The Clash of Macromolecular Titans: Replication-Transcription Conflicts in Bacteria

Abstract

Within the last decade, it has become clear that DNA replication and transcription are routinely in conflict with each other in growing cells. Much of the seminal work on this topic has been carried out in bacteria, specifically, Escherichia coli and Bacillus subtilis; therefore, studies of conflicts in these species deserve special attention. Collectively, the recent findings on conflicts have fundamentally changed the way we think about DNA replication in vivo. Furthermore, new insights on this topic have revealed that the conflicts between replication and transcription significantly influence many key parameters of cellular function, including genome organization, mutagenesis, and evolution of stress response and virulence genes. In this review, we discuss the consequences of replication-transcription conflicts on the life of bacteria and describe some key strategies cells use to resolve them. We put special emphasis on two critical aspects of these encounters: ( a) the consequences of conflicts on replisome stability and dynamics, and ( b) the resulting increase in spontaneous mutagenesis.

Keywords: DNA replication, transcription; replication-transcription conflicts.

Figure 1.

Replication-transcription conflicts occur in two different orientations. Codirectional conflicts (a) occur when a gene is encoded on the leading strand. Head-on conflicts (b) occur when a gene is encoded on the lagging strand. Accessory helicases and RNA polymerase (RNAP) modulators aid in the resolution of both types of conflicts. Accessory helicases (PcrA, UvrD, Rep, DinG) likely arrive at conflict regions together with the replication fork. In contrast, RNAP modulators (DksA, GreA/B) are likely present at the transcription unit through their interactions with RNAP. The modulators regulate the movement and activity of RNAP when necessary (for instance, during backtracking), helping resolve conflicts. Head-on conflicts increase the frequency and/or stability of R-loops, leading to replisome stalling, mutations, and reduced gene expression. Models of conflict-mediated topological disturbance predict that positive supercoiling builds up transiently between the replication and transcription machineries at head-on gene regions, as depicted. This could drive R-loop formation. Accessory helicases, RNases H, and possibly type II topoisomerases resolve head-on conflicts. How type II topoisomerases may be recruited to conflict regions is unclear. Figure adapted from Reference .

Figure 2.

Models of potential fork-processing pathways downstream of a head-on collision. A head-on collision between replication (purple) and transcription (green) can lead to a reversed replication fork (left pathway), which is processed by RecBC (orange) and/or Ruv proteins (blue). These collisions can also result in RecA (red) loading (right pathway). RecBC processing may result in RecA loading, or RecA loading could result in initiation of replication fork reversal (dashed arrow). In both cases, replication restart occurs through Pri protein–mediated replisome reassembly.