Abstract
BackgroundCompleted 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.ResultsWe 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.ConclusionChanges 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.
Highlights
Completed genomes and environmental genomic sequences are bringing a significant contribution to understanding the evolution of gene families, microbial metabolism and community eco-physiology
To gain insight into the evolution of function in a gene family that has been extensively sampled by environmental genomic screening and characterized biochemically, we focused on bacterial nitrilases
Phylogenetic analysis of a sequence dataset consisting of all nitrilase genes from cultivated bacteria shows that 18 sequences belong to subfamilies one and two (Fig. 1)
Summary
Completed genomes and environmental genomic sequences are bringing a significant contribution to understanding the evolution of gene families, microbial metabolism and community eco-physiology. We used comparative genomics and phylogenetic analyses in conjunction with enzymatic data to probe the evolution and functions of a microbial nitrilase gene family. A variety of functional and sequence-based approaches have been developed for discovering and characterizing genes, operons and even entire genomes directly from the environment, collectively referred to as metagenomics or environmental genomics [4]. The use of environmental genomics has already led to important discoveries such as genes responsible for novel biological functions [5], microbial community metabolic traits [6,7,8] and dramatic increases in the diversity of various enzyme families [9,10].
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