Proc. Natl. Acad. Sci. USAVol. 83, pp. 5474-5478, August 1986Biochemistry

Integration of staphylococcal phage L54a occurs by site-specificrecombination: Structural analysis of the attachment sites

(bacteriophage conversion/lipase expression)

CHIA YEN LEE AND JOHN J. IANDOLO*Division of Biology, Microbiology and Immunology Group, Kansas State University, Manhattan, KS 66506

Communicated by Myron K. Brakke, April 18, 1986

ABSTRACT Lysogenization by staphylococcal phage L54ainduces the loss of lipase (glycerol ester hydrolase) activity in itshost Staphylococcus aureus. The attachment site ofthe bacterialchromosome (attB) for the phage is at the 3' end of the lipasegene, geh. The DNA fragment containing the attB (base pairs2620-2637 inclusive) site has been sequenced. We have alsocloned and determined the nucleotide sequence of the DNAfragments containing the other three attachment sites-i.e., theattP locus on the circularly permuted phage genome and theattL and attR loci at the left and right ends of the prophage inthe lysogenized strain. These results reveal that an 18-base-paircore sequence is common to all four afu sites. These dataindicate that the crossover point must exist within the coresequence and, further, that integration is site- and orientation-specific. We also localized the viral recombinase gene to a2.1-kilobase DNA segment extending rightward to the atP site.This region was found to be essential for integration ofplasmidscontaining the attP site.

There are many well-characterized examples of site-specificrecombination among Gram-negative bacteria. The integra-tion and excision of bacteriophage X is the most thoroughlystudied system, but others include resolution of Tn3 andgamma-delta transposition (1, 2), bacteriophage P1 integra-tion (3, 4), and site-specific gene inversions (5-9). However,less is known about site-specific recombination in Gram-positive microorganisms. In Staphylococcus, studies of site-specific recombination of Tn554 transposition (10-12),cointegration of small plasmids (13), and phage-plasmidrecombination (14) have been described. Recently, the struc-ture of the recombination sites used for plasmid cointegrateformation and Tn554 insertion sites have been determined(15, 16). However, very little is known of the mechanism ofbacteriophage integration. We report here the structure oftheattachment site of the staphylococcal phage L54a, whichlysogenizes its host S. aureus PS54 by site-specific recom-bination into the glycerol ester hydrolase (geh) gene.

Bacteriophage L54a is one of the two prophages originallyfound in S. aureus PS54. It is a temperate phage, capable ofboth lytic and lysogenic life cycles. In the lysogenic form, itinactivates the extracellular lipase ofthe host strain, whereascuring restores the activity (17). Lysogenic conversion is dueto interruption of the lipase structural gene (geh) by insertionof the phage DNA near the 3' end of the reading frame (18,19). To understand the mechanism of integration and todetermine the exact integration site within the lipase gene, wecloned and determined the nucleotide sequence of (i) theattachment site contained on the phage genome, attP; (it) theattachment site contained on the bacterial chromosome,attB; and (iii) the sites created at the bacteriophage/chromo-somal DNA junctions in the lysogenized strain, attL and

attR. We found an 18-base-pair (bp) homologous core regionat all four attachment sites, which suggests a model forintegration wherein recombination of the phage genome withthe host chromosome is site- and orientation-specific. Inaddition, we localized the viral gene(s) necessary for inte-gration to a 2.1-kilobase (kb) DNA fragment rightward of theattP site.

MATERIALS AND METHODSPhage and Bacterial Strains. Staphylococcal phage L54a

was isolated from S. aureus PS54 by ultraviolet light induc-tion (18) and was propagated on S. aureus 8325-4. StrainPS54C is the prophage-cured derivative of PS54. S. aureusRN4220 (20), a restriction-deficient variant of S. aureus8325-4, was used as the recipient in transformations.Protoplast transformation was performed by the procedure ofChang and Cohen (21). Strain RN4220 was also used forintegration analyses, because it is lipase-positive and couldbe converted to the lipase-negative phenotype by bacterio-phage L54a. Escherichia coli LE392 was used for transfor-mation with cloned DNA and for preparation of plasmidDNA. Phage preparation, phage DNA extraction, and bulkchromosomalDNA purification were as previously described(18).

Chemicals and Enzymes. Medium for routine cultivationand for detection of lipase activity has been described (18).Chemicals were purchased from Sigma. Restriction en-zymes, bacteriophage T4 DNA ligase, T4 polynucleotidekinase, and nick-translation reagents were obtained fromNew England Biolabs and Bethesda Research Laboratories.The large fragment of DNA polymerase (Klenow fragment)was purchased from Boehringer Mannheim. [a-32P]dATP and[y-32P]dATP were purchased from New England Nuclear.

Hybridization. The transfer ofDNA to nitrocellulose mem-branes was by the method of Southern (22). Conditions usedfor hybridization analysis have been described (19).DNA Sequence Analysis. As we described (19), restriction

fragments were inserted into the M13 bacteriophage deriva-tives mpl8 and mpl9 and propagated in E. coli JM103. DNAsequencing was carried out by the dideoxy chain-terminationmethod of Sanger et al. (23).

Isolation of DNA Fragments Containing Attachment Sites.We had previously identified and isolated the attB site of S.aureus PS54C chromosomal DNA within the Cla I segmentD ofthe 3.0-kb DNA fragment containing the lipase gene. Thebacteriophage/chromosome junctions of strain PS54, attRand attL, were also identified respectively within 4.8-kb and3.6-kb Cla I restriction fragments (18). End-labeling (38)indicated that the genome of L54a was circularly permuted,and we were therefore able to identify the fragment contain-ing the attP site directly by hybridization analysis. Bacterio-phage L54a DNA and PS54 bulk chromosomal DNA were

Abbreviations: bp, base pair(s); kb, kilobase(s).*To whom reprint requests should be addressed.

5474

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Proc. Natl. Acad. Sci. USA 83 (1986) 5475

digested with the restriction enzyme Cla I and separated byelectrophoresis in an agarose gel. The fragments were thentransferred to nitrocellulose and hybridized to nick-translat-ed bacteriophage L54a DNA. A single, 4.5-kb bacteriophageDNA fragment that was distinct from the chromosomal*junction fragments was found and concluded to contain theL54a attP site.The restriction fragments containing the attachment sites

were isolated from agarose gels and inserted into the Cla I siteof plasmid pBR322.

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RESULTS

DNA Sequences of the aft Sites. The nucleotide sequence ofthe PS54C chromosomal DNA segment containing the attBsite was identified in an earlier report (19). The crossoverpoint of the site was confined to a 90-bp DNA segment, butthe exact site was not determined.To determine the nucleotide sequence of the DNA seg-

ments containing the prophage attachment sites, we firstlocalized the approximate attL and attR by Southern hybrid-ization. The cloned Cla I fragments containing attL (4.8 kb)and attR (3.6 kb) were digested with various restrictionenzymes and hybridized to a nick-translated 770-bp Cla IDNA segment (Cla I-segment D) of the chromosome ofPS54C, which contained attB (19). Two fragments of approx-imately 400 bp and 450 bp were found that contained attL andattR, respectively. These fragments were in turn used asprobes to localize the attP site on the 4.5-kb Cla I fragmentof bacteriophage L54a DNA. attP was confined to a 400-bpCla I-Acc I double-digest fragment. The restriction map andthe sequencing strategy of the DNA segments containing theatt sites are shown in Fig. 1.The sequence of the att sites (Fig. 2) reveals an 18-bp core

sequence common to all four. Within the geh gene, the coresequence extends from base pair 2620 to 2637 inclusive (19).This feature is similar to the bacteriophage X att sites, inwhich the common core is a 15-bp sequence (24). Unlike thecommon core of the X att sites, which has an 80% A+Tcontent, the core of the L54a att sites is only 61% A+T. TheA+T content of the DNA flanking the core region (the arms)and extending from position -50 to +50 (see Fig. 2) is 63%in the attP site and 55% in the attB site. In view of the factthat the percent A+T of the S. aureus genome andstaphylococcal phages is 62-70% (25, 26), the percent A+Tfound in the core sequence and the surrounding region is notatypical.

Also indicated in Fig. 2 are regions of dyad symmetry,inverted repeats and direct repeats. These might representbinding sites for proteins that mediate the recombination. Noattempt was made to confirm the protein-binding capacity ofthese regions.

Localization of the Recombinase Gene. In every reportedsystem of site-specific recombination, the gene encoding theenzyme that mediates the recombination reaction is locatednear the recombination site, so our initial approach to identifythe gene or genes responsible for phage L54a recombination(recombinase gene) was centered on the DNA near the attPsite. Two DNA fragments containing attP were cut from thebacteriophage genome. One (4.5 kb) contained attP withDNA extending rightward from it (Cla I restriction fragment,see Fig. 3) and the other (3.5 kb) contained attP with DNAextending leftward from it (Pvu II-HindIII restriction frag-ment, see Fig. 3). These fragments were individually clonedinto a shuttle vector, pLI50, and the resultant plasmids weredesignated pLI461 and pLI475, respectively (Fig. 3). Theplasmids were transformed into protoplasts derived from S.aureus RN4220, and the presence of recombinase activitywas tested by assaying for lipase activity. The results (Fig. 3)indicate that RN4220(pLI461) had no lipase activity, whereas

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FIG. 1. Cloned primary restriction fragments of the genomes ofS. aureus PS54 and PS54C and of the genome of bacteriophage L54acontaining the attachment sites. DNA sequencing strategy is alsoindicated. (A) attB. (B) attL. (C) attR. (D) attP. Isolation of thesefragments is described in Materials and Methods. Solid bars repre-sent bacterial DNA, and open bars L54a DNA. The approximatelocation of the geh gene is indicated in A. An expanded restrictionmap of the region containing each att site is shown under the primaryfragment. Arrows indicate the direction of sequencing. Arrowheadsabove the line represent the approximate location of the center of thecore. Numbers indicate the distance (bp) from the center of the coresequence.

RN4220(pLI475) remained lipase-positive. The recombinaseexpressed in RN4220(pLI461) mediates the recombinationbetween attP on plasmid pLI461 and attB on the lipase geneof the RN4220 chromosome, indicating that the recombinasegene is located within the segment of DNA rightward fromthe attP site.More precise mapping of the recombinase gene function

was achieved by cloning and testing recombination activity ofsequential deletions of the 4.5-kb Cla I fragment. The resultsof this experiment are schematically shown in Fig. 3, indi-cating the size of the deletion along with an indication of theeffect of the deletion on integration. These data indicate thatone end of the recombinase gene is located to the left of theEcoRV site (about 2.1 kb rightward of the attP site). Inaddition, since there is no promoter in the vector precedingthe cloning site, the 2.1-kb fragment must contain thepromoter of the recombinase gene.

Confirmation that the lipase-negative phenotype was due tointegration of the plasmid containing the attP site and therecombinase gene was obtained from Southern hybridizationanalyses (22). Cla I-digested bulk chromosomal DNA preparedfrom transformants of various plasmids was hybridized to a

probe of the 770-bp Cla I fragment D of the lipase gene, which

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Biochemistry: Lee and Iandolo

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5476 Biochemistry: Lee and Iandolo

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FIG. 2. Nucleotide sequences of the regions containing the att sites. Sequences are numbered from the center of the core; the base

immediately to the right is + 1 and the base immediately to the left is -1. (A) The central 130 bp of each of the four att sites that encompasses65 bp on each side. (B) Distal portions of the four arms extending 100 bases leftward from -60 and 100 bases rightward from +60. Nomenclatureshown at left of each region (BOB', etc.) is adapted from that of the bacteriophage X system (24). Solid bars represent bacterial DNA; openbars, L54a DNA; hatched bars, core sequences. Molecular palindromes (_-4), inverted repeats ( >-), and direct repeats (a A) are indicated.

Direct repeats are omitted in B, except one set, found in the P and P' arm, that is of special importance and is discussed in the text. Dotted

lines connect the pairs of repeats. The criteria used in marking the sequence features are as follows: minimum of 6 bp with no mismatches in

inverted repeats and direct repeats; a single or no central mismatch with at least 3 bp to each side, or two central mismatches with at least 4

bp to each side, in molecular palindromes.

contains the attB site (i.e., the DNA fragment from base pair-430 to +340 of Fig. 1A). Since Cla I cleaves each of theplasmids at least once but does not cleave the Cla I fragment Dof the lipase gene, the probe would identify two bands ifintegration had occurred, whereas it would identify only oneband if there had been no integration. Fig. 4 shows the resultsof this analysis, which confirm that integration has occurred.

DISCUSSIONPreviously, we used deletion analysis to approximate thelocation of the insertion site (attB) of the bacteriophage L54a

in the lipase structural gene (geh) of S. aureus (18, 19). It waslocated within the terminal 360 bp of the gene; in thiscommunication, we have precisely fixed its position, whichspans base pairs 2620 to 2637. Results of this investigationhave clarified the location and sequence of the other threerecombination attachment sites, and we have also identifiedthe recombinase gene function of phage L54a responsible forintegration.The most striking feature of the att sites is the 18-bp

common core found in all four. Inasmuch as there areunaltered tandem direct repeats ofthe core sequence flanking

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Proc. Natl. Acad Sci. USA 83 (1986)

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Proc. Natl. Acad. Sci. USA 83 (1986) 5477

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FIG. 3. Localization ofthe recombinase gene near the attP site. Relevant restriction sites are indicated. Arrowhead indicates the approximateattP site. Vertical line indicates the approximate location of the core sequences. Lipase phenotype of transformants generated by transformingthe various deleted plasmids is indicated. Integration as determined by lipase activity is also indicated.

the prophage as a result of integration, the crossover pointmust occur within the core sequence. Furthermore, theflanking core sequences also suggest that recombinationoccurs via staggered cuts and that recombination is not onlysite-specific but also orientation-specific.Lysogenization of phage group III strains of S. aureus by

bacteriophage L54a results in loss of lipase activity (17). Thisis caused by insertion of the prophage genome at the 3' endof the lipase structural gene, which is essential for catalysis.By examination of the nucleotide sequence of the leftjunction of the bacterial chromosome and L54a DNA (i.e.,attL), a stop codon (TAA) was found adjacent to the coresequence (Fig. 2A, BOP'). This indicates that a truncated,catalytically inactive lipase protein lacking 46 amino acidresidues should be produced by the lysogenized strain.Indeed, immunodiffusion analysis indicates that thelysogenized strain does produce a crossreactive material thatlacks lipase activity (data not shown). The sequence analy-ses, therefore, support the mechanism of the lysogenicconversion of the lipase.Comparison to the X site-specific recombination system

indicates that a high degree of similarity exists between thetwo systems. Among the similarities are (0) the existence ofthe common core, (ii) specificity and directionality of therecombination, and (iii) the presence and location of therecombinase gene. Despite these similar characteristics,there are also differences. In L54a, the core is 18 bp, whereasin X, it is 15 bp; in L54a, the percentage of A+T within theatt sites is similar to the staphylococcal chromosome and thephage genome, whereas in X, the A+T content of the att siteis much higher than that of the phage or host DNA (24). The

1 2 3 4 5 6

FIG. 4. Southern hybridizationanalysis of integration. DNA from thetransformants containing the deletedplasmids was digested with Cla I,

subjected to electrophoresis in agar-ose, blotted to nitrocellulose, and hy-bridized with 32P-labeled probe pre-pared from the Cla I fragment Dcontaining the attB site (i.e., the DNAfragment from base pair -430 to +340of Fig. L4). Digested DNA was fromRN4220 (lane 1), RN4220(pLI461)(lane 2), RN4220(pLI462) (lane 3),RN4220(pLI463) (lane 4), RN4220-(pLI464) (lane 5), and RN4220-(pLI475) (lane 6).

unenriched A+T level within the L54a/host att sites maysuggest that staphylococci have a site-specific recombinationsystem that is not highly dependent on high A+T content topromote local denaturation at the crossover site (27, 28). Onthe other hand, the similarities between these two unrelatedbacteriophages may suggest that other controls relating torecombination are also similar.The gene function(s) required for site-specific recombina-

tion is located within a 2.1-kb DNA segment rightward oftheattP site. Our results also suggest the functioning of morethan one gene and are supported by the following argument.Our assay for integration is the loss of lipase activityconsequent to insertion. However, after prolonged incuba-tion of strain PS54, lipase activity could be detected at afrequency of 1o-4 to 1O-3 due to loss ofthe prophage (17). Thesame phenomenon was observed with transformants carryingthe cloned attachment sites. The plasmids pLI461, pLI462,and pLI463 would convert these cultures to the lipase-negative phenotype and also revert at a frequency of 10-4.Consequently, this implies that the excision gene is locatedwithin the same 2.1-kb cloned DNA fragment as the gene forintegration. On the other hand, it is conceivable that excisionof these elements could result by homologous recombinationbetween the flanking 18-bp core sequences. To test this,strain RN4220(pLI475) was infected with phage L54a as ahelper to provide the recombinase gene product necessary forpLI475 integration. The resultant lipase-negative colonieswere screened for a lysogen-free clone in which the attB sitewas occupied by pLI475. This strain (KSI1150) did not revertto the lipase-positive phenotype (below detectable limits, ata frequency less than 1 in 107). Since pLI475 does not carrythe region of the phage genome containing the recombinasegene, this result suggests that lipase reversion (at the rateobserved in this study) is not due to homologous recombi-nation mediated by host recombination functions. It ispossible that in L54a, two enzymes are responsible forrecombination and are located within the 2.1-kb DNA seg-ment. In support ofthis, X "integrase" and "excisionase" arelinked as partially overlapping genes within a 1.4-kb segment(29). On balance, however, it must be pointed out that thesearguments do not preclude the possibility that only oneenzyme is required for both integration and excision, asexemplified by the cre gene required for bacteriophage P1site-specific recombination (4).A search of the DNA sequence features (molecular palin-

dromes, inverted repeats, and direct repeats) for potentialprotein-binding sites (Fig. 2) indicates that attP containsmore features than attB. This may imply that attP plays amore important role than attB in recombination. In X recom-

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bination, attP contains five binding sites for integrase(30-34), two sites for excisionase (35), and three sites for IHF(integration host factor) (36, 37); the E. coli attB onlyprovides two sites, in core-arm junctures, for integrasebinding (30, 31). The X integrase and E. coli IHF bind almost240 bp surrounding the attP. In L54a, although there aremany potential protein binding sites at attP, one particulardirect repeat warrants specific mention because of its long (12bp) and nearly perfect repeat sequence. This sequence(AAAAAGGACARA; R = A or G) is found four times in theP and P' arms and spans the region from -135 in the P armto +95 in the P' arm. These most likely represent the sites forrecombinase binding because of the similarity ofthis arrange-ment to the X integrase binding sites. However, it is onlysuggestive, and the actual sites remain to be determined bynuclease protection assay.

In conclusion, we have described the structure of attach-ment sites of bacteriophage L54a site-specific recombinationin S. aureus. The system is very similar to X integration andexcision, yet differences were observed. We have alsoidentified the recombinase gene required for integration.However, mutants have yet to be isolated so that the numberof genes involved can be determined. To elucidate theinteraction between recombinase and the att sites, moreexperiments, such as nuclease protection assays, are needed.

This work was supported in part by Grant AI17474 from theNational Institute of Allergy and Infectious Diseases and in part byU.S. Army Contract DAMD17-86-C-6055. This is contribution no.86-328-J from the Kansas Agricultural Experiment Station, Manhat-tan, KS.

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Proc. Natl. Acad. Sci. USA 83 (1986)