Determinants of translation efficiency and accuracy

[1]  Yitzhak Pilpel,et al.  The role of codon selection in regulation of translation efficiency deduced from synthetic libraries , 2011, Genome Biology.

[2]  Harkamal Walia,et al.  Protein abundances are more conserved than mRNA abundances across diverse taxa , 2010, Proteomics.

[3]  Michael D. Rice,et al.  The mRNA landscape at yeast translation initiation sites , 2010, Bioinform..

[4]  M. Bushell,et al.  Translational regulation of gene expression during conditions of cell stress. , 2010, Molecular cell.

[5]  Jian-Rong Yang,et al.  Impact of translational error-induced and error-free misfolding on the rate of protein evolution , 2010, Molecular systems biology.

[6]  Svetlana A. Shabalina,et al.  Differential Arginylation of Actin Isoforms Is Regulated by Coding Sequence–Dependent Degradation , 2010, Science.

[7]  P. Higgs,et al.  The influence of anticodon-codon interactions and modified bases on codon usage bias in bacteria. , 2010, Molecular biology and evolution.

[8]  S. Le,et al.  Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line , 2010, Molecular systems biology.

[9]  S. Ben-Yehuda,et al.  Visualizing high error levels during gene expression in living bacterial cells , 2010, Proceedings of the National Academy of Sciences.

[10]  Y. Pilpel,et al.  An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation , 2010, Cell.

[11]  Nicol N. Schraudolph,et al.  A Role for Codon Order in Translation Dynamics , 2010, Cell.

[12]  Eytan Ruppin,et al.  Translation efficiency is determined by both codon bias and folding energy , 2010, Proceedings of the National Academy of Sciences.

[13]  Haiwei Song,et al.  Structural and mechanistic insights into translation termination. , 2010, Current opinion in structural biology.

[14]  R. Jackson,et al.  The mechanism of eukaryotic translation initiation and principles of its regulation , 2010, Nature Reviews Molecular Cell Biology.

[15]  J. Parsch,et al.  Experimentally Increased Codon Bias in the Drosophila Adh Gene Leads to an Increase in Larval, But Not Adult, Alcohol Dehydrogenase Activity , 2010, Genetics.

[16]  Tong Zhou,et al.  A Universal Trend of Reduced mRNA Stability near the Translation-Initiation Site in Prokaryotes and Eukaryotes , 2010, PLoS Comput. Biol..

[17]  Tobias Warnecke,et al.  GroEL dependency affects codon usage—support for a critical role of misfolding in gene evolution , 2010, Molecular systems biology.

[18]  Premal Shah,et al.  Measuring and Detecting Molecular Adaptation in Codon Usage Against Nonsense Errors During Protein Translation , 2009, Genetics.

[19]  E. Marcotte,et al.  Global signatures of protein and mRNA expression levelsw , 2009 .

[20]  J. Yewdell,et al.  Innate Immune and Chemically Triggered Oxidative Stress Modifies Translational Fidelity , 2009, Nature.

[21]  David G Hendrickson,et al.  Concordant Regulation of Translation and mRNA Abundance for Hundreds of Targets of a Human microRNA , 2009, PLoS biology.

[22]  Michal Linial,et al.  Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferences , 2009, Molecular systems biology.

[23]  Alan Villalobos,et al.  Design Parameters to Control Synthetic Gene Expression in Escherichia coli , 2009, PloS one.

[24]  D. Lipman,et al.  Selection for minimization of translational frameshifting errors as a factor in the evolution of codon usage , 2009, Nucleic acids research.

[25]  Tobias Warnecke,et al.  Why there is more to protein evolution than protein function: splicing, nucleosomes and dual-coding sequence. , 2009, Biochemical Society transactions.

[26]  Tong Zhou,et al.  Translationally optimal codons associate with structurally sensitive sites in proteins. , 2009, Molecular biology and evolution.

[27]  T. Pan,et al.  Genome-wide Analysis of tRNA Charging and Activation of the eIF2 Kinase Gcn2p*♦ , 2009, The Journal of Biological Chemistry.

[28]  M. Mirande,et al.  Dynamic Organization of Aminoacyl-tRNA Synthetase Complexes in the Cytoplasm of Human Cells* , 2009, Journal of Biological Chemistry.

[29]  Nicholas T. Ingolia,et al.  Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling , 2009, Science.

[30]  Zoya Ignatova,et al.  Transient ribosomal attenuation coordinates protein synthesis and co-translational folding , 2009, Nature Structural &Molecular Biology.

[31]  R. Aebersold,et al.  Comparative Functional Analysis of the Caenorhabditis elegans and Drosophila melanogaster Proteomes , 2009, PLoS biology.

[32]  Lorenz Wernisch,et al.  Estimating Translational Selection in Eukaryotic Genomes , 2008, Molecular biology and evolution.

[33]  Reinhard Wolf,et al.  Coding-Sequence Determinants of Gene Expression in Escherichia coli , 2009 .

[34]  S. Teichmann,et al.  Tight Regulation of Unstructured Proteins: From Transcript Synthesis to Protein Degradation , 2008, Science.

[35]  Ruth Nussinov,et al.  Synonymous mutations and ribosome stalling can lead to altered folding pathways and distinct minima. , 2008, Journal of molecular biology.

[36]  Z. Gu,et al.  Relaxation of yeast mitochondrial functions after whole-genome duplication. , 2008, Genome research.

[37]  Claus O. Wilke,et al.  Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution , 2008, Cell.

[38]  M. Gerstein,et al.  The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing , 2008, Science.

[39]  Ignacio Tinoco,et al.  Following translation by single ribosomes one codon at a time , 2008, Nature.

[40]  Gang Wu,et al.  Integrative Analyses of Posttranscriptional Regulation in the Yeast Saccharomyces cerevisiae Using Transcriptomic and Proteomic Data , 2008, Current Microbiology.

[41]  Daniel M. Stoebel,et al.  The Cost of Expression of Escherichia coli lac Operon Proteins Is in the Process, Not in the Products , 2008, Genetics.

[42]  Alessandra Carbone,et al.  Codon Bias is a Major Factor Explaining Phage Evolution in Translationally Biased Hosts , 2008, Journal of Molecular Evolution.

[43]  Joel L Sussman,et al.  Operational definition of intrinsically unstructured protein sequences based on susceptibility to the 20S proteasome , 2007, Proteins.

[44]  Joshua B. Plotkin,et al.  Genome Landscapes and Bacteriophage Codon Usage , 2007, PLoS Comput. Biol..

[45]  C. Ponting,et al.  Variable Strength of Translational Selection Among 12 Drosophila Species , 2007, Genetics.

[46]  Massimo Vergassola,et al.  Causes for the intriguing presence of tRNAs in phages. , 2007, Genome research.

[47]  Joost Schymkowitz,et al.  The stability effects of protein mutations appear to be universally distributed. , 2007, Journal of molecular biology.

[48]  J. Mata,et al.  A Network of Multiple Regulatory Layers Shapes Gene Expression in Fission Yeast , 2007, Molecular cell.

[49]  Yitzhak Pilpel,et al.  Differential translation efficiency of orthologous genes is involved in phenotypic divergence of yeast species , 2007, Nature Genetics.

[50]  Lippincott-Schwartz,et al.  Supporting Online Material Materials and Methods Som Text Figs. S1 to S8 Table S1 Movies S1 to S3 a " Silent " Polymorphism in the Mdr1 Gene Changes Substrate Specificity Corrected 30 November 2007; See Last Page , 2022 .

[51]  A. Eyre-Walker,et al.  Synonymous codon usage in Escherichia coli: selection for translational accuracy. , 2006, Molecular biology and evolution.

[52]  Gang Wu,et al.  Correlation of mRNA Expression and Protein Abundance Affected by Multiple Sequence Features Related to Translational Efficiency in Desulfovibrio vulgaris: A Quantitative Analysis , 2006, Genetics.

[53]  Tao Pan,et al.  Tissue-Specific Differences in Human Transfer RNA Expression , 2006, PLoS genetics.

[54]  N. Gregersen,et al.  Protein misfolding disorders: Pathogenesis and intervention , 2006, Journal of Inherited Metabolic Disease.

[55]  L. Hurst,et al.  Hearing silence: non-neutral evolution at synonymous sites in mammals , 2006, Nature Reviews Genetics.

[56]  Kevin Camphausen,et al.  Radiation-induced changes in gene expression involve recruitment of existing messenger RNAs to and away from polysomes. , 2006, Cancer research.

[57]  M. Kozak,et al.  Regulation of translation via mRNA structure in prokaryotes and eukaryotes. , 2005, Gene.

[58]  Yanda Li,et al.  The relationship among gene expression, folding free energy and codon usage bias in Escherichia coli , 2005, FEBS letters.

[59]  M. Takagi,et al.  Regulation of p53 Translation and Induction after DNA Damage by Ribosomal Protein L26 and Nucleolin , 2005, Cell.

[60]  U. Alon,et al.  Optimality and evolutionary tuning of the expression level of a protein , 2005, Nature.

[61]  Yizhar Lavner,et al.  Codon bias as a factor in regulating expression via translation rate in the human genome. , 2005, Gene.

[62]  D. McConnell,et al.  Selection pressures on codon usage in the complete genome of bacteriophage T7 , 1985, Journal of Molecular Evolution.

[63]  N. Sonenberg,et al.  Mammalian poly(A)-binding protein is a eukaryotic translation initiation factor, which acts via multiple mechanisms. , 2005, Genes & development.

[64]  J. M. Comeron,et al.  Selective and Mutational Patterns Associated With Gene Expression in Humans , 2004, Genetics.

[65]  G. Crooks,et al.  WebLogo: a sequence logo generator. , 2004, Genome research.

[66]  T. Pan,et al.  Exploring the regulation of tRNA distribution on the genomic scale. , 2004, Journal of molecular biology.

[67]  L. Wernisch,et al.  Solving the riddle of codon usage preferences: a test for translational selection. , 2004, Nucleic acids research.

[68]  Clifford H. Taubes,et al.  Towards a theory of evolutionary adaptation , 2004, Genetica.

[69]  H. Margalit,et al.  Hierarchy of sequence-dependent features associated with prokaryotic translation. , 2003, Genome research.

[70]  Araxi O. Urrutia,et al.  A unification of mosaic structures in the human genome. , 2003, Human molecular genetics.

[71]  C. Dobson,et al.  Protein aggregation and aggregate toxicity: new insights into protein folding, misfolding diseases and biological evolution , 2003, Journal of Molecular Medicine.

[72]  J. Elf,et al.  Selective Charging of tRNA Isoacceptors Explains Patterns of Codon Usage , 2003, Science.

[73]  John D. Storey,et al.  Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[74]  M. Kozak,et al.  Pushing the limits of the scanning mechanism for initiation of translation , 2002, Gene.

[75]  Ricardo Ehrlich,et al.  Silent mutations affect in vivo protein folding in Escherichia coli. , 2002, Biochemical and biophysical research communications.

[76]  C. Dobson,et al.  Inherent toxicity of aggregates implies a common mechanism for protein misfolding diseases , 2002, Nature.

[77]  '. T.A.THANARAJ Ribosome-mediated translational pause and protein domain organization , 2002 .

[78]  Shigehiko Kanaya,et al.  Codon Usage and tRNA Genes in Eukaryotes: Correlation of Codon Usage Diversity with Translation Efficiency and with CG-Dinucleotide Usage as Assessed by Multivariate Analysis , 2001, Journal of Molecular Evolution.

[79]  M. Sørensen,et al.  Charging levels of four tRNA species in Escherichia coli Rel(+) and Rel(-) strains during amino acid starvation: a simple model for the effect of ppGpp on translational accuracy. , 2001, Journal of molecular biology.

[80]  S. Wessler,et al.  Role of mRNA secondary structure in translational repression of the maize transcriptional activator Lc(1,2). , 2001, Plant physiology.

[81]  M. Rodnina,et al.  Fidelity of aminoacyl-tRNA selection on the ribosome: kinetic and structural mechanisms. , 2001, Annual review of biochemistry.

[82]  V. Uversky,et al.  Why are “natively unfolded” proteins unstructured under physiologic conditions? , 2000, Proteins.

[83]  L. Duret,et al.  tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes. , 2000, Trends in genetics : TIG.

[84]  D. Söll,et al.  Aminoacyl-tRNA synthesis. , 2000, Annual review of biochemistry.

[85]  A. Komar,et al.  Synonymous codon substitutions affect ribosome traffic and protein folding during in vitro translation , 1999, FEBS letters.

[86]  S. Kanaya,et al.  Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: gene expression level and species-specific diversity of codon usage based on multivariate analysis. , 1999, Gene.

[87]  L. Duret,et al.  Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[88]  P. Farabaugh,et al.  How translational accuracy influences reading frame maintenance , 1999, The EMBO journal.

[89]  W. V. Shaw,et al.  Missense translation errors in Saccharomyces cerevisiae. , 1998, Journal of molecular biology.

[90]  Etsuko N. Moriyama,et al.  Codon Usage Bias and tRNA Abundance in Drosophila , 1997, Journal of Molecular Evolution.

[91]  A. Pavesi,et al.  Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae. , 1997, Journal of molecular biology.

[92]  A. Sachs,et al.  Association of the yeast poly(A) tail binding protein with translation initiation factor eIF‐4G. , 1996, The EMBO journal.

[93]  P Argos,et al.  Protein secondary structural types are differentially coded on messenger RNA , 1996, Protein science : a publication of the Protein Society.

[94]  C. Kurland,et al.  Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates. , 1996, Journal of molecular biology.

[95]  P Argos,et al.  Ribosome‐mediated translational pause and protein domain organization , 1996, Protein science : a publication of the Protein Society.

[96]  J. Carson,et al.  Protein translation components are colocalized in granules in oligodendrocytes. , 1995, Journal of cell science.

[97]  Coevolution of RNA helix stability and Shine‐Dalgarno complementarity in a translational start region , 1995, Molecular microbiology.

[98]  A. Brown,et al.  The folding of the bifunctional TRP3 protein in yeast is influenced by a translational pause which lies in a region of structural divergence with Escherichia coli indoleglycerol-phosphate synthase. , 1994, European journal of biochemistry.

[99]  Paul M. Sharp,et al.  Codon usage in Caenorhabditis elegans: delineation of translational selection and mutational biases , 1994, Nucleic Acids Res..

[100]  H. Akashi Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy. , 1994, Genetics.

[101]  J. van Duin,et al.  Translational initiation on structured messengers. Another role for the Shine-Dalgarno interaction. , 1994, Journal of molecular biology.

[102]  A. Brown,et al.  Protein folding within the cell is influenced by controlled rates of polypeptide elongation. , 1992, Journal of molecular biology.

[103]  D. Gallie The cap and poly(A) tail function synergistically to regulate mRNA translational efficiency. , 1991, Genes & development.

[104]  M. Bulmer The selection-mutation-drift theory of synonymous codon usage. , 1991, Genetics.

[105]  E. Goldman,et al.  Low-usage codons in Escherichia coli, yeast, fruit fly and primates. , 1991, Gene.

[106]  C. Kurland,et al.  Codon preferences in free-living microorganisms. , 1990, Microbiological reviews.

[107]  F. Wright The 'effective number of codons' used in a gene. , 1990, Gene.

[108]  C. Kurland,et al.  Codon usage determines translation rate in Escherichia coli. , 1989, Journal of molecular biology.

[109]  J. McCarthy,et al.  The role of bases upstream of the Shine-Dalgarno region and in the coding sequence in the control of gene expression in Escherichia coli: translation and stability of mRNAs in vivo. , 1989, Gene.

[110]  D C Shields,et al.  "Silent" sites in Drosophila genes are not neutral: evidence of selection among synonymous codons. , 1988, Molecular biology and evolution.

[111]  E. Olson,et al.  Acylation of proteins with myristic acid occurs cotranslationally. , 1987, Science.

[112]  J. Parker,et al.  Missense misreading of asparagine codons as a function of codon identity and context. , 1987, The Journal of biological chemistry.

[113]  M. Santer,et al.  A single base change in the Shine-Dalgarno region of 16S rRNA of Escherichia coli affects translation of many proteins. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[114]  C. Watanabe,et al.  Compilation and comparison of the sequence context around the AUG startcodons in Saccharomyces cerevisiae mRNAs. , 1987, Nucleic acids research.

[115]  P. Sharp,et al.  The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications. , 1987, Nucleic acids research.

[116]  P. Sharp,et al.  Codon usage in regulatory genes in Escherichia coli does not reflect selection for 'rare' codons. , 1986, Nucleic acids research.

[117]  M. Kozak Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes , 1986, Cell.

[118]  T. Ikemura Codon usage and tRNA content in unicellular and multicellular organisms. , 1985, Molecular biology and evolution.

[119]  R. Lloubès,et al.  Translation is a non-uniform process. Effect of tRNA availability on the rate of elongation of nascent polypeptide chains. , 1984, Journal of molecular biology.

[120]  S. Pedersen Escherichia coli ribosomes translate in vivo with variable rate. , 1984, The EMBO journal.

[121]  W. Konigsberg,et al.  Evidence for use of rare codons in the dnaG gene and other regulatory genes of Escherichia coli. , 1983, Proceedings of the National Academy of Sciences of the United States of America.

[122]  H. Ozeki,et al.  Codon usage and transfer RNA contents: organism-specific codon-choice patterns in reference to the isoacceptor contents. , 1983, Cold Spring Harbor symposia on quantitative biology.

[123]  M. Gouy,et al.  Codon usage in bacteria: correlation with gene expressivity. , 1982, Nucleic acids research.

[124]  J. Bennetzen,et al.  Codon selection in yeast. , 1982, The Journal of biological chemistry.

[125]  T. Ikemura Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. , 1981, Journal of molecular biology.

[126]  C. Yanofsky Attenuation in the control of expression of bacterial operons , 1981, Nature.

[127]  Manolo Gouy,et al.  Codon catalog usage is a genome strategy modulated for gene expressivity , 1981, Nucleic Acids Res..

[128]  J. Steitz,et al.  How ribosomes select initiator regions in mRNA: base pair formation between the 3' terminus of 16S rRNA and the mRNA during initiation of protein synthesis in Escherichia coli. , 1975, Proceedings of the National Academy of Sciences of the United States of America.

[129]  J. Shine,et al.  The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. , 1974, Proceedings of the National Academy of Sciences of the United States of America.

[130]  F. Crick Codon--anticodon pairing: the wobble hypothesis. , 1966, Journal of molecular biology.