Artykuły w czasopismach: „RecR”

1

Sawitzke, J. A., i F. W. Stahl. "Phage lambda has an analog of Escherichia coli recO, recR and recF genes." Genetics 130, nr 1 (1.01.1992): 7–16. http://dx.doi.org/10.1093/genetics/130.1.7.

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Abstract The RecF pathway catalyzes generalized recombination in Escherichia coli that is mutant for recBC, sbcB and sbcC. This pathway operating on conjugational recombination requires the recA, recF, recJ, recN, recO, recQ, recR, ruvA, ruvB and ruvC genes. In contrast, lambda mutant for its own recombination genes, int, red alpha and red beta, requires only the recA and recJ genes to recombine efficiently in recBC sbcB sbcC cells. Deletion of an open reading frame in the ninR region of lambda results in an additional requirement for recO, recR and recF in order to recombine in recBC sbcB sbcC mutant cells. This function, designated orf for recO-, recR- and recF-like function, is largely RecF pathway specific.

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Shiraishi, Kouya, Katsuhiro Hanada, Yoichiro Iwakura i Hideo Ikeda. "Roles of RecJ, RecO, and RecR in RecET-Mediated Illegitimate Recombination in Escherichia coli". Journal of Bacteriology 184, nr 17 (1.09.2002): 4715–21. http://dx.doi.org/10.1128/jb.184.17.4715-4721.2002.

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ABSTRACT We analyzed effects of overexpression of RecE and RecT on illegitimate recombination during prophage induction in Escherichia coli and found that frequencies of spontaneous and UV-induced illegitimate recombination are enhanced by coexpression of RecE and RecT in the wild type, but the enhanced recombination was reduced by recJ, recO, or recR mutation. The results indicated that RecET-mediated illegitimate recombination depends on the functions of RecJ, RecO, and RecR, suggesting that the RecE and RecJ exonucleases play different roles in this recombination pathway and that the RecO and RecR proteins also play important roles in the recombination. On the other hand, the frequency of the RecET-mediated illegitimate recombination was enhanced by a recQ mutation, implying that the RecQ protein plays a role in suppression of RecET-mediated illegitimate recombination. It was also found that RecET-mediated illegitimate recombination is independent of the RecA function with UV irradiation, but it is enhanced by the recA mutation without UV irradiation. Based on these results, we propose a model for the roles of RecJOR on RecET-mediated illegitimate recombination.

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3

Luisi-DeLuca, C., S. T. Lovett i R. D. Kolodner. "Genetic and physical analysis of plasmid recombination in recB recC sbcB and recB recC sbcA Escherichia coli K-12 mutants." Genetics 122, nr 2 (1.06.1989): 269–78. http://dx.doi.org/10.1093/genetics/122.2.269.

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Abstract The effect of mutations in known recombination genes (recA, recB, recC, recE, recF, recJ, recN, recO, recQ and ruv) on intramolecular recombination of plasmids was studied in recB recC sbcB and recB recC sbcA Escherichia coli mutants. The rate of recombination of circular dimer plasmids was at least 1000-fold higher in recB recC sbcB or recB recC sbcA mutants as compared to wild-type cells. The rate was decreased by mutations in recA, recF, recJ, recO, ruv or mutS in recB recC sbcB mutants, and by mutations in recE, recN, recO, recQ, ruv or mutS in recB recC sbcA mutants. In addition to measuring the recombination rate of circular dimer plasmids, the recombination-mediated transformation of linear dimer plasmids was also studied. Linear dimer plasmids transformed recB recC sbcB and recB recC sbcA mutants 20- to 40-fold more efficiently than wild-type cells. The transformation efficiency of linear dimer plasmids in recB recC sbcB mutants was decreased by mutations in recA, recF, recJ, recO, recQ or lexA (lexA3). In recB recC sbcA mutants the transformation efficiency of linear dimers was decreased only by a recE mutation. Physical analysis of linear dimer- or circular dimer-transformed recB recC sbcB mutants revealed that all transformants contained recombinant monomer genotypes. This suggests that recombination in recB recC sbcB cells is very efficient.

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4

Lovett, S. T., C. Luisi-DeLuca i R. D. Kolodner. "The genetic dependence of recombination in recD mutants of Escherichia coli." Genetics 120, nr 1 (1.09.1988): 37–45. http://dx.doi.org/10.1093/genetics/120.1.37.

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Abstract RecBCD enzyme has multiple activities including helicase, exonuclease and endonuclease activities. Mutations in the genes recB or recC, encoding two subunits of the enzyme, reduce the frequency of many types of recombinational events. Mutations in recD, encoding the third subunit, do not reduce recombination even though most of the activities of the RecBCD enzyme are severely reduced. In this study, the genetic dependence of different types of recombination in recD mutants has been investigated. The effects of mutations in genes in the RecBCD pathway (recA and recC) as well as the genes specific for the RecF pathway (recF, recJ, recN, recO, recQ, ruv and lexA) were tested on conjugational, transductional and plasmid recombination, and on UV survival. recD mutants were hyper-recombinogenic for all the monitored recombination events, especially those involving plasmids, and all recombination events in recD strains required recA and recC. In addition, unlike recD+ strains, chromosomal recombination events and the repair of UV damage to DNA in recD strains were dependent on one RecF pathway gene, recJ. Only a subset of the tested recombination events were affected by ruv, recN, recQ, recO and lexA mutations.

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5

Lee, Su-jin, Si Yeon Ahn, Han Byeol Oh, Seung Yeon Kim, Wan Seok Song i Sung-il Yoon. "Structural and Biochemical Analysis of the Recombination Mediator Protein RecR from Campylobacter jejuni". International Journal of Molecular Sciences 24, nr 16 (18.08.2023): 12947. http://dx.doi.org/10.3390/ijms241612947.

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The recombination mediator complex RecFOR, consisting of the RecF, RecO, and RecR proteins, is needed to initiate homologous recombination in bacteria by positioning the recombinase protein RecA on damaged DNA. Bacteria from the phylum Campylobacterota, such as the pathogen Campylobacter jejuni, lack the recF gene and trigger homologous recombination using only RecR and RecO. To elucidate the functional properties of C. jejuni RecR (cjRecR) in recombination initiation that differ from or are similar to those in RecF-expressing bacteria, we determined the crystal structure of cjRecR and performed structure-based binding analyses. cjRecR forms a rectangular ring-like tetrameric structure and coordinates a zinc ion using four cysteine residues, as observed for RecR proteins from RecF-expressing bacteria. However, the loop of RecR that has been shown to recognize RecO and RecF in RecF-expressing bacteria is substantially shorter in cjRecR as a canonical feature of Campylobacterota RecR proteins, indicating that cjRecR lost a part of the loop in evolution due to the lack of RecF and has a low RecO-binding affinity. Furthermore, cjRecR features a larger positive patch and exhibits substantially higher ssDNA-binding affinity than RecR from RecF-expressing bacteria. Our study provides a framework for a deeper understanding of the RecOR-mediated recombination pathway.

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6

Poteete, Anthony R. "Modulation of DNA Repair and Recombination by the Bacteriophage λ Orf Function in Escherichia coli K-12". Journal of Bacteriology 186, nr 9 (1.05.2004): 2699–707. http://dx.doi.org/10.1128/jb.186.9.2699-2707.2004.

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ABSTRACT The orf gene of bacteriophage λ, fused to a promoter, was placed in the galK locus of Escherichia coli K-12. Orf was found to suppress the recombination deficiency and sensitivity to UV radiation of mutants, in a Δ(recC ptr recB recD)::P tac gam bet exo pae cI ΔrecG background, lacking recF, recO, recR, ruvAB, and ruvC functions. It also suppressed defects of these mutants in establishing replication of a pSC101-related plasmid. Compared to orf, the recA803 allele had only small effects on recF, recO, and recR mutant phenotypes and no effect on a ruvAB mutant. In a fully wild-type background with respect to known recombination and repair functions, orf partially suppressed the UV sensitivity of ruvAB and ruvC mutants.

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7

Ivančić-Baće, Ivana, Petra Peharec, Sunčana Moslavac, Nikolina Škrobot, Erika Salaj-Šmic† i Krunoslav Brčić-Kostić. "RecFOR Function Is Required for DNA Repair and Recombination in a RecA Loading-Deficient recB Mutant of Escherichia coli". Genetics 163, nr 2 (1.02.2003): 485–94. http://dx.doi.org/10.1093/genetics/163.2.485.

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Abstract The RecA loading activity of the RecBCD enzyme, together with its helicase and 5′ → 3′ exonuclease activities, is essential for recombination in Escherichia coli. One particular mutant in the nuclease catalytic center of RecB, i.e., recB1080, produces an enzyme that does not have nuclease activity and is unable to load RecA protein onto single-stranded DNA. There are, however, previously published contradictory data on the recombination proficiency of this mutant. In a recF– background the recB1080 mutant is recombination deficient, whereas in a recF+ genetic background it is recombination proficient. A possible explanation for these contrasting phenotypes may be that the RecFOR system promotes RecA-single-strand DNA filament formation and replaces the RecA loading defect of the RecB1080CD enzyme. We tested this hypothesis by using three in vivo assays. We compared the recombination proficiencies of recB1080, recO, recR, and recF single mutants and recB1080 recO, recB1080 recR, and recB1080 recF double mutants. We show that RecFOR functions rescue the repair and recombination deficiency of the recB1080 mutant and that RecA loading is independent of RecFOR in the recB1080 recD double mutant where this activity is provided by the RecB1080C(D–) enzyme. According to our results as well as previous data, three essential activities for the initiation of recombination in the recB1080 mutant are provided by different proteins, i.e., helicase activity by RecB1080CD, 5′ → 3′ exonuclease by RecJ- and RecA-single-stranded DNA filament formation by RecFOR.

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8

Liu, Ying-Hsiu, Ann-Joy Cheng i Tzu-chien V. Wang. "Involvement of recF, recO, and recR Genes in UV-Radiation Mutagenesis ofEscherichia coli". Journal of Bacteriology 180, nr 7 (1.04.1998): 1766–70. http://dx.doi.org/10.1128/jb.180.7.1766-1770.1998.

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ABSTRACT The recF, recO, and recR genes were originally identified as those affecting the RecF pathway of recombination in Escherichia coli cells. Several lines of evidence suggest that the recF, recO, andrecR genes function at the same step of recombination and postreplication repair. In this work, we report that null mutations inrecF, recO, or recR greatly reduce UV-radiation mutagenesis (UVM) in an assay for reversion from a Trp− (trpE65) to a Trp+phenotypes. Introduction of the defective lexA51 mutation [lexA51(Def)] and/or UmuD′ into recF,recO, and recR mutants failed to restore normal UVM in the mutants. On the other hand, the presence ofrecA2020, a suppressor mutation for recF,recO, and recR mutations, restored normal UVM in recF, recO, and recR mutants. These results indicate an involvement of the recF,recO, and recR genes and their products in UVM, possibly by affecting the third role of RecA in UVM.

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9

Stohl, Elizabeth A., i H. Steven Seifert. "Neisseria gonorrhoeae DNA Recombination and Repair Enzymes Protect against Oxidative Damage Caused by Hydrogen Peroxide". Journal of Bacteriology 188, nr 21 (25.08.2006): 7645–51. http://dx.doi.org/10.1128/jb.00801-06.

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ABSTRACT The strict human pathogen Neisseria gonorrhoeae is exposed to oxidative damage during infection. N. gonorrhoeae has many defenses that have been demonstrated to counteract oxidative damage. However, recN is the only DNA repair and recombination gene upregulated in response to hydrogen peroxide (H2O2) by microarray analysis and subsequently shown to be important for oxidative damage protection. We therefore tested the importance of RecA and DNA recombination and repair enzymes in conferring resistance to H2O2 damage. recA mutants, as well as RecBCD (recB, recC, and recD) and RecF-like pathway mutants (recJ, recO, and recQ), all showed decreased resistance to H2O2. Holliday junction processing mutants (ruvA, ruvC, and recG) showed decreased resistance to H2O2 resistance as well. Finally, we show that RecA protein levels did not increase as a result of H2O2 treatment. We propose that RecA, recombinational DNA repair, and branch migration are all important for H2O2 resistance in N. gonorrhoeae but that constitutive levels of these enzymes are sufficient for providing protection against oxidative damage by H2O2.

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10

Marinus, M. G. "Recombination Is Essential for Viability of anEscherichia coli dam (DNA Adenine Methyltransferase) Mutant". Journal of Bacteriology 182, nr 2 (15.01.2000): 463–68. http://dx.doi.org/10.1128/jb.182.2.463-468.2000.

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ABSTRACT Double mutants of Escherichia coli dam (DNA adenine methyltransferase) strains with ruvA, ruvB, orruvC could not be constructed, whereas damderivatives with recD, recF, recJ, and recR were viable. The ruv gene products are required for Holliday junction translocation and resolution of recombination intermediates. A dam recG (Holliday junction translocation) mutant strain was isolated but at a very much lower frequency than expected. The inviability of a dam lexA(Ind−) host was abrogated by the simultaneous presence of plasmids encoding both recA and ruvAB. This result indicates that of more than 20 SOS genes, only recAand ruvAB need to be derepressed to allow fordam mutant survival. The presence of mutS ormutL mutations allowed the construction of dam lexA (Ind−) derivatives. The requirement forrecA, recB, recC, ruvA,ruvB, ruvC, and possibly recG gene expression indicates that recombination is essential for viability ofdam bacteria probably to repair DNA double-strand breaks. The effect of mutS and mutL mutations indicates that DNA mismatch repair is the ultimate source of most of these DNA breaks. The requirement for recombination also suggests an explanation for the sensitivity of dam cells to certain DNA-damaging agents.

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11

Gupta, Richa, Stewart Shuman i Michael S. Glickman. "RecF and RecR Play Critical Roles in the Homologous Recombination and Single-Strand Annealing Pathways of Mycobacteria". Journal of Bacteriology 197, nr 19 (20.07.2015): 3121–32. http://dx.doi.org/10.1128/jb.00290-15.

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ABSTRACTMycobacteria 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 ofadnABorrecOindividually causes partial impairment of HR, but loss ofadnABandrecOin combination abolishes HR. RecO, which can accelerate annealing of single-stranded DNAin vitro, also participates in the SSA pathway. The functions of RecF and RecR, which, in other model bacteria, function in concert with RecO as mediators of RecA loading, have not been examined in mycobacteria. Here, we present a genetic analysis ofrecFandrecRin mycobacterial recombination. We find that RecF, like RecO, participates in the AdnAB-independent arm of the HR pathway and in SSA. In contrast, RecR is required for all HR in mycobacteria and for SSA. The essentiality of RecR as an agent of HR is yet another distinctive feature of mycobacterial DNA repair.IMPORTANCEThis study clarifies the molecular requirements for homologous recombination in mycobacteria. Specifically, we demonstrate that RecF and RecR play important roles in both the RecA-dependent homologous recombination and RecA-independent single-strand annealing pathways. Coupled with our previous findings (R. Gupta, M. Ryzhikov, O. Koroleva, M. Unciuleac, S. Shuman, S. Korolev, and M. S. Glickman, Nucleic Acids Res 41:2284–2295, 2013,http://dx.doi.org/10.1093/nar/gks1298), these results revise our view of mycobacterial recombination and place the RecFOR system in a central position in homology-dependent DNA repair.

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12

Centore, Richard C., i Steven J. Sandler. "UvrD Limits the Number and Intensities of RecA-Green Fluorescent Protein Structures in Escherichia coli K-12". Journal of Bacteriology 189, nr 7 (26.01.2007): 2915–20. http://dx.doi.org/10.1128/jb.01777-06.

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ABSTRACT RecA is important for recombination, DNA repair, and SOS induction. In Escherichia coli, RecBCD, RecFOR, and RecJQ prepare DNA substrates onto which RecA binds. UvrD is a 3′-to-5′ helicase that participates in methyl-directed mismatch repair and nucleotide excision repair. uvrD deletion mutants are sensitive to UV irradiation, hypermutable, and hyper-rec. In vitro, UvrD can dissociate RecA from single-stranded DNA. Other experiments suggest that UvrD removes RecA from DNA where it promotes unproductive reactions. To test if UvrD limits the number and/or the size of RecA-DNA structures in vivo, an uvrD mutation was combined with recA-gfp. This recA allele allows the number of RecA structures and the amount of RecA at these structures to be assayed in living cells. uvrD mutants show a threefold increase in the number of RecA-GFP foci, and these foci are, on average, nearly twofold higher in relative intensity. The increased number of RecA-green fluorescent protein foci in the uvrD mutant is dependent on recF, recO, recR, recJ, and recQ. The increase in average relative intensity is dependent on recO and recQ. These data support an in vivo role for UvrD in removing RecA from the DNA.

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Belle, Jerilyn J., Andrew Casey, Charmain T. Courcelle i Justin Courcelle. "Inactivation of the DnaB Helicase Leads to the Collapse and Degradation of the Replication Fork: a Comparison to UV-Induced Arrest". Journal of Bacteriology 189, nr 15 (25.05.2007): 5452–62. http://dx.doi.org/10.1128/jb.00408-07.

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ABSTRACT Replication forks face a variety of structurally diverse impediments that can prevent them from completing their task. The mechanism by which cells overcome these hurdles is likely to vary depending on the nature of the obstacle and the strand in which the impediment is encountered. Both UV-induced DNA damage and thermosensitive replication proteins have been used in model systems to inhibit DNA replication and characterize the mechanism by which it recovers. In this study, we examined the molecular events that occur at replication forks following inactivation of a thermosensitive DnaB helicase and found that they are distinct from those that occur following arrest at UV-induced DNA damage. Following UV-induced DNA damage, the integrity of replication forks is maintained and protected from extensive degradation by RecA, RecF, RecO, and RecR until replication can resume. By contrast, inactivation of DnaB results in extensive degradation of the nascent and leading-strand template DNA and a loss of replication fork integrity as monitored by two-dimensional agarose gel analysis. The degradation that occurs following DnaB inactivation partially depends on several genes, including recF, recO, recR, recJ, recG, and xonA. Furthermore, the thermosensitive DnaB allele prevents UV-induced DNA degradation from occurring following arrest even at the permissive temperature, suggesting a role for DnaB prior to loading of the RecFOR proteins. We discuss these observations in relation to potential models for both UV-induced and DnaB(Ts)-mediated replication inhibition.

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14

Ryder, L., M. C. Whitby i R. G. Lloyd. "Mutation of recF, recJ, recO, recQ, or recR improves Hfr recombination in resolvase-deficient ruv recG strains of Escherichia coli." Journal of Bacteriology 176, nr 6 (1994): 1570–77. http://dx.doi.org/10.1128/jb.176.6.1570-1577.1994.

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15

Che, Shiyou, Yujing Chen, Yakun Liang, Qionglin Zhang i Mark Bartlam. "Crystal structure of RecR, a member of the RecFOR DNA-repair pathway, fromPseudomonas aeruginosaPAO1". Acta Crystallographica Section F Structural Biology Communications 74, nr 4 (22.03.2018): 222–30. http://dx.doi.org/10.1107/s2053230x18003503.

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DNA damage is usually lethal to all organisms. Homologous recombination plays an important role in the DNA damage-repair process in prokaryotic organisms. Two pathways are responsible for homologous recombination inPseudomonas aeruginosa: the RecBCD pathway and the RecFOR pathway. RecR is an important regulator in the RecFOR homologous recombination pathway inP. aeruginosa. It forms complexes with RecF and RecO that can facilitate the loading of RecA onto ssDNA in the RecFOR pathway. Here, the crystal structure of RecR fromP. aeruginosaPAO1 (PaRecR) is reported.PaRecR crystallizes in space groupP6122, with two monomers per asymmetric unit. Analytical ultracentrifugation data show thatPaRecR forms a stable dimer, but can exist as a tetramer in solution. The crystal structure shows that dimericPaRecR forms a ring-like tetramer architectureviacrystal symmetry. The presence of a ligand in the Walker B motif of one RecR subunit suggests a putative nucleotide-binding site.

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Ivančić-Baće, Ivana, Erika Salaj-Šmic i Krunoslav Brčić-Kostić. "Effects of recJ, recQ, and recFOR Mutations on Recombination in Nuclease-Deficient recB recD Double Mutants of Escherichia coli". Journal of Bacteriology 187, nr 4 (15.02.2005): 1350–56. http://dx.doi.org/10.1128/jb.187.4.1350-1356.2005.

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ABSTRACT The two main recombination pathways in Escherichia coli (RecBCD and RecF) have different recombination machineries that act independently in the initiation of recombination. Three essential enzymatic activities are required for early recombinational processing of double-stranded DNA ends and breaks: a helicase, a 5′→3′ exonuclease, and loading of RecA protein onto single-stranded DNA tails. The RecBCD enzyme performs all of these activities, whereas the recombination machinery of the RecF pathway consists of RecQ (helicase), RecJ (5′→3′ exonuclease), and RecFOR (RecA-single-stranded DNA filament formation). The recombination pathway operating in recB (nuclease-deficient) mutants is a hybrid because it includes elements of both the RecBCD and RecF recombination machineries. In this study, genetic analysis of recombination in a recB (nuclease-deficient) recD double mutant was performed. We show that conjugational recombination and DNA repair after UV and gamma irradiation in this mutant are highly dependent on recJ, partially dependent on recFOR, and independent of recQ. These results suggest that the recombination pathway operating in a nuclease-deficient recB recD double mutant is also a hybrid. We propose that the helicase and RecA loading activities belong to the RecBCD recombination machinery, while the RecJ-mediated 5′→3′ exonuclease is an element of the RecF recombination machinery.

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Lestini, Roxane, i Bénédicte Michel. "UvrD and UvrD252 Counteract RecQ, RecJ, and RecFOR in a rep Mutant of Escherichia coli". Journal of Bacteriology 190, nr 17 (20.06.2008): 5995–6001. http://dx.doi.org/10.1128/jb.00620-08.

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ABSTRACT Rep and UvrD are two related Escherichia coli helicases, and inactivating both is lethal. Based on the observation that the synthetic lethality of rep and uvrD inactivation is suppressed in the absence of the recombination presynaptic proteins RecF, RecO, or RecR, it was proposed that UvrD is essential in the rep mutant to counteract a deleterious RecFOR-dependent RecA binding. We show here that the synthetic lethality of rep and uvrD mutations is also suppressed by recQ and recJ inactivation but not by rarA inactivation. Furthermore, it is independent of the action of UvrD in nucleotide excision repair and mismatch repair. These observations support the idea that UvrD counteracts a deleterious RecA binding to forks blocked in the rep mutant. An ATPase-deficient mutant of UvrD [uvrD(R284A)] is dominant negative in a rep mutant, but only in the presence of all RecQJFOR proteins, suggesting that the UvrD(R284A) mutant protein is deleterious when it counteracts one of these proteins. In contrast, the uvrD252 mutant (G30D), which exhibits a strongly decreased ATPase activity, is viable in a rep mutant, where it allows replication fork reversal. We conclude that the residual ATPase activity of UvrD252 prevents a negative effect on the viability of the rep mutant and allows UvrD to counteract the action of RecQ, RecJ, and RecFOR at forks blocked in the rep mutant. Models for the action of UvrD at blocked forks are proposed.

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Morimatsu, Katsumi, Yun Wu i Stephen C. Kowalczykowski. "RecFOR Proteins Target RecA Protein to a DNA Gap with Either DNA or RNA at the 5′ Terminus". Journal of Biological Chemistry 287, nr 42 (17.08.2012): 35621–30. http://dx.doi.org/10.1074/jbc.m112.397034.

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The repair of single-stranded gaps in duplex DNA by homologous recombination requires the proteins of the RecF pathway. The assembly of RecA protein onto gapped DNA (gDNA) that is complexed with the single-stranded DNA-binding protein is accelerated by the RecF, RecO, and RecR (RecFOR) proteins. Here, we show the RecFOR proteins specifically target RecA protein to gDNA even in the presence of a thousand-fold excess of single-stranded DNA (ssDNA). The binding constant of RecF protein, in the presence of the RecOR proteins, to the junction of ssDNA and dsDNA within a gap is 1–2 nm, suggesting that a few RecF molecules in the cell are sufficient to recognize gDNA. We also found that the nucleation of a RecA filament on gDNA in the presence of the RecFOR proteins occurs at a faster rate than filament elongation, resulting in a RecA nucleoprotein filament on ssDNA for 1000–2000 nucleotides downstream (5′ → 3′) of the junction with duplex DNA. Thus, RecA loading by RecFOR is localized to a region close to a junction. 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.

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Sawitzke, James A., i Franklin W. Stahl. "Roles for λ Orf and Escherichia coli RecO, RecR and RecF in λ Recombination". Genetics 147, nr 2 (1.10.1997): 357–69. http://dx.doi.org/10.1093/genetics/147.2.357.

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Bacteriophage λ lacking its Red recombination functions requires either its own gene product, Orf, or the product of Escherichia coli's recO, recR and recF genes (RecORF) for efficient recombination in recBC sbcB sbcC mutant cells (the RecF pathway). Phage crosses under conditions of a partial block to DNA replication have revealed the following: (1) In the presence of Orf, RecF pathway recombination is similar to λ Red recombination; (2) Orf is necessary for focusing recombination toward the right end of the chromosome as λ is conventionally drawn; (3) RecORF-mediated RecF pathway recombination is not focused toward the right end of the chromosome, which may indicate that RecORF travels along the DNA; (4) both Orf- and RecORF-mediated RecF pathway recombination are stimulated by DNA replication; and (5) low level recombination in the simultaneous absence of Orf and RecORF may occur by a break-copy mechanism that is not initiated by a double strand break. Models for the roles of Orf and RecO, RecR and RecF in recombination are presented.

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20

Wang, Tzu-Chien V., Hai-Yin Chang i Jia-Li Hung. "Cosuppression of recF, recR and recO mutations by mutant recA alleles in Escherichia coli cells". Mutation Research/DNA Repair 294, nr 2 (sierpień 1993): 157–66. http://dx.doi.org/10.1016/0921-8777(93)90024-b.

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21

Jain, Kanika, Elizabeth A. Wood i Michael M. Cox. "The rarA gene as part of an expanded RecFOR recombination pathway: Negative epistasis and synthetic lethality with ruvB, recG, and recQ". PLOS Genetics 17, nr 12 (22.12.2021): e1009972. http://dx.doi.org/10.1371/journal.pgen.1009972.

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The RarA protein, homologous to human WRNIP1 and yeast MgsA, is a AAA+ ATPase and one of the most highly conserved DNA repair proteins. With an apparent role in the repair of stalled or collapsed replication forks, the molecular function of this protein family remains obscure. Here, we demonstrate that RarA acts in late stages of recombinational DNA repair of post-replication gaps. A deletion of most of the rarA gene, when paired with a deletion of ruvB or ruvC, produces a growth defect, a strong synergistic increase in sensitivity to DNA damaging agents, cell elongation, and an increase in SOS induction. Except for SOS induction, these effects are all suppressed by inactivating recF, recO, or recJ, indicating that RarA, along with RuvB, acts downstream of RecA. SOS induction increases dramatically in a rarA ruvB recF/O triple mutant, suggesting the generation of large amounts of unrepaired ssDNA. The rarA ruvB defects are not suppressed (and in fact slightly increased) by recB inactivation, suggesting RarA acts primarily downstream of RecA in post-replication gaps rather than in double strand break repair. Inactivating rarA, ruvB and recG together is synthetically lethal, an outcome again suppressed by inactivation of recF, recO, or recJ. A rarA ruvB recQ triple deletion mutant is also inviable. Together, the results suggest the existence of multiple pathways, perhaps overlapping, for the resolution or reversal of recombination intermediates created by RecA protein in post-replication gaps within the broader RecF pathway. One of these paths involves RarA.

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Sanchez, Humberto, Dawit Kidane, M. Castillo Cozar, Peter L. Graumann i Juan C. Alonso. "Recruitment of Bacillus subtilis RecN to DNA Double-Strand Breaks in the Absence of DNA End Processing". Journal of Bacteriology 188, nr 2 (15.01.2006): 353–60. http://dx.doi.org/10.1128/jb.188.2.353-360.2006.

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ABSTRACT The recognition and processing of double-strand breaks (DSBs) to a 3′ single-stranded DNA (ssDNA) overhang structure in Bacillus subtilis is poorly understood. Mutations in addA and addB or null mutations in recJ (ΔrecJ), recQ (ΔrecQ), or recS (ΔrecS) genes, when present in otherwise-Rec+ cells, render cells moderately sensitive to the killing action of different DNA-damaging agents. Inactivation of a RecQ-like helicase (ΔrecQ or ΔrecS) in addAB cells showed an additive effect; however, when ΔrecJ was combined with addAB, a strong synergistic effect was observed with a survival rate similar to that of ΔrecA cells. RecF was nonepistatic with RecJ or AddAB. After induction of DSBs, RecN-yellow fluorescent protein (YFP) foci were formed in addAB ΔrecJ cells. AddAB and RecJ were required for the formation of a single RecN focus, because in their absence multiple RecN-YFP foci accumulated within the cells. Green fluorescent protein-RecA failed to form filamentous structures (termed threads) in addAB ΔrecJ cells. We propose that RecN is one of the first recombination proteins detected as a discrete focus in live cells in response to DSBs and that either AddAB or RecQ(S)-RecJ are required for the generation of a duplex with a 3′-ssDNA tail needed for filament formation of RecA.

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Saveson, Catherine J., i Susan T. Lovett. "Tandem Repeat Recombination Induced by Replication Fork Defects in Escherichia coli Requires a Novel Factor, RadC". Genetics 152, nr 1 (1.05.1999): 5–13. http://dx.doi.org/10.1093/genetics/152.1.5.

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Abstract DnaB is the helicase associated with the DNA polymerase III replication fork in Escherichia coli. Previously we observed that the dnaB107(ts) mutation, at its permissive temperature, greatly stimulated deletion events at chromosomal tandem repeats. This stimulation required recA, which suggests a recombinational mechanism. In this article we examine the genetic dependence of recombination stimulated by the dnaB107 mutation. Gap repair genes recF, recO, and recR were not required. Mutations in recB, required for double-strand break repair, and in ruvC, the Holliday junction resolvase gene, were synthetically lethal with dnaB107, causing enhanced temperature sensitivity. The hyperdeletion phenotype of dnaB107 was semidominant, and in dnaB107/dnaB+ heterozygotes recB was partially required for enhanced deletion, whereas ruvC was not. We believe that dnaB107 causes the stalling of replication forks, which may become broken and require repair. Misalignment of repeated sequences during RecBCD-mediated repair may account for most, but not all, of deletion stimulated by dnaB107. To our surprise, the radC gene, like recA, was required for virtually all recombination stimulated by dnaB107. The biochemical function of RadC is unknown, but is reported to be required for growth-medium-dependent repair of DNA strand breaks. Our results suggest that RadC functions specifically in recombinational repair that is associated with the replication fork.

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24

Whitby, Matthew C., i Robert G. Lloyd. "Altered SOS induction associated with mutations in recF, recO and recR". Molecular and General Genetics MGG 246, nr 2 (marzec 1995): 174–79. http://dx.doi.org/10.1007/bf00294680.

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Hegde, S. P., M. h. Qin, X. h. Li, M. A. L. Atkinson, A. J. Clark, M. Rajagopalan i M. V. V. S. Madiraju. "Interactions of RecF protein with RecO, RecR, and single-stranded DNA binding proteins reveal roles for the RecF-RecO-RecR complex in DNA repair and recombination". Proceedings of the National Academy of Sciences 93, nr 25 (10.12.1996): 14468–73. http://dx.doi.org/10.1073/pnas.93.25.14468.

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Vlašić, Ignacija, Ramona Mertens, Elena M. Seco, Begoña Carrasco, Silvia Ayora, Günther Reitz, Fabian M. Commichau, Juan C. Alonso i Ralf Moeller. "Bacillus subtilis RecA and its accessory factors, RecF, RecO, RecR and RecX, are required for spore resistance to DNA double-strand break". Nucleic Acids Research 42, nr 4 (26.11.2013): 2295–307. http://dx.doi.org/10.1093/nar/gkt1194.

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Abstract Bacillus subtilis RecA is important for spore resistance to DNA damage, even though spores contain a single non-replicating genome. We report that inactivation of RecA or its accessory factors, RecF, RecO, RecR and RecX, drastically reduce survival of mature dormant spores to ultrahigh vacuum desiccation and ionizing radiation that induce single strand (ss) DNA nicks and double-strand breaks (DSBs). The presence of non-cleavable LexA renders spores less sensitive to DSBs, and spores impaired in DSB recognition or end-processing show sensitivities to X-rays similar to wild-type. In vitro RecA cannot compete with SsbA for nucleation onto ssDNA in the presence of ATP. RecO is sufficient, at least in vitro, to overcome SsbA inhibition and stimulate RecA polymerization on SsbA-coated ssDNA. In the presence of SsbA, RecA slightly affects DNA replication in vitro, but addition of RecO facilitates RecA-mediated inhibition of DNA synthesis. We propose that repairing of the DNA lesions generates a replication stress to germinating spores, and the RecA·ssDNA filament might act by preventing potentially dangerous forms of DNA repair occurring during replication. RecA might stabilize a stalled fork or prevent or promote dissolution of reversed forks rather than its cleavage that should require end-processing.

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27

Odsbu, Ingvild, i Kirsten Skarstad. "DNA compaction in the early part of the SOS response is dependent on RecN and RecA". Microbiology 160, nr 5 (1.05.2014): 872–82. http://dx.doi.org/10.1099/mic.0.075051-0.

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The nucleoids of undamaged Escherichia coli cells have a characteristic shape and number, which is dependent on the growth medium. Upon induction of the SOS response by a low dose of UV irradiation an extensive reorganization of the nucleoids occurred. Two distinct phases were observed by fluorescence microscopy. First, the nucleoids were found to change shape and fuse into compact structures at midcell. The compaction of the nucleoids lasted for 10–20 min and was followed by a phase where the DNA was dispersed throughout the cells. This second phase lasted for ~1 h. The compaction was found to be dependent on the recombination proteins RecA, RecO and RecR as well as the SOS-inducible, SMC (structural maintenance of chromosomes)-like protein RecN. RecN protein is produced in high amounts during the first part of the SOS response. It is possible that the RecN-mediated ‘compact DNA’ stage at the beginning of the SOS response serves to stabilize damaged DNA prior to recombination and repair.

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28

Handa, Naofumi, Asao Ichige i Ichizo Kobayashi. "Contribution of RecFOR machinery of homologous recombination to cell survival after loss of a restriction–modification gene complex". Microbiology 155, nr 7 (1.07.2009): 2320–32. http://dx.doi.org/10.1099/mic.0.026401-0.

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Loss of a type II restriction–modification (RM) gene complex, such as EcoRI, from a bacterial cell leads to death of its descendent cells through attack by residual restriction enzymes on undermethylated target sites of newly synthesized chromosomes. Through such post-segregational host killing, these gene complexes impose their maintenance on their host cells. This finding led to the rediscovery of type II RM systems as selfish mobile elements. The host prokaryote cells were found to cope with such attacks through a variety of means. The RecBCD pathway of homologous recombination in Escherichia coli repairs the lethal lesions on the chromosome, whilst it destroys restricted non-self DNA. recBCD homologues, however, appear very limited in distribution among bacterial genomes, whereas homologues of the RecFOR proteins, responsible for another pathway, are widespread in eubacteria, just like the RM systems. In the present work, therefore, we examined the possible contribution of the RecFOR pathway to cell survival after loss of an RM gene complex. A recF mutation reduced survival in an otherwise rec-positive background and, more severely, in a recBC sbcBC background. We also found that its effect is prominent in the presence of specific non-null mutant forms of the RecBCD enzyme: the resistance to killing seen with recC1002, recC1004, recC2145 and recB2154 is severely reduced to the level of a null recBC allele when combined with a recF, recO or recR mutant allele. Such resistance was also dependent on RecJ and RecQ functions. UV resistance of these non-null recBCD mutants is also reduced by recF, recJ or recQ mutation. These results demonstrate that the RecFOR pathway of recombination can contribute greatly to resistance to RM-mediated host killing, depending on the genetic background.

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29

Henry, Camille, i Sarah S. Henrikus. "Elucidating Recombination Mediator Function Using Biophysical Tools". Biology 10, nr 4 (1.04.2021): 288. http://dx.doi.org/10.3390/biology10040288.

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The recombination mediator proteins (RMPs) are ubiquitous and play a crucial role in genome stability. RMPs facilitate the loading of recombinases like RecA onto single-stranded (ss) DNA coated by single-strand binding proteins like SSB. Despite sharing a common function, RMPs are the products of a convergent evolution and differ in (1) structure, (2) interaction partners and (3) molecular mechanisms. The RMP function is usually realized by a single protein in bacteriophages and eukaryotes, respectively UvsY or Orf, and RAD52 or BRCA2, while in bacteria three proteins RecF, RecO and RecR act cooperatively to displace SSB and load RecA onto a ssDNA region. Proteins working alongside to the RMPs in homologous recombination and DNA repair notably belongs to the RAD52 epistasis group in eukaryote and the RecF epistasis group in bacteria. Although RMPs have been studied for several decades, molecular mechanisms at the single-cell level are still not fully understood. Here, we summarize the current knowledge acquired on RMPs and review the crucial role of biophysical tools to investigate molecular mechanisms at the single-cell level in the physiological context.

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30

Baitin, Dmitry M., Irina V. Bakhlanova, Yury V. Kil, Michael M. Cox i Vladislav A. Lanzov. "Distinguishing Characteristics of Hyperrecombinogenic RecA Protein from Pseudomonas aeruginosa Acting in Escherichia coli". Journal of Bacteriology 188, nr 16 (15.08.2006): 5812–20. http://dx.doi.org/10.1128/jb.00358-06.

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ABSTRACT In Escherichia coli, a relatively low frequency of recombination exchanges (FRE) is predetermined by the activity of RecA protein, as modulated by a complex regulatory program involving both autoregulation and other factors. The RecA protein of Pseudomonas aeruginosa (RecAPa) exhibits a more robust recombinase activity than its E. coli counterpart (RecAEc). Low-level expression of RecAPa in E. coli cells results in hyperrecombination (an increase of FRE) even in the presence of RecAEc. This genetic effect is supported by the biochemical finding that the RecAPa protein is more efficient in filament formation than RecA K72R, a mutant protein with RecAEc-like DNA-binding ability. Expression of RecAPa also partially suppresses the effects of recF, recO, and recR mutations. In concordance with the latter, RecAPa filaments initiate recombination equally from both the 5′ and 3′ ends. Besides, these filaments exhibit more resistance to disassembly from the 5′ ends that makes the ends potentially appropriate for initiation of strand exchange. These comparative genetic and biochemical characteristics reveal that multiple levels are used by bacteria for a programmed regulation of their recombination activities.

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31

Lee, Su-jin, Han Byeol Oh i Sung-il Yoon. "Crystal Structure of the Recombination Mediator Protein RecO from Campylobacter jejuni and Its Interaction with DNA and a Zinc Ion". International Journal of Molecular Sciences 23, nr 17 (26.08.2022): 9667. http://dx.doi.org/10.3390/ijms23179667.

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Homologous recombination is involved in repairing DNA damage, contributing to maintaining the integrity and stability of viral and cellular genomes. In bacteria, the recombination mediator proteins RecO and RecR are required to load the RecA recombinase on ssDNA for homologous recombination. To structurally and functionally characterize RecO, we determined the crystal structure of RecO from Campylobacter jejuni (cjRecO) at a 1.8 Å resolution and biochemically assessed its capacity to interact with DNA and a metal ion. cjRecO folds into a curved rod-like structure that consists of an N-terminal domain (NTD), C-terminal domain (CTD), and Zn2+-binding domain (ZnD). The ZnD at the end of the rod-like structure coordinates three cysteine residues and one histidine residue to accommodate a Zn2+ ion. Based on an extensive comparative analysis of RecO structures and sequences, we propose that the Zn2+-binding consensus sequence of RecO is CxxC…C/HxxC/H/D. The interaction with Zn2+ is indispensable for the protein stability of cjRecO but does not seem to be required for the recombination mediator function. cjRecO also interacts with ssDNA as part of its biological function, potentially using the positively charged patch in the NTD and CTD. However, cjRecO displays a low ssDNA-binding affinity, suggesting that cjRecO requires RecR to efficiently recognize ssDNA for homologous recombination.

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32

Nakayama, Koji, Susumu Shiota i Hiroaki Nakayama. "Thymineless death in Escherichia coli mutants deficient in the RecF recombination pathway". Canadian Journal of Microbiology 34, nr 7 (1.07.1988): 905–7. http://dx.doi.org/10.1139/m88-157.

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Like recF and recQ mutants studied earlier, two other classes of Escherichia coli mutants defective in the RecF conjugal recombination pathway, recJ and recO, were found to be partially resistant to thymineless death. In contrast, a recN mutant, also belonging to the pathway, was indistinguishable from the wild type with respect to thymineless death.

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33

Pandya, Gagan A., In-Young Yang, Arthur P. Grollman i Masaaki Moriya. "Escherichia coli Responses to a Single DNA Adduct". Journal of Bacteriology 182, nr 23 (1.12.2000): 6598–604. http://dx.doi.org/10.1128/jb.182.23.6598-6604.2000.

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ABSTRACT To study the mechanisms by which Escherichia colimodulates the genotoxic effects of DNA damage, a novel system has been developed which permits quantitative measurements of various E. coli pathways involved in mutagenesis and DNA repair. Events measured include fidelity and efficiency of translesion DNA synthesis, excision repair, and recombination repair. Our strategy involves heteroduplex plasmid DNA bearing a single site-specific DNA adduct and several mismatched regions. The plasmid replicates in a mismatch repair-deficient host with the mismatches serving as strand-specific markers. Analysis of progeny plasmid DNA for linkage of the strand-specific markers identifies the pathway from which the plasmid is derived. Using this approach, a single 1,N 6-ethenodeoxyadenosine adduct was shown to be repaired inefficiently by excision repair, to inhibit DNA synthesis by approximately 80 to 90%, and to direct the incorporation of correct dTMP opposite this adduct. This approach is especially useful in analyzing the damage avoidance-tolerance mechanisms. Our results also show that (i) progeny derived from the damage avoidance-tolerance pathway(s) accounts for more than 15% of all progeny; (ii) this pathway(s) requires functional recA, recF,recO, and recR genes, suggesting the mechanism to be daughter strand gap repair; (iii) the ruvABC genes or the recG gene is also required; and (iv) the RecG pathway appears to be more active than the RuvABC pathway. Based on these results, the mechanism of the damage avoidance-tolerance pathway is discussed.

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34

Ren, Li, Abu Amar M. Al Mamun i M. Zafri Humayun. "Requirement for Homologous Recombination Functions for Expression of the mutA Mistranslator tRNA-Induced Mutator Phenotype in Escherichia coli". Journal of Bacteriology 182, nr 5 (1.03.2000): 1427–31. http://dx.doi.org/10.1128/jb.182.5.1427-1431.2000.

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ABSTRACT Expression of the Escherichia coli mutA mutator phenotype requires recA, recB,recC, ruvA, and ruvC gene, but notrecD, recF, recO, orrecR genes. Thus, the recBCD-dependent homologous recombination system is a component of the signal pathway that activates an error-prone DNA polymerase inmutA cells.

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35

Beam, Cynthia E., Catherine J. Saveson i Susan T. Lovett. "Role for radA/sms in Recombination Intermediate Processing in Escherichia coli". Journal of Bacteriology 184, nr 24 (15.12.2002): 6836–44. http://dx.doi.org/10.1128/jb.184.24.6836-6844.2002.

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ABSTRACT RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and Lon protease. We examined mutations in the radA/sms gene of Escherichia coli for effects on conjugational recombination and sensitivity to DNA-damaging agents, including UV irradiation, methyl methanesulfonate (MMS), mitomycin C, phleomycin, hydrogen peroxide, and hydroxyurea (HU). Null mutants of radA were modestly sensitive to the DNA-methylating agent MMS and to the DNA strand breakage agent phleomycin, with conjugational recombination decreased two- to threefold. We combined a radA mutation with other mutations in recombination genes, including recA, recB, recG, recJ, recQ, ruvA, and ruvC. A radA mutation was strongly synergistic with the recG Holliday junction helicase mutation, producing profound sensitivity to all DNA-damaging agents tested. Lesser synergy was noted between a mutation in radA and recJ, recQ, ruvA, ruvC, and recA for sensitivity to various genotoxins. For survival after peroxide and HU exposure, a radA mutation surprisingly suppressed the sensitivity of recA and recB mutants, suggesting that RadA may convert some forms of damage into lethal intermediates in the absence of these functions. Loss of radA enhanced the conjugational recombination deficiency conferred by mutations in Holliday junction-processing function genes, recG, ruvA, and ruvC. A radA recG ruv triple mutant had severe recombinational defects, to the low level exhibited by recA mutants. These results establish a role for RadA/Sms in recombination and recombinational repair, most likely involving the stabilization or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC.

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Umezu, K., N. W. Chi i R. D. Kolodner. "Biochemical interaction of the Escherichia coli RecF, RecO, and RecR proteins with RecA protein and single-stranded DNA binding protein." Proceedings of the National Academy of Sciences 90, nr 9 (1.05.1993): 3875–79. http://dx.doi.org/10.1073/pnas.90.9.3875.

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Carrasco, Begoña, Silvia Fernández, Marie-Agnes Petit i Juan C. Alonso. "Genetic Recombination in Bacillus subtilis 168: Effect of ΔhelD on DNA Repair and Homologous Recombination". Journal of Bacteriology 183, nr 19 (1.10.2001): 5772–77. http://dx.doi.org/10.1128/jb.183.19.5772-5777.2001.

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ABSTRACT The B. subtilis ΔhelD allele rendered cells proficient in transformational recombination and moderately sensitive to methyl methanesulfonate when present in an otherwise Rec+ strain. The ΔhelD allele was introduced into rec-deficient strains representative of the α (recF strain), β (addA addB), γ (recH), ɛ (ΔrecU), and ζ (ΔrecS) epistatic groups. The ΔhelDmutation increased the sensitivity to DNA-damaging agents ofaddAB, ΔrecU, and ΔrecS cells, did not affect the survival ofrecH cells, and decreased the sensitivity ofrecF cells. ΔhelD also partially suppressed the DNA repair phenotype of other mutations classified within the α epistatic group, namely the recL, ΔrecO, and recR mutations. The ΔhelD allele marginally reduced plasmid transformation (three- to sevenfold) of mutations classified within the α, β, and γ epistatic groups. Altogether, these data indicate that the loss of helicase IV might stabilize recombination repair intermediates formed in the absence of recFLOR and renderrecFLOR, addAB, andrecH cells impaired in plasmid transformation.

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38

Fernández, Silvia, Alexei Sorokin i Juan C. Alonso. "Genetic Recombination in Bacillus subtilis 168: Effects of recU and recSMutations on DNA Repair and Homologous Recombination". Journal of Bacteriology 180, nr 13 (1.07.1998): 3405–9. http://dx.doi.org/10.1128/jb.180.13.3405-3409.1998.

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ABSTRACT Bacillus subtilis recombination-deficient mutants were constructed by inserting a selectable marker (cat gene) into the yppB and ypbC coding regions. TheyppB:cat and ypbC:catnull alleles rendered cells sensitive to DNA-damaging agents, impaired plasmid transformation (25- and 100-fold), and moderately affected chromosomal transformation when present in an otherwise Rec+ B. subtilis strain. The yppBgene complemented the defect of the recG40 strain.yppB and ypbC and their respective null alleles were termed “recU” and “recU1” (recU:cat) and “recS” and “recS1” (recS:cat), respectively. The recU and recS mutations were introduced into rec-deficient strains representative of the α (recF), β (addA5 addB72), γ (recH342), and ɛ (recG40) epistatic groups. The recU mutation did not modify the sensitivity ofrecH cells to DNA-damaging agents, but it did affect inter- and intramolecular recombination in recH cells. TherecS mutation did not modify the sensitivity ofaddAB cells to DNA-damaging agents, and it marginally affected recF, recH, and recUcells. The recS mutation markedly reduced (about 250-fold) intermolecular recombination in recH cells, and there were reductions of 10- to 20-fold in recF, addAB, and recU cells. Intramolecular recombination was blocked inrecS recF, recS addAB, and recS recU cells. RecU and RecS have no functional counterparts inEscherichia coli. Altogether, these data indicate that therecU and recS proteins are required for DNA repair and intramolecular recombination and that the recF(α epistatic group), addAB (β), recH (γ),recU (ɛ), and recS genes provide overlapping activities that compensate for the effects of single mutation. We tentatively placed recS within a new group, termed “ζ.”

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39

Honda, Masayoshi, Jin Inoue, Masatoshi Yoshimasu, Yutaka Ito, Takehiko Shibata i Tsutomu Mikawa. "Identification of the RecR Toprim Domain as the Binding Site for both RecF and RecO". Journal of Biological Chemistry 281, nr 27 (4.05.2006): 18549–59. http://dx.doi.org/10.1074/jbc.m512658200.

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Shan, Qun, Julie M. Bork, Brian L. Webb, Ross B. Inman i Michael M. Cox. "RecA protein filaments: end-dependent dissociation from ssDNA and stabilization by RecO and RecR proteins". Journal of Molecular Biology 265, nr 5 (styczeń 1997): 519–40. http://dx.doi.org/10.1006/jmbi.1996.0748.

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Tang, Qun, Pu Gao, Yan-Ping Liu, Ang Gao, Xiao-Min An, Shun Liu, Xiao-Xue Yan i Dong-Cai Liang. "RecOR complex including RecR N-N dimer and RecO monomer displays a high affinity for ssDNA". Nucleic Acids Research 40, nr 21 (27.09.2012): 11115–25. http://dx.doi.org/10.1093/nar/gks889.

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Diaz-Martinez, Laura A., Aimee A. Hernandez, Christina E. D’Arcy, Stephanie Corral, Jay M. Bhatt, David Esparza, Martina Rosenberg i Jeffrey T. Olimpo. "Current Approaches for Integrating Responsible and Ethical Conduct of Research (RECR) Education into Course-based Undergraduate Research Experiences: A National Assessment". CBE—Life Sciences Education 20, nr 3 (wrzesień 2021): ar38. http://dx.doi.org/10.1187/cbe.20-08-0179.

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Incorporation of responsible and ethical conduct of research (RECR) education into course-based undergraduate research experiences (CUREs) remains largely unexplored despite the importance of RECR practices to the broader scientific enterprise. To address this concern, a mixed methods approach was employed to characterize the state of RECR education in biological sciences CUREs nationwide.

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43

Lenhart, J. S., E. R. Brandes, J. W. Schroeder, R. J. Sorenson, H. D. Showalter i L. A. Simmons. "RecO and RecR Are Necessary for RecA Loading in Response to DNA Damage and Replication Fork Stress". Journal of Bacteriology 196, nr 15 (2.06.2014): 2851–60. http://dx.doi.org/10.1128/jb.01494-14.

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ZETTNER, C. M., i M. YODA. "Moderate-aspect-ratio elliptical cylinders in simple shear with inertia". Journal of Fluid Mechanics 442 (24.08.2001): 241–66. http://dx.doi.org/10.1017/s0022112001005006.

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The effects of fluid inertia, geometry and flow confinement upon the dynamics of neutrally buoyant elliptical and non-elliptical cylinders over a wide range of aspect ratios in simple shear are studied experimentally for moderate shear-based Reynolds numbers Re. Unlike circular cylinders, elliptical cylinders of moderate aspect ratio cease to rotate, coming to rest at a nearly horizontal equilibrium orientation above a critical Reynolds number Recr (‘stationary behaviour’). Simple dynamics arguments are proposed to explain the effects of aspect ratio and flow confinement upon critical Reynolds number and particle dynamics. Experiments confirm results from previous numerical simulations that the normalized rotation period for Re < Recr (‘periodic behaviour’) is proportional to (Recr − Re)−0.5 for small Recr − Re. For periodic behaviour, maximum and minimum angular cylinder speeds both decrease, and period increases, as Recr − Re decreases. For stationary behaviour, the cylinder rotates until it achieves a nearly horizontal equilibrium orientation, which increases as the Reynolds number approaches the critical value. The experimental results are in good agreement with previous lattice-Boltzmann simulations for a 0.5 aspect ratio cylinder.Variation in angular speed over a rotation period decreases as aspect ratio increases, while Recr increases as flow confinement and aspect ratio increase. A non-elliptical cylinder of 0.33 aspect ratio also ceases to rotate above a certain Reynolds number. Although Recr is different from the corresponding elliptical case, the scaling of the normalized rotation period for this body as Recr → Re is identical to that for the elliptical cylinder, suggesting that this scaling is independent of particle shape (i.e. ‘universal’, as conjectured in previous numerical studies). The results also demonstrate that a variety of centrosymmetric bodies with aspect ratios below unity transition from periodic to stationary behaviour.

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Mendonca, V. M., i S. W. Matson. "Genetic analysis of delta helD and delta uvrD mutations in combination with other genes in the RecF recombination pathway in Escherichia coli: suppression of a ruvB mutation by a uvrD deletion." Genetics 141, nr 2 (1.10.1995): 443–52. http://dx.doi.org/10.1093/genetics/141.2.443.

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Abstract Helicase II (uvrD gene product) and helicase IV (helD gene product) have been shown previously to be involved in the RecF pathway of recombination. To better understand the role of these two proteins in homologous recombination in the RecF pathway [recBCsbcB(C) background, we investigated the interactions between helD, uvrD and the following RecF pathway genes: recF, recO, recN and ruvAB. We observed synergistic interactions between uvrD ant the recF, recN, recO and recG genes in both conjugational recombination and the repair of methylmethane sulfonate (MMS)-induced DNA damage. No synergistic interactions were detected between helD and the recF, recO and regN genes when conjugational recombination was analyzed. We did, however, detect synergistic interactions between helD and recF/recO in recombinational repair. Surprisingly, the uvrD deletion completely suppressed the phenotype of a ruvB mutation in a recBCsbcB(C) background. Both conjugational recombination efficiency and MMS-damaged DNA repair proficiency returned to wild-type levels in the deltauvrDruvB9 double mutant. Suppression of the effects of the ruvB mutation by a uvrD deletion was dependent on the recG and recN genes and not dependent on the recF/O/R genes. These data are discussed in the context of two "RecF" homologous recombination pathways operating in a recBCsbcB(C) strain background.

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46

Lloyd, R. G., i C. Buckman. "Conjugational recombination in Escherichia coli: genetic analysis of recombinant formation in Hfr x F- crosses." Genetics 139, nr 3 (1.03.1995): 1123–48. http://dx.doi.org/10.1093/genetics/139.3.1123.

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Abstract The formation of recombinants during conjugation between Hfr and F- strains of Escherichia coli was investigated using unselected markers to monitor integration of Hfr DNA into the circular recipient chromosome. In crosses selecting a marker located approximately 500 kb from the Hfr origin, 60-70% of the recombinants appeared to inherit the Hfr DNA in a single segment, with the proximal exchange located > 300 kb from the selected marker. The proportion of recombinants showing multiple exchanges increased in matings selecting more distal markers located 700-2200 kb from the origin, but they were always in the minority. This effect was associated with decreased linkage of unselected proximal markers. Mutation of recB, or recD plus recJ, in the recipient reduced the efficiency of recombination and shifted the location of the proximal exchange(s) closer to the selected marker. Mutation of recF, recO or recQ produced recombinants in which this exchange tended to be closer to the origin, though the effect observed was rather small. Up to 25% of recombinant colonies in rec+ crosses showed segregation of both donor and recipient alleles at a proximal unselected locus. Their frequency varied with the distance between the selected and unselected markers and was also related directly to the efficiency of recombination. Mutation of recD increased their number by twofold in certain crosses to a value of 19%, a feature associated with an increase in the survival of linear DNA in the absence of RecBCD exonuclease. Mutation of recN reduced sectored recombinants in these crosses to approximately 1% in all the strains examined, including recD. A model for conjugational recombination is proposed in which recombinant chromosomes are formed initially by two exchanges that integrate a single piece of duplex Hfr DNA into the recipient chromosome. Additional pairs of exchanges involving the excised recipient DNA, RecBCD enzyme and RecN protein, can subsequently modify the initial product to generate the spectrum of recombinants normally observed.

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Ying, Xiangxian, Jie Zhang, Can Wang, Meijuan Huang, Yuting Ji, Feng Cheng, Meilan Yu, Zhao Wang i Meirong Ying. "Characterization of a Carbonyl Reductase from Rhodococcus erythropolis WZ010 and Its Variant Y54F for Asymmetric Synthesis of (S)-N-Boc-3-Hydroxypiperidine". Molecules 23, nr 12 (28.11.2018): 3117. http://dx.doi.org/10.3390/molecules23123117.

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The recombinant carbonyl reductase from Rhodococcus erythropolis WZ010 (ReCR) demonstrated strict (S)-stereoselectivity and catalyzed the irreversible reduction of N-Boc-3-piperidone (NBPO) to (S)-N-Boc-3-hydroxypiperidine [(S)-NBHP], a key chiral intermediate in the synthesis of ibrutinib. The NAD(H)-specific enzyme was active within broad ranges of pH and temperature and had remarkable activity in the presence of higher concentration of organic solvents. The amino acid residue at position 54 was critical for the activity and the substitution of Tyr54 to Phe significantly enhanced the catalytic efficiency of ReCR. The kcat/Km values of ReCR Y54F for NBPO, (R/S)-2-octanol, and 2-propanol were 49.17 s−1 mM−1, 56.56 s−1 mM−1, and 20.69 s−1 mM−1, respectively. In addition, the (S)-NBHP yield was as high as 95.92% when whole cells of E. coli overexpressing ReCR variant Y54F catalyzed the asymmetric reduction of 1.5 M NBPO for 12 h in the aqueous/(R/S)-2-octanol biphasic system, demonstrating the great potential of ReCR variant Y54F for practical applications.

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48

Kidane, Dawit, i Peter L. Graumann. "Dynamic formation of RecA filaments at DNA double strand break repair centers in live cells". Journal of Cell Biology 170, nr 3 (1.08.2005): 357–66. http://dx.doi.org/10.1083/jcb.200412090.

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We show that RecN protein is recruited to a defined DNA double strand break (DSB) in Bacillus subtilis cells at an early time point during repair. Because RecO and RecF are successively recruited to DSBs, it is now clear that dynamic DSB repair centers (RCs) exist in prokaryotes. RecA protein was also recruited to RCs and formed highly dynamic filamentous structures, which we term threads, across the nucleoids. Formation of RecA threads commenced ∼30 min after the induction of DSBs, after RecN recruitment to RCs, and disassembled after 2 h. Time-lapse microscopy showed that the threads rapidly changed in length, shape, and orientation within minutes and can extend at 1.02 μm/min. The formation of RecA threads was abolished in recJ addAB mutant cells but not in each of the single mutants, suggesting that RecA filaments can be initiated via two pathways. Contrary to proteins forming RCs, DNA polymerase I did not form foci but was present throughout the nucleoids (even after induction of DSBs or after UV irradiation), suggesting that it continuously scans the chromosome for DNA lesions.

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49

Thaler, David S., Elizabeth Sampson, Imran Siddiqi, Susan M. Rosenberg, Lynn C. Thomason, Franklin W. Stahl i Mary M. Stahl. "Recombination of bacteriophage λ in recD mutants of Escherichia coli". Genome 31, nr 1 (1.01.1989): 53–67. http://dx.doi.org/10.1139/g89-013.

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RecBCD enzyme is centrally important in homologous recombination in Escherichia coli and is the source of ExoV activity. Null alleles of either the recB or the recC genes, which encode the B and C subunits, respectively, manifest no recombination and none of the nuclease functions characteristic of the holoenzyme. Loss of the D subunit, by a recD mutation, likewise results in loss of ExoV activity. However, mutants lacking the D subunit are competent for homologous recombination. We report that the distribution of exchanges along the chromosome of Red−Gam−phage λ is strikingly altered by recD null mutations in the host. When λ DNA replication is blocked, recombination in recD mutant strains is high near λ's right end. In contrast, recombination in isogenic recD+ strains is approximately uniform along λ unless the λ chromosome contains a χ sequence. Recombination in recD mutant strains is focused toward the site of action of a type II restriction enzyme acting in vivo on λ. The distribution of exchanges in isogenic recD+ strains is scarcely altered by the restriction enzyme (unless the phage contains an otherwise silent χ). The distribution of exchanges in recD mutants is strongly affected by λ DNA replication. The distribution of exchanges on λ growing in rec+ cells is not influenced by DNA replication. The exchange distribution along λ in recD mutant cells is independent of χ in a variety of conditions. Recombination in rec+ cells is χ influenced. Recombination in recD mutants depends on recC function, occurs in strains deleted for rac prophage, and is independent of recJ, which is known to be required for λ recombination via the RecF pathway. We entertain two models for recombination in recD mutants: (i) recombination in recD mutants may proceed via double-chain break–repair, as it does in λ's Red pathway and E. coli's RecE pathway; (ii) the RecBC enzyme, missing its D subunit, is equivalent to the wild-type, RecBCD, enzyme after that enzyme has been activated by a χ sequence.Key words: χ sequence, RecBCD pathway, Red pathway, RecBC‡ pathway.

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Webb, Brian L., Michael M. Cox i Ross B. Inman. "Recombinational DNA Repair: The RecF and RecR Proteins Limit the Extension of RecA Filaments beyond Single-Strand DNA Gaps". Cell 91, nr 3 (październik 1997): 347–56. http://dx.doi.org/10.1016/s0092-8674(00)80418-3.

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