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J Proteome Res. 2007 Jul;6(7):2502-8. Epub 2007 May 26.

Robust determinants of thermostability highlighted by a codon frequency index capable of discriminating thermophilic from mesophilic genomes.

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  • 1Biocomputing Group, CIRB/Dept of Biology, University of Bologna, Bologna, Italy.

Abstract

Can genome analysis tell us about the lifestyle of an organism? We ask this question considering a thorough cross comparison of thermophilic and mesophilic genomes, since presently the number of available genomes is enough to ensure statistical significance of the results. We analyze, by means of principal component analysis (PCA), the codon composition of a database comprising 116 genomes, selected so as to include one species for each genus and show that a cross genomic approach can allow the extraction of common determinants of thermostability at the genome level. The results of our analysis indicate that all the known features of thermostability can be found in the 64 component loadings of the second principal axis of PCA. By this, we develop an index of thermostability whose discriminative power between mesophiles and thermophiles scores with 98% accuracy at the genome level and with 95% accuracy at the protein sequence level. We also prove that these results are not due to phylogenetic differences between archaea and bacteria.

PMID:
17530792
[PubMed - indexed for MEDLINE]
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