Nucleotide Composition and Amino Acid Usage in AT-Rich Hyperthermophilic Species
RESEARCH ARTICLE

Nucleotide Composition and Amino Acid Usage in AT-Rich Hyperthermophilic Species

The Open Bioinformatics Journal 01 Apr 2008 RESEARCH ARTICLE DOI: 10.2174/1875036200802010011

Abstract

Nucleotide composition, codon usage and amino acid content are important molecular signatures that vary in different groups of organisms. AT-rich (or GC poor) hyperthermophiles have relatively been unexplored in these aspects. In this study, we have examined the compositional characteristics of AT rich genomes viz. Methanococcus jannaschii, Sulfolobus solfataricus, Sulfolobus tokodaii and Nanoarcheum equitans by their comparison with four mesophiles having similar genomic GC content. The analysis revealed a significant increase in purine content of ORFs due to increase in guanine content. Moreover, the influence of dinucleotide composition on protein thermostability was found even larger. Accordingly, increased usage of codons that are constituted of dinucleotides RR was observed. Arginine, proline, valine and tyrosine were most abundant amino acids in hyperthermophilic proteomes, and similar bias was seen when dipeptidic composition of proteins was compared. Further amino acid composition analysis of alpha helices indicates an increased usage of E, K, R and decreased usage of N and Q. Summing up, the study suggested that elevated growth temperature impose selective constraints at all the three molecular levels- nucleotide composition, codon usage and amino acid content.

Keywords: Hyperthermophiles, nucleotide bias, codon usage, amino acid composition.