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. 1991 Jul;173(13):4079–4087. doi: 10.1128/jb.173.13.4079-4087.1991

Site-specific recombinase genes in three Shigella subgroups and nucleotide sequences of a pinB gene and an invertible B segment from Shigella boydii.

A Tominaga 1, S Ikemizu 1, M Enomoto 1
PMCID: PMC208056  PMID: 2061288

Abstract

Inversional switching systems in procaryotes are composed of an invertible DNA segment and a site-specific recombinase gene adjacent to or contained in the segment. Four related but functionally distinct systems have previously been characterized in detail: the Salmonella typhimurium H segment-hin gene (H-hin), phage Mu G-gin, phage P1 C-cin, and Escherichia coli e14 P-pin. In this article we report the isolation and characterization of three new recombinase genes: pinB, pinD, and defective pinF from Shigella boydii, Shigella dysenteriae, and Shigella flexneri, respectively. The genes pinB and pinD were detected by the complementation of a hin mutation of Salmonella and were able to mediate inversion of the H, P, and C segments. pinB mediated H inversion as efficiently as the hin gene did and mediated C inversion with a frequency three orders of magnitude lower than that of the cin gene. pinD mediated inversion of H and P segments with frequencies ten times as high as those for the genes intrinsic to each segment and mediated C inversion with a frequency ten times lower than that for cin. Therefore, the pinB and pinD genes were inferred to be different from each other. The invertible B segment-pinB gene cloned from S. boydii is highly homologous to the G-gin in size, organization, and nucleotide sequence of open reading frames, but the 5' constant region outside the segment is quite different in size and predicted amino acid sequence. The B segment underwent inversion in the presence of hin, pin, or cin. The defective pinF gene is suggested to hae the same origin as P-pin on e14 by the restriction map of the fragment cloned from a Pin+ transductant that was obtained in transduction from S. flexneri to E. coli delta pin.

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Selected References

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  1. Birnboim H. C., Doly J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 1979 Nov 24;7(6):1513–1523. doi: 10.1093/nar/7.6.1513. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bolivar F., Rodriguez R. L., Greene P. J., Betlach M. C., Heyneker H. L., Boyer H. W., Crosa J. H., Falkow S. Construction and characterization of new cloning vehicles. II. A multipurpose cloning system. Gene. 1977;2(2):95–113. [PubMed] [Google Scholar]
  3. Brody H., Greener A., Hill C. W. Excision and reintegration of the Escherichia coli K-12 chromosomal element e14. J Bacteriol. 1985 Mar;161(3):1112–1117. doi: 10.1128/jb.161.3.1112-1117.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bruist M. F., Horvath S. J., Hood L. E., Steitz T. A., Simon M. I. Synthesis of a site-specific DNA-binding peptide. Science. 1987 Feb 13;235(4790):777–780. doi: 10.1126/science.3027895. [DOI] [PubMed] [Google Scholar]
  5. Casadaban M. J., Martinez-Arias A., Shapira S. K., Chou J. Beta-galactosidase gene fusions for analyzing gene expression in escherichia coli and yeast. Methods Enzymol. 1983;100:293–308. doi: 10.1016/0076-6879(83)00063-4. [DOI] [PubMed] [Google Scholar]
  6. Chang A. C., Cohen S. N. Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the P15A cryptic miniplasmid. J Bacteriol. 1978 Jun;134(3):1141–1156. doi: 10.1128/jb.134.3.1141-1156.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Csonka L. N., Clark A. J. Construction of an Hfr strain useful for transferring recA mutations between Escherichia coli strains. J Bacteriol. 1980 Jul;143(1):529–530. doi: 10.1128/jb.143.1.529-530.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Enomoto M., Oosawa K., Momota H. Mapping of the pin locus coding for a site-specific recombinase that causes flagellar-phase variation in Escherichia coli K-12. J Bacteriol. 1983 Nov;156(2):663–668. doi: 10.1128/jb.156.2.663-668.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Enomoto M., Sakai A., Tominaga A. Expression of an Escherichia coli flagellin gene, hag48, in the presence of a Salmonella H1-repressor. Mol Gen Genet. 1985;201(1):133–135. doi: 10.1007/BF00397999. [DOI] [PubMed] [Google Scholar]
  10. Enomoto M., Stocker B. A. Integration, at hag or elsewhere, of H2 (phase-2 flagellin) genes transduced from Salmonella to Escherichia coli. Genetics. 1975 Dec;81(4):595–614. doi: 10.1093/genetics/81.4.595. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Feinberg A. P., Vogelstein B. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal Biochem. 1983 Jul 1;132(1):6–13. doi: 10.1016/0003-2697(83)90418-9. [DOI] [PubMed] [Google Scholar]
  12. Hiestand-Nauer R., Iida S. Sequence of the site-specific recombinase gene cin and of its substrates serving in the inversion of the C segment of bacteriophage P1. EMBO J. 1983;2(10):1733–1740. doi: 10.1002/j.1460-2075.1983.tb01650.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Huber H. E., Iida S., Arber W., Bickle T. A. Site-specific DNA inversion is enhanced by a DNA sequence element in cis. Proc Natl Acad Sci U S A. 1985 Jun;82(11):3776–3780. doi: 10.1073/pnas.82.11.3776. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Hübner P., Arber W. Mutational analysis of a prokaryotic recombinational enhancer element with two functions. EMBO J. 1989 Feb;8(2):577–585. doi: 10.1002/j.1460-2075.1989.tb03412.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Iida S. Bacteriophage P1 carries two related sets of genes determining its host range in the invertible C segment of its genome. Virology. 1984 Apr 30;134(2):421–434. doi: 10.1016/0042-6822(84)90309-x. [DOI] [PubMed] [Google Scholar]
  16. Iida S., Hiestand-Nauer R. Localized conversion at the crossover sequences in the site-specific DNA inversion system of bacteriophage P1. Cell. 1986 Apr 11;45(1):71–79. doi: 10.1016/0092-8674(86)90539-8. [DOI] [PubMed] [Google Scholar]
  17. Iida S., Meyer J., Kennedy K. E., Arber W. A site-specific, conservative recombination system carried by bacteriophage P1. Mapping the recombinase gene cin and the cross-over sites cix for the inversion of the C segment. EMBO J. 1982;1(11):1445–1453. doi: 10.1002/j.1460-2075.1982.tb01336.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Johnson R. C., Simon M. I. Hin-mediated site-specific recombination requires two 26 bp recombination sites and a 60 bp recombinational enhancer. Cell. 1985 Jul;41(3):781–791. doi: 10.1016/s0092-8674(85)80059-3. [DOI] [PubMed] [Google Scholar]
  19. Kahmann R., Rudt F., Koch C., Mertens G. G inversion in bacteriophage Mu DNA is stimulated by a site within the invertase gene and a host factor. Cell. 1985 Jul;41(3):771–780. doi: 10.1016/s0092-8674(85)80058-1. [DOI] [PubMed] [Google Scholar]
  20. Kamp D., Kahmann R. The relationship of two invertible segments in bacteriophage Mu and Salmonella typhimurium DNA. Mol Gen Genet. 1981;184(3):564–566. doi: 10.1007/BF00352543. [DOI] [PubMed] [Google Scholar]
  21. Kamp D., Kardas E., Ritthaler W., Sandulache R., Schmucker R., Stern B. Comparative analysis of invertible DNA in phage genomes. Cold Spring Harb Symp Quant Biol. 1984;49:301–311. doi: 10.1101/sqb.1984.049.01.036. [DOI] [PubMed] [Google Scholar]
  22. Kutsukake K., Iino T. A trans-acting factor mediates inversion of a specific DNA segment in flagellar phase variation of Salmonella. Nature. 1980 Apr 3;284(5755):479–481. doi: 10.1038/284479a0. [DOI] [PubMed] [Google Scholar]
  23. Maloy S. R., Nunn W. D. Selection for loss of tetracycline resistance by Escherichia coli. J Bacteriol. 1981 Feb;145(2):1110–1111. doi: 10.1128/jb.145.2.1110-1111.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Olszewska E., Jones K. Vacuum blotting enhances nucleic acid transfer. Trends Genet. 1988 Apr;4(4):92–94. doi: 10.1016/0168-9525(88)90095-9. [DOI] [PubMed] [Google Scholar]
  25. Parker L. L., Betts P. W., Hall B. G. Activation of a cryptic gene by excision of a DNA fragment. J Bacteriol. 1988 Jan;170(1):218–222. doi: 10.1128/jb.170.1.218-222.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Plasterk R. H., Brinkman A., van de Putte P. DNA inversions in the chromosome of Escherichia coli and in bacteriophage Mu: relationship to other site-specific recombination systems. Proc Natl Acad Sci U S A. 1983 Sep;80(17):5355–5358. doi: 10.1073/pnas.80.17.5355. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Plasterk R. H., van de Putte P. Inversion of DNA in vivo and in vitro by gin and pin proteins. Cold Spring Harb Symp Quant Biol. 1984;49:295–300. doi: 10.1101/sqb.1984.049.01.035. [DOI] [PubMed] [Google Scholar]
  28. Plasterk R. H., van de Putte P. The invertible P-DNA segment in the chromosome of Escherichia coli. EMBO J. 1985 Jan;4(1):237–242. doi: 10.1002/j.1460-2075.1985.tb02341.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Rosner J. L. Formation, induction, and curing of bacteriophage P1 lysogens. Virology. 1972 Jun;48(3):679–689. doi: 10.1016/0042-6822(72)90152-3. [DOI] [PubMed] [Google Scholar]
  30. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Scott J. R. Genetic studies on bacteriophage P1. Virology. 1968 Dec;36(4):564–574. doi: 10.1016/0042-6822(68)90188-8. [DOI] [PubMed] [Google Scholar]
  32. Silverman M., Zieg J., Hilmen M., Simon M. Phase variation in Salmonella: genetic analysis of a recombinational switch. Proc Natl Acad Sci U S A. 1979 Jan;76(1):391–395. doi: 10.1073/pnas.76.1.391. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Simon M., Zieg J., Silverman M., Mandel G., Doolittle R. Phase variation: evolution of a controlling element. Science. 1980 Sep 19;209(4463):1370–1374. doi: 10.1126/science.6251543. [DOI] [PubMed] [Google Scholar]
  34. Southern E. M. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol. 1975 Nov 5;98(3):503–517. doi: 10.1016/s0022-2836(75)80083-0. [DOI] [PubMed] [Google Scholar]
  35. Szekely E., Simon M. Homology between the invertible deoxyribonucleic acid sequence that controls flagellar-phase variation in Salmonella sp. and deoxyribonucleic acid sequences in other organisms. J Bacteriol. 1981 Dec;148(3):829–836. doi: 10.1128/jb.148.3.829-836.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Tominaga A., Enomoto M. Magnesium-dependent plaque formation by bacteriophage P1cinC(-) on Escherichia coli C and Shigella sonnei. Virology. 1986 Nov;155(1):284–288. doi: 10.1016/0042-6822(86)90190-x. [DOI] [PubMed] [Google Scholar]
  37. Vieira J., Messing J. Production of single-stranded plasmid DNA. Methods Enzymol. 1987;153:3–11. doi: 10.1016/0076-6879(87)53044-0. [DOI] [PubMed] [Google Scholar]
  38. Wood W. B. Host specificity of DNA produced by Escherichia coli: bacterial mutations affecting the restriction and modification of DNA. J Mol Biol. 1966 Mar;16(1):118–133. doi: 10.1016/s0022-2836(66)80267-x. [DOI] [PubMed] [Google Scholar]
  39. Zieg J., Simon M. Analysis of the nucleotide sequence of an invertible controlling element. Proc Natl Acad Sci U S A. 1980 Jul;77(7):4196–4200. doi: 10.1073/pnas.77.7.4196. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. van de Putte P., Plasterk R., Kuijpers A. A Mu gin complementing function and an invertible DNA region in Escherichia coli K-12 are situated on the genetic element e14. J Bacteriol. 1984 May;158(2):517–522. doi: 10.1128/jb.158.2.517-522.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]

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