How Acts of Infidelity Promote DNA Break Repair: Collision and Collusion Between DNA Repair and Transcription

Abstract

Transcription is a fundamental cellular process and the first step in gene regulation. Although RNA polymerase (RNAP) is highly processive, in growing cells the progression of transcription can be hindered by obstacles on the DNA template, such as damaged DNA. The authors recent findings highlight a trade-off between transcription fidelity and DNA break repair. While a lot of work has focused on the interaction between transcription and nucleotide excision repair, less is known about how transcription influences the repair of DNA breaks. The authors suggest that when the cell experiences stress from DNA breaks, the control of RNAP processivity affects the balance between preserving transcription integrity and DNA repair. Here, how the conflict between transcription and DNA double-strand break (DSB) repair threatens the integrity of both RNA and DNA are discussed. In reviewing this field, the authors speculate on cellular paradigms where this equilibrium is well sustained, and instances where the maintenance of transcription fidelity is favored over genome stability.

Keywords: DNA break repair; DNA resection; RNA polymerase; RecBCD; genome stability; transcription fidelity.

Figure 1.

The cellular balance between transcription fidelity and DNA damage survival. GreA/B and possibly the D. radiodurans protein Gfh,[48,49] increase transcription fidelity at the cost of survival during DNA damage stress. In the absence of GreA/B, transcription fidelity is reduced, but survival after DNA damage is greatly improved. Under DNA damage stress, D. radiodurans is predicted to have a balance between maintaining transcription fidelity and performing DNA repair such that both RNA and DNA fidelity is high (blue dots), while in E. coli, the equilibrium is shifted toward transcription fidelity (green dots).

Figure 2.

Collisions between backtracked RNA polymerase and RecBCD promote homologous recombination. Transcription by RNA polymerase (RNAP) and resection by RecBCD co-occur on the DNA template. RecBCD can initiate resection at a DNA break independent of ongoing transcription. A) GreA/B and DksA promote transcription elongation and prevent RNAP backtracking, allowing DNA degradation by RecBCD to continue. B) The SOS response in E. coli is activated by DNA breaks. ssDNA coated RecA filaments (RecA%) stimulates the autocatalytic cleavage of the transcriptional repressor LexA. Cleavage of LexA leads to the de-repression of genes in the SOS regulon, including RecBC and UvrD. C) A transcription error (yellow star) or UvrD along with ppGpp promote RNAP backtracking, increasing the chance for RecBCD to encounter backtracked RNAP. Stably bound backtracked RNAP stops RecBCD resection, which facilitates the switch to RecA loading and hence recombination.

Figure 3.

Backtracked RNA polymerase can act like a Chi site to reduce resection and promote recombination. A) Chi distribution across the E. coli genome is biased, with more correctly oriented Chi sites toward the origin (OriC), and fewer close to the terminus of replication (Ter). Because of this bias, resection by RecBCD is lower toward OriC compared to downstream of the DNA break site. B) RNAP can act like a Chi site. When RecBCD encounters a Chi site, the probability of RecBCD pausing increases. This pause results in a switch from exonucleolytic activity of RecBCD to the RecA loading activity. Thus, RecBCD loads RecA to allow for recombination at a Chi site. We hypothesize that backtracked RNAP acts analogously, promoting a RecBCD pause and stimulating recombination.