A novel putative DNA damage-repair system Dip in Corynebacterium glutamicum

In bacterial species, most types of environmental stresses ultimately result in varying degrees of DNA damage. The bacterial SOS response is a generalized response aimed not only at repairing DNA damage, but also at pausing cell division to avoid segregation of damaged chromosomes. This response is controlled by LexA which, under physiological conditions, represses the expression of SOS genes. In Corynebacterium glutamicum, a model organism for the cell biology of Corynebacterineae and a biotechnological workhorse, the LexA regulon consists of 48 genes. Apart from genes encoding homologous recombination systems, HNH endonucleases and others, nearly half of the LexA-regulated genes have an unknown function (1). In this project, we identified a new putative SOS-regulated operon in C. glutamicum containing the DNA damage-induced proteins (dipABCD). Having proven its induction upon exposure to the DNA-damaging compound mitomycin C, we aimed to elucidate the role of Dips in the SOS response and, more specifically, DNA repair. Using a variety of in vitro and in vivo approaches, we could show that the system comprises a divalent ion-dependent nickase and GTPase, DipA, and an ATP-dependent helicase which binds in proximity to DNA damage, DipD. Moreover, based on the single-molecule localization microscopy, we hypothesized that DipD and DipA are recruited to the DNA damage site sequentially, e.g. the DNA nicking activity of DipA precedes the unwinding activity of DipD. The Dip system as a whole might interact with DivIVA, a polar scaffold for cell elongation (RodA) and chromosome segregation (ParB-parS) machineries (2), as evidenced by pull-down assay and SMLM. In summary, our results demonstrate a putative role of the Dip system in DNA damage repair and contribute to the studies of non-canonical DNA repair systems.

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