Too Much of a Good Thing: How Ectopic DNA Replication Affects Bacterial Replication Dynamics.

Aisha H Syeda,Christian J Rudolph,Ole Skovgaard,Juachi U Dimude

doi:10.3389/fmicb.2020.00534

Aisha H Syeda, Christian J Rudolph + Show 2 more

Open Access

https://doi.org/10.3389/fmicb.2020.00534

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Abstract

Each cell division requires the complete and accurate duplication of the entire genome. In bacteria, the duplication process of the often-circular chromosomes is initiated at a single origin per chromosome, resulting in two replication forks that traverse the chromosome in opposite directions. DNA synthesis is completed once the two forks fuse in a region diametrically opposite the origin. In some bacteria, such as Escherichia coli, the region where forks fuse forms a specialized termination area. Polar replication fork pause sites flanking this area can pause the progression of replication forks, thereby allowing forks to enter but not to leave. Transcription of all required genes has to take place simultaneously with genome duplication. As both of these genome trafficking processes share the same template, conflicts are unavoidable. In this review, we focus on recent attempts to add additional origins into various ectopic chromosomal locations of the E. coli chromosome. As ectopic origins disturb the native replichore arrangements, the problems resulting from such perturbations can give important insights into how genome trafficking processes are coordinated and the problems that arise if this coordination is disturbed. The data from these studies highlight that head-on replication–transcription conflicts are indeed highly problematic and multiple repair pathways are required to restart replication forks arrested at obstacles. In addition, the existing data also demonstrate that the replication fork trap in E. coli imposes significant constraints to genome duplication if ectopic origins are active. We describe the current models of how replication fork fusion events can cause serious problems for genome duplication, as well as models of how such problems might be alleviated both by a number of repair pathways as well as the replication fork trap system. Considering the problems associated both with head-on replication-transcription conflicts as well as head-on replication fork fusion events might provide clues of how these genome trafficking issues have contributed to shape the distinct architecture of bacterial chromosomes.

Highlights

While eukaryotic cells typically contain multiple linear chromosomes, the bacterial models studied in most detail early on, such as Escherichia coli and Bacillus subtilis, have a single chromosome with a size of roughly 5 Mbp that forms a covalently closed circle
We do not have any direct information about the speed of individual forks, but these results suggest that the forks leaving the termination area and traveling in the wrong orientation have, on average, a similar speed to the forks coming from origin per chromosome (oriC) or are even slightly faster (Ivanova et al, 2015; Dimude et al, 2016, 2018b), similar to the situation observed in Vibrio cholerae where replication forks fused opposite the origin even when the origin was moved to an ectopic location (Galli et al, 2019)
The relatively mild phenotype of cells lacking a fork trap system highlights that this effect is in addition to the various processing factors that are involved in the processing of fork fusion intermediates, such as RecG, 3 exonucleases and DNA polymerase I

Summary

Introduction

While eukaryotic cells typically contain multiple linear chromosomes, the bacterial models studied in most detail early on, such as Escherichia coli and Bacillus subtilis, have a single chromosome with a size of roughly 5 Mbp that forms a covalently closed circle. We observed that the low point of the replication profiles in the presence and absence of a functional fork trap was in the same location (Rudolph et al, 2013; Ivanova et al, 2015; Dimude et al, 2016), suggesting that both replisomes traverse their replichores with similar speeds and fuse freely within the innermost ter sites.

Results

Conclusion