The implication of life style on codon usage patterns and predicted highly expressed genes for three Frankia genomes

Abstract

Frankia are nitrogen-fixing actinomycetes that form a symbiotic association with over 200 species of woody dicotyledonous plants. Recently, three Frankia genomes were completely sequenced. In this study, the synonymous codon usage patterns of three Frankia genomes (strains CcI3, ACN14a, and EAN1pec) were determined and compared to each other and to other actinobacteria. As expected for a high G+C organism, codon usage by Frankia was highly biased, but differences were observed among the three strains. Using the codon adaptation index (CAI) as a numerical estimator of gene expression level, highly expressed genes in Frankia were predicted with ribosomal protein genes as a reference. The analysis of the predicted highly expressed genes showed that Frankia strain CcI3 had a different profile from the other two strains. Strain CcI3 had fewer predicted highly expressed genes in several COG categories including lipid transport and metabolism, secondary metabolites biosynthesis, inorganic ion transport and metabolism, and general function prediction only than Frankia strains EAN1pec and ACN14a. Interestingly, Frankia EAN1pec had more predicted highly expressed genes in transcription and signal transduction mechanisms than the other two strains. These differences were not just a reflection in total gene numbers, but also based on percentage of genes within a category. These results support the hypothesis that strain CcI3 is becoming a symbiotic specialist and the other two facultative symbiotic strains are maintaining their capacity to exist as free-living soil dwellers.

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

“…[16] All of the protein coding genes, genes associated with pathogenicity, and ribosomal protein genes were examined using Codon W software (http://bioweb2.pasteur. 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).…”

“…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.…”

“…[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. [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).…”

“…[8] Mutational pressure and natural selection operating at the level of translation are the primary reasons behind codon usage variation among the genes in different organisms. [9] Codon bias is quite high in the highly expressed genes compared to lowly expressed ones inside a genome. [10][11][12][13] The bias of highly expressed genes is inß uenced by translational selection; in contrast to lowly expressed genes, which is governed by mutational bias.…”

“…[11] This index has been revealed to relate better with mRNA expression levels. [14] Over and above codon adaptation index, the effective number of codons (Nc), [15] which is described as the amount of equal codons producing the same codon usage bias as observed; and the incidence of optimal codons (Fop), [9] deÞ ned as the proportion of synonymous codons that are optimal codons, are also used.…”