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Das A, Bao C, Ermolenko DN. Comparing FRET Pairs that Report on Intersubunit Rotation in Bacterial Ribosomes. J Mol Biol 2023; 435:168185. [PMID: 37348753 PMCID: PMC10528089 DOI: 10.1016/j.jmb.2023.168185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/03/2023] [Accepted: 06/14/2023] [Indexed: 06/24/2023]
Abstract
Mediated by elongation factor G (EF-G), ribosome translocation along mRNA is accompanied by rotational movement between ribosomal subunits. Here, we reassess whether the intersubunit rotation requires GTP hydrolysis by EF-G or can occur spontaneously. To that end, we employ two independent FRET assays, which are based on labeling either ribosomal proteins (bS6 and bL9) or rRNAs (h44 of 16S and H101 of 23S rRNA). Both FRET pairs reveal three FRET states, corresponding to the non-rotated, rotated and semi-rotated conformations of the ribosome. Both FRET assays show that in the absence of EF-G, pre-translocation ribosomes containing deacylated P-site tRNA undergo spontaneous intersubunit rotations between non-rotated and rotated conformations. While the two FRET pairs exhibit largely similar behavior, they substantially differ in the fraction of ribosomes showing spontaneous fluctuations. Nevertheless, instead of being an invariable intrinsic property of each FRET pair, the fraction of spontaneously fluctuating molecules changes in both FRET assays depending on experimental conditions. Our results underscore importance of using multiple FRET pairs in studies of ribosome dynamics and highlight the role of thermally-driven large-scale ribosome rearrangements in translation.
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Affiliation(s)
- Ananya Das
- Department of Biochemistry & Biophysics, School of Medicine and Dentistry, and Center for RNA Biology, University of Rochester, Rochester, NY 14642, United States
| | - Chen Bao
- Department of Biochemistry & Biophysics, School of Medicine and Dentistry, and Center for RNA Biology, University of Rochester, Rochester, NY 14642, United States
| | - Dmitri N Ermolenko
- Department of Biochemistry & Biophysics, School of Medicine and Dentistry, and Center for RNA Biology, University of Rochester, Rochester, NY 14642, United States.
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2
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Das A, Bao C, Ermolenko DN. Comparing FRET pairs that report on intersubunit rotation in bacterial ribosomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.540051. [PMID: 37214817 PMCID: PMC10197640 DOI: 10.1101/2023.05.09.540051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Mediated by elongation factor G (EF-G), ribosome translocation along mRNA is accompanied by rotational movement between ribosomal subunits. Here, we reassess whether the intersubunit rotation requires GTP hydrolysis by EF-G or can occur spontaneously. To that end, we employ two independent FRET assays, which are based on labeling either ribosomal proteins (bS6 and bL9) or rRNAs (h44 of 16S and H101 of 23S rRNA). Both FRET pairs reveal three FRET states, corresponding to the non-rotated, rotated and semi-rotated conformations of the ribosome. Both FRET assays show that in the absence of EF-G, pre-translocation ribosomes containing deacylated P-site tRNA undergo spontaneous intersubunit rotations between non-rotated and rotated conformations. While the two FRET pairs exhibit largely similar behavior, they substantially differ in the fraction of ribosomes showing spontaneous fluctuations. Nevertheless, instead of being an invariable intrinsic property of each FRET pair, the fraction of spontaneously fluctuating molecules changes in both FRET assays depending on experimental conditions. Our results underscore importance of using multiple FRET pairs in studies of ribosome dynamics and highlight the role of thermally-driven large-scale ribosome rearrangements in translation.
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3
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Ribosomal RNA 2'- O-methylations regulate translation by impacting ribosome dynamics. Proc Natl Acad Sci U S A 2022; 119:e2117334119. [PMID: 35294285 PMCID: PMC8944910 DOI: 10.1073/pnas.2117334119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
SignificanceThe presence of RNA chemical modifications has long been known, but their precise molecular consequences remain unknown. 2'-O-methylation is an abundant modification that exists in RNA in all domains of life. Ribosomal RNA (rRNA) represents a functionally important RNA that is heavily modified by 2'-O-methylations. Although abundant at functionally important regions of the rRNA, the contribution of 2'-O-methylations to ribosome activities is unknown. By establishing a method to disturb rRNA 2'-O-methylation patterns, we show that rRNA 2'-O-methylations affect the function and fidelity of the ribosome and change the balance between different ribosome conformational states. Our work links 2'-O-methylation to ribosome dynamics and defines a set of critical rRNA 2'-O-methylations required for ribosome biogenesis and others that are dispensable.
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4
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Cook GM, Brown K, Shang P, Li Y, Soday L, Dinan AM, Tumescheit C, Mockett APA, Fang Y, Firth AE, Brierley I. Ribosome profiling of porcine reproductive and respiratory syndrome virus reveals novel features of viral gene expression. eLife 2022; 11:e75668. [PMID: 35226596 PMCID: PMC9000960 DOI: 10.7554/elife.75668] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/26/2022] [Indexed: 11/13/2022] Open
Abstract
The arterivirus porcine reproductive and respiratory syndrome virus (PRRSV) causes significant economic losses to the swine industry worldwide. Here we apply ribosome profiling (RiboSeq) and parallel RNA sequencing (RNASeq) to characterise the transcriptome and translatome of both species of PRRSV and to analyse the host response to infection. We calculated programmed ribosomal frameshift (PRF) efficiency at both sites on the viral genome. This revealed the nsp2 PRF site as the second known example where temporally regulated frameshifting occurs, with increasing -2 PRF efficiency likely facilitated by accumulation of the PRF-stimulatory viral protein, nsp1β. Surprisingly, we find that PRF efficiency at the canonical ORF1ab frameshift site also increases over time, in contradiction of the common assumption that RNA structure-directed frameshift sites operate at a fixed efficiency. This has potential implications for the numerous other viruses with canonical PRF sites. Furthermore, we discovered several highly translated additional viral ORFs, the translation of which may be facilitated by multiple novel viral transcripts. For example, we found a highly expressed 125-codon ORF overlapping nsp12, which is likely translated from novel subgenomic RNA transcripts that overlap the 3' end of ORF1b. Similar transcripts were discovered for both PRRSV-1 and PRRSV-2, suggesting a potential conserved mechanism for temporally regulating expression of the 3'-proximal region of ORF1b. We also identified a highly translated, short upstream ORF in the 5' UTR, the presence of which is highly conserved amongst PRRSV-2 isolates. These findings reveal hidden complexity in the gene expression programmes of these important nidoviruses.
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Affiliation(s)
- Georgia M Cook
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Katherine Brown
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Pengcheng Shang
- Department of Diagnostic Medicine and Pathobiology, Kansas State UniversityManhattanUnited States
| | - Yanhua Li
- Department of Diagnostic Medicine and Pathobiology, Kansas State UniversityManhattanUnited States
| | - Lior Soday
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Adam M Dinan
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | | | | | - Ying Fang
- Department of Diagnostic Medicine and Pathobiology, Kansas State UniversityManhattanUnited States
| | - Andrew E Firth
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Ian Brierley
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
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5
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Bao C, Zhu M, Nykonchuk I, Wakabayashi H, Mathews DH, Ermolenko DN. Specific length and structure rather than high thermodynamic stability enable regulatory mRNA stem-loops to pause translation. Nat Commun 2022; 13:988. [PMID: 35190568 PMCID: PMC8861025 DOI: 10.1038/s41467-022-28600-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 02/03/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractTranslating ribosomes unwind mRNA secondary structures by three basepairs each elongation cycle. Despite the ribosome helicase, certain mRNA stem-loops stimulate programmed ribosomal frameshift by inhibiting translation elongation. Here, using mutagenesis, biochemical and single-molecule experiments, we examine whether high stability of three basepairs, which are unwound by the translating ribosome, is critical for inducing ribosome pauses. We find that encountering frameshift-inducing mRNA stem-loops from the E. coli dnaX mRNA and the gag-pol transcript of Human Immunodeficiency Virus (HIV) hinders A-site tRNA binding and slows down ribosome translocation by 15-20 folds. By contrast, unwinding of first three basepairs adjacent to the mRNA entry channel slows down the translating ribosome by only 2-3 folds. Rather than high thermodynamic stability, specific length and structure enable regulatory mRNA stem-loops to stall translation by forming inhibitory interactions with the ribosome. Our data provide the basis for rationalizing transcriptome-wide studies of translation and searching for novel regulatory mRNA stem-loops.
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6
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Structural and molecular basis for Cardiovirus 2A protein as a viral gene expression switch. Nat Commun 2021; 12:7166. [PMID: 34887415 PMCID: PMC8660796 DOI: 10.1038/s41467-021-27400-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 11/12/2021] [Indexed: 12/21/2022] Open
Abstract
Programmed –1 ribosomal frameshifting (PRF) in cardioviruses is activated by the 2A protein, a multi-functional virulence factor that also inhibits cap-dependent translational initiation. Here we present the X-ray crystal structure of 2A and show that it selectively binds to a pseudoknot-like conformation of the PRF stimulatory RNA element in the viral genome. Using optical tweezers, we demonstrate that 2A stabilises this RNA element, likely explaining the increase in PRF efficiency in the presence of 2A. Next, we demonstrate a strong interaction between 2A and the small ribosomal subunit and present a cryo-EM structure of 2A bound to initiated 70S ribosomes. Multiple copies of 2A bind to the 16S rRNA where they may compete for binding with initiation and elongation factors. Together, these results define the structural basis for RNA recognition by 2A, show how 2A-mediated stabilisation of an RNA pseudoknot promotes PRF, and reveal how 2A accumulation may shut down translation during virus infection. Many RNA viruses employ programmed –1 ribosomal frameshifting (PRF) to expand their coding capacity and optimize production of viral proteins. Here, the authors report structural and biophysical analysis of protein 2A from a cardiovirus, with insights into the mechanism of its PRF-stimulatory function.
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7
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Napthine S, Hill CH, Nugent HCM, Brierley I. Modulation of Viral Programmed Ribosomal Frameshifting and Stop Codon Readthrough by the Host Restriction Factor Shiftless. Viruses 2021; 13:v13071230. [PMID: 34202160 PMCID: PMC8310280 DOI: 10.3390/v13071230] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/15/2021] [Accepted: 06/19/2021] [Indexed: 12/18/2022] Open
Abstract
The product of the interferon-stimulated gene C19orf66, Shiftless (SHFL), restricts human immunodeficiency virus replication through downregulation of the efficiency of the viral gag/pol frameshifting signal. In this study, we demonstrate that bacterially expressed, purified SHFL can decrease the efficiency of programmed ribosomal frameshifting in vitro at a variety of sites, including the RNA pseudoknot-dependent signals of the coronaviruses IBV, SARS-CoV and SARS-CoV-2, and the protein-dependent stimulators of the cardioviruses EMCV and TMEV. SHFL also reduced the efficiency of stop-codon readthrough at the murine leukemia virus gag/pol signal. Using size-exclusion chromatography, we confirm the binding of the purified protein to mammalian ribosomes in vitro. Finally, through electrophoretic mobility shift assays and mutational analysis, we show that expressed SHFL has strong RNA binding activity that is necessary for full activity in the inhibition of frameshifting, but shows no clear specificity for stimulatory RNA structures.
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Affiliation(s)
| | | | | | - Ian Brierley
- Correspondence: ; Tel.: +44-12-2333-6914; Fax: +44-12-2333-6926
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8
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Chang KC, Wen JD. Programmed -1 ribosomal frameshifting from the perspective of the conformational dynamics of mRNA and ribosomes. Comput Struct Biotechnol J 2021; 19:3580-3588. [PMID: 34257837 PMCID: PMC8246090 DOI: 10.1016/j.csbj.2021.06.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 06/11/2021] [Accepted: 06/12/2021] [Indexed: 11/01/2022] Open
Abstract
Programmed -1 ribosomal frameshifting (-1 PRF) is a translation mechanism that regulates the relative expression level of two proteins encoded on the same messenger RNA (mRNA). This regulation is commonly used by viruses such as coronaviruses and retroviruses but rarely by host human cells, and for this reason, it has long been considered as a therapeutic target for antiviral drug development. Understanding the molecular mechanism of -1 PRF is one step toward this goal. Minus-one PRF occurs with a certain efficiency when translating ribosomes encounter the specialized mRNA signal consisting of the frameshifting site and a downstream stimulatory structure, which impedes translocation of the ribosome. The impeded ribosome can still undergo profound conformational changes to proceed with translocation; however, some of these changes may be unique and essential to frameshifting. In addition, most stimulatory structures exhibit conformational dynamics and sufficient mechanical strength, which, when under the action of ribosomes, may in turn further promote -1 PRF efficiency. In this review, we discuss how the dynamic features of ribosomes and mRNA stimulatory structures may influence the occurrence of -1 PRF and propose a hypothetical frameshifting model that recapitulates the role of conformational dynamics.
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Affiliation(s)
- Kai-Chun Chang
- Department of Bioengineering and Therapeutic Sciences, Schools of Medicine and Pharmacy, University of California, San Francisco, CA 94158, United States
| | - Jin-Der Wen
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan
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9
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Bao C, Loerch S, Ling C, Korostelev AA, Grigorieff N, Ermolenko DN. mRNA stem-loops can pause the ribosome by hindering A-site tRNA binding. eLife 2020; 9:e55799. [PMID: 32427100 PMCID: PMC7282821 DOI: 10.7554/elife.55799] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 05/18/2020] [Indexed: 12/27/2022] Open
Abstract
Although the elongating ribosome is an efficient helicase, certain mRNA stem-loop structures are known to impede ribosome movement along mRNA and stimulate programmed ribosome frameshifting via mechanisms that are not well understood. Using biochemical and single-molecule Förster resonance energy transfer (smFRET) experiments, we studied how frameshift-inducing stem-loops from E. coli dnaX mRNA and the gag-pol transcript of Human Immunodeficiency Virus (HIV) perturb translation elongation. We find that upon encountering the ribosome, the stem-loops strongly inhibit A-site tRNA binding and ribosome intersubunit rotation that accompanies translation elongation. Electron cryo-microscopy (cryo-EM) reveals that the HIV stem-loop docks into the A site of the ribosome. Our results suggest that mRNA stem-loops can transiently escape the ribosome helicase by binding to the A site. Thus, the stem-loops can modulate gene expression by sterically hindering tRNA binding and inhibiting translation elongation.
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Affiliation(s)
- Chen Bao
- Department of Biochemistry and Biophysics at School of Medicine and Dentistry and Center for RNA Biology, University of RochesterRochesterUnited States
| | - Sarah Loerch
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Clarence Ling
- Department of Biochemistry and Biophysics at School of Medicine and Dentistry and Center for RNA Biology, University of RochesterRochesterUnited States
| | - Andrei A Korostelev
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical SchoolWorcesterUnited States
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Nikolaus Grigorieff
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Dmitri N Ermolenko
- Department of Biochemistry and Biophysics at School of Medicine and Dentistry and Center for RNA Biology, University of RochesterRochesterUnited States
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10
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Rodnina MV, Korniy N, Klimova M, Karki P, Peng BZ, Senyushkina T, Belardinelli R, Maracci C, Wohlgemuth I, Samatova E, Peske F. Translational recoding: canonical translation mechanisms reinterpreted. Nucleic Acids Res 2020; 48:1056-1067. [PMID: 31511883 PMCID: PMC7026636 DOI: 10.1093/nar/gkz783] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/21/2019] [Accepted: 08/30/2019] [Indexed: 01/15/2023] Open
Abstract
During canonical translation, the ribosome moves along an mRNA from the start to the stop codon in exact steps of one codon at a time. The collinearity of the mRNA and the protein sequence is essential for the quality of the cellular proteome. Spontaneous errors in decoding or translocation are rare and result in a deficient protein. However, dedicated recoding signals in the mRNA can reprogram the ribosome to read the message in alternative ways. This review summarizes the recent advances in understanding the mechanisms of three types of recoding events: stop-codon readthrough, –1 ribosome frameshifting and translational bypassing. Recoding events provide insights into alternative modes of ribosome dynamics that are potentially applicable to other non-canonical modes of prokaryotic and eukaryotic translation.
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Affiliation(s)
- Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Natalia Korniy
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Mariia Klimova
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Prajwal Karki
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Bee-Zen Peng
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Tamara Senyushkina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Riccardo Belardinelli
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Cristina Maracci
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Ingo Wohlgemuth
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Ekaterina Samatova
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Frank Peske
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
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11
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Wang H, Sun L, Gaba A, Qu X. An in vitro single-molecule assay for eukaryotic cap-dependent translation initiation kinetics. Nucleic Acids Res 2020; 48:e6. [PMID: 31722415 PMCID: PMC7145701 DOI: 10.1093/nar/gkz1066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 10/18/2019] [Accepted: 10/29/2019] [Indexed: 11/12/2022] Open
Abstract
Eukaryotic mRNAs are predominantly translated via the cap-dependent pathway. Initiation is a rate-limiting step in cap-dependent translation and is the main target of translational control mechanisms. There is a lack of high-resolution techniques for characterizing the cap-dependent initiation kinetics. Here, we report an in vitro single-molecule assay that allows characterization of both initiation and peptide chain elongation kinetics for cap-dependent translation. Surprisingly, the histogram of the first-round initiation time is highly asymmetrical and spans a large time range that is several-fold greater than the average peptide synthesis time in translation reactions with a firefly luciferase-encoding mRNA. Both the histogram and single-molecule trajectories reveal an unexpected high-degree of asynchrony in translation activity between mRNA molecules. Furthermore, by inserting a small stem-loop (ΔG = -4.8 kcal/mol) in the middle of the mRNA 5' untranslated region (UTR), our assay robustly detects small changes in budding yeast initiation kinetics, which could not be resolved by bulk luminescence kinetics. Lastly, we demonstrate the general applicability of this assay to distinct cell-free translation systems by using extracts prepared from budding yeast, wheat germ, and rabbit reticulocyte lysates. This assay should facilitate mechanistic studies of eukaryotic cap-dependent translation initiation and translational control.
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Affiliation(s)
- Hongyun Wang
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Lexi Sun
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Department of Physiology, Biophysics and Systems Biology, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA
| | - Anthony Gaba
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Xiaohui Qu
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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12
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Choi J, O’Loughlin S, Atkins JF, Puglisi JD. The energy landscape of -1 ribosomal frameshifting. SCIENCE ADVANCES 2020; 6:eaax6969. [PMID: 31911945 PMCID: PMC6938710 DOI: 10.1126/sciadv.aax6969] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 11/04/2019] [Indexed: 05/02/2023]
Abstract
Maintenance of translational reading frame ensures the fidelity of information transfer during protein synthesis. Yet, programmed ribosomal frameshifting sequences within the coding region promote a high rate of reading frame change at predetermined sites thus enriching genomic information density. Frameshifting is typically stimulated by the presence of 3' messenger RNA (mRNA) structures, but how these mRNA structures enhance -1 frameshifting remains debatable. Here, we apply single-molecule and ensemble approaches to formulate a mechanistic model of ribosomal -1 frameshifting. Our model suggests that the ribosome is intrinsically susceptible to frameshift before its translocation and this transient state is prolonged by the presence of a precisely positioned downstream mRNA structure. We challenged this model using temperature variation in vivo, which followed the prediction made based on in vitro results. Our results provide a quantitative framework for analyzing other frameshifting enhancers and a potential approach to control gene expression dynamically using programmed frameshifting.
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Affiliation(s)
- Junhong Choi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA
- Department of Applied Physics, Stanford University, Stanford, CA 94305-4090, USA
| | - Sinéad O’Loughlin
- Schools of Biochemistry and Microbiology, University College Cork, Western Gateway Building, Western Road, Cork, Ireland
| | - John F. Atkins
- Schools of Biochemistry and Microbiology, University College Cork, Western Gateway Building, Western Road, Cork, Ireland
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA
| | - Joseph D. Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA
- Corresponding author.
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13
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Chang KC, Salawu EO, Chang YY, Wen JD, Yang LW. Resolution-exchanged structural modeling and simulations jointly unravel that subunit rolling underlies the mechanism of programmed ribosomal frameshifting. Bioinformatics 2019; 35:945-952. [PMID: 30169551 DOI: 10.1093/bioinformatics/bty762] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 07/26/2018] [Accepted: 08/28/2018] [Indexed: 12/20/2022] Open
Abstract
MOTIVATION Programmed ribosomal frameshifting (PRF) is widely used by viruses and bacteria to produce different proteins from a single mRNA template. How steric hindrance of a PRF-stimulatory mRNA structure transiently modifies the conformational dynamics of the ribosome, and thereby allows tRNA slippage, remains elusive. RESULTS Here, we leverage linear response theories and resolution-exchanged simulations to construct a structural/dynamics model that connects and rationalizes existing structural, single-molecule and mutagenesis data by resolution-exchanged structural modelling and simulations. Our combined theoretical techniques provide a temporal and spatial description of PRF with unprecedented mechanistic details. We discover that ribosomal unfolding of the PRF-stimulating pseudoknot exerts resistant forces on the mRNA entrance of the ribosome, and thereby drives 30S subunit rolling. Such motion distorts tRNAs, leads to tRNA slippage, and in turn serves as a delicate control of cis-element's unwinding forces over PRF. AVAILABILITY AND IMPLEMENTATION All the simulation scripts and computational implementations of our methods/analyses (including linear response theory) are included in the bioStructureM suite, provided through GitHub at https://github.com/Yuan-Yu/bioStructureM. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Kai-Chun Chang
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
| | - Emmanuel Oluwatobi Salawu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan.,TIGP Bioinformatics Program, Institute of Information Sciences, Academia Sinica, Taipei, Taiwan
| | - Yuan-Yu Chang
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Jin-Der Wen
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
| | - Lee-Wei Yang
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan.,TIGP Bioinformatics Program, Institute of Information Sciences, Academia Sinica, Taipei, Taiwan.,Physics Division, National Center for Theoretical Sciences, Hsinchu, Taiwan
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14
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Ribosome collisions alter frameshifting at translational reprogramming motifs in bacterial mRNAs. Proc Natl Acad Sci U S A 2019; 116:21769-21779. [PMID: 31591196 PMCID: PMC6815119 DOI: 10.1073/pnas.1910613116] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Ribosomes move along mRNAs in 3-nucleotide steps as they interpret codons that specify which amino acid is required at each position in the protein. There are multiple examples of genes with DNA sequences that do not match the produced proteins because ribosomes move to a new reading frame in the message before finishing translation (so-called frameshifting). This report shows that, when ribosomes stall at mRNA regions prone to cause frameshifting events, trailing ribosomes that collide with them can significantly change the outcome and potentially regulate protein production. This work highlights the principle that biological macromolecules do not function in isolation, and it provides an example of how physical interactions between neighboring complexes can be used to augment their performance. Translational frameshifting involves the repositioning of ribosomes on their messages into decoding frames that differ from those dictated during initiation. Some messenger RNAs (mRNAs) contain motifs that promote deliberate frameshifting to regulate production of the encoded proteins. The mechanisms of frameshifting have been investigated in many systems, and the resulting models generally involve single ribosomes responding to stimulator sequences in their engaged mRNAs. We discovered that the abundance of ribosomes on messages containing the IS3, dnaX, and prfB frameshift motifs significantly influences the levels of frameshifting. We show that this phenomenon results from ribosome collisions that occur during translational stalling, which can alter frameshifting in both the stalled and trailing ribosomes. Bacteria missing ribosomal protein bL9 are known to exhibit a reduction in reading frame maintenance and to have a strong dependence on elongation factor P (EFP). We discovered that ribosomes lacking bL9 become compacted closer together during collisions and that the E-sites of the stalled ribosomes appear to become blocked, which suggests subsequent transpeptidation in transiently stalled ribosomes may become compromised in the absence of bL9. In addition, we determined that bL9 can suppress frameshifting of its host ribosome, likely by regulating E-site dynamics. These findings provide mechanistic insight into the behavior of colliding ribosomes during translation and suggest naturally occurring frameshift elements may be regulated by the abundance of ribosomes relative to an mRNA pool.
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15
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Klimova M, Senyushkina T, Samatova E, Peng BZ, Pearson M, Peske F, Rodnina MV. EF-G-induced ribosome sliding along the noncoding mRNA. SCIENCE ADVANCES 2019; 5:eaaw9049. [PMID: 31183409 PMCID: PMC6551183 DOI: 10.1126/sciadv.aaw9049] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 04/25/2019] [Indexed: 05/02/2023]
Abstract
Translational bypassing is a recoding event during which ribosomes slide over a noncoding region of the messenger RNA (mRNA) to synthesize one protein from two discontinuous reading frames. Structures in the mRNA orchestrate forward movement of the ribosome, but what causes ribosomes to start sliding remains unclear. Here, we show that elongation factor G (EF-G) triggers ribosome take-off by a pseudotranslocation event using a small mRNA stem-loop as an A-site transfer RNA mimic and requires hydrolysis of about two molecules of guanosine 5'-triphosphate per nucleotide of the noncoding gap. Bypassing ribosomes adopt a hyper-rotated conformation, also observed with ribosomes stalled by the SecM sequence, suggesting common ribosome dynamics during translation stalling. Our results demonstrate a new function of EF-G in promoting ribosome sliding along the mRNA, in contrast to codon-wise ribosome movement during canonical translation, and suggest a mechanism by which ribosomes could traverse untranslated parts of mRNAs.
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16
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Amiri H, Noller HF. A tandem active site model for the ribosomal helicase. FEBS Lett 2019; 593:1009-1019. [PMID: 30972734 DOI: 10.1002/1873-3468.13383] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 03/31/2019] [Accepted: 04/06/2019] [Indexed: 12/12/2022]
Abstract
During protein synthesis, the messenger RNA (mRNA) helicase activity of the ribosome ensures that codons are made single stranded before decoding. Here, based on recent structural and functional findings, a quantitative model is presented for a tandem arrangement of two helicase active sites on the ribosome. A distal site encounters mRNA structures first, one elongation cycle earlier than a proximal site. Although unwinding of encountered mRNA structures past the proximal site is required for translocation, two routes exist for translocation past the distal site: sliding, which requires unwinding, and stick-slip, which does not. The model accounts in detail for a number of findings related to the ribosomal helicase and provides a testable framework to further study mRNA unwinding.
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Affiliation(s)
- Hossein Amiri
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA.,Department of Molecular, Cell and Developmental Biology, Center for Molecular Biology of RNA, University of California at Santa Cruz, Santa Cruz, CA, USA
| | - Harry F Noller
- Department of Molecular, Cell and Developmental Biology, Center for Molecular Biology of RNA, University of California at Santa Cruz, Santa Cruz, CA, USA
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17
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Levi M, Whitford PC. Dissecting the Energetics of Subunit Rotation in the Ribosome. J Phys Chem B 2019; 123:2812-2823. [PMID: 30844276 DOI: 10.1021/acs.jpcb.9b00178] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The accurate expression of proteins requires the ribosome to efficiently undergo elaborate conformational rearrangements. The most dramatic of these motions is subunit rotation, which is necessary for tRNA molecules to transition between ribosomal binding sites. While rigid-body descriptions provide a qualitative picture of the process, obtaining quantitative mechanistic insights requires one to account for the relationship between molecular flexibility and collective dynamics. Using simulated rotation events, we assess the quality of experimentally accessible measures for describing the collective displacement of the ∼4000-residue small subunit. For this, we ask whether each coordinate is able to identify the underlying free-energy barrier and transition state ensemble (TSE). We find that intuitive structurally motivated coordinates (e.g., rotation angle, interprotein distances) can distinguish between the endpoints, though they are poor indicators of barrier-crossing events, and they underestimate the free-energy barrier. In contrast, coordinates based on intersubunit bridges can identify the TSE. We additionally verify that the committor probability for the putative TSE configurations is 0.5, a hallmark feature of any transition state. In terms of structural properties, these calculations implicate a transition state in which flexibility allows for asynchronous rearrangements of the bridges, as the ribosome adopts a partially rotated orientation. This provides a theoretical foundation, upon which experimental techniques may precisely quantify the energy landscape of the ribosome.
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Affiliation(s)
- Mariana Levi
- Department of Physics , Northeastern University , Dana Research Center 111, 360 Huntington Avenue , Boston , Massachusetts 02115 , United States
| | - Paul C Whitford
- Department of Physics , Northeastern University , Dana Research Center 111, 360 Huntington Avenue , Boston , Massachusetts 02115 , United States
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18
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Adio S, Sharma H, Senyushkina T, Karki P, Maracci C, Wohlgemuth I, Holtkamp W, Peske F, Rodnina MV. Dynamics of ribosomes and release factors during translation termination in E. coli. eLife 2018; 7:34252. [PMID: 29889659 PMCID: PMC5995542 DOI: 10.7554/elife.34252] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 05/11/2018] [Indexed: 12/28/2022] Open
Abstract
Release factors RF1 and RF2 promote hydrolysis of peptidyl-tRNA during translation termination. The GTPase RF3 promotes recycling of RF1 and RF2. Using single molecule FRET and biochemical assays, we show that ribosome termination complexes that carry two factors, RF1–RF3 or RF2–RF3, are dynamic and fluctuate between non-rotated and rotated states, whereas each factor alone has its distinct signature on ribosome dynamics and conformation. Dissociation of RF1 depends on peptide release and the presence of RF3, whereas RF2 can dissociate spontaneously. RF3 binds in the GTP-bound state and can rapidly dissociate without GTP hydrolysis from termination complex carrying RF1. In the absence of RF1, RF3 is stalled on ribosomes if GTP hydrolysis is blocked. Our data suggest how the assembly of the ribosome–RF1–RF3–GTP complex, peptide release, and ribosome fluctuations promote termination of protein synthesis and recycling of the release factors. Inside cells, molecular machines called ribosomes make proteins using messenger RNA as a template. However, the template contains more than just the information needed to create the protein. A ‘stop codon’ in the mRNA marks where the ribosome should stop. When this is reached a group of proteins called release factors removes the newly made protein from the ribosome. Bacteria typically have three types of release factors. RF1 and RF2 recognize the stop codon, and RF3 helps to release RF1 or RF2 from the ribosome so that it can be recycled to produce another protein. It was not fully understood how the release factors interact with the ribosome and how this terminates protein synthesis. Adio et al. used TIRF microscopy to study individual ribosomes from the commonly studied bacteria species Escherichia coli. This technique allows researchers to monitor movements of the ribosome and record how release factors bind to it. The results of the experiments performed by Adio et al. show that although RF1 and RF2 are very similar to each other, they interact with the ribosome in different ways. In addition, only RF1 relies upon RF3 to release it from the ribosome; RF2 can release itself. RF3 releases RF1 by forcing the ribosome to change shape. RF3 then uses energy produced by the breakdown of a molecule called GTP to help release itself from the ribosome. Most importantly, the findings presented by Adio et al. highlight that the movements of ribosomes and release factors during termination are only loosely coupled rather than occur in a set order. Other molecular machines are likely to work in a similar way. The results could also help us to understand the molecular basis of several human diseases, such as Duchenne muscular dystrophy and cystic fibrosis, that result from ribosomes not recognizing stop codons in the mRNA.
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Affiliation(s)
- Sarah Adio
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Heena Sharma
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Tamara Senyushkina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Prajwal Karki
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Cristina Maracci
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Ingo Wohlgemuth
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Wolf Holtkamp
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, 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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19
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Casy W, Prater AR, Cornish PV. Operative Binding of Class I Release Factors and YaeJ Stabilizes the Ribosome in the Nonrotated State. Biochemistry 2018; 57:1954-1966. [PMID: 29499110 DOI: 10.1021/acs.biochem.7b00824] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
During translation, the small subunit of the ribosome rotates with respect to the large subunit primarily between two states as mRNA is being translated into a protein. At the termination of bacterial translation, class I release factors (RFs) bind to a stop codon in the A-site and catalyze the release of the peptide chain from the ribosome. Periodically, mRNA is truncated prematurely, and the translating ribosome stalls at the end of the mRNA forming a nonstop complex requiring one of several ribosome rescue factors to intervene. One factor, YaeJ, is structurally homologous with the catalytic region of RFs but differs by binding to the ribosome directly through its C-terminal tail. Structures of the ribosome show that the ribosome adopts the nonrotated state conformation when these factors are bound. However, these studies do not elucidate the influence of binding to cognate or noncognate codons on the dynamics of intersubunit rotation. Here, we investigate the effects of wild-type and mutant forms of RF1, RF2, and YaeJ binding on ribosome intersubunit rotation using single-molecule Förster resonance energy transfer. We show that both RF1 binding and RF2 binding are sufficient to shift the population of posthydrolysis ribosome complexes from primarily the rotated to the nonrotated state only when a cognate stop codon is present in the A-site. Similarly, YaeJ binding stabilizes nonstop ribosomal complexes in the nonrotated state. Along with previous studies, these results are consistent with the idea that directed conformational changes and binding of subsequent factors to the ribosome are requisite for efficient termination and ribosome recycling.
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Affiliation(s)
- Widler Casy
- Department of Biochemistry , University of Missouri , Columbia , Missouri 65211 , United States
| | - Austin R Prater
- Department of Biochemistry , University of Missouri , Columbia , Missouri 65211 , United States
| | - Peter V Cornish
- Department of Biochemistry , University of Missouri , Columbia , Missouri 65211 , United States
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20
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Zhang Y, Hong S, Ruangprasert A, Skiniotis G, Dunham CM. Alternative Mode of E-Site tRNA Binding in the Presence of a Downstream mRNA Stem Loop at the Entrance Channel. Structure 2018; 26:437-445.e3. [PMID: 29456023 PMCID: PMC5842130 DOI: 10.1016/j.str.2018.01.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 09/14/2017] [Accepted: 01/19/2018] [Indexed: 12/23/2022]
Abstract
Structured mRNAs positioned downstream of the ribosomal decoding center alter gene expression by slowing protein synthesis. Here, we solved the cryo-EM structure of the bacterial ribosome bound to an mRNA containing a 3' stem loop that regulates translation. Unexpectedly, the E-site tRNA adopts two distinct orientations. In the first structure, normal interactions with the 50S and 30S E site are observed. However, in the second structure, although the E-site tRNA makes normal interactions with the 50S E site, its anticodon stem loop moves ∼54 Å away from the 30S E site to interact with the 30S head domain and 50S uL5. This position of the E-site tRNA causes the uL1 stalk to adopt a more open conformation that likely represents an intermediate state during E-site tRNA dissociation. These results suggest that structured mRNAs at the entrance channel restrict 30S subunit movement required during translation to slow E-site tRNA dissociation.
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Affiliation(s)
- Yan Zhang
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Samuel Hong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | | | - Georgios Skiniotis
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Christine M Dunham
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.
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21
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Puah RY, Jia H, Maraswami M, Toh DFK, Ero R, Yang L, Patil KM, Ong AAL, Krishna MS, Sun R, Tong C, Huang M, Chen X, Loh TP, Gao YG, Liu DX, Chen G. Selective Binding to mRNA Duplex Regions by Chemically Modified Peptide Nucleic Acids Stimulates Ribosomal Frameshifting. Biochemistry 2017; 57:149-159. [PMID: 29116759 DOI: 10.1021/acs.biochem.7b00744] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Minus-one programmed ribosomal frameshifting (-1 PRF) allows the precise maintenance of the ratio between viral proteins and is involved in the regulation of the half-lives of cellular mRNAs. Minus-one ribosomal frameshifting is activated by several stimulatory elements such as a heptameric slippery sequence (X XXY YYZ) and an mRNA secondary structure (hairpin or pseudoknot) that is positioned 2-8 nucleotides downstream from the slippery site. Upon -1 RF, the ribosomal reading frame is shifted from the normal zero frame to the -1 frame with the heptameric slippery sequence decoded as XXX YYY Z instead of X XXY YYZ. Our research group has developed chemically modified peptide nucleic acid (PNA) L and Q monomers to recognize G-C and C-G Watson-Crick base pairs, respectively, through major-groove parallel PNA·RNA-RNA triplex formation. L- and Q-incorporated PNAs show selective binding to double-stranded RNAs (dsRNAs) over single-stranded RNAs (ssRNAs). The sequence specificity and structural selectivity of L- and Q-modified PNAs may allow the precise targeting of desired viral and cellular RNA structures, and thus may serve as valuable biological tools for mechanistic studies and potential therapeutics for fighting diseases. Here, for the first time, we demonstrate by cell-free in vitro translation assays using rabbit reticulocyte lysate that the dsRNA-specific chemically modified PNAs targeting model mRNA hairpins stimulate -1 RF (from 2% to 32%). An unmodified control PNA, however, shows nonspecific inhibition of translation. Our results suggest that the modified dsRNA-binding PNAs may be advantageous for targeting structured RNAs.
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Affiliation(s)
| | | | | | | | - Rya Ero
- School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore 637551
| | | | | | | | | | | | | | - Mei Huang
- School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore 637551
| | | | | | - Yong-Gui Gao
- School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore 637551
| | - Ding Xiang Liu
- School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore 637551.,Guangdong Province Key Laboratory Microbial Signals & Disease Co, and Integrative Microbiology Research Centre, South China Agricultural University , Guangzhou 510642, Guangdong, People's Republic of China
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22
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Ribosome structural dynamics in translocation: yet another functional role for ribosomal RNA. Q Rev Biophys 2017; 50:e12. [DOI: 10.1017/s0033583517000117] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
AbstractRibosomes are remarkable ribonucleoprotein complexes that are responsible for protein synthesis in all forms of life. They polymerize polypeptide chains programmed by nucleotide sequences in messenger RNA in a mechanism mediated by transfer RNA. One of the most challenging problems in the ribosome field is to understand the mechanism of coupled translocation of mRNA and tRNA during the elongation phase of protein synthesis. In recent years, the results of structural, biophysical and biochemical studies have provided extensive evidence that translocation is based on the structural dynamics of the ribosome itself. Detailed structural analysis has shown that ribosome dynamics, like aminoacyl-tRNA selection and catalysis of peptide bond formation, is made possible by the properties of ribosomal RNA.
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23
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Kim HK, Tinoco I. EF-G catalyzed translocation dynamics in the presence of ribosomal frameshifting stimulatory signals. Nucleic Acids Res 2017; 45:2865-2874. [PMID: 27799473 PMCID: PMC5389563 DOI: 10.1093/nar/gkw1020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 10/20/2016] [Indexed: 12/05/2022] Open
Abstract
Programmed -1 ribosomal frameshifting (-1PRF) is tightly regulated by messenger RNA (mRNA) sequences and structures in expressing two or more proteins with precise ratios from a single mRNA. Using single-molecule fluorescence resonance energy transfer (smFRET) between (Cy5)EF-G and (Cy3)tRNALys, we studied the translational elongation dynamics of -1PRF in the Escherichia coli dnaX gene, which contains three frameshifting signals: a slippery sequence (A AAA AAG), a Shine-Dalgarno (SD) sequence and a downstream hairpin. The frameshift promoting signals mostly impair the EF-G-catalyzed translocation step of the two tRNALys and the slippery codons from the A- and P- sites. The hairpin acts as a road block slowing the translocation rate. The upstream SD sequence together with the hairpin promotes dissociation of futile EF-G and thus causes multiple EF-G driven translocation attempts. A slippery sequence also helps dissociation of the EF-G by providing alternative base-pairing options. These results indicate that frameshifting takes place during the repetitive ribosomal conformational changes associated with EF-G dissociation upon unsuccessful translocation attempts of the second slippage codon from the A- to the P- sites.
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Affiliation(s)
- Hee-Kyung Kim
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Ignacio Tinoco
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
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24
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Xie P, Chen H. Mechanism of ribosome translation through mRNA secondary structures. Int J Biol Sci 2017; 13:712-722. [PMID: 28655997 PMCID: PMC5485627 DOI: 10.7150/ijbs.19508] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 03/07/2017] [Indexed: 02/03/2023] Open
Abstract
A ribosome is a macromolecular machine that is responsible for translating the genetic codes in messenger RNA (mRNA) into polypeptide chains. It has been determined that besides translating through the single-stranded region, the ribosome can also translate through the duplex region of mRNA by unwinding the duplex. To understand the mechanism of ribosome translation through the duplex, several models have been proposed to study the dynamics of mRNA unwinding. Here, we present a comprehensive review of these models and also discuss other possible models. We evaluate each model and discuss the consistency and/or inconsistency between the theoretical results that are obtained based on each model and the available experimental data, thus determining which model is the most reasonable one to describe the mRNA unwinding mechanism and dynamics of the ribosome. Moreover, a framework for future studies in this subject is provided.
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Affiliation(s)
- Ping Xie
- School of Materials Science and Energy Engineering, FoShan University, Guangdong, 528000, China.,Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Hong Chen
- School of Materials Science and Energy Engineering, FoShan University, Guangdong, 528000, China
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25
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Zhong Z, Yang L, Zhang H, Shi J, Vandana JJ, Lam DTUH, Olsthoorn RCL, Lu L, Chen G. Mechanical unfolding kinetics of the SRV-1 gag-pro mRNA pseudoknot: possible implications for -1 ribosomal frameshifting stimulation. Sci Rep 2016; 6:39549. [PMID: 28000744 PMCID: PMC5175198 DOI: 10.1038/srep39549] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 11/24/2016] [Indexed: 12/19/2022] Open
Abstract
Minus-one ribosomal frameshifting is a translational recoding mechanism widely utilized by many RNA viruses to generate accurate ratios of structural and catalytic proteins. An RNA pseudoknot structure located in the overlapping region of the gag and pro genes of Simian Retrovirus type 1 (SRV-1) stimulates frameshifting. However, the experimental characterization of SRV-1 pseudoknot (un)folding dynamics and the effect of the base triple formation is lacking. Here, we report the results of our single-molecule nanomanipulation using optical tweezers and theoretical simulation by steered molecular dynamics. Our results directly reveal that the energetic coupling between loop 2 and stem 1 via minor-groove base triple formation enhances the mechanical stability. The terminal base pair in stem 1 (directly in contact with a translating ribosome at the slippery site) also affects the mechanical stability of the pseudoknot. The -1 frameshifting efficiency is positively correlated with the cooperative one-step unfolding force and inversely correlated with the one-step mechanical unfolding rate at zero force. A significantly improved correlation was observed between -1 frameshifting efficiency and unfolding rate at forces of 15-35 pN, consistent with the fact that the ribosome is a force-generating molecular motor with helicase activity. No correlation was observed between thermal stability and -1 frameshifting efficiency.
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Affiliation(s)
- Zhensheng Zhong
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, 637371 Singapore
| | - Lixia Yang
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, 637371 Singapore
| | - Haiping Zhang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Jiahao Shi
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, 637371 Singapore
| | - J. Jeya Vandana
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, 637371 Singapore
| | - Do Thuy Uyen Ha Lam
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, 637371 Singapore
- St Andrew’s Junior College, 5 Sorby Adams Drive, 357691 Singapore
| | - René C. L. Olsthoorn
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Lanyuan Lu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, 637371 Singapore
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26
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Belardinelli R, Sharma H, Peske F, Wintermeyer W, Rodnina MV. Translocation as continuous movement through the ribosome. RNA Biol 2016; 13:1197-1203. [PMID: 27801619 DOI: 10.1080/15476286.2016.1240140] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In each round of translation elongation, tRNAs and mRNA move within the ribosome by one codon at a time. tRNA-mRNA translocation is promoted by elongation factor G (EF-G) at the cost of GTP hydrolysis. The key questions for understanding translocation are how and when the tRNAs move and how EF-G coordinates motions of the ribosomal subunits with tRNA movement. Here we present 2 recent papers which describe the choreography of movements over the whole trajectory of translocation. We present the view that EF-G accelerates translocation by promoting the steps that lead to GTPase-dependent ribosome unlocking. EF-G facilitates the formation of the rotated state of the ribosome and uncouples the backward motions of the ribosomal subunits, forming an open conformation in which the tRNAs can rapidly move. Ribosome dynamics are important not only in translocation, but also in recoding events, such as frameshifting and bypassing, and mediate sensitivity to antibiotics.
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Affiliation(s)
- Riccardo Belardinelli
- a Max Planck Institute for Biophysical Chemistry , Department of Physical Biochemistry , Göttingen , Germany
| | - Heena Sharma
- a Max Planck Institute for Biophysical Chemistry , Department of Physical Biochemistry , Göttingen , Germany
| | - Frank Peske
- a Max Planck Institute for Biophysical Chemistry , Department of Physical Biochemistry , Göttingen , Germany
| | - Wolfgang Wintermeyer
- a Max Planck Institute for Biophysical Chemistry , Department of Physical Biochemistry , Göttingen , Germany
| | - Marina V Rodnina
- a Max Planck Institute for Biophysical Chemistry , Department of Physical Biochemistry , Göttingen , Germany
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27
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Sharma H, Adio S, Senyushkina T, Belardinelli R, Peske F, Rodnina MV. Kinetics of Spontaneous and EF-G-Accelerated Rotation of Ribosomal Subunits. Cell Rep 2016; 16:2187-2196. [PMID: 27524615 DOI: 10.1016/j.celrep.2016.07.051] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 05/30/2016] [Accepted: 07/20/2016] [Indexed: 11/18/2022] Open
Abstract
Ribosome dynamics play an important role in translation. The rotation of the ribosomal subunits relative to one another is essential for tRNA-mRNA translocation. An important unresolved question is whether subunit rotation limits the rate of translocation. Here, we monitor subunit rotation relative to peptide bond formation and translocation using ensemble kinetics and single-molecule FRET. We observe that spontaneous forward subunit rotation occurs at a rate of 40 s(-1), independent of the rate of preceding peptide bond formation. Elongation factor G (EF-G) accelerates forward subunit rotation to 200 s(-1). tRNA-mRNA movement is much slower (10-40 s(-1)), suggesting that forward subunit rotation does not limit the rate of translocation. The transition back to the non-rotated state of the ribosome kinetically coincides with tRNA-mRNA movement. Thus, large-scale movements of the ribosome are intrinsically rapid and gated by its ligands such as EF-G and tRNA.
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Affiliation(s)
- Heena Sharma
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Sarah Adio
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Tamara Senyushkina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Riccardo Belardinelli
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Frank Peske
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
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28
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Atkins JF, Loughran G, Bhatt PR, Firth AE, Baranov PV. Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use. Nucleic Acids Res 2016; 44:7007-78. [PMID: 27436286 PMCID: PMC5009743 DOI: 10.1093/nar/gkw530] [Citation(s) in RCA: 161] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/26/2016] [Indexed: 12/15/2022] Open
Abstract
Genetic decoding is not ‘frozen’ as was earlier thought, but dynamic. One facet of this is frameshifting that often results in synthesis of a C-terminal region encoded by a new frame. Ribosomal frameshifting is utilized for the synthesis of additional products, for regulatory purposes and for translational ‘correction’ of problem or ‘savior’ indels. Utilization for synthesis of additional products occurs prominently in the decoding of mobile chromosomal element and viral genomes. One class of regulatory frameshifting of stable chromosomal genes governs cellular polyamine levels from yeasts to humans. In many cases of productively utilized frameshifting, the proportion of ribosomes that frameshift at a shift-prone site is enhanced by specific nascent peptide or mRNA context features. Such mRNA signals, which can be 5′ or 3′ of the shift site or both, can act by pairing with ribosomal RNA or as stem loops or pseudoknots even with one component being 4 kb 3′ from the shift site. Transcriptional realignment at slippage-prone sequences also generates productively utilized products encoded trans-frame with respect to the genomic sequence. This too can be enhanced by nucleic acid structure. Together with dynamic codon redefinition, frameshifting is one of the forms of recoding that enriches gene expression.
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Affiliation(s)
- John F Atkins
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland School of Microbiology, University College Cork, Cork, Ireland Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Gary Loughran
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Pramod R Bhatt
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Andrew E Firth
- Division of Virology, Department of Pathology, University of Cambridge, Hills Road, Cambridge CB2 0QQ, UK
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
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29
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The molecular choreography of protein synthesis: translational control, regulation, and pathways. Q Rev Biophys 2016; 49:e11. [PMID: 27658712 DOI: 10.1017/s0033583516000056] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Translation of proteins by the ribosome regulates gene expression, with recent results underscoring the importance of translational control. Misregulation of translation underlies many diseases, including cancer and many genetic diseases. Decades of biochemical and structural studies have delineated many of the mechanistic details in prokaryotic translation, and sketched the outlines of eukaryotic translation. However, translation may not proceed linearly through a single mechanistic pathway, but likely involves multiple pathways and branchpoints. The stochastic nature of biological processes would allow different pathways to occur during translation that are biased by the interaction of the ribosome with other translation factors, with many of the steps kinetically controlled. These multiple pathways and branchpoints are potential regulatory nexus, allowing gene expression to be tuned at the translational level. As research focus shifts toward eukaryotic translation, certain themes will be echoed from studies on prokaryotic translation. This review provides a general overview of the dynamic data related to prokaryotic and eukaryotic translation, in particular recent findings with single-molecule methods, complemented by biochemical, kinetic, and structural findings. We will underscore the importance of viewing the process through the viewpoints of regulation, translational control, and heterogeneous pathways.
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30
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Shebl B, Menke DE, Pennella M, Poudyal RR, Burke DH, Cornish PV. Preparation of ribosomes for smFRET studies: A simplified approach. Arch Biochem Biophys 2016; 603:118-30. [PMID: 27208427 DOI: 10.1016/j.abb.2016.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 05/11/2016] [Accepted: 05/12/2016] [Indexed: 11/18/2022]
Abstract
During the past decade, single-molecule studies of the ribosome have significantly advanced our understanding of protein synthesis. The broadest application of these methods has been towards the investigation of ribosome conformational dynamics using single-molecule Förster resonance energy transfer (smFRET). The recent advances in fluorescently labeled ribosomes and translation components have resulted in success of smFRET experiments. Various methods have been employed to target fluorescent dyes to specific locations within the ribosome. Primarily, these methods have involved additional steps including subunit dissociation and/or full reconstitution, which could result in ribosomes of reduced activity and translation efficiency. In addition, substantial time and effort are required to produce limited quantities of material. To enable rapid and large-scale production of highly active, fluorescently labeled ribosomes, we have developed a procedure that combines partial reconstitution with His-tag purification. This allows for a homogeneous single-step purification of mutant ribosomes and subsequent integration of labeled proteins. Ribosomes produced with this method are shown to be as active as ribosomes purified using classical methods. While we have focused on two labeling sites in this report, the method is generalizable and can in principle be extended to any non-essential ribosomal protein.
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Affiliation(s)
- Bassem Shebl
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Drew E Menke
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Min Pennella
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Raghav R Poudyal
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Donald H Burke
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Peter V Cornish
- Department of Biochemistry, University of Missouri, Columbia, MO, USA.
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31
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Frank J. Whither Ribosome Structure and Dynamics Research? (A Perspective). J Mol Biol 2016; 428:3565-9. [PMID: 27178840 DOI: 10.1016/j.jmb.2016.04.034] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 03/24/2016] [Accepted: 04/29/2016] [Indexed: 12/24/2022]
Abstract
As high-resolution cryogenic electron microscopy (cryo-EM) structures of ribosomes proliferate, at resolutions that allow atomic interactions to be visualized, this article attempts to give a perspective on the way research on ribosome structure and dynamics may be headed, and particularly the new opportunities we have gained through recent advances in cryo-EM. It is pointed out that single-molecule FRET and cryo-EM form natural complements in the characterization of ribosome dynamics and transitions among equilibrating states of in vitro translational systems.
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Affiliation(s)
- Joachim Frank
- Howard Hughes Medical Institute, Columbia University, 116th and Broadway, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, 650 W. 168th Street, New York, NY 10032, USA; Department of Biological Sciences, Columbia University, 1212 Amsterdam Avenue, New York, NY 10027, USA
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32
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Coupling of mRNA Structure Rearrangement to Ribosome Movement during Bypassing of Non-coding Regions. Cell 2016; 163:1267-1280. [PMID: 26590426 DOI: 10.1016/j.cell.2015.10.064] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 09/07/2015] [Accepted: 10/21/2015] [Indexed: 01/13/2023]
Abstract
Nearly half of the ribosomes translating a particular bacteriophage T4 mRNA bypass a region of 50 nt, resuming translation 3' of this gap. How this large-scale, specific hop occurs and what determines whether a ribosome bypasses remain unclear. We apply single-molecule fluorescence with zero-mode waveguides to track individual Escherichia coli ribosomes during translation of T4's gene 60 mRNA. Ribosomes that bypass are characterized by a 10- to 20-fold longer pause in a non-canonical rotated state at the take-off codon. During the pause, mRNA secondary structure rearrangements are coupled to ribosome forward movement, facilitated by nascent peptide interactions that disengage the ribosome anticodon-codon interactions for slippage. Close to the landing site, the ribosome then scans mRNA in search of optimal base-pairing interactions. Our results provide a mechanistic and conformational framework for bypassing, highlighting a non-canonical ribosomal state to allow for mRNA structure refolding to drive large-scale ribosome movements.
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33
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Dunkle JA, Dunham CM. Mechanisms of mRNA frame maintenance and its subversion during translation of the genetic code. Biochimie 2015; 114:90-6. [PMID: 25708857 PMCID: PMC4458409 DOI: 10.1016/j.biochi.2015.02.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 02/11/2015] [Indexed: 01/26/2023]
Abstract
Important viral and cellular gene products are regulated by stop codon readthrough and mRNA frameshifting, processes whereby the ribosome detours from the reading frame defined by three nucleotide codons after initiation of translation. In the last few years, rapid progress has been made in mechanistically characterizing both processes and also revealing that trans-acting factors play important regulatory roles in frameshifting. Here, we review recent biophysical studies that bring new molecular insights to stop codon readthrough and frameshifting. Lastly, we consider whether there may be common mechanistic themes in -1 and +1 frameshifting based on recent X-ray crystal structures of +1 frameshift-prone tRNAs bound to the ribosome.
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Affiliation(s)
- Jack A Dunkle
- Emory University School of Medicine, Department of Biochemistry, 1510 Clifton Road NE, Suite G223, Atlanta, GA 30322, USA
| | - Christine M Dunham
- Emory University School of Medicine, Department of Biochemistry, 1510 Clifton Road NE, Suite G223, Atlanta, GA 30322, USA.
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34
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Bock LV, Blau C, Vaiana AC, Grubmüller H. Dynamic contact network between ribosomal subunits enables rapid large-scale rotation during spontaneous translocation. Nucleic Acids Res 2015; 43:6747-60. [PMID: 26109353 PMCID: PMC4538834 DOI: 10.1093/nar/gkv649] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 06/10/2015] [Indexed: 11/13/2022] Open
Abstract
During ribosomal translation, the two ribosomal subunits remain associated through intersubunit bridges, despite rapid large-scale intersubunit rotation. The absence of large barriers hindering rotation is a prerequisite for rapid rotation. Here, we investigate how such a flat free-energy landscape is achieved, in particular considering the large shifts the bridges undergo at the periphery. The dynamics and energetics of the intersubunit contact network are studied using molecular dynamics simulations of the prokaryotic ribosome in intermediate states of spontaneous translocation. Based on observed occupancies of intersubunit contacts, residues were grouped into clusters. In addition to the central contact clusters, peripheral clusters were found to maintain strong steady interactions by changing contacts in the course of rotation. The peripheral B1 bridges are stabilized by a changing contact pattern of charged residues that adapts to the rotational state. In contrast, steady strong interactions of the B4 bridge are ensured by the flexible helix H34 following the movement of protein S15. The tRNAs which span the subunits contribute to the intersubunit binding enthalpy to an almost constant degree, despite their different positions in the ribosome. These mechanisms keep the intersubunit interaction strong and steady during rotation, thereby preventing dissociation and enabling rapid rotation.
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Affiliation(s)
- Lars V Bock
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Christian Blau
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Andrea C Vaiana
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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35
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Caliskan N, Peske F, Rodnina MV. Changed in translation: mRNA recoding by -1 programmed ribosomal frameshifting. Trends Biochem Sci 2015; 40:265-74. [PMID: 25850333 PMCID: PMC7126180 DOI: 10.1016/j.tibs.2015.03.006] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 03/09/2015] [Accepted: 03/09/2015] [Indexed: 12/19/2022]
Abstract
–1PRF occurs when ribosomes move over a slippery sequence. A frameshifting pseudoknot/stem-loop element stalls ribosomes in a metastable state. –1PRF may contribute to the quality-control machinery in eukaryotes. Trans-acting factors (proteins, miRNAs, or antibiotics) can modulate –1PRF.
Programmed −1 ribosomal frameshifting (−1PRF) is an mRNA recoding event commonly utilized by viruses and bacteria to increase the information content of their genomes. Recent results have implicated −1PRF in quality control of mRNA and DNA stability in eukaryotes. Biophysical experiments demonstrated that the ribosome changes the reading frame while attempting to move over a slippery sequence of the mRNA – when a roadblock formed by a folded downstream segment in the mRNA stalls the ribosome in a metastable conformational state. The efficiency of −1PRF is modulated not only by cis-regulatory elements in the mRNA but also by trans-acting factors such as proteins, miRNAs, and antibiotics. These recent results suggest a molecular mechanism and new important cellular roles for −1PRF.
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Affiliation(s)
- Neva Caliskan
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany
| | - Frank Peske
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany.
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36
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Mathew SF, Crowe-McAuliffe C, Graves R, Cardno TS, McKinney C, Poole ES, Tate WP. The highly conserved codon following the slippery sequence supports -1 frameshift efficiency at the HIV-1 frameshift site. PLoS One 2015; 10:e0122176. [PMID: 25807539 PMCID: PMC4373837 DOI: 10.1371/journal.pone.0122176] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 02/08/2015] [Indexed: 01/18/2023] Open
Abstract
HIV-1 utilises -1 programmed ribosomal frameshifting to translate structural and enzymatic domains in a defined proportion required for replication. A slippery sequence, U UUU UUA, and a stem-loop are well-defined RNA features modulating -1 frameshifting in HIV-1. The GGG glycine codon immediately following the slippery sequence (the 'intercodon') contributes structurally to the start of the stem-loop but has no defined role in current models of the frameshift mechanism, as slippage is inferred to occur before the intercodon has reached the ribosomal decoding site. This GGG codon is highly conserved in natural isolates of HIV. When the natural intercodon was replaced with a stop codon two different decoding molecules-eRF1 protein or a cognate suppressor tRNA-were able to access and decode the intercodon prior to -1 frameshifting. This implies significant slippage occurs when the intercodon is in the (perhaps distorted) ribosomal A site. We accommodate the influence of the intercodon in a model of frame maintenance versus frameshifting in HIV-1.
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Affiliation(s)
- Suneeth F. Mathew
- Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
| | | | - Ryan Graves
- Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
| | - Tony S. Cardno
- Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
| | - Cushla McKinney
- Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
| | - Elizabeth S. Poole
- Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
| | - Warren P. Tate
- Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
- * E-mail:
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37
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Venkataraman K, Zafar H, Karzai AW. Distinct tmRNA sequence elements facilitate RNase R engagement on rescued ribosomes for selective nonstop mRNA decay. Nucleic Acids Res 2014; 42:11192-202. [PMID: 25200086 PMCID: PMC4176180 DOI: 10.1093/nar/gku802] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
trans-Translation, orchestrated by SmpB and tmRNA, is the principal eubacterial pathway for resolving stalled translation complexes. RNase R, the leading nonstop mRNA surveillance factor, is recruited to stalled ribosomes in a trans-translation dependent process. To elucidate the contributions of SmpB and tmRNA to RNase R recruitment, we evaluated Escherichia coli–Francisella tularensis chimeric variants of tmRNA and SmpB. This evaluation showed that while the hybrid tmRNA supported nascent polypeptide tagging and ribosome rescue, it suffered defects in facilitating RNase R recruitment to stalled ribosomes. To gain further insights, we used established tmRNA and SmpB variants that impact distinct stages of the trans-translation process. Analysis of select tmRNA variants revealed that the sequence composition and positioning of the ultimate and penultimate codons of the tmRNA ORF play a crucial role in recruiting RNase R to rescued ribosomes. Evaluation of defined SmpB C-terminal tail variants highlighted the importance of establishing the tmRNA reading frame, and provided valuable clues into the timing of RNase R recruitment to rescued ribosomes. Taken together, these studies demonstrate that productive RNase R-ribosomes engagement requires active trans-translation, and suggest that RNase R captures the emerging nonstop mRNA at an early stage after establishment of the tmRNA ORF as the surrogate mRNA template.
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Affiliation(s)
- Krithika Venkataraman
- Department of Biochemistry and Cell Biology, Center for Infectious Diseases, Stony Brook University, Stony Brook, New York, NY 11794, USA
| | - Hina Zafar
- Department of Biochemistry and Cell Biology, Center for Infectious Diseases, Stony Brook University, Stony Brook, New York, NY 11794, USA
| | - A Wali Karzai
- Department of Biochemistry and Cell Biology, Center for Infectious Diseases, Stony Brook University, Stony Brook, New York, NY 11794, USA
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38
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Caliskan N, Katunin VI, Belardinelli R, Peske F, Rodnina MV. Programmed -1 frameshifting by kinetic partitioning during impeded translocation. Cell 2014; 157:1619-31. [PMID: 24949973 PMCID: PMC7112342 DOI: 10.1016/j.cell.2014.04.041] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 02/17/2014] [Accepted: 04/10/2014] [Indexed: 02/04/2023]
Abstract
Programmed –1 ribosomal frameshifting (−1PRF) is an mRNA recoding event utilized by cells to enhance the information content of the genome and to regulate gene expression. The mechanism of –1PRF and its timing during translation elongation are unclear. Here, we identified the steps that govern –1PRF by following the stepwise movement of the ribosome through the frameshifting site of a model mRNA derived from the IBV 1a/1b gene in a reconstituted in vitro translation system from Escherichia coli. Frameshifting occurs at a late stage of translocation when the two tRNAs are bound to adjacent slippery sequence codons of the mRNA. The downstream pseudoknot in the mRNA impairs the closing movement of the 30S subunit head, the dissociation of EF-G, and the release of tRNA from the ribosome. The slippage of the ribosome into the –1 frame accelerates the completion of translocation, thereby further favoring translation in the new reading frame. Kinetics of –1 ribosomal frameshifting are monitored at single-codon resolution Frameshifting occurs when the backward movement of the 30S subunit head is impeded Two tRNAs at the XXXYYYZ mRNA sequence are stalled in chimeric POST states The shift to the –1 reading frame occurs prior to EF-G release from the ribosome
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Affiliation(s)
- Neva Caliskan
- Max Planck Institute for Biophysical Chemistry, Department of Physical Biochemistry, 37077 Göttingen, Germany
| | - Vladimir I Katunin
- B.P. Konstantinov Petersburg Nuclear Physics Institute, Department of Molecular and Radiation Biophysics, 188300 Gatchina, Russia
| | - Riccardo Belardinelli
- Max Planck Institute for Biophysical Chemistry, Department of Physical Biochemistry, 37077 Göttingen, Germany
| | - Frank Peske
- Max Planck Institute for Biophysical Chemistry, Department of Physical Biochemistry, 37077 Göttingen, Germany
| | - Marina V Rodnina
- Max Planck Institute for Biophysical Chemistry, Department of Physical Biochemistry, 37077 Göttingen, Germany.
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39
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High-efficiency translational bypassing of non-coding nucleotides specified by mRNA structure and nascent peptide. Nat Commun 2014; 5:4459. [PMID: 25041899 DOI: 10.1038/ncomms5459] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 06/19/2014] [Indexed: 02/08/2023] Open
Abstract
The gene product 60 (gp60) of bacteriophage T4 is synthesized as a single polypeptide chain from a discontinuous reading frame as a result of bypassing of a non-coding mRNA region of 50 nucleotides by the ribosome. To identify the minimum set of signals required for bypassing, we recapitulated efficient translational bypassing in an in vitro reconstituted translation system from Escherichia coli. We find that the signals, which promote efficient and accurate bypassing, are specified by the gene 60 mRNA sequence. Systematic analysis of the mRNA suggests unexpected contributions of sequences upstream and downstream of the non-coding gap region as well as of the nascent peptide. During bypassing, ribosomes glide forward on the mRNA track in a processive way. Gliding may have a role not only for gp60 synthesis, but also during regular mRNA translation for reading frame selection during initiation or tRNA translocation during elongation.
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40
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Chen J, Petrov A, Johansson M, Tsai A, O'Leary SE, Puglisi JD. Dynamic pathways of -1 translational frameshifting. Nature 2014; 512:328-32. [PMID: 24919156 PMCID: PMC4472451 DOI: 10.1038/nature13428] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 05/01/2014] [Indexed: 12/16/2022]
Abstract
Spontaneous changes in the reading frame of translation are rare (frequency of 10−3 – 10−4 per codon)1, but can be induced by specific features in the messenger RNA (mRNA). In the presence of mRNA secondary structures, a heptanucleotide “slippery sequence” usually defined by the motif X XXY YYZ, and (in some prokaryotic cases) mRNA sequences that base pair with the 3′ end of the 16S ribosomal rRNA (internal Shine-Dalgarno (SD) sequences), there is an increased probability that a specific programmed change of frame occurs, wherein the ribosome shifts one nucleotide backwards into an overlapping reading frame (−1 frame) and continues by translating a new sequence of amino acids2,3. Despite extensive biochemical and genetic studies, there is no clear mechanistic description for frameshifting. Here, we apply single-molecule fluorescence to track the compositional and conformational dynamics of the individual ribosomes at each codon during translation of a frameshift-inducing mRNA from the dnaX gene in Escherichia coli. Ribosomes that frameshift into the −1 frame are characterized by a 10-fold longer pause in elongation compared to non-frameshifted ribosomes, which translate through unperturbed. During the pause, interactions of the ribosome with the mRNA stimulatory elements uncouple EF-G catalyzed translocation from normal ribosomal subunit reverse-rotation, leaving the ribosome in a non-canonical intersubunit rotated state with an exposed codon in the aminoacyl-tRNA site (A site). tRNALys sampling and accommodation to the empty A site either lead to the slippage of the tRNAs into the −1 frame or maintain the ribosome into the 0 frame. Our results provide a general mechanistic and conformational framework for −1 frameshifting, highlighting multiple kinetic branchpoints during elongation.
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Affiliation(s)
- Jin Chen
- 1] Department of Applied Physics, Stanford University, Stanford, California 94305-4090, USA [2] Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA
| | - Alexey Petrov
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA
| | - Magnus Johansson
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA
| | - Albert Tsai
- 1] Department of Applied Physics, Stanford University, Stanford, California 94305-4090, USA [2] Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA
| | - Seán E O'Leary
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA
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