scholarly journals Topoisomerase IV tracks behind the replication fork and the SeqA complex during DNA replication in Escherichia coli

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Emily Helgesen ◽  
Frank Sætre ◽  
Kirsten Skarstad
Keyword(s):  
Dna Replication ◽  
Replication Fork ◽  
Time Lag ◽  
Movement Pattern ◽  
Replication Machinery ◽  
Topoisomerase Iv ◽  
Bacterial Enzyme ◽  
Concurrent Processes ◽  
The Subject ◽  
Short Time

AbstractTopoisomerase IV (TopoIV) is a vital bacterial enzyme which disentangles newly replicated DNA and enables segregation of daughter chromosomes. In bacteria, DNA replication and segregation are concurrent processes. This means that TopoIV must continually remove inter-DNA linkages during replication. There exists a short time lag of about 10–20 min between replication and segregation in which the daughter chromosomes are intertwined. Exactly where TopoIV binds during the cell cycle has been the subject of much debate. We show here that TopoIV localizes to the origin proximal side of the fork trailing protein SeqA and follows the movement pattern of the replication machinery in the cell.

scholarly journals Separation of newly replicated bacterial chromosomes: the role of Escherichia coli Topoisomerase IV

2020 ◽  
Author(s):  
Emily Helgesen ◽  
Frank Sætre ◽  
Kirsten Skarstad
Keyword(s):  
Time Lag ◽  
Movement Pattern ◽  
Replication Machinery ◽  
Topoisomerase Iv ◽  
Bacterial Enzyme ◽  
Bacterial Chromosomes ◽  
Concurrent Processes ◽  
The Subject ◽  
Short Time

AbstractTopoisomerase IV (TopoIV) is a vital bacterial enzyme which disentangles newly replicated DNA and enables segregation of daughter chromosomes. In bacteria, DNA replication and segregation are concurrent processes. This means that TopoIV must continually remove inter-DNA linkages during replication. There exists a short time lag of about 5-10 minutes between replication and segregation in which the daughter chromosomes are intertwined. Exactly where TopoIV binds during the cell cycle has been the subject of much debate. We show here that TopoIV localizes to the origin proximal side of the fork trailing protein SeqA and follows the movement pattern of the replication machinery in the cell.

The haloarchaeal chromosome replication machinery

2009 ◽  
Vol 37 (1) ◽  
pp. 108-113 ◽  
Author(s):  
Stuart A. MacNeill
Keyword(s):  
Dna Replication ◽  
Replication Fork ◽  
Biochemical Analysis ◽  
Structure And Function ◽  
Haloferax Volcanii ◽  
Eukaryotic Cells ◽  
Replication Machinery ◽  
Chromosomal Dna ◽  
Biochemical Studies ◽  
And Function

The powerful combination of genetic and biochemical analysis has provided many key insights into the structure and function of the chromosomal DNA replication machineries of bacterial and eukaryotic cells. In contrast, in the archaea, biochemical studies have dominated, mainly due to the absence of efficient genetic systems for these organisms. This situation is changing, however, and, in this regard, the genetically tractable haloarchaea Haloferax volcanii and Halobacterium sp. NRC-1 are emerging as key models. In the present review, I give an overview of the components of the replication machinery in the haloarchaea, with particular emphasis on the protein factors presumed to travel with the replication fork.

scholarly journals Topoisomerase III Acts at the Replication Fork To Remove Precatenanes

2019 ◽  
Vol 201 (7) ◽  
Author(s):  
Chong M. Lee ◽  
Guanshi Wang ◽  
Alexandros Pertsinidis ◽  
Kenneth J. Marians
Keyword(s):  
Dna Replication ◽  
Replication Fork ◽  
Dna Helicase ◽  
Holliday Junctions ◽  
Bacterial Cells ◽  
Topoisomerase Iv ◽  
Content Type ◽  
E Coli ◽  
Topoisomerase Iii

ABSTRACTThe role of DNA topoisomerase III (Topo III) in bacterial cells has proven elusive. Whereas eukaryotic Top IIIα homologs are clearly involved with homologs of the bacterial DNA helicase RecQ in unraveling double Holliday junctions, preventing crossover exchange of genetic information at unscheduled recombination intermediates, and Top IIIβ homologs have been shown to be involved in regulation of various mRNAs involved in neuronal function, there is little evidence for similar reactions in bacteria. Instead, most data point to Topo III playing a role supplemental to that of topoisomerase IV in unlinking daughter chromosomes during DNA replication. In support of this model, we show thatEscherichia coliTopo III associates with the replication forkin vivo(likely via interactions with the single-stranded DNA-binding protein and the β clamp-loading DnaX complex of the DNA polymerase III holoenzyme), that the DnaX complex stimulates the ability of Topo III to unlink both catenated and precatenated DNA rings, and that ΔtopBcells show delayed and disorganized nucleoid segregation compared to that of wild-type cells. These data argue that Topo III normally assists topoisomerase IV in chromosome decatenation by removing excess positive topological linkages at or near the replication fork as they are converted into precatenanes.IMPORTANCETopological entanglement between daughter chromosomes has to be reduced to exactly zero every time anE. colicell divides. The enzymatic agents that accomplish this task are the topoisomerases.E. colipossesses four topoisomerases. It has been thought that topoisomerase IV is primarily responsible for unlinking the daughter chromosomes during DNA replication. We show here that topoisomerase III also plays a role in this process and is specifically localized to the replisome, the multiprotein machine that duplicates the cell’s genome, in order to do so.

scholarly journals DNA replication machinery: Insights from in vitro single-molecule approaches

2021 ◽  
Vol 19 ◽  
pp. 2057-2069
Author(s):  
Rebeca Bocanegra ◽  
G.A. Ismael Plaza ◽  
Carlos R. Pulido ◽  
Borja Ibarra
Keyword(s):  
Dna Replication ◽  
Single Molecule ◽  
Replication Machinery

scholarly journals The replication machinery of LUCA: common origin of DNA replication and transcription

BMC Biology ◽  
2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Eugene V. Koonin ◽  
Mart Krupovic ◽  
Sonoko Ishino ◽  
Yoshizumi Ishino
Keyword(s):  
Dna Replication ◽  
Common Origin ◽  
Replication Machinery ◽  
Origin Of Dna Replication

scholarly journals Reconciling Lagrangian Diffusivity and Effective Diffusivity in Contour-Based Coordinates

2019 ◽  
Vol 49 (6) ◽  
pp. 1521-1539
Author(s):  
Yu-Kun Qian ◽  
Shiqiu Peng ◽  
Chang-Xia Liang
Keyword(s):  
Time Lag ◽  
Effective Diffusivity ◽  
Delta Function ◽  
Spreading Rate ◽  
Particle Dispersion ◽  
Small Scale ◽  
Time Lags ◽  
Conservative Tracer ◽  
Stirring Effect ◽  
Short Time

AbstractThe present study reconciles theoretical differences between the Lagrangian diffusivity and effective diffusivity in a transformed spatial coordinate based on the contours of a quasi-conservative tracer. In the transformed coordinate, any adiabatic stirring effect, such as shear-induced dispersion, is naturally isolated from diabatic cross-contour motions. Therefore, Lagrangian particle motions in the transformed coordinate obey a transformed zeroth-order stochastic (i.e., random walk) model with the diffusivity replaced by the effective diffusivity. Such a stochastic model becomes the theoretical foundation on which both diffusivities are exactly unified. In the absence of small-scale diffusion, particles do not disperse at all in the transformed contour coordinate. Besides, the corresponding Lagrangian autocorrelation becomes a delta function and is thus free from pronounced overshoot and negative lobe at short time lags that may be induced by either Rossby waves or mesoscale eddies; that is, particles decorrelate immediately and Lagrangian diffusivity is already asymptotic no matter how small the time lag is. The resulting instantaneous Lagrangian spreading rate is thus conceptually identical to the effective diffusivity that only measures the instantaneous irreversible mixing. In these regards, the present study provides a new look at particle dispersion in contour-based coordinates.

scholarly journals The yeast S phase checkpoint enables replicating chromosomes to bi-orient and restrain spindle extension during S phase distress

2005 ◽  
Vol 168 (7) ◽  
pp. 999-1012 ◽  
Author(s):  
Jeff Bachant ◽  
Shannon R. Jessen ◽  
Sarah E. Kavanaugh ◽  
Candida S. Fielding
Keyword(s):  
Dna Replication ◽  
Chromosome Segregation ◽  
Replication Fork ◽  
S Phase ◽  
Origin Of Replication ◽  
Independent Manner ◽  
Checkpoint Signaling ◽  
Hydroxyurea Treatment ◽  
Chromatid Cohesion ◽  
S Phase Checkpoint

The budding yeast S phase checkpoint responds to hydroxyurea-induced nucleotide depletion by preventing replication fork collapse and the segregation of unreplicated chromosomes. Although the block to chromosome segregation has been thought to occur by inhibiting anaphase, we show checkpoint-defective rad53 mutants undergo cycles of spindle extension and collapse after hydroxyurea treatment that are distinct from anaphase cells. Furthermore, chromatid cohesion, whose dissolution triggers anaphase, is dispensable for S phase checkpoint arrest. Kinetochore–spindle attachments are required to prevent spindle extension during replication blocks, and chromosomes with two centromeres or an origin of replication juxtaposed to a centromere rescue the rad53 checkpoint defect. These observations suggest that checkpoint signaling is required to generate an inward force involved in maintaining preanaphase spindle integrity during DNA replication distress. We propose that by promoting replication fork integrity under these conditions Rad53 ensures centromere duplication. Replicating chromosomes can then bi-orient in a cohesin-independent manner to restrain untimely spindle extension.

Implications of DNA replication for eukaryotic gene expression

1991 ◽  
Vol 99 (2) ◽  
pp. 201-206 ◽  
Author(s):  
A.P. Wolffe
Keyword(s):  
Gene Expression ◽  
Dna Replication ◽  
Replication Fork ◽  
Recent Progress ◽  
Gene Activity ◽  
Nucleosome Assembly ◽  
Developmental Processes ◽  
Eukaryotic Gene Expression ◽  
Eukaryotic Gene

DNA replication has a key role in many developmental processes. Recent progress in understanding events at the replication fork suggests mechanisms for both establishing and maintaining programs of eukaryotic gene activity. In this review, I discuss the consequences of replication fork passage for preexisting chromatin structures and describe how the mechanism of nucleosome assembly at the replication fork may facilitate the formation of either transcriptionally active or repressed chromatin.

scholarly journals The TREX2 3′→ 5′ Exonuclease Physically Interacts with DNA Polymerase δ and Increases Its Accuracy

2002 ◽  
Vol 2 ◽  
pp. 275-281 ◽  
Author(s):  
Igor V. Shevelev ◽  
Kristijan Ramadan ◽  
Ulrich Hubscher
Keyword(s):  
Dna Replication ◽  
Dna Polymerase ◽  
Error Rates ◽  
High Fidelity ◽  
Replication Machinery ◽  
Dna Polymerase Δ ◽  
Pol I ◽  
Calf Thymus ◽  
Mutation Assay ◽  
Forward Mutation

Proofreading function by the 3′→ 5′ exonuclease of DNA polymerase δ (pol δ) is consistent with the observation that deficiency of the associated exonuclease can lead to a strong mutation phenotype, high error rates during DNA replication, and ultimately cancer. We have isolated pol δdfrom isotonic (pol δi) and detergent (pol δd) calf thymus extracts. Pol δdhad a 20-fold higher ratio of exonuclease to DNA polymerase than pol δi. This was due to the physical association of the TREX2 exonuclease to pol δd, which was missing from pol δi. Pol δdwas fivefold more accurate than pol δiunder error-prone conditions (1 μM dGTP and 20 dATP, dCTP, and dTTP) in a M13mp2 DNA forward mutation assay, and fourfold more accurate in an M13mp2T90 reversion assay. Under error-free conditions (20 μM each of the four dNTPs), however, both polymerases showed equal fidelity. Our data suggested that autonomous 3′→ 5′ exonucleases, such as TREX2, through its association with pol I can guarantee high fidelity under difficult conditions in the cell (e.g., imbalance of dNTPs) and can add to the accuracy of the DNA replication machinery, thus preventing mutagenesis.

Sign in / Sign up

Export Citation Format

Share Document