Three new NifA-regulated genes in the Bradyrhizobium japonicum symbiotic gene region discovered by competitive DNA-RNA hybridization

Journal of Bacteriology

Volumn 182, Issue 6, 2000, Pages 1472-1480

  Nienaber, Andrea ^a   Huber, Alexander ^a,c   Göttfert, Michael ^b   Hennecke, Hauke ^a   Fischer, Hans Martin ^a  

^a ETH ZURICH   (Switzerland)

^b DRESDEN UNIVERSITY OF TECHNOLOGY   (Germany)

^c UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BRADYRHIZOBIUM; BRADYRHIZOBIUM JAPONICUM; DNA RNA HYBRIDIZATION; GENE CLUSTER; GENE CONTROL; GENE INDUCTION; NITROGEN FIXATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; SEQUENCE ANALYSIS; SOUTHERN BLOTTING; SOYBEAN;

BACTERIA (MICROORGANISMS); BRADYRHIZOBIUM; BRADYRHIZOBIUM JAPONICUM; GLYCINE MAX; NEGIBACTERIA; PHASEOLUS (ANGIOSPERM); PROKARYOTA; RHIZOBIUM; VIGNA RADIATA VAR. RADIATA;

EID: 0034090540     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.182.6.1472-1480.2000     Document Type: Article

References (59)

1. Aguilar, O. M., J. Taormino, B. Thöny, T. Ramseier, H. Hennecke, and A. A. Szalay. 1990. The nifEN genes participating in FeMo cofactor biosynthesis and genes encoding dinitrogenase are part of the same operon in Bradyrhizobium species. Mol. Gen. Genet. 224:413-420.
2. Alexeyev, M. F. 1995. Three kanamycin resistance gene cassettes with different polylinkers. BioTechniques 18:52-54.
3. Babst, M., H. Hennecke, and H. M. Fischer. 1996. Two different mechanisms are involved in the heat shock regulation of chaperonin gene expression in Bradyrhizobium japonicum. Mol. Microbiol. 19:827-839.
4. Baron, C., and P. C. Zambryski. 1995. The plant response in pathogenesis, symbiosis, and wounding: variations on a common theme? Annu. Rev. Genet. 29:107-129.
5. Bauer, E., T. Kaspar, H. M. Fischer, and H. Hennecke. 1998. Expression of the fixR-nifA operon in Bradyrhizobium japonicum depends on a new response regulator, RegR. J. Bacteriol. 180:3853-3863.
6. Bhagwat, A. A., and D. L. Keister. 1992. Identification and cloning of Bradyrhizobium japonicum genes expressed strain-selectively in soil and rhizosphere. Appl. Environ. Microbiol. 58:1490-1495.
7. Chuang, S. E., D. L. Daniels, and F. R. Blattner. 1993. Global regulation of gene expression in Escherichia coli. J. Bacteriol. 175:2026-2036.
8. Daniel, R. M., and C. A. Appleby. 1972. Anaerobic-nitrate, symbiotic and aerobic growth of Rhizobium japonicum: effects on cytochrome P450, other haemoproteins, nitrate and nitrite reductases. Biochim. Biophys. Acta 275: 347-354.
9. David, M., O. Domergue, P. Pognonec, and D. Kahn. 1987. Transcription patterns of Rhizobium meliloti symbiotic plasmid pSym: identification of nifA-independent fix genes. J. Bacteriol. 169:2239-2244.
10. Dénarié, J., F. Debellé, and J. C. Promé. 1996. Rhizobium lipo-chitooligo-saccharide nodulation factors: signaling molecules mediating recognition and morphogenesis. Annu. Rev. Biochem. 65:503-535.
11. Dixon, R. 1998. The oxygen-responsive NIFL-NIFA complex: a novel two-component regulatory system controlling nitrogenase synthesis in γ-Proteobacteria. Arch. Microbiol. 169:371-380.
12. Ebeling, S., M. Hahn, H. M. Fischer, and H. Hennecke. 1987. Identification of nifE-, nifN-and nifS-like genes in Bradyrhizobium japonicum. Mol. Gen. Genet. 207:503-508.
13. Ebeling, S., J. D. Noti, and H. Hennecke. 1988. Identification of a new Bradyrhizobium japonicum gene (frxA) encoding a ferredoxin-like protein. J. Bacteriol. 170:1999-2001.
14. Fellay, R., X. Perret, V. Viprey, W. J. Broughton, and S. Brenner. 1995. Organisation of host-inducible transcripts on the symbiotic plasmid of Rhizobium sp. NGR234. Mol. Microbiol. 16:657-667.
15. Fischer, H. M. 1994. Genetic regulation of nitrogen fixation in rhizobia. Microbiol. Rev. 58:352-386.
16. Fischer, H. M. 1996. Environmental regulation of rhizobial symbiotic nitrogen fixation genes. Trends Microbiol. 4:317-320.
17. Fischer, H. M., A. Alvarez-Morales, and H. Hennecke. 1986. The pleiotropic nature of symbiotic regulatory mutants: Bradyrhizobium japonicum nifA gene is involved in control of nif gene expression and formation of determinate symbiosis. EMBO J. 5:1165-1173.
18. Fischer, H. M., M. Babst, T. Kaspar, G. Acuña, F. Arigoni, and H. Hennecke. 1993. One member of a groESL-like chaperonin multigene family in Bradyrhizobium japonicum is co-regulated with symbiotic nitrogen fixation genes. EMBO J. 12:2901-2912.
19. Fuhrmann, M., and H. Hennecke. 1984. Rhizobium japonicum nitrogenase Fe protein gene (nifH). J. Bacteriol. 158:1005-1011.
20. Fuhrmann, M., H. M. Fischer, and H. Hennecke. 1985. Mapping of Rhizobium japonicum nifB-, fixBC-, and fixA-like genes and identification of the fixA promoter. Mol. Gen. Genet. 199:315-322.
21. Gibson, T. J., A. Rosenthal, and R. H. Waterston. 1987. Lorist6, a cosmid vector with BamHI, NotI, ScaI and HindIII cloning sites and altered neomycin phosphotransferase gene expression. Gene 53:283-286.
22. Girard, L., B. Valderrama, R. Palacios, D. Romero, and G. Dávila. 1996. Transcriptional activity of the symbiotic plasmid of Rhizobium etli is affected by different environmental conditions. Microbiology 142:2847-2856.
23. Göttfert, M., S. Hitz, and H. Hennecke. 1990. Identification of nodS and nodU, two inducible genes inserted between the Bradyrhizobium japonicum nodYABC and nod1J genes. Mol. Plant-Microbe Interact. 3:308-316.
24. Gubler, M., and H. Hennecke. 1986. FixA, B and C genes are essential for symbiotic and free-living, microaerobic nitrogen fixation. FEBS Lett. 200: 186-192.
25. Hahn, M. 1986. Genomstruktur von Bradyrhizobium japonicum: gemeinsames Vorkommen von repetitiven Sequenzen und Genen für die Wurzelknöllchensymbiose. Ph.D. thesis. Eidgenössische Technische Hochschule, Zürich, Switzerland.
26. Hahn, M., and H. Hennecke. 1984. Localized mutagenesis in Rhizobium japonicum. Mol. Gen. Genet. 193:46-52.
27. Hart, S., R. Kirby, and D. R. Woods. 1990. Structure of a Rhodococcus gene encoding pigment product in Escherichia coli. J. Gen. Microbiol. 136:1357-1363.
28. Hawkins, F. K. L., and A. W. B. Johnston. 1988. Transcription of a Rhizobium leguminosarum biovar phaseoli gene needed for melanin synthesis is activated by nifA of Rhizobium and Klebsiella pneumoniae. Mol. Microbiol. 2: 331-337.
29. Howard, J. B., and D. C. Rees. 1994. Nitrogenase: a nucleotide-dependent molecular switch. Annu. Rev. Biochem. 63:235-264.
30. Kaluza, K., and H. Hennecke. 1984. Fine structure analysis of the nifDK operon encoding the α and β subunits of dinitrogenase from Rhizobium japonicum. Mol. Gen. Genet. 196:35-42.
31. Kaluza, K., M. Hahn, and H. Hennecke. 1985. Repeated sequences similar to insertion elements clustered around the nif region of the Rhizobium japonicum genome. J. Bacteriol. 162:535-542.
32. Kaminski, P. A., J. Batut, and P. Boistard. 1998. A survey of symbiotic nitrogen fixation by rhizobia, p. 431-460. In H. P. Spaink, A. Kondorosi, and P. J. J. Hooykaas (ed.), The Rhizobiaceae. Kluwer Academic Publishers, Dordrecht, The Netherlands.
33. Kim, I. C., and P. J. Oriel. 1995. Characterization of the Bacillus stearothermophilus BR219 phenol hydroxylase gene. Appl. Environ. Microbiol. 61: 1252-1256.
34. Klement, Z. 1982. Hypersensitivity, p. 149-177. In M. S. Mount and G. H. Lacy (ed.), Phytopathogenic prokaryotes, Academic Press Inc., New York, N.Y.
35. Kohara, Y., K. Akiyama, and K. Isono. 1987. The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell 50:495-508.
36. 54 gene (rpoN). J. Bacteriol. 173:1125-1138.
37. Kündig, C. 1994. Untersuchungen zur Genomstruktur und Charakterisierung des einzigen rRNA-Operons von Bradyrhizobium japonicum. Ph.D. thesis. Eidgenössische Technische Hochschule, Zürich, Switzerland.
38. Kündig, C., H. Hennecke, and M. Göttfert. 1993. Correlated physical and genetic map of the Bradyrhizobium japonicum 110 genome. J. Bacteriol. 175: 613-622.
39. Martin, G. B., K. A. Chapman, and B. K. Chelm. 1988. Role of the Bradyrhizobium japonicum ntrC gene product in differential regulation of the glutamine synthetase II gene (glnII). J. Bacteriol. 170:5452-5459.
40. Miller, J. H. 1972. Experiments in molecular genetics, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
41. Murphy, P. J., N. Heycke, S. T. Trenz, P. Ratet, F. J. de Bruijn, and J. Schell. 1988. Synthesis of an opine-like compound, a rhizopine, in alfalfa nodules is symbotically regulated. Proc. Natl. Acad. Sci. USA 85:9133-9137.
42. 2, a crucial distributor in the FixLJ-dependent regulatory cascade for control of genes inducible by low oxygen levels. J. Bacteriol. 180:5251-5255.
43. Norrander, J., T. Kempe, and J. Messing. 1983. Construction of improved M13 vectors using oligonucleotide-directed mutagenesis. Gene 26:101-106.
44. Parniske, M., H. M. Fischer, H. Hennecke, and D. Werner. 1991. Accumulation of the phytoalexin glyceollin I in soybean nodules infected by a Bradyrhizobium japonicum nifA mutant. Z. Naturforsch. 46:318-320.
45. Perret, X., R. Fellay, A. J. Bjourson, J. E. Cooper, S. Brenner, and W. J. Broughton. 1994. Subtraction hybridisation and shot-gun sequencing: a new approach to identify symbiotic loci. Nucleic Acids Res. 22:1335-1341.
46. Perret, X., C. Freiberg, A. Rosenthal, W. J. Broughton, and R. Fellay. 1999. High-resolution transcriptional analysis of the symbiotic plasmid of Rhizobium sp. NGR234. Mol. Microbiol. 32:415-425.
47. Phillips, D. A., and Y. Kapulnik. 1995. Plant isoflavonoids, pathogens and symbionts. Trends Microbiol. 3:58-64.
48. Ramseier, T. M., and M. Göttfert. 1991. Codon usage and G + C content in Bradyrhizobium japonicum genes are not uniform. Arch. Microbiol. 156: 270-276.
49. Regensburger, B., and H. Hennecke. 1983. RNA polymerase from Rhizobium japonicum. Arch. Microbiol. 135:103-109.
50. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
51. Schmidt, P. E., M. Parniske, and D. Werner. 1992. Production of the phytoalexin glyceollin-I by soybean roots in response to symbiotic and pathogenic infection. Bot. Acta 105:18-25.
52. Simon, R., U. Priefer, and A. Pühler. 1983. Vector plasmids for in vivo and in vitro manipulation of Gram-negative bacteria, p. 98-106. In A. Pühler (ed.), Molecular genetics of the bacteria-plant interaction, Springer Verlag, Heidelberg, Germany.
53. 2-fixation gene expression within the alfalfa root nodule. Proc. Natl. Acad. Sci. USA 92:3759-3763.
54. Studer, D., T. Gloudemans, H. J. Franssen, H. M. Fischer, T. Bisseling, and H. Hennecke. 1987. Involvement of the bacterial nitrogen fixation regulatory gene (nifA) in control of nodule-specific host-plant gene expression. Eur. J. Cell Biol. 45:177-184.
55. Thöny, B., K. Kaluza, and H. Hennecke. 1985. Structural and functional homology between the α and β subunits of the nitrogenase MoFe protein as revealed by sequencing the Rhizobium japonicum nifK gene. Mol. Gen. Genet. 198:441-448.
56. Thöny, B., H. M. Fischer, D. Anthamatten, T. Bruderer, and H. Hennecke. 1987. The symbiotic nitrogen fixation regulatory operon (fixRnifA) of Bradyrhizobium japonicum is expressed aerobically and is subject to a novel, nifA-independent type of activation. Nucleic Acids Res. 15:8479-8499.
57. van Rhijn, P., and J. Vanderleyden. 1995. The Rhizobium-plant symbiosis. Microbiol. Rev. 59:124-142.
58. Weidenhaupt, M., H. M. Fischer, G. Acuña, J. Sanjuan, and H. Hennecke. 1993. Use of a promoter-probe vector system in the cloning of a new NifA-dependent promoter (ndp) from Bradyrhizobium japonicum. Gene 129:33-40.
59. Willis, L. B., and G. C. Walker. 1998. The phbC (poly-β-hydroxyburyrate synthase) gene of Rhizobium (Sinorhizobium) meliloti and characterization of phbC mutants. Can. J. Microbiol. 44:554-564.