A Magic Spot in Genome Maintenance

Abstract

Nucleotide excision repair (NER) is the key DNA repair system that eliminates the majority of DNA helix-distorting lesions. RNA polymerase (RNAP) expedites the recognition of DNA damage by NER components via transcription-coupled DNA repair (TCR). In bacteria, a modified nucleotide ppGpp ('magic spot') is a pleiotropic second messenger that mediates the response to nutrient deficiencies by altering the initiation properties of RNAP. In this review, we discuss newly elucidated roles of guanosine 5'-diphosphate 3'-diphosphate (ppGpp) in transcription elongation that couple this alarmone to DNA damage repair and maintenance.

Keywords: DNA repair; backtracking; mutation rate; ppGpp; transcription elongation.

Figure 1, Key Figure. Schematics of UvrD/ppGpp-dependent TCR

(A) When RNAP encounters a bulky DNA lesion in the template strand it stalls and obscures the access of repair enzymes to the site of damage. (B) SOS response leads to transient accumulation of UvrD. ppGpp binds RNAP and renders it backtracking-prone. Active UvrD dimers then pull RNAP backwards to expose the lesions to the repair machinery. (C) UvrD and NusA then recruit UvrA and UvrB to the lesion site to initiate the process of NER.

Figure 2. Possible indirect activities of ppGpp that promote backtracking

(A) ppGpp may facilitate TCR at ribosomal operons during genotoxic stress by partially suppressing initiation at their promoters. Top: When RNAP encounters a lesion in the highly transcribed rRNA genes it cannot backtrack due to tightly packed arrays of RNAP molecules. Such arrays would also be resistant to Mfd- and Rho-dependent termination. Middle: Transient accumulation of ppGpp during genotoxic stress may partially inhibit initiation at rrn operons thereby reducing the number of elongating RNAPs. This should increase the space between adjacent RNAPs and create room for backtracking. Bottom: RNAP can now backtrack at the site of damage to enable TCR. (B) ppGpp can promote TCR by controlling the number of ribosomes during genotoxic stress. Top: Ribosomes act as anti-backtracking factors [44]. Middle: ppGpp can diminish the number of ribosomes, thereby increasing the probability of uncoupling transcription from translation. Bottom: Fewer ribosomes increase the probability of backtracking.