Genomes and Genes
Summary: A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).
Publications338 found, 100 shown here
- Coding-sequence determinants of gene expression in Escherichia coliGrzegorz Kudla
Department of Biology and Program in Applied Mathematics and Computational Science, University of Pennsylvania, Philadelphia, PA 19104, USA
Science 324:255-8. 2009..GFP messenger RNA (mRNA) levels, mRNA degradation patterns, and bacterial growth rates also varied, but codon bias did not correlate with gene expression...
- Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profilingNicholas T Ingolia
Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, and California Institute for Quantitative Biosciences, San Francisco, CA 94158, USA
Science 324:218-23. 2009..Ribosome profiling is readily adaptable to other organisms, making high-precision investigation of protein translation experimentally accessible...
- Synonymous but not the same: the causes and consequences of codon biasJoshua B Plotkin
Department of Biology and Program in Applied Mathematics and Computational Science, University of Pennsylvania, 433 South University Avenue, Philadelphia, Pennsylvania 19104, USA
Nat Rev Genet 12:32-42. 2011..As a result, an understanding of codon bias is central to fields as diverse as molecular evolution and biotechnology...
- Not so different after all: a comparison of methods for detecting amino acid sites under selectionSergei L Kosakovsky Pond
Antiviral Research Center, University of California San Diego, USA
Mol Biol Evol 22:1208-22. 2005..We demonstrate our methods on sequence data from the human immunodeficiency virus type 1 env and pol genes and simulated alignments...
- An evolutionarily conserved mechanism for controlling the efficiency of protein translationTamir Tuller
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
Cell 141:344-54. 2010..We suggest that the slow "ramp" at the beginning of mRNAs serves as a late stage of translation initiation, forming an optimal and robust means to reduce ribosomal traffic jams, thus minimizing the cost of protein expression...
- Selection on codon biasRuth Hershberg
Department of Biological Sciences, Stanford University, Stanford, California 94305, USA
Annu Rev Genet 42:287-99. 2008In a wide variety of organisms, synonymous codons are used with different frequencies, a phenomenon known as codon bias...
- The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteriaGene Wei Li
Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, California 94158, USA
Nature 484:538-41. 2012..protein-coding sequences, internal SD sequences are disfavoured, which leads to biased usage, avoiding codons and codon pairs that resemble canonical SD sites...
- Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular levelJianzhi Zhang
Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, USA
Mol Biol Evol 22:2472-9. 2005..Recently, Yang, Z., and R. Nielsen (2002. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol. Biol...
- Synonymous codon usage in Escherichia coli: selection for translational accuracyNina Stoletzki
Ludwig Maximilan Universität, Biocenter, Planegg Martinsried, Germany
Mol Biol Evol 24:374-81. 2007..Using several data sets, we find evidence that codon use in Escherichia coli is biased to reduce the costs of both missense and nonsense translational errors...
- A "silent" polymorphism in the MDR1 gene changes substrate specificityChava Kimchi-Sarfaty
Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
Science 315:525-8. 2007..We hypothesize that the presence of a rare codon, marked by the synonymous polymorphism, affects the timing of cotranslational folding and insertion of P-gp into ..
- Balanced codon usage optimizes eukaryotic translational efficiencyWenfeng Qian
Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
PLoS Genet 8:e1002603. 2012..We hypothesize that this phenomenon is a result of codon usage in proportion to cognate tRNA concentrations, the optimal strategy in enhancing translational efficiency ..
- Composite effects of gene determinants on the translation speed and density of ribosomesTamir Tuller
Department of Biomedical Engineering, Tel Aviv University, Israel
Genome Biol 12:R110. 2011....
- General rules for optimal codon choiceRuth Hershberg
Department of Biology, Stanford University, Stanford, California, United States of America
PLoS Genet 5:e1000556. 2009..Once the effect of the genomic GC content on selectively favored codon choice is taken into account, additional universal amino acid specific rules governing the identity of favored ..
- Determinants of translation efficiency and accuracyHila Gingold
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
Mol Syst Biol 7:481. 2011..A practical demonstration of a better understanding of the process would be a more accurate prediction of the proteome, given the transcriptome at a diversity of biological conditions...
- Translation efficiency is determined by both codon bias and folding energyTamir Tuller
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
Proc Natl Acad Sci U S A 107:3645-50. 2010..mechanisms by which this effect is achieved are controversial; although some previous studies have suggested that codon bias is the most important determinant of translation efficiency, a recent study suggested that mRNA folding at ..
- Differential arginylation of actin isoforms is regulated by coding sequence-dependent degradationFangliang Zhang
Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
Science 329:1534-7. 2010..This degradation mechanism, coupled to nucleotide coding sequence, may regulate protein arginylation in vivo...
- Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequencesBeth Shapiro
Mol Biol Evol 23:7-9. 2006..This problem is exacerbated by the exclusion of codon-based models from commonly employed model selection techniques, presumably due to the computational cost ..
- Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and ArabidopsisL Duret
Laboratoire de Biometrie, Génétique et Biologie des Populations, Unité Mixte de Recherche Centre National de la Recherche Scientifique 5558, Villeurbanne Cedex, France
Proc Natl Acad Sci U S A 96:4482-7. 1999We measured the expression pattern and analyzed codon usage in 8,133, 1,550, and 2,917 genes, respectively, from Caenorhabditis elegans, Drosophila melanogaster, and Arabidopsis thaliana...
- Solving the riddle of codon usage preferences: a test for translational selectionMario dos Reis
School of Crystallography, Birkbeck College, University of London, Malet Street, London WC1E 7HX, UK
Nucleic Acids Res 32:5036-44. 2004..Accordingly, genome size also presents upper and lower boundaries beyond which selection on codon usage is not possible...
- PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignmentsMikita Suyama
European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
Nucleic Acids Res 34:W609-12. 2006PAL2NAL is a web server that constructs a multiple codon alignment from the corresponding aligned protein sequences...
- tRNA's wobble decoding of the genome: 40 years of modificationPaul F Agris
Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695 7622, USA
J Mol Biol 366:1-13. 2007..Francis Crick hypothesized that the cell's limited number of tRNAs decoded the genome by recognizing more than one codon. The ambiguity of that recognition resided in the third base-pair, giving rise to the Wobble Hypothesis...
- Genome sequence of the recombinant protein production host Pichia pastorisKristof De Schutter
Unit for Molecular Glycobiology, Department for Molecular Biomedical Research, VIB, Ghent Zwijnaarde, Belgium
Nat Biotechnol 27:561-6. 2009..pastoris. To facilitate progress in these areas, we present the 9.43 Mbp genomic sequence of the GS115 strain of P. pastoris. We also provide manually curated annotation for its 5,313 protein-coding genes...
- Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic driftPremal Shah
Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA
Proc Natl Acad Sci U S A 108:10231-6. 2011The genetic code is redundant with most amino acids using multiple codons. In many organisms, codon usage is biased toward particular codons...
- Design parameters to control synthetic gene expression in Escherichia coliMark Welch
DNA2 0, Menlo Park, CA, USA
PLoS ONE 4:e7002. 2009..Protein-coding sequences are commonly re-designed to enhance expression, but there are no experimentally supported design principles...
- A role for codon order in translation dynamicsGina Cannarozzi
Institute of Computational Science, ETH Zurich, 8092 Zurich, Switzerland
Cell 141:355-67. 2010..Here, we show that in coding sequences, once a particular codon has been used, subsequent occurrences of the same amino acid do not use codons randomly, but favor codons that use ..
- Predicting the evolution of human influenza AR M Bush
Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
Science 286:1921-5. 1999..However, not all codons in these sites had predictive value. Monitoring new H3 isolates for additional changes in positively selected codons might help identify the most fit extant viral strains that arise during antigenic drift...
- The complete mitochondrial genome and novel gene arrangement of the unique-headed bug Stenopirates sp. (Hemiptera: Enicocephalidae)Hu Li
Department of Entomology, China Agricultural University, Beijing, China
PLoS ONE 7:e29419. 2012..A microsatellite was identified in the putative control region. Finally, phylogenetic reconstruction suggests that Enicocephalomorpha is the sister group to all the remaining Heteroptera...
- Accounting for background nucleotide composition when measuring codon usage biasJohn A Novembre
Mol Biol Evol 19:1390-4. 2002
- Mitochondrial genome sequence and expression profiling for the legume pod borer Maruca vitrata (Lepidoptera: Crambidae)Venu M Margam
Department of Entomology, Purdue University, West Lafayette, Indiana, United States of America
PLoS ONE 6:e16444. 2011..and terminates at standard mitochondrial codons, except for the coxI gene, which may start from an arginine CGA codon. The genomic copy of coxII terminates at a T nucleotide, and a proposed polyadenylation mechanism for completion ..
- Isocitrate dehydrogenase 1 codon 132 mutation is an important prognostic biomarker in gliomasMarc Sanson
L Institut National de la Santé et de la Recherche Médicale U711, Fédération de Neurologie Mazarin, Groupe Hospitalier Pitie Salpetriere, 75651, Paris Cedex 13, France
J Clin Oncol 27:4150-4. 2009Unexpected mutations affecting the isocitrate dehydrogenase (IDH1) gene at codon 132 have been found in 12% of glioblastomas.
- Translationally optimal codons associate with structurally sensitive sites in proteinsTong Zhou
Center for Computational Biology and Bioinformatics, The University of Texas at Austin, TX, USA
Mol Biol Evol 26:1571-80. 2009..To test this hypothesis, we analyzed the relationship between codon usage bias and protein structure in the genomes of four model organisms, Escherichia coli, yeast, fly, and mouse...
- A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolutionJoseph P Bielawski
Department of Biology, University College London, London, WC1E 6BT, UK
J Mol Evol 59:121-32. 2004..The method is based on a codon model of evolution and uses the nonsynonymous-to-synonymous rate ratio (omega) as a measure of selection on the ..
- Deciphering synonymous codons in the three domains of life: co-evolution with specific tRNA modification enzymesHenri Grosjean
Universite Paris Sud, CNRS, UMR8621, Institut de Génétique et de Microbiologie, Orsay F 91405, France
FEBS Lett 584:252-64. 2010....
- Gene expression and protein length influence codon usage and rates of sequence evolution in Populus tremulaPar K Ingvarsson
Umea Plant Science Centre, Department of Ecology and Environmental Science, Umea University, Umea, Sweden
Mol Biol Evol 24:836-44. 2007b>Codon bias is generally thought to be determined by a balance between mutation, genetic drift, and natural selection on translational efficiency...
- Germ-line mutations of the RET proto-oncogene in multiple endocrine neoplasia type 2AL M Mulligan
Department of Pathology, University of Cambridge, UK
Nature 363:458-60. 1993..Further, 19 of these 20 mutations affect the same conserved cysteine residue at the boundary of the RET extracellular and transmembrane domains...
- Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov modelsStephan Waack
Institut fur Informatik, Universitat Gottingen, Lotzestr, 16 18, 37083 Göttingen, Germany
BMC Bioinformatics 7:142. 2006..Frequently, the transferred pieces of DNA have a considerable length, comprise several genes and are called genomic islands (GIs) or more specifically pathogenicity or symbiotic islands...
- A general model of codon bias due to GC mutational biasGareth A Palidwor
Ottawa Hospital Research Institute, Ottawa, Canada
PLoS ONE 5:e13431. 2010In spite of extensive research on the effect of mutation and selection on codon usage, a general model of codon usage bias due to mutational bias has been lacking...
- Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiaeManolis Kellis
The Broad Institute, Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02138, USA
Nature 428:617-24. 2004..Strikingly, 95% of cases of accelerated evolution involve only one member of a gene pair, providing strong support for a specific model of evolution, and allowing us to distinguish ancestral and derived functions...
- Datamonkey: rapid detection of selective pressure on individual sites of codon alignmentsSergei L Kosakovsky Pond
Antiviral Research Center, University of California, San Diego, CA 92103, USA
Bioinformatics 21:2531-3. 2005..The methods range from very fast data exploration to the some of the most complex models available in public domain software, and are implemented to run in parallel on a cluster of computers...
- Parallel on-chip gene synthesis and application to optimization of protein expressionJiayuan Quan
Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
Nat Biotechnol 29:449-52. 2011..19 errors per kb. We applied this approach to synthesize pools of thousands of codon-usage variants of lacZα and 74 challenging Drosophila protein antigens, which were then screened for expression ..
- Forces that influence the evolution of codon biasPaul M Sharp
Institute of Evolutionary Biology, University of Edinburgh, Kings Buildings, Edinburgh EH9 3JT, UK
Philos Trans R Soc Lond B Biol Sci 365:1203-12. 2010..The strength of selection on codon usage can be estimated by two different approaches...
- How the sequence of a gene can tune its translationKurt Fredrick
Department of Microbiology, Ohio State Biochemistry Program, and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
Cell 141:227-9. 2010..Two new studies (Cannarrozzi et al., 2010; Tuller et al., 2010) now foster the idea that patterns of codon usage can control ribosome speed, fine-tuning translation to increase the efficiency of protein synthesis.
- Codon usage in twelve species of DrosophilaSaverio Vicario
Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520 8105, USA
BMC Evol Biol 7:226. 2007b>Codon usage bias (CUB), the uneven use of synonymous codons, is a ubiquitous observation in virtually all organisms examined...
- Natural selection on synonymous and nonsynonymous mutations shapes patterns of polymorphism in Populus tremulaPar K Ingvarsson
Umea Plant Science Centre, Department of Ecology and Environmental Science, Umea University, Umea, Sweden
Mol Biol Evol 27:650-60. 2010..tremula. The results presented here show that this has resulted in an increase in codon bias in P. tremula, consistent with stronger selection acting on synonymous codon usage...
- Frequent somatic mutations of GNAQ in uveal melanoma and blue naeviCatherine D Van Raamsdonk
Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6T1Z3, Canada
Nature 457:599-602. 2009..The mutations occur exclusively in codon 209 in the Ras-like domain and result in constitutive activation, turning GNAQ into a dominant acting oncogene...
- A multicenter blinded study to evaluate KRAS mutation testing methodologies in the clinical settingVicki Whitehall
Queensland Institute of Medical Research, Bancroft Building, 300 Herston Road, Herston Queensland 4029, Australia
J Mol Diagn 11:543-52. 2009..These results demonstrate that a variety of detection methodologies are suitable and provide comparable results for KRAS mutation analysis of clinical samples...
- Real-time tRNA transit on single translating ribosomes at codon resolutionSotaro Uemura
Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305 5126, USA
Nature 464:1012-7. 2010..Translation at each codon is monitored by stable binding of transfer RNAs (tRNAs)-labelled with distinct fluorophores-to translating ..
- Impact of translational error-induced and error-free misfolding on the rate of protein evolutionJian Rong Yang
Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat Sen University, Guangzhou, PR China
Mol Syst Biol 6:421. 2010..These findings provide unambiguous support to the role of protein-misfolding-avoidance in determining the rate of protein sequence evolution...
- A mutation in the RET proto-oncogene associated with multiple endocrine neoplasia type 2B and sporadic medullary thyroid carcinomaR M Hofstra
Department of Medical Genetics, University of Groningen, The Netherlands
Nature 367:375-6. 1994..We now show that MEN 2B is also associated with mutation of the RET proto-oncogene. A mutation in codon 664, causing the substitution of a threonine for a methionine in the tyrosine kinase domain of the protein, was ..
- RET codon 804 mutations in multiple endocrine neoplasia 2: genotype-phenotype correlations and implications in clinical managementS Mukherjee
Beaumont Cancer Genetics Program, Beaumont Cancer Institute, William Beaumont Hospital, Royal Oak, MI 48073, USA
Clin Genet 79:1-16. 2011..This review summarizes the genotypic and phenotypic characteristics of RET codon 804 mutation, a prototype for the less well-defined non-cysteine RET mutations associated with MEN 2.
- Two germline missense mutations at codons 804 and 806 of the RET proto-oncogene in the same allele in a patient with multiple endocrine neoplasia type 2B without codon 918 mutationA Miyauchi
Kuma Hospital, Kobe
Jpn J Cancer Res 90:1-5. 1999..Combinations of mutations of the RET proto-oncogene may cause oncogenic activities different from those of single mutations...
- Microsatellites within genes: structure, function, and evolutionYou Chun Li
Institute of Evolution, University of Haifa, Haifa, Israel
Mol Biol Evol 21:991-1007. 2004..These SSRs may provide a molecular basis for fast adaptation to environmental changes in both prokaryotes and eukaryotes...
- Codon-usage-based inhibition of HIV protein synthesis by human schlafen 11Manqing Li
Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA
Nature 491:125-8. 2012..SLFN11 acts at the late stage of virus production by selectively inhibiting the expression of viral proteins in a codon-usage-dependent manner...
- The complete mitochondrial genome sequence of the planthopper, Sivaloka damnosusNan Song
Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, P R China
J Insect Sci 10:76. 2010..In the phylogenetic analyses based on protein-coding genes, Cicadomorpha is a sister to Fulgoromorpha+Sternorrhyncha, and Heteroptera is a sister to all other Hemiptera...
- Evolution in regulatory regions rapidly compensates the cost of nonoptimal codon usageDolors Amorós-Moya
Genomics and Health, Centre for Public Health Research Centro Superior de Investigación en Salud Pública, CSISP, Valencia, Spain
Mol Biol Evol 27:2141-51. 2010The redundant genetic code contains synonymous codons, whose relative frequencies vary among species. Nonoptimal codon usage lowers gene translation efficiency, potentially leading to a fitness cost...
- Atypical MEN type 2B associated with two germline RET mutations on the same allele not involving codon 918Fred H Menko
Department of Clinical Genetics and Human Genetics, Vrije Universiteit Medical Center, 1007 MB Amsterdam, The Netherlands
J Clin Endocrinol Metab 87:393-7. 2002..Mutation analysis revealed a double RET germline mutation, Val804Met and Ser904Cys, in affected individuals. The clinical phenotype, the functional effect of the mutations, and the clinical implications of our findings are discussed...
- Recombination and base composition: the case of the highly self-fertilizing plant Arabidopsis thalianaG Marais
Institute of Cell, Animal and Population Biology, University of Edinburgh, EH9 3JT Edinburgh, UK
Genome Biol 5:R45. 2004....
- Determinants of synonymous and nonsynonymous variability in three species of DrosophilaPenelope R Haddrill
Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
Mol Biol Evol 28:1731-43. 2011..We found evidence for stronger selection at X-linked loci, consistent with their higher levels of codon usage bias...
- Estimating translational selection in eukaryotic genomesMario dos Reis
School of Crystallography, Birkbeck College, London, UK
Mol Biol Evol 26:451-61. 2009Natural selection on codon usage is a pervasive force that acts on a large variety of prokaryotic and eukaryotic genomes...
- Extreme reconfiguration of plastid genomes in the angiosperm family Geraniaceae: rearrangements, repeats, and codon usageMary M Guisinger
Section of Integrative Biology, University of Texas, Austin, USA
Mol Biol Evol 28:583-600. 2011..Geraniaceae plastomes were found to be highly variable in size, gene content and order, repetitive DNA, and codon usage...
- Investigating protein-coding sequence evolution with probabilistic codon substitution modelsMaria Anisimova
Institute of Computational Science, Swiss Federal Institute of Technology, Zurich, Switzerland
Mol Biol Evol 26:255-71. 2009..by the true explosion in the number of recent studies both developing and ameliorating probabilistic models of codon evolution...
- The aflatoxin-induced TP53 mutation at codon 249 (R249S): biomarker of exposure, early detection and target for therapyDoriane Gouas
International Agency for Research on Cancer, 150 cours Albert Thomas, 69372 Lyon Cedex 08, France
Cancer Lett 286:29-37. 2009..HCC) in high-incidence areas (sub-Saharan Africa, South-Eastern Asia) often contains a somatic mutation at codon 249 in TP53 (R249S). This mutation is rare in low-incidence areas of Europe and the United States...
- An empirical codon model for protein sequence evolutionCarolin Kosiol
EMBL European corrected Bioinformatics Institute, Hinxton, United Kingdom
Mol Biol Evol 24:1464-79. 2007In the past, 2 kinds of Markov models have been considered to describe protein sequence evolution. Codon-level models have been mechanistic with a small number of parameters designed to take into account features, such as transition-..
- Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimizationEduardo P C Rocha
Unité Génétique des Génomes Bactériens, Institut Pasteur, 75724 Paris Cedex 15, France
Genome Res 14:2279-86. 2004The selection-mutation-drift theory of codon usage plays a major role in the theory of molecular evolution by explaining the co-evolution of codon usage bias and tRNA content in the framework of translation optimization...
- Phylogenetic dependency networks: inferring patterns of CTL escape and codon covariation in HIV-1 GagJonathan M Carlson
eScience Group, Microsoft Research, Redmond, Washington, United States of America
PLoS Comput Biol 4:e1000225. 2008..I alleles, previous population-based studies have been limited by the inability to simultaneously account for HIV codon covariation, linkage disequilibrium among HLA alleles, and the confounding effects of HIV phylogeny when ..
- Assays to detect beta-tubulin codon 200 polymorphism in Trichuris trichiura and Ascaris lumbricoidesAissatou Diawara
Institute of Parasitology, McGill University, Quebec, Canada
PLoS Negl Trop Dis 3:e397. 2009..We have developed pyrosequencer assays for codon 200 (TTC or TAC) in A. lumbricoides and T. trichiura to screen for this single nucleotide polymorphism (SNP).
- Codon bias and heterologous protein expressionClaes Gustafsson
DNA 2 0, 1455 Adams Drive, Menlo Park, CA 94025, USA
Trends Biotechnol 22:346-53. 2004..Redesign strategies are discussed here, including modification of translation initiation regions, alteration of mRNA structural elements and use of different codon biases.
- Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomesMichael F Lin
Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Genome Res 21:1916-28. 2011..alignment provides statistical power to locate more than 10,000 such regions with resolution down to nine-codon windows, which are found within more than a quarter of all human protein-coding genes and contain ∼2% of their ..
- Comparison of Sanger sequencing, pyrosequencing, and melting curve analysis for the detection of KRAS mutations: diagnostic and clinical implicationsAthanasios C Tsiatis
The Johns Hopkins Medical Institutions, Department of Pathology, 600 N Wolfe Street, Park SB202, Baltimore, MD 21287, USA
J Mol Diagn 12:425-32. 2010..Therefore, we assessed Sanger sequencing, pyrosequencing, and melting curve analysis for the detection of KRAS codon 12/13 mutations in formalin-fixed paraffin-embedded samples, including 58 primary and 42 metastatic colorectal ..
- Effective population size and the efficacy of selection on the X chromosomes of two closely related Drosophila speciesPeter Andolfatto
Department of Ecology and Evolutionary Biology and Lewis Sigler Institute for Integrative Genomics, Princeton University, USA
Genome Biol Evol 3:114-28. 2011..We observe significantly higher levels of polymorphism and evidence for stronger selection on codon usage bias in D...
- Estimating selection intensity on synonymous codon usage in a nonequilibrium populationKai Zeng
Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
Genetics 183:651-62, 1SI-23SI. 2009b>Codon usage bias is the nonrandom use of synonymous codons for the same amino acid. Most population genetic models of codon usage evolution assume that the population is at mutation-selection-drift equilibrium...
- The complete mitochondrial genome of Diadegma semiclausum (hymenoptera: ichneumonidae) indicates extensive independent evolutionary eventsShu jun Wei
Institute of Insect Sciences, Zhejiang University, Hangzhou 310029, China
Genome 52:308-19. 2009....
- Translation efficiency in humans: tissue specificity, global optimization and differences between developmental stagesYedael Y Waldman
Blavatnik School of Computer Science, Tel Aviv University, Ramat Aviv 69978, Israel
Nucleic Acids Res 38:2964-74. 2010Various studies in unicellular and multicellular organisms have shown that codon bias plays a significant role in translation efficiency (TE) by co-adaptation to the tRNA pool...
- GroEL dependency affects codon usage--support for a critical role of misfolding in gene evolutionTobias Warnecke
Department of Biology and Biochemistry, University of Bath, Bath, UK
Mol Syst Biol 6:340. 2010..We propose that putative error limitation in cis can be elucidated by examining the interaction between codon usage and chaperoning processes...
- The codon 620 tryptophan allele of the lymphoid tyrosine phosphatase (LYP) gene is a major determinant of Graves' diseaseM R Velaga
Institute of Human Genetics, University of Newcastle upon Tyne NE1 3BZ, United Kingdom
J Clin Endocrinol Metab 89:5862-5. 2004..a single nucleotide polymorphism (SNP), encoding a functional arginine to tryptophan residue change at LYP codon 620 has been shown to be associated with type 1 diabetes and other autoimmune disorders...
- Heterologous protein expression is enhanced by harmonizing the codon usage frequencies of the target gene with those of the expression hostEvelina Angov
Molecular Parasitology, Division of Malaria Vaccine Development, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
PLoS ONE 3:e2189. 2008Synonymous codon replacement can change protein structure and function, indicating that protein structure depends on DNA sequence...
- Germline dinucleotide mutation in codon 883 of the RET proto-oncogene in multiple endocrine neoplasia type 2B without codon 918 mutationO Gimm
Translational Research Laboratory, Dana Farber Cancer Institute, Boston, Massachusetts, USA
J Clin Endocrinol Metab 82:3902-4. 1997..More than 95% of all MEN 2B cases are caused by germline mutation at codon 918 (M918T) in exon 16 of the RET proto-oncogene...
- Live attenuated influenza virus vaccines by computer-aided rational designSteffen Mueller
Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York, USA
Nat Biotechnol 28:723-6. 2010..A/PR/8/34 to rationally design live attenuated influenza virus vaccine candidates through genome-scale changes in codon-pair bias...
- Characterization of mammalian selenoproteomesGregory V Kryukov
Department of Biochemistry, University of Nebraska, Lincoln, NE 68588 0664, USA
Science 300:1439-43. 2003In the genetic code, UGA serves as a stop signal and a selenocysteine codon, but no computational methods for identifying its coding function are available. Consequently, most selenoprotein genes are misannotated...
- Evolutionary basis of codon usage and nucleotide composition bias in vertebrate DNA virusesLaura A Shackelton
Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
J Mol Evol 62:551-63. 2006Understanding the extent and causes of biases in codon usage and nucleotide composition is essential to the study of viral evolution, particularly the interplay between viruses and host cells or immune responses...
- Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymesManfred T Reetz
Max Planck Institut fur Kohlenforschung, Kaiser Wilhelm Platz 1, 45470 Mulheim Ruhr, Germany
Nat Protoc 2:891-903. 2007..The pronounced increase in thermostability of the lipase from Bacillus subtilis (Lip A) as a result of applying ISM is illustrated here...
- Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferencesIris Bahir
Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
Mol Syst Biol 5:311. 2009..We consider their respective amino acid and codon usages and compare them among the viruses and their hosts...
- Instruction of translating ribosome by nascent peptideFeng Gong
Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA
Science 297:1864-7. 2002..Replacing the tnaC stop codon with a tryptophan codon allows tryptophan-charged tryptophan transfer RNA to substitute for tryptophan as inducer...
- Trichinella spiralis mtDNA: a nematode mitochondrial genome that encodes a putative ATP8 and normally structured tRNAS and has a gene arrangement relatable to those of coelomate metazoansD V Lavrov
Department of Biology, University of Michigan, Ann Arbor, Michigan 48109 1048, USA
Genetics 157:621-37. 2001..The sequence also contains a large repeat region that is polymorphic in size at the population and/or individual level...
- Generation and immunogenicity of novel HIV/AIDS vaccine candidates targeting HIV-1 Env/Gag-Pol-Nef antigens of clade CCarmen Elena Gómez
Department of Molecular and Cellular Biology, Centro Nacional de Biotecnologia, CSIC, Ciudad Universitaria Cantoblanco, 28049 Madrid, Spain
Vaccine 25:1969-92. 2007..in transgenic HHD mice the immunogenicity of two attenuated poxvirus vectors expressing in a single locus (TK) the codon optimized HIV-1 genes encoding gp120 and Gag-Pol-Nef (GPN) polyprotein of clade C (referred as MVA-C and NYVAC-C)...
- Mutations at embB codon 306 are an important molecular indicator of ethambutol resistance in Mycobacterium tuberculosisAngela M Starks
Division of Tuberculosis Elimination, National Center for HIV AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
Antimicrob Agents Chemother 53:1061-6. 2009..However, recent reports have described the presence of embB mutations, especially those at embB codon 306, in isolates susceptible to ethambutol...
- Patterns of codon usage bias in Silene latifoliaSuo Qiu
State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of the Ministry of Education, Sun Yat Sen University, Guangzhou 510275, China
Mol Biol Evol 28:771-80. 2011Patterns of codon usage bias (CUB) convey useful information about the selection on synonymous codons induced by gene expression and contribute to an understanding of substitution patterns observed at synonymous sites...
- Biased gene conversion affects patterns of codon usage and amino acid usage in the Saccharomyces sensu stricto group of yeastsRichard J Harrison
Institute of Evolutionary Biology, School of Biological Sciences, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, United Kingdom
Mol Biol Evol 28:117-29. 2011Patterns of synonymous codon usage vary between organisms and are controlled by neutral processes (such as drift and mutation) as well as by selection...
- Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usageZiheng Yang
Department of Biology, Galton Laboratory, University College London, London, United Kingdom
Mol Biol Evol 25:568-79. 2008Current models of codon substitution are formulated at the levels of nucleotide substitution and do not explicitly consider the separate effects of mutation and selection...
- Codon usage bias and the evolution of influenza A viruses. Codon Usage Biases of Influenza VirusEmily H M Wong
Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong, China
BMC Evol Biol 10:253. 2010..As the replication of the influenza virus is based on its host's machinery, codon usage of its viral genes might be subject to host selection pressures, especially after interspecies transmission...
- Gene disruption in Candida albicans using a synthetic, codon-optimised Cre-loxP systemPaul M J Dennison
Aberdeen Fungal Group, School of Medical Sciences, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
Fungal Genet Biol 42:737-48. 2005..These markers were then resolved from the C. albicans genome using a synthetic codon-optimised cre recombinase gene, with near 100% efficiency...
- Following translation by single ribosomes one codon at a timeJin Der Wen
Department of Chemistry, University of California, Berkeley, California 94720, USA
Nature 452:598-603. 2008..Each translocation step measures three bases--one codon-and occurs in less than 0.1 s...
- The mitochondrial genome of the smaller tea tortrix Adoxophyes honmai (Lepidoptera: Tortricidae)Eun Seung Lee
Department of Plant Medicine, Chungbuk National University, Cheongju, Republic of Korea
Gene 373:52-7. 2006..Nucleotide composition, amino acid composition and codon usage are in the range of values estimated from other insect mitogenomes. In AT rich region of A...
- Characterization and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strainsJustin S Hogg
Allegheny General Hospital, Allegheny Singer Research Institute, Center for Genomic Sciences, Pittsburgh, Pennsylvania 15212, USA
Genome Biol 8:R103. 2007..Studies based on random sequencing of multiple strain libraries suggested that free-living bacterial species possess a supragenome that is much larger than the genome of any single bacterium...
- RET codon 634 mutations in multiple endocrine neoplasia type 2: variable clinical features and clinical outcomeMarcia K Puñales
Endocrine Division, Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Porto Alegre 90035 003, Rio Grande do Sul, Brazil
J Clin Endocrinol Metab 88:2644-9. 2003..Sixty-nine individuals from 12 different families presented a codon 634 mutation, the most prevailing missense mutation in our series...
- Patterns of molecular evolution in Caenorhabditis preclude ancient origins of selfingAsher D Cutter
Department of Ecology and Evolutionary Biology and the Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3G5, Canada
Genetics 178:2093-104. 2008..Here we contrast rates of nucleotide substitution and codon usage bias among thousands of orthologous groups of genes in six species of Caenorhabditis, including the classic ..
- Trm9-catalyzed tRNA modifications link translation to the DNA damage responseUlrike Begley
Department of Biomedical Sciences, GenNYsis Center for Excellence in Cancer Genomics, University at Albany, State University of New York, Rensselaer, NY 12144, USA
Mol Cell 28:860-70. 2007..Additionally, we identified 425 genes, which included YEF3, RNR1, and RNR3, with a unique codon usage pattern linked to Trm9...
- Effect of codon optimization and subcellular targeting on Toxoplasma gondii antigen SAG1 expression in tobacco leaves to use in subcutaneous and oral immunization in miceMelina Laguía-Becher
IIB INTECH, Camino de Circunvalación Km 6, Provincia de Buenos Aires, Argentina
BMC Biotechnol 10:52. 2010b>Codon optimization and subcellular targeting were studied with the aim to increase the expression levels of the SAG178-322 antigen of Toxoplasma gondii in tobacco leaves...
- Improved characterisation of among-lineage rate variation in cetacean mitogenomes using codon-partitioned relaxed clocksSimon Y W Ho
Research School of Biology, Centre for Macroevolution and Macroecology, Australian National University, Canberra, ACT, 0200, Australia
Mitochondrial DNA 21:138-46. 2010..However, this is rarely the case for differences in the lineage-specific patterns of rate variation among sites...
- Transfer of embB codon 306 mutations into clinical Mycobacterium tuberculosis strains alters susceptibility to ethambutol, isoniazid, and rifampinHassan Safi
Division of Infectious Disease and Center for Emerging Pathogens, Department of Medicine, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey 07103, USA
Antimicrob Agents Chemother 52:2027-34. 2008..a major mechanism of ethambutol (EMB) resistance in clinical studies of Mycobacterium tuberculosis, mutations in codon 306 of the embB gene (embB306) have also been detected in EMB-susceptible clinical isolates...
- Positive selection at sites of multiple amino acid replacements since rat-mouse divergenceGeorgii A Bazykin
Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey 08544, USA
Nature 429:558-62. 2004..This pattern cannot be explained by correlated mutation or episodes of relaxed negative selection, but instead indicates that positive selection acts at many sites of rapid, successive amino acid replacement...
Research Grants104 found, 100 shown here
- Role of troponin T isoforms in nemaline myopathyJian Ping Jin; Fiscal Year: 2009..In an alternative approach, suppression of the ANM nonsense stop codon will also be explored using emerging reagents...
- Role of troponin T isoforms in nemaline myopathyJian Ping Jin; Fiscal Year: 2010..In an alternative approach, suppression of the ANM nonsense stop codon will also be explored using emerging reagents...
- BIOCHEMISTRY OF PRE-MRNA SPLICINGADRIAN KRAINER; Fiscal Year: 2009..NMD degrades mature mRNAs with a premature termination codon (PTC)...
- BIOCHEMISTRY OF PRE-MRNA SPLICINGADRIAN KRAINER; Fiscal Year: 2007..NMD degrades mature mRNAs with a premature termination codon (PTC)...
- A SARS-CoV Spike Protein VaccineB Sim; Fiscal Year: 2005..Our experience with expression of proteins in Pichia pastoris indicates that altering codon usage based on our proprietary information leads to enhanced expression of recombinant proteins and in vivo ..
- APOLIPOPROTEIN B48 AND LIPOPROTEIN METABOLISMLawrence Chan; Fiscal Year: 2004..ApoB mRNA editing is a process whereby the cytidine (C) in a CAA codon in apoB-100 mRNA, encoding Gln-2153, is deaminated to a uridine (U), producing an in-frame UAA stop codon in apoB-..
- Resolution of Epithelial Cell HyperplasiaYohannes Tesfaigzi; Fiscal Year: 2009..A polymorphism in the p53 gene at codon 72 (Arg/Pro) differentially affects Bcl-2 expression; p53Pro increases more efficiently than p53Arg, the pro-..
- Resolution of Epithelial Cell HyperplasiaYohannes Tesfaigzi; Fiscal Year: 2010..A polymorphism in the p53 gene at codon 72 (Arg/Pro) differentially affects Bcl-2 expression;p53Pro increases more efficiently than p53Arg, the pro-..
- Ribosomal scanning and initiation codon selectionTatyana V Pestova; Fiscal Year: 2010..It occurs in two stages: formation of a 48S initiation complex at the initiation codon of mRNA and its joining with a 60S ribosomal subunit...
- STRUCTURE OF VIRAL RNA IN RIBOSOMAL FRAMESHIFTINGAlexander Rich; Fiscal Year: 2004..The - 1 shift in reading frames causes stop codon readthrough, and results in production of a single fusion protein...
- RNA Modifications as Biomarkers of Environmental Stress and InflammationThomas J Begley; Fiscal Year: 2010..have recently demonstrated that enzyme-catalyzed methylation of a modified uridine (mcm5U) in tRNA plays a role in codon- specific translational control after DNA damage, and we have preliminary data demonstrating that the levels of ..
- FUNCTIONAL CHARACTERIZATION OF AGT GENETIC POLYMORPHISMJun yan Hong; Fiscal Year: 2001..One missense alteration occurs at the codon 143 (isoleucine to valine)...
- Ribosomal scanning and initiation codon selectionTatyana V Pestova; Fiscal Year: 2011..It occurs in two stages: formation of a 48S initiation complex at the initiation codon of mRNA and its joining with a 60S ribosomal subunit...
- CONTROL OF ARG-2 GENE EXPRESSION IN NEUROSPORAMATTHEW SACHS; Fiscal Year: 2007..These data support a regulatory model in which ribosome stalling at the uORF termination codon in response to Arg destabilizes CPA1 mRNA by increasing the extent of nonsense codon recognition by NMD...
- CONTROL OF ARG-2 GENE EXPRESSION IN NEUROSPORAMATTHEW SACHS; Fiscal Year: 2006..This data supports a regulatory model in which ribosome stalling at the uORF termination codon in response to Arg destabilizes CPA1 mRNA by increasing the extent of nonsense codon recognition by NMD...
- CONTROL OF ARG-2 GENE EXPRESSION IN NEUROSPORAMATTHEW SACHS; Fiscal Year: 2009..These data support a regulatory model in which ribosome stalling at the uORF termination codon in response to Arg destabilizes CPA1 mRNA by increasing the extent of nonsense codon recognition by NMD...
- CONTROL OF ARG-2 GENE EXPRESSION IN NEUROSPORAMATTHEW SACHS; Fiscal Year: 2007..These data support a regulatory model in which ribosome stalling at the uORF termination codon in response to Arg destabilizes CPA1 mRNA by increasing the extent of nonsense codon recognition by NMD...
- ENTEROHEPATIC LIPID FLUX AND APOPROTEIN BIOSYNTHESIS.NICHOLAS DAVIDSON; Fiscal Year: 2007..RNA modification that results in C to U deaminaton of a single cytidine base and creates a translational stop codon. This process occurs in the mammalian small intestine and is mediated by a multicomponent enzyme complex ..
- Gene Expression Levels Across Diverse GenomesSamuel Karlin; Fiscal Year: 2006..The main focus of our research is to evaluate gene expression levels based on codon usage...
- BACTERIAL LIVE VECTOR-BASED VACCINE AGAINST MALARIAMyron Levine; Fiscal Year: 2004..the priming potential of Shigella live vectors harboring DNA vaccines, we propose to use DNA vaccines in which codon usage has been optimized for expression by mammalian (human) cells...
- STRUCTURE AND FUNCTION OF TRANSFER RIBONUCLEIC ACIDSUttam L RajBhandary; Fiscal Year: 2010..In eubacteria, ochre suppressor tRNAs, which read the UAA stop codon also read the amber stop codon UAG. In eukaryotes, however, ochre suppressors are specific for UAA...
- EDITING OF APOLIPOPROTEIN-B MRNADONNA DRISCOLL; Fiscal Year: 2004..The editing of apolipoprotein-B (apo-B) mRNA involves the deamination of C6666 to U which converts a glutamine codon (CAA) to an in-frame stop codon (UAA)...
- tRNA editing by deamination: Balancing affinity and specificityJuan D Alfonzo; Fiscal Year: 2010..amino acids and, with the exception of methionine and tryptophan, each amino acid is encoded by more than one codon. This discrepancy between codon and amino acid numbers was first explained by Crick's wobble hypothesis, ..
- tRNA editing by deamination: Balancing affinity and specificityJuan Alfonzo; Fiscal Year: 2009..amino acids and, with the exception of methionine and tryptophan, each amino acid is encoded by more than one codon. This discrepancy between codon and amino acid numbers was first explained by Crick's wobble hypothesis, ..
- Listeria Immunotherapy for Pancreatic and Ovarian CancerThomas Dubensky; Fiscal Year: 2006..is to continue development of our Listeria monocytogenes (Lm)-based immunotherapy to target Mesothelin and codon 12-mutated activated K-ras antigens in patients with pancreatic and ovarian cancers...
- Regulation of the Na/K Pump by RNA EditingJoshua J C Rosenthal; Fiscal Year: 2010..A central premise to our approach is that naturally occurring codon changes, caused by RNA editing, can lead us to functionally important regions of the Na/K pump...
- 'RECODING: DYNAMIC REPROGRAMMING OF GENETIC READOUT'John Atkins; Fiscal Year: 2004..cassettes with different defects in the gene 60 bypassing signals: poorly functioning matched take-off and landing codon pairs, extended coding gap, extended stem loop and related studies with mutants of nascent peptide affecting frame ..
- The Biological and Chemical Function of Selenium in EnzymesROBERT J contact HONDAL; Fiscal Year: 2010..of selenocysteine (Sec) into a protein is much more complicated than the other 20 amino acids because a UGA stop codon must be recoded as a sense codon for Sec and this process requires complex cellular machinery...
- Translational Research in the DystrophinopathiesKevin Flanigan; Fiscal Year: 2002..The remainder consist of point mutations (primarily premature stop codon mutations), small deletions resulting in shift of the reading frame, and (in less than 5%) duplications...
- Translation Regulation in Giardia lambliaCHING CHUNG WANG; Fiscal Year: 2010..analysis of an internal ribosomal entry site (IRES) in the Giardia-virus transcript, we identified the AUG start codon at the center of an unstructured 31 nucleotide stretch between two stem-loops, suggesting a direct recruitment of ..
- The Role of Osteoactivin in Osteoblast Development and FunctionFayez F Safadi; Fiscal Year: 2010..in mice with the null allele for OA and in mice with a natural mutation in the OA gene caused a premature stop codon that results in the generation of a truncated OA protein...
- MOLECULAR ANALYSIS OF SITE-SPECIFIC TRANSLATIONAL FRAMESPhilip Farabaugh; Fiscal Year: 1993..This sequence includes no obvious secondary structure, but does include an unusual codon, AGG. This codon is recognized by a rare tRNA encoded by a single genetic locus...
- APOLIPOPROTEIN B48 AND LIPOPROTEIN METABOLISMLawrence Chan; Fiscal Year: 1999..The apoB-48 mRNA is the product of RNA editing, whereby the first nucleotide (C) for the codon CAA, encoding Gln-2153, in apoB-100 mRNA is converted to U producing an in-frame stop codon...
- Ribosomal scanning and initiation codon selectionTatyana Pestova; Fiscal Year: 2007The ribosomal scanning model postulates a three-step mechanism for initiation codon selection...