Abstract
Microbes are known for their unique ability to adapt to varying lifestyle and environment, even to the extreme or adverse ones. The genomic architecture of a microbe may bear the signatures not only of its phylogenetic position, but also of the kind of lifestyle to which it is adapted. The present review aims to provide an account of the specific genome signatures observed in microbes acclimatized to distinct lifestyles or ecological niches. Niche-specific signatures identified at different levels of microbial genome organization like base composition, GC-skew, purine-pyrimidine ratio, dinucleotide abundance, codon bias, oligonucleotide composition etc. have been discussed. Among the specific cases highlighted in the review are the phenomena of genome shrinkage in obligatory host-restricted microbes, genome expansion in strictly intra-amoebal pathogens, strand-specific codon usage in intracellular species, acquisition of genome islands in pathogenic or symbiotic organisms, discriminatory genomic traits of marine microbes with distinct trophic strategies, and conspicuous sequence features of certain extremophiles like those adapted to high temperature or high salinity.
Keywords: Reductive genome evolution, Intra-amoeba pathogens, Strand-specific codon bias, Genome islands, Trophic, strategies, Thermophiles, Halophiles, GC-skew, codon bias, intra-amoebal pathogens
Current Genomics
Title:Microbial Lifestyle and Genome Signatures
Volume: 13 Issue: 2
Author(s): Chitra Dutta, Sandip Paul
Affiliation:
Keywords: Reductive genome evolution, Intra-amoeba pathogens, Strand-specific codon bias, Genome islands, Trophic, strategies, Thermophiles, Halophiles, GC-skew, codon bias, intra-amoebal pathogens
Abstract:
Microbes are known for their unique ability to adapt to varying lifestyle and environment, even to the extreme or adverse ones. The genomic architecture of a microbe may bear the signatures not only of its phylogenetic position, but also of the kind of lifestyle to which it is adapted. The present review aims to provide an account of the specific genome signatures observed in microbes acclimatized to distinct lifestyles or ecological niches. Niche-specific signatures identified at different levels of microbial genome organization like base composition, GC-skew, purine-pyrimidine ratio, dinucleotide abundance, codon bias, oligonucleotide composition etc. have been discussed. Among the specific cases highlighted in the review are the phenomena of genome shrinkage in obligatory host-restricted microbes, genome expansion in strictly intra-amoebal pathogens, strand-specific codon usage in intracellular species, acquisition of genome islands in pathogenic or symbiotic organisms, discriminatory genomic traits of marine microbes with distinct trophic strategies, and conspicuous sequence features of certain extremophiles like those adapted to high temperature or high salinity.
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Cite this article as:
Chitra Dutta, Sandip Paul , Microbial Lifestyle and Genome Signatures, Current Genomics 2012; 13 (2) . https://dx.doi.org/10.2174/138920212799860698
DOI https://dx.doi.org/10.2174/138920212799860698 |
Print ISSN 1389-2029 |
Publisher Name Bentham Science Publisher |
Online ISSN 1875-5488 |
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