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Low PM, Kong Q, Blaschek L, Ma Z, Lim PK, Yang Y, Quek T, Lim CJR, Singh SK, Crocoll C, Engquist E, Thorsen JS, Pattanaik S, Tee WT, Mutwil M, Miao Y, Yuan L, Xu D, Persson S, Ma W. ZINC FINGER PROTEIN2 suppresses funiculus lignification to ensure seed loading efficiency in Arabidopsis. Dev Cell 2025; 60:1719-1729.e6. [PMID: 39999844 DOI: 10.1016/j.devcel.2025.01.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 11/07/2024] [Accepted: 01/31/2025] [Indexed: 02/27/2025]
Abstract
The plant funiculus anchors the developing seed to the placenta within the inner dorsal pod strands of the silique wall and directly transports nutrients to the seeds. The lignified vasculature critically supports nutrient transport through the funiculus. However, molecular mechanisms underlying lignified secondary cell wall (SCW) biosynthesis in the funiculus remain elusive. Here, we show that the transcription factor ZINC FINGER PROTEIN2 (ZFP2) represses SCW formation in the cortex cells that surround the vasculature. This function is essential for efficient nutrient loading into the seeds. Notably, ZFP2 directly acts on the SCW transcription factor NAC SECONDARY WALL THICKENING PROMOTING FACTOR1 (NST1) to repress cortex cell lignification, providing a mechanism of how SCW biosynthesis is restricted to the vasculature of the funiculus to ensure proper seed loading in Arabidopsis.
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Affiliation(s)
- Pui Man Low
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Que Kong
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Leonard Blaschek
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark
| | - Zhiming Ma
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Peng Ken Lim
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Yuzhou Yang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Trisha Quek
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Cuithbert J R Lim
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Sanjay K Singh
- Department of Plant and Soil Sciences, Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY 40546, USA
| | - Christoph Crocoll
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark
| | - Ellen Engquist
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark
| | - Jakob S Thorsen
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark
| | - Sitakanta Pattanaik
- Department of Plant and Soil Sciences, Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY 40546, USA
| | - Wan Ting Tee
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Yansong Miao
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Ling Yuan
- Department of Plant and Soil Sciences, Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY 40546, USA
| | - Deyang Xu
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark
| | - Staffan Persson
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark; Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Wei Ma
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.
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Cai JL, Zhang Y, Gao H, Wang Q, Huang W, Cai YJ, Jia WX, Wang JJ, Chen X, Sun HY. Molecular characterization, expression pattern and the function of TRAF2 from blood parrot Amphilophus citrinellus ×Vieja melanura response to LPS stimulation. FISH & SHELLFISH IMMUNOLOGY 2025; 163:110362. [PMID: 40280260 DOI: 10.1016/j.fsi.2025.110362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2024] [Revised: 04/18/2025] [Accepted: 04/20/2025] [Indexed: 04/29/2025]
Abstract
Tumor necrosis factor receptor-associated factor (TRAF) family is a critical signal transduction protein, and plays important roles in cell growth, apoptosis, and immune response, etc. In this study, molecular characteristics, expression patterns, and the role of TRAF2 in blood parrot Vieja synspila ♀ × Amphilophus citrinellus ♂, an important ornamental fish, were explored response to lipopolysaccharide (LPS) challenge. The full length of blood parrot TRAF2 was 2725 bp, with an open reading frame (ORF) of 1551 bp encoding 516 amino acids, and a molecular weight of 58.58 kDa. Blood parrot TRAF2 contained four conserved domains: RING, TRAF-type zinc finger, TRAF_BIRC3_bd, and MATH (Meprin and TRAF-C homology). Analysis of phylogenetic relationships showed that TRAF2 were conserved in different species, indicating that its role might be similar. Blood parrot TRAF2 mRNA could be detected in all of the tissues examined, and was distributed in both the cytoplasm and nucleus. The expression of blood parrot TRAF2 was up-regulated during LPS challenge. Overexpression of TRAF2 could significantly inhibit the activities of nuclear factor κB (NF-κB) and activated protein 1 (AP-1), and reduce the ratio of Bax/Bcl-2. This study indicated that the TRAF2 might play important roles in organisms during pathogen infection.
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Affiliation(s)
- Jie-Li Cai
- College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong, China; School of Life Sciences, South China Normal University, Guangzhou, Guangdong, China; College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China
| | - Yue Zhang
- College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong, China; College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China
| | - Hui Gao
- College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong, China; College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China
| | - Qi Wang
- College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong, China
| | - Wei Huang
- College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong, China
| | - Yi-Jie Cai
- College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong, China
| | - Wei-Xin Jia
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jun-Jie Wang
- School of Life Sciences, South China Normal University, Guangzhou, Guangdong, China.
| | - Xiao Chen
- College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong, China.
| | - Hong-Yan Sun
- College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong, China.
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Kim SM, Choi DM, Chun JI, Kim SY, Kim SH, Kim JI, Jang JI, Kim K, Park SJ, Seo JK, Jung C, Kang JH. SlH3 and SlH4 promote multicellular trichome formation and elongation by upregulating woolly in tomato. HORTICULTURE RESEARCH 2025; 12:uhaf008. [PMID: 40093379 PMCID: PMC11908826 DOI: 10.1093/hr/uhaf008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2024] [Accepted: 01/05/2025] [Indexed: 03/19/2025]
Abstract
Trichomes are tiny outgrowths on the plant epidermis that serve defensive purposes against various stresses. While the regulatory mechanisms underlying unicellular trichome development are well understood, those governing multicellular trichome formation remain largely unexplored. In this study, we reveal a new regulatory pathway involving the Hair3 (H3) and H4 genes, which encode C2H2 zinc finger proteins that participate in multicellular trichome development in tomato (Solanum lycopersicum). Using CRISPR-Cas9 to generate single- and double-knockout lines, we found that h3 and h4 single-mutant plants did not show altered trichome characteristics compared to wild-type plants. However, h3/h4 double-knockout plants displayed decreased densities of Types I, VI, and VII trichomes, increased densities of Types III and V trichomes, and reduced leaf and stem lengths of Type I trichomes, revealing that H3 and H4 redundantly regulate trichome development. Notably, protein interaction assays demonstrated that H3 and H4 formed both homo- and heterodimers, supporting their cooperative role. Transcriptome and gene expression analyses identified H3 and H4 as key regulators of several genes involved in trichome development, including Woolly (Wo) and its downstream targets, such as Wox3b, MX1, H, and HD8. Protein-promoter assays showed that H3 and H4 did not directly bind to the Wo promoter but rather interacted with Wo, thereby enhancing the expression of Wo and Wox3b. These findings establish H3 and H4 as key regulators of trichome development and provide novel insights into the mechanisms controlling multicellular trichome development in tomato plants.
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Affiliation(s)
- Seong-Min Kim
- Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Crop Biotechnology Institute, Institutes of Green-bio Science and Technology, Seoul National University, Pyeongchang 25354, Republic of Korea
| | - Da-Min Choi
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jae-In Chun
- Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Crop Biotechnology Institute, Institutes of Green-bio Science and Technology, Seoul National University, Pyeongchang 25354, Republic of Korea
| | - Seong-Yeop Kim
- Department of International Agricultural Technology, Seoul National University, Pyeongchang 25354, Republic of Korea
- Integrated Major in Global Smart Farm, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Seong-Hyeon Kim
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jeong-Il Kim
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Ji-in Jang
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC) and Division of Biological Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Keunhwa Kim
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC) and Division of Biological Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Soon Ju Park
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC) and Division of Biological Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Jang-Kyun Seo
- Crop Biotechnology Institute, Institutes of Green-bio Science and Technology, Seoul National University, Pyeongchang 25354, Republic of Korea
- Department of International Agricultural Technology, Seoul National University, Pyeongchang 25354, Republic of Korea
| | - Choonkyun Jung
- Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Crop Biotechnology Institute, Institutes of Green-bio Science and Technology, Seoul National University, Pyeongchang 25354, Republic of Korea
- Department of International Agricultural Technology, Seoul National University, Pyeongchang 25354, Republic of Korea
- Integrated Major in Global Smart Farm, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jin-Ho Kang
- Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Crop Biotechnology Institute, Institutes of Green-bio Science and Technology, Seoul National University, Pyeongchang 25354, Republic of Korea
- Department of International Agricultural Technology, Seoul National University, Pyeongchang 25354, Republic of Korea
- Integrated Major in Global Smart Farm, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
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Hammers KL, Urriola PE, Ramirez-Camba CD, Schwartz M, Ryu MS, Gomez A, Abrahante Lloréns JE, Johnston LJ. Piglet birth weight but not the timing of zinc supplementation in gestation diets affects tissue mineral concentrations and gene expression. J Anim Sci 2025; 103:skaf097. [PMID: 40152474 PMCID: PMC12124254 DOI: 10.1093/jas/skaf097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2024] [Accepted: 03/26/2025] [Indexed: 03/29/2025] Open
Abstract
Sows were supplemented with high dietary zinc (Zn) at different times in gestation to determine effects on piglet tissue mineral concentrations and gene expression. Ten sows per treatment were assigned to dietary treatments: 1) Control-sows fed a corn-soybean meal-based diet containing 206 ppm total supplemental zinc supplied by zinc hydroxychloride from mating to farrowing; 2) Breed-to-Farrow-as Control + additional 147 ppm supplemental Zn as ZnSO4 fed from 5 d post-breeding to farrowing; and 3) Day 110-to-Farrow-as Control + additional 4,079 ppm supplemental Zn as ZnSO4 starting on day 110 of gestation until farrowing. Final supplemental Zn concentrations of the Control, Breed-to-Farrow, and Day 110-to-Farrow treatments were 206, 353, and 4,285 ppm, respectively. Serum, colostrum, and milk were collected from each sow. At farrowing, 2 average birth weight (ABW) and 2 low birth weight (LBW) piglets from each sow were selected for collection of serum and tail samples within 2 d of birth. Liver tissue was collected from 65 piglets that died naturally (n = 35) or were euthanized (n = 30). Blood was collected from a different group of piglets (9 LBW piglets per treatment and 8 ABW Control piglets) for RNA-sequencing to evaluate differentially expressed genes (DEGs) and pathways. Mineral concentration data were analyzed using a generalized linear mixed model and RNAseq data were analyzed using the edgeR program. Diet did not affect mineral concentrations of sow serum, colostrum, and milk (P > 0.05). Mineral concentrations of piglet serum were not influenced by maternal Zn treatment or piglet birth weight. Tail Cu for LBW piglets born to sows fed high Zn tended to be lower than Control piglets (P = 0.082) while piglets of LBW had greater concentrations of Fe (P = 0.018) and Cu (P = 0.031) in tails compared to ABW piglets. Piglets that died naturally had greater hepatic Fe concentrations (P < 0.001) than healthy euthanized piglets. Only 2 to 3 DEGs were noted between Control LBW and LBW piglets born to sows fed high Zn. However, 262 DEGs were identified between LBW and ABW piglets. Genes affected by birth weight were associated with pathways of translation and ribosomal activity. In conclusion, the timing of feeding high Zn concentrations to gestating sows had minimal influence on concentrations of trace minerals in sows and their offspring, while piglet birth weight may have meaningful effects on mineral metabolism and protein synthesis of neonatal piglets.
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Affiliation(s)
- Kelsey L Hammers
- Department of Animal Science, University of Minnesota, St. Paul, MN, 55108, USA
| | - Pedro E Urriola
- Department of Animal Science, University of Minnesota, St. Paul, MN, 55108, USA
| | | | | | - Moon-Suhn Ryu
- Department of Food and Nutrition, Yonsei University, Seoul, South Korea
| | - Andres Gomez
- Department of Animal Science, University of Minnesota, St. Paul, MN, 55108, USA
| | - Juan E Abrahante Lloréns
- Minnesota Supercomputing Institute, University of Minnesota University of Minnesota, Minneapolis, MN 55455, USA
| | - Lee J Johnston
- Department of Animal Science, University of Minnesota, St. Paul, MN, 55108, USA
- West Central Research and Outreach Center, University of Minnesota, Morris, MN 56267, USA
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5
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Zhao JJ, Xiang X, Yang P, Li J, Li H, Wei SY, Wang RQ, Wang T, Huang J, Chen LH, Wan XQ, He F. Genome-wide analysis of C2H2.2 gene family in Populus Trichocarpa and the function exploration of PtrC2H2.2-6 in osmotic stress. Int J Biol Macromol 2024; 283:137937. [PMID: 39579826 DOI: 10.1016/j.ijbiomac.2024.137937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Revised: 11/18/2024] [Accepted: 11/20/2024] [Indexed: 11/25/2024]
Abstract
C2H2 transcription factors are essential for increasing a plant's ability to withstand extreme conditions. However, research on the functions of C2H2 transcription factors in woody plants, particularly their responses to osmotic stress, is limited. This research identified 109 C2H2 genes, and the PtrC2H2.2 subfamily, which contains 28 genes, captured our keen interest, prompting an extensive molecular characterization. Evolutionarily, PtrC2H2.2 s have undergone 30 fragment duplications and 2 tandem duplications. PtrC2H2.2-6 acts as a core transcription factor, whose expression was decreased after both ABA and drought treatments, implying it may play a negative regulatory role in the osmotic stress response by regulating the expression of targets. Specifically, the PtrC2H2.2-6-RNAi poplar showed improved osmotic stress tolerance compared to the overexpressing line, which was more sensitive, and transcriptome data analyses flanked the molecular mechanisms of their possible regulation. In this research, we dissected the molecular features of the PtrC2H2.2 subfamily genes and elucidated the role of a specific member, the PtrC2H2.2-6 gene, in the ability of poplar to respond to osmotic stress. This discovery not only establishes a foundation for further exploration of its biological functions but also presents precious genetic assets for the development of drought-tolerant forest tree varieties through genetic engineering.
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Affiliation(s)
- Jiu-Jiu Zhao
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiang Xiang
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Peng Yang
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Jing Li
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Hao Li
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Shu-Ying Wei
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Rui-Quan Wang
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Ting Wang
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Jinliang Huang
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Liang-Hua Chen
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Xue-Qin Wan
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Fang He
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China.
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6
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Negrón-Piñeiro LJ, Di Gregorio A. Single-cell Transcriptomic Studies Unveil Potential Nodes of the Notochord Gene Regulatory Network. Integr Comp Biol 2024; 64:1194-1213. [PMID: 38914463 PMCID: PMC11579531 DOI: 10.1093/icb/icae084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 06/01/2024] [Accepted: 06/16/2024] [Indexed: 06/26/2024] Open
Abstract
Transcription factors (TFs) are DNA-binding proteins able to modulate the timing, location, and levels of gene expression by binding to regulatory DNA regions. Therefore, the repertoire of TFs present in the genome of a multicellular organism and the expression of variable constellations of TFs in different cellular cohorts determine the distinctive characteristics of developing tissues and organs. The information on tissue-specific assortments of TFs, their cross-regulatory interactions, and the genes/regulatory regions targeted by each TF is summarized in gene regulatory networks (GRNs), which provide genetic blueprints for the specification, development, and differentiation of multicellular structures. In this study, we review recent transcriptomic studies focused on the complement of TFs expressed in the notochord, a distinctive feature of all chordates. We analyzed notochord-specific datasets available from organisms representative of the three chordate subphyla, and highlighted lineage-specific variations in the suite of TFs expressed in their notochord. We framed the resulting findings within a provisional evolutionary scenario, which allows the formulation of hypotheses on the genetic/genomic changes that sculpted the structure and function of the notochord on an evolutionary scale.
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Affiliation(s)
- Lenny J Negrón-Piñeiro
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY 10010, USA
| | - Anna Di Gregorio
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY 10010, USA
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7
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Li J, Li M, Shen T, Guo Q, Zhang R, Chen Y, Zhang Y, Luo K. Molecular characterization of cassava zinc finger-homeodomain (ZF-HD) transcription factors reveals their role in disease resistance. Int J Biol Macromol 2024; 279:134846. [PMID: 39179062 DOI: 10.1016/j.ijbiomac.2024.134846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 08/07/2024] [Accepted: 08/16/2024] [Indexed: 08/26/2024]
Abstract
The production of cassava (Manihot esculenta Crantz) is constantly threatened by cassava bacterial blight (CBB), caused by Xanthomonas phaseoli pv. manihotis (Xpm). Zinc finger-homeodomain (ZF-HD) belongs to a family of homozygous heterotypic cassette genes widely implicated in various developmental and physiological processes in plants. Despite their importance, a comprehensive analysis of ZF-HD genes, particularly those involved in disease resistance, has not been performed for cassava. In the present study, we utilized bioinformatics methods to identify 21 ZF-HD genes distributed across 11 chromosomes of cassava genome, with the majority exhibiting gene structure without introns. Phylogenetic analysis categorized these genes into two major groups (MIF and ZHD) with five subgroups. We observed fourteen pairs of duplicated genes, suggesting that segmental duplication has likely facilitated the expansion of the cassava ZF-HD gene family. Comparative orthologous analyses between cassava and other plant species shed light on the evolutionary trajectory of this gene family. Promoter analyses revealed multiple hormone- and stress-related elements, indicative of a functional role in stress responses. Expression profiling through RNA-seq and quantitative real-time PCR (qRT-PCR) demonstrated that certain cassava ZF-HD genes are up-regulated in response to Xpm infection, suggesting their involvement in defense mechanisms. Notably, MeZHD7 gene was identified via virus induced gene silencing (VIGS) as potentially crucial in conferring resistance against CBB. Results from subcellular localization experiments indicated that MeZHD7 was localized in the nucleus. The Luciferase reporter assay demonstrated an interaction between MeZHD7 and MeMIF5. These findings may lay the foundation for further cloning and functional analyses of cassava ZF-HD genes, particularly those associated with pathogen resistance.
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Affiliation(s)
- Junyi Li
- School of Breeding and Multiplication (Sanya institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Mingchao Li
- School of Breeding and Multiplication (Sanya institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Tiantian Shen
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Qiying Guo
- School of Breeding and Multiplication (Sanya institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Rui Zhang
- School of Breeding and Multiplication (Sanya institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Yinhua Chen
- School of Breeding and Multiplication (Sanya institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Yindong Zhang
- Key Laboratory of Plant Disease and Pest Control of Hainan Province/Institute of Plant Protection, Hainan Academy of Agricultural Sciences, Haikou 571100, China
| | - Kai Luo
- School of Breeding and Multiplication (Sanya institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China.
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8
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Armentrout PB. Perspective: intrinsic interactions of metal ions with biological molecules as studied by threshold collision-induced dissociation and infrared multiple photon dissociation. Phys Chem Chem Phys 2024. [PMID: 39042103 DOI: 10.1039/d4cp00897a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
In this perspective, gas-phase studies of group 1 monocations and group 12 dications with amino acids and small peptides are highlighted. Although the focus is on two experimental techniques, threshold collision-induced dissociation and infrared multiple photon dissociation action spectroscopy, these methods as well as complementary approaches are summarized. The synergistic interplay with theory, made particularly powerful by the small sizes of the systems explored and the absence of solvent and support, is also elucidated. Importantly, these gas-phase methods permit quantitative insight into the structures and thermodynamics of metal cations interacting with biological molecules. Periodic trends in how these interactions vary as the metal cations get heavier are discussed as are quantitative trends with changes in the amino acid side chain and effects of hydration. Such trends allow these results to transcend the limitations associated with the biomimetic model systems.
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Affiliation(s)
- P B Armentrout
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA.
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9
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Kang YK, Eom J, Min B, Park JS. SETDB1 deletion causes DNA demethylation and upregulation of multiple zinc-finger genes. Mol Biol Rep 2024; 51:778. [PMID: 38904842 PMCID: PMC11192681 DOI: 10.1007/s11033-024-09703-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 06/04/2024] [Indexed: 06/22/2024]
Abstract
BACKGROUND SETDB1 (SET domain bifurcated-1) is a histone H3-lysine 9 (H3K9)-specific methyltransferase that mediates heterochromatin formation and repression of target genes. Despite the assumed functional link between DNA methylation and SETDB1-mediated H3K9 trimethylations, several studies have shown that SETDB1 operates autonomously of DNA methylation in a region- and cell-specific manner. This study analyzes SETDB1-null HAP1 cells through a linked methylome and transcriptome analysis, intending to explore genes controlled by SETDB1-involved DNA methylation. METHODS AND RESULTS We investigated SETDB1-mediated regulation of DNA methylation and gene transcription in human HAP1 cells using reduced-representation bisulfite sequencing (RRBS) and RNA sequencing. While two-thirds of differentially methylated CpGs (DMCs) in genic regions were hypomethylated in SETDB1-null cells, we detected a plethora of C2H2-type zinc-finger protein genes (C2H2-ZFP, 223 of 749) among the DMC-associated genes. Most C2H2-ZFPs with DMCs in their promoters were found hypomethylated in SETDB1-KO cells, while other non-ZFP genes with promoter DMCs were not. These C2H2-ZFPs with DMCs in their promoters were significantly upregulated in SETDB1-KO cells. Similarly, C2H2-ZFP genes were upregulated in SETDB1-null 293T cells, suggesting that SETDB1's function in ZFP gene repression is widespread. There are several C2H2-ZFP gene clusters on chromosome 19, which were selectively hypomethylated in SETDB1-KO cells. CONCLUSIONS SETDB1 collectively and specifically represses a substantial fraction of the C2H2-ZFP gene family. Through the en-bloc silencing of a set of ZFP genes, SETDB1 may help establish a panel of ZFP proteins that are expressed cell-type specifically and thereby can serve as signature proteins for cellular identity.
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Affiliation(s)
- Yong-Kook Kang
- Development and Differentiation Research Center, Aging Convergence Research Center (ACRC), Korea Research Institute of Bioscience Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, South Korea.
- Department of Functional Genomics, University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, South Korea.
| | - Jaemin Eom
- Development and Differentiation Research Center, Aging Convergence Research Center (ACRC), Korea Research Institute of Bioscience Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, South Korea
- Department of Functional Genomics, University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, South Korea
| | - Byungkuk Min
- Development and Differentiation Research Center, Aging Convergence Research Center (ACRC), Korea Research Institute of Bioscience Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, South Korea
| | - Jung Sun Park
- Development and Differentiation Research Center, Aging Convergence Research Center (ACRC), Korea Research Institute of Bioscience Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, South Korea
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10
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Xie Q, Tong C, Xiong X. An overview of the co-transcription factor NACC1: Beyond its pro-tumor effects. Life Sci 2024; 336:122314. [PMID: 38030057 DOI: 10.1016/j.lfs.2023.122314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/20/2023] [Accepted: 11/26/2023] [Indexed: 12/01/2023]
Abstract
Nucleus accumbens-associated protein 1 (NACC1) is a member of the broad complex, tramtrack, bric-a-brac/poxvirus and zinc finger (BTB/POZ) protein families, mainly exerting its biological functions as a transcription co-regulator. NACC1 forms homo- or hetero-dimers through the BTB/POZ or BANP, E5R, and NACC1 (BEN) domain with other transcriptional regulators to regulate downstream signals. Recently, the overexpression of NACC1 has been observed in various tumors and is positively associated with tumor progression, high recurrence rate, indicating poor prognosis. NACC1 also regulates biological processes such as embryonic development, stem cell pluripotency, innate immunity, and related diseases. Our review combines recent research to summarize advancements in the structure, biological functions, and relative molecular mechanisms of NACC1. The future development of NACC1 clinical appliances is also discussed.
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Affiliation(s)
- Qing Xie
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Nanchang University, Nanchang, 330006, China; School of Basic Medical Sciences, Nanchang University, Nanchang, 330006, China
| | - Chang Tong
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Nanchang University, Nanchang, 330006, China
| | - Xiangyang Xiong
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Nanchang University, Nanchang, 330006, China; Province Key Laboratory of Tumor Pathogens and Molecular Pathology, Nanchang University, Nanchang 330006, China.
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11
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Mozumdar D, Roy RN. Origin of ribonucleotide recognition motifs through ligand mimicry at early earth. RNA Biol 2024; 21:107-121. [PMID: 39526332 PMCID: PMC11556283 DOI: 10.1080/15476286.2024.2423149] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 10/23/2024] [Accepted: 10/25/2024] [Indexed: 11/16/2024] Open
Abstract
In an RNA world, the emergence of template-specific self-replication and catalysis necessitated the presence of motifs facilitating reliable recognition between RNA molecules. What did these motifs entail, and how did they evolve into the proteinaceous RNA recognition entities observed today? Direct observation of these primordial entities is hindered by rapid degradation over geological time scales. To overcome this challenge, researchers employ diverse approaches, including scrutiny of conserved sequences and structural motifs across extant organisms and employing directed evolution experiments to generate RNA molecules with specific catalytic abilities. In this review, we delve into the theme of ribonucleotide recognition across key periods of early Earth's evolution. We explore scenarios of RNA interacting with small molecules and examine hypotheses regarding the role of minerals and metal ions in enabling structured ribonucleotide recognition and catalysis. Additionally, we highlight instances of RNA-protein mimicry in interactions with other RNA molecules. We propose a hypothesis where RNA initially recognizes small molecules and metal ions/minerals, with subsequent mimicry by proteins leading to the emergence of proteinaceous RNA binding domains.
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Affiliation(s)
- Deepto Mozumdar
- Department of Immunology & Microbiology, University of California San Francisco, San Francisco, CA, USA
| | - Raktim N. Roy
- Department of pathology & laboratory medicine, Indiana University School of Medicine, Indianapolis, IN, USA
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12
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Islam MAU, Nupur JA, Shafiq M, Ali Q, Sami A, Shahid MA. In silico and computational analysis of zinc finger motif-associated homeodomain (ZF-HD) family genes in chilli (Capsicum annuum L). BMC Genomics 2023; 24:603. [PMID: 37821819 PMCID: PMC10566081 DOI: 10.1186/s12864-023-09682-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 09/18/2023] [Indexed: 10/13/2023] Open
Abstract
Zinc finger-homeodomain (ZHD) proteins are mostly expressed in plants and are involved in proper growth and development and minimizing biotic and abiotic stress. A recent study identified and characterized the ZHD gene family in chilli (Capsicum annuum L.) to determine their probable molecular function. ZHD genes with various physicochemical characteristics were discovered on twelve chromosomes in chilli. We separated ZHD proteins into two major groups using sequence alignment and phylogenetic analysis. These groups differ in gene structure, motif distribution, and a conserved ZHD and micro-zinc finger ZF domain. The majority of the CaZHDs genes are preserved, early duplication occurred recently, and significant pure selection took place throughout evolution, according to evolutionary study. According to expression profiling, the genes were found to be equally expressed in tissues above the ground, contribute to plant growth and development and provide tolerance to biotic and abiotic stress. This in silico analysis, taken as a whole, hypothesized that these genes perform distinct roles in molecular and phytohormone signaling processes, which may serve as a foundation for subsequent research into the roles of these genes in other crops.
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Affiliation(s)
- Md Abir Ul Islam
- United Graduate School of Agricultural Science, Faculty of Biological Sciences, Gifu University, Yanagido, Gifu, 501-1193, Japan
| | - Juthy Abedin Nupur
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2R3, Canada
| | - Muhammad Shafiq
- Department of Horticulture, University of Panjab, Lahore, 54000, Pakistan.
| | - Qurban Ali
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, P.O BOX. 54590, Lahore, Pakistan.
| | - Adnan Sami
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, P.O BOX. 54590, Lahore, Pakistan
| | - Muhammad Adnan Shahid
- Horticultural Science Department, North Florida Research and Education Center, University of Florida/IFAS, Quincy, FL, USA
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13
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Sahoo BR, Bardwell JCA. SERF, a family of tiny highly conserved, highly charged proteins with enigmatic functions. FEBS J 2023; 290:4150-4162. [PMID: 35694898 DOI: 10.1111/febs.16555] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 06/07/2022] [Accepted: 06/10/2022] [Indexed: 11/27/2022]
Abstract
Amyloid formation is a misfolding process that has been linked to age-related diseases, including Alzheimer's and Huntington's. Understanding how cellular factors affect this process in vivo is vital in realizing the dream of controlling this insidious process that robs so many people of their humanity. SERF (small EDRK-rich factor) was initially isolated as a factor that accelerated polyglutamine amyloid formation in a C. elegans model. SERF knockouts inhibit amyloid formation of a number of proteins that include huntingtin, α-synuclein and β-amyloid which are associated with Huntington's, Parkinson's and Alzheimer's disease, respectively, and purified SERF protein speeds their amyloid formation in vitro. SERF proteins are highly conserved, highly charged and conformationally dynamic proteins that form a fuzzy complex with amyloid precursors. They appear to act by specifically accelerating the primary step of amyloid nucleation. Brain-specific SERF knockout mice, though viable, appear to be more prone to deposition of amyloids, and show modified fibril morphology. Whole-body knockouts are perinatally lethal due to an apparently unrelated developmental issue. Recently, it was found that SERF binds RNA and is localized to nucleic acid-rich membraneless compartments. SERF-related sequences are commonly found fused to zinc finger sequences. These results point towards a nucleic acid-binding function. How this function relates to their ability to accelerate amyloid formation is currently obscure. In this review, we discuss the possible biological functions of SERF family proteins in the context of their structural fuzziness, modulation of amyloid pathway, nucleic acid binding and their fusion to folded proteins.
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Affiliation(s)
- Bikash R Sahoo
- Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
| | - James C A Bardwell
- Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
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14
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Wang S, Liu R. Insights into the pleiotropic roles of ZNF703 in cancer. Heliyon 2023; 9:e20140. [PMID: 37810156 PMCID: PMC10559930 DOI: 10.1016/j.heliyon.2023.e20140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 09/05/2023] [Accepted: 09/12/2023] [Indexed: 10/10/2023] Open
Abstract
Zinc finger proteins (ZNFs) belong to the NET/NLZ protein family. In physiological functions, ZNF703 play significant roles in embryonic development, especially in the nervous system. As an transcription factors with zinc finger domains, abnormal regulation of the ZNF703 protein is associated with enhanced proliferation, invasion, and metastasis as well as drug resistance in many tumors, although mechanisms of action vary depending on the specific tumor microenvironment. ZNF703 lacks a nuclear localization sequence despite its function requiring nuclear DNA binding. The purpose of this review is to summarize the architecture of ZNF703, its roles in tumorigenesis, and tumor progression, as well as future oncology therapeutic prospects, which have implications for understanding tumor susceptibility and progression.
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Affiliation(s)
- Shuang Wang
- Department of Obstetrics and Gynaecology, Tianjin Central Hospital of Gynecology Obstetrics, No. 156 Nan Kai San Ma Lu, Tianjin, 300000, China
- Tianjin Key Laboratory of Human Development and Reproductive Regulation, Tianjin, 300000, China
- Department of Obstetrics and Gynaecology, Nankai University Maternity Hospital, Tianjin, 300000, China
| | - Rong Liu
- Department of Obstetrics and Gynecology, Tianjin First Center Hospital, Tianjin, China
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15
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Zou X, Ma L, Zhang Y, Zhang Q, Xu C, Zhang D, Chu Y, Zhang J, Li M, Zhang H, Wang J, Peng C, Wei G, Wu Y, Hou Z, Jia H. GATA zinc finger protein p66β promotes breast cancer cell migration by acting as a co-activator of Snail. Cell Death Dis 2023; 14:382. [PMID: 37380643 DOI: 10.1038/s41419-023-05887-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 05/15/2023] [Accepted: 06/12/2023] [Indexed: 06/30/2023]
Abstract
The transcriptional repressor Snail induces EMT during embryonic development and tumor metastasis. Growing evidence indicates that Snail functions as a trans-activator to induce gene expression; however, the underlying mechanism remains elusive. Here, we report that Snail cooperates with GATA zinc finger protein p66β to transactivate genes in breast cancer cells. Biologically, depletion of p66β reduces cell migration and lung metastasis in BALB/c mice. Mechanistically, Snail interacts with p66β and cooperatively induces gene transcription. Notably, a group of genes induced by Snail harbor conserved G-rich cis-elements (5'-GGGAGG-3', designated as G-box) in their proximal promoter regions. Snail directly binds to G-box via its zinc fingers and transactivates the G-box-containing promoters. p66β enhances Snail binding affinity to G-box, whereas depletion of p66β results in a decreased binding affinity of Snail to the endogenous promoters and concomitantly reduces the transcription of Snail-induced genes. Taken together, these data demonstrated that p66β is critical for Snail-mediated cell migration by acting as a co-activator of Snail to induce genes containing G-box elements in the promoters.
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Affiliation(s)
- Xiuqun Zou
- Hongqiao Institute of Medicine, Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry & Molecular Cellular Biology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Li Ma
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute of Computational Biology, Shanghai Institute for Biological Science, Chinese Academy of Sciences, Shanghai, China
| | - Yihong Zhang
- Hongqiao Institute of Medicine, Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry & Molecular Cellular Biology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Qun Zhang
- Hongqiao Institute of Medicine, Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry & Molecular Cellular Biology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Chu Xu
- Hongqiao Institute of Medicine, Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry & Molecular Cellular Biology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Dan Zhang
- Hongqiao Institute of Medicine, Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry & Molecular Cellular Biology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yimin Chu
- Digestive Endoscopy Center, Shanghai Tongren Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jie Zhang
- Hongqiao Institute of Medicine, Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry & Molecular Cellular Biology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Mengying Li
- Hongqiao Institute of Medicine, Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry & Molecular Cellular Biology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Hui Zhang
- Hongqiao Institute of Medicine, Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry & Molecular Cellular Biology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jiamin Wang
- Hongqiao Institute of Medicine, Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry & Molecular Cellular Biology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Chicheng Peng
- Naruiboen Biomedical Technology Corporation Limited, Linyi, Shandong, China
| | - Gang Wei
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute of Computational Biology, Shanghai Institute for Biological Science, Chinese Academy of Sciences, Shanghai, China
| | - Yingjie Wu
- Shandong Provincial Hospital, Shandong Laboratory Animal Center, Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China.
| | - Zhaoyuan Hou
- Hongqiao Institute of Medicine, Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiaotong University School of Medicine, Shanghai, China.
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry & Molecular Cellular Biology, Shanghai Jiaotong University School of Medicine, Shanghai, China.
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai, China.
- Linyi University-Shanghai Jiaotong University Joint Institute of Translational Medicine, Linyi, Shandong, China.
| | - Hao Jia
- Hongqiao Institute of Medicine, Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiaotong University School of Medicine, Shanghai, China.
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry & Molecular Cellular Biology, Shanghai Jiaotong University School of Medicine, Shanghai, China.
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16
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Li Y, Zhou Z, Xu Y, Wang ZR. Novel mutation c.2090_2091del in neurodevelopmental-craniofacial syndrome with variable renal and cardiac abnormalities in an 18.5-mo-old boy: A case report. World J Clin Cases 2023; 11:3891-3898. [PMID: 37383123 PMCID: PMC10294165 DOI: 10.12998/wjcc.v11.i16.3891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/06/2023] [Accepted: 04/14/2023] [Indexed: 06/02/2023] Open
Abstract
BACKGROUND Neurodevelopmental-craniofacial syndrome with variable renal and cardiac abnormalities (NECRC) is a rare, autosomal, dominant neurological disorder caused by mutations in the ZMYM2 gene. To date, the clinical and functional characteristics of the novel ZMYM2 mutation c.2090_2091del have not yet been reported.
CASE SUMMARY The patient was an 18.5-mo-old Chinese boy with motor and language delay, microcephaly, facial dysmorphism, moderate malnutrition, single palmar crease on the left hand, synpolydactyly of the right foot, hypotonia and feeding problems. The boy who was diagnosed with NECRC was enrolled in the First Affiliated Hospital, Henan University of Chinese Medicine, and his clinical data were collected. From the whole-exon sequencing (WES) data, the pathogenic SNVs/InDels were identified, and the molecular findings were characterized. WES revealed that the heterozygous variant in the ZMYM2 gene was c.2090_2091del, p.Ser697TrpfsTer3, a frameshift mutation, which is a NECRC-related gene mutation.
CONCLUSION We performed a systematic literature review to identify and characterize NECRC. Substantial evidence from the literature indicated that patients with ZMYM2 gene mutation showed different degrees of intellectual disability, motor and language retardation, facial dysmorphism, and a few had congenital heart defects, kidney and urinary tract abnormalities. Early diagnosis and prompt management with comprehensive rehabilitation training are beneficial, but may not improve long-term outcomes.
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Affiliation(s)
- Yi Li
- College of Pediatrics, Henan University of Chinese Medicine, Zhengzhou 450000, Henan Province, China
| | - Zheng Zhou
- Department of Pediatrics, The First Affiliated Hospital, Henan University of Chinese Medicine, Zhengzhou 450000, Henan Province, China
| | - Yan Xu
- Department of Pediatrics, The First Affiliated Hospital, Henan University of Chinese Medicine, Zhengzhou 450000, Henan Province, China
| | - Zhi-Ru Wang
- Department of Pediatrics, The First Affiliated Hospital, Henan University of Chinese Medicine, Zhengzhou 450000, Henan Province, China
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17
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You SL, Jiang XX, Zhang GR, Ji W, Ma XF, Zhou X, Wei KJ. Molecular Characterization of Nine TRAF Genes in Yellow Catfish ( Pelteobagrus fulvidraco) and Their Expression Profiling in Response to Edwardsiella ictaluri Infection. Int J Mol Sci 2023; 24:ijms24098363. [PMID: 37176078 PMCID: PMC10179116 DOI: 10.3390/ijms24098363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/27/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023] Open
Abstract
The yellow catfish (Pelteobagrus fulvidraco) is an economic fish with a large breeding scale, and diseases have led to huge economic losses. Tumor necrosis factor receptor-associated factors (TRAFs) are a class of intracellular signal transduction proteins that play an important role in innate and adaptive immune responses by mediating NF-κB, JNK and MAPK signaling pathways. However, there are few studies on the TRAF gene family in yellow catfish. In this study, the open reading frame (ORF) sequences of TRAF1, TRAF2a, TRAF2b, TRAF3, TRAF4a, TRAF4b, TRAF5, TRAF6 and TRAF7 genes were cloned and identified in yellow catfish. The ORF sequences of the nine TRAF genes of yellow catfish (Pf_TRAF1-7) were 1413-2025 bp in length and encoded 470-674 amino acids. The predicted protein structures of Pf_TRAFs have typically conserved domains compared to mammals. The phylogenetic relationships showed that TRAF genes are conserved during evolution. Gene structure, motifs and syntenic analyses of TRAF genes showed that the exon-intron structure and conserved motifs of TRAF genes are diverse among seven vertebrate species, and the TRAF gene family is relatively conserved evolutionarily. Among them, TRAF1 is more closely related to TRAF2a and TRAF2b, and they may have evolved from a common ancestor. TRAF7 is quite different and distantly related to other TRAFs. Real-time quantitative PCR (qRT-PCR) results showed that all nine Pf_TRAF genes were constitutively expressed in 12 tissues of healthy yellow catfish, with higher mRNA expression levels in the gonad, spleen, brain and gill. After infection with Edwardsiella ictaluri, the expression levels of nine Pf_TRAF mRNAs were significantly changed in the head kidney, spleen, gill and brain tissues of yellow catfish, of which four genes were down-regulated and one gene was up-regulated in the head kidney; four genes were up-regulated and four genes were down-regulated in the spleen; two genes were down-regulated, one gene was up-regulated, and one gene was up-regulated and then down-regulated in the gill; one gene was up-regulated, one gene was down-regulated, and four genes were down-regulated and then up-regulated in the brain. These results indicate that Pf_TRAF genes might be involved in the immune response against bacterial infection. Subcellular localization results showed that all nine Pf_TRAFs were found localized in the cytoplasm, and Pf_TRAF2a, Pf_TRAF3 and Pf_TRAF4a could also be localized in the nucleus, uncovering that the subcellular localization of TRAF protein may be closely related to its structure and function in cellular mechanism. The results of this study suggest that the Pf_TRAF gene family plays important roles in the immune response against pathogen invasion and will provide basic information to further understand the roles of TRAF gene against bacterial infection in yellow catfish.
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Affiliation(s)
- Shen-Li You
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Xin-Xin Jiang
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Gui-Rong Zhang
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Wei Ji
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Xu-Fa Ma
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Xu Zhou
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Kai-Jian Wei
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
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18
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Hajdu B, Hunyadi-Gulyás É, Kato K, Kawaguchi A, Nagata K, Gyurcsik B. Zinc binding of a Cys2His2-type zinc finger protein is enhanced by the interaction with DNA. J Biol Inorg Chem 2023; 28:301-315. [PMID: 36820987 PMCID: PMC10036435 DOI: 10.1007/s00775-023-01988-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 01/10/2023] [Indexed: 02/24/2023]
Abstract
Zinc finger proteins specifically recognize DNA sequences and, therefore, play a crucial role in living organisms. In this study the Zn(II)-, and DNA-binding of 1MEY#, an artificial zinc finger protein consisting of three finger units was characterized by multiple methods. Fluorimetric, circular dichroism and isothermal calorimetric titrations were applied to determine the accurate stability constant of a zinc finger protein. Assuming that all three zinc finger subunits behave identically, the obtained thermodynamic data for the Zn(II) binding were ΔHbinding site = - (23.5 - 28.0) kcal/mol (depending on the applied protonation state of the cysteines) and logβ'pH 7.4 = 12.2 ± 0.1, being similar to those of the CP1 consensus zinc finger peptide. The specific DNA binding of the protein can be characterized by logβ'pH 7.4 = 8.20 ± 0.08, which is comparable to the affinity of the natural zinc finger proteins (Sp1, WT1, TFIIIA) toward DNA. This value is ~ 1.9 logβ' unit higher than those determined for semi- or nonspecific DNA binding. Competitive circular dichroism and electrophoretic mobility shift measurements revealed that the conditional stability constant characteristic for Zn(II) binding of 1MEY# protein increased by 3.4 orders of magnitude in the presence of its target DNA sequence.
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Affiliation(s)
- Bálint Hajdu
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm Tér 7, 6720, Szeged, Hungary
| | - Éva Hunyadi-Gulyás
- Laboratory of Proteomics Research, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Temesvári Krt. 62, 6726, Szeged, Hungary
| | - Kohsuke Kato
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan
| | - Atsushi Kawaguchi
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan
| | - Kyosuke Nagata
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan
| | - Béla Gyurcsik
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm Tér 7, 6720, Szeged, Hungary.
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19
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Interactions of an Artificial Zinc Finger Protein with Cd(II) and Hg(II): Competition and Metal and DNA Binding. INORGANICS 2023. [DOI: 10.3390/inorganics11020064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Cys2His2 zinc finger proteins are important for living organisms, as they—among other functions—specifically recognise DNA when Zn(II) is coordinated to the proteins, stabilising their ββα secondary structure. Therefore, competition with other metal ions may alter their original function. Toxic metal ions such as Cd(II) or Hg(II) might be especially dangerous because of their similar chemical properties to Zn(II). Most competition studies carried out so far have involved small zinc finger peptides. Therefore, we have investigated the interactions of toxic metal ions with a zinc finger proteins consisting of three finger units and the consequences on the DNA binding properties of the protein. Binding of one Cd(II) per finger subunit of the protein was shown by circular dichroism spectroscopy, fluorimetry and electrospray ionisation mass spectrometry. Cd(II) stabilised a similar secondary structure to that of the Zn(II)-bound protein but with a slightly lower affinity. In contrast, Hg(II) could displace Zn(II) quantitatively (logβ′ ≥ 16.7), demolishing the secondary structure, and further Hg(II) binding was also observed. Based on electrophoretic gel mobility shift assays, the Cd(II)-bound zinc finger protein could recognise the specific DNA target sequence similarly to the Zn(II)-loaded form but with a ~0.6 log units lower stability constant, while Hg(II) could destroy DNA binding completely.
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20
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Shi B, Haq IU, Fiaz S, Alharthi B, Xu ML, Wang JL, Hou WH, Feng XB. Genome-wide identification and expression analysis of the ZF-HD gene family in pea ( Pisum sativum L.). Front Genet 2023; 13:1089375. [PMID: 36685917 PMCID: PMC9849798 DOI: 10.3389/fgene.2022.1089375] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/19/2022] [Indexed: 01/07/2023] Open
Abstract
Pea is a conventional grain-feed-grass crop in Tibet and the only high-protein legume in the region; therefore, it plays an important role in Tibetan food and grass security. Zinc finger-homeodomain (ZF-HD) belongs to a family of homozygous heterotypic cassette genes, which play an important role in plant growth, development, and response to adversity stress. Using a bioinformatics approach, 18 PsZF-HD family members were identified. These genes were distributed across seven chromosomes and two scaffold fragments, and evolutionary analysis classified them into two subgroups, MIF and ZHD. The MIF subgroup was subdivided into three subclasses (PsMIFⅠ-III), and the ZHD subgroup was subdivided into five subclasses (ZHDⅠ-V). The PsZF-HD members were named PsMIF1-PsMIF4 and PsZHD1-PsZHD14. Twelve conserved motifs and four conserved domains were identified from PsZF-HD family, of which MIF subgroup only contained one domain, while ZHD subgroup contained two types of domains. In addition, there were significant differences in the three-dimensional structures of the protein members of the two subgroups. Most PsZF-HD genes had no introns (13/18), and only five genes had one intron. Forty-five cis-acting elements were predicted and screened, involving four categories: light response, stress, hormone, and growth and development. Transcriptome analysis of different tissues during pea growth and development showed that PsZHD11, 8, 13, 14 and MIF4 were not expressed or were individually expressed in low amounts in the tissues, while the other 13 PsZF-HDs genes were differentially expressed and showed tissue preference, as seen in aboveground reproductive organs, where PsZHD6, 2, 10 and MIF1 (except immature seeds) were highly expressed. In the aerial vegetative organs, PsZHD6, 1, and 10 were significantly overexpressed, while in the underground root system, PsMIF3 was specifically overexpressed. The leaf transcriptome under a low-nitrogen environment showed that the expression levels of 17 PsZF-HDs members were upregulated in shoot organs. The leaf transcriptome analysis under a low-temperature environment showed stress-induced upregulation of PsZHD10 and one genes and down-regulation of PsZHD6 gene. These results laid the foundation for deeper exploration of the functions of the PsZF-HD genes and also improved the reference for molecular breeding for stress resistance in peas.
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Affiliation(s)
- Bowen Shi
- Plant Sciences College, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, China
| | - Inzamam Ul Haq
- College of Plant Protection, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | - Badr Alharthi
- Department of Biology, University College of Al Khurmah, Taif University, Saudi Arabia
| | - Ming-Long Xu
- Plant Sciences College, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, China
| | - Jian-Lin Wang
- Plant Sciences College, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, China
| | - Wei-Hai Hou
- Plant Sciences College, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, China,*Correspondence: Wei-Hai Hou, ; Xi-Bo Feng,
| | - Xi-Bo Feng
- Plant Sciences College, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, China,*Correspondence: Wei-Hai Hou, ; Xi-Bo Feng,
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21
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Dai X, Zhai R, Lin J, Wang Z, Meng D, Li M, Mao Y, Gao B, Ma H, Zhang B, Sun Y, Li S, Zhou C, Lin YCJ, Wang JP, Chiang VL, Li W. Cell-type-specific PtrWOX4a and PtrVCS2 form a regulatory nexus with a histone modification system for stem cambium development in Populus trichocarpa. NATURE PLANTS 2023; 9:96-111. [PMID: 36624255 PMCID: PMC9873556 DOI: 10.1038/s41477-022-01315-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 11/17/2022] [Indexed: 05/20/2023]
Abstract
Stem vascular cambium cells in forest trees produce wood for materials and energy. WOX4 affects the proliferation of such cells in Populus. Here we show that PtrWOX4a is the most highly expressed stem vascular-cambium-specific (VCS) gene in P. trichocarpa, and its expression is controlled by the product of the second most highly expressed VCS gene, PtrVCS2, encoding a zinc finger protein. PtrVCS2 binds to the PtrWOX4a promoter as part of a PtrWOX13a-PtrVCS2-PtrGCN5-1-PtrADA2b-3 protein tetramer. PtrVCS2 prevented the interaction between PtrGCN5-1 and PtrADA2b-3, resulting in H3K9, H3K14 and H3K27 hypoacetylation at the PtrWOX4a promoter, which led to fewer cambium cell layers. These effects on cambium cell proliferation were consistent across more than 20 sets of transgenic lines overexpressing individual genes, gene-edited mutants and RNA interference lines in P. trichocarpa. We propose that the tetramer-PtrWOX4a system may coordinate genetic and epigenetic regulation to maintain normal vascular cambium development for wood formation.
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Affiliation(s)
- Xiufang Dai
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Rui Zhai
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Jiaojiao Lin
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Zhifeng Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- National Key Laboratory of Plant Molecular Genetics and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Dekai Meng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Meng Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yuli Mao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Boyuan Gao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Hongyan Ma
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Baofeng Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yi Sun
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Shuang Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Chenguang Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Ying-Chung Jimmy Lin
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan, China
| | - Jack P Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, USA
| | - Vincent L Chiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, USA
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China.
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22
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Ilyas M, Hussain Shah S, Fujita Y, Maruyama K, Nakashima K, Yamaguchi-Shinozaki K, Jan A. OsTZF1, a CCCH-tandem zinc finger protein gene, driven under own promoter produces no pleiotropic effects and confers salt and drought tolerance in rice. PLANT SIGNALING & BEHAVIOR 2022; 17:2142725. [PMID: 36398733 PMCID: PMC9677997 DOI: 10.1080/15592324.2022.2142725] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
Different abiotic stresses induce OsTZF1, a tandem CCCH-type zinc finger domain gene, in rice. Here, we report that transgenic rice plants overexpressing OsTZF1 under own promoter (POsTZF1:OsTZF1-OX [for overexpression]) transferred to soil showed normal growth similar to vector control plants. The POsTZF1:OsTZF1-OX produced normal leaves without any lesion mimic phenotype and exhibited normal seed setting. The POsTZF1:OsTZF1-OX plants showed significantly increased tolerance to salt and drought stresses and enhanced post stress recovery. Microarray analysis revealed a total of 846 genes up-regulated and 360 genes down-regulated in POsTZF1:OsTZF1-OX salt-treated plants. Microarray analysis of POsTZF1:OsTZF1-OX plants showed the regulation of many abiotic stress tolerance genes. These results suggest that OsTZF1-OX under own promoter show abiotic stress tolerance and produces no pleiotropic effect on phenotype of transgenic rice plant.
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Affiliation(s)
- Muhammad Ilyas
- Institute of Biotechnology and Genetic Engineering, the University of Agriculture Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Safdar Hussain Shah
- Institute of Biotechnology and Genetic Engineering, the University of Agriculture Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Yasunari Fujita
- Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, Japan
| | - Kyonoshin Maruyama
- Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, Japan
| | - Kazuo Nakashima
- Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, Japan
| | - Kazuko Yamaguchi-Shinozaki
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Research Institute for Agricultural and Life Sciences, Tokyo University of Agriculture, Tokyo, Japan
| | - Asad Jan
- Institute of Biotechnology and Genetic Engineering, the University of Agriculture Peshawar, Khyber Pakhtunkhwa, Pakistan
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23
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Li S, Xie H, Zhou L, Dong D, Liu Y, Jia C, Han L, Chao Y, Chen Y. Overexpression of MsSAG113 gene promotes leaf senescence in alfalfa via participating in the hormone regulatory network. FRONTIERS IN PLANT SCIENCE 2022; 13:1085497. [PMID: 36570962 PMCID: PMC9774027 DOI: 10.3389/fpls.2022.1085497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
Introduction Alfalfa (Medicago sativa) is a kind of high quality leguminous forage species, which was widely cultivated in the world. Leaf senescence is an essential process in plant development and life cycle. Here, we reported the isolation and functional analysis of an alfalfa SENESCENCE-ASSOCIATED GENE113 (MsSAG113), which belongs to the PP2C family and mainly plays a role in promoting plant senescence. Methods In the study, Agrobacterium-mediated, gene expression analysis, next generation sequencing, DNA pull-down, yeast single hybridization and transient expression were used to identify the function of MsSAG113 gene. Results The MsSAG113 gene was isolated from alfalfa, and the transgenic plants were obtained by Agrobacterium-mediated method. Compared with the wildtype, transgenic plants showed premature senescence in leaves, especially when cultivated under dark conditions. Meanwhile, application of exogenous hormones ABA, SA, MeJA, obviously acclerated leaf senescence of transgenic plants. Furthermore, the detached leaves from transgenic plants turned yellow earlier with lower chlorophyll content. Transcriptome analysis identified a total of 1,392 differentially expressed genes (DEGs), involving 13 transcription factor families. Of which, 234 genes were related to phytohormone synthesis, metabolism and transduction. Pull-down assay and yeast one-hybrid assay confirmed that alfalfa zinc finger CCCH domain-containing protein 39 (MsC3H-39) could directly bind the upstream of MsSAG113 gene. In conclusion, the MsSAG113 gene plays a crucial role in promoting leaf senescence in alfalfa via participating in the hormone regulatory network. Discussion This provides an essential basis for further analysis on the regulatory network involving senescence-associated genes in alfalfa.
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Affiliation(s)
- Shuwen Li
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Hong Xie
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Lingfang Zhou
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Di Dong
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Yaling Liu
- Inner Mongolia M-Grass Ecology And Environment (Group) Co., Ltd, Hohhot, China
| | - Chenyan Jia
- Inner Mongolia M-Grass Ecology And Environment (Group) Co., Ltd, Hohhot, China
| | - Liebao Han
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Yuehui Chao
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Yinglong Chen
- The University of Western Australia (UWA) Institute of Agriculture, and University of Western Australia School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
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24
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Hussain A, Liu J, Mohan B, Burhan A, Nasim Z, Bano R, Ameen A, Zaynab M, Mukhtar MS, Pajerowska-Mukhtar KM. A genome-wide comparative evolutionary analysis of zinc finger-BED transcription factor genes in land plants. Sci Rep 2022; 12:12328. [PMID: 35853967 PMCID: PMC9296551 DOI: 10.1038/s41598-022-16602-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 07/12/2022] [Indexed: 11/09/2022] Open
Abstract
Zinc finger (Zf)-BED proteins are a novel superfamily of transcription factors that controls numerous activities in plants including growth, development, and cellular responses to biotic and abiotic stresses. Despite their important roles in gene regulation, little is known about the specific functions of Zf-BEDs in land plants. The current study identified a total of 750 Zf-BED-encoding genes in 35 land plant species including mosses, bryophytes, lycophytes, gymnosperms, and angiosperms. The gene family size was somewhat proportional to genome size. All identified genes were categorized into 22 classes based on their specific domain architectures. Of these, class I (Zf-BED_DUF-domain_Dimer_Tnp_hAT) was the most common in the majority of the land plants. However, some classes were family-specific, while the others were species-specific, demonstrating diversity at different classification levels. In addition, several novel functional domains were also predicated including WRKY and nucleotide-binding site (NBS). Comparative genomics, transcriptomics, and proteomics provided insights into the evolutionary history, duplication, divergence, gene gain and loss, species relationship, expression profiling, and structural diversity of Zf-BEDs in land plants. The comprehensive study of Zf-BEDs in Gossypium sp., (cotton) also demonstrated a clear footprint of polyploidization. Overall, this comprehensive evolutionary study of Zf-BEDs in land plants highlighted significant diversity among plant species.
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Affiliation(s)
- Athar Hussain
- Genomics Lab, School of Food and Agricultural Sciences (SFAS), University of Management and Technology (UMT), Lahore, 54770, Pakistan
| | - Jinbao Liu
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, AL, 35294, USA
| | - Binoop Mohan
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, AL, 35294, USA
| | - Akif Burhan
- Department of Life Science, University of Management and Technology (UMT), Lahore, 54770, Pakistan
| | - Zunaira Nasim
- Department of Life Science, University of Management and Technology (UMT), Lahore, 54770, Pakistan
| | - Raveena Bano
- Department of Life Science, University of Management and Technology (UMT), Lahore, 54770, Pakistan
| | - Ayesha Ameen
- Office of Research Innovation and Commercialization, University of Management and Technology, Lahore, 54770, Pakistan
| | - Madiha Zaynab
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Sciences, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 51807, Guangdong, China
| | - M Shahid Mukhtar
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, AL, 35294, USA.
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25
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Hao M, Zhang J, Sun M, Diao K, Wang J, Li S, Cao Q, Dai S, Mi X. TRAF4 Inhibits the Apoptosis and Promotes the Proliferation of Breast Cancer Cells by Inhibiting the Ubiquitination of Spindle Assembly-Associated Protein Eg5. Front Oncol 2022; 12:855139. [PMID: 35692762 PMCID: PMC9174544 DOI: 10.3389/fonc.2022.855139] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
Tumor necrosis factor receptor associated factor 4 (TRAF4) is a RING domain E3 ubiquitin ligase that mediates the ubiquitination of various proteins and plays an important role in driving tumor progression. By studying the relationship between TRAF4 and Eg5, a member of the kinesin family that plays a critical role in spindle assembly, we demonstrated that TRAF4 regulated Eg5 ubiquitination and contributed to Eg5-mediated breast cancer proliferation and inhibited breast cancer apoptosis. TRAF4 and Eg5 were both highly expressed in breast cancer and their protein level was positively correlated. Relying on its Zinc fingers domain, TRAF4 interacted with Eg5 in the cytoplasm of breast cancer cells. TRAF4 was a mitosis-related protein, and by up-regulating the protein level of Eg5 TRAF4 participated in spindle assembly. Loss of TRAF4 resulted in monopolar spindles formation, but loss of function could be rescued by Eg5. Relying on its RING domain, TRAF4 up-regulated Eg5 protein levels by inhibition of Eg5 ubiquitination, thus stabilizing Eg5 protein level during mitosis. Furthermore, we found that Smurf2, a TRAF4-targeted ubiquitination substrate, mediated the regulation of Eg5 ubiquitination by TRAF4. TRAF4 inhibited the interaction between Smurf2 and Eg5, and down-regulated the protein level of Smurf2 by promoting its ubiquitination, thereby inhibited the Smurf2-catalyzed ubiquitination of Eg5 and up-regulated Eg5 protein levels. We also demonstrate that TRAF4 plays an important role in promoting cell proliferation and in inhibiting cell apoptosis induced by Eg5. In summary, our study suggests a new direction for investigating the role of TRAF4 in driving breast cancer progression.
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Affiliation(s)
- Miaomiao Hao
- Department of Pathology, College of Basic Medical Sciences, China Medical University, Shenyang, China
- Department of Pathology, Shanghai Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Jie Zhang
- Department of Pathology, School of Basic Medical Sciences, Hebei University, Baoding, China
| | - Mingfang Sun
- Department of Pathology, College of Basic Medical Sciences, First Affiliated Hospital, China Medical University, Shenyang, China
| | - Kexin Diao
- Department of Pathology, College of Basic Medical Sciences, First Affiliated Hospital, China Medical University, Shenyang, China
| | - Jian Wang
- Department of Pathology, College of Basic Medical Sciences, First Affiliated Hospital, China Medical University, Shenyang, China
| | - Shiping Li
- Department of Pathology, College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Qixue Cao
- Department of Pathology, Shanghai Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Shundong Dai
- Department of Pathology, Shanghai Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Xiaoyi Mi
- Department of Pathology, College of Basic Medical Sciences, First Affiliated Hospital, China Medical University, Shenyang, China
- *Correspondence: Xiaoyi Mi,
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26
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Fischer F, Grigolon G, Benner C, Ristow M. Evolutionarily conserved transcription factors as regulators of longevity and targets for geroprotection. Physiol Rev 2022; 102:1449-1494. [PMID: 35343830 DOI: 10.1152/physrev.00017.2021] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Aging is the single largest risk factor for many debilitating conditions, including heart diseases, stroke, cancer, diabetes, and neurodegenerative disorders. While far from understood in its full complexity, it is scientifically well-established that aging is influenced by genetic and environmental factors, and can be modulated by various interventions. One of aging's early hallmarks are aberrations in transcriptional networks, controlling for example metabolic homeostasis or the response to stress. Evidence in different model organisms abounds that a number of evolutionarily conserved transcription factors, which control such networks, can affect lifespan and healthspan across species. These transcription factors thus potentially represent conserved regulators of longevity and are emerging as important targets in the challenging quest to develop treatments to mitigate age-related diseases, and possibly even to slow aging itself. This review provides an overview of evolutionarily conserved transcription factors that impact longevity or age-related diseases in at least one multicellular model organism (nematodes, flies, or mice), and/or are tentatively linked to human aging. Discussed is the general evidence for transcriptional regulation of aging and disease, followed by a more detailed look at selected transcription factor families, the common metabolic pathways involved, and the targeting of transcription factors as a strategy for geroprotective interventions.
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Affiliation(s)
- Fabian Fischer
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland
| | - Giovanna Grigolon
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland
| | - Christoph Benner
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland
| | - Michael Ristow
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland
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Maderazo D, Flegg JA, Algama M, Ramialison M, Keith J. Detection and identification of cis-regulatory elements using change-point and classification algorithms. BMC Genomics 2022; 23:78. [PMID: 35078412 PMCID: PMC8790847 DOI: 10.1186/s12864-021-08190-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 11/19/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Transcriptional regulation is primarily mediated by the binding of factors to non-coding regions in DNA. Identification of these binding regions enhances understanding of tissue formation and potentially facilitates the development of gene therapies. However, successful identification of binding regions is made difficult by the lack of a universal biological code for their characterisation. RESULTS We extend an alignment-based method, changept, and identify clusters of biological significance, through ontology and de novo motif analysis. Further, we apply a Bayesian method to estimate and combine binary classifiers on the clusters we identify to produce a better performing composite. CONCLUSIONS The analysis we describe provides a computational method for identification of conserved binding sites in the human genome and facilitates an alternative interrogation of combinations of existing data sets with alignment data.
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Affiliation(s)
- Dominic Maderazo
- School of Mathematics and Statistics, The University of Melbourne, Melbourne, 3010, VIC, Australia.
| | - Jennifer A Flegg
- School of Mathematics and Statistics, The University of Melbourne, Melbourne, 3010, VIC, Australia
| | - Manjula Algama
- School of Mathematics, Monash University, Melbourne, 3800, VIC, Australia
| | - Mirana Ramialison
- Australian Regenerative Medicine Institute, Monash University, Melbourne, 3800, VIC, Australia
| | - Jonathan Keith
- School of Mathematics, Monash University, Melbourne, 3800, VIC, Australia
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28
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Hua B, Chang J, Han X, Xu Z, Hu S, Li S, Wang R, Yang L, Yang M, Wu S, Shen J, Yu X, Wu S. H and HL synergistically regulate jasmonate-triggered trichome formation in tomato. HORTICULTURE RESEARCH 2022; 9:uhab080. [PMID: 35048113 PMCID: PMC8973001 DOI: 10.1093/hr/uhab080] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/21/2021] [Accepted: 11/25/2021] [Indexed: 06/14/2023]
Abstract
The development of trichomes, which protect plants against herbivores, is affected by various stresses. In tomato, previous studies showed that stress triggered JA signaling influences trichome formation, but the underlying mechanism is not fully resolved. Here, we found two C2H2 zinc finger proteins synergistically regulate JA-induced trichome formation in tomato. The naturally occurring mutations in H and its close homolog H-like gene in a spontaneous mutant, LA3172 cause severely affected trcihome development. Compared with respective single mutant, h/hl double mutant displayed more severe trichome defects in all tissues. Despite the partially redundant function, H and HL genes regulate the trichome formation in the spatially distinct manner, with HL more involved in hypocotyls and leaves, while H more involved in stems and sepals. Furthermore,the activity of H/HL is essential for JA-triggered trichome formation. JA signaling inhibitor SlJAZ2 represses the activity of H and HL via physical interaction, resulting in the activation of THM1, a negative regulator of trichome formation. Our results provide novel insight into the mechanism of the trichome formation in response to stress induced JA signaling in tomato.
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Affiliation(s)
- Bing Hua
- College of Horticulture, FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Jiang Chang
- College of Horticulture, FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaoqian Han
- College of Horticulture, FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhijing Xu
- College of Horticulture, FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shourong Hu
- College of Horticulture, FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shuang Li
- College of Horticulture, FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Renyin Wang
- College of Horticulture, FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Liling Yang
- College of Horticulture, FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Meina Yang
- College of Horticulture, FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shasha Wu
- College of Horticulture, FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jingyuan Shen
- College of Horticulture, FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaomin Yu
- College of Horticulture, FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shuang Wu
- College of Horticulture, FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Zheng F, Cui L, Li C, Xie Q, Ai G, Wang J, Yu H, Wang T, Zhang J, Ye Z, Yang C. Hair interacts with SlZFP8-like to regulate the initiation and elongation of trichomes by modulating SlZFP6 expression in tomato. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:228-244. [PMID: 34499170 DOI: 10.1093/jxb/erab417] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 09/09/2021] [Indexed: 06/13/2023]
Abstract
Trichomes are specialized glandular or non-glandular structures that provide physical or chemical protection against insect and pathogen attack. Trichomes in Arabidopsis have been extensively studied as typical non-glandular structures. By contrast, the molecular mechanism underlying glandular trichome formation and elongation remains largely unknown. We previously demonstrated that Hair is essential for the formation of type I and type VI trichomes. Here, we found that overexpression of Hair increased the density and length of tomato trichomes. Biochemical assays revealed that Hair physically interacts with its close homolog SlZFP8-like (SlZFP8L), and SlZFP8L also directly interacts with Woolly. SlZFP8L-overexpressing plants showed increased trichome density and length. We further found that the expression of SlZFP6, which encodes a C2H2 zinc finger protein, is positively regulated by Hair. Using chromatin immunoprecipitation, yeast one-hybrid, and dual-luciferase assays we identified that SlZFP6 is a direct target of Hair. Similar to Hair and SlZFP8L, the overexpression of SlZFP6 also increased the density and length of tomato trichomes. Taken together, our results suggest that Hair interacts with SlZFP8-like to regulate the initiation and elongation of trichomes by modulating SlZFP6 expression in tomato.
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Affiliation(s)
- Fangyan Zheng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Long Cui
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Changxing Li
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Qingmin Xie
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Guo Ai
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Junqiang Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Huiyang Yu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Taotao Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Junhong Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Zhibiao Ye
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Changxian Yang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
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30
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Lin DZ, Pan QW, Wang XM, Chen Y, Pan XB, Dong YJ. Mutation of the rice AN1-type zinc-finger protein gene ASL4 causes chloroplast development defects and seedling lethality. PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:95-103. [PMID: 34724300 DOI: 10.1111/plb.13334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 06/20/2021] [Accepted: 07/20/2021] [Indexed: 06/13/2023]
Abstract
Plant zinc-finger proteins play a crucial role in biosynthesis and plant development. However, it is not known whether certain zinc-finger proteins play a role in rice chloroplast development. In this study, a novel rice zinc-finger protein mutant asl4 (albino seedling lethality4), which exhibits an albino lethal phenotype at the seedling stage, was used. Chlorophyll fluorescence analysis and TEM were used to investigate features of the asl4 mutant. The genetic behaviour and function of ASL4 gene were then analysed thorough map-based cloning, transgenic complement and subcellular localization. The albino lethal phenotype was caused by a single nucleotide (G*) deletion mutation on the exon of the ASL4 (LOC_Os09g21710) gene. The ASL4 gene encoded a novel zinc-finger protein containing two ZnF-AN1 domains, which was localized to the nucleocytoplasm. The ASL4 transcripts were highly expressed in all leaves but relatively less in other tissues, suggesting its tissue-specific expression. The transcript levels of associated genes for Chl biosynthesis, photosynthesis and chloroplast development were severely suppressed in asl4 mutants. In conclusion, the absence of ASL4 function caused a defect in chloroplast development and seedling lethality. This is the first published report on the importance of the ZnF-AN1 type zinc-finger protein gene in chloroplast development in rice.
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Affiliation(s)
- D Z Lin
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Q W Pan
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - X M Wang
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Y Chen
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - X B Pan
- Crop Institute, Taizhou Academy of Agricultural Sciences, Zhejiang Linhai, China
| | - Y J Dong
- College of Life Sciences, Shanghai Normal University, Shanghai, China
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai, China
- Institute of Genetics, Shanghai Normal University, Shanghai, China
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31
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Grochowska KM, Bär J, Gomes GM, Kreutz MR, Karpova A. Jacob, a Synapto-Nuclear Protein Messenger Linking N-methyl-D-aspartate Receptor Activation to Nuclear Gene Expression. Front Synaptic Neurosci 2021; 13:787494. [PMID: 34899262 PMCID: PMC8662305 DOI: 10.3389/fnsyn.2021.787494] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/01/2021] [Indexed: 11/13/2022] Open
Abstract
Pyramidal neurons exhibit a complex dendritic tree that is decorated by a huge number of spine synapses receiving excitatory input. Synaptic signals not only act locally but are also conveyed to the nucleus of the postsynaptic neuron to regulate gene expression. This raises the question of how the spatio-temporal integration of synaptic inputs is accomplished at the genomic level and which molecular mechanisms are involved. Protein transport from synapse to nucleus has been shown in several studies and has the potential to encode synaptic signals at the site of origin and decode them in the nucleus. In this review, we summarize the knowledge about the properties of the synapto-nuclear messenger protein Jacob with special emphasis on a putative role in hippocampal neuronal plasticity. We will elaborate on the interactome of Jacob, the signals that control synapto-nuclear trafficking, the mechanisms of transport, and the potential nuclear function. In addition, we will address the organization of the Jacob/NSMF gene, its origin and we will summarize the evidence for the existence of splice isoforms and their expression pattern.
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Affiliation(s)
- Katarzyna M Grochowska
- Research Group (RG) Neuroplasticity, Leibniz Institute for Neurobiology, Magdeburg, Germany.,Leibniz Group 'Dendritic Organelles and Synaptic Function', University Medical Center Hamburg-Eppendorf, Center for Molecular Neurobiology Hamburg, Hamburg, Germany
| | - Julia Bär
- Research Group (RG) Neuroplasticity, Leibniz Institute for Neurobiology, Magdeburg, Germany.,Research Group (RG) Neuronal Protein Transport, University Medical Center Hamburg-Eppendorf, Center for Molecular Neurobiology Hamburg, Hamburg, Germany.,Research Group (RG) Optobiology, Institute of Biology, HU Berlin, Berlin, Germany
| | - Guilherme M Gomes
- Research Group (RG) Neuroplasticity, Leibniz Institute for Neurobiology, Magdeburg, Germany.,Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany
| | - Michael R Kreutz
- Research Group (RG) Neuroplasticity, Leibniz Institute for Neurobiology, Magdeburg, Germany.,Leibniz Group 'Dendritic Organelles and Synaptic Function', University Medical Center Hamburg-Eppendorf, Center for Molecular Neurobiology Hamburg, Hamburg, Germany.,Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany.,German Research Center for Neurodegenerative Diseases (DZNE), Magdeburg, Germany
| | - Anna Karpova
- Research Group (RG) Neuroplasticity, Leibniz Institute for Neurobiology, Magdeburg, Germany.,Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany
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32
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Tan Q, Jiang S, Wang N, Liu X, Zhang X, Wen B, Fang Y, He H, Chen X, Fu X, Li D, Xiao W, Li L. OVATE Family Protein PpOFP1 Physically Interacts With PpZFHD1 and Confers Salt Tolerance to Tomato and Yeast. FRONTIERS IN PLANT SCIENCE 2021; 12:759955. [PMID: 34868154 PMCID: PMC8633955 DOI: 10.3389/fpls.2021.759955] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/04/2021] [Indexed: 06/13/2023]
Abstract
The OVATE family protein (OFP) genes (OFPs) have been shown to respond to salt stress in plants. However, the regulatory mechanism for salt tolerance of the peach (Prunus persica) OFP gene PpOFP1 has not been elucidated. In this study, using yeast two-hybrid screening, we isolated a nucleus-localized ZF-HD_dimer domain protein PpZFHD1, which interacts with the PpOFP1 protein in the peach cultivar "Zhongnongpan No.10". A segmentation experiment further suggested that the interaction happens more specifically between the N-terminal, contains ZF-HD_dimer domain, of PpZFHD1 and the C-terminal, consists of OVATE domain, of PpOFP1. Additionally, quantitative real-time polymerase chain reaction (qRT-PCR) experiments indicate that transcription of these two genes are induced by 200 mmol/L (mM) NaCl treatment. Heterogeneous transformation experiments suggested that the growth status of transformed yeast strain over-expressing each of these two genes was more robust than that of control (CK). Furthermore, transgenic tomato plants over-expressing PpOFP1 were also more robust. They had a higher content of chlorophyll, soluble proteins, soluble sugars, and proline. Activities of the superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) in these plants were higher, and tissues from these plants exhibited a lower relative conductivity and malondialdehyde (MDA) content. These results suggest that PpOFP1 physically interacts with PpZFHD1 and confers salt tolerance to tomato and yeast, thus revealing a novel mechanism for regulating salt tolerance in peach and other perennial deciduous trees.
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Affiliation(s)
- Qiuping Tan
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Tai’an, China
- College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Shan Jiang
- Shandong Huayu University of Technology, Dezhou, China
| | - Ning Wang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Tai’an, China
| | - Xiao Liu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Tai’an, China
| | - Xinhao Zhang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Tai’an, China
| | - Binbin Wen
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Tai’an, China
| | - Yuhui Fang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Tai’an, China
| | - Huajie He
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Tai’an, China
| | - Xiude Chen
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Tai’an, China
| | - Xiling Fu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Tai’an, China
| | - Dongmei Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Tai’an, China
| | - Wei Xiao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Tai’an, China
| | - Ling Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Tai’an, China
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Yang F, Zhang Z, Hu B, Yu Y, Tan A. A CCCH zinc finger gene regulates doublesex alternative splicing and male development in Bombyx mori. INSECT SCIENCE 2021; 28:1253-1261. [PMID: 33029871 DOI: 10.1111/1744-7917.12876] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/26/2020] [Accepted: 09/28/2020] [Indexed: 06/11/2023]
Abstract
Recent identification of a Piwi-interacting RNA (piRNA)-initiated sex determination cascade in the silkworm, Bombyx mori, provides novel insights into high diversity of insect sex determination pathways. In this system, the W-chromosome-derived Fem piRNA is the primary sex determination signal. A CCCH-type zinc finger gene Masculinizer (Masc), which is targeted by Fem piRNA-PIWI complex in female animals, is indispensable for male-specific splicing of B. mori doublesex (Bmdsx). Although many genes involved in this cascade have been identified, the regulatory mechanisms of silkworm sex determination remain to be elucidated. Here we show that another CCCH-type zinc finger gene, Bmznf-2, is a masculinization factor in B. mori. Bmznf-2 shows testis-abundant expression and loss of Bmznf-2 function via clustered regularly interspaced short palindromic repeats / single-guide RNA-mediated mutagenesis results in feminized differentiation and appearance of the female-specific splicing variants of Bmdsx transcripts in males. In contrast, there is no phenotypic consequence in mutant females. In mutant males, relative messenger RNA expression levels of female-dominant genes such as vitellogenin and sex-specific storage protein 1 are significantly elevated while several male-dominant genes are significantly down-regulated. Furthermore, male mutants show delayed developmental timing, smaller body sizes of larvae and malformation of moth wings. Our data thus reveal that Bmznf-2 plays an indispensable role in silkworm male sexual differentiation.
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Affiliation(s)
- Fangying Yang
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhongjie Zhang
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bo Hu
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ye Yu
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Anjiang Tan
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
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Niu H, Xia P, Hu Y, Zhan C, Li Y, Gong S, Li Y, Ma D. Genome-wide identification of ZF-HD gene family in Triticum aestivum: Molecular evolution mechanism and function analysis. PLoS One 2021; 16:e0256579. [PMID: 34559835 PMCID: PMC8462724 DOI: 10.1371/journal.pone.0256579] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/11/2021] [Indexed: 12/04/2022] Open
Abstract
ZF-HD family genes play important roles in plant growth and development. Studies about the whole genome analysis of ZF-HD gene family have been reported in some plant species. In this study, the whole genome identification and expression profile of the ZF-HD gene family were analyzed for the first time in wheat. A total of 37 TaZF-HD genes were identified and divided into TaMIF and TaZHD subfamilies according to the conserved domain. The phylogeny tree of the TaZF-HD proteins was further divided into six groups based on the phylogenetic relationship. The 37 TaZF-HDs were distributed on 18 of 21 chromosomes, and almost all the genes had no introns. Gene duplication and Ka/Ks analysis showed that the gene family may have experienced powerful purification selection pressure during wheat evolution. The qRT-PCR analysis showed that TaZF-HD genes had significant expression patterns in different biotic stress and abiotic stress. Through subcellular localization experiments, we found that TaZHD6-3B was located in the nucleus, while TaMIF4-5D was located in the cell membrane and nucleus. Our research contributes to a comprehensive understanding of the TaZF-HD family, provides a new perspective for further research on the biological functions of TaZF-HD genes in wheat.
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Affiliation(s)
- Hongli Niu
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
| | - Pengliang Xia
- Enshi Tobacco Company of Hubei Province, Enshi, China
| | - Yifeng Hu
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
| | - Chuang Zhan
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
| | - Yiting Li
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
| | - Shuangjun Gong
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
| | - Yan Li
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
- * E-mail: (YL); (DM)
| | - Dongfang Ma
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
- Key Laboratory of Integrated Pest Management on Crop in Central China, Ministry of Agriculture/Hubei Province Key Laboratory for Control of Crop Diseases, Pest and Weeds/Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, China
- * E-mail: (YL); (DM)
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35
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Nikonov OS, Nevskaya NA, Garber MB, Nikonov SV. Structure and Function of Archaeal Translation Initiation Factor 2 Fragments Containing Cys2-Cys2 Motifs. BIOCHEMISTRY (MOSCOW) 2021; 86:1003-1011. [PMID: 34488576 DOI: 10.1134/s0006297921080101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The heterotrimeric (αβγ) translation initiation factor 2 of archaea and eukaryotes (a/eIF2) supplies the P-site of the ribosome with the initiation tRNA. Its two subunits (β and γ) contain the Cys2-Cys2 motif, which is capable of forming a stable zinc finger structure in the presence of zinc ions. In this work, comparative analysis of the fragments containing Cys2-Cys2 motifs in the aIF2β and aIF2γ structures from different organisms was carried out and their environments in crystals was analyzed. Based on the obtained data, a conclusion was made that the conformation and role of these fragments in the β- and γ-subunits of the aIF2 are different.
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Affiliation(s)
- Oleg S Nikonov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
| | - Natalia A Nevskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Maria B Garber
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Stanislav V Nikonov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
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Tahir MS, Tian L. HD2-type histone deacetylases: unique regulators of plant development and stress responses. PLANT CELL REPORTS 2021; 40:1603-1615. [PMID: 34041586 DOI: 10.1007/s00299-021-02688-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
Plants have developed sophisticated and complex epigenetic regulation-based mechanisms to maintain stable growth and development under diverse environmental conditions. Histone deacetylases (HDACs) are important epigenetic regulators in eukaryotes that are involved in the deacetylation of lysine residues of histone H3 and H4 proteins. Plants have developed a unique HDAC family, HD2, in addition to the RPD3 and Sir2 families, which are also present in other eukaryotes. HD2s are well conserved plant-specific HDACs, which were first identified as nucleolar phosphoproteins in maize. The HD2 family plays important roles not only in fundamental developmental processes, including seed germination, root and leaf development, floral transition, and seed development but also in regulating plant responses to biotic and abiotic stresses. Some of the HD2 members coordinate with each other to function. The HD2 family proteins also show functional association with RPD3-type HDACs and other transcription factors as a part of repression complexes in gene regulatory networks involved in environmental stress responses. This review aims to analyse and summarise recent research progress in the HD2 family, and to describe their role in plant growth and development and in response to different environmental stresses.
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Affiliation(s)
- Muhammad Sufyan Tahir
- Department of Biology, University of Western Ontario, London, ON, Canada.
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada.
| | - Lining Tian
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
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Rakhra G, Rakhra G. Zinc finger proteins: insights into the transcriptional and post transcriptional regulation of immune response. Mol Biol Rep 2021; 48:5735-5743. [PMID: 34304391 PMCID: PMC8310398 DOI: 10.1007/s11033-021-06556-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 07/08/2021] [Indexed: 12/18/2022]
Abstract
BACKGROUND Zinc finger proteins encompass one of the unique and large families of proteins with diversified biological functions in the human body. These proteins are primarily considered to be DNA binding transcription factors; however, owing to the diverse array of zinc-finger domains, they are able to interact with molecules other than DNA like RNA, proteins, lipids and PAR (poly-ADP-ribose). Evidences from recent scientific studies have provided an insight into the potential functions of zinc finger proteins in immune system regulation both at the transcriptional and post transcriptional level. However, the mechanism and importance of zinc finger proteins in the regulation of immune response is not very well defined and understood. This review highlights in detail the importance of zinc finger proteins in the regulation of immune system at transcriptional and post transcriptional level. CONCLUSION Different types of zinc finger proteins are involved in immune system regulation and their mechanism of regulation is discussed herewith.
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Affiliation(s)
- Gurseen Rakhra
- Department of Nutrition & Dietetics, Faculty of Allied Health Sciences, Manav Rachna International Institute of Research & Studies, Faridabad, Haryana, 121004, India
| | - Gurmeen Rakhra
- Department of Biochemistry, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, India.
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Shehzad M, Zhou Z, Ditta A, Khan M, Cai X, Xu Y, Maqbool A, Khalofah A, Shaban M, Naeem M, Ansari MJ, Wang K, Liu F. Identification and characterization of genes related to salt stress tolerance within segregation distortion regions of genetic map in F2 population of upland cotton. PLoS One 2021; 16:e0247593. [PMID: 33770112 PMCID: PMC7997035 DOI: 10.1371/journal.pone.0247593] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/09/2021] [Indexed: 12/12/2022] Open
Abstract
Segregation distortion (SD) is a genetic mechanism commonly found in segregating or stable populations. The principle behind this puzzles many researchers. The F2 generation developed from wild Gossypium darwinii and G. hirsutum CCRI12 species was used to investigate the possible transcription factors within the segregation distortion regions (SDRs). The 384 out of 2763 markers were distorted in 29 SDRs on 18 chromosomes. Good collinearity was observed among genetic and physical maps of G. hirsutum and G. barbadense syntenic blocks. Total 568 genes were identified from SDRs of 18 chromosomes. Out of these genes, 128 belonged to three top-ranked salt-tolerant gene families. The DUF597 contained 8 uncharacterized genes linked to Pkinase (PF00069) gene family in the phylogenetic tree, while 15 uncharacterized genes clustered with the zinc finger gene family. Two hundred thirty four miRNAs targeted numerous genes, including ghr-miR156, ghr-miR399 and ghr-miR482, while others targeted top-ranked stress-responsive transcription factors. Moreover, these genes were involved in the regulation of numerous stress-responsive cis-regulatory elements. The RNA sequence data of fifteen upregulated genes were verified through the RT-qPCR. The expression profiles of two highly upregulated genes (Gh_D01G2015 and Gh_A01G1773) in salt-tolerant G. darwinii showed antagonistic expression in G. hirsutum. The results indicated that salt-tolerant genes have been possibly transferred from the wild G. darwinii species. A detailed functional analysis of these genes can be carried out which might be helpful in the future for gene cloning, transformation, gene editing and the development of salt-resistant cotton varieties.
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Affiliation(s)
- Muhammad Shehzad
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R China
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R China
| | - Allah Ditta
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R China
- Plant Breeding, and Genetics Division, Cotton Group, Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad, Punjab, Pakistan
| | - Majid Khan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R China
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R China
| | - Yanchao Xu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R China
| | - Amir Maqbool
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, Nigde, Turkey
| | - Ahlam Khalofah
- Biology Department, Faculty of Science, King Khalid University, Abha, Saudi Arabia
| | - Muhammad Shaban
- Department of Plant Breeding and Genetics, Faculty of Agricultural Science & Technology, Bahauddin Zakariya University, Multan, Pakistan
| | - Muhammad Naeem
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, Nigde, Turkey
| | - Mohammad Javed Ansari
- Department of Botany, Hindu College Moradabad (Mahatma Jyotiba Phule Rohilkhand University Bareilly), Bareilly, India
| | - Kunbo Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R China
- * E-mail: (KW); (FL)
| | - Fang Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- * E-mail: (KW); (FL)
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Manceau A, Nagy KL, Glatzel P, Bourdineaud JP. Acute Toxicity of Divalent Mercury to Bacteria Explained by the Formation of Dicysteinate and Tetracysteinate Complexes Bound to Proteins in Escherichia coli and Bacillus subtilis. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:3612-3623. [PMID: 33629845 DOI: 10.1021/acs.est.0c05202] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Bacteria are the most abundant organisms on Earth and also the major life form affected by mercury (Hg) poisoning in aquatic and terrestrial food webs. In this study, we applied high energy-resolution X-ray absorption near edge structure (HR-XANES) spectroscopy to bacteria with intracellular concentrations of Hg as low as 0.7 ng/mg (ppm) for identifying the intracellular molecular forms and trafficking pathways of Hg in bacteria at environmentally relevant concentrations. Gram-positive Bacillus subtilis and Gram-negative Escherichia coli were exposed to three Hg species: HgCl2, Hg-dicysteinate (Hg(Cys)2), and Hg-dithioglycolate (Hg(TGA)2). In all cases, Hg was transformed into new two- and four-coordinate cysteinate complexes, interpreted to be bound, respectively, to the consensus metal-binding CXXC motif and zinc finger domains of proteins, with glutathione acting as a transfer ligand. Replacement of zinc cofactors essential to gene regulatory proteins with Hg would inhibit vital functions such as DNA transcription and repair and is suggested to be a main cause of Hg genotoxicity.
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Affiliation(s)
- Alain Manceau
- Université Grenoble Alpes, CNRS, ISTerre, CS 40700, 38058 Grenoble, France
| | - Kathryn L Nagy
- Department of Earth and Environmental Sciences, University of Illinois at Chicago, MC-186, 845 West Taylor Street, Chicago, Illinois 60607, United States
| | - Pieter Glatzel
- European Synchrotron Radiation Facility (ESRF), 71 Rue des Martyrs, 38000 Grenoble, France
| | - Jean-Paul Bourdineaud
- Institut Européen de Chimie et Biologie, Université de Bordeaux, CNRS, UMR 5234, 2 rue Escarpit, 33607 Pessac, France
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Stevenson BC, Martens J, Berden G, Oomens J, Schäfer M, Armentrout PB. IRMPD Spectroscopic and Theoretical Structural Investigations of Zinc and Cadmium Dications Bound to Histidine Dimers. J Phys Chem A 2020; 124:10266-10276. [PMID: 33241937 DOI: 10.1021/acs.jpca.0c08861] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metallated gas-phase structures consisting of a deprotonated and an intact histidine (His) ligand, yielding M(His-H)(His)+, where M = Zn and Cd, were examined with infrared multiple photon dissociation (IRMPD) action spectroscopy utilizing light from a free-electron laser (FEL). In parallel, quantum chemical calculations identified several low-energy isomers for each complex. Experimental action spectra were compared to linear spectra calculated at the B3LYP level of theory using the 6-311+G(d,p) and def2-TZVP basis sets for the zinc and cadmium complexes, respectively. For both Zn and Cd species, the definitive assignment is complicated by conflicting relative energetics, which were calculated at B3LYP, B3LYP-GD3BJ, B3P86, and MP2(full) levels. Spectral comparison for both species indicates that the dominant conformation, [Nα,Nπ,CO-][CO2-](NπH+), has the deprotonated His chelating the metal at the amine nitrogen, π nitrogen of the imidazole ring, and the deprotonated carbonyl oxygen and that the intact His ligand adopts a salt-bridge bidentate binding motif, coordinating the metal with both carboxylate oxygens. There is also evidence for a conformation where the deprotonated His coordination is maintained, but the intact His ligand adopts a more canonical structure, coordinating with the metal atom at the amine nitrogen and π nitrogen, [Nα,Nπ,CO-][Nα,Nπ]gtgg. For both metallated species, B3LYP, B3P86, and B3LYP-GD3BJ levels of theory appear to describe the relative stability of the dominant zwitterionic species more accurately than the MP2(full) level.
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Affiliation(s)
- Brandon C Stevenson
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Jonathan Martens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands.,van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, NL, 1098 XH Amsterdam, The Netherlands
| | - Mathias Schäfer
- Department of Chemistry, University of Cologne, 50939 Cologne, Germany
| | - P B Armentrout
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
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Yang C, Xiao X, Huang L, Zhou F, Chen LH, Zhao YY, Qu SL, Zhang C. Role of Kruppel-like factor 4 in atherosclerosis. Clin Chim Acta 2020; 512:135-141. [PMID: 33181148 DOI: 10.1016/j.cca.2020.11.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/29/2020] [Accepted: 11/02/2020] [Indexed: 01/13/2023]
Abstract
Atherosclerosis is one of the chronic progressive diseases, which is caused by vascular injury and promoted by the interaction of various inflammatory factors and inflammatory cells. In recent years, kruppel-like factor 4 (KLF4), a significant transcription factor that participated in cell growth, differentiation and proliferation, has been proved to cause substantial impacts on regulating cardiovascular disease. This paper will give a comprehensive summary to highlight KLF4 as a crucial regulator of foam cell formation, vascular smooth muscle cells (VSMCs) phenotypic transformation, macrophage polarization, endothelial cells inflammation, lymphocyte differentiation and cell proliferation in the process of atherosclerosis. Recent studies show that KLF4 may be an important "molecular switch" in the process of improving vascular injury and inflammation under harmful stimulation, suggesting that KLF4 is a latent disease biomarker for the therapeutic target of atherosclerosis and vascular disease.
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Affiliation(s)
- Chen Yang
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, Hengyang Medical College, University of South China, Hengyang, Hunan 421001, People's Republic of China
| | - Xuan Xiao
- Research Lab for Clinical & Translational Medicine, Hengyang Medical College, University of South China, Hengyang, Hunan 421001, People's Republic of China
| | - Liang Huang
- Research Lab for Clinical & Translational Medicine, Hengyang Medical College, University of South China, Hengyang, Hunan 421001, People's Republic of China
| | - Fan Zhou
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, Hengyang Medical College, University of South China, Hengyang, Hunan 421001, People's Republic of China
| | - Lin-Hui Chen
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, Hengyang Medical College, University of South China, Hengyang, Hunan 421001, People's Republic of China
| | - Yu-Yan Zhao
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, Hengyang Medical College, University of South China, Hengyang, Hunan 421001, People's Republic of China
| | - Shun-Lin Qu
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, Hengyang Medical College, University of South China, Hengyang, Hunan 421001, People's Republic of China
| | - Chi Zhang
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, Hengyang Medical College, University of South China, Hengyang, Hunan 421001, People's Republic of China.
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Syed Lal Badshah, Ullah A, Syed S. The Role of Zinc-Finger Antiviral Proteins in Immunity against Viruses. MOLECULAR GENETICS MICROBIOLOGY AND VIROLOGY 2020. [DOI: 10.3103/s0891416820020020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Kumar A, Rathi E, Hariharapura RC, Kini SG. Is viral E6 oncoprotein a viable target? A critical analysis in the context of cervical cancer. Med Res Rev 2020; 40:2019-2048. [PMID: 32483862 DOI: 10.1002/med.21697] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 05/18/2020] [Accepted: 05/21/2020] [Indexed: 12/15/2022]
Abstract
An understanding of the pathology of cervical cancer (CC) mediated by E6/E7 oncoproteins of high-risk human papillomavirus (HPV) was developed by late 80's. But if we look at the present scenario, not a single drug could be developed to inhibit these oncoproteins and in turn, be used specifically for the treatment of CC. The readers are advised not to presume the "viability of E6 protein" as mentioned in the title relates to just druggability of E6. The viability aspect will cover almost everything a researcher should know to develop E6 inhibitors until the preclinical stage. Herein, we have analysed the achievements and shortcomings of the scientific community in the last four decades in targeting HPV E6 against CC. Role of all HPV proteins has been briefly described for better perspective with a little detailed discussion of the role of E6. We have reviewed the articles from 1985 onward, reporting in vitro inhibition of E6. Recently, many computational studies have reported potent E6 inhibitors and these have also been reviewed. Subsequently, a critical analysis has been reported to cover the in vitro assay protocols and in vivo models to develop E6 inhibitors. A paragraph has been devoted to the role of public policy to fight CC employing vaccines and whether the vaccine against HPV has quenched the zeal to develop drugs against it. The review concludes with the challenges and the way forward.
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Affiliation(s)
- Avinash Kumar
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Ekta Rathi
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Raghu Chandrashekar Hariharapura
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Suvarna G Kini
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
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Han G, Lu C, Guo J, Qiao Z, Sui N, Qiu N, Wang B. C2H2 Zinc Finger Proteins: Master Regulators of Abiotic Stress Responses in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:115. [PMID: 32153617 PMCID: PMC7044346 DOI: 10.3389/fpls.2020.00115] [Citation(s) in RCA: 193] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 01/24/2020] [Indexed: 05/04/2023]
Abstract
Abiotic stresses such as drought and salinity are major environmental factors that limit crop yields. Unraveling the molecular mechanisms underlying abiotic stress resistance is crucial for improving crop performance and increasing productivity under adverse environmental conditions. Zinc finger proteins, comprising one of the largest transcription factor families, are known for their finger-like structure and their ability to bind Zn2+. Zinc finger proteins are categorized into nine subfamilies based on their conserved Cys and His motifs, including the Cys2/His2-type (C2H2), C3H, C3HC4, C2HC5, C4HC3, C2HC, C4, C6, and C8 subfamilies. Over the past two decades, much progress has been made in understanding the roles of C2H2 zinc finger proteins in plant growth, development, and stress signal transduction. In this review, we focus on recent progress in elucidating the structures, functions, and classifications of plant C2H2 zinc finger proteins and their roles in abiotic stress responses.
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Affiliation(s)
- Guoliang Han
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Chaoxia Lu
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Jianrong Guo
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Ziqi Qiao
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Na Sui
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Nianwei Qiu
- College of Life Sciences, Qufu Normal University, Qufu, China
| | - Baoshan Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
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Functional analysis of SlNCED1 in pistil development and fruit set in tomato (Solanum lycopersicum L.). Sci Rep 2019; 9:16943. [PMID: 31729411 PMCID: PMC6858371 DOI: 10.1038/s41598-019-52948-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 10/25/2019] [Indexed: 12/19/2022] Open
Abstract
Abscisic acid (ABA) is an important regulator of many plant developmental processes, although its regulation in the pistil during anthesis is unclear. We investigated the role of 9-cis-epoxycarotenoid dioxygenase (SlNCED1), a key ABA biosynthesis enzyme, through overexpression and transcriptome analysis in the tomato pistil. During pistil development, ABA accumulates and SlNCED1 expression increases continually, peaking one day before full bloom, when the maximum amount of ethylene is released in the pistil. ABA accumulation and SlNCED1 expression in the ovary remained high for three days before and after full bloom, but then both declined rapidly four days after full bloom following senescence and petal abscission and expansion of the young fruits. Overexpression of SlNCED1 significantly increased ABA levels and also up-regulated SlPP2C5 expression, which reduced ABA signaling activity. Overexpression of SlNCED1 caused up-regulation of pistil-specific Zinc finger transcription factor genes SlC3H29, SlC3H66, and SlC3HC4, which may have affected the expression of SlNCED1-mediated pistil development-related genes, causing major changes in ovary development. Increased ABA levels are due to SlNCED1 overexpresson which caused a hormonal imbalance resulting in the growth of parthenocarpic fruit. Our results indicate that SlNCED1 plays a crucial role in the regulation of ovary/pistil development and fruit set.
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Shalmani A, Muhammad I, Sharif R, Zhao C, Ullah U, Zhang D, Jing XQ, Amin B, Jia P, Mobeen Tahir M, Xu Z, Chen KM, An N. Zinc Finger-Homeodomain Genes: Evolution, Functional Differentiation, and Expression Profiling Under Flowering-Related Treatments and Abiotic Stresses in Plants. Evol Bioinform Online 2019; 15:1176934319867930. [PMID: 31523124 PMCID: PMC6728664 DOI: 10.1177/1176934319867930] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 07/11/2019] [Indexed: 11/15/2022] Open
Abstract
Zinc finger-homeodomain (ZHD) proteins constitute a plant-specific transcription factor family that play important roles in plant growth, development, and stress responses. In this study, we investigated a total of 10, 17, and 31 ZHD gene members in the peach, Arabidopsis, and apple genome, respectively. The phylogenetic tree divided the identified ZHD genes into 4 subfamilies based on their domain organization, gene structure, and motif distribution with minor variations. The ZHD gene family members were unevenly distributed throughout in apple, peach, and Arabidopsis genomes. Segmental duplication was observed for 14 pairs of genes in apple. Transcript analysis found that ZHD genes mostly expressed in various tissues, particularly in leaves and flowers. Moreover, the transcript of most ZHD genes was significantly affected at different time points in response to various flowering-related exogenous hormones (sugar, gibberellin [GA], and 6-benzylaminopurine [6-BA]), signifying their possible role in the flowering induction in apple. Furthermore, the transcripts of CaZHD6, CaZHD7, CaZHD3, and CaZHD8 have induced in response to abiotic stresses including heat, drought, salt, and cold, indicating their possible involvement in response to abiotic stresses. Our research work systemically presents the different roles of ZHD genes. We believe that this study will provide a platform for future functional characterization of ZHD genes and to deeply unfold their roles in the regulation of flowering induction in plants.
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Affiliation(s)
- Abdullah Shalmani
- College of Horticulture, Northwest
A&F University, Yangling, China
- State Key Laboratory of Crop Stress
Biology in Arid Areas, College of Life Sciences, Northwest A&F University,
Yangling, China
| | - Izhar Muhammad
- State Key Laboratory of Crop Stress
Biology in Arid Areas, College of Life Sciences, Northwest A&F University,
Yangling, China
| | - Rahat Sharif
- College of Horticulture, Northwest
A&F University, Yangling, China
| | - CaiPing Zhao
- College of Horticulture, Northwest
A&F University, Yangling, China
| | - Uzair Ullah
- Department of Agriculture, Hazara
University, Mansehra, KPK, Pakistan
| | - Dong Zhang
- College of Horticulture, Northwest
A&F University, Yangling, China
| | - Xiu-Qing Jing
- State Key Laboratory of Crop Stress
Biology in Arid Areas, College of Life Sciences, Northwest A&F University,
Yangling, China
| | - Bakht Amin
- College of Horticulture, Northwest
A&F University, Yangling, China
| | - Peng Jia
- College of Horticulture, Northwest
A&F University, Yangling, China
| | | | - Ze Xu
- College of Horticulture, Northwest
A&F University, Yangling, China
| | - Kun-Ming Chen
- State Key Laboratory of Crop Stress
Biology in Arid Areas, College of Life Sciences, Northwest A&F University,
Yangling, China
| | - Na An
- College of Horticulture, Northwest
A&F University, Yangling, China
- State Key Laboratory of Crop Stress
Biology in Arid Areas, College of Life Sciences, Northwest A&F University,
Yangling, China
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Liu M, Wang X, Sun W, Ma Z, Zheng T, Huang L, Wu Q, Tang Z, Bu T, Li C, Chen H. Genome-wide investigation of the ZF-HD gene family in Tartary buckwheat (Fagopyrum tataricum). BMC PLANT BIOLOGY 2019; 19:248. [PMID: 31185913 PMCID: PMC6558689 DOI: 10.1186/s12870-019-1834-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 05/15/2019] [Indexed: 05/29/2023]
Abstract
BACKGROUND ZF-HD is a family of genes that play an important role in plant growth, development, some studies have found that after overexpression AtZHD1 in Arabidopsis thaliana, florescence advance, the seeds get bigger and the life span of seeds is prolonged, moreover, ZF-HD genes are also participate in responding to adversity stress. The whole genome of the ZF-HD gene family has been studied in several model plants, such as Arabidopsis thaliana and rice. However, there has been little research on the ZF-HD genes in Tartary buckwheat (Fagopyrum tataricum), which is an important edible and medicinal crop. The recently published whole genome sequence of Tartary buckwheat allows us to study the tissue and expression profiles of the ZF-HD gene family in Tartary buckwheat on a genome-wide basis. RESULTS In this study, the whole genome and expression profile of the ZF-HD gene family were analyzed for the first time in Tartary buckwheat. We identified 20 FtZF-HD genes and divided them into MIF and ZHD subfamilies according to phylogeny. The ZHD genes were divided into 5 subfamilies. Twenty FtZF-HD genes were distributed on 7 chromosomes, and almost all the genes had no introns. We detected seven pairs of chromosomes with fragment repeats, but no tandem repeats were detected. In different tissues and at different fruit development stages, the FtZF-HD genes obtained by a real-time quantitative PCR analysis showed obvious expression patterns. CONCLUSIONS In this study, 20 FtZF-HD genes were identified in Tartary buckwheat, and the structures, evolution and expression patterns of the proteins were studied. Our findings provide a valuable basis for further analysis of the biological function of the ZF-HD gene family. Our study also laid a foundation for the improvement of Tartary buckwheat crops.
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Affiliation(s)
- Moyang Liu
- College of Life Science, Sichuan Agricultural University, Ya’an, China
- School of Agriculture and Biolog, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoxiang Wang
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Wenjun Sun
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Zhaotang Ma
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Tianrun Zheng
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Li Huang
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Qi Wu
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Zizhong Tang
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Tongliang Bu
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Chenglei Li
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Hui Chen
- College of Life Science, Sichuan Agricultural University, Ya’an, China
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Comprehensive genomic survey, structural classification and expression analysis of C2H2 zinc finger protein gene family in Brassica rapa L. PLoS One 2019; 14:e0216071. [PMID: 31059545 PMCID: PMC6502316 DOI: 10.1371/journal.pone.0216071] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 04/12/2019] [Indexed: 12/20/2022] Open
Abstract
C2H2 zinc finger protein (ZFP) genes have been extensively studied in many organisms and can function as transcription factors and be involved in many biological processes including plant growth and development and stress responses. In the current study, a comprehensive genomics analysis of the C2H2-ZFP genes in B. rapa was performed. A total of 301 B. rapa putative C2H2-ZFP (BrC2H2-ZFP) genes were identified from the available Brassica genome databases, and further characterized through analysis of conserved amino acid residues in C2H2-ZF domains and their organization, subcellular localization, phylogeny, additional domain, chromosomal location, synteny relationship, Ka/Ks ratio, and expression pattern. We also analyzed the expression patterns of eight B. rapa C2H2-ZFP genes under salt and drought stress conditions by using qRT-PCR technique. Our results showed that about one-third of these B. rapa C2H2-ZFP genes were originated from segmental duplication caused by the WGT around 13 to 17 MYA, one-third of them were highly and consecutively expressed in all tested tissues, and 92% of them were located in nucleus by prediction supporting then their functional roles as transcription factors, of which some may play important roles in plant growth and development. The Ka/Ks ratios of 264 orthologous C2H2-ZFP gene pairs between A. thaliana and B. rapa were all, except two, inferior to 1 (varied from 0.0116 to 1.4919, with an average value of 0.3082), implying that these genes had mainly experienced purifying selection during species evolution. The estimated divergence times of the same set of gene pairs ranged from 6.23 to 38.60 MY, with an average value of 18.29 MY, indicating that these gene members have undergone different selective pressures resulting in different evolutionary rates during species evolution. In addition, a few of these B. rapa C2H2-ZFPs were shown to be involved in stress responses in a similar way as their orthologs in A. thaliana. Comparison between A. thaliana and B. rapa orthologous C2H2-ZFP genes showed that the majority of these C2H2-ZFP gene members encodes proteins with conserved subcellular localization and functional domains between the two species but differed in their expression patterns in five tissues or organs. Thus, our study provides valuable information for further functional determination of each C2H2-ZFP gene across the Brassica species, and may help to select the appropriate gene targets for further in-depth studies, and genetic engineering and improvement of Brassica crops.
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Xu L, Xu J, Zhu J, Yao Z, Yu N, Deng W, Wang Y, Lin B. Universal Anticancer Cu(DTC)
2
Discriminates between Thiols and Zinc(II) Thiolates Oxidatively. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201814519] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Luyan Xu
- School of Physical Science and TechnologyShanghaiTech University 393 Middle Huaxia Road, Pudong new area Shanghai 201210 P. R. China
- Shanghai Institute of Organic ChemistryChinese Academy of Sciences 345 Lingling Road Shanghai 200032 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Jialin Xu
- School of Physical Science and TechnologyShanghaiTech University 393 Middle Huaxia Road, Pudong new area Shanghai 201210 P. R. China
| | - Jingwei Zhu
- School of Chemical and Environmental EngineeringShanghai Institute of Technology 100 Haiquan Road, Fengxian District Shanghai 201418 P. R. China
| | - Zijian Yao
- School of Chemical and Environmental EngineeringShanghai Institute of Technology 100 Haiquan Road, Fengxian District Shanghai 201418 P. R. China
| | - Na Yu
- School of Physical Science and TechnologyShanghaiTech University 393 Middle Huaxia Road, Pudong new area Shanghai 201210 P. R. China
| | - Wei Deng
- School of Chemical and Environmental EngineeringShanghai Institute of Technology 100 Haiquan Road, Fengxian District Shanghai 201418 P. R. China
| | - Yu Wang
- Shanghai Synchrotron Radiation FacilityShanghai Advanced Research InstituteChinese Academy of Sciences 239 Zhangheng Road, Pudong New District Shanghai 201204 China
| | - Bo‐Lin Lin
- School of Physical Science and TechnologyShanghaiTech University 393 Middle Huaxia Road, Pudong new area Shanghai 201210 P. R. China
- Shanghai Institute of Organic ChemistryChinese Academy of Sciences 345 Lingling Road Shanghai 200032 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 China
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50
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Xu L, Xu J, Zhu J, Yao Z, Yu N, Deng W, Wang Y, Lin B. Universal Anticancer Cu(DTC)
2
Discriminates between Thiols and Zinc(II) Thiolates Oxidatively. Angew Chem Int Ed Engl 2019; 58:6070-6073. [DOI: 10.1002/anie.201814519] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Indexed: 01/10/2023]
Affiliation(s)
- Luyan Xu
- School of Physical Science and TechnologyShanghaiTech University 393 Middle Huaxia Road, Pudong new area Shanghai 201210 P. R. China
- Shanghai Institute of Organic ChemistryChinese Academy of Sciences 345 Lingling Road Shanghai 200032 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Jialin Xu
- School of Physical Science and TechnologyShanghaiTech University 393 Middle Huaxia Road, Pudong new area Shanghai 201210 P. R. China
| | - Jingwei Zhu
- School of Chemical and Environmental EngineeringShanghai Institute of Technology 100 Haiquan Road, Fengxian District Shanghai 201418 P. R. China
| | - Zijian Yao
- School of Chemical and Environmental EngineeringShanghai Institute of Technology 100 Haiquan Road, Fengxian District Shanghai 201418 P. R. China
| | - Na Yu
- School of Physical Science and TechnologyShanghaiTech University 393 Middle Huaxia Road, Pudong new area Shanghai 201210 P. R. China
| | - Wei Deng
- School of Chemical and Environmental EngineeringShanghai Institute of Technology 100 Haiquan Road, Fengxian District Shanghai 201418 P. R. China
| | - Yu Wang
- Shanghai Synchrotron Radiation FacilityShanghai Advanced Research InstituteChinese Academy of Sciences 239 Zhangheng Road, Pudong New District Shanghai 201204 China
| | - Bo‐Lin Lin
- School of Physical Science and TechnologyShanghaiTech University 393 Middle Huaxia Road, Pudong new area Shanghai 201210 P. R. China
- Shanghai Institute of Organic ChemistryChinese Academy of Sciences 345 Lingling Road Shanghai 200032 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 China
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