Mol Gen Genet (1992) 234:1-13

© Springer-Verlag 1992

Gene conversion in the Escherichia coli RecF pathway: a successive half crossing-over model Kenji Yamamoto 1., Kohji Kusano 2, Noriko K. Takahashi 1'3, Hiroshi Yoshikura 1, and Ichizo Kobayashi 1'2'3

1 Department of Bacteriology, Medical School, University of Tokyo, 7-3-1 Hongo, Tokyo 113, Japan 2 Department of Molecular Biology, Institute of Medical Science, University of Tokyo, 4-6~1 Shiroganedai, Tokyo 108, Japan a National Children's Medical Research Center, Tokyo 154, Japan

Received July 24, 1991

Summary. Gene conversion - apparently non-reciprocal transfer of sequence information between homologous DNA sequences - has been reported in various organ- isms. Frequent association of gene conversion with recip- rocal exchange (crossing-over) of the flanking sequen- ces in meiosis has formed the basis of the current view that gene conversion reflects events at the site of interac- tion during homologous recombination. In order to analyze mechanisms of gene conversion and homologous recombination in an E s c h e r i c h i a co l i strain with an active RecF pathway ( r e c B C s b c B C ) , we first established in cells of this strain a plasmid carrying two mutant n e o

genes, each deleted for a different gene segment, in in- verted orientation. We then selected kanamycin-resistant plasmids that had reconstituted an intact n e o + gene by homologous recombination. We found that all the n e o +

plasmids from these clones belonged to the gene-conver- sion type in the sense that they carried one n e o + gene and retained one of the mutant n e o genes. This apparent gene conversion was, however, only very rarely accompanied by apparent crossing-over of the flanking sequences. This is in contrast to the case in a r e c + strain or in a strain with an active RecE pathway ( r e c B C s b c A ) . Our further analyses, especially comparisons with apparent gene con- version in the r e c + strain, led us to propose a mechanism for this biased gene conversion. This "successive half crossing-over model" proposes that the elementary re- combinational process is half crossing-over in the sense that it generates only one recombinant DNA duplex molecule, and leaves one or two free end(s), out of two parental DNA duplexes. The resulting free end is, the model assumes, recombinogenic and frequently engages in a second round of half crossing-ove, r with the recom- binant duplex. The products resulting from such interac- tion involving two molecules of the plasmid would be classified as belonging to the gene-conversion type with- out crossing-over. We constructed a dimeric molecule

* Present address: Department of Bacteriology, The National In- stitute of Health (Yoken), Tokyo 141, Japan Correspondence to: I. Kobayashi at address 21

that mimics the intermediate form hypothesized in this model and introduced it into cells. Biased gene conver- sion products were obtained in this reconstruction ex- periment. The half crossing-over mechanism can also explain formation of huge linear multimers of bacterial plasmids, the nature of transcribable recombination products in bacterial conjugation, chromosomal gene conversion not accompanied by flanking exchange (like that in yeast mating-type switching), and antigenic varia- tion in microorganisms.

Key words: Homologous recombination - Plasmid linear multimer - Yeast mating-type switching - Antigenic variation

Introduction

Gene conversion, replicative transfer of a stretch of sequence information from one DNA molecule to anoth- er homolog, has been observed in various organisms. Frequent association of gene conversion with reciprocal exchange (crossing-over) of the flanking sequences (Fig. 1A) in fungal meiosis has led to the current view that gene conversion reflects events at the site of interac- tion during homologous recombination as revealed by distant markers (Stahl 1979; Meselson and Radding 1975).

The extent of association of gene conversion and crossing-over varies, however, among different systems (for example, see Klein 1984). It has been suggested that gene convesion and crossing-over represent separate events in meiosis and mitosis (Rossignol et al. 1984; Roman and Fabre 1983). A specialized case of gene con- version not accompanied by crossing-over is mating-type switching in yeasts (Strathern 1988). Such a system of gene conversion has an obvious advantage: it allows transfer of information between homologous sequences at different sites without altering chromosome organiza- tion by deletion or inversion. Possible molecular mecha-

/ \

gene conve r s ion gene c o n v e r s i o n wi thou t wi th c r o s s i n g - o v e r c r o s s i n g - o v e r

B BB B

I ' [ neo~--~ .Iqg p I K 4 3 ]]

ikb ~ B RI

C

4~rap+ ~ ~ V

"gene c o n v e r s i o n "gene c o n v e r s i o n a t a w i thou t a t a wi th c r o s s i n g - o v e r " c r o s s i n g - o v e r " (Type 5) (Type 6)

Fig. 1. A Gene conversion and crossing-over (reciprocal exchange) of flanking sequences. B Substrate plasmid (pIK43). The two homologous duplex segments are drawn in parallel. The top seg- ment has a 283 bp deletion (deletion a) between two NaeI sites, which removes one (C-terminal encoding) end of the neo gene. The NaeI site was inactivated by insertion of an 8 bp XhoI linker sequence. The bottom segment has a 248 bp deletion (deletion b), which removes the other (N-terminal) end of the neo gene. The two deletions are separated by 506 bp homology and are flanked by 1079 bp homology to their left and 231 bp homology to their right. The left, non-homologous "arm" (2321 bp long), including the ampicil- lin resistance gene and the replication origin, is derived from pBR322. The entire plasmid length is 14 795 bp. The restriction enzymes are: X, XhoI; RI, EcoRI; RV, EcoRV ; N, NaeI; B, BglII. Details of construction of the plasmid are given elsewhere (Ya- mamoto et al. 1988a). C "Gene conversion" type products. These two types of neo + plasmid have a structure that could be formed by intramolecular gene conversion at site a. The XhoI site in the top neo segment has been replaced by two NaeI sites. The EcoRI pattern has been changed only in the crossing-over type

nisms for gene conversion without crossing-over have been the subjects of much speculation (Rossignol et al. 1984; Roman and Fabre 1983; Duckett et al. 1988; Strathern 1988; Sobell 1972).

We have been analyzing apparent gene conversion involving two mutant alleles of a gene in plasmids in various mutant strains of Escherichia eoli (Yamamoto et al. 1988a, b). We found that apparent gene conversion in a plasmid in an E. coli strain (recBC sbcBC), which is thought to have an activated RecF pathway, is not ac- companied by crossing-over. Our further analyses lead us to propose a mechanism for this type of gene conversion. This "successive half crossing-over model" (Fig. 2) proposes that the elementary recombinational process is a half crossing-over in the sense that it generates only one

A

wi thou t

i i i l U l l l l l l l U l l l l l l l l l l l l l i i i i n l n l l l U l l l l

................... [ .......................... 1st h a l f c r o s s i n g - o v e r

i = i i i i i l U l l l l l l l l l l n l l ~

t

_1- _U

i 2nd h a l f c r o s s i n g - o v e r

=F" l =

gene c o n v e r s i o n gene c o n v e r s i o n w i t h o u t

c r o s s i n g - o v e r c r o s s i n g - o v e r

Fig. 2A and B. Apparent gene conversion without crossing-over by two rounds of half crossing-over. A Half crossing-over between two intact duplex molecules generating one recombinant duplex and two ends. One end engages in a second event of half crossing-over with this recombinant duplex at a site at some distance from that of the first event, presumably after degradation and generation of a single-stranded tail. The final products are one duplex, with two closely spaced double-strand exchanges with heteroduplex regions, and two ends. B Half crossing-over between one intact duplex and one duplex with an end. The resulting end engages in a second event of half crossing-over as in A. The final products are one duplex, with two closely spaced double-strand exchanges, and one end

recombinant DNA duplex molecule out of two parental DNA duplexes and leaves one or two free end(s). The resulting end is, the model assumes, recombinogenic and engages in a second round of half crossing-over with the recombinant duplex. Our reconstruction experiments with a putative intermediate form gave results in accor- dance with this model. We show that this successive half crossing-over model can resolve several mysteries in homologous recombination.

Materials and methods

Bacterial strains and plasmids. The following isogenic E. coli K12 strains were from Dr. A.J. Clark: JC7623 (= recB21 recC22 sbcB15 sbcC201) (Kushner et al. 1971 ; Lloyd and Buckman 1985), JC8111 (as JC7623 but reeF143), JC12190 (as JC7623 but recJ153), and JC7940 (as JC7623 but reeA142) (Horii and Clark 1973; Lovett and Clark 1984). BIK1212, a recN262 tyrA16: :TnlO derivative of JC7623, was made by P1 transduction from SP256 (Picksley et al. 1984), a gift from Dr. R. Lloyd. KEN88, a ruvC53 eda-51::TnlO (Shurvinton et al. 1984; Sharples et al. 1990) derivative of JC7623 was made by P1 transduction from KD2245 (Kusano et al. 1989), a gift from Dr. H. Nakayama. JC5519 (recB21 recC22) (Willetts and Clark 1969) is isogenic with JC7623 and was from Dr. A. Miura. ABl157 rec +) and JC8679 (= recB21 recC22 sbcA23), with similar genetic backgrounds, have been described previously (Yamamo-

to et al. 1988a, b; Kobayashi and Takahashi 1988), as have two recA1 strains, DH1 and DH5, not isogenic with the above strains.

The plasmids used are described in the figure legends.

Detection o f recombination. Each ampicillin-resistant (Amp ~) colony obtained by transformation with plK43 was grown with ampicillin selection (50 ~tg/ml with 200 ~tg/ml methicillin) to saturation in 5 rnl. The culture was then plated on kanamycin (Kan) agar (50 gg/ml) and on ampicillin agar.

Electrophoresis. Intact plasmids (not cut with enzymes) were electrophoresed through 0.4% agarose in a low sodium buffer (40 mM TRIS-acetate, 2 mM Na2EDTA, pH 8.0) with 0.5 gg/ml ethidium bromide at a low voltage (70 V/35 cm) for 16 36 h. The restriction enzyme digests were electrophoresed through 0.7% agarose in a high sodium buffer (40 mM sodium acetate., 2 mM EDTA, pH 8.0) with 0.5 btg/ml ethidium bromide at a voltage of 100 V/12 cm for 30 min. Linear plasmid multimers were isolated by electrophoresis in 1% agarose in 8 9 m M TRIS-borate, 0.2 mM EDTA, pH 8.0 with 0.5 btg/ml ethidium bromide at 300 V /24 cm for 1 h.

Other methods. Substrate plasmid preparation, trans- formation by the calcium method, plasmid preparation by the boiling method, and other procedures have been described (Yamamoto et al. 1988a, b; Kobayashi and Takahashi 1988; Takahashi and Kobayashi 1990).

Table 1. Plasmid recombination by the RecF pathway

Bacterial strain

Recombinant frequency

(Kanr colony former/Amp r colony former) x 104

recBC sbcBC 56.7 +- 29.3 (n = 5) recBC sbcBC recA 1.59 +_ 0.47 (n=5) recBC sbeBC recF 2.56 +_ 0.93 (n=5) recBC sbcBC recJ 10.8 _+ 2.5 (n=5) recBC sbcBC recN 2.96 ± 1.13 (n=5) recBC sbcBC ruvC 2.80 +_ 2.15 (n=4) recBC 12.5 +_ 3.3 (n=5)

f e ca l 0.0696+_0.0348 (n= 10)

Each of n ampicillin-resistant (Amp r) colonies (50 btg/ml ampicillin and 200 btg/ml methicillin) obtained by transformation with pIK43 was grown in liquid medium with ampicillin selection (50 gg/ml ampicillin and 200 gg/ml methicillin) to an OD6o o of 0.3. The culture was diluted and plated on kanamycin agar (50 gg/ml) and on ampicillin agar for overnight incubation. The recombinant fre- quency is shown together with the standard deviation among n clones examined. The data for the recA1 strain, DH1, is from Yamamoto et al. (1988a). DH1 is not isogenic with the other strains and was used for preparation of substrate plasmid molecules with low background recombination. Relative plating efficiency (kan- amycin/ampicillin) of DH 1 carrying a neo + plasmid ("gene conver- sion at a without crossing-over" type; Fig. 1C, left) was 1.07 and 1.21 in two experiments

plasmid in rec + and recBC sbcA strains (Yamamoto et al., 1988a, b).

Results

Experimental system

Our starting plasmid pIK43 (Fig. 1B) carries two homol- ogous neo segments in inverted orientation. The upper segment has a deletion (deletion a) removing one end (C-terminus) of the neo gene, and the lower segment has a deletion (deletion b) removing the other end. This plasmid was introduced into an E. coli strain with recB recC sbcB sbcC mutations (JC7623) using ampicillin selection. The resulting strain (JC7623 [plK43]) generated Kan ~ clones at a frequency of 6 x 10 -3 (No. of Kan r colony formers/No, of Amp ~ colony formers) (Table 1).

Plasmid D N A preparations isolated from these Kan ~ clones as well as the parental strain showed three bands on gel electrophoresis: bands at positions expected for a closed circle and an open circle of approximately the size of the parental plasmid and one broad band migrating more slowly (data not shown). This last species was identified as plasmid linear multimer (Cohen and Clark 1986; Kusano et al. 1989) by its behavior as a long linear molecule under different electrophoresis conditions (de- scribed in Materials and methods).

We could not detect any circular dimers, closed or open, by ethidium bromide staining. This is in contrast to the presence of many circular dimeric forms of this

Apparent 9ene conversion not accompanied by crossinf f-ol)er

We recovered monomer closed circle DNA from these Kanr clones by electrophoresis and analyzed it with the restriction enzymes XhoI, EcoRI, NaeI, and Bg/II. No heterogeneity in plasmid structure was observed within a given Kan ~ clone. We were able to assign each of the clones to one of the predicted forms (Yamamoto et al. 1988a), as summarized in Table 2. The linear multimer fraction produced the restriction patterns expected for head-to-tail multimers of the monomer closed circle plasmid present in the same clone in all the cases exam- ined (6/6).

Plasmids in most of the Kanr clones had the restriction patterns shown in Fig. 3 and belonged to the type shown on the left, in Fig. 1C (Table 2). We define this as a gene conversion type (gene conversion at deletion a) because it possesses one recombinant allele and one parental allele. Plasmids in some of the clones showed the restric- tion patterns expected from gene conversion at deletion b. If the responsible gene conversion events were intra- molecular and accompanied by reciprocal exchange (crossing-over) of the flanking sequences, the region be- tween the two homologous segments (the left "arm" in Fig. 1B) would be inverted with respect to the outside markers (the right arm in Fig. 1B) to give the form on the right in Fig. 1C. We found, however, only one clone

4

Table 2. Classification of recombinant (neo +) plasmids

Bacterial Plasmid strain

Product

Gene conversion type

at s i t ea at s i t ea at s i teb without with without crossing- crossing- crossing- over over over

Other Mixture Total

r e c B C s b e B C pIK43

r e c B C s b c A plK43

rec + pIK43

Exp. 1 Exp. 2 Exp. 3 Exp. 4 Exp. 5 Total

8 0 1 0 0 9 18 0 2 0 0 20 11 0 3 0 0 14 9 0 0 0 0 9

16 1 4 0 0 21 62 1 10 0 0 73

60 17 1 8 0 87

(43) (67) (0) (15) - (125)

Kan ~ clones generated during growth of the cells carrying pIK43 were isolated as colonies. Plasmid DNA (monomer closed circles) from each of them was analyzed with XhoI, NaeI, EeoRI, and BglII and classified (Yamamoto et al. 1988a). In the ree + strain, plasmid molecules from the primary Kan ~ transformants showed heterogeneous forms. These were introduced into a reeA strain, and the resulting secondary transformants were analyzed and classified. The results for the reeBC sbeA strain and the rec + strain are from earlier publica- tions (Yamamoto et al. 1988a, b). Mixture, mixture of crossing-over and non-crossing-over types

N a e I E c o R I

Fig. 3. Form of neo ÷ plasmids. Plasmid DNA was isolated from each of three Kanr colonies obtained by streaking of an Amp r pIK43 transformant of JC7623. Closed circle monomer DNA was purified by agarose gel electrophoresis. It was cut with restriction enzymes and electrophoresed through 0.7% agarose. The NaeI pattern reveals apparent gene conversion at site a. The EcoRI pattern shows absence of apparent crossing-over. The numbers indicate fragment lengths in kb. The white triangle indicates the origin. Parent, pIK43

carrying plasmid molecules of this crossing-over type (Table 2).

This strong bias towards the non-crossing-over types is in contrast to the case in a r e c B C sbcA strain and in a rec ÷ strain (Table 2). In a r e c B C sbcA strain we found a significant number of clones carrying the "gene conver- sion with crossing-over" type (Yamamoto et al. 1988a). In a rec + strain each Kanr clone contained multiple types of recombinant plasmid molecules. There were many gene conversion with crossing-over "type molecules" (Table 2; Y a m a m o t o et al. 1988a).

This bias is not likely to have resulted f rom a selective advantage of the non-crossing-over types in the r e c B C

s b c B C strain for the following reasons. All of the four plasmid species - gene conversion at a without crossing- over, gene conversion at a with crossing-over, reciprocal crossing-over between a and b, and gene conversion at b without crossing-over - prepared in a recombination- defective strain (DH1) t ransformed the host bacterial strain with similar efficiencies. They produced, f rom 10ng DNA, 1.09x103 ' 1.51x103 , 0 .73x103 , and 1.83x 10 a of Kanr transformants, respectively. We analyzed more than 11 t ransformants f rom each of the four types but found no clone in which the starting plasmid type had been replaced by another type. We found that the doubling times of bacteria carrying type 5 and type 6 plasmids in the presence of ampicillin selec- tion were not significantly different. JC7623 [type 5] showed a doubling time of 95 +__ 12 min (n = 3) for Amp r colony former and 91 + 10 min (n=3) for Kanr colony former. JC7623 [type 6] showed a doubling time of 90+23 min (n=3) for Amp r colony former and 90_+ 16 min (n = 3) for Kanr colony former.

Compar i son with apparent gene conversion in a rec + strain

Several current models can provide explanations for this biased conversion. These include format ion of "patch- type" heteroduplex and double-strand break repair, which will be discussed later. We were led to consider another model after we had analyzed this apparent con- version in comparison with apparent conversion in a rec + strain (Yamamoto et al. 1988a), for which we dem- onstrated the mechanism illustrated in Fig. 4A. We here describe our experiments and ideas and will compare this model with other models in more detail in Discussion.

A 1s t c r o s s i n g - o v e r

Type 1 dimer

2nd c r o s s i n g - o v e r ~ 0 0 +

Type 5 Type 6

B 1st h a l f c r o s s i n g - o v e r

~ ----~ 'd

L inear dimer 2nd h a l f c r o s s i n g - o v e r ~ O ( ~

Type 5

Fig. 4A-C. Proposed origins of the gene-conversion type products in A ree + and B, C r e c B C s b e B C bacteria. A ree +. Reciprocal crossing-over involving two plasmid molecules at some site between deletion a and deletion b produces a "type 1" dimer. Descendant molecules of this type 1 dimer then produce, by a second, intramo- lecular crossing-over between direct repeats, various neo + mon- omers. These include gene conversion type products with and with- out apparent crossing-over. B r e e B C s b c B C . Half crossing-over be- tween the bottom neo segment of one mole, cule and the top neo

C 1s t h a l f c r o s s i n g - o v e r

L inea r mul t imer

2nd L i n e a r mul t imer h a l f c r o s s i n g - o v e r ~ O q )

Type 6 Type 5 Type 6

segment of another molecule produces a linear dimer intermediate. This linear dimer then produces, by a second, intramoleeular ex- change between direct repeats, various types of neo + monomers including the two gene conversion types. The end favors the route leading to the gene conversion type without apparent crossing-over. C r e c B C s b c B C (involving plasmid linear multimers). The first half crossing-over is initiated by an end of a plasmid linear multimer. The neo + monomers are produced as in B

In r ec + cells the "bottom" n e o segment of one plasmid molecule and the "top" n e o segment of a second molecule undergo i n t e r - m o l e c u l a r reciprocal crossing-over be- tween site a and site b as illustrated in Fig. 4A. The resulting n e o + dimer, which we call a type 1 dimer (Fig. 4A top right), renders the host cell Kanr. Descen- dants of this type 1 dimer produce various n e o + mon- omers by intra-molecular crossing-over within the result- ing Kan r clone. Figure 4A indicates two routes for the second crossing-over: the left one leads to a plasmid of the type gene conversion at a without crossing-over, and the right one leads to a plasmid of the type gene conver- sion at a with crossing-over.

This mechanism in the r ec + strain, involving the type 1 dimer, however, cannot account for the apparent biased gene conversion observed in the r e c B C s b c B C

strain for the following reasons. First, each of the Kan r clones from the r ec + strain contained the type 1 dimer (Yamamoto et al. 1988a). No circular dimer was, how- ever, detected in the r e c B C s b c B C strain as mentioned above. Second, each of the Kan r clones from the r e c +

strain contained multiple types of n e o + plasmid (Ya- mamoto et al. 1988a). These are proposed to be "cous- ins" generated by different recombination events from replicating type 1 dimer molecules within one clone (Fig. 4A; Yamamoto et al. 1988a). Each of the Kan r clones from the r e c B C s b c B C strain, however, had only one type of n e o + plasmid. Third, when the type 1 dimer was introduced into the r e c B C s b c B C strain, each of the resulting colonies carried both the non-crossing-over type (gene conversion at a without crossing-over; Fig. 1C left) and the crossing-over type (gene conversion at a with crossing-over; Fig. 1C right) as shown in Fig. 5C, (right-hand lanes of the gel) and summarized in Table 3. The bias toward the non-crossing-over type was not seen.

A B C

pKEN1 1 / X h o I p K E N 1 2 / X h o I pKEN10

f I I I i I

T y p e 5 p e 6

Fig. 5A-C. Reconstruction experiments introducing dimeric plas- mids into the cells. Top The dimeric plasmids, pKENI0 is a type 1 dimer (Fig. 4A), a neo + dimer produced by reciprocal crossing-over between two parental molecules (pIK43) (Yamamoto et al. 1988a). p K E N l l and pKEN12 are its derivatives carrying only one X h o I

site. They were obtained by partial digestion of pKEN 10 with X h o I ,

filling-in by Klenow fragment of DNA polymerase I, and ligation. pKEN11 and pKEN12 were cut with X h o I before transfer into the r e c B C s b c B C strain. Bottom The neo + plasmids in the resulting transformants. Monomer closed circle plasmids were recovered from each of the resulting Kanr colonies. They were cut with E c o R I

and electrophoresed to distinguish between the non-crossing-over type (8 and 7 kb) and the crossing-over type (10 and 5 kb). Results for four Kanr clones are shown for each transformation. Numbers indicate fragment lengths in kb. Lane 11 shows small but significant amounts of 7 and 8 kb fragments

Table 3. Classification of recombinant (neo +) plasmids in the reconstruction ex- periments

Bacterial strain

Plasmid Product

Gene conversion type

at sitea at sitea at siteb without with without crossing- crossing- crossing- over over over

Other Mixture Total

recBC sbcBC pKENI0 0 0 0 0 3 3 recBC sbcBC pKEN11 0 0 0 0 4 4 recBC sbcBC pKENll/XhoI Exp. 1 11 0 0 0 1 12

Exp. 2 12 0 0 0 0 12 Exp. 3 12 0 0 0 0 12 Total 35 0 0 0 1 36

recBC sbeBC pKEN12 0 0 0 0 4 4 reeBC sbeBC pKEN12/Xhol Exp. 1 0 12 0 0 0 12

Exp. 2 0 12 0 0 0 12 Exp. 3 0 10 0 0 0 10 Total 0 34 0 0 0 34

Kan ~ colonies were selected immediately after expression following transformation with the dimeric plasmids pKEN 10, pKEN 11, and pKEN 12. The plasmids were classified as in Table 2. In a fourth experiment the plasmids were analyzed only with EeoRI. All the clones derived from pKEN11/XhoI (6/6) showed the non-crossing-over pattern (as in Fig. 5, bottom left). All the clones from pKEN12/XhoI (6/6) showed the crossing-over pattern (as in Fig. 5, bottom middle), but one of them showed an extra band of approximately 6 kb. All the clones from intact pKEN10 (6/6) showed the mixture pattern (as in Fig. 5, bottom right). Mixture, mixture of the crossing-over type and the non-crossing-over type as analyzed with EcoRI. pKEN11/XhoI, pKEN11 cut with XhoI. pKEN12/XhoI, pKEN12 cut with XhoI

I f the type 1 dimer were an intermediate as illustrated in Fig. 4A, both the crossing-over type and the non-crossing- over type would result. We observed only the non-cross- ing-over type. Therefore, the type 1 dimer is not likely to be an intermediate form.

A mechanism: Two rounds o f half crossino-over

A modification (Fig. 4B) of the above scheme (Fig. 4A) can, however, explain the biased gene conversion we observed in the reeBC sbeBC strain. Here we assume that the elementary recombinat ion process in the recBC sbcBC strain is half crossing-over rather than full cross- ing-over. We define half crossing-over as a homologous recombinat ion process generating only one recombinant D N A duplex, and leaving two ends (or one end) free, out of two parental D N A duplexes (Fig. 2A and B). (This is a specific type of non-conservative recombination, which is defined here as recombinat ion between two duplexes generating only one recombinant duplex.) The resulting end is, we assume, recombinogenic and engages in a second round of exchange with the recombinant duplex at some distance f rom the first exchange. The net out- come is a duplex with two close double-stranded ex- changes (Fig. 2A).

In the modified scheme in Fig. 4B, a half crossing-over between the bo t tom neo segment of one plasmid and the top neo segment of another plasmid generates a linear dimer instead of a circular dimer. Two alternative routes of second exchange lead to the non-crossing-over type product and to the crossing-over type product as in the case with type 1 dimer. The recombinogenic nature of

the end, however, causes bias toward the former route (Fig. 4B, left).

The order of the two exchanges may be reversed in producing gene conversion at a without crossing-over. Generat ion of gene conversion at b without crossing-over can be explained in a similar way.

Reconstruction f rom the intermediate form

The mechanism in Fig. 4B predicts that the dimeric intermediate form will produce only "gene conversion without crossing-over" type monomers and no "gene conversion with crossing-over" type monomer in the recBC sbcBC strain. This prediction was borne out in the reconstruction experiments shown in Fig. 5.

We prepared a linear dimer molecule that mimics the proposed intermediate form as follows. The type 1 dimer (pKEN10) carries two XhoI sites (compare Fig. 1B and Fig. 5C). We inactivated the upper one (see Fig. 5 legend) and the resulting plasmid (pKEN11) was cut with J(hoI (Fig. 5A). This linear dimer resembles the hypothetical intermediate in Fig. 4B in that a double-strand break is present opposite to the recombinant segment. We in- troduced this linear dimer form into the recBC sbcBC cells. Plasmid preparat ions f rom these t ransformants contained monomers and linear multimers but no detect- able circular dimers. We analyzed monomer closed cir- cles and found only the non-crossing-over type as shown in Fig. 5A (bottom) in all the clones examined (sum- marized in Table 3 and its legend).

The opposite result was obtained when a double- strand break was present on a segment not involved in

Table 4. Effect of sbcBC mutations in the reconstruction experi- ments

Plasmid Selection Colony forming units

recBC sbcBC recBC sbc +

Exp. 1 pKEN11/J(hoI Amp

pKEN11/XhoI Kan

pKEN 11 Amp

Exp. 2 pKENll/XhoI Kan

pKEN11 Kan

300 48 340 43 280 40 260 35

28000 39000 36000 37000

400 64 470 56

18500 26000 21000 24000

Equal aliquots of a plasmid DNA preparation were incubated with or without J(hoI. Approximately 0.25 gg was introduced into the bacteria in duplicate. Kan, kanamycin selection. Amp, ampicillin selection, pKEN11/J(hoI, pKEN11 cut with XhoI

the hypothetical first exchange (Fig. 5B). In this case we inactivated the other XhoI site of pKEN10 to construct pKEN 12. pKEN 12 cut with J(hoI produced clones carry- ing only the crossing-over type plasmids (Fig, 5B and Table 3). The intact form of these two plasmids (pKENll and pKEN12) produced clones containing both the non-crossing-over type and the crossing-over type (as did the type 1 dimer) when introduced into the cells (Table 3).

The ratio of Kanr transformants to Amp ~ transfor- mants from pKEN11 cut with J(hoI was close to unity (Table 4). This is consistent with our hypothesis that this form resembles one of the recombination intermediate forms.

Effect o f sbc and rec mutations

The strain we used in this study (JC7623) carries recB21, recC22, sbcB15 and sbcC201 mutatio~s. The recB21 and recC22 mutations inactivate the RecBCD enzyme and decrease recombination between bacterial chromosomes following conjugation. The sbcB- and sbcC- mutations suppress the latter defect (Kushner et al. 1971 ; Lloyd and Buckman 1985). Mutations in the recA, recF, recJ, recN, and ruvC genes again decrease recombination associated with conjugation in this recBC sbcBC background (Horii and Clark 1973; Lovett and Clark 1984; Lloyd et al. 1983, 1984). It is assumed that the products of these genes constitute the RecF pathway of recombination in this background (Clark and Low 1988).

The recombination frequency of our plasmid (pIK43) in the recBC- sbcBC- background we described was also decreased by mutations in the recA, recF, recJ, recN, and ruvC genes (Table 1) although the decrease was not so great as in conjugtion. These results indicate that the RecF pathway as defined by bacterial recombination is responsible for the gene conversion we observed.

We also found that the recombination frequency of our plasmid was lower in a recBC sbc + strain than in our recBC sbcBC strain (Table 1) in accord with the observa- tions on conjugation.

The effect of the sbcBC mutations was also observed in the reconstruction experiments shown in Fig. 5. A recBC- sbc ÷ strain and a recBC- sbcBC- strain were transformed with approximately the same efficiency by the circular form of the dimer. However, when the lin- earized form was introduced, the recBC sbc + cells produced fewer transformants than did recBC sbc- cells (Table 4).

Discussion

The successive half crossing-over mechanism illustrated in Fig. 2 can explain production of "gone-conversion without crossing-over" type plasmids. If half crossing- over takes place betwen two plasmid molecules as illus- trated in Fig. 4B, the resulting intermediate form should produce biased conversion products as shown by the reconstruction experiments (Fig. 5 and Table 3).

The hypothesis of half crossing-over implies that re- combination is non-conservative in the sense that recom- bination between two duplexes generates only one re- combinant duplex. We have demonstrated that recom- bination is non-conservative in the recBC sbcBC strain that we used in the present study (Takahashi et al. 1992). The ends generated by restriction enzymes and by )~ terminase at cos are recombinogenic in this genetic back- ground (Luisi-DeLuca et al. 1989; Takahashi et al. 1992; Thaler et al. 1989). The hypothesis of half crossing-over also implies that non-conservative recombination creates DNA molecules with one or two broken end(s). We are now testing this prediction. We did not detect linear dimers in the present experiment. This is not surprising for the following reasons: (1) the recombination rate of circular plasmids is relatively low. It is approximately 10 .3 per generation according to Luisi-DeLuca et al. (1989), and our results with transformation with a cir- cular dimer in Fig. 5C are consistent with this order of magnitude. (2) This intermediate might be very short lived.

Luisi-DeLuca et al. (1989) have reported that the recombination rate observed with a plasmid carrying direct repeats is much higher in a recBC sbcBC strain than in a rec ÷ strain. With our plasmid the recombina- tion rates do not differ greatly in the recBC sbcBC and rec + strains (Table 1 and Yamamoto et al. 1988a). This is readily explained by the successive half crossing-over model. Only one round of half crossing-over is sufficient to produce a recombinant monomer from direct repeats, whereas successive rounds of half crossing-over are necessary to produce a recombinant monomer from in- verted repeats (Fig. 4B, C).

In our reconstruction experiments many fewer trans- formants were produced with the linear form than with the intact form of the plasmid (Table 4). Luisi-DeLuca et al. (1989) found that transformation by a linear form of a head-to-tail dimer of a plasmid is as efficient as that

A (i)

Replicating ~ ~ ( i ~ {(~'~ )) plasmid {f~'~-. '~ t s t half recA + ~ H F ° r k ~ _ _ x . ~ x~ossing_ove r recJ +recF + ~ all er°$sing-°ver 0 [ ~ recO" --'%~

"transcribable dii~ recombination recBCD + product"

/ ,~nd tlalf crossing-over sbcB-c- -% J - r e c N + ruvB +

viable recombinant Rolling circle progeny

(ii)

( iv)

(ii~ di i )

0 0 l l @

@* O "O

©

© Fig. 6A-C. Implications of the half crossing-over model. A Possible contribution of half crossing-over mechanism to plasmid linear multimer formation. (i) Half crossing-over between a replicating circle and another circle would generate a rolling circle. (ii) Half crossing-over between the end of a linear multimer and a replicating circle would generate a double rolling circle. (iii) Half crossing-over between the end of one rolling circle and the tail of another rolling circle would also generate a double rolling circle. (iv) Half crossing-

(iv)

0 1.

0 0 over between the end of a linear multimer and a circle would elongate the multimer. B Transcribable recombination products in bacterial conjugation. C Gene conversion as explained by successive half crossing-over. The donor chromosome is assumed to be parti- ally replicated prior to the first exchange. (i) Chromosomal gene conversion without crossing-over. (ii) Chromosomal gene conver- sion with crossing-over. (iii) Apparent gap repair without crossing- over. (iv) Aparent gap repair with crossing-over

by its circular form. This contrast can be explained by the nature of the recombination event being selected. In their experiment recombination between any pair of homolo- gous sequences could produce a monomer circle. Our experiments selected recombination between a pair of specific regions (neo regions). Homologous recombina- tion elsewhere would not produce a circular molecule.

We do not know what triggers the first exchange in the model in Fig. 2A. One of the duplexes may first suffer a double-strand break, which would result in two recom- binogenic ends. Alternatively, one parent might carry only one end, to begin with, as illustrated in Fig. 2B. This end might be produced by rolling-circle replication.

A large amount of huge plasmid linear multimers are formed in recBC sbcBC strains (Cohen and Clark 1986). The ends of these linear multimers may initiate half crossing-over. This and a second half crossing-over, which is intramolecular, might lead to monomers of the non-crossing-over gene conversion type as illustrated in Fig. 4C.

Possible contribution of half crossing-over to plasmid muhimer formation

On the other hand, formation of these linear multimers depends on gene functions involved in the ReeF pathway of recombination (recA, recF, recJ, and reeO) (Cohen and Clark 1986; Silberstein and Cohen 1987; Kusano et al. 1989). Half crossing-over between a replicating circle and another circle might generate a rolling circle as illus- trated in Fig. 6A (i). [Another possible role for the recom- bination functions is protection of the end of a rolling circle by homologous pairing (Niki et al. 1990).]

Half crossing-over between an end of a rolling circle and a replicating circle will generate a double rolling circle as illustrated in Fig. 6A (ii). Half crossing-over be- tween an end of a rolling circle and a tail of another rolling circle will have the same consequence (Fig. 6A (iii)). These double rolling circles may be the exonu- clease-resistant multimers described by Kusano et al. (1989). Elongation of the linear multimers can be ex- plained by the rolling-circle replication mechanism

(Cohen and Clark 1986). Half crossing-over between an end of a linear multimer and a circle is, however, another way of causing elongation of the multimer as illustrated in Fig. 6A (iv). Kinetic experiments (Cohen and Clark 1986) and density-shift experiments (Silberstein et al. 1990) indicate that the former route of elongation is the major route (although the genetic ba,ckgrounds of their strains are not identical with ours). But they cannot exclude a contribution of the latter route. If these kinds of intermolecular half crossing-over events happen to take place frequently between the inve, rted repeats of our plasmids, this would result in characteristic restriction patterns (head-to-head instead of head-to-tail). We did not see these after ethidium bromide staining (see Re- sults), but we may need a more sensitive assay for their detection.

Roles of rec and sbc gene products

We found parallelism in genetic requirements between bacterial conjugative recombination through the ReeF pathway and our plasmid recombination. Mutations in the recA, recF, reeJ, recN, and ruvC genes decreased recombination in a recBC sbcBC background. The reeBC sbcBC strain showed higher recombination than the recBC sbc + strain.

We propose that the sbcBC mutations affect at least the second recombination event in the two-step model (in Fig. 2 and Fig. 4B) because on effect of sbcBC muta- tions was observed in the reconstruction experiments (Table 4).

Homologous recombination between direct repeats on a linear molecule has been reporl:ed to need only a subset of these gene functions (recA, recF, recJ, and recO) but not recN or ruvB functions (Luisi-DeLuca et al. 1989). We observed an effect of recN and ruvC muta- tions on apparent gene conversion with a plasmid with inverted repeats (Table 1). If we assume that the two steps in Fig. 2 have different genetic requirements, these contrasting results can be explained. The first step might need only the primary subset (recA, recF, recJ, and recO) of the RecF pathway genes. The second step might need the second subset (recN and ruvC) (and possibly the primary subset as well). Recombination between di- rect repeats might require only one event of intramole- cular half crossing-over and hence only the first subset of genes. This hypothesis needs to be tested experimentally. Examination of the effects of rec mutations in our recon- struction experiments, however, has been difficult for technical reasons (including low transformation effi- ciency of the strains).

The known and inferred properties of these and other gene products revealed by many researchers have helped us to speculate on the details of the hypothesized two- step half crossing-over process. Replication or some other process may produce double-strand ends in a DNA duplex. Distribution of crossing-over along the lambda chromosome is more or less uniform in the presence of replication but is concentrated at the end (cos) in the

absence of replication (Thaler et al. 1989). The recQ helicase (Umezu et al. 1990) may expose two single- strand tails at the end. The recJ gene product, a 5' to 3' single-strand specific exonuclease (Lovett and Kolodner 1989), may digest the 5' tailed end. The remaining 3' tailed single-strand may stimulate recombination. Exo- nuclease I (ExoI), the sbcB gene product, when it is present, may degrade this 3' tailed single strand (Lehman 1960). The RecA and RecF proteins may help the 3' tailed single strand to pair with a homologous duplex (Shibata et al. 1979; Madiraju et al. 1988). The RuvA/ RuvB complex renatures cruciform structures (Shiba et al. 1991), and RuvC protein resolves the Holliday struc- ture (Connolly et al. 1991; Iwasaki et al. 1991). We propose that proper processing of the above intermediate form by these Ruv proteins produces one recombinant duplex and one 3' tailed recombinogenic single-stranded end. The latter is ready for another round of recombina- tion unless erased by ExoI, the sbcB gene product. The former is completed by repair synthesis and ligation at the single-strand interruptions. Processing other than by these Ruv gene products would somehow produce one recombinant duplex but would not leave a recom- binogenic end. The resulting recombinant duplex carries a heteroduplex with a 3' overhang as demonstrated (Sid- diqi et al. 1991).

Bacterial recombination: Transcribable recombination products

Our model of successive half crossing-over (Fig. 2) can explain recombination following bacterial conjugation, and especially the nature of transcribable recombination products (Birge and Low 1974).

Although recB- sbcBC + mutants do not produce recombinant colonies, they synthesize products of re- combinant type genes and, therefore, transcribable re- combination products (Birge and Low 1974). Their formation depends on the function of a subset of the above genes (recA, reeF, reeJ, and reeO) but not on the function of recN or ruv (Lloyd et al. 1987).

We propose that this transcribable recombination product is a linearized bacterial chromosome produced by the first half crossing-over in our model as illustrated in Fig. 6B. In the recB strain, a first half crossing-over by reeA, reeF, reeJ, and recO functions would generate a linear chromosome of the recombinant genotype, which would produce recombinant type protein but would not replicate to produce a recombinant colony. Some special feature of the incoming DNA might make this recombination resistant to ExoI.

We propose that, in the presence of sbeBC mutations only, a second half crossing-over would restore a circular chromosome of the recombinant genotype, which can generate a recombinant colony. The slow time course and the clustering of exchanges in reeBC sbcBC cells (Maha- jan and Datta 1988) are consistent with our two-step model.

10

Alternative mechanisms

We briefly discuss here three other models that might provide an explanation for the bias in gene conversion that we observe.

The first is formation of a heteroduplex of the patch type. A patch covering one of the deletion mutations would replicate to give the "gene-conversion without crossing-over" type plasmid. A large region of heterology can be included in a heteroduplex at least in a 9am + rec ÷ background (Lichten and Fox 1983, 1984). The bias toward the non-crossing-over type as opposed to the crossing-over type [patch vs splice (Stahl 1979)] can be explained if an end of a linear multimer attacks a circular molecule. Splice formation would result in an elongated linear multimer. Patch formation, however, could result in a neo ÷ monomer after replication. Alternatively a heteroduplex is formed within one plasmid molecule, and some topological constraint on crossing-over leads primarily to the patch type.

This model and our model are difficult to distinguish because a patch and a pair of close double-stranded exchanges are difficult to distinguish (Stahl 1979). Our recent demonstration of the non-conservative nature of exchange in the recB recC sbcB sbcC strain (Takahashi et al. 1992), however, implies that patch formation must be non-reciprocal even if it is part of the mechanism.

The second type of model, involving double-strand break repair (Szostak et al. 1983; Kobayashi 1991), can explain apparent conversion of deletions in plasmids like the one we observed (Kobayashi 1991; Kobayashi and Takahashi 1988; Takahashi and Kobayashi 1990). We, however, failed to detect double-strand gap repair reac- tion or double-strand break repair reaction following transfer of a gapped form of the plasmid into the recBC sbcBC strain (N. Takahashi, K. Kusano, Y. Kitamura, H. Yoshikura, I. Kobayashi unpublished) while such repair can be observed with the E. coli RecE (Kobayashi and Takahashi 1988) and the )~ Red pathways (Takahashi and Kobayashi 1990). These latter gap repair events were often accompanied by crossing-over (Kobayashi and Takahashi 1988; Takahashi and Kobayashi 1990). These models must be modified in some way in order to explain the bias toward the non-crossing-over type (see Strathern 1988).

The third type of model we consider emerged from analysis of recombination between homologous se- quences on the Salmonella chromosome (Mahan and Roth 1989, 1990). Homologous recombination between direct repeats on this chromosome was not decreased by a recB- mutation. Some pairs of repeats in inverted orientation did not undergo crossing-over of flanking sequences, which should result in chromosomal inver- sion. The latter observation is similar to our present result in the plasmid system. The observations in Sal- monella can he explained well by our two-route theory: non-conservative recombination for the RecF pathway and conservative recombination for the RecBCD path- way. We assume that the non-conservative RecF path- way rather than the apparently conservative (Kobayashi et al. 1984a) RecBCD pathway makes a large contribu-

tion to homologous recombination in some regions along the chromosome.

Mahan and Roth (1989, 1990), however, have proposed a one-pathway, two-step, model to explain their findings. Its first step is a recBC-independent "half reciprocal" recombination, which produces one recom- binant molecule and two ends. In the second step, they propose, the RecBCD enzyme enters DNA from the end, as in the case of Z activation (Kobayashi et al. 1982, 1984a, b; Taylor et al. i985). Its action completes the second recombinant molecule. Thus the overall process is "fully reciprocal" recombination. We think this model is unlikely for the following reasons: (i) there has been no evidence for recombination enhancement in the im- mediate vicinity of double-strand breaks by the RecBCD enzyme. The RecBCD enzyme rather appears to inhibit enhancement at double-strand breaks, at least, by the £ Red pathway (Stahl et al. 1985; Thaler et al. 1987b). (ii) In this model the end must be similar to a blunt end in shape in order to serve as an entry site for the RecBCD enzyme. An end with a long single-strand tail cannot serve as an entry site (Kobayashi et al. 1982; Taylor and Smith 1985). Then the first exchange is likely to leave a double-strand gap around the break. If this is the case, this one-pathway model has to assume a conservative double-strand gap repair reaction by the RecBCD system in the second step. We have failed to detect such conser- vative double-strand gap repair in a recBC + strain (N. Takahashi, K. Kusano, H. Yoshikura, I. Kobayashi, unpublished). (iii) They found fully reciprocal exchange (by their definition) in a recB strain. This is in contrast to an economical prediction of their one-pathway model (Mahan and Roth 1989).

Other organisms: yeasts, mammals, Trypanosoma and Borrelia

Our successive half crossing-over model can explain chromosomal gene conversion if we assume that donor DNA is partially replicated prior to the first exchange (Fig. 6C, i, ii). This version is formally equivalent to the uni-sex circle model proposed earlier (Stahl 1979, 1969) although emphasis in our model is on generation of recombinogenic end(s) by a non-conservative exchange. We applied this concept to mating-type switching in the yeast Saccharomyces (Fig. 7), which has been explained by various versions of the double-strand break repair model (Strathern 1988). We are testing the possibility that our plasmid gene conversion takes place within a replicating molecule as in this scheme.

Previous results interpreted in terms of the double- strand break repair models in vegetatively growing yeast cells (Orr-Weaver et al. 1981; Orr-Weaver and Szostak 1983; Jayaram 1985; Rudin et al. 1989) can also be explained by this model, as illustrated in Fig. 6C (Camp- bell 1984) and in Fig. 4 of our earlier publication (Taka- hashi and Kobayashi 1990). Although £ Red recombina- tion initiated by a double-strand break often involves invasion of different homologs by the two ends (Thaler et al. 1987a), it can carry out true double-strand break

A E Ya Z l (a!s (ars) X )

H M R a

. . . . - = ~ - - M A T ( ~

X Y(t Zl

HOcut

D

E X Ya z1 - - ~ ~ ~ ~ H M R a

MAT a X Ya Z l

Fig. 7A-E. A successive half crossing-over model for Sac- charomyces mating-type switching. A HMRa is a donor duplex. MATc~ is the recipient duplex. Y a and Ya are non-homologous. X and Z1 are common to the donor and the recipient. The donor HMR is flanked by silencers, E and I, which have ars (plasmid replication origin) activity. B HO endonuc][ease makes a double- strand break at the Y-Z junction of the recipient. The donor duplex is partially replicated by the ars activity of the silencers. Cell type (a vs a) determines which donor (HMLa or HMRa) is to be repli- cated (directionality). At least one of the daughter duplexes is recombinogenic. C The end in the Z region initiates a first half crossing-over with one of the daughter duplexes of the donor. The other end is degraded to a variable extent into the X region. A single-strand tail is produced. D This single-strand tail initiates a second half crossing-over with the same daughter. The extra DNA of the donor is trimed off. E The recipient has a coconversion and heteroduplex pattern as observed (McGill et al. 1989). The donor genotype remains unchanged. Scheduled re.plication of the chro- mosome and cell division produce two cells of the switched mating type. This model can explain the observed intermediates (White and Haber 1990)

repair by gene conversion as demonstrated by our con- trol experiments with marked plasmids (Takahashi and Kobayashi 1990).

Various aspects of mammalian homologous recom- bination can be explained by the half crossing-over mechanism (see Kobayashi 1992 for review). (i) Homolo- gous recombination events between incoming DNA molecules in mammalian somatic cells have been ex- plained by non-conserva t ive mechanisms (Chakrabar t i and Se idman 1986; Lin et al. 1987; Brouillette and Char- t r and 1987; K i t a m u r a et al. 1990). These non-conser - vative r ecombina t ion events might generate D N A ends and thus might be similar to hal f crossing-over as defined here. (ii) Previous results of homologous r ecombina t ion involving ch romosoma l D N A can be explained by the

11

half crossing-over model rather than conservative mech- anisms (including the double-strand break repair models) (Fig. 6C) (Kobayashi 1992).

Antigenic variation in unicellular microorganisms can be explained by post-replicational half crossing-over (Kobayashi 1992). Antigenic variation can be effected by only one half crossing-over event between mini-chro- mosomes in Trypanosoma ("telomere conversion") (Pays etal. 1985) and between linear plasmids in Borrelia (Plas- terk et al. 1985).

Acknowledgments. We thank Drs. A.J. Clark, R. Lloyd, H. Nakaya- ma, A. Miura and their colleagues for gifts of bacterial strains. T. Tohda and Y. Sunohara helped us in preparation of the manu- script. We are grateful to Drs. Y. Kitamura and I. Saito for advice in experiments, and to Drs. H. Shinagawa, H. Nakayama, S. Hira- ga, C.I. White and J. Haber for communication of unpublished results. Drs. J. Roth, J. Haber, D. Carrol, I. Herskowitz, A.J. Clark, and J. Rine provided critical and helpful discussion. Drs. M.S. Fox and F.W. Stahl provided comments on the manuscript. Drs. T. Takeda and H. Ikeda supported us in part. K.Y. was supported by a fellowship from the Japan Society for the Promotion of Science.

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C o m m u n i c a t e d by M. Sekiguchi