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Chadani Y, Kanamori T, Niwa T, Ichihara K, Nakayama KI, Matsumoto A, Taguchi H. Mechanistic dissection of premature translation termination induced by acidic residues-enriched nascent peptide. Cell Rep 2023; 42:113569. [PMID: 38071619 DOI: 10.1016/j.celrep.2023.113569] [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: 08/14/2023] [Revised: 10/18/2023] [Accepted: 11/24/2023] [Indexed: 12/30/2023] Open
Abstract
Ribosomes polymerize nascent peptides through repeated inter-subunit rearrangements between the classic and hybrid states. The peptidyl-tRNA, the intermediate species during translation elongation, stabilizes the translating ribosome to ensure robust continuity of elongation. However, the translation of acidic residue-rich sequences destabilizes the ribosome, leading to a stochastic premature translation cessation termed intrinsic ribosome destabilization (IRD), which is still ill-defined. Here, we dissect the molecular mechanisms underlying IRD in Escherichia coli. Reconstitution of the IRD event reveals that (1) the prolonged ribosome stalling enhances IRD-mediated translation discontinuation, (2) IRD depends on temperature, (3) the destabilized 70S ribosome complex is not necessarily split, and (4) the destabilized ribosome is subjected to peptidyl-tRNA hydrolase-mediated hydrolysis of the peptidyl-tRNA without subunit splitting or recycling factors-mediated subunit splitting. Collectively, our data indicate that the translation of acidic-rich sequences alters the conformation of the 70S ribosome to an aberrant state that allows the noncanonical premature termination.
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Affiliation(s)
- Yuhei Chadani
- Faculty of Environmental, Life, Natural Science and Technology, Okayama University, Okayama 700-8530, Japan.
| | | | - Tatsuya Niwa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan; School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Kazuya Ichihara
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Keiichi I Nakayama
- Anticancer Strategies Laboratory, TMDU Advanced Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan; Division of Cell Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Akinobu Matsumoto
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Hideki Taguchi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan; School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8503, Japan.
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2
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Nagao A, Nakanishi Y, Yamaguchi Y, Mishina Y, Karoji M, Toya T, Fujita T, Iwasaki S, Miyauchi K, Sakaguchi Y, Suzuki T. Quality control of protein synthesis in the early elongation stage. Nat Commun 2023; 14:2704. [PMID: 37198183 PMCID: PMC10192219 DOI: 10.1038/s41467-023-38077-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 04/14/2023] [Indexed: 05/19/2023] Open
Abstract
In the early stage of bacterial translation, peptidyl-tRNAs frequently dissociate from the ribosome (pep-tRNA drop-off) and are recycled by peptidyl-tRNA hydrolase. Here, we establish a highly sensitive method for profiling of pep-tRNAs using mass spectrometry, and successfully detect a large number of nascent peptides from pep-tRNAs accumulated in Escherichia coli pthts strain. Based on molecular mass analysis, we found about 20% of the peptides bear single amino-acid substitutions of the N-terminal sequences of E. coli ORFs. Detailed analysis of individual pep-tRNAs and reporter assay revealed that most of the substitutions take place at the C-terminal drop-off site and that the miscoded pep-tRNAs rarely participate in the next round of elongation but dissociate from the ribosome. These findings suggest that pep-tRNA drop-off is an active mechanism by which the ribosome rejects miscoded pep-tRNAs in the early elongation, thereby contributing to quality control of protein synthesis after peptide bond formation.
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Affiliation(s)
- Asuteka Nagao
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan.
| | - Yui Nakanishi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Yutaro Yamaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Yoshifumi Mishina
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Minami Karoji
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Takafumi Toya
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Tomoya Fujita
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan
| | - Kenjyo Miyauchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Yuriko Sakaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan.
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3
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tRNA methylation resolves codon usage bias at the limit of cell viability. Cell Rep 2022; 41:111539. [PMID: 36288695 PMCID: PMC9643105 DOI: 10.1016/j.celrep.2022.111539] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/31/2022] [Accepted: 09/29/2022] [Indexed: 11/21/2022] Open
Abstract
Codon usage of each genome is closely correlated with the abundance of tRNA isoacceptors. How codon usage bias is resolved by tRNA post-transcriptional modifications is largely unknown. Here we demonstrate that the N1-methylation of guanosine at position 37 (m1G37) on the 3′-side of the anticodon, while not directly responsible for reading of codons, is a neutralizer that resolves differential decoding of proline codons. A genome-wide suppressor screen of a non-viable Escherichia coli strain, lacking m1G37, identifies proS suppressor mutations, indicating a coupling of methylation with tRNA prolyl-aminoacylation that sets the limit of cell viability. Using these suppressors, where prolyl-aminoacylation is decoupled from tRNA methylation, we show that m1G37 neutralizes differential translation of proline codons by the major isoacceptor. Lack of m1G37 inactivates this neutralization and exposes the need for a minor isoacceptor for cell viability. This work has medical implications for bacterial species that exclusively use the major isoacceptor for survival. Masuda et al. show that loss of m1G37 from the 3′ side of the tRNA anticodon renders a modified wobble nucleotide of the anticodon insufficient to decode a set of rare codons, providing a functional underpinning for the “modification circuit” between position 37 and the wobble position of the tRNA anticodon.
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4
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Minigene as a Novel Regulatory Element in Toxin-Antitoxin Systems. Int J Mol Sci 2021; 22:ijms222413389. [PMID: 34948189 PMCID: PMC8708949 DOI: 10.3390/ijms222413389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 12/05/2022] Open
Abstract
The axe-txe type II toxin-antitoxin (TA) system is characterized by a complex and multilayered mode of gene expression regulation. Precise and tight control of this process is crucial to keep the toxin in an appropriate balance with the cognate antitoxin until its activation is needed for the cell. In this report, we provide evidence that a minigene encoded within the axe-txe operon influences translation of the Txe toxin. This is the first example to date of such a regulatory mechanism identified in the TA modules. Here, in a series of genetic studies, we employed translational reporter gene fusions to establish the molecular basis of this phenomenon. Our results show that translation of the two-codon mini-ORF displays an in cis mode of action, and positively affects the expression of txe, possibly by increasing its mRNA stability through protection from an endonuclease attack. Moreover, we established that the reading frame in which the two cistrons are encoded, as well as the distance between them, are critical parameters that affect the level of such regulation. In addition, by searching for two-codon ORFs we found sequences of several potential minigenes in the leader sequences of several other toxins belonging to the type II TA family. These findings suggest that this type of gene regulation may not only apply for the axe-txe cassette, but could be more widespread among other TA systems.
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5
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Yang J, Han YH, Im J, Seo SW. Synthetic protein quality control to enhance full-length translation in bacteria. Nat Chem Biol 2021; 17:421-427. [PMID: 33542534 DOI: 10.1038/s41589-021-00736-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 01/08/2021] [Indexed: 01/30/2023]
Abstract
Coupled transcription and translation processes in bacteria cause indiscriminate translation of intact and truncated messenger RNAs, inevitably generating nonfunctional polypeptides. Here, we devised a synthetic protein quality control (ProQC) system that enables translation only when both ends of mRNAs are present and followed by circularization based on sequence-specific RNA-RNA hybridization. We demonstrate that the ProQC system dramatically improved the fraction of full-length proteins among all synthesized polypeptides by selectively translating intact mRNA and reducing abortive translation. As a result, full-length protein synthesis increased up to 2.5-fold without changing the transcription or translation efficiency. Furthermore, we applied the ProQC system for 3-hydroxypropionic acid, violacein and lycopene production by ensuring full-length expression of enzymes in biosynthetic pathways, resulting in 1.6- to 2.3-fold greater biochemical production. We believe that our ProQC system can be universally applied to improve not only the quality of recombinant protein production but also efficiencies of metabolic pathways.
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Affiliation(s)
- Jina Yang
- School of Chemical and Biological Engineering, Seoul National University, Seoul, Korea.,Institute of Chemical Processes, Seoul National University, Seoul, Korea
| | - Yong Hee Han
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, Korea
| | - Jongwon Im
- School of Chemical and Biological Engineering, Seoul National University, Seoul, Korea
| | - Sang Woo Seo
- School of Chemical and Biological Engineering, Seoul National University, Seoul, Korea. .,Institute of Chemical Processes, Seoul National University, Seoul, Korea. .,Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, Korea. .,Bio-MAX Institute, Seoul National University, Seoul, Korea. .,Institute of Engineering Research, Seoul National University, Seoul, Korea.
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6
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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: 36] [Impact Index Per Article: 12.0] [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.
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Affiliation(s)
| | | | - Daniel N. Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
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7
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Pavlov MY, Ehrenberg M. Substrate-Induced Formation of Ribosomal Decoding Center for Accurate and Rapid Genetic Code Translation. Annu Rev Biophys 2019; 47:525-548. [PMID: 29792818 DOI: 10.1146/annurev-biophys-060414-034148] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Accurate translation of genetic information is crucial for synthesis of functional proteins in all organisms. We use recent experimental data to discuss how induced fit affects accuracy of initial codon selection on the ribosome by aminoacyl transfer RNA in ternary complex ( T3) with elongation factor Tu (EF-Tu) and guanosine-5'-triphosphate (GTP). We define actual accuracy ([Formula: see text]) of a particular protein synthesis system as its current accuracy and the effective selectivity ([Formula: see text]) as [Formula: see text] in the limit of zero ribosomal binding affinity for T3. Intrinsic selectivity ([Formula: see text]), defined as the upper thermodynamic limit of [Formula: see text], is determined by the free energy difference between near-cognate and cognate T3 in the pre-GTP hydrolysis state on the ribosome. [Formula: see text] is much larger than [Formula: see text], suggesting the possibility of a considerable increase in [Formula: see text] and [Formula: see text] at negligible kinetic cost. Induced fit increases [Formula: see text] and [Formula: see text] without affecting [Formula: see text], and aminoglycoside antibiotics reduce [Formula: see text] and [Formula: see text] at unaltered [Formula: see text].
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Affiliation(s)
- Michael Y Pavlov
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 75124, Sweden;
| | - Måns Ehrenberg
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 75124, Sweden;
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8
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Reiterative Synthesis by the Ribosome and Recognition of the N-Terminal Formyl Group by Biosynthetic Machinery Contribute to Evolutionary Conservation of the Length of Antibiotic Microcin C Peptide Precursor. mBio 2019; 10:mBio.00768-19. [PMID: 31040244 PMCID: PMC6495379 DOI: 10.1128/mbio.00768-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli microcin C (McC) is a representative member of peptide-nucleotide antibiotics produced by diverse microorganisms. The vast majority of biosynthetic gene clusters responsible for McC-like compound production encode 7-amino-acid-long precursor peptides, which are C-terminally modified by dedicated biosynthetic enzymes with a nucleotide moiety to produce a bioactive compound. In contrast, the sequences of McC-like compound precursor peptides are not conserved. Here, we studied the consequences of E. coli McC precursor peptide length increase on antibiotic production and activity. We show that increasing the precursor peptide length strongly decreases McC production by affecting multiple biosynthetic steps, suggesting that the McC biosynthesis system has evolved under significant functional constraints to maintain the precursor peptide length. Microcin C (McC) is a peptide adenylate antibiotic produced by Escherichiacoli cells bearing a plasmid-borne mcc gene cluster. Most MccA precursors, encoded by validated mcc operons from diverse bacteria, are 7 amino acids long, but the significance of this precursor length conservation has remained unclear. Here, we created derivatives of E. colimcc operons encoding longer precursors and studied their synthesis and bioactivities. We found that increasing the precursor length to 11 amino acids and beyond strongly decreased antibiotic production. We found this decrease to depend on several parameters. First, reiterative synthesis of the MccA peptide by the ribosome was decreased at longer mccA open reading frames, leading to less efficient competition with other messenger RNAs. Second, the presence of a formyl group at the N-terminal methionine of the heptameric peptide had a strong stimulatory effect on adenylation by the MccB enzyme. No such formyl group stimulation was observed for longer peptides. Finally, the presence of the N-terminal formyl on the heptapeptide adenylate stimulated bioactivity, most likely at the uptake stage. Together, these factors should contribute to optimal activity of McC-like compounds as 7-amino-acid peptide moieties and suggest convergent evolution of several steps of the antibiotic biosynthesis pathway and their adjustment to sensitive cell uptake machinery to create a potent drug.
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9
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Doerr A, de Reus E, van Nies P, van der Haar M, Wei K, Kattan J, Wahl A, Danelon C. Modelling cell-free RNA and protein synthesis with minimal systems. Phys Biol 2019; 16:025001. [DOI: 10.1088/1478-3975/aaf33d] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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10
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Cambray G, Guimaraes JC, Arkin AP. Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in Escherichia coli. Nat Biotechnol 2018; 36:1005-1015. [DOI: 10.1038/nbt.4238] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 08/02/2018] [Indexed: 01/01/2023]
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11
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Burks GL, McFeeters H, McFeeters RL. Expression, purification, and buffer solubility optimization of the putative human peptidyl-tRNA hydrolase PTRHD1. Protein Expr Purif 2016; 126:49-54. [DOI: 10.1016/j.pep.2016.05.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Revised: 05/16/2016] [Accepted: 05/23/2016] [Indexed: 11/24/2022]
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12
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Beck HJ, Fleming IMC, Janssen GR. 5'-Terminal AUGs in Escherichia coli mRNAs with Shine-Dalgarno Sequences: Identification and Analysis of Their Roles in Non-Canonical Translation Initiation. PLoS One 2016; 11:e0160144. [PMID: 27467758 PMCID: PMC4965119 DOI: 10.1371/journal.pone.0160144] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 07/14/2016] [Indexed: 01/18/2023] Open
Abstract
Analysis of the Escherichia coli transcriptome identified a unique subset of messenger RNAs (mRNAs) that contain a conventional untranslated leader and Shine-Dalgarno (SD) sequence upstream of the gene’s start codon while also containing an AUG triplet at the mRNA’s 5’- terminus (5’-uAUG). Fusion of the coding sequence specified by the 5’-terminal putative AUG start codon to a lacZ reporter gene, as well as primer extension inhibition assays, reveal that the majority of the 5’-terminal upstream open reading frames (5’-uORFs) tested support some level of lacZ translation, indicating that these mRNAs can function both as leaderless and canonical SD-leadered mRNAs. Although some of the uORFs were expressed at low levels, others were expressed at levels close to that of the respective downstream genes and as high as the naturally leaderless cI mRNA of bacteriophage λ. These 5’-terminal uORFs potentially encode peptides of varying lengths, but their functions, if any, are unknown. In an effort to determine whether expression from the 5’-terminal uORFs impact expression of the immediately downstream cistron, we examined expression from the downstream coding sequence after mutations were introduced that inhibit efficient 5’-uORF translation. These mutations were found to affect expression from the downstream cistrons to varying degrees, suggesting that some 5’-uORFs may play roles in downstream regulation. Since the 5’-uAUGs found on these conventionally leadered mRNAs can function to bind ribosomes and initiate translation, this indicates that canonical mRNAs containing 5’-uAUGs should be examined for their potential to function also as leaderless mRNAs.
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Affiliation(s)
- Heather J Beck
- Department of Microbiology, Miami University, Oxford, Ohio, United States of America
| | - Ian M C Fleming
- Department of Microbiology, Miami University, Oxford, Ohio, United States of America
| | - Gary R Janssen
- Department of Microbiology, Miami University, Oxford, Ohio, United States of America
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13
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Kushwaha M, Salis HM. A portable expression resource for engineering cross-species genetic circuits and pathways. Nat Commun 2015; 6:7832. [PMID: 26184393 PMCID: PMC4518296 DOI: 10.1038/ncomms8832] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 06/16/2015] [Indexed: 12/24/2022] Open
Abstract
Genetic circuits and metabolic pathways can be reengineered to allow organisms to process signals and manufacture useful chemicals. However, their functions currently rely on organism-specific regulatory parts, fragmenting synthetic biology and metabolic engineering into host-specific domains. To unify efforts, here we have engineered a cross-species expression resource that enables circuits and pathways to reuse the same genetic parts, while functioning similarly across diverse organisms. Our engineered system combines mixed feedback control loops and cross-species translation signals to autonomously self-regulate expression of an orthogonal polymerase without host-specific promoters, achieving nontoxic and tuneable gene expression in diverse Gram-positive and Gram-negative bacteria. Combining 50 characterized system variants with mechanistic modelling, we show how the cross-species expression resource's dynamics, capacity and toxicity are controlled by the control loops' architecture and feedback strengths. We also demonstrate one application of the resource by reusing the same genetic parts to express a biosynthesis pathway in both model and non-model hosts. Organism-specific genetic parts are often used to express circuits and pathways, limiting their portability. Here the authors engineer a cross-species expression resource, without using host-specific parts, to control protein and pathway expression in non-model bacteria.
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Affiliation(s)
- Manish Kushwaha
- Department of Biological Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Howard M Salis
- 1] Department of Biological Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, USA [2] Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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14
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O’Connor M. Interactions of release factor RF3 with the translation machinery. Mol Genet Genomics 2015; 290:1335-44. [DOI: 10.1007/s00438-015-0994-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 01/09/2015] [Indexed: 10/24/2022]
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15
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Wang Y, Xiao M, Li Y. Heterogeneity of single molecule FRET signals reveals multiple active ribosome subpopulations. Proteins 2013; 82:1-9. [PMID: 23609951 DOI: 10.1002/prot.24308] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 03/28/2013] [Accepted: 04/03/2013] [Indexed: 11/06/2022]
Abstract
Single molecule methods have revealed that heterogeneity is common in biological systems. However, interpretations of the complex signals are challenging. By tracking the fluorescence resonance energy transfer (FRET) signals between the A-site tRNA and L27 protein in single ribosomes, we attempt to develop a qualitative method to subtract the inherent patterns of the heterogeneous single molecule FRET data. Seven ribosome subpopulations are identified using this method and spontaneous exchanges among these subpopulations are observed. All of the pretranslocation subpopulations are competent in real-time translocation, but via distinguished pathways. These observations suggest that the ribosome may function through multiple reaction pathways.
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Affiliation(s)
- Yuhong Wang
- Department of Biology and Biochemistry, University of Houston, 4800 Calhoun Rd, Houston, Texas, 77214
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16
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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]
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17
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Gilchrist MA, Shah P, Zaretzki R. Measuring and detecting molecular adaptation in codon usage against nonsense errors during protein translation. Genetics 2009; 183:1493-505. [PMID: 19822731 PMCID: PMC2787434 DOI: 10.1534/genetics.109.108209] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Accepted: 09/26/2009] [Indexed: 11/18/2022] Open
Abstract
Codon usage bias (CUB) has been documented across a wide range of taxa and is the subject of numerous studies. While most explanations of CUB invoke some type of natural selection, most measures of CUB adaptation are heuristically defined. In contrast, we present a novel and mechanistic method for defining and contextualizing CUB adaptation to reduce the cost of nonsense errors during protein translation. Using a model of protein translation, we develop a general approach for measuring the protein production cost in the face of nonsense errors of a given allele as well as the mean and variance of these costs across its coding synonyms. We then use these results to define the nonsense error adaptation index (NAI) of the allele or a contiguous subset thereof. Conceptually, the NAI value of an allele is a relative measure of its elevation on a specific and well-defined adaptive landscape. To illustrate its utility, we calculate NAI values for the entire coding sequence and across a set of nonoverlapping windows for each gene in the Saccharomyces cerevisiae S288c genome. Our results provide clear evidence of adaptation to reduce the cost of nonsense errors and increasing adaptation with codon position and expression. The magnitude and nature of this adaptation are also largely consistent with simulation results in which nonsense errors are the only selective force driving CUB evolution. Because NAI is derived from mechanistic models, it is both easier to interpret and more amenable to future refinement than other commonly used measures of codon bias. Further, our approach can also be used as a starting point for developing other mechanistically derived measures of adaptation such as for translational accuracy.
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Affiliation(s)
- Michael A Gilchrist
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee 37996-1610, USA.
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18
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Janssen BD, Hayes CS. Kinetics of paused ribosome recycling in Escherichia coli. J Mol Biol 2009; 394:251-67. [PMID: 19761774 DOI: 10.1016/j.jmb.2009.09.020] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2009] [Revised: 08/09/2009] [Accepted: 09/09/2009] [Indexed: 11/29/2022]
Abstract
The bacterial tmRNA.SmpB system recycles stalled translation complexes in a process termed 'ribosome rescue.' tmRNA.SmpB specifically recognizes ribosomes that are paused at or near the 3' end of truncated mRNA; therefore, nucleolytic mRNA processing is required before paused ribosomes can be rescued from full-length transcripts. Here, we examine the recycling of ribosomes paused on both full-length and truncated mRNAs. Peptidyl-tRNAs corresponding to each paused translation complex were identified, and their turnover kinetics was used to estimate the half-lives of paused ribosomes in vivo. Ribosomes were paused at stop codons on full-length mRNA using a nascent peptide motif that interferes with translation termination and elicits tmRNA.SmpB activity. Peptidyl-tRNA turnover from these termination-paused ribosomes was slightly more rapid in tmRNA(+) cells (T(1/2)=22+/-2.2 s) than in DeltatmRNA cells (T(1/2)=32+/-1.6 s). Overexpression of release factor (RF) 1 greatly accelerated peptidyl-tRNA turnover from termination-paused ribosomes in both tmRNA(+) and DeltatmRNA cells, whereas other termination factors had little or no effect on recycling. In contrast to inefficient translation termination, ribosome recycling from truncated transcripts lacking in-frame stop codons was dramatically accelerated by tmRNA.SmpB. However, peptidyl-tRNA still turned over from nonstop-paused ribosomes at a significant rate (t(1/2)=61+/-7.3 s) in DeltatmRNA cells. Overexpression of RF-1, RF-3, and ribosome recycling factor in DeltatmRNA cells failed to accelerate ribosome recycling from nonstop mRNA. These results indicate that tmRNA.SmpB activity is rate limited by mRNA cleavage, and that RF-3 and ribosome recycling factor do not constitute a tmRNA-independent rescue pathway, as previously suggested. Peptidyl-tRNA turnover from nonstop-paused ribosomes in DeltatmRNA cells suggests the existence of another uncharacterized ribosome rescue pathway.
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Affiliation(s)
- Brian D Janssen
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106-9610, USA
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19
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Jacinto-Loeza E, Vivanco-Domínguez S, Guarneros G, Hernández-Sánchez J. Minigene-like inhibition of protein synthesis mediated by hungry codons near the start codon. Nucleic Acids Res 2008; 36:4233-41. [PMID: 18583364 PMCID: PMC2490762 DOI: 10.1093/nar/gkn395] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Rare AGA or AGG codons close to the initiation codon inhibit protein synthesis by a tRNA-sequestering mechanism as toxic minigenes do. To further understand this mechanism, a parallel analysis of protein synthesis and peptidyl-tRNA accumulation was performed using both a set of lacZ constructs where AGAAGA codons were moved codon by codon from +2, +3 up to +7, +8 positions and a series of 3–8 codon minigenes containing AGAAGA codons before the stop codon. β-Galactosidase synthesis from the AGAAGA lacZ constructs (in a Pth defective in vitro system without exogenous tRNA) diminished as the AGAAGA codons were closer to AUG codon. Likewise, β-galactosidase expression from the reporter +7 AGA lacZ gene (plus tRNA, 0.25 μg/μl) waned as the AGAAGAUAA minigene shortened. Pth counteracted both the length-dependent minigene effect on the expression of β-galactosidase from the +7 AGA lacZ reporter gene and the positional effect from the AGAAGA lacZ constructs. The +2, +3 AGAAGA lacZ construct and the shortest +2, +3 AGAAGAUAA minigene accumulated the highest percentage of peptidyl-tRNAArg4. These observations lead us to propose that hungry codons at early positions, albeit with less strength, inhibit protein synthesis by a minigene-like mechanism involving accumulation of peptidyl-tRNA.
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Affiliation(s)
- Eva Jacinto-Loeza
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 14-740, México DF, 07000, México
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20
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Delgado-Olivares L, Zamora-Romo E, Guarneros G, Hernandez-Sanchez J. Codon-specific and general inhibition of protein synthesis by the tRNA-sequestering minigenes. Biochimie 2006; 88:793-800. [PMID: 16488066 DOI: 10.1016/j.biochi.2006.01.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2005] [Accepted: 01/10/2006] [Indexed: 11/21/2022]
Abstract
The expression of minigenes in bacteria inhibits protein synthesis and cell growth. Presumably, the translating ribosomes, harboring the peptides as peptidyl-tRNAs, pause at the last sense codon of the minigene directed mRNAs. Eventually, the peptidyl-tRNAs drop off and, under limiting activity of peptidyl-tRNA hydrolase, accumulate in the cells reducing the concentration of specific aminoacylable tRNA. Therefore, the extent of inhibition is associated with the rate of starvation for a specific tRNA. Here, we used minigenes harboring various last sense codons that sequester specific tRNAs with different efficiency, to inhibit the translation of reporter genes containing, or not, these codons. A prompt inhibition of the protein synthesis directed by genes containing the codons starved for their cognate tRNA (hungry codons) was observed. However, a non-specific in vitro inhibition of protein synthesis, irrespective of the codon composition of the gene, was also evident. The degree of inhibition correlated directly with the number of hungry codons in the gene. Furthermore, a tRNA(Arg4)-sequestering minigene promoted the production of an incomplete beta-galactosidase polypeptide interrupted, during bacterial polypeptide chain elongation at sites where AGA codons were inserted in the lacZ gene suggesting ribosome pausing at the hungry codons.
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MESH Headings
- Base Sequence
- Codon/genetics
- Codon, Terminator/genetics
- Escherichia coli/genetics
- Lac Operon/genetics
- Peptide Chain Termination, Translational/genetics
- Plasmids/genetics
- Protein Biosynthesis/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- RNA, Transfer, Amino Acyl/genetics
- RNA, Transfer, Amino Acyl/metabolism
- Ribosomes/genetics
- Ribosomes/metabolism
- beta-Galactosidase/metabolism
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Affiliation(s)
- Luis Delgado-Olivares
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 14-740, México DF 07000, Mexico
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21
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Jin H, Zhao Q, Gonzalez de Valdivia EI, Ardell DH, Stenström M, Isaksson LA. Influences on gene expression in vivo by a Shine-Dalgarno sequence. Mol Microbiol 2006; 60:480-92. [PMID: 16573696 DOI: 10.1111/j.1365-2958.2006.05110.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Shine-Dalgarno (SD+: 5'-AAGGAGG-3') sequence anchors the mRNA by base pairing to the 16S rRNA in the small ribosomal subunit during translation initiation. We have here compared how an SD+ sequence influences gene expression, if located upstream or downstream of an initiation codon. The positive effect of an upstream SD+ is confirmed. A downstream SD+ gives decreased gene expression. This effect is also valid for appropriately modified natural Escherichia coli genes. If an SD+ is placed between two potential initiation codons, initiation takes place predominantly at the second start site. The first start site is activated if the distance between this site and the downstream SD+ is enlarged and/or if the second start site is weakened. Upstream initiation is eliminated if a stable stem-loop structure is placed between this SD+ and the upstream start site. The results suggest that the two start sites compete for ribosomes that bind to an SD+ located between them. A minor positive contribution to upstream initiation resulting from 3' to 5' ribosomal diffusion along the mRNA is suggested. Analysis of the E. coli K12 genome suggests that the SD+ or SD-like sequences are systematically avoided in the early coding region suggesting an evolutionary significance.
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MESH Headings
- Base Sequence
- Binding Sites
- Codon, Initiator/genetics
- Codon, Initiator/metabolism
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression Regulation, Bacterial
- Genes, Bacterial/genetics
- Genes, Reporter
- Molecular Sequence Data
- Nucleic Acid Conformation
- Protein Biosynthesis/genetics
- RNA, Bacterial/metabolism
- RNA, Messenger/metabolism
- RNA, Ribosomal, 16S/metabolism
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/metabolism
- Ribosomes/metabolism
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Affiliation(s)
- Haining Jin
- Department of Genetics, Microbiology and Toxicology, Stockholm University, S-106 91 Stockholm, Sweden
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22
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Gilchrist MA, Wagner A. A model of protein translation including codon bias, nonsense errors, and ribosome recycling. J Theor Biol 2006; 239:417-34. [PMID: 16171830 DOI: 10.1016/j.jtbi.2005.08.007] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2005] [Revised: 08/05/2005] [Accepted: 08/08/2005] [Indexed: 11/15/2022]
Abstract
We present and analyse a model of protein translation at the scale of an individual messenger RNA (mRNA) transcript. The model we develop is unique in that it incorporates the phenomena of ribosome recycling and nonsense errors. The model conceptualizes translation as a probabilistic wave of ribosome occupancy traveling down a heterogeneous medium, the mRNA transcript. Our results show that the heterogeneity of the codon translation rates along the mRNA results in short-scale spikes and dips in the wave. Nonsense errors attenuate this wave on a longer scale while ribosome recycling reinforces it. We find that the combination of nonsense errors and codon usage bias can have a large effect on the probability that a ribosome will completely translate a transcript. We also elucidate how these forces interact with ribosome recycling to determine the overall translation rate of an mRNA transcript. We derive a simple cost function for nonsense errors using our model and apply this function to the yeast (Saccharomyces cervisiae) genome. Using this function we are able to detect position dependent selection on codon bias which correlates with gene expression levels as predicted a priori. These results indirectly validate our underlying model assumptions and confirm that nonsense errors can play an important role in shaping codon usage bias.
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Affiliation(s)
- Michael A Gilchrist
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, 37996, USA.
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23
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Petersen CP, Bordeleau ME, Pelletier J, Sharp PA. Short RNAs Repress Translation after Initiation in Mammalian Cells. Mol Cell 2006; 21:533-42. [PMID: 16483934 DOI: 10.1016/j.molcel.2006.01.031] [Citation(s) in RCA: 499] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2005] [Revised: 11/22/2005] [Accepted: 01/30/2006] [Indexed: 12/13/2022]
Abstract
MicroRNAs (miRNAs) are predicted to regulate 30% of mammalian protein-encoding genes by interactions with their 3' untranslated regions (UTRs). We use partially complementary siRNAs to investigate the mechanism by which miRNAs mediate translational repression in human cells. Repressed mRNAs are associated with polyribosomes that are engaged in translation elongation, as shown by puromycin sensitivity. The inhibition appears to be postinitiation because translation driven by the cap-independent processes of HCV IRES and CrPV IRES is repressed by short RNAs. Further, metabolic labeling suggests that silencing occurs before completion of the nascent polypeptide chain. In addition, silencing by short RNAs causes a decrease in translational readthrough at a stop codon, and ribosomes on repressed mRNAs dissociate more rapidly after a block of initiation of translation than those on control mRNAs. These results suggest that repression by short RNAs, and thus probably miRNAs, is primarily due to ribosome drop off during elongation of translation.
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Affiliation(s)
- Christian P Petersen
- Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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24
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Gonzalez de Valdivia EI, Isaksson LA. Abortive translation caused by peptidyl-tRNA drop-off at NGG codons in the early coding region of mRNA. FEBS J 2005; 272:5306-16. [PMID: 16218960 DOI: 10.1111/j.1742-4658.2005.04926.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
In Escherichia coli the codons CGG, AGG, UGG or GGG (NGG codons) but not GGN or GNG (where N is non-G) are associated with low expression of a reporter gene, if located at positions +2 to +5. Induction of a lacZ reporter gene with any one of the NGG codons at position +2 to +5 does not influence growth of a normal strain, but growth of a strain with a defective peptidyl-tRNA hydrolase (Pth) enzyme is inhibited. The same codons, if placed at position +7, did not give this effect. Other codons, such as CGU and AGA, at location +2 to +5, did not give any growth inhibition of either the wild-type or the mutant strain. The inhibitory effect on the pth mutant strain by NGG codons at location +5 was suppressed by overexpression of the Pth enzyme from a plasmid. However, the overexpression of cognate tRNAs for AGG or GGG did not rescue from the growth inhibition associated with these codons early in the induced model gene. The data suggest that the NGG codons trigger peptidyl-tRNA drop-off if located at early coding positions in mRNA, thereby strongly reducing gene expression. This does not happen if these codons are located further down in the mRNA at position +7, or later.
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MESH Headings
- Base Sequence
- Carboxylic Ester Hydrolases/genetics
- Carboxylic Ester Hydrolases/metabolism
- Cell Division/genetics
- Codon/genetics
- Escherichia coli/genetics
- Gene Expression Regulation, Bacterial/genetics
- Genes, Reporter/genetics
- Lac Operon/genetics
- Molecular Sequence Data
- Mutation/genetics
- Plasmids/genetics
- Protein Biosynthesis/genetics
- RNA, Messenger/genetics
- RNA, Transfer, Amino Acyl/genetics
- RNA, Transfer, Amino Acyl/metabolism
- RNA, Transfer, Arg/genetics
- RNA, Transfer, Arg/metabolism
- RNA, Transfer, Gly/genetics
- RNA, Transfer, Gly/metabolism
- Staphylococcal Protein A/genetics
- Temperature
- Transformation, Bacterial
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25
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Vestergaard B, Sanyal S, Roessle M, Mora L, Buckingham RH, Kastrup JS, Gajhede M, Svergun DI, Ehrenberg M. The SAXS Solution Structure of RF1 Differs from Its Crystal Structure and Is Similar to Its Ribosome Bound Cryo-EM Structure. Mol Cell 2005; 20:929-38. [PMID: 16364917 DOI: 10.1016/j.molcel.2005.11.022] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2005] [Revised: 11/15/2005] [Accepted: 11/28/2005] [Indexed: 10/25/2022]
Abstract
Bacterial class I release factors (RFs) are seen by cryo-electron microscopy (cryo-EM) to span the distance between the ribosomal decoding and peptidyl transferase centers during translation termination. The compact conformation of bacterial RF1 and RF2 observed in crystal structures will not span this distance, and large structural rearrangements of RFs have been suggested to play an important role in termination. We have collected small-angle X-ray scattering (SAXS) data from E. coli RF1 and from a functionally active truncated RF1 derivative. Theoretical scattering curves, calculated from crystal and cryo-EM structures, were compared with the experimental data, and extensive analyses of alternative conformations were made. Low-resolution models were constructed ab initio, and by rigid-body refinement using RF1 domains. The SAXS data were compatible with the open cryo-EM conformation of ribosome bound RFs and incompatible with the crystal conformation. These conclusions obviate the need for assuming large conformational changes in RFs during termination.
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Affiliation(s)
- Bente Vestergaard
- Biostructural Research, Department of Medicinal Chemistry, Danish University of Pharmaceutical Sciences, Copenhagen
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26
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Graille M, Heurgué-Hamard V, Champ S, Mora L, Scrima N, Ulryck N, van Tilbeurgh H, Buckingham RH. Molecular Basis for Bacterial Class I Release Factor Methylation by PrmC. Mol Cell 2005; 20:917-27. [PMID: 16364916 DOI: 10.1016/j.molcel.2005.10.025] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2005] [Revised: 10/19/2005] [Accepted: 10/25/2005] [Indexed: 11/20/2022]
Abstract
Class I release factors bind to ribosomes in response to stop codons and trigger peptidyl-tRNA hydrolysis at the P site. Prokaryotic and eukaryotic RFs share one motif: a GGQ tripeptide positioned in a loop at the end of a stem region that interacts with the ribosomal peptidyl transferase center. The glutamine side chain of this motif is specifically methylated in both prokaryotes and eukaryotes. Methylation in E. coli is due to PrmC and results in strong stimulation of peptide chain release. We have solved the crystal structure of the complex between E. coli RF1 and PrmC bound to the methyl donor product AdoHCy. Both the GGQ domain (domain 3) and the central region (domains 2 and 4) of RF1 interact with PrmC. Structural and mutagenic data indicate a compact conformation of RF1 that is unlike its conformation when it is bound to the ribosome but is similar to the crystal structure of the protein alone.
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Affiliation(s)
- Marc Graille
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, CNRS, UMR8619, Université Paris-Sud, Orsay, France
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27
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Singh NS, Das G, Seshadri A, Sangeetha R, Varshney U. Evidence for a role of initiation factor 3 in recycling of ribosomal complexes stalled on mRNAs in Escherichia coli. Nucleic Acids Res 2005; 33:5591-601. [PMID: 16199751 PMCID: PMC1240113 DOI: 10.1093/nar/gki864] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Specific interactions between ribosome recycling factor (RRF) and elongation factor-G (EFG) mediate disassembly of post-termination ribosomal complexes for new rounds of initiation. The interactions between RRF and EFG are also important in peptidyl-tRNA release from stalled pre-termination complexes. Unlike the post-termination complexes (harboring deacylated tRNA), the pre-termination complexes (harboring peptidyl-tRNA) are not recycled by RRF and EFG in vitro, suggesting participation of additional factor(s) in the process. Using a combination of biochemical and genetic approaches, we show that, (i) Inclusion of IF3 with RRF and EFG results in recycling of the pre-termination complexes; (ii) IF3 overexpression in Escherichia coli LJ14 rescues its temperature sensitive phenotype for RRF; (iii) Transduction of infC135 (which encodes a functionally compromised IF3) in E.coli LJ14 generates a ‘synthetic severe’ phenotype; (iv) The infC135 and frr1 (containing an insertion in the RRF gene promoter) alleles synergistically rescue a temperature sensitive mutation in peptidyl-tRNA hydrolase in E.coli; and (v) IF3 facilitates ribosome recycling by Thermus thermophilus RRF and E.coli EFG in vivo and in vitro. These lines of evidence clearly demonstrate the physiological importance of IF3 in the overall mechanism of ribosome recycling in E.coli.
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Affiliation(s)
| | | | | | | | - U. Varshney
- To whom correspondence should be addressed. Tel: +91 80 2293 2686; Fax: +91 80 2360 2697;
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28
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Zavialov AV, Hauryliuk VV, Ehrenberg M. Splitting of the Posttermination Ribosome into Subunits by the Concerted Action of RRF and EF-G. Mol Cell 2005; 18:675-86. [PMID: 15949442 DOI: 10.1016/j.molcel.2005.05.016] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2005] [Revised: 05/02/2005] [Accepted: 05/23/2005] [Indexed: 10/25/2022]
Abstract
After peptide release by a class-1 release factor, the ribosomal subunits must be recycled back to initiation. We have demonstrated that the distance between a strong Shine-Dalgarno (SD) sequence and a codon in the P site is crucial for the binding stability of the deacylated tRNA in the P site of the posttermination ribosome and the in-frame maintenance of its mRNA. We show that the elongation factor EF-G and the ribosomal recycling factor RRF split the ribosome into subunits in the absence of initiation factor 3 (IF3) by a mechanism that requires both GTP and GTP hydrolysis. Taking into account that EF-G in the GTP form and RRF bind with positive cooperativity to the free 50S subunit but with negative cooperativity to the 70S ribosome, we suggest a mechanism for ribosome recycling that specifies distinct roles for EF-G, RRF, and IF3.
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Affiliation(s)
- Andrey V Zavialov
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Sweden
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29
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Bucklin DJ, Wills NM, Gesteland RF, Atkins JF. P-site pairing subtleties revealed by the effects of different tRNAs on programmed translational bypassing where anticodon re-pairing to mRNA is separated from dissociation. J Mol Biol 2005; 345:39-49. [PMID: 15567409 DOI: 10.1016/j.jmb.2004.10.037] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2004] [Revised: 10/11/2004] [Accepted: 10/13/2004] [Indexed: 11/29/2022]
Abstract
Programmed ribosomal bypassing occurs in decoding phage T4 gene 60 mRNA. Half the ribosomes bypass a 50 nucleotide gap between codons 46 and 47. Peptidyl-tRNA dissociates from the "take-off" GGA, codon 46, and re-pairs to mRNA at a matched GGA "landing site" codon directly 5' of codon 47 where translation resumes. The system described here allows the contribution of peptidyl-tRNA re-pairing to be measured independently of dissociation. The matched GGA codons have been replaced by 62 other matched codons, giving a wide range of bypassing efficiencies. Codons with G or C in either or both of the first two codon positions yielded high levels of bypassing. The results are compared with those from a complementary study of non-programmed bypassing, where the combined effects of peptidyl-tRNA dissociation and reassociation were measured. The wild-type, GGA, matched codons are the most efficient in their gene 60 context in contrast to the relatively low value in the non-programmed bypassing study.
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Affiliation(s)
- Douglas J Bucklin
- Department of Human Genetics, University of Utah, 15N 2030E Rm7410, Salt Lake City, UT 84112-5330, USA
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30
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Singh NS, Varshney U. A physiological connection between tmRNA and peptidyl-tRNA hydrolase functions in Escherichia coli. Nucleic Acids Res 2004; 32:6028-37. [PMID: 15547251 PMCID: PMC534616 DOI: 10.1093/nar/gkh924] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The bacterial ssrA gene codes for a dual function RNA, tmRNA, which possesses tRNA-like and mRNA-like regions. The tmRNA appends an oligopeptide tag to the polypeptide on the P-site tRNA by a trans-translation process that rescues ribosomes stalled on the mRNAs and targets the aberrant protein for degradation. In cells, processing of the stalled ribosomes is also pioneered by drop-off of peptidyl-tRNAs. The ester bond linking the peptide to tRNA is hydrolyzed by peptidyl-tRNA hydrolase (Pth), an essential enzyme, which releases the tRNA and the aberrant peptide. As the trans-translation mechanism utilizes the peptidyl-transferase activity of the stalled ribosomes to free the tRNA (as opposed to peptidyl-tRNA drop-off), the need for Pth to recycle such tRNAs is bypassed. Thus, we hypothesized that tmRNA may rescue a defect in Pth. Here, we show that overexpression of tmRNA rescues the temperature-sensitive phenotype of Escherichia coli (pth(ts)). Conversely, a null mutation in ssrA enhances the temperature-sensitive phenotype of the pth(ts) strain. Consistent with our hypothesis, overexpression of tmRNA results in decreased accumulation of peptidyl-tRNA in E.coli. Furthermore, overproduction of tmRNA in E.coli strains deficient in ribosome recycling factor and/or lacking the release factor 3 enhances the rescue of pth(ts) strains. We discuss the physiological relevance of these observations to highlight a major role of tmRNA in decreasing cellular peptidyl-tRNA load.
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31
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Cruz-Vera LR, Magos-Castro MA, Zamora-Romo E, Guarneros G. Ribosome stalling and peptidyl-tRNA drop-off during translational delay at AGA codons. Nucleic Acids Res 2004; 32:4462-8. [PMID: 15317870 PMCID: PMC516057 DOI: 10.1093/nar/gkh784] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Minigenes encoding the peptide Met-Arg-Arg have been used to study the mechanism of toxicity of AGA codons proximal to the start codon or prior to the termination codon in bacteria. The codon sequences of the 'mini-ORFs' employed were initiator, combinations of AGA and CGA, and terminator. Both, AGA and CGA are low-usage Arg codons in ORFs of Escherichia coli but, whilst AGA is translated by the scarce tRNA(Arg4), CGA is recognized by the abundant tRNA(Arg2). Overexpression of minigenes harbouring AGA in the third position, next to a termination codon, was deleterious to the cell and led to the accumulation of peptidyl-tRNA(Arg4) and of the peptidyl-tRNA cognate to the preceding CGA or AGA Arg triplet. The minigenes carrying CGA in the third position were not toxic. Minigene-mediated toxicity and peptidyl-tRNA accumulation were suppressed by overproduction of tRNA(Arg4) but not by overproduction of peptidyl-tRNA hydrolase, an enzyme that is only active on substrates that have been released from the ribosome. Consistent with these findings, peptidyl-tRNA(Arg4) was identified to be mainly associated with ribosomes in a stand-by complex. These and previous results support the hypothesis that the primary mechanism of inhibition of protein synthesis by AGA triplets in pth+ cells involves sequestration of tRNAs as peptidyl-tRNA on the stalled ribosome.
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Affiliation(s)
- Luis Rogelio Cruz-Vera
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 14-740, 07000 México D.F
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32
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Oviedo de Anda NA, Kameyama L, Galindo JM, Guarneros G, Hernandez-Sanchez J. Evidence of bar minigene expression and tRNA2Ile sequestration as peptidyl-tRNA2Ile during lambda bacteriophage development. J Bacteriol 2004; 186:5533-7. [PMID: 15292158 PMCID: PMC490872 DOI: 10.1128/jb.186.16.5533-5537.2004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lambda bacteriophage development is impaired in Escherichia coli cells defective for peptidyl (pep)-tRNA hydrolase (Pth). Single-base-pair mutations (bar(-)) that affect translatable two-codon open reading frames named bar minigenes (barI or barII) in the lambda phage genome promote the development of this phage in Pth-defective cells (rap cells). When the barI minigene is cloned and overexpressed from a plasmid, it inhibits protein synthesis and cell growth in rap cells by sequestering tRNA(2)(Ile) as pep-tRNA(2)(Ile). Either tRNA(2)(Ile) or Pth may reverse these effects. In this paper we present evidence that both barI and barII minigenes are translatable elements that sequester tRNA(2)(Ile) as pep-tRNA(2)(Ile). In addition, overexpression of the barI minigene impairs the development even of bar(-) phages in rap cells. Interestingly, tRNA or Pth may reestablish lambda phage development. These results suggest that lambda bar minigenes are expressed and tRNA(2)(Ile) is sequestered as pep-tRNA(2)(Ile) during lambda phage development.
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33
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Olivares-Trejo JJ, Bueno-Martínez JG, Guarneros G, Hernández-Sánchez J. The pair of arginine codons AGA AGG close to the initiation codon of the lambda int gene inhibits cell growth and protein synthesis by accumulating peptidyl-tRNAArg4. Mol Microbiol 2003; 49:1043-9. [PMID: 12890027 DOI: 10.1046/j.1365-2958.2003.03611.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
To analyse the mechanism by which rare codons near the initiation codon inhibit cell growth and protein synthesis, we used the bacteriophage lambda int gene or early codon substitution derivatives. The lambda int gene has a high frequency of rare ATA, AGA and AGG codons; two of them (AGA AGG) located at positions 3 and 4 of the int open reading frame (ORF). Escherichia coli pth (rap) cells, which are defective in peptidyl-tRNA hydrolase (Pth) activity, are more susceptible to the inhibitory effects of int expression as compared with wild-type cells. Cell growth and Int protein synthesis were enhanced by overexpression of Pth and tRNAArg4 cognate to AGG and AGA but not of tRNAIle2a specific for ATA. The increase of Int protein synthesis also takes place when the rare arginine codons AGA and AGG at positions 3 and 4 are changed to common arginine CGT or lysine AAA codons but not to rare isoleucine ATA codons. In addition, overexpression of int in Pth defective cells provokes accumulation of peptidyl-tRNAArg4 in the soluble fraction. Therefore, cell growth and Int synthesis inhibition may be due to ribosome stalling and premature release of peptidyl-tRNAArg4 from the ribosome at the rare arginine codons of the first tandem, which leads to cell starvation for the specific tRNA.
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Affiliation(s)
- José J Olivares-Trejo
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Mexico City, Mexico
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34
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Cruz-Vera LR, Hernandez-Ramon E, Perez-Zamorano B, Guarneros G. The rate of peptidyl-tRNA dissociation from the ribosome during minigene expression depends on the nature of the last decoding interaction. J Biol Chem 2003; 278:26065-70. [PMID: 12716898 DOI: 10.1074/jbc.m301129200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The expression of some very short open reading frames (ORFs) in Escherichia coli results in peptidyl-tRNA accumulation that is lethal to cells defective in peptidyl-tRNA hydrolase activity. In an attempt to understand the factors that affect this phenotype, we have surveyed the toxicity of a complete set of two-codon ORFs cloned as minigenes in inducible expression vectors. The minigenes were tested in hydrolase-defective hosts and classified according to their degree of toxicity. In general, minigenes harboring codons belonging to the same box in the standard table of the genetic code mediated similar degrees of toxicity. Moreover, the levels of peptidyl-tRNA accumulation for synonymous minigenes decoded by the same tRNA were comparable. However, two exceptions were observed: (i) expression of minigenes harboring the Arg codons CGA, CGU, and CGC, resulted in the accumulation of different levels of the unique peptidyl-tRNAArg-2 and (ii) the toxicity of minigenes containing CUG and UCU codons, each recognized by two different tRNAs, depended on peptidyl-tRNA accumulation of only one of them. Non-toxic, or partly toxic, minigenes prompted higher accumulation levels of peptidyl-tRNA upon deprivation of active RF1, implying that translation termination occurred efficiently. Our data indicate that the nature of the last decoding tRNA is crucial in the rate of peptidyl-tRNA release from the ribosome.
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Affiliation(s)
- L Rogelio Cruz-Vera
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 14-740, México Distrito Federal 07000
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35
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Kaji A, Kiel MC, Hirokawa G, Muto AR, Inokuchi Y, Kaji H. The fourth step of protein synthesis: disassembly of the posttermination complex is catalyzed by elongation factor G and ribosome recycling factor, a near-perfect mimic of tRNA. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2003; 66:515-29. [PMID: 12762054 DOI: 10.1101/sqb.2001.66.515] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- A Kaji
- Microbiology Department, Medical School, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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36
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Abstract
Ribosome bypassing refers to the ability of the ribosome::peptidyl-tRNA complex to slide down the message without translation to a site several or dozens of nucleotides downstream and resume protein chain elongation there. The product is an isoform of a protein with a 'coding' gap corresponding to the region of the message which was bypassed. Previous work showed that ribosome bypassing was strongly stimulated at 'hungry' codons calling for a tRNA whose aminoacylation was limited. We have now used the 'minigene' phenomenon to ascertain whether depletion of the pool of specific isoacceptors has a similar effect. High level expression of plasmid-borne minigenes results in the sequestration as peptidyl-tRNA of tRNA cognate to the last triplet of the minigene, thereby limiting protein synthesis for lack of the tRNA in question. We find that induction of a minigene ending in AUA stimulates bypassing at an AUA codon, but not in a control sequence with AGA at the test position; induction of a minigene ending in AGA stimulates bypassing at the latter but not the former. Induction of the AUA minigene also stimulates both leftward and rightward frameshifting at 'shifty' sequences containing an AUA codon. The normal, background frequency of bypassing at an AUA codon is markedly reduced by increasing the cellular level of the tRNA which reads the codon. Thus, the frequency of bypassing can be increased or decreased by lowering or raising the concentration of a relevant tRNA isoacceptor. These observations suggest that the occurrence of ribosome bypassing reflects the length of the pause at a given codon.
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Affiliation(s)
- Dale Lindsley
- University of Washington, Department of Genome Sciences, Box no. 357730, Seattle 98105, USA
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37
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Mora L, Heurgué-Hamard V, Champ S, Ehrenberg M, Kisselev LL, Buckingham RH. The essential role of the invariant GGQ motif in the function and stability in vivo of bacterial release factors RF1 and RF2. Mol Microbiol 2003; 47:267-75. [PMID: 12492870 DOI: 10.1046/j.1365-2958.2003.03301.x] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Release factors RF1 and RF2 are required in bacteria for the cleavage of peptidyl-tRNA. A single sequence motif, GGQ, is conserved in all eubacterial, archaebacterial and eukaryotic release factors and may mimic the CCA end of tRNA, although the position of the motif in the crystal structures of human eRF1 and Escherichia coli RF2 is strikingly different. Mutations have been introduced at each of the three conserved positions. Changing the Gln residue to Ala or Glu allowed the factors to retain about 22% of tetrapeptide release activity in vitro, but these mutants could not complement thermosensitive RF mutants in vivo. None of several mutants with altered Gly residues retained activity in vivo or in vitro. Many GGQ mutants were poorly expressed and are presumably unstable; many were also toxic to the cell. The toxic mutant factors or their degradation products may bind to ribosomes inhibiting the action of the normal factor. These data are consistent with a common role for the GGQ motif in bacterial and eukaryotic release factors, despite strong divergence in primary, secondary and tertiary structure, but are difficult to reconcile with the hypothesis that the amide nitrogen of the Gln plays a vital role in peptidyl-tRNA hydrolysis.
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Affiliation(s)
- Liliana Mora
- UPR9073 du CNRS, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, Paris 75005, France
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38
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Rosas-Sandoval G, Ambrogelly A, Rinehart J, Wei D, Cruz-Vera LR, Graham DE, Stetter KO, Guarneros G, Söll D. Orthologs of a novel archaeal and of the bacterial peptidyl-tRNA hydrolase are nonessential in yeast. Proc Natl Acad Sci U S A 2002; 99:16707-12. [PMID: 12475929 PMCID: PMC139208 DOI: 10.1073/pnas.222659199] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Peptidyl-tRNA hydrolase (encoded by pth) is an essential enzyme in all bacteria, where it releases tRNA from the premature translation termination product peptidyl-tRNA. Archaeal genomes lack a recognizable peptidyl-tRNA hydrolase (Pth) ortholog, although it is present in most eukaryotes. However, we detected Pth-like activity in extracts of the archaeon Methanocaldococcus jannaschii. The uncharacterized MJ0051 ORF was shown to correspond to a protein with Pth activity. Heterologously expressed MJ0051 enzyme catalyzed in vitro the cleavage of the Pth substrates diacetyl-[14C]lysyl-tRNA and acetyl-[14C]phenylalanyl-tRNA. On transformation of an Escherichia coli pth(ts) mutant, the MJ0051 gene (named pth2) rescued the temperature-sensitive phenotype of the strain. Analysis of known genomes revealed the presence of highly conserved orthologs of the archaeal pth2 gene in all archaea and eukaryotes but not in bacteria. The phylogeny of pth2 homologs suggests that the gene has been vertically inherited throughout the archaeal and eukaryal domains. Deletions in Saccharomyces cerevisiae of the pth2 (YBL057c) or pth (YHR189w) orthologs were viable, as was the double deletion strain, implying that the canonical Pth and Pth2 enzymes are not essential for yeast viability.
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Affiliation(s)
- Guillermina Rosas-Sandoval
- Departments of Molecular Biophysics and Biochemistry and Chemistry, Yale University, New Haven, CT 06520-8114, USA
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39
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Cruz-Vera LR, Galindo JM, Guarneros G. Transcriptional analysis of the gene encoding peptidyl-tRNA hydrolase in Escherichia coli. MICROBIOLOGY (READING, ENGLAND) 2002; 148:3457-3466. [PMID: 12427937 DOI: 10.1099/00221287-148-11-3457] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Gene pth encodes peptidyl-tRNA hydrolase (Pth), an enzyme that cleaves peptidyl-tRNAs released abortively from ribosomes during protein synthesis. In the Escherichia coli chromosome, pth is flanked by ychH and ychF, two genes of unknown function. Pth is essential for cell viability, especially under conditions leading to overproduction of peptidyl-tRNA. In an attempt to unveil the elements that affect pth expression, the transcriptional features of the pth region were investigated. Northern blot experiments showed that both pth and ychF, the 3'-proximal gene, are cotranscribed in a bicistronic transcript. However, transcripts containing each of the individual messages were also detected. Accordingly, two transcriptional promoters were identified by primer extension experiments: one located upstream of pth, which presumably gives rise to both the mono and bicistronic pth transcripts, and the other, preceding ychF, which generates its monocistronic message. Deletion analysis indicates that pth transcript stability depends on ychF integrity. Also, a defect in RNase E activity resulted in Pth overproduction. It is proposed that RNase E processing within ychF in the bicistronic message limits pth expression.
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Affiliation(s)
- L Rogelio Cruz-Vera
- Departamento de Genética y Biologı́a Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 14-740, México DF 07000, Mexico1
| | - José Manuel Galindo
- Departamento de Genética y Biologı́a Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 14-740, México DF 07000, Mexico1
| | - Gabriel Guarneros
- Departamento de Genética y Biologı́a Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 14-740, México DF 07000, Mexico1
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40
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Jin H, Björnsson A, Isaksson LA. Cis control of gene expression in E.coli by ribosome queuing at an inefficient translational stop signal. EMBO J 2002; 21:4357-67. [PMID: 12169638 PMCID: PMC126163 DOI: 10.1093/emboj/cdf424] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
An UGA stop codon context which is inefficient because of the 3'-flanking context and the last two amino acids in the gene protein product has a negative effect on gene expression, as shown using a model protein A' gene. This is particularly true at low mRNA levels, corresponding to a high intracellular ribosome/mRNA ratio. The negative effect is smaller if this ratio is decreased, or if the distance between the initiation and termination signals is increased. The results suggest that an inefficient termination codon can cause ribosomal pausing and queuing along the upstream mRNA region, thus blocking translation initiation of short genes. This cis control effect is dependent on the stop codon context, including the C-terminal amino acids in the gene product, the translation initiation signal strength, the ribosome/mRNA ratio and the size of the mRNA coding region. A large proportion of poorly expressed natural Escherichia coli genes are small, and the weak termination codon UGA is under-represented in small, highly expressed E.coli genes as compared with the efficient stop codon UAA.
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Affiliation(s)
| | - Asgeir Björnsson
- Department of Microbiology, Stockholm University, S-10691 Stockholm, Sweden
Present address: deCODE Genetics, Sturlugata 8, IS-101 Reykjavik, Iceland Corresponding author e-mail:
| | - Leif A. Isaksson
- Department of Microbiology, Stockholm University, S-10691 Stockholm, Sweden
Present address: deCODE Genetics, Sturlugata 8, IS-101 Reykjavik, Iceland Corresponding author e-mail:
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41
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Menez J, Buckingham RH, de Zamaroczy M, Campelli CK. Peptidyl-tRNA hydrolase in Bacillus subtilis, encoded by spoVC, is essential to vegetative growth, whereas the homologous enzyme in Saccharomyces cerevisiae is dispensable. Mol Microbiol 2002; 45:123-9. [PMID: 12100553 DOI: 10.1046/j.1365-2958.2002.02992.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Peptidyl-tRNA hydrolase in Escherichia coli, encoded by pth, is essential for recycling tRNA molecules sequestered as peptidyl-tRNA as a result of pre-mature dissociation from the ribosome during translation. Genes homologous to pth are present in other bacteria, yeast and man, but not in archaea. The homologous gene in Bacillus subtilis, spoVC, was first identified as a gene involved in sporulation. A second copy of spoVC, under the control of the xyl promoter, was integrated into B. subtilis at the amy locus. In this background, interruption of the original gene was possible provided that expression of the copy at the amy locus was induced. When spoVC was interrupted, both vegetative growth and sporulation were dependent on xylose, showing that SpoVC is essential. The role of SpoVC in sporulation is discussed and appears to be consistent with previous hypotheses that a relaxation of translational accuracy may occur during sporulation. The homologous gene in Saccharomyces cerevisiae, yHR189W, has been interrupted in both haploid and diploid strains. The mutant haploid strains remain viable, as do the yHR189W mutant spores obtained by tetrad dis-section, with either glucose or glycerol as carbon source, showing that the yHR189W gene product is dispensable for cell growth and for mitochondrial respiration.
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Affiliation(s)
- Jeanne Menez
- UPR 9073 du CNRS, Institut de Biologie Physico-Chimique, Paris, France
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42
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Heurgué-Hamard V, Champ S, Engström Å, Ehrenberg M, Buckingham RH. The hemK gene in Escherichia coli encodes the N(5)-glutamine methyltransferase that modifies peptide release factors. EMBO J 2002; 21:769-78. [PMID: 11847124 PMCID: PMC125846 DOI: 10.1093/emboj/21.4.769] [Citation(s) in RCA: 116] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Class 1 peptide release factors (RFs) in Escherichia coli are N(5)-methylated on the glutamine residue of the universally conserved GGQ motif. One other protein alone has been shown to contain N(5)-methylglutamine: E.coli ribosomal protein L3. We identify the L3 methyltransferase as YfcB and show that it methylates ribosomes from a yfcB strain in vitro, but not RF1 or RF2. HemK, a close orthologue of YfcB, is shown to methylate RF1 and RF2 in vitro. hemK is immediately downstream of and co-expressed with prfA. Its deletion in E.coli K12 leads to very poor growth on rich media and abolishes methylation of RF1. The activity of unmethylated RF2 from K12 strains is extremely low due to the cumulative effects of threonine at position 246, in place of alanine or serine present in all other bacterial RFs, and the lack of N(5)-methylation of Gln252. Fast-growing spontaneous revertants in hemK K12 strains contain the mutations Thr246Ala or Thr246Ser in RF2. HemK and YfcB are the first identified methyltransferases modifying glutamine, and are widely distributed in nature.
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Affiliation(s)
| | | | - Åke Engström
- UPR9073 du CNRS, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, Paris 75005, France and Departments of
Medical Biochemistry and Microbiology and Cell and Molecular Biology, BMC, Uppsala University, Box 596, S-751 24 Uppsala, Sweden Corresponding author e-mail:
| | - Måns Ehrenberg
- UPR9073 du CNRS, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, Paris 75005, France and Departments of
Medical Biochemistry and Microbiology and Cell and Molecular Biology, BMC, Uppsala University, Box 596, S-751 24 Uppsala, Sweden Corresponding author e-mail:
| | - Richard H. Buckingham
- UPR9073 du CNRS, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, Paris 75005, France and Departments of
Medical Biochemistry and Microbiology and Cell and Molecular Biology, BMC, Uppsala University, Box 596, S-751 24 Uppsala, Sweden Corresponding author e-mail:
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43
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Menez J, Remy E, Buckingham RH. Suppression of thermosensitive peptidyl-tRNA hydrolase mutation in Escherichia coli by gene duplication. MICROBIOLOGY (READING, ENGLAND) 2001; 147:1581-1589. [PMID: 11390689 DOI: 10.1099/00221287-147-6-1581] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Peptidyl-tRNA hydrolase (Pth) in Escherichia coli is required to recycle tRNA molecules that dissociate from the ribosome as peptidyl-tRNA during protein synthesis. At non-permissive temperatures, strains with a thermosensitive mutation affecting the enzyme accumulate peptidyl-tRNA, cease protein synthesis and die. The rate of reversion of this mutation to thermoresistance varies widely according to the genetic background of the cell and the temperature of selection; under certain conditions, reversion can occur at rates approaching 10(-3) per cell per generation. In such revertants, a chromosomal pth gene can be replaced by an inactivated gene, restoring thermosensitive growth in most cases. PCR amplification experiments and Southern blots show the presence of both normal and inactivated copies of the gene, demonstrating that gene duplication has occurred in the revertants. Estimation of intracellular peptidyl-tRNA hydrolase by Western blotting confirms this explanation of the mechanism of high-frequency reversion to thermoresistance.
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Affiliation(s)
- Jeanne Menez
- UPR9073 du CNRS, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, F-75005 Paris, France1
| | - Elisabeth Remy
- Aventis Pharma SA, 13 Quai Jules Guesde, 94403 Vitry sur Seine Cedex, France2
| | - Richard H Buckingham
- UPR9073 du CNRS, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, F-75005 Paris, France1
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44
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Abstract
Translational bypassing joins the information found within two disparate open reading frames into a single polypeptide chain. The underlying mechanism centers on the decoding properties of peptidyl-transfer RNA (tRNA) and involves three stages: take-off, scanning, and landing. In take-off, the peptidyl-tRNA/messenger RNA (mRNA) complex in the P site of the ribosome dissociates, and the mRNA begins to move through the ribosome. In scanning, the peptidyl-tRNA probes the mRNA sliding through the decoding center. In landing, the peptidyl-tRNA re-pairs with a codon with which it can form a stable interaction. Although few examples of genes are known that rely on translational bypassing to couple open reading frames, ribosomes appear to have an innate capacity for bypassing. This suggests that the strategy of translational bypassing may be more common than presently appreciated. The best characterized example of this phenomenon is T4 gene 60, in which a complex set of signals stimulates bypassing of 50 nucleotides between the two open reading frames. In this review, we focus on the bypassing mechanism of gene 60 in terms of take-off, scanning, and landing.
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MESH Headings
- Amino Acid Sequence
- Base Sequence
- Genes, Bacterial
- Models, Biological
- Models, Molecular
- Molecular Sequence Data
- Open Reading Frames
- Peptide Chain Termination, Translational
- Protein Biosynthesis
- Protein Sorting Signals/genetics
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/metabolism
- RNA, Transfer, Amino Acyl/genetics
- RNA, Transfer, Amino Acyl/metabolism
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
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Affiliation(s)
- A J Herr
- Department of Human Genetics, The University of Utah, Salt Lake City, Utah 84112-5330, USA.
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45
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Valadez JG, Hernández-Sánchez J, Magos MA, Ontiveros C, Guarneros G. Increased bar minigene mRNA stability during cell growth inhibition. Mol Microbiol 2001; 39:361-9. [PMID: 11136457 DOI: 10.1046/j.1365-2958.2001.02214.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Bacteriophage lambda is unable to grow vegetatively on Escherichia coli mutants defective in peptidyl-tRNA hydrolase (Pth) activity. Mutations which allow phage growth on the defective host have been located at regions named bar in the lambda genome. Expression of wild-type bar regions from plasmid constructs results in inhibition of protein synthesis and lethality to Pth-defective cells. Two of these wild-type bar regions, barI+ and barII+, contain minigenes with similar AUG-AUA-stop codon sequences preceded by different Shine-Dalgarno (SD) and spacer regions. The induced expression of barI+ and barII+ regions from plasmid constructs resulted in similar patterns of protein synthesis inhibition and cell growth arrest. Therefore, these deleterious effects may stem from translation of the transcripts containing the minigene two-codon 'ORF' (open reading frame). To test for this possibility, we assayed the effect of point mutations within the barI minigene. The results showed that a base pair substitution within the SD and the two-codon 'ORF' sequences affected protein synthesis and cell growth inhibition. In addition, mRNA stability was altered in each mutant. Higher mRNA stability correlated with the more toxic minigenes. We argue that this effect may be caused by ribosome protection of the mRNA in paused complexes as a result of deficiency of specific tRNA.
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Affiliation(s)
- J G Valadez
- Departamento de Biotecnología y Bioingeniería, CINVESTAV-IPN, Mexico City, Mexico
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46
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Dinçbas-Renqvist V, Engström A, Mora L, Heurgué-Hamard V, Buckingham R, Ehrenberg M. A post-translational modification in the GGQ motif of RF2 from Escherichia coli stimulates termination of translation. EMBO J 2000; 19:6900-7. [PMID: 11118225 PMCID: PMC305885 DOI: 10.1093/emboj/19.24.6900] [Citation(s) in RCA: 114] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A post-translational modification affecting the translation termination rate was identified in the universally conserved GGQ sequence of release factor 2 (RF2) from Escherichia coli, which is thought to mimic the CCA end of the tRNA molecule. It was shown by mass spectrometry and Edman degradation that glutamine in position 252 is N:(5)-methylated. Overexpression of RF2 yields protein lacking the methylation. RF2 from E.coli K12 is unique in having Thr246 near the GGQ motif, where all other sequenced bacterial class 1 RFs have alanine or serine. Sequencing the prfB gene from E.coli B and MRE600 strains showed that residue 246 is coded as alanine, in contrast to K12 RF2. Thr246 decreases RF2-dependent termination efficiency compared with Ala246, especially for short peptidyl-tRNAs. Methylation of Gln252 increases the termination efficiency of RF2, irrespective of the identity of the amino acid in position 246. We propose that the previously observed lethal effect of overproducing E.coli K12 RF2 arises through accumulating the defects due to lack of Gln252 methylation and Thr246 in place of alanine.
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Affiliation(s)
- V Dinçbas-Renqvist
- Department of Cell and Molecular Biology and Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, S-751 24, Uppsala, Sweden
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47
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Menez J, Heurgué-Hamard V, Buckingham RH. Sequestration of specific tRNA species cognate to the last sense codon of an overproduced gratuitous protein. Nucleic Acids Res 2000; 28:4725-32. [PMID: 11095683 PMCID: PMC115180 DOI: 10.1093/nar/28.23.4725] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
High-level expression of non-functional model proteins, derived from elongation factor EF-Tu by the deletion of an essential domain, greatly inhibits the growth of Escherichia coli partly deficient in peptidyl-tRNA hydrolase. High-level expression in wild-type cells has little effect on growth. The inhibitory effect is therefore presumably due to the sequestration of essential tRNA species, partly in the form of free peptidyl-tRNA. The growth inhibitory effect can be modulated by changing the last sense codon in the genes encoding the model proteins. Thus, replacement of Ser by Lys or His at this position increases growth inhibition. The effects of 11 changes studied are related to the rates of accumulation previously observed of the corresponding families of peptidyl-tRNA. Two non-exclusive hypotheses are proposed to account for these observations: first, the last sense codon of mRNA is a preferred site of peptidyl-tRNA drop-off in cells, due to the slow rate of translation termination compared with sense codon translation; secondly, the relatively long pause of the ribosome at the stop codon (of the order of 1 s), results in significant temporary sequestration on the ribosome of the tRNA cognate to the last sense codon.
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MESH Headings
- Bacterial Proteins/genetics
- Binding Sites/genetics
- Carboxylic Ester Hydrolases/deficiency
- Carboxylic Ester Hydrolases/genetics
- Cell Division/genetics
- Codon/genetics
- DNA, Recombinant
- Escherichia coli/genetics
- Escherichia coli/growth & development
- Gene Expression Regulation, Bacterial
- Models, Molecular
- Mutation
- Peptide Chain Elongation, Translational/genetics
- Peptide Elongation Factor Tu/chemistry
- Peptide Elongation Factor Tu/genetics
- Plasmids/genetics
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- RNA, Transfer, Amino Acyl/metabolism
- RNA, Transfer, Lys/genetics
- RNA, Transfer, Lys/metabolism
- Temperature
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Affiliation(s)
- J Menez
- UPR9073 du CNRS, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, F-75005 Paris, France
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48
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Heurgué-Hamard V, Dinçbas V, Buckingham RH, Ehrenberg M. Origins of minigene-dependent growth inhibition in bacterial cells. EMBO J 2000; 19:2701-9. [PMID: 10835367 PMCID: PMC212743 DOI: 10.1093/emboj/19.11.2701] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The expression of very short open reading frames in Escherichia coli can lead to the inhibition of translation and an arrest in cell growth. Inhibition occurs because peptidyl-tRNA hydrolase fails to recycle sufficiently rapidly peptidyl-tRNA released from ribosomes at the stop signal in competition with normal termination, causing starvation for essential species of tRNA. Previous studies have shown that the last sense codon, the strength of the Shine-Dalgarno sequence and the nature and context of the stop codon affect the toxicity associated with mini-gene expression. Here, several important parameters are studied as a function of the length of the mini-gene coding sequence. The rate of peptidyl-tRNA drop-off catalysed by translation factors decreases dramatically for peptides longer than a hexamer. The probability that ribosomes recycle without dissociation of the mini-gene mRNA varies strongly with the length of the coding sequence. The peptidyl-tRNA hydrolase rap mutant, unlike the wild-type enzyme, is highly sensitive to the length and sequence of the peptide. Together, these parameters explain the length dependence of mini-gene toxicity.
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MESH Headings
- Bacterial Proteins/biosynthesis
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Carboxylic Ester Hydrolases/genetics
- Carboxylic Ester Hydrolases/metabolism
- Cell-Free System
- Escherichia coli/genetics
- Escherichia coli/growth & development
- Genes, Bacterial
- Molecular Weight
- Open Reading Frames
- Peptide Chain Termination, Translational
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/metabolism
- Regulatory Sequences, Nucleic Acid
- Sequence Deletion
- Substrate Specificity
- Terminator Regions, Genetic
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Affiliation(s)
- V Heurgué-Hamard
- Department of Cell and Molecular Biology, BMC, Box 596, S-75124 Uppsala, Sweden
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49
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Cruz-Vera LR, Toledo I, Hernández-Sánchez J, Guarneros G. Molecular basis for the temperature sensitivity of Escherichia coli pth(Ts). J Bacteriol 2000; 182:1523-8. [PMID: 10692356 PMCID: PMC94448 DOI: 10.1128/jb.182.6.1523-1528.2000] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The gene pth, encoding peptidyl-tRNA hydrolase (Pth), is essential for protein synthesis and viability of Escherichia coli. Two pth mutants have been studied in depth: a pth(Ts) mutant isolated as temperature sensitive and a pth(rap) mutant selected as nonpermissive for bacteriophage lambda vegetative growth. Here we show that each mutant protein is defective in a different way. The Pth(Ts) protein was very unstable in vivo, both at 43 degrees C and at permissive temperatures, but its specific activity was comparable to that of the wild-type enzyme, Pth(wt). Conversely, the mutant Pth(rap) protein had the same stability as Pth(wt), but its specific activity was low. The thermosensitivity of the pth(Ts) mutant, presumably, ensues after Pth(Ts) protein levels are reduced at 43 degrees C. Conditions that increased the cellular Pth(Ts) concentration, a rise in gene copy number or diminished protein degradation, allowed cell growth at a nonpermissive temperature. Antibiotic-mediated inhibition of mRNA and protein synthesis, but not of peptidyl-tRNA drop-off, reduced pth(Ts) cell viability even at a permissive temperature. Based on these results, we suggest that Pth(Ts) protein, being unstable in vivo, supports cell viability only if its concentration is maintained above a threshold that allows general protein synthesis.
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Affiliation(s)
- L R Cruz-Vera
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del IPN, México City, Mexico
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50
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Freistroffer DV, Kwiatkowski M, Buckingham RH, Ehrenberg M. The accuracy of codon recognition by polypeptide release factors. Proc Natl Acad Sci U S A 2000; 97:2046-51. [PMID: 10681447 PMCID: PMC15751 DOI: 10.1073/pnas.030541097] [Citation(s) in RCA: 126] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The precision with which individual termination codons in mRNA are recognized by protein release factors (RFs) has been measured and compared with the decoding of sense codons by tRNA. An Escherichia coli system for protein synthesis in vitro with purified components was used to study the accuracy of termination by RF1 and RF2 in the presence or absence of RF3. The efficiency of factor-dependent termination at all sense codons differing from any of the three stop codons by a single mutation was measured and compared with the efficiency of termination at the three stop codons. RF1 and RF2 discriminate against sense codons related to stop codons by between 3 and more than 6 orders of magnitude. This high level of accuracy is obtained without energy-driven error correction (proofreading), in contrast to codon-dependent aminoacyl-tRNA recognition by ribosomes. Two codons, UAU and UGG, stand out as hotspots for RF-dependent premature termination.
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Affiliation(s)
- D V Freistroffer
- Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Box 596, S-75124 Uppsala, Sweden
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