Discrepancy among the synonymous codons with respect to their selection as optimal codon in bacteria

Abstract

The different triplets encoding the same amino acid, termed as synonymous codons, are not equally abundant in a genome. Factors such as G + C% and tRNA are known to influence their abundance in a genome. However, the order of the nucleotide in each codon per se might also be another factor impacting on its abundance values. Of the synonymous codons for specific amino acids, some are preferentially used in the high expression genes that are referred to as the ‘optimal codons’ (OCs). In this study, we compared OCs of the 18 amino acids in 221 species of bacteria. It is observed that there is amino acid specific influence for the selection of OCs. There is also influence of phylogeny in the choice of OCs for some amino acids such as Glu, Gln, Lys and Leu. The phenomenon of codon bias is also supported by the comparative studies of the abundance values of the synonymous codons with same G + C. It is likely that the order of the nucleotides in the triplet codon is also perhaps involved in the phenomenon of codon usage bias in organisms.

Codon degeneracy and amino acid abundance influence the measures of codon usage bias: improved Nc (N̂c) and ENCprime (N̂′c) measures

“…However, it is now widely accepted that the codon usage bias widely differs among amino acids (Satapathy et al . ), and therefore, it would be appropriate to calculate contributions toward value for different amino acids separately as given in Eqn . With this modification, value may fall below 20.0 when some of the amino acids are absent in a coding sequence.…”

Polymorphism at four-fold degenerate site, but not at the intergenic regions, explains nucleotide compositional strand asymmetry in bacteria

“…However, the reason for the high and low G+C% in these phyla is not clearly understood. But phylogeny specific optimal codon selection has been reported recently (Satapathy et al 2016). Future understanding of translational decoding by the ribosome might explain the phylogeny specific codon usage bias and genome composition.…”

“…However, we have observed a lack of correlation between the genome size and genome G+C% in different phylogeny (Supplementary Table 3). It has been reported that the strength of selection on codon usage bias is variable among the bacteria (Sharp et al 2005;Satapathy et al 2012Satapathy et al , 2014Satapathy et al , 2016. In that case bacteria with poor selection on codon usage bias should exhibit low genome G+C%, while bacteria with high genome G+C% must exhibit high selection on codon usage bias.…”

“…In case of Ec, the polymorphism pattern between complementary nucleotide pairs revealed that Pro and Gly often behaved opposite to each other. Considering the previous knowledge that Gending codon in Pro (CCG) is the most preferred whereas the G-ending codon (GGG) in Gly is the least preferred (Satapathy et al 2016), we analysed both forward and reverse nucleotide polymorphisms. In case of Gly, G→C and G→T transversions were more frequent than C→G and T→G respectively, that supported the higher abundance of GGT/GGC over GGG in the genome.…”

Adaptation of codon and amino acid use for translational functions in highly expressed cricket genes

“…Synonymous codons in protein-coding genes are not used randomly [1]. The preferential use of synonymous codons per amino acid in highly transcribed genes, often called optimal codons, has been observed in diverse organisms including bacteria, fungi, plants and animals [2][3][4][5][6][7][8][9][10][11][12][13][14], including insects such as flies, mosquitoes, beetles and crickets [10,11,13,15,16]. When optimal codons co-occur with a high count of iso-accepting tRNA gene copies in the genome, which reflects an organism's tRNA abundance [3-5, 12, 17-20], it suggests a history of selection favoring translational optimization [1,3,5,12,13,[20][21][22][23][24][25].…”