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https://www.readbyqxmd.com/read/29129691/recbcd-exonuclease-v-is-inhibited-by-dna-adducts-produced-by-cisplatin-and-ultraviolet-light
#1
Wai Y Leung, Long H Chung, Hieronimus W Kava, Vincent Murray
The presence of adducts on the DNA double-helix can have major consequences for the efficient functioning of DNA repair enzymes. E. coli RecBCD (exonuclease V) is involved in recombinational repair of double-strand breaks that are caused by defective DNA replication, DNA damaging agents and other factors. The holoenzyme possesses a bipolar helicase activity which helps unwind DNA from both 3'- and 5'-directions and is coupled with a potent exonuclease activity that is also capable of digesting DNA from both 3'- and 5'-ends...
November 9, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29058747/cobalt-and-nickel-impair-dna-metabolism-by-the-oxidative-stress-independent-pathway
#2
Vineet Kumar, Rajesh Kumar Mishra, Gursharan Kaur, Dipak Dutta
The oxidative stress that evolves under cobalt and nickel exposure is thought to exert toxicity, though the exact routes of such metal poisoning remain ambiguous. We revisited the metal toxicity in Escherichia coli to show that cobalt and nickel exposure at levels as low as 0.5 and 1 mM, respectively, visibly inhibits growth. We also observed that acidic conditions aggravated, while alkaline conditions alleviated the metal toxicity. Besides, 1 mM manganese, which is non-cytotoxic, as judged by the growth of E...
November 15, 2017: Metallomics: Integrated Biometal Science
https://www.readbyqxmd.com/read/29032606/how-chi-sequence-modifies-recbcd-single-stranded-dna-translocase-activities
#3
Chia-Chuan Cho, Cinya Chung, Hung-Wen Li
E. coli RecBCD initiates homologous repair as well as degrades foreign DNA. Recognition of chi sequence (5'-GCTGGTGG-3') switches RecBCD from a destructive, nucleolytic mode into a repair-active one that promotes RecA-mediated recombination. It includes a 3'-to-5'ssDNA translocase in RecB subunit, a 5'-to-3' translocase in RecD, and a secondary translocase activity associated with RecBC. To understand how chi specifically affects each translocase activities, we directly visualized individual RecBCD translocating along DNA substrates containing a ssDNA gap of different polarities, with chi or not...
October 15, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
https://www.readbyqxmd.com/read/28976965/the-transcription-fidelity-factor-grea-impedes-dna-break-repair
#4
Priya Sivaramakrishnan, Leonardo A Sepúlveda, Jennifer A Halliday, Jingjing Liu, María Angélica Bravo Núñez, Ido Golding, Susan M Rosenberg, Christophe Herman
Homologous recombination repairs DNA double-strand breaks and must function even on actively transcribed DNA. Because break repair prevents chromosome loss, the completion of repair is expected to outweigh the transcription of broken templates. However, the interplay between DNA break repair and transcription processivity is unclear. Here we show that the transcription factor GreA inhibits break repair in Escherichia coli. GreA restarts backtracked RNA polymerase and hence promotes transcription fidelity. We report that removal of GreA results in markedly enhanced break repair via the classic RecBCD-RecA pathway...
October 12, 2017: Nature
https://www.readbyqxmd.com/read/28968392/division-induced-dna-double-strand-breaks-in-the-chromosome-terminus-region-of-escherichia-coli-lacking-recbcd-dna-repair-enzyme
#5
Anurag Kumar Sinha, Adeline Durand, Jean-Michel Desfontaines, Ielyzaveta Iurchenko, Hélène Auger, David R F Leach, François-Xavier Barre, Bénédicte Michel
Marker frequency analysis of the Escherichia coli recB mutant chromosome has revealed a deficit of DNA in a specific zone of the terminus, centred on the dif/TerC region. Using fluorescence microscopy of a marked chromosomal site, we show that the dif region is lost after replication completion, at the time of cell division, in one daughter cell only, and that the phenomenon is transmitted to progeny. Analysis by marker frequency and microscopy shows that the position of DNA loss is not defined by the replication fork merging point since it still occurs in the dif/TerC region when the replication fork trap is displaced in strains harbouring ectopic Ter sites...
October 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28927723/antimutagenic-activity-of-vitamin-b1-against-damages-induced-by-chemical-and-physical-mutagens-in-salmonella-typhimurium-and-escherichia-coli
#6
Jaime Sánchez-Navarrete, Myriam Arriaga-Alba, Nancy Jannet Ruiz-Pérez, Julia Dolores Toscano-Garibay
Thiamine (vitamin B1) is an essential nutrient acting mainly as an enzymatic cofactor on diverse cell processes. It has been reported that vitamin B1 has a significant role in the signaling pathways related to the response to adverse environmental conditions (chemical and physical). The objectives of this study were to evaluate the antimutagenic potential of vitamin B1 in front of DNA-alkylating agents in the presence/absence of ogt and ada repairing genes in Salmonella typhimurium strains and against damage induced by ultraviolet light type C in Escherichia coli strains mutated at the uvrABC system and recBCD enzymes...
December 2017: Toxicology in Vitro: An International Journal Published in Association with BIBRA
https://www.readbyqxmd.com/read/28716908/sequential-eviction-of-crowded-nucleoprotein-complexes-by-the-exonuclease-recbcd-molecular-motor
#7
Tsuyoshi Terakawa, Sy Redding, Timothy D Silverstein, Eric C Greene
In physiological settings, all nucleic acids motor proteins must travel along substrates that are crowded with other proteins. However, the physical basis for how motor proteins behave in these highly crowded environments remains unknown. Here, we use real-time single-molecule imaging to determine how the ATP-dependent translocase RecBCD travels along DNA occupied by tandem arrays of high-affinity DNA binding proteins. We show that RecBCD forces each protein into its nearest adjacent neighbor, causing rapid disruption of the protein-nucleic acid interaction...
August 1, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28689072/nucleolytic-degradation-of-3-ending-overhangs-is-essential-for-dna-end-resection-in-reca-loading-deficient-recb-mutants-of-escherichia-coli
#8
Siniša Ivanković, Dušica Vujaklija, Damir Đermić
Degradation of a 5'-ending strand is the hallmark of the universal process of DNA double strand break (DSB) resection, which results in creation of the central recombination intermediate, a 3'-ending overhang. Here we show that in Escherichia coli recB1080/recB1067 mutants, which are devoid of RecBCD's nuclease and RecA loading activities, degradation of the unwound 3' tail is as essential as is degradation of its 5'-ending complement. Namely, a synergistic action of ExoI, ExoVII, SbcCD and ExoX single-strand specific exonucleases (ssExos) of 3'-5' polarity was essential for preserving cell viability, DNA repair and homologous recombination in the recB1080/recB1067 mutants, to the same extent as the redundant action of 5'-tail trimming ssExos RecJ and ExoVII...
June 27, 2017: DNA Repair
https://www.readbyqxmd.com/read/28475211/short-dna-containing-%C3%AF-sites-enhances-dna-stability-and-gene-expression-in-e-coli-cell-free-transcription-translation-systems
#9
Ryan Marshall, Colin S Maxwell, Scott P Collins, Chase L Beisel, Vincent Noireaux
Escherichia coli cell-free transcription-translation (TXTL) systems offer versatile platforms for advanced biomanufacturing and for prototyping synthetic biological parts and devices. Production and testing could be accelerated with the use of linear DNA, which can be rapidly and cheaply synthesized. However, linear DNA is efficiently degraded in TXTL preparations from E. coli. Here, we show that double-stranded DNA encoding χ sites-eight base-pair sequences preferentially bound by the RecBCD recombination machinery-stabilizes linear DNA and greatly enhances the TXTL-based expression and activity of a fluorescent reporter gene, simple regulatory cascades, and T7 bacteriophage particles...
September 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28369478/a-non-catalytic-role-of-recbcd-in-homology-directed-gap-repair-and-translesion-synthesis
#10
Luisa Laureti, Lara Lee, Gaëlle Philippin, Vincent Pagès
The RecBCD complex is a key factor in DNA metabolism. This protein complex harbors a processive nuclease and two helicases activities that give it the ability to process duplex DNA ends. These enzymatic activities make RecBCD a major player in double strand break repair, conjugational recombination and degradation of linear DNA. In this work, we unravel a new role of the RecBCD complex in the processing of DNA single-strand gaps that are generated at DNA replication-blocking lesions. We show that independently of its nuclease or helicase activities, the entire RecBCD complex is required for recombinational repair of the gap and efficient translesion synthesis...
June 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28202049/costs-and-benefits-of-natural-transformation-in-acinetobacter-baylyi
#11
Nils Hülter, Vidar Sørum, Kristina Borch-Pedersen, Mikkel M Liljegren, Ane L G Utnes, Raul Primicerio, Klaus Harms, Pål J Johnsen
BACKGROUND: Natural transformation enables acquisition of adaptive traits and drives genome evolution in prokaryotes. Yet, the selective forces responsible for the evolution and maintenance of natural transformation remain elusive since taken-up DNA has also been hypothesized to provide benefits such as nutrients or templates for DNA repair to individual cells. RESULTS: We investigated the immediate effects of DNA uptake and recombination on the naturally competent bacterium Acinetobacter baylyi in both benign and genotoxic conditions...
February 15, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28009252/structural-basis-for-the-inhibition-of-recbcd-by-gam-and-its-synergistic-antibacterial-effect-with-quinolones
#12
Martin Wilkinson, Lucy Troman, Wan Ak Wan Nur Ismah, Yuriy Chaban, Matthew B Avison, Mark S Dillingham, Dale B Wigley
Our previous paper (Wilkinson et al, 2016) used high-resolution cryo-electron microscopy to solve the structure of the Escherichia coli RecBCD complex, which acts in both the repair of double-stranded DNA breaks and the degradation of bacteriophage DNA. To counteract the latter activity, bacteriophage λ encodes a small protein inhibitor called Gam that binds to RecBCD and inactivates the complex. Here, we show that Gam inhibits RecBCD by competing at the DNA-binding site. The interaction surface is extensive and involves molecular mimicry of the DNA substrate...
December 23, 2016: ELife
https://www.readbyqxmd.com/read/27999939/heat-survival-and-phenotype-microarray-profiling-of-salmonella-typhimurium-mutants
#13
Turki M Dawoud, Anita Khatiwara, Si Hong Park, Morgan L Davis, Christopher A Baker, Steven C Ricke, Young Min Kwon
Contamination of food products by pathogenic microorganisms continues to be a major public health and food industry concern. Non-typhoidal Salmonella species have led to numerous outbreaks associated with various foods. A wide variety of methods have been applied and introduced for treatment of fresh foods to eliminate pathogenic as well as spoilage microorganisms. Salmonella can become exposed to elevated temperatures while associated with hosts such as poultry. In addition, heat treatment is also applied at various stages of processing to retain the shelf life of food products...
February 2017: Current Microbiology
https://www.readbyqxmd.com/read/27899634/homologous-recombination-mediated-by-the-mycobacterial-adnab-helicase-without-end-resection-by-the-adnab-nucleases
#14
Richa Gupta, Mihaela-Carmen Unciuleac, Stewart Shuman, Michael S Glickman
Current models of bacterial homologous recombination (HR) posit that extensive resection of a DNA double-strand break (DSB) by a multisubunit helicase-nuclease machine (e.g. RecBCD, AddAB or AdnAB) generates the requisite 3' single-strand DNA substrate for RecA-mediated strand invasion. AdnAB, the helicase-nuclease implicated in mycobacterial HR, consists of two subunits, AdnA and AdnB, each composed of an N-terminal ATPase domain and a C-terminal nuclease domain. DSB unwinding by AdnAB in vitro is stringently dependent on the ATPase activity of the 'lead' AdnB motor translocating on the 3' ssDNA strand, but not on the putative 'lagging' AdnA ATPase...
January 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27881980/comparative-genomics-of-dna-recombination-and-repair-in-cyanobacteria-biotechnological-implications
#15
REVIEW
Corinne Cassier-Chauvat, Théo Veaudor, Franck Chauvat
Cyanobacteria are fascinating photosynthetic prokaryotes that are regarded as the ancestors of the plant chloroplast; the purveyors of oxygen and biomass for the food chain; and promising cell factories for an environmentally friendly production of chemicals. In colonizing most waters and soils of our planet, cyanobacteria are inevitably challenged by environmental stresses that generate DNA damages. Furthermore, many strains engineered for biotechnological purposes can use DNA recombination to stop synthesizing the biotechnological product...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27644322/mechanism-for-nuclease-regulation-in-recbcd
#16
Martin Wilkinson, Yuriy Chaban, Dale B Wigley
In bacterial cells, processing of double-stranded DNA breaks for repair by homologous recombination is catalysed by AddAB, AdnAB or RecBCD-type helicase-nucleases. These enzyme complexes are highly processive, duplex unwinding and degrading machines that require tight regulation. Here, we report the structure of E.coli RecBCD, determined by cryoEM at 3.8 Å resolution, with a DNA substrate that reveals how the nuclease activity of the complex is activated once unwinding progresses. Extension of the 5'-tail of the unwound duplex induces a large conformational change in the RecD subunit, that is transferred through the RecC subunit to activate the nuclease domain of the RecB subunit...
September 20, 2016: ELife
https://www.readbyqxmd.com/read/27607601/correction-to-the-nuclease-domain-of-the-escherichia-coli-recbcd-enzyme-catalyzes-degradation-of-linear-and-circular-single-stranded-and-double-stranded-dna
#17
Jian-Zhong Sun, Douglas A Julin, Jin-Shan Hu
No abstract text is available yet for this article.
September 20, 2016: Biochemistry
https://www.readbyqxmd.com/read/27422010/processive-dna-unwinding-by-recbcd-helicase-in-the-absence-of-canonical-motor-translocation
#18
Michael J Simon, Joshua E Sokoloski, Linxuan Hao, Elizabeth Weiland, Timothy M Lohman
Escherichia coli RecBCD is a DNA helicase/nuclease that functions in double-stranded DNA break repair. RecBCD possesses two motors (RecB, a 3' to 5' translocase, and RecD, a 5' to 3' translocase). Current DNA unwinding models propose that motor translocation is tightly coupled to base pair melting. However, some biochemical evidence suggests that DNA melting of multiple base pairs may occur separately from single-stranded DNA translocation. To test this hypothesis, we designed DNA substrates containing reverse backbone polarity linkages that prevent ssDNA translocation of the canonical RecB and RecD motors...
July 31, 2016: Journal of Molecular Biology
https://www.readbyqxmd.com/read/27401752/recbcd-enzyme-chi-recognition-mutants-recognize-chi-recombination-hotspots-in-the-right-dna-context
#19
Susan K Amundsen, Jake W Sharp, Gerald R Smith
RecBCD enzyme is a complex, three-subunit protein machine essential for the major pathway of DNA double-strand break repair and homologous recombination in Escherichia coli Upon encountering a Chi recombination-hotspot during DNA unwinding, RecBCD nicks DNA to produce a single-stranded DNA end onto which it loads RecA protein. Conformational changes that regulate RecBCD's helicase and nuclease activities are induced upon its interaction with Chi, defined historically as 5' GCTGGTGG 3'. Chi is thought to be recognized as single-stranded DNA passing through a tunnel in RecC...
September 2016: Genetics
https://www.readbyqxmd.com/read/27330137/unexpected-dna-context-dependence-identifies-a-new-determinant-of-chi-recombination-hotspots
#20
Andrew F Taylor, Susan K Amundsen, Gerald R Smith
Homologous recombination occurs especially frequently near special chromosomal sites called hotspots. In Escherichia coli, Chi hotspots control RecBCD enzyme, a protein machine essential for the major pathway of DNA break-repair and recombination. RecBCD generates recombinogenic single-stranded DNA ends by unwinding DNA and cutting it a few nucleotides to the 3' side of 5' GCTGGTGG 3', the sequence historically equated with Chi. To test if sequence context affects Chi activity, we deep-sequenced the products of a DNA library containing 10 random base-pairs on each side of the Chi sequence and cut by purified RecBCD...
September 30, 2016: Nucleic Acids Research
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