Decoding the similarities and differences among mycobacterial species.
PLoS Negl Trop Dis 2017;
11:e0005883. [PMID:
28854187 PMCID:
PMC5595346 DOI:
10.1371/journal.pntd.0005883]
[Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 09/12/2017] [Accepted: 08/18/2017] [Indexed: 11/19/2022] Open
Abstract
Mycobacteriaceae comprises pathogenic species such as Mycobacterium tuberculosis, M. leprae and M. abscessus, as well as non-pathogenic species, for example, M. smegmatis and M. thermoresistibile. Genome comparison and annotation studies provide insights into genome evolutionary relatedness, identify unique and pathogenicity-related genes in each species, and explore new targets that could be used for developing new diagnostics and therapeutics. Here, we present a comparative analysis of ten-mycobacterial genomes with the objective of identifying similarities and differences between pathogenic and non-pathogenic species. We identified 1080 core orthologous clusters that were enriched in proteins involved in amino acid and purine/pyrimidine biosynthetic pathways, DNA-related processes (replication, transcription, recombination and repair), RNA-methylation and modification, and cell-wall polysaccharide biosynthetic pathways. For their pathogenicity and survival in the host cell, pathogenic species have gained specific sets of genes involved in repair and protection of their genomic DNA. M. leprae is of special interest owing to its smallest genome (1600 genes and ~1300 psuedogenes), yet poor genome annotation. More than 75% of the pseudogenes were found to have a functional ortholog in the other mycobacterial genomes and belong to protein families such as transferases, oxidoreductases and hydrolases.
Members of the Mycobacteriaceae family, which are known to adapt to different environmental niches, comprise bacterial species with varied genome sizes. They are unique in their cell-wall composition, which is remarkably thick and lipid-rich as compared to other bacteria. We performed a comparative analysis at the proteome level for ten mycobacterial species that differ in their pathogenicity, genome size and environmental niches. A total of 1080 orthologous clusters with representation from all ten species were obtained, and these were further examined for their domain annotations, domain architecture similarities and enriched GO terms. These core orthologous clusters are enriched in various biosynthetic pathways. The proteins that are specific to each of the ten species were also investigated for their GO functions. The M. leprae genome has a large number of pseudogenes and we searched for their functional orthologs in other mycobacterial species in order to understand the functions that are lost from the M. leprae genome. The proteins present exclusively in M. leprae genome were studied in more detail, in order to predict putative drug targets and diagnostic markers. These findings, which have implications in understanding evolution of mycobacterial genomes, identify species-specific proteins that have potential for use in developing new diagnostic tools and therapeutics.
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