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Ero R, Leppik M, Reier K, Liiv A, Remme J. Ribosomal RNA modification enzymes stimulate large ribosome subunit assembly in E. coli. Nucleic Acids Res 2024; 52:6614-6628. [PMID: 38554109 PMCID: PMC11194073 DOI: 10.1093/nar/gkae222] [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: 12/07/2023] [Revised: 03/12/2024] [Accepted: 03/15/2024] [Indexed: 04/01/2024] Open
Abstract
Ribosomal RNA modifications are introduced by specific enzymes during ribosome assembly in bacteria. Deletion of individual modification enzymes has a minor effect on bacterial growth, ribosome biogenesis, and translation, which has complicated the definition of the function of the enzymes and their products. We have constructed an Escherichia coli strain lacking 10 genes encoding enzymes that modify 23S rRNA around the peptidyl-transferase center. This strain exhibits severely compromised growth and ribosome assembly, especially at lower temperatures. Re-introduction of the individual modification enzymes allows for the definition of their functions. The results demonstrate that in addition to previously known RlmE, also RlmB, RlmKL, RlmN and RluC facilitate large ribosome subunit assembly. RlmB and RlmKL have functions in ribosome assembly independent of their modification activities. While the assembly stage specificity of rRNA modification enzymes is well established, this study demonstrates that there is a mutual interdependence between the rRNA modification process and large ribosome subunit assembly.
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MESH Headings
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Escherichia coli Proteins/metabolism
- Escherichia coli Proteins/genetics
- Methyltransferases/metabolism
- Methyltransferases/genetics
- Ribosome Subunits, Large/metabolism
- Ribosome Subunits, Large/genetics
- Ribosome Subunits, Large, Bacterial/metabolism
- Ribosome Subunits, Large, Bacterial/genetics
- Ribosomes/metabolism
- Ribosomes/genetics
- RNA, Ribosomal/metabolism
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 23S/metabolism
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/chemistry
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Affiliation(s)
- Rya Ero
- IMCB University of Tartu, Riia 23, 51010 Tartu, Estonia
| | - Margus Leppik
- IMCB University of Tartu, Riia 23, 51010 Tartu, Estonia
| | - Kaspar Reier
- IMCB University of Tartu, Riia 23, 51010 Tartu, Estonia
| | - Aivar Liiv
- IMCB University of Tartu, Riia 23, 51010 Tartu, Estonia
| | - Jaanus Remme
- IMCB University of Tartu, Riia 23, 51010 Tartu, Estonia
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2
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Höfler S, Duss O. Interconnections between m 6A RNA modification, RNA structure, and protein-RNA complex assembly. Life Sci Alliance 2024; 7:e202302240. [PMID: 37935465 PMCID: PMC10629537 DOI: 10.26508/lsa.202302240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 11/09/2023] Open
Abstract
Protein-RNA complexes exist in many forms within the cell, from stable machines such as the ribosome to transient assemblies like the spliceosome. All protein-RNA assemblies rely on spatially and temporally coordinated interactions between specific proteins and RNAs to achieve a functional form. RNA folding and structure are often critical for successful protein binding and protein-RNA complex formation. RNA modifications change the chemical nature of a given RNA and often alter its folding kinetics. Both these alterations can affect how and if proteins or other RNAs can interact with the modified RNA and assemble into complexes. N6-methyladenosine (m6A) is the most common base modification on mRNAs and regulatory noncoding RNAs and has been shown to impact RNA structure and directly modulate protein-RNA interactions. In this review, focusing on the mechanisms and available quantitative information, we discuss first how the METTL3/14 m6A writer complex is specifically targeted to RNA assisted by protein-RNA and other interactions to enable site-specific and co-transcriptional RNA modification and, once introduced, how the m6A modification affects RNA folding and protein-RNA interactions.
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Affiliation(s)
- Simone Höfler
- https://ror.org/03mstc592 Structural and Computational Biology Unit, EMBL Heidelberg, Heidelberg, Germany
| | - Olivier Duss
- https://ror.org/03mstc592 Structural and Computational Biology Unit, EMBL Heidelberg, Heidelberg, Germany
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3
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Deng L, Kumar J, Rose R, McIntyre W, Fabris D. Analyzing RNA posttranscriptional modifications to decipher the epitranscriptomic code. MASS SPECTROMETRY REVIEWS 2024; 43:5-38. [PMID: 36052666 DOI: 10.1002/mas.21798] [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: 02/14/2022] [Revised: 05/23/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
The discovery of RNA silencing has revealed that non-protein-coding sequences (ncRNAs) can cover essential roles in regulatory networks and their malfunction may result in severe consequences on human health. These findings have prompted a general reassessment of the significance of RNA as a key player in cellular processes. This reassessment, however, will not be complete without a greater understanding of the distribution and function of the over 170 variants of the canonical ribonucleotides, which contribute to the breathtaking structural diversity of natural RNA. This review surveys the analytical approaches employed for the identification, characterization, and detection of RNA posttranscriptional modifications (rPTMs). The merits of analyzing individual units after exhaustive hydrolysis of the initial biopolymer are outlined together with those of identifying their position in the sequence of parent strands. Approaches based on next generation sequencing and mass spectrometry technologies are covered in depth to provide a comprehensive view of their respective merits. Deciphering the epitranscriptomic code will require not only mapping the location of rPTMs in the various classes of RNAs, but also assessing the variations of expression levels under different experimental conditions. The fact that no individual platform is currently capable of meeting all such demands implies that it will be essential to capitalize on complementary approaches to obtain the desired information. For this reason, the review strived to cover the broadest possible range of techniques to provide readers with the fundamental elements necessary to make informed choices and design the most effective possible strategy to accomplish the task at hand.
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Affiliation(s)
- L Deng
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - J Kumar
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - R Rose
- Department of Advanced Research Technologies, New York University Langone Health Center, New York, USA
| | - W McIntyre
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - Daniele Fabris
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
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4
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Wu S, Xie H, Su Y, Jia X, Mi Y, Jia Y, Ying H. The landscape of implantation and placentation: deciphering the function of dynamic RNA methylation at the maternal-fetal interface. Front Endocrinol (Lausanne) 2023; 14:1205408. [PMID: 37720526 PMCID: PMC10499623 DOI: 10.3389/fendo.2023.1205408] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 08/15/2023] [Indexed: 09/19/2023] Open
Abstract
The maternal-fetal interface is defined as the interface between maternal tissue and sections of the fetus in close contact. RNA methylation modifications are the most frequent kind of RNA alterations. It is effective throughout both normal and pathological implantation and placentation during pregnancy. By influencing early embryo development, embryo implantation, endometrium receptivity, immune microenvironment, as well as some implantation and placentation-related disorders like miscarriage and preeclampsia, it is essential for the establishment of the maternal-fetal interface. Our review focuses on the role of dynamic RNA methylation at the maternal-fetal interface, which has received little attention thus far. It has given the mechanistic underpinnings for both normal and abnormal implantation and placentation and could eventually provide an entirely novel approach to treating related complications.
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Affiliation(s)
- Shengyu Wu
- Department of Clinical Medicine, Tongji University School of Medicine, Shanghai, China
- Department of Obstetrics, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Han Xie
- Department of Obstetrics, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yao Su
- Department of Clinical Medicine, Tongji University School of Medicine, Shanghai, China
- Department of Obstetrics, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xinrui Jia
- Department of Clinical Medicine, Tongji University School of Medicine, Shanghai, China
- Department of Obstetrics, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yabing Mi
- Department of Clinical Medicine, Tongji University School of Medicine, Shanghai, China
- Department of Obstetrics, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yuanhui Jia
- Clinical and Translational Research Center, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Hao Ying
- Department of Obstetrics, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
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5
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Sun RX, Zuo MQ, Zhang JS, Dong MQ. Charge-State-Dependent Collision-Induced Dissociation Behaviors of RNA Oligonucleotides via High-Resolution Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023. [PMID: 37463304 DOI: 10.1021/jasms.3c00073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Mass spectrometry (MS)-based analysis of RNA oligonucleotides (oligos) plays an increasingly important role in the development of RNA therapeutics and epitranscriptomics research. However, MS fragmentation behaviors of RNA oligomers are understood insufficiently. Herein, we characterized the negative-ion-mode fragmentation behaviors of 26 synthetic RNA oligos containing four to eight nucleotides using collision-induced dissociation (CID) on a high-resolution, accurate-mass instrument. We found that in CID spectra acquired under the normalized collision energy (NCE) of 35%, approximately 70% of the total peak intensity was attributed to sequencing ions (a-B, a, b, c, d, w, x, y, z), around 25% of the peak intensity came from precursor ions that experienced complete or partial loss of a nucleobase in the form of either a neutral or an anion, and the remainder were internal ions and anionic nucleobases. The top five sequencing ions were the y, c, w, a-B, and a ions. Furthermore, we observed that CID fragmentation behaviors of RNA oligos were significantly impacted by their precursor charge. Specifically, when the precursors had a charge from 1- to 5-, the fractional intensity of sequencing ions decreased, while that of precursors that underwent either neutral or charged losses of a nucleobase increased. Additionally, we found that RNA oligos containing 3'-U tended to produce precursors with HNCO and/or NCO- losses, which presumably corresponded to isocyanic acid and cyanate anion, respectively. These findings provide valuable insights for better comprehending the mechanism behind RNA fragmentation by MS/MS, thereby facilitating the future automated identification of RNA oligos based on their CID spectra in a more efficient manner.
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Affiliation(s)
- Rui-Xiang Sun
- National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084, China
| | - Mei-Qing Zuo
- National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084, China
| | - Ji-Shuai Zhang
- National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084, China
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6
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Chen YN, Shen XY, Yu Y, Xue CY, Zhou YL, Zhang XX. In-source fragmentation of nucleosides in electrospray ionization towards more sensitive and accurate nucleoside analysis. Analyst 2023; 148:1500-1506. [PMID: 36883656 DOI: 10.1039/d3an00047h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Nucleosides have been found to suffer in-source fragmentation (ISF) in electrospray ionization mass spectrometry, which leads to reduced sensitivity and ambiguous identification. In this work, a combination of theoretical calculations and nuclear magnetic resonance analysis revealed the key role of protonation at N3 near the glycosidic bond during ISF. Therefore, an ultrasensitive liquid chromatography-tandem mass spectrometry system for 5-formylcytosine detection was developed with 300 fold signal enhancement. Also, we established a MS1-only platform for nucleoside profiling and successfully identified sixteen nucleosides in the total RNA of MCF-7 cells. Taking ISF into account, we can realize analysis with higher sensitivity and less ambiguity, not only for nucleosides, but for other molecules with similar protonation and fragmentation behaviors.
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Affiliation(s)
- Yu-Nan Chen
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
| | - Xu-Yang Shen
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
| | - Yue Yu
- Institute of Biotechnology Development, Qilu Pharmaceutical, Jinan, China
| | - Chen-Yu Xue
- Key Laboratory of Forensic Toxicology, Ministry of Public Security, Beijing, China
| | - Ying-Lin Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
| | - Xin-Xiang Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
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7
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Ye Y, Liu M, Wu F, Ou S, Wang W, Fei J, Xie F, Bai L. TRMT6 promotes hepatocellular carcinoma progression through the PI3K/AKT signaling pathway. Eur J Med Res 2023; 28:48. [PMID: 36707905 PMCID: PMC9881333 DOI: 10.1186/s40001-022-00951-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 12/14/2022] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma is one of the most common and deadly cancers. The aim of this study was to elucidate the role of tRNA methyltransferase 6 (TRMT6) during HCC progression. METHODS The role of TRMT6 in the progression and prognosis of HCC was confirmed by analysis of online databases and clinical human samples. The effects of up-regulation or down-regulation of TRMT6 on HCC cell proliferation and PI3K/AKT pathway-related protein expressions were verified. The molecular mechanism was investigated in vivo by constructing subcutaneous xenograft tumor model. RESULTS TRMT6 was overexpressed in HCC tissues and associated with Tumour-Node-Metastasis (TNM) stage, primary tumor (T) and regional lymph node (N) classification. TRMT6 expressions in HCC cell lines were higher than that in normal liver cell. TRMT6 overexpression can promote HCC cell proliferation, increase the number of S phase cells. Interference with TRMT6 reduced the PI3K/AKT pathway-related protein expressions, and was reversed by the addition of IGF1. Interference with TRMT6 inhibited tumor growth in vivo and was related to PI3K/AKT pathway. CONCLUSIONS Overexpression of TRMT6 promote HCC cell proliferation in vivo and in vitro through PI3K/AKT/mTOR axis, which provides a potential choice for the treatment of HCC in clinical practice.
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Affiliation(s)
- Yanqing Ye
- grid.284723.80000 0000 8877 7471Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Avenue, Guangzhou, 510515 Guangdong People’s Republic of China ,grid.452437.3Department of Gastroenterology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000 Jiangxi People’s Republic of China
| | - Maosheng Liu
- grid.452437.3Department of Gastroenterology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000 Jiangxi People’s Republic of China
| | - Fengfei Wu
- grid.284723.80000 0000 8877 7471Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Avenue, Guangzhou, 510515 Guangdong People’s Republic of China
| | - Shiyu Ou
- grid.460075.0Department of Gastroenterology, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, 545005 Guangxi People’s Republic of China
| | - Weidong Wang
- grid.284723.80000 0000 8877 7471Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Avenue, Guangzhou, 510515 Guangdong People’s Republic of China
| | - Jieying Fei
- grid.284723.80000 0000 8877 7471Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Avenue, Guangzhou, 510515 Guangdong People’s Republic of China
| | - Fang Xie
- grid.284723.80000 0000 8877 7471Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Avenue, Guangzhou, 510515 Guangdong People’s Republic of China
| | - Lan Bai
- grid.284723.80000 0000 8877 7471Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Avenue, Guangzhou, 510515 Guangdong People’s Republic of China
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8
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Cooke MS, Chang YJ, Chen YR, Hu CW, Chao MR. Nucleic acid adductomics - The next generation of adductomics towards assessing environmental health risks. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:159192. [PMID: 36195140 DOI: 10.1016/j.scitotenv.2022.159192] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 09/07/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
This Discussion article aims to explore the potential for a new generation of assay to emerge from cellular and urinary DNA adductomics which brings together DNA-RNA- and, to some extent, protein adductomics, to better understand the role of the exposome in environmental health. Components of the exposome have been linked to an increased risk of various, major diseases, and to identify the precise nature, and size, of risk, in this complex mixture of exposures, powerful tools are needed. Modification of nucleic acids (NA) is a key consequence of environmental exposures, and a goal of cellular DNA adductomics is to evaluate the totality of DNA modifications in the genome, on the basis that this will be most informative. Consequently, an approach which encompasses modifications of all nucleic acids (NA) would be potentially yet more informative. This article focuses on NA adductomics, which brings together the assessment of both DNA and RNA modifications, including modified (2'-deoxy)ribonucleosides (2'-dN/rN), modified nucleobases (nB), plus: DNA-DNA, RNA-RNA, DNA-RNA, DNA-protein, and RNA-protein crosslinks (DDCL, RRCL, DRCL, DPCL, and RPCL, respectively). We discuss the need for NA adductomics, plus the pros and cons of cellular vs. urinary NA adductomics, and present some evidence for the feasibility of this approach. We propose that NA adductomics provides a more comprehensive approach to the study of nucleic acid modifications, which will facilitate a range of advances, including the identification of novel, unexpected modifications e.g., RNA-RNA, and DNA-RNA crosslinks; key modifications associated with mutagenesis; agent-specific mechanisms; and adductome signatures of key environmental agents, leading to the dissection of the exposome, and its role in human health/disease, across the life course.
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Affiliation(s)
- Marcus S Cooke
- Oxidative Stress Group, Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, USA.
| | - Yuan-Jhe Chang
- Department of Occupational Safety and Health, Chung Shan Medical University, Taichung 402, Taiwan
| | - Yet-Ran Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chiung-Wen Hu
- Department of Public Health, Chung Shan Medical University, Taichung 402, Taiwan.
| | - Mu-Rong Chao
- Department of Occupational Safety and Health, Chung Shan Medical University, Taichung 402, Taiwan; Department of Occupational Medicine, Chung Shan Medical University Hospital, Taichung 402, Taiwan.
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Takahashi H, Hase H, Yoshida T, Tashiro J, Hirade Y, Kitae K, Tsujikawa K. Discovery of two novel ALKBH5 selective inhibitors that exhibit uncompetitive or competitive type and suppress the growth activity of glioblastoma multiforme. Chem Biol Drug Des 2022; 100:1-12. [PMID: 35384315 DOI: 10.1111/cbdd.14051] [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] [Received: 11/25/2021] [Revised: 02/20/2022] [Accepted: 03/26/2022] [Indexed: 12/12/2022]
Abstract
A group of RNA methylation enzymes is currently of interest as a new target for cancer therapy. Alpha-ketoglutarate-dependent dioxygenase B (AlkB) homolog 5 (ALKBH5) is an N6 -methyladenosine (m6 A) demethylation enzyme, and by high-throughput screening from pure small molecule compounds, we identified two novel inhibitors, Ena15 and Ena21, against it. Each compound showed either uncompetitive or competitive inhibition for 2-oxoglutarate (2OG). In addition, Ena21 had little inhibitory activity for fat mass and obesity-associated protein (FTO), which is another N6 -methyladenosine demethylation enzyme, while Ena15 enhanced the demethylase activity of FTO. The predicted binding poses of both compounds with the crystal structure of ALKBH5 (PDB ID: 4NRO) were comparable with these observations pertaining to the interaction of the 2OG catalytic site in this enzyme kinetics. Furthermore, either knockdown of ALKBH5 or inhibition with Ena15 or Ena21 inhibited cell proliferation of glioblastoma multiforme-derived cell lines, decreased cell population in the synthesis phase of the cell cycle, increased m6 A RNA level, and stabilized FOXM1 mRNA. Based on these results, Ena15 and Ena21 were found to be potential candidates that might help in further research into the biological function of ALKBH5.
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Affiliation(s)
- Hikaru Takahashi
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Hiroaki Hase
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Takuya Yoshida
- Laboratory of Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Junki Tashiro
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Yoshihiro Hirade
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Kaori Kitae
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Kazutake Tsujikawa
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
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10
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Sun X, Wu W, Yang Y, Wilson I, Shao F, Qiu D. Genome-Wide Identification of m6A Writers, Erasers and Readers in Poplar 84K. Genes (Basel) 2022; 13:genes13061018. [PMID: 35741780 PMCID: PMC9223284 DOI: 10.3390/genes13061018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/28/2022] [Accepted: 05/31/2022] [Indexed: 11/16/2022] Open
Abstract
N6-methyladenosine (m6A) RNA modification is a conserved mechanism to regulate gene expression that plays vital roles in the development of plants. However, the m6A RNA modification in forest trees remains limited. Here, we performed a complete analysis of m6A writers, erasers and readers in Poplar 84K, including gene location, gene structures, conserved motifs, phylogenetic relationships, promoter analysis, expression profiles and the homology modeling. We have identified 61 m6A pathway genes in Poplar 84K (Populus alba × Populus glandulosa), including 14 m6A writers, 14 m6A erasers and 33 m6A readers. Phylogenetic analysis indicated that the m6A writers and erasers were clustered into four groups and m6A readers were clustered into two groups. Promoter analysis showed that m6A pathway genes were mainly responsive to low oxygen followed by ABA and ethylene. The expression of the identified m6A pathway genes showed tissue-specific expression patterns in leaves, xylem, phloem and roots. Moreover, 17 genes were significantly up-regulated and 13 genes were significantly down-regulated in poplar overexpressing the transcription factor LBD15. Homology modeling and molecular docking results suggested that PagFIP37b was most likely to be regulated by LBD15, and the qPCRshowed that PagFIP37b were up-regulated in the LBD15-oe plants. The results provide insights that aid in the future elucidation of the functions of these m6A pathway genes and the epigenetic regulation mechanism of these genes in Poplar 84K.
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Affiliation(s)
- Xiaochen Sun
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (X.S.); (W.W.); (Y.Y.); (D.Q.)
| | - Wenli Wu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (X.S.); (W.W.); (Y.Y.); (D.Q.)
| | - Yanfang Yang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (X.S.); (W.W.); (Y.Y.); (D.Q.)
| | - Iain Wilson
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia;
| | - Fenjuan Shao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (X.S.); (W.W.); (Y.Y.); (D.Q.)
- Correspondence: ; Tel.: +86-10-62889641; Fax: +86-10-62872015
| | - Deyou Qiu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (X.S.); (W.W.); (Y.Y.); (D.Q.)
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11
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“Superwobbling” and tRNA-34 Wobble and tRNA-37 Anticodon Loop Modifications in Evolution and Devolution of the Genetic Code. Life (Basel) 2022; 12:life12020252. [PMID: 35207539 PMCID: PMC8879553 DOI: 10.3390/life12020252] [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: 01/19/2022] [Revised: 01/25/2022] [Accepted: 02/01/2022] [Indexed: 11/17/2022] Open
Abstract
The genetic code evolved around the reading of the tRNA anticodon on the primitive ribosome, and tRNA-34 wobble and tRNA-37 modifications coevolved with the code. We posit that EF-Tu, the closing mechanism of the 30S ribosomal subunit, methylation of wobble U34 at the 5-carbon and suppression of wobbling at the tRNA-36 position were partly redundant and overlapping functions that coevolved to establish the code. The genetic code devolved in evolution of mitochondria to reduce the size of the tRNAome (all of the tRNAs of an organism or organelle). “Superwobbling” or four-way wobbling describes a major mechanism for shrinking the mitochondrial tRNAome. In superwobbling, unmodified wobble tRNA-U34 can recognize all four codon wobble bases (A, G, C and U), allowing a single unmodified tRNA-U34 to read a 4-codon box. During code evolution, to suppress superwobbling in 2-codon sectors, U34 modification by methylation at the 5-carbon position appears essential. As expected, at the base of code evolution, tRNA-37 modifications mostly related to the identity of the adjacent tRNA-36 base. TRNA-37 modifications help maintain the translation frame during elongation.
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12
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Biedenbänder T, de Jesus V, Schmidt-Dengler M, Helm M, Corzilius B, Fürtig B. RNA modifications stabilize the tertiary structure of tRNAfMet by locally increasing conformational dynamics. Nucleic Acids Res 2022; 50:2334-2349. [PMID: 35137185 PMCID: PMC8887418 DOI: 10.1093/nar/gkac040] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/29/2021] [Accepted: 01/14/2022] [Indexed: 11/12/2022] Open
Abstract
A plethora of modified nucleotides extends the chemical and conformational space for natural occurring RNAs. tRNAs constitute the class of RNAs with the highest modification rate. The extensive modification modulates their overall stability, the fidelity and efficiency of translation. However, the impact of nucleotide modifications on the local structural dynamics is not well characterized. Here we show that the incorporation of the modified nucleotides in tRNAfMet from Escherichia coli leads to an increase in the local conformational dynamics, ultimately resulting in the stabilization of the overall tertiary structure. Through analysis of the local dynamics by NMR spectroscopic methods we find that, although the overall thermal stability of the tRNA is higher for the modified molecule, the conformational fluctuations on the local level are increased in comparison to an unmodified tRNA. In consequence, the melting of individual base pairs in the unmodified tRNA is determined by high entropic penalties compared to the modified. Further, we find that the modifications lead to a stabilization of long-range interactions harmonizing the stability of the tRNA's secondary and tertiary structure. Our results demonstrate that the increase in chemical space through introduction of modifications enables the population of otherwise inaccessible conformational substates.
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Affiliation(s)
- Thomas Biedenbänder
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, Frankfurt am Main 60438, Germany.,Institute of Chemistry and Department Life, Light & Matter, University of Rostock, Rostock 18059, Germany
| | - Vanessa de Jesus
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, Frankfurt am Main 60438, Germany
| | - Martina Schmidt-Dengler
- Institut für pharmazeutische und biomedizinische Wissenschaften (IPBW), Johannes Gutenberg-Universität, Mainz 55128, Germany
| | - Mark Helm
- Institut für pharmazeutische und biomedizinische Wissenschaften (IPBW), Johannes Gutenberg-Universität, Mainz 55128, Germany
| | - Björn Corzilius
- Institute of Chemistry and Department Life, Light & Matter, University of Rostock, Rostock 18059, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, Frankfurt am Main 60438, Germany
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13
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Leptidis S, Papakonstantinou E, Diakou KI, Pierouli K, Mitsis T, Dragoumani K, Bacopoulou F, Sanoudou D, Chrousos GP, Vlachakis D. Epitranscriptomics of cardiovascular diseases (Review). Int J Mol Med 2022; 49:9. [PMID: 34791505 PMCID: PMC8651226 DOI: 10.3892/ijmm.2021.5064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/20/2021] [Indexed: 11/09/2022] Open
Abstract
RNA modifications have recently become the focus of attention due to their extensive regulatory effects in a vast array of cellular networks and signaling pathways. Just as epigenetics is responsible for the imprinting of environmental conditions on a genetic level, epitranscriptomics follows the same principle at the RNA level, but in a more dynamic and sensitive manner. Nevertheless, its impact in the field of cardiovascular disease (CVD) remains largely unexplored. CVD and its associated pathologies remain the leading cause of death in Western populations due to the limited regenerative capacity of the heart. As such, maintenance of cardiac homeostasis is paramount for its physiological function and its capacity to respond to environmental stimuli. In this context, epitranscriptomic modifications offer a novel and promising therapeutic avenue, based on the fine‑tuning of regulatory cascades, necessary for cardiac function. This review aimed to provide an overview of the most recent findings of key epitranscriptomic modifications in both coding and non‑coding RNAs. Additionally, the methods used for their detection and important associations with genetic variations in the context of CVD were summarized. Current knowledge on cardiac epitranscriptomics, albeit limited still, indicates that the impact of epitranscriptomic editing in the heart, in both physiological and pathological conditions, holds untapped potential for the development of novel targeted therapeutic approaches in a dynamic manner.
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Affiliation(s)
- Stefanos Leptidis
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Eleni Papakonstantinou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Kalliopi Io Diakou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Katerina Pierouli
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Thanasis Mitsis
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Konstantina Dragoumani
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Flora Bacopoulou
- Laboratory of Molecular Endocrinology, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
- First Department of Pediatrics, Center for Adolescent Medicine and UNESCO Chair on Adolescent Health Care, Medical School, Aghia Sophia Children's Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Despina Sanoudou
- Fourth Department of Internal Medicine, Clinical Genomics and Pharmacogenomics Unit, Medical School, 'Attikon' Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
- Molecular Biology Division, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
- Center for New Biotechnologies and Precision Medicine, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - George P. Chrousos
- Laboratory of Molecular Endocrinology, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
- First Department of Pediatrics, Center for Adolescent Medicine and UNESCO Chair on Adolescent Health Care, Medical School, Aghia Sophia Children's Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Dimitrios Vlachakis
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
- Laboratory of Molecular Endocrinology, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
- First Department of Pediatrics, Center for Adolescent Medicine and UNESCO Chair on Adolescent Health Care, Medical School, Aghia Sophia Children's Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
- School of Informatics, Faculty of Natural and Mathematical Sciences, King's College London, London WC2R 2LS, UK
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14
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Single-molecule RNA sequencing for simultaneous detection of m6A and 5mC. Sci Rep 2021; 11:19304. [PMID: 34588546 PMCID: PMC8481274 DOI: 10.1038/s41598-021-98805-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 09/15/2021] [Indexed: 11/09/2022] Open
Abstract
Epitranscriptomics is the study of RNA base modifications involving functionally relevant changes to the transcriptome. In recent years, epitranscriptomics has been an active area of research. However, a major issue has been the development of sequencing methods to map transcriptome-wide RNA base modifications. We have proposed a single-molecule quantum sequencer for mapping RNA base modifications in microRNAs (miRNAs), such as N6-methyladenosine (m6A) or 5-methylcytidine (5mC), which are related to cancer cell propagation and suppression. Here, we investigated 5mC and m6A in hsa-miR-200c-5p extracted from colorectal cancer cells and determined their methylation sites and rates; the data were comparable to those determined by mass spectrometry. Furthermore, we evaluated the methylation ratio of cytidine and adenosine at each site in the sequences and its relationship. These results suggest that the methylation ratio of cytidine and adenosine is facilitated by the presence of vicinal methylation. Our work provides a robust new tool for sequencing various types of RNA base modifications in their RNA context.
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15
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Liu X, Wang H, Liu B, Qi Z, Li J, Xu B, Liu W, Xu Z, Deng Y. The Latest Research Progress of m 6A Modification and Its Writers, Erasers, Readers in Infertility: A Review. Front Cell Dev Biol 2021; 9:681238. [PMID: 34568313 PMCID: PMC8461070 DOI: 10.3389/fcell.2021.681238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 07/06/2021] [Indexed: 01/22/2023] Open
Abstract
Eukaryotic messenger mRNAs contain many RNA methyl chemical modifications, in which N6-methyladenosine (m6A) plays a very important role. The modification process of RNA methylation is a dynamic reversible regulatory process that is mainly catalyzed by "Writer" m6A methyltransferase, removed by "Eraser" m6A demethylase, and recognized by the m6A binding protein, thereby, linking m6A modification with other mRNA pathways. At various stages of the life cycle, m6A modification plays an extremely important role in regulating mRNA splicing, processing, translation, as well as degradation, and is associated with gametogenesis and fertility for both sexes. Normal gametogenesis is a basic guarantee of fertility. Infertility leads to trauma, affects harmony in the family and seriously affects the quality of life. We review the roles and mechanisms of RNA m6A methylation modification in infertility and provide a potential target for infertility treatment, which can be used for drug development.
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Affiliation(s)
- Xuda Liu
- Department of Public Health, China Medical University, Shenyang, China
| | - Haiying Wang
- Department of Public Health, China Medical University, Shenyang, China
| | - Bingchen Liu
- Department of Public Health, China Medical University, Shenyang, China
| | - Zhipeng Qi
- Department of Public Health, China Medical University, Shenyang, China
| | - Jiashuo Li
- Department of Public Health, China Medical University, Shenyang, China
| | - Bin Xu
- Department of Public Health, China Medical University, Shenyang, China
| | - Wei Liu
- Department of Public Health, China Medical University, Shenyang, China
| | - Zhaofa Xu
- Department of Public Health, China Medical University, Shenyang, China
| | - Yu Deng
- Department of Public Health, China Medical University, Shenyang, China
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16
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Tavares JF, Davis NK, Poim A, Reis A, Kellner S, Sousa I, Soares AR, Moura GMR, Dedon PC, Santos M. tRNA-modifying enzyme mutations induce codon-specific mistranslation and protein aggregation in yeast. RNA Biol 2021; 18:563-575. [PMID: 32893724 PMCID: PMC7971265 DOI: 10.1080/15476286.2020.1819671] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 01/28/2023] Open
Abstract
Protein synthesis rate and accuracy are tightly controlled by the cell and are essential for proteome homoeostasis (proteostasis); however, the full picture of how mRNA translational factors maintain protein synthesis accuracy and co-translational protein folding are far from being fully understood. To address this question, we evaluated the role of 70 yeast tRNA-modifying enzyme genes on protein aggregation and used mass spectrometry to identify the aggregated proteins. We show that modification of uridine at anticodon position 34 (U34) by the tRNA-modifying enzymes Elp1, Elp3, Sml3 and Trm9 is critical for proteostasis, the mitochondrial tRNA-modifying enzyme Slm3 plays a fundamental role in general proteostasis and that stress response proteins whose genes are enriched in codons decoded by tRNAs lacking mcm5U34, mcm5s2U34, ncm5U34, ncm5Um34, modifications are overrepresented in protein aggregates of the ELP1, SLM3 and TRM9 KO strains. Increased rates of amino acid misincorporation were also detected in these strains at protein sites that specifically mapped to the codons sites that are decoded by the hypomodified tRNAs, demonstrating that U34 tRNA modifications safeguard the proteome from translational errors, protein misfolding and proteotoxic stress.
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Affiliation(s)
- Joana F Tavares
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
| | - Nick K. Davis
- Department of Biological Engineering, Massachusetts Institute of Technology – MIT, Cambridge, US
| | - Ana Poim
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
| | - Andreia Reis
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
| | - Stefanie Kellner
- Department of Biological Engineering, Massachusetts Institute of Technology – MIT, Cambridge, US
| | - Inês Sousa
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
| | - Ana R. Soares
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
| | - Gabriela M R Moura
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
| | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology – MIT, Cambridge, US
- Singapore-MIT Alliance for Research and Technology, Campus for Research Excellence and Technical Enterprise – CREATE, Singapore
| | - Manuel Santos
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
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17
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Kösters M, Leufken J, Leidel SA. SMITER-A Python Library for the Simulation of LC-MS/MS Experiments. Genes (Basel) 2021; 12:396. [PMID: 33799543 PMCID: PMC8000309 DOI: 10.3390/genes12030396] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/05/2021] [Accepted: 03/08/2021] [Indexed: 12/24/2022] Open
Abstract
SMITER (Synthetic mzML writer) is a Python-based command-line tool designed to simulate liquid-chromatography-coupled tandem mass spectrometry LC-MS/MS runs. It enables the simulation of any biomolecule amenable to mass spectrometry (MS) since all calculations are based on chemical formulas. SMITER features a modular design, allowing for an easy implementation of different noise and fragmentation models. By default, SMITER uses an established noise model and offers several methods for peptide fragmentation, and two models for nucleoside fragmentation and one for lipid fragmentation. Due to the rich Python ecosystem, other modules, e.g., for retention time (RT) prediction, can easily be implemented for the tailored simulation of any molecule of choice. This facilitates the generation of defined gold-standard LC-MS/MS datasets for any type of experiment. Such gold standards, where the ground truth is known, are required in computational mass spectrometry to test new algorithms and to improve parameters of existing ones. Similarly, gold-standard datasets can be used to evaluate analytical challenges, e.g., by predicting co-elution and co-fragmentation of molecules. As these challenges hinder the detection or quantification of co-eluents, a comprehensive simulation can identify and thus, prevent such difficulties before performing actual MS experiments. SMITER allows the creation of such datasets easily, fast, and efficiently.
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Affiliation(s)
| | | | - Sebastian A. Leidel
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences (DCBP), University of Bern, Freiestrasse 3, 3012 Bern, Switzerland; (M.K.); (J.L.)
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18
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Schwark DG, Schmitt MA, Biddle W, Fisk JD. The Influence of Competing tRNA Abundance on Translation: Quantifying the Efficiency of Sense Codon Reassignment at Rarely Used Codons. Chembiochem 2020; 21:2274-2286. [PMID: 32203635 DOI: 10.1002/cbic.202000052] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/12/2020] [Indexed: 11/07/2022]
Abstract
A quantitative understanding of how system composition and molecular properties conspire to determine the fidelity of translation is lacking. Our strategy directs an orthogonal tRNA to directly compete against endogenous tRNAs to decode individual targeted codons in a GFP reporter. Sets of directed sense codon reassignment measurements allow the isolation of particular factors contributing to translational fidelity. In this work, we isolated the effect of tRNA concentration on translational fidelity by evaluating reassignment of the 15 least commonly employed E. coli sense codons. Eight of the rarely used codons are reassigned with greater than 20 % efficiency. Both tRNA abundance and codon demand moderately inversely correlate with reassignment efficiency. Furthermore, the reassignment of rarely used codons does not appear to confer a fitness advantage relative to reassignment of other codons. These direct competition experiments also map potential targets for genetic code expansion. The isoleucine AUA codon is particularly attractive for the incorporation of noncanonical amino acids, with a nonoptimized reassignment efficiency of nearly 70 %.
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Affiliation(s)
- David G Schwark
- Department of Chemistry, University of Colorado Denver Campus Box 194, P.O. Box 173364, Denver, CO 80217-3364, USA
| | - Margaret A Schmitt
- Department of Chemistry, University of Colorado Denver Campus Box 194, P.O. Box 173364, Denver, CO 80217-3364, USA
| | - Wil Biddle
- Department of Chemistry, University of Colorado Denver Campus Box 194, P.O. Box 173364, Denver, CO 80217-3364, USA
| | - John D Fisk
- Department of Chemistry, University of Colorado Denver Campus Box 194, P.O. Box 173364, Denver, CO 80217-3364, USA
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19
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Challenges in Analysis of Hydrophilic Metabolites Using Chromatography Coupled with Mass Spectrometry. JOURNAL OF ANALYSIS AND TESTING 2020. [DOI: 10.1007/s41664-020-00126-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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20
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Leonardi A, Evke S, Lee M, Melendez JA, Begley TJ. Epitranscriptomic systems regulate the translation of reactive oxygen species detoxifying and disease linked selenoproteins. Free Radic Biol Med 2019; 143:573-593. [PMID: 31476365 PMCID: PMC7650020 DOI: 10.1016/j.freeradbiomed.2019.08.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/28/2019] [Accepted: 08/29/2019] [Indexed: 02/07/2023]
Abstract
Here we highlight the role of epitranscriptomic systems in post-transcriptional regulation, with a specific focus on RNA modifying writers required for the incorporation of the 21st amino acid selenocysteine during translation, and the pathologies linked to epitranscriptomic and selenoprotein defects. Epitranscriptomic marks in the form of enzyme-catalyzed modifications to RNA have been shown to be important signals regulating translation, with defects linked to altered development, intellectual impairment, and cancer. Modifications to rRNA, mRNA and tRNA can affect their structure and function, while the levels of these dynamic tRNA-specific epitranscriptomic marks are stress-regulated to control translation. The tRNA for selenocysteine contains five distinct epitranscriptomic marks and the ALKBH8 writer for the wobble uridine (U) has been shown to be vital for the translation of the glutathione peroxidase (GPX) and thioredoxin reductase (TRXR) family of selenoproteins. The reactive oxygen species (ROS) detoxifying selenocysteine containing proteins are a prime examples of how specialized translation can be regulated by specific tRNA modifications working in conjunction with distinct codon usage patterns, RNA binding proteins and specific 3' untranslated region (UTR) signals. We highlight the important role of selenoproteins in detoxifying ROS and provide details on how epitranscriptomic marks and selenoproteins can play key roles in and maintaining mitochondrial function and preventing disease.
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Affiliation(s)
- Andrea Leonardi
- Colleges of Nanoscale Science and Engineering, University at Albany, State University of New York, Albany, NY, USA
| | - Sara Evke
- Colleges of Nanoscale Science and Engineering, State University of New York Polytechnic Institute, Albany, NY, USA
| | - May Lee
- Colleges of Nanoscale Science and Engineering, State University of New York Polytechnic Institute, Albany, NY, USA
| | - J Andres Melendez
- Colleges of Nanoscale Science and Engineering, State University of New York Polytechnic Institute, Albany, NY, USA.
| | - Thomas J Begley
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA; RNA Institute, University at Albany, State University of New York, Albany, NY, USA.
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21
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He CC, Hamlow LA, Zhu Y, Nei YW, Fan L, McNary CP, Maître P, Steinmetz V, Schindler B, Compagnon I, Armentrout PB, Rodgers MT. Structural and Energetic Effects of O2'-Ribose Methylation of Protonated Pyrimidine Nucleosides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2318-2334. [PMID: 31435890 DOI: 10.1007/s13361-019-02300-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/18/2019] [Accepted: 07/23/2019] [Indexed: 06/10/2023]
Abstract
The 2'-substituents distinguish DNA from RNA nucleosides. 2'-O-methylation occurs naturally in RNA and plays important roles in biological processes. Such 2'-modifications may alter the hydrogen-bonding interactions of the nucleoside and thus may affect the conformations of the nucleoside in an RNA chain. Structures of the protonated 2'-O-methylated pyrimidine nucleosides were examined by infrared multiple photon dissociation (IRMPD) action spectroscopy, assisted by electronic structure calculations. The glycosidic bond stabilities of the protonated 2'-O-methylated pyrimidine nucleosides, [Nuom+H]+, were also examined and compared to their DNA and RNA nucleoside analogues via energy-resolved collision-induced dissociation (ER-CID). The preferred sites of protonation of the 2'-O-methylated pyrimidine nucleosides parallel their canonical DNA and RNA nucleoside analogues, [dNuo+H]+ and [Nuo+H]+, yet their nucleobase orientation and sugar puckering differ. The glycosidic bond stabilities of the protonated pyrimidine nucleosides follow the order: [dNuo+H]+ < [Nuo+H]+ < [Nuom+H]+. The slightly altered structures help explain the stabilization induced by 2'-O-methylation of the pyrimidine nucleosides.
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Affiliation(s)
- C C He
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - L A Hamlow
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - Y Zhu
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - Y-W Nei
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - L Fan
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - C P McNary
- Department of Chemistry, University of Utah, Salt Lake City, UT, 84112, USA
| | - P Maître
- Laboratoire de Chimie Physique (UMR8000), Université Paris-Sud, CNRS, Université Paris Saclay, 91405, Orsay, France
| | - V Steinmetz
- Laboratoire de Chimie Physique (UMR8000), Université Paris-Sud, CNRS, Université Paris Saclay, 91405, Orsay, France
| | - B Schindler
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Villeurbanne, France
| | - I Compagnon
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Villeurbanne, France
| | - P B Armentrout
- Department of Chemistry, University of Utah, Salt Lake City, UT, 84112, USA
| | - M T Rodgers
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA.
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22
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Mosca P, Leheup B, Dreumont N. Nutrigenomics and RNA methylation: Role of micronutrients. Biochimie 2019; 164:53-59. [DOI: 10.1016/j.biochi.2019.07.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 07/06/2019] [Indexed: 12/24/2022]
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23
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Jin X, Lv Z, Gao J, Zhang R, Zheng T, Yin P, Li D, Peng L, Cao X, Qin Y, Persson S, Zheng B, Chen P. AtTrm5a catalyses 1-methylguanosine and 1-methylinosine formation on tRNAs and is important for vegetative and reproductive growth in Arabidopsis thaliana. Nucleic Acids Res 2019; 47:883-898. [PMID: 30508117 PMCID: PMC6344853 DOI: 10.1093/nar/gky1205] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 11/20/2018] [Indexed: 12/21/2022] Open
Abstract
Modified nucleosides on tRNA are critical for decoding processes and protein translation. tRNAs can be modified through 1-methylguanosine (m1G) on position 37; a function mediated by Trm5 homologs. We show that AtTRM5a (At3g56120) is a Trm5 ortholog in Arabidopsis thaliana. AtTrm5a is localized to the nucleus and its function for m1G and m1I methylation was confirmed by mutant analysis, yeast complementation, m1G nucleoside level on single tRNA, and tRNA in vitro methylation. Arabidopsis attrm5a mutants were dwarfed and had short filaments, which led to reduced seed setting. Proteomics data indicated differences in the abundance of proteins involved in photosynthesis, ribosome biogenesis, oxidative phosphorylation and calcium signalling. Levels of phytohormone auxin and jasmonate were reduced in attrm5a mutant, as well as expression levels of genes involved in flowering, shoot apex cell fate determination, and hormone synthesis and signalling. Taken together, loss-of-function of AtTrm5a impaired m1G and m1I methylation and led to aberrant protein translation, disturbed hormone homeostasis and developmental defects in Arabidopsis plants.
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Affiliation(s)
- Xiaohuan Jin
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China.,Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
| | - Zhengyi Lv
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China.,Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
| | - Junbao Gao
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China.,Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
| | - Rui Zhang
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China.,Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
| | - Ting Zheng
- College of Life Science, HuaZhong Agricultural University, Wuhan 430070, China.,National Key Laboratory of Crop Genetic Improvement, HuaZhong Agricultural University, Wuhan 430070, China
| | - Ping Yin
- College of Life Science, HuaZhong Agricultural University, Wuhan 430070, China.,National Key Laboratory of Crop Genetic Improvement, HuaZhong Agricultural University, Wuhan 430070, China
| | - Dongqin Li
- National Key Laboratory of Crop Genetic Improvement, HuaZhong Agricultural University, Wuhan 430070, China
| | - Liangcai Peng
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China.,Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
| | - Xintao Cao
- Institute of Biophysics, Chinese Academy of Sciences, China
| | - Yan Qin
- Institute of Biophysics, Chinese Academy of Sciences, China
| | - Staffan Persson
- School of Biosciences, University of Melbourne, Parkville 3010, VIC, Australia.,Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bo Zheng
- College of Horticulture and Forestry Sciences, HuaZhong Agricultural University, Wuhan 430070, China
| | - Peng Chen
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China.,Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
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24
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Bhat A, Chakraborty R, Adlakha K, Agam G, Chakraborty K, Sengupta S. Ncl1-mediated metabolic rewiring critical during metabolic stress. Life Sci Alliance 2019; 2:2/4/e201900360. [PMID: 31416893 PMCID: PMC6696984 DOI: 10.26508/lsa.201900360] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 08/02/2019] [Accepted: 08/05/2019] [Indexed: 11/24/2022] Open
Abstract
Accumulation of cysteine induces translational defects and metabolic rewiring that are abrogated by leucine in a transfer RNA (tRNA) methyltransferase NCL1-dependent manner in yeast. Nutritional limitation has been vastly studied; however, there is limited knowledge of how cells maintain homeostasis in excess nutrients. In this study, using yeast as a model system, we show that some amino acids are toxic at higher concentrations. With cysteine as a physiologically relevant example, we delineated the pathways/processes that are altered and those that are involved in survival in the presence of elevated levels of this amino acid. Using proteomics and metabolomics approach, we found that cysteine up-regulates proteins involved in amino acid metabolism, alters amino acid levels, and inhibits protein translation—events that are rescued by leucine supplementation. Through a comprehensive genetic screen, we show that leucine-mediated effect depends on a transfer RNA methyltransferase (NCL1), absence of which decouples transcription and translation in the cell, inhibits the conversion of leucine to ketoisocaproate, and leads to tricarboxylic acid cycle block. We therefore propose a role of NCL1 in regulating metabolic homeostasis through translational control.
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Affiliation(s)
- Ajay Bhat
- Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Rahul Chakraborty
- Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Khushboo Adlakha
- Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Ganesh Agam
- Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Kausik Chakraborty
- Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, New Delhi, India .,Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Shantanu Sengupta
- Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, New Delhi, India .,Academy of Scientific and Innovative Research, Ghaziabad, India
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25
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Konno M, Taniguchi M, Ishii H. Significant epitranscriptomes in heterogeneous cancer. Cancer Sci 2019; 110:2318-2327. [PMID: 31187550 PMCID: PMC6676114 DOI: 10.1111/cas.14095] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/03/2019] [Accepted: 06/05/2019] [Indexed: 02/06/2023] Open
Abstract
Precision medicine places significant emphasis on techniques for the identification of DNA mutations and gene expression by deep sequencing of gene panels to obtain medical data. However, other diverse information that is not easily readable using bioinformatics, including RNA modifications, has emerged as a novel diagnostic and innovative therapy owing to its multifunctional aspects. It is suggested that this breakthrough innovation might open new avenues for the elucidation of uncharacterized cancer cellular functions to develop more precise medical applications. The functional characteristics and regulatory mechanisms of RNA modifications, ie, the epitranscriptome (ETR), which reflects RNA metabolism, remains unclear, mainly due to detection methods being limited. Recent studies have revealed that N6‐methyl adenosine, the most common modification in mRNA in eukaryotes, is affected in various types of cancer and, in some cases, cancer stem cells, but also affects cellular responses to viral infections. The ETR can control cancer cell fate through mRNA splicing, stability, nuclear export, and translation. Here we report on the recent progress of ETR detection methods, and biological findings regarding the significance of ETR in cancer precision medicine.
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Affiliation(s)
- Masamitsu Konno
- Department of Frontier Science for Cancer and Chemotherapy, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Masateru Taniguchi
- The Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan
| | - Hideshi Ishii
- Department of Medical Data Science, Graduate School of Medicine, Osaka University, Osaka, Japan
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26
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Chawla M, Minenkov Y, Vu KB, Oliva R, Cavallo L. Structural and Energetic Impact of Non-natural 7-Deaza-8-azaguanine, 7-Deaza-8-azaisoguanine, and Their 7-Substituted Derivatives on Hydrogen-Bond Pairing with Cytosine and Isocytosine. Chembiochem 2019; 20:2262-2270. [PMID: 30983115 DOI: 10.1002/cbic.201900245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Indexed: 12/12/2022]
Abstract
The impact of 7-deaza-8-azaguanine (DAG) and 7-deaza-8-azaisoguanine (DAiG) modifications on the geometry and stability of the G:C Watson-Crick (cWW) base pair and the G:iC and iG:C reverse Watson-Crick (tWW) base pairs has been characterized theoretically. In addition, the effect on the same base pairs of seven C7-substituted DAG and DAiG derivatives, some of which have been previously experimentally characterized, has been investigated. Calculations indicate that all of these modifications have a negligible impact on the geometry of the above base pairs, and that modification of the heterocycle skeleton has a small impact on the base-pair interaction energies. Instead, base-pair interaction energies are dependent on the nature of the C7 substituent. For the 7-substituted DAG-C cWW systems, a linear correlation between the base-pair interaction energy and the Hammett constant of the 7-substituent is found, with higher interaction energies corresponding to more electron-withdrawing substituents. Therefore, the explored modifications are expected to be accommodated in both parallel and antiparallel nucleic acid duplexes without perturbing their geometry, while the strength of a base pair (and duplex) featuring a DAG modification can, in principle, be tuned by incorporating different substituents at the C7 position.
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Affiliation(s)
- Mohit Chawla
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal, 23955-6900, Saudi Arabia
| | - Yury Minenkov
- Moscow Institute of Physics and Technology, Institutskiy Pereulok 9, Dolgoprudny, Moscow Region, 141700, Russia
| | - Khanh B Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, 298-300A Nguyen Tat Thanh Street, Ho Chi Minh City, Vietnam
| | - Romina Oliva
- Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, 80143, Naples, Italy
| | - Luigi Cavallo
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal, 23955-6900, Saudi Arabia
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27
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Saha A, Dutta S, Nandi N. Inhibition of seryl tRNA synthetase by seryl nucleoside moiety (SB-217452) of albomycin antibiotic. J Biomol Struct Dyn 2019; 38:2440-2454. [PMID: 31241419 DOI: 10.1080/07391102.2019.1635912] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Amrita Saha
- Department of Chemistry, University of Kalyani, Kalyani, West Bengal, India
| | - Saheb Dutta
- Department of Chemistry, University of Kalyani, Kalyani, West Bengal, India
| | - Nilashis Nandi
- Department of Chemistry, University of Kalyani, Kalyani, West Bengal, India
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28
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Advani VM, Ivanov P. Translational Control under Stress: Reshaping the Translatome. Bioessays 2019; 41:e1900009. [PMID: 31026340 PMCID: PMC6541386 DOI: 10.1002/bies.201900009] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/06/2019] [Indexed: 01/01/2023]
Abstract
Adequate reprogramming of cellular metabolism in response to stresses or suboptimal growth conditions involves a myriad of coordinated changes that serve to promote cell survival. As protein synthesis is an energetically expensive process, its regulation under stress is of critical importance. Reprogramming of messenger RNA (mRNA) translation involves well-understood stress-activated kinases that target components of translation initiation machinery, resulting in the robust inhibition of general translation and promotion of the translation of stress-responsive proteins. Translational arrest of mRNAs also results in the accumulation of transcripts in cytoplasmic foci called stress granules. Recent studies focus on the key roles of transfer RNA (tRNA) in stress-induced translational reprogramming. These include stress-specific regulation of tRNA pools, codon-biased translation influenced by tRNA modifications, tRNA miscoding, and tRNA cleavage. In combination, signal transduction pathways and tRNA metabolism changes regulate translation during stress, resulting in adaptation and cell survival. This review examines molecular mechanisms that regulate protein synthesis in response to stress.
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Affiliation(s)
- Vivek M. Advani
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Pavel Ivanov
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- The Broad Institute of Harvard and M.I.T., Cambridge, Massachusetts, United States of America
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29
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Xie J, de Souza Alves V, von der Haar T, O’Keefe L, Lenchine RV, Jensen KB, Liu R, Coldwell MJ, Wang X, Proud CG. Regulation of the Elongation Phase of Protein Synthesis Enhances Translation Accuracy and Modulates Lifespan. Curr Biol 2019; 29:737-749.e5. [DOI: 10.1016/j.cub.2019.01.029] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 12/12/2018] [Accepted: 01/11/2019] [Indexed: 02/07/2023]
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30
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Slama K, Galliot A, Weichmann F, Hertler J, Feederle R, Meister G, Helm M. Determination of enrichment factors for modified RNA in MeRIP experiments. Methods 2018; 156:102-109. [PMID: 30394295 DOI: 10.1016/j.ymeth.2018.10.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 10/23/2018] [Accepted: 10/24/2018] [Indexed: 11/18/2022] Open
Abstract
In the growing field of RNA modification, precipitation techniques using antibodies play an important role. However, little is known about their specificities and protocols are missing to assess their effectiveness. Here we present a method to assess enrichment factors after MeRIP-type pulldown experiments, here exemplified with a commercial antibody against N6-methyladenosine (m6A). Testing different pulldown and elution conditions, we measure enrichment factors of 4-5 using m6A-containing mRNAs against an unmodified control of identical sequence. Both types of mRNA carry 32P labels at different nucleotides, allowing their relative quantification in a mixture after digestion to nucleotides, separation by TLC and quantitative phosphorimaging of the labels.
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Affiliation(s)
- Kaouthar Slama
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, Germany
| | - Aurellia Galliot
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, Germany
| | - Franziska Weichmann
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Regensburg, Germany
| | - Jasmin Hertler
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, Germany
| | - Regina Feederle
- Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Institute for Diabetes and Obesity, Monoclonal Antibody Core Facility and Research Group, Munich, Germany
| | - Gunter Meister
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Regensburg, Germany
| | - Mark Helm
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, Germany.
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31
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He CC, Hamlow LA, Devereaux ZJ, Zhu Y, Nei YW, Fan L, McNary CP, Maitre P, Steinmetz V, Schindler B, Compagnon I, Armentrout PB, Rodgers MT. Structural and Energetic Effects of O2'-Ribose Methylation of Protonated Purine Nucleosides. J Phys Chem B 2018; 122:9147-9160. [PMID: 30203656 DOI: 10.1021/acs.jpcb.8b07687] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The chemical difference between DNA and RNA nucleosides is their 2'-hydrogen versus 2'-hydroxyl substituents. Modification of the ribosyl moiety at the 2'-position and 2'-O-methylation in particular, is common among natural post-transcriptional modifications of RNA. 2'-Modification may alter the electronic properties and hydrogen-bonding characteristics of the nucleoside and thus may lead to enhanced stabilization or malfunction. The structures and relative glycosidic bond stabilities of the protonated forms of the 2'-O-methylated purine nucleosides, 2'-O-methyladenosine (Adom) and 2'-O-methylguanosine (Guom), were examined using two complementary tandem mass spectrometry approaches, infrared multiple photon dissociation action spectroscopy and energy-resolved collision-induced dissociation. Theoretical calculations were also performed to predict the structures and relative stabilities of stable low-energy conformations of the protonated forms of the 2'-O-methylated purine nucleosides and their infrared spectra in the gas phase. Low-energy conformations highly parallel to those found for the protonated forms of the canonical DNA and RNA purine nucleosides are also found for the protonated 2'-O-methylated purine nucleosides. Importantly, the preferred site of protonation, nucleobase orientation, and sugar puckering are preserved among the DNA, RNA, and 2'-O-methylated variants of the protonated purine nucleosides. The 2'-substituent does however influence hydrogen-bond stabilization as the 2'-O-methyl and 2'-hydroxyl substituents enable a hydrogen-bonding interaction between the 2'- and 3'-substituents, whereas a 2'-hydrogen atom does not. Further, 2'-O-methylation reduces the number of stable low-energy hydrogen-bonded conformations possible and importantly inverts the preferred polarity of this interaction versus that of the RNA analogues. Trends in the CID50% values extracted from survival yield analyses of the 2'-O-methylated and canonical DNA and RNA forms of the protonated purine nucleosides are employed to elucidate their relative glycosidic bond stabilities. The glycosidic bond stability of Adom is found to exceed that of its DNA and RNA analogues. The glycosidic bond stability of Guom is also found to exceed that of its DNA analogue; however, this modification weakens this bond relative to its RNA counterpart. The glycosidic bond stability of the protonated purine nucleosides appears to be correlated with the hydrogen-bond stabilization of the sugar moiety.
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Affiliation(s)
- C C He
- Department of Chemistry , Wayne State University , Detroit , Michigan 48202 , United States
| | - L A Hamlow
- Department of Chemistry , Wayne State University , Detroit , Michigan 48202 , United States
| | - Zachary J Devereaux
- Department of Chemistry , Wayne State University , Detroit , Michigan 48202 , United States
| | - Y Zhu
- Department of Chemistry , Wayne State University , Detroit , Michigan 48202 , United States
| | - Y-W Nei
- Department of Chemistry , Wayne State University , Detroit , Michigan 48202 , United States
| | - L Fan
- Department of Chemistry , Wayne State University , Detroit , Michigan 48202 , United States
| | - C P McNary
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112 , United States
| | - P Maitre
- Laboratoire de Chimie Physique (UMR8000), CNRS, Université Paris-Sud, Université Paris-Saclay , 91405 Orsay , France
| | - V Steinmetz
- Laboratoire de Chimie Physique (UMR8000), CNRS, Université Paris-Sud, Université Paris-Saclay , 91405 Orsay , France
| | - B Schindler
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière , F-69622 Villeurbanne , France
| | - I Compagnon
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière , F-69622 Villeurbanne , France
| | - P B Armentrout
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112 , United States
| | - M T Rodgers
- Department of Chemistry , Wayne State University , Detroit , Michigan 48202 , United States
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32
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Abstract
Codon usage depends on mutation bias, tRNA-mediated selection, and the need for high efficiency and accuracy in translation. One codon in a synonymous codon family is often strongly over-used, especially in highly expressed genes, which often leads to a high dN/dS ratio because dS is very small. Many different codon usage indices have been proposed to measure codon usage and codon adaptation. Sense codon could be misread by release factors and stop codons misread by tRNAs, which also contribute to codon usage in rare cases. This chapter outlines the conceptual framework on codon evolution, illustrates codon-specific and gene-specific codon usage indices, and presents their applications. A new index for codon adaptation that accounts for background mutation bias (Index of Translation Elongation) is presented and contrasted with codon adaptation index (CAI) which does not consider background mutation bias. They are used to re-analyze data from a recent paper claiming that translation elongation efficiency matters little in protein production. The reanalysis disproves the claim.
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33
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Oerum S, Roovers M, Rambo RP, Kopec J, Bailey HJ, Fitzpatrick F, Newman JA, Newman WG, Amberger A, Zschocke J, Droogmans L, Oppermann U, Yue WW. Structural insight into the human mitochondrial tRNA purine N1-methyltransferase and ribonuclease P complexes. J Biol Chem 2018; 293:12862-12876. [PMID: 29880640 PMCID: PMC6102140 DOI: 10.1074/jbc.ra117.001286] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 04/24/2018] [Indexed: 01/17/2023] Open
Abstract
Mitochondrial tRNAs are transcribed as long polycistronic transcripts of precursor tRNAs and undergo posttranscriptional modifications such as endonucleolytic processing and methylation required for their correct structure and function. Among them, 5'-end processing and purine 9 N1-methylation of mitochondrial tRNA are catalyzed by two proteinaceous complexes with overlapping subunit composition. The Mg2+-dependent RNase P complex for 5'-end cleavage comprises the methyltransferase domain-containing protein tRNA methyltransferase 10C, mitochondrial RNase P subunit (TRMT10C/MRPP1), short-chain oxidoreductase hydroxysteroid 17β-dehydrogenase 10 (HSD17B10/MRPP2), and metallonuclease KIAA0391/MRPP3. An MRPP1-MRPP2 subcomplex also catalyzes the formation of 1-methyladenosine/1-methylguanosine at position 9 using S-adenosyl-l-methionine as methyl donor. However, a lack of structural information has precluded insights into how these complexes methylate and process mitochondrial tRNA. Here, we used a combination of X-ray crystallography, interaction and activity assays, and small angle X-ray scattering (SAXS) to gain structural insight into the two tRNA modification complexes and their components. The MRPP1 N terminus is involved in tRNA binding and monomer-monomer self-interaction, whereas the C-terminal SPOUT fold contains key residues for S-adenosyl-l-methionine binding and N1-methylation. The entirety of MRPP1 interacts with MRPP2 to form the N1-methylation complex, whereas the MRPP1-MRPP2-MRPP3 RNase P complex only assembles in the presence of precursor tRNA. This study proposes low-resolution models of the MRPP1-MRPP2 and MRPP1-MRPP2-MRPP3 complexes that suggest the overall architecture, stoichiometry, and orientation of subunits and tRNA substrates.
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Affiliation(s)
- Stephanie Oerum
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
| | | | - Robert P Rambo
- Diamond Light Source, Harwell Science and Innovation Center, Didcot OX11 0QG, United Kingdom
| | - Jola Kopec
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Henry J Bailey
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Fiona Fitzpatrick
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Joseph A Newman
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - William G Newman
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, University of Manchester, Manchester, M13 9WL, United Kingdom
| | - Albert Amberger
- Division of Human Genetics, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Johannes Zschocke
- Division of Human Genetics, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Louis Droogmans
- Laboratoire de Microbiologie, Universite libre de Bruxelles, 1050 Belgium
| | - Udo Oppermann
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom; Botnar Research Centre, NIHR Oxford Biomedical Research Unit, Oxford OX3 7LD, United Kingdom.
| | - Wyatt W Yue
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom.
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34
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Schneider C, Becker S, Okamura H, Crisp A, Amatov T, Stadlmeier M, Carell T. Noncanonical RNA Nucleosides as Molecular Fossils of an Early Earth-Generation by Prebiotic Methylations and Carbamoylations. Angew Chem Int Ed Engl 2018. [PMID: 29533524 DOI: 10.1002/anie.201801919] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The RNA-world hypothesis assumes that life on Earth started with small RNA molecules that catalyzed their own formation. Vital to this hypothesis is the need for prebiotic routes towards RNA. Contemporary RNA, however, is not only constructed from the four canonical nucleobases (A, C, G, and U), it also contains many chemically modified (noncanonical) bases. A still open question is whether these noncanonical bases were formed in parallel to the canonical bases (chemical origin) or later, when life demanded higher functional diversity (biological origin). Here we show that isocyanates in combination with sodium nitrite establish methylating and carbamoylating reactivity compatible with early Earth conditions. These reactions lead to the formation of methylated and amino acid modified nucleosides that are still extant. Our data provide a plausible scenario for the chemical origin of certain noncanonical bases, which suggests that they are fossils of an early Earth.
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Affiliation(s)
- Christina Schneider
- Center for Integrated Protein Science (CiPSM) at the Department, of Chemistry, LMU München, Butenandtstrasse 5-13, 81377, München, Germany
| | - Sidney Becker
- Center for Integrated Protein Science (CiPSM) at the Department, of Chemistry, LMU München, Butenandtstrasse 5-13, 81377, München, Germany
| | - Hidenori Okamura
- Center for Integrated Protein Science (CiPSM) at the Department, of Chemistry, LMU München, Butenandtstrasse 5-13, 81377, München, Germany
| | - Antony Crisp
- Center for Integrated Protein Science (CiPSM) at the Department, of Chemistry, LMU München, Butenandtstrasse 5-13, 81377, München, Germany
| | - Tynchtyk Amatov
- Center for Integrated Protein Science (CiPSM) at the Department, of Chemistry, LMU München, Butenandtstrasse 5-13, 81377, München, Germany
| | - Michael Stadlmeier
- Center for Integrated Protein Science (CiPSM) at the Department, of Chemistry, LMU München, Butenandtstrasse 5-13, 81377, München, Germany
| | - Thomas Carell
- Center for Integrated Protein Science (CiPSM) at the Department, of Chemistry, LMU München, Butenandtstrasse 5-13, 81377, München, Germany
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35
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Schneider C, Becker S, Okamura H, Crisp A, Amatov T, Stadlmeier M, Carell T. Nicht-kanonische RNA-Nukleoside als molekulare Fossilien einer frühen Erde - Generierung durch präbiotische Methylierungen und Carbamoylierungen. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201801919] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Christina Schneider
- Center for Integrated Protein Science (CiPS ) am, Department Chemie; LMU München; Butenandtstraße 5-13 81377 München Deutschland
| | - Sidney Becker
- Center for Integrated Protein Science (CiPS ) am, Department Chemie; LMU München; Butenandtstraße 5-13 81377 München Deutschland
| | - Hidenori Okamura
- Center for Integrated Protein Science (CiPS ) am, Department Chemie; LMU München; Butenandtstraße 5-13 81377 München Deutschland
| | - Antony Crisp
- Center for Integrated Protein Science (CiPS ) am, Department Chemie; LMU München; Butenandtstraße 5-13 81377 München Deutschland
| | - Tynchtyk Amatov
- Center for Integrated Protein Science (CiPS ) am, Department Chemie; LMU München; Butenandtstraße 5-13 81377 München Deutschland
| | - Michael Stadlmeier
- Center for Integrated Protein Science (CiPS ) am, Department Chemie; LMU München; Butenandtstraße 5-13 81377 München Deutschland
| | - Thomas Carell
- Center for Integrated Protein Science (CiPS ) am, Department Chemie; LMU München; Butenandtstraße 5-13 81377 München Deutschland
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36
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Bartsakoulia M, Mϋller JS, Gomez-Duran A, Yu-Wai-Man P, Boczonadi V, Horvath R. Cysteine Supplementation May be Beneficial in a Subgroup of Mitochondrial Translation Deficiencies. J Neuromuscul Dis 2018; 3:363-379. [PMID: 27854233 DOI: 10.3233/jnd-160178] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Mitochondrial encephalomyopathies are severe, relentlessly progressive conditions and there are very few effective therapies available to date. We have previously suggested that in two rare forms of reversible mitochondrial disease (reversible infantile respiratory chain deficiency and reversible infantile hepatopathy) supplementation with L-cysteine can improve mitochondrial protein synthesis, since cysteine is required for the 2-thiomodification of mitochondrial tRNAs. OBJECTIVES We studied whether supplementation with L-cysteine or N-acetyl-cysteine (NAC) results in any improvement of the mitochondrial function in vitro in fibroblasts of patients with different genetic forms of abnormal mitochondrial translation. METHODS We studied in vitro in fibroblasts of patients carrying the common m.3243A>G and m.8344A>G mutations or autosomal recessive mutations in genes affecting mitochondrial translation, whether L-cysteine or N-acetyl-cysteine supplementation have an effect on mitochondrial respiratory chain function. RESULTS Here we show that supplementation with L-cysteine, but not with N-acetyl-cysteine partially rescues the mitochondrial translation defect in vitro in fibroblasts of patients carrying the m.3243A>G and m.8344A>G mutations. In contrast, N-acetyl-cysteine had a beneficial effect on mitochondrial translation in TRMU and MTO1 deficient fibroblasts. CONCLUSIONS Our results suggest that L-cysteine or N-acetyl-cysteine supplementation may be a potential treatment for selected subgroups of patients with mitochondrial translation deficiencies. Further studies are needed to explore the full potential of cysteine supplementation as a treatment for patients with mitochondrial disease.
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Affiliation(s)
- Marina Bartsakoulia
- Wellcome Trust Mitochondrial Research Centre and the John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK
| | - Juliane S Mϋller
- Wellcome Trust Mitochondrial Research Centre and the John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK
| | - Aurora Gomez-Duran
- Wellcome Trust Mitochondrial Research Centre and the John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK.,Present address: Department of Clinical Neurosciences, Cambridge and MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Patrick Yu-Wai-Man
- Wellcome Trust Mitochondrial Research Centre and the John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK.,Newcastle Eye Centre, Royal Victoria Infirmary, Newcastle upon Tyne, UK.,NIHR Biomedical Research Centre at Moorfields Eye Hospital and UCL Institute of Ophthalmology, London, UK
| | - Veronika Boczonadi
- Wellcome Trust Mitochondrial Research Centre and the John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK
| | - Rita Horvath
- Wellcome Trust Mitochondrial Research Centre and the John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK
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37
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Chou HJ, Donnard E, Gustafsson HT, Garber M, Rando OJ. Transcriptome-wide Analysis of Roles for tRNA Modifications in Translational Regulation. Mol Cell 2017; 68:978-992.e4. [PMID: 29198561 DOI: 10.1016/j.molcel.2017.11.002] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/19/2017] [Accepted: 10/31/2017] [Indexed: 12/17/2022]
Abstract
Covalent nucleotide modifications in noncoding RNAs affect a plethora of biological processes, and new functions continue to be discovered even for well-known modifying enzymes. To systematically compare the functions of a large set of noncoding RNA modifications in gene regulation, we carried out ribosome profiling in budding yeast to characterize 57 nonessential genes involved in tRNA modification. Deletion mutants exhibited a range of translational phenotypes, with enzymes known to modify anticodons, or non-tRNA substrates such as rRNA, exhibiting the most dramatic translational perturbations. Our data build on prior reports documenting translational upregulation of the nutrient-responsive transcription factor Gcn4 in response to numerous tRNA perturbations, and identify many additional translationally regulated mRNAs throughout the yeast genome. Our data also uncover unexpected roles for tRNA-modifying enzymes in regulation of TY retroelements, and in rRNA 2'-O-methylation. This dataset should provide a rich resource for discovery of additional links between tRNA modifications and gene regulation.
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Affiliation(s)
- Hsin-Jung Chou
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Elisa Donnard
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - H Tobias Gustafsson
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Manuel Garber
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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38
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Vahdati AR, Sprouffske K, Wagner A. Effect of Population Size and Mutation Rate on the Evolution of RNA Sequences on an Adaptive Landscape Determined by RNA Folding. Int J Biol Sci 2017; 13:1138-1151. [PMID: 29104505 PMCID: PMC5666329 DOI: 10.7150/ijbs.19436] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 07/05/2017] [Indexed: 02/04/2023] Open
Abstract
The dynamics of populations evolving on an adaptive landscape depends on multiple factors, including the structure of the landscape, the rate of mutations, and effective population size. Existing theoretical work often makes ad hoc and simplifying assumptions about landscape structure, whereas experimental work can vary important parameters only to a limited extent. We here overcome some of these limitations by simulating the adaptive evolution of RNA molecules, whose fitness is determined by the thermodynamics of RNA secondary structure folding. We study the influence of mutation rates and population sizes on final mean population fitness, on the substitution rates of mutations, and on population diversity. We show that evolutionary dynamics cannot be understood as a function of mutation rate µ, population size N, or population mutation rate Nµ alone. For example, at a given mutation rate, clonal interference prevents the fixation of beneficial mutations as population size increases, but larger populations still arrive at a higher mean fitness. In addition, at the highest population mutation rates we study, mean final fitness increases with population size, because small populations are driven to low fitness by the relatively higher incidence of mutations they experience. Our observations show that mutation rate and population size can interact in complex ways to influence the adaptive dynamics of a population on a biophysically motivated fitness landscape.
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Affiliation(s)
- Ali R Vahdati
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,The Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Kathleen Sprouffske
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,The Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Andreas Wagner
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,The Swiss Institute of Bioinformatics, Lausanne, Switzerland.,The Santa Fe Institute, Santa Fe, USA
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39
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Xu J, Gu AY, Thumati NR, Wong JMY. Quantification of Pseudouridine Levels in Cellular RNA Pools with a Modified HPLC-UV Assay. Genes (Basel) 2017; 8:genes8090219. [PMID: 28872587 PMCID: PMC5615352 DOI: 10.3390/genes8090219] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 08/28/2017] [Accepted: 08/30/2017] [Indexed: 12/26/2022] Open
Abstract
Pseudouridine (Ψ) is the most abundant post-transcriptionally modified ribonucleoside. Different Ψ modifications correlate with stress responses and are postulated to coordinate the distinct biological responses to a diverse panel of cellular stresses. With the help of different guide RNAs, the dyskerin complex pseudouridylates ribosomal RNA, small nuclear RNA and selective messenger RNAs. To monitor Ψ levels quantitatively, a previously reported high performance liquid chromatography method coupled with ultraviolet detection (HPLC-UV) was modified to determine total Ψ levels in different cellular RNA fractions. Our method was validated to be accurate and precise within the linear range of 0.06-15.36 pmol/μL and to have absolute Ψ quantification levels as low as 3.07 pmol. Using our optimized HPLC assay, we found that 1.20% and 1.94% of all ribonucleosides in nuclear-enriched RNA and small non-coding RNA pools from the HEK293 cell line, and 1.77% and 0.98% of ribonucleosides in 18S and 28S rRNA isolated from the HeLa cell line, were pseudouridylated. Upon knockdown of dyskerin expression, a consistent and significant reduction in total Ψ levels in nuclear-enriched RNA pools was observed. Our assay provides a fast and accurate quantification method to measure changes in Ψ levels of different RNA pools without sample derivatization.
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Affiliation(s)
- Jialin Xu
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
| | - Alice Y Gu
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
| | - Naresh R Thumati
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
| | - Judy M Y Wong
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
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40
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Bednářová A, Hanna M, Durham I, VanCleave T, England A, Chaudhuri A, Krishnan N. Lost in Translation: Defects in Transfer RNA Modifications and Neurological Disorders. Front Mol Neurosci 2017; 10:135. [PMID: 28536502 PMCID: PMC5422465 DOI: 10.3389/fnmol.2017.00135] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 04/20/2017] [Indexed: 11/13/2022] Open
Abstract
Transfer RNAs (tRNAs) are key molecules participating in protein synthesis. To augment their functionality they undergo extensive post-transcriptional modifications and, as such, are subject to regulation at multiple levels including transcription, transcript processing, localization and ribonucleoside base modification. Post-transcriptional enzyme-catalyzed modification of tRNA occurs at a number of base and sugar positions and influences specific anticodon-codon interactions and regulates translation, its efficiency and fidelity. This phenomenon of nucleoside modification is most remarkable and results in a rich structural diversity of tRNA of which over 100 modified nucleosides have been characterized. Most often these hypermodified nucleosides are found in the wobble position of tRNAs, where they play a direct role in codon recognition as well as in maintaining translational efficiency and fidelity, etc. Several recent studies have pointed to a link between defects in tRNA modifications and human diseases including neurological disorders. Therefore, defects in tRNA modifications in humans need intensive characterization at the enzymatic and mechanistic level in order to pave the way to understand how lack of such modifications are associated with neurological disorders with the ultimate goal of gaining insights into therapeutic interventions.
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Affiliation(s)
- Andrea Bednářová
- Department of Biochemistry and Physiology, Institute of Entomology, Biology Centre, Academy of SciencesČeské Budějovice, Czechia.,Laboratory of Molecular Biology and Biochemistry, Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State UniversityMississippi State, MS, USA
| | - Marley Hanna
- Molecular Biosciences Program, Arkansas State UniversityJonesboro, AR, USA
| | - Isabella Durham
- Department of Wildlife, Fisheries and Aquaculture, Mississippi State UniversityMississippi State, MS, USA
| | - Tara VanCleave
- Laboratory of Molecular Biology and Biochemistry, Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State UniversityMississippi State, MS, USA
| | - Alexis England
- Laboratory of Molecular Biology and Biochemistry, Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State UniversityMississippi State, MS, USA
| | | | - Natraj Krishnan
- Laboratory of Molecular Biology and Biochemistry, Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State UniversityMississippi State, MS, USA
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41
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Trm5 and TrmD: Two Enzymes from Distinct Origins Catalyze the Identical tRNA Modification, m¹G37. Biomolecules 2017; 7:biom7010032. [PMID: 28335556 PMCID: PMC5372744 DOI: 10.3390/biom7010032] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 03/07/2017] [Accepted: 03/16/2017] [Indexed: 11/17/2022] Open
Abstract
The N¹-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. The resultant modified nucleotide m¹G37 positively regulates the aminoacylation of the tRNA, and simultaneously functions to prevent the +1 frameshift on the ribosome. Interestingly, Trm5 and TrmD have completely distinct origins, and therefore bear different tertiary folds. In this review, we describe the different strategies utilized by Trm5 and TrmD to recognize their substrate tRNAs, mainly based on their crystal structures complexed with substrate tRNAs.
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42
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MicroRNA MultiTool: A Software for Identifying Modified and Unmodified Human microRNA Using Mass Spectrometry. Noncoding RNA 2017; 3:ncrna3010013. [PMID: 29657285 PMCID: PMC5832007 DOI: 10.3390/ncrna3010013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Revised: 03/10/2017] [Accepted: 03/10/2017] [Indexed: 12/11/2022] Open
Abstract
microRNA (miRNA) are short endogenous non-coding RNA that play a crucial role in post-transcriptional gene regulation and have been implicated in the initiation and progression of 160+ human diseases. Excellent analytical methods have been developed for the measurement of miRNA by mass spectrometry. However, interpretation of mass spectrometric data has been an incapacitating bottleneck in miRNA identification. This study details the development of MicroRNA MultiTool, a software for the identification of miRNA from mass spectrometric data. The software includes capabilities such as miRNA search and mass calculator, modified miRNA mass calculator, and miRNA fragment search. MicroRNA MultiTool bridges the gap between experimental data and identification of miRNA by providing a rapid means of mass spectrometric data interpretation.
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43
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Sharma U, Rando OJ. Metabolic Inputs into the Epigenome. Cell Metab 2017; 25:544-558. [PMID: 28273477 DOI: 10.1016/j.cmet.2017.02.003] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 12/14/2016] [Accepted: 01/07/2017] [Indexed: 12/30/2022]
Abstract
A number of molecular pathways play key roles in transmitting information in addition to the genomic sequence-epigenetic information-from one generation to the next. However, so-called epigenetic marks also impact an enormous variety of physiological processes, even under circumstances that do not result in heritable consequences. Perhaps inevitably, the epigenetic regulatory machinery is highly responsive to metabolic cues, as, for example, central metabolites are the substrates for the enzymes that catalyze the deposition of covalent modifications on histones, DNA, and RNA. Interestingly, in addition to the effects that metabolites exert over biological regulation in somatic cells, over the past decade multiple studies have shown that ancestral nutrition can alter the metabolic phenotype of offspring, raising the question of how metabolism regulates the epigenome of germ cells. Here, we review the widespread links between metabolism and epigenetic modifications, both in somatic cells and in the germline.
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Affiliation(s)
- Upasna Sharma
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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44
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Fitzsimmons CM, Fujimori DG. Determinants of tRNA Recognition by the Radical SAM Enzyme RlmN. PLoS One 2016; 11:e0167298. [PMID: 27902775 PMCID: PMC5130265 DOI: 10.1371/journal.pone.0167298] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 11/12/2016] [Indexed: 11/19/2022] Open
Abstract
RlmN, a bacterial radical SAM methylating enzyme, has the unusual ability to modify two distinct types of RNA: 23S rRNA and tRNA. In rRNA, RlmN installs a methyl group at the C2 position of A2503 of 23S rRNA, while in tRNA the modification occurs at nucleotide A37, immediately adjacent to the anticodon triplet. Intriguingly, only a subset of tRNAs that contain an adenosine at position 37 are substrates for RlmN, suggesting that the enzyme carefully probes the highly conserved tRNA fold and sequence features to identify its targets. Over the past several years, multiple studies have addressed rRNA modification by RlmN, while relatively few investigations have focused on the ability of this enzyme to modify tRNAs. In this study, we utilized in vitro transcribed tRNAs as model substrates to interrogate RNA recognition by RlmN. Using chimeras and point mutations, we probed how the structure and sequence of RNA influences methylation, identifying position 38 of tRNAs as a critical determinant of substrate recognition. We further demonstrate that, analogous to previous mechanistic studies with fragments of 23S rRNA, tRNA methylation requirements are consistent with radical SAM reactivity. Together, our findings provide detailed insight into tRNA recognition by a radical SAM methylating enzyme.
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Affiliation(s)
- Christina M. Fitzsimmons
- Chemistry and Chemical Biology Graduate Program, University of California San Francisco, San Francisco, California, United States of America
| | - Danica Galonić Fujimori
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, United States of America
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
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45
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Biddle W, Schmitt MA, Fisk JD. Modification of orthogonal tRNAs: unexpected consequences for sense codon reassignment. Nucleic Acids Res 2016; 44:10042-10050. [PMID: 27915288 PMCID: PMC5137457 DOI: 10.1093/nar/gkw948] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 10/05/2016] [Accepted: 10/10/2016] [Indexed: 12/25/2022] Open
Abstract
Breaking the degeneracy of the genetic code via sense codon reassignment has emerged as a way to incorporate multiple copies of multiple non-canonical amino acids into a protein of interest. Here, we report the modification of a normally orthogonal tRNA by a host enzyme and show that this adventitious modification has a direct impact on the activity of the orthogonal tRNA in translation. We observed nearly equal decoding of both histidine codons, CAU and CAC, by an engineered orthogonal M. jannaschii tRNA with an AUG anticodon: tRNAOpt. We suspected a modification of the tRNAOptAUG anticodon was responsible for the anomalous lack of codon discrimination and demonstrate that adenosine 34 of tRNAOptAUG is converted to inosine. We identified tRNAOptAUG anticodon loop variants that increase reassignment of the histidine CAU codon, decrease incorporation in response to the histidine CAC codon, and improve cell health and growth profiles. Recognizing tRNA modification as both a potential pitfall and avenue of directed alteration will be important as the field of genetic code engineering continues to infiltrate the genetic codes of diverse organisms.
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Affiliation(s)
- Wil Biddle
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
| | - Margaret A Schmitt
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523, USA
| | - John D Fisk
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA .,Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523, USA.,School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523, USA
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46
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Li GQ, Liu Z, Shen HB, Yu DJ. TargetM6A: Identifying N6-Methyladenosine Sites From RNA Sequences via Position-Specific Nucleotide Propensities and a Support Vector Machine. IEEE Trans Nanobioscience 2016; 15:674-682. [DOI: 10.1109/tnb.2016.2599115] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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47
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Abstract
tRNAs are fundamental components of translation and emerging evidence places them more centrally in various other cellular processes. However, rather than being uniformly conserved, tRNA abundance is instead highly variable and adaptable. The amount of tRNA genes greatly differs among species. Moreover, even within the same genome, tRNA abundance shapes the proteome in a tissue- and cell-specific manner and is dynamically regulated in response to stress. Here, we review approaches for identification and quantification of tRNAs and their functional integrity. We discuss the resolution of each method and highlight new approaches with cell-wide resolution based on deep-sequencing technologies.
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48
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Haag S, Sloan KE, Ranjan N, Warda AS, Kretschmer J, Blessing C, Hübner B, Seikowski J, Dennerlein S, Rehling P, Rodnina MV, Höbartner C, Bohnsack MT. NSUN3 and ABH1 modify the wobble position of mt-tRNAMet to expand codon recognition in mitochondrial translation. EMBO J 2016; 35:2104-2119. [PMID: 27497299 PMCID: PMC5048346 DOI: 10.15252/embj.201694885] [Citation(s) in RCA: 175] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 07/20/2016] [Indexed: 12/22/2022] Open
Abstract
Mitochondrial gene expression uses a non‐universal genetic code in mammals. Besides reading the conventional AUG codon, mitochondrial (mt‐)tRNAMet mediates incorporation of methionine on AUA and AUU codons during translation initiation and on AUA codons during elongation. We show that the RNA methyltransferase NSUN3 localises to mitochondria and interacts with mt‐tRNAMet to methylate cytosine 34 (C34) at the wobble position. NSUN3 specifically recognises the anticodon stem loop (ASL) of the tRNA, explaining why a mutation that compromises ASL basepairing leads to disease. We further identify ALKBH1/ABH1 as the dioxygenase responsible for oxidising m5C34 of mt‐tRNAMet to generate an f5C34 modification. In vitro codon recognition studies with mitochondrial translation factors reveal preferential utilisation of m5C34 mt‐tRNAMet in initiation. Depletion of either NSUN3 or ABH1 strongly affects mitochondrial translation in human cells, implying that modifications generated by both enzymes are necessary for mt‐tRNAMet function. Together, our data reveal how modifications in mt‐tRNAMet are generated by the sequential action of NSUN3 and ABH1, allowing the single mitochondrial tRNAMet to recognise the different codons encoding methionine.
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Affiliation(s)
- Sara Haag
- Institute for Molecular Biology, University Medical Center Göttingen Georg-August-University, Göttingen, Germany
| | - Katherine E Sloan
- Institute for Molecular Biology, University Medical Center Göttingen Georg-August-University, Göttingen, Germany
| | - Namit Ranjan
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Ahmed S Warda
- Institute for Molecular Biology, University Medical Center Göttingen Georg-August-University, Göttingen, Germany
| | - Jens Kretschmer
- Institute for Molecular Biology, University Medical Center Göttingen Georg-August-University, Göttingen, Germany
| | - Charlotte Blessing
- Institute for Molecular Biology, University Medical Center Göttingen Georg-August-University, Göttingen, Germany
| | - Benedikt Hübner
- Institute for Molecular Biology, University Medical Center Göttingen Georg-August-University, Göttingen, Germany
| | - Jan Seikowski
- Institute for Organic and Biomolecular Chemistry, Georg-August-University, Göttingen, Germany Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Sven Dennerlein
- Institute for Cellular Biochemistry, University Medical Center Göttingen Georg-August-University, Göttingen, Germany
| | - Peter Rehling
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany Institute for Cellular Biochemistry, University Medical Center Göttingen Georg-August-University, Göttingen, Germany Göttingen Centre for Molecular Biosciences, Georg-August-University, Göttingen, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Claudia Höbartner
- Institute for Organic and Biomolecular Chemistry, Georg-August-University, Göttingen, Germany
| | - Markus T Bohnsack
- Institute for Molecular Biology, University Medical Center Göttingen Georg-August-University, Göttingen, Germany Göttingen Centre for Molecular Biosciences, Georg-August-University, Göttingen, Germany
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49
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Kılıç S, Sagitova DM, Wolfish S, Bely B, Courtot M, Ciufo S, Tatusova T, O'Donovan C, Chibucos MC, Martin MJ, Erill I. From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw055. [PMID: 27114493 PMCID: PMC4843526 DOI: 10.1093/database/baw055] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 03/20/2016] [Indexed: 11/12/2022]
Abstract
Domain-specific databases are essential resources for the biomedical community, leveraging expert knowledge to curate published literature and provide access to referenced data and knowledge. The limited scope of these databases, however, poses important challenges on their infrastructure, visibility, funding and usefulness to the broader scientific community. CollecTF is a community-oriented database documenting experimentally validated transcription factor (TF)-binding sites in the Bacteria domain. In its quest to become a community resource for the annotation of transcriptional regulatory elements in bacterial genomes, CollecTF aims to move away from the conventional data-repository paradigm of domain-specific databases. Through the adoption of well-established ontologies, identifiers and collaborations, CollecTF has progressively become also a portal for the annotation and submission of information on transcriptional regulatory elements to major biological sequence resources (RefSeq, UniProtKB and the Gene Ontology Consortium). This fundamental change in database conception capitalizes on the domain-specific knowledge of contributing communities to provide high-quality annotations, while leveraging the availability of stable information hubs to promote long-term access and provide high-visibility to the data. As a submission portal, CollecTF generates TF-binding site information through direct annotation of RefSeq genome records, definition of TF-based regulatory networks in UniProtKB entries and submission of functional annotations to the Gene Ontology. As a database, CollecTF provides enhanced search and browsing, targeted data exports, binding motif analysis tools and integration with motif discovery and search platforms. This innovative approach will allow CollecTF to focus its limited resources on the generation of high-quality information and the provision of specialized access to the data.Database URL: http://www.collectf.org/.
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Affiliation(s)
- Sefa Kılıç
- Department of Biological Sciences, University of Maryland Baltimore County (UMBC), 1000 Hilltop Circle, Baltimore, MD, 21250, USA
| | - Dinara M Sagitova
- Department of Biological Sciences, University of Maryland Baltimore County (UMBC), 1000 Hilltop Circle, Baltimore, MD, 21250, USA
| | - Shoshannah Wolfish
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Benoit Bely
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Mélanie Courtot
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stacy Ciufo
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, Rockville Pike, Bethesda, MD, 20894, USA
| | - Tatiana Tatusova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, Rockville Pike, Bethesda, MD, 20894, USA
| | - Claire O'Donovan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Marcus C Chibucos
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Maria J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Ivan Erill
- Department of Biological Sciences, University of Maryland Baltimore County (UMBC), 1000 Hilltop Circle, Baltimore, MD, 21250, USA
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Huang HY, Hopper AK. Multiple Layers of Stress-Induced Regulation in tRNA Biology. Life (Basel) 2016; 6:life6020016. [PMID: 27023616 PMCID: PMC4931453 DOI: 10.3390/life6020016] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/14/2016] [Accepted: 03/17/2016] [Indexed: 01/28/2023] Open
Abstract
tRNAs are the fundamental components of the translation machinery as they deliver amino acids to the ribosomes during protein synthesis. Beyond their essential function in translation, tRNAs also function in regulating gene expression, modulating apoptosis and several other biological processes. There are multiple layers of regulatory mechanisms in each step of tRNA biogenesis. For example, tRNA 3′ trailer processing is altered upon nutrient stress; tRNA modification is reprogrammed under various stresses; nuclear accumulation of tRNAs occurs upon nutrient deprivation; tRNA halves accumulate upon oxidative stress. Here we address how environmental stresses can affect nearly every step of tRNA biology and we describe the possible regulatory mechanisms that influence the function or expression of tRNAs under stress conditions.
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Affiliation(s)
- Hsiao-Yun Huang
- Department of Biology, Indiana University, 915 E third St., Myers 300, Bloomington, IN 47405, USA.
| | - Anita K Hopper
- Department of Molecular Genetics and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
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