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1.
EMBO J ; 42(20): e110844, 2023 10 16.
Article in English | MEDLINE | ID: mdl-37661798

ABSTRACT

Homologous recombination (HR) is a prominent DNA repair pathway maintaining genome integrity. Mutations in many HR genes lead to cancer predisposition. Paradoxically, the implication of the pivotal HR factor RAD51 on cancer development remains puzzling. Particularly, no RAD51 mouse models are available to address the role of RAD51 in aging and carcinogenesis in vivo. We engineered a mouse model with an inducible dominant-negative form of RAD51 (SMRad51) that suppresses RAD51-mediated HR without stimulating alternative mutagenic repair pathways. We found that in vivo expression of SMRad51 led to replicative stress, systemic inflammation, progenitor exhaustion, premature aging and reduced lifespan, but did not trigger tumorigenesis. Expressing SMRAD51 in a breast cancer predisposition mouse model (PyMT) decreased the number and the size of tumors, revealing an anti-tumor activity of SMRAD51. We propose that these in vivo phenotypes result from chronic endogenous replication stress caused by HR decrease, which preferentially targets progenitors and tumor cells. Our work underlines the importance of RAD51 activity for progenitor cell homeostasis, preventing aging and more generally for the balance between cancer and aging.


Subject(s)
Neoplasms , Rad51 Recombinase , Animals , Mice , Aging/genetics , Carcinogenesis/genetics , Cell Transformation, Neoplastic , DNA Damage , DNA Repair , Homologous Recombination , Rad51 Recombinase/genetics , Rad51 Recombinase/metabolism
2.
Nucleic Acids Res ; 52(12): 7337-7353, 2024 Jul 08.
Article in English | MEDLINE | ID: mdl-38828772

ABSTRACT

In vertebrates, the BRCA2 protein is essential for meiotic and somatic homologous recombination due to its interaction with the RAD51 and DMC1 recombinases through FxxA and FxPP motifs (here named A- and P-motifs, respectively). The A-motifs present in the eight BRC repeats of BRCA2 compete with the A-motif of RAD51, which is responsible for its self-oligomerization. BRCs thus disrupt RAD51 nucleoprotein filaments in vitro. The role of the P-motifs is less studied. We recently found that deletion of Brca2 exons 12-14 encoding one of them (the prototypical 'PhePP' motif), disrupts DMC1 but not RAD51 function in mouse meiosis. Here we provide a mechanistic explanation for this phenotype by solving the crystal structure of the complex between a BRCA2 fragment containing the PhePP motif and DMC1. Our structure reveals that, despite sharing a conserved phenylalanine, the A- and P-motifs bind to distinct sites on the ATPase domain of the recombinases. The P-motif interacts with a site that is accessible in DMC1 octamers and nucleoprotein filaments. Moreover, we show that this interaction also involves the adjacent protomer and thus increases the stability of the DMC1 nucleoprotein filaments. We extend our analysis to other P-motifs from RAD51AP1 and FIGNL1.


Subject(s)
Amino Acid Motifs , BRCA2 Protein , Cell Cycle Proteins , DNA-Binding Proteins , Protein Binding , Rad51 Recombinase , Rad51 Recombinase/metabolism , Rad51 Recombinase/genetics , Rad51 Recombinase/chemistry , BRCA2 Protein/metabolism , BRCA2 Protein/chemistry , BRCA2 Protein/genetics , Animals , Cell Cycle Proteins/metabolism , Cell Cycle Proteins/genetics , Cell Cycle Proteins/chemistry , DNA-Binding Proteins/metabolism , DNA-Binding Proteins/genetics , DNA-Binding Proteins/chemistry , Mice , Humans , Binding Sites , Models, Molecular , Crystallography, X-Ray , Homologous Recombination , Phosphate-Binding Proteins
3.
Nucleic Acids Res ; 51(6): 2800-2817, 2023 04 11.
Article in English | MEDLINE | ID: mdl-36806960

ABSTRACT

RecA-mediated homologous recombination (HR) is a key mechanism for genome maintenance and plasticity in bacteria. It proceeds through RecA assembly into a dynamic filament on ssDNA, the presynaptic filament, which mediates DNA homology search and ordered DNA strand exchange. Here, we combined structural, single molecule and biochemical approaches to characterize the ATP-dependent assembly mechanism of the presynaptic filament of RecA from Streptococcus pneumoniae (SpRecA), in comparison to the Escherichia coli RecA (EcRecA) paradigm. EcRecA polymerization on ssDNA is assisted by the Single-Stranded DNA Binding (SSB) protein, which unwinds ssDNA secondary structures that block EcRecA nucleofilament growth. We report by direct microscopic analysis of SpRecA filamentation on ssDNA that neither of the two paralogous pneumococcal SSBs could assist the extension of SpRecA nucleopolymers. Instead, we found that the conserved RadA helicase promotes SpRecA nucleofilamentation in an ATP-dependent manner. This allowed us to solve the atomic structure of such a long native SpRecA nucleopolymer by cryoEM stabilized with ATPγS. It was found to be equivalent to the crystal structure of the EcRecA filament with a marked difference in how RecA mediates nucleotide orientation in the stretched ssDNA. Then, our results show that SpRecA and EcRecA HR activities are different, in correlation with their distinct ATP-dependent ssDNA binding modes.


Subject(s)
Rec A Recombinases , Streptococcus pneumoniae , Adenosine Triphosphate/metabolism , DNA/metabolism , DNA, Single-Stranded/genetics , DNA, Single-Stranded/metabolism , Escherichia coli/genetics , Escherichia coli/metabolism , Rec A Recombinases/metabolism , Rec A Recombinases/ultrastructure , Streptococcus pneumoniae/genetics , Streptococcus pneumoniae/metabolism , Cryoelectron Microscopy
4.
J Med Genet ; 60(11): 1116-1126, 2023 Nov.
Article in English | MEDLINE | ID: mdl-37308287

ABSTRACT

BACKGROUND: Mirror movements are involuntary movements of one hand that mirror intentional movements of the other hand. Congenital mirror movements (CMM) is a rare genetic disorder with autosomal dominant inheritance, in which mirror movements are the main neurological manifestation. CMM is associated with an abnormal decussation of the corticospinal tract, a major motor tract for voluntary movements. RAD51 is known to play a key role in homologous recombination with a critical function in DNA repair. While RAD51 haploinsufficiency was first proposed to explain CMM, other mechanisms could be involved. METHODS: We performed Sanger sequencing of RAD51 in five newly identified CMM families to identify new pathogenic variants. We further investigated the expression of wild-type and mutant RAD51 in the patients' lymphoblasts at mRNA and protein levels. We then characterised the functions of RAD51 altered by non-truncating variants using biochemical approaches. RESULTS: The level of wild-type RAD51 protein was lower in the cells of all patients with CMM compared with their non-carrier relatives. The reduction was less pronounced in asymptomatic carriers. In vitro, mutant RAD51 proteins showed loss-of-function for polymerisation, DNA binding and strand exchange activity. CONCLUSION: Our study demonstrates that RAD51 haploinsufficiency, including loss-of-function of non-truncating variants, results in CMM. The incomplete penetrance likely results from post-transcriptional compensation. Changes in RAD51 levels and/or polymerisation properties could influence guidance of the corticospinal axons during development. Our findings open up new perspectives to understand the role of RAD51 in neurodevelopment.

5.
Nucleic Acids Res ; 50(17): 9909-9929, 2022 09 23.
Article in English | MEDLINE | ID: mdl-36107774

ABSTRACT

DNA lesions in S phase threaten genome stability. The DNA damage tolerance (DDT) pathways overcome these obstacles and allow completion of DNA synthesis by the use of specialised translesion (TLS) DNA polymerases or through recombination-related processes. However, how these mechanisms coordinate with each other and with bulk replication remains elusive. To address these issues, we monitored the variation of replication intermediate architecture in response to ultraviolet irradiation using transmission electron microscopy. We show that the TLS polymerase η, able to accurately bypass the major UV lesion and mutated in the skin cancer-prone xeroderma pigmentosum variant (XPV) syndrome, acts at the replication fork to resolve uncoupling and prevent post-replicative gap accumulation. Repriming occurs as a compensatory mechanism when this on-the-fly mechanism cannot operate, and is therefore predominant in XPV cells. Interestingly, our data support a recombination-independent function of RAD51 at the replication fork to sustain repriming. Finally, we provide evidence for the post-replicative commitment of recombination in gap repair and for pioneering observations of in vivo recombination intermediates. Altogether, we propose a chronology of UV damage tolerance in human cells that highlights the key role of polη in shaping this response and ensuring the continuity of DNA synthesis.


Subject(s)
DNA Repair , Xeroderma Pigmentosum , DNA Damage , DNA Replication , DNA-Directed DNA Polymerase/genetics , DNA-Directed DNA Polymerase/metabolism , Humans , Ultraviolet Rays , Xeroderma Pigmentosum/genetics
6.
Nucleic Acids Res ; 50(5): 2651-2666, 2022 03 21.
Article in English | MEDLINE | ID: mdl-35137208

ABSTRACT

Selection of the appropriate DNA double-strand break (DSB) repair pathway is decisive for genetic stability. It is proposed to act according to two steps: 1-canonical nonhomologous end-joining (C-NHEJ) versus resection that generates single-stranded DNA (ssDNA) stretches; 2-on ssDNA, gene conversion (GC) versus nonconservative single-strand annealing (SSA) or alternative end-joining (A-EJ). Here, we addressed the mechanisms by which RAD51 regulates this second step, preventing nonconservative repair in human cells. Silencing RAD51 or BRCA2 stimulated both SSA and A-EJ, but not C-NHEJ, validating the two-step model. Three different RAD51 dominant-negative forms (DN-RAD51s) repressed GC and stimulated SSA/A-EJ. However, a fourth DN-RAD51 repressed SSA/A-EJ, although it efficiently represses GC. In living cells, the three DN-RAD51s that stimulate SSA/A-EJ failed to load efficiently onto damaged chromatin and inhibited the binding of endogenous RAD51, while the fourth DN-RAD51, which inhibits SSA/A-EJ, efficiently loads on damaged chromatin. Therefore, the binding of RAD51 to DNA, rather than its ability to promote GC, is required for SSA/A-EJ inhibition by RAD51. We showed that RAD51 did not limit resection of endonuclease-induced DSBs, but prevented spontaneous and RAD52-induced annealing of complementary ssDNA in vitro. Therefore, RAD51 controls the selection of the DSB repair pathway, protecting genome integrity from nonconservative DSB repair through ssDNA occupancy, independently of the promotion of CG.


Subject(s)
DNA Breaks, Double-Stranded , Rad51 Recombinase , Chromatin , DNA End-Joining Repair , DNA Repair , DNA, Single-Stranded/genetics , Humans , Rad51 Recombinase/metabolism
7.
Mol Cell ; 48(4): 560-71, 2012 Nov 30.
Article in English | MEDLINE | ID: mdl-23084832

ABSTRACT

The E. coli chromosome is condensed into insulated regions termed macrodomains (MDs), which are essential for genomic packaging. How chromosomal MDs are specifically organized and compacted is unknown. Here, we report studies revealing the molecular basis for Terminus-containing (Ter) chromosome condensation by the Ter-specific factor MatP. MatP contains a tripartite fold with a four-helix bundle DNA-binding motif, ribbon-helix-helix and C-terminal coiled-coil. Strikingly, MatP-matS structures show that the MatP coiled-coils form bridged tetramers that flexibly link distant matS sites. Atomic force microscopy and electron microscopy studies demonstrate that MatP alone loops DNA. Mutation of key coiled-coil residues destroys looping and causes a loss of Ter condensation in vivo. Thus, these data reveal the molecular basis for a protein-mediated DNA-bridging mechanism that mediates condensation of a large chromosomal domain in enterobacteria.


Subject(s)
Chromosomal Proteins, Non-Histone/metabolism , Chromosomes, Bacterial/metabolism , DNA, Bacterial/metabolism , Escherichia coli K12/genetics , Escherichia coli K12/metabolism , Escherichia coli Proteins/metabolism , Chromosomal Proteins, Non-Histone/chemistry , Chromosomal Proteins, Non-Histone/genetics , Chromosomal Proteins, Non-Histone/ultrastructure , Chromosomes, Bacterial/genetics , Chromosomes, Bacterial/ultrastructure , DNA, Bacterial/genetics , DNA, Bacterial/ultrastructure , Escherichia coli K12/cytology , Escherichia coli K12/ultrastructure , Escherichia coli Proteins/chemistry , Escherichia coli Proteins/genetics , Escherichia coli Proteins/ultrastructure , Microscopy, Atomic Force , Microscopy, Electron , Models, Molecular , Protein Binding
8.
EMBO J ; 31(14): 3198-211, 2012 May 11.
Article in English | MEDLINE | ID: mdl-22580828

ABSTRACT

Initiation of chromosome segregation in bacteria is achieved by proteins acting near the origin of replication. Here, we report that the precise choreography of the terminus region of the Escherichia coli chromosome is also tightly controlled. The segregation of the terminus (Ter) macrodomain (MD) involves the structuring factor MatP. We characterized that migration of the Ter MD from the new pole to mid-cell and its subsequent persistent localization at mid-cell relies on several processes. First, the replication of the Ter DNA is concomitant with its recruitment from the new pole to mid-cell in a sequential order correlated with the position on the genetic map. Second, using a strain carrying a linear chromosome with the Ter MD split in two parts, we show that replisomes are repositioned at mid-cell when replication of the Ter occurs. Third, we demonstrate that anchoring the Ter MD at mid-cell depends on the specific interaction of MatP with the division apparatus-associated protein ZapB. Our results reveal how segregation of the Ter MD is integrated in the cell-cycle control.


Subject(s)
Cell Cycle Proteins/metabolism , Cell Division/physiology , Chromosomal Proteins, Non-Histone/metabolism , Chromosomes, Bacterial/metabolism , DNA, Bacterial/metabolism , Escherichia coli Proteins/metabolism , Cell Cycle Proteins/genetics , Chromosomal Proteins, Non-Histone/genetics , Chromosomes, Bacterial/genetics , DNA, Bacterial/genetics , Escherichia coli , Escherichia coli Proteins/genetics
9.
PLoS Genet ; 9(10): e1003833, 2013.
Article in English | MEDLINE | ID: mdl-24130504

ABSTRACT

The budding yeast Srs2 is the archetype of helicases that regulate several aspects of homologous recombination (HR) to maintain genomic stability. Srs2 inhibits HR at replication forks and prevents high frequencies of crossing-over. Additionally, sensitivity to DNA damage and synthetic lethality with replication and recombination mutants are phenotypes that can only be attributed to another role of Srs2: the elimination of lethal intermediates formed by recombination proteins. To shed light on these intermediates, we searched for mutations that bypass the requirement of Srs2 in DNA repair without affecting HR. Remarkably, we isolated rad52-L264P, a novel allele of RAD52, a gene that encodes one of the most central recombination proteins in yeast. This mutation suppresses a broad spectrum of srs2Δ phenotypes in haploid cells, such as UV and γ-ray sensitivities as well as synthetic lethality with replication and recombination mutants, while it does not significantly affect Rad52 functions in HR and DNA repair. Extensive analysis of the genetic interactions between rad52-L264P and srs2Δ shows that rad52-L264P bypasses the requirement for Srs2 specifically for the prevention of toxic Rad51 filaments. Conversely, this Rad52 mutant cannot restore viability of srs2Δ cells that accumulate intertwined recombination intermediates which are normally processed by Srs2 post-synaptic functions. The avoidance of toxic Rad51 filaments by Rad52-L264P can be explained by a modification of its Rad51 filament mediator activity, as indicated by Chromatin immunoprecipitation and biochemical analysis. Remarkably, sensitivity to DNA damage of srs2Δ cells can also be overcome by stimulating Rad52 sumoylation through overexpression of the sumo-ligase SIZ2, or by replacing Rad52 by a Rad52-SUMO fusion protein. We propose that, like the rad52-L264P mutation, sumoylation modifies Rad52 activity thereby changing the properties of Rad51 filaments. This conclusion is strengthened by the finding that Rad52 is often associated with complete Rad51 filaments in vitro.


Subject(s)
DNA Helicases/genetics , Homologous Recombination/genetics , Rad51 Recombinase/genetics , Rad52 DNA Repair and Recombination Protein/genetics , Saccharomyces cerevisiae Proteins/genetics , Cytoskeleton/genetics , DNA Damage/genetics , DNA Repair/genetics , DNA-Binding Proteins/genetics , Saccharomyces cerevisiae/genetics , Small Ubiquitin-Related Modifier Proteins/genetics , Sumoylation
10.
Life Sci Alliance ; 7(3)2024 Mar.
Article in English | MEDLINE | ID: mdl-38081641

ABSTRACT

Homologous recombination (HR) is a DNA repair mechanism of double-strand breaks and blocked replication forks, involving a process of homology search leading to the formation of synaptic intermediates that are regulated to ensure genome integrity. RAD51 recombinase plays a central role in this mechanism, supported by its RAD52 and BRCA2 partners. If the mediator function of BRCA2 to load RAD51 on RPA-ssDNA is well established, the role of RAD52 in HR is still far from understood. We used transmission electron microscopy combined with biochemistry to characterize the sequential participation of RPA, RAD52, and BRCA2 in the assembly of the RAD51 filament and its activity. Although our results confirm that RAD52 lacks a mediator activity, RAD52 can tightly bind to RPA-coated ssDNA, inhibit the mediator activity of BRCA2, and form shorter RAD51-RAD52 mixed filaments that are more efficient in the formation of synaptic complexes and D-loops, resulting in more frequent multi-invasions as well. We confirm the in situ interaction between RAD51 and RAD52 after double-strand break induction in vivo. This study provides new molecular insights into the formation and regulation of presynaptic and synaptic intermediates by BRCA2 and RAD52 during human HR.


Subject(s)
Rad51 Recombinase , Replication Protein A , Humans , Replication Protein A/genetics , Replication Protein A/metabolism , Rad51 Recombinase/genetics , DNA, Single-Stranded/genetics , DNA Repair/genetics , Homologous Recombination/genetics , Rad52 DNA Repair and Recombination Protein/genetics , Rad52 DNA Repair and Recombination Protein/metabolism
11.
DNA Repair (Amst) ; 102: 103097, 2021 06.
Article in English | MEDLINE | ID: mdl-33812231

ABSTRACT

During meiosis, programmed double-strand breaks are repaired by homologous recombination (HR) to form crossovers that are essential to homologous chromosome segregation. Single-stranded DNA (ssDNA) containing intermediates are key features of HR, which must be highly regulated. RPA, the ubiquitous ssDNA binding complex, was thought to play similar roles during mitotic and meiotic HR until the recent discovery of MEIOB and its partner, SPATA22, two essential meiosis-specific proteins. Here, we show that like MEIOB, SPATA22 resembles RPA subunits and binds ssDNA. We studied the physical and functional interactions existing between MEIOB, SPATA22, and RPA, and show that MEIOB and SPATA22 interact with the preformed RPA complex through their interacting domain and condense RPA-coated ssDNA in vitro. In meiotic cells, we show that MEIOB and SPATA22 modify the immunodetection of the two large subunits of RPA. Given these results, we propose that MEIOB-SPATA22 and RPA form a functional ssDNA-interacting complex to satisfy meiotic HR requirements by providing specific properties to the ssDNA.


Subject(s)
Cell Cycle Proteins/metabolism , Chromosome Pairing , Crossing Over, Genetic , DNA, Single-Stranded/metabolism , DNA-Binding Proteins/metabolism , Replication Protein A/metabolism , Animals , Cell Line, Tumor , HEK293 Cells , Homologous Recombination , Humans , Meiosis , Mice , Models, Molecular , Multiprotein Complexes , Protein Conformation
12.
Nucleic Acids Res ; 36(15): 4964-74, 2008 Sep.
Article in English | MEDLINE | ID: mdl-18658248

ABSTRACT

Saccharomyces cerevisiae Srs2 helicase plays at least two distinct functions. One is to prevent recombinational repair through its recruitment by sumoylated Proliferating Cell Nuclear Antigen (PCNA), evidenced in postreplication-repair deficient cells, and a second one is to eliminate potentially lethal intermediates formed by recombination proteins. Both actions are believed to involve the capacity of Srs2 to displace Rad51 upon translocation on single-stranded DNA (ssDNA), though a role of its helicase activity may be important to remove some toxic recombination structures. Here, we described two new mutants, srs2R1 and srs2R3, that have lost the ability to hinder recombinational repair in postreplication-repair mutants, but are still able to remove toxic recombination structures. Although the mutants present very similar phenotypes, the mutated proteins are differently affected in their biochemical activities. Srs2R1 has lost its capacity to interact with sumoylated PCNA while the biochemical activities of Srs2R3 are attenuated (ATPase, helicase, DNA binding and ability to displace Rad51 from ssDNA). In addition, crossover (CO) frequencies are increased in both mutants. The different roles of Srs2, in relation to its eventual recruitment by sumoylated PCNA, are discussed.


Subject(s)
DNA Helicases/genetics , DNA Helicases/metabolism , DNA Repair , Proliferating Cell Nuclear Antigen/metabolism , Recombination, Genetic , SUMO-1 Protein/metabolism , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism , DNA/ultrastructure , DNA Helicases/chemistry , DNA Repair Enzymes , DNA-Binding Proteins/genetics , Gene Deletion , Mutation , Rad51 Recombinase/ultrastructure , RecQ Helicases/genetics , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae/radiation effects , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae Proteins/ultrastructure , Suppression, Genetic , Ultraviolet Rays
13.
Biol Methods Protoc ; 5(1): bpaa012, 2020.
Article in English | MEDLINE | ID: mdl-32913896

ABSTRACT

DNA intermediate structures are formed in all major pathways of DNA metabolism. Transmission electron microscopy (TEM) is a tool of choice to study their choreography and has led to major advances in the understanding of these mechanisms, particularly those of homologous recombination (HR) and replication. In this article, we describe specific TEM procedures dedicated to the structural characterization of DNA intermediates formed during these processes. These particular DNA species contain single-stranded DNA regions and/or branched structures, which require controlling both the DNA molecules spreading and their staining for subsequent visualization using dark-field imaging mode. Combining BAC (benzyl dimethyl alkyl ammonium chloride) film hyperphase with positive staining and dark-field TEM allows characterizing synthetic DNA substrates, joint molecules formed during not only in vitro assays mimicking HR, but also in vivo DNA intermediates.

14.
Nucleic Acids Res ; 35(8): e58, 2007.
Article in English | MEDLINE | ID: mdl-17392343

ABSTRACT

DNA in living cells is generally processed via the generation and the protection of single-stranded DNA involving the binding of ssDNA-binding proteins (SSBs). The studies of SSB-binding mode transition and cooperativity are therefore critical to many cellular processes like DNA repair and replication. However, only a few atomic force microscopy (AFM) investigations of ssDNA nucleoprotein filaments have been conducted so far. The point is that adsorption of ssDN A-SSB complexes on mica, necessary for AFM imaging, is not an easy task. Here, we addressed this issue by using spermidine as a binding agent. This trivalent cation induces a stronger adsorption on mica than divalent cations, which are commonly used by AFM users but are ineffective in the adsorption of ssDNA-SSB complexes. At low spermidine concentration (<0.3 mM), we obtained AFM images of ssDNA-SSB complexes (E. coli SSB, gp32 and yRPA) on mica at both low and high ionic strengths. In addition, partially or fully saturated nucleoprotein filaments were studied at various monovalent salt concentrations thus allowing the observation of SSB-binding mode transition. In association with conventional biochemical techniques, this work should make it possible to study the dynamics of DNA processes involving DNA-SSB complexes as intermediates by AFM.


Subject(s)
DNA, Single-Stranded/ultrastructure , DNA-Binding Proteins/ultrastructure , Microscopy, Atomic Force/methods , Aluminum Silicates/chemistry , Electrophoresis, Agar Gel , Escherichia coli Proteins/ultrastructure , Spermidine/chemistry
15.
Nat Commun ; 10(1): 4058, 2019 09 06.
Article in English | MEDLINE | ID: mdl-31492866

ABSTRACT

Homologous recombination (HR) uses a homologous template to accurately repair DNA double-strand breaks and stalled replication forks to maintain genome stability. During homology search, Rad51 nucleoprotein filaments probe and interact with dsDNA, forming the synaptic complex that is stabilized on a homologous sequence. Strand intertwining leads to the formation of a displacement-loop (D-loop). In yeast, Rad54 is essential for HR in vivo and required for D-loop formation in vitro, but its exact role remains to be fully elucidated. Using electron microscopy to visualize the DNA-protein complexes, here we find that Rad54 is crucial for Rad51-mediated synaptic complex formation and homology search. The Rad54-K341R ATPase-deficient mutant protein promotes formation of synaptic complexes but not D-loops and leads to the accumulation of stable heterologous associations, suggesting that the Rad54 ATPase is involved in preventing non-productive intermediates. We propose that Rad51/Rad54 form a functional unit operating in homology search, synaptic complex and D-loop formation.


Subject(s)
DNA Helicases/metabolism , DNA Repair Enzymes/metabolism , DNA, Single-Stranded/metabolism , DNA/metabolism , Macromolecular Substances/metabolism , Rad51 Recombinase/metabolism , Saccharomyces cerevisiae Proteins/metabolism , DNA/chemistry , DNA/ultrastructure , DNA Helicases/chemistry , DNA Helicases/genetics , DNA Repair Enzymes/chemistry , DNA Repair Enzymes/genetics , DNA, Single-Stranded/chemistry , DNA, Single-Stranded/ultrastructure , Homologous Recombination , Macromolecular Substances/chemistry , Macromolecular Substances/ultrastructure , Microscopy, Electron , Mutation , Protein Binding , Rad51 Recombinase/chemistry , Rad51 Recombinase/genetics , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae Proteins/genetics
16.
Methods Mol Biol ; 1805: 251-270, 2018.
Article in English | MEDLINE | ID: mdl-29971722

ABSTRACT

Transmission electron microscopy (TEM) and atomic force microscopy (AFM) are powerful tools to study the behavior of various actors in homologous recombination including molecular motors such as recombinases and helicases/translocases. Here we present specific approaches developed in terms of sample preparation and imaging methods to contribute to the understanding of homologous recombination process and its regulation focusing on the interplay between recombinases and other related proteins such as mediators or antirecombinase actors.Homologous recombination (HR) is a high-fidelity DNA repair pathway since it uses a homologous DNA as template. Recombinases such as RecA in bacteria, RadA in archaea, and Rad51 in eukaryotes are key proteins in the HR pathway: HR is initiated with formation of an ssDNA overhang on which recombinases polymerize and form a dynamic active nucleoprotein filament able to search for homology and to exchange DNA strand in an ATP-dependent manner. We provide practical methods to analyze presynaptic filament formation on ssDNA, its composition and regulation in presence of mediator partners, antirecombinase activity of translocase, and chromatin remodeling events.


Subject(s)
Homologous Recombination , Microscopy/methods , Recombinases/metabolism , Chromatin Assembly and Disassembly , DNA/ultrastructure , DNA Breaks, Single-Stranded , Humans , Microscopy, Atomic Force , Nucleosomes/metabolism , Polymerization , Proteins/metabolism
17.
Elife ; 72018 07 09.
Article in English | MEDLINE | ID: mdl-29985128

ABSTRACT

Homology search and strand exchange mediated by Rad51 nucleoprotein filaments are key steps of the homologous recombination process. In budding yeast, Rad52 is the main mediator of Rad51 filament formation, thereby playing an essential role. The current model assumes that Rad51 filament formation requires the interaction between Rad52 and Rad51. However, we report here that Rad52 mutations that disrupt this interaction do not affect γ-ray- or HO endonuclease-induced gene conversion frequencies. In vivo and in vitro studies confirmed that Rad51 filaments formation is not affected by these mutations. Instead, we found that Rad52-Rad51 association makes Rad51 filaments toxic in Srs2-deficient cells after exposure to DNA damaging agents, independently of Rad52 role in Rad51 filament assembly. Importantly, we also demonstrated that Rad52 is essential for protecting Rad51 filaments against dissociation by the Srs2 DNA translocase. Our findings open new perspectives in the understanding of the role of Rad52 in eukaryotes.


Subject(s)
DNA Helicases/metabolism , Rad51 Recombinase/metabolism , Rad52 DNA Repair and Recombination Protein/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/metabolism , Alleles , Amino Acid Sequence , DNA Breaks, Double-Stranded , DNA, Fungal/metabolism , Gene Conversion , Homologous Recombination , Models, Biological , Mutant Proteins/metabolism , Mutation/genetics , Protein Binding , Protein Domains , Rad52 DNA Repair and Recombination Protein/chemistry , Saccharomyces cerevisiae Proteins/chemistry , Sumoylation
18.
PLoS One ; 12(5): e0177751, 2017.
Article in English | MEDLINE | ID: mdl-28542368

ABSTRACT

The bacterium Deinococcus radiodurans possesses a set of Deinococcus-specific genes highly induced after DNA damage. Among them, ddrC (dr0003) was recently re-annotated, found to be in the inverse orientation and called A2G07_00380. Here, we report the first in vivo and in vitro characterization of the corrected DdrC protein to better understand its function in irradiated cells. In vivo, the ΔddrC null mutant is sensitive to high doses of UV radiation and the ddrC deletion significantly increases UV-sensitivity of ΔuvrA or ΔuvsE mutant strains. We show that the expression of the DdrC protein is induced after γ-irradiation and is under the control of the regulators, DdrO and IrrE. DdrC is rapidly recruited into the nucleoid of the irradiated cells. In vitro, we show that DdrC is able to bind single- and double-stranded DNA with a preference for the single-stranded DNA but without sequence or shape specificity and protects DNA from various nuclease attacks. DdrC also condenses DNA and promotes circularization of linear DNA. Finally, we show that the purified protein exhibits a DNA strand annealing activity. Altogether, our results suggest that DdrC is a new DNA binding protein with pleiotropic activities. It might maintain the damaged DNA fragments end to end, thus limiting their dispersion and extensive degradation after exposure to ionizing radiation. DdrC might also be an accessory protein that participates in a single strand annealing pathway whose importance in DNA repair becomes apparent when DNA is heavily damaged.


Subject(s)
Bacterial Proteins/metabolism , DNA Damage , Deinococcus/genetics , Deinococcus/metabolism , Bacterial Proteins/chemistry , DNA Repair , DNA, Single-Stranded/genetics , DNA, Single-Stranded/metabolism , Deinococcus/radiation effects , Dose-Response Relationship, Radiation , Gamma Rays/adverse effects , Gene Deletion , Plasmids/genetics , Protein Multimerization , Protein Structure, Quaternary , Ultraviolet Rays/adverse effects
19.
PLoS One ; 5(2): e9342, 2010 Feb 22.
Article in English | MEDLINE | ID: mdl-20179769

ABSTRACT

BACKGROUND: The pro-apoptotic effector Bid induces mitochondrial apoptosis in synergy with Bax and Bak. In response to death receptors activation, Bid is cleaved by caspase-8 into its active form, tBid (truncated Bid), which then translocates to the mitochondria to trigger cytochrome c release and subsequent apoptosis. Accumulating evidence now indicate that the binding of tBid initiates an ordered sequences of events that prime mitochondria from the action of Bax and Bak: (1) tBid interacts with mitochondria via a specific binding to cardiolipin (CL) and immediately disturbs mitochondrial structure and function idependently of its BH3 domain; (2) Then, tBid activates through its BH3 domain Bax and/or Bak and induces their subsequent oligomerization in mitochondrial membranes. To date, the underlying mechanism responsible for targeting tBid to mitochondria and disrupting mitochondrial bioenergetics has yet be elucidated. PRINCIPAL FINDINGS: The present study investigates the mechanism by which tBid interacts with mitochondria issued from mouse hepatocytes and perturbs mitochondrial function. We show here that the helix alphaH6 is responsible for targeting tBid to mitochondrial CL and disrupting mitochondrial bioenergetics. In particular, alphaH6 interacts with mitochondria through electrostatic interactions involving the lysines 157 and 158 and induces an inhibition of state-3 respiration and an uncoupling of state-4 respiration. These changes may represent a key event that primes mitochondria for the action of Bax and Bak. In addition, we also demonstrate that tBid required its helix alphaH6 to efficiently induce cytochrome c release and apoptosis. CONCLUSIONS: Our findings provide new insights into the mechanism of action of tBid, and particularly emphasize the importance of the interaction of the helix alphaH6 with CL for both mitochondrial targeting and pro-apoptotic activity of tBid. These support the notion that tBid acts as a bifunctional molecule: first, it binds to mitochondrial CL via its helix alphaH6 and destabilizes mitochondrial structure and function, and then it promotes through its BH3 domain the activation and oligomerization of Bax and/or Bak, leading to cytochrome c release and execution of apoptosis. Our findings also imply an active role of the membrane in modulating the interactions between Bcl-2 proteins that has so far been underestimated.


Subject(s)
BH3 Interacting Domain Death Agonist Protein/metabolism , Cardiolipins/metabolism , Mitochondrial Proteins/metabolism , src Homology Domains , Amino Acid Sequence , Animals , Apoptosis , BH3 Interacting Domain Death Agonist Protein/chemistry , BH3 Interacting Domain Death Agonist Protein/genetics , Cardiolipins/genetics , Cells, Cultured , Cytochromes c/metabolism , Cytoplasm/metabolism , Female , Hepatocytes/cytology , Hepatocytes/metabolism , Luminescent Proteins/genetics , Luminescent Proteins/metabolism , Male , Mice , Mice, Congenic , Mice, Inbred C57BL , Mice, Knockout , Microscopy, Fluorescence , Mitochondria/metabolism , Mitochondrial Proteins/genetics , Molecular Sequence Data , Mutation , Protein Binding , Reactive Oxygen Species/metabolism , Transfection
20.
FEBS J ; 276(21): 6338-54, 2009 Nov.
Article in English | MEDLINE | ID: mdl-19796174

ABSTRACT

BH3 interacting domain death agonist (Bid), a pro-apoptotic member of the Bcl-2 family of proteins, is activated through cleavage by caspase-8. The active C-terminal fragment of Bid (tBid) translocates to the mitochondria where it interacts with cardiolipins at contact sites and induces the release of cytochrome c by a mechanism that is not yet fully understood. It has been shown that the alpha-helices alphaH6 and alphaH7 (which create the hairpin-forming domain of tBid) mediate the insertion of Bid into mitochondrial membranes and are essential for the cytochrome c-releasing activity. In the present study, we focused on the interaction between the alphaH6 and the mitochondrial membrane. By the use of single-cell electropermeabilization associated with flow cytometric analysis of intact cells, we demonstrated that H6 is able to induce cell death when used in the micromolar range. We also studied the interactions of the alphaH6 with artificial monolayers. We showed that the presence of negatively charged cardiolipins greatly enhances the insertion of alphaH6 into the phospholipid monolayer. The modification of two charged amino acid residues in alphaH6 abolished its insertion and also its in vivo effects. Furthermore, the negative values of the excess areas of mixing indicate that attractive interactions between cardiolipins and alphaH6 occur in the mixed monolayers. Fluorescence microscopy observations revealed that alphaH6 significantly disrupts cardiolipin packing and stabilizes the fluid lipid phase. These results suggest that cardiolipins at the contact sites between the two mitochondrial membranes could mediate the binding of tBid via alphaH6.


Subject(s)
BH3 Interacting Domain Death Agonist Protein/chemistry , Cardiolipins/chemistry , Amino Acid Sequence , Animals , Apoptosis , Energy Metabolism , Mice , Microscopy, Fluorescence , Mitochondria/metabolism , Molecular Sequence Data , Protein Structure, Secondary
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