In silico analysis of cholesterol catabolic genes/proteins in the genus mycobacterium

Abstract

It is well known that Mycobacterium tuberculosis, the causative agent of one of the deadliest human diseases, tuberculosis, uses human cholesterol as a carbon source both in the latent and active phases of its lifestyle. The discovery of the ability of M. tuberculosis to degrade and use cholesterol as a sole source of carbon and energy has opened up the possibility of using genes/proteins involved in cholesterol degradation as novel drug targets. If one can find the highly conserved genes/proteins across the mycobacteria that are capable of degrading cholesterol, then in future these genes can possibly be used as universal drug targets against mycobacterial infections. However, to date, data on how many mycobacterial species utilise cholesterol has not been reported. Furthermore, performing laboratory experiments is laborious and time- and money-consuming, considering each of the mycobacterial species has different lifestyle and culture conditions. The study is aimed at using the available genomic data to perform comparative genomic studies to unravel the nature of cholesterol catabolic genes/proteins in the genus Mycobacterium to determine which mycobacterial species are capable of degrading cholesterol. This study is a first of its kind comprehensive analysis of the genes/proteins involved in cholesterol degradation across 93 mycobacterial species, using bioinformatic tools. Ninety-three mycobacterial species whose genomes are available for public use at the KEGG database were used in this study. Literature on cholesterol degradation by bacteria was collected and the cholesterol degradation pathway was deduced. The intermediate metabolites and enzymes involved in each of the steps were identified and mapped using ChemDraw software. A software program that extracts homolog data across 93 mycobacterial species was developed. The hit proteins’ domains/functions were identified using software programs: NCBI Batch Web CD-search tool and the KEGG functional database. Based on the sequence identity, functional motifs and functional data, if available, the hit proteins were sorted into specific enzymatic reactions of cholesterol degradation. After thorough literature analysis, 152 genes/proteins were identified as cholesterol catabolic genes/proteins and grouped into four different categories. The four categories are: (i) genes predicted to be specifically required for growth on cholesterol, (ii) cholesterol catabolic genes proven to be or predicted to be essential for the survival of M. tuberculosis in macrophage cells and in murine infection, (iii) genes/proteins that are up-regulated during growth on cholesterol, and (iv) genes involved in cholesterol degradation by M. tuberculosis H37Rv, but not confirmed or predicted to be essential. In silico analysis of 152 genes across 93 mycobacterial species revealed that 51 mycobacterial species are unable to degrade cholesterol.