Modulating DNA bending affects NodD-mediated transcriptional control in Rhizobium leguminosarum

Nucleic Acids Research

Volumn 33, Issue 8, 2005, Pages 2540-2548

  Chen, Xiao Chun ^a   Feng, Jie ^a   Hou, Bi He ^a   Li, Feng Qing ^a   Li, Qiang ^a   Hong, Guo Fan ^a  

^a INSTITUTE OF BIOCHEMISTRY AND CELL BIOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; CURVED DNA; NARINGENIN; PROTEIN NOD; PROTEIN NODA; PROTEIN NODD; TRANSACTIVATOR PROTEIN; UNCLASSIFIED DRUG; BACTERIAL DNA; FLAVANONE DERIVATIVE; NODD PROTEIN, BACTERIA; TRANSCRIPTION FACTOR;

ARTICLE; BASE PAIRING; CONTROLLED STUDY; CORRELATION ANALYSIS; DNA MODIFICATION; DNA STRUCTURE; GEL MOBILITY SHIFT ASSAY; GENE DELETION; GENE INDUCTION; GENE INSERTION; GENETIC DISTANCE; NONHUMAN; PRIORITY JOURNAL; RHIZOBIUM LEGUMINOSARUM; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION; WILD TYPE; BINDING SITE; CHEMISTRY; CONFORMATION; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROMOTER REGION; TRANSACTIVATION;

RHIZOBIUM LEGUMINOSARUM;

BACTERIAL PROTEINS; BASE SEQUENCE; BINDING SITES; DNA, BACTERIAL; ELECTROPHORETIC MOBILITY SHIFT ASSAY; FLAVANONES; GENE EXPRESSION REGULATION, BACTERIAL; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PROMOTER REGIONS (GENETICS); RHIZOBIUM LEGUMINOSARUM; TRANS-ACTIVATION (GENETICS); TRANSCRIPTION FACTORS;

EID: 18244389706     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki537     Document Type: Article

References (44)

1. Schultze, M. and Kondorosi, A. (1998) Regulation of symbiotic root nodule development. Annu. Rev. Genet., 32, 33-57.
2. Long, S.R. (1989) Rhizobium-legume nodulation: Life together in the underground. Cell, 56, 203-214.
3. Firmin, J.L., Wilson, K.E., Rossen, L. and Johnston, A.W.B. (1986) Flavonoid activation of nodulation genes in Rhizobium, reversed by other compounds present in plants. Nature, 324, 90-92.
4. Hong, G.F., Burn J.E. and Johnston, A.W.B. (1987) Evidence that DNA involved in the expression of nodulation (nod) genes in Rhizobium binds to the product of the regulatory gene nodD. Nucleic Acids Res., 15, 9677-9689.
5. Fisher, R.F., Egellhoff, T.T., Mulligan, J.T. and Long, S.R. (1988) Specific binding of proteins from Rhizobium meliloti cell-free extracts containing NodD to DNA sequences upstream of inducible nodulation genes. Genes Dev., 2, 282-293.
6. Schell, M.A. (1993) Molecular biology of the LysR family of transcriptional regulators. Annu. Rev. Microbiol., 47, 597-626.
7. Colyer, T.E. and Kredich, N.M. (1994) Residue threonine- 149 of the Salmonella typhimurium CysB transcription activator: Mutations causing constitutive expression of positively regulated genes of the cysteine regulon. Mol. Microbiol., 13, 797-805.
8. van den Bergh, E.R., Dijkhuizen, L. and Meijer, W.G. (1993) CbnR, a LysR-type transcriptional activator, is required for expression of the autotrophic CO2 fixation enzymes of Xanthobacter flavus. J. Bacteriol., 175, 6097-6104.
9. Rothmel, R.K., Shinabarger, D.L., Parsek, M.R., Aldrich, T.L. and Chakrabarty, A.M. (1991) Functional analysis of the Pseudomonas putida regulatory protein CatR: Transcriptional studies and determination of the CatR DNA-binding site by hydroxyl-radical footprinting. J. Bacteriol., 173, 4717-4724.
10. Doty, S.L., Chang, M. and Nester, E.W. (1993) The chromosomal virulence gene, chvE, of Agrobacterium tumefaciens is regulated by a LysR family member. J. Bacteriol., 175, 7880-7886.
11. Henikoff, S., Haughn, G.W., Calvo, J.M. and Wallace, J.C. (1988) A large family of bacterial activator proteins. Proc. Natl Acad. Sci. USA, 85, 6602-6606.
12. Viale, A.M., Kobayashi, H., Akazawa, T. and Henikoff, S. (1991) rbcR [correction of rcbR], a gene coding for a member of the LysR family of transcriptional regulators, is located upstream of the expressed set of ribulose 1,5-bisphosphate carboxylase/oxygenase genes in the photosynthetic bacterium Chromatium vinosum. J. Bacteriol., 173, 5224-5229.
13. Mao, C., Downie, J.A. and Hong, G.F. (1994) Two inverted repeats in the nodD promoter region are involved in nodD regulation in Rhizobium leguminosarum. Gene, 144, 87-90.
14. Hu, H.L., Liu, S.T., Yang, Y., Chang, W.Z. and Hong, G.F. (2000) In Rhizobium leguminosarum, NodD represses its own transcription by competing with RNA polymerase for binding sites. Nucleic Acids Res.. 28, 2784-2793.
15. Tyrrell, R., Verschueren, K.H., Dodson, E., Murshudov, G.N., Addy, C. and Wilkinson, A.J. (1997) The structure of the cofactor-binding fragment of the LysR family member, CysB: A family fold with a surprising subunit arrangement. Structure, 5, 1017-1031.
16. Wang, L. and Winans, S.C. (1995) The sixty nucleotide of OccR operator contains a subsite essential and sufficient for OccR binding and a second subsite required for ligand-responsive DNA bending. J. Mol. Biol., 253, 691-702.
17. Coco, W.M., Parsek, M.R. and Chakrabarty, A.M. (1994) Purification of the LysR family regulator, ClcR, and its interaction with the Pseudomonas putida clcABD chlorocatechol operon promoter. J. Bacteriol., 176, 5530-5533.
18. Jourlin-Castelli, C., Mani, N., Nakano, M.M. and Sonenshein, A.L. (2000) CcpC, a novel regulator of the LysR family required for glucose repression of the citB gene in Bacillus subtilis. J. Mol. Biol., 295, 865-878.
19. Lamblin, A.J. and Fuchs, J.A. (1994) Functional analysis of the Escherichia coli K-12 cyn operon transcriptional regulation. J. Bacteriol.. 176, 6613-6622.
20. Chang, M. and Crawford, I. (1990) The roles of indoleglycerol phosphate and the TrpI protein in the expression of trpBA from Pseudomonas aeruginosa. Nucleic Acids Res., 18, 979-988.
21. Fisher, R.F. and Long, S.R. (1993) Interaction of NodD at the nod box: NodD binds to two distinct sites on the same face of the helix and induces a bend in the DNA. J. Mol. Biol., 233, 336-348.
22. Wang, L., Helmann, J.D. and Winans, S.C. (1992) The A. tumefaciens transcriptional activator OccR causes a bend at a target promoter, which is partially relaxed by a plant tumor metabolite. Cell, 69, 659-667.
23. Mcfall, S.M., Klem, T.J., Fujita, N., Ishihama, A. and Chakrabarty, A.M. (1997) DNase I footprinting, DNA bending and in vitro transcription analyses of ClcR and CatR interactions with the clcABD promoter: evidence of a conserved transcriptional activation mechanism. Mol. Microbiol.. 24, 965-976.
24. Feng, J., Li, Q., Hu, H.L., Chen, X.C. and Hong, G.F. (2003) Inactivation of the nod box distal half-site allows tetrameric NodD to activate nodA transcription in an inducer-independent manner. Nucleic Acids Res., 31, 3143-3156.
25. Shin, M., Rumi, O., Naoto, O., Takamasa, N., Kiyotaka, M. and Toshiya, S. (2003) Crystal structure of a full-length LysR-type transcriptional regulator, CbnR: Unusual combination of two subunit forms and molecular bases for causing and changing DNA bend. J. Mol. Biol., 328, 555-566.
26. Ansari, A.Z., Bradner, J.E. and O'Halloran, T.V. (1995) DNA-bend modulation in a repressor-to-activator switching mechanism. Nature, 374, 371-375.
27. Toledano, M.B., Kullik, I.. Trinh, F., Baird, P.T., Schneider, T.D. and Storz, G. (1994) Redox-dependent shift of OxyR-DNA contacts along an extended DNA-binding site: A mechanism for differential promoter selection. Cell, 78, 897-909.
28. Simon, R., Priefer, V. and Puhler, A. (1983) A broad host range mobilization system for in vivo genetic engineering: Transposon mutagenesis in gram-negative bacteria. Biotechnology, 1, 784.
29. Huang, W.H., Zhai, F. and Hong, G.F. (1999) Cloning, expression, characterization and application of Bst DNA polymerase large Fragment. Sheng WU Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai), 31, 379-384.
30. Chang, W.Z. and Hong, G.F. (1997) Two functional regions were discovered within nodA promoter. Chin. J. Biotechnol., 13, 83-87.
31. Spaink, H.P., Okker, R.J.H., Wijffelman, C.A., Pees, E. and Lugtenberg, B.J.J. (1987) Promoters in the nodulation region of the Rhizobium leguminosarum Sym plasmid pRL1JI. Plant Mol. Biol., 9, 27-39.
32. Sambrook, J., Fritsch, E.F. and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
33. Goethals, K., van Montagu, M. and Holsters, M. (1992) Conserved motifs in a divergent nod box of Azorhizobiuim caulinodans ORS571 reveal a common structure in promoters regulated by the LysR-type protein. Proc. Natl Acad. Sci. USA, 89, 1646-1650.
34. Wu, H.M. and Crothers, D.M. (1984) The locus of sequence-directed and protein induced DNA bending. Nature, 308, 509-513.
35. Thompson, J.F. and Landy, A. (1988) Empirical estimation of protein-induced DNA bending angles: Applications to lambda site-specific recombination complexes. Nucleic Acids Res., 16, 9687-9705.
36. Akakura, R. and Winans, S.C. (2002) Constitutive mutations of the OccR regulatory protein affect DNA bending in response to metabolites released from plant tumors. J. Biol. Chem., 277, 5866-5874.
37. Park, W., Jeon, C.O. and Madsen, E.L. (2002) Interaction of NahR, a LysR-type transcriptional regulator, with the alpha subunit of RNA polymerase in the naphthalene degrading bacterium. Pseudomonas putida NCIB 9816-4. FEMS Microbiol. Lett., 213, 159-165.
38. Kondorosi, E., Gyuris, J., Schmidt, J., John, M., Duda, E., Hoffman, B., Schell, J. and Kondorosi, A. (1989) Positive and negative control of nod gene expression in Rhizobium meliloti is required for optimal nodulation. EMBO J., 8, 1331-1340.
39. Cren, M., Kondorosi, A. and Kondorosi, E. (1995) NoIR controls expression of the Rhizobium meliloti nodulations genes involved in the core Nod factor synthesis. Mol. Microbiol., 15, 733-747.
40. Liu, S.T., Chang, W.Z., Cao, H.M., Hu, H.L., Chen, Z.H., Ni, F.D. and Hong, G.F. (1998) A HU-like protein binds to specific sites within nod promoters of Rhizobium leguminosarum. J. Biol. Chem., 273 20568-20574.
41. Li, Q., Feng, J., Hu, H.L., Chen, X.C., Li, F.Q. and Hong, G.F. (2004) A HU-Like gene mutation in Rhizobium leguminosarum. bv. viciae affects the expression of nodulation genes. Mol. Microbiol., 51, 861-871.
42. Ogawa, J. and Long, S.R. (1995) The Rhizobium meliloti groELc locus is required for regulation of early nod genes by the transcription activator NodD. Genes Dev., 9, 714-729.
43. Lamb, J.W., Hombrecher, G. and Johnston, A.W.B. (1982) Plasmid-determined nodulation and nitrogen-fixation abilities in Rhizobium phaseoli. Mol. Gen. Genet., 186, 449-452.
44. Bagdasarian, M., Lurz, R., Ruckert, B., Franklin, F.C.H., Bagdasarian, M.M., Frey, J. and Timmis, K.N. (1981) Specific-purpose plasmid cloning vectors. II. Broad host range, high copy number, RSF1010-derived vectors, and a host-vector system for gene cloning in. Pseudomonas Gene, 16, 237-247.