TraM protein of plasmid R1: In vitro selection of the target region reveals two consensus 7 bp binding motifs spaced by a 4 bp linker of defined sequence

Plasmid

Volumn 59, Issue 1, 2008, Pages 20-35

  Geist, Carsten ^a   Brantl, Sabine ^a  

^a FRIEDRICH SCHILLER UNIVERSITY JENA   (Germany)

Author keywords

Conjugation; In vitro selection; Plasmid; R1; SELEX; Transcriptional regulator

Indexed keywords

PROTEIN; PROTEIN TRAM; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; AUTOREGULATION; BACTERIAL GENETICS; CONSENSUS SEQUENCE; DNA CLEAVAGE; GENE EXPRESSION; NONHUMAN; PLASMID; PROTEIN BINDING; PROTEIN MOTIF;

AMINO ACID MOTIFS; BACTERIAL PROTEINS; BASE SEQUENCE; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; R FACTORS; SELEX APTAMER TECHNIQUE;

EID: 37549039508     PISSN: 0147619X     EISSN: 10959890     Source Type: Journal    
DOI: 10.1016/j.plasmid.2007.10.001     Document Type: Article

References (38)

1. Becker E.C., and Meyer R.J. Recognition of oriT for DNA processing at termination of a round of conjugal transfer. J. Mol. Biol. 30 (2000) 1067-1077
2. Beranek A., Zettl M., Lorenzoni K., Schauer A., Manhart M., and Koraimann G. Thirty-eight C-terminal amino acids of the coupling protein TraD of the F-like conjugative resistance plasmid R1 are required and sufficient to confer binding to the substrate selector protein TraM. J. Bacteriol. 186 (2004) 6999-7006
3. Brantl S., and Wagner E.G.H. An antisense RNA-mediated transcriptional attenuation mechanism functions in Escherichia coli. J. Bacteriol. 184 (2002) 2740-2747
4. Clerget M., Chandler M., and Caro L. The structure of R1drd19: a revised physical map of the plasmid. Mol. Gen. Genet. 181 (1981) 183-191
5. Czernik P.J., Shin D.S., and Hurlburt B.K. Functional selection and characterization of DNA binding sites for trp repressor of Escherichia coli. J. Biol. Chem. 269 (1994) 27869-27875
6. Daniels D.A., Cheng H., Hicke B.J., Swidereck K.M., and Gold L. A tenascin-C aptamer identified by tumor cell SELEX: Systematic evolution of ligands by exponential enrichment. Proc. Natl. Acad. Sci. USA 100 (2003) 15416-15421
7. De Vuyst G., Aci S., Genest D., and Culard F. Atypical recognition of particular DNA sequences by the archaeal chromosomal MC1 protein. Biochemistry 44 (2005) 10369-10377
8. Di Laurenzio L., Frost L.S., Finlay B.B., and Paranchych W. Characterization of the oriT region of the IncFV plasmid pED208. Mol. Microbiol. 5 (1991) 1779-1790
9. Disque-Kochem C., and Dreiseikelmann B. The cytoplasmic DNA-binding protein TraM binds to the inner membrane protein TraD in vitro. J. Bacteriol. 179 (1997) 6133-6137
10. Ellington A.D., and Szostak J.W. In vitro selection of RNA molecules that bind specific ligands. Nature 346 (1990) 818-822
11. Emmerich R., Strehler P., Hennecke H., and Fischer H.-M. An imperfect inverted repeat is critical for DNA binding of the response regulator RegR of Bradyrhizobium japonicum. Nucleic Acids Res. 28 (2000) 4166-4171
12. Firth N., Ippen-Ihler K., and Skurray R.A. Structure and function of the F factor and mechanism of conjugation. In: Neidhart F.C., Curtiss III R., Ingraham J.L., Lin E.C.C., Low K.B., Magasanik B., Reznikoff W.S., Riley M., Schaechter M., and Umbarger H.E. (Eds). Escherichia coli and Salomonella typhimurium (1996), American Society for Microbioloy Press, Washington, DC 2377-2401
13. Freede P., and Brantl S. Transcriptional repressor CopR: Use of SELEX to study the copR operator indicates that evolution was directed at maximal binding efficiency. J. Bacteriol. 186 (2004) 6254-6264
14. Fürste J.P., Pansegrau W., Frank R., Blocker H., Scholz P., Bagdasarian M., and Lanka E. Molecular cloning of the plasmid RP4 primase region in a multi-host-range tacP expression vector. Gene 48 (1986) 119-131
15. Gaal T., Ross W., Estrem S.T., Nguyen L.H., Burgess R.R., and Gourse R.L. Promoter recognition and discrimination by EσS RNA polymerase. Mol. Microbiol. 42 (2001) 939-954
16. Goebel W., Lindenmaier W., Pfeifer F., Schrempf H., and Schelle B. Transposition and insertion of intact, deleted and enlarged ampicillin transposon Tn3 from mini-R1 (Rsc) plasmids into transfer factors. Mol. Gen. Genet. 157 (1977) 119-129
17. Goodman S.D., Velten N.J., Gao Q., Robinson S., and Segall A.M. In vitro selection of integration host factor binding sites. J. Bacteriol. 181 (1999) 3246-3255
18. He Y.-y., Stockley P.G., and Gold L. In vitro evolution of the DNA binding sites of Escherichia coli methionine repressor, MetJ. J. Mol. Biol. 255 (1996) 55-66
19. Johnston W.K., Unrau P.J., Lawrence M.S., Glasner M.E., and Bartel D.P. RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension. Science 292 (2001) 1319-1325
20. Klug S.J., Hüttenhofer A., Kromayer M., and Famulok M. In vitro and in vivo characterization of novel mRNA motifs that bind special elongation factor SelB. Biochemistry 94 (1997) 6676-6681
21. Koraimann G., Koraimann C., Koronakis V., Schlager S., and Högenauer G. Repression and derepression of conjugation of plasmid R1 by wild-type and mutated finP antisense RNA. Mol. Microbiol. 5 (1991) 77-87
22. Koronakis V.E., Bauer E., and Högenauer G. The traM gene of the resistance plasmid R1: comparison with the corresponding sequence of the Escherichia coli F factor. Gene 36 (1985) 79-86
23. Kupelwieser G., Schwab M., Högenauer G., Koraimann G., and Zechner E.L. Transfer protein TraM stimulates TraI-catalyzed cleavage of the transfer origin of plasmid R1 in vivo. J. Mol. Biol. 275 (1998) 81-94
24. Lee N., Bessho Y., Wei K., Szostak J.W., and Suga H. Ribozyme-catalyzed tRNA aminoacylation. Nat. Struct. Biol. 7 (2000) 28-33
25. Lu J., and Frost L.S. Mutations in the C-terminal region of TraM provide evidence for in vivo TraM-TraD interactions during F-plasmid conjugation. J. Bacteriol. 187 (2005) 4767-4773
26. Pölzleitner E., Zechner E.L., Renner W., Fratte R., Jauk B., Högenauer G., and Koraimann G. TraM of plasmid R1 controls transfer gene expression as an integrated control element in a complex regulatory network. Mol. Microbiol. 25 (1997) 495-508
27. Sambrook J., Fritsch E.F., and Maniatis T. Molecular Cloning. A Laboratory Manual. second ed. (1989), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York
28. Sanger F., Nicklen S., and Coulson A.R. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 74 (1977) 5463-5467
29. Schwab M., Reisenzein H., and Högenauer G. TraM of plasmid R1 regulates its own expression. Mol. Microbiol. 7 (1993) 795-803
30. Stockner T., Plugariu C., Koraimann G., Högenauer G., Bermel W., Prytulla S., and Sterk H. Solution structure of the DNA-binding domain of TraM. Biochemistry 40 (2001) 3370-3377
31. Strohmaier H., Noiges R., Kotschan S., Sawers G., Högenauer G., Zechner E.L., and Koraimann G. Signal transduction and bacterial conjugation: characterization of the role of ArcA in regulating conjugative transfer of the resistance plasmid R1. J. Mol. Biol. 277 (1998) 309-316
32. Tuerk C., and Gold L. Systematic evolution of ligands by exponential enrichment. Science 249 (1990) 505-510
33. van Biesen T., and Frost L.S. The FinO protein of IncF plasmids binds FinP antisense RNA and its target, traJ mRNA, and promotes duplex formation. Mol. Micobiol. 14 (1994) 427-436
34. Verdino P., Keller W., Strohmaier H., Bischof K., Lindner H., and Koraimann G. The essential transfer protein TraM binds to DNA as a tetramer. J. Biol. Chem. 274 (1999) 37421-37428
35. Vieira J., and Messing J. The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers. Gene 19 (1982) 259-268
36. Will W.R., and Frost L.S. Hfq is a regulator of F-plasmid TraJ and TraM synthesis in Escherichia coli. J. Bacteriol. 188 (2006) 124-131
37. Yu D., Ellis H.M., Lee E.C., Jenkins N.A., Copeland N.G., and Court D.L. An efficient recombination system for chromosome engineering in Escherichia coli. Proc. Natl. Acad. Sci. USA 97 (2000) 5978-5983
38. Zechner E.L., Prüger H., Grohmann E., Espinosa M., and Högenauer G. Specific cleavage of chromosomal and plasmid DNA strands in gram-positive and gram-negative bacteria can be detected with nucleotide resolution. Proc. Natl. Acad. Sci. USA 94 (1997) 7435-7440