Predicted highly expressed genes in the genomes of Streptomyces coelicolor and Streptomyces avermitilis and the implications for their metabolism

Abstract

Highly expressed genes in bacteria often have a stronger codon bias than genes expressed at lower levels, due to translational selection. In this study, a comparative analysis of predicted highly expressed (PHX) genes in the Streptomyces coelicolor and Streptomyces avermitilis genomes was performed using the codon adaptation index (CAI) as a numerical estimator of gene expression level. Although it has been suggested that there is little heterogeneity in codon usage in G+C-rich bacteria, considerable heterogeneity was found among genes in these two G+C-rich Streptomyces genomes. Using ribosomal protein genes as references,~10 % of the genes were predicted to be PHX genes using a CAI cutoff value of greater than 0?78 and 0?75 in S. coelicolor and S. avermitilis, respectively. The PHX genes showed good agreement with the experimental data on expression levels obtained from proteomic analysis by previous workers. Among 724 and 730 PHX genes identified from S. coelicolor and S. avermitilis, 368 are orthologue genes present in both genomes, which were mostly 'housekeeping' genes involved in cell growth. In addition, 61 orthologous gene pairs with unknown functions were identified as PHX. Only one polyketide synthase gene from each Streptomyces genome was predicted as PHX. Nevertheless, several key genes responsible for producing precursors for secondary metabolites, such as crotonyl-CoA reductase and propionyl-CoA carboxylase, and genes necessary for initiation of secondary metabolism, such as adenosylmethionine synthetase, were among the PHX genes in the two Streptomyces species. The PHX genes exclusive to each genome, and what they imply regarding cellular metabolism, are also discussed.

Comparative analysis of codon usage patterns and identification of predicted highly expressed genes in fiveSalmonellagenomes

“…fr) [9] and CAI Calculator 2 (http://www.evolvingcode.net/ codon/CalculateCAIs.php). [17] The software Codon W [9] was employed to inspect G or C in the third position of codons (GC3s), as well as to determine the effective number of codons (Nc) [15] and the frequency of optimal codons (Fop). [9] Nc is a straightforward measure of codon bias.…”

“…[9] Nc is a straightforward measure of codon bias. [17] It ranges from 20 (when merely one codon is used per amino acid) to 61 (when each and every codon is used in equal likelihood). Fop [9] determines the section of synonymous codons that are optimal codons.…”

“…The 'codon adaptation index' (CAI) [9] values were computed using the web-based application 'the CAI Calculator 2' (http://www.evolvingcode.net/codon/cai/ cais.php) [17] taking the ribosomal genes as a reference. It quantiÞ es the relative adaptiveness of a gene's codon usage, which is its codon usage as compared to the codon usage of highly expressed genes.…”

“…This phenomenon has been previously reported in E. coli and Streptomyces. [17] Table 1 shows that the mean Nc values of the total protein coding genes in the studied strains are in the range of 46-47, with the mean standard deviation value hovering around 6. With the exception of the ribosomal protein genes, the mean Nc values of the other categories of genes in the studied strains are quite high.…”

Mutational Pressure Drives Evolution of Synonymous Codon Usage in Genetically Distinct Oenothera plastomes

“…Online version of codonW (45; http://mobyle.pasteur.fr/cgibin/portal.py) was used to estimate ENC, hydropathy score (a number indicating hydrophobic/hydrophilic properties of side chain of an amino acid) and aromaticity (frequency of aromatic amino acids) values. CAI values were calculated by using CAI calculator 2 (46). CodonO (47) was employed to compute SCUO values (35).…”