The Mycobacterial LexA/RecA-Independent DNA Damage Response Is Controlled by PafBC and the Pup-Proteasome System

• Published in: Cell reports (Cambridge) Vol. 23; no. 12; pp. 3551 - 3564
• Main Authors: Müller, Andreas U., Imkamp, Frank, Weber-Ban, Eilika
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 19.06.2018
• Subjects: Amino Acid Sequence; bacterial proteasome; Bacterial Proteins - metabolism; Base Sequence; Clp gene regulator ClgR; DNA Damage; DNA damage response; DNA Repair - drug effects; DNA Repair - genetics; DNA, Bacterial - genetics; Gene Expression Regulation, Bacterial - drug effects; LexA/RecA-independent pathway; Mitomycin - pharmacology; Mycobacterium - drug effects; Mycobacterium - genetics; Mycobacterium - metabolism; Mycobacterium smegmatis; Nucleotide Motifs - genetics; PafBC regulon; Promoter Regions, Genetic; Proteasome Endopeptidase Complex - metabolism; pupylation; Rec A Recombinases - chemistry; Rec A Recombinases - metabolism; RecA-NDp promoter; Recombination, Genetic - genetics; Regulon - genetics; Serine Endopeptidases - metabolism; Stress, Physiological - drug effects; Stress, Physiological - genetics; Trans-Activators - metabolism; Transcriptome - drug effects; Transcriptome - genetics; Up-Regulation - drug effects; Up-Regulation - genetics; PafBC regulon; pupylation; Clp gene regulator ClgR; bacterial proteasome; DNA damage response; Mycobacterium smegmatis; RecA-NDp promoter; LexA/RecA-independent pathway
• ISSN: 2211-1247; 2211-1247
• DOI: 10.1016/j.celrep.2018.05.073

Mycobacteria exhibit two DNA damage response pathways: the LexA/RecA-dependent SOS response and a LexA/RecA-independent pathway. Using a combination of transcriptomics and genome-wide binding site analysis, we demonstrate that PafBC (proteasome accessory factor B and C), encoded in the Pup-proteasome system (PPS) gene locus, is the transcriptional regulator of the predominant LexA/RecA-independent pathway. Comparison of the resulting PafBC regulon with the DNA damage response of Mycobacterium smegmatis reveals that the majority of induced DNA repair genes are upregulated by PafBC. We further demonstrate that RecA, a member of the PafBC regulon and principal regulator of the SOS response, is degraded by the PPS when DNA damage stress has been overcome. Our results suggest a model for the regulation of the mycobacterial DNA damage response that employs the concerted action of PafBC as master transcriptional activator and the PPS for removal of DNA repair proteins to maintain a temporally controlled stress response. [Display omitted] •PafBC is the key transcriptional activator of the mycobacterial DNA damage response•PafBC upregulates 150 genes via the RecA-NDp motif•Induced genes are involved in DNA damage repair and the oxidative stress response•The Pup-proteasome system removes DNA repair proteins during stress recovery Müller et al. demonstrate that the Pup-proteasome gene locus harbors a transcriptional activator, PafBC, acting as the principal regulator of the mycobacterial DNA damage response, upregulating the majority of DNA repair genes. During stress recovery, the Pup-proteasome system removes DNA repair proteins to return the cell to its normal state.