A Fork Trap in the Chromosomal Termination Area Is Highly Conserved across All Escherichia coli Phylogenetic Groups.

Daniel J Goodall,Katie H Jameson,Michelle Hawkins,Christian J Rudolph

doi:10.3390/ijms22157928

Daniel J Goodall, Katie H Jameson + Show 2 more

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https://doi.org/10.3390/ijms22157928

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Abstract

Termination of DNA replication, the final stage of genome duplication, is surprisingly complex, and failures to bring DNA synthesis to an accurate conclusion can impact genome stability and cell viability. In Escherichia coli, termination takes place in a specialised termination area opposite the origin. A ‘replication fork trap’ is formed by unidirectional fork barriers via the binding of Tus protein to genomic ter sites. Such a fork trap system is found in some bacterial species, but it appears not to be a general feature of bacterial chromosomes. The biochemical properties of fork trap systems have been extensively characterised, but little is known about their precise physiological roles. In this study, we compare locations and distributions of ter terminator sites in E. coli genomes across all phylogenetic groups, including Shigella. Our analysis shows that all ter sites are highly conserved in E. coli, with slightly more variability in the Shigella genomes. Our sequence analysis of ter sites and Tus proteins shows that the fork trap is likely to be active in all strains investigated. In addition, our analysis shows that the dif chromosome dimer resolution site is consistently located between the innermost ter sites, even if rearrangements have changed the location of the innermost termination area. Our data further support the idea that the replication fork trap has an important physiological role that provides an evolutionary advantage.

Highlights

In all domains of life, chromosome duplication initiates at origins of replication by the assembly of two multi-subunit ‘replisomes’
The Replication Fork Trap in Salmonella and Klebsiella. Another important question is how the replication fork trap might be structured in other bacterial species. tus-related sequences have been found in most Enterobacteriales [24], and it has been shown before that the expression of tus genes from Salmonella enterica, Klebsiella ozaenae and Yersinia pestis in E. coli resulted in the formation of functional ter/Tus complexes, even though the blocking activity of the heterologous complexes were not as strong [25,63]
While the biochemical aspects of ter/Tus complexes have been studied extensively, we still know surprisingly little about the precise physiological function of the replication we still know surprisingly little about the precise physiological function of the replication fork trap. tus-related sequences have been found in most Enterobacteriales, in the Pseufork trap. tus-related sequences have been found in most Enterobacteriales, in the Pseudoalteromonas and in most Aeromonadales [24]

Summary

Introduction

In all domains of life, chromosome duplication initiates at origins of replication by the assembly of two multi-subunit ‘replisomes’. These replisome–DNA replication fork complexes (called ‘replication forks’ from here onwards for simplicity) move in opposite directions until they either merge with another replication fork or reach a chromosome end [1,2,3]. DNA replication is completed once the two replication forks merge opposite oriC in the terminus area of the chromosome, which is located in the Ter macrodomain. The main protein involved in the organisation of the Ter macrodomain is the DNA-binding protein MatP, which binds to matS sequences located in the Ter domain [9].

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