scholarly journals Differential Binding of Replication Proteins across the Human c-myc Replicator

2006 ◽  
Vol 26 (14) ◽  
pp. 5270-5283 ◽  
Author(s):  
Maloy Ghosh ◽  
Michael Kemp ◽  
Guoqi Liu ◽  
Marion Ritzi ◽  
Aloys Schepers ◽  
...  
Keyword(s):  
Trichostatin A ◽  
Qualitative Change ◽  
Replication Initiation ◽  
Dna Unwinding ◽  
The Novel ◽  
Replication Proteins ◽  
Structural Elements ◽  
Histone Hyperacetylation ◽  
M Phase ◽  
Differential Binding

ABSTRACT The binding of the prereplication complex proteins Orc1, Orc2, Mcm3, Mcm7, and Cdc6 and the novel DNA unwinding element (DUE) binding protein DUE-B to the endogenous human c-myc replicator was studied by chromatin immunoprecipitation. In G1-arrested HeLa cells, Mcm3, Mcm7, and DUE-B were prominent near the DUE, while Orc1 and Orc2 were least abundant near the DUE and more abundant at flanking sites. Cdc6 binding mirrored that of Orc2 in G1-arrested cells but decreased in asynchronous or M-phase cells. Similarly, the signals from Orc1, Mcm3, and Mcm7 were at background levels in cells arrested in M phase, whereas Orc2 retained the distribution seen in G1-phase cells. Previously shown to cause histone hyperacetylation and delocalization of replication initiation, trichostatin A treatment of cells led to a parallel qualitative change in the distribution of Mcm3, but not Orc2, across the c-myc replicator. Orc2, Mcm3, and DUE-B were also bound at an ectopic c-myc replicator, where deletion of sequences essential for origin activity was associated with the loss of DUE-B binding or the alteration of chromatin structure and loss of Mcm3 binding. These results show that proteins implicated in replication initiation are selectively and differentially bound across the c-myc replicator, dependent on discrete structural elements in DNA or chromatin.

scholarly journals Putative Cooperative ATP–DnaA Binding to Double-Stranded DnaA Box and Single-Stranded DnaA-Trio Motif upon Helicobacter pylori Replication Initiation Complex Assembly

2021 ◽  
Vol 22 (12) ◽  
pp. 6643
Author(s):  
Pawel Jaworski ◽  
Dorota Zyla-Uklejewicz ◽  
Malgorzata Nowaczyk-Cieszewska ◽  
Rafal Donczew ◽  
Thorsten Mielke ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Replication Initiation ◽  
Dna Unwinding ◽  
Rich Region ◽  
Initiator Protein ◽  
New Class ◽  
H Pylori ◽  
General Architecture ◽  
Dnaa Box

oriC is a region of the bacterial chromosome at which the initiator protein DnaA interacts with specific sequences, leading to DNA unwinding and the initiation of chromosome replication. The general architecture of oriCs is universal; however, the structure of oriC and the mode of orisome assembly differ in distantly related bacteria. In this work, we characterized oriC of Helicobacter pylori, which consists of two DnaA box clusters and a DNA unwinding element (DUE); the latter can be subdivided into a GC-rich region, a DnaA-trio and an AT-rich region. We show that the DnaA-trio submodule is crucial for DNA unwinding, possibly because it enables proper DnaA oligomerization on ssDNA. However, we also observed the reverse effect: DNA unwinding, enabling subsequent DnaA–ssDNA oligomer formation—stabilized DnaA binding to box ts1. This suggests the interplay between DnaA binding to ssDNA and dsDNA upon DNA unwinding. Further investigation of the ts1 DnaA box revealed that this box, together with the newly identified c-ATP DnaA box in oriC1, constitute a new class of ATP–DnaA boxes. Indeed, in vitro ATP–DnaA unwinds H. pylori oriC more efficiently than ADP–DnaA. Our results expand the understanding of H. pylori orisome formation, indicating another regulatory pathway of H. pylori orisome assembly.

scholarly journals Protein Phosphatase 2A and Cdc7 Kinase Regulate the DNA Unwinding Element-binding Protein in Replication Initiation

2014 ◽  
Vol 289 (52) ◽  
pp. 35987-36000 ◽  
Author(s):  
Yanzhe Gao ◽  
Jianhong Yao ◽  
Sumeet Poudel ◽  
Eric Romer ◽  
Lubna Abu-Niaaj ◽  
...  
Keyword(s):  
Protein Phosphatase ◽  
Binding Protein ◽  
Protein Phosphatase 2A ◽  
Replication Initiation ◽  
Dna Unwinding ◽  
Element Binding Protein ◽  
Phosphatase 2A ◽  
Cdc7 Kinase

scholarly journals Expression of Differentiation-related Markers in Teratocarcinoma Cells via Histone Hyperacetylation by Trichostatin A.

1991 ◽  
Vol 55 (6) ◽  
pp. 1491-1495 ◽  
Author(s):  
Yutaka HOSHIKAWA ◽  
Masako KIJIMA ◽  
Minoru YOSHIDA ◽  
Teruhiko BEPPU
Keyword(s):  
Trichostatin A ◽  
Histone Hyperacetylation ◽  
Teratocarcinoma Cells

scholarly journals Evolution of CDK1 paralog specializations in a lineage with fast developing planktonic embryos

2019 ◽  
Author(s):  
Xiaofei Ma ◽  
Jan Inge Øvrebø ◽  
Eric M Thompson
Keyword(s):  
General Rule ◽  
Embryonic Cell ◽  
Cyclin B ◽  
Gene Duplications ◽  
Structural Elements ◽  
Oikopleura Dioica ◽  
Cell Cycles ◽  
Protein Levels ◽  
Binding Interface ◽  
M Phase

AbstractThe active site of the essential, eukaryotic CDK1 kinase is generated by core structural elements, among which the PSTAIRE motif in the critical αC-helix, is universally conserved in metazoans. The CDK2 kinase, sharing the PSTAIRE, arose early in metazoan evolution and permitted subdivision of tasks along the S-M-phase axis. The marine chordate, Oikopleura dioica, is the only metazoan known to possess more than a single CDK1 ortholog, and all of its 5 paralogs show sequence divergences in the PSTAIRE. Through assessing CDK1 gene duplications in the appendicularian lineage, we show that the CDK1 activation loop substrate binding platform, ATP entrance site, hinge region, and main Cyclin binding interface, have all diversified under positive selection. Three of the 5 CDK1 paralogs are required for embryonic divisions and knockdown phenotypes illustrate further subdivision of functions along the S-M-phase axis. In parallel to CDK1 gene duplications, there has also been amplification in the Cyclin B complement. Among these, the CDK1d:Cyclin Ba pairing is required for oogenic meiosis and early embryogenesis and shows evidence of coevolution of an exclusive interaction. In an intriguing twist on the general rule that Cyclin B oscillations on a background of stable CDK1 levels regulate M-phase MPF activity, it is CDK1d protein levels that oscillate, rather than Cyclin Ba levels, to drive rapid, early embryonic cell cycles. Strikingly, the modified PSTAIRE of odCDK1d shows convergence over great evolutionary distance with plant CDKB, and in both O. dioica, and plants, these variants exhibit increased specialization to M-phase.

scholarly journals Processes of digitalization in the context of philosophical-technical interpretation

2020 ◽  
Vol 65 (1) ◽  
pp. 15-24
Author(s):  
A. Yu. Kosenkov
Keyword(s):  
Digital Technologies ◽  
Qualitative Change ◽  
Structural Elements ◽  
Information Communication ◽  
Digital Products ◽  
Digital Product ◽  
Production Economic

Based on the analysis of transformations of the technical reality of the last century related to the development of computers and digital technologies, the article discusses the processes of digitalization and digital transformations. It has been established that digitalization can be understood as the process of creating, through digital technologies, a specific real or virtual digital product with information, communication, production, economic and other purposes. It is noted that the digitalization process leads to digital transformations – processes of a qualitative change in the structural elements of reality associated with the development and use of digital technologies and digital products. The study also establishes that digitalization processes, due to the advent of computer devices and digital technologies, are transforming technical reality.

scholarly journals Mechanical phenotyping of acute promyelocytic leukemia reveals unique biomechanical responses in retinoic acid-resistant populations

2021 ◽  
Author(s):  
Brian Li ◽  
Annie Maslan ◽  
Aaron M Streets ◽  
Lydia L. Sohn
Keyword(s):  
Retinoic Acid ◽  
Acute Promyelocytic Leukemia ◽  
Dna Content ◽  
Trichostatin A ◽  
Chromatin Condensation ◽  
Promyelocytic Leukemia ◽  
Mechanical Responses ◽  
Nuclear Mechanics ◽  
All Trans Retinoic Acid ◽  
M Phase

While all-trans retinoic acid (ATRA) is an essential therapy in the treatment of acute promyelocytic leukemia (APL), an aggressive subtype of acute myeloid leukemia, nearly 20% of APL patients are resistant to ATRA. As no biomarkers for ATRA resistance yet exist, we investigated whether cell mechanics could be associated with this pathological phenotype. Using mechano-node-pore sensing, a single-cell mechanical phenotyping platform, and patient-derived APL cell lines, NB4 (ATRA-sensitive) and AP-1060 (ATRA-resistant), we discovered that ATRA-resistant APL cells are less mechanically pliable. By investigating how different subcellular components of APL cells contribute to whole-cell mechanical phenotype, we determined that nuclear mechanics strongly influence APL cell mechanical responses. By arresting APL cells in S-phase or M-phase in the cell cycle, we found cell pliability to be inversely related to DNA content. In addition to DNA content affecting cell pliability, we observed that chromatin condensation also affects nuclear mechanics: decondensing chromatin with trichostatin A is especially effective in softening ATRA-resistant APL cells. RNA-Seq allowed us to compare the transcriptomic differences between ATRA-resistant and ATRA-responsive APL cells and highlighted gene expression changes that could be associated with mechanical changes. Overall, we demonstrate the potential of physical biomarkers in identifying APL resistance.

scholarly journals The zinc-binding motif of human RECQ5β suppresses the intrinsic strand-annealing activity of its DExH helicase domain and is essential for the helicase activity of the enzyme

2008 ◽  
Vol 412 (3) ◽  
pp. 425-433 ◽  
Author(s):  
Hua Ren ◽  
Shuo-Xing Dou ◽  
Xing-Dong Zhang ◽  
Peng-Ye Wang ◽  
Radhakrishnan Kanagaraj ◽  
...  
Keyword(s):  
Structural Similarity ◽  
Zinc Binding ◽  
Binding Motif ◽  
Dna Unwinding ◽  
Helicase Domain ◽  
The Novel ◽  
Quantitative Measurements ◽  
Strand Annealing ◽  
Zinc Binding Motif

RecQ family helicases, functioning as caretakers of genomic integrity, contain a zinc-binding motif which is highly conserved among these helicases, but does not have a substantial structural similarity with any other known zinc-finger folds. In the present study, we show that a truncated variant of the human RECQ5β helicase comprised of the conserved helicase domain only, a splice variant named RECQ5α, possesses neither ATPase nor DNA-unwinding activities, but surprisingly displays a strong strand-annealing activity. In contrast, fragments of RECQ5β including the intact zinc-binding motif, which is located immediately downstream of the helicase domain, exhibit much reduced strand-annealing activity but are proficient in DNA unwinding. Quantitative measurements indicate that the regulatory role of the zinc-binding motif is achieved by enhancing the DNA-binding affinity of the enzyme. The novel intramolecular modulation of RECQ5β catalytic activity mediated by the zinc-binding motif may represent a universal regulation mode for all RecQ family helicases.

Effects of histone hyperacetylation on the preimplantation development of male and female bovine embryos

2010 ◽  
Vol 22 (6) ◽  
pp. 1041 ◽  
Author(s):  
Clara S. Oliveira ◽  
Naiara Z. Saraiva ◽  
Marcela M. de Souza ◽  
Tatiane A. D. Tetzner ◽  
Marina R. de Lima ◽  
...  
Keyword(s):  
Histone Deacetylases ◽  
Trichostatin A ◽  
Preimplantation Development ◽  
Bovine Embryos ◽  
In Vitro Production ◽  
Male And Female ◽  
Beneficial Effects ◽  
Histone Hyperacetylation ◽  
Vitro Production

Trichostatin A (TSA) induces histone hyperacetylation by inhibiting histone deacetylases and consequently increasing gene expression. The hypothesis was that TSA supplementation during the in vitro culture (IVC) of bovine embryos would increase the blastocyst rate, particularly in low-quality and female embryos. Oocytes were fertilised separately with X and Y spermatozoa and, 70 h after IVF, the IVC medium was supplemented with 5 nM and 15 nM TSA for 48 or 144 h. Incubation of female embryos with 5 nM and 15 nM TSA resulted in similar increases in acetylated histone H3K9 levels. However, to see comparable effects on acetylated histone H3K9 levels in male embryos, the culture medium needed to be supplemented with 15 nM TSA (as opposed to 5 nM TSA for female embryos). Treatment of male and female embryos with 5 nM TSA for 48 h or female embryos with 5 nM for 144 h had no effect on blastocyst rates, although 15 nM TSA compromised embryonic development. The terminal deoxyribonucleotidyl transferase-mediated dUTP–digoxigenin nick end-labelling (TUNEL) assay revealed increased apoptosis in female embryos treated with 5 nM TSA for 144 h, as well as in male and female embryos treated with 15 nM TSA for 48 h, but this increase in apoptosis was not observed in low-quality embryos. The results of the present study suggest that TSA treatment promotes histone hyperacetylation, but has no beneficial effects on the in vitro production of male and female bovine embryos during preimplantation development.

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