Codon usage data for 56 Bacillus subtilis genes show that synonymous codon usage in B. subtilis is less biased than in Escherichia coli, or in Saccharomyces cerevisiae. Nevertheless, certain genes with a high codon bias can be identified by correspondence analysis, and also by various indices of codon bias. These genes are very highly expressed, and a general trend (a decrease) in codon bias across genes seems to correspond to decreasing expression level. This, then, may be a general phenomenon in unicellular organisms. The unusually small effect of translational selection on the pattern of codon usage in lowly expressed genes in B. subtilis yields similar dinucleotide frequencies among different codon positions, and on complementary strands. These patterns could arise through selection on DNA structure, but more probably are largely determined by mutation. This prevalence of mutational bias could lead to difficulties in assessing whether open reading frames encode proteins.
Sequence analysis of the cDNA encoding human liver glycogen phosphorylase reveals tissue-specific codon usage
Codon-defined ribosomal pausing in Escherichia coli detected by using the pyrE attenuator to probe the coupling between transcription and translation
The DNA sequence of the gene for the secreted Bacillus subtilis enzyme levansucrase and its genetic control sites
Constraints on codon context in Escherichia coli genes. Their possible role in modulating the efficiency of translation
Effect of distribution of unfavourable codons on the maximum rate of gene expression by an heterologous organism
Unusually high-level expression of a foreign gene (hepatitis B virus core antigen) in Saccharomyces cerevisiae
The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications
Synthetic oligonucleotide probes deduced from amino acid sequence data. Theoretical and practical considerations
Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes
Measurements of the effects that coding for a protein has on a DNA sequence and their use for finding genes
The codon preference plot: graphic analysis of protein coding sequences and prediction of gene expression
Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs
Method to determine the reading frame of a protein from the purine/pyrimidine genome sequence and its possible evolutionary justification
Sequence analyses and evolutionary relationships among the energy-coupling proteins Enzyme I and HPr of the bacterial phosphoenolpyruvate: sugar phosphotransferase system
Characterization of the S1 binding site of the glutamic acid-specific protease from Streptomyces griseus
Molecular cloning and nucleotide sequence of the glycogen branching enzyme gene (glgB) from Bacillus stearothermophilus and expression in Escherichia coli and Bacillus subtilis
Insights on the evolution of metabolic networks of unicellular translationally biased organisms from transcriptomic data and sequence analysis
IS257 from Staphylococcus aureus: member of an insertion sequence superfamily prevalent among gram-positive and gram-negative bacteria
Comparison of the nucleotide and amino acid sequences of the RsrI and EcoRI restriction endonucleases
Characterisation of a repressor gene (xre) and a temperature-sensitive allele from the Bacillus subtilis prophage, PBSX
Sequence analysis of the sbsA gene encoding the 130-kDa surface-layer protein of Bacillus stearothermophilus strain PV72
Differences in codon usage among genes encoding proteins of different function in Rhodobacter capsulatus
The PAUSE software for analysis of translational control over protein targeting: application to E. nidulans membrane proteins
Thermophilic prokaryotes have characteristic patterns of codon usage, amino acid composition and nucleotide content
Predicting gene expression level from relative codon usage bias: an application to Escherichia coli genome
Universal pattern and diverse strengths of successive synonymous codon bias in three domains of life, particularly among prokaryotic genomes
Codon usage patterns in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens; a review of the considerable within-species diversity
Codon usage and gene expression level in Dictyostelium discoideum: highly expressed genes do 'prefer' optimal codons
Molecular analysis of the replication region of the conjugative Streptococcus agalactiae plasmid pIP501 in Bacillus subtilis. Comparison with plasmids pAM beta 1 and pSM19035
Role of GC-biased mutation pressure on synonymous codon choice in Micrococcus luteus, a bacterium with a high genomic GC-content
Codon usage in Chlamydia trachomatis is the result of strand-specific mutational biases and a complex pattern of selective forces
Evolution of nucleotide substitutions and gene regulation in the amylase multigenes in Drosophila kikkawai and its sibling species
Bacillus subtilis genome project: cloning and sequencing of the 97 kb region from 325 degrees to 333 degrees
Codon usage bias: causative factors, quantification methods and genome-wide patterns: with emphasis on insect genomes
Comparative study of the hemagglutinin and neuraminidase genes of influenza A virus H3N2, H9N2, and H5N1 subtypes using bioinformatics techniques
Analysis of synonymous codon usage in Shigella flexneri 2a strain 301 and other Shigella and Escherichia coli strains
Comparison of codon usage measures and their applicability in prediction of microbial gene expressivity
Genome-wide identification and characterization of cytochrome P450 monooxygenase genes in the ciliate Tetrahymena thermophila
Comparative study of synonymous codon usage variations between the nucleocapsid and spike genes of coronavirus, and C-type lectin domain genes of human and mouse
Site-directed mutations reveal long-range compensatory interactions in the Adh gene of Drosophila melanogaster
Differentiation of single-cell organisms according to elongation stages crucial for gene expression efficacy
Construction of a novel, stable, food-grade expression system by engineering the endogenous toxin-antitoxin system in Bacillus subtilis
Analyzing gene expression from relative codon usage bias in Yeast genome: a statistical significance and biological relevance
Automated isolation of translational efficiency bias that resists the confounding effect of GC(AT)-content
Codon-biased translation can be regulated by wobble-base tRNA modification systems during cellular stress responses
The Synthetic Gene Designer: a flexible web platform to explore sequence manipulation for heterologous expression
High-level extracellular production of alkaline polygalacturonate lyase in Bacillus subtilis with optimized regulatory elements
Cancer, Warts, or Asymptomatic Infections: Clinical Presentation Matches Codon Usage Preferences in Human Papillomaviruses
Genes and regulatory sites of the "host-takeover module" in the terminal redundancy of Bacillus subtilis bacteriophage SPO1
Novel third-letter bias in Escherichia coli codons revealed by rigorous treatment of coding constraints
Association of the phi nucleotide with codon bias, amino acid usage and expressivity: differences between Bacillus subtilis and Escherichia coli
Evolution of Synonymous Codon Usage in the Mitogenomes of Certain Species of Bilaterian Lineage with Special Reference to Chaetognatha
Understanding molecular biology of codon usage in mitochondrial complex IV genes of electron transport system: Relevance to mitochondrial diseases
Transcript free energy positively correlates with codon usage bias in mitochondrial genes of Calypogeia species (Calypogeiaceae, Marchantiophyta)
Genome-wide comparison of codon usage dynamics in mitochondrial genes across different species of amphibian genus Bombina
Widespread selection for extremely high and low levels of secondary structure in coding sequences across all domains of life
An improved distribution of codon frequencies allowing for inhomogeneity of DNA's primary-structure evolution
Genome-wide patterns of codon bias are shaped by natural selection in the purple sea urchin, Strongylocentrotus purpuratus
Transcripts of the genes sacB, amyE, sacC and csn expressed in Bacillus subtilis under the control of the 5' untranslated sacR region display different stabilities that can be modulated
Similarities and dissimilarities of codon usage in mitochondrial ATP genes among fishes, aves, and mammals
Mutation pressure and natural selection on codon usage in chloroplast genes of two species in Pisum L. (Fabaceae: Faboideae)
Codon usage pattern and evolutionary forces of mitochondrial ND genes among orders of class Amphibia.
Comparative analysis of codon usage pattern and its influencing factors in Schistosoma japonicum and Ascaris suum
Effect of host bacteria genotype on spontaneous reversions of Bacillus subtilis bacteriophage phi29 sus17 nonsense codon
Using the IPTG-Inducible Pgrac212 Promoter for Overexpression of Human Rhinovirus 3C Protease Fusions in the Cytoplasm of Bacillus subtilis Cells
Codon usage pattern and its influencing factors for mitochondrial CO genes among different classes of Arthropoda
Compositional properties and codon usage pattern of mitochondrial ATP gene in different classes of Arthropoda
Display of Escherichia coli Phytase on the Surface of Bacillus subtilis Spore Using CotG as an Anchor Protein
Composition, codon usage pattern, protein properties, and influencing factors in the genomes of members of the family Anelloviridae.
Co-expression of alcohol dehydrogenase and aldehyde dehydrogenase in Bacillus subtilis for alcohol detoxification
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