Sequence relations among the IncY plasmid p15B, P1, and P7 prophages

PLASMID

16,8 l-89 ( 1986)

Sequence

Relations

among

the IncY

Plasmid

~158,

Pl , and P7 Prophages

JURGMEYER,MARGARETHAST~LHAMMAR-CARLEMALM,MARKUSSTREIFF, SHIGERU IIDA, AND WERNER ARBER Department of Microbiology,

Biozemrum,

University ofBase1, KIingeIbergstrasse

70. CH-4056 Basel, Switzerland

Received October 1, 1985 Electron microscopic analysis of heteroduplex molecules between the 94-kb plasmid p 1SB and the 92-kb phage PI genome revealed nine regions of nonhomology, eight substitutions, and two neighboring insertions. Overall, the homologous segments correspond to 83% of the Pl genome and 8 1% of p 15B. Heteroduplex molecules between p 15B and the 99-kb phagc P7 genome showed nonhomology in eight of the same nine regions; in addition, two new nonhomologous segments are present and P7 carries a 5-kb insertion representing Tn902. The DNA homology between those two genomes amounts to 79% of P7 DNA and 83% of p15B. Plasmid p15B contains two stem-loop structures. One of them has no equivalent structure on Pl and P7 DNA. The other substitutes the invertible C segments of PI and P7 and their flanking sequences including tin, the gene for the site-specific recombinasc mediating inversion. Q 1986 Academic PESS. hc. The

temperate

coliphages

Pl

0.6-kb-long inverted repeats, one of which carries a deletion in P7 (Lee et al., 1974; Yun and Vapnek, 1977; Chow et al., 1978; Iida et al., 1982, 1985b). As another structural characteristic, Pl DNA carries a copy of the insertion element ISI as a natural constituent, while this region is substituted in the P7 genome (Yun and Vapnek, 1977; Iida et al., 1978; Iida and Arber, 1979). Another IncY plasmid, p15B, resident in Escherichia co/i 15T- has extensive sequence homology to P 1 DNA and can recombine with the Pl genome to give rise to plaque-forming Pl- 15 hybrid phages (Arber and WautersWillems, 1970; Ikeda et al., 1970; Hedges et al., 1975; Meyer et al., 1983). The Pl-15 hybrids and p 15B determine the restriction and modification system EcoPl5, which is functionally related to the EcoP 1 system of phages Pl and P7 although it has a different DNA specificity (Arber and Wauters-Willems, 1970; Bachi et al., 1979; Iida et al., 1983; Hadi et al., 1983). Two different temperate phages can be induced in several E. coli 15 strains, but there is no correlation between the presence of p 15B and the production of phage particles, and the DNAs in the different particles do not hybridize to PI DNA (Ikeda et al., 1970). Thus, plasmid p 15B may be considered to be

(Bertani,

195 1) and P7, originally called 4Amp (Smith, 1972) are heteroimmune relatives able to complement each other for many functions and to form viable genetic recombinants (Chesney and Scott, 1975; Walker and Walker, 1976; Wandersman and Yarmolinsky, 1977; Iida and Arber, 1979). In lysogenic cells the prophages replicate as autonomous plasmids of about 92 and 99 kb, respectively, at one to two copies per host chromosome (Ikeda and Tomizawa, 1968; Prentki et al., 1977; Yun and Vapnek, 1977). Both of these plasmids belong to the incompatibility group Y (Hedges et al., 1975; Cowan and Scott, 198 1). Restriction cleavage maps of the two phage genomes and an electron microscope heteroduplex map have been established (Blchi and Arber, 1977; Yun and Vapnek, 1977; Chow et al., 1978; Iida and Arber, 1979). They showed that DNA homology corresponds to 90% of Pl DNA and 83% of P7 DNA, respectively, and that there are seven regions of nonhomology. The P7 genome is larger mainly due to the insertion of a T&-related ampicillin (AP) resistance transposon, Tn902. As a structural feature, both genomes contain a homologous, invertible C segment consisting of a 3.0-kb unique sequence flanked by 81

0147-619X/86

$3.00

Copyrigbf 8 1986 by Academic Press, Inc. All rights of reproduction in any form resewed.

82

MEYER

ET AL.

a PI-related defective prophage. However, corresponding to plasmids designated p 15A, cells carrying pl5B are not Pl-immune. p 15B, and p 15C, respectively (Cozzarelli et al., In this study we determined, by electron 1968; Ikeda et al., 1970). microscopic heteroduplex analysis, the size and location of homologous and nonhomol- Physical Homology betweenp15B ogous DNA segmentsin these plasmids. and Pl DNA MATERIALS

AND METHODS

Bacterial and bacteriophage strains. E. coli K 12strain WA92 I, usedashost for the phages, and E. coli 15T- were grown as described (Arber and Wauters-Willems, 1970). The phages usedwerePlmod202::Tn10(Iidaet al., 1983), P7clts48 (Scott et al., 1977; Iida and Arber, 1979), and PI-15Km 9H-7 which is a Pl-15 hybrid 2 derivative carrying an IS2 in the Cloop and Tn5 in fragment BamHI- 11 (Meyer et al., 1983; Iida, 1984). Preparation of plasmid and phage DNA. The procedure used for the isolation of plasmids from E. coli 15T- involved lysis by Triton X- 100 as given by Kupersztoch and Helinski (1973). Phage DNA was extracted from phage P 1 and P7 particles as described (Meyer and Iida, 1979; Iida and Arber, 1979). Electron microscopy. For measurements of double-stranded molecules, DNA was mounted by cytochrome c spreadings. Heteroduplex molecules between uv-nicked p 15B and phage DNA were prepared by alkali denaturation and renaturation in formamide (Davis et al., 1971; Meyer et al., 1981). Cytochrome c spreadingswere done maintaining identical denaturing conditions in spreading solution and hypophase (Davis and Hyman, 1971) usually from solutions containing 50% formamide. Phage PM2 DNA and phage fd DNA were added to samplesbefore spreading as double- and single-strand standards, respectively. The DNA molecules were measured from tenfold enlarged electron micrographs with an electronic planimeter (Numonies Corp.). RESULTS

Plasmid preparations isolated from E. coli 15T- contained three kinds of plasmids of sizes 2.34 f 0.12, 93.9 +- 2.9, and 144.5 -t 4.9 kb,

A heteroduplex analysis was carried out to determine the extent of homology between pl5B and Pl DNA. Since plasmid mixtures were used, the pertinent heteroduplex molecules were identified by their size and the two stem-loop structures of TnlO and of the Cloop present on the DNA of the particular P 1 derivative. These snap-back structures also provided convenient physical markers on the circular heteroduplex molecules and allowed unambiguous orientation. A representative molecule is shown in Fig. 1 and the results of the analysis are summarized in Table I and Fig. 2. There were nine regions of nonhomology between p 15B and P 1. Most of these seemed to overlap with nonhomologous segments which had been defined in PI :P7 heteroduplexes by Yun and Vapnek (1977), and we therefore followed and extended their alphabetic designations.Regions M and B have been mapped on a Pl- 15 hybrid phage DNA (Iida et al., 1983; Meyer et al., 1983) and are identical on the parental p15B. Ml and M2 rep resent the partial homology in res and the nonhomology in mod, respectively. B2 contains the ISI element present on the Pl genome, while Bl represents an insertion in p 15B. C is an almost symmetrical substitution of about 5 kb. On the PI DNA it includes the invertible C segment consisting of 3.0-kb unique DNA and flanking 0.6-kb inverted repeatstogether with adjacent sequenceson both sides. The corresponding DNA in pl5B also contains a unique sequence (about 1.5 kb) flanked by inverted repeatsof 0.6 kb. We have no evidence for homology between these repeats of similar length which form characteristic stem-loop structures on both strands of heteroduplex molecules (Fig. 1, inset). Rather, we observed considerable heterogeneity in the position within the substituted segment and

DNA HOMOLOGY

BETWEEN IncY PLASMIDS

83

FIG. 1. Electron micrograph of a heteroduplex molecule between p15B and PI: :TnlO. The TnlO and C snap-backsallowed proper orientation. The nonhomologous segmentsare labeled according to the map in Fig. 2. The inset shows a disentangled C region and a contiguous C-D segment.

in the size of the C stem-loop structure of pl5B, reflected in the higher standard deviations. This may indicate that there is not just one pair of inverted repeats but a more complex pattern of repetitive DNA. In region D there is a second stem-loop structure on p 15B of O.&kb-long inverted repeats flanking a segment of about 1S-kb DNA substituting a 1.Ikb segment on PI DNA. E is a symmetrical substitution; H, F, and G are asymmetrical

substitutions; and L represents a region of partial nonhomology. The overall homology between pl SB and PI DNA amounts to 76.1 kb, while 18.4 kb of p15B and 15.6 kb of Pl DNA are nonhomologous.

SequenceHomology betweenp15B and P7 DNA Heteroduplex molecules between p 15B and P7 DNA revealed 11 segmentsof nonhomol-

84

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ET AL.

TABLE MEASUREMENTS OF Ho~oux;ous

1

AND N~NH~M~LLK%XJ~ DNA SEGMENTS IN HETER~DUPLEX MOLECULES Heteroduplex

Segment A A-M I MI MI-M2 M2 M2-BI Bl BI-B2 B2 B2-Cl Cl Cl-c2

plSB:Pl

1

K-F1 Fl

FI-F2 F2 F2-G G G-L L L-A

7.61 + 0.21

-

1 J

0.33

0.49 zk0.15 0.66 + 0.08 0.29 3.02 f 0.28 0.36 0.68 + 0.14 9.24 + 0.55 0.11

1.53 + 0.20 1.09 + 0.14 0.84 -+ 0.07 I 3.74 2 0.18 0.71 f 0.13 1.85 + 0.31 5.47 f 0.28 2.62 f 0.32’

1

0.58 f 0.38 f 1.29 + 0.32 2.98 + I .26 f 0.26 0.78 f 9.24 +_0.33

1.81 f 0.28

0.20 0.11 0.48Ir 0.24

13.2 T!Z0.3 0.34 zk0.10 partial 70% 2.22 * 0.12 0.94 * 0.22 partial 60% 14.4 + 0.5 0.54 f 0.19 partial 90% 0.75 + 0.13 0.65 + 0.21 partial 90% 1.55 It 0.15

0.30 f 0.19

1.26 f 0.10

-

2.17 + 0.42

6.97 f 0.25 0.49 * 0.15

1.63 f 0.32 1.19 * 0.39 0.82 0.51 f* 0.13 0.10 I 3.44 + 0.26 0.72 + 0.15 1.90 ?I 0.32

J

0.94 f 0.19 0.53 * 0.11 5.26 + 0.36 0.28 f 0.08 partial 25%

1.20 + 0.21

12.3 + 0.5

6.87 + 0.38 0.43 2 0.10 0.24 ?I 0.10

22.3 k 1.2

2.81 f 0.36

4.12 k 0.34

1

2.00 ? 0.33

1.07 + 0.31 0.61 + 0.28

-

4.88 f 0.48

4.90 f 0.53

1.15 + 0.18 12.2 k 0.6

7.35 f 0.47 1.08 f 0.67 + 1.51 + 1.47 f

W:Pl-15

4.04 Lk0.44

0.49 f 0.11 partial” 0.77 f 0.08 1.18 + 0.12 12.3 zk0.7 0.74 k 0.16 0.84 k 0.09 1.73 * 0.31

C2 left C2 stem c2 loop c2 right C2-D D stem D loop D flanking D-H H H-E E E-l I I-K K

pl5B:W

1.10 k 0.21

5.66 + 0.23 0.44 + 0.20 partial 20% 4.53 * 0.71

1

0.66 f 0.32 0.37 zi 0.1 I 3.60 lk o.33b

0.63 k 0.1 I 3.05 + 0.40

10.4 _+0.5

I I

1.54 + 0.33

10.7 f 0.4

2.86 + 0.31’ 5.68 f 0.22 0.28 ?I 0.12 partial 85% 2.25 + 0.19 1.09 + 0.14 partial 80% 14.1 + 0.8

1) 3.32 f 0.57

J

0.32 zk0.14

1.35 f 0.23 1.95 * 0.45 0.42 f 0.21

1

10.7 f 0.6

Note. The meansf standard deviations given (in kb) are basedon measurementsof 13-27 heteroduplex molecules. Data in the center of eachcolumn indicate segmentsof equal length in both partners. Unequal lengths are assignedto the respectiveDNA. “Partial” means that a particular loop is seenonly in a fraction (given as W below) of the heteroduplex molecules. n Seenonly at high formmru‘de concentration (Iida et al., 1983). b Reduced by 1.33 kb to compensatefor the IS2 inserted in the C loop. ‘Some molecules contain one me loop; others have two smaller loops separatedby a homologous segmentof 0.2-0.6 kb.

ogy (Fig. 2; Table I), five of which locate in stem-loop structure of P7 carries an internal the same regions as on the p 15B:P1 hetero- deletion (Iida et al., 1985b) and the D substiduplex map. Regions M2, H, and L appear tution appears slightly larger, perhaps due to identical, while in the C2 substitution the local melting of the flanking A+T-rich DNA

DNA HOMOLOGY

MlMZ

8182

85

BETWEEN IncY PLASMIDS

c2

0

H

H

A

II2

B

ClC2

0

A

M2

a

ClC2

0

E

I

E

K

I

K

FG

L

FlFZG

L

F

G

10kb

FIG. 2. Heteroduplex maps between p15B plasmid, PI and P7 DNAs. The circular maps are drawn in a linear form with insertion A of P7 at the left and located at map unit 3 of the conventional PI map (Yarmolinsky, 1984). A single line indicates homologous DNA, while substitutions are marked by two separatelines. Two lines at half the distance (e.g., regions MI, E, L) delineate regions of partial homology. Stem-loop structures in C2 and D denote snapback DNA due to the presenceof inverted repeats.The upper two maps are aligned relative to p 15B sequences.

(Meyer et al., 1981) under the spreading conditions used. Region A representsthe insert of Tn902 in P7 (Yun and Vapnek, 1977). Although P7 lacks an ISZ and contains a shorter segment nonhomologous to PI in this part of the genome, the B region is also nonhomologousto pl5B. There are one additional small nonhomologous segment,C 1, to the left of the C2 region and two segments of partial DNA homology, I and K. While region E is completely homologous, the FG region is only partly complementary and contains an insertion in P7. P7 and p15B share 78.3-kb DNA sequences, while nonhomologous segments correspond to 20.7 kb of P7 DNA and 15.8 kb of p15B. P7:Pl-15 Heteroduplex Map As a control for the EM measurements and particularly as a search for partial nonhomology in regions I, K, and L we prepared a heteroduplex map between P7 and P 1- 15 derivative DNA (Fig. 2, Table 1). All the expected insertions, substitutions and snap-back struc-

tures A-G and M2 were found (Yun and Vapnek, 1977;Chow et al., 1978;Ii& et al., 1983). Partial nonhomologies were observed in regions I and K but not in L. p15B Homoduplex Analysis In an attempt to determine whether one or both of the stem-loop structures of p 15B represent an invertible DNA segment similar to the C segmentsof P 1 and P7 we analyzed p 15B after denaturation and reannealing. A small fraction of these homoduplex molecules showed one loop of about 1.5 kb. Only one of them (Fig. 3) contained such a non-base-paired region in addition to a stem-loop structure at a distance corresponding to the distance between regions C2 and D. These observations could indicate that one of the DNA segments flanked by long inverted repeats may alter its orientation. DISCUSSION

The heteroduplex maps between p 15B, P 1, and P7 define 12 regions of nonhomology

ET AL.

PIG. 3. Relevant part of a p 15B homoduplex molecule showing a IS-kb loop (arrowhead) and an “undenvound loop” (arrow) (Broker et al., 1977) which is produced by annealing of the loops of two stem-loop structures (C or D).

called A to M which are correlated to genetic data and the BgfiI restriction map in Fig. 4. Insert A representsthe Ap’ transposon Tn902 carried by phage P7 (Yun and Vapnek, 1977). Tn902 is probably identical to the 4957-bp transposon Tn3 (Heffron et al., 1979; Iida et al., 1985~). Segments Ml, M2, Bl, and B2 have been characterized on a hybrid phagebetween p 15B and P 1, and are located in the res mod and the ISI regions, respectively, of the PI genome (Iida et al., 1983; Meyer et al., 1983). Since the flanking nonhomologies C2

and L were not found on this Pl- 15 hybrid phage (hybrid 2; Meyer et al., 1983), the recombination crossoversresulting in its emergencemust have occurred in DNA between L and Ml on the left and between B2 and C2 on the right. The C regions of Pl and P7 are largely homologous and contain an invertible DNA segment consisting of 0.6-kb inverted repeatsand 3.0-kb unique sequences,and immediately to its left the 561-bp-long gene tin for the sitespecific recombinase mediating inversion (Yun and Vapnek, 1977; Chow et al., 1978; Iida et al., 1982, 1984, 1985b,Hiestand-Nauer and Iida, 1983). To the right of the C segment probably lies a leftward promoter which initiates late transcription of tail fiber genes(S) and (U) or (S’) and (U’) residing in the invertible DNA segment, thus regulating the phages’ host range (Iida, 1984; Iida et al., 1985b). This whole functional unit is substituted in p 15B by a slightly shorter DNA segment which also contains inverted repeats. Although we have observedp 15B homoduplex molecules suggestingthat this DNA segment is invertible, we do not know whether inversion is mediated by a plasmid-encoded recombinase or by a general recombination function of E. coli 15T-. The C 1 nonhomol-

PIG. 4. Correlation of the phage PI genetic map (I) and BgfiI restriction fragment map (II) to the Pl:P7 (III) and the Pl:plSB (IV) heteroduplex maps and to insertion sites of IS elements and transposons into plaque-forming PI, Pl-I 5, or P7 phages (V). The genetic symbols and mapping data are taken from Yarmolinsky (1984),the Bg/II restriction map of Pl from B&&i and Arber (1977).The black box in the restriction map represent ISI and the boxes with the triangle mark the inverted repeats of the C segment, respectively. In the heteroduplex maps (III, IV) black boxes indicate substitutions, black triangles represent insertions, and white boxes indicate segments of partial nonhomology, respectively. The data are derived from Yun and Vapnek (1977) and this study. The insertions in V represent (A) ISI or ISI-flanked transposons, (A) IS3, (A) ISJO, (A) Tn5, and (t) TnlO, respectively, and have been mapped by Arber et al. (1978, 1980), Casperset al. (1984), Iida (1983, 1984), Ii& et al. (1980, 1981a,b, 1985a), and S. Iida (unpublished). The brackets in V indicate nonessential regions in the Pl genome in which DNA rearrangements have been observed repeatedly (Iida et al., 1982, 1983).

DNA HOMOLOGY

BETWEEN IncY PLASMIDS

ogy seenin P7:p15B and P7:Pl heteroduplexes startsabout 700 bp to the left of the C segment, and thus some 100 bp to the left of the tin structural gene where the regulatory elements for the tin gene lie (Hiestand-Nauer and Iida, 1983). Segment Cl is probably related to the segment called X by Chow et al., (1978). The D segment of nonhomology contains the ImmI region which determines the Pl- and P7-specific immunity, respectively (Yun and Vapnek, 1977; Iida and Arber, 1979; Scott, 1980). Plasmid p 1SB carries an unrelated sequence flanked by 0.8-kb-long inverted repeats, which might be related to the observation that cells harboring pl5B are immune neither to PI nor to P7. The Pl plasmid can be replicated from either one of the two physically and functionally distinct replication origins designatedoriL and oriR (Stemberg and Austin, 1981; Stemberg and Hoess, 1983). Since the PI plasmid replication does not reflect the properties of the L replicon but rather those of the R replicon, replication from oriL is postulated to be repressed in the PI prophage, perhaps by the gene products of the immunity repressorscl and c4 (Stemberg and Hoess, 1983; D. Chattoraj and N. Stemberg cited therein). While the oriL region of p 15B is not homologous to that of Pl (segment H), the plasmids share DNA homology in the oriR region, which in addition to functions for autonomous replication also contains incompatibility determinants (Abeles et al., 1984; Austin et al., 1985). The 2.8-kb segmentE could include the 2.5kb region essential for stable plasmid maintenance (par) (Austin and Abeles, 1983ab). The Pl par region acts in cis and is sufficient to promote equipartition of plasmids. The substitution in p 15B may contain a poor homology to the PI sequencein its middle part, but the two flanking parts are not homologous to Pl DNA. Interestingly, this segment of p 15B is identical to the substitution in P7. This sequence difference between PI and P7 could provide an explanation for the observation that homologous pairs of Pl or P7 plasmid prophages segregatemore rapidly than heterologous pairs (Cowan and Scott, 1981). We

87

take this as evidence that the E substitution provides indeed a par function of distinct specificity. Neither in region I-K nor in region F-G have there been any PI or P7 genesmapped. Region L is close to or overlaps with the cl gene coding for a repressor that maintains lysogeny but is not responsible for immunity specificity. This DNA segmentis homologous between P 1 and P7 (Chesney and Scott, 1975; Wandersman and Yarmolinsky, 1977; Yun and Vapnek, 1977; Scott, 1980). Plasmid p 15B is considered to be a Pl-related defective prophage. Whether the reason(s) for the defectivenessof p15B resides in one or several of the substituted DNA segments, in additional mutations in genes or their regulatory elements responsible for head and tail morphogenesisor for vegetative phage DNA replication, or in the E. coli 15 host remains to be investigated. Comparison of the DNA sequencesof plasmids pl5B, PI, and P7 by electron microscopic heteroduplex mapping reveals eight regions in which divergence occurred by substitution of about gene-sized or larger DNA segments.For three of them (B, D, FG) there are three different DNA sequences.Four regions with partial nonhomology could indicate extensive sequencevariation by accumulation of point mutations. Interestingly, in the PI (or PI-1 5) and P7 genomesthe regions A, B, C, D, and FG have repeatedly served as target regions for IS elements and transposons (Fig. 4, V). Since these PI and P7 mutants carrying insertions are plaque-forming derivatives, the regions contain dispensable sites or segments. Four of these regions contain a relatively high A+T content which may have facilitated repeated ISZ-mediated DNA insertions (Meyer et al., 1980, 1981). Furthermore, isolation of a plaque-forming P 1 derivative carrying the genome region between B and D in inverted orientation indicates that the orientation of the transcription units in this region is not important for Pl growth, both for vegetative phagereplication and for plasmid propagation in the lysogenic state (Iida et al., 1985a). In

88

MEYER ET AL.

view of the comparison presentedhere, P 1 and its related IncY plasmids provide yet another example of the significant contribution of exchange of DNA “modules” in the evolution of plasmids and phages (Campbell and Botstein, 1983; Storchovi et al., 1985; Jarvis and Meyer, 1986). ACKNOWLEDGMENTS We thank Gordon Lark for critical comments on the manuscript and Heini Sandmeier for providing a plasmid preparation. This work was supported by Grants 3.038.81 and 3.392.83from the SwissNational ScienceFoundation.

REFERENCES ABELES,A. L., SNYDER,K. M., AND CHATTORAJ,D. K. (1984). PI plasmid replication: replicon structure. J. Mol. Biol. 173, 307-324. ARBER,W., IIDA, S., JOVE, H., CASPERS, P., MEYER,J., AND HKNNI, C. (1978). Rearrangementsof genetic material in Escherichia coli as observed on the bacteriophage Pl plasmid. Cold Spring Harbor Symp. Quant. Biol. 43, 1197-1208. ARBER, W., H~~MBELIN,M., CASPERS,P., REIF, H. J., IIDA, S., AND MEYER,J. (1980). Spontaneousmutations in the Escherichia coli prophage Pl and IS-mediated processes.Cold Spring Harbor Symp. Quant. Biol. 45, 38-40. ARBER,W., AND WAUTERS-WILLEMS,D. (1970). Host specificity of DNA produced by E. coli. XII. The two restriction and modification systemsof strain 15T-. Mol. Gen. Genet. 108,203-2 17. AUSTIN, S., AND ABELES, A. (1983a). Partition of unitcopy miniplasmids to daughter cells. I. PI and F miniplasmids contain discrete interchangeable sequences sufficient to promote equipartition. J. Mol. Biol. 169, 353-372. AUSTIN, S., AND ABELES,A. (1983b). Partition of unitcopy miniplasmids to daughter cells. II. The partition region of miniplasmid PI encodesan essential protein and a centromere-like site at which it acts. J. Mol. Biol. 169,373-387.

AUSTIN, S. J., MURAL, R. J., CHATTORAJ,D. K., AND ABEL& A. L. (1985). Tram- and cis-acting elements for the replication of Pl miniplasmids. J. Mol. Biol. 183, 195-202. BACHI, B., AND ARBER,W. (I 977). Physical mapping of Bg/II, BamHI, EcoRI, Hind111and PsfI restriction fragments ofbacteriophage Pl DNA. Mol. Gen. Genet. 153, 31l-324. BKCHI, B., REISER,J., AND PIRROTTA,V. (1979). Methylation and cleavagesequencesof the EcoP1 restrictionmodification enzyme. J. Mol. Bio/. 128, 143-163.

BERTANI,G. (195 1). Studies of lysogenesis.I. The mode of phage liberation by lysogenic Escherichia co/i. J. Bacterial. 62, 293-300. BROKER,T. A., SOLL,L., AND CHOW,L. T. (1977). Underwound loops in self-renaturedDNA can be diagnostic of inverted duplications and translocated sequences.J. Mol. Biol. 113, 579-589. CAMPBELL,A., AND BOTSTEIN,D. (1983). Evolution of the lambdoid phages.In ‘Lambda II” (R. W. Hendrix, J. W. Roberts, F. W. Stahl, and R. Weisberg, eds.),pp. 365-380. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. CASPERS,P., DALRYMPLE,B., IIDA, S., AND ARBER,W. (1984). ISJO, a new insertion sequence of Escherichia coli K12. Mol. Gen. Genet. 196, 68-73. CHESNEY,R. H., AND Scorr, J. R. (1975). Superinfection immunity and prophage repression in phage Pl. II. Mapping of the immunitydifference and ampicillin resistanceloci of Pl and $Amp. Virology 67, 375-384. CHOW,L. T., BROKER,T. R., KAHMANN, R., AND KAMP, D. ( 1978).Comparison of the G DNA inversion in bacteriophages Mu, PI and P7. In “Microbiology-1978” (D. Schlessinger,ed.), pp. 55-56. Amer. Sot. for Microbiol., Washington, D.C. COWAN,J. A., AND SCOTT,J. R. (1981). Incompatibility among group Y plasmids. Plasmid 6,202-22 1. COZZARELLI,N. R., KELLY, R. B., AND KORNBERG,A. (1968). A minute circular DNA from E. co/i 15. Proc. Nat/. Acad. Sci. USA 60,992-999. DAVIS, R. W., AND HYMAN, R. W. (1971). A study in evolution: The DNA base sequencehomology between coliphages T7 and T3. J. Mol. Biol. 62, 287-30 1. DAVIS, R. W., SIMON, M., AND DAVIDSON,N. (1971). Electron microscopeheteroduplex methods for mapping regions of base sequencehomology in nucleic acids. In “Methods in Enzymology” (L. Grossman and K. Moldave, eds.),Vol. 2 1, pp. 4 13-428. Academic Press,New York. HADI, S. M., BACHI,B., IIDA, S.,ANDBICKLE,T. A. (1983). DNA restriction-modification enzymesof phage PI and plasmid pl5B. Subunit functions and structural homologies. J. Mol. Biol. 165, 19-34. HEDGES,R. W., JACOB,A. E., BARTH, P. T., AND GRINTER, N. J. (1975). Compatibility properties of Pl and +Amp prophages. Mol. Gen. Genet. 141, 263-267. HEFFRON,F., MCCARTHY, J. B., OHTSUBO,H., AND OHTSUBO,E. (1979). DNA sequence analysis of the transposon Tn3: Three genes and three sites involved in transposition of Tn3. Cell 18, 1153-I 163. HIESTANDNAUER,R., AND IIDA, S. (1983). Sequenceof the site-specificrecombinasegenetin and of its substrates serving in the inversion of the C segment of bacteriophage Pl. EMBO J. 2, 1733-1740. IIDA, S. (1983). On the origin of the chloramphenicol resistancetransposon Tn9. J. Gen. Microbial. 129, 12171225. IIDA, S. (1984). Bacteriophage Pl carries two related sets

DNA

HOMOLOGY

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