Impact of lifestyle on cytochrome P450 monooxygenase repertoire is clearly evident in the bacterial phylum Firmicutes

Tiara Padayachee,Khajamohiddin Syed,Wanping Chen,Nomfundo Nzuza,David R Nelson

doi:10.1038/s41598-020-70686-8

Abstract

Cytochrome P450 monooxygenases (CYPs/P450s), heme thiolate proteins, are well known for their role in organisms’ primary and secondary metabolism. Research on eukaryotes such as animals, plants, oomycetes and fungi has shown that P450s profiles in these organisms are affected by their lifestyle. However, the impact of lifestyle on P450 profiling in bacteria is scarcely reported. This study is such an example where the impact of lifestyle seems to profoundly affect the P450 profiles in the bacterial species belonging to the phylum Firmicutes. Genome-wide analysis of P450s in 972 Firmicutes species belonging to 158 genera revealed that only 229 species belonging to 37 genera have P450s; 38% of Bacilli species, followed by 14% of Clostridia and 2.7% of other Firmicutes species, have P450s. The pathogenic or commensal lifestyle influences P450 content to such an extent that species belonging to the genera Streptococcus, Listeria, Staphylococcus, Lactobacillus, Lactococcus and Leuconostoc do not have P450s, with the exception of a handful of Staphylococcus species that have a single P450. Only 18% of P450s are found to be involved in secondary metabolism and 89 P450s that function in the synthesis of specific secondary metabolites are predicted. This study is the first report on comprehensive analysis of P450s in Firmicutes.

Highlights

Among the bacteria that inhabit the human gut, species belonging to the bacterial phylum Firmicutes and Bacteroides are d ominant[1,2,3]
We examined such a phenomenon where Firmicutes species that are pathogens and adapted to simple lifestyles lost P450s in their genomes
Analysis of P450s in Firmicutes species revealed the presence of the lowest number of P450s and the lowest P450 diversity in these species compared to bacterial species belonging to the genera Streptomyces and Mycobacterium and from the phylum Cyanobacterium

Summary

Introduction

Among the bacteria that inhabit the human gut, species belonging to the bacterial phylum Firmicutes and Bacteroides are d ominant[1,2,3]. Firmicutes species are gram-positive microorganisms with rod or sphere shapes and reproduce via binary fission This phylum contains bacteria possessing diverse characteristics that are adapted to diverse ecological niches. Species belonging to the subphyla Bacilli are well known for the production of secondary metabolites valuable to humans, organic compounds that have medicinal properties (Table 1). Because of the potential biotechnological applications of secondary metabolites produced mostly by Bacillus species (Table 1), comprehensive analysis of cytochrome P450 monooxygenases (CYPs/P450s) in the species. The study revealed the presence of 507 P450s belonging to 13 P450 families and 28 P450 subfamilies in 128 Bacillus species and 112 P450s were found to be part of secondary metabolite biosynthetic gene clusters (BGCs)[30]. None of the species belonging to other genera or a comprehensive analysis of P450s in Firmicutes species has been reported

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Results

Conclusion