Chemotherapy Side-Effects: Not All DNA Damage Is Equal by Winnie M. C. van den Boogaard, Daphne S. J. Komninos, Wilbert P. Vermeij

“…However, there are numerous types of chemotherapeutic drugs that are genotoxic and interfere with DNA metabolism in different ways, each with their own biodistribution, kinetics, and biological fate. …”
Get full text

The Role of Topoisomerase II in DNA Repair and Recombination in <i>Arabidopsis thaliana</i> by Marina Martinez-Garcia, Charles I. White, F. Chris. H. Franklin, Eugenio Sanchez-Moran

“…DNA entanglements and supercoiling arise frequently during normal DNA metabolism. DNA topoisomerases are highly conserved enzymes that resolve the topological problems that these structures create. …”
Get full text

The Last Chance Saloon by Ye Hong, Hongtao Zhang, Anton Gartner

“…Finally, we describe a recently identified mechanism uncovered in C. elegans where the conserved midbody associated endonuclease LEM-3/ANKLE1 is able to resolve chromatin bridges generated by various perturbations of DNA metabolism at the final stage of cell division. We also discuss how LEM-3 dependent chromatin bridge resolution may be coordinated with abscission checkpoint (NoCut) to achieve an error-free cleavage, therefore acting as a “last chance saloon” to facilitate genome integrity and organismal survival.…”
Get full text

RNA-seq profiling reveals novel target genes of LexA in the cyanobacterium Synechocystis sp. PCC 6803 by Ayumi eKizawa, Akihito eKawahara, Yasushi eTakimura, Yoshitaka eNishiyama, Yukako eHihara, Yukako eHihara

“…However, none of the genes related to DNA metabolism were affected by disruption of lexA. DNA gel mobility shift assay using the recombinant LexA protein suggested that LexA binds to the upstream region of pilA7, pilA9, ggpS and slr1670 to directly regulate their expression, but changes in the expression level of photosystem I genes by disruption of lexA is likely a secondary effect.…”
Get full text

Interdomain dynamics in human Replication Protein A regulates kinetics and thermodynamics of its binding to ssDNA by Sangeeta, Arnab Bhattacherjee

“…Human Replication Protein A (hRPA) is a multidomain protein that interacts with ssDNA intermediates to provide the latter much-needed stability during DNA metabolism and maintain genomic integrity. Although the ssDNA organization with hRPA was studied recently through experimental means, characterizing the underlying mechanism at the atomic level remains challenging because of the dynamic domain architecture of hRPA and poorly understood heterogeneity of ssDNA-protein interactions. …”
Get full text

Proline-specific aminopeptidase P prevents replication-associated genome instability. by Nicola Silva, Maikel Castellano-Pozo, Kenichiro Matsuzaki, Consuelo Barroso, Monica Roman-Trufero, Hannah Craig, Darren R Brooks, R Elwyn Isaac, Simon J Boulton, Enrique Martinez-Perez

“…Defects at different steps of DNA metabolism are known to induce replication stress, but the contribution of other aspects of cellular metabolism is less understood. …”
Get full text

Biochemical characterization of DNA damage checkpoint complexes: clamp loader and clamp complexes with specificity for 5' recessed DNA. by Viola Ellison, Bruce Stillman

“…The observation that RSR loads its clamp onto a 5' recessed end supports a potential role for RHR and RSR in diverse DNA metabolism, such as stalled DNA replication forks, recombination-linked DNA repair, and telomere maintenance, among other processes.…”
Get full text

Alternative sigma factor σ^Hactivates competence gene expression in <it>Lactobacillus sakei</it> by Schmid Solveig, Bevilacqua Claudia, Crutz-Le Coq Anne-Marie

“…More than half of them are involved in the synthesis of a DNA uptake machinery linked to genetic competence, and in DNA metabolism; however, σ^Hoverproduction did not allow detectable genetic transformation. σ^Hwas found to be conserved in the <it>L. sakei </it>species.…”
Get full text

The inner side of yeast PCNA contributes to genome stability by mediating interactions with Rad18 and the replicative DNA polymerase δ by Robert Toth, Miklos Halmai, Zsuzsanna Gyorfy, Eva Balint, Ildiko Unk

“…Abstract PCNA is a central orchestrator of cellular processes linked to DNA metabolism. It is a binding platform for a plethora of proteins and coordinates and regulates the activity of several pathways. …”
Get full text

Role of protein phosphorylation in the regulation of cell cycle and DNA-related processes in bacteria by Transito eGarcia-Garcia, Sandrine ePoncet, Lei eShi, Abderahmane eDerouiche, Ivan eMijakovic, Marie-Françoise eNoirot-Gros

“…Recent phosphoproteomics and interactomics studies identified numerous phosphoproteins involved in various aspect of DNA metabolism strongly supporting the existence of such level of regulation in bacteria. …”
Get full text

Genome-wide prediction of topoisomerase IIβ binding by architectural factors and chromatin accessibility. by Pedro Manuel Martínez-García, Miguel García-Torres, Federico Divina, José Terrón-Bautista, Irene Delgado-Sainz, Francisco Gómez-Vela, Felipe Cortés-Ledesma

“…DNA topoisomerase II-β (TOP2B) is fundamental to remove topological problems linked to DNA metabolism and 3D chromatin architecture, but its cut-and-reseal catalytic mechanism can accidentally cause DNA double-strand breaks (DSBs) that can seriously compromise genome integrity. …”
Get full text

Experimental evolution of UV resistance in a phage by Eric F. Tom, Ian J. Molineux, Matthew L. Paff, James J. Bull

“…At the end point, a 2.1 kb deletion of early genes and three substitutions in structural-genes were the only changes observed at high frequency throughout the 40 kb genome; no changes were observed in genes affecting DNA metabolism. The deletion accounted for only a two-fold improvement in survival. …”
Get full text

Topoisomerase III is essential for accurate nuclear division in Schizosaccharomyces pombe. by Goodwin, A, Wang, S, Toda, T, Norbury, C, Hickson, I

“…Topoisomerases catalyse changes in the topological state of DNA and are required for many aspects of DNA metabolism. While the functions of topoisomerases I and II in eukaryotes are well established, the role of topoisomerase III remains poorly defined. …”

Defensive function of transposable elements in bacteria by Fan, C, Wu, Y, Decker, C, Rohani, R, Gesell Salazar, M, Ye, H, Cui, Z, Schmidt, F, Huang, W

“…The DNA damage caused by the leaky expression of I-CeuI was enough to trigger a SOS response and alter lipid synthesis, ribosomal activity, RNA/DNA metabolism, central dogma and cell cycle processes in E. coli DH5a. …”

Identification of a second proliferating cell nuclear antigen in the human malarial pathogen Plasmodium falciparum. by Li, J, Warren, A, Cox, L

“…Northern blot analyses revealed two different transcripts of Pfpcna2, one expressed in both asexual and sexual erythrocytic stages, while the other existed only in the sexual stage, implying that PfPCNA2 may play multiple roles in DNA metabolism in different stages of the parasite. Recombinant protein of PfPCNA2, overexpressed in Escherichia coli, has been purified to near homogeneity and shown to form an oligomer, probably a trimer, as revealed by a size-exclusion chromatography and a native gel electrophoresis, suggesting that PfPCNA2, like its higher eukaryotic counterparts, may serve as a sliding platform which is capable of interaction with diverse proteins and regulation of their activities.…”

PROBING GENOME MAINTENANCE FUNCTIONS OF HUMAN RECQ1 by Furqan Sami, Sudha Sharma

“…Delineating what aspects of RECQ1 catalytic functions contribute to the observed cellular phenotypes, and how this is regulated is critical to establish its biological functions in DNA metabolism.'Recent studies have identified functional specialization of RECQ1 in DNA repair; however, identification of fundamental similarities will be just as critical in developing a unifying theme for RecQ actions, allowing the functions revealed from studying one homolog to be extrapolated and generalized to other RecQ homologs.…”
Get full text

Enzymatic activities and DNA substrate specificity of Mycobacterium tuberculosis DNA helicase XPB. by Seetha V Balasingham, Ephrem Debebe Zegeye, Håvard Homberset, Marie L Rossi, Jon K Laerdahl, Vilhelm A Bohr, Tone Tønjum

“…However, more insight into the function of bacterial helicases is central to understanding the mechanism of DNA metabolism and pathogenesis in general. Here, we characterized Mycobacterium tuberculosis XPB (Mtb XPB), a 3'→5' DNA helicase with DNA-dependent ATPase activity. …”
Get full text

Mutational signatures of redox stress in yeast single-strand DNA and of aging in human mitochondrial DNA share a common feature. by Natalya P Degtyareva, Natalie Saini, Joan F Sterling, Victoria C Placentra, Leszek J Klimczak, Dmitry A Gordenin, Paul W Doetsch

“…Clustered mutations discovered in several cancer genomes were linked to single-strand DNA (ssDNA) intermediates in various processes of DNA metabolism. Previously, only one clustered mutational signature had been clearly associated with a subclass of ssDNA-specific apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like (APOBEC) cytidine deaminases. …”
Get full text

A FRET-Based Assay for the Identification of PCNA Inhibitors by Sarah Hardebeck, Sebastian Schreiber, Annika Adick, Klaus Langer, Joachim Jose

“…Proliferating cell nuclear antigen (PCNA) is the key regulator of human DNA metabolism. One important interaction partner is p15, involved in DNA replication and repair. …”
Get full text

Algal rhodopsins encoding diverse signal sequence holds potential for expansion of organelle optogenetics by Kumari Sushmita, Sunita Sharma, Manish Singh Kaushik, Suneel Kateriya

“…Several identified channelrhodopsins and ion-pumping rhodopsins possess effector domains associated with DNA metabolism (repair, replication, and recombination) and gene regulation. …”
Get full text