title: Selection on GGU and CGU codons in the high expression genes in bacteria.
abstract: The fourfold degenerate site (FDS) in coding sequences is important for studying the effect of any selection pressure on codon usage bias (CUB) because nucleotide substitution per se is not under any such pressure at the site due to the unaltered amino acid sequence in a protein. We estimated the frequency variation of nucleotides at the FDS across the eight family boxes (FBs) defined as Um(g), the unevenness measure of a gene g. The study was made in 545 species of bacteria. In many bacteria, the Um(g) correlated strongly with Nc'-a measure of the CUB. Analysis of the strongly correlated bacteria revealed that the U-ending codons (GGU, CGU) were preferred to the G-ending codons (GGG, CGG) in Gly and Arg FBs even in the genomes with G+C % higher than 65.0. Further evidence suggested that these codons can be used as a good indicator of selection pressure on CUB in genomes with higher G+C %.
authors.affiliation: Department of Computer Science and Engineering, Tezpur University, Tezpur, 784028, Assam, India.
authors.forename: Siddhartha Sankar
authors.initials: SS
authors.lastname: Satapathy
authors.forename: Bhesh Raj
authors.initials: BR
authors.lastname: Powdel
authors.forename: Malay
authors.initials: M
authors.lastname: Dutta
authors.forename: Alak Kumar
authors.initials: AK
authors.lastname: Buragohain
authors.forename: Suvendra Kumar
authors.initials: SK
authors.lastname: Ray
mesh_terms: D019943:Amino Acid Substitution / Q000235:genetics; D000596:Amino Acids / Q000235:genetics; D001419:Bacteria / Q000235:genetics*; D001482:Base Composition / Q000235:genetics*; D003062:Codon / Q000235:genetics*; D009710:Nucleotide Mapping; D009711:Nucleotides / Q000235:genetics*; D012641:Selection, Genetic
chemical_list: D000596:Amino Acids; D003062:Codon; D009711:Nucleotides