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. 2021 Mar 11;26(6):1538.
doi: 10.3390/molecules26061538.

In Silico Analysis of P450s and Their Role in Secondary Metabolism in the Bacterial Class Gammaproteobacteria

Ntombizethu Nokuphiwa Msomi  1 , Tiara Padayachee  1 , Nomfundo Nzuza  1 , Puleng Rosinah Syed  2 , Justyna Dorota Kryś  3 , Wanping Chen  4 , Dominik Gront  3 , David R Nelson  5 , Khajamohiddin Syed  1
Affiliations

In Silico Analysis of P450s and Their Role in Secondary Metabolism in the Bacterial Class Gammaproteobacteria

Ntombizethu Nokuphiwa Msomi et al. Molecules. .

Abstract

The impact of lifestyle on shaping the genome content of an organism is a well-known phenomenon and cytochrome P450 enzymes (CYPs/P450s), heme-thiolate proteins that are ubiquitously present in organisms, are no exception. Recent studies focusing on a few bacterial species such as Streptomyces, Mycobacterium, Cyanobacteria and Firmicutes revealed that the impact of lifestyle affected the P450 repertoire in these species. However, this phenomenon needs to be understood in other bacterial species. We therefore performed genome data mining, annotation, phylogenetic analysis of P450s and their role in secondary metabolism in the bacterial class Gammaproteobacteria. Genome-wide data mining for P450s in 1261 Gammaproteobacterial species belonging to 161 genera revealed that only 169 species belonging to 41 genera have P450s. A total of 277 P450s found in 169 species grouped into 84 P450 families and 105 P450 subfamilies, where 38 new P450 families were found. Only 18% of P450s were found to be involved in secondary metabolism in Gammaproteobacterial species, as observed in Firmicutes as well. The pathogenic or commensal lifestyle of Gammaproteobacterial species influences them to such an extent that they have the lowest number of P450s compared to other bacterial species, indicating the impact of lifestyle on shaping the P450 repertoire. This study is the first report on comprehensive analysis of P450s in Gammaproteobacteria.

Keywords: Cyanobacteria; Firmicutes; Gammaproteobacteria; Mycobacterium; Streptomyces; biosynthetic gene clusters; cytochrome P450 monooxygenases; genome data mining; lifestyle; secondary metabolism.

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Conflict of interest statement

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

Figures

Figure 1
Figure 1
Analysis of P450s in Gammaproteobacterial species. Detailed analysis of the species and P450s is presented in Supplementary Dataset 1.
Figure 2
Figure 2
Phylogenetic analysis of Gammaproteobacterial species P450s. P450 families that are expanded in these species were highlighted in different colors and indicated in the figure.
Figure 3
Figure 3
Heat map figure representing the presence or absence of cytochrome P450 families in 169 species of Gammaproteobacterial species. The data have been represented as −3 for family absence (green) and 3 for family presence (red). One-hundred and sixty-nine Gammaproteobacterial species form the horizontal axis and 84 P450 families form the vertical axis.
Figure 4
Figure 4
Comparative analysis of P450s involved in secondary metabolism in Gammaproteobacterial species. The P450 family name, number of P450s and the percentage of the total number of P450s that are part of BGCs are presented in the figure. Detailed information on secondary metabolite clusters, species and P450s is presented in Supplementary Dataset 1: Sheet 2.
See this image and copyright information in PMC

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