Open AccessFactors Influencing the Synonymous Codon and Amino Acid Usage Bias in AT‐rich Pseudomonas aeruginosa Phage PhiKZ
Author(s) -
SAU K.,
SAU S.,
MANDAL S. C.,
GHOSH T. C.
Publication year - 2005
Publication title -
acta biochimica et biophysica sinica
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.771
H-Index - 57
eISSN - 1745-7270
pISSN - 1672-9145
DOI - 10.1111/j.1745-7270.2005.00089.x
Subject(s) - codon usage bias , amino acid , pseudomonas aeruginosa , gc content , bacteriophage , biology , genetics , genetic code , genome , escherichia coli , cysteine , gene , biochemistry , bacteria , enzyme
To reveal how the AT‐rich genome of bacteriophage PhiKZ has been shaped in order to carry out its growth in the GC‐rich host Pseudomonas aeruginosa , synonymous codon and amino acid usage bias of PhiKZ was investigated and the data were compared with that of P. aeruginosa. It was found that synonymous codon and amino acid usage of PhiKZ was distinct from that of P. aeruginosa. In contrast to P. aeruginosa , the third codon position of the synonymous codons of PhiKZ carries mostly A or T base; codon usage bias in PhiKZ is dictated mainly by mutational bias and, to a lesser extent, by translational selection. A cluster analysis of the relative synonymous codon usage values of 16 myoviruses including PhiKZ shows that PhiKZ is evolutionary much closer to Escherichia coli phage T4. Further analysis reveals that the three factors of mean molecular weight, aromaticity and cysteine content are mostly responsible for the variation of amino acid usage in PhiKZ proteins, whereas amino acid usage of P. aeruginosa proteins is mainly governed by grand average of hydropathicity, aromaticity and cysteine content. Based on these observations, we suggest that codons of the phage‐like PhiKZ have evolved to preferentially incorporate the smaller amino acid residues into their proteins during translation, thereby economizing the cost of its development in GC‐rich P. aeruginosa. Edited by Zu‐Hong LU