Dataset Information

Gene and whole genome analyses reveal that the mycobacterial strain JS623 is not a member of the species Mycobacterium smegmatis.

ABSTRACT: Unexpected differences were found between the genome of strain JS623, used in bioremediation studies, and the genome of strain mc(2) 155, a model organism for investigating basic biology of mycobacteria. Both strains are currently assigned in the databases to the species Mycobacterium smegmatis and, consequently, the environmental isolate JS623 is increasingly included as a representative of that species in comparative genome-based approaches aiming at identifying distinctive traits of the different members of the genus Mycobacterium. We applied traditional molecular taxonomic procedures--inference of single and concatenated gene trees--to re-evaluate the membership of both strains to the same species, adopting the latest accepted cut-off values for species delimitation. Additionally, modern whole genome-based in silico methods where performed in a comprehensive molecular phylogenetic analysis of JS623 and other members of the genus Mycobacterium. These analyses showed that all relevant genome parameters of JS623 clearly separate this strain from M. smegmatis. The strain JS623 should be corrected as Mycobacterium sp. not only in the literature but, even more importantly, in the database entries, as inclusion of the genome wrongly attributed to the M. smegmatis species in comparative studies will result in misleading conclusions.

SUBMITTER: Garcia MJ

PROVIDER: S-EPMC4767285 | biostudies-literature | 2016 Mar

REPOSITORIES: biostudies-literature

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Gene and whole genome analyses reveal that the mycobacterial strain JS623 is not a member of the species Mycobacterium smegmatis.

Garcia Maria J MJ Gola Susanne S

Microbial biotechnology 20160201 2

Unexpected differences were found between the genome of strain JS623, used in bioremediation studies, and the genome of strain mc(2) 155, a model organism for investigating basic biology of mycobacteria. Both strains are currently assigned in the databases to the species Mycobacterium smegmatis and, consequently, the environmental isolate JS623 is increasingly included as a representative of that species in comparative genome-based approaches aiming at identifying distinctive traits of the diffe ...[more]

PMID: 26834038

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Project description:Mycobacterium neoaurum strains can transform phytosterols to 4-androstene-3,17-dione (4-AD), a key intermediate for the synthesis of advanced steroidal medicines. In this work, we presented the complete genome sequence of the M. neoaurum strain HGMS2, which transforms β-sitosterol to 4-AD. Through genome annotation, a phytosterol-degrading pathway in HGMS2 was predicted and further shown to form a 9,10-secosteroid intermediate by five groups of enzymes. These five groups of enzymes included three cholesterol oxidases (ChoM; group 1: ChoM1, ChoM2 and Hsd), two monooxygenases (Mon; group 2: Mon164 and Mon197), a set of enzymes for side-chain degradation (group 3), one 3-ketosteroid-1,2-dehydrogenase (KstD; group 4: KstD211) and three 3-ketosteroid-9a-hydroxylases (Ksh; group 5: KshA226, KshA395 and KshB122). A gene cluster encoding Mon164, KstD211, KshA226, KshB122 and fatty acid β-oxidoreductases constituted one integrated metabolic pathway, while genes encoding other key enzymes were sporadically distributed. All key enzymes except those from group 3 were prepared as recombinant proteins and their activities were evaluated, and the proteins exhibited distinct activities compared with enzymes identified from other bacterial species. Importantly, we found that the KstD211 and KshA395 enzymes in the HGMS2 strain retained weak activities and caused the occurrence of two major impurities, i.e., 1,4-androstene-3,17-dione (ADD) and 9-hydroxyl-4-androstene-3,17-dione (9OH-AD) during β-sitosterol fermentation. The concurrence of these two 4-AD analogs not only lowered 4-AD production yield but also hampered 4-AD purification. HGMS2 has the least number of genes encoding KstD and Ksh enzymes compared with current industrial strains. Therefore, HGMS2 could be a potent strain by which the 4-AD production yield could be enhanced by disabling the KstD211 and KshA395 enzymes. Our work also provides new insight into the engineering of the HGMS2 strain to produce ADD and 9OH-AD for industrial application.

Dataset Information

Gene and whole genome analyses reveal that the mycobacterial strain JS623 is not a member of the species Mycobacterium smegmatis.

Publications

Gene and whole genome analyses reveal that the mycobacterial strain JS623 is not a member of the species Mycobacterium smegmatis.

Similar Datasets

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