Evolution of a microbial nitrilase gene family: a comparative and environmental genomics study
<p>Abstract</p> <p>Background</p> <p>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...
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| Format: | Article |
| Language: | English |
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BMC
2005-08-01
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| Series: | BMC Evolutionary Biology |
| Online Access: | http://www.biomedcentral.com/1471-2148/5/42 |
| _version_ | 1798029552842178560 |
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| author | Eads Jonathan R Podar Mircea Richardson Toby H |
| author_facet | Eads Jonathan R Podar Mircea Richardson Toby H |
| author_sort | Eads Jonathan R |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>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.</p> |
| first_indexed | 2024-04-11T19:26:00Z |
| format | Article |
| id | doaj.art-062e8ee3de2a434ca9b524b30a937750 |
| institution | Directory Open Access Journal |
| issn | 1471-2148 |
| language | English |
| last_indexed | 2024-04-11T19:26:00Z |
| publishDate | 2005-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Evolutionary Biology |
| spelling | doaj.art-062e8ee3de2a434ca9b524b30a9377502022-12-22T04:07:08ZengBMCBMC Evolutionary Biology1471-21482005-08-01514210.1186/1471-2148-5-42Evolution of a microbial nitrilase gene family: a comparative and environmental genomics studyEads Jonathan RPodar MirceaRichardson Toby H<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>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.</p>http://www.biomedcentral.com/1471-2148/5/42 |
| spellingShingle | Eads Jonathan R Podar Mircea Richardson Toby H Evolution of a microbial nitrilase gene family: a comparative and environmental genomics study BMC Evolutionary Biology |
| title | Evolution of a microbial nitrilase gene family: a comparative and environmental genomics study |
| title_full | Evolution of a microbial nitrilase gene family: a comparative and environmental genomics study |
| title_fullStr | Evolution of a microbial nitrilase gene family: a comparative and environmental genomics study |
| title_full_unstemmed | Evolution of a microbial nitrilase gene family: a comparative and environmental genomics study |
| title_short | Evolution of a microbial nitrilase gene family: a comparative and environmental genomics study |
| title_sort | evolution of a microbial nitrilase gene family a comparative and environmental genomics study |
| url | http://www.biomedcentral.com/1471-2148/5/42 |
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