Comparative Analysis Of Secondary Metabolite Biosynthetic Gene Clusters And Associated P450S In The Genera Streptomyces And Mycobacterium

Abstract

Species belonging to the genera Streptomyces and Mycobacterium are well known for their contrasting lifestyle and impact on humans. Streptomyces species produce two-thirds of antibiotics, secondary metabolites, used in the world, whereas mycobacterial species are well known to be the deadliest human pathogens, although a few are environmentally useful. Mycobacterial species also produce secondary metabolites that play a role in pathogenesis. It is a well known fact that genes involved in the synthesis of secondary metabolites form clusters known as biosynthetic gene clusters (BGCs). To date, comparative analysis of secondary metabolite BGCs in species belonging to these two genera has not been reported. Among the genes involved in synthesis of secondary metabolites, cytochrome P450 monooxygenases (CYPs/P450s) play a key role, as these enzymes contribute to the diversity of secondary metabolites owing to their chemo-, stereo- and regio-specific oxidation of substrates. Despite this importance of P450s in the synthesis of secondary metabolites, to date, identification of P450s involved in the synthesis of secondary metabolites in species belonging to these two genera has not been reported. Thus, this study is aimed at addressing these two research gaps by conducting comprehensive comparative analysis of secondary metabolite BGCs and associated P450s in the species belonging to the genera Streptomyces (48 species) and Mycobacterium (60 species). Genome-wide analysis revealed the presence of a large and diverse number of secondary metabolite BGCs in Streptomyces species compared to mycobacteria species. In total 1 461 secondary metabolite BGCs belonging to 159 types were found in 48 Streptomyces species compared to 898 secondary metabolite BGCs belonging to only 18 types found in 60 mycobacterial species. Among Streptomyces species, S. griseochromogenes has the highest number of secondary metabolite BGCs (49) and Streptomyces sp. 4F has the lowest number of secondary metabolite BGCs (19) in their genomes. Mycobacterium marinum has the highest number of secondary metabolite BGCs (29) and two strains of M. leprae have the lowest number of secondary metabolite BGCs (five each) in their genomes. Quite a big difference was observed with respect to the types of secondary metabolite BGCs between Streptomyces and mycobacterial species. Among 159 types of secondary metabolite BGCs found in Streptomyces species, only 13 types of BGCs contributed 80% to the total percentage of BGCs, suggesting that the secondary metabolites produced by these BGCs were highly important in Streptomyces species’ physiology. The secondary metabolite BGC, terpene, was dominant, followed by siderophores, nonribosomal peptides (Nrps) and Type 1 polyketides (T1pks) in Streptomyces species. Among 18 types of secondary metabolite BGCs identified in mycobacterial species, Nrps was the dominant secondary metabolite BGC, followed by ‘other’, T1pks and T1pks-Nrps. Despite the presence of 15 common types of secondary metabolite BGCs between the genera Streptomyces and Mycobacterium, large differences were observed in terms of the number of BGCs, indicating that the selective enrichment of particular secondary metabolite BGCs in both genera is possibly due to the different lifestyle, as discussed in the subsequent section. Comparative analysis of P450s that are part of secondary metabolite BGCs revealed the presence of a large number of diverse P450s as part of these secondary metabolite BGCs in Streptomyces, compared to Mycobacterium. Not all secondary metabolite BGCs found in Streptomyces and Mycobacterium have P450s. Among 1 461 Streptomyces species, only 554 secondary metabolite BGCs were found to have P450s, whereas in mycobacterial species, among 898 only 204 secondary metabolite BGCs have P450s. Overall, 554 and 204 P450s were found to be part of secondary metabolite BGCs in respectively Streptomyces and mycobacterial species. Among 88 P450 families that are part of different secondary metabolite BGCs, some P450 families are highly dominant in Streptomyces species, indicating their key role in the synthesis of different secondary metabolites. These P450 families were found to be the same that are highly populated in Streptomyces species, with some exceptions. This strongly indicates that these P450 families provide an advantage to Streptomyces species by generating diverse secondary metabolites, thus letting these species thrive in nature. Mycobacterial species’ secondary metabolite BGC P450 profiles are contrasted with Streptomyces species, where the dominant P450 families are not necessarily dominant as part of secondary metabolite BGCs. Ten P450 families, namely CYP51, CYP123, CYP125, CYP130, CYP135, CYP136, CYP138, CYP140, CYP144 and CYP1128, are conserved and highly populated across 60 mycobacterial species. However, none of these P450 families is dominant as part of different secondary metabolite BGCs. The CYP139 P450 family was found to be the dominant family as part of secondary metabolite BGCs. Although eight P450 families, namely CYP124, CYP121, CYP105, CYP125, CYP102, CYP147, CYP136 and CYP161, which are part of secondary metabolite BGCs, were commonly found between the genera Streptomyces and Mycobacterium, the number of P450s in these families was found to be different. Based on the above data, it is clear that different lifestyles influenced the gene content in Streptomyces and Mycobacterium, hence differences in the number and type of secondary metabolite BGCs and P450s that are associated with secondary metabolite BGCs were observed. The saprophytic and symbiotic lifestyle of Streptomyces resulted in the highest diversity of secondary metabolite BGCs and P450s, thus helping these organisms to generate chemically diverse secondary metabolites to adapt to different ecological niches. For this reason, Streptomyces species have been found to have large and diverse secondary metabolite BGCs and P450s compared to mycobacterial species. Based on the evidence presented in this study, the researcher hereby proposes that lifestyle or ecological niches play a key role in the evolution of secondary metabolite BGCs and associated P450s in species belonging to the genera Streptomyces and Mycobacterium.