Mycobacterial phage TM4 requires a eukaryotic-like Ser/Thr protein kinase to silence and escape anti-phage immunity

Insertion sequence transposition activates antimycobacteriophage immunity through an lsr2‐silenced lipid metabolism gene island

“…Very few antiphage mechanisms have been clearly characterized in mycobacterial species, although these bacterial genomes encode potential adaptive immune systems such as the CRISPR‐Cas system 28 and some innate immune systems 29 , 30 . In this study, we found that, under the pressure of phage infection, the transposition of IS 1096 into the lsr2 gene endowed M. smegmatis with a broad‐spectrum antiphage ability.…”

“…It has been proposed that M. smegmatis I3 uses glycopeptide lipids as receptors 42 , and Wetzel et al suggested that the surface component trehalose polyphylenates of mycobacteria may be a potential receptor for phage BPs and Muddy 43 . A very recent study suggested that phage‐binding receptors in M. smegmatis are associated with the metabolic homeostasis of phospholipids 30 . Consistently, in the present study, when comparing differential lipid components between the wild‐type and Δ lsr2 strains, the contents of eight different Ac 1 PIMs in the Δ lsr2 strain significantly increased (Figure 5B ), resulting in a phage absorption defect.…”

“…Deletions of the lsr2 gene in the wild‐type M. smegmatis strain, or the genes including MSMEG_4728 , MSMEG_4731 , MSMEG_4733 , MSMEG_4734 , MSMEG_4737 , MSMEG_4727–4737 , MSMEG_4727–4732 , MSMEG_4728–4732 , and MSMEG_4733–4737 , or the promoters such as S1 ( MSMEG_4727 p), S2 ( MSMEG_4735 p), and S3 ( MSMEG_4737 p) in the lsr2 deletion strain, were performed according to previously described procedures 30 . In brief, a recombinant suicide plasmid was constructed and transferred into the corresponding mycobacterial strains according to the reported procedures.…”

“…Lipidomic assays were performed with several modifications as described previously 30 . In brief, mycobacterial strains were grown in 7H9 medium and then harvested when an OD 600 of 1.0 was reached.…”

“…Mycobacterial genomes contain abundant IS elements, of which IS 6110 has been widely used as a marker in the molecular epidemiology of tuberculosis 24 , and its transposition can help produce antibiotic resistance 25 ; IS 1096 is considered unique to M. smegmatis 26 , and plays a crucial role in mycobacterial genome evolution 27 . Recently, it has been found that mycobacterial genomes encode some potential immune systems that resist phage infection, including the CRISPR‐Cas system 28 , the toxin–antitoxin system 29 , the restriction–modification system 29 , and the BREX‐like system 30 . However, their roles in phage defense are still largely unclear.…”