Structure and Function of the Bacterial Genome. Charles J. Dorman

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Structure and Function of the Bacterial Genome - Charles J. Dorman


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      The linking number of DNA is changed at a local level by the processes of transcription and DNA replication. In 1987, Liu and Wang proposed, in a landmark theoretical paper, that the process of transcription would induce overwinding of the DNA template ahead of RNA polymerase and underwinding behind (Liu and Wang 1987) (Figure 1.15). Experimental studies provided support for the proposal, leading to the realisation that topoisomerases play important roles in transcription by relieving the torsional stress that the process creates (Ahmed et al. 2017; Chong et al. 2014; Higgins 2014; Rahmouni and Wells 1992; Rani and Nagaraja 2019; Wu et al. 1988). The role of local DNA supercoiling in the modulation of transcription and in gene‐to‐gene communication will be addressed in Section 8.2. Here we will consider the impact of transcription on nucleoid architecture and on DNA replication.

      

      Several investigations have made links between patterns of transcription and the superstructure of the bacterial nucleoid. At a practical level, replication fork movement must be reconciled with the needs of transcription (initiation, elongation, and termination), so aligning replisome movement with the direction of gene transcription avoids significant conflicts between DNA and RNA polymerases. Collisions between the replisome and RNA polymerase are known to cause severe inhibition of replisome progression (Mirkin and Mirkin 2005). Transcriptional promoters that oppose the direction of replisome movement serve to pause the replication fork, while transcription terminators that are aligned with the direction of replisome movement also act as replication fork pause sites (Mirkin et al. 2006). Conflicts between the replisome and RNA polymerase can generate R‐loops, stalling replication, and transcription in the affected region until RNase H removes the R‐loop (Kuziminov 2018). Unresolved R‐loops also result in hyper‐recombination and genome instability, so avoiding replication–transcription conflicts is very desirable (Figure 1.16).

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