FUS Microphase Separation: Regulation by Nucleic Acid Polymers and DNA Repair Proteins by Maria V. Sukhanova, Rashid O. Anarbaev, Ekaterina A. Maltseva, David Pastré, Olga I. Lavrik

“…Fused in sarcoma (FUS) is involved in the regulation of RNA and DNA metabolism. FUS participates in the formation of biomolecular condensates driven by phase transition. …”
Get full text

Forty Years without Family: Three Novel Bacteriophages with High Similarity to SPP1 Reveal Decades of Evolutionary Stasis since the Isolation of Their Famous Relative by Véronique A. Delesalle, Brianne E. Tomko, Albert C. Vill, Katherine B. Lichty, Greg P. Krukonis

“…Gene conservation connotes purifying selection and is observed in structural genes and genes involved in DNA metabolism, but also in genes of unknown function, suggesting an important role in phage survival independent of the environment. …”
Get full text

OB-Folds and Genome Maintenance: Targeting Protein–DNA Interactions for Cancer Therapy by Sui Par, Sofia Vaides, Pamela S. VanderVere-Carozza, Katherine S. Pawelczak, Jason Stewart, John J. Turchi

“…We discuss their individual roles in DNA metabolism, progress toward drugging these motifs and their utility as potential cancer therapeutics. …”
Get full text

Probing hyper-negatively supercoiled mini-circles with nucleases and DNA binding proteins. by Carole Saintomé, Emmanuelle Delagoutte

“…Our goals in this study were to use radiolabeled double-stranded DNA mini-circles (dsMCs) to locate the unpaired bases on dsMCs whose topology ranged from relaxed to hyper-negatively supercoiled states, and to characterize the binding of proteins involved in the DNA metabolism. Our results show that the Nuclease SI is nearly ten times more active on hyper-negatively supercoiled than relaxed DNA. …”
Get full text

Immunomodulatory Roles of PARP-1 and PARP-2: Impact on PARP-Centered Cancer Therapies by José Yélamos, Lucia Moreno-Lama, Jaime Jimeno, Syed O. Ali

“…The central role of these PARPs in DNA metabolism in cancer cells has led to the development of PARP inhibitors as new cancer therapeutics, both as adjuvant treatment potentiating chemo-, radio-, and immuno-therapies and as monotherapy exploiting cancer-specific defects in DNA repair. …”
Get full text

Chl1, an ATP-Dependent DNA Helicase, Inhibits DNA:RNA Hybrids Formation at DSB Sites to Maintain Genome Stability in <i>S. pombe</i> by Deyun He, Zhen Du, Huiling Xu, Xiaoming Bao

“…Studies have demonstrated that ChlR1 plays a vital role in preserving genome stability by participating in DNA repair and sister chromatid cohesion, whereas the ways in which the biochemical features of ChlR1 function in DNA metabolism are not well understood. Here, we illustrate that Chl1 localizes to double-strand DNA break (DSB) sites and restrains DNA:RNA hybrid accumulation at these loci. …”
Get full text

FAM72 family proteins as poor prognostic markers in clear cell renal carcinoma by Hui Gou, Ping Chen, Wenbing Wu

“…GO and GSEA analyses indicated that FAM72 was enriched in biological processes related to mitosis, cell cycle, and DNA metabolism. Moreover, we found a significant correlation between FAM72 and immune cell infiltration and the level of methylation in ccRCC patients. …”
Get full text

The adjacent positioning of co-regulated gene pairs is widely conserved across eukaryotes by Arnone James T, Robbins-Pianka Adam, Arace Jeffrey R, Kass-Gergi Sara, McAlear Michael A

“…</p> <p>Results</p> <p>We investigated co-regulated gene sets in <it>S. cerevisiae</it> beyond those related to ribosome biogenesis, and found that a number of these regulons, including those involved in DNA metabolism, heat shock, and the response to cellular stressors were also significantly enriched for adjacent gene pairs. …”
Get full text

<it>Arabidopsis </it>gene co-expression network and its functional modules by Dash Sudhansu, Van Hemert John L, Mao Linyong, Dickerson Julie A

“…The cell cycle module orchestrated the coordinated expression of hundreds of genes involved in cell cycle, DNA metabolism, and cytoskeleton organization and biogenesis. …”
Get full text

Transcriptional analysis of the <it>recA </it>gene of <it>Streptococcus thermophilus</it> by Cordone Angelina, Baccigalupi Loredana, Giliberti Gabriele, Ricca Ezio, De Felice Maurilio

“…<p>Abstract</p> <p>Background</p> <p>RecA is a highly conserved prokaryotic protein that not only plays several important roles connected to DNA metabolism but also affects the cell response to various stress conditions. …”
Get full text

Computational Insights into the Dynamic Structural Features and Binding Characteristics of Recombinase UvsX Compared with RecA by Yue Pan, Ningkang Xie, Xin Zhang, Shuo Yang, Shaowu Lv

“…The UvsX protein from bacteriophage T4 is a member of the RecA family recombinases and plays a central role in T4 phage DNA repair and replication, which provides an important model for the biochemistry and genetics of DNA metabolism. UvsX shares a high degree of structural similarity and function with RecA, which is the most deeply studied member of the RecA family. …”
Get full text

Comparative genomic analysis of East Asian and non-Asian Helicobacter pylori strains identifies rapidly evolving genes. by Stacy S Duncan, Pieter L Valk, Mark S McClain, Carrie L Shaffer, Jason A Metcalf, Seth R Bordenstein, Timothy L Cover

“…The most highly represented functional groups are hypothetical proteins, cell envelope proteins and proteins involved in DNA metabolism. Among the divergent genes with known or predicted functions, population genetic analyses indicate that 86% exhibit evidence of positive selection. …”
Get full text

Structural characterization of human RPA70N association with DNA damage response proteins by Yeyao Wu, Wangmi Fu, Ning Zang, Chun Zhou

“…The heterotrimeric Replication protein A (RPA) is the ubiquitous eukaryotic single-stranded DNA (ssDNA) binding protein and participates in nearly all aspects of DNA metabolism, especially DNA damage response. The N-terminal OB domain of the RPA70 subunit (RPA70N) is a major protein-protein interaction element for RPA and binds to more than 20 partner proteins. …”
Get full text

Mechanism of Growth Inhibition of Human Cancer Cells by Conjugated Eicosapentaenoic Acid, an Inhibitor of DNA Polymerase and Topoisomerase by Yoshiyuki Mizushina, Hiromi Yoshida, Yuko Yonezawa

“…DNA topoisomerases (topos) and DNA polymerases (pols) are involved in manyaspects of DNA metabolism such as replication reactions. We found that long chainunsaturated fatty acids such as polyunsaturated fatty acids (PUFA) (i.e., eicosapentaenoicacid (EPA) and docosahexaenoic acid (DHA)) inhibited the activities of eukaryotic pols andtopos in vitro, and the inhibitory effect of conjugated fatty acids converted from EPA andDHA (cEPA and cDHA) on pols and topos was stronger than that of normal EPA and DHA.cEPA and cDHA did not affect the activities of plant and prokaryotic pols or other DNAmetabolic enzymes tested. cEPA was a stronger inhibitor than cDHA with IC50 values formammalian pols and human topos of 11.0 - 31.8 and 0.5 - 2.5 μM, respectively. cEPAinhibited the proliferation of two human leukemia cell lines, NALM-6, which is a p53-wildtype, and HL-60, which is a p53-null mutant, and the inhibitory effect was stronger than thatof normal EPA. …”
Get full text

Interaction of Proteins with Inverted Repeats and Cruciform Structures in Nucleic Acids by Richard P. Bowater, Natália Bohálová, Václav Brázda

“…It is, therefore, becoming clear that inverted repeats play important roles in regulating many aspects of DNA metabolism, including replication, gene expression, and recombination. …”
Get full text

Analyses of six homologous proteins of <it>Protochlamydia amoebophila </it>UWE25 encoded by large GC-rich genes (<it>lgr</it>): a model of evolution and concatenation of leucine-ri... by Roten Claude-Alain H, Eugster Myriam, Greub Gilbert

“…Interestingly, <it>lgrE</it>, which is present on Pam100G like the <it>tra </it>operon, exhibits Pfam domains related to DNA metabolism.</p> <p>Conclusion</p> <p>Comparison of the LRRs, enable us to propose a parsimonious evolutionary scenario of these domains driven by adjacent concatenations of LRRs. …”
Get full text

Endogenous and Foreign Nucleoid-Associated Proteins of Bacteria: Occurrence, Interactions and Effects on Mobile Genetic Elements and Host's Biology by Rodrigo Flores-Ríos, Raquel Quatrini, Alejandra Loyola

“…These small, basic, highly abundant proteins bind and bend DNA, altering its topology and folding, thereby affecting all known essential DNA metabolism related processes. Both chromosomally- (endogenous) and MGE- (foreign) encoded NAPs have been shown to exist in bacteria. …”
Get full text

Data of transcriptional effects of the merbarone-mediated inhibition of TOP2 by Fernando M. Delgado-Chaves, Pedro Manuel Martínez-García, Andrés Herrero-Ruiz, Francisco Gómez-Vela, Federico Divina, Silvia Jimeno-González, Felipe Cortés-Ledesma

“…Therefore, they are essential to overcome topological problems associated with DNA metabolism. Their aberrant activity results in the generation of DNA double-strand breaks, which can seriously compromise cell survival and genome integrity. …”
Get full text

Polynucleotide phosphorylase is implicated in homologous recombination and DNA repair in Escherichia coli by Thomas Carzaniga, Giulia Sbarufatti, Federica Briani, Gianni Dehò

“…Conclusions Our data suggest that PNPase may participate both directly and indirectly through regulation of gene expression to several aspects of DNA metabolism such as recombination, DNA repair and resistance to genotoxic agents.…”
Get full text

Nucleoside Hydrolase NH 36: A Vital Enzyme for the Leishmania Genus in the Development of T-Cell Epitope Cross-Protective Vaccines by Clarisa Beatriz Palatnik-de-Sousa, Clarisa Beatriz Palatnik-de-Sousa

“…NH36 is a vital enzyme of the DNA metabolism and a specific target for anti-Leishmania chemotherapy. …”
Get full text