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

BMC Genomics

Research Article

Anindya Roy Chowdhury¹  Chitra Dutta¹ 

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

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

DOI  :  10.1186/1471-2164-13-236

 received in 2012-01-25, accepted in 2012-06-12,  发布年份 2012

来源: Springer

【 摘 要 】

BackgroundArchaea 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.ResultsOverall 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.ConclusionsDivergences 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.

【 授权许可】

CC BY   
© Roy Chowdhury and Dutta; licensee BioMed Central Ltd. 2012