101
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Fattahi M, Malekpour A, Mortazavi M, Safarpour A, Naseri N. The characteristics of rare codon clusters in the genome and proteins of hepatitis C virus; a bioinformatics look. Middle East J Dig Dis 2014; 6:214-27. [PMID: 25349685 PMCID: PMC4208930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 09/12/2014] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Recent studies suggest that rare codon clusters are functionally important for protein activity. METHODS Here, for the first time we analyzed and reported rare codon clusters in Hepatitis C Virus (HCV) genome and then identified the location of these rare codon clusters in the structure of HCV protein. This analysis was performed using the Sherlocc program that detects statistically relevant conserved rare codon clusters. RESULTS By this program, we identified the rare codon cluster in three regions of HCV genome; NS2, NS3, and NS5A coding sequence of HCV genome. For further understanding of the role of these rare codon clusters, we studied the location of these rare codon clusters and critical residues in the structure of NS2, NS3 and NS5A proteins. We identified some critical residues near or within rare codon clusters. It should be mentioned that characteristics of these critical residues such as location and situation of side chains are important in assurance of the HCV life cycle. CONCLUSION The characteristics of these residues and their relative status showed that these rare codon clusters play an important role in proper folding of these proteins. Thus, it is likely that these rare codon clusters may have an important role in the function of HCV proteins. This information is helpful in development of new avenues for vaccine and treatment protocols.
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Affiliation(s)
- Mohammadreza Fattahi
- 1 Gastroenterohepatology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
,Corresponding Author: Mohammadreza Fattahi, MD Gastroenterohepatology Research Center, Shiraz University of Medical Sciences, P.O. Box: 71935-1311, Shiraz, Iran Telefax: + 98 71 36474263
| | - Abdorrasoul Malekpour
- 1 Gastroenterohepatology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mojtaba Mortazavi
- 2 Department of Biotechnology, Institute of Science and High Technology and Environmental Science, Graduate University of Advanced Technology, Kerman, Iran
| | - Alireza Safarpour
- 1 Gastroenterohepatology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nasrin Naseri
- 1 Gastroenterohepatology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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102
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The effects of the context-dependent codon usage bias on the structure of the nsp1α of porcine reproductive and respiratory syndrome virus. BIOMED RESEARCH INTERNATIONAL 2014; 2014:765320. [PMID: 25162025 PMCID: PMC4137607 DOI: 10.1155/2014/765320] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 06/05/2014] [Accepted: 06/19/2014] [Indexed: 11/18/2022]
Abstract
The information about the crystal structure of porcine reproductive and respiratory syndrome virus (PRRSV) leader protease nsp1α is available to analyze the roles of tRNA abundance of pigs and codon usage of the nsp1 α gene in the formation of this protease. The effects of tRNA abundance of the pigs and the synonymous codon usage and the context-dependent codon bias (CDCB) of the nsp1 α on shaping the specific folding units (α-helix, β-strand, and the coil) in the nsp1α were analyzed based on the structural information about this protease from protein data bank (PDB: 3IFU) and the nsp1 α of the 191 PRRSV strains. By mapping the overall tRNA abundance along the nsp1 α, we found that there is no link between the fluctuation of the overall tRNA abundance and the specific folding units in the nsp1α, and the low translation speed of ribosome caused by the tRNA abundance exists in the nsp1 α. The strong correlation between some synonymous codon usage and the specific folding units in the nsp1α was found, and the phenomenon of CDCB exists in the specific folding units of the nsp1α. These findings provide an insight into the roles of the synonymous codon usage and CDCB in the formation of PRRSV nsp1α structure.
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103
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Dixit G, Baker R, Sacks CM, Torres MP, Dohlman HG. Guanine nucleotide-binding protein (Gα) endocytosis by a cascade of ubiquitin binding domain proteins is required for sustained morphogenesis and proper mating in yeast. J Biol Chem 2014; 289:15052-63. [PMID: 24722989 PMCID: PMC4031556 DOI: 10.1074/jbc.m114.566117] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Revised: 04/07/2014] [Indexed: 01/10/2023] Open
Abstract
Heterotrimeric G proteins are well known to transmit signals from cell surface receptors to intracellular effector proteins. There is growing appreciation that G proteins are also present at endomembrane compartments, where they can potentially interact with a distinct set of signaling proteins. Here, we examine the cellular trafficking function of the G protein α subunit in yeast, Gpa1. Gpa1 contains a unique 109-amino acid insert within the α-helical domain that undergoes a variety of posttranslational modifications. Among these is monoubiquitination, catalyzed by the NEDD4 family ubiquitin ligase Rsp5. Using a newly optimized method for G protein purification together with biophysical measures of structure and function, we show that the ubiquitination domain does not influence enzyme activity. By screening a panel of 39 gene deletion mutants, each lacking a different ubiquitin binding domain protein, we identify seven that are necessary to deliver Gpa1 to the vacuole compartment including four proteins (Ede1, Bul1, Ddi1, and Rup1) previously not known to be involved in this process. Finally, we show that proper endocytosis of the G protein is needed for sustained cellular morphogenesis and mating in response to pheromone stimulation. We conclude that a cascade of ubiquitin-binding proteins serves to deliver the G protein to its final destination within the cell. In this instance and in contrast to the previously characterized visual system, endocytosis from the plasma membrane is needed for proper signal transduction rather than for signal desensitization.
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Affiliation(s)
- Gauri Dixit
- From the Department of Biochemistry and Biophysics
| | | | | | - Matthew P Torres
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Henrik G Dohlman
- From the Department of Biochemistry and Biophysics, Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 and
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104
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O’Brien EP, Ciryam P, Vendruscolo M, Dobson CM. Understanding the influence of codon translation rates on cotranslational protein folding. Acc Chem Res 2014; 47:1536-44. [PMID: 24784899 DOI: 10.1021/ar5000117] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Protein domains can fold into stable tertiary structures while they are synthesized by the ribosome in a process known as cotranslational folding. If a protein does not fold cotranslationally, however, it has the opportunity to do so post-translationally, that is, after the nascent chain has been fully synthesized and released from the ribosome. The rate at which a ribosome adds an amino acid encoded by a particular codon to the elongating nascent chain can vary significantly and is called the codon translation rate. Recent experiments have illustrated the profound impact that codon translation rates can have on the cotranslational folding process and the acquisition of function by nascent proteins. Synonymous codon mutations in an mRNA molecule change the chemical identity of a codon and its translation rate without changing the sequence of the synthesized protein. This change in codon translation rate can, however, cause a nascent protein to malfunction as a result of cotranslational misfolding. In some situations, such dysfunction can have profound implications; for example, it can alter the substrate specificity of an ABC transporter protein, resulting in patients who are nonresponsive to chemotherapy treatment. Thus, codon translation rates are crucial in coordinating protein folding in a cellular environment and can affect downstream cellular processes that depend on the proper functioning of newly synthesized proteins. As the importance of codon translation rates makes clear, a necessary aspect of fully understanding cotranslational folding lies in considering the kinetics of the process in addition to its thermodynamics. In this Account, we examine the contributions that have been made to elucidating the mechanisms of cotranslational folding by using the theoretical and computational tools of chemical kinetics, molecular simulations, and systems biology. These efforts have extended our ability to understand, model, and predict the influence of codon translation rates on cotranslational protein folding and misfolding. The application of such approaches to this important problem is creating a framework for making quantitative predictions of the impact of synonymous codon substitutions on cotranslational folding that has led to a novel hypothesis regarding the role of fast-translating codons in coordinating cotranslational folding. In addition, it is providing new insights into proteome-wide cotranslational folding behavior and making it possible to identify potential molecular mechanisms by which molecular chaperones can influence such behavior during protein synthesis. As we discuss in this Account, bringing together these theoretical developments with experimental approaches is increasingly helping answer fundamental questions about the nature of nascent protein folding on the ribosome.
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Affiliation(s)
- Edward P. O’Brien
- Department
of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Prajwal Ciryam
- Department
of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Michele Vendruscolo
- Department
of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
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105
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Charoensri N, Suphatrakul A, Sriburi R, Yasanga T, Junjhon J, Keelapang P, Utaipat U, Puttikhunt C, Kasinrerk W, Malasit P, Sittisombut N. An optimized expression vector for improving the yield of dengue virus-like particles from transfected insect cells. J Virol Methods 2014; 205:116-23. [PMID: 24814967 DOI: 10.1016/j.jviromet.2014.04.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 04/23/2014] [Accepted: 04/29/2014] [Indexed: 10/25/2022]
Abstract
Recombinant virus-like particles (rVLPs) of flaviviruses are non-infectious particles released from cells expressing the envelope glycoproteins prM and E. Dengue virus rVLPs are recognized as a potential vaccine candidate, but large scale production of these particles is hindered by low yields and the occurrence of cytopathic effects. In an approach to improve the yield of rVLPs from transfected insect cells, several components of a dengue serotype 2 virus prM+E expression cassette were modified and the effect of these modifications was assessed during transient expression. Enhancement of extracellular rVLP levels by simultaneous substitutions of the prM signal peptide and the stem-anchor region of E with homologous cellular and viral counterparts, respectively, was further augmented by codon optimization. Extensive formation of multinucleated cells following transfection with the codon-optimized expression cassette was abrogated by introducing an E fusion loop mutation. This mutation also helped restore the extracellular E levels affected negatively by alteration of a charged residue at the pr-M junction, which was intended to promote maturation of rVLPs during export. Optimized expression cassettes generated in this multiple add-on modification approach should be useful in the generation of stably expressing clones and production of dengue virus rVLPs for immunogenicity studies.
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Affiliation(s)
- Nicha Charoensri
- Center for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Amporn Suphatrakul
- Medical Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Bangkok 10700, Thailand
| | - Rungtawan Sriburi
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Thippawan Yasanga
- Medical Science Research Equipment Center, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Jiraphan Junjhon
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok 10400, Thailand
| | - Poonsook Keelapang
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Utaiwan Utaipat
- Research Institute for Health Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Chunya Puttikhunt
- Medical Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Bangkok 10700, Thailand; Dengue Hemorrhagic Fever Research Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Watchara Kasinrerk
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; Biomedical Technology Research Center, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency at the Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Prida Malasit
- Medical Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Bangkok 10700, Thailand; Dengue Hemorrhagic Fever Research Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Nopporn Sittisombut
- Medical Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Bangkok 10700, Thailand; Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand.
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106
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Sander IM, Chaney JL, Clark PL. Expanding Anfinsen's principle: contributions of synonymous codon selection to rational protein design. J Am Chem Soc 2014; 136:858-61. [PMID: 24392935 PMCID: PMC3959793 DOI: 10.1021/ja411302m] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
![]()
Anfinsen’s principle asserts
that all information required
to specify the structure of a protein is encoded in its amino acid
sequence. However, during protein synthesis by the ribosome, the N-terminus
of the nascent chain can begin to fold before the C-terminus is available.
We tested whether this cotranslational folding can alter the folded
structure of an encoded protein in vivo, versus the structure formed
when refolded in vitro. We designed a fluorescent protein consisting
of three half-domains, where the N- and C-terminal half-domains compete
with each other to interact with the central half-domain. The outcome
of this competition determines the fluorescence properties of the
resulting folded structure. Upon refolding after chemical denaturation,
this protein produced equimolar amounts of the N- and C-terminal folded
structures, respectively. In contrast, translation in Escherichia coli resulted in a 2-fold enhancement
in the formation of the N-terminal folded structure. Rare synonymous
codon substitutions at the 5′ end of the C-terminal half-domain
further increased selection for the N-terminal folded structure. These
results demonstrate that the rate at which a nascent protein emerges
from the ribosome can specify the folded structure of a protein.
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Affiliation(s)
- Ian M Sander
- Department of Chemistry & Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
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107
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Gloge F, Becker AH, Kramer G, Bukau B. Co-translational mechanisms of protein maturation. Curr Opin Struct Biol 2013; 24:24-33. [PMID: 24721450 DOI: 10.1016/j.sbi.2013.11.004] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2013] [Revised: 11/05/2013] [Accepted: 11/21/2013] [Indexed: 10/25/2022]
Abstract
Protein biogenesis integrates multiple finely regulated mechanisms, ensuring nascent polypeptide chains are correctly enzymatically processed, targeted to membranes and folded to native structure. Recent studies show that the cellular translation machinery serves as hub that coordinates the maturation events in space and time at various levels. The ribosome itself serves as docking site for a multitude of nascent chain-interacting factors. The movement of ribosomes along open reading frames is non-uniformous and includes pausing sites, which facilitates nascent chain folding and perhaps factor engagement. Here we summarize current knowledge and discuss emerging concepts underlying the critical interplay between translation and protein maturation in E. coli.
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Affiliation(s)
- Felix Gloge
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Deutsches Krebsforschungszentrum (DKFZ), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany
| | - Annemarie H Becker
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Deutsches Krebsforschungszentrum (DKFZ), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany
| | - Günter Kramer
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Deutsches Krebsforschungszentrum (DKFZ), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany.
| | - Bernd Bukau
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Deutsches Krebsforschungszentrum (DKFZ), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany.
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108
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Van Zyl LJ, Taylor MP, Eley K, Tuffin M, Cowan DA. Engineering pyruvate decarboxylase-mediated ethanol production in the thermophilic host Geobacillus thermoglucosidasius. Appl Microbiol Biotechnol 2013; 98:1247-59. [DOI: 10.1007/s00253-013-5380-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 10/30/2013] [Accepted: 11/02/2013] [Indexed: 11/25/2022]
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109
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Kim YE, Hipp MS, Bracher A, Hayer-Hartl M, Hartl FU. Molecular chaperone functions in protein folding and proteostasis. Annu Rev Biochem 2013; 82:323-55. [PMID: 23746257 DOI: 10.1146/annurev-biochem-060208-092442] [Citation(s) in RCA: 1004] [Impact Index Per Article: 91.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The biological functions of proteins are governed by their three-dimensional fold. Protein folding, maintenance of proteome integrity, and protein homeostasis (proteostasis) critically depend on a complex network of molecular chaperones. Disruption of proteostasis is implicated in aging and the pathogenesis of numerous degenerative diseases. In the cytosol, different classes of molecular chaperones cooperate in evolutionarily conserved folding pathways. Nascent polypeptides interact cotranslationally with a first set of chaperones, including trigger factor and the Hsp70 system, which prevent premature (mis)folding. Folding occurs upon controlled release of newly synthesized proteins from these factors or after transfer to downstream chaperones such as the chaperonins. Chaperonins are large, cylindrical complexes that provide a central compartment for a single protein chain to fold unimpaired by aggregation. This review focuses on recent advances in understanding the mechanisms of chaperone action in promoting and regulating protein folding and on the pathological consequences of protein misfolding and aggregation.
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Affiliation(s)
- Yujin E Kim
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
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110
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Zhou JH, Zhang J, Sun DJ, Ma Q, Chen HT, Ma LN, Ding YZ, Liu YS. The distribution of synonymous codon choice in the translation initiation region of dengue virus. PLoS One 2013; 8:e77239. [PMID: 24204777 PMCID: PMC3808402 DOI: 10.1371/journal.pone.0077239] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 08/30/2013] [Indexed: 11/18/2022] Open
Abstract
Dengue is the most common arthropod-borne viral (Arboviral) illness in humans. The genetic features concerning the codon usage of dengue virus (DENV) were analyzed by the relative synonymous codon usage, the effective number of codons and the codon adaptation index. The evolutionary distance between DENV and the natural hosts (Homo sapiens, Pan troglodytes, Aedes albopictus and Aedes aegypti) was estimated by a novel formula. Finally, the synonymous codon usage preference for the translation initiation region of this virus was also analyzed. The result indicates that the general trend of the 59 synonymous codon usage of the four genotypes of DENV are similar to each other, and this pattern has no link with the geographic distribution of the virus. The effect of codon usage pattern of Aedes albopictus and Aedes aegypti on the formation of codon usage of DENV is stronger than that of the two primates. Turning to the codon usage preference of the translation initiation region of this virus, some codons pairing to low tRNA copy numbers in the two primates have a stronger tendency to exist in the translation initiation region than those in the open reading frame of DENV. Although DENV, like other RNA viruses, has a high mutation to adapt its hosts, the regulatory features about the synonymous codon usage have been 'branded' on the translation initiation region of this virus in order to hijack the translational mechanisms of the hosts.
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Affiliation(s)
- Jian-hua Zhou
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences. Lanzhou, Gansu, P.R. China
| | - Jie Zhang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences. Lanzhou, Gansu, P.R. China
| | - Dong-jie Sun
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences. Lanzhou, Gansu, P.R. China
| | - Qi Ma
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences. Lanzhou, Gansu, P.R. China
| | - Hao-tai Chen
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences. Lanzhou, Gansu, P.R. China
| | - Li-na Ma
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences. Lanzhou, Gansu, P.R. China
| | - Yao-zhong Ding
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences. Lanzhou, Gansu, P.R. China
| | - Yong-sheng Liu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences. Lanzhou, Gansu, P.R. China
- * E-mail:
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111
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Rosenblum G, Chen C, Kaur J, Cui X, Zhang H, Asahara H, Chong S, Smilansky Z, Goldman YE, Cooperman BS. Quantifying elongation rhythm during full-length protein synthesis. J Am Chem Soc 2013; 135:11322-9. [PMID: 23822614 DOI: 10.1021/ja405205c] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Pauses regulate the rhythm of ribosomal protein synthesis. Mutations disrupting even minor pauses can give rise to improperly formed proteins and human disease. Such minor pauses are difficult to characterize by ensemble methods, but can be readily examined by single-molecule (sm) approaches. Here we use smFRET to carry out real-time monitoring of the expression of a full-length protein, the green fluorescent protein variant Emerald GFP. We demonstrate significant correlations between measured elongation rates and codon and isoacceptor tRNA usage, and provide a quantitative estimate of the effect on elongation rate of replacing a codon recognizing an abundant tRNA with a synonymous codon cognate to a rarer tRNA. Our results suggest that tRNA selection plays an important general role in modulating the rates and rhythms of protein synthesis, potentially influencing simultaneous co-translational processes such as folding and chemical modification.
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Affiliation(s)
- Gabriel Rosenblum
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA
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112
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Zhou JH, You YN, Chen HT, Zhang J, Ma LN, Ding YZ, Pejsak Z, Liu YS. The effects of the synonymous codon usage and tRNA abundance on protein folding of the 3C protease of foot-and-mouth disease virus. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2013; 16:270-4. [PMID: 23499709 DOI: 10.1016/j.meegid.2013.02.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 02/18/2013] [Accepted: 02/22/2013] [Indexed: 11/22/2022]
Abstract
The 3C protease of foot-and-mouth disease virus (FMDV) has a conserved amino acid sequence and is responsible for most cleavage in the viral polyprotein. The effects of the synonymous codon usage of FMDV 3C gene and tRNA abundance of the hosts on shaping different folding units (α-helix, β-strand and the coil) in the 3C protease were analyzed based on the structural information of the FMDV 3C protease from Protein Data Bank (PDB: 2BHG) and 210 genes of 3C for all serotypes of FMDV. The strong correlation between some codons usage and the specific folding unit in the FMDV 3C protease is found. As for the effect of translation speed caused by tRNA abundance on the formation of folding units, the codon positions with lowly abundant tRNA scatter in the 3C gene and there is the obvious fluctuation of tRNA abundance locating in the transition boundaries from the β-strand to the α-helix and the coil, respectively. However, codon positions with lowly abundant tRNA clustering into these boundaries are not found, suggesting that the adjustment of translation speed is likely also achieved by the single codon position with low tRNA abundance rather than a cluster. The observations can provide the information for insight into the role of the synonymous codon usage in the formation of 3C protease of FMDV and effect of the tRNA abundance of the hosts on this formation of protease.
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Affiliation(s)
- Jian-hua Zhou
- State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046 Gansu, PR China
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113
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Ma XX, Feng YP, Liu JL, Ma B, Chen L, Zhao YQ, Guo PH, Guo JZ, Ma ZR, Zhang J. The effects of the codon usage and translation speed on protein folding of 3Dpol of foot-and-mouth disease virus. Vet Res Commun 2013; 37:243-50. [DOI: 10.1007/s11259-013-9564-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/10/2013] [Indexed: 10/26/2022]
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114
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Kahali B, Ghosh TC. Disorderness inEscherichia coliproteome: perception of folding fidelity and protein–protein interactions. J Biomol Struct Dyn 2013; 31:472-6. [DOI: 10.1080/07391102.2012.706071] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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115
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Abstract
Cells face a constant challenge as they produce new proteins. The newly synthesized polypeptides must be folded properly to avoid aggregation. If proteins do misfold, they must be cleared to maintain a functional and healthy proteome. Recent work is revealing the complex mechanisms that work cotranslationally to ensure protein quality control during biogenesis at the ribosome. Indeed, the ribosome is emerging as a central hub in coordinating these processes, particularly in sensing the nature of the nascent protein chain, recruiting protein folding and translocation components, and integrating mRNA and nascent chain quality control. The tiered and complementary nature of these decision-making processes confers robustness and fidelity to protein homeostasis during protein synthesis.
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Affiliation(s)
- Sebastian Pechmann
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA
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116
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Hilterbrand A, Saelens J, Putonti C. CBDB: the codon bias database. BMC Bioinformatics 2012; 13:62. [PMID: 22536831 PMCID: PMC3463423 DOI: 10.1186/1471-2105-13-62] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 03/26/2012] [Indexed: 02/01/2023] Open
Abstract
Background In many genomes, a clear preference in the usage of particular codons exists. The mechanisms that induce codon biases remain an open question; studies have attributed codon usage to translational selection, mutational bias and drift. Furthermore, correlations between codon usage within host genomes and their viral pathogens have been observed for a myriad of host-virus systems. As such, numerous studies have investigated codon usage and codon bias in an effort to better understand how species evolve. Numerous metrics have been developed to identify biases in codon usage. In addition, a few data repositories of codon bias data are available, differing in the metrics reported as well as the number and taxonomy of strains examined. Description We have created a new web resource called the Codon Bias Database (CBDB) which provides information regarding the codon bias within the set of highly expressed genes for 300+ bacterial genomes. CBDB was developed to provide a resource for researchers investigating codon bias in bacteria, facilitating comparisons between strains and species. Furthermore, the site was created to serve those studying adaptation in phage; the genera selected for this first release of CBDB all have sequenced, annotated bacteriophages. The annotations and sequences for the highly expressed gene set are available for each strain in addition to the strain’s codon bias measurements. Conclusions Comparing species and strains provides a comprehensive look at how codon usage has been shaped over evolutionary time and can elucidate the putative mechanisms behind it. The Codon Bias Database provides a centralized repository of look-up tables and codon usage bias measures for a wide variety of genera, species and strains. Through our analysis of the variation in codon usage within the strains presently available, we find that most members of a genus have a codon composition most similar to other members of its genus, although not necessarily other members of its species.
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Affiliation(s)
- Adam Hilterbrand
- Department of Biology, Loyola University Chicago, 1032 W Sheridan Road, Chicago, IL 60660, USA
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117
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Weiss C, Bertalan I, Johanningmeier U. Effects of rare codon clusters on the expression of a high-turnover chloroplast protein in Chlamydomonas reinhardtii. J Biotechnol 2012; 160:105-11. [PMID: 22561172 DOI: 10.1016/j.jbiotec.2012.04.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Revised: 02/14/2012] [Accepted: 04/13/2012] [Indexed: 10/28/2022]
Abstract
Expression of foreign proteins in chloroplasts has become an important field of plant genetic engineering. Optimized codon usage is generally thought to increase translational efficiency, but high speed translation of codon bias-adjusted mRNAs can also result in protein misfolding due to a lack of rare codons. In order to analyze the effect of rare codons on a native chloroplast protein in vivo, we modified the D1 subunit of photosystem II by fusing small peptides with different codons into a loop region which tolerates insertions without loss of function. Because of its high-turnover properties, the D1 protein represents an excellent test object to investigate the impact of rare codons on its translation. We choose codons for amino acids Arg, Leu, Ser, Ala and Gly which are rarely used and compared translation of the modified D1 proteins with the respective mutant proteins containing insertions with frequently used codons. Our data indicate that only rare Arg codons drastically affect synthesis of the D1 protein and cluster of rare Ser-codon can induce strategic ribosomal pausing sites.
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Affiliation(s)
- Caroline Weiss
- Institute of Biology, Plant Physiology, Martin-Luther-University Halle-Wittenberg, Weinbergweg 10, 06120 Halle (Saale), Germany
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118
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Chartier M, Gaudreault F, Najmanovich R. Large-scale analysis of conserved rare codon clusters suggests an involvement in co-translational molecular recognition events. ACTA ACUST UNITED AC 2012; 28:1438-45. [PMID: 22467916 DOI: 10.1093/bioinformatics/bts149] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
MOTIVATION An increasing amount of evidence from experimental and computational analysis suggests that rare codon clusters are functionally important for protein activity. Most of the studies on rare codon clusters were performed on a limited number of proteins or protein families. In the present study, we present the Sherlocc program and how it can be used for large scale protein family analysis of evolutionarily conserved rare codon clusters and their relation to protein function and structure. This large-scale analysis was performed using the whole Pfam database covering over 70% of the known protein sequence universe. Our program Sherlocc, detects statistically relevant conserved rare codon clusters and produces a user-friendly HTML output. RESULTS Statistically significant rare codon clusters were detected in a multitude of Pfam protein families. The most statistically significant rare codon clusters were predominantly identified in N-terminal Pfam families. Many of the longest rare codon clusters are found in membrane-related proteins which are required to interact with other proteins as part of their function, for example in targeting or insertion. We identified some cases where rare codon clusters can play a regulating role in the folding of catalytically important domains. Our results support the existence of a widespread functional role for rare codon clusters across species. Finally, we developed an online filter-based search interface that provides access to Sherlocc results for all Pfam families. AVAILABILITY The Sherlocc program and search interface are open access and are available at http://bcb.med.usherbrooke.ca
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Affiliation(s)
- Matthieu Chartier
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Université de Sherbrooke, 12e Avenue Nord, Sherbrooke, Québec, Canada
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119
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Spencer PS, Barral JM. Genetic code redundancy and its influence on the encoded polypeptides. Comput Struct Biotechnol J 2012; 1:e201204006. [PMID: 24688635 PMCID: PMC3962081 DOI: 10.5936/csbj.201204006] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 02/29/2012] [Accepted: 03/10/2012] [Indexed: 11/22/2022] Open
Abstract
The genetic code is said to be redundant in that the same amino acid residue can be encoded by multiple, so-called synonymous, codons. If all properties of synonymous codons were entirely equivalent, one would expect that they would be equally distributed along protein coding sequences. However, many studies over the last three decades have demonstrated that their distribution is not entirely random. It has been postulated that certain codons may be translated by the ribosome faster than others and thus their non-random distribution dictates how fast the ribosome moves along particular segments of the mRNA. The reasons behind such segmental variability in the rates of protein synthesis, and thus polypeptide emergence from the ribosome, have been explored by theoretical and experimental approaches. Predictions of the relative rates at which particular codons are translated and their impact on the nascent chain have not arrived at unequivocal conclusions. This is probably due, at least in part, to variation in the basis for classification of codons as “fast” or “slow”, as well as variability in the number and types of genes and proteins analyzed. Recent methodological advances have allowed nucleotide-resolution studies of ribosome residency times in entire transcriptomes, which confirm the non-uniform movement of ribosomes along mRNAs and shed light on the actual determinants of rate control. Moreover, experiments have begun to emerge that systematically examine the influence of variations in ribosomal movement and the fate of the emerging polypeptide chain.
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Affiliation(s)
- Paige S Spencer
- Department of Biochemistry & Molecular Biology, The University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0620
| | - José M Barral
- Department of Biochemistry & Molecular Biology, The University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0620 ; Department of Neuroscience & Cell Biology, The University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0620 ; Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0620
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120
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Beaber JW, Tam EM, Lao LS, Rondon IJ. A new helper phage for improved monovalent display of Fab molecules. J Immunol Methods 2012; 376:46-54. [PMID: 22119405 DOI: 10.1016/j.jim.2011.11.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Revised: 11/10/2011] [Accepted: 11/10/2011] [Indexed: 10/15/2022]
Abstract
Phage display technology is a powerful tool for the identification of novel antibodies for drug discovery. Phage display libraries have been constructed with massive diversity, but their use may be hindered by limited antibody display levels when rescued with the M13KO7 helper phage. Variants of M13KO7 have been constructed previously that increase the levels of display of rescued phage, but all produce phage that display multiple copies of the antibody fragment on their surface and have reduced titer and infectivity. In this study, we describe a new helper phage, XP5, which increased the display level of Fab molecules more than two-fold compared to phage rescued with M13KO7. XP5 uses a combination of ribosome binding site spacing alterations and rare codon clusters to reduce the expression of pIII from the helper phage. This reduction in pIII expression leads to an increase in the incorporation of pIII-Fab fusions during phage rescue. The rescued phage displayed a single copy of the Fab molecule, preventing any avidity effects during the selection process. This also suggests that the percentage of the population of phage displaying a Fab molecule is increased when rescued with XP5. Additionally, the phage titers and infectivity are comparable to libraries rescued with M13KO7. After two rounds of panning we observed a nearly 5-fold increase in the number of antigen binding Fab molecules compared to panning conducted with the same library rescued with M13KO7. The nature of the mutations in XP5 makes it a universal substitute for M13KO7 in pIII-based phage display, compatible with most phagemids and bacterial strains.
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Affiliation(s)
- John W Beaber
- Preclinical Research and Development, XOMA (US) LLC, Berkeley, CA 94710, United States.
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121
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Theodosiou A, Promponas VJ. LaTcOm: a web server for visualizing rare codon clusters in coding sequences. Bioinformatics 2012; 28:591-2. [PMID: 22199385 DOI: 10.1093/bioinformatics/btr706] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
UNLABELLED We present LaTcOm, a new web tool, which offers several alternative methods for 'rare codon cluster' (RCC) identification from a single and simple graphical user interface. In the current version, three RCC detection schemes are implemented: the recently described %MinMax algorithm and a simplified sliding window approach, along with a novel modification of a linear-time algorithm for the detection of maximally scoring subsequences tailored to the RCC detection problem. Among a number of user tunable parameters, several codon-based scales relevant for RCC detection are available, including tRNA abundance values from Escherichia coli and several codon usage tables from a selection of genomes. Furthermore, useful scale transformations may be performed upon user request (e.g. linear, sigmoid). Users may choose to visualize RCC positions within the submitted sequences either with graphical representations or in textual form for further processing. AVAILABILITY LaTcOm is freely available online at the URL http://troodos.biol.ucy.ac.cy/latcom.html.
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Affiliation(s)
- Athina Theodosiou
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, PO Box 20537, CY 1678, Nicosia, Cyprus
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122
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Nørholm MHH, Light S, Virkki MTI, Elofsson A, von Heijne G, Daley DO. Manipulating the genetic code for membrane protein production: what have we learnt so far? BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:1091-6. [PMID: 21884679 DOI: 10.1016/j.bbamem.2011.08.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Revised: 08/04/2011] [Accepted: 08/15/2011] [Indexed: 12/19/2022]
Abstract
With synthetic gene services, molecular cloning is as easy as ordering a pizza. However choosing the right RNA code for efficient protein production is less straightforward, more akin to deciding on the pizza toppings. The possibility to choose synonymous codons in the gene sequence has ignited a discussion that dates back 50 years: Does synonymous codon use matter? Recent studies indicate that replacement of particular codons for synonymous codons can improve expression in homologous or heterologous hosts, however it is not always successful. Furthermore it is increasingly apparent that membrane protein biogenesis can be codon-sensitive. Single synonymous codon substitutions can influence mRNA stability, mRNA structure, translational initiation, translational elongation and even protein folding. Synonymous codon substitutions therefore need to be carefully evaluated when membrane proteins are engineered for higher production levels and further studies are needed to fully understand how to select the codons that are optimal for higher production. This article is part of a Special Issue entitled: Protein Folding in Membranes.
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Affiliation(s)
- Morten H H Nørholm
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91, Sweden.
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123
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Zhou JH, Zhang J, Chen HT, Ma LN, Ding YZ, Pejsak Z, Liu YS. The codon usage model of the context flanking each cleavage site in the polyprotein of foot-and-mouth disease virus. INFECTION GENETICS AND EVOLUTION 2011; 11:1815-9. [PMID: 21801856 DOI: 10.1016/j.meegid.2011.07.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Revised: 06/03/2011] [Accepted: 07/13/2011] [Indexed: 11/18/2022]
Abstract
To investigate the codon usage pattern of the contexts flanking 11 cleavage sites of foot-and-mouth disease virus (FMDV) polyprotein, the codon usage model of the corresponding codon position and the synonymous codon usage in the target contexts of 66 strains were characterized by two simple methods based on the relative synonymous codon usage value. The synonymous codons usage pattern was also compared between this virus and two species of hosts (cattle and domestic pig). It is indicated that FMDV bore a general resemblance to the hosts in terms of the synonymous codon usage pattern. This feature may help FMDV to utilize translational resources of host efficiently. The two amino acid residues constituting each cleavage site contain at least one conserved residue. It was noticed that the codon usage model with the strong bias appeared in some specific positions in the target contexts, and the under-represented synonymous codons, AUA for Ile, CUA for Leu, UUA for Leu and GUA for Val, are preferentially used in these positions. These under-represented synonymous codons likely play role in regulating the translation rate and influencing the secondary structure of the contexts flanking the cleavage sites.
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Affiliation(s)
- Jian-Hua Zhou
- State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, PR China
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124
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An Y, Chen L, Sun S, Lv A, Wu W. QuikChange shuffling: a convenient and robust method for site-directed mutagenesis and random recombination of homologous genes. N Biotechnol 2011; 28:320-5. [DOI: 10.1016/j.nbt.2011.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 02/12/2011] [Accepted: 03/02/2011] [Indexed: 11/25/2022]
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125
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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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126
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Jha S, Komar AA. Birth, life and death of nascent polypeptide chains. Biotechnol J 2011; 6:623-40. [PMID: 21538896 PMCID: PMC3130931 DOI: 10.1002/biot.201000327] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Revised: 02/26/2011] [Accepted: 03/15/2011] [Indexed: 01/16/2023]
Abstract
The journey of nascent polypeptides from synthesis at the peptidyl transferase center of the ribosome (“birth”) to full function (“maturity”) involves multiple interactions, constraints, modifications and folding events. Each step of this journey impacts the ultimate expression level and functional capacity of the translated protein. It has become clear that the kinetics of protein translation is predominantly modulated by synonymous codon usage along the mRNA, and that this provides an active mechanism for coordinating the synthesis, maturation and folding of nascent polypeptides. Multiple quality control systems ensure that proteins achieve their native, functional form. Unproductive co-translational folding intermediates that arise during protein synthesis may undergo enhanced interaction with components of these systems, such as chaperones, and/or be subjects of co-translational degradation (“death”). This review provides an overview of our current understanding of the complex co-translational events that accompany the synthesis, maturation, folding and degradation of nascent polypeptide chains.
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Affiliation(s)
- Sujata Jha
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH 44115, USA
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127
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Abstract
Over five decades of research have yielded a large body of information on how purified proteins attain their native state when refolded in the test tube, starting from a chemically or thermally denatured state. Nevertheless, we still know little about how proteins fold and unfold in their natural biological habitat: the living cell. Indeed, a variety of cellular components, including molecular chaperones, the ribosome, and crowding of the intracellular medium, modulate folding mechanisms in physiologically relevant environments. This review focuses on the current state of knowledge in protein folding in the cell with emphasis on the early stage of a protein's life, as the nascent polypeptide traverses and emerges from the ribosomal tunnel. Given the vectorial nature of ribosome-assisted translation, the transient degree of chain elongation becomes a relevant variable expected to affect nascent protein foldability, aggregation propensity and extent of interaction with chaperones and the ribosome.
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Affiliation(s)
- Daria V Fedyukina
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
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128
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Zhang G, Ignatova Z. Folding at the birth of the nascent chain: coordinating translation with co-translational folding. Curr Opin Struct Biol 2010; 21:25-31. [PMID: 21111607 DOI: 10.1016/j.sbi.2010.10.008] [Citation(s) in RCA: 147] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Revised: 10/27/2010] [Accepted: 10/29/2010] [Indexed: 11/29/2022]
Abstract
In the living cells, the folding of many proteins is largely believed to begin co-translationally, during their biosynthesis at the ribosomes. In the ribosomal tunnel, the nascent peptide may establish local interactions and stabilize α-helical structures. Long-range contacts are more likely outside the ribosomes after release of larger segments of the nascent chain. Examples suggest that domains can attain native-like structure on the ribosome with and without population of folding intermediates. The co-translational folding is limited by the speed of the gradual extrusion of the nascent peptide which imposes conformational restraints on its folding landscape. Recent experimental and in silico modeling studies indicate that translation kinetics fine-tunes co-translational folding by providing a time delay for sequential folding of distinct portions of the nascent chain.
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Affiliation(s)
- Gong Zhang
- Department of Biochemistry, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14467 Potsdam, Germany
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129
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Horton AA, Lee Y, Coulibaly CA, Rashbrook VK, Cornel AJ, Lanzaro GC, Luckhart S. Identification of three single nucleotide polymorphisms in Anopheles gambiae immune signaling genes that are associated with natural Plasmodium falciparum infection. Malar J 2010; 9:160. [PMID: 20540770 PMCID: PMC2896950 DOI: 10.1186/1475-2875-9-160] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Accepted: 06/11/2010] [Indexed: 01/26/2023] Open
Abstract
Background Laboratory studies have demonstrated that a variety of immune signaling pathways regulate malaria parasite infection in Anopheles gambiae, the primary vector species in Africa. Methods To begin to understand the importance of these associations under natural conditions, an association mapping approach was adopted to determine whether single nucleotide polymorphisms (SNPs) in selected immune signaling genes in A. gambiae collected in Mali were associated with the phenotype of Plasmodium falciparum infection. Results Three SNPs were identified in field-collected mosquitoes that were associated with parasite infection in molecular form-dependent patterns: two were detected in the Toll5B gene and one was detected in the gene encoding insulin-like peptide 3 precursor. In addition, one infection-associated Toll5B SNP was in linkage disequilibrium with a SNP in sequence encoding a mitogen-activated protein kinase that has been associated with Toll signaling in mammalian cells. Both Toll5B SNPs showed divergence from Hardy-Weinberg equilibrium, suggesting that selection pressure(s) are acting on these loci. Conclusions Seven of these eight infection-associated and linked SNPs alter codon frequency or introduce non-synonymous changes that would be predicted to alter protein structure and, hence, function, suggesting that these SNPs could alter immune signaling and responsiveness to parasite infection.
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Affiliation(s)
- Ashley A Horton
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA
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130
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Saunders R, Deane CM. Synonymous codon usage influences the local protein structure observed. Nucleic Acids Res 2010; 38:6719-28. [PMID: 20530529 PMCID: PMC2965230 DOI: 10.1093/nar/gkq495] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Translation of mRNA into protein is a unidirectional information flow process. Analysing the input (mRNA) and output (protein) of translation, we find that local protein structure information is encoded in the mRNA nucleotide sequence. The Coding Sequence and Structure (CSandS) database developed in this work provides a detailed mapping between over 4000 solved protein structures and their mRNA. CSandS facilitates a comprehensive analysis of codon usage over many organisms. In assigning translation speed, we find that relative codon usage is less informative than tRNA concentration. For all speed measures, no evidence was found that domain boundaries are enriched with slow codons. In fact, genes seemingly avoid slow codons around structurally defined domain boundaries. Translation speed, however, does decrease at the transition into secondary structure. Codons are identified that have structural preferences significantly different from the amino acid they encode. However, each organism has its own set of ‘significant codons’. Our results support the premise that codons encode more information than merely amino acids and give insight into the role of translation in protein folding.
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Affiliation(s)
- Rhodri Saunders
- Department of Statistics, Oxford University, 1 South Parks Road, Oxford OX1 3TG, UK.
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131
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Ellis JJ, Huard FPE, Deane CM, Srivastava S, Wood GR. Directionality in protein fold prediction. BMC Bioinformatics 2010; 11:172. [PMID: 20374616 PMCID: PMC2871273 DOI: 10.1186/1471-2105-11-172] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Accepted: 04/07/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ever since the ground-breaking work of Anfinsen et al. in which a denatured protein was found to refold to its native state, it has been frequently stated by the protein fold prediction community that all the information required for protein folding lies in the amino acid sequence. Recent in vitro experiments and in silico computational studies, however, have shown that cotranslation may affect the folding pathway of some proteins, especially those of ancient folds. In this paper aspects of cotranslational folding have been incorporated into a protein structure prediction algorithm by adapting the Rosetta program to fold proteins as the nascent chain elongates. This makes it possible to conduct a pairwise comparison of folding accuracy, by comparing folds created sequentially from each end of the protein. RESULTS A single main result emerged: in 94% of proteins analyzed, following the sense of translation, from N-terminus to C-terminus, produced better predictions than following the reverse sense of translation, from the C-terminus to N-terminus. Two secondary results emerged. First, this superiority of N-terminus to C-terminus folding was more marked for proteins showing stronger evidence of cotranslation and second, an algorithm following the sense of translation produced predictions comparable to, and occasionally better than, Rosetta. CONCLUSIONS There is a directionality effect in protein fold prediction. At present, prediction methods appear to be too noisy to take advantage of this effect; as techniques refine, it may be possible to draw benefit from a sequential approach to protein fold prediction.
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Affiliation(s)
- Jonathan J Ellis
- Department of Statistics, Macquarie University, Sydney, NSW 2109, Australia
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Zhou T, Gu W, Wilke CO. Detecting positive and purifying selection at synonymous sites in yeast and worm. Mol Biol Evol 2010; 27:1912-22. [PMID: 20231333 DOI: 10.1093/molbev/msq077] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We present a new computational method to identify positive and purifying selection at synonymous sites in yeast and worm. We define synonymous substitutions that change codons from preferred to unpreferred or vice versa as nonconservative synonymous substitutions and all other substitutions as conservative. Using a maximum-likelihood framework, we then test whether conservative and nonconservative synonymous substitutions occur at equal rates. Our approach replaces the standard rate of synonymous substitutions per synonymous site, dS, with two new rates, the conservative synonymous substitution rate (dS(C)) and the nonconservative synonymous substitution rate (dS(N)). Based on the ratio dS(N)/dS(C), we find that 0.05% of all yeast genes and none of worm genes show evidence of positive selection at synonymous sites (dS(N)/dS(C) > 1). On the other hand, 9.44% of all yeast genes and 5.12% of all worm genes show evidence of significant purifying selection on synonymous sites (dS(N)/dS(C) < 1). We also find that dS(N) correlates strongly with gene expression level, whereas the correlation between expression level and dS(C) is very weak. Thus, dS(N) captures most of the signal of selection for translational accuracy and speed, whereas dS(C) is not strongly influenced by this selection pressure. We suggest that the ratio dN/dS(C) may be more appropriate than the ratio dN/dS to identify positive or purifying selection on amino acids.
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Affiliation(s)
- Tong Zhou
- Center for Computational Biology and Bioinformatics, University of Texas at Austin, TX, USA
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133
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Increased incidence of rare codon clusters at 5' and 3' gene termini: implications for function. BMC Genomics 2010; 11:118. [PMID: 20167116 PMCID: PMC2833160 DOI: 10.1186/1471-2164-11-118] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Accepted: 02/18/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The process of translation can be affected by the use of rare versus common codons within the mRNA transcript. RESULTS Here, we show that rare codons are enriched at the 5' and 3' termini of genes from E. coli and other prokaryotes. Genes predicted to be secreted show significant enrichment in 5' rare codon clusters, but not 3' rare codon clusters. Surprisingly, no correlation between 5' mRNA structure and rare codon usage was observed. CONCLUSIONS Potential functional roles for the enrichment of rare codons at terminal positions are explored.
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134
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Hoffmann A, Bukau B, Kramer G. Structure and function of the molecular chaperone Trigger Factor. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2010; 1803:650-61. [PMID: 20132842 DOI: 10.1016/j.bbamcr.2010.01.017] [Citation(s) in RCA: 164] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2009] [Accepted: 01/22/2010] [Indexed: 01/16/2023]
Abstract
Newly synthesized proteins often require the assistance of molecular chaperones to efficiently fold into functional three-dimensional structures. At first, ribosome-associated chaperones guide the initial folding steps and protect growing polypeptide chains from misfolding and aggregation. After that folding into the native structure may occur spontaneously or require support by additional chaperones which do not bind to the ribosome such as DnaK and GroEL. Here we review the current knowledge on the best-characterized ribosome-associated chaperone at present, the Escherichia coli Trigger Factor. We describe recent progress on structural and dynamic aspects of Trigger Factor's interactions with the ribosome and substrates and discuss how these interactions affect co-translational protein folding. In addition, we discuss the newly proposed ribosome-independent function of Trigger Factor as assembly factor of multi-subunit protein complexes. Finally, we cover the functional cooperation between Trigger Factor, DnaK and GroEL in folding of cytosolic proteins and the interplay between Trigger Factor and other ribosome-associated factors acting in enzymatic processing and translocation of nascent polypeptide chains.
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Affiliation(s)
- Anja Hoffmann
- Zentrum für Molekulare Biologie der Universität Heidelberg, Heidelberg, Germany
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135
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Frugier M, Bour T, Ayach M, Santos MAS, Rudinger-Thirion J, Théobald-Dietrich A, Pizzi E. Low Complexity Regions behave as tRNA sponges to help co-translational folding of plasmodial proteins. FEBS Lett 2009; 584:448-54. [PMID: 19900443 DOI: 10.1016/j.febslet.2009.11.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Revised: 11/02/2009] [Accepted: 11/03/2009] [Indexed: 10/20/2022]
Abstract
In most organisms, the information necessary to specify the native 3D-structures of proteins is encoded in the corresponding mRNA sequences. Translational accuracy and efficiency are coupled and sequences that are slowly translated play an essential role in the concomitant folding of protein domains. Here, we suggest that the well-known mechanisms for the regulation of translational efficiency, which involves mRNA structure and/or asymmetric tRNA abundance, do not apply to all organisms. We propose that Plasmodium, the parasite responsible for malaria, uses an alternative strategy to slow down ribosomal speed and avoid multidomain protein misfolding during translation. In our model, the abundant Low Complexity Regions present in Plasmodium proteins replace the codon preferences, which influence the assembly of protein secondary structures.
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Affiliation(s)
- Magali Frugier
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, 67084 Strasbourg Cedex, France.
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136
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Clark PL, Ugrinov KG. Measuring cotranslational folding of nascent polypeptide chains on ribosomes. Methods Enzymol 2009; 466:567-90. [PMID: 21609877 DOI: 10.1016/s0076-6879(09)66024-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Protein folding has been studied extensively in vitro, but much less is known about how folding proceeds in vivo. A particular distinction of folding in vivo is that folding begins while the nascent polypeptide chain is still undergoing synthesis by the ribosome. Studies of cotranslational protein folding are inherently much more complex than classical in vitro protein folding studies, and historically there have been few methods available to produce the quantities of pure material required for biophysical studies of the nascent chain, or assays to specifically interrogate its conformation. However, the past few years have produced dramatic methodological advances, which now place cotranslational folding studies within reach of more biochemists, enabling a detailed comparison of the earliest stages of protein folding on the ribosome to the wealth of information available for the refolding of full-length polypeptide chains in vitro.
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Affiliation(s)
- Patricia L Clark
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
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137
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Davidsen T, Beck E, Ganapathy A, Montgomery R, Zafar N, Yang Q, Madupu R, Goetz P, Galinsky K, White O, Sutton G. The comprehensive microbial resource. Nucleic Acids Res 2009; 38:D340-5. [PMID: 19892825 PMCID: PMC2808947 DOI: 10.1093/nar/gkp912] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Comprehensive Microbial Resource or CMR (http://cmr.jcvi.org) provides a web-based central resource for the display, search and analysis of the sequence and annotation for complete and publicly available bacterial and archaeal genomes. In addition to displaying the original annotation from GenBank, the CMR makes available secondary automated structural and functional annotation across all genomes to provide consistent data types necessary for effective mining of genomic data. Precomputed homology searches are stored to allow meaningful genome comparisons. The CMR supplies users with over 50 different tools to utilize the sequence and annotation data across one or more of the 571 currently available genomes. At the gene level users can view the gene annotation and underlying evidence. Genome level information includes whole genome graphical displays, biochemical pathway maps and genome summary data. Comparative tools display analysis between genomes with homology and genome alignment tools, and searches across the accessions, annotation, and evidence assigned to all genes/genomes are available. The data and tools on the CMR aid genomic research and analysis, and the CMR is included in over 200 scientific publications. The code underlying the CMR website and the CMR database are freely available for download with no license restrictions.
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138
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Ponnala L. On finding poorly translated codons based on their usage frequency. Bioinformation 2009; 4:63-5. [PMID: 20198170 PMCID: PMC2823382 DOI: 10.6026/97320630004063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Accepted: 07/18/2009] [Indexed: 11/23/2022] Open
Abstract
Long stretches of “rare” codons are known to severely inhibit the efficiency of translation. Understanding the distribution of such rare codons is
of critical importance in improving the efficiency of heterologous gene expression systems. Accurate estimates of codon usage take the
abundance of each protein into consideration. In this paper, we analyze the correlation between approximate measures of codon usage and the
availability of tRNA at various growth rates in E coli. We show that the computationally derived estimates of tRNA isoacceptor concentration
enable the finding of poorly translated codons.
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Affiliation(s)
- Lalit Ponnala
- Computational Biology Service Unit, Cornell University, Ithaca, NY 14853, USA.
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139
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The ribosome as a platform for co-translational processing, folding and targeting of newly synthesized proteins. Nat Struct Mol Biol 2009; 16:589-97. [PMID: 19491936 DOI: 10.1038/nsmb.1614] [Citation(s) in RCA: 347] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The early events in the life of newly synthesized proteins in the cellular environment are remarkably complex. Concurrently with their synthesis by the ribosome, nascent polypeptides are subjected to enzymatic processing, chaperone-assisted folding or targeting to translocation pores at membranes. The ribosome itself has a key role in these different tasks and governs the interplay between the various factors involved. Indeed, the ribosome serves as a platform for the spatially and temporally regulated association of enzymes, targeting factors and chaperones that act upon the nascent polypeptides emerging from the exit tunnel. Furthermore, the ribosome provides opportunities to coordinate the protein-synthesis activity of its peptidyl transferase center with the protein targeting and folding processes. Here we review the early co-translational events involving the ribosome that guide cytosolic proteins to their native state.
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140
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Clustering of codons with rare cognate tRNAs in human genes suggests an extra level of expression regulation. PLoS Genet 2009; 5:e1000548. [PMID: 19578405 PMCID: PMC2697378 DOI: 10.1371/journal.pgen.1000548] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2008] [Accepted: 06/03/2009] [Indexed: 12/31/2022] Open
Abstract
In species with large effective population sizes, highly expressed genes tend to be encoded by codons with highly abundant cognate tRNAs to maximize translation rate. However, there has been little evidence for a similar bias of synonymous codons in highly expressed human genes. Here, we ask instead whether there is evidence for the selection for codons associated with low abundance tRNAs. Rather than averaging the codon usage of complete genes, we scan the genes for windows with deviating codon usage. We show that there is a significant over representation of human genes that contain clusters of codons with low abundance cognate tRNAs. We name these regions, which on average have a 50% reduction in the amount of cognate tRNA available compared to the remainder of the gene, RTS (rare tRNA score) clusters. We observed a significant reduction in the substitution rate between the human RTS clusters and their orthologous chimp sequence, when compared to non-RTS cluster sequences. Overall, the genes with an RTS cluster have higher tissue specificity than the non-RTS cluster genes. Furthermore, these genes are functionally enriched for transcription regulation. As genes that regulate transcription in lower eukaryotes are known to be involved in translation on demand, this suggests that the mechanism of translation level expression regulation also exists within the human genome.
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141
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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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