Abstract
Cytochrome P450 monooxygenases (CYPs/P450s) are among the most catalytically-diverse enzymes, capable of performing enzymatic reactions with chemo-, regio-, and stereo-selectivity. Our understanding of P450s’ role in secondary metabolite biosynthesis is becoming broader. Among bacteria, Bacillus species are known to produce secondary metabolites, and recent studies have revealed the presence of secondary metabolite biosynthetic gene clusters (BGCs) in these species. However, a comprehensive comparative analysis of P450s and P450s involved in the synthesis of secondary metabolites in Bacillus species has not been reported. This study intends to address these two research gaps. In silico analysis of P450s in 128 Bacillus species revealed the presence of 507 P450s that can be grouped into 13 P450 families and 28 subfamilies. No P450 family was found to be conserved in Bacillus species. Bacillus species were found to have lower numbers of P450s, P450 families and subfamilies, and a lower P450 diversity percentage compared to mycobacterial species. This study revealed that a large number of P450s (112 P450s) are part of different secondary metabolite BGCs, and also identified an association between a specific P450 family and secondary metabolite BGCs in Bacillus species. This study opened new vistas for further characterization of secondary metabolite BGCs, especially P450s in Bacillus species.
Highlights
Cytochrome P450 monooxygenases, known as CYPs/P450s, are undoubtedly among the most catalytically-diverse enzymes, performing enzymatic reactions with chemo, regio- and stereo-selectivity [1,2,3,4,5,6]
The catalytic diversity combined with chemo, regio- and stereo-specific oxidation of substrates exerted by P450s are used in diverse biotechnological applications ranging from drug discovery to bioethanol production and synthesis of different secondary metabolites [7,8,9,10,11,12]
This gives us the opportunity to perform comprehensive a comparative analysis of P450s in Bacillus species as per international P450 nomenclature committee rules [27,28,29], and to identify P450s involved in the synthesis of different secondary metabolites
Summary
Cytochrome P450 monooxygenases, known as CYPs/P450s, are undoubtedly among the most catalytically-diverse enzymes, performing enzymatic reactions with chemo-, regio- and stereo-selectivity [1,2,3,4,5,6]. Analysis of 1566 Bacillus species’ genomes revealed the presence of 20,000 BGCs, most of which were found to produce known secondary metabolites that play a key role in the physiology and development of Bacillus species [21]. Quite a large number of Bacillus species genome sequences are available for public use at Kyoto Encyclopedia of Genes and Genomes—GenomeNet (KEGG) [26] This gives us the opportunity to perform comprehensive a comparative analysis of P450s in Bacillus species as per international P450 nomenclature committee rules [27,28,29], and to identify P450s involved in the synthesis of different secondary metabolites. We report genome data mining, annotation, phylogenetic and comparative analysis of P450s in 128 Bacillus species, including identification of P450s involved in the synthesis of different secondary metabolites. A previous study reporting BGCs in Bacillus species did not clearly indicate BGCs on genomic DNA (gDNA) and plasmid DNA [21]; in this study, gDNA and plasmid DNAs were individually subjected to BGC analysis
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