2'-O-methylation in mRNA disrupts tRNA decoding during translation elongation

Choi, Junhong; Indrisiunaite, Gabriele; DeMirci, Hasan; Ieong, Ka -Weng; Wang, Jinfan; Petrov, Alexey; Prabhakar, Arjun; Rechavi, Gideon; Dominissini, Dan; He, Chuan; Ehrenberg, Mans; Puglisi, Joseph D.

doi:10.1038/s41594-018-0030-z

2'-O-methylation in mRNA disrupts tRNA decoding during translation elongation

Journal Article · Mon Feb 19 00:00:00 EST 2018 · Nature Structural & Molecular Biology

DOI:https://doi.org/10.1038/s41594-018-0030-z· OSTI ID:1460737

^[1]; Indrisiunaite, Gabriele ^[2]; ^[3]; Ieong, Ka -Weng ^[2]; ^[4]; Petrov, Alexey ^[5]; Prabhakar, Arjun ^[1]; Rechavi, Gideon ^[6]; Dominissini, Dan ^[6]; ^[7]; Ehrenberg, Mans ^[2]; ^[4]

Stanford Univ. School of Medicine, Stanford, CA (United States); Stanford Univ., Stanford, CA (United States)
Uppsala Univ., Uppsala (Sweden)
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Stanford Univ. School of Medicine, Stanford, CA (United States)
Stanford Univ. School of Medicine, Stanford, CA (United States); Auburn Univ., Auburn, AL (United States)
Chaim Sheba Medical Center, Tel-Hashomer (Israel); Tel Aviv Univ., Tel Aviv (Israel)
The Univ. of Chicago, Chicago, IL (United States)

Chemical modifications of mRNA may regulate many aspects of mRNA processing and protein synthesis. Recently, 2'-O-methylation of nucleotides was identified as a frequent modification in translated regions of human mRNA, showing enrichment in codons for certain amino acids. Here, using single-molecule, bulk kinetics and structural methods, we show that 2'-O-methylation within coding regions of mRNA disrupts key steps in codon reading during cognate tRNA selection. Our results suggest that 2'-O-methylation sterically perturbs interactions of ribosomal-monitoring bases (G530, A1492 and A1493) with cognate codon–anticodon helices, thereby inhibiting downstream GTP hydrolysis by elongation factor Tu (EF-Tu) and A-site tRNA accommodation, leading to excessive rejection of cognate aminoacylated tRNAs in initial selection and proofreading. In conclusion, our current and prior findings highlight how chemical modifications of mRNA tune the dynamics of protein synthesis at different steps of translation elongation.

View Accepted Manuscript (DOE)

Research Organization:: SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC02-76SF00515

OSTI ID:: 1460737

Journal Information:: Nature Structural & Molecular Biology, Journal Name: Nature Structural & Molecular Biology Journal Issue: 3 Vol. 25; ISSN 1545-9993

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

References (52)

Coordinated Conformational and Compositional Dynamics Drive Ribosome Translocation Chen, Jin; Petrov, Alexey; Tsai Seán, Albert Biophysical Journal, Vol. 104, Issue 2 https://doi.org/10.1016/j.bpj.2012.11.1457	journal	January 2013
“Modified tRNA: Fully Equipped and Ready to Strike” Alfonzo, Juan D. Journal of Molecular Biology, Vol. 416, Issue 4 https://doi.org/10.1016/j.jmb.2012.01.045	journal	March 2012
Site-Specific Ribose Methylation of Preribosomal RNA: A Novel Function for Small Nucleolar RNAs Kiss-László, Zsuzsanna; Henry, Yves; Bachellerie, Jean-Pierre Cell, Vol. 85, Issue 7 https://doi.org/10.1016/s0092-8674(00)81308-2	journal	June 1996
Selection of tRNA by the Ribosome Requires a Transition from an Open to a Closed Form Ogle, James M.; Murphy, Frank V.; Tarry, Michael J. Cell, Vol. 111, Issue 5 https://doi.org/10.1016/s0092-8674(02)01086-3	journal	November 2002
Kinetic amplification of enzyme discrimination Ninio, Jacques Biochimie, Vol. 57, Issue 5 https://doi.org/10.1016/s0300-9084(75)80139-8	journal	July 1975
Structure-Based Energetics of mRNA Decoding on the Ribosome Satpati, Priyadarshi; Sund, Johan; Åqvist, Johan Biochemistry, Vol. 53, Issue 10 https://doi.org/10.1021/bi5000355	journal	March 2014
Structure and Thermodynamics of N ⁶ -Methyladenosine in RNA: A Spring-Loaded Base Modification Roost, Caroline; Lynch, Stephen R.; Batista, Pedro J. Journal of the American Chemical Society, Vol. 137, Issue 5 https://doi.org/10.1021/ja513080v	journal	January 2015
N6-methyladenosine-dependent RNA structural switches regulate RNA–protein interactions Liu, Nian; Dai, Qing; Zheng, Guanqun Nature, Vol. 518, Issue 7540 https://doi.org/10.1038/nature14234	journal	February 2015
Nm-seq maps 2′-O-methylation sites in human mRNA with base precision Dai, Qing; Moshitch-Moshkovitz, Sharon; Han, Dali Nature Methods, Vol. 14, Issue 7 https://doi.org/10.1038/nmeth.4294	journal	May 2017
Following the intersubunit conformation of the ribosome during translation in real time Aitken, Colin Echeverría; Puglisi, Joseph D. Nature Structural & Molecular Biology, Vol. 17, Issue 7 https://doi.org/10.1038/nsmb.1828	journal	June 2010
N6-methyladenosine in mRNA disrupts tRNA selection and translation-elongation dynamics Choi, Junhong; Ieong, Ka-Weng; Demirci, Hasan Nature Structural & Molecular Biology, Vol. 23, Issue 2 https://doi.org/10.1038/nsmb.3148	journal	January 2016
tRNA selection and kinetic proofreading in translation Blanchard, Scott C.; Gonzalez, Ruben L.; Kim, Harold D. Nature Structural & Molecular Biology, Vol. 11, Issue 10 https://doi.org/10.1038/nsmb831	journal	September 2004
Irreversible chemical steps control intersubunit dynamics during translation Marshall, R. Andrew; Dorywalska, Magdalena; Puglisi, Joseph D. Proceedings of the National Academy of Sciences, Vol. 105, Issue 40 https://doi.org/10.1073/pnas.0805299105	journal	September 2008
High-throughput platform for real-time monitoring of biological processes by multicolor single-molecule fluorescence Chen, J.; Dalal, R. V.; Petrov, A. N. Proceedings of the National Academy of Sciences, Vol. 111, Issue 2 https://doi.org/10.1073/pnas.1315735111	journal	December 2013
Accuracy of initial codon selection by aminoacyl-tRNAs on the mRNA-programmed bacterial ribosome Zhang, Jingji; Ieong, Ka-Weng; Johansson, Magnus Proceedings of the National Academy of Sciences, Vol. 112, Issue 31 https://doi.org/10.1073/pnas.1506823112	journal	July 2015
Kinetic Proofreading: A New Mechanism for Reducing Errors in Biosynthetic Processes Requiring High Specificity Hopfield, J. J. Proceedings of the National Academy of Sciences, Vol. 71, Issue 10 https://doi.org/10.1073/pnas.71.10.4135	journal	October 1974
Characterization of fully 2'-modified oligoribonucleotide hetero- and homoduplex hybridization and nuclease sensitivity Cummins, L. L.; Owens, S. R.; Risen, L. M. Nucleic Acids Research, Vol. 23, Issue 11 https://doi.org/10.1093/nar/23.11.2019	journal	June 1995
Site-specific labeling of the ribosome for single-molecule spectroscopy Dorywalska, M. Nucleic Acids Research, Vol. 33, Issue 1 https://doi.org/10.1093/nar/gki151	journal	January 2005
The structure of a bacterial 30S ribosomal subunit Ramakrishnan, V.; Brodersen, D.; Carter, A. P. Acta Crystallographica Section A Foundations of Crystallography, Vol. 56, Issue s1 https://doi.org/10.1107/s0108767300021279	journal	August 2000
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/s0907444909047337	journal	January 2010
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/s0907444910007493	journal	March 2010
Recognition of the Codon-Anticodon Helix by Ribosomal RNA Yoshizawa, S. Science, Vol. 285, Issue 5434 https://doi.org/10.1126/science.285.5434.1722	journal	September 1999
Nucleolar methyltransferase fibrillarin: Evolution of structure and functions Shubina, M. Y.; Musinova, Y. R.; Sheval, E. V. Biochemistry (Moscow), Vol. 81, Issue 9 https://doi.org/10.1134/s0006297916090030	journal	September 2016
Characterization of two homologous 2′-O-methyltransferases showing different specificities for their tRNA substrates Somme, Jonathan; Van Laer, Bart; Roovers, Martine RNA, Vol. 20, Issue 8 https://doi.org/10.1261/rna.044503.114	journal	June 2014
Modification of 16S ribosomal RNA by the KsgA methyltransferase restructures the 30S subunit to optimize ribosome function Demirci, H.; Murphy, F.; Belardinelli, R. RNA, Vol. 16, Issue 12 https://doi.org/10.1261/rna.2357210	journal	October 2010
PHENIX: a comprehensive Python-based system for macromolecular structure solution. Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.45787	text	January 2010
Studies on the Enzyme Enolase Wold, Finn; Ballou, Clinton E. Journal of Biological Chemistry, Vol. 227, Issue 1 https://doi.org/10.1016/S0021-9258(18)70816-8	journal	July 1957
Site-Specific Ribose Methylation of Preribosomal RNA: A Novel Function for Small Nucleolar RNAs Kiss-László, Zsuzsanna; Henry, Yves; Bachellerie, Jean-Pierre Cell, Vol. 85, Issue 7 https://doi.org/10.1016/S0092-8674(00)81308-2	journal	June 1996
Selection of tRNA by the Ribosome Requires a Transition from an Open to a Closed Form Ogle, James M.; Murphy, Frank V.; Tarry, Michael J. Cell, Vol. 111, Issue 5 https://doi.org/10.1016/S0092-8674(02)01086-3	journal	November 2002
Kinetic amplification of enzyme discrimination Ninio, Jacques Biochimie, Vol. 57, Issue 5 https://doi.org/10.1016/S0300-9084(75)80139-8	journal	July 1975
rRNA modifications and ribosome function Decatur, Wayne A.; Fournier, Maurille J. Trends in Biochemical Sciences, Vol. 27, Issue 7 https://doi.org/10.1016/S0968-0004(02)02109-6	journal	July 2002
Pausing on Polyribosomes: Make Way for Elongation in Translational Control Richter, Joel D.; Coller, Jeff Cell, Vol. 163, Issue 2 https://doi.org/10.1016/j.cell.2015.09.041	journal	October 2015
Human tRNALys3UUU Is Pre-Structured by Natural Modifications for Cognate and Wobble Codon Binding through Keto–Enol Tautomerism Vendeix, Franck A. P.; Murphy, Frank V.; Cantara, William A. Journal of Molecular Biology, Vol. 416, Issue 4 https://doi.org/10.1016/j.jmb.2011.12.048	journal	March 2012
Nonfluorescent Quenchers To Correlate Single-Molecule Conformational and Compositional Dynamics Chen, Jin; Tsai, Albert; Petrov, Alexey Journal of the American Chemical Society, Vol. 134, Issue 13 https://doi.org/10.1021/ja2119964	journal	March 2012
Structure of the 30S ribosomal subunit Wimberly, Brian T.; Brodersen, Ditlev E.; Clemons, William M. Nature, Vol. 407, Issue 6802 https://doi.org/10.1038/35030006	journal	September 2000
Targeted ribose methylation of RNA in vivo directed by tailored antisense RNA guides Cavaillé, Jérôme; Nicoloso, Monique; Bachellerie, Jean-Pierre Nature, Vol. 383, Issue 6602 https://doi.org/10.1038/383732a0	journal	October 1996
Real-time tRNA transit on single translating ribosomes at codon resolution Uemura, Sotaro; Aitken, Colin Echeverría; Korlach, Jonas Nature, Vol. 464, Issue 7291 https://doi.org/10.1038/nature08925	journal	April 2010
Ensemble cryo-EM elucidates the mechanism of translation fidelity Loveland, Anna B.; Demo, Gabriel; Grigorieff, Nikolaus Nature, Vol. 546, Issue 7656 https://doi.org/10.1038/nature22397	journal	May 2017
Gene expression regulation mediated through reversible m6A RNA methylation Fu, Ye; Dominissini, Dan; Rechavi, Gideon Nature Reviews Genetics, Vol. 15, Issue 5 https://doi.org/10.1038/nrg3724	journal	March 2014
Post-transcriptional gene regulation by mRNA modifications Zhao, Boxuan Simen; Roundtree, Ian A.; He, Chuan Nature Reviews Molecular Cell Biology, Vol. 18, Issue 1 https://doi.org/10.1038/nrm.2016.132	journal	November 2016
Coordinated conformational and compositional dynamics drive ribosome translocation Chen, Jin; Petrov, Alexey; Tsai, Albert Nature Structural & Molecular Biology, Vol. 20, Issue 6 https://doi.org/10.1038/nsmb.2567	journal	April 2013
m1A and m1G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs Zhou, Huiqing; Kimsey, Isaac J.; Nikolova, Evgenia N. Nature Structural & Molecular Biology, Vol. 23, Issue 9 https://doi.org/10.1038/nsmb.3270	journal	August 2016
PARP1 exhibits enhanced association and catalytic efficiency with γH2A.X-nucleosome Sharma, Deepti; De Falco, Louis; Padavattan, Sivaraman Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-13641-0	journal	December 2019
Genetic code translation displays a linear trade-off between efficiency and accuracy of tRNA selection Johansson, M.; Zhang, J.; Ehrenberg, M. Proceedings of the National Academy of Sciences, Vol. 109, Issue 1 https://doi.org/10.1073/pnas.1116480109	journal	December 2011
Two proofreading steps amplify the accuracy of genetic code translation Ieong, Ka-Weng; Uzun, Ülkü; Selmer, Maria Proceedings of the National Academy of Sciences, Vol. 113, Issue 48 https://doi.org/10.1073/pnas.1610917113	journal	November 2016
Modified Uridines with C5-methylene Substituents at the First Position of the tRNA Anticodon Stabilize U·G Wobble Pairing during Decoding Kurata, Shinya; Weixlbaumer, Albert; Ohtsuki, Takashi Journal of Biological Chemistry, Vol. 283, Issue 27 https://doi.org/10.1074/jbc.M800233200	journal	May 2008
Advantages of 2'-O-methyl oligoribonucleotide probes for detecting RNA targets Majlessi, M. Nucleic Acids Research, Vol. 26, Issue 9 https://doi.org/10.1093/nar/26.9.2224	journal	May 1998
Nucleotide modifications within bacterial messenger RNAs regulate their translation and are able to rewire the genetic code Hoernes, Thomas Philipp; Clementi, Nina; Faserl, Klaus Nucleic Acids Research, Vol. 44, Issue 2 https://doi.org/10.1093/nar/gkv1182	journal	November 2015
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/S0907444909047337	journal	January 2010
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
Recognition of Cognate Transfer RNA by the 30S Ribosomal Subunit Ogle, J. M. Science, Vol. 292, Issue 5518 https://doi.org/10.1126/science.1060612	journal	May 2001
HNRNPA2B1 promotes multiple myeloma progression by increasing AKT3 expression via m6A-dependent stabilization of ILF3 mRNA Jiang, Fengjie; Tang, Xiaozhu; Tang, Chao Journal of Hematology & Oncology, Vol. 14, Issue 1 https://doi.org/10.1186/s13045-021-01066-6	journal	April 2021

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