1887

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Volume 157, Issue 10

Regulation of the integrase and cassette promoters of the class 1 integron by nucleoid-associated proteins Free

Abstract

The integrase IntI1 catalyses recombination of antibiotic-resistance gene cassettes in the integron, a widely found bacterial mobile element active in spreading antibiotic multi-resistance. We have previously shown that resistance cassette recombination rate and specificity depend on the amount of intracellular integrase. Here, we used and methods to examine convergent expression of the integrase promoter () and of the cassette promoters ( and ) in the prototypical plasmid-borne class 1 integron, In Highly conserved has near consensus −10 and −35 hexamers for σ RNA polymerase, but there are 11 naturally occurring arrangements of alone or combinations of the + cassette promoters (note that occurs with a 14 or 17 bp spacer). Using a bi-directional reporter vector, we found that is a strong promoter , but its expression is reduced by converging transcription from and . In addition to -acting convergence control of integrase expression, the regulator site prediction program, 8.9, identified sites for global regulators FIS, LexA, IHF and H-NS in and near the integron promoters. In strains mutated in each global regulator, we found that: (1) FIS repressed integrase and cassette expression; (2) LexA repressed and with the 14 bp spacer version of and FIS was necessary for maximum LexA repression; (3) IHF activated when it faced the strong 17 bp spacer but did not elevate its expression versus LexA-repressed with the 14 bp spacer; and (4) H-NS repressed both and the 14 bp but activated the 17 bp cassette promoters. Mobility shift assays showed that FIS and IHF interact directly with the promoter regions and DNase I footprinting confirmed extensive protection by FIS of wild-type In integron promoter sequence. Thus, nucleoid-associated proteins, known to act directly in site-specific recombination, also control integron gene expression directly and possibly indirectly.

  • Received:
  • Accepted:
  • Revised:
  • Published Online:
Funding
This study was supported by the:
  • United States Department of Agriculture (USDA) (Award 99-35212-8680)
  • National Science Foundation (NSF) (Award 06-26940)
© 2011 SGM
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2011-10-01
2024-04-27
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References

  1. Ali B. M., Amit R., Braslavsky I., Oppenheim A. B., Gileadi O., Stavans J. ( 2001). Compaction of single DNA molecules induced by binding of integration host factor (IHF). Proc Natl Acad Sci U S A 98:10658–10663 [View Article][PubMed]
     [Google Scholar]
  2. Ali Azam T., Iwata A., Nishimura A., Ueda S., Ishihama A. ( 1999). Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. J Bacteriol 181:6361–6370[PubMed]
     [Google Scholar]
  3. Arfin S. M., Long A. D., Ito E. T., Tolleri L., Riehle M. M., Paegle E. S., Hatfield G. W. ( 2000). Global gene expression profiling in Escherichia coli K12. The effects of integration host factor. J Biol Chem 275:29672–29684 [View Article][PubMed]
     [Google Scholar]
  4. Burr T., Mitchell J., Kolb A., Minchin S., Busby S. ( 2000). DNA sequence elements located immediately upstream of the −10 hexamer in Escherichia coli promoters: a systematic study. Nucleic Acids Res 28:1864–1870 [View Article][PubMed]
     [Google Scholar]
  5. Butala M., Zgur-Bertok D., Busby S. J. ( 2009). The bacterial LexA transcriptional repressor. Cell Mol Life Sci 66:82–93 [View Article][PubMed]
     [Google Scholar]
  6. Collis C. M., Hall R. M. ( 1992). Site-specific deletion and rearrangement of integron insert genes catalyzed by the integron DNA integrase. J Bacteriol 174:1574–1585[PubMed]
     [Google Scholar]
  7. Dame R. T., Wyman C., Goosen N. ( 2001). Structural basis for preferential binding of H-NS to curved DNA. Biochimie 83:231–234 [View Article][PubMed]
     [Google Scholar]
  8. Dorman C. J. ( 2009). Nucleoid-associated proteins and bacterial physiology. Adv Appl Microbiol 67:47–64 [View Article][PubMed]
     [Google Scholar]
  9. Drlica K., Zhao X. ( 1997). DNA gyrase, topoisomerase IV, and the 4-quinolones. Microbiol Mol Biol Rev 61:377–392[PubMed]
     [Google Scholar]
  10. Freundlich M., Ramani N., Mathew E., Sirko A., Tsui P. ( 1992). The role of integration host factor in gene expression in Escherichia coli. Mol Microbiol 6:2557–2563 [View Article][PubMed]
     [Google Scholar]
  11. Gottesman S. ( 1984). Bacterial regulation: global regulatory networks. Annu Rev Genet 18:415–441 [View Article][PubMed]
     [Google Scholar]
  12. Guerin E., Cambray G., Sanchez-Alberola N., Campoy S., Erill I., Da Re S., Gonzalez-Zorn B., Barbé J., Ploy M. C., Mazel D. ( 2009). The SOS response controls integron recombination. Science 324:1034 [View Article][PubMed]
     [Google Scholar]
  13. Hall R. M., Collis C. M. ( 1995). Mobile gene cassettes and integrons: capture and spread of genes by site-specific recombination. Mol Microbiol 15:593–600 [View Article][PubMed]
     [Google Scholar]
  14. Hall R. M., Stokes H. W. ( 1993). Integrons: novel DNA elements which capture genes by site-specific recombination. Genetica 90:115–132 [View Article][PubMed]
     [Google Scholar]
  15. Hansson K., Sköld O., Sundström L. ( 1997). Non-palindromic attl sites of integrons are capable of site-specific recombination with one another and with secondary targets. Mol Microbiol 26:441–453 [View Article][PubMed]
     [Google Scholar]
  16. Jové T., Da Re S., Denis F., Mazel D., Ploy M. C. ( 2010). Inverse correlation between promoter strength and excision activity in class 1 integrons. PLoS Genet 6:e1000793 [View Article][PubMed]
     [Google Scholar]
  17. Kelley W. L. ( 2006). Lex marks the spot: the virulent side of SOS and a closer look at the LexA regulon. Mol Microbiol 62:1228–1238 [View Article][PubMed]
     [Google Scholar]
  18. Kostrewa D., Granzin J., Koch C., Choe H. W., Raghunathan S., Wolf W., Labahn J., Kahmann R., Saenger W. ( 1991). Three-dimensional structure of the E. coli DNA-binding protein FIS. Nature 349:178–180 [View Article][PubMed]
     [Google Scholar]
  19. Lévesque C., Brassard S., Lapointe J., Roy P. H. ( 1994). Diversity and relative strength of tandem promoters for the antibiotic-resistance genes of several integrons. Gene 142:49–54 [View Article][PubMed]
     [Google Scholar]
  20. Lewin C. S., Amyes S. G. ( 1991). The role of the SOS response in bacteria exposed to zidovudine or trimethoprim. J Med Microbiol 34:329–332 [View Article][PubMed]
     [Google Scholar]
  21. Luijsterburg M. S., Noom M. C., Wuite G. J., Dame R. T. ( 2006). The architectural role of nucleoid-associated proteins in the organization of bacterial chromatin: a molecular perspective. J Struct Biol 156:262–272 [View Article][PubMed]
     [Google Scholar]
  22. Mazón G., Erill I., Campoy S., Cortés P., Forano E., Barbé J. ( 2004). Reconstruction of the evolutionary history of the LexA-binding sequence. Microbiology 150:3783–3795 [View Article][PubMed]
     [Google Scholar]
  23. Miller J. H. ( 1972). Experiments in Molecular Genetics Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
     [Google Scholar]
  24. Miller C., Thomsen L. E., Gaggero C., Mosseri R., Ingmer H., Cohen S. N. ( 2004). SOS response induction by β-lactams and bacterial defense against antibiotic lethality. Science 305:1629–1631 [View Article][PubMed]
     [Google Scholar]
  25. Münch R., Hiller K., Barg H., Heldt D., Linz S., Wingender E., Jahn D. ( 2003). PRODORIC: prokaryotic database of gene regulation. Nucleic Acids Res 31:266–269 [View Article][PubMed]
     [Google Scholar]
  26. Navarre W. W., Porwollik S., Wang Y., McClelland M., Rosen H., Libby S. J., Fang F. C. ( 2006). Selective silencing of foreign DNA with low GC content by the H-NS protein in Salmonella. Science 313:236–238 [View Article][PubMed]
     [Google Scholar]
  27. Nesvera J., Hochmannová J., Pátek M. ( 1998). An integron of class 1 is present on the plasmid pCG4 from Gram-positive bacterium Corynebacterium glutamicum. FEMS Microbiol Lett 169:391–395 [View Article][PubMed]
     [Google Scholar]
  28. Papagiannitsis C. C., Tzouvelekis L. S., Miriagou V. ( 2009). Relative strengths of the class 1 integron promoter hybrid 2 and the combinations of strong and hybrid 1 with an active P2 promoter. Antimicrob Agents Chemother 53:277–280 [View Article][PubMed]
     [Google Scholar]
  29. Recchia G. D., Hall R. M. ( 1995). Plasmid evolution by acquisition of mobile gene cassettes: plasmid pIE723 contains the aadB gene cassette precisely inserted at a secondary site in the incQ plasmid RSF1010. Mol Microbiol 15:179–187 [View Article][PubMed]
     [Google Scholar]
  30. Rice P. A., Yang S., Mizuuchi K., Nash H. A. ( 1996). Crystal structure of an IHF–DNA complex: a protein-induced DNA U-turn. Cell 87:1295–1306 [View Article][PubMed]
     [Google Scholar]
  31. Ross W., Park S. J., Summers A. O. ( 1989). Genetic analysis of transcriptional activation and repression in the Tn21 mer operon. J Bacteriol 171:4009–4018[PubMed]
     [Google Scholar]
  32. Schneider K., Beck C. F. ( 1986). Promoter-probe vectors for the analysis of divergently arranged promoters. Gene 42:37–48 [View Article][PubMed]
     [Google Scholar]
  33. Schröder O., Wagner R. ( 2002). The bacterial regulatory protein H-NS–a versatile modulator of nucleic acid structures. Biol Chem 383:945–960 [View Article][PubMed]
     [Google Scholar]
  34. Shao Y., Feldman-Cohen L. S., Osuna R. ( 2008). Functional characterization of the Escherichia coli Fis-DNA binding sequence. J Mol Biol 376:771–785 [View Article][PubMed]
     [Google Scholar]
  35. Shearer J. E., Summers A. O. ( 2009). Intracellular steady-state concentration of integron recombination products varies with integrase level and growth phase. J Mol Biol 386:316–331 [View Article][PubMed]
     [Google Scholar]
  36. Stokes H. W., Hall R. M. ( 1989). A novel family of potentially mobile DNA elements encoding site-specific gene-integration functions: integrons. Mol Microbiol 3:1669–1683 [View Article][PubMed]
     [Google Scholar]
  37. Stokes H. W., Hall R. M. ( 1991). Sequence analysis of the inducible chloramphenicol resistance determinant in the Tn1696 integron suggests regulation by translational attenuation. Plasmid 26:10–19 [View Article][PubMed]
     [Google Scholar]
  38. Tolmasky M. E., Crosa J. H. ( 1993). Genetic organization of antibiotic resistance genes (aac(6′)-Ib, aadA, and oxa9) in the multiresistance transposon Tn1331. Plasmid 29:31–40 [View Article][PubMed]
     [Google Scholar]
  39. Yang S. W., Nash H. A. ( 1995). Comparison of protein binding to DNA in vivo and in vitro: defining an effective intracellular target. EMBO J 14:6292–6300[PubMed]
     [Google Scholar]
  40. Yildiz F. H., Liu X. S., Heydorn A., Schoolnik G. K. ( 2004). Molecular analysis of rugosity in a Vibrio cholerae O1 El Tor phase variant. Mol Microbiol 53:497–515 [View Article][PubMed]
     [Google Scholar]
  41. Yindeeyoungyeon W., Schell M. A. ( 2000). Footprinting with an automated capillary DNA sequencer. Biotechniques 29:1034–1036, 1038, 1040–1041[PubMed]
     [Google Scholar]
  42. Zhang X., Bremer H. ( 1995). Control of the Escherichia coli rrnB P1 promoter strength by ppGpp. J Biol Chem 270:11181–11189 [View Article][PubMed]
     [Google Scholar]
  43. Zhang Z., Schwartz S., Wagner L., Miller W. ( 2000). A greedy algorithm for aligning DNA sequences. J Comput Biol 7:203–214 [View Article][PubMed]
     [Google Scholar]
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Regulation of the integrase and cassette promoters of the class 1 integron by nucleoid-associated proteins
Microbiology 157, 2841 (2011); https://doi.org/10.1099/mic.0.046987-0
/content/journal/micro/10.1099/mic.0.046987-0
/content/journal/micro/10.1099/mic.0.046987-0
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