Affiliations: Bioinformatics Centre, Institute of Life Sciences,
Department of Biotechnology, Nalco Square, Bhubaneswar, 751 023, India. Tel.:
+91 674 2301500; Fax: +91 674 2300728; E-mail: [email protected],
[email protected]
Abstract: In this study major factors shaping codon and amino acid usage
variation in Thermobifida fusca YX are reported. It is a major degrader
of plant cell walls. It produces spores that can be allergenic and has been
associated with a condition called farmers lung. For comparison, two other
closely related Actinobacteria, S. coelicolor and N.
farcinica were considered. Correspondence analysis on RSCU (Relative
Synonymous Codon Usage) showed significant correlation between the major trend
of codon usage variation and gene expression level assessed by the "Codon
Adaptation Index" (CAI) values. The result was further confirmed from
distribution of genes along the first axis. In addition,
N_{c} (effective number of codons) plot, SCUO (synonymous
codon usage order) plot and correlation analyses showed that base composition
and mutational bias have a dominant role in codon usage variation. Furthermore,
gene expression level, hydrophobicity and aromaticity have played a significant
role in the source of variations for amino acid usage. In addition, codon
preference for genes at higher expression level was found to be similar among
three different genera. Notably, 14 codons optimally used by Thermobifida
fusca YX and its comparative study with S. coelicolor and N.
farcinica might provide some useful information for their further study of
molecular evolution and genetic engineering.
