1
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McNutt ZA, Roy B, Gemler BT, Shatoff EA, Moon KM, Foster L, Bundschuh R, Fredrick K. Ribosomes lacking bS21 gain function to regulate protein synthesis in Flavobacterium johnsoniae. Nucleic Acids Res 2023; 51:1927-1942. [PMID: 36727479 PMCID: PMC9976891 DOI: 10.1093/nar/gkad047] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/12/2023] [Accepted: 01/16/2023] [Indexed: 02/03/2023] Open
Abstract
Ribosomes of Bacteroidia (formerly Bacteroidetes) fail to recognize Shine-Dalgarno (SD) sequences even though they harbor the anti-SD (ASD) of 16S rRNA. Inhibition of SD-ASD pairing is due to sequestration of the 3' tail of 16S rRNA in a pocket formed by bS21, bS18, and bS6 on the 30S platform. Interestingly, in many Flavobacteriales, the gene encoding bS21, rpsU, contains an extended SD sequence. In this work, we present genetic and biochemical evidence that bS21 synthesis in Flavobacterium johnsoniae is autoregulated via a subpopulation of ribosomes that specifically lack bS21. Mutation or depletion of bS21 in the cell increases translation of reporters with strong SD sequences, such as rpsU'-gfp, but has no effect on other reporters. Purified ribosomes lacking bS21 (or its C-terminal region) exhibit higher rates of initiation on rpsU mRNA and lower rates of initiation on other (SD-less) mRNAs than control ribosomes. The mechanism of autoregulation depends on extensive pairing between mRNA and 16S rRNA, and exceptionally strong SD sequences, with predicted pairing free energies of < -13 kcal/mol, are characteristic of rpsU across the Bacteroidota. This work uncovers a clear example of specialized ribosomes in bacteria.
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Affiliation(s)
- Zakkary A McNutt
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Bappaditya Roy
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Bryan T Gemler
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| | - Elan A Shatoff
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Kyung-Mee Moon
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V3T1Z4, Canada
| | - Leonard J Foster
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V3T1Z4, Canada
| | - Ralf Bundschuh
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Kurt Fredrick
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
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2
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Thommen M, Draycheva A, Rodnina MV. Ribosome selectivity and nascent chain context in modulating the incorporation of fluorescent non-canonical amino acid into proteins. Sci Rep 2022; 12:12848. [PMID: 35896582 PMCID: PMC9329280 DOI: 10.1038/s41598-022-16932-7] [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: 03/11/2022] [Accepted: 07/18/2022] [Indexed: 11/09/2022] Open
Abstract
Fluorescence reporter groups are important tools to study the structure and dynamics of proteins. Genetic code reprogramming allows for cotranslational incorporation of non-canonical amino acids at any desired position. However, cotranslational incorporation of bulky fluorescence reporter groups is technically challenging and usually inefficient. Here we analyze the bottlenecks for the cotranslational incorporation of NBD-, BodipyFL- and Atto520-labeled Cys-tRNACys into a model protein using a reconstituted in-vitro translation system. We show that the modified Cys-tRNACys can be rejected during decoding due to the reduced ribosome selectivity for the modified aa-tRNA and the competition with native near-cognate aminoacyl-tRNAs. Accommodation of the modified Cys-tRNACys in the A site of the ribosome is also impaired, but can be rescued by one or several Gly residues at the positions −1 to −4 upstream of the incorporation site. The incorporation yield depends on the steric properties of the downstream residue and decreases with the distance from the protein N-terminus to the incorporation site. In addition to the full-length translation product, we find protein fragments corresponding to the truncated N-terminal peptide and the C-terminal fragment starting with a fluorescence-labeled Cys arising from a StopGo-like event due to a defect in peptide bond formation. The results are important for understanding the reasons for inefficient cotranslational protein labeling with bulky reporter groups and for designing new approaches to improve the yield of fluorescence-labeled protein.
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Affiliation(s)
- Michael Thommen
- Department of Physical Biochemistry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Albena Draycheva
- Department of Physical Biochemistry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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3
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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: 11] [Impact Index Per Article: 5.5] [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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4
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Tajima K, Katoh T, Suga H. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2736-2753. [PMID: 35188576 PMCID: PMC8934632 DOI: 10.1093/nar/gkac068] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 01/13/2022] [Accepted: 02/07/2022] [Indexed: 11/13/2022] Open
Abstract
In ribosomal translation, peptidyl transfer occurs between P-site peptidyl-tRNA and A-site aminoacyl-tRNA, followed by translocation of the resulting P-site deacylated-tRNA and A-site peptidyl-tRNA to E and P site, respectively, mediated by EF-G. Here, we report that mistranslocation of P-site peptidyl-tRNA and A-site aminoacyl-tRNA toward E and A site occurs when high concentration of EF-G triggers the migration of two tRNAs prior to completion of peptidyl transfer. Consecutive incorporation of less reactive amino acids, such as Pro and d-Ala, makes peptidyl transfer inefficient and thus induces the mistranslocation event. Consequently, the E-site peptidyl-tRNA drops off from ribosome to give a truncated peptide lacking the C-terminal region. The P-site aminoacyl-tRNA allows for reinitiation of translation upon accommodation of a new aminoacyl-tRNA at A site, leading to synthesis of a truncated peptide lacking the N-terminal region, which we call the ‘reinitiated peptide’. We also revealed that such a drop-off-reinitiation event can be alleviated by EF-P that promotes peptidyl transfer of Pro. Moreover, this event takes place both in vitro and in cell, showing that reinitiated peptides during protein synthesis could be accumulated in this pathway in cells.
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Affiliation(s)
- Kenya Tajima
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | | | - Hiroaki Suga
- To whom correspondence should be addressed. Tel: +81 3 5841 8372; Fax: +81 3 5841 8372;
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5
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Jha V, Roy B, Jahagirdar D, McNutt ZA, Shatoff EA, Boleratz BL, Watkins DE, Bundschuh R, Basu K, Ortega J, Fredrick K. Structural basis of sequestration of the anti-Shine-Dalgarno sequence in the Bacteroidetes ribosome. Nucleic Acids Res 2021; 49:547-567. [PMID: 33330920 PMCID: PMC7797042 DOI: 10.1093/nar/gkaa1195] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 11/18/2020] [Accepted: 11/24/2020] [Indexed: 11/25/2022] Open
Abstract
Genomic studies have indicated that certain bacterial lineages such as the Bacteroidetes lack Shine-Dalgarno (SD) sequences, and yet with few exceptions ribosomes of these organisms carry the canonical anti-SD (ASD) sequence. Here, we show that ribosomes purified from Flavobacterium johnsoniae, a representative of the Bacteroidetes, fail to recognize the SD sequence of mRNA in vitro. A cryo-electron microscopy structure of the complete 70S ribosome from F. johnsoniae at 2.8 Å resolution reveals that the ASD is sequestered by ribosomal proteins bS21, bS18 and bS6, explaining the basis of ASD inhibition. The structure also uncovers a novel ribosomal protein—bL38. Remarkably, in F. johnsoniae and many other Flavobacteriia, the gene encoding bS21 contains a strong SD, unlike virtually all other genes. A subset of Flavobacteriia have an alternative ASD, and in these organisms the fully complementary sequence lies upstream of the bS21 gene, indicative of natural covariation. In other Bacteroidetes classes, strong SDs are frequently found upstream of the genes for bS21 and/or bS18. We propose that these SDs are used as regulatory elements, enabling bS21 and bS18 to translationally control their own production.
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Affiliation(s)
- Vikash Jha
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada.,Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Bappaditya Roy
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Dushyant Jahagirdar
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada.,Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Zakkary A McNutt
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.,Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Elan A Shatoff
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.,Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Bethany L Boleratz
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Dean E Watkins
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Ralf Bundschuh
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.,Department of Physics, The Ohio State University, Columbus, OH 43210, USA.,Department of Chemistry & Biochemistry, Division of Hematology, The Ohio State University, Columbus, OH 43210, USA
| | - Kaustuv Basu
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada.,Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Joaquin Ortega
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada.,Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Kurt Fredrick
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.,Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
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6
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Wakabayashi H, Warnasooriya C, Ermolenko DN. Extending the Spacing between the Shine-Dalgarno Sequence and P-Site Codon Reduces the Rate of mRNA Translocation. J Mol Biol 2020; 432:4612-4622. [PMID: 32544497 DOI: 10.1016/j.jmb.2020.06.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 12/24/2022]
Abstract
By forming base-pairing interactions with the 3' end of 16S rRNA, mRNA Shine-Dalgarno (SD) sequences positioned upstream of open reading frames facilitate translation initiation. During the elongation phase of protein synthesis, intragenic SD-like sequences stimulate ribosome frameshifting and may also slow down ribosome movement along mRNA. Here, we show that the length of the spacer between the SD sequence and P-site codon strongly affects the rate of ribosome translocation. Increasing the spacer length beyond 6 nt destabilizes mRNA-tRNA-ribosome interactions and results in a 5- to 10-fold reduction of the translocation rate. These observations suggest that during translation, the spacer between the SD sequence and P-site codon undergoes structural rearrangements, which slow down mRNA translocation and promote mRNA frameshifting.
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Affiliation(s)
- Hironao Wakabayashi
- Department of Biochemistry & Biophysics at School of Medicine and Dentistry and Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA
| | - Chandani Warnasooriya
- Department of Biochemistry & Biophysics at School of Medicine and Dentistry and Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA
| | - Dmitri N Ermolenko
- Department of Biochemistry & Biophysics at School of Medicine and Dentistry and Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA.
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7
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Bhagdikar D, Grundy FJ, Henkin TM. Transcriptional and translational S-box riboswitches differ in ligand-binding properties. J Biol Chem 2020; 295:6849-6860. [PMID: 32209653 DOI: 10.1074/jbc.ra120.012853] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/20/2020] [Indexed: 01/27/2023] Open
Abstract
There are a number of riboswitches that utilize the same ligand-binding domain to regulate transcription or translation. S-box (SAM-I) riboswitches, including the riboswitch present in the Bacillus subtilis metI gene, which encodes cystathionine γ-synthase, regulate the expression of genes involved in methionine metabolism in response to SAM, primarily at the level of transcriptional attenuation. A rarer class of S-box riboswitches is predicted to regulate translation initiation. Here we identified and characterized a translational S-box riboswitch in the metI gene from Desulfurispirillum indicum The regulatory mechanisms of riboswitches are influenced by the kinetics of ligand interaction. The half-life of the translational D. indicum metI RNA-SAM complex is significantly shorter than that of the transcriptional B. subtilis metI RNA. This finding suggests that, unlike the transcriptional RNA, the translational metI riboswitch can make multiple reversible regulatory decisions. Comparison of both RNAs revealed that the second internal loop of helix P3 in the transcriptional RNA usually contains an A residue, whereas the translational RNA contains a C residue that is conserved in other S-box RNAs that are predicted to regulate translation. Mutational analysis indicated that the presence of an A or C residue correlates with RNA-SAM complex stability. Biochemical analyses indicate that the internal loop sequence critically determines the stability of the RNA-SAM complex by influencing the flexibility of residues involved in SAM binding and thereby affects the molecular mechanism of riboswitch function.
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Affiliation(s)
- Divyaa Bhagdikar
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210
| | - Frank J Grundy
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210
| | - Tina M Henkin
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210
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8
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Egorova T, Sokolova E, Shuvalova E, Matrosova V, Shuvalov A, Alkalaeva E. Fluorescent toeprinting to study the dynamics of ribosomal complexes. Methods 2019; 162-163:54-59. [PMID: 31201933 DOI: 10.1016/j.ymeth.2019.06.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 06/08/2019] [Accepted: 06/10/2019] [Indexed: 12/20/2022] Open
Abstract
Classical toeprinting is generally used to determine the position of ribosomes on mRNA; however, it has several disadvantages. We describe a fluorescent toeprinting assay that enables easier identification of ribosomal complexes bound to mRNA in vitro. The procedure involves the use of stable and safe fluorescently labeled oligonucleotides for reverse transcription reactions as primers, followed by the analysis of cDNA products using an automatic sequencer. This procedure allows the multiplexing and simultaneous analysis of a large number of samples. Over the past ten years, fluorescent toeprinting was applied to determine the activities of eukaryotic release factors and additional proteins involved in translation termination, to study the dynamics of translation initiation and elongation complexes, and to quantitatively evaluate the observed ribosomal complexes. Because of the simplicity and small amounts of material required, fluorescent toeprinting provides a highly scalable and versatile tool to study ribosomal complexes.
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Affiliation(s)
- Tatiana Egorova
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia
| | - Elizaveta Sokolova
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia
| | - Ekaterina Shuvalova
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia
| | - Vera Matrosova
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexey Shuvalov
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia
| | - Elena Alkalaeva
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia.
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9
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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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10
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Ying L, Zhu H, Shoji S, Fredrick K. Roles of specific aminoglycoside-ribosome interactions in the inhibition of translation. RNA (NEW YORK, N.Y.) 2019; 25:247-254. [PMID: 30413565 PMCID: PMC6348987 DOI: 10.1261/rna.068460.118] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 11/06/2018] [Indexed: 05/18/2023]
Abstract
Aminoglycosides containing a 2-deoxystreptamine core (AGs) represent a large family of antibiotics that target the ribosome. These compounds promote miscoding, inhibit translocation, and inhibit ribosome recycling. AG binding to helix h44 of the small subunit induces rearrangement of A-site nucleotides A1492 and A1493, which promotes a key open-to-closed conformational change of the subunit and thereby increases miscoding. Mechanisms by which AGs inhibit translocation and recycling remain less clear. Structural studies have revealed a secondary AG binding site in H69 of the large subunit, and it has been proposed that interaction at this site is crucial for inhibition of translocation and recycling. Here, we analyze ribosomes with mutations targeting either or both AG binding sites. Assaying translocation, we find that ablation of the h44 site increases the IC50 values for AGs dramatically, while removal of the H69 site increases these values modestly. This suggests that the AG-h44 interaction is primarily responsible for inhibition, with H69 playing a minor role. Assaying recycling, we find that mutation of h44 has no effect on AG inhibition, consistent with a primary role for AG-H69 interaction. Collectively, these findings help clarify the roles of the two AG binding sites in mechanisms of inhibition by these compounds.
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Affiliation(s)
- Lanqing Ying
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Hongkun Zhu
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Shinichiro Shoji
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Kurt Fredrick
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
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11
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Dever TE, Dinman JD, Green R. Translation Elongation and Recoding in Eukaryotes. Cold Spring Harb Perspect Biol 2018; 10:cshperspect.a032649. [PMID: 29610120 DOI: 10.1101/cshperspect.a032649] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In this review, we highlight the current understanding of translation elongation and recoding in eukaryotes. In addition to providing an overview of the process, recent advances in our understanding of the role of the factor eIF5A in both translation elongation and termination are discussed. We also highlight mechanisms of translation recoding with a focus on ribosomal frameshifting during elongation. We see that the balance between the basic steps in elongation and the less common recoding events is determined by the kinetics of the different processes as well as by specific sequence determinants.
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Affiliation(s)
- Thomas E Dever
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - Jonathan D Dinman
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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12
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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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13
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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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14
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Mailliot J, Martin F. Viral internal ribosomal entry sites: four classes for one goal. WILEY INTERDISCIPLINARY REVIEWS. RNA 2018; 9. [PMID: 29193740 DOI: 10.1002/wrna.1458] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 09/19/2017] [Accepted: 10/02/2017] [Indexed: 12/22/2022]
Abstract
To ensure efficient propagation, viruses need to rapidly produce viral proteins after cell entrance. Since viral genomes do not encode any components of the protein biosynthesis machinery, viral proteins must be produced by the host cell. To hi-jack the host cellular translation, viruses use a great variety of distinct strategies. Many single-stranded positive-sensed RNA viruses contain so-called internal ribosome entry sites (IRESs). IRESs are structural RNA motifs that have evolved to specific folds that recruit the host ribosomes on the viral coding sequences in order to synthesize viral proteins. In host canonical translation, recruitment of the translation machinery components is essentially guided by the 5' cap (m7 G) of mRNA. In contrast, IRESs are able to promote efficient ribosome assembly internally and in cap-independent manner. IRESs have been categorized into four classes, based on their length, nucleotide sequence, secondary and tertiary structures, as well as their mode of action. Classes I and II require the assistance of cellular auxiliary factors, the eukaryotic intiation factors (eIF), for efficient ribosome assembly. Class III IRESs require only a subset of eIFs whereas Class IV, which are the more compact, can promote translation without any eIFs. Extensive functional and structural investigations of IRESs over the past decades have allowed a better understanding of their mode of action for viral translation. Because viral translation has a pivotal role in the infectious program, IRESs are therefore attractive targets for therapeutic purposes. WIREs RNA 2018, 9:e1458. doi: 10.1002/wrna.1458 This article is categorized under: Translation > Ribosome Structure/Function Translation > Translation Mechanisms RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Justine Mailliot
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR7104, INSERM U964, Illkirch-Graffenstaden, France
| | - Franck Martin
- Institut de Biologie Moléculaire et Cellulaire, "Architecture et Réactivité de l'ARN" CNRS UPR9002, Université De Strasbourg, Strasbourg, France
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15
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Johnson AG, Grosely R, Petrov AN, Puglisi JD. Dynamics of IRES-mediated translation. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2016.0177. [PMID: 28138065 DOI: 10.1098/rstb.2016.0177] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2016] [Indexed: 12/19/2022] Open
Abstract
Viral internal ribosome entry sites (IRESs) are unique RNA elements, which use stable and dynamic RNA structures to recruit ribosomes and drive protein synthesis. IRESs overcome the high complexity of the canonical eukaryotic translation initiation pathway, often functioning with a limited set of eukaryotic initiation factors. The simplest types of IRESs are typified by the cricket paralysis virus intergenic region (CrPV IGR) and hepatitis C virus (HCV) IRESs, both of which independently form high-affinity complexes with the small (40S) ribosomal subunit and bypass the molecular processes of cap-binding and scanning. Owing to their simplicity and ribosomal affinity, the CrPV and HCV IRES have been important models for structural and functional studies of the eukaryotic ribosome during initiation, serving as excellent targets for recent technological breakthroughs in cryogenic electron microscopy (cryo-EM) and single-molecule analysis. High-resolution structural models of ribosome : IRES complexes, coupled with dynamics studies, have clarified decades of biochemical research and provided an outline of the conformational and compositional trajectory of the ribosome during initiation. Here we review recent progress in the study of HCV- and CrPV-type IRESs, highlighting important structural and dynamics insights and the synergy between cryo-EM and single-molecule studies.This article is part of the themed issue 'Perspectives on the ribosome'.
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Affiliation(s)
- Alex G Johnson
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA.,Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
| | - Rosslyn Grosely
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
| | - Alexey N Petrov
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
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16
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Miscoding-induced stalling of substrate translocation on the bacterial ribosome. Proc Natl Acad Sci U S A 2017; 114:E8603-E8610. [PMID: 28973849 DOI: 10.1073/pnas.1707539114] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Directional transit of the ribosome along the messenger RNA (mRNA) template is a key determinant of the rate and processivity of protein synthesis. Imaging of the multistep translocation mechanism using single-molecule FRET has led to the hypothesis that substrate movements relative to the ribosome resolve through relatively long-lived late intermediates wherein peptidyl-tRNA enters the P site of the small ribosomal subunit via reversible, swivel-like motions of the small subunit head domain within the elongation factor G (GDP)-bound ribosome complex. Consistent with translocation being rate-limited by recognition and productive engagement of peptidyl-tRNA within the P site, we now show that base-pairing mismatches between the peptidyl-tRNA anticodon and the mRNA codon dramatically delay this rate-limiting, intramolecular process. This unexpected relationship between aminoacyl-tRNA decoding and translocation suggests that miscoding antibiotics may impact protein synthesis by impairing the recognition of peptidyl-tRNA in the small subunit P site during EF-G-catalyzed translocation. Strikingly, we show that elongation factor P (EF-P), traditionally known to alleviate ribosome stalling at polyproline motifs, can efficiently rescue translocation defects arising from miscoding. These findings help reveal the nature and origin of the rate-limiting steps in substrate translocation on the bacterial ribosome and indicate that EF-P can aid in resuming translation elongation stalled by miscoding errors.
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17
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Fan Y, Evans CR, Barber KW, Banerjee K, Weiss KJ, Margolin W, Igoshin OA, Rinehart J, Ling J. Heterogeneity of Stop Codon Readthrough in Single Bacterial Cells and Implications for Population Fitness. Mol Cell 2017; 67:826-836.e5. [PMID: 28781237 PMCID: PMC5591071 DOI: 10.1016/j.molcel.2017.07.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 05/22/2017] [Accepted: 07/07/2017] [Indexed: 12/30/2022]
Abstract
Gene expression noise (heterogeneity) leads to phenotypic diversity among isogenic individual cells. Our current understanding of gene expression noise is mostly limited to transcription, as separating translational noise from transcriptional noise has been challenging. It also remains unclear how translational heterogeneity originates. Using a transcription-normalized reporter system, we discovered that stop codon readthrough is heterogeneous among single cells, and individual cells with higher UGA readthrough grow faster from stationary phase. Our work also revealed that individual cells with lower protein synthesis levels exhibited higher UGA readthrough, which was confirmed with ribosome-targeting antibiotics (e.g., chloramphenicol). Further experiments and mathematical modeling suggest that varied competition between ternary complexes and release factors perturbs the UGA readthrough level. Our results indicate that fluctuations in the concentrations of translational components lead to UGA readthrough heterogeneity among single cells, which enhances phenotypic diversity of the genetically identical population and facilitates its adaptation to changing environments.
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MESH Headings
- Bacterial Proteins/biosynthesis
- Bacterial Proteins/genetics
- Codon, Terminator
- Escherichia coli/genetics
- Escherichia coli/growth & development
- Escherichia coli/metabolism
- Escherichia coli Proteins/biosynthesis
- Escherichia coli Proteins/genetics
- Gene Expression Regulation, Bacterial
- Genes, Reporter
- Genetic Fitness
- Genotype
- Kinetics
- Luminescent Proteins/biosynthesis
- Luminescent Proteins/genetics
- Microscopy, Fluorescence
- Models, Genetic
- One-Carbon Group Transferases
- Phenotype
- RNA, Bacterial/biosynthesis
- RNA, Bacterial/genetics
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- Transcription, Genetic
- Red Fluorescent Protein
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Affiliation(s)
- Yongqiang Fan
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Christopher R Evans
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Karl W Barber
- Department of Cellular & Molecular Physiology, Yale University, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Kinshuk Banerjee
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
| | - Kalyn J Weiss
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - William Margolin
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Oleg A Igoshin
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA; Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Jesse Rinehart
- Department of Cellular & Molecular Physiology, Yale University, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Jiqiang Ling
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, Houston, TX 77030, USA.
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18
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Novel Translation Initiation Regulation Mechanism in Escherichia coli ptrB Mediated by a 5'-Terminal AUG. J Bacteriol 2017; 199:JB.00091-17. [PMID: 28484048 DOI: 10.1128/jb.00091-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 05/01/2017] [Indexed: 11/20/2022] Open
Abstract
Alternative translation initiation mechanisms, distinct from the Shine-Dalgarno (SD) sequence-dependent mechanism, are more prevalent in bacteria than once anticipated. Translation of Escherichia coliptrB instead requires an AUG triplet at the 5' terminus of its mRNA. The 5'-terminal AUG (5'-uAUG) acts as a ribosomal recognition signal to attract ribosomes to the ptrB mRNA rather than functioning as an initiation codon to support translation of an upstream open reading frame. ptrB expression exhibits a stronger dependence on the 5'-uAUG than the predicted SD sequence; however, strengthening the predicted ptrB SD sequence relieves the necessity for the 5'-uAUG. Additional sequences within the ptrB 5' untranslated region (5'-UTR) work cumulatively with the 5'-uAUG to control expression of the downstream ptrB coding sequence (CDS), thereby compensating for the weak SD sequence. Replacement of 5'-UTRs from other mRNAs with the ptrB 5'-UTR sequence showed a similar dependence on the 5'-uAUG for CDS expression, suggesting that the regulatory features contained within the ptrB 5'-UTR are sufficient to control the expression of other E. coli CDSs. Demonstration that the 5'-uAUG present on the ptrB leader mRNA is involved in ribosome binding and expression of the downstream ptrB CDS revealed a novel form of translational regulation. Due to the abundance of AUG triplets at the 5' termini of E. coli mRNAs and the ability of ptrB 5'-UTR regulation to function independently of gene context, the regulatory effects of 5'-uAUGs on downstream CDSs may be widespread throughout the E. coli genome.IMPORTANCE As the field of synthetic biology continues to grow, a complete understanding of basic biological principles will be necessary. The increasing complexity of the synthetic systems highlights the gaps in our current knowledge of RNA regulation. This study demonstrates that there are novel ways to regulate canonical Shine-Dalgarno-led mRNAs in Escherichia coli, illustrating that our understanding of the fundamental processes of translation and RNA regulation is still incomplete. Even for E. coli, one of the most-studied model organisms, genes with translation initiation mechanisms that do not fit the canonical Shine-Dalgarno sequence paradigm are being revealed. Uncovering diverse mechanisms that control translational expression will allow synthetic biologists to finely tune protein production of desired gene products.
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19
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Beck HJ, Fleming IMC, Janssen GR. 5'-Terminal AUGs in Escherichia coli mRNAs with Shine-Dalgarno Sequences: Identification and Analysis of Their Roles in Non-Canonical Translation Initiation. PLoS One 2016; 11:e0160144. [PMID: 27467758 PMCID: PMC4965119 DOI: 10.1371/journal.pone.0160144] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 07/14/2016] [Indexed: 01/18/2023] Open
Abstract
Analysis of the Escherichia coli transcriptome identified a unique subset of messenger RNAs (mRNAs) that contain a conventional untranslated leader and Shine-Dalgarno (SD) sequence upstream of the gene’s start codon while also containing an AUG triplet at the mRNA’s 5’- terminus (5’-uAUG). Fusion of the coding sequence specified by the 5’-terminal putative AUG start codon to a lacZ reporter gene, as well as primer extension inhibition assays, reveal that the majority of the 5’-terminal upstream open reading frames (5’-uORFs) tested support some level of lacZ translation, indicating that these mRNAs can function both as leaderless and canonical SD-leadered mRNAs. Although some of the uORFs were expressed at low levels, others were expressed at levels close to that of the respective downstream genes and as high as the naturally leaderless cI mRNA of bacteriophage λ. These 5’-terminal uORFs potentially encode peptides of varying lengths, but their functions, if any, are unknown. In an effort to determine whether expression from the 5’-terminal uORFs impact expression of the immediately downstream cistron, we examined expression from the downstream coding sequence after mutations were introduced that inhibit efficient 5’-uORF translation. These mutations were found to affect expression from the downstream cistrons to varying degrees, suggesting that some 5’-uORFs may play roles in downstream regulation. Since the 5’-uAUGs found on these conventionally leadered mRNAs can function to bind ribosomes and initiate translation, this indicates that canonical mRNAs containing 5’-uAUGs should be examined for their potential to function also as leaderless mRNAs.
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Affiliation(s)
- Heather J Beck
- Department of Microbiology, Miami University, Oxford, Ohio, United States of America
| | - Ian M C Fleming
- Department of Microbiology, Miami University, Oxford, Ohio, United States of America
| | - Gary R Janssen
- Department of Microbiology, Miami University, Oxford, Ohio, United States of America
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20
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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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21
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Salsi E, Farah E, Ermolenko DN. EF-G Activation by Phosphate Analogs. J Mol Biol 2016; 428:2248-58. [PMID: 27063503 DOI: 10.1016/j.jmb.2016.03.032] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 03/25/2016] [Accepted: 03/29/2016] [Indexed: 01/31/2023]
Abstract
Elongation factor G (EF-G) is a universally conserved translational GTPase that promotes the translocation of tRNA and mRNA through the ribosome. EF-G binds to the ribosome in a GTP-bound form and subsequently catalyzes GTP hydrolysis. The contribution of the ribosome-stimulated GTP hydrolysis by EF-G to tRNA/mRNA translocation remains debated. Here, we show that while EF-G•GDP does not stably bind to the ribosome and induce translocation, EF-G•GDP in complex with phosphate group analogs BeF3(-) and AlF4(-) promotes the translocation of tRNA and mRNA. Furthermore, the rates of mRNA translocation induced by EF-G in the presence of GTP and a non-hydrolyzable analog of GTP, GDP•BeF3(-) are similar. Our results are consistent with the model suggesting that GTP hydrolysis is not directly coupled to mRNA/tRNA translocation. Hence, GTP binding is required to induce the activated, translocation-competent conformation of EF-G while GTP hydrolysis triggers EF-G release from the ribosome.
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Affiliation(s)
- Enea Salsi
- Department of Biochemistry and Biophysics & Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA
| | - Elie Farah
- Department of Biochemistry and Biophysics & Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA
| | - Dmitri N Ermolenko
- Department of Biochemistry and Biophysics & Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA.
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22
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Petrov A, Grosely R, Chen J, O'Leary SE, Puglisi JD. Multiple Parallel Pathways of Translation Initiation on the CrPV IRES. Mol Cell 2016; 62:92-103. [PMID: 27058789 PMCID: PMC4826567 DOI: 10.1016/j.molcel.2016.03.020] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 12/28/2015] [Accepted: 03/17/2016] [Indexed: 02/05/2023]
Abstract
The complexity of eukaryotic translation allows fine-tuned regulation of protein synthesis. Viruses use internal ribosome entry sites (IRESs) to minimize or, like the CrPV IRES, eliminate the need for initiation factors. Here, by exploiting the CrPV IRES, we observed the entire process of initiation and transition to elongation in real time. We directly tracked the CrPV IRES, 40S and 60S ribosomal subunits, and tRNA using single-molecule fluorescence spectroscopy and identified multiple parallel initiation pathways within the system. Our results distinguished two pathways of 80S:CrPV IRES complex assembly that produce elongation-competent complexes. Following 80S assembly, the requisite eEF2-mediated translocation results in an unstable intermediate that is captured by binding of the elongator tRNA. Whereas initiation can occur in the 0 and +1 frames, the arrival of the first tRNA defines the reading frame and strongly favors 0 frame initiation. Overall, even in the simplest system, an intricate reaction network regulates translation initiation.
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Affiliation(s)
- Alexey Petrov
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA
| | - Rosslyn Grosely
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA
| | - Jin Chen
- 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
| | - Seán E O'Leary
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.
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23
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Ying L, Fredrick K. Epistasis analysis of 16S rRNA ram mutations helps define the conformational dynamics of the ribosome that influence decoding. RNA (NEW YORK, N.Y.) 2016; 22:499-505. [PMID: 26873598 PMCID: PMC4793206 DOI: 10.1261/rna.054486.115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 01/14/2016] [Indexed: 06/05/2023]
Abstract
The ribosome actively participates in decoding, with a tRNA-dependent rearrangement of the 30S A site playing a key role. Ribosomal ambiguity (ram) mutations have mapped not only to the A site but also to the h12/S4/S5 region and intersubunit bridge B8, implicating other conformational changes such as 30S shoulder rotation and B8 disruption in the mechanism of decoding. Recent crystallographic data have revealed that mutation G299A in helix h12 allosterically promotes B8 disruption, raising the question of whether G299A and/or other ram mutations act mainly via B8. Here, we compared the effects of each of several ram mutations in the absence and presence of mutation h8Δ2, which effectively takes out bridge B8. The data obtained suggest that a subset of mutations including G299A act in part via B8 but predominantly through another mechanism. We also found that G299A in h12 and G347U in h14 each stabilize tRNA in the A site. Collectively, these data support a model in which rearrangement of the 30S A site, inward shoulder rotation, and bridge B8 disruption are loosely coupled events, all of which promote progression along the productive pathway toward peptide bond formation.
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Affiliation(s)
- Lanqing Ying
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Kurt Fredrick
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
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24
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Castro-Roa D, Zenkin N. Methodology for the analysis of transcription and translation in transcription-coupled-to-translation systems in vitro. Methods 2015; 86:51-9. [PMID: 26080048 DOI: 10.1016/j.ymeth.2015.05.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Revised: 05/26/2015] [Accepted: 05/29/2015] [Indexed: 11/27/2022] Open
Abstract
The various properties of RNA polymerase (RNAP) complexes with nucleic acids during different stages of transcription involve various types of regulation and different cross-talk with other cellular entities and with fellow RNAP molecules. The interactions of transcriptional apparatus with the translational machinery have been focused mainly in terms of outcomes of gene expression, whereas the study of the physical interaction of the ribosome and the RNAP remains obscure partly due to the lack of a system that allows such observations. In this article we will describe the methodology needed to set up a pure, transcription-coupled-to-translation system in which the translocation of the ribosome can be performed in a step-wise manner towards RNAP allowing investigation of the interactions between the two machineries at colliding and non-colliding distances. In the same time RNAP can be put in various types of states, such as paused, roadblocked, backtracked, etc. The experimental system thus allows studying the effects of the ribosome on different aspects of transcription elongation and the effects by RNAP on translation.
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Affiliation(s)
- Daniel Castro-Roa
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Baddiley-Clark Building, Richardson Road, Newcastle upon Tyne NE2 4AX, UK.
| | - Nikolay Zenkin
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Baddiley-Clark Building, Richardson Road, Newcastle upon Tyne NE2 4AX, UK
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25
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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: 90] [Impact Index Per Article: 10.0] [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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26
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T box riboswitches in Actinobacteria: translational regulation via novel tRNA interactions. Proc Natl Acad Sci U S A 2015; 112:1113-8. [PMID: 25583497 DOI: 10.1073/pnas.1424175112] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The T box riboswitch regulates many amino acid-related genes in Gram-positive bacteria. T box riboswitch-mediated gene regulation was shown previously to occur at the level of transcription attenuation via structural rearrangements in the 5' untranslated (leader) region of the mRNA in response to binding of a specific uncharged tRNA. In this study, a novel group of isoleucyl-tRNA synthetase gene (ileS) T box leader sequences found in organisms of the phylum Actinobacteria was investigated. The Stem I domains of these RNAs lack several highly conserved elements that are essential for interaction with the tRNA ligand in other T box RNAs. Many of these RNAs were predicted to regulate gene expression at the level of translation initiation through tRNA-dependent stabilization of a helix that sequesters a sequence complementary to the Shine-Dalgarno (SD) sequence, thus freeing the SD sequence for ribosome binding and translation initiation. We demonstrated specific binding to the cognate tRNA(Ile) and tRNA(Ile)-dependent structural rearrangements consistent with regulation at the level of translation initiation, providing the first biochemical demonstration, to our knowledge, of translational regulation in a T box riboswitch.
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27
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Castro-Roa D, Zenkin N. Methods for the assembly and analysis of in vitro transcription-coupled-to-translation systems. Methods Mol Biol 2015; 1276:81-99. [PMID: 25665559 DOI: 10.1007/978-1-4939-2392-2_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
RNA polymerase is a complex machinery, which is further embedded in interactions with other cellular components that interplay with either the transcribed DNA (DNA polymerases, topoisomerases, etc.) or the nascent RNA (RNA processing enzymes, ribosomes, etc.). In prokaryotes, coupling of transcription and translation is thought to play many regulatory roles but the mechanistic understanding of their interactions has been hindered by the lack of a defined experimental system. Here, we describe a pure transcription-coupled-to-translation system in which control of the ribosome has been achieved through its stepwise translocation towards RNA polymerase. This system can be used to study the effects of concurrent translation on RNA chain elongation and to elucidate the interface between the two macromolecular complexes.
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Affiliation(s)
- Daniel Castro-Roa
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Baddiley-Clark Building, Richardson Road, Newcastle Upon Tyne, NE2 4AX, UK,
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28
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Salsi E, Farah E, Netter Z, Dann J, Ermolenko DN. Movement of elongation factor G between compact and extended conformations. J Mol Biol 2014; 427:454-67. [PMID: 25463439 DOI: 10.1016/j.jmb.2014.11.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 10/28/2014] [Accepted: 11/10/2014] [Indexed: 11/19/2022]
Abstract
Previous structural studies suggested that ribosomal translocation is accompanied by large interdomain rearrangements of elongation factor G (EF-G). Here, we follow the movement of domain IV of EF-G relative to domain II of EF-G using ensemble and single-molecule Förster resonance energy transfer. Our results indicate that ribosome-free EF-G predominantly adopts a compact conformation that can also, albeit infrequently, transition into a more extended conformation in which domain IV moves away from domain II. By contrast, ribosome-bound EF-G predominantly adopts an extended conformation regardless of whether it is interacting with pretranslocation ribosomes or with posttranslocation ribosomes. Our data suggest that ribosome-bound EF-G may also occasionally sample at least one more compact conformation. GTP hydrolysis catalyzed by EF-G does not affect the relative stability of the observed conformations in ribosome-free and ribosome-bound EF-G. Our data support a model suggesting that, upon binding to a pretranslocation ribosome, EF-G moves from a compact to a more extended conformation. This transition is not coupled to but likely precedes both GTP hydrolysis and mRNA/tRNA translocation.
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Affiliation(s)
- Enea Salsi
- Department of Biochemistry and Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA
| | - Elie Farah
- Department of Biochemistry and Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA
| | - Zoe Netter
- Department of Biochemistry and Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA
| | - Jillian Dann
- Department of Biochemistry and Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA
| | - Dmitri N Ermolenko
- Department of Biochemistry and Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA.
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29
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Balakrishnan R, Oman K, Shoji S, Bundschuh R, Fredrick K. The conserved GTPase LepA contributes mainly to translation initiation in Escherichia coli. Nucleic Acids Res 2014; 42:13370-83. [PMID: 25378333 PMCID: PMC4245954 DOI: 10.1093/nar/gku1098] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
LepA is a paralog of EF-G found in all bacteria. Deletion of lepA confers no obvious growth defect in Escherichia coli, and the physiological role of LepA remains unknown. Here, we identify nine strains (ΔdksA, ΔmolR1, ΔrsgA, ΔtatB, ΔtonB, ΔtolR, ΔubiF, ΔubiG or ΔubiH) in which ΔlepA confers a synthetic growth phenotype. These strains are compromised for gene regulation, ribosome assembly, transport and/or respiration, indicating that LepA contributes to these functions in some way. We also use ribosome profiling to deduce the effects of LepA on translation. We find that loss of LepA alters the average ribosome density (ARD) for hundreds of mRNA coding regions in the cell, substantially reducing ARD in many cases. By contrast, only subtle and codon-specific changes in ribosome distribution along mRNA are seen. These data suggest that LepA contributes mainly to the initiation phase of translation. Consistent with this interpretation, the effect of LepA on ARD is related to the sequence of the Shine–Dalgarno region. Global perturbation of gene expression in the ΔlepA mutant likely explains most of its phenotypes.
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Affiliation(s)
- Rohan Balakrishnan
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Kenji Oman
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Shinichiro Shoji
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Ralf Bundschuh
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Kurt Fredrick
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
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30
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Following movement of domain IV of elongation factor G during ribosomal translocation. Proc Natl Acad Sci U S A 2014; 111:15060-5. [PMID: 25288752 DOI: 10.1073/pnas.1410873111] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Translocation of mRNA and tRNAs through the ribosome is catalyzed by a universally conserved elongation factor (EF-G in prokaryotes and EF-2 in eukaryotes). Previous studies have suggested that ribosome-bound EF-G undergoes significant structural rearrangements. Here, we follow the movement of domain IV of EF-G, which is critical for the catalysis of translocation, relative to protein S12 of the small ribosomal subunit using single-molecule FRET. We show that ribosome-bound EF-G adopts distinct conformations corresponding to the pre- and posttranslocation states of the ribosome. Our results suggest that, upon ribosomal translocation, domain IV of EF-G moves toward the A site of the small ribosomal subunit and facilitates the movement of peptidyl-tRNA from the A to the P site. We found no evidence of direct coupling between the observed movement of domain IV of EF-G and GTP hydrolysis. In addition, our results suggest that the pretranslocation conformation of the EF-G-ribosome complex is significantly less stable than the posttranslocation conformation. Hence, the structural rearrangement of EF-G makes a considerable energetic contribution to promoting tRNA translocation.
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31
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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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32
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Taura syndrome virus IRES initiates translation by binding its tRNA-mRNA-like structural element in the ribosomal decoding center. Proc Natl Acad Sci U S A 2014; 111:9139-44. [PMID: 24927574 DOI: 10.1073/pnas.1406335111] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In cap-dependent translation initiation, the open reading frame (ORF) of mRNA is established by the placement of the AUG start codon and initiator tRNA in the ribosomal peptidyl (P) site. Internal ribosome entry sites (IRESs) promote translation of mRNAs in a cap-independent manner. We report two structures of the ribosome-bound Taura syndrome virus (TSV) IRES belonging to the family of Dicistroviridae intergenic IRESs. Intersubunit rotational states differ in these structures, suggesting that ribosome dynamics play a role in IRES translocation. Pseudoknot I of the IRES occupies the ribosomal decoding center at the aminoacyl (A) site in a manner resembling that of the tRNA anticodon-mRNA codon. The structures reveal that the TSV IRES initiates translation by a previously unseen mechanism, which is conceptually distinct from initiator tRNA-dependent mechanisms. Specifically, the ORF of the IRES-driven mRNA is established by the placement of the preceding tRNA-mRNA-like structure in the A site, whereas the 40S P site remains unoccupied during this initial step.
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33
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McClory SP, Devaraj A, Fredrick K. Distinct functional classes of ram mutations in 16S rRNA. RNA (NEW YORK, N.Y.) 2014; 20:496-504. [PMID: 24572811 PMCID: PMC3964911 DOI: 10.1261/rna.043331.113] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 01/20/2014] [Indexed: 06/03/2023]
Abstract
During decoding, the ribosome selects the correct (cognate) aminoacyl-tRNA (aa-tRNA) from a large pool of incorrect aa-tRNAs through a two-stage mechanism. In the initial selection stage, aa-tRNA is delivered to the ribosome as part of a ternary complex with elongation factor EF-Tu and GTP. Interactions between codon and anticodon lead to activation of the GTPase domain of EF-Tu and GTP hydrolysis. Then, in the proofreading stage, aa-tRNA is released from EF-Tu and either moves fully into the A/A site (a step termed "accommodation") or dissociates from the ribosome. Cognate codon-anticodon pairing not only stabilizes aa-tRNA at both stages of decoding but also stimulates GTP hydrolysis and accommodation, allowing the process to be both accurate and fast. In previous work, we isolated a number of ribosomal ambiguity (ram) mutations in 16S rRNA, implicating particular regions of the ribosome in the mechanism of decoding. Here, we analyze a representative subset of these mutations with respect to initial selection, proofreading, RF2-dependent termination, and overall miscoding in various contexts. We find that mutations that disrupt inter-subunit bridge B8 increase miscoding in a general way, causing defects in both initial selection and proofreading. Mutations in or near the A site behave differently, increasing miscoding in a codon-anticodon-dependent manner. These latter mutations may create spurious favorable interactions in the A site for certain near-cognate aa-tRNAs, providing an explanation for their context-dependent phenotypes in the cell.
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MESH Headings
- Anticodon/genetics
- Codon/genetics
- Guanosine Triphosphate/metabolism
- Kinetics
- Models, Molecular
- Mutation/genetics
- Nucleic Acid Conformation
- Peptide Termination Factors/chemistry
- Peptide Termination Factors/genetics
- Peptide Termination Factors/metabolism
- Protein Biosynthesis
- RNA, Messenger/genetics
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/genetics
- RNA, Transfer, Amino Acyl/metabolism
- Ribosomes/chemistry
- Ribosomes/genetics
- Ribosomes/metabolism
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Affiliation(s)
- Sean P. McClory
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Aishwarya Devaraj
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Kurt Fredrick
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
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34
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Ermolenko DN, Cornish PV, Ha T, Noller HF. Antibiotics that bind to the A site of the large ribosomal subunit can induce mRNA translocation. RNA (NEW YORK, N.Y.) 2013; 19:158-66. [PMID: 23249745 PMCID: PMC3543091 DOI: 10.1261/rna.035964.112] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
In the absence of elongation factor EF-G, ribosomes undergo spontaneous, thermally driven fluctuation between the pre-translocation (classical) and intermediate (hybrid) states of translocation. These fluctuations do not result in productive mRNA translocation. Extending previous findings that the antibiotic sparsomycin induces translocation, we identify additional peptidyl transferase inhibitors that trigger productive mRNA translocation. We find that antibiotics that bind the peptidyl transferase A site induce mRNA translocation, whereas those that do not occupy the A site fail to induce translocation. Using single-molecule FRET, we show that translocation-inducing antibiotics do not accelerate intersubunit rotation, but act solely by converting the intrinsic, thermally driven dynamics of the ribosome into translocation. Our results support the idea that the ribosome is a Brownian ratchet machine, whose intrinsic dynamics can be rectified into unidirectional translocation by ligand binding.
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MESH Headings
- Anti-Bacterial Agents/metabolism
- Anti-Bacterial Agents/pharmacology
- Chloramphenicol/metabolism
- Chloramphenicol/pharmacology
- Clindamycin/metabolism
- Clindamycin/pharmacology
- Enzyme Inhibitors/metabolism
- Enzyme Inhibitors/pharmacology
- Escherichia coli/drug effects
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Escherichia coli Proteins/drug effects
- Escherichia coli Proteins/metabolism
- Fluorescence Resonance Energy Transfer
- Lincomycin/metabolism
- Lincomycin/pharmacology
- Peptide Elongation Factor G/drug effects
- Peptide Elongation Factor G/metabolism
- Peptidyl Transferases/drug effects
- Peptidyl Transferases/metabolism
- Protein Biosynthesis/drug effects
- RNA Transport/drug effects
- RNA, Bacterial/drug effects
- RNA, Bacterial/metabolism
- RNA, Messenger/drug effects
- RNA, Messenger/metabolism
- RNA, Transfer/drug effects
- RNA, Transfer/metabolism
- Ribosome Subunits, Large, Bacterial/drug effects
- Ribosome Subunits, Large, Bacterial/metabolism
- Sparsomycin/metabolism
- Sparsomycin/pharmacology
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Affiliation(s)
- Dmitri N Ermolenko
- Department of Biochemistry and Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA.
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35
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Zenkin N. Hypothesis: Emergence of Translation as a Result of RNA Helicase Evolution. J Mol Evol 2012; 74:249-56. [DOI: 10.1007/s00239-012-9503-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2011] [Accepted: 04/13/2012] [Indexed: 10/28/2022]
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36
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Harish A, Caetano-Anollés G. Ribosomal history reveals origins of modern protein synthesis. PLoS One 2012; 7:e32776. [PMID: 22427882 PMCID: PMC3299690 DOI: 10.1371/journal.pone.0032776] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2011] [Accepted: 01/30/2012] [Indexed: 02/06/2023] Open
Abstract
The origin and evolution of the ribosome is central to our understanding of the cellular world. Most hypotheses posit that the ribosome originated in the peptidyl transferase center of the large ribosomal subunit. However, these proposals do not link protein synthesis to RNA recognition and do not use a phylogenetic comparative framework to study ribosomal evolution. Here we infer evolution of the structural components of the ribosome. Phylogenetic methods widely used in morphometrics are applied directly to RNA structures of thousands of molecules and to a census of protein structures in hundreds of genomes. We find that components of the small subunit involved in ribosomal processivity evolved earlier than the catalytic peptidyl transferase center responsible for protein synthesis. Remarkably, subunit RNA and proteins coevolved, starting with interactions between the oldest proteins (S12 and S17) and the oldest substructure (the ribosomal ratchet) in the small subunit and ending with the rise of a modern multi-subunit ribosome. Ancestral ribonucleoprotein components show similarities to in vitro evolved RNA replicase ribozymes and protein structures in extant replication machinery. Our study therefore provides important clues about the chicken-or-egg dilemma associated with the central dogma of molecular biology by showing that ribosomal history is driven by the gradual structural accretion of protein and RNA structures. Most importantly, results suggest that functionally important and conserved regions of the ribosome were recruited and could be relics of an ancient ribonucleoprotein world.
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Affiliation(s)
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana-Champaign, Illinois, United States of America
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37
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Giliberti J, O'Donnell S, Van Etten WJ, Janssen GR. A 5'-terminal phosphate is required for stable ternary complex formation and translation of leaderless mRNA in Escherichia coli. RNA (NEW YORK, N.Y.) 2012; 18:508-518. [PMID: 22291205 PMCID: PMC3285938 DOI: 10.1261/rna.027698.111] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Accepted: 12/01/2011] [Indexed: 05/31/2023]
Abstract
The bacteriophage λ's cI mRNA was utilized to examine the importance of the 5'-terminal phosphate on expression of leadered and leaderless mRNA in Escherichia coli. A hammerhead ribozyme was used to produce leadered and leaderless mRNAs, in vivo and in vitro, that contain a 5'-hydroxyl. Although these mRNAs may not occur naturally in the bacterial cell, they allow for the study of the importance of the 5'-phosphorylation state in ribosome binding and translation of leadered and leaderless mRNAs. Analyses with mRNAs containing either a 5'-phosphate or a 5'-hydroxyl indicate that leaderless cI mRNA requires a 5'-phosphate for stable ribosome binding in vitro as well as expression in vivo. Ribosome-binding assays show that 30S subunits and 70S ribosomes do not bind as strongly to 5'-hydroxyl as they do to 5'-phosphate containing leaderless mRNA and the tRNA-dependent ternary complex is less stable. Additionally, filter-binding assays revealed that the 70S ternary complex formed with a leaderless mRNA containing a 5'-hydroxyl has a dissociation rate (k(off)) that is 4.5-fold higher compared with the complex formed with a 5'-phosphate leaderless mRNA. Fusion to a lacZ reporter gene revealed that leaderless cI mRNA expression with a 5'-hydroxyl was >100-fold lower than the equivalent mRNA with a 5'-phosphate. These data indicate that a 5'-phosphate is an important feature of leaderless mRNA for stable ribosome binding and expression.
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Affiliation(s)
| | - Sean O'Donnell
- Grifols, Inc., Research Triangle Park, North Carolina 27709, USA
| | | | - Gary R. Janssen
- Department of Microbiology, Miami University, Oxford, Ohio 45056, USA
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38
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Qin D, Liu Q, Devaraj A, Fredrick K. Role of helix 44 of 16S rRNA in the fidelity of translation initiation. RNA (NEW YORK, N.Y.) 2012; 18:485-95. [PMID: 22279149 PMCID: PMC3285936 DOI: 10.1261/rna.031203.111] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Accepted: 12/08/2011] [Indexed: 05/30/2023]
Abstract
The molecular mechanisms that govern translation initiation to ensure accuracy remain unclear. Here, we provide evidence that the subunit-joining step of initiation is controlled in part by a conformational change in the 1408 region of helix h44. First, chemical probing of 30S initiation complexes formed with either a cognate (AUG) or near-cognate (AUC) start codon shows that an IF1-dependent enhancement at A1408 is reduced in the presence of AUG. This change in reactivity is due to a conformational change rather than loss of IF1, because other portions of the IF1 footprint are unchanged and high concentrations of IF1 fail to diminish the reactivity difference seen at A1408. Second, mutations in h44 such as A1413C stimulate 50S docking and cause reduced reactivity at A1408. Third, streptomycin, which has been shown by Rodnina and coworkers to stimulate 50S docking by reversing the inhibitory effects of IF1, also causes reduced reactivity at A1408. Collectively, these data support a model in which IF1 alters the A1408 region of h44 in a way that makes 50S docking unfavorable, and canonical codon-anticodon pairing in the P site restores h44 to a docking-favorable conformation. We also find that, in the absence of factors, the cognate 30S•AUG•fMet-tRNA ternary complex is >1000-fold more stable than the near-cognate 30S•AUC•fMet-tRNA complex. Hence, the selectivity of ternary complex formation is inherently high, exceeding that of initiation in vivo by more than 10-fold.
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MESH Headings
- Codon, Initiator/genetics
- Codon, Initiator/metabolism
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Mutation
- Nucleic Acid Conformation
- Peptide Chain Initiation, Translational/drug effects
- RNA, Messenger/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Ribosome Subunits, Small, Bacterial/metabolism
- Streptomycin/pharmacology
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Affiliation(s)
- Daoming Qin
- Department of Microbiology, Ohio State Biochemistry Program, and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Qi Liu
- Department of Microbiology, Ohio State Biochemistry Program, and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Aishwarya Devaraj
- Department of Microbiology, Ohio State Biochemistry Program, and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Kurt Fredrick
- Department of Microbiology, Ohio State Biochemistry Program, and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
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39
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Liu CY, Qureshi MT, Lee TH. Interaction strengths between the ribosome and tRNA at various steps of translocation. Biophys J 2011; 100:2201-8. [PMID: 21539788 DOI: 10.1016/j.bpj.2011.03.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Revised: 02/28/2011] [Accepted: 03/24/2011] [Indexed: 10/18/2022] Open
Abstract
Transfer RNA (tRNA) translocates inside the ribosome during translation. We studied the interaction strengths between the ribosome and tRNA at various stages of translocation. We utilized an optical trap to measure the mechanical force to rupture tRNA from the ribosome. We measured the rupture forces of aminoacyl tRNA or peptidyl tRNA mimic from the ribosome in a prepeptidyl transfer state, the pretranslocational state, and the posttranslocational state. In addition, we measured the interaction strength between the ribosome and aminoacyl-tRNA in presence of viomycin. Based on the interaction strengths between the ribosome and tRNA under these conditions, 1), we concluded that tRNA interaction with the 30S subunit is far more important than the interaction with the 50S subunit in the mechanism of translocation; and 2), we propose a mechanism of translocation where the ribosomal ratchet motion, with the aid of EF-G, drives tRNA translocation.
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Affiliation(s)
- Chen-Yu Liu
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA
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40
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Devaraj A, Fredrick K. Short spacing between the Shine-Dalgarno sequence and P codon destabilizes codon-anticodon pairing in the P site to promote +1 programmed frameshifting. Mol Microbiol 2010; 78:1500-9. [PMID: 21143320 DOI: 10.1111/j.1365-2958.2010.07421.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Programmed frameshifting in the RF2 gene (prfB) involves an intragenic Shine-Dalgarno (SD) sequence. To investigate the role of SD-ASD pairing in the mechanism of frameshifting, we have analysed the effect of spacing between the SD sequence and P codon on P-site tRNA binding and RF2-dependent termination. When the spacing between an extended SD sequence and the P codon is decreased from 4 to 1 nucleotide (nt), the dissociation rate (k(off) ) for P-site tRNA increases by > 100-fold. Toeprinting analysis shows that pre-translocation complexes cannot be formed when the spacer sequence is ≤ 2 nt. Instead, the tRNA added secondarily to fill the A site and its corresponding codon move spontaneously into the P site, resulting in a complex with a 3 nt longer spacer between the SD-ASD helix and the P codon. While close proximity of the SD clearly destabilizes P-site tRNA, RF2-dependent termination and EF-Tu-dependent decoding are largely unaffected in analogous complexes. These data support a model in which formation of the SD-ASD helix in ribosomes stalled at the in-frame UGA codon of prfB generates tension on the mRNA that destabilizes codon-anticodon pairing in the P site and promotes slippage of the mRNA in the 5' direction.
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Affiliation(s)
- Aishwarya Devaraj
- Ohio State Biochemistry Program Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
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41
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Abstract
Our current understanding of the mechanism of translation is based on nearly fifty years of biochemical and biophysical studies. This mechanism, which requires the ribosome to manipulate tRNA and step repetitively along the mRNA, implies movement. High-resolution structures of the ribosome and its ligands have recently described translation in atomic detail, capturing the endpoints of large-scale rearrangements of the ribosome. Direct observation of the dynamic events that underlie the mechanism of translation is challenged by ensemble averaging in bulk solutions. Single-molecule methods, which eliminate these averaging effects, have emerged as powerful tools to probe the mechanism of translation. Single-molecule fluorescence experiments have described the dynamic motion of the ribosome and tRNA. Single-molecule force measurements have directly probed the forces stabilizing ribosomal complexes. Recent developments have allowed real-time observation of ribosome movement and dynamics during translation. This review covers the contributions of single-molecule studies to our understanding of the dynamic nature of translation.
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42
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Mazauric MH, Seol Y, Yoshizawa S, Visscher K, Fourmy D. Interaction of the HIV-1 frameshift signal with the ribosome. Nucleic Acids Res 2010; 37:7654-64. [PMID: 19812214 PMCID: PMC2794165 DOI: 10.1093/nar/gkp779] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Ribosomal frameshifting on viral RNAs relies on the mechanical properties of structural elements, often pseudoknots and more rarely stem-loops, that are unfolded by the ribosome during translation. In human immunodeficiency virus (HIV)-1 type B a long hairpin containing a three-nucleotide bulge is responsible for efficient frameshifting. This three-nucleotide bulge separates the hairpin in two domains: an unstable lower stem followed by a GC-rich upper stem. Toeprinting and chemical probing assays suggest that a hairpin-like structure is retained when ribosomes, initially bound at the slippery sequence, were allowed multiple EF-G catalyzed translocation cycles. However, while the upper stem remains intact the lower stem readily melts. After the first, and single step of translocation of deacylated tRNA to the 30 S P site, movement of the mRNA stem-loop in the 5′ direction is halted, which is consistent with the notion that the downstream secondary structure resists unfolding. Mechanical stretching of the hairpin using optical tweezers only allows clear identification of unfolding of the upper stem at a force of 12.8 ± 1.0 pN. This suggests that the lower stem is unstable and may indeed readily unfold in the presence of a translocating ribosome.
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Affiliation(s)
- Marie-Hélène Mazauric
- Laboratoire de Chimie et Biologie Structurales, FRC 3115 ICSN-CNRS 1 ave de la terrasse, 91190 Gif-sur-Yvette, France
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Allosteric collaboration between elongation factor G and the ribosomal L1 stalk directs tRNA movements during translation. Proc Natl Acad Sci U S A 2009; 106:15702-7. [PMID: 19717422 DOI: 10.1073/pnas.0908077106] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Determining the mechanism by which tRNAs rapidly and precisely transit through the ribosomal A, P, and E sites during translation remains a major goal in the study of protein synthesis. Here, we report the real-time dynamics of the L1 stalk, a structural element of the large ribosomal subunit that is implicated in directing tRNA movements during translation. Within pretranslocation ribosomal complexes, the L1 stalk exists in a dynamic equilibrium between open and closed conformations. Binding of elongation factor G (EF-G) shifts this equilibrium toward the closed conformation through one of at least two distinct kinetic mechanisms, where the identity of the P-site tRNA dictates the kinetic route that is taken. Within posttranslocation complexes, L1 stalk dynamics are dependent on the presence and identity of the E-site tRNA. Collectively, our data demonstrate that EF-G and the L1 stalk allosterically collaborate to direct tRNA translocation from the P to the E sites, and suggest a model for the release of E-site tRNA.
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Garza-Sánchez F, Shoji S, Fredrick K, Hayes CS. RNase II is important for A-site mRNA cleavage during ribosome pausing. Mol Microbiol 2009; 73:882-97. [PMID: 19627501 DOI: 10.1111/j.1365-2958.2009.06813.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In Escherichia coli, translational arrest can elicit cleavage of codons within the ribosomal A site. This A-site mRNA cleavage is independent of RelE, and has been proposed to be an endonucleolytic activity of the ribosome. Here, we show that the 3'-->5' exonuclease RNase II plays an important role in RelE-independent A-site cleavage. Instead of A-site cleavage, translational pausing in DeltaRNase II cells produces transcripts that are truncated +12 and +28 nucleotides downstream of the A-site codon. Deletions of the genes encoding polynucleotide phosphorylase (PNPase) and RNase R had little effect on A-site cleavage. However, PNPase overexpression restored A-site cleavage activity to DeltaRNase II cells. Purified RNase II and PNPase were both unable to directly catalyse A-site cleavage in vitro. Instead, these exonucleases degraded ribosome-bound mRNA to positions +18 and +24 nucleotides downstream of the ribosomal A site respectively. Finally, a stable structural barrier to exoribonuclease activity inhibited A-site cleavage when introduced immediately downstream of paused ribosomes. These results demonstrate that 3'-->5' exonuclease activity is an important prerequisite for efficient A-site cleavage. We propose that RNase II degrades mRNA to the downstream border of paused ribosomes, facilitating cleavage of the A-site codon by an unknown RNase.
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Affiliation(s)
- Fernando Garza-Sánchez
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106-9610, USA
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Abstract
In the cell, proteins are synthesized by ribosomes in a multi-step process called translation. The ribosome translocates along the messenger RNA to read the codons that encode the amino acid sequence of a protein. Elongation factors, including EF-G and EF-Tu, are used to catalyze the process. Recently, we have shown that translation can be followed at the single-molecule level using optical tweezers; this technique allows us to study the kinetics of translation by measuring the lifetime the ribosome spends at each codon. Here, we analyze the data from single-molecule experiments and fit the data with simple kinetic models. We also simulate the translation kinetics based on a multi-step mechanism from ensemble kinetic measurements. The mean lifetimes from the simulation were consistent with our experimental single-molecule measurements. We found that the calculated lifetime distributions were fit in general by equations with up to five rate-determining steps. Two rate-determining steps were only obtained at low concentrations of elongation factors. These analyses can be used to design new single-molecule experiments to better understand the kinetics and mechanism of translation.
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Affiliation(s)
- Ignacio Tinoco
- Department of Chemistry, University of California, Berkeley, CA 94720-1460, USA.
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Shoji S, Abdi NM, Bundschuh R, Fredrick K. Contribution of ribosomal residues to P-site tRNA binding. Nucleic Acids Res 2009; 37:4033-42. [PMID: 19417061 PMCID: PMC2709574 DOI: 10.1093/nar/gkp296] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Structural studies have revealed multiple contacts between the ribosomal P site and tRNA, but how these contacts contribute to P-tRNA binding remains unclear. In this study, the effects of ribosomal mutations on the dissociation rate (k(off)) of various tRNAs from the P site were measured. Mutation of the 30S P site destabilized tRNAs to various degrees, depending on the mutation and the species of tRNA. These data support the idea that ribosome-tRNA interactions are idiosyncratically tuned to ensure stable binding of all tRNA species. Unlike deacylated elongator tRNAs, N-acetyl-aminoacyl-tRNAs and tRNA(fMet) dissociated from the P site at a similar low rate, even in the presence of various P-site mutations. These data provide evidence for a stability threshold for P-tRNA binding and suggest that ribosome-tRNA(fMet) interactions are uniquely tuned for tight binding. The effects of 16S rRNA mutation G1338U were suppressed by 50S E-site mutation C2394A, suggesting that G1338 is particularly important for stabilizing tRNA in the P/E site. Finally, mutation C2394A or the presence of an N-acetyl-aminoacyl group slowed the association rate (k(on)) of tRNA dramatically, suggesting that deacylated tRNA binds the P site of the ribosome via the E site.
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Affiliation(s)
- Shinichiro Shoji
- Department of Microbiology, The Ohio State University, 484 W., 12th Ave, Columbus, OH 43210, USA
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A thermal ratchet model of tRNA–mRNA translocation by the ribosome. Biosystems 2009; 96:19-28. [DOI: 10.1016/j.biosystems.2008.11.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2008] [Revised: 11/07/2008] [Accepted: 11/10/2008] [Indexed: 11/23/2022]
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Following movement of the L1 stalk between three functional states in single ribosomes. Proc Natl Acad Sci U S A 2009; 106:2571-6. [PMID: 19190181 DOI: 10.1073/pnas.0813180106] [Citation(s) in RCA: 143] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The L1 stalk is a mobile domain of the large ribosomal subunit E site that interacts with the elbow of deacylated tRNA during protein synthesis. Here, by using single-molecule FRET, we follow the real-time dynamics of the L1 stalk and observe its movement relative to the body of the large subunit between at least 3 distinct conformational states: open, half-closed, and fully closed. Pretranslocation ribosomes undergo spontaneous fluctuations between the open and fully closed states. In contrast, posttranslocation ribosomes containing peptidyl-tRNA and deacylated tRNA in the classical P/P and E/E states, respectively, are fixed in the half-closed conformation. In ribosomes with a vacant E site, the L1 stalk is observed either in the fully closed or fully open conformation. Several lines of evidence show that the L1 stalk can move independently of intersubunit rotation. Our findings support a model in which the mobility of the L1 stalk facilitates binding, movement, and release of deacylated tRNA by remodeling the structure of the 50S subunit E site between 3 distinct conformations, corresponding to the E/E vacant, P/E hybrid, and classical states.
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Lancaster L, Lambert NJ, Maklan EJ, Horan LH, Noller HF. The sarcin-ricin loop of 23S rRNA is essential for assembly of the functional core of the 50S ribosomal subunit. RNA (NEW YORK, N.Y.) 2008; 14:1999-2012. [PMID: 18755834 PMCID: PMC2553751 DOI: 10.1261/rna.1202108] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The sarcin-ricin loop (SRL) of 23S rRNA in the large ribosomal subunit is a factor-binding site that is essential for GTP-catalyzed steps in translation, but its precise functional role is thus far unknown. Here, we replaced the 15-nucleotide SRL with a GAAA tetraloop and affinity purified the mutant 50S subunits for functional and structural analysis in vitro. The SRL deletion caused defects in elongation-factor-dependent steps of translation and, unexpectedly, loss of EF-Tu-independent A-site tRNA binding. Detailed chemical probing analysis showed disruption of a network of rRNA tertiary interactions that hold together the 23S rRNA elements of the functional core of the 50S subunit, accompanied by loss of ribosomal protein L16. Our results reveal an influence of the SRL on the higher-order structure of the 50S subunit, with implications for its role in translation.
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Affiliation(s)
- Laura Lancaster
- Center for Molecular Biology of RNA, University of California at Santa Cruz, Santa Cruz, California 95064, USA
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50
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Abstract
Decades of studies have established translation as a multistep, multicomponent process that requires intricate communication to achieve high levels of speed, accuracy, and regulation. A crucial next step in understanding translation is to reveal the functional significance of the large-scale motions implied by static ribosome structures. This requires determining the trajectories, timescales, forces, and biochemical signals that underlie these dynamic conformational changes. Single-molecule methods have emerged as important tools for the characterization of motion in complex systems, including translation. In this review, we chronicle the key discoveries in this nascent field, which have demonstrated the power and promise of single-molecule techniques in the study of translation.
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Affiliation(s)
- R Andrew Marshall
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
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