Genomes and Genes
rec a recombinases
Summary: A family of recombinases initially identified in BACTERIA. They catalyze the ATP-driven exchange of DNA strands in GENETIC RECOMBINATION. The product of the reaction consists of a duplex and a displaced single-stranded loop, which has the shape of the letter D and is therefore called a D-loop structure.
- Danilowicz C, Feinstein E, Conover A, Coljee V, Vlassakis J, Chan Y, et al. RecA homology search is promoted by mechanical stress along the scanned duplex DNA. Nucleic Acids Res. 2012;40:1717-27 pubmed publisher..The stress resulting from different levels of tension on its constitutive strands causes rapid dsDNA unbinding unless sufficient homology is present. ..
- Zhang A, Pigli Y, Rice P. Structure of the LexA-DNA complex and implications for SOS box measurement. Nature. 2010;466:883-6 pubmed publisher..However, the wings of these two DNA-binding domains bind to the same minor groove of the DNA. These wing-wing contacts may explain why the spacing between the two half-sites of E. coli SOS boxes is invariant. ..
- Ayora S, Carrasco B, Cardenas P, César C, Cañas C, Yadav T, et al. Double-strand break repair in bacteria: a view from Bacillus subtilis. FEMS Microbiol Rev. 2011;35:1055-81 pubmed publisher..In this review, we examine the functions that are known to contribute to DNA DSB repair in B. subtilis, and compare their properties with those of other bacterial phyla. ..
- Cardenas P, Carrasco B, Defeu Soufo C, César C, Herr K, Kaufenstein M, et al. RecX facilitates homologous recombination by modulating RecA activities. PLoS Genet. 2012;8:e1003126 pubmed publisher..RecX, by modulating the "length or packing" of a RecA filament, facilitates the initiation of recombination and increases recombination across species. ..
- Long J, Renzette N, Centore R, Sandler S. Differential requirements of two recA mutants for constitutive SOS expression in Escherichia coli K-12. PLoS ONE. 2008;3:e4100 pubmed publisher..RecFOR regulate the activity of RecX to destabilize the RecA filament. RecA730 causes SOS(C) expression by binding to ssDNA in a mechanism yet to be determined. ..
- Sakai A, Cox M. RecFOR and RecOR as distinct RecA loading pathways. J Biol Chem. 2009;284:3264-72 pubmed publisher..The RecOR pathway is more efficient for RecA loading onto ssDNA when no proximal dsDNA is available. A merger of new and published results leads to a new model for RecFOR function. ..
- Gruenig M, Renzette N, Long E, Chitteni Pattu S, Inman R, Cox M, et al. RecA-mediated SOS induction requires an extended filament conformation but no ATP hydrolysis. Mol Microbiol. 2008;69:1165-79 pubmed publisher..The RecA E38K/K72R protein represents an improved reagent for studies of the function of ATP hydrolysis by RecA in vivo and in vitro. ..
- van der Veen S, Abee T. Contribution of Listeria monocytogenes RecA to acid and bile survival and invasion of human intestinal Caco-2 cells. Int J Med Microbiol. 2011;301:334-40 pubmed publisher..This mutant also showed a deficiency in adhesion and invasion of Caco-2 cells. These results suggest that RecA may contribute to the colonization of the human gastro-intestinal tract and crossing of the intestinal barrier...
- Feinstein E, Danilowicz C, Conover A, Gunaratne R, Kleckner N, Prentiss M. Single-molecule studies of the stringency factors and rates governing the polymerization of RecA on double-stranded DNA. Nucleic Acids Res. 2011;39:3781-91 pubmed publisher..We propose that force reduces the off-rate for nucleation site binding and that nucleation site stability is the stringency factor that prevents in vivo polymerization. ..
- Britt R, Chitteni Pattu S, Page A, Cox M. RecA K72R filament formation defects reveal an oligomeric RecA species involved in filament extension. J Biol Chem. 2011;286:7830-40 pubmed publisher..Thus, RecA K72R inhibits hydrolysis-proficient RecA proteins by interacting with them in solution and preventing the extension phase of filament assembly. ..
- Butala M, Klose D, Hodnik V, Rems A, Podlesek Z, Klare J, et al. Interconversion between bound and free conformations of LexA orchestrates the bacterial SOS response. Nucleic Acids Res. 2011;39:6546-57 pubmed publisher..We show that, while LexA exhibits diverse dissociation rates from operators, it interacts extremely rapidly with DNA target sites. Modulation of LexA activity changes the occurrence of persister cells in bacterial populations. ..
- Fan H, Cox M, Li H. Developing single-molecule TPM experiments for direct observation of successful RecA-mediated strand exchange reaction. PLoS ONE. 2011;6:e21359 pubmed publisher..In addition, the Brownian motion time-courses suggest that the strand exchange process progresses uni-directionally in the 5'-to-3' fashion, using a synapse segment with a wide and continuous size distribution. ..
- Wang Y, Huang Y, Xue C, He Y, He Z. ClpR protein-like regulator specifically recognizes RecA protein-independent promoter motif and broadly regulates expression of DNA damage-inducible genes in mycobacteria. J Biol Chem. 2011;286:31159-67 pubmed publisher..These results enhance our understanding of the function of the ClpR regulator and the regulatory mechanism of RecA-independent DNA repair in mycobacteria. ..
- Patel M, Jiang Q, Woodgate R, Cox M, Goodman M. A new model for SOS-induced mutagenesis: how RecA protein activates DNA polymerase V. Crit Rev Biochem Mol Biol. 2010;45:171-84 pubmed publisher..Based on unforeseen properties of RecA*, we describe a new model for pol V-catalyzed SOS-induced mutagenesis. ..
- Indiani C, Patel M, Goodman M, O Donnell M. RecA acts as a switch to regulate polymerase occupancy in a moving replication fork. Proc Natl Acad Sci U S A. 2013;110:5410-5 pubmed publisher..In sharp contrast, RecA severely inhibits the Pol III replisome. Given the opposite effects of RecA on Pol III and TLS replisomes, we propose that RecA acts as a switch to regulate the occupancy of polymerases within a moving replisome...
- Roy R, Kozlov A, Lohman T, Ha T. SSB protein diffusion on single-stranded DNA stimulates RecA filament formation. Nature. 2009;461:1092-7 pubmed publisher..This observation of diffusional movement of a protein on ssDNA introduces a new model for how an SSB protein can be redistributed, while remaining tightly bound to ssDNA during recombination and repair processes. ..
- Gaasbeek E, van der Wal F, van Putten J, de Boer P, van der Graaf van Bloois L, de Boer A, et al. Functional characterization of excision repair and RecA-dependent recombinational DNA repair in Campylobacter jejuni. J Bacteriol. 2009;191:3785-93 pubmed publisher..jejuni and may contribute to the genetic heterogeneity of the C. jejuni population...
- Inagaki S, Matsumoto Nakano M, Fujita K, Nagayama K, Funao J, Ooshima T. Effects of recombinase A deficiency on biofilm formation by Streptococcus mutans. Oral Microbiol Immunol. 2009;24:104-8 pubmed publisher..These results suggest that RecA has a relationship with biofilm formation. ..
- Jeong K, Hung K, Baumler D, Byrd J, Kaspar C. Acid stress damage of DNA is prevented by Dps binding in Escherichia coli O157:H7. BMC Microbiol. 2008;8:181 pubmed publisher..Further investigation into the precise interplay between DNA protection and damage repair pathways during acid stress are underway to gain additional insight. ..
- Crismani W, Portemer V, Froger N, Chelysheva L, Horlow C, Vrielynck N, et al. MCM8 is required for a pathway of meiotic double-strand break repair independent of DMC1 in Arabidopsis thaliana. PLoS Genet. 2013;9:e1003165 pubmed publisher..We propose that MCM8 is involved with RAD51 in a backup pathway that repairs meiotic DSB without giving CO when the major pathway, which relies on DMC1, fails. ..
- Fagerburg M, Schauer G, Thickman K, Bianco P, Khan S, Leuba S, et al. PcrA-mediated disruption of RecA nucleoprotein filaments--essential role of the ATPase activity of RecA. Nucleic Acids Res. 2012;40:8416-24 pubmed..Our findings demonstrate that translocation of PcrA is not sufficient to displace RecA from the DNA and assigns an essential role for the ATPase activity of RecA in helicase-mediated disruption of its filaments. ..
- Kurzbauer M, Uanschou C, Chen D, Schlögelhofer P. The recombinases DMC1 and RAD51 are functionally and spatially separated during meiosis in Arabidopsis. Plant Cell. 2012;24:2058-70 pubmed publisher..Taken together, these results demonstrate that DMC1 functions independently and spatially separated from RAD51 during meiosis and that ATR is an integral part of the regular meiotic program. ..
- Amundsen S, Fero J, Hansen L, Cromie G, Solnick J, Smith G, et al. Helicobacter pylori AddAB helicase-nuclease and RecA promote recombination-related DNA repair and survival during stomach colonization. Mol Microbiol. 2008;69:994-1007 pubmed publisher..Our results reveal requirements for double-strand break repair and recombination during both acute and chronic phases of H. pylori stomach infection...
- Yadav T, Carrasco B, Myers A, George N, Keck J, Alonso J. Genetic recombination in Bacillus subtilis: a division of labor between two single-strand DNA-binding proteins. Nucleic Acids Res. 2012;40:5546-59 pubmed publisher..Our results provide a mechanistic framework for rationalizing the coordinated events modulated by SsbA, SsbB and RecO that are crucial for RecA-dependent chromosomal transformation and RecA-independent plasmid transformation. ..
- Singh P, Patil K, Khanduja J, Kumar P, Williams A, Rossi F, et al. Mycobacterium tuberculosis UvrD1 and UvrA proteins suppress DNA strand exchange promoted by cognate and noncognate RecA proteins. Biochemistry. 2010;49:4872-83 pubmed publisher..These observations are consistent with a molecular mechanism, whereby M. tuberculosis UvrA and UvrD1, acting together, block DNA strand exchange promoted by cognate and noncognate RecA proteins...
- Peterson E, Janzen W, Kireev D, Singleton S. High-throughput screening for RecA inhibitors using a transcreener adenosine 5'-O-diphosphate assay. Assay Drug Dev Technol. 2012;10:260-8 pubmed publisher..This set of compounds comprises previously unidentified scaffolds for RecA inhibition and represents tractable hit structures for efforts aimed at tuning RecA inhibitory activity in both biochemical and bacteriological assays. ..
- Haldenby S, White M, Allers T. RecA family proteins in archaea: RadA and its cousins. Biochem Soc Trans. 2009;37:102-7 pubmed publisher..On the basis of phylogenetic analysis, we propose that a family of archaeal proteins with a single RecA domain, which are currently annotated as KaiC, be renamed aRadC. ..
- Gruenig M, Lu D, Won S, Dulberger C, Manlick A, Keck J, et al. Creating directed double-strand breaks with the Ref protein: a novel RecA-dependent nuclease from bacteriophage P1. J Biol Chem. 2011;286:8240-51 pubmed publisher..We propose that enhancement of recombination by Ref reflects the introduction of directed, recombinogenic double-strand breaks...
- Khan S, Kuzminov A. Replication forks stalled at ultraviolet lesions are rescued via RecA and RuvABC protein-catalyzed disintegration in Escherichia coli. J Biol Chem. 2012;287:6250-65 pubmed publisher..Thus, chromosomes fragment when replication forks stall at UV lesions and regress, generating Holliday junctions. Remarkably, cells specifically utilize fork breakage to rescue stalled replication and avoid lethality. ..
- Petrova V, Chitteni Pattu S, Drees J, Inman R, Cox M. An SOS inhibitor that binds to free RecA protein: the PsiB protein. Mol Cell. 2009;36:121-30 pubmed publisher..However, PsiB binds to RecA protein that is free in solution. The RecA-PsiB complex impedes formation of RecA nucleoprotein filaments on DNA. ..
- Ragunathan K, Joo C, Ha T. Real-time observation of strand exchange reaction with high spatiotemporal resolution. Structure. 2011;19:1064-73 pubmed publisher..This finding could have important implications for the irreversibility of strand exchange. Our model for strand exchange links structural models of RecA to its catalytic function. ..
- Manfredi C, Carrasco B, Ayora S, Alonso J. Bacillus subtilis RecO nucleates RecA onto SsbA-coated single-stranded DNA. J Biol Chem. 2008;283:24837-47 pubmed publisher..We herein discuss the possible mechanisms of RecO involvement in the regulation of double strand break repair and genetic transformation. ..
- Seeliger K, Dukowic Schulze S, Wurz Wildersinn R, Pacher M, Puchta H. BRCA2 is a mediator of RAD51- and DMC1-facilitated homologous recombination in Arabidopsis thaliana. New Phytol. 2012;193:364-75 pubmed publisher..We further show that AtBRCA2 is required for proper meiotic synapsis and mediates the recruitment of AtRAD51 and AtDMC1. Our results suggest that BRCA2 controls single-strand invasion steps during homologous recombination in plants. ..
- Phue J, Lee S, Trinh L, Shiloach J. Modified Escherichia coli B (BL21), a superior producer of plasmid DNA compared with Escherichia coli K (DH5alpha). Biotechnol Bioeng. 2008;101:831-6 pubmed publisher..The produced plasmid, which was constructed for HIV clinical study, was found to have identical properties to the plasmid currently produced by E. coli DH5alpha. ..
- Quevillon Cheruel S, Campo N, Mirouze N, Mortier Barrière I, Brooks M, Boudes M, et al. Structure-function analysis of pneumococcal DprA protein reveals that dimerization is crucial for loading RecA recombinase onto DNA during transformation. Proc Natl Acad Sci U S A. 2012;109:E2466-75 pubmed publisher..We propose a model in which RecA interaction promotes rearrangement or disruption of the DprA dimer, enabling the subsequent nucleation of RecA and its polymerization onto ssDNA. ..
- Peacock Villada A, Yang D, Danilowicz C, Feinstein E, Pollock N, McShan S, et al. Complementary strand relocation may play vital roles in RecA-based homology recognition. Nucleic Acids Res. 2012;40:10441-51 pubmed publisher..This differential extension drives strand exchange forward for homologs and increases the free energy penalty for strand exchange of non-homologs. ..
- Carrasco B, Manfredi C, Ayora S, Alonso J. Bacillus subtilis SsbA and dATP regulate RecA nucleation onto single-stranded DNA. DNA Repair (Amst). 2008;7:990-6 pubmed publisher..We propose that dATP binding and hydrolysis as well as SsbA provide different levels of regulation of the dynamic RecA nucleoprotein filament. ..
- Wu D, Wu M, Halpern A, Rusch D, Yooseph S, Frazier M, et al. Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees. PLoS ONE. 2011;6:e18011 pubmed publisher..If there exist any major, but so-far-undiscovered, deeply branching lineages in the tree of life, we suggest that methods such as those described herein currently offer the best way to search for them. ..
- Britt R, Haruta N, Lusetti S, Chitteni Pattu S, Inman R, Cox M. Disassembly of Escherichia coli RecA E38K/DeltaC17 nucleoprotein filaments is required to complete DNA strand exchange. J Biol Chem. 2010;285:3211-26 pubmed publisher..A requirement for RecA filament disassembly in DNA strand exchange has a variety of ramifications for the current models linking ATP hydrolysis to DNA strand exchange. ..
- Gruenig M, Stohl E, Chitteni Pattu S, Seifert H, Cox M. Less is more: Neisseria gonorrhoeae RecX protein stimulates recombination by inhibiting RecA. J Biol Chem. 2010;285:37188-97 pubmed publisher..Thus, in N. gonorrhoeae, recombinational processes are facilitated by RecX(Ng) protein-mediated limitations on RecA(Ng) filament presence and/or length to achieve maximal function...
- Masuda T, Ito Y, Terada T, Shibata T, Mikawa T. A non-canonical DNA structure enables homologous recombination in various genetic systems. J Biol Chem. 2009;284:30230-9 pubmed publisher..Thus, HP includes the common non-canonical DNA structure and uses a common core mechanism, independent of the species of HP proteins. We discuss the significance of multiple types of HP proteins. ..
- Krishnamurthy M, Tadesse S, Rothmaier K, Graumann P. A novel SMC-like protein, SbcE (YhaN), is involved in DNA double-strand break repair and competence in Bacillus subtilis. Nucleic Acids Res. 2010;38:455-66 pubmed publisher..In agreement with this idea, we found that RecN-YFP damage-induced assemblies also arise in the absence of ongoing replication. ..
- Handa N, Amitani I, Gumlaw N, Sandler S, Kowalczykowski S. Single molecule analysis of a red fluorescent RecA protein reveals a defect in nucleoprotein filament nucleation that relates to its reduced biological functions. J Biol Chem. 2009;284:18664-73 pubmed publisher..Thus, RecA-RFP reveals that its attenuated biological functions correlate with a reduced frequency of nucleoprotein filament nucleation at the single molecule level. ..
- Savir Y, Tlusty T. RecA-mediated homology search as a nearly optimal signal detection system. Mol Cell. 2010;40:388-96 pubmed publisher..Our analysis suggests a possible role for DNA extension by RecA, in which deformation enhances detection. The present signal detection approach provides a general recipe for testing the optimality of other molecular recognition systems. ..
- Galkin V, Yu X, Bielnicki J, Ndjonka D, Bell C, Egelman E. Cleavage of bacteriophage lambda cI repressor involves the RecA C-terminal domain. J Mol Biol. 2009;385:779-87 pubmed publisher..These observations provide a framework for understanding previous genetic and biochemical observations. ..
- Adikesavan A, Katsonis P, Marciano D, Lua R, Herman C, Lichtarge O. Separation of recombination and SOS response in Escherichia coli RecA suggests LexA interaction sites. PLoS Genet. 2011;7:e1002244 pubmed publisher..These new sites can provide new drug targets to modulate one or more RecA functions, with the potential to address the problem of evolution of antibiotic resistance at its root. ..
- Cardenas P, Carzaniga T, Zangrossi S, Briani F, Garcia Tirado E, Dehò G, et al. Polynucleotide phosphorylase exonuclease and polymerase activities on single-stranded DNA ends are modulated by RecN, SsbA and RecA proteins. Nucleic Acids Res. 2011;39:9250-61 pubmed publisher..subtilis PNPase might also contribute to repair via NHEJ. ..
- Lee C, Wang T. The N-terminal domain of Escherichia coli RecA have multiple functions in promoting homologous recombination. J Biomed Sci. 2009;16:37 pubmed publisher..A two-step model is proposed to explain how a RecA-ssDNA presynaptic nucleoprotein filament interacts with donor dsDNA. ..
- van Loenhout M, van der Heijden T, Kanaar R, Wyman C, Dekker C. Dynamics of RecA filaments on single-stranded DNA. Nucleic Acids Res. 2009;37:4089-99 pubmed publisher..Taken together, our results demonstrate that ATP hydrolysis has a major influence on the structure and state of RecA filaments on ssDNA. ..
- Mani A, Braslavsky I, Arbel Goren R, Stavans J. Caught in the act: the lifetime of synaptic intermediates during the search for homology on DNA. Nucleic Acids Res. 2010;38:2036-43 pubmed publisher..These results suggest the need for facilitated homology search mechanisms to locate homology successfully within the timescales observed in vivo. ..
- Pages V, Mazon G, Naiman K, Philippin G, Fuchs R. Monitoring bypass of single replication-blocking lesions by damage avoidance in the Escherichia coli chromosome. Nucleic Acids Res. 2012;40:9036-43 pubmed publisher..With this novel assay, we show that in Escherichia coli DA events massively outweigh TLS events and that in contrast to plasmid, chromosome-borne lesions partially require RecA for tolerance. ..
- Morimatsu K, Wu Y, Kowalczykowski S. RecFOR proteins target RecA protein to a DNA gap with either DNA or RNA at the 5' terminus: implication for repair of stalled replication forks. J Biol Chem. 2012;287:35621-30 pubmed publisher..RecFOR proteins also recognize RNA at the 5'-end of an RNA-DNA junction within an ssDNA gap, which is compatible with their role in the repair of lagging strand gaps at stalled replication forks. ..
- Ragone S, Maman J, Furnham N, Pellegrini L. Structural basis for inhibition of homologous recombination by the RecX protein. EMBO J. 2008;27:2259-69 pubmed publisher..Collectively, our data support a model in which RecX binding to the helical groove of the filament causes local dissociation of RecA protomers, leading to filament destabilisation and HR inhibition. ..
- Butala M, Zgur Bertok D, Busby S. The bacterial LexA transcriptional repressor. Cell Mol Life Sci. 2009;66:82-93 pubmed publisher..These may provide new starting points in the battle against the emergence of bacterial pathogens and the spread of drug resistance among them. ..
- Galkin V, Britt R, Bane L, Yu X, Cox M, Egelman E. Two modes of binding of DinI to RecA filament provide a new insight into the regulation of SOS response by DinI protein. J Mol Biol. 2011;408:815-24 pubmed publisher..Polymorphic binding of DinI to RecA filaments implies an even more complex role of DinI in the bacterial SOS response. ..