THE JOURNAL OF BIOLOGICAL CHEMISTRY Vol. 275, No. 16, Issue of April 21, pp. 12261–12265, 2000 © 2000 by The American Society for Biochemistry and Molecular Biology, Inc. Printed in U.S.A. Facilitated Loading of RecA Protein Is Essential to Recombination by RecBCD Enzyme* (Received for publication, November 5, 1999) Deana A. Arnold‡§ and Stephen C. Kowalczykowski‡¶ʈ From the ¶Sections of Microbiology and of Molecular and Cellular Biology, and ‡Genetics Graduate Group, University of California, Davis, California 95616 Although the RecB2109CD enzyme retains most of the Although the majority of homologous recombination in wild- biochemical functions associated with the wild-type type E. coli is initiated at ␹ by the combined actions of RecBCD RecBCD enzyme, it is completely defective for genetic enzyme and RecA protein (18, 19), there are recBCD mutants recombination. Here, we demonstrate that the mutant that promote wild-type levels of recombination, and yet are enzyme exhibits an aberrant double-stranded DNA exo- ␹-insensitive. For example, E. coli strains that lack a functional nuclease activity, intrinsically producing a 3؅-terminal RecD subunit are recombination-proficient, but recombination single-stranded DNA overhang that is an ideal substrate is completely independent of ␹ (20–22). Biochemical character- for RecA protein-promoted strand invasion. Thus, the ization of the RecBC(DϪ) enzyme revealed that it is nuclease- mutant enzyme constitutively processes double- deficient, but retains helicase activity, and can unwind dsDNA ␹ stranded DNA in the same manner as the -modified molecules to produce long tracts of ssDNA. Like the RecBCD wild-type RecBCD enzyme. However, we further show enzyme after ␹ recognition, RecBC enzyme also coordinates the that the RecB2109CD enzyme is unable to coordinate the loading of RecA protein onto the 3Ј-terminal ssDNA it pro- loading of RecA protein onto the single-stranded DNA duces, further defining the way in which this enzyme promotes produced, and we conclude that this inability results in ␹ the recombination-defective phenotype of the recB2109 -independent recombination (23). In contrast to the nuclease- allele. Our findings argue that the facilitated loading of deficient RecBC enzyme, an inability of the nuclease-proficient ␹ RecA protein by the ␹-activated RecBCD enzyme is es- mutants to respond properly to can also manifest itself in vivo sential for RecBCD-mediated homologous recombina- as a drastic reduction in homologous recombination, as well as tion in vivo. a heightened sensitivity to DNA-damaging agents. Strains bearing the recB2109 mutation are phenotypically similar to a recB null strain; both display a severe reduction in conjugal The RecBCD enzyme is a multifunctional protein complex recombination, sensitivity to mitomycin C, and a lack of ␹-me- essential to the main pathway of homologous recombination in diated recombinational hotspot activity (24). Unlike a recB null Escherichia coli (1, 2). The holoenzyme, composed of the RecB, strain, however, recB2109 cells do not facilitate plaque forma- Ϫ RecC, and RecD subunits, possesses DNA-dependent ATPase, tion by phage T4 gene 2 , demonstrating that the RecB2109CD helicase, and nuclease activities (3–8). Proper function of enzyme is functional in vivo and that it retains a significant RecBCD enzyme in the initiation of recombination is depend- amount of helicase or nuclease activity. Biochemical character- 2109 ent upon its response to a specific DNA sequence, the recom- ization of the RecB CD enzyme demonstrated that it pos- bination hotspot, ␹ (9, 10). Interaction with a ␹ site results in sesses all the biochemical activities of the wild-type enzyme as an attenuation of the 3Ј to 5Ј nuclease activity and an activa- follows: ATPase, helicase, and ds- and ssDNA nuclease (25). 2109 tion of the 5Ј to 3Ј nuclease activity (11, 12). This nuclease The only significant defect of the RecB CD enzyme observed modification allows the production of a long 3Ј-terminal in vitro was an absence of nuclease modification at ␹. This ssDNA1 tail, which is the preferred substrate for RecA protein- discovery offered a possible explanation for the failure to pro- promoted DNA strand exchange (13–15). Upon modification of mote ␹-stimulated recombination; this enzyme was unable to nuclease activity, RecBCD enzyme also promotes the loading of modify 3Ј to 5Ј nuclease activity and so proceeded through a RecA protein onto this ssDNA tail (16). The RecA protein- dsDNA molecule degrading the potentially recombinogenic 3Ј- ssDNA complex, or presynaptic filament, can then initiate terminal ssDNA. 2109 strand invasion into a homologous duplex DNA molecule (17). However, here we show that the RecB CD enzyme dis- plays an asymmetry of dsDNA degradation that is uncharac- teristic of the wild-type enzyme but is, instead, characteristic of * This work was supported by National Institutes of Health Grant the ␹-activated RecBCD enzyme. The mutant enzyme degrades GM-41347. The costs of publication of this article were defrayed in part dsDNA primarily in the 5Ј to 3Ј direction, producing processed by the payment of page charges. This article must therefore be hereby Ј 2109 marked “advertisement” in accordance with 18 U.S.C. Section 1734 dsDNA with a 3 -terminal overhang. Although the RecB CD solely to indicate this fact. nuclease activity produces a substrate suitable for RecA pro- The nucleotide sequence(s) reported in this paper has been submitted tein action, the RecB2109CD enzyme is unable to facilitate the TM to the GenBank /EBI Data Bank with accession number(s) AF179304. loading of RecA protein onto these ssDNA products. We con- § Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in genetics at the University of California, Davis clude that RecA protein loading is an essential function of the (36). RecBCD enzyme and that the generation of a recombinogenic ʈ To whom correspondence should be addressed: Section of Microbi- 3Ј-terminal ssDNA, although necessary, is not sufficient for ology, University of California, One Shields Ave., Davis, CA 95616. Tel.: initiation of recombination by the RecBCD enzyme. 530-752-5938; Fax: 530-752-5939; E-mail: sckowalczykowski@ ucdavis.edu. EXPERIMENTAL PROCEDURES 1 The abbreviations used are: ssDNA, single-stranded DNA; dsDNA, double-stranded DNA; SSB, Escherichia coli single-stranded DNA- Chemicals and Buffers—All solutions were made using reagent binding protein; PCR, polymerase chain reaction. grade chemicals and Barnstead NANOpure water. Radiolabel was pur- This paper is available on line at http://www.jbc.org 12261 12262 RecA Loading Is Essential FIG.1. RecB2109CD enzyme prefer- entially degrades linear dsDNA in -the 5؅ to 3؅ direction. A, the construc tion of the differentially labeled, tailed dsDNA substrates is shown. B, wild-type RecBCD (w) and mutant RecB2109CD (m) enzymes were allowed to act on tailed dsDNA substrates over a range of condi- tions as described under “Experimental Procedures” as follows: AseI-cut, 3Ј-end- labeled dsDNA in lanes 1–11; uncut, 3Ј- end-labeled dsDNA in lanes 12–14; AseI- cut, 5Ј-end-labeled dsDNA in lanes 15–25; uncut, 5Ј-end-labeled dsDNA in lanes 26–28. chased from NEN Life Science Products. The 1-kilobase pair DNA The reactions were performed at 37 °C and initiated by addition of 0.46 ladder was purchased from Life Technologies, Inc. All other chemicals nM RecBCD or RecB2109CD enzyme (one enzyme per 2.5 accessible were purchased from vendors as listed and were used as described dsDNA ends). The 30-␮l reactions were stopped after 4 min with 10 ␮l previously (26). of 5ϫ stop mix and 14 ␮g of proteinase K, as described previously (26). Enzymes—Wild-type RecBCD, RecB2109CD, SSB, and RecA proteins The reactions were separated by native gel electrophoresis on 1% aga- were purified as described previously (25, 26). Restriction endonucle- rose in TAE buffer for 550 V-h. The gels were exposed to PhosphorIm- ases, Klenow fragment lacking exonuclease, and T4 polynucleotide ki- ager screens that were later scanned by a Molecular Dynamics STORM nase were purchased from New England Biolabs. Shrimp alkaline phos- 840 PhosphorImager; the gel images were analyzed using ImageQuaNT phatase and exonuclease I were acquired from United States version 4.1a software. Biochemical Corp.. Exonuclease III and Taq DNA polymerase were Exonuclease I Protection Assays—These reactions were performed as obtained from Promega Corp. Proteinase K was purchased from Roche described previously in reaction buffer containing 8 mM magnesium Molecular Biochemicals. acetate and 5 mM ATP (16). 40 ␮M nucleotides of plasmid DNA was DNA Substrates—Plasmid DNA substrates were purified, linearized, treated with 0.92 nM functional RecBCD or RecB2109CD enzyme in the and radioactively end-labeled as described previously (26). All concen- presence of 4 ␮M SSB and 20 ␮M RecA proteins for 3 min prior to trations of DNA are given in nucleotides, unless otherwise indicated. addition of 11 units of exonuclease I. The tailed plasmid was created as The strain containing the recB2109 gene that was sequenced, V1000 described for the dsDNA exonuclease asymmetry assays; the plasmid (27), is the same as that used to purify the RecB2109CD enzyme (25). The containing the ␹ site was linearized with AvaI restriction endonuclease recB2109 gene was sequenced from both a plasmid template purified and 5Ј-end-labeled as previously reported (26). using a Qiagen midi-prep (Qiagen) and a PCR-amplified 3649-base