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Open Access Research article

A pursuit of lineage-specific and niche-specific proteome features in the world of archaea

Anindya Roy Chowdhury and Chitra Dutta*

Author Affiliations

Structural Biology & Bioinformatics Division, CSIR Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata, 700032, India

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BMC Genomics 2012, 13:236  doi:10.1186/1471-2164-13-236

Published: 12 June 2012

Abstract

Background

Archaea evoke interest among researchers for two enigmatic characteristics –a combination of bacterial and eukaryotic components in their molecular architectures and an enormous diversity in their life-style and metabolic capabilities. Despite considerable research efforts, lineage- specific/niche-specific molecular features of the whole archaeal world are yet to be fully unveiled. The study offers the first large-scale in silico proteome analysis of all archaeal species of known genome sequences with a special emphasis on methanogenic and sulphur-metabolising archaea.

Results

Overall amino acid usage in archaea is dominated by GC-bias. But the environmental factors like oxygen requirement or thermal adaptation seem to play important roles in selection of residues with no GC-bias at the codon level. All methanogens, irrespective of their thermal/salt adaptation, show higher usage of Cys and have relatively acidic proteomes, while the proteomes of sulphur-metabolisers have higher aromaticity and more positive charges. Despite of exhibiting thermophilic life-style, korarchaeota possesses an acidic proteome. Among the distinct trends prevailing in COGs (Cluster of Orthologous Groups of proteins) distribution profiles, crenarchaeal organisms display higher intra-order variations in COGs repertoire, especially in the metabolic ones, as compared to euryarchaea. All methanogens are characterised by a presence of 22 exclusive COGs.

Conclusions

Divergences in amino acid usage, aromaticity/charge profiles and COG repertoire among methanogens and sulphur-metabolisers, aerobic and anaerobic archaea or korarchaeota and nanoarchaeota, as elucidated in the present study, point towards the presence of distinct molecular strategies for niche specialization in the archaeal world.

Keywords:
Amino acid usage; Isoelectric point; COG distribution; Methanogen; Sulphur metaboliser; Korarachaeota; Oxygen requirement