1
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Warner BR, Bundschuh R, Fredrick K. Roles of the leader-trailer helix and antitermination complex in biogenesis of the 30S ribosomal subunit. Nucleic Acids Res 2023; 51:5242-5254. [PMID: 37102690 PMCID: PMC10250234 DOI: 10.1093/nar/gkad316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 04/07/2023] [Accepted: 04/13/2023] [Indexed: 04/28/2023] Open
Abstract
Ribosome biogenesis occurs co-transcriptionally and entails rRNA folding, ribosomal protein binding, rRNA processing, and rRNA modification. In most bacteria, the 16S, 23S and 5S rRNAs are co-transcribed, often with one or more tRNAs. Transcription involves a modified RNA polymerase, called the antitermination complex, which forms in response to cis-acting elements (boxB, boxA and boxC) in the nascent pre-rRNA. Sequences flanking the rRNAs are complementary and form long helices known as leader-trailer helices. Here, we employed an orthogonal translation system to interrogate the functional roles of these RNA elements in 30S subunit biogenesis in Escherichia coli. Mutations that disrupt the leader-trailer helix caused complete loss of translation activity, indicating that this helix is absolutely essential for active subunit formation in the cell. Mutations of boxA also reduced translation activity, but by only 2- to 3-fold, suggesting a smaller role for the antitermination complex. Similarly modest drops in activity were seen upon deletion of either or both of two leader helices, termed here hA and hB. Interestingly, subunits formed in the absence of these leader features exhibited defects in translational fidelity. These data suggest that the antitermination complex and precursor RNA elements help to ensure quality control during ribosome biogenesis.
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Affiliation(s)
- Benjamin R Warner
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
- 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
- Department of Chemistry and 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
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
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2
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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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3
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Sharma H, Anand B. Ribosome assembly defects subvert initiation Factor3 mediated scrutiny of bona fide start signal. Nucleic Acids Res 2020; 47:11368-11386. [PMID: 31586395 PMCID: PMC6868393 DOI: 10.1093/nar/gkz825] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 08/17/2019] [Accepted: 10/03/2019] [Indexed: 12/02/2022] Open
Abstract
In bacteria, the assembly factors tightly orchestrate the maturation of ribosomes whose competency for protein synthesis is validated by translation machinery at various stages of translation cycle. However, what transpires to the quality control measures when the ribosomes are produced with assembly defects remains enigmatic. In Escherichia coli, we show that 30S ribosomes that harbour assembly defects due to the lack of assembly factors such as RbfA and KsgA display suboptimal initiation codon recognition and bypass the critical codon–anticodon proofreading steps during translation initiation. These premature ribosomes on entering the translation cycle compromise the fidelity of decoding that gives rise to errors during initiation and elongation. We show that the assembly defects compromise the binding of initiation factor 3 (IF3), which in turn appears to license the rapid transition of 30S (pre) initiation complex to 70S initiation complex by tempering the validation of codon–anticodon interaction during translation initiation. This suggests that the premature ribosomes harbouring the assembly defects subvert the IF3 mediated proofreading of cognate initiation codon to enter the translation cycle.
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Affiliation(s)
- Himanshu Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - B Anand
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
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4
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Vinogradova DS, Zegarra V, Maksimova E, Nakamoto JA, Kasatsky P, Paleskava A, Konevega AL, Milón P. How the initiating ribosome copes with ppGpp to translate mRNAs. PLoS Biol 2020; 18:e3000593. [PMID: 31995552 PMCID: PMC7010297 DOI: 10.1371/journal.pbio.3000593] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 02/10/2020] [Accepted: 01/16/2020] [Indexed: 11/18/2022] Open
Abstract
During host colonization, bacteria use the alarmones (p)ppGpp to reshape their proteome by acting pleiotropically on DNA, RNA, and protein synthesis. Here, we elucidate how the initiating ribosome senses the cellular pool of guanosine nucleotides and regulates the progression towards protein synthesis. Our results show that the affinity of guanosine triphosphate (GTP) and the inhibitory concentration of ppGpp for the 30S-bound initiation factor IF2 vary depending on the programmed mRNA. The TufA mRNA enhanced GTP affinity for 30S complexes, resulting in improved ppGpp tolerance and allowing efficient protein synthesis. Conversely, the InfA mRNA allowed ppGpp to compete with GTP for IF2, thus stalling 30S complexes. Structural modeling and biochemical analysis of the TufA mRNA unveiled a structured enhancer of translation initiation (SETI) composed of two consecutive hairpins proximal to the translation initiation region (TIR) that largely account for ppGpp tolerance under physiological concentrations of guanosine nucleotides. Furthermore, our results show that the mechanism enhancing ppGpp tolerance is not restricted to the TufA mRNA, as similar ppGpp tolerance was found for the SETI-containing Rnr mRNA. Finally, we show that IF2 can use pppGpp to promote the formation of 30S initiation complexes (ICs), albeit requiring higher factor concentration and resulting in slower transitions to translation elongation. Altogether, our data unveil a novel regulatory mechanism at the onset of protein synthesis that tolerates physiological concentrations of ppGpp and that bacteria can exploit to modulate their proteome as a function of the nutritional shift happening during stringent response and infection.
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Affiliation(s)
- Daria S. Vinogradova
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC “Kurchatov Institute”, Gatchina, Russia
- NanoTemper Technologies Rus, Saint Petersburg, Russia
| | - Victor Zegarra
- Centre for Research and Innovation, Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas (UPC), Lima, Peru
| | - Elena Maksimova
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC “Kurchatov Institute”, Gatchina, Russia
| | - Jose Alberto Nakamoto
- Centre for Research and Innovation, Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas (UPC), Lima, Peru
| | - Pavel Kasatsky
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC “Kurchatov Institute”, Gatchina, Russia
| | - Alena Paleskava
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC “Kurchatov Institute”, Gatchina, Russia
- Peter the Great Saint Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Andrey L. Konevega
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC “Kurchatov Institute”, Gatchina, Russia
- Peter the Great Saint Petersburg Polytechnic University, Saint Petersburg, Russia
- NRC “Kurchatov Institute,” Moscow, Russia
- * E-mail: (PM); (ALK)
| | - Pohl Milón
- Centre for Research and Innovation, Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas (UPC), Lima, Peru
- * E-mail: (PM); (ALK)
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5
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Roy B, Liu Q, Shoji S, Fredrick K. IF2 and unique features of initiator tRNA fMet help establish the translational reading frame. RNA Biol 2017; 15:604-613. [PMID: 28914580 DOI: 10.1080/15476286.2017.1379636] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Translation begins at AUG, GUG, or UUG codons in bacteria. Start codon recognition occurs in the P site, which may help explain this first-position degeneracy. However, the molecular basis of start codon specificity remains unclear. In this study, we measured the codon dependence of 30S•mRNA•tRNAfMet and 30S•mRNA•tRNAMet complex formation. We found that complex stability varies over a large range with initiator tRNAfMet, following the same trend as reported previously for initiation rate in vivo (AUG > GUG, UUG > CUG, AUC, AUA > ACG). With elongator tRNAMet, the codon dependence of binding differs qualitatively, with virtually no discrimination between GUG and CUG. A unique feature of initiator tRNAfMet is a series of three G-C basepairs in the anticodon stem, which are known to be important for efficient initiation in vivo. A mutation targeting the central of these G-C basepairs causes the mRNA binding specificity pattern to change in a way reminiscent of elongator tRNAMet. Unexpectedly, for certain complexes containing fMet-tRNAfMet, we observed mispositioning of mRNA, such that codon 2 is no longer programmed in the A site. This mRNA mispositioning is exacerbated by the anticodon stem mutation and suppressed by IF2. These findings suggest that both IF2 and the unique anticodon stem of fMet-tRNAfMet help constrain mRNA positioning to set the correct reading frame during initiation.
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Affiliation(s)
- Bappaditya Roy
- a Department of Microbiology and Center for RNA Biology , Ohio State University , Columbus , Ohio , USA
| | - Qi Liu
- a Department of Microbiology and Center for RNA Biology , Ohio State University , Columbus , Ohio , USA
| | - Shinichiro Shoji
- a Department of Microbiology and Center for RNA Biology , Ohio State University , Columbus , Ohio , USA
| | - Kurt Fredrick
- a Department of Microbiology and Center for RNA Biology , Ohio State University , Columbus , Ohio , USA
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6
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Chengguang H, Sabatini P, Brandi L, Giuliodori AM, Pon CL, Gualerzi CO. Ribosomal selection of mRNAs with degenerate initiation triplets. Nucleic Acids Res 2017; 45:7309-7325. [PMID: 28575317 PMCID: PMC5499595 DOI: 10.1093/nar/gkx472] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Accepted: 05/12/2017] [Indexed: 12/27/2022] Open
Abstract
To assess the influence of degenerate initiation triplets on mRNA recruitment by ribosomes, five mRNAs identical but for their start codon (AUG, GUG, UUG, AUU and AUA) were offered to a limiting amount of ribosomes, alone or in competition with an identical AUGmRNA bearing a mutation conferring different electrophoretic mobility to the product. Translational efficiency and competitiveness of test mRNAs toward this AUGmRNA were determined quantifying the relative amounts of the electrophoretically separated wt and mutated products synthesized in vitro and found to be influenced to different extents by the nature of their initiation triplet and by parameters such as temperature and nutrient availability in the medium. The behaviors of AUAmRNA, UUGmRNA and AUGmRNA were the same between 20 and 40°C whereas the GUG and AUUmRNAs were less active and competed poorly with the AUGmRNA, especially at low temperature. Nutrient limitation and preferential inhibition by ppGpp severely affected activity and competitiveness of all mRNAs bearing non-AUG starts, the UUGmRNA being the least affected. Overall, our data indicate that beyond these effects exclusively due to the degenerate start codons within an optimized translational initiation region, an important role is played by the context in which the rare start codons are present.
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Affiliation(s)
- He Chengguang
- College of Life Sciences, Engineering Research Centre of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, Jilin, China.,Laboratory of Genetics, University of Camerino 62032 Camerino, Italy
| | - Paola Sabatini
- Laboratory of Genetics, University of Camerino 62032 Camerino, Italy
| | - Letizia Brandi
- Laboratory of Genetics, University of Camerino 62032 Camerino, Italy
| | - Anna M Giuliodori
- Laboratory of Genetics, University of Camerino 62032 Camerino, Italy
| | - Cynthia L Pon
- Laboratory of Genetics, University of Camerino 62032 Camerino, Italy
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7
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Hussain T, Llácer JL, Wimberly BT, Kieft JS, Ramakrishnan V. Large-Scale Movements of IF3 and tRNA during Bacterial Translation Initiation. Cell 2016; 167:133-144.e13. [PMID: 27662086 PMCID: PMC5037330 DOI: 10.1016/j.cell.2016.08.074] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 08/04/2016] [Accepted: 08/23/2016] [Indexed: 11/19/2022]
Abstract
In bacterial translational initiation, three initiation factors (IFs 1–3) enable the selection of initiator tRNA and the start codon in the P site of the 30S ribosomal subunit. Here, we report 11 single-particle cryo-electron microscopy (cryoEM) reconstructions of the complex of bacterial 30S subunit with initiator tRNA, mRNA, and IFs 1–3, representing different steps along the initiation pathway. IF1 provides key anchoring points for IF2 and IF3, thereby enhancing their activities. IF2 positions a domain in an extended conformation appropriate for capturing the formylmethionyl moiety charged on tRNA. IF3 and tRNA undergo large conformational changes to facilitate the accommodation of the formylmethionyl-tRNA (fMet-tRNAfMet) into the P site for start codon recognition. Structures of the 30S ribosomal subunit with initiation factors, tRNA and mRNA IF3 helps to position the correct start codon in the P site before binding of tRNA Large-scale conformational changes of IF3 and tRNA are observed IF3 movements facilitate the accommodation of initiator tRNA in P site
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Affiliation(s)
| | - Jose L Llácer
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Brian T Wimberly
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK; Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA
| | - Jeffrey S Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA; RNA BioScience Initiative, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA
| | - V Ramakrishnan
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
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8
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Chulluncuy R, Espiche C, Nakamoto JA, Fabbretti A, Milón P. Conformational Response of 30S-bound IF3 to A-Site Binders Streptomycin and Kanamycin. Antibiotics (Basel) 2016; 5:antibiotics5040038. [PMID: 27983590 PMCID: PMC5187519 DOI: 10.3390/antibiotics5040038] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 10/22/2016] [Accepted: 12/06/2016] [Indexed: 11/16/2022] Open
Abstract
Aminoglycoside antibiotics are widely used to treat infectious diseases. Among them, streptomycin and kanamycin (and derivatives) are of importance to battle multidrug-resistant (MDR) Mycobacterium tuberculosis. Both drugs bind the small ribosomal subunit (30S) and inhibit protein synthesis. Genetic, structural, and biochemical studies indicate that local and long-range conformational rearrangements of the 30S subunit account for this inhibition. Here, we use intramolecular FRET between the C- and N-terminus domains of the flexible IF3 to monitor real-time perturbations of their binding sites on the 30S platform. Steady and pre-steady state binding experiments show that both aminoglycosides bring IF3 domains apart, promoting an elongated state of the factor. Binding of Initiation Factor IF1 triggers closure of IF3 bound to the 30S complex, while both aminoglycosides revert the IF1-dependent conformation. Our results uncover dynamic perturbations across the 30S subunit, from the A-site to the platform, and suggest that both aminoglycosides could interfere with prokaryotic translation initiation by modulating the interaction between IF3 domains with the 30S platform.
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Affiliation(s)
- Roberto Chulluncuy
- Centro de Investigación e Innovación, Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas-UPC, Lima L-33, Peru.
| | - Carlos Espiche
- Centro de Investigación e Innovación, Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas-UPC, Lima L-33, Peru.
| | - Jose Alberto Nakamoto
- Centro de Investigación e Innovación, Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas-UPC, Lima L-33, Peru.
- Facultad de Ciencias y Filosofía Alberto Cazorla Talleri, Universidad Peruana Cayetano Heredia-UPCH, Lima L-31, Peru.
| | - Attilio Fabbretti
- Laboratory of Genetics, Department of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy.
| | - Pohl Milón
- Centro de Investigación e Innovación, Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas-UPC, Lima L-33, Peru.
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9
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Schureck MA, Repack A, Miles SJ, Marquez J, Dunham CM. Mechanism of endonuclease cleavage by the HigB toxin. Nucleic Acids Res 2016; 44:7944-53. [PMID: 27378776 PMCID: PMC5027501 DOI: 10.1093/nar/gkw598] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 06/17/2016] [Accepted: 06/22/2016] [Indexed: 01/11/2023] Open
Abstract
Bacteria encode multiple type II toxin-antitoxin modules that cleave ribosome-bound mRNAs in response to stress. All ribosome-dependent toxin family members structurally characterized to date adopt similar microbial RNase architectures despite possessing low sequence identities. Therefore, determining which residues are catalytically important in this specialized RNase family has been a challenge in the field. Structural studies of RelE and YoeB toxins bound to the ribosome provided significant insights but biochemical experiments with RelE were required to clearly demonstrate which residues are critical for acid-base catalysis of mRNA cleavage. Here, we solved an X-ray crystal structure of the wild-type, ribosome-dependent toxin HigB bound to the ribosome revealing potential catalytic residues proximal to the mRNA substrate. Using cell-based and biochemical assays, we further determined that HigB residues His54, Asp90, Tyr91 and His92 are critical for activity in vivo, while HigB H54A and Y91A variants have the largest effect on mRNA cleavage in vitro Comparison of X-ray crystal structures of two catalytically inactive HigB variants with 70S-HigB bound structures reveal that HigB active site residues undergo conformational rearrangements likely required for recognition of its mRNA substrate. These data support the emerging concept that ribosome-dependent toxins have diverse modes of mRNA recognition.
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Affiliation(s)
- Marc A Schureck
- Emory University School of Medicine, Department of Biochemistry, 1510 Clifton Road NE, Atlanta, GA 30322, USA
| | - Adrienne Repack
- Emory University School of Medicine, Department of Biochemistry, 1510 Clifton Road NE, Atlanta, GA 30322, USA
| | - Stacey J Miles
- Emory University School of Medicine, Department of Biochemistry, 1510 Clifton Road NE, Atlanta, GA 30322, USA
| | - Jhomar Marquez
- Emory University School of Medicine, Department of Biochemistry, 1510 Clifton Road NE, Atlanta, GA 30322, USA
| | - Christine M Dunham
- Emory University School of Medicine, Department of Biochemistry, 1510 Clifton Road NE, Atlanta, GA 30322, USA
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10
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Liu Q, Fredrick K. Intersubunit Bridges of the Bacterial Ribosome. J Mol Biol 2016; 428:2146-64. [PMID: 26880335 DOI: 10.1016/j.jmb.2016.02.009] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 01/29/2016] [Accepted: 02/05/2016] [Indexed: 02/02/2023]
Abstract
The ribosome is a large two-subunit ribonucleoprotein machine that translates the genetic code in all cells, synthesizing proteins according to the sequence of the mRNA template. During translation, the primary substrates, transfer RNAs, pass through binding sites formed between the two subunits. Multiple interactions between the ribosomal subunits, termed intersubunit bridges, keep the ribosome intact and at the same time govern dynamics that facilitate the various steps of translation such as transfer RNA-mRNA movement. Here, we review the molecular nature of these intersubunit bridges, how they change conformation during translation, and their functional roles in the process.
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Affiliation(s)
- Qi Liu
- Ohio State Biochemistry Program, Department of Microbiology, and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Kurt Fredrick
- Ohio State Biochemistry Program, Department of Microbiology, and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
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11
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The Pathogen-Derived Aminoglycoside Resistance 16S rRNA Methyltransferase NpmA Possesses Dual m1A1408/m1G1408 Specificity. Antimicrob Agents Chemother 2015; 59:7862-5. [PMID: 26416864 DOI: 10.1128/aac.01872-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 09/20/2015] [Indexed: 01/08/2023] Open
Abstract
Chemical modification of 16S rRNA can confer exceptionally high-level resistance to a diverse set of aminoglycoside antibiotics. Here, we show that the pathogen-derived enzyme NpmA possesses dual m(1)A1408/m(1)G1408 activity, an unexpected property apparently unique among the known aminoglycoside resistance 16S rRNA (m(1)A1408) methyltransferases. Although the biological significance of this activity remains to be determined, such mechanistic variation in enzymes acquired by pathogens has significant implications for development of inhibitors of these emerging resistance determinants.
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12
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Goyal A, Belardinelli R, Maracci C, Milón P, Rodnina MV. Directional transition from initiation to elongation in bacterial translation. Nucleic Acids Res 2015; 43:10700-12. [PMID: 26338773 PMCID: PMC4678851 DOI: 10.1093/nar/gkv869] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 08/18/2015] [Indexed: 01/21/2023] Open
Abstract
The transition of the 30S initiation complex (IC) to the translating 70S ribosome after 50S subunit joining provides an important checkpoint for mRNA selection during translation in bacteria. Here, we study the timing and control of reactions that occur during 70S IC formation by rapid kinetic techniques, using a toolbox of fluorescence-labeled translation components. We present a kinetic model based on global fitting of time courses obtained with eight different reporters at increasing concentrations of 50S subunits. IF1 and IF3 together affect the kinetics of subunit joining, but do not alter the elemental rates of subsequent steps of 70S IC maturation. After 50S subunit joining, IF2-dependent reactions take place independent of the presence of IF1 or IF3. GTP hydrolysis triggers the efficient dissociation of fMet-tRNA(fMet) from IF2 and promotes the dissociation of IF2 and IF1 from the 70S IC, but does not affect IF3. The presence of non-hydrolyzable GTP analogs shifts the equilibrium towards a stable 70S-mRNA-IF1-IF2-fMet-tRNA(fMet) complex. Our kinetic analysis reveals the molecular choreography of the late stages in translation initiation.
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Affiliation(s)
- Akanksha Goyal
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Riccardo Belardinelli
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Cristina Maracci
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Pohl Milón
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
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13
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Abstract
Initiation of translation involves the assembly of a ribosome complex with initiator tRNA bound to the peptidyl site and paired to the start codon of the mRNA. In bacteria, this process is kinetically controlled by three initiation factors--IF1, IF2, and IF3. Here, we show that deletion of helix H69 (∆H69) of 23S rRNA allows rapid 50S docking without concomitant IF3 release and virtually eliminates the dependence of subunit joining on start codon identity. Despite this, overall accuracy of start codon selection, based on rates of formation of elongation-competent 70S ribosomes, is largely uncompromised in the absence of H69. Thus, the fidelity function of IF3 stems primarily from its interplay with initiator tRNA rather than its anti-subunit association activity. While retaining fidelity, ∆H69 ribosomes exhibit much slower rates of overall initiation, due to the delay in IF3 release and impedance of an IF3-independent step, presumably initiator tRNA positioning. These findings clarify the roles of H69 and IF3 in the mechanism of translation initiation and explain the dominant lethal phenotype of the ∆H69 mutation.
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14
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Gualerzi CO, Pon CL. Initiation of mRNA translation in bacteria: structural and dynamic aspects. Cell Mol Life Sci 2015; 72:4341-67. [PMID: 26259514 PMCID: PMC4611024 DOI: 10.1007/s00018-015-2010-3] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/28/2015] [Accepted: 07/30/2015] [Indexed: 01/12/2023]
Abstract
Initiation of mRNA translation is a major checkpoint for regulating level and fidelity of protein synthesis. Being rate limiting in protein synthesis, translation initiation also represents the target of many post-transcriptional mechanisms regulating gene expression. The process begins with the formation of an unstable 30S pre-initiation complex (30S pre-IC) containing initiation factors (IFs) IF1, IF2 and IF3, the translation initiation region of an mRNA and initiator fMet-tRNA whose codon and anticodon pair in the P-site following a first-order rearrangement of the 30S pre-IC produces a locked 30S initiation complex (30SIC); this is docked by the 50S subunit to form a 70S complex that, following several conformational changes, positional readjustments of its ligands and ejection of the IFs, becomes a 70S initiation complex productive in initiation dipeptide formation. The first EF-G-dependent translocation marks the beginning of the elongation phase of translation. Here, we review structural, mechanistic and dynamical aspects of this process.
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MESH Headings
- Bacteria/genetics
- Bacteria/metabolism
- Binding Sites/genetics
- Codon, Initiator/genetics
- Codon, Initiator/metabolism
- Models, Genetic
- Nucleic Acid Conformation
- Peptide Initiation Factors/genetics
- Peptide Initiation Factors/metabolism
- Protein Biosynthesis
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Transfer, Met/chemistry
- RNA, Transfer, Met/genetics
- RNA, Transfer, Met/metabolism
- Ribosomes/metabolism
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Affiliation(s)
| | - Cynthia L Pon
- Laboratory of Genetics, University of Camerino, 62032, Camerino, Italy.
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15
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Maehigashi T, Ruangprasert A, Miles SJ, Dunham CM. Molecular basis of ribosome recognition and mRNA hydrolysis by the E. coli YafQ toxin. Nucleic Acids Res 2015; 43:8002-12. [PMID: 26261214 PMCID: PMC4652777 DOI: 10.1093/nar/gkv791] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 07/22/2015] [Indexed: 01/30/2023] Open
Abstract
Bacterial type II toxin-antitoxin modules are protein–protein complexes whose functions are finely tuned by rapidly changing environmental conditions. E. coli toxin YafQ is suppressed under steady state growth conditions by virtue of its interaction with its cognate antitoxin, DinJ. During stress, DinJ is proteolytically degraded and free YafQ halts translation by degrading ribosome-bound mRNA to slow growth until the stress has passed. Although structures of the ribosome with toxins RelE and YoeB have been solved, it is unclear what residues among ribosome-dependent toxins are essential for mediating both recognition of the ribosome and the mRNA substrate given their low sequence identities. Here we show that YafQ coordinates binding to the 70S ribosome via three surface-exposed patches of basic residues that we propose directly interact with 16S rRNA. We demonstrate that YafQ residues H50, H63, D67 and H87 participate in acid-base catalysis during mRNA hydrolysis and further show that H50 and H63 functionally complement as general bases to initiate the phosphodiester cleavage reaction. Moreover YafQ residue F91 likely plays an important role in mRNA positioning. In summary, our findings demonstrate the plasticity of ribosome-dependent toxin active site residues and further our understanding of which toxin residues are important for function.
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Affiliation(s)
- Tatsuya Maehigashi
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | | | - Stacey J Miles
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Christine M Dunham
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
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16
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Fosso MY, Zhu H, Green KD, Garneau-Tsodikova S, Fredrick K. Tobramycin Variants with Enhanced Ribosome-Targeting Activity. Chembiochem 2015; 16:1565-70. [PMID: 26033429 DOI: 10.1002/cbic.201500256] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Indexed: 01/16/2023]
Abstract
With the increased evolution of aminoglycoside (AG)-resistant bacterial strains, the need to develop AGs with 1) enhanced antimicrobial activity, 2) the ability to evade resistance mechanisms, and 3) the capability of targeting the ribosome with higher efficiency is more and more pressing. The chemical derivatization of the naturally occurring tobramycin (TOB) by attachment of 37 different thioether groups at the 6''-position led to the identification of generally poorer substrates of TOB-targeting AG-modifying enzymes (AMEs). Thirteen of these displayed better antibacterial activity than the parent TOB while retaining ribosome-targeting specificity. Analysis of these compounds in vitro shed light on the mechanism by which they act and revealed three with clearly enhanced ribosome-targeting activity.
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Affiliation(s)
- Marina Y Fosso
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 S. Limestone, Lexington, KY 40536-0596 (USA)
| | - Hongkun Zhu
- Department of Microbiology, Center for RNA Biology, Ohio State University, 484 W. 12th Avenue, Columbus, OH 43210-1292 (USA)
| | - Keith D Green
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 S. Limestone, Lexington, KY 40536-0596 (USA)
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 S. Limestone, Lexington, KY 40536-0596 (USA).
| | - Kurt Fredrick
- Department of Microbiology, Center for RNA Biology, Ohio State University, 484 W. 12th Avenue, Columbus, OH 43210-1292 (USA).
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17
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Caban K, Gonzalez RL. The emerging role of rectified thermal fluctuations in initiator aa-tRNA- and start codon selection during translation initiation. Biochimie 2015; 114:30-8. [PMID: 25882682 DOI: 10.1016/j.biochi.2015.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 04/02/2015] [Indexed: 11/30/2022]
Abstract
Decades of genetic, biochemical, biophysical, and structural studies suggest that the conformational dynamics of the translation machinery (TM), of which the ribosome is the central component, play a fundamental role in the mechanism and regulation of translation. More recently, single-molecule fluorescence resonance energy transfer (smFRET) studies have provided a unique and powerful approach for directly monitoring the real-time dynamics of the TM. Indeed, smFRET studies of the elongation stage of translation have significantly enriched our understanding of the mechanisms through which stochastic, thermally driven conformational fluctuations of the TM are exploited to drive and regulate the individual steps of translation elongation [1]. Beyond translation elongation, smFRET studies of the conformational dynamics of the initiation stage of translation offer great potential for providing mechanistic information that has thus far remained difficult or impossible to obtain using traditional methods. This is particularly true of the mechanisms through which the accuracy of initiator tRNA- and start codon selection is established during translation initiation. Given that translation initiation is a major checkpoint for regulating the translation of mRNAs, obtaining such mechanistic information holds great promise for our understanding of the translational regulation of gene expression. Here, we provide an overview of the bacterial translation initiation pathway, summarize what is known regarding the biochemical functions of the IFs, and discuss various new and exciting mechanistic insights that have emerged from several recently published smFRET studies of the mechanisms that guide initiator tRNA- and start codon selection during translation initiation. These studies provide a springboard for future investigations of the conformational dynamics of the more complex eukaryotic translation initiation pathway and mechanistic studies of the role of translational regulation of gene expression in human health and disease.
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Affiliation(s)
- Kelvin Caban
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Ruben L Gonzalez
- Department of Chemistry, Columbia University, New York, NY 10027, USA.
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18
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Fan Y, Wu J, Ung MH, De Lay N, Cheng C, Ling J. Protein mistranslation protects bacteria against oxidative stress. Nucleic Acids Res 2015; 43:1740-8. [PMID: 25578967 PMCID: PMC4330365 DOI: 10.1093/nar/gku1404] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Accurate flow of genetic information from DNA to protein requires faithful translation. An increased level of translational errors (mistranslation) has therefore been widely considered harmful to cells. Here we demonstrate that surprisingly, moderate levels of mistranslation indeed increase tolerance to oxidative stress in Escherichia coli. Our RNA sequencing analyses revealed that two antioxidant genes katE and osmC, both controlled by the general stress response activator RpoS, were upregulated by a ribosomal error-prone mutation. Mistranslation-induced tolerance to hydrogen peroxide required rpoS, katE and osmC. We further show that both translational and post-translational regulation of RpoS contribute to peroxide tolerance in the error-prone strain, and a small RNA DsrA, which controls translation of RpoS, is critical for the improved tolerance to oxidative stress through mistranslation. Our work thus challenges the prevailing view that mistranslation is always detrimental, and provides a mechanism by which mistranslation benefits bacteria under stress conditions.
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Affiliation(s)
- Yongqiang Fan
- Department of Microbiology and Molecular Genetics, Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Jiang Wu
- Department of Microbiology and Molecular Genetics, Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Matthew H Ung
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Nicholas De Lay
- Department of Microbiology and Molecular Genetics, Medical School, University of Texas Health Science Center, Houston, TX 77030, USA Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Chao Cheng
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Jiqiang Ling
- Department of Microbiology and Molecular Genetics, 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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19
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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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20
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Pon CL, Fabbretti A, Brandi L. Antibiotics Targeting Translation Initiation in Prokaryotes. Antibiotics (Basel) 2013. [DOI: 10.1002/9783527659685.ch17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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21
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Weisser M, Voigts-Hoffmann F, Rabl J, Leibundgut M, Ban N. The crystal structure of the eukaryotic 40S ribosomal subunit in complex with eIF1 and eIF1A. Nat Struct Mol Biol 2013; 20:1015-7. [PMID: 23851459 DOI: 10.1038/nsmb.2622] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 05/23/2013] [Indexed: 11/09/2022]
Abstract
Eukaryotic translation initiation factors (eIFs) 1A and 1 are central players in the complex process of start-codon recognition. To improve mechanistic understanding of this process, we determined the crystal structure of the 40S ribosomal subunit in complex with eIF1A and eIF1 from Tetrahymena thermophila at a resolution of 3.7 Å. It reveals the positions of the two factors on the 40S and the conformational changes that accompany their binding.
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Affiliation(s)
- Melanie Weisser
- Institute of Molecular Biology and Biophysics, Swiss Federal Institute of Technology (ETH Zürich), Zürich, Switzerland
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22
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Fabbretti A, Brandi L, Petrelli D, Pon CL, Castañedo NR, Medina R, Gualerzi CO. The antibiotic Furvina® targets the P-site of 30S ribosomal subunits and inhibits translation initiation displaying start codon bias. Nucleic Acids Res 2012; 40:10366-74. [PMID: 22941660 PMCID: PMC3488254 DOI: 10.1093/nar/gks822] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Furvina®, also denominated G1 (MW 297), is a synthetic nitrovinylfuran [2-bromo-5-(2-bromo-2-nitrovinyl)-furan] antibiotic with a broad antimicrobial spectrum. An ointment (Dermofural®) containing G1 as the only active principle is currently marketed in Cuba and successfully used to treat dermatological infections. Here we describe the molecular target and mechanism of action of G1 in bacteria and demonstrate that in vivo G1 preferentially inhibits protein synthesis over RNA, DNA and cell wall synthesis. Furthermore, we demonstrate that G1 targets the small ribosomal subunit, binds at or near the P-decoding site and inhibits its function interfering with the ribosomal binding of fMet-tRNA during 30S initiation complex (IC) formation ultimately inhibiting translation. Notably, this G1 inhibition displays a bias for the nature (purine vs. pyrimidine) of the 3′-base of the codon, occurring efficiently only when the mRNA directing 30S IC formation and translation contains the canonical AUG initiation triplet or the rarely found AUA triplet, but hardly occurs when the mRNA start codon is either one of the non-canonical triplets AUU or AUC. This codon discrimination by G1 is reminiscent, though of opposite type of that displayed by IF3 in its fidelity function, and remarkably does not occur in the absence of this factor.
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Affiliation(s)
- Attilio Fabbretti
- Laboratory of Genetics, Department of Biosciences & Biotechnology, University of Camerino, 62032 Camerino, MC, Italy.
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23
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Milón P, Maracci C, Filonava L, Gualerzi CO, Rodnina MV. Real-time assembly landscape of bacterial 30S translation initiation complex. Nat Struct Mol Biol 2012; 19:609-15. [PMID: 22562136 DOI: 10.1038/nsmb.2285] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 05/21/2012] [Indexed: 11/09/2022]
Abstract
Initiation factors guide the ribosome in the selection of mRNA and translational reading frame. We determined the kinetically favored assembly pathway of the 30S preinitiation complex (30S PIC), an early intermediate in 30S initiation complex formation in Escherichia coli. IF3 and IF2 are the first factors to arrive, forming an unstable 30S-IF2-IF3 complex. Subsequently, IF1 joins and locks the factors in a kinetically stable 30S PIC to which fMet-tRNA(fMet) is recruited. Binding of mRNA is independent of initiation factors and can take place at any time during 30S PIC assembly, depending on the cellular concentration of the mRNA and the structural determinants at the ribosome-binding site. The kinetic analysis shows both specific and cumulative effects of initiation factors as well as kinetic checkpoints of mRNA selection at the entry into translation.
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Affiliation(s)
- Pohl Milón
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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24
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Abstract
Translation initiation is a crucial step of protein synthesis which largely defines how the composition of the cellular transcriptome is converted to the proteome and controls the response and adaptation to environmental stimuli. The efficiency of translation of individual mRNAs, and hence the basal shape of the proteome, is defined by the structures of the mRNA translation initiation regions. Initiation efficiency can be regulated by small molecules, proteins, or antisense RNAs, underscoring its importance in translational control. Although initiation has been studied in bacteria for decades, many aspects remain poorly understood. Recent evidence has suggested an unexpected diversity of pathways by which mRNAs can be recruited to the bacterial ribosome, the importance of structural dynamics of initiation intermediates, and the complexity of checkpoints for mRNA selection. In this review, we discuss how the ribosome shapes the landscape of translation initiation by non-linear kinetic processing of the transcriptome information. We summarize the major pathways by which mRNAs enter the ribosome depending on the structure of their 5' untranslated regions, the assembly and the structure of initiation intermediates, the individual and synergistic roles of initiation factors, and the mechanisms of mRNA and initiator tRNA selection.
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Affiliation(s)
- Pohl Milón
- Department of Physical Biochemistry, Max Planck Institute of Biophysical Chemistry, Goettingen, Germany
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25
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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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26
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Molecular mechanism of scanning and start codon selection in eukaryotes. Microbiol Mol Biol Rev 2012; 75:434-67, first page of table of contents. [PMID: 21885680 DOI: 10.1128/mmbr.00008-11] [Citation(s) in RCA: 281] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The correct translation of mRNA depends critically on the ability to initiate at the right AUG codon. For most mRNAs in eukaryotic cells, this is accomplished by the scanning mechanism, wherein the small (40S) ribosomal subunit attaches to the 5' end of the mRNA and then inspects the leader base by base for an AUG in a suitable context, using complementarity with the anticodon of methionyl initiator tRNA (Met-tRNAiMet) as the key means of identifying AUG. Over the past decade, a combination of yeast genetics, biochemical analysis in reconstituted systems, and structural biology has enabled great progress in deciphering the mechanism of ribosomal scanning. A robust molecular model now exists, describing the roles of initiation factors, notably eukaryotic initiation factor 1 (eIF1) and eIF1A, in stabilizing an "open" conformation of the 40S subunit with Met-tRNAiMet bound in a low-affinity state conducive to scanning and in triggering rearrangement into a "closed" conformation incompatible with scanning, which features Met-tRNAiMet more tightly bound to the "P" site and base paired with AUG. It has also emerged that multiple DEAD-box RNA helicases participate in producing a single-stranded "landing pad" for the 40S subunit and in removing the secondary structure to enable the mRNA to traverse the 40S mRNA-binding channel in the single-stranded form for base-by-base inspection in the P site.
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27
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Abstract
Selection of correct start codons on messenger RNAs is a key step required for faithful translation of the genetic message. Such a selection occurs in a complex process, during which a translation-competent ribosome assembles, eventually having in its P site a specialized methionyl-tRNAMet base-paired with the start codon on the mRNA. This chapter summarizes recent advances describing at the molecular level the successive steps involved in the process. Special emphasis is put on the roles of the three initiation factors and of the initiator tRNA, which are crucial for the efficiency and the specificity of the process. In particular, structural analyses concerning complexes containing ribosomal subunits, as well as detailed kinetic studies, have shed new light on the sequence of events leading to faithful initiation of protein synthesis in Bacteria.
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28
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Belotserkovsky JM, Isak GI, Isaksson LA. Suppression of a cold-sensitive mutant initiation factor 1 by alterations in the 23S rRNA maturation region. FEBS J 2011; 278:1745-56. [DOI: 10.1111/j.1742-4658.2011.08099.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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29
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Insertion domain within mammalian mitochondrial translation initiation factor 2 serves the role of eubacterial initiation factor 1. Proc Natl Acad Sci U S A 2011; 108:3918-23. [PMID: 21368145 DOI: 10.1073/pnas.1017425108] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mitochondria have their own translational machineries for the synthesis of thirteen polypeptide chains that are components of the complexes that participate in the process of oxidative phosphorylation (or ATP generation). Translation initiation in mammalian mitochondria requires two initiation factors, IF2(mt) and IF3(mt), instead of the three that are present in eubacteria. The mammalian IF2(mt) possesses a unique 37 amino acid insertion domain, which is known to be important for the formation of the translation initiation complex. We have obtained a three-dimensional cryoelectron microscopic map of the mammalian IF2(mt) in complex with initiator fMet-tRNA(iMet) and the eubacterial ribosome. We find that the 37 amino acid insertion domain interacts with the same binding site on the ribosome that would be occupied by the eubacterial initiation factor IF1, which is absent in mitochondria. Our finding suggests that the insertion domain of IF2(mt) mimics the function of eubacterial IF1, by blocking the ribosomal aminoacyl-tRNA binding site (A site) at the initiation step.
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30
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McClory SP, Leisring JM, Qin D, Fredrick K. Missense suppressor mutations in 16S rRNA reveal the importance of helices h8 and h14 in aminoacyl-tRNA selection. RNA (NEW YORK, N.Y.) 2010; 16:1925-34. [PMID: 20699303 PMCID: PMC2941101 DOI: 10.1261/rna.2228510] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The molecular basis of the induced-fit mechanism that determines the fidelity of protein synthesis remains unclear. Here, we isolated mutations in 16S rRNA that increase the rate of miscoding and stop codon read-through. Many of the mutations clustered along interfaces between the 30S shoulder domain and other parts of the ribosome, strongly implicating shoulder movement in the induced-fit mechanism of decoding. The largest subset of mutations mapped to helices h8 and h14. These helices interact with each other and with the 50S subunit to form bridge B8. Previous cryo-EM studies revealed a contact between h14 and the switch 1 motif of EF-Tu, raising the possibility that h14 plays a direct role in GTPase activation. To investigate this possibility, we constructed both deletions and insertions in h14. While ribosomes harboring a 2-base-pair (bp) insertion in h14 were completely inactive in vivo, those containing a 2-bp deletion retained activity but were error prone. In vitro, the truncation of h14 accelerated GTP hydrolysis for EF-Tu bearing near-cognate aminoacyl-tRNA, an effect that can largely account for the observed miscoding in vivo. These data show that h14 does not help activate EF-Tu but instead negatively controls GTP hydrolysis by the factor. We propose that bridge B8 normally acts to counter inward rotation of the shoulder domain; hence, mutations in h8 and h14 that compromise this bridge decrease the stringency of aminoacyl-tRNA selection.
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MESH Headings
- Binding Sites/genetics
- Codon, Nonsense
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Kinetics
- Models, Molecular
- Mutation, Missense
- Nucleic Acid Conformation
- Protein Biosynthesis
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- RNA, Transfer, Amino Acyl/metabolism
- Ribosomes/genetics
- Ribosomes/metabolism
- Suppression, Genetic
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Affiliation(s)
- Sean P McClory
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, USA
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31
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Abstract
Protein biosynthesis, or translation, occurs on the ribosome, a large RNA-protein assembly universally conserved in all forms of life. Over the last decade, structures of the small and large ribosomal subunits and of the intact ribosome have begun to reveal the molecular details of how the ribosome works. Both cryo-electron microscopy and X-ray crystallography continue to provide fresh insights into the mechanism of translation. In this review, we describe the most recent structural models of the bacterial ribosome that shed light on the movement of messenger RNA and transfer RNA on the ribosome after each peptide bond is formed, a process termed translocation. We also discuss recent structures that reveal the molecular basis for stop codon recognition during translation termination. Finally, we review recent advances in understanding how bacteria handle errors in both translocation and termination.
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Affiliation(s)
- Jack A Dunkle
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
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32
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Gualerzi C, Fabbretti A, Brandi L, Milon P, Pon C. Role of the Initiation Factors in mRNA Start Site Selection and fMet-tRNA Recruitment by Bacterial Ribosomes. Isr J Chem 2010. [DOI: 10.1002/ijch.201000006] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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33
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Kimura S, Suzuki T. Fine-tuning of the ribosomal decoding center by conserved methyl-modifications in the Escherichia coli 16S rRNA. Nucleic Acids Res 2009; 38:1341-52. [PMID: 19965768 PMCID: PMC2831307 DOI: 10.1093/nar/gkp1073] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
In bacterial 16S rRNAs, methylated nucleosides are clustered within the decoding center, and these nucleoside modifications are thought to modulate translational fidelity. The N4, 2′-O-dimethylcytidine (m4Cm) at position 1402 of the Escherichia coli 16S rRNA directly interacts with the P-site codon of the mRNA. The biogenesis and function of this modification remain unclear. We have identified two previously uncharacterized genes in E. coli that are required for m4Cm formation. mraW (renamed rsmH) and yraL (renamed rsmI) encode methyltransferases responsible for the N4 and 2′-O-methylations of C1402, respectively. Recombinant RsmH and RsmI proteins employed the 30S subunit (not the 16S rRNA) as a substrate to reconstitute m4Cm1402 in the presence of S-adenosylmethionine (Ado-Met) as the methyl donor, suggesting that m4Cm1402 is formed at a late step during 30S assembly in the cell. A luciferase reporter assay indicated that the lack of N4 methylation of C1402 increased the efficiency of non-AUG initiation and decreased the rate of UGA read-through. These results suggest that m4Cm1402 plays a role in fine-tuning the shape and function of the P-site, thus increasing decoding fidelity.
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Affiliation(s)
- Satoshi Kimura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bldg. 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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