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Fu Y, Jiang F, Zhang X, Pan Y, Xu R, Liang X, Wu X, Li X, Lin K, Shi R, Zhang X, Ferrandon D, Liu J, Pei D, Wang J, Wang T. Perturbation of METTL1-mediated tRNA N 7- methylguanosine modification induces senescence and aging. Nat Commun 2024; 15:5713. [PMID: 38977661 PMCID: PMC11231295 DOI: 10.1038/s41467-024-49796-8] [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: 11/07/2023] [Accepted: 06/14/2024] [Indexed: 07/10/2024] Open
Abstract
Cellular senescence is characterized by a decrease in protein synthesis, although the underlying processes are mostly unclear. Chemical modifications to transfer RNAs (tRNAs) frequently influence tRNA activity, which is crucial for translation. We describe how tRNA N7-methylguanosine (m7G46) methylation, catalyzed by METTL1-WDR4, regulates translation and influences senescence phenotypes. Mettl1/Wdr4 and m7G gradually diminish with senescence and aging. A decrease in METTL1 causes a reduction in tRNAs, especially those with the m7G modification, via the rapid tRNA degradation (RTD) pathway. The decreases cause ribosomes to stall at certain codons, impeding the translation of mRNA that is essential in pathways such as Wnt signaling and ribosome biogenesis. Furthermore, chronic ribosome stalling stimulates the ribotoxic and integrative stress responses, which induce senescence-associated secretory phenotype. Moreover, restoring eEF1A protein mitigates senescence phenotypes caused by METTL1 deficiency by reducing RTD. Our findings demonstrate that tRNA m7G modification is essential for preventing premature senescence and aging by enabling efficient mRNA translation.
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Affiliation(s)
- Yudong Fu
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou, China
- GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fan Jiang
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou, China
- GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou, China
| | - Xiao Zhang
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou, China
- GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yingyi Pan
- Sino-French Hoffmann Institute, Guangzhou Medical University, Guangzhou, China
| | - Rui Xu
- Department of pediatrics, Foshan maternal and children's hospital affiliated to southern medical university, 528000, Foshan, Guangdong, China
| | - Xiu Liang
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou, China
- GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou, China
| | - Xiaofen Wu
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou, China
- GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou, China
| | | | - Kaixuan Lin
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou, China
- GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou, China
| | - Ruona Shi
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou, China
- GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou, China
| | - Xiaofei Zhang
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou, China
- GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dominique Ferrandon
- Sino-French Hoffmann Institute, Guangzhou Medical University, Guangzhou, China
- Université de Strasbourg, Strasbourg, France
- Modèles Insectes de l'Immunité Innée, UPR 9022 du CNRS, Strasbourg, France
| | - Jing Liu
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou, China
- GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou, China
- Joint School of Lifesciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China, Guangzhou Medical University, 511436, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Duanqing Pei
- School of Life Sciences, Westlake University, Hangzhou, China
| | - Jie Wang
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou, China.
- GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou, China.
- Joint School of Lifesciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China, Guangzhou Medical University, 511436, Guangzhou, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Tao Wang
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou, China.
- GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou, China.
- University of Chinese Academy of Sciences, Beijing, China.
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2
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Hasan M, Nishat ZS, Hasan MS, Hossain T, Ghosh A. Identification of m 6A RNA methylation genes in Oryza sativa and expression profiling in response to different developmental and environmental stimuli. Biochem Biophys Rep 2024; 38:101677. [PMID: 38511186 PMCID: PMC10950732 DOI: 10.1016/j.bbrep.2024.101677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/27/2024] [Accepted: 02/27/2024] [Indexed: 03/22/2024] Open
Abstract
Eukaryotic messenger RNAs (mRNAs) transcend their predominant function of protein encoding by incorporating auxiliary components that ultimately contribute to their processing, transportation, translation, and decay. In doing so, additional layers of modifications are incorporated in mRNAs at post-transcriptional stage. Among them, N6-methyladenosine (m6A) is the most frequently found mRNA modification that plays crucial roles in plant development and stress response. In the overall mechanism of m6A methylation, key proteins classified based on their functions such as writers, readers, and erasers dynamically add, read, and subtract methyl groups respectively to deliver relevant functions in response to external stimuli. In this study, we identified 30 m6A regulatory genes (9 writers, 5 erasers, and 16 readers) in rice that encode 53 proteins (13 writers, 7 erasers, and 33 readers) where segmental duplication was found in one writer and four reader gene pairs. Reproductive cells such as sperm, anther and panicle showed high levels of expression for most of the m6A regulatory genes. Notably, writers like OsMTA, OsMTD, and OsMTC showed varied responses in different stress and infection contexts, with initial upregulation in response to early exposure followed by downregulation later. OsALKBH9A, a noteworthy eraser, displayed varied expression in response to different stresses at different time intervals, but upregulation in certain infections. Reader genes like OsECT5, OsCPSF30-L3, and OsECT8 showed continuous upregulation in exertion of all kinds of stress relevant here. Conversely, other reader genes along with OsECT11 and OsCPSF30-L2 were observed to be consistently downregulated. The apparent correlation between the expression patterns of m6A regulatory genes and stress modulation pathways in this study underscores the need for additional research to unravel their intricate regulatory mechanisms that could ultimately contribute to the substantial development of enhanced stress tolerance in rice through mRNA modification.
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Affiliation(s)
| | | | - Md. Soyib Hasan
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Tanvir Hossain
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Ajit Ghosh
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
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3
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Rabolli CP, Accornero F. Cardiac cryptographers: cracking the code of the epitranscriptome. Eur Heart J 2024; 45:2034-2036. [PMID: 38339963 PMCID: PMC11177708 DOI: 10.1093/eurheartj/ehae057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/12/2024] Open
Affiliation(s)
- Charles P Rabolli
- Department of Biomedical Engineering, The Ohio State University, Columbus, OH 43210, USA
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Sidney E Frank Hall for Life Sciences, 185 Meeting St, Providence, RI 02912, USA
| | - Federica Accornero
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Sidney E Frank Hall for Life Sciences, 185 Meeting St, Providence, RI 02912, USA
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4
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Qiu Y, Tian Z, Miao TY, Shen L, Chen J, Li PF, Zhu ZX, Zhu ZF, Wu WJ, Xu X, Shen WG. The METTL3-m 6A-YTHDC1-AMIGO2 axis contributes to cell proliferation and migration in esophageal squamous cell carcinoma. Gene 2024; 908:148281. [PMID: 38360124 DOI: 10.1016/j.gene.2024.148281] [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: 10/06/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/17/2024]
Abstract
The upregulation of methyltransferase-like 3 (METTL3) has been associated with the progression of esophageal cancer. However, METTL3-induced N6-methyladenosine (m6A) alterations on the downstream target mRNAs in esophageal squamous cell carcinoma (ESCC) are not yet fully understood. Our study revealed that silencing METTL3 resulted in a significant decrease in ESCC cell proliferation and metastasis in vitro and in vivo. Additionally, the adhesion molecule with Ig like domain 2 (AMIGO2) was identified as a potential downstream target of both METTL3 and YTH Domain-Containing Protein 1 (YTHDC1) in ESCC cells. Functionally, AMIGO2 augmented the malignant behaviors of ESCC cells in vitro and in vivo, and its overexpression can rescue the inhibition of the proliferation and migration in ESCC cells induced by METTL3 or YTHDC1 knockdown. Furthermore, our findings revealed that knockdown of METTL3 decreased m6A modification in the 5'-untranslated regions (5'UTR) of AMIGO2 precursor mRNA (pre-mRNA), and YTHDC1 interacted with AMIGO2 pre-mRNA to regulate AMIGO2 expression by modulating the splicing process of AMIGO2 pre-mRNA in ESCC cells. These findings highlighted a novel role of the METTL3-m6A-YTHDC1-AMIGO2 axis in regulating ESCC cell proliferation and motility, suggesting its potential as a therapeutic target for ESCC.
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Affiliation(s)
- Yue Qiu
- Department of Cell Biology, Yangzhou University Medical College, Yangzhou, Jiangsu, China
| | - Zhen Tian
- Department of Cell Biology, Yangzhou University Medical College, Yangzhou, Jiangsu, China
| | - Ting-Yu Miao
- Department of Cell Biology, Yangzhou University Medical College, Yangzhou, Jiangsu, China
| | - Lin Shen
- Department of Cell Biology, Yangzhou University Medical College, Yangzhou, Jiangsu, China
| | - Jing Chen
- Department of Cell Biology, Yangzhou University Medical College, Yangzhou, Jiangsu, China
| | - Pei-Fen Li
- Department of Cell Biology, Yangzhou University Medical College, Yangzhou, Jiangsu, China
| | - Zi-Xuan Zhu
- Department of Cell Biology, Yangzhou University Medical College, Yangzhou, Jiangsu, China
| | - Zi-Fan Zhu
- Department of Cell Biology, Yangzhou University Medical College, Yangzhou, Jiangsu, China
| | - Wen-Juan Wu
- Department of Oncology, Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu, China
| | - Xiao Xu
- Department of Oncology, Taizhou Hospital of Traditional Chinese Medicine, Taizhou, Jiangsu, China.
| | - Wei-Gan Shen
- Department of Cell Biology, Yangzhou University Medical College, Yangzhou, Jiangsu, China; Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou University, Yangzhou, Jiangsu, China.
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5
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Leppik M, Pomerants L, Põldes A, Mihkelson P, Remme J, Tamm T. Loss of Conserved rRNA Modifications in the Peptidyl Transferase Center Leads to Diminished Protein Synthesis and Cell Growth in Budding Yeast. Int J Mol Sci 2024; 25:5194. [PMID: 38791231 PMCID: PMC11121408 DOI: 10.3390/ijms25105194] [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: 04/05/2024] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Ribosomal RNAs (rRNAs) are extensively modified during the transcription and subsequent maturation. Three types of modifications, 2'-O-methylation of ribose moiety, pseudouridylation, and base modifications, are introduced either by a snoRNA-driven mechanism or by stand-alone enzymes. Modified nucleotides are clustered at the functionally important sites, including peptidyl transferase center (PTC). Therefore, it has been hypothesised that the modified nucleotides play an important role in ensuring the functionality of the ribosome. In this study, we demonstrate that seven 25S rRNA modifications, including four evolutionarily conserved modifications, in the proximity of PTC can be simultaneously depleted without loss of cell viability. Yeast mutants lacking three snoRNA genes (snR34, snR52, and snR65) and/or expressing enzymatically inactive variants of spb1(D52A/E679K) and nop2(C424A/C478A) were constructed. The results show that rRNA modifications in PTC contribute collectively to efficient translation in eukaryotic cells. The deficiency of seven modified nucleotides in 25S rRNA resulted in reduced cell growth, cold sensitivity, decreased translation levels, and hyperaccurate translation, as indicated by the reduced missense and nonsense suppression. The modification m5C2870 is crucial in the absence of the other six modified nucleotides. Thus, the pattern of rRNA-modified nucleotides around the PTC is essential for optimal ribosomal translational activity and translational fidelity.
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Affiliation(s)
| | | | | | | | | | - Tiina Tamm
- Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia; (M.L.); (L.P.); (A.P.); (P.M.); (J.R.)
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6
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Zheng X, Su C, Duan L, Jin M, Sun Y, Zhu L, Zhang W. Molecular basis of A. thaliana KEOPS complex in biosynthesizing tRNA t6A. Nucleic Acids Res 2024; 52:4523-4540. [PMID: 38477398 PMCID: PMC11077089 DOI: 10.1093/nar/gkae179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/19/2024] [Accepted: 03/01/2024] [Indexed: 03/14/2024] Open
Abstract
In archaea and eukaryotes, the evolutionarily conserved KEOPS is composed of four core subunits-Kae1, Bud32, Cgi121 and Pcc1, and a fifth Gon7/Pcc2 that is found in fungi and metazoa. KEOPS cooperates with Sua5/YRDC to catalyze the biosynthesis of tRNA N6-threonylcarbamoyladenosine (t6A), an essential modification needed for fitness of cellular organisms. Biochemical and structural characterizations of KEOPSs from archaea, yeast and humans have determined a t6A-catalytic role for Kae1 and auxiliary roles for other subunits. However, the precise molecular workings of KEOPSs still remain poorly understood. Here, we investigated the biochemical functions of A. thaliana KEOPS and determined a cryo-EM structure of A. thaliana KEOPS dimer. We show that A. thaliana KEOPS is composed of KAE1, BUD32, CGI121 and PCC1, which adopts a conserved overall arrangement. PCC1 dimerization leads to a KEOPS dimer that is needed for an active t6A-catalytic KEOPS-tRNA assembly. BUD32 participates in direct binding of tRNA to KEOPS and modulates the t6A-catalytic activity of KEOPS via its C-terminal tail and ATP to ADP hydrolysis. CGI121 promotes the binding of tRNA to KEOPS and potentiates the t6A-catalytic activity of KEOPS. These data and findings provide insights into mechanistic understanding of KEOPS machineries.
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Affiliation(s)
- Xinxing Zheng
- School of Life Sciences, Key Laboratory of Cell Activities and Stress Adaptation of the Ministry of Education, Lanzhou University, Lanzhou 730000, China
| | - Chenchen Su
- School of Life Sciences, Key Laboratory of Cell Activities and Stress Adaptation of the Ministry of Education, Lanzhou University, Lanzhou 730000, China
| | - Lei Duan
- School of Life Sciences, Key Laboratory of Cell Activities and Stress Adaptation of the Ministry of Education, Lanzhou University, Lanzhou 730000, China
| | - Mengqi Jin
- School of Life Sciences, Key Laboratory of Cell Activities and Stress Adaptation of the Ministry of Education, Lanzhou University, Lanzhou 730000, China
| | - Yongtao Sun
- School of Life Sciences, Key Laboratory of Cell Activities and Stress Adaptation of the Ministry of Education, Lanzhou University, Lanzhou 730000, China
| | - Li Zhu
- School of Life Sciences, Key Laboratory of Cell Activities and Stress Adaptation of the Ministry of Education, Lanzhou University, Lanzhou 730000, China
| | - Wenhua Zhang
- School of Life Sciences, Key Laboratory of Cell Activities and Stress Adaptation of the Ministry of Education, Lanzhou University, Lanzhou 730000, China
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7
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Manning AC, Bashir MM, Jimenez AR, Upton HE, Collins K, Lowe TM, Tucker JM. Gammaherpesvirus infection triggers the formation of tRNA fragments from premature tRNAs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.592122. [PMID: 38746336 PMCID: PMC11092647 DOI: 10.1101/2024.05.01.592122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Transfer RNAs (tRNAs) are fundamental for both cellular and viral gene expression during viral infection. In addition, mounting evidence supports biological function for tRNA cleavage products, including in the control of gene expression during conditions of stress and infection. We previously reported that infection with the model murine gammaherpesvirus, MHV68, leads to enhanced tRNA transcription. However, whether this has any influence on tRNA transcript processing, viral replication, or the host response is not known. Here, we combined two new approaches, sequencing library preparation by Ordered Two Template Relay (OTTR) and tRNA bioinformatic analysis by tRAX, to quantitatively profile full-length tRNAs and tRNA fragment (tRF) identities during MHV68 infection. We find that MHV68 infection triggers both pre-tRNA and mature tRNA cleavage, resulting in the accumulation of specific tRFs. OTTR-tRAX revealed not only host tRNAome changes, but also the expression patterns of virally-encoded tRNAs (virtRNAs) and virtRFs made from the MHV68 genome, including their base modification signatures. Because the transcript ends of several host tRFs matched tRNA splice junctions, we tested and confirmed the role of tRNA splicing factors TSEN2 and CLP1 in MHV68-induced tRF biogenesis. Further, we show that CLP1 kinase, and by extension tRNA splicing, is required for productive MHV68 infection. Our findings provide new insight into how gammaherpesvirus infection both impacts and relies on tRNA transcription and processing.
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Affiliation(s)
- Aidan C. Manning
- Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Mahmoud M. Bashir
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Ariana R. Jimenez
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
- Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA, 52242, USA
| | - Heather E. Upton
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Kathleen Collins
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Todd M. Lowe
- Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Jessica M. Tucker
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
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8
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Martinez-Feduchi P, Jin P, Yao B. Epigenetic modifications of DNA and RNA in Alzheimer's disease. Front Mol Neurosci 2024; 17:1398026. [PMID: 38726308 PMCID: PMC11079283 DOI: 10.3389/fnmol.2024.1398026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 04/15/2024] [Indexed: 05/12/2024] Open
Abstract
Alzheimer's disease (AD) is a complex neurodegenerative disorder and the most common form of dementia. There are two main types of AD: familial and sporadic. Familial AD is linked to mutations in amyloid precursor protein (APP), presenilin-1 (PSEN1), and presenilin-2 (PSEN2). On the other hand, sporadic AD is the more common form of the disease and has genetic, epigenetic, and environmental components that influence disease onset and progression. Investigating the epigenetic mechanisms associated with AD is essential for increasing understanding of pathology and identifying biomarkers for diagnosis and treatment. Chemical covalent modifications on DNA and RNA can epigenetically regulate gene expression at transcriptional and post-transcriptional levels and play protective or pathological roles in AD and other neurodegenerative diseases.
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Affiliation(s)
| | | | - Bing Yao
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, United States
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9
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Čáp M, Palková Z. Non-Coding RNAs: Regulators of Stress, Ageing, and Developmental Decisions in Yeast? Cells 2024; 13:599. [PMID: 38607038 PMCID: PMC11012152 DOI: 10.3390/cells13070599] [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: 02/15/2024] [Revised: 03/19/2024] [Accepted: 03/27/2024] [Indexed: 04/13/2024] Open
Abstract
Cells must change their properties in order to adapt to a constantly changing environment. Most of the cellular sensing and regulatory mechanisms described so far are based on proteins that serve as sensors, signal transducers, and effectors of signalling pathways, resulting in altered cell physiology. In recent years, however, remarkable examples of the critical role of non-coding RNAs in some of these regulatory pathways have been described in various organisms. In this review, we focus on all classes of non-coding RNAs that play regulatory roles during stress response, starvation, and ageing in different yeast species as well as in structured yeast populations. Such regulation can occur, for example, by modulating the amount and functional state of tRNAs, rRNAs, or snRNAs that are directly involved in the processes of translation and splicing. In addition, long non-coding RNAs and microRNA-like molecules are bona fide regulators of the expression of their target genes. Non-coding RNAs thus represent an additional level of cellular regulation that is gradually being uncovered.
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Affiliation(s)
- Michal Čáp
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, 128 00 Prague, Czech Republic
| | - Zdena Palková
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, 128 00 Prague, Czech Republic
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10
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Li X, Wang Y, Zhang S, Zhang P, Huang S. Nanopore Identification of N-Acetylation by Hydroxylamine Deacetylation (NINAHD). ACS Sens 2024; 9:1359-1371. [PMID: 38449100 DOI: 10.1021/acssensors.3c02350] [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] [Indexed: 03/08/2024]
Abstract
N-Acetyl modification, a chemical modification commonly found on biomacromolecules, plays a crucial role in the regulation of cell activities and is related to a variety of diseases. However, due to the instability of N-acetyl modification, accurate and rapid identification of N-acetyl modification with a low measurement cost is still technically challenging. Here, based on hydroxylamine deacetylation and nanopore single molecule chemistry, a universal sensing strategy for N-acetyl modification has been developed. Acetohydroxamic acid (AHA), which is produced by the hydroxylamine deacetylation reaction and serves as a reporter for N-acetylation identification, is specifically sensed by a phenylboronic acid (PBA)-modified Mycobacterium smegmatis porin A (MspA). With this strategy, N-acetyl modifications on RNA, DNA, proteins, and glycans were identified, demonstrating its generality. Specifically, histones can be treated with hydroxylamine deacetylation, from which the generated AHA can represent the amount of N-acetyl modification detected by a nanopore sensor. The unique event features of AHA also demonstrate the robustness of sensing against other interfering analytes in the environment.
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Affiliation(s)
- Xinyue Li
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, China
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, China
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, China
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11
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Yared MJ, Marcelot A, Barraud P. Beyond the Anticodon: tRNA Core Modifications and Their Impact on Structure, Translation and Stress Adaptation. Genes (Basel) 2024; 15:374. [PMID: 38540433 PMCID: PMC10969862 DOI: 10.3390/genes15030374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 06/14/2024] Open
Abstract
Transfer RNAs (tRNAs) are heavily decorated with post-transcriptional chemical modifications. Approximately 100 different modifications have been identified in tRNAs, and each tRNA typically contains 5-15 modifications that are incorporated at specific sites along the tRNA sequence. These modifications may be classified into two groups according to their position in the three-dimensional tRNA structure, i.e., modifications in the tRNA core and modifications in the anticodon-loop (ACL) region. Since many modified nucleotides in the tRNA core are involved in the formation of tertiary interactions implicated in tRNA folding, these modifications are key to tRNA stability and resistance to RNA decay pathways. In comparison to the extensively studied ACL modifications, tRNA core modifications have generally received less attention, although they have been shown to play important roles beyond tRNA stability. Here, we review and place in perspective selected data on tRNA core modifications. We present their impact on tRNA structure and stability and report how these changes manifest themselves at the functional level in translation, fitness and stress adaptation.
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Affiliation(s)
| | | | - Pierre Barraud
- Expression Génétique Microbienne, Université Paris Cité, CNRS, Institut de Biologie Physico-Chimique, F-75005 Paris, France; (M.-J.Y.); (A.M.)
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12
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Nowzari ZR, D'Esposito RJ, Vangaveti S, Chen AA. Elucidating the influence of RNA modifications and Magnesium ions on tRNA Phe conformational dynamics in S. cerevisiae : Insights from Replica Exchange Molecular Dynamics simulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.11.584441. [PMID: 38559076 PMCID: PMC10979867 DOI: 10.1101/2024.03.11.584441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Post-transcriptional modifications in RNA can significantly impact their structure and function. In particular, transfer RNAs (tRNAs) are heavily modified, with around 100 different naturally occurring nucleotide modifications contributing to codon bias and decoding efficiency. Here, we describe our efforts to investigate the impact of RNA modifications on the structure and stability of tRNA Phenylalanine (tRNA Phe ) from S. cerevisiae using molecular dynamics (MD) simulations. Through temperature replica exchange MD (T-REMD) studies, we explored the unfolding pathway to understand how RNA modifications influence the conformational dynamics of tRNA Phe , both in the presence and absence of magnesium ions (Mg 2+ ). We observe that modified nucleotides in key regions of the tRNA establish a complex network of hydrogen bonds and stacking interactions which is essential for tertiary structure stability of the tRNA. Furthermore, our simulations show that modifications facilitate the formation of ion binding sites on the tRNA. However, high concentrations of Mg 2+ ions can stabilize the tRNA tertiary structure in the absence of modifications. Our findings illuminate the intricate interactions between modifications, magnesium ions, and RNA structural stability.
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13
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Cheung K, Amos TG, Shine R, DeVore JL, Ducatez S, Edwards RJ, Rollins LA. Whole-mitogenome analysis unveils previously undescribed genetic diversity in cane toads across their invasion trajectory. Ecol Evol 2024; 14:e11115. [PMID: 38435005 PMCID: PMC10909579 DOI: 10.1002/ece3.11115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 02/16/2024] [Accepted: 02/22/2024] [Indexed: 03/05/2024] Open
Abstract
Invasive species offer insights into rapid adaptation to novel environments. The iconic cane toad (Rhinella marina) is an excellent model for studying rapid adaptation during invasion. Previous research using the mitochondrial NADH dehydrogenase 3 (ND3) gene in Hawai'ian and Australian invasive populations found a single haplotype, indicating an extreme genetic bottleneck following introduction. Nuclear genetic diversity also exhibited reductions across the genome in these two populations. Here, we investigated the mitochondrial genomics of cane toads across this invasion trajectory. We created the first reference mitochondrial genome for this species using long-read sequence data. We combined whole-genome resequencing data of 15 toads with published transcriptomic data of 125 individuals to construct nearly complete mitochondrial genomes from the native (French Guiana) and introduced (Hawai'i and Australia) ranges for population genomic analyses. In agreement with previous investigations of these populations, we identified genetic bottlenecks in both Hawai'ian and Australian introduced populations, alongside evidence of population expansion in the invasive ranges. Although mitochondrial genetic diversity in introduced populations was reduced, our results revealed that it had been underestimated: we identified 45 mitochondrial haplotypes in Hawai'ian and Australian samples, none of which were found in the native range. Additionally, we identified two distinct groups of haplotypes from the native range, separated by a minimum of 110 base pairs (0.6%). These findings enhance our understanding of how invasion has shaped the genetic landscape of this species.
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Affiliation(s)
- Kelton Cheung
- Evolution & Ecology Research Centre, School of Biological, Earth & Environmental SciencesUniversity of New South WalesSydneyNew South WalesAustralia
- School of Biotechnology & Biomolecular SciencesUniversity of New South WalesSydneyNew South WalesAustralia
| | - Timothy G. Amos
- School of Biotechnology & Biomolecular SciencesUniversity of New South WalesSydneyNew South WalesAustralia
- Garvan Institute of Medical ResearchSydneyNew South WalesAustralia
| | - Rick Shine
- Department of Biological SciencesMacquarie UniversitySydneyNew South WalesAustralia
| | - Jayna L. DeVore
- Univ. Polynésie FrancaiseUMR 241 EIO (UPF, IRD, IFREMER, ILM) BP 6570 Faa'aTahitiFrench Polynesia
| | - Simon Ducatez
- Institut de Recherche pour le Développement (IRD)UMR 241 EIO (UPF, IRD, IFREMER, ILM) BP 6570 Faa'aTahitiFrench Polynesia
| | - Richard J. Edwards
- School of Biotechnology & Biomolecular SciencesUniversity of New South WalesSydneyNew South WalesAustralia
- Minderoo OceanOmics Centre at UWA, Oceans InstituteThe University of Western AustraliaPerthWestern AustraliaAustralia
| | - Lee Ann Rollins
- Evolution & Ecology Research Centre, School of Biological, Earth & Environmental SciencesUniversity of New South WalesSydneyNew South WalesAustralia
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14
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Manning AC, Bashir MM, Jimenez AR, Upton HE, Collins K, Lowe TM, Tucker JM. Gammaherpesvirus infection alters transfer RNA splicing and triggers tRNA cleavage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.16.580780. [PMID: 38405876 PMCID: PMC10888928 DOI: 10.1101/2024.02.16.580780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Transfer RNAs (tRNAs) are fundamental for both cellular and viral gene expression during viral infection. Moreover, mounting evidence supports a noncanonical role for tRNA cleavage products in the control of gene expression during diverse conditions of stress and infection. We previously reported that infection with the model murine gammaherpesvirus, MHV68, leads to altered tRNA transcription, suggesting that tRNA regulation may play an important role in mediating viral replication or the host response. To better understand how viral infection alters tRNA expression, we combined Ordered Two Template Relay (OTTR) with tRNA-specific bioinformatic software called tRAX to profile full-length tRNAs and fragmented tRNA-derived RNAs (tDRs) during infection with MHV68. We find that OTTR-tRAX is a powerful sequencing strategy for combined tRNA/tDR profiling and reveals that MHV68 infection triggers pre-tRNA and mature tRNA cleavage, resulting in the accumulation of specific tDRs. Fragments of virally-encoded tRNAs (virtRNAs), as well as virtRNA base modification signatures are also detectable during infection. We present evidence that tRNA splicing factors are involved in the biogenesis of MHV68-induced cleavage products from pre-tRNAs and, in the case of CLP1 kinase, impact infectious virus production. Our data offers new insights into the importance of tRNA processing during gammaherpesvirus infection.
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Affiliation(s)
- Aidan C Manning
- Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Mahmoud M Bashir
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Ariana R Jimenez
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
- Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA, 52242, USA
| | - Heather E Upton
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Kathleen Collins
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Todd M Lowe
- Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Jessica M Tucker
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
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15
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Ding D, Fang Z, Kim SC, O’Flaherty DK, Jia X, Stone TB, Zhou L, Szostak JW. Unusual Base Pair between Two 2-Thiouridines and Its Implication for Nonenzymatic RNA Copying. J Am Chem Soc 2024; 146:3861-3871. [PMID: 38293747 PMCID: PMC10870715 DOI: 10.1021/jacs.3c11158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 02/01/2024]
Abstract
2-Thiouridine (s2U) is a nucleobase modification that confers enhanced efficiency and fidelity both on modern tRNA codon translation and on nonenzymatic and ribozyme-catalyzed RNA copying. We have discovered an unusual base pair between two 2-thiouridines that stabilizes an RNA duplex to a degree that is comparable to that of a native A:U base pair. High-resolution crystal structures indicate similar base-pairing geometry and stacking interactions in duplexes containing s2U:s2U compared to those with U:U pairs. Notably, the C═O···H-N hydrogen bond in the U:U pair is replaced with a C═S···H-N hydrogen bond in the s2U:s2U base pair. The thermodynamic stability of the s2U:s2U base pair suggested that this self-pairing might lead to an increased error frequency during nonenzymatic RNA copying. However, competition experiments show that s2U:s2U base-pairing induces only a low level of misincorporation during nonenzymatic RNA template copying because the correct A:s2U base pair outcompetes the slightly weaker s2U:s2U base pair. In addition, even if an s2U is incorrectly incorporated, the addition of the next base is greatly hindered. This strong stalling effect would further increase the effective fidelity of nonenzymatic RNA copying with s2U. Our findings suggest that s2U may enhance the rate and extent of nonenzymatic copying with only a minimal cost in fidelity.
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Affiliation(s)
- Dian Ding
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
- Department
of Molecular Biology and Center for Computational and Integrative
Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Ziyuan Fang
- Howard
Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Seohyun Chris Kim
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
- Department
of Molecular Biology and Center for Computational and Integrative
Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department
of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Derek K. O’Flaherty
- Department
of Chemistry, College of Engineering and Physical Sciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Xiwen Jia
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
- Department
of Molecular Biology and Center for Computational and Integrative
Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Talbot B. Stone
- Department
of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn
Institute for RNA Innovation, University
of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Lijun Zhou
- Department
of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn
Institute for RNA Innovation, University
of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Jack W. Szostak
- Howard
Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
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16
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Bowles IE, Jackman JE. A tRNA-specific function for tRNA methyltransferase Trm10 is associated with a new tRNA quality control mechanism in Saccharomyces cerevisiae. RNA (NEW YORK, N.Y.) 2024; 30:171-187. [PMID: 38071471 PMCID: PMC10798241 DOI: 10.1261/rna.079861.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 11/28/2023] [Indexed: 01/18/2024]
Abstract
In Saccharomyces cerevisiae, a single homolog of the tRNA methyltransferase Trm10 performs m1G9 modification on 13 different tRNAs. Here we provide evidence that the m1G9 modification catalyzed by S. cerevisiae Trm10 plays a biologically important role for one of these tRNA substrates, tRNATrp Overexpression of tRNATrp (and not any of 38 other elongator tRNAs) rescues growth hypersensitivity of the trm10Δ strain in the presence of the antitumor drug 5-fluorouracil (5FU). Mature tRNATrp is depleted in trm10Δ cells, and its levels are further decreased upon growth in 5FU, while another Trm10 substrate (tRNAGly) is not affected under these conditions. Thus, m1G9 in S. cerevisiae is another example of a tRNA modification that is present on multiple tRNAs but is only essential for the biological function of one of those species. In addition to the effects of m1G9 on mature tRNATrp, precursor tRNATrp species accumulate in the same strains, an effect that is due to at least two distinct mechanisms. The levels of mature tRNATrp are rescued in the trm10Δmet22Δ strain, consistent with the known role of Met22 in tRNA quality control, where deletion of met22 causes inhibition of 5'-3' exonucleases that catalyze tRNA decay. However, none of the known Met22-associated exonucleases appear to be responsible for the decay of hypomodified tRNATrp, based on the inability of mutants of each enzyme to rescue the growth of the trm10Δ strain in the presence of 5FU. Thus, the surveillance of tRNATrp appears to constitute a distinct tRNA quality control pathway in S. cerevisiae.
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Affiliation(s)
- Isobel E Bowles
- Department of Chemistry and Biochemistry, Center for RNA Biology, and Ohio State Biochemistry Program, Columbus, Ohio 43210, USA
| | - Jane E Jackman
- Department of Chemistry and Biochemistry, Center for RNA Biology, and Ohio State Biochemistry Program, Columbus, Ohio 43210, USA
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17
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Lucas MC, Pryszcz LP, Medina R, Milenkovic I, Camacho N, Marchand V, Motorin Y, Ribas de Pouplana L, Novoa EM. Quantitative analysis of tRNA abundance and modifications by nanopore RNA sequencing. Nat Biotechnol 2024; 42:72-86. [PMID: 37024678 DOI: 10.1038/s41587-023-01743-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 03/08/2023] [Indexed: 04/08/2023]
Abstract
Transfer RNAs (tRNAs) play a central role in protein translation. Studying them has been difficult in part because a simple method to simultaneously quantify their abundance and chemical modifications is lacking. Here we introduce Nano-tRNAseq, a nanopore-based approach to sequence native tRNA populations that provides quantitative estimates of both tRNA abundances and modification dynamics in a single experiment. We show that default nanopore sequencing settings discard the vast majority of tRNA reads, leading to poor sequencing yields and biased representations of tRNA abundances based on their transcript length. Re-processing of raw nanopore current intensity signals leads to a 12-fold increase in the number of recovered tRNA reads and enables recapitulation of accurate tRNA abundances. We then apply Nano-tRNAseq to Saccharomyces cerevisiae tRNA populations, revealing crosstalks and interdependencies between different tRNA modification types within the same molecule and changes in tRNA populations in response to oxidative stress.
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Affiliation(s)
- Morghan C Lucas
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Leszek P Pryszcz
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Rebeca Medina
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ivan Milenkovic
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Noelia Camacho
- Institute for Research in Biomedicine (IRB), Barcelona, Spain
| | - Virginie Marchand
- CNRS-Université de Lorraine, UAR2008 IBSLor/UMR7365 IMoPA, Nancy, France
| | - Yuri Motorin
- CNRS-Université de Lorraine, UAR2008 IBSLor/UMR7365 IMoPA, Nancy, France
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB), Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Eva Maria Novoa
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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18
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De Zoysa T, Hauke AC, Iyer NR, Marcus E, Ostrowski SM, Stegemann F, Ermolenko DN, Fay JC, Phizicky EM. A connection between the ribosome and two S. pombe tRNA modification mutants subject to rapid tRNA decay. PLoS Genet 2024; 20:e1011146. [PMID: 38295128 PMCID: PMC10861057 DOI: 10.1371/journal.pgen.1011146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 02/12/2024] [Accepted: 01/22/2024] [Indexed: 02/02/2024] Open
Abstract
tRNA modifications are crucial in all organisms to ensure tRNA folding and stability, and accurate translation. In both the yeast Saccharomyces cerevisiae and the evolutionarily distant yeast Schizosaccharomyces pombe, mutants lacking certain tRNA body modifications (outside the anticodon loop) are temperature sensitive due to rapid tRNA decay (RTD) of a subset of hypomodified tRNAs. Here we show that for each of two S. pombe mutants subject to RTD, mutations in ribosomal protein genes suppress the temperature sensitivity without altering tRNA levels. Prior work showed that S. pombe trm8Δ mutants, lacking 7-methylguanosine, were temperature sensitive due to RTD, and that one class of suppressors had mutations in the general amino acid control (GAAC) pathway, which was activated concomitant with RTD, resulting in further tRNA loss. We now find that another class of S. pombe trm8Δ suppressors have mutations in rpl genes, encoding 60S subunit proteins, and that suppression occurs with minimal restoration of tRNA levels and reduced GAAC activation. Furthermore, trm8Δ suppression extends to other mutations in the large or small ribosomal subunit. We also find that S. pombe tan1Δ mutants, lacking 4-acetylcytidine, are temperature sensitive due to RTD, that one class of suppressors have rpl mutations, associated with minimal restoration of tRNA levels, and that suppression extends to other rpl and rps mutations. However, although S. pombe tan1Δ temperature sensitivity is associated with some GAAC activation, suppression by an rpl mutation only modestly inhibits GAAC activation. We propose a model in which ribosomal protein mutations result in reduced ribosome concentrations, leading to both reduced ribosome collisions and a reduced requirement for tRNA, with these effects having different relative importance in trm8Δ and tan1Δ mutants. This model is consistent with our results in S. cerevisiae trm8Δ trm4Δ mutants, known to undergo RTD, fueling speculation that this model applies across eukaryotes.
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Affiliation(s)
- Thareendra De Zoysa
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York, United States of America
| | - Alayna C. Hauke
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York, United States of America
| | - Nivedita R. Iyer
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York, United States of America
| | - Erin Marcus
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York, United States of America
| | - Sarah M. Ostrowski
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York, United States of America
| | - Franziska Stegemann
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York, United States of America
| | - Dmitri N. Ermolenko
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York, United States of America
| | - Justin C. Fay
- Department of Biology, University of Rochester, Rochester, New York, United States of America
| | - Eric M. Phizicky
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York, United States of America
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19
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Bowles IE, Jackman JE. Diversity in Biological Function and Mechanism of the tRNA Methyltransferase Trm10. Acc Chem Res 2023; 56:3595-3603. [PMID: 38048440 PMCID: PMC11210281 DOI: 10.1021/acs.accounts.3c00533] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2023]
Abstract
Transfer ribonucleic acid (tRNA) is the most highly modified RNA species in the cell, and loss of tRNA modifications can lead to growth defects in yeast as well as metabolic, neurological, and mitochondrial disorders in humans. Significant progress has been made toward identifying the enzymes that are responsible for installing diverse modifications in tRNA, revealing a landscape of fascinating biological and mechanistic diversity that remains to be fully explored. Most early discoveries of tRNA modification enzymes were in model systems, where many enzymes were not strictly required for viability, an observation somewhat at odds with the extreme conservation of many of the same enzymes throughout multiple domains of life. Moreover, many tRNA modification enzymes act on more than one type of tRNA substrate, which is not necessarily surprising given the similar overall secondary and tertiary structures of tRNA, yet biochemical characterization has revealed interesting patterns of substrate specificity that can be challenging to rationalize on a molecular level. Questions about how many enzymes efficiently select a precise set of target tRNAs from among a structurally similar pool of molecules persist.The tRNA methyltransferase Trm10 provides an exciting paradigm to study the biological and mechanistic questions surrounding tRNA modifications. Even though the enzyme was originally characterized in Saccharomyces cerevisiae where its deletion causes no detectable phenotype under standard lab conditions, several more recently identified phenotypes provide insight into the requirement for this modification in the overall quality control of the tRNA pool. Studies of Trm10 in yeast also revealed another characteristic feature that has turned out to be a conserved feature of enzymes throughout the Trm10 family tree. We were initially surprised to see that purified S. cerevisiae Trm10 was capable of modifying tRNA substrates that were not detectably modified by the enzyme in vivo in yeast. This pattern has continued to emerge as we and others have studied Trm10 orthologs from Archaea and Eukarya, with enzymes exhibiting in vitro substrate specificities that can differ significantly from in vivo patterns of modification. While this feature complicates efforts to predict substrate specificities of Trm10 enzymes in the absence of appropriate genetic systems, it also provides an exciting opportunity for studying how enzyme activities can be regulated to achieve dynamic patterns of biological tRNA modification, which have been shown to be increasingly important for stress responses and human disease. Finally, the intriguing diversity in target nucleotide modification that has been revealed among Trm10 orthologs is distinctive among known tRNA modifying enzymes and necessitates unusual and likely novel catalytic strategies for methylation that are being revealed by biochemical and structural studies directed toward various family members. These efforts will no doubt yield more surprising discoveries in terms of tRNA modification enzymology.
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Affiliation(s)
- Isobel E. Bowles
- Department of Chemistry and Biochemistry, Center for RNA Biology and Ohio State Biochemistry Program, 484 W. 12th Avenue, Columbus, OH, 43210, USA
| | - Jane E. Jackman
- Department of Chemistry and Biochemistry, Center for RNA Biology and Ohio State Biochemistry Program, 484 W. 12th Avenue, Columbus, OH, 43210, USA
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20
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Madhwani KR, Sayied S, Ogata CH, Hogan CA, Lentini JM, Mallik M, Dumouchel JL, Storkebaum E, Fu D, O’Connor-Giles KM. tRNA modification enzyme-dependent redox homeostasis regulates synapse formation and memory. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.14.566895. [PMID: 38014328 PMCID: PMC10680711 DOI: 10.1101/2023.11.14.566895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Post-transcriptional modification of RNA regulates gene expression at multiple levels. ALKBH8 is a tRNA modifying enzyme that methylates wobble uridines in specific tRNAs to modulate translation. Through methylation of tRNA-selenocysteine, ALKBH8 promotes selenoprotein synthesis and regulates redox homeostasis. Pathogenic variants in ALKBH8 have been linked to intellectual disability disorders in the human population, but the role of ALKBH8 in the nervous system is unknown. Through in vivo studies in Drosophila, we show that ALKBH8 controls oxidative stress in the brain to restrain synaptic growth and support learning and memory. ALKBH8 null animals lack wobble uridine methylation and exhibit a global reduction in protein synthesis, including a specific decrease in selenoprotein levels. Loss of ALKBH8 or independent disruption of selenoprotein synthesis results in ectopic synapse formation. Genetic expression of antioxidant enzymes fully suppresses synaptic overgrowth in ALKBH8 null animals, confirming oxidative stress as the underlying cause of dysregulation. ALKBH8 animals also exhibit associative learning and memory impairments that are reversed by pharmacological antioxidant treatment. Together, these findings demonstrate the critical role of tRNA modification in redox homeostasis in the nervous system and reveal antioxidants as a potential therapy for ALKBH8-associated intellectual disability.
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Affiliation(s)
| | - Shanzeh Sayied
- Department of Neuroscience, Brown University, Providence, RI, USA
| | | | - Caley A. Hogan
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Jenna M. Lentini
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY, USA
| | - Moushami Mallik
- Molecular Neurobiology Laboratory, Donders Institute for Brain, Cognition, and Behaviour, Radboud University, Nijmegen, NL
| | | | - Erik Storkebaum
- Molecular Neurobiology Laboratory, Donders Institute for Brain, Cognition, and Behaviour, Radboud University, Nijmegen, NL
| | - Dragony Fu
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY, USA
| | - Kate M. O’Connor-Giles
- Department of Neuroscience, Brown University, Providence, RI, USA
- Carney Institute for Brain Sciences, Brown University, Providence, RI, USA
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21
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Sun X, Wang G, Luo W, Gu H, Ma W, Wei X, Liu D, Jia S, Cao S, Wang Y, Yuan Z. Small but strong: the emerging role of small nucleolar RNA in cardiovascular diseases. Front Cell Dev Biol 2023; 11:1292925. [PMID: 38033868 PMCID: PMC10682241 DOI: 10.3389/fcell.2023.1292925] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023] Open
Abstract
Cardiovascular diseases (CVDs) are the leading cause of mortality and disability worldwide. Numerous studies have demonstrated that non-coding RNAs (ncRNAs) play a primary role in CVD development. Therefore, studies on the mechanisms of ncRNAs are essential for further efforts to prevent and treat CVDs. Small nucleolar RNAs (snoRNAs) are a novel species of non-conventional ncRNAs that guide post-transcriptional modifications and the subsequent maturation of small nuclear RNA and ribosomal RNA. Evidently, snoRNAs are extensively expressed in human tissues and may regulate different illnesses. Particularly, as the next-generation sequencing techniques have progressed, snoRNAs have been shown to be differentially expressed in CVDs, suggesting that they may play a role in the occurrence and progression of cardiac illnesses. However, the molecular processes and signaling pathways underlying the function of snoRNAs remain unidentified. Therefore, it is of great value to comprehensively investigate the association between snoRNAs and CVDs. The aim of this review was to collate existing literature on the biogenesis, characteristics, and potential regulatory mechanisms of snoRNAs. In particular, we present a scientific update on these snoRNAs and their relevance to CVDs in an effort to cast new light on the functions of snoRNAs in the clinical diagnosis of CVDs.
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Affiliation(s)
- Xue Sun
- Department of Ultrasound, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Gebang Wang
- Department of Thoracic Surgery, Liaoning Cancer Hospital and Institute, Cancer Hospital of Dalian University of Technology, Shenyang, Liaoning, China
| | - Wenting Luo
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Hui Gu
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Wei Ma
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Xiaowei Wei
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Dan Liu
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Shanshan Jia
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Songying Cao
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yu Wang
- Department of Ultrasound, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Zhengwei Yuan
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
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22
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Chen H, Luo W, Lu X, Zhang T. Regulatory role of RNA modifications in the treatment of pancreatic ductal adenocarcinoma (PDAC). Heliyon 2023; 9:e20969. [PMID: 37928039 PMCID: PMC10623179 DOI: 10.1016/j.heliyon.2023.e20969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 09/22/2023] [Accepted: 10/12/2023] [Indexed: 11/07/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is an extremely life-threatening malignancy with a relatively unfavorable prognosis. The early occurrence of metastasis and local recurrence subsequent to surgery contribute to the poor survival rates of PDAC patients, thereby limiting the effectiveness of surgical intervention. Additionally, the desmoplastic and immune-suppressive tumor microenvironment of PDAC diminishes its responsiveness to conventional treatment modalities such as chemotherapy, radiotherapy, and immunotherapy. Therefore, it is imperative to identify novel therapeutic targets for PDAC treatment. Chemical modifications are prevalent in various types of RNA and exert significant influence on their structure and functions. RNA modifications, exemplified by m6A, m5C, m1A, and Ψ, have been identified as general regulators of cellular functions. The abundance of specific modifications, such as m6A, has been correlated with cell proliferation, invasion, migration, and patient prognosis in PDAC. Pre-clinical data has indicated that manipulating RNA modification regulators could enhance the efficacy of chemotherapy, radiotherapy, and immunotherapy. Therefore, targeting RNA modifications in conjunction with current adjuvant or neoadjuvant therapy holds promise. The objective of this review is to provide a comprehensive overview of RNA modifications in PDAC treatment, encompassing their behaviors, mechanisms, and potential treatment targets. Therefore, it aims to stimulate the development of novel therapeutic approaches and future clinical trials.
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Affiliation(s)
- Hao Chen
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Wenhao Luo
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaoyue Lu
- Peking Union Medical College, Beijing, China
| | - Taiping Zhang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
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23
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Yared MJ, Yoluç Y, Catala M, Tisné C, Kaiser S, Barraud P. Different modification pathways for m1A58 incorporation in yeast elongator and initiator tRNAs. Nucleic Acids Res 2023; 51:10653-10667. [PMID: 37650648 PMCID: PMC10602860 DOI: 10.1093/nar/gkad722] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 08/18/2023] [Indexed: 09/01/2023] Open
Abstract
As essential components of the protein synthesis machinery, tRNAs undergo a tightly controlled biogenesis process, which include the incorporation of numerous posttranscriptional modifications. Defects in these tRNA maturation steps may lead to the degradation of hypomodified tRNAs by the rapid tRNA decay (RTD) and nuclear surveillance pathways. We previously identified m1A58 as a late modification introduced after modifications Ψ55 and T54 in yeast elongator tRNAPhe. However, previous reports suggested that m1A58 is introduced early during the tRNA modification process, in particular on primary transcripts of initiator tRNAiMet, which prevents its degradation by RNA decay pathways. Here, aiming to reconcile this apparent inconsistency on the temporality of m1A58 incorporation, we examined its introduction into yeast elongator and initiator tRNAs. We used specifically modified tRNAs to report on the molecular aspects controlling the Ψ55 → T54 → m1A58 modification circuit in elongator tRNAs. We also show that m1A58 is efficiently introduced on unmodified tRNAiMet, and does not depend on prior modifications. Finally, we show that m1A58 has major effects on the structural properties of initiator tRNAiMet, so that the tRNA elbow structure is only properly assembled when this modification is present. This observation provides a structural explanation for the degradation of hypomodified tRNAiMet lacking m1A58 by the nuclear surveillance and RTD pathways.
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Affiliation(s)
- Marcel-Joseph Yared
- Expression génétique microbienne, Université Paris Cité, CNRS, Institut de biologie physico-chimique, Paris, France
| | - Yasemin Yoluç
- Department of Chemistry, Ludwig Maximilians University, Munich, Germany
| | - Marjorie Catala
- Expression génétique microbienne, Université Paris Cité, CNRS, Institut de biologie physico-chimique, Paris, France
| | - Carine Tisné
- Expression génétique microbienne, Université Paris Cité, CNRS, Institut de biologie physico-chimique, Paris, France
| | - Stefanie Kaiser
- Department of Chemistry, Ludwig Maximilians University, Munich, Germany
- Institute of Pharmaceutical Chemistry, Goethe-University, Frankfurt, Germany
| | - Pierre Barraud
- Expression génétique microbienne, Université Paris Cité, CNRS, Institut de biologie physico-chimique, Paris, France
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24
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Wang Z, Xu X, Li X, Fang J, Huang Z, Zhang M, Liu J, Qiu X. Investigations of Single-Subunit tRNA Methyltransferases from Yeast. J Fungi (Basel) 2023; 9:1030. [PMID: 37888286 PMCID: PMC10608323 DOI: 10.3390/jof9101030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 10/28/2023] Open
Abstract
tRNA methylations, including base modification and 2'-O-methylation of ribose moiety, play critical roles in the structural stabilization of tRNAs and the fidelity and efficiency of protein translation. These modifications are catalyzed by tRNA methyltransferases (TRMs). Some of the TRMs from yeast can fully function only by a single subunit. In this study, after performing the primary bioinformatic analyses, the progress of the studies of yeast single-subunit TRMs, as well as the studies of their homologues from yeast and other types of eukaryotes and the corresponding TRMs from other types of organisms was systematically reviewed, which will facilitate the understanding of the evolutionary origin of functional diversity of eukaryotic single-subunit TRM.
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Affiliation(s)
- Zhongyuan Wang
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China; (Z.W.); (X.L.); (J.F.); (Z.H.); (M.Z.); (J.L.)
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China;
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Centre, Ningbo University, Ningbo 315800, China
| | - Xiangbin Xu
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China;
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Centre, Ningbo University, Ningbo 315800, China
| | - Xinhai Li
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China; (Z.W.); (X.L.); (J.F.); (Z.H.); (M.Z.); (J.L.)
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China;
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Centre, Ningbo University, Ningbo 315800, China
| | - Jiaqi Fang
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China; (Z.W.); (X.L.); (J.F.); (Z.H.); (M.Z.); (J.L.)
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China;
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Centre, Ningbo University, Ningbo 315800, China
| | - Zhenkuai Huang
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China; (Z.W.); (X.L.); (J.F.); (Z.H.); (M.Z.); (J.L.)
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China;
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Centre, Ningbo University, Ningbo 315800, China
| | - Mengli Zhang
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China; (Z.W.); (X.L.); (J.F.); (Z.H.); (M.Z.); (J.L.)
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China;
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Centre, Ningbo University, Ningbo 315800, China
| | - Jiameng Liu
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China; (Z.W.); (X.L.); (J.F.); (Z.H.); (M.Z.); (J.L.)
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China;
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Centre, Ningbo University, Ningbo 315800, China
| | - Xiaoting Qiu
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China; (Z.W.); (X.L.); (J.F.); (Z.H.); (M.Z.); (J.L.)
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China;
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Centre, Ningbo University, Ningbo 315800, China
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25
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De Zoysa T, Hauke AC, Iyer NR, Marcus E, Ostrowski SM, Fay JC, Phizicky EM. A connection between the ribosome and two S. pombe tRNA modification mutants subject to rapid tRNA decay. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.18.558340. [PMID: 37790432 PMCID: PMC10542129 DOI: 10.1101/2023.09.18.558340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
tRNA modifications are crucial in all organisms to ensure tRNA folding and stability, and accurate translation in the ribosome. In both the yeast Saccharomyces cerevisiae and the evolutionarily distant yeast Schizosaccharomyces pombe, mutants lacking certain tRNA body modifications (outside the anticodon loop) are temperature sensitive due to rapid tRNA decay (RTD) of a subset of hypomodified tRNAs. Here we show that for each of two S. pombe mutants subject to RTD, mutations in ribosomal protein genes suppress the temperature sensitivity without altering tRNA levels. Prior work showed that S. pombe trm8Δ mutants, lacking 7-methylguanosine, were temperature sensitive due to RTD and that one class of suppressors had mutations in the general amino acid control (GAAC) pathway, which was activated concomitant with RTD, resulting in further tRNA loss. We now find that another class of S. pombe trm8Δ suppressors have mutations in rpl genes, encoding 60S subunit proteins, and that suppression occurs with minimal restoration of tRNA levels and reduced GAAC activation. Furthermore, trm8Δ suppression extends to other mutations in the large or small ribosomal subunit. We also find that S. pombe tan1Δ mutants, lacking 4-acetylcytidine, are temperature sensitive due to RTD, that one class of suppressors have rpl mutations, associated with minimal restoration of tRNA levels, and that suppression extends to other rpl and rps mutations. However, although S. pombe tan1Δ temperature sensitivity is associated with some GAAC activation, suppression by an rpl mutation does not significantly inhibit GAAC activation. These results suggest that ribosomal protein mutations suppress the temperature sensitivity of S. pombe trm8Δ and tan1Δ mutants due to reduced ribosome concentrations, leading to both a reduced requirement for tRNA, and reduced ribosome collisions and GAAC activation. Results with S. cerevisiae trm8Δ trm4Δ mutants are consistent with this model, and fuel speculation that similar results will apply across eukaryotes.
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Affiliation(s)
- Thareendra De Zoysa
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, NY, USA 14642
| | - Alayna C. Hauke
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, NY, USA 14642
| | - Nivedita R. Iyer
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, NY, USA 14642
| | - Erin Marcus
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, NY, USA 14642
| | - Sarah M. Ostrowski
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, NY, USA 14642
| | - Justin C. Fay
- Department of Biology, University of Rochester, Rochester, NY, USA 14627
| | - Eric M. Phizicky
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, NY, USA 14642
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26
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Jin M, Zhang Z, Yu Z, Chen W, Wang X, Lei D, Zhang W. Structure-function analysis of an ancient TsaD-TsaC-SUA5-TcdA modular enzyme reveals a prototype of tRNA t6A and ct6A synthetases. Nucleic Acids Res 2023; 51:8711-8729. [PMID: 37427786 PMCID: PMC10484737 DOI: 10.1093/nar/gkad587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/22/2023] [Accepted: 06/29/2023] [Indexed: 07/11/2023] Open
Abstract
N 6-threonylcarbamoyladenosine (t6A) is a post-transcriptional modification found uniquely at position 37 of tRNAs that decipher ANN-codons in the three domains of life. tRNA t6A plays a pivotal role in promoting translational fidelity and maintaining protein homeostasis. The biosynthesis of tRNA t6A requires members from two evolutionarily conserved protein families TsaC/Sua5 and TsaD/Kae1/Qri7, and a varying number of auxiliary proteins. Furthermore, tRNA t6A is modified into a cyclic hydantoin form of t6A (ct6A) by TcdA in bacteria. In this work, we have identified a TsaD-TsaC-SUA5-TcdA modular protein (TsaN) from Pandoraviruses and determined a 3.2 Å resolution cryo-EM structure of P. salinus TsaN. The four domains of TsaN share strong structural similarities with TsaD/Kae1/Qri7 proteins, TsaC/Sua5 proteins, and Escherichia coli TcdA. TsaN catalyzes the formation of threonylcarbamoyladenylate (TC-AMP) using L-threonine, HCO3- and ATP, but does not participate further in tRNA t6A biosynthesis. We report for the first time that TsaN catalyzes a tRNA-independent threonylcarbamoyl modification of adenosine phosphates, leading to t6ADP and t6ATP. Moreover, TsaN is also active in catalyzing tRNA-independent conversion of t6A nucleoside to ct6A. Our results imply that TsaN from Pandoraviruses might be a prototype of the tRNA t6A- and ct6A-modifying enzymes in some cellular organisms.
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Affiliation(s)
- Mengqi Jin
- School of Life Sciences, Key Laboratory of Cell Activities and Stress Adaptation of the Ministry of Education, Lanzhou University, Lanzhou 730000, China
| | - Zelin Zhang
- Key Laboratory for Magnetism and Magnetic Materials of the Ministry of Education, Electron Microscopy Centre of Lanzhou University, Lanzhou University, Lanzhou 730000, China
| | - Zhijiang Yu
- School of Life Sciences, Key Laboratory of Cell Activities and Stress Adaptation of the Ministry of Education, Lanzhou University, Lanzhou 730000, China
| | - Wei Chen
- School of Life Sciences, Key Laboratory of Cell Activities and Stress Adaptation of the Ministry of Education, Lanzhou University, Lanzhou 730000, China
| | - Xiaolei Wang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Dongsheng Lei
- Key Laboratory for Magnetism and Magnetic Materials of the Ministry of Education, Electron Microscopy Centre of Lanzhou University, Lanzhou University, Lanzhou 730000, China
| | - Wenhua Zhang
- School of Life Sciences, Key Laboratory of Cell Activities and Stress Adaptation of the Ministry of Education, Lanzhou University, Lanzhou 730000, China
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27
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Biela A, Hammermeister A, Kaczmarczyk I, Walczak M, Koziej L, Lin TY, Glatt S. The diverse structural modes of tRNA binding and recognition. J Biol Chem 2023; 299:104966. [PMID: 37380076 PMCID: PMC10424219 DOI: 10.1016/j.jbc.2023.104966] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/20/2023] [Accepted: 06/22/2023] [Indexed: 06/30/2023] Open
Abstract
tRNAs are short noncoding RNAs responsible for decoding mRNA codon triplets, delivering correct amino acids to the ribosome, and mediating polypeptide chain formation. Due to their key roles during translation, tRNAs have a highly conserved shape and large sets of tRNAs are present in all living organisms. Regardless of sequence variability, all tRNAs fold into a relatively rigid three-dimensional L-shaped structure. The conserved tertiary organization of canonical tRNA arises through the formation of two orthogonal helices, consisting of the acceptor and anticodon domains. Both elements fold independently to stabilize the overall structure of tRNAs through intramolecular interactions between the D- and T-arm. During tRNA maturation, different modifying enzymes posttranscriptionally attach chemical groups to specific nucleotides, which not only affect translation elongation rates but also restrict local folding processes and confer local flexibility when required. The characteristic structural features of tRNAs are also employed by various maturation factors and modification enzymes to assure the selection, recognition, and positioning of specific sites within the substrate tRNAs. The cellular functional repertoire of tRNAs continues to extend well beyond their role in translation, partly, due to the expanding pool of tRNA-derived fragments. Here, we aim to summarize the most recent developments in the field to understand how three-dimensional structure affects the canonical and noncanonical functions of tRNA.
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Affiliation(s)
- Anna Biela
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Igor Kaczmarczyk
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland; Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Marta Walczak
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland; Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Lukasz Koziej
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Ting-Yu Lin
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
| | - Sebastian Glatt
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
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28
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Piperi C, Markouli M, Gargalionis AN, Papavassiliou KA, Papavassiliou AG. Deciphering glioma epitranscriptome: focus on RNA modifications. Oncogene 2023:10.1038/s41388-023-02746-y. [PMID: 37322070 DOI: 10.1038/s41388-023-02746-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/17/2023]
Abstract
Gliomas are highly malignant tumors accounting for the majority of brain neoplasms. They are characterized by nuclear atypia, high mitotic rate and cellular polymorphism that often contributes to aggressiveness and resistance to standard therapy. They often associate with challenging treatment approaches and poor outcomes. New treatment strategies or regimens to improve the efficacy of glioma treatment require a deeper understanding of glioma occurrence and development as well as elucidation of their molecular biological characteristics. Recent studies have revealed RNA modifications as a key regulatory mechanism involved in tumorigenesis, tumor progression, immune regulation, and response to therapy. The present review discusses research advances on several RNA modifications involved in glioma progression and tumor microenvironment (TME) immunoregulation as well as in the development of adaptive drug resistance, summarizing current progress on major RNA modification targeting strategies.
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Affiliation(s)
- Christina Piperi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens, Greece.
| | - Mariam Markouli
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Antonios N Gargalionis
- Department of Biopathology, 'Eginition' Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Kostas A Papavassiliou
- First University Department of Respiratory Medicine, 'Sotiria' Hospital, Medical School, National and Kapodistrian University of Athens, 11527, Athens, Greece
| | - Athanasios G Papavassiliou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens, Greece.
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29
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Wang W, Yang Y, Guo H, Li MH, Chen XQ, Wei XY, Chen Y, Elsheikha HM, Zhang XX. Unravelling Strain-Specific Modifications of Toxoplasma gondii tRNA and sncRNA Using LC-MS/MS. Microbiol Spectr 2023; 11:e0356422. [PMID: 37036375 PMCID: PMC10269570 DOI: 10.1128/spectrum.03564-22] [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: 09/08/2022] [Accepted: 03/21/2023] [Indexed: 04/11/2023] Open
Abstract
Many RNA modifications have been detected in rRNA, tRNA and small noncoding RNA (sncRNA) as well as in low-abundance RNA species such mRNA. Although RNA modifications play roles in many cellular and biological processes in various domains of life, knowledge about the diversity and role of RNA modifications in Toxoplasma gondii is limited. In this study, RNA modifications in three T. gondii strains (RH type I, PRU type II, and VEG type III) with distinct virulence abilities were determined by liquid chromatography-tandem mass spectrometry. We compared the levels of modifications of four nucleotides in tRNA and sncRNA, characterized RNA modification patterns of different T. gondii strains, and determined the diversity of RNA modifications. We detected and quantified 22 modified nucleosides in both tRNA and sncRNA. Significant differences in the diversity of the modified nucleosides were found between the three T. gondii strains. RNA modifications were correlated with the expression of many T. gondii virulence proteins. Some of the identified modifications (e.g., 2'-O-methylinosine, pseudouridine) play a role in mediating the host-parasite interaction. These results provide novel insight into the global modifications in tRNA and sncRNA, and the diversity of RNA modifications between T. gondii strains with different virulence backgrounds. IMPORTANCE Although RNA modifications play roles in many cellular and developmental processes in various domains of life, knowledge about the patterns and functions of RNA modifications in T. gondii is limited. Here, a quantitative liquid chromatography-tandem mass spectrometry (LC-MS/MS) approach was used to study global RNA modifications in T. gondii strains of distinct virulence backgrounds. We quantified 22 modified nucleosides in both tRNA and sncRNA. Significant T. gondii strain-specific differences in RNA modifications were detected. More tRNA modifications correlated with T. gondii virulence proteins than sncRNA modifications. RNA modifications were significantly correlated with virulence proteins. Our data provide the first comprehensive profiling of the modifications tRNA and sncRNA in T. gondii, expanding the diversity of RNA modifications in this parasite and suggesting new regulators for modulating its virulence.
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Affiliation(s)
- Wei Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, People’s Republic of China
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agriculture University, Daqing, People’s Republic of China
| | - Yi Yang
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Institute of Preventive Veterinary Medicine, Zhejiang University, Hangzhou, People’s Republic of China
| | - Huanping Guo
- Medical Center of Hematology, The Second Affiliated Hospital of Army Medical University, Chongqing, People’s Republic of China
| | - Ming-Han Li
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, People’s Republic of China
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, People’s Republic of China
| | - Xiao-Qing Chen
- Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, People’s Republic of China
| | - Xin-Yu Wei
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, People’s Republic of China
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agriculture University, Daqing, People’s Republic of China
| | - Yu Chen
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, People’s Republic of China
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agriculture University, Daqing, People’s Republic of China
| | - Hany M. Elsheikha
- Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Xiao-Xuan Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, People’s Republic of China
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30
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Wang X, Yu D, Chen L. Antimicrobial resistance and mechanisms of epigenetic regulation. Front Cell Infect Microbiol 2023; 13:1199646. [PMID: 37389209 PMCID: PMC10306973 DOI: 10.3389/fcimb.2023.1199646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/26/2023] [Indexed: 07/01/2023] Open
Abstract
The rampant use of antibiotics in animal husbandry, farming and clinical disease treatment has led to a significant issue with pathogen resistance worldwide over the past decades. The classical mechanisms of resistance typically investigate antimicrobial resistance resulting from natural resistance, mutation, gene transfer and other processes. However, the emergence and development of bacterial resistance cannot be fully explained from a genetic and biochemical standpoint. Evolution necessitates phenotypic variation, selection, and inheritance. There are indications that epigenetic modifications also play a role in antimicrobial resistance. This review will specifically focus on the effects of DNA modification, histone modification, rRNA methylation and the regulation of non-coding RNAs expression on antimicrobial resistance. In particular, we highlight critical work that how DNA methyltransferases and non-coding RNAs act as transcriptional regulators that allow bacteria to rapidly adapt to environmental changes and control their gene expressions to resist antibiotic stress. Additionally, it will delve into how Nucleolar-associated proteins in bacteria perform histone functions akin to eukaryotes. Epigenetics, a non-classical regulatory mechanism of bacterial resistance, may offer new avenues for antibiotic target selection and the development of novel antibiotics.
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Affiliation(s)
- Xinrui Wang
- Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian, China
- National Health Commission Key Laboratory of Technical Evaluation of Fertility Regulation for Non-Human Primate, Fujian Maternity and Child Health Hospital, Fuzhou, Fujian, China
| | - Donghong Yu
- Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian, China
- National Health Commission Key Laboratory of Technical Evaluation of Fertility Regulation for Non-Human Primate, Fujian Maternity and Child Health Hospital, Fuzhou, Fujian, China
| | - Lu Chen
- Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian, China
- National Health Commission Key Laboratory of Technical Evaluation of Fertility Regulation for Non-Human Primate, Fujian Maternity and Child Health Hospital, Fuzhou, Fujian, China
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Patel A, Clark KD. Characterizing RNA modifications in the central nervous system and single cells by RNA sequencing and liquid chromatography-tandem mass spectrometry techniques. Anal Bioanal Chem 2023:10.1007/s00216-023-04604-y. [PMID: 36840809 DOI: 10.1007/s00216-023-04604-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 02/26/2023]
Abstract
Post-transcriptional modifications to RNA constitute a newly appreciated layer of translation regulation in the central nervous system (CNS). The identity, stoichiometric quantity, and sequence position of these unusual epitranscriptomic marks are central to their function, making analytical methods that are capable of accurate and reproducible measurements paramount to the characterization of the neuro-epitranscriptome. RNA sequencing-based methods and liquid chromatography-tandem mass spectrometry (LC-MS/MS) techniques have been leveraged to provide an early glimpse of the landscape of RNA modifications in bulk CNS tissues. However, recent advances in sample preparation, separations, and detection methods have revealed that individual cells display remarkable heterogeneity in their RNA modification profiles, raising questions about the prevalence and function of cell-specific distributions of post-transcriptionally modified nucleosides in the brain. In this Trends article, we present an overview of RNA sequencing and LC-MS/MS methodologies for the analysis of RNA modifications in the CNS with special emphasis on recent advancements in techniques that facilitate single-cell and subcellular detection.
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Affiliation(s)
- Arya Patel
- Department of Chemistry, Tufts University, Medford, MA, 02155, USA
| | - Kevin D Clark
- Department of Chemistry, Tufts University, Medford, MA, 02155, USA.
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Volná A, Bartas M, Nezval J, Pech R, Pečinka P, Špunda V, Červeň J. Beyond the Primary Structure of Nucleic Acids: Potential Roles of Epigenetics and Noncanonical Structures in the Regulations of Plant Growth and Stress Responses. Methods Mol Biol 2023; 2642:331-361. [PMID: 36944887 DOI: 10.1007/978-1-0716-3044-0_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Epigenetics deals with changes in gene expression that are not caused by modifications in the primary sequence of nucleic acids. These changes beyond primary structures of nucleic acids not only include DNA/RNA methylation, but also other reversible conversions, together with histone modifications or RNA interference. In addition, under particular conditions (such as specific ion concentrations or protein-induced stabilization), the right-handed double-stranded DNA helix (B-DNA) can form noncanonical structures commonly described as "non-B DNA" structures. These structures comprise, for example, cruciforms, i-motifs, triplexes, and G-quadruplexes. Their formation often leads to significant differences in replication and transcription rates. Noncanonical RNA structures have also been documented to play important roles in translation regulation and the biology of noncoding RNAs. In human and animal studies, the frequency and dynamics of noncanonical DNA and RNA structures are intensively investigated, especially in the field of cancer research and neurodegenerative diseases. In contrast, noncanonical DNA and RNA structures in plants have been on the fringes of interest for a long time and only a few studies deal with their formation, regulation, and physiological importance for plant stress responses. Herein, we present a review focused on the main fields of epigenetics in plants and their possible roles in stress responses and signaling, with special attention dedicated to noncanonical DNA and RNA structures.
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Affiliation(s)
- Adriana Volná
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Martin Bartas
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Jakub Nezval
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Radomír Pech
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Petr Pečinka
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Vladimír Špunda
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- Global Change Research Institute, Czech Academy of Sciences, Brno, Czech Republic
| | - Jiří Červeň
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic.
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Arzumanian VA, Dolgalev GV, Kurbatov IY, Kiseleva OI, Poverennaya EV. Epitranscriptome: Review of Top 25 Most-Studied RNA Modifications. Int J Mol Sci 2022; 23:ijms232213851. [PMID: 36430347 PMCID: PMC9695239 DOI: 10.3390/ijms232213851] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/12/2022] Open
Abstract
The alphabet of building blocks for RNA molecules is much larger than the standard four nucleotides. The diversity is achieved by the post-transcriptional biochemical modification of these nucleotides into distinct chemical entities that are structurally and functionally different from their unmodified counterparts. Some of these modifications are constituent and critical for RNA functions, while others serve as dynamic markings to regulate the fate of specific RNA molecules. Together, these modifications form the epitranscriptome, an essential layer of cellular biochemistry. As of the time of writing this review, more than 300 distinct RNA modifications from all three life domains have been identified. However, only a few of the most well-established modifications are included in most reviews on this topic. To provide a complete overview of the current state of research on the epitranscriptome, we analyzed the extent of the available information for all known RNA modifications. We selected 25 modifications to describe in detail. Summarizing our findings, we describe the current status of research on most RNA modifications and identify further developments in this field.
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Affiliation(s)
- Viktoriia A. Arzumanian
- Correspondence: (V.A.A.); (G.V.D.); Tel.: +7-960-889-7117 (V.A.A.); +7-967-236-36-79 (G.V.D.)
| | - Georgii V. Dolgalev
- Correspondence: (V.A.A.); (G.V.D.); Tel.: +7-960-889-7117 (V.A.A.); +7-967-236-36-79 (G.V.D.)
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Conservation and Diversification of tRNA t6A-Modifying Enzymes across the Three Domains of Life. Int J Mol Sci 2022; 23:ijms232113600. [PMID: 36362385 PMCID: PMC9654439 DOI: 10.3390/ijms232113600] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 10/28/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
The universal N6-threonylcarbamoyladenosine (t6A) modification occurs at position 37 of tRNAs that decipher codons starting with adenosine. Mechanistically, t6A stabilizes structural configurations of the anticodon stem loop, promotes anticodon–codon pairing and safeguards the translational fidelity. The biosynthesis of tRNA t6A is co-catalyzed by two universally conserved protein families of TsaC/Sua5 (COG0009) and TsaD/Kae1/Qri7 (COG0533). Enzymatically, TsaC/Sua5 protein utilizes the substrates of L-threonine, HCO3−/CO2 and ATP to synthesize an intermediate L-threonylcarbamoyladenylate, of which the threonylcarbamoyl-moiety is subsequently transferred onto the A37 of substrate tRNAs by the TsaD–TsaB –TsaE complex in bacteria or by the KEOPS complex in archaea and eukaryotic cytoplasm, whereas Qri7/OSGEPL1 protein functions on its own in mitochondria. Depletion of tRNA t6A interferes with protein homeostasis and gravely affects the life of unicellular organisms and the fitness of higher eukaryotes. Pathogenic mutations of YRDC, OSGEPL1 and KEOPS are implicated in a number of human mitochondrial and neurological diseases, including autosomal recessive Galloway–Mowat syndrome. The molecular mechanisms underscoring both the biosynthesis and cellular roles of tRNA t6A are presently not well elucidated. This review summarizes current mechanistic understandings of the catalysis, regulation and disease implications of tRNA t6A-biosynthetic machineries of three kingdoms of life, with a special focus on delineating the structure–function relationship from perspectives of conservation and diversity.
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Borišek J, Aupič J, Magistrato A. Establishing the catalytic and regulatory mechanism of
RNA
‐based machineries. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Jure Borišek
- Theory Department National Institute of Chemistry Ljubljana Slovenia
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Highlighting the Unique Roles of Radical S-Adenosylmethionine Enzymes in Methanogenic Archaea. J Bacteriol 2022; 204:e0019722. [PMID: 35880875 PMCID: PMC9380564 DOI: 10.1128/jb.00197-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Radical S-adenosylmethionine (SAM) enzymes catalyze an impressive variety of difficult biochemical reactions in various pathways across all domains of life. These metalloenzymes employ a reduced [4Fe-4S] cluster and SAM to generate a highly reactive 5'-deoxyadenosyl radical that is capable of initiating catalysis on otherwise unreactive substrates. Interestingly, the genomes of methanogenic archaea encode many unique radical SAM enzymes with underexplored or completely unknown functions. These organisms are responsible for the yearly production of nearly 1 billion tons of methane, a potent greenhouse gas as well as a valuable energy source. Thus, understanding the details of methanogenic metabolism and elucidating the functions of essential enzymes in these organisms can provide insights into strategies to decrease greenhouse gas emissions as well as inform advances in bioenergy production processes. This minireview provides an overview of the current state of the field regarding the functions of radical SAM enzymes in methanogens and discusses gaps in knowledge that should be addressed.
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Dound AS, Fandilolu PM, Sonawane KD. Structural Significance of Conformational Preferences and Ribose-Ring-Puckering of Hyper Modified Nucleotide 5'-Monophosphate 2-Methylthio Cyclic N 6-Threonylcarbamoyladenosine (p-ms 2ct 6A) Present at 37th Position in Anticodon Loop of tRNA Lys. Cell Biochem Biophys 2022; 80:665-680. [PMID: 35965304 DOI: 10.1007/s12013-022-01086-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 07/28/2022] [Indexed: 12/01/2022]
Abstract
Structural significance of conformational preferences and ribose ring puckering of newly discovered hyper modified nucleotide, 5'-monophosphate 2-methylthio cyclic N6-threonylcarbamoyladenosine (p-ms2ct6A) have been investigated using quantum chemical semi-empirical RM1 and molecular dynamics simulation techniques. Automated geometry optimization of most stable structure of p-ms2ct6A has also been carried out with the help of abinitio (HF SCF, DFT) as well as semi empirical quantum chemical (RM1, AM1, PM3, and PM6) methods. Most stable structure of p-ms2ct6A is stabilized by intramolecular interactions between N(3)…HC(2'), N(1)…HC(16), O(13)…HC(15), and O(13)…HO(14). The torsion angles alpha (α) and beta (β) show the significant characteristic patterns with the involvement of intramolecular hydrogen bonding to provide stability to the p-ms2ct6A. Further, molecular dynamics simulations of p-ms2ct6A revealed the role of ribose sugar ring puckering i.e. C2'-endo and C3'-endo on the structural dynamics of ms2ct6A side chain. The modified nucleotide p-ms2ct6A periodically prefers both the C2'-endo and C3'-endo sugar with 'anti' and 'syn' conformations. This property of p-ms2ct6A could be useful to recognize the starting ANN codons. All atom explicit MD simulation of anticodon loop (ACL) of tRNALys of Bacillus subtilis containing ms2ct6A at 37th position showed the U-turn feature, base stacking ability with other adjacent bases and hydrogen bonding interactions similar to the isolated base p-ms2ct6A. The ribose sugar puckering contributes to the orientation of the side chain conformation of p-ms2ct6A. Thus, the present study could be helpful to understand the structure-function relationship of the hypermodified nucleoside, ms2ct6A in recognition of the proper codons AAA/AAG during protein biosynthesis.
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Affiliation(s)
- Ambika S Dound
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur, 416 004, Maharashtra, India
| | - Prayagraj M Fandilolu
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur, 416 004, Maharashtra, India
| | - Kailas D Sonawane
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur, 416 004, Maharashtra, India.
- Department of Microbiology, Shivaji University, Kolhapur, 416004, Maharashtra, India.
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Abstract
Small RNAs are ubiquitous regulators of gene expression that participate in nearly all aspects of physiology in a wide range of organisms. There are many different classes of eukaryotic small RNAs that play regulatory roles at every level of gene expression, including transcription, RNA stability, and translation. While eukaryotic small RNAs display diverse functions across and within classes, they are generally grouped functionally based on the machinery required for their biogenesis, the effector proteins they associate with, and their molecular characteristics. The development of techniques to clone and sequence small RNAs has been critical for their identification, yet the ligation-dependent addition of RNA adapters and the use of reverse transcriptase to generate cDNA in traditional library preparation protocols can be unsuitable to detect certain small RNA subtypes. In particular, 3' or 5' chemical modifications that are characteristic of specific types of small RNAs can impede the ligation-dependent addition of RNA adapters, while internal RNA modifications can interfere with accurate reverse transcription. The inability to clone certain small RNA subtypes with traditional protocols results in an inaccurate assessment of small RNA abundance and diversity, where some RNAs appear over-represented and others are not detected. This overview aims to guide users on how to design small RNA cloning workflows in eukaryotes to more accurately capture specific small RNAs of interest. Hence, we discuss the molecular biology underlying the identification and quantitation of small RNAs, explore the limitations of commonly used protocols, and detail the alternative approaches that can be used to enrich specific small RNA classes. © 2022 Wiley Periodicals LLC.
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Affiliation(s)
- Olivia J Crocker
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Departments of Genetics and Pediatrics - Penn Epigenetics Institute, Institute of Regenerative Medicine, and Center for Research on Reproduction and Women's Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Natalie A Trigg
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Departments of Genetics and Pediatrics - Penn Epigenetics Institute, Institute of Regenerative Medicine, and Center for Research on Reproduction and Women's Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Colin C Conine
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Departments of Genetics and Pediatrics - Penn Epigenetics Institute, Institute of Regenerative Medicine, and Center for Research on Reproduction and Women's Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
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Fleming BA, Blango MG, Rousek AA, Kincannon WM, Tran A, Lewis A, Russell C, Zhou Q, Baird LM, Barber A, Brannon JR, Beebout C, Bandarian V, Hadjifrangiskou M, Howard M, Mulvey M. A tRNA modifying enzyme as a tunable regulatory nexus for bacterial stress responses and virulence. Nucleic Acids Res 2022; 50:7570-7590. [PMID: 35212379 PMCID: PMC9303304 DOI: 10.1093/nar/gkac116] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 02/02/2022] [Accepted: 02/08/2022] [Indexed: 11/16/2022] Open
Abstract
Post-transcriptional modifications can impact the stability and functionality of many different classes of RNA molecules and are an especially important aspect of tRNA regulation. It is hypothesized that cells can orchestrate rapid responses to changing environmental conditions by adjusting the specific types and levels of tRNA modifications. We uncovered strong evidence in support of this tRNA global regulation hypothesis by examining effects of the well-conserved tRNA modifying enzyme MiaA in extraintestinal pathogenic Escherichia coli (ExPEC), a major cause of urinary tract and bloodstream infections. MiaA mediates the prenylation of adenosine-37 within tRNAs that decode UNN codons, and we found it to be crucial to the fitness and virulence of ExPEC. MiaA levels shifted in response to stress via a post-transcriptional mechanism, resulting in marked changes in the amounts of fully modified MiaA substrates. Both ablation and forced overproduction of MiaA stimulated translational frameshifting and profoundly altered the ExPEC proteome, with variable effects attributable to UNN content, changes in the catalytic activity of MiaA, or availability of metabolic precursors. Cumulatively, these data indicate that balanced input from MiaA is critical for optimizing cellular responses, with MiaA acting much like a rheostat that can be used to realign global protein expression patterns.
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Affiliation(s)
- Brittany A Fleming
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Matthew G Blango
- Junior Research Group RNA Biology of Fungal Infections, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (Leibniz-HKI), 07745 Jena, Germany
| | - Alexis A Rousek
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | | | - Alexander Tran
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Adam J Lewis
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Colin W Russell
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Qin Zhou
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Lisa M Baird
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Amelia E Barber
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - John R Brannon
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Connor J Beebout
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Vahe Bandarian
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Maria Hadjifrangiskou
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Michael T Howard
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Matthew A Mulvey
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
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Brégeon D, Pecqueur L, Toubdji S, Sudol C, Lombard M, Fontecave M, de Crécy-Lagard V, Motorin Y, Helm M, Hamdane D. Dihydrouridine in the Transcriptome: New Life for This Ancient RNA Chemical Modification. ACS Chem Biol 2022; 17:1638-1657. [PMID: 35737906 DOI: 10.1021/acschembio.2c00307] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Until recently, post-transcriptional modifications of RNA were largely restricted to noncoding RNA species. However, this belief seems to have quickly dissipated with the growing number of new modifications found in mRNA that were originally thought to be primarily tRNA-specific, such as dihydrouridine. Recently, transcriptomic profiling, metabolic labeling, and proteomics have identified unexpected dihydrouridylation of mRNAs, greatly expanding the catalog of novel mRNA modifications. These data also implicated dihydrouridylation in meiotic chromosome segregation, protein translation rates, and cell proliferation. Dihydrouridylation of tRNAs and mRNAs are introduced by flavin-dependent dihydrouridine synthases. In this review, we will briefly outline the current knowledge on the distribution of dihydrouridines in the transcriptome, their chemical labeling, and highlight structural and mechanistic aspects regarding the dihydrouridine synthases enzyme family. A special emphasis on important research directions to be addressed will also be discussed. This new entry of dihydrouridine into mRNA modifications has definitely added a new layer of information that controls protein synthesis.
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Affiliation(s)
- Damien Brégeon
- IBPS, Biology of Aging and Adaptation, Sorbonne Université, Paris 75252, France
| | - Ludovic Pecqueur
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75231 Paris, Cedex 05, France
| | - Sabrine Toubdji
- IBPS, Biology of Aging and Adaptation, Sorbonne Université, Paris 75252, France
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75231 Paris, Cedex 05, France
| | - Claudia Sudol
- IBPS, Biology of Aging and Adaptation, Sorbonne Université, Paris 75252, France
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75231 Paris, Cedex 05, France
| | - Murielle Lombard
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75231 Paris, Cedex 05, France
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75231 Paris, Cedex 05, France
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611, United States
- Genetics Institute, University of Florida, Gainesville, Florida 32610, United States
| | - Yuri Motorin
- Université de Lorraine, CNRS, INSERM, UMS2008/US40 IBSLor, EpiRNA-Seq Core Facility, Nancy F-54000, France
- Université de Lorraine, CNRS, UMR7365 IMoPA, Nancy F-54000, France
| | - Mark Helm
- Institut für pharmazeutische und biomedizinische Wissenschaften (IPBW), Johannes Gutenberg-Universität, Mainz 55128, Germany
| | - Djemel Hamdane
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75231 Paris, Cedex 05, France
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Dysregulation of Small Nucleolar RNAs in B-Cell Malignancies. Biomedicines 2022; 10:biomedicines10061229. [PMID: 35740251 PMCID: PMC9219770 DOI: 10.3390/biomedicines10061229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 01/17/2023] Open
Abstract
Small nucleolar RNAs (snoRNAs) are responsible for post-transcriptional modification of ribosomal RNAs, transfer RNAs and small nuclear RNAs, and thereby have important regulatory functions in mRNA splicing and protein translation. Several studies have shown that snoRNAs are dysregulated in human cancer and may play a role in cancer initiation and progression. In this review, we focus on the role of snoRNAs in normal and malignant B-cell development. SnoRNA activity appears to be essential for normal B-cell differentiation and dysregulated expression of sno-RNAs is determined in B-cell acute lymphoblastic leukemia, chronic lymphocytic leukemia, B-cell non-Hodgkin’s lymphoma, and plasma cell neoplasms. SnoRNA expression is associated with cytogenetic/molecular subgroups and clinical outcome in patients with B-cell malignancies. Translocations involving snoRNAs have been described as well. Here, we discuss the different aspects of snoRNAs in B-cell malignancies and report on their role in oncogenic transformation, which may be useful for the development of novel diagnostic biomarkers or therapeutic targets.
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Shoaib Y, Usman B, Kang H, Jung KH. Epitranscriptomics: An Additional Regulatory Layer in Plants' Development and Stress Response. PLANTS (BASEL, SWITZERLAND) 2022; 11:1033. [PMID: 35448761 PMCID: PMC9027318 DOI: 10.3390/plants11081033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 04/04/2022] [Accepted: 04/04/2022] [Indexed: 06/14/2023]
Abstract
Epitranscriptomics has added a new layer of regulatory machinery to eukaryotes, and the advancement of sequencing technology has revealed more than 170 post-transcriptional modifications in various types of RNAs, including messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA), and long non-coding RNA (lncRNA). Among these, N6-methyladenosine (m6A) and N5-methylcytidine (m5C) are the most prevalent internal mRNA modifications. These regulate various aspects of RNA metabolism, mainly mRNA degradation and translation. Recent advances have shown that regulation of RNA fate mediated by these epitranscriptomic marks has pervasive effects on a plant's development and responses to various biotic and abiotic stresses. Recently, it was demonstrated that the removal of human-FTO-mediated m6A from transcripts in transgenic rice and potatoes caused a dramatic increase in their yield, and that the m6A reader protein mediates stress responses in wheat and apple, indicating that regulation of m6A levels could be an efficient strategy for crop improvement. However, changing the overall m6A levels might have unpredictable effects; therefore, the identification of precise m6A levels at a single-base resolution is essential. In this review, we emphasize the roles of epitranscriptomic modifications in modulating molecular, physiological, and stress responses in plants, and provide an outlook on epitranscriptome engineering as a promising tool to ensure food security by editing specific m6A and m5C sites through robust genome-editing technology.
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Affiliation(s)
- Yasira Shoaib
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin-si 17104, Korea; (Y.S.); (B.U.)
| | - Babar Usman
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin-si 17104, Korea; (Y.S.); (B.U.)
| | - Hunseung Kang
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea;
| | - Ki-Hong Jung
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin-si 17104, Korea; (Y.S.); (B.U.)
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Brown IN, Lafita-Navarro MC, Conacci-Sorrell M. Regulation of Nucleolar Activity by MYC. Cells 2022; 11:cells11030574. [PMID: 35159381 PMCID: PMC8834138 DOI: 10.3390/cells11030574] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/02/2022] [Accepted: 02/03/2022] [Indexed: 01/20/2023] Open
Abstract
The nucleolus harbors the machinery necessary to produce new ribosomes which are critical for protein synthesis. Nucleolar size, shape, and density are highly dynamic and can be adjusted to accommodate ribosome biogenesis according to the needs for protein synthesis. In cancer, cells undergo continuous proliferation; therefore, nucleolar activity is elevated due to their high demand for protein synthesis. The transcription factor and universal oncogene MYC promotes nucleolar activity by enhancing the transcription of ribosomal DNA (rDNA) and ribosomal proteins. This review summarizes the importance of nucleolar activity in mammalian cells, MYC’s role in nucleolar regulation in cancer, and discusses how a better understanding (and the potential inhibition) of aberrant nucleolar activity in cancer cells could lead to novel therapeutics.
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Affiliation(s)
- Isabella N. Brown
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
| | - M. Carmen Lafita-Navarro
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
- Correspondence: (M.C.L.-N.); (M.C.-S.)
| | - Maralice Conacci-Sorrell
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Correspondence: (M.C.L.-N.); (M.C.-S.)
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44
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Chemical modifications to mRNA nucleobases impact translation elongation and termination. Biophys Chem 2022; 285:106780. [DOI: 10.1016/j.bpc.2022.106780] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/03/2022] [Accepted: 02/13/2022] [Indexed: 12/15/2022]
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45
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Kleiber N, Lemus-Diaz N, Stiller C, Heinrichs M, Mai MMQ, Hackert P, Richter-Dennerlein R, Höbartner C, Bohnsack KE, Bohnsack MT. The RNA methyltransferase METTL8 installs m 3C 32 in mitochondrial tRNAs Thr/Ser(UCN) to optimise tRNA structure and mitochondrial translation. Nat Commun 2022; 13:209. [PMID: 35017528 PMCID: PMC8752778 DOI: 10.1038/s41467-021-27905-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 12/14/2021] [Indexed: 12/30/2022] Open
Abstract
Modified nucleotides in tRNAs are important determinants of folding, structure and function. Here we identify METTL8 as a mitochondrial matrix protein and active RNA methyltransferase responsible for installing m3C32 in the human mitochondrial (mt-)tRNAThr and mt-tRNASer(UCN). METTL8 crosslinks to the anticodon stem loop (ASL) of many mt-tRNAs in cells, raising the question of how methylation target specificity is achieved. Dissection of mt-tRNA recognition elements revealed U34G35 and t6A37/(ms2)i6A37, present concomitantly only in the ASLs of the two substrate mt-tRNAs, as key determinants for METTL8-mediated methylation of C32. Several lines of evidence demonstrate the influence of U34, G35, and the m3C32 and t6A37/(ms2)i6A37 modifications in mt-tRNAThr/Ser(UCN) on the structure of these mt-tRNAs. Although mt-tRNAThr/Ser(UCN) lacking METTL8-mediated m3C32 are efficiently aminoacylated and associate with mitochondrial ribosomes, mitochondrial translation is mildly impaired by lack of METTL8. Together these results define the cellular targets of METTL8 and shed new light on the role of m3C32 within mt-tRNAs.
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MESH Headings
- Anticodon/chemistry
- Anticodon/metabolism
- Base Pairing
- Cytosine/metabolism
- Gene Expression Regulation
- HEK293 Cells
- Humans
- Methylation
- Methyltransferases/genetics
- Methyltransferases/metabolism
- Mitochondria/genetics
- Mitochondria/metabolism
- Nucleic Acid Conformation
- Protein Binding
- Protein Biosynthesis
- RNA, Mitochondrial/chemistry
- RNA, Mitochondrial/genetics
- RNA, Mitochondrial/metabolism
- RNA, Transfer, Ser/chemistry
- RNA, Transfer, Ser/genetics
- RNA, Transfer, Ser/metabolism
- RNA, Transfer, Thr/chemistry
- RNA, Transfer, Thr/genetics
- RNA, Transfer, Thr/metabolism
- Signal Transduction
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Affiliation(s)
- Nicole Kleiber
- Department of Molecular Biology, University Medical Centre Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Nicolas Lemus-Diaz
- Department of Molecular Biology, University Medical Centre Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Carina Stiller
- Institute of Organic Chemistry, Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Marleen Heinrichs
- Department of Cellular Biochemistry, University Medical Centre Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Mandy Mong-Quyen Mai
- Department of Cellular Biochemistry, University Medical Centre Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Philipp Hackert
- Department of Molecular Biology, University Medical Centre Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Ricarda Richter-Dennerlein
- Department of Cellular Biochemistry, University Medical Centre Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), Göttingen, Germany
| | - Claudia Höbartner
- Institute of Organic Chemistry, Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Centre Göttingen, Humboldtallee 23, 37073, Göttingen, Germany.
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Centre Göttingen, Humboldtallee 23, 37073, Göttingen, Germany.
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), Göttingen, Germany.
- Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, Justus-von-Liebig-Weg 11, Göttingen, 37077, Germany.
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46
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Dixit S, Kessler AC, Henderson J, Pan X, Zhao R, D'Almeida GS, Kulkarni S, Rubio MAT, Hegedűsová E, Ross RL, Limbach PA, Green BD, Paris Z, Alfonzo JD. Dynamic queuosine changes in tRNA couple nutrient levels to codon choice in Trypanosoma brucei. Nucleic Acids Res 2021; 49:12986-12999. [PMID: 34883512 PMCID: PMC8682783 DOI: 10.1093/nar/gkab1204] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 11/16/2021] [Accepted: 12/08/2021] [Indexed: 11/22/2022] Open
Abstract
Every type of nucleic acid in cells undergoes programmed chemical post-transcriptional modification. Generally, modification enzymes use substrates derived from intracellular metabolism, one exception is queuine (q)/queuosine (Q), which eukaryotes obtain from their environment; made by bacteria and ultimately taken into eukaryotic cells via currently unknown transport systems. Here, we use a combination of molecular, cell biology and biophysical approaches to show that in Trypanosoma brucei tRNA Q levels change dynamically in response to concentration variations of a sub-set of amino acids in the growth media. Most significant were variations in tyrosine, which at low levels lead to increased Q content for all the natural tRNAs substrates of tRNA-guanine transglycosylase (TGT). Such increase results from longer nuclear dwell time aided by retrograde transport following cytoplasmic splicing. In turn high tyrosine levels lead to rapid decrease in Q content. Importantly, the dynamic changes in Q content of tRNAs have negligible effects on global translation or growth rate but, at least, in the case of tRNATyr it affected codon choice. These observations have implications for the occurrence of other tunable modifications important for ‘normal’ growth, while connecting the intracellular localization of modification enzymes, metabolites and tRNAs to codon selection and implicitly translational output.
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Affiliation(s)
- Sameer Dixit
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Alan C Kessler
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Jeremy Henderson
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Xiaobei Pan
- School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, UK
| | - Ruoxia Zhao
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | | | - Sneha Kulkarni
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Mary Anne T Rubio
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Eva Hegedűsová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Robert L Ross
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Brian D Green
- School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, UK
| | - Zdeněk Paris
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Juan D Alfonzo
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA
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47
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Chen R, Zhou J, Liu L, Mao XL, Zhou X, Xie W. Crystal structure of human METTL6, the m 3C methyltransferase. Commun Biol 2021; 4:1361. [PMID: 34862464 PMCID: PMC8642396 DOI: 10.1038/s42003-021-02890-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 11/10/2021] [Indexed: 01/27/2023] Open
Abstract
In tRNA, the epigenetic m3C modification at position 32 in the anticodon loop is highly conserved in eukaryotes, which maintains the folding and basepairing functions of the anticodon. However, the responsible enzymes METTL2 and METTL6 were identified only in recent years. The loss of human METTL6 (hMETTL6) affects the translational process and proteostasis in cells, while in mESCs cells, it leads to defective pluripotency potential. Despite its important functions, the catalytic mechanism of the C32 methylation by this enzyme is poorly understood. Here we present the 1.9 Å high-resolution crystal structure of hMETTL6 bound by SAH. The key residues interacting with the ligand were identified and their roles were confirmed by ITC. We generated a docking model for the hMETTL6-SAH-CMP ternary complex. Interestingly, the CMP molecule binds into a cavity in a positive patch with the base ring pointing to the inside, suggesting a flipped-base mechanism for methylation. We further generated a model for the quaternary complex with tRNASer as a component, which reasonably explained the biochemical behaviors of hMETTL6. Taken together, our crystallographic and biochemical studies provide important insight into the molecular recognition mechanism by METTL6 and may aid in the METTL-based rational drug design in the future.
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Affiliation(s)
- Ran Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou, Guangdong, 510006, People's Republic of China.,Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou, 511458, People's Republic of China
| | - Jie Zhou
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou, Guangdong, 510006, People's Republic of China
| | - Ling Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou, Guangdong, 510006, People's Republic of China
| | - Xue-Ling Mao
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, People's Republic of China
| | - Xiaolong Zhou
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, People's Republic of China
| | - Wei Xie
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou, Guangdong, 510006, People's Republic of China.
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48
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Clifton BE, Fariz MA, Uechi GI, Laurino P. Evolutionary repair reveals an unexpected role of the tRNA modification m1G37 in aminoacylation. Nucleic Acids Res 2021; 49:12467-12485. [PMID: 34761260 PMCID: PMC8643618 DOI: 10.1093/nar/gkab1067] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/13/2021] [Accepted: 10/20/2021] [Indexed: 11/13/2022] Open
Abstract
The tRNA modification m1G37, introduced by the tRNA methyltransferase TrmD, is thought to be essential for growth in bacteria because it suppresses translational frameshift errors at proline codons. However, because bacteria can tolerate high levels of mistranslation, it is unclear why loss of m1G37 is not tolerated. Here, we addressed this question through experimental evolution of trmD mutant strains of Escherichia coli. Surprisingly, trmD mutant strains were viable even if the m1G37 modification was completely abolished, and showed rapid recovery of growth rate, mainly via duplication or mutation of the proline-tRNA ligase gene proS. Growth assays and in vitro aminoacylation assays showed that G37-unmodified tRNAPro is aminoacylated less efficiently than m1G37-modified tRNAPro, and that growth of trmD mutant strains can be largely restored by single mutations in proS that restore aminoacylation of G37-unmodified tRNAPro. These results show that inefficient aminoacylation of tRNAPro is the main reason for growth defects observed in trmD mutant strains and that proS may act as a gatekeeper of translational accuracy, preventing the use of error-prone unmodified tRNAPro in translation. Our work shows the utility of experimental evolution for uncovering the hidden functions of essential genes and has implications for the development of antibiotics targeting TrmD.
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Affiliation(s)
- Ben E Clifton
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Okinawa 904-0495, Japan
| | - Muhammad A Fariz
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Okinawa 904-0495, Japan
| | - Gen-Ichiro Uechi
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Okinawa 904-0495, Japan
| | - Paola Laurino
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Okinawa 904-0495, Japan
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49
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Lei K, Lin S, Yuan Q. N6-methyladenosine (m6A) modification of ribosomal RNAs (rRNAs): Critical roles in mRNA translation and diseases. Genes Dis 2021; 10:126-134. [PMID: 37013049 PMCID: PMC10066336 DOI: 10.1016/j.gendis.2021.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 10/14/2021] [Accepted: 10/22/2021] [Indexed: 11/18/2022] Open
Abstract
As key components of the ribosome and the most abundant RNA species, the rRNAs are modified during ribosome formation. N6-methyladenosine (m6A) is a conserved RNA modification occurring on different RNA species including rRNAs. Recently, it has been reported that ZCCHC4 and METTL5 are methyltransferases that mediate m6A modification of human 28S and 18S rRNA, respectively. The newly discovered biological functions of the two methyltransferases include regulation of mRNA translation, cell proliferation, cell differentiation, stress response, and other biological processes. Both of them, especially METTL5, have been proved to be associated with a variety of diseases such as intellectual disability, cancer, congenital dysplasia and have potential clinical application as biomarkers and therapeutic targets.
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Affiliation(s)
- Kexin Lei
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, China
| | - Shuibin Lin
- Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Quan Yuan
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, China
- Corresponding author. State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No.14, 3rd Section, South Renmin Road, Chengdu, Sichuan 610041, China.
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50
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Interplay between Host tRNAs and HIV-1: A Structural Perspective. Viruses 2021; 13:v13091819. [PMID: 34578400 PMCID: PMC8473020 DOI: 10.3390/v13091819] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/06/2021] [Accepted: 09/09/2021] [Indexed: 12/23/2022] Open
Abstract
The cellular metabolism of host tRNAs and life cycle of HIV-1 cross paths at several key virus-host interfaces. Emerging data suggest a multi-faceted interplay between host tRNAs and HIV-1 that plays essential roles, both structural and regulatory, in viral genome replication, genome packaging, and virion biogenesis. HIV-1 not only hijacks host tRNAs and transforms them into obligatory reverse transcription primers but further commandeers tRNAs to regulate the localization of its major structural protein, Gag, via a specific interface. This review highlights recent advances in understanding tRNA-HIV-1 interactions, primarily from a structural perspective, which start to elucidate their underlying molecular mechanisms, intrinsic specificities, and biological significances. Such understanding may provide new avenues toward developing HIV/AIDS treatments and therapeutics including small molecules and RNA biologics that target these host-virus interfaces.
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