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

Agarwal, Subhash Mohan; Grover, Atul

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

Subhash Mohan Agarwal^{1, *}, Atul Grover²

¹ Bioinformatics Center, School of Information Technology, Jawaharlal Nehru University, New Delhi 110067, India and

² Department of Bioscience and Biotechnology, Banasthali University, Banasthali 304022, India

Article Information

Identifiers and Pagination:

Year: 2008
Volume: 2
First Page: 11
Last Page: 19
Publisher ID: TOBIOIJ-2-11
DOI: 10.2174/1875036200802010011

Article History:

Received Date: 04/02/2008
Revision Received Date: 04/03/2008
Acceptance Date: 04/03/2008
Electronic publication date: 01/04/2008
Collection year: 2008

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© 2008 Agarwal and Grover

open-access license: This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International Public License (CC-BY 4.0), a copy of which is available at: https://creativecommons.org/licenses/by/4.0/legalcode. This license permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

^* Address correspondence to this author at the Bioinformatics Center, School of Information Technology, Jawaharlal Nehru University, New Delhi 110067, India; E-mail: smagarwal@yahoo.co.in

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.

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RESEARCH ARTICLE

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

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