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Ishida S, Ngo PHT, Gundlach A, Ellington A. Engineering Ribosomal Machinery for Noncanonical Amino Acid Incorporation. Chem Rev 2024; 124:7712-7730. [PMID: 38829723 DOI: 10.1021/acs.chemrev.3c00912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
The introduction of noncanonical amino acids into proteins has enabled researchers to modify fundamental physicochemical and functional properties of proteins. While the alteration of the genetic code, via the introduction of orthogonal aminoacyl-tRNA synthetase:tRNA pairs, has driven many of these efforts, the various components involved in the process of translation are important for the development of new genetic codes. In this review, we will focus on recent advances in engineering ribosomal machinery for noncanonical amino acid incorporation and genetic code modification. The engineering of the ribosome itself will be considered, as well as the many factors that interact closely with the ribosome, including both tRNAs and accessory factors, such as the all-important EF-Tu. Given the success of genome re-engineering efforts, future paths for radical alterations of the genetic code will require more expansive alterations in the translation machinery.
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Affiliation(s)
- Satoshi Ishida
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Phuoc H T Ngo
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Arno Gundlach
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Andrew Ellington
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
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2
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Weiss JL, Decker JC, Bolano A, Krahn N. Tuning tRNAs for improved translation. Front Genet 2024; 15:1436860. [PMID: 38983271 PMCID: PMC11231383 DOI: 10.3389/fgene.2024.1436860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 06/06/2024] [Indexed: 07/11/2024] Open
Abstract
Transfer RNAs have been extensively explored as the molecules that translate the genetic code into proteins. At this interface of genetics and biochemistry, tRNAs direct the efficiency of every major step of translation by interacting with a multitude of binding partners. However, due to the variability of tRNA sequences and the abundance of diverse post-transcriptional modifications, a guidebook linking tRNA sequences to specific translational outcomes has yet to be elucidated. Here, we review substantial efforts that have collectively uncovered tRNA engineering principles that can be used as a guide for the tuning of translation fidelity. These principles have allowed for the development of basic research, expansion of the genetic code with non-canonical amino acids, and tRNA therapeutics.
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Affiliation(s)
- Joshua L Weiss
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - J C Decker
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Ariadna Bolano
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Natalie Krahn
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
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3
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Fujino T, Sonoda R, Higashinagata T, Mishiro-Sato E, Kano K, Murakami H. Ser/Leu-swapped cell-free translation system constructed with natural/in vitro transcribed-hybrid tRNA set. Nat Commun 2024; 15:4143. [PMID: 38755134 PMCID: PMC11099018 DOI: 10.1038/s41467-024-48056-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
The Ser/Leu-swapped genetic code can act as a genetic firewall, mitigating biohazard risks arising from horizontal gene transfer in genetically modified organisms. Our prior work demonstrated the orthogonality of this swapped code to the standard genetic code using a cell-free translation system comprised of 21 in vitro transcribed tRNAs. In this study, to advance this system for protein engineering, we introduce a natural/in vitro transcribed-hybrid tRNA set. This set combines natural tRNAs from Escherichia coli (excluding Ser, Leu, and Tyr) and in vitro transcribed tRNAs, encompassing anticodon-swapped tRNASerGAG and tRNALeuGGA. This approach reduces the number of in vitro transcribed tRNAs required from 21 to only 4. In this optimized system, the production of a model protein, superfolder green fluorescent protein, increases to 3.5-fold. With this hybrid tRNA set, the Ser/Leu-swapped cell-free translation system will stand as a potent tool for protein production with reduced biohazard concerns in future biological endeavors.
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MESH Headings
- Cell-Free System
- Protein Biosynthesis
- Escherichia coli/genetics
- Escherichia coli/metabolism
- RNA, Transfer, Leu/genetics
- RNA, Transfer, Leu/metabolism
- RNA, Transfer, Ser/metabolism
- RNA, Transfer, Ser/genetics
- Genetic Code
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Green Fluorescent Proteins/metabolism
- Green Fluorescent Proteins/genetics
- Protein Engineering/methods
- Transcription, Genetic
- Anticodon/genetics
- Anticodon/metabolism
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Affiliation(s)
- Tomoshige Fujino
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Ryogo Sonoda
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Taito Higashinagata
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Emi Mishiro-Sato
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
| | - Keiko Kano
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
| | - Hiroshi Murakami
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan.
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya, Japan.
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4
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Flügel T, Schacherl M, Unbehaun A, Schroeer B, Dabrowski M, Bürger J, Mielke T, Sprink T, Diebolder CA, Guillén Schlippe YV, Spahn CMT. Transient disome complex formation in native polysomes during ongoing protein synthesis captured by cryo-EM. Nat Commun 2024; 15:1756. [PMID: 38409277 PMCID: PMC10897467 DOI: 10.1038/s41467-024-46092-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 02/13/2024] [Indexed: 02/28/2024] Open
Abstract
Structural studies of translating ribosomes traditionally rely on in vitro assembly and stalling of ribosomes in defined states. To comprehensively visualize bacterial translation, we reactivated ex vivo-derived E. coli polysomes in the PURE in vitro translation system and analyzed the actively elongating polysomes by cryo-EM. We find that 31% of 70S ribosomes assemble into disome complexes that represent eight distinct functional states including decoding and termination intermediates, and a pre-nucleophilic attack state. The functional diversity of disome complexes together with RNase digest experiments suggests that paused disome complexes transiently form during ongoing elongation. Structural analysis revealed five disome interfaces between leading and queueing ribosomes that undergo rearrangements as the leading ribosome traverses through the elongation cycle. Our findings reveal at the molecular level how bL9's CTD obstructs the factor binding site of queueing ribosomes to thwart harmful collisions and illustrate how translation dynamics reshape inter-ribosomal contacts.
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Affiliation(s)
- Timo Flügel
- Charité - Univesitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Magdalena Schacherl
- Charité - Univesitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Anett Unbehaun
- Charité - Univesitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Birgit Schroeer
- Charité - Univesitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Marylena Dabrowski
- Charité - Univesitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Jörg Bürger
- Charité - Univesitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
- Max Planck Institute for Molecular Genetics, Microscopy and Cryo-Electron Microscopy Service Group, Berlin, Germany
| | - Thorsten Mielke
- Max Planck Institute for Molecular Genetics, Microscopy and Cryo-Electron Microscopy Service Group, Berlin, Germany
| | - Thiemo Sprink
- Core Facility for Cryo-Electron Microscopy, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Technology Platform Cryo-EM, Berlin, Germany
| | - Christoph A Diebolder
- Core Facility for Cryo-Electron Microscopy, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Technology Platform Cryo-EM, Berlin, Germany
| | - Yollete V Guillén Schlippe
- Charité - Univesitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany.
| | - Christian M T Spahn
- Charité - Univesitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany.
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5
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Smith TJ, Giles RN, Koutmou KS. Anticodon stem-loop tRNA modifications influence codon decoding and frame maintenance during translation. Semin Cell Dev Biol 2024; 154:105-113. [PMID: 37385829 DOI: 10.1016/j.semcdb.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 07/01/2023]
Abstract
RNAs are central to protein synthesis, with ribosomal RNA, transfer RNAs and messenger RNAs comprising the core components of the translation machinery. In addition to the four canonical bases (uracil, cytosine, adenine, and guanine) these RNAs contain an array of enzymatically incorporated chemical modifications. Transfer RNAs (tRNAs) are responsible for ferrying amino acids to the ribosome, and are among the most abundant and highly modified RNAs in the cell across all domains of life. On average, tRNA molecules contain 13 post-transcriptionally modified nucleosides that stabilize their structure and enhance function. There is an extensive chemical diversity of tRNA modifications, with over 90 distinct varieties of modifications reported within tRNA sequences. Some modifications are crucial for tRNAs to adopt their L-shaped tertiary structure, while others promote tRNA interactions with components of the protein synthesis machinery. In particular, modifications in the anticodon stem-loop (ASL), located near the site of tRNA:mRNA interaction, can play key roles in ensuring protein homeostasis and accurate translation. There is an abundance of evidence indicating the importance of ASL modifications for cellular health, and in vitro biochemical and biophysical studies suggest that individual ASL modifications can differentially influence discrete steps in the translation pathway. This review examines the molecular level consequences of tRNA ASL modifications in mRNA codon recognition and reading frame maintenance to ensure the rapid and accurate translation of proteins.
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Affiliation(s)
- Tyler J Smith
- University of Michigan, Department of Chemistry, 930 N University, Ann Arbor, MI 48109, USA
| | - Rachel N Giles
- University of Michigan, Department of Chemistry, 930 N University, Ann Arbor, MI 48109, USA
| | - Kristin S Koutmou
- University of Michigan, Department of Chemistry, 930 N University, Ann Arbor, MI 48109, USA.
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6
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Xiao Y, Wang R, Han X, Wang W, Liang A. The Deficiency of Hypusinated eIF5A Decreases the Putrescine/Spermidine Ratio and Inhibits +1 Programmed Ribosomal Frameshifting during the Translation of Ty1 Retrotransposon in Saccharomyces cerevisiae. Int J Mol Sci 2024; 25:1766. [PMID: 38339043 PMCID: PMC10855120 DOI: 10.3390/ijms25031766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
Programmed ribosomal frameshifting (PRF) exists in all branches of life that regulate gene expression at the translational level. The eukaryotic translation initiation factor 5A (eIF5A) is a highly conserved protein essential in all eukaryotes. It is identified initially as an initiation factor and functions broadly in translation elongation and termination. The hypusination of eIF5A is specifically required for +1 PRF at the shifty site derived from the ornithine decarboxylase antizyme 1 (OAZ1) in Saccharomyces cerevisiae. However, whether the regulation of +1 PRF by yeast eIF5A is universal remains unknown. Here, we found that Sc-eIF5A depletion decreased the putrescine/spermidine ratio. The re-introduction of Sc-eIF5A in yeast eIF5A mutants recovered the putrescine/spermidine ratio. In addition, the Sc-eIF5A depletion decreases +1 PRF during the decoding of Ty1 retrotransposon mRNA, but has no effect on -1 PRF during the decoding of L-A virus mRNA. The re-introduction of Sc-eIF5A in yeast eIF5A mutants restored the +1 PRF rate of Ty1. The inhibition of the hypusine modification of yeast eIF5A by GC7 treatment or by mutating the hypusination site Lys to Arg caused decreases of +1 PRF rates in the Ty1 retrotransposon. Furthermore, mutational studies of the Ty1 frameshifting element support a model where the efficient removal of ribosomal subunits at the first Ty1 frame 0 stop codon is required for the frameshifting of trailing ribosomes. This dependency is likely due to the unique position of the frame 0 stop codon distance from the slippery sequence of Ty1. The results showed that eIF5A is a trans-regulator of +1 PRF for Ty1 retrotransposon and could function universally in yeast.
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Affiliation(s)
- Yu Xiao
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (Y.X.); (R.W.); (X.H.)
- Shanxi Key Laboratory of Biotechnology, Taiyuan 030006, China
| | - Ruanlin Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (Y.X.); (R.W.); (X.H.)
- Shanxi Key Laboratory of Biotechnology, Taiyuan 030006, China
| | - Xiaxia Han
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (Y.X.); (R.W.); (X.H.)
- Shanxi Key Laboratory of Biotechnology, Taiyuan 030006, China
| | - Wei Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (Y.X.); (R.W.); (X.H.)
- Shanxi Key Laboratory of Biotechnology, Taiyuan 030006, China
| | - Aihua Liang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (Y.X.); (R.W.); (X.H.)
- Shanxi Key Laboratory of Biotechnology, Taiyuan 030006, China
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7
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del Dedo JE, Segundo RLS, Vázquez-Bolado A, Sun J, García-Blanco N, Suárez MB, García P, Tricquet P, Chen JS, Dedon PC, Gould KL, Hidalgo E, Hermand D, Moreno S. The Greatwall-Endosulfine-PP2A/B55 pathway controls entry into quiescence by promoting translation of Elongator-tuneable transcripts. RESEARCH SQUARE 2023:rs.3.rs-3616701. [PMID: 38105947 PMCID: PMC10723533 DOI: 10.21203/rs.3.rs-3616701/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Quiescent cells require a continuous supply of proteins to maintain protein homeostasis. In fission yeast, entry into quiescence is triggered by nitrogen stress, leading to the inactivation of TORC1 and the activation of TORC2. Here, we report that the Greatwall-Endosulfine-PPA/B55 pathway connects the downregulation of TORC1 with the upregulation of TORC2, resulting in the activation of Elongator-dependent tRNA modifications essential for sustaining the translation programme during entry into quiescence. This process promotes U34 and A37 tRNA modifications at the anticodon stem loop, enhancing translation efficiency and fidelity of mRNAs enriched for AAA versus AAG lysine codons. Notably, some of these mRNAs encode inhibitors of TORC1, activators of TORC2, tRNA modifiers, and proteins necessary for telomeric and subtelomeric functions. Therefore, we propose a novel mechanism by which cells respond to nitrogen stress at the level of translation, involving a coordinated interplay between the tRNA epitranscriptome and biased codon usage.
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Affiliation(s)
- Javier Encinar del Dedo
- Instituto de Biología Funcional y Genómica, CSIC, University of Salamanca, 37007 Salamanca, Spain
| | - Rafael López-San Segundo
- Instituto de Biología Funcional y Genómica, CSIC, University of Salamanca, 37007 Salamanca, Spain
| | - Alicia Vázquez-Bolado
- Instituto de Biología Funcional y Genómica, CSIC, University of Salamanca, 37007 Salamanca, Spain
| | - Jingjing Sun
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
| | - Natalia García-Blanco
- Instituto de Biología Funcional y Genómica, CSIC, University of Salamanca, 37007 Salamanca, Spain
| | - M. Belén Suárez
- Instituto de Biología Funcional y Genómica, University of Salamanca, CSIC, 37007 Salamanca, Spain
- Departamento de Microbiología y Genética, University of Salamanca, 37007 Salamanca, Spain
| | - Patricia García
- Instituto de Biología Funcional y Genómica, University of Salamanca, CSIC, 37007 Salamanca, Spain
- Departamento de Microbiología y Genética, University of Salamanca, 37007 Salamanca, Spain
| | - Pauline Tricquet
- URPHYM-GEMO, University of Namur, rue de Bruxelles, 61, Namur 5000, Belgium
| | - Jun-Song Chen
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, United States
| | - Peter C. Dedon
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
- Department of Biological Engineering and Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Kathleen L. Gould
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, United States
| | - Elena Hidalgo
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Damien Hermand
- URPHYM-GEMO, University of Namur, rue de Bruxelles, 61, Namur 5000, Belgium
| | - Sergio Moreno
- Instituto de Biología Funcional y Genómica, CSIC, University of Salamanca, 37007 Salamanca, Spain
- Lead contact
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8
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Mao Y, Jia L, Dong L, Shu XE, Qian SB. Start codon-associated ribosomal frameshifting mediates nutrient stress adaptation. Nat Struct Mol Biol 2023; 30:1816-1825. [PMID: 37957305 DOI: 10.1038/s41594-023-01119-z] [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: 12/06/2022] [Accepted: 09/07/2023] [Indexed: 11/15/2023]
Abstract
A translating ribosome is typically thought to follow the reading frame defined by the selected start codon. Using super-resolution ribosome profiling, here we report pervasive out-of-frame translation immediately from the start codon. Start codon-associated ribosomal frameshifting (SCARF) stems from the slippage of ribosomes during the transition from initiation to elongation. Using a massively paralleled reporter assay, we uncovered sequence elements acting as SCARF enhancers or repressors, implying that start codon recognition is coupled with reading frame fidelity. This finding explains thousands of mass spectrometry spectra that are unannotated in the human proteome. Mechanistically, we find that the eukaryotic initiation factor 5B (eIF5B) maintains the reading frame fidelity by stabilizing initiating ribosomes. Intriguingly, amino acid starvation induces SCARF by proteasomal degradation of eIF5B. The stress-induced SCARF protects cells from starvation by enabling amino acid recycling and selective mRNA translation. Our findings illustrate a beneficial effect of translational 'noise' in nutrient stress adaptation.
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Affiliation(s)
- Yuanhui Mao
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Longfei Jia
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
| | - Leiming Dong
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
| | - Xin Erica Shu
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
| | - Shu-Bing Qian
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA.
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9
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Bubunenko MG, Korepanov AP. The P-Site Loop of the Universally Conserved Bacterial Ribosomal Protein L5 Is Required for Maintaining Both Translation Rate and Fidelity. Int J Mol Sci 2023; 24:14285. [PMID: 37762588 PMCID: PMC10531944 DOI: 10.3390/ijms241814285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/07/2023] [Accepted: 09/09/2023] [Indexed: 09/29/2023] Open
Abstract
The bacterial ribosomal 5S rRNA-binding protein L5 is universally conserved (uL5). It contains the so-called P-site loop (PSL), which contacts the P-site tRNA in the ribosome. Certain PSL mutations in yeast are lethal, suggesting that the loop plays an important role in translation. In this work, for the first time, a viable Escherichia coli strain was obtained with the deletion of the major part of the PSL (residues 73-80) of the uL5 protein. The deletion conferred cold sensitivity and drastically reduced the growth rate and overall protein synthesizing capacity of the mutant. Translation rate is decreased in mutant cells as compared to the control. At the same time, the deletion causes increased levels of -1 frameshifting and readthrough of all three stop codons. In general, the results show that the PSL of the uL5 is required for maintaining both the accuracy and rate of protein synthesis in vivo.
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Affiliation(s)
- Mikhail G. Bubunenko
- Basic Science Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA;
| | - Alexey P. Korepanov
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
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10
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Biela A, Hammermeister A, Kaczmarczyk I, Walczak M, Koziej L, Lin TY, Glatt S. The diverse structural modes of tRNA binding and recognition. J Biol Chem 2023; 299:104966. [PMID: 37380076 PMCID: PMC10424219 DOI: 10.1016/j.jbc.2023.104966] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/20/2023] [Accepted: 06/22/2023] [Indexed: 06/30/2023] Open
Abstract
tRNAs are short noncoding RNAs responsible for decoding mRNA codon triplets, delivering correct amino acids to the ribosome, and mediating polypeptide chain formation. Due to their key roles during translation, tRNAs have a highly conserved shape and large sets of tRNAs are present in all living organisms. Regardless of sequence variability, all tRNAs fold into a relatively rigid three-dimensional L-shaped structure. The conserved tertiary organization of canonical tRNA arises through the formation of two orthogonal helices, consisting of the acceptor and anticodon domains. Both elements fold independently to stabilize the overall structure of tRNAs through intramolecular interactions between the D- and T-arm. During tRNA maturation, different modifying enzymes posttranscriptionally attach chemical groups to specific nucleotides, which not only affect translation elongation rates but also restrict local folding processes and confer local flexibility when required. The characteristic structural features of tRNAs are also employed by various maturation factors and modification enzymes to assure the selection, recognition, and positioning of specific sites within the substrate tRNAs. The cellular functional repertoire of tRNAs continues to extend well beyond their role in translation, partly, due to the expanding pool of tRNA-derived fragments. Here, we aim to summarize the most recent developments in the field to understand how three-dimensional structure affects the canonical and noncanonical functions of tRNA.
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Affiliation(s)
- Anna Biela
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Igor Kaczmarczyk
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland; Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Marta Walczak
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland; Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Lukasz Koziej
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Ting-Yu Lin
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
| | - Sebastian Glatt
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
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11
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Fromm SA, O'Connor KM, Purdy M, Bhatt PR, Loughran G, Atkins JF, Jomaa A, Mattei S. The translating bacterial ribosome at 1.55 Å resolution generated by cryo-EM imaging services. Nat Commun 2023; 14:1095. [PMID: 36841832 PMCID: PMC9968351 DOI: 10.1038/s41467-023-36742-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 02/15/2023] [Indexed: 02/26/2023] Open
Abstract
Our understanding of protein synthesis has been conceptualised around the structure and function of the bacterial ribosome. This complex macromolecular machine is the target of important antimicrobial drugs, an integral line of defence against infectious diseases. Here, we describe how open access to cryo-electron microscopy facilities combined with bespoke user support enabled structural determination of the translating ribosome from Escherichia coli at 1.55 Å resolution. The obtained structures allow for direct determination of the rRNA sequence to identify ribosome polymorphism sites in the E. coli strain used in this study and enable interpretation of the ribosomal active and peripheral sites at unprecedented resolution. This includes scarcely populated chimeric hybrid states of the ribosome engaged in several tRNA translocation steps resolved at ~2 Å resolution. The current map not only improves our understanding of protein synthesis but also allows for more precise structure-based drug design of antibiotics to tackle rising bacterial resistance.
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Affiliation(s)
- Simon A Fromm
- EMBL Imaging Centre, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Kate M O'Connor
- School of Biochemistry and Cell Biology, University College Cork, Cork, T12 XF62, Ireland
| | - Michael Purdy
- Department of Molecular Physiology and Biological Physics, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Pramod R Bhatt
- School of Biochemistry and Cell Biology, University College Cork, Cork, T12 XF62, Ireland
| | - Gary Loughran
- School of Biochemistry and Cell Biology, University College Cork, Cork, T12 XF62, Ireland
| | - John F Atkins
- School of Biochemistry and Cell Biology, University College Cork, Cork, T12 XF62, Ireland. .,MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK.
| | - Ahmad Jomaa
- Department of Molecular Physiology and Biological Physics, School of Medicine, University of Virginia, Charlottesville, VA, USA. .,Centre for Cell and Membrane Physiology, University of Virginia, Charlottesville, VA, USA.
| | - Simone Mattei
- EMBL Imaging Centre, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117, Heidelberg, Germany. .,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117, Heidelberg, Germany.
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12
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Mao Y, Jia L, Dong L, Shu XE, Qian SB. Start codon-associated ribosomal frameshifting mediates nutrient stress adaptation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.15.528768. [PMID: 36824937 PMCID: PMC9949036 DOI: 10.1101/2023.02.15.528768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
A translating ribosome is typically thought to follow the reading frame defined by the selected start codon. Using super-resolution ribosome profiling, here we report pervasive out-of-frame translation immediately from the start codon. The start codon-associated ribosome frameshifting (SCARF) stems from the slippage of ribosomes during the transition from initiation to elongation. Using a massively paralleled reporter assay, we uncovered sequence elements acting as SCARF enhancers or repressors, implying that start codon recognition is coupled with reading frame fidelity. This finding explains thousands of mass spectrometry spectra unannotated from human proteome. Mechanistically, we find that the eukaryotic initiation factor 5B (eIF5B) maintains the reading frame fidelity by stabilizing initiating ribosomes. Intriguingly, amino acid starvation induces SCARF by proteasomal degradation of eIF5B. The stress-induced SCARF protects cells from starvation by enabling amino acid recycling and selective mRNA translation. Our findings illustrate a beneficial effect of translational "noise" in nutrient stress adaptation.
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13
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Chen Y, He X, Ma B, Liu K, Gao T, Niu W, Guo J. Noncanonical amino acid mutagenesis in response to recoding signal-enhanced quadruplet codons. Nucleic Acids Res 2022; 50:e94. [PMID: 35657094 PMCID: PMC9458425 DOI: 10.1093/nar/gkac474] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/13/2022] [Accepted: 04/19/2022] [Indexed: 12/01/2022] Open
Abstract
While amber suppression is the most common approach to introduce noncanonical amino acids into proteins in live cells, quadruplet codon decoding has potential to enable a greatly expanded genetic code with up to 256 new codons for protein biosynthesis. Since triplet codons are the predominant form of genetic code in nature, quadruplet codon decoding often displays limited efficiency. In this work, we exploited a new approach to significantly improve quadruplet UAGN and AGGN (N = A, U, G, C) codon decoding efficiency by using recoding signals imbedded in mRNA. With representative recoding signals, the expression level of mutant proteins containing UAGN and AGGN codons reached 48% and 98% of that of the wild-type protein, respectively. Furthermore, this strategy mitigates a common concern of reading-through endogenous stop codons with amber suppression-based system. Since synthetic recoding signals are rarely found near the endogenous UAGN and AGGN sequences, a low level of undesirable suppression is expected. Our strategy will greatly enhance the utility of noncanonical amino acid mutagenesis in live-cell studies.
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Affiliation(s)
- Yan Chen
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Xinyuan He
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Bin Ma
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Kun Liu
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Tianyu Gao
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Wei Niu
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE 68588, USA
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14
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Ribosome collisions induce mRNA cleavage and ribosome rescue in bacteria. Nature 2022; 603:503-508. [PMID: 35264790 DOI: 10.1038/s41586-022-04416-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 01/07/2022] [Indexed: 01/17/2023]
Abstract
Ribosome rescue pathways recycle stalled ribosomes and target problematic mRNAs and aborted proteins for degradation1,2. In bacteria, it remains unclear how rescue pathways distinguish ribosomes stalled in the middle of a transcript from actively translating ribosomes3-6. Here, using a genetic screen in Escherichia coli, we discovered a new rescue factor that has endonuclease activity. SmrB cleaves mRNAs upstream of stalled ribosomes, allowing the ribosome rescue factor tmRNA (which acts on truncated mRNAs3) to rescue upstream ribosomes. SmrB is recruited to ribosomes and is activated by collisions. Cryo-electron microscopy structures of collided disomes from E. coli and Bacillus subtilis show distinct and conserved arrangements of individual ribosomes and the composite SmrB-binding site. These findings reveal the underlying mechanisms by which ribosome collisions trigger ribosome rescue in bacteria.
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15
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Riegger RJ, Caliskan N. Thinking Outside the Frame: Impacting Genomes Capacity by Programmed Ribosomal Frameshifting. Front Mol Biosci 2022; 9:842261. [PMID: 35281266 PMCID: PMC8915115 DOI: 10.3389/fmolb.2022.842261] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 01/26/2022] [Indexed: 01/08/2023] Open
Abstract
Translation facilitates the transfer of the genetic information stored in the genome via messenger RNAs to a functional protein and is therefore one of the most fundamental cellular processes. Programmed ribosomal frameshifting is a ubiquitous alternative translation event that is extensively used by viruses to regulate gene expression from overlapping open reading frames in a controlled manner. Recent technical advances in the translation field enabled the identification of precise mechanisms as to how and when ribosomes change the reading frame on mRNAs containing cis-acting signals. Several studies began also to illustrate that trans-acting RNA modulators can adjust the timing and efficiency of frameshifting illuminating that frameshifting can be a dynamically regulated process in cells. Here, we intend to summarize these new findings and emphasize how it fits in our current understanding of PRF mechanisms as previously described.
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Affiliation(s)
- Ricarda J. Riegger
- Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for RNA-Based Infection Research (HIRI), Würzburg, Germany
- Graduate School of Life Sciences (GSLS), University of Würzburg, Würzburg, Germany
| | - Neva Caliskan
- Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for RNA-Based Infection Research (HIRI), Würzburg, Germany
- Medical Faculty, University of Würzburg, Würzburg, Germany
- *Correspondence: Neva Caliskan,
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16
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Gamper H, Masuda I, Hou YM. Genome Expansion by tRNA +1 Frameshifting at Quadruplet Codons. J Mol Biol 2022; 434:167440. [PMID: 34995554 PMCID: PMC9643101 DOI: 10.1016/j.jmb.2021.167440] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 12/27/2021] [Accepted: 12/30/2021] [Indexed: 11/29/2022]
Abstract
Inducing tRNA +1 frameshifting to read a quadruplet codon has the potential to incorporate a non-canonical amino acid (ncAA) into the polypeptide chain. While this strategy is attractive for genome expansion in biotechnology and bioengineering endeavors, improving the yield is hampered by a lack of understanding of where the shift can occur in an elongation cycle of protein synthesis. Lacking a clear answer to this question, current efforts have focused on designing +1-frameshifting tRNAs with an extra nucleotide inserted to the anticodon loop for pairing with a quadruplet codon in the aminoacyl-tRNA binding (A) site of the ribosome. However, the designed and evolved +1-frameshifting tRNAs vary broadly in achieving successful genome expansion. Here we summarize recent work on +1-frameshifting tRNAs. We suggest that, rather than engineering the quadruplet anticodon-codon pairing scheme at the ribosome A site, efforts should be made to engineer the pairing scheme at steps after the A site, including the step of the subsequent translocation and the step that stabilizes the pairing scheme in the +1-frame in the peptidyl-tRNA binding (P) site.
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Affiliation(s)
- Howard Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, USA
| | - Isao Masuda
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, USA
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, USA.
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17
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Guo J, Niu W. Genetic Code Expansion Through Quadruplet Codon Decoding. J Mol Biol 2021; 434:167346. [PMID: 34762896 PMCID: PMC9018476 DOI: 10.1016/j.jmb.2021.167346] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/25/2021] [Accepted: 10/30/2021] [Indexed: 12/31/2022]
Abstract
Noncanonical amino acid mutagenesis has emerged as a powerful tool for the study of protein structure and function. While triplet nonsense codons, especially the amber codon, have been widely employed, quadruplet codons have attracted attention for the potential of creating additional blank codons for noncanonical amino acids mutagenesis. In this review, we discuss methodologies and applications of quadruplet codon decoding in genetic code expansion both in vitro and in vivo.
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Affiliation(s)
- Jiantao Guo
- Department of Chemistry, University of Nebraska-Lincoln, United States; The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States.
| | - Wei Niu
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, United States; The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
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18
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DeBenedictis EA, Carver GD, Chung CZ, Söll D, Badran AH. Multiplex suppression of four quadruplet codons via tRNA directed evolution. Nat Commun 2021; 12:5706. [PMID: 34588441 PMCID: PMC8481270 DOI: 10.1038/s41467-021-25948-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 09/10/2021] [Indexed: 11/20/2022] Open
Abstract
Genetic code expansion technologies supplement the natural codon repertoire with assignable variants in vivo, but are often limited by heterologous translational components and low suppression efficiencies. Here, we explore engineered Escherichia coli tRNAs supporting quadruplet codon translation by first developing a library-cross-library selection to nominate quadruplet codon-anticodon pairs. We extend our findings using a phage-assisted continuous evolution strategy for quadruplet-decoding tRNA evolution (qtRNA-PACE) that improved quadruplet codon translation efficiencies up to 80-fold. Evolved qtRNAs appear to maintain codon-anticodon base pairing, are typically aminoacylated by their cognate tRNA synthetases, and enable processive translation of adjacent quadruplet codons. Using these components, we showcase the multiplexed decoding of up to four unique quadruplet codons by their corresponding qtRNAs in a single reporter. Cumulatively, our findings highlight how E. coli tRNAs can be engineered, evolved, and combined to decode quadruplet codons, portending future developments towards an exclusively quadruplet codon translation system.
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Affiliation(s)
- Erika A DeBenedictis
- The Broad Institute of MIT & Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Christina Z Chung
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Ahmed H Badran
- The Broad Institute of MIT & Harvard, Cambridge, MA, USA.
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA.
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19
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Gamper H, Mao Y, Masuda I, McGuigan H, Blaha G, Wang Y, Xu S, Hou YM. Twice exploration of tRNA +1 frameshifting in an elongation cycle of protein synthesis. Nucleic Acids Res 2021; 49:10046-10060. [PMID: 34417618 PMCID: PMC8464047 DOI: 10.1093/nar/gkab734] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/07/2021] [Accepted: 08/13/2021] [Indexed: 12/18/2022] Open
Abstract
Inducing tRNA +1 frameshifting to read a quadruplet codon has the potential to incorporate a non-natural amino acid into the polypeptide chain. While this strategy is being considered for genome expansion in biotechnology and bioengineering endeavors, a major limitation is a lack of understanding of where the shift occurs in an elongation cycle of protein synthesis. Here, we use the high-efficiency +1-frameshifting SufB2 tRNA, containing an extra nucleotide in the anticodon loop, to address this question. Physical and kinetic measurements of the ribosome reading frame of SufB2 identify twice exploration of +1 frameshifting in one elongation cycle, with the major fraction making the shift during translocation from the aminoacyl-tRNA binding (A) site to the peptidyl-tRNA binding (P) site and the remaining fraction making the shift within the P site upon occupancy of the A site in the +1-frame. We demonstrate that the twice exploration of +1 frameshifting occurs during active protein synthesis and that each exploration is consistent with ribosomal conformational dynamics that permits changes of the reading frame. This work indicates that the ribosome itself is a determinant of changes of the reading frame and reveals a mechanistic parallel of +1 frameshifting with –1 frameshifting.
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Affiliation(s)
- Howard Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Yujia Mao
- Department of Chemistry, University of Houston, Houston, TX 77204, USA
| | - Isao Masuda
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Henri McGuigan
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Gregor Blaha
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Yuhong Wang
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
| | - Shoujun Xu
- Department of Chemistry, University of Houston, Houston, TX 77204, USA
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
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20
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Masuda I, Hwang JY, Christian T, Maharjan S, Mohammad F, Gamper H, Buskirk AR, Hou YM. Loss of N1-methylation of G37 in tRNA induces ribosome stalling and reprograms gene expression. eLife 2021; 10:70619. [PMID: 34382933 PMCID: PMC8384417 DOI: 10.7554/elife.70619] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 08/09/2021] [Indexed: 01/20/2023] Open
Abstract
N1-methylation of G37 is required for a subset of tRNAs to maintain the translational reading-frame. While loss of m1G37 increases ribosomal +1 frameshifting, whether it incurs additional translational defects is unknown. Here, we address this question by applying ribosome profiling to gain a genome-wide view of the effects of m1G37 deficiency on protein synthesis. Using E coli as a model, we show that m1G37 deficiency induces ribosome stalling at codons that are normally translated by m1G37-containing tRNAs. Stalling occurs during decoding of affected codons at the ribosomal A site, indicating a distinct mechanism than that of +1 frameshifting, which occurs after the affected codons leave the A site. Enzyme- and cell-based assays show that m1G37 deficiency reduces tRNA aminoacylation and in some cases peptide-bond formation. We observe changes of gene expression in m1G37 deficiency similar to those in the stringent response that is typically induced by deficiency of amino acids. This work demonstrates a previously unrecognized function of m1G37 that emphasizes its role throughout the entire elongation cycle of protein synthesis, providing new insight into its essentiality for bacterial growth and survival.
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Affiliation(s)
- Isao Masuda
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, United States
| | - Jae-Yeon Hwang
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Thomas Christian
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, United States
| | - Sunita Maharjan
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, United States
| | - Fuad Mohammad
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Howard Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, United States
| | - Allen R Buskirk
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, United States
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21
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Demo G, Gamper HB, Loveland AB, Masuda I, Carbone CE, Svidritskiy E, Hou YM, Korostelev AA. Structural basis for +1 ribosomal frameshifting during EF-G-catalyzed translocation. Nat Commun 2021; 12:4644. [PMID: 34330903 PMCID: PMC8324841 DOI: 10.1038/s41467-021-24911-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 07/12/2021] [Indexed: 12/25/2022] Open
Abstract
Frameshifting of mRNA during translation provides a strategy to expand the coding repertoire of cells and viruses. How and where in the elongation cycle +1-frameshifting occurs remains poorly understood. We describe seven ~3.5-Å-resolution cryo-EM structures of 70S ribosome complexes, allowing visualization of elongation and translocation by the GTPase elongation factor G (EF-G). Four structures with a + 1-frameshifting-prone mRNA reveal that frameshifting takes place during translocation of tRNA and mRNA. Prior to EF-G binding, the pre-translocation complex features an in-frame tRNA-mRNA pairing in the A site. In the partially translocated structure with EF-G•GDPCP, the tRNA shifts to the +1-frame near the P site, rendering the freed mRNA base to bulge between the P and E sites and to stack on the 16S rRNA nucleotide G926. The ribosome remains frameshifted in the nearly post-translocation state. Our findings demonstrate that the ribosome and EF-G cooperate to induce +1 frameshifting during tRNA-mRNA translocation.
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MESH Headings
- Biocatalysis
- Cryoelectron Microscopy
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Escherichia coli Proteins/chemistry
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- Frameshifting, Ribosomal/genetics
- Models, Molecular
- Nucleic Acid Conformation
- Peptide Chain Elongation, Translational/genetics
- Peptide Elongation Factor G/chemistry
- Peptide Elongation Factor G/genetics
- Peptide Elongation Factor G/metabolism
- Protein Conformation
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Ribosomes/genetics
- Ribosomes/metabolism
- Ribosomes/ultrastructure
- tRNA Methyltransferases/genetics
- tRNA Methyltransferases/metabolism
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Affiliation(s)
- Gabriel Demo
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, MA, USA
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Howard B Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Anna B Loveland
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, MA, USA
| | - Isao Masuda
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Christine E Carbone
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, MA, USA
| | - Egor Svidritskiy
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, MA, USA
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA.
| | - Andrei A Korostelev
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, MA, USA.
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22
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Atkins JF, O’Connor KM, Bhatt PR, Loughran G. From Recoding to Peptides for MHC Class I Immune Display: Enriching Viral Expression, Virus Vulnerability and Virus Evasion. Viruses 2021; 13:1251. [PMID: 34199077 PMCID: PMC8310308 DOI: 10.3390/v13071251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/11/2021] [Accepted: 06/19/2021] [Indexed: 01/02/2023] Open
Abstract
Many viruses, especially RNA viruses, utilize programmed ribosomal frameshifting and/or stop codon readthrough in their expression, and in the decoding of a few a UGA is dynamically redefined to specify selenocysteine. This recoding can effectively increase viral coding capacity and generate a set ratio of products with the same N-terminal domain(s) but different C-terminal domains. Recoding can also be regulatory or generate a product with the non-universal 21st directly encoded amino acid. Selection for translation speed in the expression of many viruses at the expense of fidelity creates host immune defensive opportunities. In contrast to host opportunism, certain viruses, including some persistent viruses, utilize recoding or adventitious frameshifting as part of their strategy to evade an immune response or specific drugs. Several instances of recoding in small intensively studied viruses escaped detection for many years and their identification resolved dilemmas. The fundamental importance of ribosome ratcheting is consistent with the initial strong view of invariant triplet decoding which however did not foresee the possibility of transitory anticodon:codon dissociation. Deep level dynamics and structural understanding of recoding is underway, and a high level structure relevant to the frameshifting required for expression of the SARS CoV-2 genome has just been determined.
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Affiliation(s)
- John F. Atkins
- Schools of Biochemistry and Microbiology, University College Cork, T12 XF62 Cork, Ireland; (K.M.O.); (P.R.B.); (G.L.)
| | - Kate M. O’Connor
- Schools of Biochemistry and Microbiology, University College Cork, T12 XF62 Cork, Ireland; (K.M.O.); (P.R.B.); (G.L.)
| | - Pramod R. Bhatt
- Schools of Biochemistry and Microbiology, University College Cork, T12 XF62 Cork, Ireland; (K.M.O.); (P.R.B.); (G.L.)
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Gary Loughran
- Schools of Biochemistry and Microbiology, University College Cork, T12 XF62 Cork, Ireland; (K.M.O.); (P.R.B.); (G.L.)
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23
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Kimura S. Distinct evolutionary pathways for the synthesis and function of tRNA modifications. Brief Funct Genomics 2021; 20:125-134. [PMID: 33454776 DOI: 10.1093/bfgp/elaa027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 12/23/2022] Open
Abstract
Transfer ribonucleicacids (RNAs) (tRNAs) are essential adaptor molecules for translation. The functions and stability of tRNAs are modulated by their post-transcriptional modifications (tRNA modifications). Each domain of life has a specific set of modifications that include ones shared in multiple domains and ones specific to a domain. In some cases, different tRNA modifications across domains have similar functions to each other. Recent studies uncovered that distinct enzymes synthesize the same modification in different organisms, suggesting that such modifications are acquired through independent evolution. In this short review, I outline the mechanisms by which various modifications contribute to tRNA function, including modulation of decoding and tRNA stability, using recent findings. I also focus on modifications that are synthesized by distinct biosynthetic pathways.
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Affiliation(s)
- Satoshi Kimura
- Dr Matthew Waldor's lab at the Brigham and Women's Hospital. He completed his PhD and early postdoc work in Dr Tsutomu Suzuki's lab at the University of Tokyo
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24
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Gamper H, Li H, Masuda I, Miklos Robkis D, Christian T, Conn AB, Blaha G, Petersson EJ, Gonzalez RL, Hou YM. Insights into genome recoding from the mechanism of a classic +1-frameshifting tRNA. Nat Commun 2021; 12:328. [PMID: 33436566 PMCID: PMC7803779 DOI: 10.1038/s41467-020-20373-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/30/2020] [Indexed: 12/18/2022] Open
Abstract
While genome recoding using quadruplet codons to incorporate non-proteinogenic amino acids is attractive for biotechnology and bioengineering purposes, the mechanism through which such codons are translated is poorly understood. Here we investigate translation of quadruplet codons by a +1-frameshifting tRNA, SufB2, that contains an extra nucleotide in its anticodon loop. Natural post-transcriptional modification of SufB2 in cells prevents it from frameshifting using a quadruplet-pairing mechanism such that it preferentially employs a triplet-slippage mechanism. We show that SufB2 uses triplet anticodon-codon pairing in the 0-frame to initially decode the quadruplet codon, but subsequently shifts to the +1-frame during tRNA-mRNA translocation. SufB2 frameshifting involves perturbation of an essential ribosome conformational change that facilitates tRNA-mRNA movements at a late stage of the translocation reaction. Our results provide a molecular mechanism for SufB2-induced +1 frameshifting and suggest that engineering of a specific ribosome conformational change can improve the efficiency of genome recoding. Genome recoding with quadruplet codons requires a +1-frameshift-suppressor tRNA able to insert an amino acid at quadruplet codons of interest. Here the authors identify the mechanisms resulting in +1 frameshifting and the steps of the elongation cycle in which it occurs.
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Affiliation(s)
- Howard Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Haixing Li
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Isao Masuda
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - D Miklos Robkis
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Thomas Christian
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Adam B Conn
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA
| | - Gregor Blaha
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ruben L Gonzalez
- Department of Chemistry, Columbia University, New York, NY, 10027, USA.
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA.
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25
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Nesterov-Mueller A, Popov R, Seligmann H. Combinatorial Fusion Rules to Describe Codon Assignment in the Standard Genetic Code. Life (Basel) 2020; 11:life11010004. [PMID: 33374866 PMCID: PMC7824455 DOI: 10.3390/life11010004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/15/2020] [Accepted: 12/21/2020] [Indexed: 11/16/2022] Open
Abstract
We propose combinatorial fusion rules that describe the codon assignment in the standard genetic code simply and uniformly for all canonical amino acids. These rules become obvious if the origin of the standard genetic code is considered as a result of a fusion of four protocodes: Two dominant AU and GC protocodes and two recessive AU and GC protocodes. The biochemical meaning of the fusion rules consists of retaining the complementarity between cognate codons of the small hydrophobic amino acids and large charged or polar amino acids within the protocodes. The proto tRNAs were assembled in form of two kissing hairpins with 9-base and 10-base loops in the case of dominant protocodes and two 9-base loops in the case of recessive protocodes. The fusion rules reveal the connection between the stop codons, the non-canonical amino acids, pyrrolysine and selenocysteine, and deviations in the translation of mitochondria. Using fusion rules, we predicted the existence of additional amino acids that are essential for the development of the standard genetic code. The validity of the proposed partition of the genetic code into dominant and recessive protocodes is considered referring to state-of-the-art hypotheses. The formation of two aminoacyl-tRNA synthetase classes is compatible with four-protocode partition.
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Affiliation(s)
- Alexander Nesterov-Mueller
- Institute of Microstructure Technology, Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany; (R.P.); (H.S.)
- Correspondence:
| | - Roman Popov
- Institute of Microstructure Technology, Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany; (R.P.); (H.S.)
| | - Hervé Seligmann
- Institute of Microstructure Technology, Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany; (R.P.); (H.S.)
- The National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
- Laboratory AGEIS EA 7407, Team Tools for e-GnosisMedical & LabcomCNRS/UGA/OrangeLabs Telecoms4Health, Faculty of Medicine, Université Grenoble Alpes, F-38700 La Tronche, France
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26
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Fisher KE, Bradbury SP, Coates BS. Prediction of mitochondrial genome-wide variation through sequencing of mitochondrion-enriched extracts. Sci Rep 2020; 10:19123. [PMID: 33154458 PMCID: PMC7645498 DOI: 10.1038/s41598-020-76088-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/19/2020] [Indexed: 11/08/2022] Open
Abstract
Although mitochondrial DNA (mtDNA) haplotype variation is often applied for estimating population dynamics and phylogenetic relationships, economical and generalized methods for entire mtDNA genome enrichment prior to high-throughput sequencing are not readily available. This study demonstrates the utility of differential centrifugation to enrich for mitochondrion within cell extracts prior to DNA extraction, short-read sequencing, and assembly using exemplars from eight maternal lineages of the insect species, Ostrinia nubilalis. Compared to controls, enriched extracts showed a significant mean increase of 48.2- and 86.1-fold in mtDNA based on quantitative PCR, and proportion of subsequent short sequence reads that aligned to the O. nubilalis reference mitochondrial genome, respectively. Compared to the reference genome, our de novo assembled O. nubilalis mitochondrial genomes contained 82 intraspecific substitution and insertion/deletion mutations, and provided evidence for correction of mis-annotated 28 C-terminal residues within the NADH dehydrogenase subunit 4. Comparison to a more recent O. nubilalis mtDNA assembly from unenriched short-read data analogously showed 77 variant sites. Twenty-eight variant positions, and a triplet ATT codon (Ile) insertion within ATP synthase subunit 8, were unique within our assemblies. This study provides a generalizable pipeline for whole mitochondrial genome sequence acquisition adaptable to applications across a range of taxa.
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Affiliation(s)
- Kelsey E Fisher
- Department of Entomology, Iowa State University, Ames, IA, 50011, USA.
| | - Steven P Bradbury
- Department of Entomology, Iowa State University, Ames, IA, 50011, USA
- Department of Natural Resource Ecology and Management, Iowa State University, Ames, IA, 50011, USA
| | - Brad S Coates
- Department of Agriculture, Agriculture Research Station, Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA
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27
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Flegel WA, Srivastava K. Frameshift variations in the RHD coding sequence: Molecular mechanisms permitting protein expression. Transfusion 2020; 60:2737-2744. [PMID: 33037655 DOI: 10.1111/trf.16123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 07/08/2020] [Accepted: 07/17/2020] [Indexed: 12/31/2022]
Affiliation(s)
- Willy A Flegel
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Kshitij Srivastava
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
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28
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Simms CL, Yan LL, Qiu JK, Zaher HS. Ribosome Collisions Result in +1 Frameshifting in the Absence of No-Go Decay. Cell Rep 2020; 28:1679-1689.e4. [PMID: 31412239 PMCID: PMC6701860 DOI: 10.1016/j.celrep.2019.07.046] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 06/17/2019] [Accepted: 07/15/2019] [Indexed: 12/22/2022] Open
Abstract
During translation, an mRNA is typically occupied by multiple ribosomes sparsely distributed across the coding sequence. This distribution, mediated by slow rates of initiation relative to elongation, ensures that they rarely collide with each other, but given the stochastic nature of protein synthesis, collision events do occur. Recent work from our lab suggested that collisions signal for mRNA degradation through no-go decay (NGD). We have explored the impact of stalling on ribosome function when NGD is compromised and found it to result in +1 frameshifting. We used reporters that limit the number of ribosomes on a transcript to show that +1 frameshifting is induced through ribosome collision in yeast and bacteria. Furthermore, we observe a positive correlation between ribosome density and frameshifting efficiency. It is thus tempting to speculate that NGD, in addition to its role in mRNA quality control, evolved to cope with stochastic collision events to prevent deleterious frameshifting events. Ribosome collisions, resulting from stalling, activate quality control processes to degrade the aberrant mRNA and the incomplete peptide. mRNA degradation proceeds through an endonucleolytic cleavage between the stacked ribosomes, which resolves the collisions. Simms et al. show that, when cleavage is inhibited, colliding ribosomes move out of frame.
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Affiliation(s)
- Carrie L Simms
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Liewei L Yan
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Jessica K Qiu
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Hani S Zaher
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA.
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29
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Antibiotic resistance by high-level intrinsic suppression of a frameshift mutation in an essential gene. Proc Natl Acad Sci U S A 2020; 117:3185-3191. [PMID: 31992637 PMCID: PMC7022156 DOI: 10.1073/pnas.1919390117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Frameshift mutations have been reported in rpoB, an essential gene encoding the beta-subunit of RNA polymerase, in rifampicin-resistant clinical isolates of Mycobacterium tuberculosis. These have never been experimentally validated, and no mechanisms of action have been proposed. We show that Escherichia coli with a +1-nt frameshift mutation centrally located in rpoB is viable and highly resistant to rifampicin. Spontaneous frameshifting occurs at a high rate on a heptanucleotide sequence downstream of the mutation, with production of active protein increased to 61–71% of wild-type level by a feedback mechanism that increases translation initiation. Accordingly, apparently lethal mutations can be viable and cause clinically relevant phenotypes, a finding that has broad significance for predictions of phenotype from genotype. A fundamental feature of life is that ribosomes read the genetic code in messenger RNA (mRNA) as triplets of nucleotides in a single reading frame. Mutations that shift the reading frame generally cause gene inactivation and in essential genes cause loss of viability. Here we report and characterize a +1-nt frameshift mutation, centrally located in rpoB, an essential gene encoding the beta-subunit of RNA polymerase. Mutant Escherichia coli carrying this mutation are viable and highly resistant to rifampicin. Genetic and proteomic experiments reveal a very high rate (5%) of spontaneous frameshift suppression occurring on a heptanucleotide sequence downstream of the mutation. Production of active protein is stimulated to 61–71% of wild-type level by a feedback mechanism increasing translation initiation. The phenomenon described here could have broad significance for predictions of phenotype from genotype. Several frameshift mutations have been reported in rpoB in rifampicin-resistant clinical isolates of Mycobacterium tuberculosis (Mtb). These mutations have never been experimentally validated, and no mechanisms of action have been proposed. This work shows that frameshift mutations in rpoB can be a mutational mechanism generating antibiotic resistance. Our analysis further suggests that genetic elements supporting productive frameshifting could rapidly evolve de novo, even in essential genes.
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30
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Structural basis for ribosome recycling by RRF and tRNA. Nat Struct Mol Biol 2019; 27:25-32. [PMID: 31873307 DOI: 10.1038/s41594-019-0350-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 11/12/2019] [Indexed: 11/08/2022]
Abstract
The bacterial ribosome is recycled into subunits by two conserved proteins, elongation factor G (EF-G) and the ribosome recycling factor (RRF). The molecular basis for ribosome recycling by RRF and EF-G remains unclear. Here, we report the crystal structure of a posttermination Thermus thermophilus 70S ribosome complexed with EF-G, RRF and two transfer RNAs at a resolution of 3.5 Å. The deacylated tRNA in the peptidyl (P) site moves into a previously unsuspected state of binding (peptidyl/recycling, p/R) that is analogous to that seen during initiation. The terminal end of the p/R-tRNA forms nonfavorable contacts with the 50S subunit while RRF wedges next to central inter-subunit bridges, illuminating the active roles of tRNA and RRF in dissociation of ribosomal subunits. The structure uncovers a missing snapshot of tRNA as it transits between the P and exit (E) sites, providing insights into the mechanisms of ribosome recycling and tRNA translocation.
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31
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Molecular Dynamics Simulations Suggest a Non-Doublet Decoding Model of -1 Frameshifting by tRNA Ser3. Biomolecules 2019; 9:biom9110745. [PMID: 31752208 PMCID: PMC6920855 DOI: 10.3390/biom9110745] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/14/2019] [Accepted: 11/14/2019] [Indexed: 12/28/2022] Open
Abstract
In-frame decoding in the ribosome occurs through canonical or wobble Watson-Crick pairing of three mRNA codon bases (a triplet) with a triplet of anticodon bases in tRNA. Departures from the triplet-triplet interaction can result in frameshifting, meaning downstream mRNA codons are then read in a different register. There are many mechanisms to induce frameshifting, and most are insufficiently understood. One previously proposed mechanism is doublet decoding, in which only codon bases 1 and 2 are read by anticodon bases 34 and 35, which would lead to -1 frameshifting. In E. coli, tRNASer3GCU can induce -1 frameshifting at alanine (GCA) codons. The logic of the doublet decoding model is that the Ala codon's GC could pair with the tRNASer3's GC, leaving the third anticodon residue U36 making no interactions with mRNA. Under that model, a U36C mutation would still induce -1 frameshifting, but experiments refute this. We perform all-atom simulations of wild-type tRNASer3, as well as a U36C mutant. Our simulations revealed a hydrogen bond between U36 of the anticodon and G1 of the codon. The U36C mutant cannot make this interaction, as it lacks the hydrogen-bond-donating H3. The simulation thus suggests a novel, non-doublet decoding mechanism for -1 frameshifting by tRNASer3 at Ala codons.
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32
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Zinoviev A, Kuroha K, Pestova TV, Hellen CUT. Two classes of EF1-family translational GTPases encoded by giant viruses. Nucleic Acids Res 2019; 47:5761-5776. [PMID: 31216040 PMCID: PMC6582330 DOI: 10.1093/nar/gkz296] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 04/10/2019] [Accepted: 04/12/2019] [Indexed: 01/31/2023] Open
Abstract
Giant viruses have extraordinarily large dsDNA genomes, and exceptionally, they encode various components of the translation apparatus, including tRNAs, aminoacyl-tRNA synthetases and translation factors. Here, we focused on the elongation factor 1 (EF1) family of viral translational GTPases (trGTPases), using computational and functional approaches to shed light on their functions. Multiple sequence alignment indicated that these trGTPases clustered into two groups epitomized by members of Mimiviridae and Marseilleviridae, respectively. trGTPases in the first group were more closely related to GTP-binding protein 1 (GTPBP1), whereas trGTPases in the second group were closer to eEF1A, eRF3 and Hbs1. Functional characterization of representative GTPBP1-like trGTPases (encoded by Hirudovirus, Catovirus and Moumouvirus) using in vitro reconstitution revealed that they possess eEF1A-like activity and can deliver cognate aa-tRNAs to the ribosomal A site during translation elongation. By contrast, representative eEF1A/eRF3/Hbs1-like viral trGTPases, encoded by Marseillevirus and Lausannevirus, have eRF3-like termination activity and stimulate peptide release by eRF1. Our analysis identified specific aspects of the functioning of these viral trGTPases with eRF1 of human, amoebal and Marseillevirus origin.
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Affiliation(s)
- Alexandra Zinoviev
- Department of Cell Biology, SUNY Downstate Medical Center, 450 Clarkson Avenue, MSC 44, Brooklyn, NY 11203, USA
| | - Kazushige Kuroha
- Department of Cell Biology, SUNY Downstate Medical Center, 450 Clarkson Avenue, MSC 44, Brooklyn, NY 11203, USA
| | - Tatyana V Pestova
- Department of Cell Biology, SUNY Downstate Medical Center, 450 Clarkson Avenue, MSC 44, Brooklyn, NY 11203, USA
| | - Christopher U T Hellen
- Department of Cell Biology, SUNY Downstate Medical Center, 450 Clarkson Avenue, MSC 44, Brooklyn, NY 11203, USA
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33
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Korniy N, Samatova E, Anokhina MM, Peske F, Rodnina MV. Mechanisms and biomedical implications of -1 programmed ribosome frameshifting on viral and bacterial mRNAs. FEBS Lett 2019; 593:1468-1482. [PMID: 31222875 PMCID: PMC6771820 DOI: 10.1002/1873-3468.13478] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/14/2019] [Accepted: 05/26/2019] [Indexed: 12/11/2022]
Abstract
Some proteins are expressed as a result of a ribosome frameshifting event that is facilitated by a slippery site and downstream secondary structure elements in the mRNA. This review summarizes recent progress in understanding mechanisms of –1 frameshifting in several viral genes, including IBV 1a/1b, HIV‐1 gag‐pol, and SFV 6K, and in Escherichia coli dnaX. The exact frameshifting route depends on the availability of aminoacyl‐tRNAs: the ribosome normally slips into the –1‐frame during tRNA translocation, but can also frameshift during decoding at condition when aminoacyl‐tRNA is in limited supply. Different frameshifting routes and additional slippery sites allow viruses to maintain a constant production of their key proteins. The emerging idea that tRNA pools are important for frameshifting provides new direction for developing antiviral therapies.
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Affiliation(s)
- Natalia Korniy
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Ekaterina Samatova
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Maria M Anokhina
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Frank Peske
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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34
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Nguyen HA, Hoffer ED, Dunham CM. Importance of a tRNA anticodon loop modification and a conserved, noncanonical anticodon stem pairing in tRNACGGProfor decoding. J Biol Chem 2019; 294:5281-5291. [PMID: 30782843 PMCID: PMC6462517 DOI: 10.1074/jbc.ra119.007410] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 02/13/2019] [Indexed: 01/15/2023] Open
Abstract
Modification of anticodon nucleotides allows tRNAs to decode multiple codons, expanding the genetic code. Additionally, modifications located in the anticodon loop, outside the anticodon itself, stabilize tRNA–codon interactions, increasing decoding fidelity. Anticodon loop nucleotide 37 is 3′ to the anticodon and, in tRNA CGG Pro , is methylated at the N1 position in its nucleobase (m1G37). The m1G37 modification in tRNA CGG Pro stabilizes its interaction with the codon and maintains the mRNA frame. However, it is unclear how m1G37 affects binding at the decoding center to both cognate and +1 slippery codons. Here, we show that the tRNA CGG Pro m1G37 modification is important for the association step during binding to a cognate CCG codon. In contrast, m1G37 prevented association with a slippery CCC-U or +1 codon. Similar analyses of frameshift suppressor tRNASufA6, a tRNA CGG Pro derivative containing an extra nucleotide in its anticodon loop that undergoes +1 frameshifting, reveal that m1G37 destabilizes interactions with both the cognate CCG and slippery codons. One reason for this destabilization is the disruption of a conserved U32·A38 nucleotide pairing in the anticodon stem through insertion of G37.5. Restoring the tRNASufA6 U32·A37.5 pairing results in a high-affinity association on the slippery CCC-U codon. Further, an X-ray crystal structure of the 70S ribosome bound to tRNASufA6 U32·A37.5 at 3.6 Å resolution shows a reordering of the anticodon loop consistent with the findings from the high-affinity measurements. Our results reveal how the tRNA modification at nucleotide 37 stabilizes interactions with the mRNA codon to preserve the mRNA frame.
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Affiliation(s)
- Ha An Nguyen
- From the Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322 and
- the Department of Chemistry, Emory University, Atlanta, Georgia 30322
| | - Eric D Hoffer
- From the Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322 and
| | - Christine M Dunham
- From the Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322 and
- the Department of Chemistry, Emory University, Atlanta, Georgia 30322
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35
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Numerous cultivated and uncultivated viruses encode ribosomal proteins. Nat Commun 2019; 10:752. [PMID: 30765709 PMCID: PMC6375957 DOI: 10.1038/s41467-019-08672-6] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 01/18/2019] [Indexed: 01/04/2023] Open
Abstract
Viruses modulate ecosystems by directly altering host metabolisms through auxiliary metabolic genes. However, viral genomes are not known to encode the core components of translation machinery, such as ribosomal proteins (RPs). Here, using reference genomes and global-scale viral metagenomic datasets, we identify 14 different RPs across viral genomes arising from cultivated viral isolates and metagenome-assembled viruses. Viruses tend to encode dynamic RPs, easily exchangeable between ribosomes, suggesting these proteins can replace cellular versions in host ribosomes. Functional assays confirm that the two most common virus-encoded RPs, bS21 and bL12, are incorporated into 70S ribosomes when expressed in Escherichia coli. Ecological distribution of virus-encoded RPs suggests some level of ecosystem adaptations as aquatic viruses and viruses of animal-associated bacteria are enriched for different subsets of RPs. Finally, RP genes are under purifying selection and thus likely retained an important function after being horizontally transferred into virus genomes.
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36
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Wang J, Zhou J, Yang Q, Grayhack EJ. Multi-protein bridging factor 1(Mbf1), Rps3 and Asc1 prevent stalled ribosomes from frameshifting. eLife 2018; 7:39637. [PMID: 30465652 PMCID: PMC6301793 DOI: 10.7554/elife.39637] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 11/21/2018] [Indexed: 12/17/2022] Open
Abstract
Reading frame maintenance is critical for accurate translation. We show that the conserved eukaryotic/archaeal protein Mbf1 acts with ribosomal proteins Rps3/uS3 and eukaryotic Asc1/RACK1 to prevent frameshifting at inhibitory CGA-CGA codon pairs in the yeast Saccharomyces cerevisiae. Mutations in RPS3 that allow frameshifting implicate eukaryotic conserved residues near the mRNA entry site. Mbf1 and Rps3 cooperate to maintain the reading frame of stalled ribosomes, while Asc1 also mediates distinct events that result in recruitment of the ribosome quality control complex and mRNA decay. Frameshifting occurs through a +1 shift with a CGA codon in the P site and involves competition between codons entering the A site, implying that the wobble interaction of the P site codon destabilizes translation elongation. Thus, eukaryotes have evolved unique mechanisms involving both a universally conserved ribosome component and two eukaryotic-specific proteins to maintain the reading frame at ribosome stalls. Proteins perform all the chemical reactions needed to keep a cell alive; thus, it is essential to assemble them correctly. They are made by molecular machines called ribosomes, which follow a sequence of instructions written in genetic code in molecules known as mRNAs. Ribosomes essentially read the genetic code three letters at a time; each triplet either codes for the insertion of one of 20 building blocks into the emerging protein, or serves as a signal to stop the process. It is critical that, after reading one triplet, the ribosome moves precisely three letters to read the next triplet. If, for example, the ribosome shifted just two letters instead of three – a phenomenon known as “frameshifting” – it would completely change the building blocks that were used to make the protein. This could lead to atypical or aberrant proteins that either do not work or are even toxic to the cell. For a variety of reasons, ribosomes will often stall before they have finished building a protein. When this happens, the ribosome is more likely to frameshift. Cells commonly respond to stalled ribosomes by recruiting other molecules that work as quality control systems, some of which can disassemble the ribosome and break down the mRNA. In budding yeast, one part of the ribosome – named Asc1 – plays a key role in recruiting these quality control systems and in mRNA breakdown. If this component is removed, stalled ribosomes frameshift more frequently and, as a result, aberrant proteins accumulate in the cell. Since the Asc1 recruiter protein sits on the outside of the ribosome, it seemed likely that it might act through other factors to stop the ribosome from frameshifting when it stalls. However, it was unknown if such factors exist, what they are, or how they might work. Now, Wang et al. have identified two additional yeast proteins, named Mbf1 and Rps3, which cooperate to stop the ribosome from frameshifting after it stalls. Rps3, like Asc1, is a component of the ribosome, while Mbf1 is not. It appears that Rps3 likely stops frameshifting via an interaction with the incoming mRNA, because a region of Rps3 near the mRNA entry site to the ribosome is important for its activity. Further experiments then showed that the known Asc1-mediated breakdown of mRNAs did not depend on Mbf1 and Rps3, but also assists in stopping frameshifting. Thus, frameshifting of stalled ribosomes is prevented via two distinct ways: one that directly involves Mbf1 and Rps3 and one that is promoted by Asc1, which reduces the amounts of mRNAs on which ribosomes frameshift. These newly identified factors may provide insights into the precisely controlled protein-production machinery in the cell and into roles of the quality control systems. An improved understanding of mechanisms that prevent frameshifting could eventually lead to better treatments for some human diseases that result when these processes go awry, which include certain neurological conditions.
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Affiliation(s)
- Jiyu Wang
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York.,Center for RNA Biology, University of Rochester, Rochester, New York
| | - Jie Zhou
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York
| | - Qidi Yang
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York
| | - Elizabeth J Grayhack
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York.,Center for RNA Biology, University of Rochester, Rochester, New York
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37
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Joshi K, Bhatt MJ, Farabaugh PJ. Codon-specific effects of tRNA anticodon loop modifications on translational misreading errors in the yeast Saccharomyces cerevisiae. Nucleic Acids Res 2018; 46:10331-10339. [PMID: 30060218 PMCID: PMC6212777 DOI: 10.1093/nar/gky664] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 07/03/2018] [Accepted: 07/12/2018] [Indexed: 01/10/2023] Open
Abstract
Protein synthesis requires both high speed and accuracy to ensure a healthy cellular environment. Estimates of errors during protein synthesis in Saccharomyces cerevisiae have varied from 10-3 to 10-4 errors per codon. Here, we show that errors made by ${\rm{tRNA}}^{\rm Glu}_{\rm UUC}$ in yeast can vary 100-fold, from 10-6 to 10-4 errors per codon. The most frequent errors require a G•U mismatch at the second position for the near cognate codon GGA (Gly). We also show, contrary to our previous results, that yeast tRNAs can make errors involving mismatches at the wobble position but with low efficiency. We have also assessed the effect on misreading frequency of post-transcriptional modifications of tRNAs, which are known to regulate cognate codon decoding in yeast. We tested the roles of mcm5s2U34 and t6A37 and show that their effects depend on details of the codon anticodon interaction including the position of the modification with respect to the base mismatch and the nature of that mismatch. Both mcm5 and s2 modification of wobble uridine strongly stabilizes G2•U35 mismatches when ${\rm{tRNA}}^{\rm Glu}_{\rm UUC}$ misreads the GGA Gly codon but has weaker effects on other mismatches. By contrast, t6A37 destabilizes U1•U36 mismatches when ${\rm{tRNA}}^{\rm Lys}_{\rm UUU}$ misreads UAA or UAG but stabilizes mismatches at the second and wobble positions.
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Affiliation(s)
- Kartikeya Joshi
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Monika J Bhatt
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Philip J Farabaugh
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250, USA
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38
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Culmination of a half-century quest reveals insight into mutant tRNA-mediated frameshifting after tRNA departure from the decoding site. Proc Natl Acad Sci U S A 2018; 115:11121-11123. [PMID: 30341222 DOI: 10.1073/pnas.1815837115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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39
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Abrahams L, Hurst LD. Refining the Ambush Hypothesis: Evidence That GC- and AT-Rich Bacteria Employ Different Frameshift Defence Strategies. Genome Biol Evol 2018; 10:1153-1173. [PMID: 29617761 PMCID: PMC5909447 DOI: 10.1093/gbe/evy075] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2018] [Indexed: 12/13/2022] Open
Abstract
Stop codons are frequently selected for beyond their regular termination function for error control. The “ambush hypothesis” proposes out-of-frame stop codons (OSCs) terminating frameshifted translations are selected for. Although early indirect evidence was partially supportive, recent evidence suggests OSC frequencies are not exceptional when considering underlying nucleotide content. However, prior null tests fail to control amino acid/codon usages or possible local mutational biases. We therefore return to the issue using bacterial genomes, considering several tests defining and testing against a null. We employ simulation approaches preserving amino acid order but shuffling synonymous codons or preserving codons while shuffling amino acid order. Additionally, we compare codon usage in amino acid pairs, where one codon can but the next, otherwise identical codon, cannot encode an OSC. OSC frequencies exceed expectations typically in AT-rich genomes, the +1 frame and for TGA/TAA but not TAG. With this complex evidence, simply rejecting or accepting the ambush hypothesis is not warranted. We propose a refined post hoc model, whereby AT-rich genomes have more accidental frameshifts, handled by RF2–RF3 complexes (associated with TGA/TAA) and are mostly +1 (or −2) slips. Supporting this, excesses positively correlate with in silico predicted frameshift probabilities. Thus, we propose a more viable framework, whereby genomes broadly adopt one of the two strategies to combat frameshifts: preventing frameshifting (GC-rich) or permitting frameshifts but minimizing impacts when most are caught early (AT-rich). Our refined framework holds promise yet some features, such as the bias of out-of-frame sense codons, remain unexplained.
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Affiliation(s)
- Liam Abrahams
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, United Kingdom
| | - Laurence D Hurst
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, United Kingdom
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Abstract
Accurate translation of the genetic code is critical to ensure expression of proteins with correct amino acid sequences. Certain tRNAs can cause a shift out of frame (i.e., frameshifting) due to imbalances in tRNA concentrations, lack of tRNA modifications or insertions or deletions in tRNAs (called frameshift suppressors). Here, we determined the structural basis for how frameshift-suppressor tRNASufA6 (a derivative of tRNAPro) reprograms the mRNA frame to translate a 4-nt codon when bound to the bacterial ribosome. After decoding at the aminoacyl (A) site, the crystal structure of the anticodon stem-loop of tRNASufA6 bound in the peptidyl (P) site reveals ASL conformational changes that allow for recoding into the +1 mRNA frame. Furthermore, a crystal structure of full-length tRNASufA6 programmed in the P site shows extensive conformational rearrangements of the 30S head and body domains similar to what is observed in a translocation intermediate state containing elongation factor G (EF-G). The 30S movement positions tRNASufA6 toward the 30S exit (E) site disrupting key 16S rRNA-mRNA interactions that typically define the mRNA frame. In summary, this tRNA-induced 30S domain change in the absence of EF-G causes the ribosome to lose its grip on the mRNA and uncouples the canonical forward movement of the tRNAs during elongation.
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Wan J, Gao X, Mao Y, Zhang X, Qian SB. A Coding Sequence-Embedded Principle Governs Translational Reading Frame Fidelity. RESEARCH (WASHINGTON, D.C.) 2018; 2018:7089174. [PMID: 31549036 PMCID: PMC6750092 DOI: 10.1155/2018/7089174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 08/28/2018] [Indexed: 06/10/2023]
Abstract
Upon initiation at a start codon, the ribosome must maintain the correct reading frame for hundreds of codons in order to produce functional proteins. While some sequence elements are able to trigger programmed ribosomal frameshifting (PRF), very little is known about how the ribosome normally prevents spontaneous frameshift errors that can have dire consequences if uncorrected. Using high resolution ribosome profiling data sets, we discovered that the translating ribosome uses the 3' end of 18S rRNA to scan the AUG-like codons after the decoding process. The postdecoding mRNA:rRNA interaction not only contributes to predominant translational pausing, but also provides a retrospective mechanism to safeguard the ribosome in the correct reading frame. Partially eliminating the AUG-like "sticky" codons in the reporter message leads to increased +1 frameshift errors. Remarkably, mutating the highly conserved CAU triplet of 18S rRNA globally changes the codon "stickiness". Further supporting the role of "sticky" sequences in reading frame maintenance, the codon composition of open reading frames is highly optimized across eukaryotic genomes. These results suggest an important layer of information embedded within the protein-coding sequences that instructs the ribosome to ensure reading frame fidelity during translation.
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Affiliation(s)
- Ji Wan
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Xiangwei Gao
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Yuanhui Mao
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Xingqian Zhang
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Shu-Bing Qian
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
- Graduate Programs in Genetics Genomics and Development, Biochemistry Molecular and Cellular Biology, Cornell University, Ithaca, NY 14853, USA
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Chen Y, Wan Y, Wang N, Yuan Z, Niu W, Li Q, Guo J. Controlling the Replication of a Genomically Recoded HIV-1 with a Functional Quadruplet Codon in Mammalian Cells. ACS Synth Biol 2018; 7:1612-1617. [PMID: 29787233 DOI: 10.1021/acssynbio.8b00096] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Large efforts have been devoted to genetic code engineering in the past decade, aiming for unnatural amino acid mutagenesis. Recently, an increasing number of studies were reported to employ quadruplet codons to encode unnatural amino acids. We and others have demonstrated that the quadruplet decoding efficiency could be significantly enhanced by an extensive engineering of tRNAs bearing an extra nucleotide in their anticodon loops. In this work, we report the identification of tRNA mutants derived from directed evolution to efficiently decode a UAGA quadruplet codon in mammalian cells. Intriguingly, the trend of quadruplet codon decoding efficiency among the tested tRNA variants in mammalian cells was largely the same as that in E. coli. We subsequently demonstrate the utility of quadruplet codon decoding by the construction of the first HIV-1 mutant that lacks any in-frame amber nonsense codons and can be precisely activated by the decoding of a genomically embedded UAGA codon with an unnatural amino acid. Such conditionally activatable HIV-1 mutant can likely facilitate both fundamental investigations of HIV-1 as well as vaccine developments. The use of quadruplet codon, instead of an amber nonsense codon, to control HIV-1 replication has the advantage in that the correction of a frameshift caused by a quadruplet codon is much less likely than the reversion of an amber codon back into a sense codon in HIV-1.
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Johansson MJO, Xu F, Byström AS. Elongator-a tRNA modifying complex that promotes efficient translational decoding. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1861:401-408. [PMID: 29170010 DOI: 10.1016/j.bbagrm.2017.11.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 11/19/2017] [Indexed: 12/22/2022]
Abstract
Naturally occurring modifications of the nucleosides in the anticodon region of tRNAs influence their translational decoding properties. Uridines present at the wobble position in eukaryotic cytoplasmic tRNAs often contain a 5-carbamoylmethyl (ncm(5)) or 5-methoxycarbonylmethyl (mcm(5)) side-chain and sometimes also a 2-thio or 2'-O-methyl group. The first step in the formation of the ncm(5) and mcm(5) side-chains requires the conserved six-subunit Elongator complex. Although Elongator has been implicated in several different cellular processes, accumulating evidence suggests that its primary, and possibly only, cellular function is to promote modification of tRNAs. In this review, we discuss the biosynthesis and function of modified wobble uridines in eukaryotic cytoplasmic tRNAs, focusing on the in vivo role of Elongator-dependent modifications in Saccharomyces cerevisiae. This article is part of a Special Issue entitled: SI: Regulation of tRNA synthesis and modification in physiological conditions and disease edited by Dr. Boguta Magdalena.
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Affiliation(s)
| | - Fu Xu
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
| | - Anders S Byström
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden.
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Tuorto F, Lyko F. Genome recoding by tRNA modifications. Open Biol 2017; 6:rsob.160287. [PMID: 27974624 PMCID: PMC5204126 DOI: 10.1098/rsob.160287] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 11/14/2016] [Indexed: 11/12/2022] Open
Abstract
RNA modifications are emerging as an additional regulatory layer on top of the primary RNA sequence. These modifications are particularly enriched in tRNAs where they can regulate not only global protein translation, but also protein translation at the codon level. Modifications located in or in the vicinity of tRNA anticodons are highly conserved in eukaryotes and have been identified as potential regulators of mRNA decoding. Recent studies have provided novel insights into how these modifications orchestrate the speed and fidelity of translation to ensure proper protein homeostasis. This review highlights the prominent modifications in the tRNA anticodon loop: queuosine, inosine, 5-methoxycarbonylmethyl-2-thiouridine, wybutosine, threonyl-carbamoyl-adenosine and 5-methylcytosine. We discuss the functional relevance of these modifications in protein translation and their emerging role in eukaryotic genome recoding during cellular adaptation and disease.
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Affiliation(s)
- Francesca Tuorto
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
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45
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DEEPN as an Approach for Batch Processing of Yeast 2-Hybrid Interactions. Cell Rep 2017; 17:303-315. [PMID: 27681439 DOI: 10.1016/j.celrep.2016.08.095] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/06/2016] [Accepted: 08/29/2016] [Indexed: 01/06/2023] Open
Abstract
We adapted the yeast 2-hybrid assay to simultaneously uncover multiple transient protein interactions within a single screen by using a strategy termed DEEPN (dynamic enrichment for evaluation of protein networks). This approach incorporates high-throughput DNA sequencing and computation to follow competition among a plasmid population encoding interacting partners. To demonstrate the capacity of DEEPN, we identify a wide range of ubiquitin-binding proteins, including interactors that we verify biochemically. To demonstrate the specificity of DEEPN, we show that DEEPN allows simultaneous comparison of candidate interactors across multiple bait proteins, allowing differential interactions to be identified. This feature was used to identify interactors that distinguish between GTP- and GDP-bound conformations of Rab5.
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46
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Pei H, Han S, Yang S, Lei Z, Zheng J, Jia Z. Phosphorylation of bacterial L9 and its functional implication in response to starvation stress. FEBS Lett 2017; 591:3421-3430. [PMID: 28898405 DOI: 10.1002/1873-3468.12840] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 08/20/2017] [Accepted: 08/28/2017] [Indexed: 11/10/2022]
Abstract
The bacterial L9 (bL9) protein expressed and purified from Escherichia coli is stably phosphorylated. We mapped seven Ser/Thr phosphorylation sites, all of which but one are located at the carboxyl-terminal domain (CTD). When a histidine tag is fused to the C-terminus, bL9 is no longer phosphorylated. Phosphorylation of bL9 causes complete disordering of its CTD and helps cell survival under nutrient-limiting conditions. Previous structural studies of the ribosome have shown that bL9 exhibits two distinct conformations, one of which competes with binding of RelA to the 30s rRNA and prevents RelA activation. Taken together, we suggest that the flexibility of the bL9 CTD enabled by phosphorylation would remove the steric hindrance, serving as a previously unknown mechanism to regulate RelA function and help cell survival under starvation stress.
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Affiliation(s)
- Hairun Pei
- College of Chemistry, Beijing Normal University, China.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology & Business University, China
| | - Shengnan Han
- College of Chemistry, Beijing Normal University, China
| | - Shaoyuan Yang
- College of Chemistry, Beijing Normal University, China
| | - Zhen Lei
- College of Chemistry, Beijing Normal University, China
| | - Jimin Zheng
- College of Chemistry, Beijing Normal University, China
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada
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47
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Agris PF, Eruysal ER, Narendran A, Väre VYP, Vangaveti S, Ranganathan SV. Celebrating wobble decoding: Half a century and still much is new. RNA Biol 2017; 15:537-553. [PMID: 28812932 PMCID: PMC6103715 DOI: 10.1080/15476286.2017.1356562] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/04/2017] [Accepted: 07/06/2017] [Indexed: 10/25/2022] Open
Abstract
A simple post-transcriptional modification of tRNA, deamination of adenosine to inosine at the first, or wobble, position of the anticodon, inspired Francis Crick's Wobble Hypothesis 50 years ago. Many more naturally-occurring modifications have been elucidated and continue to be discovered. The post-transcriptional modifications of tRNA's anticodon domain are the most diverse and chemically complex of any RNA modifications. Their contribution with regards to chemistry, structure and dynamics reveal individual and combined effects on tRNA function in recognition of cognate and wobble codons. As forecast by the Modified Wobble Hypothesis 25 years ago, some individual modifications at tRNA's wobble position have evolved to restrict codon recognition whereas others expand the tRNA's ability to read as many as four synonymous codons. Here, we review tRNA wobble codon recognition using specific examples of simple and complex modification chemistries that alter tRNA function. Understanding natural modifications has inspired evolutionary insights and possible innovation in protein synthesis.
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Affiliation(s)
- Paul F. Agris
- The RNA Institute, State University of New York, Albany, NY, USA
- Department of Biology, State University of New York, Albany, NY, USA
- Department of Chemistry, State University of New York, Albany, NY, USA
| | - Emily R. Eruysal
- Department of Biology, State University of New York, Albany, NY, USA
| | - Amithi Narendran
- Department of Biology, State University of New York, Albany, NY, USA
| | - Ville Y. P. Väre
- Department of Biology, State University of New York, Albany, NY, USA
| | - Sweta Vangaveti
- The RNA Institute, State University of New York, Albany, NY, USA
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Reviewing evidence for systematic transcriptional deletions, nucleotide exchanges, and expanded codons, and peptide clusters in human mitochondria. Biosystems 2017; 160:10-24. [PMID: 28807694 DOI: 10.1016/j.biosystems.2017.08.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 07/26/2017] [Accepted: 08/04/2017] [Indexed: 12/12/2022]
Abstract
Polymerization sometimes transforms sequences by (a) systematic deletions of mono-, dinucleotides after trinucleotides, or (b) 23 systematic nucleotide exchanges (9 symmetric, X<>Y, e.g. G<>T, 14 asymmetric, X > Y > Z > X, e.g. A > G > T > A), producing del- and swinger RNAs. Some peptides correspond to del- and swinger RNA translations, also according to tetracodons, codons expanded by a silent nucleotide. Here new analyzes assume different proteolytic patterns, partially alleviating false negative peptide detection biases, expanding noncanonical mitoproteome profiles. Mito-genomic, -transcriptomic and -proteomic evidence for noncanonical transcriptions and translations are reviewed and clusters of del- and swinger peptides (also along tetracodons) are described. Noncanonical peptide clusters indicate regulated expression of cryptically encoded mitochondrial protein coding genes. These candidate noncanonical proteins don't resemble known proteins.
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Seligmann H. Natural mitochondrial proteolysis confirms transcription systematically exchanging/deleting nucleotides, peptides coded by expanded codons. J Theor Biol 2016; 414:76-90. [PMID: 27899286 DOI: 10.1016/j.jtbi.2016.11.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 11/11/2016] [Accepted: 11/22/2016] [Indexed: 12/19/2022]
Abstract
Protein sequences have higher linguistic complexities than human languages. This indicates undeciphered multilayered, overprinted information/genetic codes. Some superimposed genetic information is revealed by detections of transcripts systematically (a) exchanging nucleotides (nine symmetric, e.g. A<->C, fourteen asymmetric, e.g. A->C->G->A, swinger RNAs) translated according to tri-, tetra- and pentacodons, and (b) deleting mono-, dinucleotides after each trinucleotide (delRNAs). Here analyses of two independent proteomic datasets considering natural proteolysis confirm independently translation of these non-canonical RNAs, also along tetra- and pentacodons, increasing coverage of putative, cryptically encoded proteins. Analyses assuming endoproteinase GluC and elastase digestions (cleavages after residues D, E, and A, L, I, V, respectively) detect additional peptides colocalizing with detected non-canonical RNAs. Analyses detect fewer peptides matching GluC-, elastase- than trypsin-digestions: artificial trypsin-digestion outweighs natural proteolysis. Results suggest occurrences of complete proteins entirely matching non-canonical, superimposed encoding(s). Protein-coding after bijective transformations could explain genetic code symmetries, such as along Rumer's transformation.
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Affiliation(s)
- Hervé Seligmann
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes, Faculté de Médecine, URMITE CNRS-IRD 198 UMER 6236, IHU (Institut Hospitalo-Universitaire), Aix-Marseille University, Marseille, France.
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50
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Seligmann H. Natural chymotrypsin-like-cleaved human mitochondrial peptides confirm tetra-, pentacodon, non-canonical RNA translations. Biosystems 2016; 147:78-93. [PMID: 27477600 DOI: 10.1016/j.biosystems.2016.07.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Revised: 07/15/2016] [Accepted: 07/26/2016] [Indexed: 12/22/2022]
Abstract
Mass spectra of human mitochondrial peptides match non-canonical transcripts systematically (a) deleting mono/dinucleotides after trinucleotides (delRNA), (b) exchanging nucleotides (swinger RNA), translated according to tri, (c) tetra- and pentacodons (codons expanded by a 4th (and 5th) silent nucleotide(s)). Swinger transcriptions are 23 bijective transformations, nine symmetric (X<->Y, e.g. A<->C) and fourteen asymmetric exchanges (X->Y->Z->X, e.g. A->C->G->A). Here, proteomic analyses assuming cleavage after W,Y, F (chymotrypsin-like, for trypsinized samples) detect fewer chymotrypsinized than trypsinized peptides. Detected non-canonical peptides map preferentially on detected non-canonical RNAs for chymotrypsinized peptides, as previously found for trypsinized peptides. This suggests residual natural chymotrypsin-like digestion detectable within experimentally trypsinized peptide data. Some trypsinized peptides are detected twice, by analyses assuming trypsin, and those assuming chymotrypsin cleavages. They have higher spectra counts than peptides detected only once, meaning that abundant peptides are more frequently detected, but detection certainties resemble those for peptides detected only once. Analyses assuming 'incorrect' digestions are inadequate negative controls for digestion enzymes naturally active in biological samples. Chymotrypsin-analyses confirm non-canonical transcriptions/translations independently of results obtained assuming trypsinization, increase non-canonical peptidome coverage, indicating mitogenome-encoding of yet undetected proteins.
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Affiliation(s)
- Hervé Seligmann
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes, Faculté de Médecine, Université d'Aix-Marseille, URMITE CNRS-IRD 198 UMER 6236, Marseille, France.
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