1
|
Nishizawa C, Aburaya S, Kosaka Y, Sugase K, Aoki W. Optimizing in vitro expression balance of central dogma-related genes using parallel reaction monitoring. J Biosci Bioeng 2024; 138:97-104. [PMID: 38762340 DOI: 10.1016/j.jbiosc.2024.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/05/2024] [Accepted: 04/25/2024] [Indexed: 05/20/2024]
Abstract
The creation of a self-replicating synthetic cell is an essential to understand life self-replication. One method to create self-replicating artificial cells is to reconstitute the self-replication system of living organisms in vitro. In a living cell, self-replication is achieved via a system called the autonomous central dogma, a system in which central dogma-related factors are autonomously synthesized and genome replication, transcription, and translation are driven by nascent factors. Various studies to reconstitute some processes of the autonomous central dogma in vitro have been conducted. However, in vitro reconstitution of the entire autonomous central dogma system is difficult as it requires balanced expression of several related genes. Therefore, we developed a method to simultaneously quantify and optimize the in vitro expression balance of multiple genes. First, we developed a quantitative mass spectrometry method targeting genome replication-related proteins as a model of central dogma-related factors and acquired in vitro expression profiles of these genes. Additionally, we demonstrated that the in vitro expression balance of these genes can be easily optimized by adjusting the input gene ratio based on the data obtained by the developed method. This study facilitated the easy optimization of the in vitro expression balance of multiple genes. Therefore, extending the scope of this method to other central dogma-related factors will accelerate attempts of self-replicating synthetic cells creation.
Collapse
Affiliation(s)
- Chisato Nishizawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan.
| | - Shunsuke Aburaya
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan.
| | - Yuishin Kosaka
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan; Japan Society for the Promotion of Science 606-8502, Kyoto, Japan.
| | - Kenji Sugase
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan.
| | - Wataru Aoki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka 565-0871, Japan; Kyoto Integrated Science & Technology Bio-Analysis Center, Kyoto 600-8815, Japan.
| |
Collapse
|
2
|
Pandey R, Kaul G, Akhir A, Saxena D, Shukla M, Mundra S, Zohib M, Singh S, Pal RK, Tripathi S, Jain A, Chopra S, Arora A. Characterization of structure of peptidyl-tRNA hydrolase from Enterococcus faecium and its inhibition by a pyrrolinone compound. Int J Biol Macromol 2024; 275:133445. [PMID: 38945334 DOI: 10.1016/j.ijbiomac.2024.133445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/15/2024] [Accepted: 06/24/2024] [Indexed: 07/02/2024]
Abstract
In bacteria, peptidyl-tRNA hydrolase (Pth, E.C. 3.1.1.29) is a ubiquitous and essential enzyme for preventing the accumulation of peptidyl-tRNA and sequestration of tRNA. Pth is an esterase that cleaves the ester bond between peptide and tRNA. Here, we present the crystal structure of Pth from Enterococcus faecium (EfPth) at a resolution of 1.92 Å. The two molecules in the asymmetric unit differ in the orientation of sidechain of N66, a conserved residue of the catalytic site. Enzymatic hydrolysis of substrate α-N-BODIPY-lysyl-tRNALys (BLT) by EfPth was characterized by Michaelis-Menten parameters KM 163.5 nM and Vmax 1.9 nM/s. Compounds having pyrrolinone scaffold were tested for inhibition of Pth and one compound, 1040-C, was found to have IC50 of 180 nM. Antimicrobial activity profiling was done for 1040-C. It exhibited equipotent activity against drug-susceptible and resistant S. aureus (MRSA and VRSA) and Enterococcus (VSE and VRE) with MICs 2-8 μg/mL. 1040-C synergized with gentamicin and the combination was effective against the gentamicin resistant S. aureus strain NRS-119. 1040-C was found to reduce biofilm mass of S. aureus to an extent similar to Vancomycin. In a murine model of infection, 1040-C was able to reduce bacterial load to an extent comparable to Vancomycin.
Collapse
Affiliation(s)
- Roumya Pandey
- Biochemistry and Structural Biology Division, CSIR - Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Grace Kaul
- Molecular Microbiology and Immunology Division, CSIR - Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Abdul Akhir
- Molecular Microbiology and Immunology Division, CSIR - Central Drug Research Institute, Lucknow 226031, India
| | - Deepanshi Saxena
- Molecular Microbiology and Immunology Division, CSIR - Central Drug Research Institute, Lucknow 226031, India
| | - Manjulika Shukla
- Molecular Microbiology and Immunology Division, CSIR - Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Surbhi Mundra
- Biochemistry and Structural Biology Division, CSIR - Central Drug Research Institute, Lucknow 226031, India; Department of Science and Technology, New Delhi 110016, India
| | - Muhammad Zohib
- Biochemistry and Structural Biology Division, CSIR - Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sneha Singh
- Biochemistry and Structural Biology Division, CSIR - Central Drug Research Institute, Lucknow 226031, India
| | - Ravi Kant Pal
- X-ray Crystallography Facility, National Institute of Immunology, New Delhi 110067, India
| | - Sarita Tripathi
- Biochemistry and Structural Biology Division, CSIR - Central Drug Research Institute, Lucknow 226031, India
| | - Anupam Jain
- Biochemistry and Structural Biology Division, CSIR - Central Drug Research Institute, Lucknow 226031, India
| | - Sidharth Chopra
- Molecular Microbiology and Immunology Division, CSIR - Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| | - Ashish Arora
- Biochemistry and Structural Biology Division, CSIR - Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| |
Collapse
|
3
|
Cruz-Navarrete FA, Griffin WC, Chan YC, Martin MI, Alejo JL, Brady RA, Natchiar SK, Knudson IJ, Altman RB, Schepartz A, Miller SJ, Blanchard SC. β-Amino Acids Reduce Ternary Complex Stability and Alter the Translation Elongation Mechanism. ACS CENTRAL SCIENCE 2024; 10:1262-1275. [PMID: 38947208 PMCID: PMC11212133 DOI: 10.1021/acscentsci.4c00314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 07/02/2024]
Abstract
Templated synthesis of proteins containing non-natural amino acids (nnAAs) promises to expand the chemical space available to biological therapeutics and materials, but existing technologies are still limiting. Addressing these limitations requires a deeper understanding of the mechanism of protein synthesis and how it is perturbed by nnAAs. Here we examine the impact of nnAAs on the formation and ribosome utilization of the central elongation substrate: the ternary complex of native, aminoacylated tRNA, thermally unstable elongation factor, and GTP. By performing ensemble and single-molecule fluorescence resonance energy transfer measurements, we reveal that both the (R)- and (S)-β2 isomers of phenylalanine (Phe) disrupt ternary complex formation to levels below in vitro detection limits, while (R)- and (S)-β3-Phe reduce ternary complex stability by 1 order of magnitude. Consistent with these findings, (R)- and (S)-β2-Phe-charged tRNAs were not utilized by the ribosome, while (R)- and (S)-β3-Phe stereoisomers were utilized inefficiently. (R)-β3-Phe but not (S)-β3-Phe also exhibited order of magnitude defects in the rate of translocation after mRNA decoding. We conclude from these findings that non-natural amino acids can negatively impact the translation mechanism on multiple fronts and that the bottlenecks for improvement must include the consideration of the efficiency and stability of ternary complex formation.
Collapse
Affiliation(s)
- F. Aaron Cruz-Navarrete
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, Memphis, Tennessee 38105, United States
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Wezley C. Griffin
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, Memphis, Tennessee 38105, United States
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Yuk-Cheung Chan
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Maxwell I. Martin
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, Memphis, Tennessee 38105, United States
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Jose L. Alejo
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, Memphis, Tennessee 38105, United States
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Ryan A. Brady
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, Memphis, Tennessee 38105, United States
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - S. Kundhavai Natchiar
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, Memphis, Tennessee 38105, United States
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Isaac J. Knudson
- College
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Roger B. Altman
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, Memphis, Tennessee 38105, United States
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Alanna Schepartz
- College
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
- Molecular
and Cell Biology, University of California,
Berkeley, Berkeley, California 94720, United States
- California
Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California 94720, United States
- Chan
Zuckerberg Biohub, San Francisco, California 94158, United States
- Innovation
Investigator, ARC Institute, Palo Alto, California 94304, United States
| | - Scott J. Miller
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Scott C. Blanchard
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, Memphis, Tennessee 38105, United States
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| |
Collapse
|
4
|
Weiss JL, Decker JC, Bolano A, Krahn N. Tuning tRNAs for improved translation. Front Genet 2024; 15:1436860. [PMID: 38983271 PMCID: PMC11231383 DOI: 10.3389/fgene.2024.1436860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 06/06/2024] [Indexed: 07/11/2024] Open
Abstract
Transfer RNAs have been extensively explored as the molecules that translate the genetic code into proteins. At this interface of genetics and biochemistry, tRNAs direct the efficiency of every major step of translation by interacting with a multitude of binding partners. However, due to the variability of tRNA sequences and the abundance of diverse post-transcriptional modifications, a guidebook linking tRNA sequences to specific translational outcomes has yet to be elucidated. Here, we review substantial efforts that have collectively uncovered tRNA engineering principles that can be used as a guide for the tuning of translation fidelity. These principles have allowed for the development of basic research, expansion of the genetic code with non-canonical amino acids, and tRNA therapeutics.
Collapse
Affiliation(s)
- Joshua L Weiss
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - J C Decker
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Ariadna Bolano
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Natalie Krahn
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| |
Collapse
|
5
|
Awad S, Valleriani A, Chiarugi D. A data-driven estimation of the ribosome drop-off rate in S. cerevisiae reveals a correlation with the genes length. NAR Genom Bioinform 2024; 6:lqae036. [PMID: 38638702 PMCID: PMC11025885 DOI: 10.1093/nargab/lqae036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 03/08/2024] [Accepted: 04/03/2024] [Indexed: 04/20/2024] Open
Abstract
Ribosomes are the molecular machinery that catalyse all the fundamental steps involved in the translation of mRNAs into proteins. Given the complexity of this process, the efficiency of protein synthesis depends on a large number of factors among which ribosome drop-off (i.e. the premature detachment of the ribosome from the mRNA template) plays an important role. However, an in vitro quantification of the extent to which ribosome drop-off occurs is not trivial due to difficulties in obtaining the needed experimental evidence. In this work we focus on the study of ribosome drop-off in Saccharomyces cerevisiae by using 'Ribofilio', a novel software tool that relies on a high sensitive strategy to estimate the ribosome drop-off rate from ribosome profiling data. Our results show that ribosome drop-off events occur at a significant rate also when S. cerevisiae is cultured in standard conditions. In this context, we also identified a correlation between the ribosome drop-off rate and the genes length: the longer the gene, the lower the drop-off rate.
Collapse
Affiliation(s)
- Sherine Awad
- Genomics and Bioinformatics Core Facility, Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Angelo Valleriani
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany
| | - Davide Chiarugi
- Max Planck Institute for Human Cognitive and Brain Sciences, Stephanstraße 1a, 04103 Leipzig - Germany
| |
Collapse
|
6
|
Svetlov MS, Dunand CF, Nakamoto JA, Atkinson GC, Safdari HA, Wilson DN, Vázquez-Laslop N, Mankin AS. Peptidyl-tRNA hydrolase is the nascent chain release factor in bacterial ribosome-associated quality control. Mol Cell 2024; 84:715-726.e5. [PMID: 38183984 DOI: 10.1016/j.molcel.2023.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/08/2023] [Accepted: 12/01/2023] [Indexed: 01/08/2024]
Abstract
Rescuing stalled ribosomes often involves their splitting into subunits. In many bacteria, the resultant large subunits bearing peptidyl-tRNAs are processed by the ribosome-associated quality control (RQC) apparatus that extends the C termini of the incomplete nascent polypeptides with polyalanine tails to facilitate their degradation. Although the tailing mechanism is well established, it is unclear how the nascent polypeptides are cleaved off the tRNAs. We show that peptidyl-tRNA hydrolase (Pth), the known role of which has been to hydrolyze ribosome-free peptidyl-tRNA, acts in concert with RQC factors to release nascent polypeptides from large ribosomal subunits. Dislodging from the ribosomal catalytic center is required for peptidyl-tRNA hydrolysis by Pth. Nascent protein folding may prevent peptidyl-tRNA retraction and interfere with the peptide release. However, oligoalanine tailing makes the peptidyl-tRNA ester bond accessible for Pth-catalyzed hydrolysis. Therefore, the oligoalanine tail serves not only as a degron but also as a facilitator of Pth-catalyzed peptidyl-tRNA hydrolysis.
Collapse
Affiliation(s)
- Maxim S Svetlov
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA; Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA.
| | - Clémence F Dunand
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA; Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Jose A Nakamoto
- Department of Experimental Medicine, University of Lund, 221 00 Lund, Sweden
| | - Gemma C Atkinson
- Department of Experimental Medicine, University of Lund, 221 00 Lund, Sweden
| | - Haaris A Safdari
- Institute for Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany
| | - Nora Vázquez-Laslop
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA; Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Alexander S Mankin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA; Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA.
| |
Collapse
|
7
|
Insights into the ribosome function from the structures of non-arrested ribosome-nascent chain complexes. Nat Chem 2023; 15:143-153. [PMID: 36316410 PMCID: PMC9840698 DOI: 10.1038/s41557-022-01073-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 09/23/2022] [Indexed: 12/24/2022]
Abstract
During protein synthesis, the growing polypeptide threads through the ribosomal exit tunnel and modulates ribosomal activity by itself or by sensing various small molecules, such as metabolites or antibiotics, appearing in the tunnel. While arrested ribosome-nascent chain complexes (RNCCs) have been extensively studied structurally, the lack of a simple procedure for the large-scale preparation of peptidyl-tRNAs, intermediates in polypeptide synthesis that carry the growing chain, means that little attention has been given to RNCCs representing functionally active states of the ribosome. Here we report the facile synthesis of stably linked peptidyl-tRNAs through a chemoenzymatic approach based on native chemical ligation and use them to determine several structures of RNCCs in the functional pre-attack state of the peptidyl transferase centre. These structures reveal that C-terminal parts of the growing peptides adopt the same uniform β-strand conformation stabilized by an intricate network of hydrogen bonds with the universally conserved 23S rRNA nucleotides, and explain how the ribosome synthesizes growing peptides containing various sequences with comparable efficiencies.
Collapse
|
8
|
Safdari HA, Kasvandik S, Polte C, Ignatova Z, Tenson T, Wilson D. Structure of Escherichia coli heat shock protein Hsp15 in complex with the ribosomal 50S subunit bearing peptidyl-tRNA. Nucleic Acids Res 2022; 50:12515-12526. [PMID: 36370110 PMCID: PMC9757039 DOI: 10.1093/nar/gkac1035] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/13/2022] [Accepted: 11/09/2022] [Indexed: 11/14/2022] Open
Abstract
In Escherichia coli, the heat shock protein 15 (Hsp15) is part of the cellular response to elevated temperature. Hsp15 interacts with peptidyl-tRNA-50S complexes that arise upon dissociation of translating 70S ribosomes, and is proposed to facilitate their rescue and recycling. A previous structure of E. coli Hsp15 in complex with peptidyl-tRNA-50S complex reported a binding site located at the central protuberance of the 50S subunit. By contrast, recent structures of RqcP, the Hsp15 homolog in Bacillus subtilis, in complex with peptidyl-tRNA-50S complexes have revealed a distinct site positioned between the anticodon-stem-loop (ASL) of the P-site tRNA and H69 of the 23S rRNA. Here we demonstrate that exposure of E. coli cells to heat shock leads to a decrease in 70S ribosomes and accumulation of 50S subunits, thus identifying a natural substrate for Hsp15 binding. Additionally, we have determined a cryo-EM reconstruction of the Hsp15-50S-peptidyl-tRNA complex isolated from heat shocked E. coli cells, revealing that Hsp15 binds to the 50S-peptidyl-tRNA complex analogously to its B. subtilis homolog RqcP. Collectively, our findings support a model where Hsp15 stabilizes the peptidyl-tRNA in the P-site and thereby promotes access to the A-site for putative rescue factors to release the aberrant nascent polypeptide chain.
Collapse
Affiliation(s)
- Haaris A Safdari
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Pl. 6, 20146 Hamburg, Germany
| | - Sergo Kasvandik
- University of Tartu, Institute of Technology, 50411 Tartu, Estonia
| | - Christine Polte
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Pl. 6, 20146 Hamburg, Germany
| | - Zoya Ignatova
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Pl. 6, 20146 Hamburg, Germany
| | - Tanel Tenson
- University of Tartu, Institute of Technology, 50411 Tartu, Estonia
| | - Daniel N Wilson
- To whom correspondence should be addressed. Tel: +49 40 42838 2841;
| |
Collapse
|
9
|
Phan T, He C, Loladze I, Prater C, Elser J, Kuang Y. Dynamics and growth rate implications of ribosomes and mRNAs interaction in E. coli. Heliyon 2022; 8:e09820. [PMID: 35800243 PMCID: PMC9254350 DOI: 10.1016/j.heliyon.2022.e09820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/15/2021] [Accepted: 06/24/2022] [Indexed: 11/30/2022] Open
Abstract
Understanding how cells grow and adapt under various nutrient conditions is pivotal in the study of biological stoichiometry. Recent studies provide empirical evidence that cells use multiple strategies to maintain an optimal protein production rate under different nutrient conditions. Mathematical models can provide a solid theoretical foundation that can explain experimental observations and generate testable hypotheses to further our understanding of the growth process. In this study, we generalize a modeling framework that centers on the translation process and study its asymptotic behaviors to validate algebraic manipulations involving the steady states. Using experimental results on the growth of E. coli under C-, N-, and P-limited environments, we simulate the expected quantitative measurements to show the feasibility of using the model to explain empirical evidence. Our results support the findings that cells employ multiple strategies to maintain a similar protein production rate across different nutrient limitations. Moreover, we find that the previous study underestimates the significance of certain biological rates, such as the binding rate of ribosomes to mRNA and the transition rate between different ribosomal stages. Furthermore, our simulation shows that the strategies used by cells under C- and P-limitations result in a faster overall growth dynamics than under N-limitation. In conclusion, the general modeling framework provides a valuable platform to study cell growth under different nutrient supply conditions, which also allows straightforward extensions to the coupling of transcription, translation, and energetics to deepen our understanding of the growth process.
Collapse
Affiliation(s)
- Tin Phan
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, AZ 85287, USA
- Division of Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Changhan He
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Irakli Loladze
- Bryan Medical Center, Bryan College of Health Sciences, Lincoln, NE 68506, USA
| | - Clay Prater
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Jim Elser
- Flathead Lake Bio Station, University of Montana, Polson, MT 59860, USA
| | - Yang Kuang
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, AZ 85287, USA
- Corresponding author.
| |
Collapse
|
10
|
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.
Collapse
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;
| |
Collapse
|
11
|
A novel PTRH2 missense mutation causing IMNEPD: a case report. Hum Genome Var 2021; 8:23. [PMID: 34112751 PMCID: PMC8192544 DOI: 10.1038/s41439-021-00147-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/11/2021] [Accepted: 03/11/2021] [Indexed: 11/08/2022] Open
Abstract
PTRH2 deficiency is associated with an extremely rare disease, infantile-onset multisystem neurologic, endocrine, and pancreatic disease (IMNEPD). We report the first Iranian patient with IMNEPD. We detected a pathogenic variant in the PTRH2 gene (NM_016077.5: c.68T > C, p.V23A). The proband has myopia, spastic diplegic cerebral palsy, urolithiasis, and a history of seizures.
Collapse
|
12
|
Müller C, Crowe-McAuliffe C, Wilson DN. Ribosome Rescue Pathways in Bacteria. Front Microbiol 2021; 12:652980. [PMID: 33815344 PMCID: PMC8012679 DOI: 10.3389/fmicb.2021.652980] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 02/23/2021] [Indexed: 12/18/2022] Open
Abstract
Ribosomes that become stalled on truncated or damaged mRNAs during protein synthesis must be rescued for the cell to survive. Bacteria have evolved a diverse array of rescue pathways to remove the stalled ribosomes from the aberrant mRNA and return them to the free pool of actively translating ribosomes. In addition, some of these pathways target the damaged mRNA and the incomplete nascent polypeptide chain for degradation. This review highlights the recent developments in our mechanistic understanding of bacterial ribosomal rescue systems, including drop-off, trans-translation mediated by transfer-messenger RNA and small protein B, ribosome rescue by the alternative rescue factors ArfA and ArfB, as well as Bacillus ribosome rescue factor A, an additional rescue system found in some Gram-positive bacteria, such as Bacillus subtilis. Finally, we discuss the recent findings of ribosome-associated quality control in particular bacterial lineages mediated by RqcH and RqcP. The importance of rescue pathways for bacterial survival suggests they may represent novel targets for the development of new antimicrobial agents against multi-drug resistant pathogenic bacteria.
Collapse
Affiliation(s)
| | | | - Daniel N. Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| |
Collapse
|
13
|
In vitro synthesis of 32 translation-factor proteins from a single template reveals impaired ribosomal processivity. Sci Rep 2021; 11:1898. [PMID: 33479285 PMCID: PMC7820420 DOI: 10.1038/s41598-020-80827-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 12/24/2020] [Indexed: 12/20/2022] Open
Abstract
The Protein synthesis Using Recombinant Elements (PURE) system enables transcription and translation of a DNA template from purified components. Therefore, the PURE system-catalyzed generation of RNAs and proteins constituting the PURE system itself represents a major challenge toward a self-replicating minimal cell. In this work, we show that all translation factors (except elongation factor Tu) and 20 aminoacyl-tRNA synthetases can be expressed in the PURE system from a single plasmid encoding 32 proteins in 30 cistrons. Cell-free synthesis of all 32 proteins is confirmed by quantitative mass spectrometry-based proteomic analysis using isotopically labeled amino acids. We find that a significant fraction of the gene products consists of proteins missing their C-terminal ends. The per-codon processivity loss that we measure lies between 1.3 × 10-3 and 13.2 × 10-3, depending on the expression conditions, the version of the PURE system, and the coding sequence. These values are 5 to 50 times higher than those measured in vivo in E. coli. With such an impaired processivity, a considerable fraction of the biosynthesis capacity of the PURE system is wasted, posing an unforeseen challenge toward the development of a self-regenerating PURE system.
Collapse
|
14
|
Datta M, Pillai M, Modak MJ, Liiv A, Khaja FT, Hussain T, Remme J, Varshney U. A mutation in the ribosomal protein uS12 reveals novel functions of its universally conserved PNSA loop. Mol Microbiol 2021; 115:1292-1308. [PMID: 33368752 DOI: 10.1111/mmi.14675] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 12/18/2020] [Accepted: 12/19/2020] [Indexed: 11/28/2022]
Abstract
The ribosomal protein uS12 is conserved across all domains of life. Recently, a heterozygous spontaneous mutation in human uS12 (corresponding to R49K mutation immediately downstream of the universally conserved 44 PNSA47 loop in Escherichia coli uS12) was identified for causing ribosomopathy, highlighting the importance of the PNSA loop. To investigate the effects of a similar mutation in the absence of any wild-type alleles, we mutated the rpsL gene (encoding uS12) in E. coli. Consistent with its pathology (in humans), we were unable to generate the R49K mutation in E. coli in the absence of a support plasmid. However, we were able to generate the L48K mutation in its immediate vicinity. The L48K mutation resulted in a cold sensitive phenotype and ribosome biogenesis defect in the strain. We show that the L48K mutation impacts the steps of initiation and elongation. Furthermore, the genetic interactions of the L48K mutation with RRF and Pth suggest a novel role of the PNSA loop in ribosome recycling. Our studies reveal new functions of the PNSA loop in uS12, which has so far been studied in the context of translation elongation.
Collapse
Affiliation(s)
- Madhurima Datta
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Maalavika Pillai
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Mamata Jayant Modak
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Aivar Liiv
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Faisal Tarique Khaja
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India
| | - Tanweer Hussain
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India
| | - Jaanus Remme
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India.,Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| |
Collapse
|
15
|
Matsumoto A, Uehara Y, Shimizu Y, Ueda T, Uchiumi T, Ito K. High-resolution crystal structure of peptidyl-tRNA hydrolase fromThermus thermophilus. Proteins 2018; 87:226-235. [DOI: 10.1002/prot.25643] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/11/2018] [Accepted: 11/29/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Ami Matsumoto
- Faculty of Science, Department of Biology; Niigata University; Niigata Japan
| | - Yuji Uehara
- Faculty of Science, Department of Biology; Niigata University; Niigata Japan
| | - Yoshihiro Shimizu
- Department of Medical Genome Sciences; Graduate School of Frontier Sciences, The University of Tokyo; Chiba Japan
- Laboratory for Cell-Free Protein Synthesis; RIKEN Center for Biosystems Dynamics Research; Osaka Japan
| | - Takuya Ueda
- Department of Medical Genome Sciences; Graduate School of Frontier Sciences, The University of Tokyo; Chiba Japan
| | - Toshio Uchiumi
- Faculty of Science, Department of Biology; Niigata University; Niigata Japan
| | - Kosuke Ito
- Faculty of Science, Department of Biology; Niigata University; Niigata Japan
| |
Collapse
|
16
|
Shahid S, Kabra A, Mundra S, Pal RK, Tripathi S, Jain A, Arora A. Role of methionine 71 in substrate recognition and structural integrity of bacterial peptidyl-tRNA hydrolase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:865-874. [DOI: 10.1016/j.bbapap.2018.05.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 04/19/2018] [Accepted: 05/03/2018] [Indexed: 01/25/2023]
|
17
|
Search of multiple hot spots on the surface of peptidyl-tRNA hydrolase: structural, binding and antibacterial studies. Biochem J 2018; 475:547-560. [DOI: 10.1042/bcj20170666] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 12/25/2017] [Accepted: 01/03/2018] [Indexed: 11/17/2022]
Abstract
Peptidyl-tRNA hydrolase (Pth) catalyzes the breakdown of peptidyl-tRNA into peptide and tRNA components. Pth from Acinetobacter baumannii (AbPth) was cloned, expressed, purified and crystallized in a native unbound (AbPth-N) state and in a bound state with the phosphate ion and cytosine arabinoside (cytarabine) (AbPth-C). Structures of AbPth-N and AbPth-C were determined at 1.36 and 1.10 Å resolutions, respectively. The structure of AbPth-N showed that the active site is filled with water molecules. In the structure of AbPth-C, a phosphate ion is present in the active site, while cytarabine is bound in a cleft which is located away from the catalytic site. The cytarabine-binding site is formed with residues: Gln19, Trp27, Glu30, Gln31, Lys152, Gln158 and Asp162. In the structure of AbPth-N, the side chains of two active-site residues, Asn70 and Asn116, were observed in two conformations. Upon binding of the phosphate ion in the active site, the side chains of both residues were ordered to single conformations. Since Trp27 is present at the cytarabine-binding site, the fluorescence studies were carried out which gave a dissociation constant (KD) of 3.3 ± 0.8 × 10−7 M for cytarabine. The binding studies using surface plasmon resonance gave a KD value of 3.7 ± 0.7 × 10−7 M. The bacterial inhibition studies using the agar diffusion method and the biofilm inhibition assay established the strong antimicrobial potential of cytarabine. It also indicated that cytarabine inhibited Gram-negative bacteria more profoundly when compared with Gram-positive bacteria in a dose-dependent manner. Cytarabine was also effective against the drug-resistant bacteria both alone as well as in combination with other antibiotics.
Collapse
|
18
|
Bonnin P, Kern N, Young NT, Stansfield I, Romano MC. Novel mRNA-specific effects of ribosome drop-off on translation rate and polysome profile. PLoS Comput Biol 2017; 13:e1005555. [PMID: 28558053 PMCID: PMC5469512 DOI: 10.1371/journal.pcbi.1005555] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 06/13/2017] [Accepted: 05/08/2017] [Indexed: 11/19/2022] Open
Abstract
The well established phenomenon of ribosome drop-off plays crucial roles in translational accuracy and nutrient starvation responses during protein translation. When cells are under stress conditions, such as amino acid starvation or aminoacyl-tRNA depletion due to a high level of recombinant protein expression, ribosome drop-off can substantially affect the efficiency of protein expression. Here we introduce a mathematical model that describes the effects of ribosome drop-off on the ribosome density along the mRNA and on the concomitant protein synthesis rate. Our results show that ribosome premature termination may lead to non-intuitive ribosome density profiles, such as a ribosome density which increases from the 5' to the 3' end. Importantly, the model predicts that the effects of ribosome drop-off on the translation rate are mRNA-specific, and we quantify their resilience to drop-off, showing that the mRNAs which present ribosome queues are much less affected by ribosome drop-off than those which do not. Moreover, among those mRNAs that do not present ribosome queues, resilience to drop-off correlates positively with the elongation rate, so that sequences using fast codons are expected to be less affected by ribosome drop-off. This result is consistent with a genome-wide analysis of S. cerevisiae, which reveals that under favourable growth conditions mRNAs coding for proteins involved in the translation machinery, known to be highly codon biased and using preferentially fast codons, are highly resilient to ribosome drop-off. Moreover, in physiological conditions, the translation rate of mRNAs coding for regulatory, stress-related proteins, is less resilient to ribosome drop-off. This model therefore allows analysis of variations in the translational efficiency of individual mRNAs by accounting for the full range of known ribosome behaviours, as well as explaining mRNA-specific variations in ribosome density emerging from ribosome profiling studies.
Collapse
Affiliation(s)
- Pierre Bonnin
- Institute for Complex Systems and Mathematical Biology, Physics Department, University of Aberdeen, Aberdeen, UK
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, UK
| | - Norbert Kern
- Université Montpellier 2, Laboratoire Charles Coulomb UMR 5221, Montpellier, France
| | - Neil T. Young
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, UK
| | - Ian Stansfield
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, UK
| | - M. Carmen Romano
- Institute for Complex Systems and Mathematical Biology, Physics Department, University of Aberdeen, Aberdeen, UK
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, UK
| |
Collapse
|
19
|
Kabra A, Shahid S, Pal RK, Yadav R, Pulavarti SVSRK, Jain A, Tripathi S, Arora A. Unraveling the stereochemical and dynamic aspects of the catalytic site of bacterial peptidyl-tRNA hydrolase. RNA (NEW YORK, N.Y.) 2017; 23:202-216. [PMID: 28096445 PMCID: PMC5238795 DOI: 10.1261/rna.057620.116] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 11/07/2016] [Indexed: 06/06/2023]
Abstract
Bacterial peptidyl-tRNA hydrolase (Pth; EC 3.1.1.29) hydrolyzes the peptidyl-tRNAs accumulated in the cytoplasm and thereby prevents cell death by alleviating tRNA starvation. X-ray and NMR studies of Vibrio cholerae Pth (VcPth) and mutants of its key residues involved in catalysis show that the activity and selectivity of the protein depends on the stereochemistry and dynamics of residues H24, D97, N118, and N14. D97-H24 interaction is critical for activity because it increases the nucleophilicity of H24. The N118 and N14 have orthogonally competing interactions with H24, both of which reduce the nucleophilicity of H24 and are likely to be offset by positioning of a peptidyl-tRNA substrate. The region proximal to H24 and the lid region exhibit slow motions that may assist in accommodating the substrate. Helix α3 exhibits a slow wobble with intermediate time scale motions of its N-cap residue N118, which may work as a flypaper to position the scissile ester bond of the substrate. Overall, the dynamics of interactions between the side chains of N14, H24, D97, and N118, control the catalysis of substrate by this enzyme.
Collapse
Affiliation(s)
- Ashish Kabra
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Salman Shahid
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
- Academy of Scientific and Innovative Research, New Delhi 110025, India
| | - Ravi Kant Pal
- X-ray Crystallography Facility, National Institute of Immunology, New Delhi 110067, India
| | - Rahul Yadav
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | | | - Anupam Jain
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Sarita Tripathi
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Ashish Arora
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
- Academy of Scientific and Innovative Research, New Delhi 110025, India
| |
Collapse
|
20
|
Kabra A, Fatma F, Shahid S, Pathak PP, Yadav R, Pulavarti SK, Tripathi S, Jain A, Arora A. Structural characterization of peptidyl-tRNA hydrolase from Mycobacterium smegmatis by NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1304-14. [DOI: 10.1016/j.bbapap.2016.06.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 06/24/2016] [Accepted: 06/28/2016] [Indexed: 10/21/2022]
|
21
|
Picker-Minh S, Mignot C, Doummar D, Hashem M, Faqeih E, Josset P, Dubern B, Alkuraya FS, Kraemer N, Kaindl AM. Phenotype variability of infantile-onset multisystem neurologic, endocrine, and pancreatic disease IMNEPD. Orphanet J Rare Dis 2016; 11:52. [PMID: 27129381 PMCID: PMC4850685 DOI: 10.1186/s13023-016-0433-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 04/19/2016] [Indexed: 11/12/2022] Open
Abstract
Infantile-onset multisystem neurologic, endocrine, and pancreatic disease (IMNEPD) has been recently linked to biallelic mutation of the peptidyl-tRNA hydrolase 2 gene PTRH2. Two index patients with IMNEPD in the original report had multiple neurological symptoms such as postnatal microcephaly, intellectual disability, developmental delay, sensorineural deafness, cerebellar atrophy, ataxia, and peripheral neuropathy. In addition, distal muscle weakness and abnormalities of thyroid, pancreas, and liver were found. Here, we report five further IMNEPD patients with a different homozygous PTRH2 mutation, broaden the phenotypic spectrum of the disease and differentiate common symptoms and interindividual variability in IMNEPD associated with a unique mutation. We thereby hope to better define IMNEPD and promote recognition and diagnosis of this novel disease entity.
Collapse
Affiliation(s)
- Sylvie Picker-Minh
- Department of Pediatric Neurology, Charité - Universitätsmedizin Berlin, Campus Virchow-Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany.,Sozialpädiatrisches Zentrum (SPZ), Center for Chronically Sick Children, Charité - Universitätsmedizin Berlin, Campus Virchow-Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany.,Institute of Cell Biology and Neurobiology Charité - Universitätsmedizin Berlin, Campus Mitte, Charitéplatz 1, 10115, Berlin, Germany
| | - Cyril Mignot
- Department of Genetics, AP-HP, Armand Trousseau Hospital, Avenue du Dr. Arnold-Netter 26, 75571, Paris, France
| | - Diane Doummar
- Department of Pediatric Neurology, AP-HP, Armand Trousseau Hospital, Avenue du Dr. Arnold-Netter 26, 75571, Paris, France
| | - Mais Hashem
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, 11211, Saudi Arabia
| | - Eissa Faqeih
- Department of Pediatric Subspecialties, Children's Specialist Hospital, King Fahad Medical City, Riyadh, 59046, Saudi Arabia
| | - Patrice Josset
- Department of Anatomy and Pathology, AP-HP, Armand Trousseau Hospital, Avenue du Dr. Arnold-Netter 26, 75571, Paris, France
| | - Béatrice Dubern
- Department of Pediatric Nutrition and Gastroenterology, AP-HP, Armand Trousseau Hospital, Avenue du Dr. Arnold-Netter 26, 75571, Paris, France
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, 11211, Saudi Arabia
| | - Nadine Kraemer
- Department of Pediatric Neurology, Charité - Universitätsmedizin Berlin, Campus Virchow-Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany.,Sozialpädiatrisches Zentrum (SPZ), Center for Chronically Sick Children, Charité - Universitätsmedizin Berlin, Campus Virchow-Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany.,Institute of Cell Biology and Neurobiology Charité - Universitätsmedizin Berlin, Campus Mitte, Charitéplatz 1, 10115, Berlin, Germany
| | - Angela M Kaindl
- Department of Pediatric Neurology, Charité - Universitätsmedizin Berlin, Campus Virchow-Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany. .,Sozialpädiatrisches Zentrum (SPZ), Center for Chronically Sick Children, Charité - Universitätsmedizin Berlin, Campus Virchow-Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany. .,Institute of Cell Biology and Neurobiology Charité - Universitätsmedizin Berlin, Campus Mitte, Charitéplatz 1, 10115, Berlin, Germany.
| |
Collapse
|
22
|
Sin C, Chiarugi D, Valleriani A. Quantitative assessment of ribosome drop-off in E. coli. Nucleic Acids Res 2016; 44:2528-37. [PMID: 26935582 PMCID: PMC4824120 DOI: 10.1093/nar/gkw137] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 02/24/2016] [Indexed: 11/14/2022] Open
Abstract
Premature ribosome drop-off is one of the major errors in translation of mRNA by ribosomes. However, repeated analyses of Ribo-seq data failed to quantify its strength inE. coli Relying on a novel highly sensitive data analysis method we show that a significant rate of ribosome drop-off is measurable and can be quantified also when cells are cultured under non-stressing conditions. Moreover, we find that the drop-off rate is highly variable, depending on multiple factors. In particular, under environmental stress such as amino acid starvation or ethanol intoxication, the drop-off rate markedly increases.
Collapse
Affiliation(s)
- Celine Sin
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14476 Potsdam, Germany
| | - Davide Chiarugi
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14476 Potsdam, Germany
| | - Angelo Valleriani
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14476 Potsdam, Germany
| |
Collapse
|
23
|
Zhang F, Song Y, Niu L, Teng M, Li X. Crystal structure of Staphylococcus aureus peptidyl-tRNA hydrolase at a 2.25 Å resolution. Acta Biochim Biophys Sin (Shanghai) 2015; 47:1005-10. [PMID: 26508479 DOI: 10.1093/abbs/gmv114] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 08/16/2015] [Indexed: 11/13/2022] Open
Abstract
Peptidyl-tRNA hydrolase (Pth) catalyzes the release of tRNA to relieve peptidyl-tRNA accumulation. Because Pth activity is essential for the viability of bacteria, Pth is regarded as a promising target for the discovery of new antimicrobial agents. Here, the structure of Pth from the Gram-positive bacterium Staphylococcus aureus (SaPth) was solved by X-ray crystallography at a 2.25 Å resolution. The SaPth structure exhibits significant structural similarity with other members of the Pth superfamily, with a conserved α/β/α sandwich fold. A molecular phylogenetic analysis and a structure database search indicated that SaPth is most similar to its homolog in Streptococcus pyogenes, but it has a different substrate-binding cleft state.
Collapse
Affiliation(s)
- Fan Zhang
- Hefei National Laboratory for Physical Sciences at Microscale, Innovation Center for Cell Signaling Network, School of Life Science, University of Science and Technology of China, Hefei 230026, China Key Laboratory of Structural Biology, Hefei Science Center, Chinese Academy of Science, Hefei 230026, China
| | - Yang Song
- Hefei National Laboratory for Physical Sciences at Microscale, Innovation Center for Cell Signaling Network, School of Life Science, University of Science and Technology of China, Hefei 230026, China Key Laboratory of Structural Biology, Hefei Science Center, Chinese Academy of Science, Hefei 230026, China
| | - Liwen Niu
- Hefei National Laboratory for Physical Sciences at Microscale, Innovation Center for Cell Signaling Network, School of Life Science, University of Science and Technology of China, Hefei 230026, China Key Laboratory of Structural Biology, Hefei Science Center, Chinese Academy of Science, Hefei 230026, China
| | - Maikun Teng
- Hefei National Laboratory for Physical Sciences at Microscale, Innovation Center for Cell Signaling Network, School of Life Science, University of Science and Technology of China, Hefei 230026, China Key Laboratory of Structural Biology, Hefei Science Center, Chinese Academy of Science, Hefei 230026, China
| | - Xu Li
- Hefei National Laboratory for Physical Sciences at Microscale, Innovation Center for Cell Signaling Network, School of Life Science, University of Science and Technology of China, Hefei 230026, China Key Laboratory of Structural Biology, Hefei Science Center, Chinese Academy of Science, Hefei 230026, China
| |
Collapse
|
24
|
Abstract
The bacterial ribosome is a complex macromolecular machine that deciphers the genetic code with remarkable fidelity. During the elongation phase of protein synthesis, the ribosome selects aminoacyl-tRNAs as dictated by the canonical base pairing between the anticodon of the tRNA and the codon of the messenger RNA. The ribosome's participation in tRNA selection is active rather than passive, using conformational changes of conserved bases of 16S rRNA to directly monitor the geometry of codon-anticodon base pairing. The tRNA selection process is divided into an initial selection step and a subsequent proofreading step, with the utilization of two sequential steps increasing the discriminating power of the ribosome far beyond that which could be achieved based on the thermodynamics of codon-anticodon base pairing stability. The accuracy of decoding is impaired by a number of antibiotics and can be either increased or decreased by various mutations in either subunit of the ribosome, in elongation factor Tu, and in tRNA. In this chapter we will review our current understanding of various forces that determine the accuracy of decoding by the bacterial ribosome.
Collapse
|
25
|
Investigating Bacterial Protein Synthesis Using Systems Biology Approaches. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 883:21-40. [PMID: 26621460 DOI: 10.1007/978-3-319-23603-2_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Protein synthesis is essential for bacterial growth and survival. Its study in Escherichia coli helped uncover features conserved among bacteria as well as universally. The pattern of discovery and the identification of some of the longest-known components of the protein synthesis machinery, including the ribosome itself, tRNAs, and translation factors proceeded through many stages of successively more refined biochemical purifications, finally culminating in the isolation to homogeneity, identification, and mapping of the smallest unit required for performing the given function. These early studies produced a wealth of information. However, many unknowns remained. Systems biology approaches provide an opportunity to investigate protein synthesis from a global perspective, overcoming the limitations of earlier ad hoc methods to gain unprecedented insights. This chapter reviews innovative systems biology approaches, with an emphasis on those designed specifically for investigating the protein synthesis machinery in E. coli.
Collapse
|
26
|
Hu H, Matter ML, Issa-Jahns L, Jijiwa M, Kraemer N, Musante L, de la Vega M, Ninnemann O, Schindler D, Damatova N, Eirich K, Sifringer M, Schrötter S, Eickholt BJ, van den Heuvel L, Casamina C, Stoltenburg-Didinger G, Ropers HH, Wienker TF, Hübner C, Kaindl AM. Mutations in PTRH2 cause novel infantile-onset multisystem disease with intellectual disability, microcephaly, progressive ataxia, and muscle weakness. Ann Clin Transl Neurol 2014; 1:1024-35. [PMID: 25574476 PMCID: PMC4284127 DOI: 10.1002/acn3.149] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 10/27/2014] [Accepted: 10/28/2014] [Indexed: 01/10/2023] Open
Abstract
OBJECTIVE To identify the cause of a so-far unreported phenotype of infantile-onset multisystem neurologic, endocrine, and pancreatic disease (IMNEPD). METHODS We characterized a consanguineous family of Yazidian-Turkish descent with IMNEPD. The two affected children suffer from intellectual disability, postnatal microcephaly, growth retardation, progressive ataxia, distal muscle weakness, peripheral demyelinating sensorimotor neuropathy, sensorineural deafness, exocrine pancreas insufficiency, hypothyroidism, and show signs of liver fibrosis. We performed whole-exome sequencing followed by bioinformatic analysis and Sanger sequencing on affected and unaffected family members. The effect of mutations in the candidate gene was studied in wild-type and mutant mice and in patient and control fibroblasts. RESULTS In a consanguineous family with two individuals with IMNEPD, we identified a homozygous frameshift mutation in the previously not disease-associated peptidyl-tRNA hydrolase 2 (PTRH2) gene. PTRH2 encodes a primarily mitochondrial protein involved in integrin-mediated cell survival and apoptosis signaling. We show that PTRH2 is highly expressed in the developing brain and is a key determinant in maintaining cell survival during human tissue development. Moreover, we link PTRH2 to the mTOR pathway and thus the control of cell size. The pathology suggested by the human phenotype and neuroimaging studies is supported by analysis of mutant mice and patient fibroblasts. INTERPRETATION We report a novel disease phenotype, show that the genetic cause is a homozygous mutation in the PTRH2 gene, and demonstrate functional effects in mouse and human tissues. Mutations in PTRH2 should be considered in patients with undiagnosed multisystem neurologic, endocrine, and pancreatic disease.
Collapse
Affiliation(s)
- Hao Hu
- Max Planck Institute for Molecular Genetics Berlin, Germany
| | | | - Lina Issa-Jahns
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin Berlin, Germany ; Department of Pediatric Neurology, Charité - Universitätsmedizin Berlin Berlin, Germany
| | - Mayumi Jijiwa
- The University of Hawaii Cancer Center Honolulu, Hawaii
| | - Nadine Kraemer
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin Berlin, Germany ; Department of Pediatric Neurology, Charité - Universitätsmedizin Berlin Berlin, Germany
| | | | | | - Olaf Ninnemann
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin Berlin, Germany
| | - Detlev Schindler
- Department of Human Genetics, University of Würzburg Würzburg, Germany
| | - Natalia Damatova
- Department of Human Genetics, University of Würzburg Würzburg, Germany
| | - Katharina Eirich
- Department of Human Genetics, University of Würzburg Würzburg, Germany
| | - Marco Sifringer
- Department of Anesthesiology and Intensive Care Medicine, Charité - Universitätsmedizin Berlin Berlin, Germany
| | - Sandra Schrötter
- Institute of Biochemistry and Cluster of Excellence Neurocure, Charité - Universitätsmedizin Berlin Berlin, Germany
| | - Britta J Eickholt
- Institute of Biochemistry and Cluster of Excellence Neurocure, Charité - Universitätsmedizin Berlin Berlin, Germany
| | - Lambert van den Heuvel
- Nijmegen Center for Mitochondrial Disorders, Radboud University Medical Center Nijmegen, The Netherlands
| | | | | | | | | | - Christoph Hübner
- Department of Pediatric Neurology, Charité - Universitätsmedizin Berlin Berlin, Germany
| | - Angela M Kaindl
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin Berlin, Germany ; Department of Pediatric Neurology, Charité - Universitätsmedizin Berlin Berlin, Germany
| |
Collapse
|
27
|
Singh A, Gautam L, Sinha M, Bhushan A, Kaur P, Sharma S, Singh TP. Crystal structure of peptidyl-tRNA hydrolase from a Gram-positive bacterium, Streptococcus pyogenes at 2.19 Å resolution shows the closed structure of the substrate-binding cleft. FEBS Open Bio 2014; 4:915-22. [PMID: 25389518 PMCID: PMC4226762 DOI: 10.1016/j.fob.2014.10.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 10/17/2014] [Accepted: 10/17/2014] [Indexed: 11/29/2022] Open
Abstract
Structure of peptidyl-tRNA hydrolase (Pth) from Streptococcus pyogenes. First structure of Pth from a Gram-positive bacterium. Conformations of the lid and gate loops are different from those observed in other Pth enzymes. The substrate-binding channel is closed at both sites of the lid and gate loops. In Pth structures from other species, the channel is fully open at the lid loop.
Peptidyl-tRNA hydrolase (Pth) catalyses the release of tRNA and peptide components from peptidyl-tRNA molecules. Pth from a Gram-positive bacterium Streptococcus pyogenes (SpPth) was cloned, expressed, purified and crystallised. Three-dimensional structure of SpPth was determined by X-ray crystallography at 2.19 Å resolution. Structure determination showed that the asymmetric unit of the unit cell contained two crystallographically independent molecules, designated A and B. The superimposition of Cα traces of molecules A and B showed an r.m.s. shift of 0.4 Å, indicating that the structures of two crystallographically independent molecules were identical. The polypeptide chain of SpPth adopted an overall α/β conformation. The substrate-binding cleft in SpPth is formed with three loops: the gate loop, Ile91–Leu102; the base loop, Gly108–Gly115; and the lid loop, Gly136–Gly150. Unlike in the structures of Pth from Gram-negative bacteria, the entry to the cleft in the structure of SpPth appeared to be virtually closed. However, the conformations of the active site residues were found to be similar.
Collapse
Affiliation(s)
- Avinash Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Lovely Gautam
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Mau Sinha
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Asha Bhushan
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Sujata Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - T P Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| |
Collapse
|
28
|
Structural and binding studies of peptidyl-tRNA hydrolase from Pseudomonas aeruginosa provide a platform for the structure-based inhibitor design against peptidyl-tRNA hydrolase. Biochem J 2014; 463:329-37. [DOI: 10.1042/bj20140631] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Peptidyl-tRNA hydrolase is a key enzyme that is required to maintain the process of protein synthesis in bacteria. The structure determinations of the native enzyme from Pseudomonas aeruginosa and its complexes have provided an excellent platform for structure-based drug design.
Collapse
|
29
|
Taylor-Creel K, Hames MC, Holloway WB, McFeeters H, McFeeters RL. Expression, purification, and solubility optimization of peptidyl-tRNA hydrolase 1 from Bacillus cereus. Protein Expr Purif 2014; 95:259-64. [PMID: 24480186 DOI: 10.1016/j.pep.2014.01.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 01/13/2014] [Accepted: 01/15/2014] [Indexed: 11/17/2022]
Abstract
Peptidyl-tRNA hydrolase 1 cleaves the ester bond of peptidyl-tRNA thereby recycling peptidyl-tRNAs generated from premature termination of translation and expression of minigenes and short ORFs. Bacterial Pth1 is essential, highly conserved, and has no essential eukaryotic homolog making it a good target for antibacterial development. Herein we describe the cloning of pth1 gene from Bacillus cereus as an N-terminal hexahistidine fusion protein. Solubility was optimized for overexpression in Escherichia coli. Purity greater than 95% was achieved in one chromatography step. Yields greater than 12mg of purified Pth1 per liter of minimal media were achieved and buffer conditions for long-term solubility were determined. Enzymatic activity of Pth1 from B. cereus was confirmed and quantification of Michaelis-Menten parameters reported.
Collapse
Affiliation(s)
- Kasey Taylor-Creel
- Department of Chemistry, University of Alabama in Huntsville, 301 Sparkman Drive, Huntsville, AL 35899, USA.
| | - Mary C Hames
- Department of Chemistry, University of Alabama in Huntsville, 301 Sparkman Drive, Huntsville, AL 35899, USA.
| | - W Blake Holloway
- Department of Chemistry, University of Alabama in Huntsville, 301 Sparkman Drive, Huntsville, AL 35899, USA.
| | - Hana McFeeters
- Department of Chemistry, University of Alabama in Huntsville, 301 Sparkman Drive, Huntsville, AL 35899, USA.
| | - Robert L McFeeters
- Department of Chemistry, University of Alabama in Huntsville, 301 Sparkman Drive, Huntsville, AL 35899, USA.
| |
Collapse
|
30
|
Arraiano CM. Post-transcriptional control of gene expression: bacterial mRNA degradation. World J Microbiol Biotechnol 2014; 9:421-32. [PMID: 24420109 DOI: 10.1007/bf00328030] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/1993] [Indexed: 11/30/2022]
Abstract
Many biological processes cannot be fully understood without detailed knowledge of RNA metabolism. The continuous breakdown and resynthesis of prokaryotic mRNA permit rapid production of new kinds of proteins. In this way, mRNA levels can regulate protein synthesis and cellular growth. Analysing mRNA degradation in prokaryotes has been particularly difficult because most mRNA undergo rapid exponential decay. Prokaryotic mRNAs differ in their susceptibility to degradation by endonucleases and exonucleases, possibly because of variation in their sequencing and structure. In spite of numerous studies, details of mRNA degradation are still largely unknown. This review highlights those aspects of mRNA metabolism which seem most influential in the regulation of gene expression.
Collapse
Affiliation(s)
- C M Arraiano
- Instituto de Tecnologia Quimica e Biológica (ITQB), Apt 127, 2780, Oeiras, Portugal
| |
Collapse
|
31
|
Premature translational termination products are rapidly degraded substrates for MHC class I presentation. PLoS One 2012; 7:e51968. [PMID: 23251665 PMCID: PMC3522582 DOI: 10.1371/journal.pone.0051968] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Accepted: 11/14/2012] [Indexed: 11/30/2022] Open
Abstract
Nearly thirty percent of all newly synthesized polypeptides are targeted for rapid proteasome-mediated degradation. These rapidly degraded polypeptides (RDPs) are a source of antigenic substrates for the MHC class I presentation pathway, allowing for immunosurveillance of newly synthesized proteins by cytotoxic T lymphocytes. Despite the recognized role of RDPs in MHC I presentation, it remains unclear what molecular characteristics distinguish RDPs from their more stable counterparts. It has been proposed that premature translational termination products may constitute a form of RDP; indeed, in prokaryotes translational drop-off products are normal by-products of protein synthesis and are subsequently rapidly degraded. To study the cellular fate of premature termination products, we used the antibiotic puromycin as a means to experimentally manipulate prematurely terminated polypeptide production in human cells. At low concentrations, puromycin enhanced flux into rapidly degraded polypeptide pools, with small polypeptides being markedly more labile then high molecular weight puromycin adducts. Immunoprecipitation experiments using anti-puromycin antisera demonstrated that the majority of peptidyl-puromycins are rapidly degraded in a proteasome-dependent manner. Low concentrations of puromycin increased the recovery of cell surface MHC I-peptide complexes, indicating that prematurely terminated polypeptides can be processed for presentation via the MHC I pathway. In the continued presence of puromycin, however, MHC I export to the cell surface was inhibited, coincident with the accumulation of polyubiquitinated proteins. The time- and dose-dependent effects of puromycin suggest that the pool of peptidyl-puromycin adducts differ in their targeting to various proteolytic pathways that, in turn, differ in the efficiency with which they access the MHC I presentation machinery. These studies highlight the diversity of cellular proteolytic pathways necessary for the metabolism and immunosurveillance of prematurely terminated polypeptides that are, by their nature, highly heterogeneous.
Collapse
|
32
|
Ito K, Murakami R, Mochizuki M, Qi H, Shimizu Y, Miura KI, Ueda T, Uchiumi T. Structural basis for the substrate recognition and catalysis of peptidyl-tRNA hydrolase. Nucleic Acids Res 2012; 40:10521-31. [PMID: 22923517 PMCID: PMC3488237 DOI: 10.1093/nar/gks790] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Peptidyl-tRNA hydrolase (Pth) cleaves the ester bond between the peptide and the tRNA of peptidyl-tRNA molecules, which are produced by aborted translation, to recycle tRNA for further rounds of protein synthesis. Pth is ubiquitous in nature, and its enzymatic activity is essential for bacterial viability. We have determined the crystal structure of Escherichia coli Pth in complex with the tRNA CCA-acceptor-TΨC domain, the enzyme-binding region of the tRNA moiety of the substrate, at 2.4 Å resolution. In combination with site-directed mutagenesis studies, the structure identified the amino acid residues involved in tRNA recognition. The structure also revealed that Pth interacts with the tRNA moiety through the backbone phosphates and riboses, and no base-specific interactions were observed, except for the interaction with the highly conserved base G53. This feature enables Pth to accept the diverse sequences of the elongator-tRNAs as substrate components. Furthermore, we propose an authentic Pth:peptidyl-tRNA complex model and a detailed mechanism for the hydrolysis reaction, based on the present crystal structure and the previous studies’ results.
Collapse
Affiliation(s)
- Kosuke Ito
- Department of Biology, Faculty of Science, Niigata University, 8050 Ikarashi 2-no-cho, Nishi-ku, Niigata 950-2181, Japan.
| | | | | | | | | | | | | | | |
Collapse
|
33
|
Paredes JA, Carreto L, Simões J, Bezerra AR, Gomes AC, Santamaria R, Kapushesky M, Moura GR, Santos MAS. Low level genome mistranslations deregulate the transcriptome and translatome and generate proteotoxic stress in yeast. BMC Biol 2012; 10:55. [PMID: 22715922 PMCID: PMC3391182 DOI: 10.1186/1741-7007-10-55] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 06/20/2012] [Indexed: 11/21/2022] Open
Abstract
Background Organisms use highly accurate molecular processes to transcribe their genes and a variety of mRNA quality control and ribosome proofreading mechanisms to maintain intact the fidelity of genetic information flow. Despite this, low level gene translational errors induced by mutations and environmental factors cause neurodegeneration and premature death in mice and mitochondrial disorders in humans. Paradoxically, such errors can generate advantageous phenotypic diversity in fungi and bacteria through poorly understood molecular processes. Results In order to clarify the biological relevance of gene translational errors we have engineered codon misreading in yeast and used profiling of total and polysome-associated mRNAs, molecular and biochemical tools to characterize the recombinant cells. We demonstrate here that gene translational errors, which have negligible impact on yeast growth rate down-regulate protein synthesis, activate the unfolded protein response and environmental stress response pathways, and down-regulate chaperones linked to ribosomes. Conclusions We provide the first global view of transcriptional and post-transcriptional responses to global gene translational errors and we postulate that they cause gradual cell degeneration through synergistic effects of overloading protein quality control systems and deregulation of protein synthesis, but generate adaptive phenotypes in unicellular organisms through activation of stress cross-protection. We conclude that these genome wide gene translational infidelities can be degenerative or adaptive depending on cellular context and physiological condition.
Collapse
Affiliation(s)
- João A Paredes
- RNA Biology Laboratory, Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
| | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Selvaraj M, Ahmad R, Varshney U, Vijayan M. Structures of new crystal forms of Mycobacterium tuberculosis peptidyl-tRNA hydrolase and functionally important plasticity of the molecule. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:124-8. [PMID: 22297982 PMCID: PMC3274386 DOI: 10.1107/s1744309111052341] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 12/04/2011] [Indexed: 11/11/2022]
Abstract
The X-ray structures of new crystal forms of peptidyl-tRNA hydrolase from M. tuberculosis reported here and the results of previous X-ray studies of the enzyme from different sources provide a picture of the functionally relevant plasticity of the protein molecule. The new X-ray results confirm the connection deduced previously between the closure of the lid at the peptide-binding site and the opening of the gate that separates the peptide-binding and tRNA-binding sites. The plasticity of the molecule indicated by X-ray structures is in general agreement with that deduced from the available solution NMR results. The correlation between the lid and the gate movements is not, however, observed in the NMR structure.
Collapse
Affiliation(s)
- M. Selvaraj
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Rais Ahmad
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Umesh Varshney
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - M. Vijayan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| |
Collapse
|
35
|
Janssen BD, Diner EJ, Hayes CS. Analysis of aminoacyl- and peptidyl-tRNAs by gel electrophoresis. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2012; 905:291-309. [PMID: 22736012 DOI: 10.1007/978-1-61779-949-5_19] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
During protein synthesis, ribosomes translate the genetic information encoded within messenger RNAs into defined amino acid sequences. Transfer RNAs (tRNAs) are crucial adaptor molecules in this process, delivering amino acid residues to the ribosome and holding the nascent peptide chain as it is assembled. Here, we present methods for the analysis of aminoacyl- and peptidyl-tRNA species isolated from Escherichia coli. These approaches utilize denaturing gel electrophoresis at acidic pH to preserve the labile ester bonds that link amino acids to tRNA. Specific aminoacyl- and peptidyl-tRNAs are detected by Northern blot hybridization using probes for tRNA isoacceptors. Small peptidyl-tRNAs can be differentiated from aminoacyl-tRNA through selective deacylation of the latter with copper sulfate. Additionally, peptidyl-tRNAs can be detected through metabolic labeling of the nascent peptide. This approach is amenable to pulse-chase analysis to examine peptidyl-tRNA turnover in vivo. We have applied these methods to study programmed translational arrests and the kinetics of paused ribosome turnover.
Collapse
Affiliation(s)
- Brian D Janssen
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | | | | |
Collapse
|
36
|
Ito K, Chadani Y, Nakamori K, Chiba S, Akiyama Y, Abo T. Nascentome analysis uncovers futile protein synthesis in Escherichia coli. PLoS One 2011; 6:e28413. [PMID: 22162769 PMCID: PMC3230602 DOI: 10.1371/journal.pone.0028413] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Accepted: 11/07/2011] [Indexed: 11/19/2022] Open
Abstract
Although co-translational biological processes attract much attention, no general and easy method has been available to detect cellular nascent polypeptide chains, which we propose to call collectively a “nascentome.” We developed a method to selectively detect polypeptide portions of cellular polypeptidyl-tRNAs and used it to study the generality of the quality control reactions that rescue dead-end translation complexes. To detect nascent polypeptides, having their growing ends covalently attached to a tRNA, cellular extracts are separated by SDS-PAGE in two dimensions, first with the peptidyl-tRNA ester bonds preserved and subsequently after their in-gel cleavage. Pulse-labeled nascent polypeptides of Escherichia coli form a characteristic line below the main diagonal line, because each of them had contained a tRNA of nearly uniform size in the first-dimension electrophoresis but not in the second-dimension. The detection of nascent polypeptides, separately from any translation-completed polypeptides or degradation products thereof, allows us to follow their fates to gain deeper insights into protein biogenesis and quality control pathways. It was revealed that polypeptidyl-tRNAs were significantly stabilized in E. coli upon dysfunction of the tmRNA-ArfA ribosome-rescuing system, whose function had only been studied previously using model constructs. Our results suggest that E. coli cells are intrinsically producing aberrant translation products, which are normally eliminated by the ribosome-rescuing mechanisms.
Collapse
Affiliation(s)
- Koreaki Ito
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan.
| | | | | | | | | | | |
Collapse
|
37
|
Ito K, Qi H, Shimizu Y, Murakami R, Miura KI, Ueda T, Uchiumi T. Crystallization and preliminary X-ray analysis of peptidyl-tRNA hydrolase from Escherichia coli in complex with the acceptor-TΨC domain of tRNA. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1566-9. [PMID: 22139168 PMCID: PMC3232141 DOI: 10.1107/s1744309111038383] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Accepted: 09/19/2011] [Indexed: 11/11/2022]
Abstract
Peptidyl-tRNA hydrolase (Pth) cleaves the ester bond between the peptide and the tRNA of peptidyl-tRNA molecules, which are the product of aborted translation. In the present work, Pth from Escherichia coli was crystallized with the acceptor-TΨC domain of tRNA using 1,4-butanediol as a precipitant. The crystals belonged to the hexagonal space group P6(1), with unit-cell parameters a = b = 55.1, c = 413.1 Å, and diffracted X-rays beyond 2.4 Å resolution. The asymmetric unit is expected to contain two complexes of Pth and the acceptor-TΨC domain of tRNA (V(M) = 2.8 Å(3) Da(-1)), with a solvent content of 60.8%. The structure is being solved by molecular replacement.
Collapse
Affiliation(s)
- Kosuke Ito
- Department of Biology, Faculty of Science, Niigata University, Nishi-ku, Niigata, Japan.
| | | | | | | | | | | | | |
Collapse
|
38
|
Suchard MA, Lange K, Sinsheimer JS. Efficiency of Protein Production from mRNA. JOURNAL OF STATISTICAL THEORY AND PRACTICE 2011. [DOI: 10.1080/15598608.2008.10411869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
39
|
Rubinstein ND, Zeevi D, Oren Y, Segal G, Pupko T. The operonic location of auto-transcriptional repressors is highly conserved in bacteria. Mol Biol Evol 2011; 28:3309-18. [PMID: 21690561 DOI: 10.1093/molbev/msr163] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Bacterial genes are commonly encoded in clusters, known as operons, which share transcriptional regulatory control and often encode functionally related proteins that take part in certain biological pathways. Operons that are coregulated are known to colocalize in the genome, suggesting that their spatial organization is under selection for efficient expression regulation. However, the internal order of genes within operons is believed to be poorly conserved, and hence expression requirements are claimed to be too weak to oppose gene rearrangements. In light of these opposing views, we set out to investigate whether the internal location of the regulatory genes within operons is under selection. Our analysis shows that transcription factors (TFs) are preferentially encoded as either first or last in their operons, in the two diverged model bacteria Escherichia coli and Bacillus subtilis. In a higher resolution, we find that TFs that repress transcription of the operon in which they are encoded (autorepressors), contribute most of this signal by specific preference of the first operon position. We show that this trend is strikingly conserved throughout highly diverged bacterial phyla. Moreover, these autorepressors regulate operons that carry out highly diverse biological functions. We propose a model according to which autorepressors are selected to be located first in their operons in order to optimize transcription regulation. Specifically, the first operon position helps autorepressors to minimize leaky transcription of the operon structural genes, thus minimizing energy waste. Our analysis provides statistically robust evidence for a paradigm of bacterial autorepressor preferential operonic location. Corroborated with our suggested model, an additional layer of operon expression control that is common throughout the bacterial domain is revealed.
Collapse
Affiliation(s)
- Nimrod D Rubinstein
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv, Israel
| | | | | | | | | |
Collapse
|
40
|
Kang TJ, Suga H. Translation of a histone H3 tail as a model system for studying peptidyl-tRNA drop-off. FEBS Lett 2011; 585:2269-74. [DOI: 10.1016/j.febslet.2011.05.051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 05/13/2011] [Accepted: 05/19/2011] [Indexed: 10/18/2022]
|
41
|
Mäkelä J, Lloyd-Price J, Yli-Harja O, Ribeiro AS. Stochastic sequence-level model of coupled transcription and translation in prokaryotes. BMC Bioinformatics 2011; 12:121. [PMID: 21521517 PMCID: PMC3113936 DOI: 10.1186/1471-2105-12-121] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Accepted: 04/26/2011] [Indexed: 12/31/2022] Open
Abstract
Background In prokaryotes, transcription and translation are dynamically coupled, as the latter starts before the former is complete. Also, from one transcript, several translation events occur in parallel. To study how events in transcription elongation affect translation elongation and fluctuations in protein levels, we propose a delayed stochastic model of prokaryotic transcription and translation at the nucleotide and codon level that includes the promoter open complex formation and alternative pathways to elongation, namely pausing, arrests, editing, pyrophosphorolysis, RNA polymerase traffic, and premature termination. Stepwise translation can start after the ribosome binding site is formed and accounts for variable codon translation rates, ribosome traffic, back-translocation, drop-off, and trans-translation. Results First, we show that the model accurately matches measurements of sequence-dependent translation elongation dynamics. Next, we characterize the degree of coupling between fluctuations in RNA and protein levels, and its dependence on the rates of transcription and translation initiation. Finally, modeling sequence-specific transcriptional pauses, we find that these affect protein noise levels. Conclusions For parameter values within realistic intervals, transcription and translation are found to be tightly coupled in Escherichia coli, as the noise in protein levels is mostly determined by the underlying noise in RNA levels. Sequence-dependent events in transcription elongation, e.g. pauses, are found to cause tangible effects in the degree of fluctuations in protein levels.
Collapse
Affiliation(s)
- Jarno Mäkelä
- Computational Systems Biology Research Group, Department of Signal Processing, Tampere University of Technology, FI-33101 Tampere, Finland
| | | | | | | |
Collapse
|
42
|
Clarke TE, Romanov V, Lam R, Gothe SA, Peddi SR, Razumova EB, Lipman RSA, Branstrom AA, Chirgadze NY. Structure of Francisella tularensis peptidyl-tRNA hydrolase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:446-9. [PMID: 21505237 PMCID: PMC3080146 DOI: 10.1107/s174430911100515x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Accepted: 02/11/2011] [Indexed: 11/11/2022]
Abstract
The rational design of novel antibiotics for bacteria involves the identification of inhibitors for enzymes involved in essential biochemical pathways in cells. In this study, the cloning, expression, purification, crystallization and structure of the enzyme peptidyl-tRNA hydrolase from Francisella tularensis, the causative agent of tularemia, was performed. The structure of F. tularensis peptidyl-tRNA hydrolase is comparable to those of other bacterial peptidyl-tRNA hydrolases, with most residues in the active site conserved amongst the family. The resultant reagents, structural data and analyses provide essential information for the structure-based design of novel inhibitors for this class of proteins.
Collapse
Affiliation(s)
- Teresa E. Clarke
- Division of Cancer Genomics and Proteomics, Ontario Cancer Institute, University Health Network, MBRC 5th Floor, 200 Elizabeth Street, Toronto, Ontario M5G 2C4, Canada
- NEXTEX Technologies Inc., Toronto, Ontario M4N 1W6, Canada
| | - Vladimir Romanov
- Division of Cancer Genomics and Proteomics, Ontario Cancer Institute, University Health Network, MBRC 5th Floor, 200 Elizabeth Street, Toronto, Ontario M5G 2C4, Canada
- NEXTEX Technologies Inc., Toronto, Ontario M4N 1W6, Canada
| | - Robert Lam
- Division of Cancer Genomics and Proteomics, Ontario Cancer Institute, University Health Network, MBRC 5th Floor, 200 Elizabeth Street, Toronto, Ontario M5G 2C4, Canada
- NEXTEX Technologies Inc., Toronto, Ontario M4N 1W6, Canada
| | - Scott A. Gothe
- PTC Therapeutics Inc., 100 Corporate Court, South Plainfield, NJ 07080-2449, USA
| | - Srinivasa R. Peddi
- PTC Therapeutics Inc., 100 Corporate Court, South Plainfield, NJ 07080-2449, USA
| | | | - Richard S. A. Lipman
- PTC Therapeutics Inc., 100 Corporate Court, South Plainfield, NJ 07080-2449, USA
| | - Arthur A. Branstrom
- PTC Therapeutics Inc., 100 Corporate Court, South Plainfield, NJ 07080-2449, USA
| | - Nickolay Y. Chirgadze
- Division of Cancer Genomics and Proteomics, Ontario Cancer Institute, University Health Network, MBRC 5th Floor, 200 Elizabeth Street, Toronto, Ontario M5G 2C4, Canada
- NEXTEX Technologies Inc., Toronto, Ontario M4N 1W6, Canada
- Department of Pharmacology and Toxicology, University of Toronto, 1 King’s College Circle, Toronto, Ontario M5S 1A8, Canada
| |
Collapse
|
43
|
Kang TJ, Hayashi Y, Suga H. Synthesis of the Backbone Cyclic Peptide Sunflower Trypsin Inhibitor-1 Promoted by the Induced Peptidyl-tRNA Drop-off. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201006963] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
44
|
Kang TJ, Hayashi Y, Suga H. Synthesis of the backbone cyclic peptide sunflower trypsin inhibitor-1 promoted by the induced peptidyl-tRNA drop-off. Angew Chem Int Ed Engl 2011; 50:2159-61. [PMID: 21344575 DOI: 10.1002/anie.201006963] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2010] [Indexed: 11/07/2022]
Affiliation(s)
- Taek Jin Kang
- Department of Chemical and Biochemical Engineering, Dongguk University-Seoul, Seoul 100-715, South Korea.
| | | | | |
Collapse
|
45
|
de Longevialle AF, Small ID, Lurin C. Nuclearly encoded splicing factors implicated in RNA splicing in higher plant organelles. MOLECULAR PLANT 2010; 3:691-705. [PMID: 20603383 DOI: 10.1093/mp/ssq025] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Plant organelles arose from two independent endosymbiosis events. Throughout evolutionary history, tight control of chloroplasts and mitochondria has been gained by the nucleus, which regulates most steps of organelle genome expression and metabolism. In particular, RNA maturation, including RNA splicing, is highly dependent on nuclearly encoded splicing factors. Most introns in organelles are group II introns, whose catalytic mechanism closely resembles that of the nuclear spliceosome. Plant group II introns have lost the ability to self-splice in vivo and require nuclearly encoded proteins as cofactors. Since the first splicing factor was identified in chloroplasts more than 10 years ago, many other proteins have been shown to be involved in splicing of one or more introns in chloroplasts or mitochondria. These new proteins belong to a variety of different families of RNA binding proteins and provide new insights into ribonucleo-protein complexes and RNA splicing machineries in organelles. In this review, we describe how splicing factors, encoded by the nucleus and targeted to the organelles, take part in post-transcriptional steps in higher plant organelle gene expression. We go on to discuss the potential for these factors to regulate organelle gene expression.
Collapse
Affiliation(s)
- Andéol Falcon de Longevialle
- Unité Mixte de Recherche en Génomique Végétale (Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique/Université d'Evry Val d'Essonne), 91057 Evry, France
| | | | | |
Collapse
|
46
|
Zhang G, Fedyunin I, Miekley O, Valleriani A, Moura A, Ignatova Z. Global and local depletion of ternary complex limits translational elongation. Nucleic Acids Res 2010; 38:4778-87. [PMID: 20360046 PMCID: PMC2919707 DOI: 10.1093/nar/gkq196] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The translation of genetic information according to the sequence of the mRNA template occurs with high accuracy and fidelity. Critical events in each single step of translation are selection of transfer RNA (tRNA), codon reading and tRNA-regeneration for a new cycle. We developed a model that accurately describes the dynamics of single elongation steps, thus providing a systematic insight into the sensitivity of the mRNA translation rate to dynamic environmental conditions. Alterations in the concentration of the aminoacylated tRNA can transiently stall the ribosomes during translation which results, as suggested by the model, in two outcomes: either stress-induced change in the tRNA availability triggers the premature termination of the translation and ribosomal dissociation, or extensive demand for one tRNA species results in a competition between frameshift to an aberrant open-reading frame and ribosomal drop-off. Using the bacterial Escherichia coli system, we experimentally draw parallels between these two possible mechanisms.
Collapse
Affiliation(s)
- Gong Zhang
- Biochemistry, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | | | | | | | | | | |
Collapse
|
47
|
Wydau S, van der Rest G, Aubard C, Plateau P, Blanquet S. Widespread distribution of cell defense against D-aminoacyl-tRNAs. J Biol Chem 2009; 284:14096-104. [PMID: 19332551 DOI: 10.1074/jbc.m808173200] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Several l-aminoacyl-tRNA synthetases can transfer a d-amino acid onto their cognate tRNA(s). This harmful reaction is counteracted by the enzyme d-aminoacyl-tRNA deacylase. Two distinct deacylases were already identified in bacteria (DTD1) and in archaea (DTD2), respectively. Evidence was given that DTD1 homologs also exist in nearly all eukaryotes, whereas DTD2 homologs occur in plants. On the other hand, several bacteria, including most cyanobacteria, lack genes encoding a DTD1 homolog. Here we show that Synechocystis sp. PCC6803 produces a third type of deacylase (DTD3). Inactivation of the corresponding gene (dtd3) renders the growth of Synechocystis sp. hypersensitive to the presence of d-tyrosine. Based on the available genomes, DTD3-like proteins are predicted to occur in all cyanobacteria. Moreover, one or several dtd3-like genes can be recognized in all cellular types, arguing in favor of the nearubiquity of an enzymatic function involved in the defense of translational systems against invasion by d-amino acids.
Collapse
Affiliation(s)
- Sandra Wydau
- Laboratoire de Biochimie and Laboratoire des Mécanismes Réactionnels, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
| | | | | | | | | |
Collapse
|
48
|
Kipper K, Hetényi C, Sild S, Remme J, Liiv A. Ribosomal Intersubunit Bridge B2a Is Involved in Factor-Dependent Translation Initiation and Translational Processivity. J Mol Biol 2009; 385:405-22. [DOI: 10.1016/j.jmb.2008.10.065] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2008] [Revised: 10/14/2008] [Accepted: 10/15/2008] [Indexed: 10/21/2022]
|
49
|
Complementary roles of initiation factor 1 and ribosome recycling factor in 70S ribosome splitting. EMBO J 2008; 27:1706-17. [PMID: 18497739 DOI: 10.1038/emboj.2008.99] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2008] [Accepted: 04/28/2008] [Indexed: 11/09/2022] Open
Abstract
We demonstrate that ribosomes containing a messenger RNA (mRNA) with a strong Shine-Dalgarno sequence are rapidly split into subunits by initiation factors 1 (IF1) and 3 (IF3), but slowly split by ribosome recycling factor (RRF) and elongation factor G (EF-G). Post-termination-like (PTL) ribosomes containing mRNA and a P-site-bound deacylated transfer RNA (tRNA) are split very rapidly by RRF and EF-G, but extremely slowly by IF1 and IF3. Vacant ribosomes are split by RRF/EF-G much more slowly than PTL ribosomes and by IF1/IF3 much more slowly than mRNA-containing ribosomes. These observations reveal complementary splitting of different ribosomal complexes by IF1/IF3 and RRF/EF-G, and suggest the existence of two major pathways for ribosome splitting into subunits in the living cell. We show that the identity of the deacylated tRNA in the PTL ribosome strongly affects the rate by which it is split by RRF/EF-G and that IF3 is involved in the mechanism of ribosome splitting by IF1/IF3 but not by RRF/EF-G. With support from our experimental data, we discuss the principally different mechanisms of ribosome splitting by IF1/IF3 and by RRF/EF-G.
Collapse
|
50
|
Pulavarti S, Jain A, Prakash Pathak P, Mahmood A, Arora A. Solution Structure and Dynamics of Peptidyl-tRNA Hydrolase from Mycobacterium tuberculosis H37Rv. J Mol Biol 2008; 378:165-77. [DOI: 10.1016/j.jmb.2008.02.027] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2007] [Revised: 01/15/2008] [Accepted: 02/14/2008] [Indexed: 11/28/2022]
|