Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria

Lo, Ian, Denef, Vincent J., VerBerkmoes, Nathan C., Shah, Manesh B., Goltsman, Daniela, DiBartolo, Genevieve, Tyson, Gene W., Allen, Eric E., Ram, Rachna J., Detter, J. Chris, Richardson, Paul, Thelen, Michael P., Hettich, Robert L. and Banfield, Jillian F. (2007) Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature, 446 7135: 537-541. doi:10.1038/nature05624


Author Lo, Ian
Denef, Vincent J.
VerBerkmoes, Nathan C.
Shah, Manesh B.
Goltsman, Daniela
DiBartolo, Genevieve
Tyson, Gene W.
Allen, Eric E.
Ram, Rachna J.
Detter, J. Chris
Richardson, Paul
Thelen, Michael P.
Hettich, Robert L.
Banfield, Jillian F.
Title Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria
Journal name Nature   Check publisher's open access policy
ISSN 0028-0836
1476-4687
Publication date 2007-03-29
Year available 2007
Sub-type Article (original research)
DOI 10.1038/nature05624
Open Access Status Not yet assessed
Volume 446
Issue 7135
Start page 537
End page 541
Total pages 5
Place of publication London, U.K.
Publisher Nature Publishing Group
Language eng
Subject 03 Chemical Sciences
0304 Medicinal and Biomolecular Chemistry
0305 Organic Chemistry
Abstract Microbes comprise the majority of extant organisms, yet much remains to be learned about the nature and driving forces of microbial diversification. Our understanding of how microorganisms adapt and evolve can be advanced by genome-wide documentation of the patterns of genetic exchange, particularly if analyses target coexisting members of natural communities. Here we use community genomic data sets to identify, with strain specificity, expressed proteins from the dominant member of a genomically uncharacterized, natural, acidophilic biofilm. Proteomics results reveal a genome shaped by recombination involving chromosomal regions of tens to hundreds of kilobases long that are derived from two closely related bacterial populations. Inter-population genetic exchange was confirmed by multilocus sequence typing of isolates and of uncultivated natural consortia. The findings suggest that exchange of large blocks of gene variants is crucial for the adaptation to specific ecological niches within the very acidic, metal-rich environment. Mass-spectrometry-based discrimination of expressed protein products that differ by as little as a single amino acid enables us to distinguish the behaviour of closely related coexisting organisms. This is important, given that microorganisms grouped together as a single species may have quite distinct roles in natural systems1, 2, 3 and their interactions might be key to ecosystem optimization. Because proteomic data simultaneously convey information about genome type and activity, strain-resolved community proteomics is an important complement to cultivation-independent genomic (metagenomic) analysis4, 5, 6 of microorganisms in the natural environment.
Keyword Microbes
Diversification
Evolution
Proteomics
Genes
Exchange
Adaptation
Acidophillic
Bacteria
Q-Index Code C1
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Excellence in Research Australia (ERA) - Collection
School of Chemistry and Molecular Biosciences
 
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Created: Tue, 22 Dec 2009, 19:45:32 EST by Macushla Boyle on behalf of Faculty of Science