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 im- pose selective constraints at all the three molecular levels- nucleotide composition, codon usage and amino acid content.
Highlights
Hyperthermophiles constantly face the challenge of maintaining the stability of their genome
The GC content of the genomes does not correlate with optimal growth temperature (OGT) [2, 3]
On comparison of occurrence of different nucleotides in four mesophiles and four thermophiles, a significant decrease in the thymine content in thermophiles was noted (Table 2). This was coupled with an overall increase in purine content (A+G) in thermophilic genomes
Summary
Hyperthermophiles constantly face the challenge of maintaining the stability of their genome. The GC content of the genomes does not correlate with optimal growth temperature (OGT) [2, 3]. Various additional attributes have been suggested that contribute in maintaining the stability of genomic DNA of hyperthermophiles [2, 3]. On the other hand GC content of rRNA and tRNA show strong correlation with optimal growth temperature [4, 5]. There is evidence that the proteins of thermophiles are characterized by a distinct pattern of amino acids [7,8,9,10]. A difference in the pattern of synonymous codon usage between thermophiles and mesophiles has been observed [7, 10]
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