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Escherichia coli RuvBL268S: a mutant RuvB protein that exhibits wild-type activities in vitro but confers a UV-sensitive ruv phenotype in vivo
Introduction
Materials And Methods
Bacterial strains
Sequence comparisons
Random mutagenesis
UV sensitivity
Proteins and reagents
DNA substrates
DNA binding, ATPase and branch migration assays
DNA unwinding assay
Holliday junction resolution
Electron microscopy
Immunoprecipitation
Results And Discussion
Random mutagenesis of the cloned ruvB gene and identification of mutants that confer UVS phenotype
Dominant negative phenotype of RuvBL268S
Purification of RuvBL268S protein
DNA binding and ATPase activities of RuvBL268S
DNA unwinding properties of RuvBL268S
Effect of RuvBL268S on RuvB- and RuvAB-mediated branch migration
RuvABC complex formation
Conclusions
Acknowledgements
References
Escherichia coli RuvBL268S: a mutant RuvB protein that exhibits wild-type activities in vitro but confers a UV-sensitive ruv phenotype in vivo
ABSTRACT
INTRODUCTION
The ruvA, ruvB and ruvC genes of Escherichia coli are required for normal levels of cellular resistance to the effects of UV- or ionising-irradiation, or to the harmful effects of DNA-damaging agents such as mitomycin C (1-3). ruv mutants are mildly defective in recombination (4), and this recombination defect is greatly enhanced by a mutation in recG (5).
Genetic studies indicate that the ruv genes are involved in a late step of recombination and the recombinational repair of DNA damage (6). Consistent with this, biochemical studies have shown that the RuvA, RuvB and RuvC proteins are involved in the processing of recombination intermediates (for review see 7). RuvA and RuvB interact to form a complex that drives the branch migration of Holliday junctions, a reaction that results in the extension of heteroduplex DNA. The third Ruv protein, RuvC, is an endonuclease that also specifically interacts with the junction, in this case to promote its resolution into two nicked duplex products that can be subsequently repaired by DNA ligase. RuvAB stimulate Holliday junction resolution by RuvC (8,9), indicating that resolution in vivo is mediated by a RuvABC complex (10-14). The formation of specific RuvABC-Holliday junction complexes was recently demonstrated in vitro (15).
The RuvA protein (a tetramer of four 22 kDa subunits) binds specifically to Holliday junctions, forming stable RuvA-junction complexes (16,17). The DNA within the complex exhibits four-fold symmetry, with the four arms of DNA extended towards the corners of a square (12,18,19). Two tetramers can interact with the junction such that it becomes sandwiched between the two concave protein faces (20,21). However, in the RuvABC resolvase complex it is thought that the junction is bound by only one RuvA tetramer, leaving the other face open for interaction with RuvC (8,9,12,22).
RuvA targets RuvB protein, a hexameric ring protein, to the site of the Holliday junction (23-27). RuvB (37 kDa) shows sequence homology and structural similarity to a family of ring helicases that includes E.coli DnaB protein (28), the bacteriophage T7 gp4 (29) and T4 gp41 helicases (30), and the viral SV40 T antigen (31). In vitro, RuvB exhibits DNA helicase activity in the presence of RuvA (32,33). When visualised by electron microscopy, RuvAB were shown to assemble on the Holliday junction as a tripartite complex with RuvA flanked by two hexameric rings of RuvB (18). The rings lie across the junction from each other and are oppositely oriented. The RuvB rings are thought to constitute an ATP-dependent molecular pump that promotes branch migration (26). A mutant RuvB protein (RuvBD113N) has been described which forms hexameric rings in solution but is defective in DNA binding and ATP-hydrolysis (34).
To better understand the molecular mechanism used by the RuvB hexameric ring to mediate branch migration, a series of ruvB mutants have been obtained and selected RuvB mutant proteins purified to homogeneity. Here, we report the generation of the mutants and the biochemical characterisation of one such protein, RuvBL268S.
MATERIALS AND METHODS
Bacterial strains
Escherichia coli strains HRS1004 (35) and H124 (1,36) are derived from AB1157. HRS1004 carries a deletion of the ruvAB operon and HI24 contains a ruvB4 mutation.
Sequence comparisons
Protein sequences of E.coli RuvB (37,38) homologues in Haemophilus influenzae (39), Mycobacterium leprae (40), Mycobacterium tuberculosis (40), Mycoplasma genitalium (41), Pseudomonas aeruginosa (42), Synechocystis sp. (GenBank accession no. U38892), Thermotoga maritima (43) and Thermus thermophilus (43) were aligned using PileUp software (Wisconsin Package Version 9.0, Genetics Computer Group, Madison, WI).
Random mutagenesis
Mutations were introduced into the ruvB gene by error-prone PCR (44). Reaction mixtures (100 µl) contained 25 mM Taps-HCl (pH 9.3), 50 mM KCl, 1 mM dithiothreitol, 2 mM MgCl2, 0.5 mM MnCl2, 1 mM dGTP, 1 mM dTTP, 1 mM dCTP, 0.1 mM dATP, 0.2 µM of each primer and 10 ng of templateDNA. The template was plasmid pGTI19 containing the wild-type ruvB gene (36). Two regions of ruvB were amplified separately: the 5[prime]-region between 1 and 432 bp (primers: 5[prime]-GCACTGCAGATGAGGTAAAGGATGATTGAAG-3[prime] and 5[prime]-CGCCGGACCTTCACCA-3[prime]) and the 3[prime]-region between 346 and 1055 bp (primers: 5[prime]-CACCGTCTATCGCCAGT-3[prime] and 5[prime]-GGCATATTGCCAGTGC-3[prime]). Taq polymerase reactions were performed at 94°C for 1 min, 50°C for 1 min and 70°C for 4 min, for 30 cycles, followed by 7 min at 70°C. Amplified DNA was gel purified and digested with KpnI and BbsI (for the 5[prime]-region) or BbsI and ClaI (for the 3[prime]-region). DNA fragments were subcloned into pGTI19 to replace the corresponding regions of ruvB. Ligation mixtures were then transformed into HI24 ruvB4 strain and clones were tested for their ability/inability to restore UV resistance.
UV sensitivity
The UV sensitivities of AB1157 ruv+ and HI24 ruvB4 containing plasmid pGTI19 (ruvB+), pME2 (ruvBL268S) or pUC19 were measured as described (34).
Proteins and reagents
RecA (13), RuvA and RuvB (45) and wheat germ topoisomerase I (46) were purified as described. RuvBL268S was purified from E.coli strain HRS1004 using a modified version of the protocol developed for the wild-type RuvB protein. In the first chromatographic step, the phosphocellulose column was omitted and the supernatant of the cell lysate was loaded directly onto a DEAE-Biogel column. RuvBL268S eluted at a lower salt concentration (170-220 mM KCl) than wild-type RuvB (240-270 mM KCl). The protein was then applied to a hydroxylapatite column in buffer containing 200 mM KCl, 10 mM potassium phosphate and eluted with a 200 mM KCl, 10-150 mM potassium phosphate gradient. Fractions eluting between 35 and 50 mM potassium phosphate were pooled. RuvBL268S was then purified to homogeneity by Mono Q FPLC as described for wild-type RuvB.
Protein concentrations are expressed in monomers and were determined using the Bradford assay. However, the concentrations of RecA and RuvB (or RuvBL268S) were determined spectro-photometrically using [epsis]280 = 2.7 × 104 (RecA) and1.64 × 104 M-1 cm-1 (RuvB). BSA (Gibco BRL), phosphocreatine (Sigma), phosphocreatine kinase (Sigma), proteinase K(Boehringer-Mannheim), glutaraldehyde (Sigma), T4 polynucleotide kinase (Pharmacia), Taq polymerase (Boehringer-Mannheim) and terminal transferase (Amersham) were purchased as indicated. Restriction enzymes were from New England Biolabs.
DNA substrates
Form I Bluescript KS, pDEA-7Z and pAKE-7Z plasmid DNAs, ØX174 single-stranded and form I duplex DNAs, gapped duplex pDEA-7Z DNA (gDNA) and linearised 3[prime]-32P-labelled pAKE-7Z DNA were prepared as described (34).
For helicase assays, a 30 nt oligonucleotide, complementary to the region 570-599 of ØX174 ssDNA, was 5[prime]-32P-end-labelled using T4 polynucleotide kinase and [[gamma]-32P]ATP (Amersham). It was annealed with ØX174 ssDNA as described (32) and purified by gel filtration through a 3 ml Bio-Gel A-0.5m column equilibrated with 10 mM Tris-HCl (pH 8.0), 1 mM EDTA and 100 mM NaCl.
Concentrations of 32P-labelled DNA substrates were determined by calculating the specific activity using DE81 filters (47), or by measuring the absorbance at 260 nm. Unless stated otherwise, DNA concentrations are expressed in moles of nucleotide residues.
DNA binding, ATPase and branch migration assays
Reactions were carried out as described (34).
DNA unwinding assay
DNA helicase reactions (20 µl) contained 1 µM annealed DNA substrate in 50 mM Tris-HCl (pH 8.0), 15 mM MgCl2, 10 mM NaCl, 2 mM ATP, 2 mM DTT and 100 µg/ml BSA. The DNA was premixed with RuvA, and the reactions initiated by addition of RuvB or RuvBL268S. After 8 min incubation at 37°C, reactions were stopped and the products deproteinised and analysed by PAGE (32). 32P-labelled DNA was visualised by autoradiography.
The unwinding of covalently closed DNA was carried out as described previously with a few modifications (48). Reactions contained 20 mM Tris-acetate (pH 7.5), 10 mM Mg(OAc)2, 0.5 mM EDTA, 0.5 mM ATP, 0.5 mM ATP[gamma]S, 2 mM DTT, 100 µg/ml BSA and 60 µM form I ØX174 DNA. After addition of RuvA (8 µM), unwinding was initiated by addition of RuvB or RuvBL268S. After 15 min at 37°C, 20 U of wheat germ topoisomerase I, an amount sufficient to relax protein-free DNA within 30 s, was added (48) and incubation at 37°C was continued for 5 min. The reactions were then stopped and deproteinised by treatment with SDS (0.8%) and proteinase K (0.8 mg/ml) for 15 min at 37°C. DNA products were purified by extraction with phenol/chloroform followed by ethanol precipitation. Agarose gel electrophoresis was carried out as described (48). Gels were dried on DE81 paper and then washed with distilled water. The DNA was denatured by soaking the gel in 0.5 M NaOH, 150 mM NaCl for 20 min and then neutralised with 0.5 M Tris-HCl (pH 8.0), 150 mM NaCl. The DNA was hybridised with a 5[prime]-32P-end-labelled 66mer complementary to the ØX174 DNA, and the gel was dried and exposed to Kodak XAR films.
Holliday junction resolution
Synthetic Holliday junctions were prepared by annealing four oligonucleotides (66 nt in length): strand 1, 5[prime]-TATCGAATCCGTCTAGTCAACGCTGCCGAATTCTACCAGTGAGGATGGACTCCTCACCTGCAGGTT-3[prime]; strand 2, 5[prime]-AACCTGCAGGTGAGGAGTCCATGGTCTTCCGTCAAGCTCGATGCCGGTTGTATGCCCACGTTGACC-3[prime]; strand 3, 5[prime]-GGTCAACGTGGGCATACAACCGGCATCGAGCTTGACGGAAGACCATCCCTGTCTAGAGGATCCGAC-3[prime]; and strand 4, 5[prime]-GTCGGATCCTCTAGACAGGGATCCTCACTGGTAGAATTCGGCAGCGTTGACTAGACGGATTCGATA-3[prime]. DNA annealing and junction purification were carried out essentially as described previously (49). Prior to annealing, strand 1 was 5[prime]-32P-end-labelled using polynucleotide kinase. Concentrations of synthetic junctions are indicated in moles of junctions.
Junctions (1 nM) were incubated with RuvC, in the presence or absence of RuvA and RuvB, in cleavage buffer [50 mM Tris-acetate (pH 8.0), 15 mM Mg(OAc)2, 1 mM ATP[gamma]S, 1 mM DTT and 100 µg/ml BSA; total volume 20 µl] for 30 min at 37°C. The products were deproteinised and analysed by 8% neutral PAGE (8).
Electron microscopy
Complexes of RuvB and RuvBL268S on pAKE-7Z linear duplex DNA were visualised as described (34).
Immunoprecipitation
Co-immunoprecipitation experiments with RuvA, RuvB (or RuvBL268S) and RuvC were carried out using synthetic Holliday junction X0 as described (15). After incubation, protein-DNA complexes were immunoprecipitated using anti-RuvC monoclonal antibodies coupled to protein-G Sepharose beads (Pharmacia). Complexes were analysed by SDS-PAGE followed by western blotting with rabbit anti-RuvA, anti-RuvB and anti-RuvC polyclonal antibodies using ECL detection (Amersham).
RESULTS AND DISCUSSION
Random mutagenesis of the cloned ruvB gene and identification of mutants that confer UVS phenotype
Error-prone PCR (44) was used to introduce random mutations into the cloned ruvB gene. Two different segments of ruvB were mutated: the 5[prime]-region between 1 and 432 bp and the 3[prime]-region between 346 and 1055 bp. The amplified fragments were cloned into the high copy number plasmid pGTI19 (ruvB+), replacing the equivalent segments of the wild-type gene. The resulting plasmids were transformed into a UV-sensitive ruvB strain (HI24) and clones were tested for their UV sensitivity. In total, 40 out of 1070 clones were identified as being unable to complement the UVS phenotype. Plasmids were recovered from these clones and tested for their ability to over-express soluble RuvB protein in strain HRS1004, which carries a ruvAB deletion. Although many plasmids expressed insoluble RuvB, 12 gave good over-expression of soluble protein and for each, the entire ruvB open reading frame was sequenced. Of these, eight plasmids were found to contain point mutations resulting in single amino acid changes in the RuvB protein sequence (Fig.
Figure 1. Alignment of the E.coli RuvB sequence with eight homologues. Identical and similar amino acids are boxed in black and grey, respectively. DNA helicase motifs I-VI are indicated above the alignment. The positions and the nature of the substitutions obtained by random mutagenesis are indicated. Their numbering relates to the amino acid sequence of E.coli RuvB. Sequence analysis of RuvB indicates the presence of a number of motifs that are characteristically found in DNA/RNA helicases (50). Helicase domains I and II (two motifs involved in nucleotide binding and hydrolysis; 51,52) and helicase motifs III and VI are highly conserved whereas motifs IV and V are not (Fig.
Dominant negative phenotype of RuvBL268S
Plasmid pME2, carrying the ruvBL268S gene under the control of the plac promoter, was transformed into E.coli strains HI24 ruvB4 and AB1157 ruv+ to assess how expression of the mutant protein affected their UV sensitivity. Due to the absence of lacIq, RuvBL268S was expressed constitutively in both strains. As expected, in view of the selection screen used after mutagenesis, expression of RuvBL268S in HI24 failed to complement the ruvB4 mutation, even at low UV doses (Fig.
Figure 2. In vivo complementation assays and SDS-PAGE analysis of purified RuvBL268S. (A) UV survival curves of HI24 and AB1157 following transformation with plasmids pME2 (ruvBL268S, [Delta]), pGTI19 (ruvB+, [squ]) or pUC19 ( [diams]). (B) SDS-PAGE of RuvB and RuvBL268S proteins. Proteins (3 µg) were analysed on a 10% polyacrylamide gel and visualised by staining with Coomassie Blue. The positions of the molecular mass markers are indicated. To characterise the biochemical defects associated with the mutation in RuvBL268S, the mutant protein was over-expressed in the ruvAB deletion strain E.coli HRS1004. The procedure used to purify RuvBL268S was similar to the protocol developed for wild-type RuvB. However, during its purification, we observed that RuvBL268S eluted from DEAE-Biogel at a significantly lower salt concentration (170-220 mM KCl) than that of wild-type protein (240-270 mM KCl), suggesting that the L268S mutation may have produced a change in the conformational state of the protein. After purification, RuvBL268S protein was found to be >95% homogeneous when analysed by SDS-PAGE (Fig. To determine whether RuvBL268S bound DNA, wild-type and mutant proteins were incubated with supercoiled circular duplex DNA in the presence of 15 mM Mg2+ and ATP[gamma]S. The resulting protein-DNA complexes were fixed with glutaraldehyde and analysed by agarose gel electrophoresis. The band-shift patterns obtained with RuvB or RuvBL268S were similar, such that the degree of DNA retardation was directly proportional to the protein concentration until saturation was reached (Fig. Figure 3. Duplex DNA binding by RuvB and RuvBL268S. (A) DNA binding assays were carried out as described in Materials and Methods using the indicated concentrations of RuvB or RuvBL268S. (B and C) Electron microscopic visualisation of RuvB and RuvBL268S, respectively, in the presence of linear duplex DNA. In previous studies, it was shown that RuvB exhibits a weak affinity for DNA at low Mg2+ concentrations ([le]10 mM Mg2+) and that under these conditions its interaction with DNA requires RuvA. Analysis of the RuvA-directed binding of RuvB or RuvBL268S, in the presence of 5 mM Mg2+, indicated that wild-type and mutant proteins bound with similar affinities (data not shown). The DNA-dependent ATPase activities of RuvB and RuvBL268S were also found to be comparable. In both cases, the amount of ATP hydrolysed in a given time was proportional to protein concentration (Fig. Figure 4. ATPase activity of RuvBL268S compared to wild-type RuvB. (A) ATPase activity analysed as a function of protein concentration. Reactions contained the indicated concentrations of RuvB ([open square]) or RuvBL268S ([open circle]) and were carried out as described in Materials and Methods. Incubation was for 20 min at 37°C. (B) Effect of RuvA on RuvB- or RuvBL268S-mediated ATP hydrolysis. Large scale reactions (100 µl) contained either RuvB (3 µM) with ([closed square]) or without ([open square]) RuvA, or RuvBL268S with ([closed circle]) or without ([open circle]) RuvA. RuvA (1 µM) was added to the preincubation mixtures immediately before initiation. Aliquots were taken at the indicated times and the percentage of ATP hydrolysed was determined. Background levels of ADP (~3%) have been subtracted. Two assays were used to determine whether RuvBL268S possessed the ability to promote DNA unwinding. First, we analysed its activity in a DNA helicase assay, which measured the displacement of a short (30 nt) 32P-labelled oligonucleotide annealed to circular single-stranded DNA (32). In the presence of RuvA, we observed that RuvBL268S displaced the 30mer with the same efficiency as wild-type RuvB (Fig. Figure 5. DNA unwinding activity of RuvBL268S compared to wild-type RuvB. (A) Displacement of a 30 nt fragment annealed to circular single-stranded DNA. Reactions were carried out as described in Materials and Methods, using the indicated amounts of RuvA and RuvB/RuvBL268S. Products were analysed by 8% PAGE. Lane m, control in which the DNA was heat-denatured at 100°C for 3 min prior to loading. (B) Unwinding of circular duplex DNA. Assays were carried out as described in Materials and Methods using the indicated concentrations of RuvA and RuvB proteins. Topoisomerase was added where indicated. DNA products were deproteinised and analysed on a 1% agarose gel. Using 32P-labelled recombination intermediates ([alpha]-structures) prepared by RecA-mediated strand exchange reactions (13) between gapped circular pDEA-7Z plasmid DNA and 32P-labelled PstI linearised duplex pAKE-7Z DNA which contains a heterologous block, we observed that wild-type RuvB catalysed branch migration to produce 32P-labelled linear duplex products (Fig. Figure 6. Branch migration activities of RuvB and RuvBL268S. (A) 32P-labelled recombination intermediates were incubated with the indicated concentrations of RuvB or RuvBL268S. Reactions were stopped and DNA products were visualised by agarose gel electrophoresis followed by autoradiography. (B) Assays were carried out as in (A), except that RuvA (30 nM) was added immediately before RuvB or RuvBL268S. Branch migration experiments were also carried out in the presence of RuvA. Because RuvA promotes the specific targeting of RuvB to the Holliday junction, these experiments were performed at low RuvB concentrations. RuvBL268S was found to promote efficient branch migration, such that >90% of the recombination intermediates were processed into branch migration products (Fig. Since RuvBL268S failed to show any obvious defect in its ability to promote branch migration, we next tested to see whether it was capable of forming functionally-active RuvABC complexes. First, we used immunoprecipitation assays to analyse whether RuvBL268S was able to form RuvABC-Holliday junction complexes in vitro (Fig. Figure 7. Formation of functional RuvABC complexes by RuvBL268S. (A) Co-immunoprecipitation of RuvABC-Holliday junction complexes using wild-type RuvB or RuvBL268S, as indicated. Complexes were prepared and pulled down using anti-RuvC MAbs as described in Materials and Methods. Aliquots were analysed by SDS-PAGE and the gels were immunoblotted with a mixture of anti-RuvA and anti-RuvB polyclonal antibodies (upper panel) or anti-RuvC antibodies (lower panel). Proteins were detected by ECL. (B) Stimulation of RuvC-mediated Holliday junction resolution by RuvAB or RuvABL268S. Resolution reactions contained 32P-labelled synthetic Holliday junctions and were carried out as described in Materials and Methods using RuvA, RuvB and RuvC as indicated. Resolution products (32P-labelled nicked duplex DNA) were analysed by 8% neutral PAGE and visualised by autoradiography. Immunoprecipitation experiments were carried out by mixing RuvA, RuvBL268S (or RuvB as a control) and RuvC with Holliday junction DNA, and the resulting complexes were immunoprecipitated using monoclonal antibodies (MAbs) raised against RuvC (15). As shown in Figure The efficiency of Holliday junction resolution by RuvC (Fig. In this paper we have described the isolation of a mutant ruvB allele that encodes a protein, RuvBL268S, which exhibits wild-type RuvB activities in vitro. The ruvBL268S mutation results in a substitution of an aliphatic amino acid (leucine 268) for a polar amino acid (serine) positioned between the poorly-conserved helicase domain V and the well-conserved helicase domain VI. In eight out of the nine RuvB sequences shown in the alignment in Figure Although RuvBL268S exhibits wild-type biochemical activities in vitro with regard to DNA binding, ATPase activity, ring formation, DNA unwinding, branch migration and ability to form functional RuvABC-Holliday junction complexes, the L268S substitution has a dramatic effect in vivo. Indeed, the ruvBL268S allele was unable to complement the ruvB4 mutation, and over-expression of RuvBL268S exerted a dominant negative effect in wild-type cells. Since associations between mutant (RuvBD113N) and wild-type RuvB proteins have been observed previously (34), it is possible that RuvBL268S interacts with wild-type RuvB to form a hetero-hexamer that is inactive for some critical RuvB function. Although RuvBL268S appeared normal when assayed in vitro, during its purification RuvBL268S eluted from the DEAE-Biogel column at lower salt concentrations than the wild-type protein, suggesting that the mutation caused a conformational change that might affect protein-protein or protein-DNA interactions. Since we have not observed any defects in self-association of the RuvB hexamer, interactions with RuvA or RuvC, nor assembly of the RuvABC-Holliday junction complex, one possibility to be considered is that RuvB associates with some other protein in E.coli and that leu268 is critical for this interaction. Alternatively, subtle changes in the way that RuvBL268S interacts with RuvA and/or RuvC, may lead to the observed cellular defect. Because our extensive in vitro analysis of RuvBL268S failed to identify the biochemical defect in this protein, the data expose the limitations of such in vitro assays which, by their necessary simplicity, can only partially reproduce the complexity of reactions that take place in vivo. For example, recombination intermediates made in vitro by RecA are naked, relaxed DNA molecules that possess free ends, whereas the natural substrates for RuvABC are likely to be supercoiled and have many associated proteins. Indeed, target DNAs may be actively undergoing DNA replication, transcription and repair, and it is possible that RuvBL268S is unable to act within the context of a DNA processing machine. We thank David Adams, Angela Eggleston, Irina Tsaneva and other members of the laboratory for their interest and providing protein reagents. This work was supported by the Imperial Cancer Research Fund, the Human Frontiers Science Program, and the Swiss-British Joint Research Program and the Swiss National Foundation. C.M. and A.J.v.G. were supported in part by fellowships from the European Molecular Biology Organisation, and D.Z. by the Centre National de la Recherche Scientifique.
Purification of RuvBL268S protein
DNA binding and ATPase activities of RuvBL268S
DNA unwinding properties of RuvBL268S
Effect of RuvBL268S on RuvB- and RuvAB-mediated branch migration
RuvABC complex formation
Conclusions
ACKNOWLEDGEMENTS
REFERENCES
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