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

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. Among the bacteria that inhabit the human gut, species belonging to the bacterial phylum Firmicutes and Bacteroides are dominant 1-3. 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. Some members are saprophytes that live in soil and aquatic environments, performing mainly decomposition and recycling of organic matter, some members are commensals of humans and some members are pathogens of animals, including humans, and plants 4. Some members have been subjected to thorough investigation to gain understanding of endospore formation and survival 5 and the biotechnological potential of these organisms has been explored for the production of dairy products 6 , enzymes 7 and antibiotics 8. The Firmicutes phylum is further divided into seven subphyla, namely Bacilli, Clostridia, Erysipelotrichia, Limnochordia, Negativicutes, Thermolithobacteria, and Tissierellia 4. 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). Clostridia consist of species that produce short chain fatty acids in the human gut, such as butyrate, which is essential fuel for colonocytes (enterocytes referred to as colonocytes in the colon) 9 and also species causing botulism, tetanus, gas gangrene, food poisoning, pseudomembranous colitis, and antibioticassociated diarrhea in humans 10,11. Quite a number of studies have explored the relation between the changes in the percentage of Firmicutes species in the human gut and human conditi...

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

“…Among these families, CYP107 P450 family members were dominantly present (37%) in secondary metabolite BGCs (Figure 4). The same phenomenon was observed in Streptomyces species [49,50] and Firmicutes species [55], where CYP107 P450 family members were dominantly present as part of BGCs. Interestingly, among six P450 families that are expanded in these species, only two P450 family members were found to be part of the clusters (Figure 4).…”

“…Recent studies from our laboratory focusing on bacterial species revealed that the lifestyle of an organism plays a key role in shaping P450 content vis à vis P450s helping microbes to adapt to ecological niches. However, these studies were limited to few groups of bacterial species belonging to the genera Streptomyces [49,50] and Mycobacterium [51][52][53] and from the phyla Cyanobacteria [54] and Firmicutes [55,56]. Furthermore, to date, a comparative analysis of P450s in the Gammaproteobacterial species has not been reported.…”

Diversification of Ferredoxins across Living Organisms

“…In this study, 241 alphaproteobacterial species and 227 Firmicutes species genomes that are available for public use at the Kyoto Encyclopedia of Genes and Genomes (KEGG) database [41] were used (Table S1). These species are known to have P450s in their genome [42,43] and thus were selected for ferredoxins analysis considering P450s need ferredoxins for their function and so, as one can expect, there is the presence of a higher number of ferredoxins in these species. The list of species used in the study along with their species codes are presented in Table S1.…”

“…Phylogenetic analysis of ferredoxins was carried out following the procedure described recently by our laboratory [43,62]. The phylogenetic tree of ferredoxins was constructed using protein sequences.…”

“…Ferredoxin subtype profile heat maps were generated following the procedure described recently by our laboratory [43,62]. The heat map was generated using the ferredoxin subtype data to show the presence or absence of ferredoxin subtypes in three domains of life, Archaea, Bacteria, and Eukarya.…”