Abstract
We provide the genome sequences of the type strains of the polychlorophenol-degrading Mycobacterium chlorophenolicum (DSM43826), the degrader of chlorinated aliphatics Mycobacterium chubuense (DSM44219) and Mycobacterium obuense (DSM44075) that has been tested for use in cancer immunotherapy. The genome sizes of M. chlorophenolicum, M. chubuense, and M. obuense are 6.93, 5.95, and 5.58 Mb with GC-contents of 68.4%, 69.2%, and 67.9%, respectively. Comparative genomic analysis revealed that 3,254 genes are common and we predicted approximately 250 genes acquired through horizontal gene transfer from different sources including proteobacteria. The data also showed that the biodegrading Mycobacterium spp. NBB4, also referred to as M. chubuense NBB4, is distantly related to the M. chubuense type strain and should be considered as a separate species, we suggest it to be named Mycobacterium ethylenense NBB4. Among different categories we identified genes with potential roles in: biodegradation of aromatic compounds and copper homeostasis. These are the first nonpathogenic Mycobacterium spp. found harboring genes involved in copper homeostasis. These findings would therefore provide insight into the role of this group of Mycobacterium spp. in bioremediation as well as the evolution of copper homeostasis within the Mycobacterium genus.
Highlights
Bacteria of the genus Mycobacterium are acid fast, robust, and can inhabit various environmental reservoirs, for example, ground and tap water, soil, animals, and humans
We decided to sequence the genomes of the type strains, M. chlorophenolicum DSM43826, M. chubuense DSM44219, and M. obuense DSM44075, and to undertake comparative genomic analysis in order to understand how some of the characteristics of these genomes with respect to genome size, common and unique genes, horizontal gene transfer (HGT), and codon usage might be manifested as phenotypic differences
We present the genome structure and functional correlation of three mycobacterial species considered to be closely related phylogenetically: the MchloDSM, M. chubuense DSM44219 (MchuDSM), and M. obuense DSM44075 (MobuDSM) type strains
Summary
Bacteria of the genus Mycobacterium are acid fast, robust, and can inhabit various environmental reservoirs, for example, ground and tap water, soil, animals, and humans. Mycobacterium chubuense was first isolated from garden soil in Japan (Saito et al 1977; Tsukamura and Mizuno 1977) It is rapidly growing, mesophilic, pigmented, and has rod- and-coccoid shaped cell morphologies and its position based on the 16S rRNA phylogenetic tree is close to M. obuense (98.5% sequence identity; Pitulle et al 1992). We decided to sequence the genomes of the type strains, M. chlorophenolicum DSM43826, M. chubuense DSM44219, and M. obuense DSM44075 (hereafter referred to as MchloDSM, MchuDSM, and MobuDSM, respectively), and to undertake comparative genomic analysis in order to understand how some of the characteristics of these genomes with respect to genome size, common and unique genes, horizontal gene transfer (HGT), and codon usage might be manifested as phenotypic differences That these three Mycobacterium spp. do change their cell shape during cultivation (Saito et al 1977; Haggblom et al 1994) made such studies relevant to our interest in mechanisms of morphological changes seen in Mycobacterium spp. We provide data showing the presence of putative genes encoding for oxygenases in all four species as well as for proteins involved in copper homeostasis in MchloDSM and in MycNBB4
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