DNA Ligase C and Prim-PolC participate in base excision repair in mycobacteria

Abstract

Prokaryotic Ligase D is a conserved DNA repair apparatus processing DNA double-strand breaks in stationary phase. An orthologous Ligase C (LigC) complex also co-exists in many bacterial species but its function is unknown. Here we show that the LigC complex interacts with core BER enzymes in vivo and demonstrate that together these factors constitute an excision repair apparatus capable of repairing damaged bases and abasic sites. The polymerase component, which contains a conserved C-terminal structural loop, preferentially binds to and fills-in short gapped DNA intermediates with RNA and LigC ligates the resulting nicks to complete repair. Components of the LigC complex, like LigD, are expressed upon entry into stationary phase and cells lacking either of these pathways exhibit increased sensitivity to oxidising genotoxins. Together, these findings establish that the LigC complex is directly involved in an excision repair pathway(s) that repairs DNA damage with ribonucleotides during stationary phase.

Bacterial NHEJ: a never ending story

“…In favor of this hypothesis, in M. smegmatis , a mutation of the PolDom of LigD abolishes the nucleotide addition but not the fill‐in activity suggesting that at least two polymerase activities (probably driven by PolD1 and/or PolD2, Bhattarai et al , ) would be required for full DSB repair achievement (Aniukwu et al , ). Finally, due to its similarity with the mycobacterial locus encoding ligC1 and prim‐polC involved in a BER system (Płociński et al , ), we surmise that the Streptomyces ligC‐polR locus could also be involved in this DNA repair pathway in addition to its role in NHEJ.…”

“…The interplay between NHEJ and BER in bacteria is reinforced by the discovery of an AP‐lyase activity driven by the other NHEJ factor: LigD (de Ory et al , ). The involvement of LigC1 Msme in BER during stationary phase of M. smegmatis (Płociński et al , ) shows that the link between NHEJ and BER can even be extended to alternative NHEJ proteins. This multiplicity of NHEJ actors involved in BER is not specific to bacteria, human DNA polymerase λ is one example (see Bebenek et al , ).…”

RecGwed: A probable novel regulator in the resolution of branched DNA structures in mycobacteria

“…Mycobacterial DNA repair is an under‐explored area, mostly understood in terms of homology . However, recent studies in the field of DNA repair have revealed the presence of several novel proteins and pathways in mycobacteria . A previous analysis of the mycobacterial genomes, in our laboratory, revealed the presence of a protein RecG wed , with a standalone wedge domain .…”

Molecular basis for DNA repair synthesis on short gaps by mycobacterial Primase-Polymerase C

“…Although Prim-PolD's roles in NHEJ repair are well established, particularly in mycobacteria, the biological functions of closely related paralogues have remained unclear. Recently, it was reported that a closely related enzyme called Prim-PolC, operonically associated with ligase C (LigC), is specifically involved in LigC-dependent repair of short DNA-gapped intermediates produced during excision-repair processing of lesions in mycobacteria 7 , further expanding the repertoire of pathways in which these diverse replicases operate. A notable feature of Prim-PolC is its favourable activity on short DNA gaps of 1-3 nucleotides, which it preferentially fills in with ribonucleotides.…”

“…A notable feature of Prim-PolC is its favourable activity on short DNA gaps of 1-3 nucleotides, which it preferentially fills in with ribonucleotides. Although the crystal structure of the apo Prim-PolC showed that it is remarkably similar to Prim-PolD, it contains a unique C-terminal extension called Loop 3, proposed to be potentially involved in gap recognition 7 .…”