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https://www.readbyqxmd.com/read/27881980/comparative-genomics-of-dna-recombination-and-repair-in-cyanobacteria-biotechnological-implications
#1
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/27466393/single-strand-transposition-at-the-host-replication-fork
#2
Laure Lavatine, Susu He, Anne Caumont-Sarcos, Catherine Guynet, Brigitte Marty, Mick Chandler, Bao Ton-Hoang
Members of the IS200/IS605 insertion sequence family differ fundamentally from classical IS essentially by their specific single-strand (ss) transposition mechanism, orchestrated by the Y1 transposase, TnpA, a small HuH enzyme which recognizes and processes ss DNA substrates. Transposition occurs by the 'peel and paste' pathway composed of two steps: precise excision of the top strand as a circular ss DNA intermediate; and subsequent integration into a specific ssDNA target. Transposition of family members was experimentally shown or suggested by in silico high-throughput analysis to be intimately coupled to the lagging strand template of the replication fork...
September 19, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27447485/structural-and-functional-studies-of-h-seropedicae-reca-protein-insights-into-the-polymerization-of-reca-protein-as-nucleoprotein-filament
#3
Wellington C Leite, Carolina W Galvão, Sérgio C Saab, Jorge Iulek, Rafael M Etto, Maria B R Steffens, Sindhu Chitteni-Pattu, Tyler Stanage, James L Keck, Michael M Cox
The bacterial RecA protein plays a role in the complex system of DNA damage repair. Here, we report the functional and structural characterization of the Herbaspirillum seropedicae RecA protein (HsRecA). HsRecA protein is more efficient at displacing SSB protein from ssDNA than Escherichia coli RecA protein. HsRecA also promotes DNA strand exchange more efficiently. The three dimensional structure of HsRecA-ADP/ATP complex has been solved to 1.7 Å resolution. HsRecA protein contains a small N-terminal domain, a central core ATPase domain and a large C-terminal domain, that are similar to homologous bacterial RecA proteins...
2016: PloS One
https://www.readbyqxmd.com/read/26305498/structural-dynamics-of-e-coli-single-stranded-dna-binding-protein-reveal-dna-wrapping-and-unwrapping-pathways
#4
Sukrit Suksombat, Rustem Khafizov, Alexander G Kozlov, Timothy M Lohman, Yann R Chemla
Escherichia coli single-stranded (ss)DNA binding (SSB) protein mediates genome maintenance processes by regulating access to ssDNA. This homotetrameric protein wraps ssDNA in multiple distinct binding modes that may be used selectively in different DNA processes, and whose detailed wrapping topologies remain speculative. Here, we used single-molecule force and fluorescence spectroscopy to investigate E. coli SSB binding to ssDNA. Stretching a single ssDNA-SSB complex reveals discrete states that correlate with known binding modes, the likely ssDNA conformations and diffusion dynamics in each, and the kinetic pathways by which the protein wraps ssDNA and is dissociated...
2015: ELife
https://www.readbyqxmd.com/read/26276393/mycobacterium-tuberculosis-recg-protein-but-not-ruvab-or-reca-protein-is-efficient-at-remodeling-the-stalled-replication-forks-implications-for-multiple-mechanisms-of-replication-restart-in-mycobacteria
#5
Roshan Singh Thakur, Shivakumar Basavaraju, Jasbeer Singh Khanduja, K Muniyappa, Ganesh Nagaraju
Aberrant DNA replication, defects in the protection, and restart of stalled replication forks are major causes of genome instability in all organisms. Replication fork reversal is emerging as an evolutionarily conserved physiological response for restart of stalled forks. Escherichia coli RecG, RuvAB, and RecA proteins have been shown to reverse the model replication fork structures in vitro. However, the pathways and the mechanisms by which Mycobacterium tuberculosis, a slow growing human pathogen, responds to different types of replication stress and DNA damage are unclear...
October 2, 2015: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/26047498/directed-evolution-of-reca-variants-with-enhanced-capacity-for-conjugational-recombination
#6
Taejin Kim, Sindhu Chitteni-Pattu, Benjamin L Cox, Elizabeth A Wood, Steven J Sandler, Michael M Cox
The recombination activity of Escherichia coli (E. coli) RecA protein reflects an evolutionary balance between the positive and potentially deleterious effects of recombination. We have perturbed that balance, generating RecA variants exhibiting improved recombination functionality via random mutagenesis followed by directed evolution for enhanced function in conjugation. A recA gene segment encoding a 59 residue segment of the protein (Val79-Ala137), encompassing an extensive subunit-subunit interface region, was subjected to degenerate oligonucleotide-mediated mutagenesis...
June 2015: PLoS Genetics
https://www.readbyqxmd.com/read/26007651/disturbance-free-rapid-solution-exchange-for-magnetic-tweezers-single-molecule-studies
#7
Shimin Le, Mingxi Yao, Jin Chen, Artem K Efremov, Sara Azimi, Jie Yan
Single-molecule manipulation technologies have been extensively applied to studies of the structures and interactions of DNA and proteins. An important aspect of such studies is to obtain the dynamics of interactions; however the initial binding is often difficult to obtain due to large mechanical perturbation during solution introduction. Here, we report a simple disturbance-free rapid solution exchange method for magnetic tweezers single-molecule manipulation experiments, which is achieved by tethering the molecules inside microwells (typical dimensions-diameter (D): 40-50 μm, height (H): 100 μm; H:D∼2:1)...
September 30, 2015: Nucleic Acids Research
https://www.readbyqxmd.com/read/25973364/functional-roles-of-n-terminal-and-c-terminal-domains-in-the-overall-activity-of-a-novel-single-stranded-dna-binding-protein-of-deinococcus-radiodurans
#8
Aman K Ujaoney, Bhakti Basu, K Muniyappa, Shree K Apte
Single-stranded DNA binding protein (Ssb) of Deinococcus radiodurans comprises N- and C-terminal oligonucleotide/oligosaccharide binding (OB) folds connected by a beta hairpin connector. To assign functional roles to the individual OB folds, we generated three Ssb variants: SsbN (N-terminal without connector), SsbNC (N-terminal with connector) and SsbC (C-terminal), each harboring one OB fold. Both SsbN and SsbNC displayed weak single-stranded DNA (ssDNA) binding activity, compared to the full-length Ssb (SsbFL)...
2015: FEBS Open Bio
https://www.readbyqxmd.com/read/25711531/assays-for-the-determination-of-the-activity-of-dna-nucleases-based-on-the-fluorometric-properties-of-the-yoyo-dye
#9
Mónica Fernández-Sierra, Edwin Quiñones
Here we characterize the fluorescence of the YOYO dye as a tool for studying DNA-protein interactions in real time and present two continuous YOYO-based assays for sensitively monitoring the kinetics of DNA digestion by λ-exonuclease and the endonuclease EcoRV. The described assays rely on the different fluorescence intensities between single- and double-stranded DNA-YOYO complexes, allowing straightforward determination of nuclease activity and quantitative determination of reaction products. The assays were also employed to assess the effect of single-stranded DNA-binding proteins on the λ-exonuclease reaction kinetics, showing that the extreme thermostable single-stranded DNA-binding protein (ET-SSB) significantly reduced the reaction rate, while the recombination protein A (RecA) displayed no effect...
March 15, 2015: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/25411316/recq-helicase-and-recj-nuclease-provide-complementary-functions-to-resect-dna-for-homologous-recombination
#10
Katsumi Morimatsu, Stephen C Kowalczykowski
Recombinational DNA repair by the RecF pathway of Escherichia coli requires the coordinated activities of RecA, RecFOR, RecQ, RecJ, and single-strand DNA binding (SSB) proteins. These proteins facilitate formation of homologously paired joint molecules between linear double-stranded (dsDNA) and supercoiled DNA. Repair starts with resection of the broken dsDNA by RecQ, a 3'→5' helicase, RecJ, a 5'→3' exonuclease, and SSB protein. The ends of a dsDNA break can be blunt-ended, or they may possess either 5'- or 3'-single-stranded DNA (ssDNA) overhangs of undefined length...
December 2, 2014: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/25138217/regression-of-replication-forks-stalled-by-leading-strand-template-damage-ii-regression-by-reca-is-inhibited-by-ssb
#11
Sankalp Gupta, Joseph T P Yeeles, Kenneth J Marians
Stalled replication forks are sites of chromosome breakage and the formation of toxic recombination intermediates that undermine genomic stability. Thus, replication fork repair and reactivation are essential processes. Among the many models of replication fork reactivation is one that invokes fork regression catalyzed by the strand exchange protein RecA as an intermediate in the processing of the stalled fork. We have investigated the replication fork regression activity of RecA using a reconstituted DNA replication system where the replisome is stalled by collision with leading-strand template damage...
October 10, 2014: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/25083707/phage-orf-family-recombinases-conservation-of-activities-and-involvement-of-the-central-channel-in-dna-binding
#12
Fiona A Curtis, Ali D Malay, Alexander J Trotter, Lindsay A Wilson, Michael M H Barradell-Black, Laura Y Bowers, Patricia Reed, Christopher R T Hillyar, Robert P Yeo, John M Sanderson, Jonathan G Heddle, Gary J Sharples
Genetic and biochemical evidence suggests that λ Orf is a recombination mediator, promoting nucleation of either bacterial RecA or phage Redβ recombinases onto single-stranded DNA (ssDNA) bound by SSB protein. We have identified a diverse family of Orf proteins that includes representatives implicated in DNA base flipping and those fused to an HNH endonuclease domain. To confirm a functional relationship with the Orf family, a distantly-related homolog, YbcN, from Escherichia coli cryptic prophage DLP12 was purified and characterized...
2014: PloS One
https://www.readbyqxmd.com/read/24891441/reco-and-recr-are-necessary-for-reca-loading-in-response-to-dna-damage-and-replication-fork-stress
#13
Justin S Lenhart, Eileen R Brandes, Jeremy W Schroeder, Roderick J Sorenson, Hollis D Showalter, Lyle A Simmons
RecA is central to maintaining genome integrity in bacterial cells. Despite the near-ubiquitous conservation of RecA in eubacteria, the pathways that facilitate RecA loading and repair center assembly have remained poorly understood in Bacillus subtilis. Here, we show that RecA rapidly colocalizes with the DNA polymerase complex (replisome) immediately following DNA damage or damage-independent replication fork arrest. In Escherichia coli, the RecFOR and RecBCD pathways serve to load RecA and the choice between these two pathways depends on the type of damage under repair...
August 2014: Journal of Bacteriology
https://www.readbyqxmd.com/read/24681881/the-key-residue-for-ssb-reco-interaction-is-dispensable-for-deinococcus-radiodurans-dna-repair-in-vivo
#14
Kaiying Cheng, Xin Xu, Ye Zhao, Liangyan Wang, Guangzhi Xu, Yuejin Hua
The RecFOR DNA repair pathway is one of the major RecA-dependent recombinatorial repair pathways in bacteria and plays an important role in double-strand breaks repair. RecO, one of the major recombination mediator proteins in the RecFOR pathway, has been shown to assist RecA loading onto single-stranded binding protein (SSB) coated single-stranded DNA (ssDNA). However, it has not been characterized whether the protein-protein interaction between RecO and SSB contributes to that process in vivo. Here, we identified the residue arginine-121 of Deinococcus radiodurans RecO (drRecO-R121) as the key residue for RecO-SSB interaction...
May 2014: Acta Biochimica et Biophysica Sinica
https://www.readbyqxmd.com/read/24307635/comparative-proteomics-reveals-key-proteins-recruited-at-the-nucleoid-of-deinococcus-after-irradiation-induced-dna-damage
#15
COMPARATIVE STUDY
Claire Bouthier de la Tour, Fanny Marie Passot, Magali Toueille, Boris Mirabella, Philippe Guérin, Laurence Blanchard, Pascale Servant, Arjan de Groot, Suzanne Sommer, Jean Armengaud
The nucleoids of radiation-resistant Deinococcus species show a high degree of compaction maintained after ionizing irradiation. We identified proteins recruited after irradiation in nucleoids of Deinococcus radiodurans and Deinococcus deserti by means of comparative proteomics. Proteins in nucleoid-enriched fractions from unirradiated and irradiated Deinococcus were identified and semiquantified by shotgun proteomics. The ssDNA-binding protein SSB, DNA gyrase subunits GyrA and GyrB, DNA topoisomerase I, RecA recombinase, UvrA excinuclease, RecQ helicase, DdrA, DdrB, and DdrD proteins were found in significantly higher amounts in irradiated nucleoids of both Deinococcus species...
December 2013: Proteomics
https://www.readbyqxmd.com/read/24296671/the-integron-integrase-efficiently-prevents-the-melting-effect-of-escherichia-coli-single-stranded-dna-binding-protein-on-folded-attc-sites
#16
Céline Loot, Vincent Parissi, José Antonio Escudero, Jihane Amarir-Bouhram, David Bikard, Didier Mazel
Integrons play a major role in the dissemination of antibiotic resistance genes among bacteria. Rearrangement of gene cassettes occurs by recombination between attI and attC sites, catalyzed by the integron integrase. Integron recombination uses an unconventional mechanism involving a folded single-stranded attC site. This site could be a target for several host factors and more precisely for proteins able to bind single-stranded DNA. One of these, Escherichia coli single-stranded DNA-binding protein (SSB), regulates many DNA processes...
February 2014: Journal of Bacteriology
https://www.readbyqxmd.com/read/24124995/kinetics-of-presynaptic-filament-assembly-in-the-presence-of-single-stranded-dna-binding-protein-and-recombination-mediator-protein
#17
Jie Liu, Christopher L Berger, Scott W Morrical
Enzymes of the RecA/Rad51 family catalyze DNA strand exchange reactions that are important for homologous recombination and for the accurate repair of DNA double-strand breaks. RecA/Rad51 recombinases are activated by their assembly into presynaptic filaments on single-stranded DNA (ssDNA), a process that is regulated by ssDNA binding protein (SSB) and mediator proteins. Mediator proteins stimulate strand exchange by accelerating the rate-limiting displacement of SSB from ssDNA by the incoming recombinase. The use of mediators is a highly conserved strategy in recombination, but the precise mechanism of mediator activity is unknown...
November 12, 2013: Biochemistry
https://www.readbyqxmd.com/read/23808153/-enzymatic-control-of-homologous-recombination-in-escherichia-coli-cells-and-hyper-recombination
#18
REVIEW
I V Bakhlanova, A V Dudkina, D M Baĭtin
The RecA protein is a major enzyme of homologous recombination in bacterial cell. Forming a right-handed helical filament on ssDNA, it provides a homology search between two DNA molecules and homologous strand exchange. The RecA protein not only defends the cell from exposure to ionizing radiation and UV-irradiation, but also ensures the recombination process in the course of normal cell growth. A number of wild-type or mutant RecA proteins demonstrate increased recombinogenic properties in vitro and in vivo as compared with the wild-type RecA protein from Escherichia coli, which leads to hyper-recombination...
March 2013: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/23779106/bacillus-subtilis-dpra-recruits-reca-onto-single-stranded-dna-and-mediates-annealing-of-complementary-strands-coated-by-ssbb-and-ssba
#19
Tribhuwan Yadav, Begoña Carrasco, James Hejna, Yuki Suzuki, Kunio Takeyasu, Juan C Alonso
Naturally transformable bacteria recombine internalized ssDNA with a homologous resident duplex (chromosomal transformation) or complementary internalized ssDNAs (plasmid or viral transformation). Bacillus subtilis competence-induced DprA, RecA, SsbB, and SsbA proteins are involved in the early processing of the internalized ssDNA, with DprA physically interacting with RecA. SsbB and SsbA bind and melt secondary structures in ssDNA but limit RecA loading onto ssDNA. DprA binds to ssDNA and facilitates partial dislodging of both single-stranded binding (SSB) proteins from ssDNA...
August 2, 2013: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/23631919/opposing-roles-for-two-molecular-forms-of-replication-protein-a-in-rad51-rad54-mediated-dna-recombination-in-plasmodium-falciparum
#20
Anusha M Gopalakrishnan, Nirbhay Kumar
UNLABELLED: The bacterial RecA protein and its eukaryotic homologue Rad51 play a central role in the homologous DNA strand exchange reaction during recombination and DNA repair. Previously, our lab has shown that PfRad51, the Plasmodium falciparum homologue of Rad51, exhibited ATPase activity and promoted DNA strand exchange in vitro. In this study, we evaluated the catalytic functions of PfRad51 in the presence of putative interacting partners, especially P. falciparum homologues of Rad54 and replication protein A...
2013: MBio
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