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[PMID]:28934502
[Au] Autor:Yakimov A; Pobegalov G; Bakhlanova I; Khodorkovskii M; Petukhov M; Baitin D
[Ad] Endereço:Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute (B.P.Konstantinov of National Research Centre 'Kurchatov Institute'), Gatchina 188300, Russia.
[Ti] Título:Blocking the RecA activity and SOS-response in bacteria with a short α-helical peptide.
[So] Source:Nucleic Acids Res;45(16):9788-9796, 2017 Sep 19.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:The RecX protein, a very active natural RecA protein inhibitor, can completely disassemble RecA filaments at nanomolar concentrations that are two to three orders of magnitude lower than that of RecA protein. Based on the structure of RecX protein complex with the presynaptic RecA filament, we designed a short first in class α-helical peptide that both inhibits RecA protein activities in vitro and blocks the bacterial SOS-response in vivo. The peptide was designed using SEQOPT, a novel method for global sequence optimization of protein α-helices. SEQOPT produces artificial peptide sequences containing only 20 natural amino acids with the maximum possible conformational stability at a given pH, ionic strength, temperature, peptide solubility. It also accounts for restrictions due to known amino acid residues involved in stabilization of protein complexes under consideration. The results indicate that a few key intermolecular interactions inside the RecA protein presynaptic complex are enough to reproduce the main features of the RecX protein mechanism of action. Since the SOS-response provides a major mechanism of bacterial adaptation to antibiotics, these results open new ways for the development of antibiotic co-therapy that would not cause bacterial resistance.
[Mh] Termos MeSH primário: Peptídeos/química
Peptídeos/farmacologia
Recombinases Rec A/antagonistas & inibidores
Resposta SOS (Genética)/efeitos dos fármacos
[Mh] Termos MeSH secundário: Dicroísmo Circular
DNA/metabolismo
Escherichia coli/efeitos dos fármacos
Escherichia coli/metabolismo
Escherichia coli/efeitos da radiação
Proteínas de Escherichia coli/química
Proteínas de Escherichia coli/metabolismo
Modelos Moleculares
Conformação Proteica
Estabilidade Proteica
Recombinases Rec A/química
Recombinases Rec A/metabolismo
Resposta SOS (Genética)/efeitos da radiação
Raios Ultravioleta
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Escherichia coli Proteins); 0 (Peptides); 0 (RecX protein, E coli); 9007-49-2 (DNA); EC 2.7.7.- (Rec A Recombinases)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171024
[Lr] Data última revisão:
171024
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170922
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gkx687


  2 / 3396 MEDLINE  
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[PMID]:28911099
[Au] Autor:Le S; Serrano E; Kawamura R; Carrasco B; Yan J; Alonso JC
[Ad] Endereço:Department of Physics, National University of Singapore, 117551, Singapore.
[Ti] Título:Bacillus subtilis RecA with DprA-SsbA antagonizes RecX function during natural transformation.
[So] Source:Nucleic Acids Res;45(15):8873-8885, 2017 Sep 06.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Bacillus subtilis DprA and RecX proteins, which interact with RecA, are crucial for efficient chromosomal and plasmid transformation. We showed that RecA, in the rATP·Mg2+ bound form (RecA·ATP), could not compete with RecX, SsbA or SsbB for assembly onto single-stranded (ss)DNA, but RecA·dATP partially displaced these proteins from ssDNA. RecX promoted reversible depolymerization of preformed RecA·ATP filaments. The two-component DprA-SsbA mediator reversed the RecX negative effect on RecA filament extension, but not DprA or DprA and SsbB. In the presence of DprA-SsbA, RecX added prior to RecA·ATP inhibited DNA strand exchange, but this inhibition was reversed when RecX was added after RecA. We propose that RecA nucleation is more sensitive to RecX action than is RecA filament growth. DprA-SsbA facilitates formation of an active RecA filament that directly antagonizes the inhibitory effects of RecX. RecX and DprA enable chromosomal transformation by altering RecA filament dynamics. DprA-SsbA and RecX proteins constitute a new regulatory network of RecA function. DprA-SsbA contributes to the formation of an active RecA filament and directly antagonizes the inhibitory effects of RecX during natural transformation.
[Mh] Termos MeSH primário: Bacillus subtilis/genética
Proteínas de Bactérias/genética
Proteínas de Ligação a DNA/genética
Regulação Bacteriana da Expressão Gênica
Proteínas de Membrana/genética
Recombinases Rec A/genética
Transformação Bacteriana
[Mh] Termos MeSH secundário: Trifosfato de Adenosina/metabolismo
Bacillus subtilis/metabolismo
Proteínas de Bactérias/metabolismo
Cromossomos Bacterianos/química
Cromossomos Bacterianos/metabolismo
DNA Bacteriano/genética
DNA Bacteriano/metabolismo
DNA de Cadeia Simples/genética
DNA de Cadeia Simples/metabolismo
Proteínas de Ligação a DNA/metabolismo
Cinética
Proteínas de Membrana/metabolismo
Plasmídeos/química
Plasmídeos/metabolismo
Recombinases Rec A/metabolismo
Recombinação Genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Bacterial Proteins); 0 (DNA, Bacterial); 0 (DNA, Single-Stranded); 0 (DNA-Binding Proteins); 0 (DprA protein, bacteria); 0 (Membrane Proteins); 0 (RecX protein, Xanthomonas campestris); 8L70Q75FXE (Adenosine Triphosphate); EC 2.7.7.- (Rec A Recombinases)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171012
[Lr] Data última revisão:
171012
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170916
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gkx583


  3 / 3396 MEDLINE  
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[PMID]:28854739
[Au] Autor:Danilowicz C; Hermans L; Coljee V; Prévost C; Prentiss M
[Ad] Endereço:Department of Physics, Harvard University, Cambridge, MA 02138, USA.
[Ti] Título:ATP hydrolysis provides functions that promote rejection of pairings between different copies of long repeated sequences.
[So] Source:Nucleic Acids Res;45(14):8448-8462, 2017 Aug 21.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:During DNA recombination and repair, RecA family proteins must promote rapid joining of homologous DNA. Repeated sequences with >100 base pair lengths occupy more than 1% of bacterial genomes; however, commitment to strand exchange was believed to occur after testing ∼20-30 bp. If that were true, pairings between different copies of long repeated sequences would usually become irreversible. Our experiments reveal that in the presence of ATP hydrolysis even 75 bp sequence-matched strand exchange products remain quite reversible. Experiments also indicate that when ATP hydrolysis is present, flanking heterologous dsDNA regions increase the reversibility of sequence matched strand exchange products with lengths up to ∼75 bp. Results of molecular dynamics simulations provide insight into how ATP hydrolysis destabilizes strand exchange products. These results inspired a model that shows how pairings between long repeated sequences could be efficiently rejected even though most homologous pairings form irreversible products.
[Mh] Termos MeSH primário: Trifosfato de Adenosina/metabolismo
Pareamento de Bases
DNA Bacteriano/metabolismo
Reparo de DNA por Recombinação
Sequências Repetitivas de Ácido Nucleico/genética
[Mh] Termos MeSH secundário: Proteínas de Bactérias/metabolismo
DNA Bacteriano/química
DNA Bacteriano/genética
DNA de Cadeia Simples/genética
Hidrólise
Modelos Genéticos
Conformação de Ácido Nucleico
Recombinases Rec A/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Bacterial Proteins); 0 (DNA, Bacterial); 0 (DNA, Single-Stranded); 8L70Q75FXE (Adenosine Triphosphate); EC 2.7.7.- (Rec A Recombinases)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171023
[Lr] Data última revisão:
171023
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170901
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gkx582


  4 / 3396 MEDLINE  
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[PMID]:28667173
[Au] Autor:Spies M
[Ad] Endereço:From the Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242 maria-spies@uiowa.edu.
[Ti] Título:A time for promiscuity in a eukaryotic recombinase.
[So] Source:J Biol Chem;292(26):11136-11137, 2017 Jun 30.
[Is] ISSN:1083-351X
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The exchange of DNA strands between broken and intact molecules lies at the heart of fundamental cellular processes ranging from repairing DNA damage by homologous recombination to generation of genetic diversity during sexual reproduction. New work by Lee and colleagues utilizes the DNA curtain method, an elegant single-molecule technique, to demonstrate common and idiosyncratic features in the DNA strand exchange mechanisms of three RecA-family recombinases, bacterial RecA, and eukaryotic Rad51 and Dmc1 proteins.
[Mh] Termos MeSH primário: Bactérias/enzimologia
Proteínas de Bactérias/metabolismo
Proteínas de Ciclo Celular/metabolismo
Reparo do DNA/fisiologia
Proteínas de Ligação a DNA/metabolismo
Rad51 Recombinase/metabolismo
Recombinases Rec A/metabolismo
Proteínas de Saccharomyces cerevisiae/metabolismo
Saccharomyces cerevisiae/enzimologia
[Pt] Tipo de publicação:JOURNAL ARTICLE; REVIEW
[Nm] Nome de substância:
0 (Bacterial Proteins); 0 (Cell Cycle Proteins); 0 (DMC1 protein, S cerevisiae); 0 (DNA-Binding Proteins); 0 (Saccharomyces cerevisiae Proteins); EC 2.7.7.- (RAD51 protein, S cerevisiae); EC 2.7.7.- (Rad51 Recombinase); EC 2.7.7.- (Rec A Recombinases)
[Em] Mês de entrada:1707
[Cu] Atualização por classe:170715
[Lr] Data última revisão:
170715
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170702
[St] Status:MEDLINE
[do] DOI:10.1074/jbc.H117.787614


  5 / 3396 MEDLINE  
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[PMID]:28542496
[Au] Autor:Bunnell BE; Escobar JF; Bair KL; Sutton MD; Crane JK
[Ad] Endereço:Department of Medicine, Division of Infectious Diseases, University at Buffalo, Buffalo, NY, United States of America.
[Ti] Título:Zinc blocks SOS-induced antibiotic resistance via inhibition of RecA in Escherichia coli.
[So] Source:PLoS One;12(5):e0178303, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Zinc inhibits the virulence of diarrheagenic E. coli by inducing the envelope stress response and inhibiting the SOS response. The SOS response is triggered by damage to bacterial DNA. In Shiga-toxigenic E. coli, the SOS response strongly induces the production of Shiga toxins (Stx) and of the bacteriophages that encode the Stx genes. In E. coli, induction of the SOS response is accompanied by a higher mutation rate, called the mutator response, caused by a shift to error-prone DNA polymerases when DNA damage is too severe to be repaired by canonical DNA polymerases. Since zinc inhibited the other aspects of the SOS response, we hypothesized that zinc would also inhibit the mutator response, also known as hypermutation. We explored various different experimental paradigms to induce hypermutation triggered by the SOS response, and found that hypermutation was induced not just by classical inducers such as mitomycin C and the quinolone antibiotics, but also by antiviral drugs such as zidovudine and anti-cancer drugs such as 5-fluorouracil, 6-mercaptopurine, and azacytidine. Zinc salts inhibited the SOS response and the hypermutator phenomenon in E. coli as well as in Klebsiella pneumoniae, and was more effective in inhibiting the SOS response than other metals. We then attempted to determine the mechanism by which zinc, applied externally in the medium, inhibits hypermutation. Our results show that zinc interferes with the actions of RecA, and protects LexA from RecA-mediated cleavage, an early step in initiation of the SOS response. The SOS response may play a role in the development of antibiotic resistance and the effect of zinc suggests ways to prevent it.
[Mh] Termos MeSH primário: Resistência Microbiana a Medicamentos/efeitos dos fármacos
Escherichia coli/efeitos dos fármacos
Regulação Bacteriana da Expressão Gênica/efeitos dos fármacos
Recombinases Rec A/antagonistas & inibidores
Resposta SOS (Genética)/efeitos dos fármacos
Zinco/farmacologia
[Mh] Termos MeSH secundário: Antibacterianos/farmacologia
Escherichia coli/genética
Escherichia coli/crescimento & desenvolvimento
Mutação/genética
Recombinases Rec A/genética
Virulência
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Anti-Bacterial Agents); EC 2.7.7.- (Rec A Recombinases); J41CSQ7QDS (Zinc)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170926
[Lr] Data última revisão:
170926
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170526
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0178303


  6 / 3396 MEDLINE  
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[PMID]:28515022
[Au] Autor:Bellio P; Di Pietro L; Mancini A; Piovano M; Nicoletti M; Brisdelli F; Tondi D; Cendron L; Franceschini N; Amicosante G; Perilli M; Celenza G
[Ad] Endereço:Department of Biotechnological and Applied Clinical Sciences, University of l'Aquila, Via Vetoio, 1, 67100 l'Aquila, Italy.
[Ti] Título:SOS response in bacteria: Inhibitory activity of lichen secondary metabolites against Escherichia coli RecA protein.
[So] Source:Phytomedicine;29:11-18, 2017 Jun 15.
[Is] ISSN:1618-095X
[Cp] País de publicação:Germany
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: RecA is a bacterial multifunctional protein essential to genetic recombination, error-prone replicative bypass of DNA damages and regulation of SOS response. The activation of bacterial SOS response is directly related to the development of intrinsic and/or acquired resistance to antimicrobials. Although recent studies directed towards RecA inactivation via ATP binding inhibition described a variety of micromolar affinity ligands, inhibitors of the DNA binding site are still unknown. PURPOSE: Twenty-seven secondary metabolites classified as anthraquinones, depsides, depsidones, dibenzofurans, diphenyl-butenolides, paraconic acids, pseudo-depsidones, triterpenes and xanthones, were investigated for their ability to inhibit RecA from Escherichia coli. They were isolated in various Chilean regions from 14 families and 19 genera of lichens. METHODS: The ATP hydrolytic activity of RecA was quantified detecting the generation of free phosphate in solution. The percentage of inhibition was calculated fixing at 100µM the concentration of the compounds. Deeper investigations were reserved to those compounds showing an inhibition higher than 80%. To clarify the mechanism of inhibition, the semi-log plot of the percentage of inhibition vs. ATP and vs. ssDNA, was evaluated. RESULTS: Only nine compounds showed a percentage of RecA inhibition higher than 80% (divaricatic, perlatolic, alpha-collatolic, lobaric, lichesterinic, protolichesterinic, epiphorellic acids, sphaerophorin and tumidulin). The half-inhibitory concentrations (IC ) calculated for these compounds were ranging from 14.2µM for protolichesterinic acid to 42.6µM for sphaerophorin. Investigations on the mechanism of inhibition showed that all compounds behaved as uncompetitive inhibitors for ATP binding site, with the exception of epiphorellic acid which clearly acted as non-competitive inhibitor of the ATP site. Further investigations demonstrated that epiphorellic acid competitively binds the ssDNA binding site. Kinetic data were confirmed by molecular modelling binding predictions which shows that epiphorellic acid is expected to bind the ssDNA site into the L2 loop of RecA protein. CONCLUSION: In this paper the first RecA ssDNA binding site ligand is described. Our study sets epiphorellic acid as a promising hit for the development of more effective RecA inhibitors. In our drug discovery approach, natural products in general and lichen in particular, represent a successful source of active ligands and structural diversity.
[Mh] Termos MeSH primário: Proteínas de Escherichia coli/antagonistas & inibidores
Líquens/química
Recombinases Rec A/antagonistas & inibidores
Resposta SOS (Genética)/efeitos dos fármacos
[Mh] Termos MeSH secundário: 4-Butirolactona/análogos & derivados
4-Butirolactona/farmacologia
Trifosfato de Adenosina/metabolismo
Antibacterianos/química
Antibacterianos/metabolismo
Antibacterianos/farmacologia
Sítios de Ligação
Chile
DNA de Cadeia Simples/metabolismo
Avaliação Pré-Clínica de Medicamentos/métodos
Escherichia coli/genética
Proteínas de Escherichia coli/metabolismo
Hidrólise
Líquens/metabolismo
Recombinases Rec A/metabolismo
Metabolismo Secundário
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Anti-Bacterial Agents); 0 (DNA, Single-Stranded); 0 (Escherichia coli Proteins); 0 (paraconic acid); 8L70Q75FXE (Adenosine Triphosphate); EC 2.7.7.- (Rec A Recombinases); OL659KIY4X (4-Butyrolactone)
[Em] Mês de entrada:1708
[Cu] Atualização por classe:170818
[Lr] Data última revisão:
170818
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170519
[St] Status:MEDLINE


  7 / 3396 MEDLINE  
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Rey, Luís
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[PMID]:28505340
[Au] Autor:Msaddak A; Rejili M; Durán D; Rey L; Imperial J; Palacios JM; Ruiz-Argüeso T; Mars M
[Ad] Endereço:Research Unit Biodiversity and Valorization of Arid Areas Bioresources (BVBAA)-Faculty of Sciences of Gabès, Erriadh, Zrig 6072, Tunisia.
[Ti] Título:Members of Microvirga and Bradyrhizobium genera are native endosymbiotic bacteria nodulating Lupinus luteus in Northern Tunisian soils.
[So] Source:FEMS Microbiol Ecol;93(6), 2017 Jun 01.
[Is] ISSN:1574-6941
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:The genetic diversity of bacterial populations nodulating Lupinus luteus (yellow lupine) in Northern Tunisia was examined. Phylogenetic analyses of 43 isolates based on recA and gyrB partial sequences grouped them in three clusters, two of which belong to genus Bradyrhizobium (41 isolates) and one, remarkably, to Microvirga (2 isolates), a genus never previously described as microsymbiont of this lupine species. Representatives of the three clusters were analysed in-depth by multilocus sequence analysis of five housekeeping genes (rrs, recA, glnII, gyrB and dnaK). Surprisingly, the Bradyrhizobium cluster with the two isolates LluI4 and LluTb2 may constitute a new species defined by a separate position between Bradyrhizobium manausense and B. denitrificans. A nodC-based phylogeny identified only two groups: one formed by Bradyrhizobium strains included in the symbiovar genistearum and the other by the Microvirga strains. Symbiotic behaviour of representative isolates was tested, and among the seven legumes inoculated only a difference was observed i.e. the Bradyrhizobium strains nodulated Ornithopus compressus unlike the two strains of Microvirga. On the basis of these data, we conclude that L. luteus root nodule symbionts in Northern Tunisia are mostly strains within the B. canariense/B. lupini lineages, and the remaining strains belong to two groups not previously identified as L. luteus endosymbionts: one corresponding to a new clade of Bradyrhizobium and the other to the genus Microvirga.
[Mh] Termos MeSH primário: Bradyrhizobium/genética
Lupinus/microbiologia
Methylobacteriaceae/genética
Nódulos Radiculares de Plantas/microbiologia
Simbiose/fisiologia
[Mh] Termos MeSH secundário: Proteínas de Bactérias/genética
Bradyrhizobium/classificação
Bradyrhizobium/isolamento & purificação
DNA Girase/genética
DNA Bacteriano/genética
Genes Essenciais/genética
Methylobacteriaceae/classificação
Methylobacteriaceae/isolamento & purificação
Tipagem de Sequências Multilocus
Filogenia
Recombinases Rec A/genética
Análise de Sequência de DNA
Solo
Microbiologia do Solo
Simbiose/genética
Tunísia
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Bacterial Proteins); 0 (DNA, Bacterial); 0 (NodD protein, Bacteria); 0 (Soil); EC 2.7.7.- (Rec A Recombinases); EC 5.99.1.3 (DNA Gyrase)
[Em] Mês de entrada:1711
[Cu] Atualização por classe:171116
[Lr] Data última revisão:
171116
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170516
[St] Status:MEDLINE
[do] DOI:10.1093/femsec/fix068


  8 / 3396 MEDLINE  
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[PMID]:28501701
[Au] Autor:Wardell K; Haldenby S; Jones N; Liddell S; Ngo GHP; Allers T
[Ad] Endereço:School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, UK.
[Ti] Título:RadB acts in homologous recombination in the archaeon Haloferax volcanii, consistent with a role as recombination mediator.
[So] Source:DNA Repair (Amst);55:7-16, 2017 Jul.
[Is] ISSN:1568-7856
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:Homologous recombination plays a central role in the repair of double-strand DNA breaks, the restart of stalled replication forks and the generation of genetic diversity. Regulation of recombination is essential since defects can lead to genome instability and chromosomal rearrangements. Strand exchange is a key step of recombination - it is catalysed by RecA in bacteria, Rad51/Dmc1 in eukaryotes and RadA in archaea. RadB, a paralogue of RadA, is present in many archaeal species. RadB has previously been proposed to function as a recombination mediator, assisting in RadA-mediated strand exchange. In this study, we use the archaeon Haloferax volcanii to provide evidence to support this hypothesis. We show that RadB is required for efficient recombination and survival following treatment with DNA-damaging agents, and we identify two point mutations in radA that suppress the ΔradB phenotype. Analysis of these point mutations leads us to propose that the role of RadB is to act as a recombination mediator, which it does by inducing a conformational change in RadA and thereby promoting its polymerisation on DNA.
[Mh] Termos MeSH primário: Proteínas Arqueais/metabolismo
Quebras de DNA de Cadeia Dupla
Haloferax volcanii/enzimologia
Recombinases Rec A/metabolismo
Reparo de DNA por Recombinação
[Mh] Termos MeSH secundário: Sequência de Aminoácidos
Proteínas Arqueais/química
DNA Arqueal/metabolismo
Haloferax volcanii/genética
Recombinases Rec A/química
Alinhamento de Sequência
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Archaeal Proteins); 0 (DNA, Archaeal); EC 2.7.7.- (Rec A Recombinases)
[Em] Mês de entrada:1708
[Cu] Atualização por classe:170810
[Lr] Data última revisão:
170810
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170515
[St] Status:MEDLINE


  9 / 3396 MEDLINE  
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[PMID]:28489851
[Au] Autor:Badrinarayanan A; Le TBK; Spille JH; Cisse II; Laub MT
[Ad] Endereço:Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States of America.
[Ti] Título:Global analysis of double-strand break processing reveals in vivo properties of the helicase-nuclease complex AddAB.
[So] Source:PLoS Genet;13(5):e1006783, 2017 May.
[Is] ISSN:1553-7404
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:In bacteria, double-strand break (DSB) repair via homologous recombination is thought to be initiated through the bi-directional degradation and resection of DNA ends by a helicase-nuclease complex such as AddAB. The activity of AddAB has been well-studied in vitro, with translocation speeds between 400-2000 bp/s on linear DNA suggesting that a large section of DNA around a break site is processed for repair. However, the translocation rate and activity of AddAB in vivo is not known, and how AddAB is regulated to prevent excessive DNA degradation around a break site is unclear. To examine the functions and mechanistic regulation of AddAB inside bacterial cells, we developed a next-generation sequencing-based approach to assay DNA processing after a site-specific DSB was introduced on the chromosome of Caulobacter crescentus. Using this assay we determined the in vivo rates of DSB processing by AddAB and found that putative chi sites attenuate processing in a RecA-dependent manner. This RecA-mediated regulation of AddAB prevents the excessive loss of DNA around a break site, limiting the effects of DSB processing on transcription. In sum, our results, taken together with prior studies, support a mechanism for regulating AddAB that couples two key events of DSB repair-the attenuation of DNA-end processing and the initiation of homology search by RecA-thereby helping to ensure that genomic integrity is maintained during DSB repair.
[Mh] Termos MeSH primário: Proteínas de Bactérias/genética
Quebras de DNA de Cadeia Dupla
Exodesoxirribonucleases/genética
Genoma Bacteriano
[Mh] Termos MeSH secundário: Proteínas de Bactérias/metabolismo
Caulobacter crescentus/genética
Exodesoxirribonucleases/metabolismo
Instabilidade Genômica
Recombinases Rec A/genética
Recombinases Rec A/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Bacterial Proteins); EC 2.7.7.- (Rec A Recombinases); EC 3.1.- (Exodeoxyribonucleases); EC 3.1.11.- (AddAB enzyme)
[Em] Mês de entrada:1706
[Cu] Atualização por classe:170819
[Lr] Data última revisão:
170819
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170511
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pgen.1006783


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[PMID]:28488863
[Au] Autor:Zwarycz AS; Fossat M; Akanyeti O; Lin Z; Rosenman DJ; Garcia AE; Royer CA; Mills KV; Wang C
[Ad] Endereço:Department of Biological Sciences, Rensselaer Polytechnic Institute , Troy, New York 12180, United States.
[Ti] Título:V67L Mutation Fills an Internal Cavity To Stabilize RecA Mtu Intein.
[So] Source:Biochemistry;56(21):2715-2722, 2017 May 30.
[Is] ISSN:1520-4995
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Inteins mediate protein splicing, which has found extensive applications in protein science and biotechnology. In the Mycobacterium tuberculosis RecA mini-mini intein (ΔΔIhh), a single valine to leucine substitution at position 67 (V67L) dramatically increases intein stability and activity. However, crystal structures show that the V67L mutation causes minimal structural rearrangements, with a root-mean-square deviation of 0.2 Å between ΔΔIhh-V67 and ΔΔIhh-L67. Thus, the structural mechanisms for V67L stabilization and activation remain poorly understood. In this study, we used intrinsic tryptophan fluorescence, high-pressure nuclear magnetic resonance (NMR), and molecular dynamics (MD) simulations to probe the structural basis of V67L stabilization of the intein fold. Guanidine hydrochloride denaturation monitored by fluorescence yielded free energy changes (ΔG °) of -4.4 and -6.9 kcal mol for ΔΔIhh-V67 and ΔΔIhh-L67, respectively. High-pressure NMR showed that ΔΔIhh-L67 is more resistant to pressure-induced unfolding than ΔΔIhh-V67 is. The change in the volume of folding (ΔV ) was significantly larger for V67 (71 ± 2 mL mol ) than for L67 (58 ± 3 mL mol ) inteins. The measured difference in ΔV (13 ± 3 mL mol ) roughly corresponds to the volume of the additional methylene group for Leu, supporting the notion that the V67L mutation fills a nearby cavity to enhance intein stability. In addition, we performed MD simulations to show that V67L decreases side chain dynamics and conformational entropy at the active site. It is plausible that changes in cavities in V67L can also mediate allosteric effects to change active site dynamics and enhance intein activity.
[Mh] Termos MeSH primário: Inteínas/genética
Leucina/genética
Mutação
Mycobacterium tuberculosis/enzimologia
Mycobacterium tuberculosis/genética
Recombinases Rec A/química
Recombinases Rec A/genética
Valina/genética
[Mh] Termos MeSH secundário: Fluorescência
Leucina/metabolismo
Simulação de Dinâmica Molecular
Ressonância Magnética Nuclear Biomolecular
Recombinases Rec A/metabolismo
Termodinâmica
Valina/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
EC 2.7.7.- (Rec A Recombinases); GMW67QNF9C (Leucine); HG18B9YRS7 (Valine)
[Em] Mês de entrada:1706
[Cu] Atualização por classe:170623
[Lr] Data última revisão:
170623
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170511
[St] Status:MEDLINE
[do] DOI:10.1021/acs.biochem.6b01264



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