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Distribution of Chi-Stimulated Recombinational Exchanges and Heteroduplex Endpoints in Phage Lambda

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Distribution of Chi-Stimulated Recombinational Exchanges and Heteroduplex Endpoints in Phage Lambda Copyright 0 1989 by the Genetics Society of America Distribution of Chi-Stimulated Recombinational Exchanges and Heteroduplex Endpoints in Phage Lambda Keith C. Cheng and Gerald R. Smith Fred Hutchinson Cancer Research Center, Seattle, Washington 98104 and Department of Pathology, University of Washington, Seattle, Washington 98195 Manuscript received December 27, 1988 Accepted for publication May 15, 1989 ABSTRACT The recombination hotspot Chi, 5’ G-C-T-G-G-T-G-G 3’, stimulates the RecBCD recombination pathway of Escherichia coli. We have determined, with precision greater than previously reported, the distribution of Chi-stimulated exchanges around a Chi site in phage X. Crosses of h phages with single base-pair mutations surroundinga Chi site were conducted in and analyzed on mismatch correction- impaired hosts to preserve heteroduplex mismatches for analysis. Among phages recombinant for flanking markers, Chi stimulated exchanges most intensely in the intervals immediately adjacent to the Chi site, both to its right and to its left. Stimulation fell off abruptly to the right but gradually to the left (with respect to the orientationof the Chi sequence written above). We have also determined that Chi stimulated the formation of heteroduplex DNA, which frequently had one endpoint to the right of Chi and the other endpoint to the left. These data support a model of Chi-stimulated recombination in which RecBCD enzyme cuts DNA immediately to the right of Chi and unwinds DNA to the left of Chi; segments of unwound single-stranded DNA are sometimes, but not always, degraded before synapsis with homologous DNA. PECIAL sites in both eukaryotes and prokaryotes respect to Chi as writtenabove; PONTICELLIet al. S affect the frequency and distribution of recom- 1985; TAYLORet al. 1985). The frequency of DNA bination events in their vicinity (STAHL1979; SMITH strand cleavage strongly correlates with the recombi- 1988b). Chi, 5’ G-C-T-G-G-T-G-G 3’ (SMITHet al. national hotspot activity of mutant forms of RecBCD 198 la), enhances break-join recombination (LAM et enzyme (PONTICELLIet al. 1985) andof mutant forms al. 1974) mediated by the primary pathway of recom- of Chi (CHENGand SMITH 1987). This correlation bination of Escherichiacoli, the RecBCD pathway indicates that the cleavage about five nucleotides to (STAHLand STAHL1977) (reviewed by STAHL1979 the right of Chi is essential for hotspot activity of Chi. and SMITH1987). Models of Chi-stimulated recombi- Does the cleavage to the rightof Chi correspond to nation incorporating known genetic and biochemical a position of Chi-stimulated exchange? Previous stud- properties of Chi and the RecBCD pathway enzymes ies have not determined the distribution of Chi-stim- have been proposed (STAHL1979; Smith et al. 1981 b). ulated exchange with sufficient precision to answer In this paper, we test predictions of one of these this question. Analysisin density gradients of the models by analyzing recombinants from phageX Red- progeny from crosses of isotopically labeled parental Gam- crosses conducted in and analyzed on mismatch X phage (e.g., LAMet al. 1974; STAHL, CRASEMANN correction-impaired hosts. and STAHL 1975; STAHLet al. 1980) has a resolution Two known components of the RecBCD pathway of several thousand base-pairs (kb) and hence cannot (CLARK1973; SMITH 1988a), RecA proteinand provide the resolution required to answer this ques- RecBCD enzyme, have been studied in vitro in detail tion. Crosses employing a large heterologyat Chi (e.g., (for reviews, see COX andLEHMAN 1987; TAYLOR STAHLet al. 1980) can detect exchange only outside 1988). RecA protein promotes interactions between the heterology, since there is no evidence that Chi homologous DNA molecules, including strand trans- stimulates nonhomologous exchange. There has been fer between double-strandedand single-stranded only one previous reportthat Chi couldstimulate DNA (SHIBATAet al. 1979). RecBCD enzyme makes exchange to its right (relative to the conventional X single strandendonucleolytic cleavages fourto six map); in that report (STAHLand STAHL1975) x+C nucleotides to the right of the Chi octamer as the opposite the largeheterology imm2’ stimulated ex- enzyme unwinds the DNA from right to left (with change in the interval imm2’-R to the right of Chi. However, this rightwardstimulation has not been The publiration costs of this article were partly defrayed by the payment of page chat-ges.This articlemust therefore be hereby marked“advertisement” reproducible (M. M. STAHLand F. W. STAHL, per- in accordance with 18 U.S.C. 3 1734 solely to indicate this fact. sonal communication). Several studies (e.g., STAHL Genetics 123: 5-17 (September, 1989) 6 and Cheng K. C. G. R. Smith and STAHL1975; STAHL et al. 1980; CHENGand SMITH 1984) have shown that Chi stimulation is greater to its left than to its right, but the absolute amount of stimulation to the right is unknown, since stimulations to the left and right were measured only relative to each other. Twoexperimental features are essential to determine if Chi can stimulate exchange immediately to its right or left: use of Chi as a marker and homology at Chi.In onereport (CHENGand SMITH 1984) using these features there were more Chi-stimulated exchanges to the left of Chi than to its right, but again only relative stimulations were meas- ured. In addition, the absence of additional nearby "---""" """""""""" markers in that report precluded determining how close to Chi (or farfrom it) these exchanges occurred. To determinethe locations of Chi-stimulated ex- changes, we have conducted X Red- Gam- crosses with Chi and additional, nearby single base-pair mu- tations as markers. - -".II In one model of Chi-stimulated recombination + * or + (SMITHet al. 1981 b, 1984),RecBCD enzyme cuts one - -le_ DNA strand to the rightof Chi as it unwinds the DNA I' from right to left (Figure 1). Continued unwinding FIGURE1.-Model for RecBCDpathway recombination. One produces a single-stranded DNA tail extending left- parental chromosome is represented by a pair of light lines, and the ward from Chi, which invades a homologous DNA other (which may be circular, but is drawn as a linear molecule for simplicity) by a pair of heavy lines. RecBCD enzyme (box) attaches duplex in a RecA protein-promotedreaction. This to a duplex end (A), unwinds the DNA to form a loop plus short model predictsthat all unreplicated Chi-stimulated tail (B) on the strand with a 3'-end (BRAEDTand SMITH1989). The recombinants have hybrid DNA at Chi (Figure 1, step ends of the loop-tail anneal to form a twin-loop (C) (TAYLORand I). After replication,half of the Chi-stimulated recom- SMITH 1980). Upon encounteringa properly oriented Chise- quence, RecBCD enzyme cuts the strand containing 5' G-C-T-G- binants exchanged for flanking markers (stepI, right) G-T-G-G 3' (Chi, denoted by * in steps D to I) to produce a 3' are predicted to have their point of genetic exchange ended "Chi tail" (F) (PONTICELLIet al. 1985; TAYLORet al. 1985). to the left of Chi, and the other half immediately to RecA and SSB proteins promote synapsis between the Chi tail and theright of Chi. If the single-stranded DNA tail the homologous parent to form a D-loop (G) (COX and LEHMAN 1987). Cleavage of the D-loop, perhaps by RecBCD enzyme, fol- extending leftward from Chi ("Chi tail") were de- lowed by synapsis of the displaced strand with the gap in the first graded more than about 10 nucleotides from its 3' parental DNA forms a Holliday junction (H), whose migration may end, therecombinants would not be hybrid atChi and be driven by RecBCD enzyme. The Holliday junction is resolved both genetic exchange points would be to the left of by cutting, perhaps by RecBCD enzyme, and ligation of homologous strands to produce recombinants with parental or recombinant Chi. In this paper we test these predictions and esti- configurations of flanking markers (left and right of I, respectively). mate the frequency of the hypothesized degradation Panels below the dashed line diagram the consequences of degra- of the Chi tail from the distribution of exchanges dation of the 3' ended "Chi tail" (F) to produce a shortertail lacking among phages recombinant for flanking markersand the Chi sequence (*)(F'). Synapsis to form a D-loop (G')and formation (H') and resolution (1') of the Holliday junction proceed from the deduced endpointsof heteroduplex DNA in as above, except that repair synthesis (-) replaces the nucleotides the Chi-stimulated recombinants. lost during degradation of the "Chi tail" (F to F'). Consequently, Genetic heterozygosity signaling thepresence of hybrid DNA does not cover the Chi site, and the points of Chi- hybrid DNA can be abolished by mismatch correction stimulated recombinational exchanges are displaced to the left. The repair synthesis drawn here is primed by a 3' end after formation (WILDENBERG andMESELSON 1975; Figure 2). There- of the Holliday junction (H'). Alternatively, repair synthesis could fore, mismatch correction-impaired hosts, such as be primed by a 3' end before formation of the Holliday junction mutL strains (MODRICH1987; RAPOSAand FOX 1987), (G'); enlargement and annealing of the D-loop to the gap would are more likely to yield recombinants reflecting the form hybrid DNA at Chi and yield genetic exchange to the right of Chi. The genetic consequences of these steps are discussed by initial break-join exchanges than are crosses permis- SMITHet al. (1 984). (Modified from SMITHet al. 198 1b.) sive for mismatch correction. For example, HUISMAN and
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