Comparative genomics of cytochrome P450 monooxygenase redox systems in mycobateria

Abstract

Cytochrome P450 monooxygenases (CYPs/P450s) are heme-thiolate proteins found in species belong to different biological kingdoms. P450s found to play key role in organism’s physiology due to their regio- and stereo-specific catalytic activity. All P450s need electrons to perform their enzymatic reactions. Except self-sufficient P450s, most P450s receive electron form different P450 redox proteins. It is logical that if one can inhibit P450 redox protein that eventually result not only in loss of all P450s functions but also led to the death of an organism. Mycobacterium tuberculosis, the deadliest pathogen of human, was found to have 20 P450s in its genome. Studies revealed that M. tuberculosis P450s can serve as novel drug targets. This suggests P450 redox proteins are very important in keeping M. tuberculosis P450s physiological function. With the exception of few studies on M. tuberculosis P450 redox proteins nothing is known about the P450 redox content in species of Mycobacterium. Therefore, the aim of this study is to perform comparative genomics of P450 redox partners in 81 mycobacterial species genomes. Genome data-mining of 81 mycobacterial species revealed presence of 1063 P450 redox proteins grouped into ferredoxins (662) and ferredoxin reductases (401). Phylogenetic anlaysis of ferredoxins revealed presence of two major clades of ferredoxins with characteristic Pfam/InterPro protein domains. The clade with domains Fer4 (PF00037), Fer4_7 (PF12838) and Fer4_9 (PF13187) was associated with the same InterPro entry (IPR17896) and it was classified under group 2 and the clade supported with 83% boostrap proportion with domains Fer4_13 (PF13370), Fer4_15 (PF13459) and Fer4_19 (PF06902) shared similar HMM-motifs which was classified under as group 1. Comparative analysis of ferredoxins across mycobacterial species revealed interesting patterns. Mycobacterial tuberculosis complex species showed 1-6 ferredoxins in their genomes. Mycobacteria causing leprosy (MCL) included two species namely mycobacterium leprae TN and mycobacterium leprae Br4923 which both contained a single ferredoxin. The other group which is known to be Nontuberculosis mycobacteria (NTM) showcased a range of 7-18 for ferredoxins. Mycobacterium avium complex species showed a range from 4 -19 ferredoxins in their genomes. Saprophytes showed a high number of ferredoxins with the range of 8-26. Phylogenetic analyses indicated presence of two major divergent clades of ferredoxin reductases (FdRs) in mycobacteria; the Bacterial-type, which belong to the Plant-type FdRs, and the Gluthatione Reductase (GR)-type. Within the GR-type FdRs, two different clades were identified: the adrenodoxin (Adr)-like clade and the oxygenase-copuled NADHferredoxin reductase (ONFR)-like clade. Mycobacterial tuberculosis complex species showed 0-8 FdRs in their genomes. MCL species contained two FdRs. NTM species contained 2-7 FdRs in their genome. Saprophytes showed a high number of FdRs with the range of 0-12. Mycobacterium avium complex species showed 3-7 FdRs in their genomes. Mycobacterium chelonae-abscessus complex ranged from 1-6 FdRs. Results generated in this study on genome data-mining, annotation and phylogenetic analysis of P450 redox proteins will be submitted to high impact factor journal. Apart from my Masters study, I supervised one B. Tech student project and also worked on a few other bioinformatics projects and earned co-authorship. Most of my research articles are published in high impact factor journals. The following is a list of my research articles: 1. SC Raselemane (co-author) (2016) Molecular evolutionary dynamics of cytochrome P450 monooxygenases across kingdoms: Special focus on mycobacterial P450s. Scientific Reports 6, Article number: 33099. 2. SC Raselemane (co-author) (2015). Diversity and evolution of cytochrome P450 monooxygenases in Oomycetes. Scientific Reports 5, Article number: 11572. In addition to the above credits, I was featured on national TV and in newspapers for discovering a novel drug target. I also presented work at both national and international (Canada) conferences.