Crystal structure of the bacterial conjugation repressor FinO

Abstract

The conjugative transfer of F-like plasmids is repressed by FinO, an RNA binding protein. FinO interacts with the F-plasmid encoded traJ mRNA and its antisense RNA, FinP, stabilizing FinP against endonucleolytic degradation and facilitating sense–antisense RNA recognition. Here we present the 2.0 Å resolution X-ray crystal structure of FinO, lacking its flexible N-terminal extension. FinO adopts a novel, elongated, largely helical conformation. An N-terminal region, previously shown to contact RNA, forms a positively charged α-helix (helix 1) that protrudes 45 Å from the central core of FinO. A C-terminal region of FinO that is implicated in RNA interactions also extends out from the central body of the protein, adopting a helical conformation and packing against the base of the N-terminal helix. A highly positively charged patch on the surface of the FinO core may present another RNA binding surface. The results of an in vitro RNA duplexing assay demonstrate that the flexible N-terminal region of FinO plays a key role in FinP–traJ RNA recognition, and supports our proposal that this region and the N-terminus of helix 1 interact with and stabilize paired, complementary RNA loops in a kissing complex.

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Figure 1: Stereo view of electron density maps around residues 152–156 (on strand β4) with the final 2.0 Å refined model superimposed.
Figure 2: Overall structure of FinO.
Figure 3: Conformational flexibility in FinO.
Figure 4: FinO–RNA interactions.

References

  1. 1

    Frost, L.S., Ippen-Ihler, K. & Skurray, R.A. Microbiol. Rev. 58, 162–210 (1994).

  2. 2

    Finnegan, D. & Willetts, N. Mol. Gen. Genet. 119, 57–66 (1972).

  3. 3

    Mullineaux, P. & Willetts, N. Basic Life. Sci. 30, 605–614 (1985).

  4. 4

    van Biesen, T. & Frost, L.S. Mol. Microbiol. 14, 427–436 (1994).

  5. 5

    Jerome, L.J., van Biesen, T. & Frost, L.S. J. Mol. Biol. 285, 1457–1473 (1999).

  6. 6

    Lee, S.H., Frost, L.S. & Paranchych, W. Mol. Gen. Genet. 235, 131–139 (1992).

  7. 7

    van Biesen, T., Soderbom, F., Wagner, E.G. & Frost, L.S. Mol. Microbiol. 10, 35–43 (1993).

  8. 8

    Koraimann, G., Teferle, K., Markolin, G., Woger, W. & Hogenauer, G. Mol. Microbiol. 21, 811–821 (1996).

  9. 9

    Ghetu, A.F., Gubbins, M.J., Oikawa, K., Kay, C.M., Frost, L.S. & Glover, J.N.M. Biochemistry 38, 14036–14044 (1999).

  10. 10

    Sandercock, J.R. & Frost, L.S. Mol. Gen. Genet. 259, 622–629 (1998).

  11. 11

    Holm, L. & Sander, C. J. Mol. Biol. 233, 123–138 (1993).

  12. 12

    Madej, T., Gibrat, J.F. & Bryant, S.H. Proteins 23, 356–369 (1995).

  13. 13

    Jerome, L.J. & Frost, L.S. J. Biol. Chem. 274, 10356–10362 (1999).

  14. 14

    Price, S.R., Evans, P.R. & Nagai, K. Nature 394, 645–650 (1998).

  15. 15

    Oubridge, C., Ito, N., Evans, P.R., Teo, C.H. & Nagai, K. Nature 372, 432–438 (1994).

  16. 16

    Legault, P., Li, J., Mogridge, J., Kay, L.E. & Greenblatt, J. Cell 93, 289–299 (1998).

  17. 17

    Predki, P.F., Nayak, L.M., Gottlieb, M.B. & Regan, L. Cell 80, 41–50 (1995).

  18. 18

    Banner, D.W., Kokkinidis, M. & Tsernoglou, D. J. Mol. Biol. 196, 657–675 (1987).

  19. 19

    Wagner, E.G. & Simons, R.W. Annu. Rev. Microbiol. 48, 713–742 (1994).

  20. 20

    Franch, T., Petersen, M., Wagner, E.G., Jacobsen, J.P. & Gerdes, K. J. Mol. Biol. 294, 1115–1125 (1999).

  21. 21

    Koraimann, G., Koraimann, C., Koronakis, V., Schlager, S. & Hogenauer, G. Mol. Microbiol. 5, 77–87 (1991).

  22. 22

    Eguchi, Y. & Tomizawa, J. J. Mol. Biol. 220, 831–842 (1991).

  23. 23

    Doublié, S. Methods Enzymol. 276, 523–530 (1997).

  24. 24

    Ho, S.N., Hunt, H.D., Horton, R.M., Pullen, J.K. & Pease, L.R. Gene 77, 51–59 (1989).

  25. 25

    Otwinowski, Z. & Minor, W. Methods Enzymol. 276, 307–326 (1997).

  26. 26

    Terwilliger, T.C.D. Acta Crystallogr. A 43, 1–5 (1987).

  27. 27

    Cowtan, K. Joint CCP4 and ESF-EACBM newsletter on protein crystallography 31, 24–28 (1994).

  28. 28

    Jones, T.A., Zhou, J.Y., Cowan, S.W. & Kjeldgaard, M. Acta Crystallogr. A 47, 110–119 (1991).

  29. 29

    McRee, D.E. J. Struct. Biol. 125, 156–165 (1999).

  30. 30

    Brünger, A.T. X-PLOR: a system for X-ray crystallography and NMR. (Yale University Press, New Haven, Connecticut; 1992).

  31. 31

    Brunger, A.T. et al. Acta Crystallogr. D 54, 905–921 (1999).

  32. 32

    Esnouf, R.M. J. Mol. Graph. Model. 15, 133–138 (1997).

  33. 33

    Kraulis, P.J. J. Appl. Crystallogr. 24, 946–950 (1991).

  34. 34

    Merritt, E.A. & Bacon, D.J. Methods Enyzmol. 277, 505–524 (1997).

  35. 35

    Nicholls, A., Sharp, K.A. & Honig, B. Proteins 11, 281–296 (1991).

  36. 36

    Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. J. Appl. Crystallogr. 26, 283–291 (1993)

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Acknowledgements

We wish to thank S. Williams, R. Sweet and the staff of beamline X12C (NSLS), and W. Schildkamp and the staff of beamline 14-BM-D (APS) for excellent technical support during crystallographic data collection. We also wish to thank M. James for encouragement and insightful comments. This work was supported by grants from the Alberta Heritage Foundation for Medical Research and the Medical Research Council of Canada (to J.N.M.G.).

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Correspondence to J. N. Mark Glover.

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Ghetu, A., Gubbins, M., Frost, L. et al. Crystal structure of the bacterial conjugation repressor FinO. Nat Struct Mol Biol 7, 565–569 (2000). https://doi.org/10.1038/76790

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