Mining of Microbial Genomes for the Novel Sources of Nitrilases

BioMed Research International
Nikhil SharmaTek Chand Bhalla

Abstract

Next-generation DNA sequencing (NGS) has made it feasible to sequence large number of microbial genomes and advancements in computational biology have opened enormous opportunities to mine genome sequence data for novel genes and enzymes or their sources. In the present communication in silico mining of microbial genomes has been carried out to find novel sources of nitrilases. The sequences selected were analyzed for homology and considered for designing motifs. The manually designed motifs based on amino acid sequences of nitrilases were used to screen 2000 microbial genomes (translated to proteomes). This resulted in identification of one hundred thirty-eight putative/hypothetical sequences which could potentially code for nitrilase activity. In vitro validation of nine predicted sources of nitrilases was done for nitrile/cyanide hydrolyzing activity. Out of nine predicted nitrilases,Gluconacetobacter diazotrophicus,Sphingopyxis alaskensis,Saccharomonospora viridis, andShimwellia blattaewere specific for aliphatic nitriles, whereas nitrilases fromGeodermatophilus obscurus,Nocardiopsis dassonvillei,Runella slithyformis, andStreptomyces albuspossessed activity for aromatic nitriles.Flavobacterium indicumwas specific towards po...Continue Reading

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Citations

Jan 23, 2018·3 Biotech·Nikhil SharmaTek Chand Bhalla
Nov 9, 2018·Molecular Biotechnology·Asmita KambleHarinder Singh
Oct 14, 2020·Critical Reviews in Biotechnology·Ji-Dong ShenYu-Guo Zheng

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Software Mentioned

MEME ( Multiple Em for Motif Elicitation )
blastp
tblastn
ExPASy
Clustal W
ProtParam
GenMark S
MAST ( Motif Alignment and Search Tool )
ProtParam Expert Protein Analysis System ( ExPASy )
MEGA

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