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Evolution of a microbial nitrilase gene family: a comparative and environmental genomics study
- Source :
- BMC Evolutionary Biology, BMC Evolutionary Biology, Vol 5, Iss 1, p 42 (2005)
- Publication Year :
- 2005
-
Abstract
- Background Completed genomes and environmental genomic sequences are bringing a significant contribution to understanding the evolution of gene families, microbial metabolism and community eco-physiology. Here, we used comparative genomics and phylogenetic analyses in conjunction with enzymatic data to probe the evolution and functions of a microbial nitrilase gene family. Nitrilases are relatively rare in bacterial genomes, their biological function being unclear. Results We examined the genetic neighborhood of the different subfamily genes and discovered conserved gene clusters or operons associated with specific nitrilase clades. The inferred evolutionary transitions that separate nitrilases which belong to different gene clusters correlated with changes in their enzymatic properties. We present evidence that Darwinian adaptation acted during one of those transitions and identified sites in the enzyme that may have been under positive selection. Conclusion Changes in the observed biochemical properties of the nitrilases associated with the different gene clusters are consistent with a hypothesis that those enzymes have been recruited to a novel metabolic pathway following gene duplication and neofunctionalization. These results demonstrate the benefits of combining environmental genomic sampling and completed genomes data with evolutionary and biochemical analyses in the study of gene families. They also open new directions for studying the functions of nitrilases and the genes they are associated with.
- Subjects :
- Genetics, Microbial
Models, Molecular
Evolution
Genomics
Bacterial genome size
Biology
Environment
Nitrilase
Evolution, Molecular
Phylogenetics
Aminohydrolases
Gene duplication
QH359-425
Gene family
Selection, Genetic
Ecology, Evolution, Behavior and Systematics
Phylogeny
Genetics
Comparative genomics
Likelihood Functions
Genome
Models, Statistical
Bacteria
Models, Genetic
Computational Biology
Biodiversity
Sequence Analysis, DNA
Genes, Bacterial
Multigene Family
Neofunctionalization
Genome, Bacterial
Research Article
Subjects
Details
- ISSN :
- 14712148
- Volume :
- 5
- Database :
- OpenAIRE
- Journal :
- BMC evolutionary biology
- Accession number :
- edsair.doi.dedup.....38e617d788dce8ff4f9bcee524a68f93