Replication-transcription conflicts in bacteria

Abstract

DNA replication and transcription use the same template and occur concurrently in bacteria. The lack of temporal and spatial separation of these two processes leads to their conflict, and failure to deal with this conflict can result in genome alterations and reduced fitness. In recent years major advances have been made in understanding how cells avoid conflicts between replication and transcription and how such conflicts are resolved when they do occur. In this Review, we summarize these findings, which shed light on the significance of the problem and on how bacterial cells deal with unwanted encounters between the replication and transcription machineries.

Figure 1. Cartoon of bidirectional replication and co-directional and head-on transcription and replication

A. Cartoon depicting a partly duplicated bacterial chromosome. Bacterial chromosomes are generally circular with a single origin of replication (oriC). The replication machinery assembles at oriC and replication occurs bi-directionally, with replication forks moving clockwise and counter-clockwise away from the origin. Partly duplicated chromosomes have two copies of oriC and other regions that have been duplicated. Replication ends in the terminus region, denoted terC. The ter region extends from ~152° to ~187° on the 360° circular map, with most termination events occurring at ~172° 91. Replication forks and their directionality are indicated by the black arrows. B. Co-directional conflicts. A co-directional conflict between replication and transcription is depicted. Co-directional conflicts occur when a gene is coded for on the leading strand. In these conflicts, transcription occurs in the same direction as leading strand replication. Small black arrows represent the direction of movement of the replication machinery on each of the two strands. The longer black arrow represents the overall movement of the replication fork and the direction of unwinding by the replicative helicase. Leading and lagging strands, and directionality of the parent strands are indicated. RNAPs are represented by pentagons pointing in the direction of transcription. A thin gray arrow marks the beginning of an open reading frame (ORF). C. Head-on conflicts. A head-on conflict between replication and transcription is depicted. Head-on conflicts occur when a gene is coded for on the lagging strand. In these conflicts, transcription occurs in the opposite direction as leading strand replication. Shapes are as described for panel B.

Figure 2. Representative mechanisms of avoiding/resolving replication-transcription conflicts

A. Conflict at DNA lesions. RNAP modulators (GreA/B, DksA, ppGpp, Mfd) are proposed to inhibit formation of arrays of stalled RNAPs at lesions on the DNA template. Mfd (orange), for instance, can dislodge the inactive RNAPs, recruit UvrA₂B complex (gold) to repair the lesion, and prevent replication forks from encountering an array of stalled RNAPs. B. Conflict due to backtracked RNAPs. Coupling transcription with translation prevents RNAP backtracking, promoting transcription processivity. The RNAP secondary channel factors, DksA and GreA/B (blue) are also proposed to reduce the replication-transcription conflict by preventing and resolving RNAP backtracking, respectively. For both panels A, and B, the replication forks are shown, but the forks likely do not need to be near RNAP for the indicated factors to function. C. Conflict at rRNA (rrn) operons. DNA accessory helicases DinG, Rep and UvrD (green) cooperate to reduce replication-transcription conflict at highly transcribed rrn operons.

Figure 3. Possible fates of a stalled replication fork due to conflicts with transcription

Three possible fates of stalled replication forks following conflict with RNAP. A. Direct replication restart. Replication restart proteins (e.g. PriA, and helicase loaders DnaB and DnaD in B. subtilis) are recruited to the stalled replication fork and directly reactivate replication without DNA recombination. B. Double strand DNA ends. Prolonged replication stalling can result in the next round of replication reaching the stalled fork and generating double strand ends, which are repaired by homologous recombination. C. Replication fork reversal. A replication fork encountering conflict with RNAP undergoes replication fork reversal. RecBC(D), RecA and RuvABC are recruited to the reversed fork for DNA degradation and homologous recombination, resulting in a replication fork at a new position further away from the conflict. Replication can then restart with the help of other auxiliary proteins.