Temperature adaptation of synonymous codon usage in different functional categories of genes: A comparative study between homologous genes of Methanococcus jannaschii and Methanococcus maripaludis

• Published in: FEBS letters Vol. 580; no. 16; pp. 3895 - 3899
• Main Authors: Basak, Surajit, Ghosh, Tapash Chandra
• Format: Journal Article
• Language: English
• Published: England Elsevier B.V 10.07.2006
• Subjects: Adaptation, Biological; Codon - genetics; Free folding energy; Gene functional categories; Genes, Archaeal - genetics; Methanocaldococcus jannaschii; Methanococcus - genetics; Methanococcus maripaludis; Non-synonymous substitution; Optimal growth temperature; Sequence Homology; Synonymous codon usage; Synonymous substitution; Temperature; Synonymous substitution; Free folding energy; Gene functional categories; Synonymous codon usage; Non-synonymous substitution; Optimal growth temperature
• ISSN: 0014-5793; 1873-3468
• DOI: 10.1016/j.febslet.2006.06.014

Synonymous codon usage of homologous sequences between Methanococcus jannaschii and Methanococcus maripaludis have been analyzed in three broad functional categories of genes namely: (i) information storage and processing; (ii) metabolism; and (iii) cellular processes and signaling. Average values of synonymous nucleotide substitutions per synonymous site are significantly lower for information processing genes compared to either metabolic or cellular processing genes. These results suggests that synonymous codon usage has been subject to greater constraint in the information storage and processing group of genes compared to other functional categories of genes. For metabolic and cellular processing genes, correspondence analysis based on relative synonymous codon usage (RSCU) values separates the genes along the first major axes according to the genome type; while in the information processing group, genes are separated along the second major axes according to the genome type. Further study on synonymous substitution rate for information processing genes shows a stronger selective constraint on synonymous codon usage of six amino acids, G, A, R, P, Y, F. Randomization of the original transcript of M. jannaschii for information processing genes suggests that variation in selective constraint between synonymous codon usage is related to the potential formation of mRNA secondary structures which contribute to the folding stability.