|
1
|
Chen X, Jin H. Essential Roles of Conserved Pseudouridines in Helix 69 for Ribosome Dynamics in Translation. J Mol Biol 2025; 437:169132. [PMID: 40194619 DOI: 10.1016/j.jmb.2025.169132] [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: 01/24/2025] [Revised: 03/20/2025] [Accepted: 04/02/2025] [Indexed: 04/09/2025]
Abstract
The widespread distribution of pseudouridine (Ψ), an isomer of the canonical uridine base, in RNA indicates its functional importance to the cell. In eukaryotes, it is estimated that around 2% of ribosomal RNA nucleotides are pseudouridines, most of which are located in functional regions of the ribosome. Defects in RNA pseudouridylation induce a range of detrimental effects from compromised cellular protein biosynthesis to disease phenotypes in humans. However, genome-wide changes to mRNA translation profiles by ribosomes lacking specific conserved pseudouridines have not been extensively studied. Here, using a new genomic method called 5PSeq and in vitro biochemistry, we investigated changes in ribosome dynamics and cellular translation profiles upon loss of Ψ2258 and Ψ2260 in helix 69, the two most conserved pseudouridines in the ribosome in yeast cells. We found that inhibiting the formation of these two pseudouridines challenges ribosomes to maintain the correct open reading frame and causes generally faster ribosome dynamics in translation. Furthermore, mutant ribosomes are more prone to pause while translating a subset of GC-rich codons, especially rare codons such as Arg (CGA) and Arg (CGG). These results demonstrate the presence of Ψ2258 and Ψ2260 contributes to the dynamics of the H69 RNA stem-loop, and helps to maintain functional interactions with the tRNAs as they move within the ribosome. The optimality of this ribosome-tRNA interaction is likely to be more critical for those limited tRNAs that decode rare codons. Consistent with the changes in ribosome dynamics, we observe that IRES-mediated translation is compromised in the mutant ribosome. These results explain the importance of Ψ2258 and Ψ2260 in H69 to maintain cellular fitness. The strong conservation of Ψ2258 and Ψ2260 in the ribosomes from bacteria to humans indicates their functional significance in modulating ribosome functions. It's likely that the identified functions of these covalent modifications are conserved across species.
Collapse
Affiliation(s)
- Xin Chen
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, United States
| | - Hong Jin
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, United States; Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, United States.
| |
Collapse
|
|
2
|
Yabaji SM, Zhernovkov V, Araveti PB, Lata S, Rukhlenko OS, Abdullatif SA, Vanvalkenburg A, Alekseev Y, Ma Q, Dayama G, Lau NC, Johnson WE, Bishai WR, Crossland NA, Campbell JD, Kholodenko BN, Gimelbrant AA, Kobzik L, Kramnik I. Lipid Peroxidation and Type I Interferon Coupling Fuels Pathogenic Macrophage Activation Causing Tuberculosis Susceptibility. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.03.05.583602. [PMID: 38496444 PMCID: PMC10942339 DOI: 10.1101/2024.03.05.583602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
A quarter of human population is infected with Mycobacterium tuberculosis, but less than 10% of those infected develop pulmonary TB. We developed a genetically defined sst1-susceptible mouse model that uniquely reproduces a defining feature of human TB: the development of necrotic lung granulomas and determined that the sst1-susceptible phenotype was driven by the aberrant macrophage activation. This study demonstrates that the aberrant response of the sst1-susceptible macrophages to prolonged stimulation with TNF is primarily driven by conflicting Myc and antioxidant response pathways leading to a coordinated failure 1) to properly sequester intracellular iron and 2) to activate ferroptosis inhibitor enzymes. Consequently, iron-mediated lipid peroxidation fueled Ifn-beta superinduction and sustained the Type I Interferon (IFN-I) pathway hyperactivity that locked the sst1-susceptible macrophages in a state of unresolving stress and compromised their resistance to Mtb. The accumulation of the aberrantly activated, stressed, macrophages within granuloma microenvironment led to the local failure of anti-tuberculosis immunity and tissue necrosis. The upregulation of Myc pathway in peripheral blood cells of human TB patients was significantly associated with poor outcomes of TB treatment. Thus, Myc dysregulation in activated macrophages results in an aberrant macrophage activation and represents a novel target for host-directed TB therapies.
Collapse
|
|
3
|
Li H, Wang G, Ye C, Zou Z, Jiang B, Yang F, He K, Ju C, Zhang L, Gao B, Liu S, Chen Y, Zhang J, He C. Quantitative RNA pseudouridine maps reveal multilayered translation control through plant rRNA, tRNA and mRNA pseudouridylation. NATURE PLANTS 2025; 11:234-247. [PMID: 39789092 DOI: 10.1038/s41477-024-01894-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 12/09/2024] [Indexed: 01/12/2025]
Abstract
Pseudouridine (Ψ) is the most abundant RNA modification, yet studies of Ψ have been hindered by a lack of robust methods to profile comprehensive Ψ maps. Here we utilize bisulfite-induced deletion sequencing to generate transcriptome-wide Ψ maps at single-base resolution across various plant species. Integrating ribosomal RNA, transfer RNA and messenger RNA Ψ stoichiometry with mRNA abundance and polysome profiling data, we uncover a multilayered regulation of translation efficiency through Ψ modifications. rRNA pseudouridylation could globally control translation, although the effects vary at different rRNA Ψ sites. Ψ in the tRNA T-arm loop shows strong positive correlations between Ψ stoichiometry and the translation efficiency of their respective codons. We observed a general inverse correlation between Ψ level and mRNA stability, but a positive correlation with translation efficiency in Arabidopsis seedlings. In conclusion, our study provides critical resources for Ψ research in plants and proposes prevalent translation regulation through rRNA, tRNA and mRNA pseudouridylation.
Collapse
Affiliation(s)
- Haoxuan Li
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, Chicago, IL, USA
| | - Guanqun Wang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, Chicago, IL, USA
- Department of Biology, Hong Kong Baptist University and School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Chang Ye
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, Chicago, IL, USA
| | - Zhongyu Zou
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, Chicago, IL, USA
| | - Bochen Jiang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Fan Yang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Kayla He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Chengwei Ju
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Lisheng Zhang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Boyang Gao
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Shun Liu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Yanming Chen
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University and School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
- Howard Hughes Medical Institute, Chicago, IL, USA.
| |
Collapse
|
|
4
|
Dai Z, Zhu W, Hou Y, Zhang X, Ren X, Lei K, Liao J, Liu H, Chen Z, Peng S, Li S, Lin S, Kuang M. METTL5-mediated 18S rRNA m 6A modification promotes oncogenic mRNA translation and intrahepatic cholangiocarcinoma progression. Mol Ther 2023; 31:3225-3242. [PMID: 37735874 PMCID: PMC10638452 DOI: 10.1016/j.ymthe.2023.09.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/14/2023] [Accepted: 09/15/2023] [Indexed: 09/23/2023] Open
Abstract
Intrahepatic cholangiocarcinoma (ICC) is a deadly cancer with rapid tumor progression. While hyperactive mRNA translation caused by mis-regulated mRNA or tRNA modifications promotes ICC development, the role of rRNA modifications remains elusive. Here, we found that 18S rRNA m6A modification and its methyltransferase METTL5 were aberrantly upregulated in ICC and associated with poorer survival (log rank test, p < 0.05). We further revealed the critical role of METTL5-mediated 18S rRNA m6A modification in regulation of ICC cell growth and metastasis using loss- and gain-of function assays in vitro and in vivo. The oncogenic function of METTL5 is corroborated using liver-specific knockout and overexpression ICC mouse models. Mechanistically, METTL5 depletion impairs 18S rRNA m6A modification that hampers ribosome synthesis and inhibits translation of G-quadruplex-containing mRNAs that are enriched in the transforming growth factor (TGF)-β pathway. Our study uncovers the important role of METTL5-mediated 18S rRNA m6A modification in ICC and unravels the mechanism of rRNA m6A modification-mediated oncogenic mRNA translation control.
Collapse
Affiliation(s)
- Zihao Dai
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
| | - Wanjie Zhu
- Department of Gastroenterology, The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong Province, China
| | - Yingdong Hou
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
| | - Xinyue Zhang
- Cancer Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
| | - Xuxin Ren
- Cancer Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
| | - Kai Lei
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
| | - Junbin Liao
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
| | - Haining Liu
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
| | - Zhihang Chen
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
| | - Sui Peng
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China; Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China; Clinical Trials Unit, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
| | - Shaoqiang Li
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.
| | - Shuibin Lin
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.
| | - Ming Kuang
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China; Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China; Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.
| |
Collapse
|
|
5
|
Liberman N, Rothi MH, Gerashchenko MV, Zorbas C, Boulias K, MacWhinnie FG, Ying AK, Flood Taylor A, Al Haddad J, Shibuya H, Roach L, Dong A, Dellacona S, Lafontaine DLJ, Gladyshev VN, Greer EL. 18S rRNA methyltransferases DIMT1 and BUD23 drive intergenerational hormesis. Mol Cell 2023; 83:3268-3282.e7. [PMID: 37689068 PMCID: PMC11990152 DOI: 10.1016/j.molcel.2023.08.014] [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: 04/07/2023] [Revised: 07/25/2023] [Accepted: 08/10/2023] [Indexed: 09/11/2023]
Abstract
Heritable non-genetic information can regulate a variety of complex phenotypes. However, what specific non-genetic cues are transmitted from parents to their descendants are poorly understood. Here, we perform metabolic methyl-labeling experiments to track the heritable transmission of methylation from ancestors to their descendants in the nematode Caenorhabditis elegans (C. elegans). We find heritable methylation in DNA, RNA, proteins, and lipids. We find that parental starvation elicits reduced fertility, increased heat stress resistance, and extended longevity in fed, naïve progeny. This intergenerational hormesis is accompanied by a heritable increase in N6'-dimethyl adenosine (m6,2A) on the 18S ribosomal RNA at adenosines 1735 and 1736. We identified DIMT-1/DIMT1 as the m6,2A and BUD-23/BUD23 as the m7G methyltransferases in C. elegans that are both required for intergenerational hormesis, while other rRNA methyltransferases are dispensable. This study labels and tracks heritable non-genetic material across generations and demonstrates the importance of rRNA methylation for regulating epigenetic inheritance.
Collapse
Affiliation(s)
- Noa Liberman
- Department of Pediatrics, HMS Initiative for RNA Medicine, Harvard Medical School, Boston, MA, USA; Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
| | - M Hafiz Rothi
- Department of Pediatrics, HMS Initiative for RNA Medicine, Harvard Medical School, Boston, MA, USA; Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Maxim V Gerashchenko
- Division of Genetics, Department of Medicine, Brigham & Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Christiane Zorbas
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université libre de Bruxelles (ULB), Biopark Campus, 6041 Gosselies, Belgium
| | - Konstantinos Boulias
- Department of Pediatrics, HMS Initiative for RNA Medicine, Harvard Medical School, Boston, MA, USA; Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Fiona G MacWhinnie
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Albert Kejun Ying
- Department of Pediatrics, HMS Initiative for RNA Medicine, Harvard Medical School, Boston, MA, USA; Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Anya Flood Taylor
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Joseph Al Haddad
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Hiroki Shibuya
- Department of Pediatrics, HMS Initiative for RNA Medicine, Harvard Medical School, Boston, MA, USA; Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Lara Roach
- Department of Pediatrics, HMS Initiative for RNA Medicine, Harvard Medical School, Boston, MA, USA; Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Anna Dong
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Scarlett Dellacona
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Denis L J Lafontaine
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université libre de Bruxelles (ULB), Biopark Campus, 6041 Gosselies, Belgium
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham & Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Eric Lieberman Greer
- Department of Pediatrics, HMS Initiative for RNA Medicine, Harvard Medical School, Boston, MA, USA; Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.
| |
Collapse
|
|
6
|
Sun X, Gao C, Xu X, Li M, Zhao X, Wang Y, Wang Y, Zhang S, Yan Z, Liu X, Wu C. FBL promotes cancer cell resistance to DNA damage and BRCA1 transcription via YBX1. EMBO Rep 2023; 24:e56230. [PMID: 37489617 PMCID: PMC10481664 DOI: 10.15252/embr.202256230] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 06/27/2023] [Accepted: 07/04/2023] [Indexed: 07/26/2023] Open
Abstract
Fibrillarin (FBL) is a highly conserved nucleolar methyltransferase responsible for methylation of ribosomal RNA and proteins. Here, we reveal a role for FBL in DNA damage response and its impact on cancer proliferation and sensitivity to DNA-damaging agents. FBL is highly expressed in various cancers and correlates with poor survival outcomes in cancer patients. Knockdown of FBL sensitizes tumor cells and xenografts to DNA crosslinking agents, and leads to homologous recombination-mediated DNA repair defects. We identify Y-box-binding protein-1 (YBX1) as a key interacting partner of FBL, and FBL increases the nuclear accumulation of YBX1 in response to DNA damage. We show that FBL promotes the expression of BRCA1 by increasing the binding of YBX1 to the BRCA1 promoter. Our study sheds light on the regulatory mechanism of FBL in tumorigenesis and DNA damage response, providing potential therapeutic targets to overcome chemoresistance in cancer.
Collapse
Affiliation(s)
- Xiaorui Sun
- College of Life SciencesHebei UniversityBaodingChina
| | - Congwen Gao
- College of Life SciencesHebei UniversityBaodingChina
| | - Xin Xu
- College of Life SciencesHebei UniversityBaodingChina
| | - Mengyuan Li
- College of Life SciencesHebei UniversityBaodingChina
| | - Xinhua Zhao
- College of Life SciencesHebei UniversityBaodingChina
| | - Yanan Wang
- Affiliated Hospital of Hebei UniversityBaodingChina
| | - Yun Wang
- Affiliated Hospital of Hebei UniversityBaodingChina
| | - Shun Zhang
- Affiliated Hospital of Hebei UniversityBaodingChina
| | - Zhenzhen Yan
- College of Life SciencesHebei UniversityBaodingChina
| | - Xiuhua Liu
- College of Life SciencesHebei UniversityBaodingChina
| | - Chen Wu
- College of Life SciencesHebei UniversityBaodingChina
- The Key Laboratory of Zoological Systematics and ApplicationHebei UniversityBaodingChina
| |
Collapse
|
|
7
|
Zhao Y, Rai J, Li H. Regulation of translation by ribosomal RNA pseudouridylation. SCIENCE ADVANCES 2023; 9:eadg8190. [PMID: 37595043 PMCID: PMC10438446 DOI: 10.1126/sciadv.adg8190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 07/18/2023] [Indexed: 08/20/2023]
Abstract
Pseudouridine is enriched in ribosomal, spliceosomal, transfer, and messenger RNA and thus integral to the central dogma. The chemical basis for how pseudouridine affects the molecular apparatus such as ribosome, however, remains elusive owing to the lack of structures without this natural modification. Here, we studied the translation of a hypopseudouridylated ribosome initiated by the internal ribosome entry site (IRES) elements. We analyzed eight cryo-electron microscopy structures of the ribosome bound with the Taura syndrome virus IRES in multiple functional states. We found widespread loss of pseudouridine-mediated interactions through water and long-range base pairings. In the presence of the translocase, eukaryotic elongation factor 2, and guanosine 5'-triphosphate hydrolysis, the hypopseudouridylated ribosome favors a rare unconducive conformation for decoding that is partially recouped in the ribosome population that remains modified at the P-site uridine. The structural principles learned establish the link between functional defects and modification loss and are likely applicable to other pseudouridine-associated processes.
Collapse
Affiliation(s)
- Yu Zhao
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Jay Rai
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Hong Li
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| |
Collapse
|
|
8
|
Ponzetti M, Rucci N, Falone S. RNA methylation and cellular response to oxidative stress-promoting anticancer agents. Cell Cycle 2023; 22:870-905. [PMID: 36648057 PMCID: PMC10054233 DOI: 10.1080/15384101.2023.2165632] [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: 10/28/2022] [Accepted: 01/03/2023] [Indexed: 01/18/2023] Open
Abstract
Disruption of the complex network that regulates redox homeostasis often underlies resistant phenotypes, which hinder effective and long-lasting cancer eradication. In addition, the RNA methylome-dependent control of gene expression also critically affects traits of cellular resistance to anti-cancer agents. However, few investigations aimed at establishing whether the epitranscriptome-directed adaptations underlying acquired and/or innate resistance traits in cancer could be implemented through the involvement of redox-dependent or -responsive signaling pathways. This is unexpected mainly because: i) the effectiveness of many anti-cancer approaches relies on their capacity to promote oxidative stress (OS); ii) altered redox milieu and reprogramming of mitochondrial function have been acknowledged as critical mediators of the RNA methylome-mediated response to OS. Here we summarize the current state of understanding on this topic, as well as we offer new perspectives that might lead to original approaches and strategies to delay or prevent the problem of refractory cancer and tumor recurrence.
Collapse
Affiliation(s)
- Marco Ponzetti
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L'Aquila, Italy
| | - Nadia Rucci
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L'Aquila, Italy
| | - Stefano Falone
- Department of Life, Health and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
| |
Collapse
|
|
9
|
Decle-Carrasco S, Rodríguez-Piña AL, Rodríguez-Zapata LC, Castano E. Current research on viral proteins that interact with fibrillarin. Mol Biol Rep 2023; 50:4631-4643. [PMID: 36928641 PMCID: PMC10018631 DOI: 10.1007/s11033-023-08343-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/15/2023] [Indexed: 03/18/2023]
Abstract
The nucleolus is a multifunctional nuclear domain primarily dedicated to ribosome biogenesis. Certain viruses developed strategies to manipulate host nucleolar proteins to facilitate their replication by modulating ribosomal RNA (rRNA) processing. This association interferes with nucleolar functions resulting in overactivation or arrest of ribosome biogenesis, induction or inhibition of apoptosis, and affecting stress response. The nucleolar protein fibrillarin (FBL) is an important target of some plant and animal viruses. FBL is an essential and highly conserved S-adenosyl methionine (SAM) dependent methyltransferase, capable of rRNA degradation by its intrinsically disordered region (IDR), the glycine/arginine-rich (GAR) domain. It forms a ribonucleoprotein complex that directs 2'-O-methylations in more than 100 sites of pre-rRNAs. It is involved in multiple cellular processes, including initiation of transcription, oncogenesis, and apoptosis, among others. The interaction with animal viruses, including human viruses, triggered its redistribution to the nucleoplasm and cytoplasm, interfering with its role in pre-rRNA processing. Viral-encoded proteins with IDRs as nucleocapsids, matrix, Tat protein, and even a viral snoRNA, can associate with FBL, forcing the nucleolar protein to undergo atypical functions. Here we review the molecular mechanisms employed by animal and human viruses to usurp FBL functions and the effect on cellular processes, particularly in ribosome biogenesis.
Collapse
Affiliation(s)
- Stefano Decle-Carrasco
- Unidad de Bioquímica y Biología Molecular de Plantas. Centro de Investigación Científica de Yucatán, A.C. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida, Yucatán, México
| | - Alma Laura Rodríguez-Piña
- Unidad de Bioquímica y Biología Molecular de Plantas. Centro de Investigación Científica de Yucatán, A.C. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida, Yucatán, México
| | - Luis Carlos Rodríguez-Zapata
- Unidad de Biotecnología. Centro de Investigación Científica de Yucatán, A.C. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida, Yucatán, México
| | - Enrique Castano
- Unidad de Bioquímica y Biología Molecular de Plantas. Centro de Investigación Científica de Yucatán, A.C. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida, Yucatán, México.
| |
Collapse
|
|
10
|
The emerging importance of METTL5-mediated ribosomal RNA methylation. Exp Mol Med 2022; 54:1617-1625. [PMID: 36266443 PMCID: PMC9636144 DOI: 10.1038/s12276-022-00869-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 07/21/2022] [Accepted: 08/11/2022] [Indexed: 01/19/2023] Open
Abstract
The study of the epitranscriptome has thus far focused largely on mRNA methylation. Recent human genetics studies suggest that methylation of ribosomal RNA also contributes to brain development and cognition. In particular, the m6A modification at the A-1832 position of the 18S rRNA is installed by METTL5. Mutations or deletions of Mettl5 in humans and mice, respectively, cause abnormal translation and gene expression that in turn mediates stem cell behaviors such as differentiation. In this review, we provide an overview of the current knowledge of the methyltransferase METTL5, as well as the molecular biology surrounding m6A on rRNA and how it regulates cell behavior.
Collapse
|
|
11
|
Dong J, Wang H, Zhang Z, Yang L, Qian X, Qian W, Han Y, Huang H, Qian P. Small but strong: Pivotal roles and potential applications of snoRNAs in hematopoietic malignancies. Front Oncol 2022; 12:939465. [PMID: 36033520 PMCID: PMC9413531 DOI: 10.3389/fonc.2022.939465] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) belong to a family of noncoding RNAs that are 60-300 nucleotides in length, and they are classified into two classes according to their structure and function: C/D box snoRNAs, playing an essential role in 2’-O-methylation modification on ribosomal RNA; H/ACA box snoRNAs, involved in the pseudouridylation of rRNA. SnoRNAs with unclear functions, no predictable targets, and unusual subcellular locations are called orphan snoRNAs. Recent studies have revealed abnormal expression and demonstrated the pivotal roles of snoRNAs and their host genes in various types of hematological malignancies. This review discusses recent discoveries concerning snoRNAs in a variety of hematological malignancies, including multiple myeloma, lymphoma and leukemia, and sheds light on the application of snoRNAs as diagnostic and prognostic markers as well as therapeutic targets of hematological malignancies in the future.
Collapse
Affiliation(s)
- Jian Dong
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Hui Wang
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Zhaoru Zhang
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Lin Yang
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Xinyue Qian
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Wenchang Qian
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Yingli Han
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - He Huang
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- *Correspondence: Pengxu Qian, ; He Huang,
| | - Pengxu Qian
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
- *Correspondence: Pengxu Qian, ; He Huang,
| |
Collapse
|
|
12
|
Small nucleolar RNA is potential as a novel player in leukemogenesis and clinical application. BLOOD SCIENCE 2021; 3:122-131. [PMID: 35402848 PMCID: PMC8975097 DOI: 10.1097/bs9.0000000000000091] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/21/2021] [Indexed: 12/19/2022] Open
Abstract
Lack of clarity of the mechanisms that underlie leukemogenesis obstructs the diagnosis, prognosis, and treatment of leukemia. Research has found that small nuclear RNA (snoRNA) plays an essential role in leukemia. These small non-coding RNAs are involved in ribosome biogenesis, including the 2′-O-methylation and pseudouridylation of precursor ribosomal RNA (pre-rRNA), and pre-rRNA splicing. Recently, many snoRNAs were found to be orphans that have no predictable RNA modification targets, but these RNAs have always been found to be located in different subcellular organelles, and they play diverse roles. Using high-throughput technology, snoRNA expression profiles have been revealed in leukemia, and some of the deregulated snoRNAs may regulate the cell cycle, differentiation, proliferation, and apoptosis in leukemic cells and confer drug resistance during leukemia treatment. In this review, we discuss the expression profiles and functions of snoRNAs, particularly orphan snoRNAs, in leukemia. It is possible that the dysregulated snoRNAs are promising diagnosis and prognosis markers for leukemia, which may serve as potential therapeutic targets in leukemia treatment.
Collapse
|
|
13
|
Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing. Nat Biotechnol 2021; 39:1278-1291. [PMID: 33986546 DOI: 10.1038/s41587-021-00915-6] [Citation(s) in RCA: 182] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 04/06/2021] [Indexed: 01/23/2023]
Abstract
Nanopore RNA sequencing shows promise as a method for discriminating and identifying different RNA modifications in native RNA. Expanding on the ability of nanopore sequencing to detect N6-methyladenosine, we show that other modifications, in particular pseudouridine (Ψ) and 2'-O-methylation (Nm), also result in characteristic base-calling 'error' signatures in the nanopore data. Focusing on Ψ modification sites, we detected known and uncovered previously unreported Ψ sites in mRNAs, non-coding RNAs and rRNAs, including a Pus4-dependent Ψ modification in yeast mitochondrial rRNA. To explore the dynamics of pseudouridylation, we treated yeast cells with oxidative, cold and heat stresses and detected heat-sensitive Ψ-modified sites in small nuclear RNAs, small nucleolar RNAs and mRNAs. Finally, we developed a software, nanoRMS, that estimates per-site modification stoichiometries by identifying single-molecule reads with altered current intensity and trace profiles. This work demonstrates that Nm and Ψ RNA modifications can be detected in cellular RNAs and that their modification stoichiometry can be quantified by nanopore sequencing of native RNA.
Collapse
|
|
14
|
Fazi F, Fatica A. Regulation of Ribosome Function by RNA Modifications in Hematopoietic Development and Leukemia: It Is Not Only a Matter of m 6A. Int J Mol Sci 2021; 22:ijms22094755. [PMID: 33946178 PMCID: PMC8125340 DOI: 10.3390/ijms22094755] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 12/15/2022] Open
Abstract
Growth and maturation of hematopoietic stem cells (HSCs) are largely controlled at both transcriptional and post-transcriptional levels. In particular, hematopoietic development requires a tight control of protein synthesis. Furthermore, translational deregulation strongly contributes to hematopoietic malignancies. Researchers have recently identified a new layer of gene expression regulation that consists of chemical modification of RNA species, which led to the birth of the epitranscriptomics field. RNA modifications provide an additional level of control in hematopoietic development by acting as post-transcriptional regulators of lineage-specific genetic programs. Other reviews have already described the important role of the N6-methylation of adenosine (m6A) within mRNA species in regulating hematopoietic differentiation and diseases. The aim of this review is to summarize the current status of the role of RNA modifications in the regulation of ribosome function, beyond m6A. In particular, we discuss the importance of RNA modifications in tRNA and rRNA molecules. By balancing translational rate and fidelity, they play an important role in regulating normal and malignant hematopoietic development.
Collapse
Affiliation(s)
- Francesco Fazi
- Department of Anatomical, Histological, Forensic & Orthopedic Sciences, Section of Histology & Medical Embryology, Sapienza University of Rome, 00165 Rome, Italy
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, 00161 Rome, Italy
- Correspondence: (F.F.); (A.F.)
| | - Alessandro Fatica
- Department of Biology and Biotechnology ‘Charles Darwin’, Sapienza University of Rome, 00165 Rome, Italy
- Correspondence: (F.F.); (A.F.)
| |
Collapse
|
|
15
|
Abstract
Post-synthesis modification of biomolecules is an efficient way of regulating and optimizing their functions. The human epitranscriptome includes a variety of more than 100 modifications known to exist in all RNA subtypes. Modifications of non-coding RNAs are particularly interesting since they can directly affect their structure, stability, interaction and function. Indeed, non-coding RNAs such as tRNA and rRNA are the most modified RNA species in eukaryotic cells. In the last 20 years, new functions of non-coding RNAs have been discovered and their involvement in human disease, including cancer, became clear. In this review, we will present the evidence connecting modifications of different non-coding RNA subtypes and their role in cancer.
Collapse
Affiliation(s)
| | | | - Luca Pandolfini
- Corresponding authors: Isaia Barbieri, University of Cambridge, Department of pathology, Division of cellular and molecular pathology, Addenbrooke's hospital, Lab block, level 3 Box 231, CB2 0QQ, Cambridge, UK. Tel.: +44 (0)1223 333917; E-mail: , Luca Pandolfini, Istituto Italiano di Tecnologia, via Enrico Melen 83, Building B, 16152 Genova, Italy. Tel.: +39 010 2897623; E-mail:
| | - Isaia Barbieri
- Corresponding authors: Isaia Barbieri, University of Cambridge, Department of pathology, Division of cellular and molecular pathology, Addenbrooke's hospital, Lab block, level 3 Box 231, CB2 0QQ, Cambridge, UK. Tel.: +44 (0)1223 333917; E-mail: , Luca Pandolfini, Istituto Italiano di Tecnologia, via Enrico Melen 83, Building B, 16152 Genova, Italy. Tel.: +39 010 2897623; E-mail:
| |
Collapse
|
|
16
|
Liu K, Santos DA, Hussmann JA, Wang Y, Sutter BM, Weissman JS, Tu BP. Regulation of translation by methylation multiplicity of 18S rRNA. Cell Rep 2021; 34:108825. [PMID: 33691096 PMCID: PMC8063911 DOI: 10.1016/j.celrep.2021.108825] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 01/04/2021] [Accepted: 02/12/2021] [Indexed: 02/01/2023] Open
Abstract
N6-methyladenosine (m6A) is a conserved ribonucleoside modification that regulates many facets of RNA metabolism. Using quantitative mass spectrometry, we find that the universally conserved tandem adenosines at the 3' end of 18S rRNA, thought to be constitutively di-methylated (m62A), are also mono-methylated (m6A). Although present at substoichiometric amounts, m6A at these positions increases significantly in response to sulfur starvation in yeast cells and mammalian cell lines. Combining yeast genetics and ribosome profiling, we provide evidence to suggest that m6A-bearing ribosomes carry out translation distinctly from m62A-bearing ribosomes, featuring a striking specificity for sulfur metabolism genes. Our work thus reveals methylation multiplicity as a mechanism to regulate translation.
Collapse
Affiliation(s)
- Kuanqing Liu
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Daniel A Santos
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Jeffrey A Hussmann
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Yun Wang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Benjamin M Sutter
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Benjamin P Tu
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| |
Collapse
|
|
17
|
Metge BJ, Kammerud SC, Pruitt HC, Shevde LA, Samant RS. Hypoxia re-programs 2'-O-Me modifications on ribosomal RNA. iScience 2020; 24:102010. [PMID: 33490918 PMCID: PMC7811136 DOI: 10.1016/j.isci.2020.102010] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 12/07/2020] [Accepted: 12/24/2020] [Indexed: 02/07/2023] Open
Abstract
Hypoxia is one of the critical stressors encountered by various cells of the human body under diverse pathophysiologic conditions including cancer and has profound impacts on several metabolic and physiologic processes. Hypoxia prompts internal ribosome entry site (IRES)-mediated translation of key genes, such as VEGF, that are vital for tumor progression. Here, we describe that hypoxia remarkably upregulates RNA Polymerase I activity. We discovered that in hypoxia, rRNA shows a different methylation pattern compared to normoxia. Heterogeneity in ribosomes due to the diversity of ribosomal RNA and protein composition has been postulated to generate “specialized ribosomes” that differentially regulate translation. We find that in hypoxia, a sub-set of differentially methylated ribosomes recognizes the VEGF-C IRES, suggesting that ribosomal heterogeneity allows for altered ribosomal functions in hypoxia.
Chronic hypoxia stimulates RNA Pol I activity In hypoxia, a pool of specialized rRNA translates VEGFC IRES Hypoxia changes 2′-O-Me modification - epitranscriptomic marks on rRNA
Collapse
Affiliation(s)
- Brandon J Metge
- Department of Pathology, University of Alabama at Birmingham, WTI 320E 1824 6 Avenue South, Birmingham, AL 35233, USA
| | - Sarah C Kammerud
- Department of Pathology, University of Alabama at Birmingham, WTI 320E 1824 6 Avenue South, Birmingham, AL 35233, USA
| | - Hawley C Pruitt
- Department of Pathology, University of Alabama at Birmingham, WTI 320E 1824 6 Avenue South, Birmingham, AL 35233, USA
| | - Lalita A Shevde
- Department of Pathology, University of Alabama at Birmingham, WTI 320E 1824 6 Avenue South, Birmingham, AL 35233, USA.,O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Rajeev S Samant
- Department of Pathology, University of Alabama at Birmingham, WTI 320E 1824 6 Avenue South, Birmingham, AL 35233, USA.,Birmingham VA Medical Center, Birmingham, AL, USA
| |
Collapse
|
|
18
|
Transcriptome Analyses and Antioxidant Activity Profiling Reveal the Role of a Lignin-Derived Biostimulant Seed Treatment in Enhancing Heat Stress Tolerance in Soybean. PLANTS 2020; 9:plants9101308. [PMID: 33023253 PMCID: PMC7601093 DOI: 10.3390/plants9101308] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 12/19/2022]
Abstract
Soybean (Glycine max Merr.) is a worldwide important legume crop, whose growth and yield are negatively affected by heat stress at germination time. Here, we tested the role of a biostimulant based on lignin derivatives, plant-derived amino acids, and molybdenum in enhancing soybean heat stress tolerance when applied on seeds. After treatment with the biostimulant at 35 °C, the seed biometric parameters were positively influenced after 24 h, meanwhile, germination percentage was increased after 72 h (+10%). RNA-Seq analyses revealed a modulation of 879 genes (51 upregulated and 828 downregulated) in biostimulant-treated seeds as compared with the control, at 24 h after incubation at 35 °C. Surprisingly, more than 33% of upregulated genes encoded for ribosomal RNA (rRNA) methyltransferases and proteins involved in the ribosome assembly, acting in a specific protein network. Conversely, the downregulated genes were involved in stress response, hormone signaling, and primary metabolism. Finally, from a biochemical point of view, the dramatic H2O2 reduction 40%) correlated to a strong increase in non-protein thiols (+150%), suggested a lower oxidative stress level in biostimulant-treated seeds, at 24 h after incubation at 35 °C. Our results provide insights on the biostimulant mechanism of action and on its application for seed treatments to improve heat stress tolerance during germination.
Collapse
|
|
19
|
Xing M, Liu Q, Mao C, Zeng H, Zhang X, Zhao S, Chen L, Liu M, Shen B, Guo X, Ma H, Chen H, Zhang J. The 18S rRNA m 6 A methyltransferase METTL5 promotes mouse embryonic stem cell differentiation. EMBO Rep 2020; 21:e49863. [PMID: 32783360 DOI: 10.15252/embr.201949863] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 07/21/2020] [Accepted: 07/23/2020] [Indexed: 12/12/2022] Open
Abstract
RNA modifications represent a novel layer of regulation of gene expression. Functional experiments revealed that N6 -methyladenosine (m6 A) on messenger RNA (mRNA) plays critical roles in cell fate determination and development. m6 A mark also resides in the decoding center of 18S ribosomal RNA (rRNA); however, the biological function of m6 A on 18S rRNA is still poorly understood. Here, we report that methyltransferase-like 5 (METTL5) methylates 18S rRNA both in vivo and in vitro, which is consistent with previous reports. Deletion of Mettl5 causes a dramatic differentiation defect in mouse embryonic stem cells (mESCs). Mechanistically, the m6 A deposited by METTL5 is involved in regulating the efficient translation of F-box and WD repeat domain-containing 7 (FBXW7), a key regulator of cell differentiation. Deficiency of METTL5 reduces FBXW7 levels and leads to the accumulation of its substrate c-MYC, thereby delaying the onset of mESC differentiation. Our study uncovers an important role of METTL5-mediated 18S m6 A in mESC differentiation through translation regulation and provides new insight into the functional significance of rRNA m6 A.
Collapse
Affiliation(s)
- Ming Xing
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Qi Liu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Cong Mao
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Hanyi Zeng
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Xin Zhang
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Shuqin Zhao
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Li Chen
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Mingxi Liu
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Bin Shen
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Honghui Ma
- Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Hao Chen
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Jun Zhang
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| |
Collapse
|
|
20
|
Janin M, Coll-SanMartin L, Esteller M. Disruption of the RNA modifications that target the ribosome translation machinery in human cancer. Mol Cancer 2020; 19:70. [PMID: 32241281 PMCID: PMC7114786 DOI: 10.1186/s12943-020-01192-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 03/24/2020] [Indexed: 12/20/2022] Open
Abstract
Genetic and epigenetic changes deregulate RNA and protein expression in cancer cells. In this regard, tumors exhibit an abnormal proteome in comparison to the corresponding normal tissues. Translation control is a crucial step in the regulation of gene expression regulation under normal and pathological conditions that ultimately determines cellular fate. In this context, evidence shows that transfer and ribosomal RNA (tRNA and rRNA) modifications affect the efficacy and fidelity of translation. The number of RNA modifications increases with the complexity of organisms, suggesting an evolutionary diversification of the possibilities for fine-tuning the functions of coding and non-coding RNAs. In this review, we focus on alterations of modifications of transfer and ribosomal RNA that affect translation in human cancer. This variation in the RNA modification status can be the result of altered modifier expression (writers, readers or erasers), but also due to components of the machineries (C/D or H/ACA boxes) or alterations of proteins involved in modifier expression. Broadening our understanding of the mechanisms by which site-specific modifications modulate ribosome activity in the context of tumorigenesis will enable us to enrich our knowledge about how ribosomes can influence cell fate and form the basis of new therapeutic opportunities.
Collapse
Affiliation(s)
- Maxime Janin
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Laia Coll-SanMartin
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain.
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain.
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain.
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.
| |
Collapse
|
|
21
|
Liberman N, O’Brown ZK, Earl AS, Boulias K, Gerashchenko MV, Wang SY, Fritsche C, Fady PE, Dong A, Gladyshev VN, Greer EL. N6-adenosine methylation of ribosomal RNA affects lipid oxidation and stress resistance. SCIENCE ADVANCES 2020; 6:eaaz4370. [PMID: 32494643 PMCID: PMC7176415 DOI: 10.1126/sciadv.aaz4370] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 01/27/2020] [Indexed: 05/26/2023]
Abstract
During stress, global translation is reduced, but specific transcripts are actively translated. How stress-responsive mRNAs are selectively translated is unknown. We show that METL-5 methylates adenosine 1717 on 18S ribosomal RNA in C. elegans, enhancing selective ribosomal binding and translation of specific mRNAs. One of these mRNAs, CYP-29A3, oxidizes the omega-3 polyunsaturated fatty acid eicosapentaenoic acid to eicosanoids, key stress signaling molecules. While metl-5-deficient animals grow normally under homeostatic conditions, they are resistant to a variety of stresses. metl-5 mutant worms also show reduced bioactive lipid eicosanoids and dietary supplementation of eicosanoid products of CYP-29A3 restores stress sensitivity of metl-5 mutant worms. Thus, methylation of a specific residue of 18S rRNA by METL-5 selectively enhances translation of cyp-29A3 to increase production of eicosanoids, and blocking this pathway increases stress resistance. This study suggests that ribosome methylation can facilitate selective translation, providing another layer of regulation of the stress response.
Collapse
Affiliation(s)
- Noa Liberman
- Division of Newborn Medicine, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Zach K. O’Brown
- Division of Newborn Medicine, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Andrew Scott Earl
- Division of Newborn Medicine, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Konstantinos Boulias
- Division of Newborn Medicine, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Maxim V. Gerashchenko
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Simon Yuan Wang
- Division of Newborn Medicine, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Colette Fritsche
- Division of Newborn Medicine, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Paul-Enguerrand Fady
- Division of Newborn Medicine, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Anna Dong
- Division of Newborn Medicine, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Eric Lieberman Greer
- Division of Newborn Medicine, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
|
22
|
Abstract
RNA plays essential roles in not only translating nucleic acids into proteins, but also in gene regulation, environmental interactions and many human diseases. Nature uses over 150 chemical modifications to decorate RNA and diversify its functions. With the fast-growing RNA research in the burgeoning field of 'epitranscriptome', a term describes post-transcriptional RNA modifications that can dynamically change the transcriptome, it becomes clear that these modifications participate in modulating gene expression and controlling the cell fate, thereby igniting the new interests in RNA-based drug discovery. The dynamics of these RNA chemical modifications is orchestrated by coordinated actions of an array of writer, reader and eraser proteins. Deregulated expression of these RNA modifying proteins can lead to many human diseases including cancer. In this review, we highlight several critical modifications, namely m6A, m1A, m5C, inosine and pseudouridine, in both coding and non-coding RNAs. In parallel, we present a few other cancer-related tRNA and rRNA modifications. We further discuss their roles in cancer promotion or tumour suppression. Understanding the molecular mechanisms underlying the biogenesis and turnover of these RNA modifications will be of great significance in the design and development of novel anticancer drugs.
Collapse
Affiliation(s)
- Phensinee Haruehanroengra
- Department of Chemistry and the RNA Institute, College of Arts and Science, University at Albany, State University of New York , Albany, NY, USA
| | - Ya Ying Zheng
- Department of Chemistry and the RNA Institute, College of Arts and Science, University at Albany, State University of New York , Albany, NY, USA
| | - Yubin Zhou
- Institute of Biosciences and Technology, Texas A&M University , Houston, TX, USA
| | - Yun Huang
- Institute of Biosciences and Technology, Texas A&M University , Houston, TX, USA
| | - Jia Sheng
- Department of Chemistry and the RNA Institute, College of Arts and Science, University at Albany, State University of New York , Albany, NY, USA
| |
Collapse
|
|
23
|
Hebras J, Krogh N, Marty V, Nielsen H, Cavaillé J. Developmental changes of rRNA ribose methylations in the mouse. RNA Biol 2019; 17:150-164. [PMID: 31566069 DOI: 10.1080/15476286.2019.1670598] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
A sequencing-based profiling method (RiboMeth-seq) for ribose methylations was used to study methylation patterns in mouse adult tissues and during development. In contrast to previous reports based on studies of human cancer cell lines, almost all methylation sites were close to fully methylated in adult tissues. A subset of sites was differentially modified in developing tissues compared to their adult counterparts and showed clear developmental dynamics. This provides the first evidence for ribosome heterogeneity at the level of rRNA modifications during mouse development. In a prominent example, the expression levels of SNORD78 during development appeared to be regulated by alternative splicing of the Gas5 host-gene and to correlate with the methylation level of its target site at LSU-G4593. The results are discussed in the context of the specialized ribosome hypothesis.
Collapse
Affiliation(s)
- Jade Hebras
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Nicolai Krogh
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Virginie Marty
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Jérôme Cavaillé
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| |
Collapse
|
|
24
|
García-Vílchez R, Sevilla A, Blanco S. Post-transcriptional regulation by cytosine-5 methylation of RNA. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:240-252. [PMID: 30593929 DOI: 10.1016/j.bbagrm.2018.12.003] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 12/04/2018] [Accepted: 12/07/2018] [Indexed: 02/02/2023]
Abstract
The recent advent of high-throughput sequencing technologies coupled with RNA modifications detection methods has allowed the detection of RNA modifications at single nucleotide resolution giving a more comprehensive landscape of post-transcriptional gene regulation pathways. In this review, we focus on the occurrence of 5-methylcytosine (m5C) in the transcriptome. We summarise the main findings of the molecular role in post-transcriptional regulation that governs m5C deposition in RNAs. Functionally, m5C deposition can regulate several cellular and physiological processes including development, differentiation and survival to stress stimuli. Despite many aspects concerning m5C deposition in RNA, such as position or sequence context and the fact that many readers and erasers still remain elusive, the overall recent findings indicate that RNA cytosine methylation is a powerful mechanism to post-transcriptionally regulate physiological processes. In addition, mutations in RNA cytosine-5 methyltransferases are associated to pathological processes ranging from neurological syndromes to cancer.
Collapse
Affiliation(s)
| | - Ana Sevilla
- Physiology, Cellular Biology and Immunology Department - Biology Faculty. University of Barcelona, Avda. Diagonal 643, 08028 Barcelona. Spain
| | - Sandra Blanco
- CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain; Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), University of Salamanca, 37007 Salamanca, Spain..
| |
Collapse
|
|
25
|
Deciphering the Role of the Non-Coding Genome in Regulating Gene-Diet Interactions. Nutrients 2018; 10:nu10121831. [PMID: 30486341 PMCID: PMC6316136 DOI: 10.3390/nu10121831] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 11/19/2018] [Accepted: 11/21/2018] [Indexed: 01/01/2023] Open
Abstract
Protein encoding genes constitute a small fraction of mammalian genomes. In addition to the protein coding genes, there are other functional units within the genome that are transcribed, but not translated into protein, the so called non-coding RNAs. There are many types of non-coding RNAs that have been identified and shown to have important roles in regulating gene expression either at the transcriptional or post-transcriptional level. A number of recent studies have highlighted that dietary manipulation in mammals can influence the expression or function of a number of classes of non-coding RNAs that contribute to the protein translation machinery. The identification of protein translation as a common target for nutritional regulation underscores the need to investigate how this may mechanistically contribute to phenotypes and diseases that are modified by nutritional intervention. Finally, we describe the state of the art and the application of emerging ‘-omics’ technologies to address the regulation of protein translation in response to diet.
Collapse
|
|
26
|
Ribosomal flavours: an acquired taste for specific mRNAs? Biochem Soc Trans 2018; 46:1529-1539. [PMID: 30420413 DOI: 10.1042/bst20180160] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 09/14/2018] [Accepted: 09/17/2018] [Indexed: 12/20/2022]
Abstract
The regulation of translation is critical in almost every aspect of gene expression. Nonetheless, the ribosome is historically viewed as a passive player in this process. However, evidence is accumulating to suggest that variations in the ribosome can have an important influence on which mRNAs are translated. Scope for variation is provided via multiple avenues, including heterogeneity at the level of both ribosomal proteins and ribosomal RNAs and their covalent modifications. Together, these variations provide the potential for hundreds, if not thousands, of flavours of ribosome, each of which could have idiosyncratic preferences for the translation of certain messenger RNAs. Indeed, perturbations to this heterogeneity appear to affect specific subsets of transcripts and manifest as cell-type-specific diseases. This review provides a historical perspective of the ribosomal code hypothesis, before outlining the various sources of heterogeneity, their regulation and functional consequences for the cell.
Collapse
|
|
27
|
2'-O-Methylation of Ribosomal RNA: Towards an Epitranscriptomic Control of Translation? Biomolecules 2018; 8:biom8040106. [PMID: 30282949 PMCID: PMC6316387 DOI: 10.3390/biom8040106] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 09/27/2018] [Accepted: 09/27/2018] [Indexed: 12/23/2022] Open
Abstract
Ribosomal RNA (rRNA) undergoes post-transcriptional modification of over 200 nucleotides, predominantly 2′-O-methylation (2′-O-Me). 2′-O-Methylation protects RNA from hydrolysis and modifies RNA strand flexibility but does not contribute to Watson-Crick base pairing. The contribution of 2′-O-Me to the translational capacity of ribosomes has been established. Yet, how 2′-O-Me participates in ribosome biogenesis and ribosome functioning remains unclear. The development of 2′-O-Me quantitative mapping methods has contributed to the demonstration that these modifications are not constitutive but rather provide heterogeneity to the ribosomal population. Moreover, recent advances in ribosome structure analysis and in vitro translation assays have proven, for the first time, that 2′-O-Me contributes to regulating protein synthesis. This review highlights the recent data exploring the impact of 2′-O-Me on ribosome structure and function, and the emerging idea that the rRNA epitranscriptome is involved in translational control.
Collapse
|
|
28
|
Tusup M, Kundig T, Pascolo S. Epitranscriptomics of cancer. World J Clin Oncol 2018; 9:42-55. [PMID: 29900123 PMCID: PMC5997933 DOI: 10.5306/wjco.v9.i3.42] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 04/18/2018] [Accepted: 05/23/2018] [Indexed: 02/06/2023] Open
Abstract
The functional impact of modifications of cellular RNAs, including mRNAs, miRNAs and lncRNAs, is a field of intense study. The role of such modifications in cancer has started to be elucidated. Diverse and sometimes opposite effects of RNA modifications have been reported. Some RNA modifications promote, while others decrease the growth and invasiveness of cancer. The present manuscript reviews the current knowledge on the potential impacts of N6-Methyladenosine, Pseudouridine, Inosine, 2’O-methylation or methylcytidine in cancer’s RNA. It also highlights the remaining questions and provides hints on research avenues and potential therapeutic applications, whereby modulating dynamic RNA modifications may be a new method to treat cancer.
Collapse
Affiliation(s)
- Marina Tusup
- Department of Dermatology, University Hospital of Zürich, Zurich 8091, Switzerland
- Faculty of Medicine, University of Zurich, Zurich 8091, Switzerland
| | - Thomas Kundig
- Department of Dermatology, University Hospital of Zürich, Zurich 8091, Switzerland
- Faculty of Medicine, University of Zurich, Zurich 8091, Switzerland
| | - Steve Pascolo
- Department of Dermatology, University Hospital of Zürich, Zurich 8091, Switzerland
- Faculty of Medicine, University of Zurich, Zurich 8091, Switzerland
| |
Collapse
|
|
29
|
Mitrea DM, Cika JA, Stanley CB, Nourse A, Onuchic PL, Banerjee PR, Phillips AH, Park CG, Deniz AA, Kriwacki RW. Self-interaction of NPM1 modulates multiple mechanisms of liquid-liquid phase separation. Nat Commun 2018; 9:842. [PMID: 29483575 PMCID: PMC5827731 DOI: 10.1038/s41467-018-03255-3] [Citation(s) in RCA: 289] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 01/31/2018] [Indexed: 12/20/2022] Open
Abstract
Nucleophosmin (NPM1) is an abundant, oligomeric protein in the granular component of the nucleolus with roles in ribosome biogenesis. Pentameric NPM1 undergoes liquid-liquid phase separation (LLPS) via heterotypic interactions with nucleolar components, including ribosomal RNA (rRNA) and proteins which display multivalent arginine-rich linear motifs (R-motifs), and is integral to the liquid-like nucleolar matrix. Here we show that NPM1 can also undergo LLPS via homotypic interactions between its polyampholytic intrinsically disordered regions, a mechanism that opposes LLPS via heterotypic interactions. Using a combination of biophysical techniques, including confocal microscopy, SAXS, analytical ultracentrifugation, and single-molecule fluorescence, we describe how conformational changes within NPM1 control valency and switching between the different LLPS mechanisms. We propose that this newly discovered interplay between multiple LLPS mechanisms may influence the direction of vectorial pre-ribosomal particle assembly within, and exit from the nucleolus as part of the ribosome biogenesis process.
Collapse
Affiliation(s)
- Diana M Mitrea
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jaclyn A Cika
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Integrative Biomedical Sciences Program, University of Tennessee Health Sciences Center, Memphis, TN, 38163, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, New York, NY, 10016, USA
| | - Christopher B Stanley
- Biology and Biomedical Sciences Group, Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Amanda Nourse
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Molecular Interaction Analysis Shared Resource, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Paulo L Onuchic
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Priya R Banerjee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Physics, University of Buffalo, Buffalo, NY, 14260, USA
| | - Aaron H Phillips
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Cheon-Gil Park
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Ashok A Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Richard W Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Sciences Center, Memphis, TN, 38163, USA.
| |
Collapse
|
|
30
|
Bustelo XR, Dosil M. Ribosome biogenesis and cancer: basic and translational challenges. Curr Opin Genet Dev 2018; 48:22-29. [DOI: 10.1016/j.gde.2017.10.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 09/13/2017] [Accepted: 10/02/2017] [Indexed: 01/08/2023]
|
|
31
|
Evidence for rRNA 2'-O-methylation plasticity: Control of intrinsic translational capabilities of human ribosomes. Proc Natl Acad Sci U S A 2017; 114:12934-12939. [PMID: 29158377 DOI: 10.1073/pnas.1707674114] [Citation(s) in RCA: 194] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ribosomal RNAs (rRNAs) are main effectors of messenger RNA (mRNA) decoding, peptide-bond formation, and ribosome dynamics during translation. Ribose 2'-O-methylation (2'-O-Me) is the most abundant rRNA chemical modification, and displays a complex pattern in rRNA. 2'-O-Me was shown to be essential for accurate and efficient protein synthesis in eukaryotic cells. However, whether rRNA 2'-O-Me is an adjustable feature of the human ribosome and a means of regulating ribosome function remains to be determined. Here we challenged rRNA 2'-O-Me globally by inhibiting the rRNA methyl-transferase fibrillarin in human cells. Using RiboMethSeq, a nonbiased quantitative mapping of 2'-O-Me, we identified a repertoire of 2'-O-Me sites subjected to variation and demonstrate that functional domains of ribosomes are targets of 2'-O-Me plasticity. Using the cricket paralysis virus internal ribosome entry site element, coupled to in vitro translation, we show that the intrinsic capability of ribosomes to translate mRNAs is modulated through a 2'-O-Me pattern and not by nonribosomal actors of the translational machinery. Our data establish rRNA 2'-O-Me plasticity as a mechanism providing functional specificity to human ribosomes.
Collapse
|
|
32
|
|
|
33
|
AML1-ETO requires enhanced C/D box snoRNA/RNP formation to induce self-renewal and leukaemia. Nat Cell Biol 2017. [PMID: 28650479 DOI: 10.1038/ncb3563] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Leukaemogenesis requires enhanced self-renewal, which is induced by oncogenes. The underlying molecular mechanisms remain incompletely understood. Here, we identified C/D box snoRNAs and rRNA 2'-O-methylation as critical determinants of leukaemic stem cell activity. Leukaemogenesis by AML1-ETO required expression of the groucho-related amino-terminal enhancer of split (AES). AES functioned by inducing snoRNA/RNP formation via interaction with the RNA helicase DDX21. Similarly, global loss of C/D box snoRNAs with concomitant loss of rRNA 2'-O-methylation resulted in decreased leukaemia self-renewal potential. Genomic deletion of either C/D box snoRNA SNORD14D or SNORD35A suppressed clonogenic potential of leukaemia cells in vitro and delayed leukaemogenesis in vivo. We further showed that AML1-ETO9a, MYC and MLL-AF9 all enhanced snoRNA formation. Expression levels of C/D box snoRNAs in AML patients correlated closely with in vivo frequency of leukaemic stem cells. Collectively, these findings indicate that induction of C/D box snoRNA/RNP function constitutes an important pathway in leukaemogenesis.
Collapse
|
|
34
|
Sloan KE, Warda AS, Sharma S, Entian KD, Lafontaine DLJ, Bohnsack MT. Tuning the ribosome: The influence of rRNA modification on eukaryotic ribosome biogenesis and function. RNA Biol 2016; 14:1138-1152. [PMID: 27911188 PMCID: PMC5699541 DOI: 10.1080/15476286.2016.1259781] [Citation(s) in RCA: 475] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
rRNAs are extensively modified during their transcription and subsequent maturation in the nucleolus, nucleus and cytoplasm. RNA modifications, which are installed either by snoRNA-guided or by stand-alone enzymes, generally stabilize the structure of the ribosome. However, they also cluster at functionally important sites of the ribosome, such as the peptidyltransferase center and the decoding site, where they facilitate efficient and accurate protein synthesis. The recent identification of sites of substoichiometric 2'-O-methylation and pseudouridylation has overturned the notion that all rRNA modifications are constitutively present on ribosomes, highlighting nucleotide modifications as an important source of ribosomal heterogeneity. While the mechanisms regulating partial modification and the functions of specialized ribosomes are largely unknown, changes in the rRNA modification pattern have been observed in response to environmental changes, during development, and in disease. This suggests that rRNA modifications may contribute to the translational control of gene expression.
Collapse
Affiliation(s)
- Katherine E Sloan
- a Institute for Molecular Biology, University Medical Center Göttingen, Georg-August-University , Göttingen , Germany
| | - Ahmed S Warda
- a Institute for Molecular Biology, University Medical Center Göttingen, Georg-August-University , Göttingen , Germany
| | - Sunny Sharma
- b RNA Molecular Biology and Center for Microscopy and Molecular Imaging, F.R.S./FNRS, Université Libre de Bruxelles , Charleroi-Gosselies , Belgium
| | - Karl-Dieter Entian
- c Institute for Molecular Biosciences, Goethe University , Frankfurt am Main , Germany
| | - Denis L J Lafontaine
- b RNA Molecular Biology and Center for Microscopy and Molecular Imaging, F.R.S./FNRS, Université Libre de Bruxelles , Charleroi-Gosselies , Belgium
| | - Markus T Bohnsack
- a Institute for Molecular Biology, University Medical Center Göttingen, Georg-August-University , Göttingen , Germany.,d Göttingen Centre for Molecular Biosciences, Georg-August-University , Göttingen , Germany
| |
Collapse
|
|
35
|
Deffrasnes C, Marsh GA, Foo CH, Rootes CL, Gould CM, Grusovin J, Monaghan P, Lo MK, Tompkins SM, Adams TE, Lowenthal JW, Simpson KJ, Stewart CR, Bean AGD, Wang LF. Genome-wide siRNA Screening at Biosafety Level 4 Reveals a Crucial Role for Fibrillarin in Henipavirus Infection. PLoS Pathog 2016; 12:e1005478. [PMID: 27010548 PMCID: PMC4806981 DOI: 10.1371/journal.ppat.1005478] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 02/08/2016] [Indexed: 12/16/2022] Open
Abstract
Hendra and Nipah viruses (genus Henipavirus, family Paramyxoviridae) are highly pathogenic bat-borne viruses. The need for high biocontainment when studying henipaviruses has hindered the development of therapeutics and knowledge of the viral infection cycle. We have performed a genome-wide siRNA screen at biosafety level 4 that identified 585 human proteins required for henipavirus infection. The host protein with the largest impact was fibrillarin, a nucleolar methyltransferase that was also required by measles, mumps and respiratory syncytial viruses for infection. While not required for cell entry, henipavirus RNA and protein syntheses were greatly impaired in cells lacking fibrillarin, indicating a crucial role in the RNA replication phase of infection. During infection, the Hendra virus matrix protein co-localized with fibrillarin in cell nucleoli, and co-associated as a complex in pulldown studies, while its nuclear import was unaffected in fibrillarin-depleted cells. Mutagenesis studies showed that the methyltransferase activity of fibrillarin was required for henipavirus infection, suggesting that this enzyme could be targeted therapeutically to combat henipavirus infections. The henipaviruses Hendra and Nipah are bat-borne paramyxoviruses that are highly pathogenic in humans. The need for high biocontainment when studying Hendra and Nipah virus biology has hindered the development of therapeutics and knowledge of the viral infection cycle. This study describes a genome-wide functional genomics screen of human host genes required for henipavirus infection, to our knowledge the first such study conducted at biosafety level 4. Our study demonstrates that henipavirus infection is critically reliant on fibrillarin, a methyltransferase enzyme residing in the cell nucleolus. Despite henipavirus genome replication occurring in the cytoplasm of infected cells, viral RNA synthesis was greatly impaired in cells lacking fibrillarin. Furthermore during the early stages of infection the Hendra virus matrix protein shuttles to the nucleolus and binds fibrillarin. Collectively these results suggest a hitherto unappreciated role for nucleolar host-virus interactions in the early replication phase of henipavirus infection. Finally, mutating the catalytic activity of fibrillarin inhibits henipavirus infection, suggesting that this enzyme could be targeted therapeutically to combat henipavirus infections.
Collapse
Affiliation(s)
- Celine Deffrasnes
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Glenn A. Marsh
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Chwan Hong Foo
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Christina L. Rootes
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Cathryn M. Gould
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | | | - Paul Monaghan
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Michael K. Lo
- Centers for Disease Control & Prevention, Viral Special Pathogens Branch, Atlanta, Georgia, United States of America
| | - S. Mark Tompkins
- Department of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America, and School of Medicine, Deakin University, Waurn Ponds, Victoria, Australia
| | | | - John W. Lowenthal
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Geelong, Victoria, Australia
- Department of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America, and School of Medicine, Deakin University, Waurn Ponds, Victoria, Australia
| | - Kaylene J. Simpson
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - Cameron R. Stewart
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Geelong, Victoria, Australia
- * E-mail:
| | - Andrew G. D. Bean
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Lin-Fa Wang
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Geelong, Victoria, Australia
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore
| |
Collapse
|
|
36
|
Translational control of PML contributes to TNFα-induced apoptosis of MCF7 breast cancer cells and decreased angiogenesis in HUVECs. Cell Death Differ 2015; 23:469-83. [PMID: 26383972 PMCID: PMC5072441 DOI: 10.1038/cdd.2015.114] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 06/06/2015] [Accepted: 06/25/2015] [Indexed: 01/21/2023] Open
Abstract
The tumor suppressor protein promyelocytic leukemia (PML) is a key regulator of inflammatory responses and tumorigenesis and functions through the assembly of subnuclear structures known as PML nuclear bodies (NBs). The inflammation-related cytokine tumor necrosis factor-α (TNFα) is known to induce PML protein accumulation and PML NB formation that mediate TNFα-induced cell death in cancer cells and inhibition of migration and capillary tube formation in endothelial cells (ECs). In this study, we uncover a novel mechanism of PML gene regulation in which the p38 MAPK and its downstream kinase MAP kinase-activated protein kinase 1 (MNK1) mediate TNFα-induced PML protein accumulation and PML NB formation. The mechanism includes the presence of an internal ribosome entry site (IRES) found within the well-conserved 100 nucleotides upstream of the PML initiation codon. The activity of the PML IRES is induced by TNFα in a manner that involves MNK1 activation. It is proposed that the p38–MNK1–PML network regulates TNFα-induced apoptosis in breast cancer cells and TNFα-mediated inhibition of migration and capillary tube formation in ECs.
Collapse
|
|
37
|
Wang CY, Yeh JK, Shie SS, Hsieh IC, Wen MS. Circadian rhythm of RNA N6-methyladenosine and the role of cryptochrome. Biochem Biophys Res Commun 2015; 465:88-94. [PMID: 26239657 DOI: 10.1016/j.bbrc.2015.07.135] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 07/28/2015] [Indexed: 11/27/2022]
Abstract
Methylation of RNA N(6)-methyladenosine has fundamental cellular functions, including translation regulation, RNA export, and stem cells renewal. However, the regulation of RNA N(6)-methyladenosine methylation is poorly understood. Here, we observed a robust circadian rhythm in N(6)-methyladenosine modifications of RNA. Deficiency of core mammalian clock genes, cryptochromes, decreased the levels of N(6)-methyladenosine in RNA. Cryptochrome1/2 knockout mice had significantly lower N(6)-methyladenosine methylation of RNA and lost the circadian rhythm of N(6)-methyladenosine levels in RNA. Global analysis of the circadian methylomes of N(6)-methyladenosine in RNA revealed that gene transcription, translation regulation, and RNA metabolism were highly correlated with N(6)-methyladenosine oscillation. Our findings extended a fundamental link between the circadian rhythm and N(6)-methyladenosine modification of RNA and suggested that this link is critical in controlling post-transcriptional gene expression and RNA metabolism.
Collapse
Affiliation(s)
- Chao-Yung Wang
- Department of Cardiology, Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taiwan.
| | - Jih-Kai Yeh
- Department of Cardiology, Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taiwan
| | - Shian-Sen Shie
- Department of Infectious Diseases, Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taiwan
| | - I-Chang Hsieh
- Department of Cardiology, Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taiwan
| | - Ming-Shien Wen
- Department of Cardiology, Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taiwan
| |
Collapse
|
|
38
|
Rodriguez-Corona U, Sobol M, Rodriguez-Zapata LC, Hozak P, Castano E. Fibrillarin from Archaea to human. Biol Cell 2015; 107:159-74. [PMID: 25772805 DOI: 10.1111/boc.201400077] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 03/05/2015] [Indexed: 12/19/2022]
Abstract
Fibrillarin is an essential protein that is well known as a molecular marker of transcriptionally active RNA polymerase I. Fibrillarin methyltransferase activity is the primary known source of methylation for more than 100 methylated sites involved in the first steps of preribosomal processing and required for structural ribosome stability. High expression levels of fibrillarin have been observed in several types of cancer cells, particularly when p53 levels are reduced, because p53 is a direct negative regulator of fibrillarin transcription. Here, we show fibrillarin domain conservation, structure and interacting molecules in different cellular processes as well as with several viral proteins during virus infection.
Collapse
Affiliation(s)
- Ulises Rodriguez-Corona
- Unidad de Bioquímica y Biología molecular de plantas, Centro de Investigación Científica de Yucatán, Colonia Chuburná de Hidalgo, Mérida, Yucatan, Mexico
| | - Margarita Sobol
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic, Prague 14220, Czech Republic
| | - Luis Carlos Rodriguez-Zapata
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Colonia Chuburná de Hidalgo, Mérida, Yucatan, Mexico
| | - Pavel Hozak
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic, Prague 14220, Czech Republic
| | - Enrique Castano
- Unidad de Bioquímica y Biología molecular de plantas, Centro de Investigación Científica de Yucatán, Colonia Chuburná de Hidalgo, Mérida, Yucatan, Mexico
| |
Collapse
|
|
39
|
Thorenoor N, Slaby O. Small nucleolar RNAs functioning and potential roles in cancer. Tumour Biol 2014; 36:41-53. [DOI: 10.1007/s13277-014-2818-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 11/04/2014] [Indexed: 11/27/2022] Open
|
|
40
|
McMahon M, Contreras A, Ruggero D. Small RNAs with big implications: new insights into H/ACA snoRNA function and their role in human disease. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 6:173-89. [PMID: 25363811 DOI: 10.1002/wrna.1266] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 07/25/2014] [Accepted: 08/07/2014] [Indexed: 12/26/2022]
Abstract
A myriad of structurally and functionally diverse noncoding RNAs (ncRNAs) have recently been implicated in numerous human diseases including cancer. Small nucleolar RNAs (snoRNAs), the most abundant group of intron-encoded ncRNAs, are classified into two families (box C/D snoRNAs and box H/ACA snoRNAs) and are required for post-transcriptional modifications on ribosomal RNA (rRNA). There is now a growing appreciation that nucleotide modifications on rRNA may impart regulatory potential to the ribosome; however, the functional consequence of site-specific snoRNA-guided modifications remains poorly defined. Discovered almost 20 years ago, H/ACA snoRNAs are required for the conversion of specific uridine residues to pseudouridine on rRNA. Interestingly, recent reports indicate that the levels of subsets of H/ACA snoRNAs required for pseudouridine modifications at specific sites on rRNA are altered in several diseases, particularly cancer. In this review, we describe recent advances in understanding the downstream consequences of H/ACA snoRNA-guided modifications on ribosome function, discuss the possible mechanism by which H/ACA snoRNAs may be regulated, and explore prospective expanding functions of H/ACA snoRNAs. Furthermore, we discuss the potential biological implications of alterations in H/ACA snoRNA expression in several human diseases.
Collapse
Affiliation(s)
- Mary McMahon
- School of Medicine and Department of Urology, Helen Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | | | | |
Collapse
|
|
41
|
Souii A, Ben M'hadheb-Gharbi M, Gharbi J. Role of RNA structure motifs in IRES-dependent translation initiation of the coxsackievirus B3: new insights for developing live-attenuated strains for vaccines and gene therapy. Mol Biotechnol 2014; 55:179-202. [PMID: 23881360 DOI: 10.1007/s12033-013-9674-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Internal ribosome entry site (IRES) elements are highly structured RNA sequences that function to recruit ribosomes for the initiation of translation. In contrast to the canonical cap-binding, the mechanism of IRES-mediated translation initiation is still poorly understood. Translation initiation of the coxsackievirus B3 (CVB3), a causative agent of viral myocarditis, has been shown to be mediated by a highly ordered structure of the 5' untranslated region (5'UTR), which harbors an IRES. Taking into account that efficient initiation of mRNA translation depends on temporally and spatially orchestrated sequence of RNA-protein and RNA-RNA interactions, and that, at present, little is known about these interactions, we aimed to describe recent advances in our understanding of molecular structures and biochemical functions of the translation initiation process. Thus, this review will explore the IRES elements as important RNA structures and the significance of these structures in providing an alternative mechanism of translation initiation of the CVB3 RNA. Since translation initiation is the first intracellular step during the CVB3 infection cycle, the IRES region provides an ideal target for antiviral therapies. Interestingly, the 5' and 3'UTRs represent promising candidates for the study of CVB3 cardiovirulence and provide new insights for developing live-attenuated vaccines.
Collapse
Affiliation(s)
- Amira Souii
- Institut Supérieur de Biotechnologie de Monastir-Université de Monastir, Avenue Tahar Hadded, BP 74, 5000, Monastir, Tunisia
| | | | | |
Collapse
|
|
42
|
Loreni F, Mancino M, Biffo S. Translation factors and ribosomal proteins control tumor onset and progression: how? Oncogene 2014; 33:2145-56. [PMID: 23644661 DOI: 10.1038/onc.2013.153] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 03/12/2013] [Accepted: 03/13/2013] [Indexed: 12/18/2022]
Abstract
Gene expression is shaped by translational control. The modalities and the extent by which translation factors modify gene expression have revealed therapeutic scenarios. For instance, eukaryotic initiation factor (eIF)4E activity is controlled by the signaling cascade of growth factors, and drives tumorigenesis by favoring the translation of specific mRNAs. Highly specific drugs target the activity of eIF4E. Indeed, the antitumor action of mTOR complex 1 (mTORc1) blockers like rapamycin relies on their capability to inhibit eIF4E assembly into functional eIF4F complexes. eIF4E biology, from its inception to recent pharmacological targeting, is proof-of-principle that translational control is druggable. The case for eIF4E is not isolated. The translational machinery is involved in the biology of cancer through many other mechanisms. First, untranslated sequences on mRNAs as well as noncoding RNAs regulate the translational efficiency of mRNAs that are central for tumor progression. Second, other initiation factors like eIF6 show a tumorigenic potential by acting downstream of oncogenic pathways. Third, genetic alterations in components of the translational apparatus underlie an entire class of inherited syndromes known as 'ribosomopathies' that are associated with increased cancer risk. Taken together, data suggest that in spite of their evolutionary conservation and ubiquitous nature, variations in the activity and levels of ribosomal proteins and translation factors generate highly specific effects. Beside, as the structures and biochemical activities of several noncoding RNAs and initiation factors are known, these factors may be amenable to rational pharmacological targeting. The future is to design highly specific drugs targeting the translational apparatus.
Collapse
Affiliation(s)
- F Loreni
- Department of Biology, University 'Tor Vergata', Roma, Italy
| | - M Mancino
- 1] San Raffaele Scientific Institute, Ospedale San Raffaele, Milan, Italy [2] DISIT, Alessandria, Italy
| | - S Biffo
- 1] San Raffaele Scientific Institute, Ospedale San Raffaele, Milan, Italy [2] DISIT, Alessandria, Italy
| |
Collapse
|
|
43
|
Baldridge KC, Contreras LM. Functional implications of ribosomal RNA methylation in response to environmental stress. Crit Rev Biochem Mol Biol 2013; 49:69-89. [PMID: 24261569 DOI: 10.3109/10409238.2013.859229] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The study of post-transcriptional RNA modifications has long been focused on the roles these chemical modifications play in maintaining ribosomal function. The field of ribosomal RNA modification has reached a milestone in recent years with the confirmation of the final unknown ribosomal RNA methyltransferase in Escherichia coli in 2012. Furthermore, the last 10 years have brought numerous discoveries in non-coding RNAs and the roles that post-transcriptional modification play in their functions. These observations indicate the need for a revitalization of this field of research to understand the role modifications play in maintaining cellular health in a dynamic environment. With the advent of high-throughput sequencing technologies, the time is ripe for leaps and bounds forward. This review discusses ribosomal RNA methyltransferases and their role in responding to external stress in Escherichia coli, with a specific focus on knockout studies and on analysis of transcriptome data with respect to rRNA methyltransferases.
Collapse
Affiliation(s)
- Kevin C Baldridge
- McKetta Department of Chemical Engineering, The University of Texas at Austin , Austin, TX , USA
| | | |
Collapse
|
|
44
|
Prokhorova IV, Osterman IA, Burakovsky DE, Serebryakova MV, Galyamina MA, Pobeguts OV, Altukhov I, Kovalchuk S, Alexeev DG, Govorun VM, Bogdanov AA, Sergiev PV, Dontsova OA. Modified nucleotides m(2)G966/m(5)C967 of Escherichia coli 16S rRNA are required for attenuation of tryptophan operon. Sci Rep 2013; 3:3236. [PMID: 24241179 PMCID: PMC3831192 DOI: 10.1038/srep03236] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 11/01/2013] [Indexed: 12/30/2022] Open
Abstract
Ribosomes contain a number of modifications in rRNA, the function of which is unclear. Here we show – using proteomic analysis and dual fluorescence reporter in vivo assays – that m2G966 and m5C967 in 16S rRNA of Escherichia coli ribosomes are necessary for correct attenuation of tryptophan (trp) operon. Expression of trp operon is upregulated in the strain where RsmD and RsmB methyltransferases were deleted, which results in the lack of m2G966 and m5C967 modifications. The upregulation requires the trpL attenuator, but is independent of the promotor of trp operon, ribosome binding site of the trpE gene, which follows trp attenuator and even Trp codons in the trpL sequence. Suboptimal translation initiation efficiency in the rsmB/rsmD knockout strain is likely to cause a delay in translation relative to transcription which causes misregulation of attenuation control of trp operon.
Collapse
Affiliation(s)
- Irina V Prokhorova
- 1] Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119899, Russia [2]
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
|
45
|
Martínez-Salas E, Lozano G, Fernandez-Chamorro J, Francisco-Velilla R, Galan A, Diaz R. RNA-binding proteins impacting on internal initiation of translation. Int J Mol Sci 2013; 14:21705-26. [PMID: 24189219 PMCID: PMC3856030 DOI: 10.3390/ijms141121705] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 10/17/2013] [Accepted: 10/22/2013] [Indexed: 12/20/2022] Open
Abstract
RNA-binding proteins (RBPs) are pivotal regulators of all the steps of gene expression. RBPs govern gene regulation at the post-transcriptional level by virtue of their capacity to assemble ribonucleoprotein complexes on certain RNA structural elements, both in normal cells and in response to various environmental stresses. A rapid cellular response to stress conditions is triggered at the step of translation initiation. Two basic mechanisms govern translation initiation in eukaryotic mRNAs, the cap-dependent initiation mechanism that operates in most mRNAs, and the internal ribosome entry site (IRES)-dependent mechanism activated under conditions that compromise the general translation pathway. IRES elements are cis-acting RNA sequences that recruit the translation machinery using a cap-independent mechanism often assisted by a subset of translation initiation factors and various RBPs. IRES-dependent initiation appears to use different strategies to recruit the translation machinery depending on the RNA organization of the region and the network of RBPs interacting with the element. In this review we discuss recent advances in understanding the implications of RBPs on IRES-dependent translation initiation.
Collapse
Affiliation(s)
- Encarnación Martínez-Salas
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Cantoblanco, Madrid 28049, Spain.
| | | | | | | | | | | |
Collapse
|
|
46
|
Marcel V, Ghayad S, Belin S, Therizols G, Morel AP, Solano-Gonzàlez E, Vendrell J, Hacot S, Mertani H, Albaret M, Bourdon JC, Jordan L, Thompson A, Tafer Y, Cong R, Bouvet P, Saurin JC, Catez F, Prats AC, Puisieux A, Diaz JJ. p53 acts as a safeguard of translational control by regulating fibrillarin and rRNA methylation in cancer. Cancer Cell 2013; 24:318-30. [PMID: 24029231 PMCID: PMC7106277 DOI: 10.1016/j.ccr.2013.08.013] [Citation(s) in RCA: 246] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 07/08/2013] [Accepted: 08/12/2013] [Indexed: 01/01/2023]
Abstract
Ribosomes are specialized entities that participate in regulation of gene expression through their rRNAs carrying ribozyme activity. Ribosome biogenesis is overactivated in p53-inactivated cancer cells, although involvement of p53 on ribosome quality is unknown. Here, we show that p53 represses expression of the rRNA methyl-transferase fibrillarin (FBL) by binding directly to FBL. High levels of FBL are accompanied by modifications of the rRNA methylation pattern, impairment of translational fidelity, and an increase of internal ribosome entry site (IRES)-dependent translation initiation of key cancer genes. FBL overexpression contributes to tumorigenesis and is associated with poor survival in patients with breast cancer. Thus, p53 acts as a safeguard of protein synthesis by regulating FBL and the subsequent quality and intrinsic activity of ribosomes.
Collapse
Affiliation(s)
- Virginie Marcel
- Centre de Recherche en Cancérologie de Lyon UMR Inserm 1052 CNRS 5286, Centre Léon Bérard, F-69373, Lyon, France
- Université de Lyon, Université Lyon 1, ISPB, Lyon F-69622, France
| | - Sandra E. Ghayad
- Centre de Recherche en Cancérologie de Lyon UMR Inserm 1052 CNRS 5286, Centre Léon Bérard, F-69373, Lyon, France
- Université de Lyon, Université Lyon 1, ISPB, Lyon F-69622, France
| | - Stéphane Belin
- Centre de Recherche en Cancérologie de Lyon UMR Inserm 1052 CNRS 5286, Centre Léon Bérard, F-69373, Lyon, France
- Université de Lyon, Université Lyon 1, ISPB, Lyon F-69622, France
| | - Gabriel Therizols
- Centre de Recherche en Cancérologie de Lyon UMR Inserm 1052 CNRS 5286, Centre Léon Bérard, F-69373, Lyon, France
- Université de Lyon, Université Lyon 1, ISPB, Lyon F-69622, France
| | - Anne-Pierre Morel
- Centre de Recherche en Cancérologie de Lyon UMR Inserm 1052 CNRS 5286, Centre Léon Bérard, F-69373, Lyon, France
- Université de Lyon, Université Lyon 1, ISPB, Lyon F-69622, France
| | - Eduardo Solano-Gonzàlez
- Université de Toulouse, UPS, TRADGENE, EA4554, Institut des Maladies Métaboliques et Cardiovasculaires, 1 Avenue Jean Poulhès, BP 84225, F-31432 Toulouse, France
| | - Julie A. Vendrell
- Centre de Recherche en Cancérologie de Lyon UMR Inserm 1052 CNRS 5286, Centre Léon Bérard, F-69373, Lyon, France
- Université de Lyon, Université Lyon 1, ISPB, Lyon F-69622, France
- ISPB, Faculté de Pharmacie, Université Lyon 1, Lyon, France
- Dundee Cancer Centre, Clinical Research Centre, University of Dundee, Dundee DD1 9SY, UK
| | - Sabine Hacot
- Centre de Recherche en Cancérologie de Lyon UMR Inserm 1052 CNRS 5286, Centre Léon Bérard, F-69373, Lyon, France
- Université de Lyon, Université Lyon 1, ISPB, Lyon F-69622, France
| | - Hichem C. Mertani
- Centre de Recherche en Cancérologie de Lyon UMR Inserm 1052 CNRS 5286, Centre Léon Bérard, F-69373, Lyon, France
- Université de Lyon, Université Lyon 1, ISPB, Lyon F-69622, France
| | - Marie Alexandra Albaret
- Centre de Recherche en Cancérologie de Lyon UMR Inserm 1052 CNRS 5286, Centre Léon Bérard, F-69373, Lyon, France
- Université de Lyon, Université Lyon 1, ISPB, Lyon F-69622, France
| | | | - Lee Jordan
- Department of Pathology, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK
| | - Alastair Thompson
- Dundee Cancer Centre, Clinical Research Centre, University of Dundee, Dundee DD1 9SY, UK
| | - Yasmine Tafer
- Centre de Recherche en Cancérologie de Lyon UMR Inserm 1052 CNRS 5286, Centre Léon Bérard, F-69373, Lyon, France
- Université de Lyon, Université Lyon 1, ISPB, Lyon F-69622, France
| | - Rong Cong
- Laboratoire Joliot-Curie, Ecole Normale Supérieure de Lyon, Université de Lyon, CNRS USR 3010, SFR BioSciences UMS3444, Lyon 69364, France
| | - Philippe Bouvet
- Laboratoire Joliot-Curie, Ecole Normale Supérieure de Lyon, Université de Lyon, CNRS USR 3010, SFR BioSciences UMS3444, Lyon 69364, France
| | - Jean-Christophe Saurin
- Centre de Recherche en Cancérologie de Lyon UMR Inserm 1052 CNRS 5286, Centre Léon Bérard, F-69373, Lyon, France
- Université de Lyon, Université Lyon 1, ISPB, Lyon F-69622, France
- Gastroenterology Unit, Édouard Herriot Hospital, Hospices Civils de Lyon, 69002 Lyon, France
| | - Frédéric Catez
- Centre de Recherche en Cancérologie de Lyon UMR Inserm 1052 CNRS 5286, Centre Léon Bérard, F-69373, Lyon, France
- Université de Lyon, Université Lyon 1, ISPB, Lyon F-69622, France
| | - Anne-Catherine Prats
- Université de Toulouse, UPS, TRADGENE, EA4554, Institut des Maladies Métaboliques et Cardiovasculaires, 1 Avenue Jean Poulhès, BP 84225, F-31432 Toulouse, France
| | - Alain Puisieux
- Centre de Recherche en Cancérologie de Lyon UMR Inserm 1052 CNRS 5286, Centre Léon Bérard, F-69373, Lyon, France
- Université de Lyon, Université Lyon 1, ISPB, Lyon F-69622, France
| | - Jean-Jacques Diaz
- Centre de Recherche en Cancérologie de Lyon UMR Inserm 1052 CNRS 5286, Centre Léon Bérard, F-69373, Lyon, France
- Université de Lyon, Université Lyon 1, ISPB, Lyon F-69622, France
- Corresponding author
| |
Collapse
|
|
47
|
Tafforeau L, Zorbas C, Langhendries JL, Mullineux ST, Stamatopoulou V, Mullier R, Wacheul L, Lafontaine D. The Complexity of Human Ribosome Biogenesis Revealed by Systematic Nucleolar Screening of Pre-rRNA Processing Factors. Mol Cell 2013; 51:539-51. [DOI: 10.1016/j.molcel.2013.08.011] [Citation(s) in RCA: 361] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 06/06/2013] [Accepted: 07/17/2013] [Indexed: 10/26/2022]
|
|
48
|
SnoRNA U50 levels are regulated by cell proliferation and rRNA transcription. Int J Mol Sci 2013; 14:14923-35. [PMID: 23867608 PMCID: PMC3742280 DOI: 10.3390/ijms140714923] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 07/01/2013] [Accepted: 07/02/2013] [Indexed: 01/08/2023] Open
Abstract
rRNA post transcriptional modifications play a role in cancer development by affecting ribosomal function. In particular, the snoRNA U50, mediating the methylation of C2848 in 28S rRNA, has been suggested as a potential tumor suppressor-like gene playing a role in breast and prostate cancers and B-cell lymphoma. Indeed, we observed the downregulation of U50 in colon cancer cell lines as well as tumors. We then investigated the relationship between U50 and proliferation in lymphocytes stimulated by phytohemagglutinin (PHA) and observed a strong decrease in U50 levels associated with a reduced C2848 methylation. This reduction was due to an alteration of U50 stability and to an increase of its consumption. Indeed, the blockade of ribosome biogenesis induced only an early decrease in U50 followed by a stabilization of U50 levels when ribosome biogenesis was almost completely blocked. Similar results were found with other snoRNAs. Lastly, we observed that U50 modulation affects ribosome efficiency in IRES-mediated translation, demonstrating that changes in the methylation levels of a single specific site on 28S rRNA may alter ribosome function. In conclusion, our results link U50 to the cellular proliferation rate and ribosome biogenesis and these findings may explain why its levels are often greatly reduced in cancers.
Collapse
|
|
49
|
Rocchi L, Pacilli A, Sethi R, Penzo M, Schneider RJ, Treré D, Brigotti M, Montanaro L. Dyskerin depletion increases VEGF mRNA internal ribosome entry site-mediated translation. Nucleic Acids Res 2013; 41:8308-18. [PMID: 23821664 PMCID: PMC3783170 DOI: 10.1093/nar/gkt587] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Dyskerin is a nucleolar protein encoded by the DKC1 gene that (i) stabilizes the RNA component of the telomerase complex, and (ii) drives the site-specific pseudouridilation of rRNA. It is known that the partial lack of dyskerin function causes a defect in the translation of a subgroup of mRNAs containing internal ribosome entry site (IRES) elements such as those encoding for the tumor suppressors p27 and p53. In this study, we aimed to analyze what is the effect of the lack of dyskerin on the IRES-mediated translation of mRNAs encoding for vascular endothelial growth factor (VEGF). We transiently reduced dyskerin expression and measured the levels of the IRES-mediated translation of the mRNA encoding for VEGF in vitro in transformed and primary cells. We demonstrated a significant increase in the VEGF IRES-mediated translation after dyskerin knock-down. This translational modulation induces an increase in VEGF production in the absence of a significant upregulation in VEGF mRNA levels. The analysis of a list of viral and cellular IRESs indicated that dyskerin depletion can differentially affect IRES-mediated translation. These results indicate for the first time that dyskerin inhibition can upregulate the IRES translation initiation of specific mRNAs.
Collapse
Affiliation(s)
- Laura Rocchi
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-Universita' di Bologna, Bologna 40126, Italy, Centro Interdipartimentale di Ricerche sul Cancro 'Giorgio Prodi'-CIRC, Alma Mater Studiorum-Universita' di Bologna 40138, Italy and Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA
| | | | | | | | | | | | | | | |
Collapse
|
|
50
|
Makarova JA, Ivanova SM, Tonevitsky AG, Grigoriev AI. New functions of small nucleolar RNAs. BIOCHEMISTRY (MOSCOW) 2013; 78:638-50. [DOI: 10.1134/s0006297913060096] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
|