Genome-wide analysis and genome mapping of essential cytochrome P450 monooxygenase CYP125 in mycobacteria

Abstract

Tuberculosis, an infectious lung disease, is a leading cause of death worldwide caused by Mycobacterium tuberculosis. Genome-wide screening for genes essential for the survival of M. tuberculosis has revealed that cytochrome P450 monooxygenase CYP125A1 is critical for M. tuberculosis survival. CYP125A1 play key role in oxidation of cholesterol and help M. tuberculosis to utilize cholesterol as a carbon source during its inhabitant in host organism. Despite this great importance, to date, genome wide identification, annotation and phylogenetic analysis of CYP125A1 and its genome mapping with respect to gene-cluster analysis across mycobacterial species has not been performed. Also, to date, P450s from prokaryote organisms has not been subjected to evolutionary analysis. This study addresses these two research gaps. Genome data-mining and annotation of CYP125 P450s across 60 mycobacterial species revealed presence of a total number of 120 CYP125 P450s that can be grouped into five subfamilies (A, D, E, F, NS). Analysis of CYP125 P450s distribution in different mycobacterial categories revealed that Mycobacterium tuberculosis complex (MTBC) species showed lowest copies of CYP125 in their genomes compared to other categories. This study revealed that CYP125 P450 is not present in Mycobacteria causing leprosy (MCL) species. Mycobacterium avium complex (MAC) and Saprophytes (SAP) species showed highest number of CYP125 subfamilies in their genomes. Analysis of CYP125 P450 subfamily patterns in mycobacterial categories revealed MAC species have highest diversity of CYP125 subfamilies followed by species belong to SAP and Nontuberculous mycobacteria (NTM). Presence of more than one copy of CYP125 in some mycobacterial categories suggests important role of this P450s in their physiology. Analysis of subfamily patterns in mycobacterial categories revealed MAC species have highest diversity of CYP125 subfamilies followed by species belong to SAP and NTM. Among subfamilies, subfamily A is more dominant across mycobacterial species. Subfamily D is present only in species belonging to MAC and NTM. Subfamily E is present only in species belonging to MAC. Subfamily F and NS is present in MAC and SAP. Analysis of CYP125 gene clusters in the genus Mycobacterium revealed presence of 28 CYP125 gene-clusters. Gene clusters 1 to 20 comprised of quite a number of CYP125 P450s ranging from 2 to 23 and gene clusters 21 – 28 named as unique gene clusters considering each of the CYP125 P450 in this cluster have different genes both in the upstream and downstream of CYP125. Overall, SAP species showed highest CYP125 gene cluster diversity (10 clusters including 1 unique cluster) followed by MAC (8 clusters including 3 unique clusters), NTM (5 clusters including 3 unique clusters), MCAC (4 clusters) and MTBC (2 clusters including one unique cluster). This study is first of its kind on analysis of gene-clusters in prokaryote P450s. Some of the CYP125 P450s in different clusters have reverse complement arrangement of genes compared to other CYP125s in the same cluster. These P450s are under investigation for further analysis of possible gene rearrangement events in the chromosome. Results generated in this study on genome data mining, identification, annotation and phylogenetic analysis of CYP125 is published as part of major article on mycobacterial P450s where I am a co-author. The article details are: R Monyaki (co-author) (2016) Molecular evolutionary dynamics of cytochrome P450 monooxygenases across kingdoms: Special focus on mycobacterial P450s. Scientific Reports 6, Article number: 33099. Apart from my Masters study, I supervised two B. Tech student projects and also worked on a few other bioinformatics projects and earned co-authorship in high impact factor journal listed below: R Monyaki (co-author) (2015) Diversity and evolution of cytochrome P450 monooxygenases in Oomycetes. Scientific Reports 5, Article number: 11572. Article as first author on CYP125 gene-cluster analysis under preparation for submission to Plos ONE. 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.