The Localization and Action of Topoisomerase IV in Escherichia coli Chromosome Segregation Is Coordinated by the SMC Complex, MukBEF

Zawadzki, Paweł; Stracy, Mathew; Ginda, Katarzyna; Zawadzka, Katarzyna; Lesterlin, Christian; Kapanidis, Achillefs N.; Sherratt, David J.

doi:10.1016/j.celrep.2015.11.034

Cited by 96 publications

(129 citation statements)

References 42 publications

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“…E. coli lacks a ParAB partition system and its chromosome is not maintained as juxtaposed as in B. subtilis . However, E. coli condensin MukBEF with TopoIV promotes timely segregation of newly replicated DNA molecules . Thus, there is no single unified system for chromosome organization and segregation in bacteria.…”

Section: Discussionmentioning

confidence: 99%

Combing Chromosomal DNA Mediated by the SMC Complex: Structure and Mechanisms

Kamada

Barillà

2017

BioEssays

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Genome maintenance requires various nucleoid-associated factors in prokaryotes. Among them, the SMC (Structural Maintenance of Chromosomes) protein has been thought to play a static role in the organization and segregation of the chromosome during cell division. However, recent studies have shown that the bacterial SMC is required to align left and right arms of the emerging chromosome and that the protein dynamically travels from origin to Ter region. A rod form of the SMC complex mediates DNA bridging and has been recognized as a machinery responsible for DNA loop extrusion, like eukaryotic condensin or cohesin complexes, which act as chromosome organizers. Attention is now turning to how the prototype of the complex is loaded on the entry site and translocated on chromosomal DNA, explaining its overall conformational changes at atomic levels. Here, we review and highlight recent findings concerning the prokaryotic SMC complex and discuss possible mechanisms from the viewpoint of protein architecture.

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Section: Discussionmentioning

confidence: 99%

Combing Chromosomal DNA Mediated by the SMC Complex: Structure and Mechanisms

Kamada

Barillà

2017

BioEssays

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“…These raw distances were aggregated across all cells and plotted. Additionally, radial distribution function analysis (Garza de Leon et al, 2017;Zawadzki et al, 2015) was used to determine the increased likelihood of localization at a distance r from the centroid of an SSB focus relative to random localization in the cell.…”

Section: Image Analysismentioning

confidence: 99%

Compartmentalization of the replication fork by single-stranded DNA binding protein regulates translesion synthesis

Chang

Thrall

Laureti

et al. 2020

Preprint

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DNA replication is mediated by the coordinated actions of multiple enzymes within replisomes. Processivity clamps tether many of these enzymes to DNA, allowing access to the primer/template junction. Many clamp-interacting proteins (CLIPs) are involved in genome maintenance pathways including translesion synthesis (TLS). Despite their abundance, DNA replication in bacteria is not perturbed by these CLIPs. Here we show that while the TLS polymerase Pol IV is largely excluded from moving replisomes, the remodeling of ssDNA binding protein (SSB) upon replisome stalling enriches Pol IV at replication forks. This enrichment is indispensable for Pol IV-mediated TLS on both the leading and lagging strands as it enables Pol IV-processivity clamp binding by overcoming the gatekeeping role of the Pol III epsilon subunit. As we have demonstrated for the Pol IV-SSB interaction, we propose that the binding of CLIPs to the processivity clamp must be preceded by interactions with factors that serve as localization markers for their site of action. Figure 4. The Pol IV-SSB interaction enriches Pol IV near lesion-stalled replisomes in cells. A. Schematic diagrams of PAmCherry fusions of Pol IV and RecQ WH -Pol IV LF variants. 303 VWP 305 , rim interacting residues; 346 QLVLGL 351 , the CBM of Pol IV; (G4S)4, a flexible linker. B. (Top panels) Representative fluorescence micrographs of an SSB-mYpet focus (left) and a single photoactivated Pol IV-PAmCherry molecule (right) with overlays showing the cell outlines. (Bottom panels) Corresponding brightfield micrographs with overlays showing SSB foci (red circle, left) or all detected Pol IV tracks (right) (Scale bars: 1 µM).C. Distributions of the mean distance between each static Pol IV track and the nearest SSB focus for Pol IV WT and mutants in cells treated with 100 mM MMS. D. Radial distribution functions g(r) for Pol IV WT and mutants in cells treated with 100 mM MMS. Also shown are random g(r) functions for each data set (dotted lines).

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“…It is also prudent to keep in mind that E. coli and related bacteria also possess DNA topoisomerase IV, an enzyme with a structure that is closely related to that of gyrase but which lacks the ability to negatively supercoil DNA (Kato et al 1990). Topo IV is also ATP dependent and is the principal decatenase of the cell, responsible for the topological separation of daughter chromosomes at the end of genome replication; Topo IV also has the ability to relax negatively supercoiled DNA (Bates and Maxwell 2007;Zawadzki et al 2015;Zechiedrich et al 2000). Like DNA gyrase, Topo IV is sensitive to adenylylation by FicT toxins that interfere with ATP binding activity (Harms et al 2015).…”

Section: Introductionmentioning

confidence: 99%

DNA supercoiling is a fundamental regulatory principle in the control of bacterial gene expression

Dorman

2016

Biophys Rev

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Although it has become routine to consider DNA in terms of its role as a carrier of genetic information, it is also an important contributor to the control of gene expression. This regulatory principle arises from its structural properties. DNA is maintained in an underwound state in most bacterial cells and this has important implications both for DNA storage in the nucleoid and for the expression of genetic information. Underwinding of the DNA through reduction in its linking number potentially imparts energy to the duplex that is available to drive DNA transactions, such as transcription, replication and recombination. The topological state of DNA also influences its affinity for some DNA binding proteins, especially in DNA sequences that have a high A + T base content. The underwinding of DNA by the ATP-dependent topoisomerase DNA gyrase creates a continuum between metabolic flux, DNA topology and gene expression that underpins the global response of the genome to changes in the intracellular and external environments. These connections describe a fundamental and generalised mechanism affecting global gene expression that underlies the specific control of transcription operating through conventional transcription factors. This mechanism also provides a basal level of control for genes acquired by horizontal DNA transfer, assisting microbial evolution, including the evolution of pathogenic bacteria.

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The Localization and Action of Topoisomerase IV in Escherichia coli Chromosome Segregation Is Coordinated by the SMC Complex, MukBEF

Cited by 96 publications

References 42 publications

Combing Chromosomal DNA Mediated by the SMC Complex: Structure and Mechanisms

Combing Chromosomal DNA Mediated by the SMC Complex: Structure and Mechanisms

Compartmentalization of the replication fork by single-stranded DNA binding protein regulates translesion synthesis

DNA supercoiling is a fundamental regulatory principle in the control of bacterial gene expression

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