RNA recognition by transcriptional antiterminators of the BgIG/SacY family: Functional and structural comparison of the CAT domain from SacY and LicT

Journal of Molecular Biology

Volumn 294, Issue 2, 1999, Pages 389-402

  Declerck, Nathalie ^a,b   Vincent, Florence ^a   Hoh, François ^b   Aymerich, Stéphane ^b   Van Tilbeurgh, Herman ^a  

^a Centre National de la Recherche Scientifique   (France)

^b CNRS   (France)

Author keywords

Antitermination; Bacillus subtilis; RNA binding; Surface plasmon resonance; X ray structure

Indexed keywords

AMINO ACID; DIMER; MESSENGER RNA; MONOMER; REGULATOR PROTEIN; RNA POLYMERASE;

AMINO ACID SEQUENCE; ARTICLE; BINDING AFFINITY; CARBOHYDRATE METABOLISM; CRYSTALLOGRAPHY; DNA TEMPLATE; ELECTRIC FIELD; GRAM NEGATIVE BACTERIUM; GRAM POSITIVE BACTERIUM; MOLECULAR RECOGNITION; NONHUMAN; OPERON; PRIORITY JOURNAL; RNA BINDING; SEQUENCE HOMOLOGY; STRUCTURE ACTIVITY RELATION; SURFACE PLASMON RESONANCE; TRANSCRIPTION REGULATION;

BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS); FELIS CATUS; NEGIBACTERIA; POSIBACTERIA;

EID: 0033607491     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.3256     Document Type: Article

References (34)

1. Amster-Choder O., Wright A. Modulation of the dimerization of a transcriptional antiterminator protein by phosphorylation. Science. 257:1992;1395-1398.
2. Amster-Choder O., Wright A. Transcriptional regulation of the bgl operon of Escherichia coli involves phosphotransferase system-mediated phosphorylation of a transcriptional antiterminator. J. Cell. Biochem. 51:1993;83-90.
3. Amster-Choder O., Wright A. BglG, the response regulator of the Escherichia coli bgl operon, is phosphorylated on a histidine residue. J. Bacteriol. 179:1997;5621-5624.
4. Arnaud M., Vary P., Zagorec M., Klier A., Débarbouillé M., Postma P., Rapoport G. Regulation of the sacPA operon of Bacillus subtilis: identification of phosphotransferase system components involved in SacT activity. J. Bacteriol. 174:1992;3161-3170.
5. Aymerich S., Steinmetz M. Specificity determinants and structural features in the RNA target of the bacterial antiterminator proteins of the BglG/SacY family. Proc. Natl Acad. Sci. USA. 89:1992;10410-10414.
6. Bachem S., Stulke J. Regulation of the Bacillus subtilis GlcT antiterminator protein by components of the phosphotransferase system. J. Bacteriol. 180:1998;5319-5326.
7. Brunger A. T. X-PLOR Version 3.1. A system for X-ray Crystallography and NMR. 1992;Yale University Press, New Haven.
8. Acta Crystallog. sect. B. 50:1994;760-763.
9. Cheong C., Varani G., Tinoco I. Jr. Solution structure of an unusually stable RNA hairpin, 5′GGAC(UUCG)GUCC. Nature. 346:1990;680-682.
10. Crutz A. M., Steinmetz M. Transcription of the Bacillus subtilis sacX and sacY genes, encoding regulators of sucrose metabolism, is both inducible by sucrose and controlled by the DegS-DegU signalling system. J. Bacteriol. 174:1992;6087-6095.
11. Débarbouillé M., Arnaud M., Fouet A., Klier A., Rapoport G. The sacT gene regulating the sacPA operon in Bacillus subtilis shares strong homology with transcriptional antiterminators. J. Bacteriol. 172:1990;3966-3973.
12. Houman F., Diaz-Torres M. R., Wright A. Transcriptional antitermination in the bgl operon of E. coli is modulated by a specific RNA binding protein. Cell. 62:1990;1153-1163.
13. Idelson M., Amster-Choder O. SacY, a transcriptional antiterminator from Bacillus subtilis, is regulated by phosphorylation in vivo. J. Bacteriol. 180:1998;660-666.
14. Laskowski R. A., MacArtur M. W., Moss D. S., Thornton J. M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallog. 26:1993;283-291.
15. Le Coq D., Lindner C., Kruger S., Steinmetz M., Stulke J. New beta-glucoside (bgl) genes in Bacillus subtilis: the bglP gene product has both transport and regulatory functions similar to those of BglF, its Escherichia coli homolog. J. Bacteriol. 177:1995;1527-1535.
16. Lewis M., Chang G., Horton N. C., Kercher M. A., Pace H. C., Schumacher M. A., Brennan R. G., Lu P. Crystal structure of the lactose operon repressor and its complexes with DNA and inducer. Science. 271:1996;1247-1254.
17. Li Y., Ferenci T. Gene organisation and regulatory sequences in the sucrose utilisation cluster of Bacillus stearothermophilus NUB36. Gene. 195:1997;195-200.
18. Lindner C., Galinier A., Hecker M., Deutscher J. Regulation of the activity of the Bacillus subtilis antiterminator LicT by multiple PEP-dependent, enzyme I- and HPr-catalysed phosphorylation. Mol. Microbiol. 31:1999;995-1006.
19. Manival X., Aymerich S., Strub M. P., Dumas C., Kochoyan M., van Tilbeurgh H. Crystallization of the RNA-binding domain of the transcriptional antiterminator protein SacY from Bacillus subtilis. Proteins: Struct. Funct. Genet. 28:1997a;590-594.
20. Manival X., Yang Y., Strub M. P., Kochoyan M., Steinmetz M., Aymerich S. From genetic to structural characterization of a new class of RNA- binding domain within the SacY/BglG family of antiterminator proteins. EMBO J. 16:1997b;5019-5029.
21. Martin-Verstraete I., Charrier V., Stulke J., Galinier A., Erni B., Rapoport G., Deutscher J. Antagonistic effects of dual PTS-catalysed phosphorylation on the Bacillus subtilis transcriptional activator LevR. Mol. Microbiol. 28:1998;293-303.
22. Navaza J. AMoRe: an automated package of molecular replacement. Acta Crystallog. sect. A. 50:1994;157-163.
23. Nicholls A., Sharp K. A., Honig B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins: Struct. Funct. Genet. 11:1991;281-296.
24. Otwinowsky A. DENZO: An Oscillation Data Processing Program for Macromolecular Crystallograph. 1993;Yale University Press, New Haven.
25. Roussel A., Cambillau C. TURBO FRODO, Silicon Graphics Geometry Partners Directory. 1991;Silicon Graphics, Mountain View.
26. Schnetz K., Stulke J., Gertz S., Kruger S., Krieg M., Hecker M., Rak B. LicT, a Bacillus subtilis transcriptional antiterminator protein of the BglG family. J. Bacteriol. 178:1996;1971-1979.
27. Steinmetz M. Carbohydrate catabolism: pathways, enzymes, genetic regulation and evolution. Sohenshein A. L., Hoch J. A., Losick R. Bacillus subtilis, and other Gram-positive Bacteria, Biochemistry, Physiology, and Molecular Genetics. 1993;157-170 American Society for Microbiology, Washington.
28. Stulke J., Arnaud M., Rapoport G., Martin-Verstraete I. PRD-a protein domain involved in PTS-dependent induction and carbon catabolite repression of catabolic operons in bacteria. Mol. Microbiol. 28:1998;865-874.
29. Tomchick D. R., Turner R. J., Switzer R. L., Smith J. L. Adaptation of an enzyme to regulatory function: structure of Bacillus subtilis PyrR, a pyr RNA-binding attenuation protein and uracil phosphoribosyltransferase. Structure. 6:1998;337-350.
30. Tortosa P., Aymerich S., Lindner C., Saier M. H. Jr, Reizer J., Le Coq D. Multiple phosphorylation of SacY, a Bacillus subtilis transcriptional antiterminator negatively controlled by the phosphotransferase system. J. Biol. Chem. 272:1997;17230-17237.
31. Valegard K., Murray J. B., Stockley P. G., Stonehouse N. J., Liljas L. Crystal structure of an RNA bacteriophage coat protein-operator complex. Nature. 371:1994;623-626.
32. van Tilbeurgh H., Manival X., Aymerich S., Lhoste J. M., Dumas C., Kochoyan M. Crystal structure of a new RNA-binding domain from the antiterminator protein SacY of Bacillus subtilis. EMBO J. 16:1997;5030-5036.
33. Weickert M. J., Adhya S. A family of bacterial regulators homologous to Gal and Lac repressors. J. Biol. Chem. 267:1992;15869-15874.
34. Wu Y., Reece R. J., Ptashne M. Quantitation of putative activator-target affinities predicts transcriptional activating potentials. EMBO J. 15:1996;3951-3963.