Rad52 oligomeric N-terminal domain stabilizes Rad51 nucleoprotein filaments and contributes to their protection against Srs2

TL;DR: In this article, mutations in Rad52 Nterminal domain also suppress the DNA damage sensitivity of Srs2-deficient cells without disturbing Rad52 mediator and pairing activity, both in vivo and in vitro.

Abstract: Homologous recombination (HR) depends on the formation of a nucleoprotein filament of the recombinase Rad51 to scan the genome and invade the homologous sequence used as template for DNA repair synthesis. Therefore, HR is highly accurate and crucial for genome stability. Rad51 filament formation is controlled by positive and negative factors. In Saccharomyces cerevisiae, the mediator protein Rad52 catalyzes Rad51 filament formation and stabilizes them, mostly by counteracting the disruptive activity of the translocase Srs2. Srs2 activity is essential to avoid the formation of toxic Rad51 filaments, as revealed by Srs2-deficient cells. We previously reported that Rad52 SUMOylation or mutations disrupting the Rad52-Rad51 interaction suppress Rad51 filament toxicity because they disengage Rad52 from Rad51 filaments and reduce their stability. Here, we found that mutations in Rad52 N-terminal domain also suppress the DNA damage sensitivity of Srs2-deficient cells without disturbing Rad52 mediator and pairing activity, both in vivo and in vitro. Structural studies showed that these mutations affect the Rad52 oligomeric ring structure. Overall, our findings indicate that Rad52 ring structure is important for protecting Rad51 filaments from Srs2, but can increase Rad51 filament stability and toxicity in Srs2-deficient cells. This stabilization function is distinct from Rad52 mediator and annealing activities.

Summary

Introduction

• Homologous recombination (HR) is an important pathway of DNA double-strand break (DSB) repair in all kingdoms of life.
• Bacterial and yeast models allowed the identification of many control mechanisms to reduce the level of HR-associated genetic instability.
• The mismatch repair machinery suppresses heteroduplexes resulting from the interaction between divergent DNA sequences, thus avoiding GC and CO between DNA sequences scattered in the genome [8] .
• This mutation strongly reduces Rad52 protection of Rad51 filaments against Srs2 destabilization in vitro.

Rad51 filament toxicity in Srs2-deficient cells

• Looking for RAD52 mutations that can suppress Srs2-deficient S. cerevisiae cells MMS sensitivity, the authors screened a RAD52 random mutation plasmid library in cells lacking RAD52 and SRS2 (rad52∆ srs2∆) exposed to methyl methanesulfonate at high dose (MMS, 0.015%).
• The authors found three mutations in conserved residues of Rad52 N-terminus: D79N, V95I and V129A .
• The authors then inserted these mutations in a centromeric plasmid carrying a RAD52-FLAG allele for subsequent in vivo analysis by coimmunoprecipitation and chromatin immunoprecipitation (ChIP).
• Evaluation of resistance to MMS by spot assay of rad52∆ srs2∆ cells transformed with these plasmids showed that each plasmid significantly restored MMS resistance in rad52∆ srs2∆ cells.
• The authors observed this suppressive effect also in γ-irradiated haploid cells where Srs2-deficient sensitivity was totally suppressed by rad52-V95I, rad52-V129A and rad52-D79N .

N-terminal Rad52 mutations that suppress Rad51 filament toxicity are proficient for HR in Srs2-deficient cells

• To measure the effect of N-terminal Rad52 mutations on Rad52 function, the authors transformed Rad52-deficient cells (but proficient for Srs2) with plasmids harboring the N-terminal RAD52 mutations.
• The rad52-V95I mutant did not fully rescue MMS sensitivity in rad52∆ cells , and it did not fully complement rad52∆ cells for γ-ray survival, as indicated by the 4-fold survival reduction upon exposure to 400Gy compared with wild type (WT) cells .
• Nevertheless, the survival rate of rad52-V95I cells was higher than that of Rad52-Rad51 interaction-defective rad52-Y376A cells and of Rad52-deficient cells [26] .
• Therefore, the Rad52 Nterminal annealing activity does not appear to be the main factor of stability provided by Rad52.
• It is important to note that Srs2 deletion in rad52-R37A cells leads to a slight increase in cell viability, suggesting that the R37A mutation might affect Rad51 filament protection against Srs2.

Structural analysis of the Rad52 N-terminal domain suggests that Rad52-V95I, rad52-V129A and rad52-D79N affect Rad52 oligomerization

• A model of the N-terminal domain of S. cerevisiae Rad52 could be obtained from the oligomeric structure of human Rad52 in its free [36] and bound to ssDNA [45] forms (PDB codes 1H2I and 5XRZ, respectively) .
• Moreover, the bulkier isoleucine residue in the mutant might induce an overpacking of the hydrophobic core that may reduce the intrinsic stability of the folded structure, as observed in other cases of substitutions in the core of folded domains [46] .
• V95T, which conserved the core geometry but reduced its hydrophobicity, behaved as WT Rad52 for MMS resistance and did not suppress the srs2∆ mutant MMS sensitivity .
• As the structural study suggested that all three mutant suppressors affect Rad52 oligomeric organization, the authors focused on Rad52-V95I that has the strongest impact on Rad52 .
• Therefore, ssDNA binding and the V95I mutation do not induce the same distortion on Rad52 rings.

Rad52-V95I affects the N-terminal ssDNA binding domain, but does not impair Rad52 global DNA binding, and only marginally reduces pairing of RPA-coated ssDNA

• The structural analysis suggested that V95I might not deeply affect Rad52 binding to DNA.
• The authors used electrophoretic mobility shift assays (EMSA) to test this hypothesis.
• The V95I mutation reduces Rad52 interaction with Rad59, but does not impair interaction with RPA, Rad51, and Srs2 The Rad52 N-terminal domain interacts with the Rad52 paralog Rad59 [48] , a protein that enhances Rad52 ssDNA annealing [49] and is important for SSA completion [50] .
• Such instability was not strong enough to influence SSA.
• As the rad52-V95I mutation and Rad52 mutations in which interaction with Rad51 is impaired can suppress Srs2-deficient cell phenotypes, the authors also quantified co-immunoprecipitation of Rad51 with Rad52-V95I-FLAG and WT Rad52-FLAG and they did not detect any difference .

The V95I mutation does not affect Rad51 filament formation at a HO-induced DSB, but increases Rad51 filament disruption by Srs2

• The authors data suggest that altering Rad52 oligomeric structure suppresses the potential toxicity of Rad51 filaments, but also induces the formation of Rad51 filaments that are more sensitive to destabilization by Srs2.
• This assay involves the formation of long 3'-end ssDNA tails generated from the DSB, thus ensuring the sensitive detection of RPA, Rad52-FLAG and Rad51 recruitment to the DSB site.
• Therefore, the reduction in Rad51 loading in rad52-V95I-FLAG cells fully depends on Srs2 activity.
• Loading was reduced by 2.6-fold compared with WT.
• Besides the defect in ssDNA pairing and SSA, Rad52-R37A also is defective for Rad51 filament protection.

The V95I mutation abrogates RPA-mediated inhibition of Rad51 filament formation in vitro

• Here, the authors found that only 24% of complete Rad51 filaments were formed in this condition.
• These experiments confirmed their previous observation that Rad52 remains associated with Rad51 filaments [26, 28] .
• The concomitant addition of Rad52 and Rad51 released the inhibition by pre-bound RPA, and led to a 1.6-fold increase in strand exchange.
• The authors genetic data and ChIP analysis suggested that V95I affects Rad51 filament protection by Rad52 against Srs2 dismantling activity.
• When Rad52 and Rad51 were added together on RPA-coated ssDNA, about 70% of complete Rad52-associated Rad51 filaments were still present after 5 minutes of incubation with Srs2.

Rad52-V95I does not destabilize Rad51 filaments in a competition assay

• Finally, the authors tested whether Rad52-V95I could challenge the stability of Rad51 filaments by incubation with excess ssDNA (ΦX174 viral (+) strand).
• The authors used the previously described optimal stoichiometric conditions, with slight modifications [28] (see Material and Methods).
• After incubation at 37°C for 20 minutes to allow Rad51 filament formation, the authors added the competing ΦX174 viral (+) strand to the reaction for 30 minutes.
• The stability of Rad51 filaments assembled with Rad52 or Rad52-V95I was comparable, indicating that Rad51 filament toxicity probably requires additional factors in vivo.

Rad52 N-terminal domain integrity is required for Rad51 filament stability

• To obtain more insight into Rad52 contribution to Rad51 filament structure and potential toxicity, the authors then screened a RAD52 random library for mutations that suppress the MMS sensitivity of Srs2-deficient cells without affecting the Rad51 filament mediator activity.
• Like the Rad52-Rad51 interaction mutants, these new mutants can suppress a broad range of srs2_ phenotypes attributed to the formation of toxic Rad51 filaments: MMS and γ-ray sensitivity in haploid cells, SSA deficiency and synthetic lethality with genes involved in DNA repair or DNA replication [28] .
• Therefore, losing the Rad52-Rad51 interaction or mutations in the Rad52 N-terminal domain alleviate the toxicity of Rad51 filaments in Srs2-deficient cells.
• These phenotypes are probably related to Srs2 post-synaptic deficiency [28] .
• On the other hand, Rad52 SUMOylation, which triggers the dissociation of Rad52 and Rad51 from DNA [30] , can suppress this protection.

Rad52-dependent stabilization of Rad51 filaments can be separated from ssDNA binding and homologous ssDNA pairing activities

• The different phenotypes conferred by the V95I and R37A mutations suggest that stabilization of Rad51 filaments can be separated from homologous ssDNA paring and Rad52 mediator activity.
• The authors genetic analysis showed that the mutations V129A, D79N and V95I only affect Rad52 capacity to stabilize Rad51 filaments.
• V95 is fully buried forming a well packed hydrophobic core with a network of hydrophobic sidechains.
• This observation can explain the strongest phenotype of the V95I mutation observed in γ-irradiated cells compared with V129A and D79N .
• The V129A, D79N and V95I mutations do not affect SSA, indicating that they do not alter Rad52 ssDNA pairing activity .

How does Rad52 stabilize Rad51 filaments?

• Rad52 clearly provides stabilization of Rad51 filaments independently of its mediator activity in vivo.
• The toxic effect of Rad52 binding to Rad51 filaments in vivo might require the association with the yeast Rad51 paralogs Rad55/Rad57 and the SHU complex, because they act as a functional ensemble with Rad52 [56] .
• Rad52 ring structure could participate in Rad51 filament stabilization through the interaction with Rad51 paralog complexes.
• Rad52 N-terminal domain also inhibits Rad51 filament removal from ssDNA by Srs2.

S. cerevisiae strains

• Experiments were mostly carried out in the FF18733 background.
• Diploid cells used in survival and recombination assays were the result of crosses between isogenic haploid strains bearing the arg4-RV and arg4-Bg frame-shift mutations.
• RAD52-3His-6FLAG fusion proteins in YCplac111 plasmids with these mutations were also used (γ-irradiation experiments and co-immunoprecipitation experiments).

Sequence alignment

• Homologous sequences of S. cerevisiae Rad52 were retrieved using PSI-Blast searches against the nr database [58, 59] .
• The full-length sequences of these homologs were aligned using the MAFFT software [60] .
• The final alignment was represented using Jalview [61] .

Irradiation and measurement of recombination rates

• Γ-ray irradiation was performed using a 137 Cs source.
• After irradiation, exponentially growing cells were plated at the appropriate dilution on rich medium (YPD) to measure the survival rate, and on synthetic plates without arginine to quantify the number of HR events.
• The mean percentage of survival from at least three independent experiments is presented.

Survival following DNA DSB formation

• Cells were grown overnight in liquid culture medium containing lactate before plating.
• Survival following HO-induced DNA DSB was measured as the number of cells growing on galactose-containing medium divided by the number of colonies growing on YPD.
• The presented results are the mean of at least three independent experiments.

Structure

• The structural model of the Rad52 11-mer was generated using the SWISSMODEL server [62] based on the template of human RAD52 (PDB code: 5xrz) that shares 47% of identity.
• Conservation was calculated using the multiple sequence alignment of the Rad52 N-terminal domain and the rate4site algorithm [63] .
• Structure are represented using PyMOL (The PyMOL Molecular Graphics System, Version 2.0 Schrödinger, LLC.).

Cycloheximide expression shut-off experiment

• For each time-point, OD at 600 nm was measured and a 2-ml fraction was removed.
• Proteins were separated on SDS-PAGE and transferred to a PVDF membrane.

Co-immunoprecipitation

• Cells were harvested and washed twice with PBS.
• Whole-cell extracts (1 mg) were incubated (4°C for 1 hour) with 0.12 µl of anti-Rad51 polyclonal antibody for Rad51 immunoprecipitation or with 1µg of anti-FLAG monoclonal for Rad52 immunoprecipitation.
• Then, 50 µl of Dynabeads coupled to Protein A or Dynabeads Pan mouse IgG (Santa Cruz Biotechnology) were added, and the incubation continued for another hour.
• Proteins were separated on 10% SDS PAGE and transferred to PVDF membranes.
• Protein-antibody complexes were visualized using the Odyssey CLx system (Li-cor Biosciences).

ChIP experiments and quantitative PCR analyses

• Cells were grown in YPD until late exponential phase.
• A 50-ml fraction was removed at the 0-hour time-point, and then galactose was added to a final concentration of 2%.
• Incubation was continued and 50-ml fractions were removed at different time-points.
• Cells were fixed in 1% formaldehyde, which was then neutralized with 125 mM glycine.
• ChIP was carried out as previously described [26] .

Protein purification

• Lysates were clarified by centrifugation and incubated with 20 mM imidazole on Ni Sepharose High Performance Resin (GE Healthcare) at 4°C for 4 hours.
• The His-SUMO tag was cut by addition of SUMO-protease at 4°C overnight.
• The Rad52-1-226-containing fractions were pooled, diluted to a final concentration of 150 mM NaCl, and glycerol was added to 10% final concentration.

Electron microscopy analysis

• A fraction of the dilution was deposited onto a 400 mesh copper grid coated with a thin carbon film, previously activated by glow-discharge in the presence of pentylamine (Merck, France).
• After 1 minute, grids were colored with aqueous 2% (w/v) uranyl acetate (Merck, France) and then dried with ashless filter paper (VWR, France).
• Observations were carried out using a Thermo fisher TECNAI 12 transmission electron microscope in filtered annular dark field mode.
• Images were acquired with a Veletta digital camera and the iTEM software (Olympus, Soft Imaging Solutions).
• For Rad51 filament transmission electron microscopy studies, a fraction of the following Rad51 filament formation reactions were used.

Electrophoretic mobility shift assay

• Complexes were separated on 8% native polyacrylamide gels.
• This experiment was also repeated with dsDNA obtained from annealing 5' end-Cy5-labeled XV2 with the complementary sequence.

DNA annealing

• Reactions were performed with 200 nM Cy5-labeled Oligo 25 and 200 nM Oligo 26, two 48nucleotide-long complementary primers described in [47] .
• An aliquot of the reaction was collected every 2 minutes and transferred to stop buffer (20 µM unlabeled Oligo 25, 0.5% SDS, 0.5 mg/ml proteinase K).
• Samples were separated on 8% native TBE polyacrylamide gels.
• Fluorescent signals were revealed with a Typhoon 9400 scanner and quantified with the ImageQuant TL software.

DNA strand exchange reaction

• Standard reactions were done by adding Rad51 prior to RPA.
• Gels were stained with ethidium bromide and fluorescent signals were imaged with a Typhoon 9400 scanner and quantified with the ImageQuant TL software.
• The ratio of nicked circular product was calculated as the ratio between the sum of the linear dsDNA substrate and the nicked circular product.

Challenging Rad51 filaments with excess amounts of DNA

• Rad52-catalyzed Rad51 filament formation was performed as follow.
• Finally, after fixation with 0.25% glutaraldehyde, 4 μl of 40% sucrose was added to facilitate loading on 0.5% agarose gel.
• After electrophoresis in 1X TAE buffer at 100 V for 1.5 hours, the fluorescent signals were imagined with a Typhoon 9400 scanner.

Full text

1
Rad52 oligomeric N-terminal domain stabilizes Rad51 nucleoprotein filaments and
contributes to their protection against Srs2
Emilie Ma
1
, Laurent Maloisel
1
, Léa Le Falher
2
, Raphaël Guérois
3
, and Eric Coïc
1,*
1 Université de Paris and Université Paris-Saclay, Inserm, LGRM/iRCM/IBFJ CEA, UMR
Stabilité Génétique Cellules Souches et Radiations, F-92265, Fontenay-aux-Roses, France.
2 Present address: Precision Oncology Genomics, Oncology Therapeutic area, Sanofi R&D, F-
94403 Vitry-Sur-Seine
3 CEA-Université Paris Saclay, DRF, i2BC, LBSR, Gif-sur-Yvette, 91191, France
*
Corresponding author: eric.coic@cea.fr
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2
Abstract
Homologous recombination (HR) depends on the formation of a nucleoprotein filament of the
recombinase Rad51 to scan the genome and invade the homologous sequence used as template
for DNA repair synthesis. Therefore, HR is highly accurate and crucial for genome stability.
Rad51 filament formation is controlled by positive and negative factors. In Saccharomyces
cerevisiae, the mediator protein Rad52 catalyzes Rad51 filament formation and stabilizes them,
mostly by counteracting the disruptive activity of the translocase Srs2. Srs2 activity is essential
to avoid the formation of toxic Rad51 filaments, as revealed by Srs2-deficient cells. We
previously reported that Rad52 SUMOylation or mutations disrupting the Rad52-Rad51
interaction suppress Rad51 filament toxicity because they disengage Rad52 from Rad51
filaments and reduce their stability. Here, we found that mutations in Rad52 N-terminal domain
also suppress the DNA damage sensitivity of Srs2-deficient cells. Structural studies showed
that these mutations affect the Rad52 oligomeric ring structure. Overall, in vivo and in vitro
analyzes of these mutants indicate that Rad52 ring structure is important for protecting Rad51
filaments from Srs2, but can increase Rad51 filament stability and toxicity in Srs2-deficient
cells. This stabilization function is distinct from Rad52 mediator and annealing activities.
Keywords: Genome stability, DNA repair, Homologous Recombination, Rad52, Rad51, Srs2
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3
Introduction
Homologous recombination (HR) is an important pathway of DNA double-strand break (DSB)
repair in all kingdoms of life. It is involved in DNA damage tolerance whereby stalled DNA
replication forks that have encountered a DNA lesion can resume their progression [1,2]. HR
also plays a central role in the correct segregation of homologous chromosomes in the first
meiotic division [3], and is implicated in telomerase-independent alternative lengthening of
telomeres by which cancer cells avoid telomer degradation [4]. HR uses a sequence
homologous to the broken DNA, found preferentially on the sister chromatid or on the
homologous chromosome, as a template for DNA repair synthesis [5]. Consequently, HR is a
very accurate process. However, its ability to link DNA sequences scattered in the genome
might promote genome instability. The two outcomes of repair by HR, gene conversion (GC)
and crossing over (CO), are potential sources of important and sudden genetic changes, through
rapid transfer of genetic information from one DNA sequence to another and also through
genomic rearrangements, such as translocation or repeated sequence shuffling [6].
Additionally, DSB repair mechanisms associated with HR, such as break-induced replication
and Single Strand Annealing (SSA), induce the loss of genetic information and can be at the
origin of translocations [1,6,7]. Bacterial and yeast models allowed the identification of many
control mechanisms to reduce the level of HR-associated genetic instability. For instance, the
mismatch repair machinery suppresses heteroduplexes resulting from the interaction between
divergent DNA sequences, thus avoiding GC and CO between DNA sequences scattered in the
genome [8]. In yeast cells in vegetative growth, HR occurs more frequently through
mechanisms that do not give rise to CO. Motor proteins such as Sgs1, Mph1 and Srs2, induce
Synthesis-Dependent Strand Annealing (SDSA) by displacing the invading strand from the
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4
displacement-loops (D-loops) after DNA synthesis [9–13]. Sgs1, with its partners Top3 and
Rmi1, can also dissolve double Holliday junctions as non-CO products [14,15].
The formation of helical nucleoprotein filaments of Rad51/RecA family recombinases on
single-stranded DNA (ssDNA) at the lesion site is a key step of HR. These proteins promote
the search and strand invasion of a homologous DNA sequence required to initiate DNA repair
synthesis [2,16]. In eukaryotes, this process is mediated by the RAD51 recombinase or by
DMC1 for meiotic recombination. The formation of RAD51 filaments is tightly regulated to
avoid the production of lethal HR intermediates. In yeast cells in vegetative growth, the
formation of Rad51 nucleoprotein filaments requires mediator proteins to mobilize the ssDNA
binding protein RPA, due to the lower affinity of Rad51 for ssDNA. Rad52 in yeast and BRCA2
in metazoans are among the most studied mediators of Rad51 filament formation [16]. Rad51
nucleoprotein filaments are formed in vitro by a two-step mechanism: nucleation of a Rad51
cluster on ssDNA, and cooperative filament growth [17–20]. Rad51 filament formation also
requires Rad51 paralog activity (Rad55/Rad57 in S. cerevisiae, RAD51B, RAD51C, RAD51D,
XRCC2 and XRCC3 in human cells, and the SHU complex in both), but they might have a
more specific role during replication stress [21].
In yeast, Rad55/Rad57, the SHU complex, and Rad52 also counterbalance Rad51 filament
disruption by Srs2 [22–27]. The reason for the regulation of Rad51 filament by positive and
negative activities is not well understood, but it is essential to avoid, during HR, the production
of lethal intermediates and notably inappropriate Rad51 filaments that are toxic for the cell. The
unproductive association of Rad51 with ssDNA might interfere with the normal progression of
the DNA replication forks or with DNA repair events [28,29]. Massive Rad52 SUMOylation
that leads to the dissociation of Rad52 and Rad51 from ssDNA [30], or Rad52 mutations
disrupting the interaction between Rad52 and Rad51 suppress most of the Srs2-deficient cell
phenotypes (e.g. DNA damaging agent sensitivity and synthetic lethality upon mutation of
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5
genes involved in DNA replication and repair) [26,28]. Rad55∆ mutants also can suppress the
DNA damaging agent sensitivity in srs2∆ cells (Maloisel, L.; Ma, E.; Coïc E., in preparation).
These findings indicate that the Rad52 and Rad55 mediator proteins are directly implicated in
Rad51 filament toxicity. Specifically, they stabilize Rad51 filaments to protect them from Srs2
disruptive activity; however, they provide excessive stability to Rad51 filaments in Srs2-
deficient cells, thus interfering with other DNA transactions.
As Rad52 is essential at several steps of HR, the stabilization it confers can be observed only
by studying separation of function mutations. Here, we describe mutations that are located in
the conserved N-terminal domain of Rad52 and that suppress the Srs2-deficient cell phenotype
without affecting Rad52 mediator activity. Rad52 N-terminal domain can bind to DNA and
carries the catalytic domain for homologous ssDNA pairing [31]. It is also involved in the
formation of Rad51 filaments because Rad52 C-terminus, which harbors the RPA and the
Rad51 binding domains, is not sufficient for suppressing RPA inhibitory effect in Rad51
filament formation as efficiently as full length Rad52 [32]. To determine how the Rad52 N-
terminal domain mutations suppress the Srs2-deficient cell phenotype we performed structural
analyses. They suggested that such mutations affect the interaction between the oligomeric ring
subunits formed by Rad52 N-terminal domain in solution [33–37]. In vivo and in vitro analyses
of one of these mutations showed that it does not affect Rad52 mediator activity and only
slightly its ssDNA binding and homologous ssDNA pairing activity. However, this mutation
strongly reduces Rad52 protection of Rad51 filaments against Srs2 destabilization in vitro.
These observations suggest that the Rad52 N-terminal domain integrity is important for Rad52
stabilization of Rad51 filaments and that this function is distinct from its mediator and
annealing activities.
.CC-BY-NC-ND 4.0 International licensemade available under a
(which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is
The copyright holder for this preprintthis version posted May 21, 2021. ; https://doi.org/10.1101/2021.05.18.444666doi: bioRxiv preprint

Frequently asked questions

Q1. What are the contributions in "Rad52 oligomeric n-terminal domain stabilizes rad51 nucleoprotein filaments and contributes to their protection against srs2" ?

In this paper, the formation of helical nucleoprotein filaments of Rad51/RecA family recombinases on single-stranded DNA ( ssDNA ) at the lesion site is studied. 

Q2. What is the reason for the formation of Rad51 filaments in yeast cells?

In yeast cells in vegetative growth, the formation of Rad51 nucleoprotein filaments requires mediator proteins to mobilize the ssDNA binding protein RPA, due to the lower affinity of Rad51 for ssDNA. 

Q3. how many nucleotides are annealed to a complementary primer?

ssDNA annealing activity of a Cy5-labelled 48 nucleotide-long to its complementary primer (upper panel) previously coated or not with RPA. 

Q4. What is the role of the mismatch repair machinery in preventing GC and CO?

For instance, the mismatch repair machinery suppresses heteroduplexes resulting from the interaction between divergent DNA sequences, thus avoiding GC and CO between DNA sequences scattered in thegenome [8]. 

Q5. What are the main mechanisms of HR-associated genetic instability?

Bacterial and yeast models allowed the identification of many control mechanisms to reduce the level of HR-associated genetic instability. 

Q6. What is the ssDNA binding site of the Rad52 subunit?

V129 is in contact with I106 in an adjacent Rad52 subunit and might contribute to the stability of the oligomeric Rad52 assembly. 

Q7. What is the effect of the mutation on the stability of the inter-subunit ss?

The mutation V129A might alter the stability of the inter-subunit Rad52-Rad52 interface by altering the intensity of the hydrophobic effect with neighboring residues. 

Q8. What is the reason why the rad51 is not detected in the immunoprecipitated?

The presence of Rad51 in the immunoprecipitated fractions could not be detected to validate the efficiency of the immunoprecipitation because it migrates at the same level as the anti-Rad51 IgG. 

Q9. What is the reason for the regulation of Rad51 filament?

The reason for the regulation of Rad51 filament by positive and negative activities is not well understood, but it is essential to avoid, during HR, the production of lethal intermediates and notably inappropriate Rad51 filaments that are toxic for the cell. 

Q10. What is the default of Rad52 in ssDNA binding?

Thismight be related to its default in ssDNA binding and pairing activity [39], making it unable to suppress the Srs2-deficient cell phenotype.