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Molecular signature of hypersaline adaptation: insights from genome and proteome composition of halophilic prokaryotes

Sandip Paul1, Sumit K Bag1, Sabyasachi Das2, Eric T Harvill3 and Chitra Dutta14*

Author affiliations

1 Bioinformatics Center, Indian Institute of Chemical Biology, 4, Raja SC Mullick Road, Kolkata - 700 032, India

2 Department of Biology, The Pennsylvania State University, Mueller Lab, University Park, PA 16802, USA

3 Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA

4 Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, 4, Raja SC Mullick Road, Kolkata - 700 032, India

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Citation and License

Genome Biology 2008, 9:R70  doi:10.1186/gb-2008-9-4-r70

Published: 9 April 2008

Abstract

Background

Halophilic prokaryotes are adapted to thrive in extreme conditions of salinity. Identification and analysis of distinct macromolecular characteristics of halophiles provide insight into the factors responsible for their adaptation to high-salt environments. The current report presents an extensive and systematic comparative analysis of genome and proteome composition of halophilic and non-halophilic microorganisms, with a view to identify such macromolecular signatures of haloadaptation.

Results

Comparative analysis of the genomes and proteomes of halophiles and non-halophiles reveals some common trends in halophiles that transcend the boundary of phylogenetic relationship and the genomic GC-content of the species. At the protein level, halophilic species are characterized by low hydrophobicity, over-representation of acidic residues, especially Asp, under-representation of Cys, lower propensities for helix formation and higher propensities for coil structure. At the DNA level, the dinucleotide abundance profiles of halophilic genomes bear some common characteristics, which are quite distinct from those of non-halophiles, and hence may be regarded as specific genomic signatures for salt-adaptation. The synonymous codon usage in halophiles also exhibits similar patterns regardless of their long-term evolutionary history.

Conclusion

The generality of molecular signatures for environmental adaptation of extreme salt-loving organisms, demonstrated in the present study, advocates the convergent evolution of halophilic species towards specific genome and amino acid composition, irrespective of their varying GC-bias and widely disparate taxonomic positions. The adapted features of halophiles seem to be related to physical principles governing DNA and protein stability, in response to the extreme environmental conditions under which they thrive.