Margrethe H Serres1 , Alastair RW Kerr2 , Thomas J McCormack3 and Monica Riley4
1 Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
2 Wellcome Trust Centre for Cell Biology, University of Edinburgh, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
3 Laboratory of Neurobiology, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
4 Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
author email corresponding author email
Biology Direct 2009, 4:46doi:10.1186/1745-6150-4-46
Published: 23 November 2009
Abstract
Background
Sequence related families of genes and proteins are common in bacterial genomes. In Escherichia coli they constitute over half of the genome. The presence of families and superfamilies of proteins suggest a history of gene duplication and divergence during evolution. Genome encoded protein families, their size and functional composition, reflect metabolic potentials of the organisms they are found in. Comparing protein families of different organisms give insight into functional differences and similarities.
Results
Equivalent enzyme families with metabolic functions were selected from the genomes of four experimentally characterized bacteria belonging to separate genera. Both similarities and differences were detected in the protein family memberships, with more similarities being detected among the more closely related organisms. Protein family memberships reflected known metabolic characteristics of the organisms. Differences in divergence of functionally characterized enzyme family members accounted for characteristics of taxa known to differ in those biochemical properties and capabilities. While some members of the gene families will have been acquired by lateral exchange and other former family members will have been lost over time, duplication and divergence of genes and functions appear to have been a significant contributor to the functional diversity of today’s microbes.
Conclusions
Protein families seem likely to have arisen during evolution by gene duplication and divergence where the gene copies that have been retained are the variants that have led to distinct bacterial physiologies and taxa. Thus divergence of the duplicate enzymes has been a major process in the generation of different kinds of bacteria.
Reviewers
This article was reviewed by Drs. Iyer Aravind, Ardcady Mushegian, and Pierre Pontarotti.
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