Insights from the Genome Sequence of Mycobacterium lepraemurium: Massive Gene Decay and Reductive Evolution

Abstract

Mycobacterium lepraemurium is the causative agent of murine leprosy, a chronic, granulomatous disease similar to human leprosy. Due to the similar clinical manifestations of human and murine leprosy and the difficulty of growing both bacilli axenically, Mycobacterium leprae and M. lepraemurium were once thought to be closely related, although it was later suggested that M. lepraemurium might be related to Mycobacterium avium In this study, the complete genome of M. lepraemurium was sequenced using a combination of PacBio and Illumina sequencing. Phylogenomic analyses confirmed that M. lepraemurium is a distinct species within the M. avium complex (MAC). The M. lepraemurium genome is 4.05 Mb in length, which is considerably smaller than other MAC genomes, and it comprises 2,682 functional genes and 1,139 pseudogenes, which indicates that M. lepraemurium has undergone genome reduction. An error-prone repair homologue of the DNA polymerase III α-subunit was found to be nonfunctional in M. lepraemurium, which might contribute to pseudogene formation due to the accumulation of mutations in nonessential genes. M. lepraemurium has retained the functionality of several genes thought to influence virulence among members of the MAC.IMPORTANCEMycobacterium lepraemurium seems to be evolving toward a minimal set of genes required for an obligatory intracellular lifestyle within its host, a niche seldom adopted by most mycobacteria, as they are free-living. M. lepraemurium could be used as a model to elucidate functions of genes shared with other members of the MAC. Its reduced gene set can be exploited for studying the essentiality of genes in related pathogenic species, which might lead to discovery of common virulence factors or clarify host-pathogen interactions. M. lepraemurium can be cultivated in vitro only under specific conditions and even then with difficulty. Elucidating the metabolic (in)capabilities of M. lepraemurium will help develop suitable axenic media and facilitate genetic studies.

Keywords: Mycobacterium lepraemurium; comparative genomics; genome sequencing; murine leprosy.

FIG 1

The genome of Mycobacterium lepraemurium strain Hawaii. (A) Graphical representation of the genome and its features. The origin of replication is at 12 o’clock, and the genome sequence runs clockwise. Ticks around the outermost circle mark million bases. Looking inwards, the outermost track or the first track (blue) shows functional genes. The second track (green) shows pseudogenes. The third track shows insertion sequences (all dysfunctional) colored to distinguish families (orange, red, black, and blue) and exaggerated in size for visibility. The fourth track shows the GC skew, calculated for a 20-kb window sliding every 1 kb, represented as a histogram with positive values pointing outward (red bars) and negative values pointing inward (blue bars). (B) Maximum parsimony tree of M. lepraemurium and selected mycobacterial species. The tree was created using MEGA7 from concatenated amino acid sequences (3,936 positions) of 11 proteins (DnaN, RplI, GrpE, MetG, RplY, PheT, FtsQ, HolA, MiaA, FtsY, and FtsX). Branches corresponding to the Mycobacterium avium complex are in blue. Bootstrap support, estimated from 500 replicates, is given below each branch. An expanded version of this tree, including additional genomes, is in Fig. S1 in the supplemental material.

FIG 2

Heatmap of the gene orthology between M. avium subsp. paratuberculosis K-10, M. lepraemurium, M. leprae, and M. ulcerans. Genes are shown in black, and the absence of genes is shown in white. The raw height corresponds to the number of genes.