scholarly journals Identification of the unwinding region in the Clostridioides difficile chromosomal origin of replication

2020 ◽  
Author(s):  
Ana M. Oliveira Paiva ◽  
Erika van Eijk ◽  
Annemieke H. Friggen ◽  
Christoph Weigel ◽  
Wiep Klaas Smits
Keyword(s):  
Dna Replication ◽  
Intergenic Region ◽  
Intestinal Inflammation ◽  
Origin Of Replication ◽  
Chromosomal Origin ◽  
Clostridioides Difficile ◽  
Origins Of Replication ◽  
Origin Region ◽  
Initiation Of Dna Replication

AbstractFaithful DNA replication is crucial for viability of cells across all kingdoms of life. Targeting DNA replication is a viable strategy for inhibition of bacterial pathogens. Clostridioides difficile is an important enteropathogen that causes potentially fatal intestinal inflammation. Knowledge about DNA replication in this organism is limited and no data is available on the very first steps of DNA replication. Here, we use a combination of in silico predictions and in vitro experiments to demonstrate that C. difficile employs a bipartite origin of replication that shows DnaA-dependent melting at oriC2, located in the dnaA-dnaN intergenic region. Analysis of putative origins of replication in different clostridia suggests that the main features of the origin architecture are conserved. This study is the first to characterize aspects of the origin region of C. difficile and contributes to our understanding of the initiation of DNA replication in clostridia.

scholarly journals Initiation of DNA replication in ColE1 plasmids containing multiple potential origins of replication.

1992 ◽  
Vol 267 (31) ◽  
pp. 22496-22505
Author(s):  
L Martín-Parras ◽  
P Hernández ◽  
M.L. Martínez-Robles ◽  
J.B. Schvartzman
Keyword(s):  
Dna Replication ◽  
Origins Of Replication ◽  
Initiation Of Dna Replication

scholarly journals Role of Papillomavirus E1 Initiator Dimerization in DNA Replication

2005 ◽  
Vol 79 (13) ◽  
pp. 8661-8664 ◽  
Author(s):  
Stephen Schuck ◽  
Arne Stenlund
Keyword(s):  
Dna Replication ◽  
Dna Binding ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Severe Effect ◽  
Origin Of Dna Replication ◽  
Initiation Of Dna Replication

ABSTRACT Viral initiator proteins are polypeptides that form oligomeric complexes on the origin of DNA replication (ori). These complexes carry out a multitude of functions related to initiation of DNA replication, and although many of these functions have been characterized biochemically, little is understood about how the complexes are assembled. Here we demonstrate that loss of one particular interaction, the dimerization between E1 DNA binding domains, has a severe effect on DNA replication in vivo but has surprisingly modest effects on most individual biochemical activities in vitro. We conclude that the dimer interaction is primarily required for initial recognition of ori.

The Escherichia coli chaperones involved in DNA replicadon

1993 ◽  
Vol 339 (1289) ◽  
pp. 271-278 ◽  
Keyword(s):  
Escherichia Coli ◽  
Dna Replication ◽  
Heat Shock ◽  
Heat Shock Proteins ◽  
Conformational Changes ◽  
Heat Shock Genes ◽  
Dnab Helicase ◽  
Initiation Of Dna Replication ◽  
Shock Proteins

Mutadons in the Escherichia coli heat shock genes, dnaK , dnaJ or grpE , alter host DNA and RNA synthesis, degradation of other proteins, cell division and expression of other heat shock genes. They also block the initiation of DNA replication of bacteriophages λ and P1, and the mini-F plasmid. An in vitro λDNA replication system, composed entirely of purified components, enabled us to describe the molecular mechanism of the dnaK , dnaJ and grpE gene products. DnaK , the bacterial hsp 70 homologue, releases λP protein from the preprimosomal complex in an ATP- and DnaJ-dependent reaction (GrpEindependent initiation of λDNA replication). In this paper, I show that, when GrpE is present, λP protein is not released from the preprimosomal complex, rather it is translocated within the complex in such a way that it does not inhibit DnaB helicase activity. Translocation of λP triggers the initiation event allowing DnaB helicase to unwind DNA near the ori λ sequence, leading to efficient λDNA replication. Chaperone activity of the DnaK -DnaJ-GrpE system is first manifested in the selective binding of these heat shock proteins to the preprimosomal complex, followed by its ATP-dependent rearrangement. I show that DnaJ not only tags the preprimosomal complex for recognition by DnaK, but also stabilizes the multi-protein structure. GrpE also participates in the binding of DnaK to the preprimosomal complex by increasing DnaK ’s affinity to those λP proteins which are already associated with DnaJ. After attracting DnaK to the preprimosomal complex, DnaJ and GrpE stimulate the ATPase activity of DnaK , triggering conformational changes in DnaK which are responsible for the rearrangement of proteins in the preprimosomal complex and recycling of these heat shock proteins. The role of DnaK , DnaJ and GrpE in λDNA replication is in sharp contrast to our understanding of their role in the oriC , P1, and probably mini-F DNA replication systems. In the cases of oriC and P1 DNA replication, these heat shock proteins activate initiation factors before they are in contact with DNA, and are not required during the subsequent steps leading to the initiation of DNA replication. The common feature of DnaK , DnaJ and GrpE action in these systems is their ATP-dependent disaggregation or rearrangement of protein complexes formed before or during initiation of DNA replication.

scholarly journals Identification of the Unwinding Region in the Clostridioides difficile Chromosomal Origin of Replication

2020 ◽  
Vol 11 ◽  
Author(s):  
Ana M. Oliveira Paiva ◽  
Erika van Eijk ◽  
Annemieke H. Friggen ◽  
Christoph Weigel ◽  
Wiep Klaas Smits
Keyword(s):  
Origin Of Replication ◽  
Chromosomal Origin ◽  
Clostridioides Difficile

scholarly journals Primer-DNA formation during simian virus 40 DNA replication in vitro.

1993 ◽  
Vol 13 (5) ◽  
pp. 2882-2890 ◽  
Author(s):  
D Denis ◽  
P A Bullock
Keyword(s):  
Dna Replication ◽  
Proliferating Cell Nuclear Antigen ◽  
Simian Virus 40 ◽  
Simian Virus ◽  
T Antigen ◽  
Nuclear Antigen ◽  
Origin Region ◽  
Sv40 Dna ◽  
Proliferating Cell

Studies of simian virus 40 (SV40) DNA replication in vitro have identified a small (approximately 30-nucleotide) RNA-DNA hybrid species termed primer-DNA. Initial experiments indicated that T antigen and the polymerase alpha-primase complex are required to form primer-DNA. Proliferating cell nuclear antigen, and presumably proliferating cell nuclear antigen-dependent polymerases, is not needed to form this species. Herein, we present an investigation of the stages at which primer-DNA functions during SV40 DNA replication in vitro. Hybridization studies indicate that primer-DNA is initially formed in the origin region and is subsequently synthesized in regions distal to the origin. At all time points, primer-DNA is synthesized from templates for lagging-strand DNA replication. These studies indicate that primer-DNA functions during both initiation and elongation stages of SV40 DNA synthesis. Results of additional experiments suggesting a precursor-product relationship between formation of primer-DNA and Okazaki fragments are presented.

Chromatin-bound Cdc6 persists in S and G2 phases in human cells, while soluble Cdc6 is destroyed in a cyclin A-cdk2 dependent process

2000 ◽  
Vol 113 (11) ◽  
pp. 1929-1938 ◽  
Author(s):  
D. Coverley ◽  
C. Pelizon ◽  
S. Trewick ◽  
R.A. Laskey
Keyword(s):  
Dna Replication ◽  
Protein Kinase ◽  
Mammalian Cell ◽  
Cyclin A ◽  
S Phase ◽  
Human Cells ◽  
Cell Extracts ◽  
In Vitro Replication ◽  
Initiation Of Dna Replication

Cdc6 is essential for the initiation of DNA replication in all organisms in which it has been studied. In addition, recombinant Cdc6 can stimulate initiation in G(1) nuclei in vitro. We have analysed the behaviour of recombinant Cdc6 in mammalian cell extracts under in vitro replication conditions. We find that Cdc6 is imported into the nucleus in G(1)phase, where it binds to chromatin and remains relatively stable. In S phase, exogenous Cdc6 is destroyed in a process that requires import into the nucleus and phosphorylation by a chromatin-bound protein kinase. Recombinant cyclin A-cdk2 can completely substitute for the nucleus in promoting destruction of soluble Xenopus and human Cdc6. Despite this regulated destruction, endogenous Cdc6 persists in the nucleus after initiation, although the amount falls. Cdc6 levels remain constant in G(2) then fall again before mitosis. We propose that cyclin A-cdk2 phosphorylation results in destruction of any Cdc6 not assembled into replication complexes, but that assembled proteins remain, in the phosphorylated state, in the nucleus. This process could contribute to the prevention of reinitiation in human cells by making free Cdc6 unavailable for re-assembly into replication complexes after G(1) phase.

scholarly journals Sequence Diversity and Functional Conservation of the Origin of Replication in Lactococcal Prolate Phages

2003 ◽  
Vol 69 (9) ◽  
pp. 5104-5114 ◽  
Author(s):  
Jasna Rakonjac ◽  
Lawrence J. H. Ward ◽  
Anja H. Schiemann ◽  
Paul P. Gardner ◽  
Mark W. Lubbers ◽  
...  
Keyword(s):  
Dna Replication ◽  
Secondary Structure ◽  
Sequence Homology ◽  
Plasmid Replication ◽  
Origin Of Replication ◽  
Functional Conservation ◽  
Origins Of Replication ◽  
Flanking Sequences ◽  
And Function ◽  
Phage Proteins

ABSTRACT Prolate or c2-like phages are a large homologous group of viruses that infect the bacterium Lactococcus lactis. In a collection of 122 prolate phages, three distinct, non-cross-hybridizing groups of origins of DNA replication were found. The nonconserved sequence was confined to the template for an untranslated transcript, PE1-T, 300 to 400 nucleotides in length, while the flanking sequences were conserved. All three origin types, despite the low sequence homology, have the same functional characteristics: they express abundant PE1-T transcripts and can function as origins of plasmid replication in the absence of phage proteins. Using chimeric constructs, we showed that hybrids of two nonhomologous origin sequences failed to function as replication origins, suggesting that preservation of a particular secondary structure of the PE1-T transcript is required for replication. This is the first systematic survey of the sequence and function of origins of replication in a group of lactococcal phages.

scholarly journals Probable Identification of a Membrane-Associated Repressor of Bacillus subtilis DNA Replication as the E2 Subunit of the Pyruvate Dehydrogenase Complex

2000 ◽  
Vol 182 (8) ◽  
pp. 2119-2124 ◽  
Author(s):  
Andrew Stein ◽  
William Firshein
Keyword(s):  
Bacillus Subtilis ◽  
Dna Replication ◽  
Pyruvate Dehydrogenase ◽  
Pyruvate Dehydrogenase Complex ◽  
E2 Protein ◽  
Reading Frame ◽  
Origin Region ◽  
Entire Open Reading Frame ◽  
Dehydrogenase Complex

ABSTRACT Two Bacillus subtilis lysogenic libraries were probed by an antibody specific for a previously described membrane-associated inhibitor of B. subtilis DNA replication (J. Laffan and W. Firshein, Proc. Natl. Acad. Sci. USA 85:7452–7456, 1988). Three clones that reacted strongly with the antibody contained an entire open reading frame. Sequencing identified one of the clones (R1-2) as containing the E2 subunit of the pyruvate dehydrogenase complex, dihydrolipoamide acetyltransferase. An AT-rich sequence in the origin region was identified initially as the site to which extracts from the R1-2 clone were bound. This sequence was almost identical to one detected in Bacillus thuringiensis that also bound the E2 subunit but which was involved in activating the Cry1 protoxin gene of the organism, not in inhibiting DNA replication (T. Walter and A. Aronson, J. Biol. Chem., 274:7901–7906, 1999). However, the exact sequence was not as important in B. subtilis as the AT-rich core region. Binding would occur as long as most of the AT character of the core remained. Purified E2 protein obtained by use of PCR and an expression vector reacted strongly with antibody prepared against the repressor protein and the protein in the R1-2 clone, but its specificity for the AT-rich region was altered. The purified E2 protein was capable of inhibiting membrane-associated DNA replication in vitro, but anti-E2 antibody was variable in its ability to rescue repression when added to the assay.

The Role of the Carboxyterminal Domain of RNA Polymerase II in Regulating Origins of DNA Replication in Saccharomyces cerevisiae

Genetics ◽  
2002 ◽  
Vol 162 (3) ◽  
pp. 1117-1129 ◽  
Author(s):  
Laura Gauthier ◽  
Renata Dziak ◽  
David J H Kramer ◽  
David Leishman ◽  
Xiaomin Song ◽  
...  
Keyword(s):  
Dna Replication ◽  
Rna Polymerase Ii ◽  
Specific Gene ◽  
Origin Of Replication ◽  
Minichromosome Maintenance ◽  
Pol Ii ◽  
Initiation Of Dna Replication ◽  
Stimulation Of ◽  
Significant Stimulatory Effect

Abstract MCM (minichromosome maintenance) proteins function as a replication licensing factor (RLF-M), which contributes to limiting initiation of DNA replication to once per cell cycle. In the present study we show that a truncation of the pol II CTD in a S. cerevisiae strain harboring a mutation in mcm5 partially reverses its ts phenotype and improves maintenance of CEN/ARS minichromosomes. We correlate this phenotype to effects on DNA replication rather than to effects on transcription or specific gene expression. We also demonstrate that a similar truncation of the CTD reduces minichromosome stability and impairs stimulation of DNA replication by trans-activators and that tethering of recombinant pol II CTD to an origin of replication has a significant stimulatory effect on minichromosome stability. Furthermore, we show that pol II is recruited to ARS1. We propose that in S. cerevisiae a mechanism of coordinating pol II transcription and DNA replication is mediated by the CTD of pol II.

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