Analysis of insertion into secondary attachment sites by phage λ and by int mutants with altered recombination specificity

Edit Rutkai, László Dorgai, Regina Sirot, Ezra Yagil, Robert A. Weisberg*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

12 Scopus citations


When phage λ lysogenizes a cell that lacks the primary bacterial attachment site, integrase catalyzes insertion of the phage chromosome into one of many secondary sites. Here, we characterize the secondary sites that are preferred by wild-type λ and by λ int mutants with altered insertion specificity. The sequences of these secondary sites resembled that of the primary site: they contained two imperfect inverted repeats flanking a short spacer. The imperfect inverted repeats of the primary site bind integrase, while the 7 bp spacer, or overlap region, swaps strands with a complementary sequence in the phage attachment site during recombination. We found substantial sequence conservation in the imperfect inverted repeats of secondary sites, and nearly perfect conservation in the leftmost three bases of the overlap region. By contrast, the rightmost bases of the overlap region were much more variable. A phage with an altered overlap region preferred to insert into secondary sites with the corresponding bases. We suggest that this difference between the left and right segments is a result of the defined order of strand exchanges during integrase-promoted recombination. This suggestion accounts for the unexpected segregation pattern of the overlap region observed after insertion into several secondary sites. Some of the altered specificity int mutants differed from wild-type in secondary site preference, but we were unable to identify simple sequence motifs that account for these differences. We propose that insertion into secondary sites is a step in the evolutionary change of phage insertion specificity and present a model of how this might occur.

Original languageEnglish
Pages (from-to)983-996
Number of pages14
JournalJournal of Molecular Biology
Issue number5
StatePublished - 20 Jun 2003


FundersFunder number
Bay Zoltán Foundation for Applied Research
Hungarian Ministry of Education
Israel Ministry of Science
National Institutes of Health
Israel Science Foundation405/98


    • Evolution
    • Lysogeny
    • Phage HK022
    • Site-specific recombination
    • Tyrosine recombinase


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