Comparison of Synonymous Codon Distribution Patterns of Bacteriophage and Host Genomes

Abstract

Synonymous codon usage patterns of bacteriophage and host genomes were compared. Two indexes, G + C base composition of a gene (fgc) and fraction of translationally optimal codons of the gene (fop), were used in the comparison. Synonymous codon usage data of all the coding sequences on a genome are represented as a cloud of points in the plane of fop vs. fgc. The Escherichia coli coding sequences appear to exhibit two phases, "rising" and "flat" phases. Genes that are essential for survival and are thought to be native are located in the flat phase, while foreign-type genes from prophages and transposons are found in the rising phase with a slope of nearly unity in the fgc vs. fop plot. Synonymous codon distribution patterns of genes from temperate phages P4, P2, N15 and lambda are similar to the pattern of E. coli rising phase genes. In contrast, genes from the virulent phage T7 or T4, for which a phage-encoded DNA polymerase is identified, fall in a linear curve with a slope of nearly zero in the fop vs. fgc plane. These results may suggest that the G + C contents for T7, T4 and E. coli flat phase genes are subject to the directional mutation pressure and are determined by the DNA polymerase used in the replication. There is significant variation in the fop values of the phage genes, suggesting an adjustment to gene expression level. Similar analyses of codon distribution patterns were carried out for Haemophilus influenzae, Bacillus subtilis, Mycobacterium tuberculosis and their phages with complete genomic sequences available.

Causes for the intriguing presence of tRNAs in phages

“…As previously noted for some of these phages (Sharp et al 1985;Kunisawa et al 1998;Kropinski and Sibbald 1999;Sau et al 2005), we find highly correlated codon frequencies: the average of the Pearson's coefficient R on all 37 couples phage-host is 0.78 ± 0.04 (standard error), and 36 of the 37 associated P-values are inferior to 0.05. This value has to be compared with the value found by computing the average correlation coefficient, 0.38 ± 0.02, between a phage and a random host (computed between the phage and a random bacterial genome from the 356 we found available in GenBank).…”

Bacteriophage T4 Genome

“…E. coli-optimal codons are in fact used more frequently for T4 proteins present in large numbers per phage particle (such as in gp23, the major capsid protein), while T4-optimal codons, defined as those recognized by the phage tRNAs, are used more frequently for T4 proteins present in small numbers per phage particle (and probably in weakly expressed genes). This may serve to enhance the expression of low-abundance T4 late proteins, whose products are required in larger amounts than the typical low-abundance E. coli protein (590)(591)(592).…”

Functional Role of Mycobacteriophage Transfer RNAs

“…As shown in Table 1, the gene copy number of E. coli tRNAs ranges from a single to six for Lys-tRNA (Blattner et al, 1997). By contrast, Mycobacterium tuberculosis tRNAs exist in a single copy on its genome except Met-tRNA genes (Cole et al, 1998), suggesting that constraints from isoacceptor tRNA species on the synonymous codon usage are less than those in E. coli (Kunisawa et al, 1998). Taken together, it seems unlikely that mycobacteriophage tRNAs serve to supplement minor host isoacceptor tRNA species for e$cient translation of rare codons.…”