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Lee HJ, Kang TG, Kim YW, Lee HS, Kim SK. Functional expression and extracellular secretion of Clostridium thermocellum Cel48S cellulase in Escherichia coli via the signal recognition particle-dependent translocation pathway. Enzyme Microb Technol 2021; 151:109918. [PMID: 34649693 DOI: 10.1016/j.enzmictec.2021.109918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/12/2021] [Accepted: 09/12/2021] [Indexed: 11/17/2022]
Abstract
As the only glycoside hydrolase family 48 member in Clostridium thermocellum, the exoglucanase Cel48S plays a crucial role in the extremely high activity of the cellulosome against crystalline cellulose. Although the importance of Cel48S in the hydrolysis of crystalline cellulose has been widely accepted, an efficient production system has not yet been established because Cel48S is usually expressed in Escherichia coli within inactive inclusion bodies. For unstable proteins like Cel48S, translocation across the inner membrane can be more advantageous than cytoplasmic production due to the presence of folding modulators in the periplasm and the absence of cytoplasmic proteases. In this study, we evaluated whether the production of Cel48S in the periplasmic space of E. coli could enhance its functional expression. To do so, we attached the PelB signal peptide, which mediates post-translational secretion, to the N-terminal end of Cel48S (P-Cel48S). The PelB signal peptide allowed catalytically active Cel48S to be successfully produced in the culture medium. In addition, we investigated the role of an alternative co-translational pathway on the extracellular production of Cel48S, finding that co-translational secretion yielded a specific activity of recombinant Cel48S of 135.1 ± 10.0 U/mg cell in the culture medium, which was 2.2 times higher than that associated with P-Cel48S expression. Therefore, we believe that our approach has potential applications for the cost-effective conversion of lignocellulosic biomass and the industrial production of other unstable proteins.
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Affiliation(s)
- Hyun-Jae Lee
- Department of Food Science and Technology, Chung-Ang University, Anseong, Gyeonggi, 17546, Republic of Korea
| | - Tae-Gu Kang
- Department of Food Science and Technology, Chung-Ang University, Anseong, Gyeonggi, 17546, Republic of Korea
| | - Young-Woo Kim
- Department of Food Science and Technology, Chung-Ang University, Anseong, Gyeonggi, 17546, Republic of Korea
| | - Hee-Seok Lee
- Department of Food Science and Technology, Chung-Ang University, Anseong, Gyeonggi, 17546, Republic of Korea.
| | - Sun-Ki Kim
- Department of Food Science and Technology, Chung-Ang University, Anseong, Gyeonggi, 17546, Republic of Korea.
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2
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Liu Y, Yang Q, Zhao F. Synonymous but Not Silent: The Codon Usage Code for Gene Expression and Protein Folding. Annu Rev Biochem 2021; 90:375-401. [PMID: 33441035 DOI: 10.1146/annurev-biochem-071320-112701] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Codon usage bias, the preference for certain synonymous codons, is found in all genomes. Although synonymous mutations were previously thought to be silent, a large body of evidence has demonstrated that codon usage can play major roles in determining gene expression levels and protein structures. Codon usage influences translation elongation speed and regulates translation efficiency and accuracy. Adaptation of codon usage to tRNA expression determines the proteome landscape. In addition, codon usage biases result in nonuniform ribosome decoding rates on mRNAs, which in turn influence the cotranslational protein folding process that is critical for protein function in diverse biological processes. Conserved genome-wide correlations have also been found between codon usage and protein structures. Furthermore, codon usage is a major determinant of mRNA levels through translation-dependent effects on mRNA decay and translation-independent effects on transcriptional and posttranscriptional processes. Here, we discuss the multifaceted roles and mechanisms of codon usage in different gene regulatory processes.
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Affiliation(s)
- Yi Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA;
| | - Qian Yang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA;
| | - Fangzhou Zhao
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA;
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3
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Liu Y. A code within the genetic code: codon usage regulates co-translational protein folding. Cell Commun Signal 2020; 18:145. [PMID: 32907610 PMCID: PMC7488015 DOI: 10.1186/s12964-020-00642-6] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 08/10/2020] [Indexed: 01/05/2023] Open
Abstract
The genetic code is degenerate, and most amino acids are encoded by two to six synonymous codons. Codon usage bias, the preference for certain synonymous codons, is a universal feature of all genomes examined. Synonymous codon mutations were previously thought to be silent; however, a growing body evidence now shows that codon usage regulates protein structure and gene expression through effects on co-translational protein folding, translation efficiency and accuracy, mRNA stability, and transcription. Codon usage regulates the speed of translation elongation, resulting in non-uniform ribosome decoding rates on mRNAs during translation that is adapted to co-translational protein folding process. Biochemical and genetic evidence demonstrate that codon usage plays an important role in regulating protein folding and function in both prokaryotic and eukaryotic organisms. Certain protein structural types are more sensitive than others to the effects of codon usage on protein folding, and predicted intrinsically disordered domains are more prone to misfolding caused by codon usage changes than other domain types. Bioinformatic analyses revealed that gene codon usage correlates with different protein structures in diverse organisms, indicating the existence of a codon usage code for co-translational protein folding. This review focuses on recent literature on the role and mechanism of codon usage in regulating translation kinetics and co-translational protein folding. Video abstract
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Affiliation(s)
- Yi Liu
- Department of Physiology, ND13.214A, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390-9040, USA.
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4
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"CodonWizard" - An intuitive software tool with graphical user interface for customizable codon optimization in protein expression efforts. Protein Expr Purif 2019; 160:84-93. [PMID: 30953700 DOI: 10.1016/j.pep.2019.03.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 03/25/2019] [Accepted: 03/31/2019] [Indexed: 11/22/2022]
Abstract
Optimization of coding sequences to maximize protein expression yield is often outsourced to external service providers during commercial gene synthesis and thus unfortunately remains a black box for many researchers. The presented software program "CodonWizard" offers scientists a powerful but easy-to-use tool for customizable codon optimization: The intuitive graphical user interface empowers even scientists inexperienced in the art to straightforward design, modify, test and save complex codon optimization strategies and to publicly share successful otimization strategies among the scientific community. "Codon Wizard" provides highly flexible features for sequence analysis and completely customizable modification/optimization of codon usage of any given input sequence data (DNA/RNA/peptide) using freely combinable algorithms, allowing for implementation of contemporary, well-established optimization strategies as well as novel, proprietary ones alike. Contrary to comparable tools, "Codon Wizard" thus finally opens up ways for an empirical approach to codon optimization and may also >be used completely offline to protect resulting intellectual property. As a benchmark, the reliability, intuitiveness and utility of the application could be demonstrated by increasing the yield of recombinant TEV-protease expressed in E. coli by several orders of magnitude after codon optimization using "CodonWizard" - Permanently available for download on the web at http://schwalbe.org.chemie.uni-frankfurt.de/node/3324.
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Mahajan S, Agashe D. Translational Selection for Speed Is Not Sufficient to Explain Variation in Bacterial Codon Usage Bias. Genome Biol Evol 2018; 10:562-576. [PMID: 29385509 PMCID: PMC5800062 DOI: 10.1093/gbe/evy018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2017] [Indexed: 02/05/2023] Open
Abstract
Increasing growth rate across bacteria strengthens selection for faster translation, concomitantly increasing the total number of tRNA genes and codon usage bias (CUB: enrichment of specific synonymous codons in highly expressed genes). Typically, enriched codons are translated by tRNAs with higher gene copy numbers (GCN). A model of tRNA–CUB coevolution based on fast growth-associated selection on translational speed recapitulates these patterns. A key untested implication of the coevolution model is that translational selection should favor higher tRNA GCN for more frequently used amino acids, potentially weakening the effect of growth-associated selection on CUB. Surprisingly, we find that CUB saturates with increasing growth rate across γ-proteobacteria, even as the number of tRNA genes continues to increase. As predicted, amino acid-specific tRNA GCN is positively correlated with the usage of corresponding amino acids, but there is no correlation between growth rate associated changes in CUB and amino acid usage. Instead, we find that some amino acids—cysteine and those in the NNA/G codon family—show weak CUB that does not increase with growth rate, despite large variation in the corresponding tRNA GCN. We suggest that amino acid-specific variation in CUB is not explained by tRNA GCN because GCN does not influence the difference between translation times of synonymous codons as expected. Thus, selection on translational speed alone cannot fully explain quantitative variation in overall or amino acid-specific CUB, suggesting a significant role for other functional constraints and amino acid-specific codon features.
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Affiliation(s)
- Saurabh Mahajan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, India
| | - Deepa Agashe
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, India
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6
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Al-Hawash AB, Zhang X, Ma F. Strategies of codon optimization for high-level heterologous protein expression in microbial expression systems. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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7
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Drögemöller BI, Monzon JG, Bhavsar AP, Borrie AE, Brooks B, Wright GEB, Liu G, Renouf DJ, Kollmannsberger CK, Bedard PL, Aminkeng F, Amstutz U, Hildebrand CA, Gunaretnam EP, Critchley C, Chen Z, Brunham LR, Hayden MR, Ross CJD, Gelmon KA, Carleton BC. Association Between SLC16A5 Genetic Variation and Cisplatin-Induced Ototoxic Effects in Adult Patients With Testicular Cancer. JAMA Oncol 2017; 3:1558-1562. [PMID: 28448657 DOI: 10.1001/jamaoncol.2017.0502] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Importance Cisplatin-induced ototoxic effects are an important complication that affects testicular cancer survivors as a consequence of treatment. The identification of genetic variants associated with this adverse drug reaction will further our mechanistic understanding of its development and potentially lead to strategies to prevent ototoxic effects. Objective To identify the genetic variants associated with cisplatin-induced ototoxic effects in adult testicular cancer patients. Design, Setting, and Participants This retrospective study was performed by the Canadian Pharmacogenomics Network for Drug Safety using patients recruited from 5 adult oncology treatment centers across Canada. Male patients who were 17 years or older, diagnosed with germ cell testicular cancer, and previously treated with cisplatin-based chemotherapy were recruited from July 2009 to April 2013 using active surveillance methodology. Cisplatin-induced ototoxic effects were independently diagnosed by 2 audiologists. Patients were genotyped for 7907 variants using a custom pharmacogenomic array. Logistic regression was used to identify genetic variants that were significantly associated with ototoxic effects. The validity of these findings was confirmed through independent replication and cell-based functional assays. Exposures Cisplatin-based chemotherapy. Main Outcomes and Measures Cisplatin-induced ototoxic effects. Results After exclusions, 188 patients (median [interquartile range] age, 31 [24-39] years) were enrolled in this study to form the discovery and replication cohorts. Association and fine-mapping analyses identified a protein-coding variant, rs4788863 in SLC16A5, that was associated with protection against cisplatin-induced ototoxic effects in 2 independent cohorts (combined cohort: odds ratio, 0.06; 95% CI, 0.02-0.22; P = 2.17 × 10-7). Functional validation of this transporter gene revealed that in vitro SLC16A5-silencing altered cellular responses to cisplatin treatment, supporting a role for SLC16A5 in the development of cisplatin-induced ototoxic effects. These results were further supported by the literature, which provided confirmatory evidence for the role that SLC16A5 plays in hearing. Conclusions and Relevance This study has identified a novel association between protein-coding variation in SLC16A5 and cisplatin-induced ototoxic effects. These findings have provided insight into the molecular mechanisms of this adverse drug reaction in adult patients with germ cell testicular cancer. Given that previous studies have shown that cimetidine, an SLC16A5-inhibitor, prevents murine cisplatin-induced ototoxic effects, the findings from this study have important implications for otoprotectant strategies in humans.
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Affiliation(s)
- Britt I Drögemöller
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | | | - Amit P Bhavsar
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Adrienne E Borrie
- Division of Translational Therapeutics, Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Pharmaceutical Outcomes Programme, BC Children's Hospital, Vancouver, British Columbia, Canada
| | - Beth Brooks
- Audiology and Speech Pathology Department, BC Children's Hospital, Vancouver, British Columbia, Canada
| | - Galen E B Wright
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada.,Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Geoffrey Liu
- Medical Oncology and Hematology, Department of Medicine, Princess Margaret Cancer Centre - University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Daniel J Renouf
- BC Cancer Agency and University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Philippe L Bedard
- Princess Margaret Cancer Centre and University of Toronto, Toronto, Ontario, Canada
| | - Folefac Aminkeng
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada.,Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ursula Amstutz
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada.,Division of Translational Therapeutics, Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,University Institute of Clinical Chemistry, Inselspital Bern University Hospital and University of Bern, Bern, Switzerland
| | - Claudette A Hildebrand
- Pharmaceutical Outcomes Programme, BC Children's Hospital, Vancouver, British Columbia, Canada
| | - Erandika P Gunaretnam
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada.,Division of Translational Therapeutics, Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Carol Critchley
- Neuro-Otology Unit, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Zhuo Chen
- Medical Oncology and Hematology, Department of Medicine, Princess Margaret Cancer Centre - University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Liam R Brunham
- Department of Medicine, Centre for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada.,Translational Laboratory in Genetic Medicine, Agency for Science Technology and Research (A*STAR), Singapore
| | - Michael R Hayden
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada.,Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Colin J D Ross
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada.,Pharmaceutical Outcomes Programme, BC Children's Hospital, Vancouver, British Columbia, Canada
| | - Karen A Gelmon
- BC Cancer Agency and University of British Columbia, Vancouver, British Columbia, Canada
| | - Bruce C Carleton
- Division of Translational Therapeutics, Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Pharmaceutical Outcomes Programme, BC Children's Hospital, Vancouver, British Columbia, Canada
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8
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Zhao F, Yu CH, Liu Y. Codon usage regulates protein structure and function by affecting translation elongation speed in Drosophila cells. Nucleic Acids Res 2017; 45:8484-8492. [PMID: 28582582 PMCID: PMC5737824 DOI: 10.1093/nar/gkx501] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 05/26/2017] [Indexed: 11/14/2022] Open
Abstract
Codon usage biases are found in all eukaryotic and prokaryotic genomes and have been proposed to regulate different aspects of translation process. Codon optimality has been shown to regulate translation elongation speed in fungal systems, but its effect on translation elongation speed in animal systems is not clear. In this study, we used a Drosophila cell-free translation system to directly compare the velocity of mRNA translation elongation. Our results demonstrate that optimal synonymous codons speed up translation elongation while non-optimal codons slow down translation. In addition, codon usage regulates ribosome movement and stalling on mRNA during translation. Finally, we show that codon usage affects protein structure and function in vitro and in Drosophila cells. Together, these results suggest that the effect of codon usage on translation elongation speed is a conserved mechanism from fungi to animals that can affect protein folding in eukaryotic organisms.
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Affiliation(s)
- Fangzhou Zhao
- Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Chien-Hung Yu
- Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Yi Liu
- Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
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9
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Koutmou KS, Radhakrishnan A, Green R. Synthesis at the Speed of Codons. Trends Biochem Sci 2015; 40:717-718. [PMID: 26526516 DOI: 10.1016/j.tibs.2015.10.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 10/15/2015] [Accepted: 10/16/2015] [Indexed: 10/22/2022]
Abstract
The possibility that different mRNA sequences encoding identical peptides are translated dissimilarly has long been of great interest. Recent work by Yu and co-workers provides striking evidence that mRNA sequences influence the rate of protein synthesis, and lends support to the emerging idea that mRNA sequence informs protein folding.
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Affiliation(s)
- Kristin S Koutmou
- Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Aditya Radhakrishnan
- Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, MD, USA.
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10
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Abstract
We review literature on the metabolism of ribo- and deoxyribonucleotides, nucleosides, and nucleobases in Escherichia coli and Salmonella,including biosynthesis, degradation, interconversion, and transport. Emphasis is placed on enzymology and regulation of the pathways, at both the level of gene expression and the control of enzyme activity. The paper begins with an overview of the reactions that form and break the N-glycosyl bond, which binds the nucleobase to the ribosyl moiety in nucleotides and nucleosides, and the enzymes involved in the interconversion of the different phosphorylated states of the nucleotides. Next, the de novo pathways for purine and pyrimidine nucleotide biosynthesis are discussed in detail.Finally, the conversion of nucleosides and nucleobases to nucleotides, i.e.,the salvage reactions, are described. The formation of deoxyribonucleotides is discussed, with emphasis on ribonucleotidereductase and pathways involved in fomation of dUMP. At the end, we discuss transport systems for nucleosides and nucleobases and also pathways for breakdown of the nucleobases.
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11
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Codon Usage Influences the Local Rate of Translation Elongation to Regulate Co-translational Protein Folding. Mol Cell 2015; 59:744-54. [PMID: 26321254 DOI: 10.1016/j.molcel.2015.07.018] [Citation(s) in RCA: 360] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 04/08/2015] [Accepted: 07/20/2015] [Indexed: 12/20/2022]
Abstract
Codon usage bias is a universal feature of eukaryotic and prokaryotic genomes and has been proposed to regulate translation efficiency, accuracy, and protein folding based on the assumption that codon usage affects translation dynamics. The roles of codon usage in translation, however, are not clear and have been challenged by recent ribosome profiling studies. Here we used a Neurospora cell-free translation system to directly monitor the velocity of mRNA translation. We demonstrated that the preferred codons enhance the rate of translation elongation, whereas non-optimal codons slow elongation. Codon usage also controls ribosome traffic on mRNA. These conclusions were supported by ribosome profiling results in vitro and in vivo with template mRNAs designed to increase the signal-to-noise ratio. Finally, we demonstrate that codon usage regulates protein function by affecting co-translational protein folding. These results resolve a long-standing fundamental question and suggest the existence of a codon usage code for protein folding.
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12
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Pop C, Rouskin S, Ingolia NT, Han L, Phizicky EM, Weissman JS, Koller D. Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation. Mol Syst Biol 2014; 10:770. [PMID: 25538139 PMCID: PMC4300493 DOI: 10.15252/msb.20145524] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Ribosome profiling data report on the distribution of translating ribosomes, at steady-state, with codon-level resolution. We present a robust method to extract codon translation rates and protein synthesis rates from these data, and identify causal features associated with elongation and translation efficiency in physiological conditions in yeast. We show that neither elongation rate nor translational efficiency is improved by experimental manipulation of the abundance or body sequence of the rare AGG tRNA. Deletion of three of the four copies of the heavily used ACA tRNA shows a modest efficiency decrease that could be explained by other rate-reducing signals at gene start. This suggests that correlation between codon bias and efficiency arises as selection for codons to utilize translation machinery efficiently in highly translated genes. We also show a correlation between efficiency and RNA structure calculated both computationally and from recent structure probing data, as well as the Kozak initiation motif, which may comprise a mechanism to regulate initiation.
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Affiliation(s)
- Cristina Pop
- Computer Science Department, Stanford University, Stanford, CA, USA
| | - Silvi Rouskin
- Department of Cellular and Molecular Pharmacology, California Institute of Quantitative Biology, Center for RNA Systems Biology, Howard Hughes Medical Institute, University of California, San Francisco, CA, USA
| | - Nicholas T Ingolia
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Lu Han
- School of Medicine and Dentistry, University of Rochester Medical Center, Rochester, NY, USA
| | - Eric M Phizicky
- School of Medicine and Dentistry, University of Rochester Medical Center, Rochester, NY, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, California Institute of Quantitative Biology, Center for RNA Systems Biology, Howard Hughes Medical Institute, University of California, San Francisco, CA, USA
| | - Daphne Koller
- Computer Science Department, Stanford University, Stanford, CA, USA
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13
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A critical analysis of codon optimization in human therapeutics. Trends Mol Med 2014; 20:604-13. [PMID: 25263172 DOI: 10.1016/j.molmed.2014.09.003] [Citation(s) in RCA: 176] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 09/02/2014] [Accepted: 09/03/2014] [Indexed: 02/01/2023]
Abstract
Codon optimization describes gene engineering approaches that use synonymous codon changes to increase protein production. Applications for codon optimization include recombinant protein drugs and nucleic acid therapies, including gene therapy, mRNA therapy, and DNA/RNA vaccines. However, recent reports indicate that codon optimization can affect protein conformation and function, increase immunogenicity, and reduce efficacy. We critically review this subject, identifying additional potential hazards including some unique to nucleic acid therapies. This analysis highlights the evolved complexity of codon usage and challenges the scientific bases for codon optimization. Consequently, codon optimization may not provide the optimal strategy for increasing protein production and may decrease the safety and efficacy of biotech therapeutics. We suggest that the use of this approach is reconsidered, particularly for in vivo applications.
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14
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Affiliation(s)
- Jacques Ninio
- Laboratoire de Physique Statistique, Ecole Normale Supérieure, 24 rue Lhomond, 75231 Paris Cedex 05, France.
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15
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Corcoran CP, Podkaminski D, Papenfort K, Urban JH, Hinton JCD, Vogel J. Superfolder GFP reporters validate diverse new mRNA targets of the classic porin regulator, MicF RNA. Mol Microbiol 2012; 84:428-45. [PMID: 22458297 DOI: 10.1111/j.1365-2958.2012.08031.x] [Citation(s) in RCA: 150] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
MicF is a textbook example of a small regulatory RNA (sRNA) that acts on a trans-encoded target mRNA through imperfect base pairing. Discovery of MicF as a post-transcriptional repressor of the major Escherichia coli porin OmpF established the paradigm for a meanwhile common mechanism of translational inhibition, through antisense sequestration of a ribosome binding site. However, whether MicF regulates additional genes has remained unknown for almost three decades. Here, we have harnessed the new superfolder variant of GFP for reporter-gene fusions to validate newly predicted targets of MicF in Salmonella. We show that the conserved 5' end of MicF acts by seed pairing to repress the mRNAs of global transcriptional regulator Lrp, and periplasmic protein YahO, while a second targeting region is also required to regulate the mRNA of the lipid A-modifying enzyme LpxR. Interestingly, MicF targets lpxR at both the ribosome binding site and deep within the coding sequence. MicF binding in the coding sequence of lpxR decreases mRNA stability through exacerbating the use of a native RNase E site proximal to the short MicF-lpxR duplex. Altogether, this study assigns the classic MicF sRNA to the growing class of Hfq-associated regulators that use diverse mechanisms to impact multiple loci.
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Affiliation(s)
- Colin P Corcoran
- Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany
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16
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Shao ZQ, Zhang YM, Feng XY, Wang B, Chen JQ. Synonymous codon ordering: a subtle but prevalent strategy of bacteria to improve translational efficiency. PLoS One 2012; 7:e33547. [PMID: 22432034 PMCID: PMC3303843 DOI: 10.1371/journal.pone.0033547] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Accepted: 02/12/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND In yeast coding sequences, once a particular codon has been used, subsequent occurrence of the same amino acid tends to use codons sharing the same tRNA. Such a phenomenon of co-tRNA codons pairing bias (CTCPB) is also found in some other eukaryotes but it is not known whether it occurs in prokaryotes. METHODOLOGY/PRINCIPAL FINDINGS In this study, we focused on a total of 773 bacterial genomes to investigate their synonymous codon pairing preferences. After calculating the actual frequencies of synonymous codon pairs and comparing them with their expected values, we detected an obvious pairing bias towards identical codon pairs. This seems consistent with the previously reported CTCPB phenomenon, since identical codons are certainly read by the same tRNA. However, among co-tRNA but non-identical codon pairs, only 22 were often found overrepresented, suggesting that many co-tRNA codons actually do not preferentially pair together in prokaryotes. Therefore, the previously reported co-tRNA codons pairing rule needs to be more rigorously defined. The affinity differences between a tRNA anticodon and its readable codons should be taken into account. Moreover, both within-gene-shuffling tests and phylogenetic analyses support the idea that translational selection played an important role in shaping the observed synonymous codon pairing pattern in prokaryotes. CONCLUSIONS Overall, a high level of synonymous codon pairing bias was detected in 73% investigated bacterial species, suggesting the synonymous codon ordering strategy has been prevalently adopted by prokaryotes to improve their translational efficiencies. The findings in this study also provide important clues to better understand the complex dynamics of translational process.
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Affiliation(s)
| | | | | | - Bin Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu Province, China
- * E-mail: (BW); (JQC)
| | - Jian-Qun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu Province, China
- * E-mail: (BW); (JQC)
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17
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Stadler M, Fire A. Wobble base-pairing slows in vivo translation elongation in metazoans. RNA (NEW YORK, N.Y.) 2011; 17:2063-73. [PMID: 22045228 PMCID: PMC3222120 DOI: 10.1261/rna.02890211] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Accepted: 08/30/2011] [Indexed: 05/24/2023]
Abstract
In the universal genetic code, most amino acids can be encoded by multiple trinucleotide codons, and the choice among available codons can influence position-specific translation elongation rates. By using sequence-based ribosome profiling, we obtained transcriptome-wide profiles of in vivo ribosome occupancy as a function of codon identity in Caenorhabditis elegans and human cells. Particularly striking in these profiles was a universal trend of higher ribosome occupancy for codons translated via G:U wobble base-pairing compared with synonymous codons that pair with the same tRNA family using G:C base-pairing. These data support a model in which ribosomal translocation is slowed at wobble codon positions.
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Affiliation(s)
- Michael Stadler
- Department of Genetics, Stanford University, Stanford, California 94305-5324, USA
| | - Andrew Fire
- Department of Genetics, Stanford University, Stanford, California 94305-5324, USA
- Department of Pathology, Stanford University, Stanford, California 94305-5324, USA
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18
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Sauna ZE, Kimchi-Sarfaty C. Understanding the contribution of synonymous mutations to human disease. Nat Rev Genet 2011; 12:683-91. [PMID: 21878961 DOI: 10.1038/nrg3051] [Citation(s) in RCA: 685] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Synonymous mutations - sometimes called 'silent' mutations - are now widely acknowledged to be able to cause changes in protein expression, conformation and function. The recent increase in knowledge about the association of genetic variants with disease, particularly through genome-wide association studies, has revealed a substantial contribution of synonymous SNPs to human disease risk and other complex traits. Here we review current understanding of the extent to which synonymous mutations influence disease, the various molecular mechanisms that underlie these effects and the implications for future research and biomedical applications.
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Affiliation(s)
- Zuben E Sauna
- Laboratory of Hemostasis, Division of Hematology, Center for Biologics Evaluation and Research, Food and Drug Administration, 29 Lincoln Drive, Bethesda, Maryland 20892, USA.
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19
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Deane CM, Saunders R. The imprint of codons on protein structure. Biotechnol J 2011; 6:641-9. [DOI: 10.1002/biot.201000329] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Revised: 03/10/2011] [Accepted: 03/23/2011] [Indexed: 12/23/2022]
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20
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Translation efficiencies of synonymous codons for arginine differ dramatically and are not correlated with codon usage in chloroplasts. Gene 2011; 472:50-4. [DOI: 10.1016/j.gene.2010.09.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Revised: 09/17/2010] [Accepted: 09/24/2010] [Indexed: 11/22/2022]
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21
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Czech A, Fedyunin I, Zhang G, Ignatova Z. Silent mutations in sight: co-variations in tRNA abundance as a key to unravel consequences of silent mutations. MOLECULAR BIOSYSTEMS 2010; 6:1767-72. [PMID: 20617253 DOI: 10.1039/c004796c] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mutations that alter the amino acid sequence are known to potentially exert deleterious effects on protein function, whereas substitutions of nucleotides without amino acid change are assumed to be neutral for the protein's functionality. However, cumulative evidence suggests that synonymous substitutions might also induce phenotypic variability by affecting splicing accuracy, translation fidelity, and conformation and function of proteins. tRNA isoacceptors mediate the translation of codons to amino acids, and asymmetric tRNA abundance causes variations in the rate of translation of each single triplet. Consequently, the effect of a silent point mutation in the coding region could be significant due to differential abundances of the cognate tRNA(s), emphasizing the importance of precise assessment of tRNA composition. Here, we provide an overview of the methods used to quantitatively determine the concentrations of tRNA species and discuss synonymous mutations in the context of tRNA composition of the cell, thus providing a new twist on the detrimental impact of the silent mutations.
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Affiliation(s)
- Andreas Czech
- Biochemistry, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str 24-25, 14467 Potsdam-Golm, Germany
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22
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Zhang G, Fedyunin I, Miekley O, Valleriani A, Moura A, Ignatova Z. Global and local depletion of ternary complex limits translational elongation. Nucleic Acids Res 2010; 38:4778-87. [PMID: 20360046 PMCID: PMC2919707 DOI: 10.1093/nar/gkq196] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The translation of genetic information according to the sequence of the mRNA template occurs with high accuracy and fidelity. Critical events in each single step of translation are selection of transfer RNA (tRNA), codon reading and tRNA-regeneration for a new cycle. We developed a model that accurately describes the dynamics of single elongation steps, thus providing a systematic insight into the sensitivity of the mRNA translation rate to dynamic environmental conditions. Alterations in the concentration of the aminoacylated tRNA can transiently stall the ribosomes during translation which results, as suggested by the model, in two outcomes: either stress-induced change in the tRNA availability triggers the premature termination of the translation and ribosomal dissociation, or extensive demand for one tRNA species results in a competition between frameshift to an aberrant open-reading frame and ribosomal drop-off. Using the bacterial Escherichia coli system, we experimentally draw parallels between these two possible mechanisms.
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Affiliation(s)
- Gong Zhang
- Biochemistry, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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23
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Gao R, Forster AC. Changeability of individual domains of an aminoacyl-tRNA in polymerization by the ribosome. FEBS Lett 2010; 584:99-105. [PMID: 19903477 DOI: 10.1016/j.febslet.2009.11.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2009] [Revised: 10/31/2009] [Accepted: 11/02/2009] [Indexed: 10/20/2022]
Abstract
The changeabilities of individual modules of aminoacyl-tRNAs are poorly understood, despite the relevance for evolution, translational accuracy and incorporation of unnatural amino acids (AAs). Here, we dissect the effect of successive changes in four domains of Ala-tRNA(3)(Ala) on translation in a purified system. Incorporating five AAs, not one, was necessary to reveal major effects on yields of peptide products. Omitting tRNA modifications had little affect, but anticodon mutations were very inhibitory. Surprisingly, changing the terminal CCA to CdCA was sometimes inhibitory and non-cognate AAs were sometimes compensatory. Results have implications for translational fidelity and engineering.
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Affiliation(s)
- Rong Gao
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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24
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Forster AC. Low modularity of aminoacyl-tRNA substrates in polymerization by the ribosome. Nucleic Acids Res 2009; 37:3747-55. [PMID: 19376831 PMCID: PMC2699524 DOI: 10.1093/nar/gkp240] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Aminoacyl-transfer RNAs contain four standardized units: amino acids, an invariant 3′-terminal CCA, trinucleotide anticodons and tRNA bodies. The degree of interchangeability of the three variable modules is poorly understood, despite its role in evolution and the engineering of translation to incorporate unnatural amino acids. Here, a purified translation system is used to investigate effects of various module swaps on the efficiency of multiple ribosomal incorporations of unnatural aminoacyl-tRNA substrates per peptide product. The yields of products containing three to five adjacent l-amino acids with unnatural side chains are low and cannot be improved by optimization or explained simply by any single factor tested. Though combinations of modules that allow quantitative single unnatural incorporations are found readily, finding combinations that enable efficient synthesis of products containing multiple unnatural amino acids is challenging. This implies that assaying multiple, as opposed to single, incorporations per product is a more stringent assay of substrate activity. The unpredictability of most results illustrates the multifactorial nature of substrate recognition and the value of synthetic biology for testing our understanding of translation. Data indicate that the degree of interchangeability of the modules of aminoacyl-tRNAs is low.
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Affiliation(s)
- Anthony C Forster
- Department of Pharmacology and Vanderbilt Institute of Chemical Biology, Vanderbilt University Medical Center, 2222 Pierce Ave., Nashville, TN 37232, USA.
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25
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Zhang G, Ignatova Z. Generic algorithm to predict the speed of translational elongation: implications for protein biogenesis. PLoS One 2009; 4:e5036. [PMID: 19343177 PMCID: PMC2661179 DOI: 10.1371/journal.pone.0005036] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2009] [Accepted: 03/03/2009] [Indexed: 11/27/2022] Open
Abstract
Synonymous codon usage and variations in the level of isoaccepting tRNAs exert a powerful selective force on translation fidelity. We have developed an algorithm to evaluate the relative rate of translation which allows large-scale comparisons of the non-uniform translation rate on the protein biogenesis. Using the complete genomes of Escherichia coli and Bacillus subtilis we show that stretches of codons pairing to minor tRNAs form putative sites to locally attenuate translation; thereby the tendency is to cluster in near proximity whereas long contiguous stretches of slow-translating triplets are avoided. The presence of slow-translating segments positively correlates with the protein length irrespective of the protein abundance. The slow-translating clusters are predominantly located down-stream of the domain boundaries presumably to fine-tune translational accuracy with the folding fidelity of multidomain proteins. Translation attenuation patterns at highly structurally and functionally conserved domains are preserved across the species suggesting a concerted selective pressure on the codon selection and species-specific tRNA abundance in these regions.
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Affiliation(s)
- Gong Zhang
- Department of Biochemistry, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
| | - Zoya Ignatova
- Department of Biochemistry, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
- * E-mail:
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26
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Atkins JF, Björk GR. A gripping tale of ribosomal frameshifting: extragenic suppressors of frameshift mutations spotlight P-site realignment. Microbiol Mol Biol Rev 2009; 73:178-210. [PMID: 19258537 PMCID: PMC2650885 DOI: 10.1128/mmbr.00010-08] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mutants of translation components which compensate for both -1 and +1 frameshift mutations showed the first evidence for framing malleability. Those compensatory mutants isolated in bacteria and yeast with altered tRNA or protein factors are reviewed here and are considered to primarily cause altered P-site realignment and not altered translocation. Though the first sequenced tRNA mutant which suppressed a +1 frameshift mutation had an extra base in its anticodon loop and led to a textbook "yardstick" model in which the number of anticodon bases determines codon size, this model has long been discounted, although not by all. Accordingly, the reviewed data suggest that reading frame maintenance and translocation are two distinct features of the ribosome. None of the -1 tRNA suppressors have anticodon loops with fewer than the standard seven nucleotides. Many of the tRNA mutants potentially affect tRNA bending and/or stability and can be used for functional assays, and one has the conserved C74 of the 3' CCA substituted. The effect of tRNA modification deficiencies on framing has been particularly informative. The properties of some mutants suggest the use of alternative tRNA anticodon loop stack conformations by individual tRNAs in one translation cycle. The mutant proteins range from defective release factors with delayed decoding of A-site stop codons facilitating P-site frameshifting to altered EF-Tu/EF1alpha to mutant ribosomal large- and small-subunit proteins L9 and S9. Their study is revealing how mRNA slippage is restrained except where it is programmed to occur and be utilized.
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Affiliation(s)
- John F Atkins
- BioSciences Institute, University College, Cork, Ireland.
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27
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de Smit MH, Verlaan PWG, van Duin J, Pleij CWA. Intracistronic transcriptional polarity enhances translational repression: a new role for Rho. Mol Microbiol 2009; 69:1278-89. [PMID: 19172759 DOI: 10.1111/j.1365-2958.2008.06360.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Transcriptional polarity in Escherichia coli occurs when cryptic Rho-dependent transcription terminators become activated as a consequence of reduced translation. Whether this is due to an increased spacing between the RNA polymerase and the leading ribosome or to prior functional inactivation of a subpopulation of the mRNAs has been a matter of discussion. Transcriptional polarity results in decreased synthesis of inefficiently translated mRNAs and therefore in decreased expression of downstream genes in the same operon (intercistronic polarity). By analogy, expression of the gene in which the conditional termination occurs is also expected to decrease, but this has so far not been demonstrated experimentally. To study the relevance of this intracistronic polarity for expression regulation in vivo, the polarity-prone IacZ reporter gene was fused to a range of mutated ribosome binding sites, repressed to different degrees by local RNA structure. Quantitative analysis of protein and mRNA synthesis shows that polarity occurs on functionally active mRNA molecules and that it indeed affects expression of the cistron carrying the terminator, thus enhancing the effect of translational repression. These findings point to a novel regulatory function of transcriptional polarity, reminiscent of transcriptional attenuation but opposite in effect.
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Affiliation(s)
- Maarten H de Smit
- Section Genexpress, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, PO Box 9502, 2300 RA Leiden, the Netherlands.
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28
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Ledoux S, Uhlenbeck OC. Different aa-tRNAs are selected uniformly on the ribosome. Mol Cell 2008; 31:114-23. [PMID: 18614050 DOI: 10.1016/j.molcel.2008.04.026] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2007] [Revised: 01/16/2008] [Accepted: 04/25/2008] [Indexed: 10/21/2022]
Abstract
Ten E. coli aminoacyl-tRNAs (aa-tRNAs) were assessed for their ability to decode cognate codons on E. coli ribosomes by using three assays that evaluate the key steps in the decoding pathway. Despite a wide variety of structural features, each aa-tRNA exhibited similar kinetic and thermodynamic properties in each assay. This surprising kinetic and thermodynamic uniformity is likely to reflect the importance of ribosome conformational changes in defining the rates and affinities of the decoding process as well as the evolutionary "tuning" of each aa-tRNA sequence to modify their individual interactions with the ribosome at each step.
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Affiliation(s)
- Sarah Ledoux
- Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, IL 60208, USA
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29
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Fluitt A, Pienaar E, Viljoen H. Ribosome kinetics and aa-tRNA competition determine rate and fidelity of peptide synthesis. Comput Biol Chem 2007; 31:335-46. [PMID: 17897886 PMCID: PMC2727733 DOI: 10.1016/j.compbiolchem.2007.07.003] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2007] [Accepted: 07/30/2007] [Indexed: 11/27/2022]
Abstract
It is generally accepted that the translation rate depends on the availability of cognate aa-tRNAs. In this study it is shown that the key factor that determines translation rate is the competition between near-cognate and cognate aa-tRNAs. The transport mechanism in the cytoplasm is diffusion, thus the competition between cognate, near-cognate and non-cognate aa-tRNAs to bind to the ribosome is a stochastic process. Two competition measures are introduced; C(i) and R(i) (i=1, 64) are quotients of the arrival frequencies of near-cognates vs. cognates and non-cognates vs. cognates, respectively. Furthermore, the reaction rates of bound cognates differ from those of bound near-cognates. If a near-cognate aa-tRNA binds to the A site of the ribosome, it may be rejected at the anti-codon recognition step or proofreading step or it may be accepted. Regardless of its fate, the near-cognates and non-cognates have caused delays of varying duration to the observed rate of translation. Rate constants have been measured at a temperature of 20 degrees C by (Gromadski, K.B., Rodnina, M.V., 2004. Kinetic determinants of high-fidelity tRNA discrimination on the ribosome. Mol. Cell 13, 191-200). These rate constants have been re-evaluated at 37 degrees C, using experimental data at 24.5 degrees C and 37 degrees C (Varenne, S., et al., 1984. Translation in a non-uniform process: effect of tRNA availability on the rate of elongation of nascent polypeptide chains. J. Mol. Biol. 180, 549-576). The key results of the study are: (i) the average time (at 37 degrees C) to add an amino acid, as defined by the ith codon, to the nascent peptide chain is: tau(i)=9.06+1.445x[10.48C(i)+0.5R(i)] (in ms); (ii) the misreading frequency is directly proportional to the near-cognate competition, E(i)=0.0009C(i); (iii) the competition from near-cognates, and not the availability of cognate aa-tRNAs, is the most important factor that determines the translation rate - the four codons with highest near-cognate competition (in the case of E. coli) are [GCC]>[CGG]>[AGG]>[GGA], which overlap only partially with the rarest codons: [AGG]<[CCA]<[GCC]<[CAC]; (iv) based on the kinetic rates at 37 degrees C, the average time to insert a cognate amino acid is 9.06ms and the average delay to process a near-cognate aa-tRNA is 10.45ms and (vii) the model also provides estimates of the vacancy times of the A site of the ribosome - an important factor in frameshifting.
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Affiliation(s)
- Aaron Fluitt
- Department of Chemical Engineering, University of Nebraska, Lincoln, NE 68588, USA
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30
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Nakamura M, Sugiura M. Translation efficiencies of synonymous codons are not always correlated with codon usage in tobacco chloroplasts. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2007; 49:128-34. [PMID: 17144890 DOI: 10.1111/j.1365-313x.2006.02945.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Codon usage in chloroplasts is different from that in prokaryotic and eukaryotic nuclear genomes. However, no experimental approach has been made to analyse the translation efficiency of individual codons in chloroplasts. We devised an in vitro assay for translation efficiencies using synthetic mRNAs, and measured the translation efficiencies of five synonymous codon groups in tobacco chloroplasts. Among four alanine codons (GCN, where N is U, C, A or G), GCU was the most efficient for translation, whereas the chloroplast genome lacks tRNA genes corresponding to GCU. Phenylalanine and tyrosine are each encoded by two codons (UUU/C and UAU/C, respectively). Phenylalanine UUC and tyrosine UAC were translated more than twice as efficiently than UUU and UAU, respectively, contrary to their codon usage, whereas translation efficiencies of synonymous codons for alanine, aspartic acid and asparagine were parallel to their codon usage. These observations indicate that translation efficiencies of individual codons are not always correlated with codon usage in vitro in chloroplasts. This raises an important issue for foreign gene expression in chloroplasts.
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Affiliation(s)
- Masayuki Nakamura
- Graduate School of Natural Sciences, Nagoya City University, Mizuhocho Yamanohata, Mizuho, Nagoya, Japan
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31
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Gonzalez de Valdivia EI, Isaksson LA. A codon window in mRNA downstream of the initiation codon where NGG codons give strongly reduced gene expression in Escherichia coli. Nucleic Acids Res 2004; 32:5198-205. [PMID: 15459289 PMCID: PMC521668 DOI: 10.1093/nar/gkh857] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The influences on gene expression by codons at positions +2, +3, +5 and +7 downstream of the initiation codon have been compared. Most of the +2 codons that are known to give low gene expression are associated with a higher expression if placed at the later positions. The NGG codons AGG, CGG, UGG and GGG, but not GGN or GNG (where N is non-G), are unique since they are associated with a very low gene expression also if located at positions +2, +3 and +5. All codons, including NGG, give a normal gene expression if placed at positions +7. The negative effect by the NGG codons is true for both the lacZ and 3A' model genes. The low expression is suggested to originate at the translational level, although it is not the result of mRNA secondary structure or a lowered intracellular mRNA pool.
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32
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Bertrand C, Prère MF, Gesteland RF, Atkins JF, Fayet O. Influence of the stacking potential of the base 3' of tandem shift codons on -1 ribosomal frameshifting used for gene expression. RNA (NEW YORK, N.Y.) 2002; 8:16-28. [PMID: 11871658 PMCID: PMC1370227 DOI: 10.1017/s1355838202012086] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Translating ribosomes can shift reading frame at specific sites with high efficiency for gene expression purposes. The most common type of shift to the -1 frame involves a tandem realignment of two anticodons from pairing with mRNA sequence of the form X XXY YYZ to XXX YYY Z where the spaces indicate the reading frame. The predominant -1 shift site of this type in eubacteria is A AAA AAG. The present work shows that in Escherichia coli the identity of the 6 nt 3' of this sequence can be responsible for a 14-fold variation in frameshift frequency. The first 3' nucleotide has the primary effect, with, in order of decreasing efficiency, U > C > A > G. This effect is independent of other stimulators of frameshifting. It is detected with other X XXA AAG sequences, but not with several other heptameric -1 shift sites. Pairing of E. coli tRNALYS with AAG is especially weak at the third codon position. We propose that strong stacking of purines 3' of AAG stabilizes pairing of tRNALys, diminishing the chance of codon:anticodon dissociation that is a prerequisite for the realignment involved in frameshifting.
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Affiliation(s)
- Claire Bertrand
- Laboratoire de Microbiologie et de Génétique Moléculaire, Centre National de la Recherche Scientifique et Université Paul Sabatier-UMR5100, Toulouse, France
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33
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Irving RA, Coia G, Roberts A, Nuttall SD, Hudson PJ. Ribosome display and affinity maturation: from antibodies to single V-domains and steps towards cancer therapeutics. J Immunol Methods 2001; 248:31-45. [PMID: 11223067 DOI: 10.1016/s0022-1759(00)00341-0] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Protein affinity maturation using molecular evolution techniques to produce high-affinity binding proteins is an important step in the generation of reagents for cancer diagnosis and treatment. Currently, the most commonly used molecular evolution processes involve mutation of a single gene into complex gene repertoires followed by selection from a display library. Fd-bacteriophage are the most popular display vectors, but are limited in their capacity for library presentation, speed of processing and mutation frequency. Recently, the potential of ribosome display for directed molecular evolution was recognised and developed into a rapid and simple affinity selection strategy using ribosome complexes to display antibody fragments (scFv). Ribosome display and selection has the potential to generate and display large libraries more representative of the theoretical optima for naïve repertoires (10(14)). Even more important is the application of ribosome display for the affinity maturation of individual proteins by rapid mutation and selection cycles. These display strategies can apply to other members of the immunoglobulin superfamily; for example single V-domains which have an important application in providing specific targeting to either novel or refractory cancer markers. We discuss the application of ribosome display and selection in conjunction with variable domain (CTLA-4) libraries as the first step towards this objective and review affinity maturation strategies for in vitro ribosome display systems.
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Affiliation(s)
- R A Irving
- CSIRO Health Sciences and Nutrition and CRC for Diagnostic Technologies, 343 Royal Parade, Parkville, 3052, Victoria, Australia.
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34
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Tsalkova T, Kramer G, Hardesty B. The effect of a hydrophobic N-terminal probe on translational pausing of chloramphenicol acetyl transferase and rhodanese. J Mol Biol 1999; 286:71-81. [PMID: 9931250 DOI: 10.1006/jmbi.1998.2481] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The effect on translational pausing of a hydrophobic probe, coumarin, at the N terminus of nascent peptides was investigated. Two different proteins, bacterial chloramphenicol acetyltransferase and bovine rhodanese, were synthesized by coupled transcription/translation in a cell-free system derived from Escherichia coli. Protein synthesis was initiated with N-formyl-Met-tRNAf or N-acetyl-S-coumarin-Met-tRNAf. Cotranslational incorporation of the coumarin derivative generated nascent polypeptides with a hydrophobic residue at their N termini. The effect of the two N-terminal groups on the size distribution and quantity of the peptides formed by translational pausing was investigated. The N-terminal coumarin caused an accumulation of nascent chloramphenicol acetyltransferase peptides in the mass range of 3.5-4.0 kDa that reflects a delay in translation at this point. No similar effect on rhodanese pause-site peptides was observed. This effect on translational pausing cannot be explained by either mRNA secondary structure or rare codons and tRNA abundance. It is suggested that the effect of N-terminal coumarin on translational pausing is the result of the interaction of the nascent peptide with components of the large ribosomal subunit along the path it follows between the peptidyl transferase center and the exit site on the distal surface.
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Affiliation(s)
- T Tsalkova
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX, 78712, USA
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35
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Oresic M, Shalloway D. Specific correlations between relative synonymous codon usage and protein secondary structure. J Mol Biol 1998; 281:31-48. [PMID: 9680473 DOI: 10.1006/jmbi.1998.1921] [Citation(s) in RCA: 121] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We found significant species-specific correlations between the use of two synonymous codons and protein secondary structure units by comparing the three-dimensional structures of human and Escherichia coli proteins with their mRNA sequences. The correlations are not explained by codon-context, expression level, GC/AU content, or positional effects. The E. coli correlation is between Asn AAC and the C-terminal regions of beta-sheet segments; it may result from selection for translational accuracy, suggesting the hypothesis that downstream Asn residues are important for beta-sheet formation. The correlation in human proteins is between Asp GAU and the N termini of alpha-helices; it may be important for eukaryote-specific sequential, cotranslational folding. The kingdom-specific correlations may reflect kingdom-specific differences in translational mechanisms. The correlations may help identify residues that are important for secondary structure formation, be useful in secondary structure prediction algorithms, and have implications for recombinant gene expression.
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Affiliation(s)
- M Oresic
- Section of Biochemistry Molecular and Cell Biology, Cornell University, Ithaca, NY 14853, USA
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36
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Abstract
Because regions on the messenger ribonucleic acid differ in the rate at which they are translated by the ribosome and because proteins can fold cotranslationally on the ribosome, a question arises as to whether the kinetics of translation influence the folding events in the growing nascent polypeptide chain. Translationally slow regions were identified on mRNAs for a set of 37 multidomain proteins from Escherichia coli with known three-dimensional structures. The frequencies of individual codons in mRNAs of highly expressed genes from E. coli were taken as a measure of codon translation speed. Analysis of codon usage in slow regions showed a consistency with the experimentally determined translation rates of codons; abundant codons that are translated with faster speeds compared with their synonymous codons were found to be avoided; rare codons that are translated at an unexpectedly higher rate were also found to be avoided in slow regions. The statistical significance of the occurrence of such slow regions on mRNA spans corresponding to the oligopeptide domain termini and linking regions on the encoded proteins was assessed. The amino acid type and the solvent accessibility of the residues coded by such slow regions were also examined. The results indicated that protein domain boundaries that mark higher-order structural organization are largely coded by translationally slow regions on the RNA and are composed of such amino acids that are stickier to the ribosome channel through which the synthesized polypeptide chain emerges into the cytoplasm. The translationally slow nucleotide regions on mRNA possess the potential to form hairpin secondary structures and such structures could further slow the movement of ribosome. The results point to an intriguing correlation between protein synthesis machinery and in vivo protein folding. Examination of available mutagenic data indicated that the effects of some of the reported mutations were consistent with our hypothesis.
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Affiliation(s)
- T A Thanaraj
- European Molecular Biology Laboratory, Heidelberg, Germany.
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37
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Gish K, Yanofsky C. Evidence suggesting cis action by the TnaC leader peptide in regulating transcription attenuation in the tryptophanase operon of Escherichia coli. J Bacteriol 1995; 177:7245-54. [PMID: 8522534 PMCID: PMC177606 DOI: 10.1128/jb.177.24.7245-7254.1995] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Expression of the tryptophanase (tna) operon in Escherichia coli is regulated by catabolite repression and transcription attenuation. Elevated levels of tryptophan induce transcription antitermination at one or more Rho factor-dependent termination sites in the leader region of the operon. Induction requires translation of a 24-residue coding region, tnaC, located in the 319-nucleotide transcribed leader region preceding tnaA, the structural gene for tryptophanase. In the present paper, we show that two bacterial species that lack tryptophanase activity, Enterobacter aerogenes and Salmonella typhimurium, allow tryptophanase induction and tna operon regulation when they carry a plasmid containing the E. coli tna operon. The role of tnaC in induction was examined by introducing mutations in a 24-nucleotide segment of tnaC of E. coli surrounding and including the crucial Trp codon 12. Some mutations resulted in a noninducible phenotype; these mostly introduced nonconservative amino acid substitutions in TnaC. Other mutations had little or no effect; these generally were in third positions of codons or introduced conservative amino acid replacements. A tryptophan-inserting, UGA-reading glutamine suppressor tRNA was observed to restore partial regulation when Trp codon 12 of tnaC was changed to UGA. Stop codons introduced downstream of Trp codon 12 in all three reading frames established that induction requires translation in the natural tnaC reading frame. Our findings suggest that the TnaC leader peptide acts in cis to prevent Rho-dependent termination.
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Affiliation(s)
- K Gish
- Department of Biological Sciences, Stanford University, California 94305-5020, USA
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38
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A small segment of the MAT alpha 1 transcript promotes mRNA decay in Saccharomyces cerevisiae: a stimulatory role for rare codons. Mol Cell Biol 1993. [PMID: 8355674 DOI: 10.1128/mcb.13.9.5141] [Citation(s) in RCA: 89] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Differences in decay rates of eukaryotic transcripts can be determined by discrete sequence elements within mRNAs. Through the analysis of chimeric transcripts and internal deletions, we have identified a 65-nucleotide segment of the MAT alpha 1 mRNA coding region, termed the MAT alpha 1 instability element, that is sufficient to confer instability to a stable PGK1 reporter transcript and that accelerates turnover of the unstable MAT alpha 1 mRNA. This 65-nucleotide element is composed of two parts, one located within the 5' 33 nucleotides and the second located in the 3' 32 nucleotides. The first part, which can be functionally replaced by sequences containing rare codons, is unable to promote rapid decay by itself but can enhance the action of the 3' 32 nucleotides (positions 234 to 266 in the MAT alpha 1 mRNA) in accelerating turnover. A second portion of the MAT alpha 1 mRNA (nucleotides 265 to 290) is also sufficient to destabilize the PGK1 reporter transcript when positioned 3' of rare codons, suggesting that the 3' half of the MAT alpha 1 instability element is functionally reiterated within the MAT alpha 1 mRNA. The observation that rare codons are part of the 65-nucleotide MAT alpha 1 instability element suggests possible mechanisms through which translation and mRNA decay may be linked.
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39
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Caponigro G, Muhlrad D, Parker R. A small segment of the MAT alpha 1 transcript promotes mRNA decay in Saccharomyces cerevisiae: a stimulatory role for rare codons. Mol Cell Biol 1993; 13:5141-8. [PMID: 8355674 PMCID: PMC360202 DOI: 10.1128/mcb.13.9.5141-5148.1993] [Citation(s) in RCA: 95] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Differences in decay rates of eukaryotic transcripts can be determined by discrete sequence elements within mRNAs. Through the analysis of chimeric transcripts and internal deletions, we have identified a 65-nucleotide segment of the MAT alpha 1 mRNA coding region, termed the MAT alpha 1 instability element, that is sufficient to confer instability to a stable PGK1 reporter transcript and that accelerates turnover of the unstable MAT alpha 1 mRNA. This 65-nucleotide element is composed of two parts, one located within the 5' 33 nucleotides and the second located in the 3' 32 nucleotides. The first part, which can be functionally replaced by sequences containing rare codons, is unable to promote rapid decay by itself but can enhance the action of the 3' 32 nucleotides (positions 234 to 266 in the MAT alpha 1 mRNA) in accelerating turnover. A second portion of the MAT alpha 1 mRNA (nucleotides 265 to 290) is also sufficient to destabilize the PGK1 reporter transcript when positioned 3' of rare codons, suggesting that the 3' half of the MAT alpha 1 instability element is functionally reiterated within the MAT alpha 1 mRNA. The observation that rare codons are part of the 65-nucleotide MAT alpha 1 instability element suggests possible mechanisms through which translation and mRNA decay may be linked.
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Affiliation(s)
- G Caponigro
- Department of Molecular and Cellular Biology, University of Arizona, Tucson 85721
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40
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Jensen KF. The Escherichia coli K-12 "wild types" W3110 and MG1655 have an rph frameshift mutation that leads to pyrimidine starvation due to low pyrE expression levels. J Bacteriol 1993; 175:3401-7. [PMID: 8501045 PMCID: PMC204738 DOI: 10.1128/jb.175.11.3401-3407.1993] [Citation(s) in RCA: 376] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The widely used and closely related Escherichia coli "wild types" W3110 and MG1655, as well as their common ancestor W1485, starve for pyrimidine in minimal medium because of a suboptimal content of orotate phosphoribosyltransferase, which is encoded by the pyrE gene. This conclusion was based on the findings that (i) the strains grew 10 to 15% more slowly in pyrimidine-free medium than in medium containing uracil; (ii) their levels of aspartate transcarbamylase were highly derepressed, as is characteristic for pyrimidine starvation conditions; and (iii) their levels of orotate phosphoribosyltransferase were low. After introduction of a plasmid carrying the rph-pyrE operon from strain HfrH, the growth rates were no longer stimulated by uracil and the levels of aspartate transcarbamylase were low and similar to the levels observed for other strains of E. coli K-12, E. coli B, and Salmonella typhimurium. To identify the mutation responsible for these phenotypes, the rph-pyrE operon of W3110 was cloned in pBR322 from Kohara bacteriophage lambda 2A6. DNA sequencing revealed that a GC base pair was missing near the end of the rph gene of W3110. This one-base-pair deletion results in a frame shift of translation over the last 15 codons and reduces the size of the rph gene product by 10 amino acid residues relative to the size of RNase PH of other E. coli strains, as confirmed by analysis of protein synthesis in minicells. The truncated protein lacks RNase PH activity, and the premature translation stop in the rph cistron explains the low levels of orotate phosphoribosyltransferase in W3110, since close coupling between transcription and translation is needed to support optimal levels of transcription past the intercistronic pyrE attenuator.
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Affiliation(s)
- K F Jensen
- Institute of Biological Chemistry, University of Copenhagen, Denmark
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41
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Sørensen MA, Vogel U, Jensen KF, Pedersen S. The rates of macromolecular chain elongation modulate the initiation frequencies for transcription and translation in Escherichia coli. Antonie Van Leeuwenhoek 1993; 63:323-31. [PMID: 7506514 DOI: 10.1007/bf00871227] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Here we show that most macromolecular biosynthesis reactions in growing bacteria are sub-saturated with substrate. The experiments should in part test predictions from a previously proposed model (Jensen & Pedersen 1990) which proposed a central role for the rates of the RNA and peptide chain elongation reactions in determining the concentration of initiation competent RNA polymerases and ribosomes and thereby the initiation frequencies for these reactions. We have shown that synthesis of ribosomal RNA and the concentration of ppGpp did not exhibit the normal inverse correlation under balanced growth conditions in batch cultures when the RNA chain elongation rate was limited by substrate supply. The RNA chain elongation rate for the polymerase transcribing lacZ mRNA was directly measured and found to be reduced by two-fold under conditions of high ppGpp levels. In the case of translation, we have shown that the peptide elongation rate varied at different types of codons and even among codons read by the same tRNA species. The faster translated codons probably have the highest cognate tRNA concentration and the highest affinity to the tRNA. Thus, the ribosome may operate close to saturation at some codons and be unsaturated at synonymous codons. Therefore, not only translation of the codons for the seven amino acids, whose biosynthesis is regulated by attenuation, but also a substantial fraction of the other translation reactions may be unsaturated. Recently, we have obtained results which indicate that also many ribosome binding sites are unsaturated with their substrate, i.e. with ribosomes.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- M A Sørensen
- Institute of Microbiology, University of Copenhagen, Denmark
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42
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Abstract
It has previously been shown that either phenylalanine codon, UUU or UUC, could be misread as leucine during phenylalanine starvation, if the codons encoded residue 8 of the Escherichia coli argI gene product, ornithine transcarbamylase (OTC). However, no leucine misincorporation was detected when either of these same codons encoded residue 3. Here we report that leucine misincorporation can be directed by a UUU codon for residue 3 of OTC during phenylalanine starvation, if the argI gene has been mutated so that the codon preceding the UUU has been changed from the rarely used glycine codon GGG to the more commonly used GGC.
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Affiliation(s)
- J Parker
- Department of Microbiology, Southern Illinois University, Carbondale, IL 62901
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43
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Parker J, Precup J, Fu C. Misreading of the argI message in Escherichia coli. FEMS Microbiol Lett 1992. [DOI: 10.1111/j.1574-6968.1992.tb05695.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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44
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Jensen K, Andersen J, Poulsen P. Overexpression and rapid purification of the orfE/rph gene product, RNase PH of Escherichia coli. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)41906-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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45
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Boyer S, Shotwell M, Larkins B. Evidence for the translational control of storage protein gene expression in oat seeds. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)41947-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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46
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Andersen JT, Poulsen P, Jensen KF. Attenuation in the rph-pyrE operon of Escherichia coli and processing of the dicistronic mRNA. EUROPEAN JOURNAL OF BIOCHEMISTRY 1992; 206:381-90. [PMID: 1375912 DOI: 10.1111/j.1432-1033.1992.tb16938.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We have substituted on a plasmid the native promoter of the Escherichia coli rph-pyrE operon with an inducible transcription-initiation signal. The plasmid was used to study the mRNA chains derived from the operon at different intracellular concentrations of UTP and as a function of time following induction of transcription. The results showed that dicistronic rph-pyrE mRNA was formed when the UTP pool was low, and that a monocistronic rph mRNa was the major transcription product in high-UTP pools, thus supporting an UTP-controlled attenuation mechanism for regulation of pyrE gene expression. However, the dicistronic rph-pyrE transcript was rapidly processed into two monocistronic mRNA units, and a cleavage site was mapped near the attenuator in the intercistronic region, close to the site where transcription was terminated in high-UTP pools. Furthermore, the major 3' end of the pyrE mRNA was mapped near a palindromic structure of similarity to the family of repetitive extragenic palindromic sequences, 35 nucleotide residues after stop codon of the pryE gene.
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MESH Headings
- Base Sequence
- Blotting, Northern
- Escherichia coli/enzymology
- Escherichia coli/genetics
- Gene Expression Regulation, Bacterial
- Gene Expression Regulation, Enzymologic
- Genes, Bacterial
- Molecular Sequence Data
- Operon
- Orotate Phosphoribosyltransferase/biosynthesis
- Orotate Phosphoribosyltransferase/genetics
- Plasmids
- Promoter Regions, Genetic
- RNA Processing, Post-Transcriptional
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Terminator Regions, Genetic
- Transcription, Genetic
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Affiliation(s)
- J T Andersen
- Institute of Biological Chemistry B, University of Copenhagen, Denmark
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47
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Abstract
Lactic acid bacteria are of major economic importance, as they occupy a key position in the manufacture of fermented foods. A considerable body of research is currently being devoted to the development of lactic acid bacterial strains with improved characteristics, that may be used to make fermentations pass of more efficiently, or to make new applications possible. Therefore, and because the lactococci are designated 'GRAS' organisms ('generally recognized as safe') which may be used for safe production of foreign proteins, detailed knowledge of homologous and heterologous gene expression in these organisms is desired. An overview is given of our current knowledge concerning gene expression in Lactococcus lactis. A general picture of gene expression signals in L. lactis emerges that shows considerable similarity to those observed in Escherichia coli and Bacillus subtilis. This feature allowed the expression of a number of L. lactis-derived genes in the latter bacterial species. Several studies have indicated, however, that in spite of the similarities, the expression signals from E. coli, B. subtilis and L. lactis are not equally efficient in these three organisms.
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Affiliation(s)
- M van de Guchte
- Department of Genetics, University of Groningen, Haren, The Netherlands
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48
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Sørensen MA, Pedersen S. Absolute in vivo translation rates of individual codons in Escherichia coli. The two glutamic acid codons GAA and GAG are translated with a threefold difference in rate. J Mol Biol 1991; 222:265-80. [PMID: 1960727 DOI: 10.1016/0022-2836(91)90211-n] [Citation(s) in RCA: 212] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We have determined the absolute translation rates for four individual codons in Escherichia coli. We used our previously described system for direct measurements of in vivo translation rates using small, in-frame inserts in the lacZ gene. The inserts consisted of multiple synthetic 30 base-pair DNA oligomers with high densities of the four individual codons, GAA (Glu), GAG (Glu), CCG (Pro) and CGA (Arg). Our method is independent of expression level, of mRNA half-life and of transcription rate. Codon GAA was found to be translated with a rate of 21.6 codons/second whereas codon GAG was translated 3.4-fold slower (6.4 codons/s). These two codons are read by the same tRNA species. Codon CCG and CGA are both read by abundant tRNA species but nevertheless we found them to be translated slowly with rates of 5.8 and 4.2 codons/second, respectively. The context of these codons were varied, but we found no significant influence of context on their translation rates and we suggest a mechanism for why context may not affect translation rates. One insert with a low translation rate gave results that most readily can be explained by assuming queue formation of ribosomes on the insert. Such a queue was found to reduce the expression level by approximately 35%. Our experiments allowed us to estimate the average distance between ribosomes and thereby the translation initiation frequency on the wild-type lacZ mRNA. This was found to be one per three seconds.
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Affiliation(s)
- M A Sørensen
- Institute of Microbiology, University of Copenhagen, Denmark
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49
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Faxén M, Plumbridge J, Isaksson LA. Codon choice and potential complementarity between mRNA downstream of the initiation codon and bases 1471-1480 in 16S ribosomal RNA affects expression of glnS. Nucleic Acids Res 1991; 19:5247-51. [PMID: 1681509 PMCID: PMC328883 DOI: 10.1093/nar/19.19.5247] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
A cis-acting expression mutation, GAG to GAA, in the third codon of the glnS gene is analyzed. Both codons code for glutamic acid but the mutation is known to increase gene expression by four fold. We show that the mutation has an effect only if it is located in the beginning of a gene but not if located internally. Data are presented that suggest that the reason for the increased expression by the mutation is the potential formation of one more base pair between the mRNA and 16S ribosomal RNA. Gene expression varies about 16 fold as the number of potential base pairs within the sequence 1471-1480 in 16S RNA increase from two to ten. We also give evidence that supports the idea that the presence of rare codons near the beginning of the mRNA can affect expression.
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Affiliation(s)
- M Faxén
- Department of Microbiology, Stockholm University, Sweden
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50
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Yasueda H, Nagase K, Hosoda A, Akiyama Y, Yamada K. High-level direct expression of semi-synthetic human interleukin-6 in Escherichia coli and production of N-terminus met-free product. Nat Biotechnol 1991; 8:1036-40. [PMID: 1366931 DOI: 10.1038/nbt1190-1036] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We have developed a direct expression system for high-level production of recombinant human interleukin-6 (rhIL-6) in Escherichia coli. In this system, (i) the natural N-terminal coding region of the hIL-6 gene was replaced by a synthetic sequence containing A-T rich codons, (ii) dual Shine-Dalgarno (SD) sequences were employed, (iii) an A-T rich segment was inserted in front of the initiation codon to avoid putative mRNA secondary structure in the region and (iv) the natural amber termination codon of the hIL-6 gene was changed to an ocher stop codon. The hIL-6 polypeptide, synthesized at a high level, formed cytoplasmic inclusion bodies. After refolding, the N-terminal methionine was removed by aminopeptidase-P in vitro. The purified recombinant hIL-6 had B-cell differentiation activity equivalent to natural IL-6 from a human T-cell culture.
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Affiliation(s)
- H Yasueda
- Central Research Laboratories, Ajinomoto Co., Inc., Kawasaki, Japan
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