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https://www.readbyqxmd.com/read/27899634/homologous-recombination-mediated-by-the-mycobacterial-adnab-helicase-without-end-resection-by-the-adnab-nucleases
#1
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...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27881980/comparative-genomics-of-dna-recombination-and-repair-in-cyanobacteria-biotechnological-implications
#2
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
#3
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...
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
#4
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
#5
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
#6
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
#7
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
https://www.readbyqxmd.com/read/27220465/sequence-dependent-nanometer-scale-conformational-dynamics-of-individual-recbcd-dna-complexes
#8
Ashley R Carter, Maasa H Seaberg, Hsiu-Fang Fan, Gang Sun, Christopher J Wilds, Hung-Wen Li, Thomas T Perkins
RecBCD is a multifunctional enzyme that possesses both helicase and nuclease activities. To gain insight into the mechanism of its helicase function, RecBCD unwinding at low adenosine triphosphate (ATP) (2-4 μM) was measured using an optical-trapping assay featuring 1 base-pair (bp) precision. Instead of uniformly sized steps, we observed forward motion convolved with rapid, large-scale (∼4 bp) variations in DNA length. We interpret this motion as conformational dynamics of the RecBCD-DNA complex in an unwinding-competent state, arising, in part, by an enzyme-induced, back-and-forth motion relative to the dsDNA that opens and closes the duplex...
July 8, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/26904381/pre-early-functions-of-bacteriophage-t5-and-its-relatives
#9
John Davison
Coliphage T5 injects its DNA in 2 steps: the first step transfer (FST) region 7.9% is injected and its genes are expressed and only then does the remainder (second step transfer, SST) of its DNA enter the cell. In the FST region, only 2 essential genes (A1 and A2) have been identified and a third (dmp) non-essential gene codes for a deoxyribonucleotide 5' monophosphatase. Thirteen additional putative ORFs are present in the FST region. Numerous properties have been attributed to FST region, including SST, host DNA degradation, inhibition of host RNA and protein synthesis, restriction insensitivity and protection of T5 DNA...
October 2015: Bacteriophage
https://www.readbyqxmd.com/read/26874520/single-strand-gap-repair-involves-both-recf-and-recbcd-pathways
#10
REVIEW
Vincent Pagès
Homologous recombination repairs discontinuities in DNA including single-strand gaps (SSGs) and double-strand breaks (DSBs). This commentary describes how the RecBCD and RecF pathways might be exchangeable for the repair of their respective DSB and SSG canonical substrates. In particular, I will discuss how the RecBCD pathway could engage in the repair of an SSG even when the latter is not associated with a DSB.
August 2016: Current Genetics
https://www.readbyqxmd.com/read/26762976/analysis-of-lexa-binding-sites-and-transcriptomics-in-response-to-genotoxic-stress-in-leptospira-interrogans
#11
Luciane Schons-Fonseca, Josefa B da Silva, Juliana S Milanez, Renan H Domingos, Janet L Smith, Helder I Nakaya, Alan D Grossman, Paulo L Ho, Renata M A da Costa
We determined the effects of DNA damage caused by ultraviolet radiation on gene expression in Leptospira interrogans using DNA microarrays. These data were integrated with DNA binding in vivo of LexA1, a regulator of the DNA damage response, assessed by chromatin immunoprecipitation and massively parallel DNA sequencing (ChIP-seq). In response to DNA damage, Leptospira induced expression of genes involved in DNA metabolism, in mobile genetic elements and defective prophages. The DNA repair genes involved in removal of photo-damage (e...
February 18, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/26471352/inhibition-of-recbcd-in-klebsiella-pneumoniae-by-gam-and-its-effect-on-the-efficiency-of-gene-replacement
#12
Chuan Chen, Dong Wei, Pengfu Liu, Min Wang, Jiping Shi, Biao Jiang, Jian Hao
Gam protein is an inhibitor of the host RecBCD exonuclease, and this inhibition is essential to the proficiency of Red recombinase-mediated gene replacement. In Klebsiella pneumoniae, the efficiency of this gene replacement was lower than that in Escherichia coli, and the minimum length of homologous extensions required was longer. Thus, it was supposed that the inhibitory effect of Gam against RecBCD was weak in K. pneumoniae. To test this hypothesis, a Gam-deficient Red recombinase expression plasmid and a ΔrecB K...
February 2016: Journal of Basic Microbiology
https://www.readbyqxmd.com/read/26261330/quantitative-genomic-analysis-of-reca-protein-binding-during-dna-double-strand-break-repair-reveals-recbcd-action-in-vivo
#13
Charlotte A Cockram, Milana Filatenkova, Vincent Danos, Meriem El Karoui, David R F Leach
Understanding molecular mechanisms in the context of living cells requires the development of new methods of in vivo biochemical analysis to complement established in vitro biochemistry. A critically important molecular mechanism is genetic recombination, required for the beneficial reassortment of genetic information and for DNA double-strand break repair (DSBR). Central to recombination is the RecA (Rad51) protein that assembles into a spiral filament on DNA and mediates genetic exchange. Here we have developed a method that combines chromatin immunoprecipitation with next-generation sequencing (ChIP-Seq) and mathematical modeling to quantify RecA protein binding during the active repair of a single DSB in the chromosome of Escherichia coli...
August 25, 2015: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/26195593/recf-and-recr-play-critical-roles-in-the-homologous-recombination-and-single-strand-annealing-pathways-of-mycobacteria
#14
Richa Gupta, Stewart Shuman, Michael S Glickman
Mycobacteria encode three DNA double-strand break repair pathways: (i) RecA-dependent homologous recombination (HR), (ii) Ku-dependent nonhomologous end joining (NHEJ), and (iii) RecBCD-dependent single-strand annealing (SSA). Mycobacterial HR has two presynaptic pathway options that rely on the helicase-nuclease AdnAB and the strand annealing protein RecO, respectively. Ablation of adnAB or recO individually causes partial impairment of HR, but loss of adnAB and recO in combination abolishes HR. RecO, which can accelerate annealing of single-stranded DNA in vitro, also participates in the SSA pathway...
October 2015: Journal of Bacteriology
https://www.readbyqxmd.com/read/26003632/recbcd-is-required-to-complete-chromosomal-replication-implications-for-double-strand-break-frequencies-and-repair-mechanisms
#15
REVIEW
Justin Courcelle, Brian M Wendel, Dena D Livingstone, Charmain T Courcelle
Several aspects of the mechanism of homologous double-strand break repair remain unclear. Although intensive efforts have focused on how recombination reactions initiate, far less is known about the molecular events that follow. Based upon biochemical studies, current models propose that RecBCD processes double-strand ends and loads RecA to initiate recombinational repair. However, recent studies have shown that RecBCD plays a critical role in completing replication events on the chromosome through a mechanism that does not involve RecA or recombination...
August 2015: DNA Repair
https://www.readbyqxmd.com/read/25874675/crispr-adaptation-biases-explain-preference-for-acquisition-of-foreign-dna
#16
Asaf Levy, Moran G Goren, Ido Yosef, Oren Auster, Miriam Manor, Gil Amitai, Rotem Edgar, Udi Qimron, Rotem Sorek
CRISPR-Cas (clustered, regularly interspaced short palindromic repeats coupled with CRISPR-associated proteins) is a bacterial immunity system that protects against invading phages or plasmids. In the process of CRISPR adaptation, short pieces of DNA ('spacers') are acquired from foreign elements and integrated into the CRISPR array. So far, it has remained a mystery how spacers are preferentially acquired from the foreign DNA while the self chromosome is avoided. Here we show that spacer acquisition is replication-dependent, and that DNA breaks formed at stalled replication forks promote spacer acquisition...
April 23, 2015: Nature
https://www.readbyqxmd.com/read/25569614/recfor-is-not-required-for-pneumococcal-transformation-but-together-with-xers-for-resolution-of-chromosome-dimers-frequently-formed-in-the-process
#17
Calum Johnston, Isabelle Mortier-Barrière, Chantal Granadel, Patrice Polard, Bernard Martin, Jean-Pierre Claverys
Homologous recombination (HR) is required for both genome maintenance and generation of diversity in eukaryotes and prokaryotes. This process initiates from single-stranded (ss) DNA and is driven by a universal recombinase, which promotes strand exchange between homologous sequences. The bacterial recombinase, RecA, is loaded onto ssDNA by recombinase loaders, RecBCD and RecFOR for genome maintenance. DprA was recently proposed as a third loader dedicated to genetic transformation. Here we assessed the role of RecFOR in transformation of the human pathogen Streptococcus pneumoniae...
January 2015: PLoS Genetics
https://www.readbyqxmd.com/read/25539914/a-new-recombineering-system-for-photorhabdus-and-xenorhabdus
#18
Jia Yin, Hongbo Zhu, Liqiu Xia, Xuezhi Ding, Thomas Hoffmann, Michael Hoffmann, Xiaoying Bian, Rolf Müller, Jun Fu, A Francis Stewart, Youming Zhang
Precise and fluent genetic manipulation is still limited to only a few prokaryotes. Ideally the highly advanced technologies available in Escherichia coli could be broadly applied. Our efforts to apply lambda Red technology, widely termed 'recombineering', in Photorhabdus and Xenorhabdus yielded only limited success. Consequently we explored the properties of an endogenous Photorhabdus luminescens lambda Red-like operon, Plu2934/Plu2935/Plu2936. Bioinformatic and functional tests indicate that Plu2936 is a 5'-3' exonuclease equivalent to Redα and Plu2935 is a single strand annealing protein equivalent to Redβ...
March 31, 2015: Nucleic Acids Research
https://www.readbyqxmd.com/read/25486468/structural-features-of-chi-recognition-in-addab-with-implications-for-recbcd
#19
Martin Wilkinson, Dale B Wigley
AddAB and RecBCD-type helicase-nuclease complexes control the first stage of bacterial homologous recombination (HR) - the resection of double strand DNA breaks. A switch in the activities of the complexes to initiate repair by HR is regulated by a short, species-specific DNA sequence known as a Crossover Hotspot Instigator (Chi) site. It has been shown that, upon encountering Chi, AddAB and RecBCD pause translocation before resuming at a reduced rate. Recently, the structure of B.subtilis AddAB in complex with its regulatory Chi sequence revealed the nature of Chi binding and the paused translocation state...
2014: Cell Cycle
https://www.readbyqxmd.com/read/25419527/the-dna-exonucleases-of-escherichia-coli
#20
Susan T Lovett
DNA exonucleases, enzymes that hydrolyze phosphodiester bonds in DNA from a free end, play important cellular roles in DNA repair, genetic recombination and mutation avoidance in all organisms. This article reviews the structure, biochemistry and biological functions of the 17 exonucleases currently identified in the bacterium Escherichia coli. These include the exonucleases associated with DNA polymerases I (polA), II (polB) and III (dnaQ/mutD), Exonucleases I (xonA/sbcB), III (xthA), IV, VII (xseAB), IX (xni/xgdG) and X (exoX), the RecBCD, RecJ, and RecE exonucleases, SbcCD endo/exonuclease, the DNA exonuclease activities of RNase T (rnt) and Endonuclease IV (nfo) and TatD...
2011: EcoSal Plus
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