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1.
Int J Biol Macromol ; 261(Pt 2): 129843, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38302027

RESUMO

Homologous recombination plays a key role in double-strand break repair, stalled replication fork repair, and meiosis. The RecA/Rad51 family recombinases catalyze the DNA strand invasion reaction that occurs during homologous recombination. However, the high sequence differences between homologous groups have hindered the thoroughly studies of this ancient protein family. The dynamic mechanisms of the family, particularly at the residual level, remain poorly understood. In this work, five representative RecA/Rad51 recombinase family members from all major kingdoms of living organisms: prokaryotes, eukaryotes, archaea, and viruses, were selected to explore the molecular mechanisms behind their conserved biological significance. A variety of techniques, including all-atom molecular dynamics simulation, perturbation response scanning, and protein structure network analysis, were used to examine the flexibility and correlation of protein domains, distribution of sensors and effectors and conserved hub residues. Furthermore, the potential communication routes between the ATP-binding region and the DNA-binding region of each recombinase were identified. Our results demonstrate the conserved molecular dynamics of these recombinases in the early stage of homologous recombination, including cooperative motions between regions, conserved sensing and effecting functional residue distribution, and conserved hub residues. Meanwhile, the unique ATP-DNA communication routes of each recombinase was also revealed. These results provide new insights into the mechanism of RecA/Rad51 family proteins, and provide new theoretical guidance for the development of allosteric inhibitors and the application of RecA/Rad51 family proteins.


Assuntos
Rad51 Recombinase , Recombinases Rec A , Rad51 Recombinase/genética , Rad51 Recombinase/química , Rad51 Recombinase/metabolismo , Recombinases Rec A/genética , Recombinases Rec A/química , Recombinases Rec A/metabolismo , Proteínas de Ligação a DNA/metabolismo , DNA de Cadeia Simples , DNA/química , Recombinases/genética , Recombinases/metabolismo , Trifosfato de Adenosina
2.
J Biomol Struct Dyn ; 42(4): 2043-2057, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38093709

RESUMO

Mycobacterium tuberculosis RecA (MtRecA), a protein involved in DNA repair, homologous recombination and SOS pathway, contributes to the development of multidrug resistance. ATP binding-site in RecA has been a drug target to disable RecA dependent DNA repair. For the first time, experiments have shown the existence and binding of c-di-AMP to a novel allosteric site in the C-terminal-Domain (CTD) of Mycobacterium smegmatis RecA (MsRecA), a close homolog of MtRecA. In addition, it was observed that the c-di-AMP was not binding to Escherichia coli RecA (EcRecA). This article analyses the possible interactions of the three RecA homologs with the various c-di-AMP conformations to gain insights into the structural basis of the natural preference of c-di-AMP to MsRecA and not to EcRecA, using the structural biology tools. The comparative analysis, based on amino acid composition, homology, motifs, residue types, docking, molecular dynamics simulations and binding free energy calculations, indeed, conclusively indicates strong binding of c-di-AMP to MsRecA. Having very similar results as MsRecA, it is highly plausible for c-di-AMP to strongly bind MtRecA as well. These insights from the in-silico studies adds a new therapeutic approach against TB through design and development of novel allosteric inhibitors for the first time against MtRecA.Communicated by Ramaswamy H. Sarma.


Assuntos
Fosfatos de Dinucleosídeos , Mycobacterium smegmatis , Mycobacterium tuberculosis , Sítios de Ligação , Mycobacterium smegmatis/metabolismo , Mycobacterium tuberculosis/genética , Sítio Alostérico , Recombinases Rec A/química , Proteínas de Bactérias/química
3.
Biochemistry ; 61(24): 2884-2896, 2022 12 20.
Artigo em Inglês | MEDLINE | ID: mdl-36473084

RESUMO

The SOS response is a bacterial DNA damage response pathway that has been heavily implicated in bacteria's ability to evolve resistance to antibiotics. Activation of the SOS response is dependent on the interaction between two bacterial proteins, RecA and LexA. RecA acts as a DNA damage sensor by forming lengthy oligomeric filaments (RecA*) along single-stranded DNA (ssDNA) in an ATP-dependent manner. RecA* can then bind to LexA, the repressor of SOS response genes, triggering LexA degradation and leading to induction of the SOS response. Formation of the RecA*-LexA complex therefore serves as the key "SOS activation signal." Given the challenges associated with studying a complex involving multiple macromolecular interactions, the essential constituents of RecA* that allow LexA cleavage are not well defined. Here, we leverage head-to-tail linked and end-capped RecA constructs as tools to define the minimal RecA* filament that can engage LexA. In contrast to previously postulated models, we found that as few as three linked RecA units are capable of ssDNA binding, LexA binding, and LexA cleavage. We further demonstrate that RecA oligomerization alone is insufficient for LexA cleavage, with an obligate requirement for ATP and ssDNA binding to form a competent SOS activation signal with the linked constructs. Our minimal system for RecA* highlights the limitations of prior models for the SOS activation signal and offers a novel tool that can inform efforts to slow acquired antibiotic resistance by targeting the SOS response.


Assuntos
Proteínas de Bactérias , Resposta SOS em Genética , Proteínas de Bactérias/química , Bactérias/metabolismo , Dano ao DNA , Trifosfato de Adenosina , Recombinases Rec A/química
4.
Chem Biol Drug Des ; 99(6): 839-856, 2022 06.
Artigo em Inglês | MEDLINE | ID: mdl-35278346

RESUMO

Antibiotics and disinfectants resistance is acquired by activating RecA-mediated DNA repair, which maintains ROS-dependent DNA damage caused by the antimicrobial molecules. To increase the efficacy of different antimicrobials, an inhibitor can be developed against RecA protein. The present study aims to design a denovo inhibitor against RecA protein of Acinetobacter baumannii. Pharmacophore-based screening, molecular mechanics, molecular dynamics simulation (MDS), retrosynthetic analysis, and combinatorial synthesis were used to design lead VTRA1.1 against RecA of A. baumannii. Pharmacophore models (structure-based and ligand-based) were created, and a phase library of FDA-approved drugs was prepared. Screening of the phase library against these pharmacophore models selected thirteen lead molecules. These filtered leads were used for the denovo fragment-based design, which produced 253 combinations. These designed molecules were further analyzed for its interaction with active site of RecA that selected a hybrid VTRA1. Further, retrosynthetic analysis and combinatorial synthesis produced 1000 analogs of VTRA1 by more than 100 modifications. These analogs were used for XP docking, binding free energy calculation, and MDS analysis which finally select lead VTRA1.1 against RecA protein. Further, mutations at the interacting residues of RecA with VTRA1.1, alter the unfolding rate of RecA, which suggests the binding of VTRA1.1 to these residues may alter the stability of RecA. It is also found that VTRA1.1 had reduced interaction of RecA with LexA and ssDNA polydT, showing the lead's efficacy in controlling the SOS response. Further, it was also observed that VTRA1.1 does not contain any predicted human off-targets and no cytotoxicity to cell lines. As functional RecA is involved in antimicrobial resistance, denovo designed lead VTRA1.1 against RecA may be further developed as a significant combination for therapeutic uses against A. baumannii.


Assuntos
Acinetobacter baumannii , Acinetobacter baumannii/metabolismo , Antibacterianos/metabolismo , Antibacterianos/farmacologia , Proteínas de Bactérias/metabolismo , Reparo do DNA , Humanos , Simulação de Dinâmica Molecular , Recombinases Rec A/química , Recombinases Rec A/genética , Recombinases Rec A/metabolismo
5.
Sci Rep ; 11(1): 21106, 2021 10 26.
Artigo em Inglês | MEDLINE | ID: mdl-34702889

RESUMO

RecA plays a central role in DNA repair and is a main actor involved in recombination and activation of the SOS response. It is also used in the context of biotechnological applications in recombinase polymerase isothermal amplification (RPA). In this work, we studied the biological properties of seven RecA variants, in particular their recombinogenic activity and their ability to induce the SOS response, to better understand the structure-function relationship of RecA and the effect of combined mutations. We also investigated the biochemical properties of RecA variants that may be useful for the development of biotechnological applications. We showed that Dickeya dadantii RecA (DdRecA) had an optimum strand exchange activity at 30 °C and in the presence of a dNTP mixture that inhibited Escherichia coli RecA (EcRecA). The differences between the CTD and C-tail of the EcRecA and DdRecA domains could explain the altered behaviour of DdRecA. D. radiodurans RecA (DrRecA) was unable to perform recombination and activation of the SOS response in an E. coli context, probably due to its inability to interact with E. coli recombination accessory proteins and SOS LexA repressor. DrRecA strand exchange activity was totally inhibited in the presence of chloride ions but worked well in acetate buffer. The overproduction of Pseudomonas aeruginosa RecA (PaRecA) in an E. coli context was responsible for a higher SOS response and defects in cellular growth. PaRecA was less inhibited by the dNTP mixture than EcRecA. Finally, the study of three variants, namely, EcPa, EcRecAV1 and EcRecAV2, that contained a combination of mutations that, taken independently, are described as improving recombination, led us to raise new hypotheses on the structure-function relationship and on the monomer-monomer interactions that perturb the activity of the protein as a whole.


Assuntos
Proteínas de Ligação a DNA/química , Deinococcus/enzimologia , Dickeya/enzimologia , Proteínas de Escherichia coli/química , Escherichia coli/enzimologia , Pseudomonas aeruginosa/enzimologia , Recombinases Rec A/química , Proteínas de Ligação a DNA/genética , Deinococcus/genética , Dickeya/genética , Escherichia coli/genética , Proteínas de Escherichia coli/genética , Pseudomonas aeruginosa/genética , Recombinases Rec A/genética , Especificidade da Espécie
6.
Curr Opin Genet Dev ; 71: 188-194, 2021 12.
Artigo em Inglês | MEDLINE | ID: mdl-34592688

RESUMO

The fundamental reaction in homologous recombination is the exchange of strands between two homologous DNA molecules. This reaction is carried out by the RecA family of ATPases that polymerize on ssDNA to form a presynaptic filament. This filament then binds to dsDNA to form a synaptic filament, a key intermediate that mediates the search for homology and subsequent strand exchange to produce a new heteroduplex. A recent cryo-EM analysis of synaptic filaments has now shed light on this process. The dsDNA strands are separated on binding to the filament. One strand is sequestrated while the other is freed to sample pairing with the ssDNA. Homology, through heteroduplex formation, promotes dsDNA opening. Lack of homology suppresses it, keeping local synapses short so that multiple synapses can form and increasing the probability of encountering homology.


Assuntos
DNA de Cadeia Simples , Recombinases Rec A , Microscopia Crioeletrônica , DNA/química , DNA de Cadeia Simples/genética , Recombinação Homóloga/genética , Recombinases Rec A/química , Recombinases Rec A/genética , Recombinases Rec A/metabolismo
7.
Int J Parasitol ; 51(10): 841-853, 2021 09.
Artigo em Inglês | MEDLINE | ID: mdl-34273392

RESUMO

Lymphatic filariasis is a debilitating disease that affects over 890 million people in 49 countries. A lack of vaccines, non-availability of adulticidal drugs, the threat of emerging drug resistance against available chemotherapeutics and an incomplete understanding of the immunobiology of the disease have sustained the problem. Characterization of Wolbachia proteins, the bacterial endosymbiont which helps in the growth and development of filarial worms, regulates fecundity in female worms and mediates immunopathogenesis of Lymphatic Filariasis, is an important approach to gain insights into the immunopathogenesis of the disease. In this study, we carried out extensive biochemical characterization of Recombinase A from Wolbachia of the filarial nematode Brugia malayi (wBmRecA) using an Electrophoretic Mobility Shift Assay, an ATP binding and hydrolysis assay, DNA strand exchange reactions, DAPI displacement assay and confocal microscopy, and evaluated anti-filarial activity of RecA inhibitors. Confocal studies showed that wBmRecA was expressed and localised within B. malayi microfilariae (Mf) and uteri and lateral chord of adult females. Recombinant wBmRecA was biochemically active and showed intrinsic binding capacity towards both single-stranded DNA and double-stranded DNA that were enhanced by ATP, suggesting ATP-induced cooperativity. wBmRecA promoted ATP hydrolysis and DNA strand exchange reactions in a concentration-dependent manner, and its binding to DNA was sensitive to temperature, pH and salt concentration. Importantly, the anti-parasitic drug Suramin, and Phthalocyanine tetrasulfonate (PcTs)-based inhibitors Fe-PcTs and 3,4-Cu-PcTs, inhibited wBmRecA activity and affected the motility and viability of Mf. The addition of Doxycycline further enhanced microfilaricidal activity of wBmRecA, suggesting potential synergism. Taken together, the omnipresence of wBmRecA in B. malayi life stages and the potent microfilaricidal activity of RecA inhibitors suggest an important role of wBmRecA in filarial pathogenesis.


Assuntos
Brugia Malayi , Filariose Linfática , Recombinases Rec A/metabolismo , Wolbachia , Animais , Feminino , Humanos , Microfilárias , Recombinases Rec A/antagonistas & inibidores , Recombinases Rec A/química
8.
Indian J Med Microbiol ; 38(3 & 4): 496-499, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33154274

RESUMO

Burkholderia cepacia complex is a Gram-negative opportunistic pathogen usually found in people with an immunocompromised condition such as cystic fibrosis (CF). In a tropical country like India, this organism has been associated with a number of hospital-acquired infections including sepsis. We present here a report of a case of Burkholderia vietnamiensis causing a non-lactational breast abscess in a non-CF patient. The pathogen was identified as B. cepacia using Vitek system and matrix-assisted laser desorption ionisation-time of flight. This was confirmed by polymerase chain reaction (PCR) using recA genus-specific gene and sequencing of the PCR amplicons. recA-restriction fragment length polymorphism and recA gene sequencing revealed that the isolate is B. vietnamiensis. This is the first description of B. vietnamiensis isolated from a clinical case from India.


Assuntos
Abscesso/microbiologia , Doenças Mamárias/microbiologia , Infecções por Burkholderia/microbiologia , Burkholderia/isolamento & purificação , Abscesso/tratamento farmacológico , Adulto , Antibacterianos/uso terapêutico , Sequência de Bases , Doenças Mamárias/tratamento farmacológico , Burkholderia/classificação , Burkholderia/genética , Infecções por Burkholderia/tratamento farmacológico , DNA Ribossômico/química , Feminino , Humanos , Índia , Levofloxacino/uso terapêutico , Polimorfismo de Fragmento de Restrição , RNA Ribossômico 16S/genética , Recombinases Rec A/química , Recombinases Rec A/genética
9.
Int J Mol Sci ; 21(19)2020 Oct 07.
Artigo em Inglês | MEDLINE | ID: mdl-33036395

RESUMO

Deinococcus radiodurans (Dr) has one of the most robust DNA repair systems, which is capable of withstanding extreme doses of ionizing radiation and other sources of DNA damage. DrRecA, a central enzyme of recombinational DNA repair, is essential for extreme radioresistance. In the presence of ATP, DrRecA forms nucleoprotein filaments on DNA, similar to other bacterial RecA and eukaryotic DNA strand exchange proteins. However, DrRecA catalyzes DNA strand exchange in a unique reverse pathway. Here, we study the dynamics of DrRecA filaments formed on individual molecules of duplex and single-stranded DNA, and we follow conformational transitions triggered by ATP hydrolysis. Our results reveal that ATP hydrolysis promotes rapid DrRecA dissociation from duplex DNA, whereas on single-stranded DNA, DrRecA filaments interconvert between stretched and compressed conformations, which is a behavior shared by E. coli RecA and human Rad51. This indicates a high conservation of conformational switching in nucleoprotein filaments and suggests that additional factors might contribute to an inverse pathway of DrRecA strand exchange.


Assuntos
Trifosfato de Adenosina/química , Proteínas de Bactérias/química , Deinococcus/enzimologia , Modelos Moleculares , Conformação Molecular , Recombinases Rec A/química , Imagem Individual de Molécula , Trifosfato de Adenosina/metabolismo , Proteínas de Bactérias/metabolismo , DNA de Cadeia Simples/química , DNA de Cadeia Simples/metabolismo , Proteínas de Ligação a DNA/química , Proteínas de Ligação a DNA/metabolismo , Hidrólise , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Recombinases Rec A/metabolismo , Imagem Individual de Molécula/métodos
10.
FEBS Lett ; 594(21): 3464-3476, 2020 11.
Artigo em Inglês | MEDLINE | ID: mdl-32880917

RESUMO

The RecA protein plays a key role in bacterial homologous recombination (HR) and acts through assembly of long helical filaments around single-stranded DNA in the presence of ATP. Large-scale conformational changes induced by ATP hydrolysis result in transitions between stretched and compressed forms of the filament. Here, using a single-molecule approach, we show that compressed RecA nucleoprotein filaments can exist in two distinct interconvertible states depending on the presence of ADP in the monomer-monomer interface. Binding of ADP promotes cooperative conformational transitions and directly affects mechanical properties of the filament. Our findings reveal that RecA nucleoprotein filaments are able to continuously cycle between three mechanically distinct states that might have important implications for RecA-mediated processes of HR.


Assuntos
DNA de Cadeia Simples/química , DNA de Cadeia Simples/metabolismo , Proteínas de Ligação a DNA/química , Proteínas de Ligação a DNA/metabolismo , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/metabolismo , Recombinases Rec A/química , Recombinases Rec A/metabolismo , Imagem Individual de Molécula , Difosfato de Adenosina/metabolismo , Trifosfato de Adenosina/metabolismo , Apoproteínas/química , Apoproteínas/metabolismo , Escherichia coli
11.
J Biol Chem ; 295(30): 10368-10379, 2020 07 24.
Artigo em Inglês | MEDLINE | ID: mdl-32513870

RESUMO

Induction of the SOS response, a cellular system triggered by DNA damage in bacteria, depends on DNA replication for the generation of the SOS signal, ssDNA. RecA binds to ssDNA, forming filaments that stimulate proteolytic cleavage of the LexA transcriptional repressor, allowing expression of > 40 gene products involved in DNA repair and cell cycle regulation. Here, using a DNA replication system reconstituted in vitro in tandem with a LexA cleavage assay, we studied LexA cleavage during DNA replication of both undamaged and base-damaged templates. Only a ssDNA-RecA filament supported LexA cleavage. Surprisingly, replication of an undamaged template supported levels of LexA cleavage like that induced by a template carrying two site-specific cyclobutane pyrimidine dimers. We found that two processes generate ssDNA that could support LexA cleavage. 1) During unperturbed replication, single-stranded regions formed because of stochastic uncoupling of the leading-strand DNA polymerase from the replication fork DNA helicase, and 2) on the damaged template, nascent leading-strand gaps were generated by replisome lesion skipping. The two pathways differed in that RecF stimulated LexA cleavage during replication of the damaged template, but not normal replication. RecF appears to facilitate RecA filament formation on the leading-strand ssDNA gaps generated by replisome lesion skipping.


Assuntos
Proteínas de Bactérias/química , Replicação do DNA , DNA Bacteriano/química , DNA de Cadeia Simples/química , Escherichia coli/química , Proteólise , Serina Endopeptidases/química , Proteínas de Bactérias/metabolismo , DNA Bacteriano/biossíntese , DNA de Cadeia Simples/biossíntese , Proteínas de Ligação a DNA/química , Proteínas de Ligação a DNA/metabolismo , Escherichia coli/metabolismo , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/metabolismo , Recombinases Rec A/química , Recombinases Rec A/metabolismo , Serina Endopeptidases/metabolismo
12.
Phys Chem Chem Phys ; 22(21): 11928-11935, 2020 Jun 04.
Artigo em Inglês | MEDLINE | ID: mdl-32432615

RESUMO

Polyamines are naturally occurring cationic molecules in cells. In addition to their roles in modulating gene expression and cell proliferation, they have been shown to stimulate DNA recombination. The molecular mechanism for stimulation is not clear. We utilized single-molecule tethered particle motion (TPM) experiments to investigate how polyamines stimulate RecA-mediated recombination. We showed that natural polyamines, spermine and spermidine, condense duplex DNA, but with different efficiencies. While ∼300 µM of spermine condenses 50% of duplex DNA, 2.0 mM of spermidine is required to achieve the same level of condensation. The condensation takes place in a stepwise manner, and is reversible upon removal of polyamines. We also showed that addition of polyamines stimulates the duplex capture activity of RecA filament and stabilizes the intermediates with longer dwell time. Through condensing duplex DNA and stabilizing the complex of RecA filaments and duplex DNA, polyamines stimulate the formation of functional intermediates by ∼20-fold, and promote recombination progression.


Assuntos
DNA/química , Recombinases Rec A/química , Recombinação Genética/efeitos dos fármacos , Espermidina/química , Espermina/química , DNA/genética , Ácidos Nucleicos Imobilizados/química , Ácidos Nucleicos Imobilizados/genética
13.
Nucleic Acids Res ; 48(12): 6640-6653, 2020 07 09.
Artigo em Inglês | MEDLINE | ID: mdl-32449930

RESUMO

G-quadruplex (G4) DNA structures can form physical barriers within the genome that must be unwound to ensure cellular genomic integrity. Here, we report unanticipated roles for the Escherichia coli Rep helicase and RecA recombinase in tolerating toxicity induced by G4-stabilizing ligands in vivo. We demonstrate that Rep and Rep-X (an enhanced version of Rep) display G4 unwinding activities in vitro that are significantly higher than the closely related UvrD helicase. G4 unwinding mediated by Rep involves repetitive cycles of G4 unfolding and refolding fueled by ATP hydrolysis. Rep-X and Rep also dislodge G4-stabilizing ligands, in agreement with our in vivo G4-ligand sensitivity result. We further demonstrate that RecA filaments disrupt G4 structures and remove G4 ligands in vitro, consistent with its role in countering cellular toxicity of G4-stabilizing ligands. Together, our study reveals novel genome caretaking functions for Rep and RecA in resolving deleterious G4 structures.


Assuntos
DNA Helicases/química , Replicação do DNA/genética , Proteínas de Ligação a DNA/química , Proteínas de Escherichia coli/química , Quadruplex G , Recombinases Rec A/química , Trifosfato de Adenosina/química , DNA Helicases/genética , Proteínas de Ligação a DNA/genética , Escherichia coli/química , Escherichia coli/genética , Proteínas de Escherichia coli/genética , Ligantes , Conformação de Ácido Nucleico , Recombinases Rec A/genética
14.
Infect Genet Evol ; 82: 104314, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32268193

RESUMO

The current study aimed to identify putative drug targets of multidrug resistant Acinetobacter baumannii (MDRAb) and study the therapeutic potential of natural epiestriol-16 by computer aided virtual screening and in vitro studies. The clinical isolates (n = 5) showed extreme dug resistance to carbapenems and colistins (p ≤ .05). Computational screening suggested that out of 236 natural molecules selected, 06 leads were qualified for drug likeliness, pharmacokinetic features and one potential molecule namely natural epiestriol-16 (16b-Hydroxy-17a-estradiol) exhibited significant binding potential towards four prioritised drug targets in comparison with the binding of faropenem to their usual target. Natural epiestriol demonstrated profound binding to the outer membrane protein (Omp38), protein RecA (RecA), orotate phosphoribosyltransferase (PyrE) and orotidine 5'-phosphate decarboxylase (PyrF) with binding energy of -6.0, -7.3, -7.3 and -8.0 kcal/mol respectively. MD simulations suggested that 16-epiestriol-receptor complexes demonstrated stability throughout the simulation. The growth curve and time kill assays revealed that MDRAb showed resistance to faropenem and polymyxin-B and the pure epiestriol-16 showed significant inhibitory properties at a concentration of 200 µg/mL (p ≤ .5). Thus, natural epiestriol-16 can be used as potential inhibitor against the prioritised targets of MDRAb and this study provide insight for drug development against carbapenem and colistin resistant A. baumannii.


Assuntos
Acinetobacter baumannii/efeitos dos fármacos , Antibacterianos/farmacologia , Proteínas de Bactérias/química , Farmacorresistência Bacteriana Múltipla/genética , Estriol/farmacologia , Infecções por Acinetobacter/microbiologia , Acinetobacter baumannii/genética , Acinetobacter baumannii/isolamento & purificação , Antibacterianos/química , Antibacterianos/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Carbapenêmicos/farmacologia , Simulação por Computador , Proteínas de Ligação a DNA/química , Proteínas de Ligação a DNA/metabolismo , Farmacorresistência Bacteriana Múltipla/efeitos dos fármacos , Estriol/química , Estriol/metabolismo , Humanos , Testes de Sensibilidade Microbiana , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Terapia de Alvo Molecular , Recombinases Rec A/química , Recombinases Rec A/metabolismo
15.
J Biomol Struct Dyn ; 38(1): 114-123, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-30688163

RESUMO

Deinococcus RecA (DrRecA) protein is a key repair enzyme and contributes to efficient DNA repair of Deinococcus radiodurans. Phosphorylation of DrRecA at Y77 (tyrosine 77) and T318 (threonine 318) residues modifies the structural and conformational switching that impart the efficiency and activity of DrRecA. Dynamics comparisons of DrRecA with its phosphorylated analogues support the idea that phosphorylation of Y77 and T318 sites could change the dynamics and conformation plasticity of DrRecA. Furthermore, docking studies showed that phosphorylation increases the binding preference of DrRecA towards dATP versus ATP and for double-strand DNA versus single-strand DNA. This work supporting the idea that phosphorylation can modulate the crucial functions of this protein and having good concordance with the experimental data. AbbreviationsDrRecADeinococcus RecADSBDNA double-strand breakshDNAheteroduplex DNASTYPKserine/threonine/tyrosine protein kinaseT318threonine 318Y77tyrosine 77Communicated by Ramaswamy H. Sarma.


Assuntos
Deinococcus/enzimologia , Deinococcus/efeitos da radiação , Tolerância a Radiação , Recombinases Rec A/química , Recombinases Rec A/metabolismo , Aminoácidos/química , Aminoácidos/metabolismo , Dano ao DNA , Reparo do DNA , DNA de Cadeia Simples , Modelos Moleculares , Fosforilação , Relação Estrutura-Atividade
16.
Biochem Soc Trans ; 47(5): 1511-1531, 2019 10 31.
Artigo em Inglês | MEDLINE | ID: mdl-31654073

RESUMO

Recombinases are responsible for homologous recombination and maintenance of genome integrity. In Escherichia coli, the recombinase RecA forms a nucleoprotein filament with the ssDNA present at a DNA break and searches for a homologous dsDNA to use as a template for break repair. During the first step of this process, the ssDNA is bound to RecA and stretched into a Watson-Crick base-paired triplet conformation. The RecA nucleoprotein filament also contains ATP and Mg2+, two cofactors required for RecA activity. Then, the complex starts a homology search by interacting with and stretching dsDNA. Thanks to supercoiling, intersegment sampling and RecA clustering, a genome-wide homology search takes place at a relevant metabolic timescale. When a region of homology 8-20 base pairs in length is found and stabilized, DNA strand exchange proceeds, forming a heteroduplex complex that is resolved through a combination of DNA synthesis, ligation and resolution. RecA activities can take place without ATP hydrolysis, but this latter activity is necessary to improve and accelerate the process. Protein flexibility and monomer-monomer interactions are fundamental for RecA activity, which functions cooperatively. A structure/function relationship analysis suggests that the recombinogenic activity can be improved and that recombinases have an inherently large recombination potential. Understanding this relationship is essential for designing RecA derivatives with enhanced activity for biotechnology applications. For example, this protein is a major actor in the recombinase polymerase isothermal amplification (RPA) used in point-of-care diagnostics.


Assuntos
DNA Bacteriano/genética , DNA de Cadeia Simples/genética , Proteínas de Ligação a DNA/genética , Proteínas de Escherichia coli/genética , Recombinases Rec A/genética , Recombinação Genética , Trifosfato de Adenosina/metabolismo , Sítios de Ligação , Proteínas de Ligação a DNA/química , Proteínas de Ligação a DNA/metabolismo , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/metabolismo , Hidrólise , Conformação Proteica , Recombinases Rec A/química , Recombinases Rec A/metabolismo
17.
Nucleic Acids Res ; 47(15): 7798-7808, 2019 09 05.
Artigo em Inglês | MEDLINE | ID: mdl-31372639

RESUMO

Homologous recombination is a fundamental process in all living organisms that allows the faithful repair of DNA double strand breaks, through the exchange of DNA strands between homologous regions of the genome. Results of three decades of investigation and recent fruitful observations have unveiled key elements of the reaction mechanism, which proceeds along nucleofilaments of recombinase proteins of the RecA family. Yet, one essential aspect of homologous recombination has largely been overlooked when deciphering the mechanism: while ATP is hydrolyzed in large quantity during the process, how exactly hydrolysis influences the DNA strand exchange reaction at the structural level remains to be elucidated. In this study, we build on a previous geometrical approach that studied the RecA filament variability without bound DNA to examine the putative implication of ATP hydrolysis on the structure, position, and interactions of up to three DNA strands within the RecA nucleofilament. Simulation results on modeled intermediates in the ATP cycle bring important clues about how local distortions in the DNA strand geometries resulting from ATP hydrolysis can aid sequence recognition by promoting local melting of already formed DNA heteroduplex and transient reverse strand exchange in a weaving type of mechanism.


Assuntos
Trifosfato de Adenosina/química , DNA de Cadeia Simples/química , DNA/química , Recombinação Homóloga , Ácidos Nucleicos Heteroduplexes/química , Recombinases Rec A/química , Trifosfato de Adenosina/metabolismo , Bactérias/genética , Bactérias/metabolismo , Sítios de Ligação , DNA/genética , DNA/metabolismo , Quebras de DNA de Cadeia Dupla , DNA de Cadeia Simples/genética , DNA de Cadeia Simples/metabolismo , Hidrólise , Simulação de Dinâmica Molecular , Conformação de Ácido Nucleico , Ácidos Nucleicos Heteroduplexes/genética , Ácidos Nucleicos Heteroduplexes/metabolismo , Ligação Proteica , Conformação Proteica , Recombinases Rec A/genética , Recombinases Rec A/metabolismo
18.
J Biol Chem ; 294(21): 8606-8616, 2019 05 24.
Artigo em Inglês | MEDLINE | ID: mdl-30975899

RESUMO

DNA recombination resulting from RecA-mediated strand exchange aided by RecBCD proteins often enables accurate repair of DNA double-strand breaks. However, the process of recombinational repair between short DNA regions of accidental similarity can lead to fatal genomic rearrangements. Previous studies have probed how effectively RecA discriminates against interactions involving a short similar sequence that is embedded in otherwise dissimilar sequences but have not yielded fully conclusive results. Here, we present results of in vitro experiments with fluorescent probes strategically located on the interacting DNA fragments used for recombination. Our findings suggest that DNA synthesis increases the stability of the recombination products. Fluorescence measurements can also probe the homology dependence of the extension of invading DNA strands in D-loops formed by RecA-mediated strand exchange. We examined the slow extension of the invading strand in a D-loop by DNA polymerase (Pol) IV and the more rapid extension by DNA polymerase LF-Bsu We found that when DNA Pol IV extends the invading strand in a D-loop formed by RecA-mediated strand exchange, the extension afforded by 82 bp of homology is significantly longer than the extension on 50 bp of homology. In contrast, the extension of the invading strand in D-loops by DNA LF-Bsu Pol is similar for intermediates with ≥50 bp of homology. These results suggest that fatal genomic rearrangements due to the recombination of small regions of accidental homology may be reduced if RecA-mediated strand exchange is immediately followed by DNA synthesis by a slow polymerase.


Assuntos
DNA Bacteriano/química , Proteínas de Ligação a DNA/química , Proteínas de Escherichia coli/química , Escherichia coli/enzimologia , Recombinação Homóloga , Recombinases Rec A/química , Sondas de DNA , DNA Bacteriano/genética , DNA Bacteriano/metabolismo , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Escherichia coli/genética , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Recombinases Rec A/genética , Recombinases Rec A/metabolismo
19.
PLoS One ; 14(4): e0214601, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30998678

RESUMO

RecA is a multifunctional protein that plays a central role in DNA repair in bacteria. The structural Make ATP Work motif (MAW) is proposed to control the ATPase activity of RecA. In the present work, we report the biochemical activity and structural effects of the L53Q mutation at the MAW motif of the RecA protein from H. seropedicae (HsRecA L53Q). In vitro studies showed that HsRecA L53Q can bind ADP, ATP, and ssDNA, as does wild-type RecA. However, the ATPase and DNA-strand exchange activities were completely lost. In vivo studies showed that the expression of HsRecA L53Q in E. coli recA1 does not change its phenotype when cells were challenged with MMS and UV. Molecular dynamics simulations showed the L53Q point mutation did not cause large conformational changes in the HsRecA structure. However, there is a difference on dynamical cross-correlation movements of the residues involved in contacts within the ATP binding site and regions that hold the DNA binding sites. Additionally, a new hydrogen bond, formed between Q53 and T49, was hypothesized to allow an independent motion of the MAW motif from the hydrophobic core, what could explain the observed loss of activity of HsRecA L53Q.


Assuntos
Trifosfato de Adenosina/metabolismo , Reparo do DNA , Herbaspirillum/genética , Recombinases Rec A/genética , Adenosina Trifosfatases/metabolismo , Motivos de Aminoácidos , Sítios de Ligação , DNA de Cadeia Simples/metabolismo , Escherichia coli/metabolismo , Escherichia coli/efeitos da radiação , Hidrólise , Simulação de Dinâmica Molecular , Mutação Puntual , Ligação Proteica , Estrutura Terciária de Proteína , Recombinases Rec A/química , Recombinases Rec A/metabolismo , Raios Ultravioleta
20.
Nucleic Acids Res ; 47(10): 5170-5180, 2019 06 04.
Artigo em Inglês | MEDLINE | ID: mdl-30941419

RESUMO

Homologous recombination (HR) maintains genome stability by promoting accurate DNA repair. Two recombinases, RAD51 and DMC1, are central to HR repair and form dynamic nucleoprotein filaments in vivo under tight regulation. However, the interplay between positive and negative regulators to control the dynamic assembly/disassembly of RAD51/DMC1 filaments in multicellular eukaryotes remains poorly characterized. Here, we report an antagonism between BRCA2, a well-studied positive mediator of RAD51/DMC1, and FIDGETIN-LIKE-1 (FIGL1), which we previously proposed as a negative regulator of RAD51/DMC1. Through forward genetic screen, we identified a mutation in one of the two Arabidopsis BRCA2 paralogs that suppresses the meiotic phenotypes of figl1. Consistent with the antagonistic roles of BRCA2 and FIGL1, the figl1 mutation in the brca2 background restores RAD51/DMC1 focus formation and homologous chromosome interaction at meiosis, and RAD51 focus formation in somatic cells. This study shows that BRCA2 and FIGL1 have antagonistic effects on the dynamics of RAD51/DMC1-dependent DNA transactions to promote accurate HR repair.


Assuntos
ATPases Associadas a Diversas Atividades Celulares/antagonistas & inibidores , Proteínas de Arabidopsis/antagonistas & inibidores , Proteínas de Ciclo Celular/antagonistas & inibidores , Proteínas de Ligação a DNA/antagonistas & inibidores , Epistasia Genética , Recombinação Homóloga , Proteínas Associadas aos Microtúbulos/antagonistas & inibidores , Nucleoproteínas/química , ATPases Associadas a Diversas Atividades Celulares/metabolismo , Arabidopsis/metabolismo , Proteínas de Arabidopsis/química , Proteínas de Arabidopsis/metabolismo , Proteínas de Ciclo Celular/química , Proteínas de Ciclo Celular/metabolismo , DNA/química , Dano ao DNA , Reparo do DNA , Proteínas de Ligação a DNA/química , Proteínas de Ligação a DNA/metabolismo , Meiose , Proteínas Associadas aos Microtúbulos/metabolismo , Modelos Genéticos , Mutação , Fenótipo , Rad51 Recombinase/química , Recombinases Rec A/química , Reparo de DNA por Recombinação
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