Genome-wide identification of essential genes in Mycobacterium intracellulare by transposon sequencing — Implication for metabolic remodeling

• Published in: Scientific reports Vol. 10; no. 1; p. 5449
• Main Authors: Tateishi, Yoshitaka, Minato, Yusuke, Baughn, Anthony D., Ohnishi, Hiroaki, Nishiyama, Akihito, Ozeki, Yuriko, Matsumoto, Sohkichi
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 25.03.2020; Nature Publishing Group
• Subjects: 45/43; 45/70; 631/326/1320; 631/326/41/2530; Aerobic conditions; Carbohydrate metabolism; DNA Transposable Elements - genetics; DNA, Bacterial - genetics; Drug Discovery; Genome, Bacterial - genetics; Genomes; Genomics - methods; Gluconeogenesis; Gluconeogenesis - genetics; Glyoxylate cycle; Glyoxylates - metabolism; Growth conditions; Humanities and Social Sciences; Humans; Hypoxia; multidisciplinary; Mycobacterium avium Complex - genetics; Mycobacterium avium Complex - growth & development; Mycobacterium avium Complex - metabolism; Mycobacterium avium Complex - pathogenicity; Mycobacterium Infections, Nontuberculous - microbiology; Mycobacterium intracellulare; Mycothiol; Proteasome Endopeptidase Complex - genetics; Proteasomes; Science; Science (multidisciplinary); Sequence Analysis, DNA - methods; Succinic Acid - metabolism; Transposons; Trehalose; Tuberculosis; Virulence; Virulence - genetics
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-020-62287-2

The global incidence of the human nontuberculous mycobacteria (NTM) disease is rapidly increasing. However, knowledge of gene essentiality under optimal growth conditions and conditions relevant to the natural ecology of NTM, such as hypoxia, is lacking. In this study, we utilized transposon sequencing to comprehensively identify genes essential for growth in Mycobacterium intracellulare . Of 5126 genes of M. intracellulare ATCC13950, 506 genes were identified as essential genes, of which 280 and 158 genes were shared with essential genes of M. tuberculosis and M. marinum , respectively. The shared genes included target genes of existing antituberculous drugs including SQ109, which targets the trehalose monomycolate transporter MmpL3. From 175 genes showing decreased fitness as conditionally essential under hypoxia, preferential carbohydrate metabolism including gluconeogenesis, glyoxylate cycle and succinate production was suggested under hypoxia. Virulence-associated genes including proteasome system and mycothiol redox system were also identified as conditionally essential under hypoxia, which was further supported by the higher effective suppression of bacterial growth under hypoxia compared to aerobic conditions in the presence of these inhibitors. This study has comprehensively identified functions essential for growth of M. intracellulare under conditions relevant to the host environment. These findings provide critical functional genomic information for drug discovery.