Nitrogen fixation genetics and regulation in a Pseudomonas stutzeri strain associated with rice

Microbiology

Volumn 149, Issue 8, 2003, Pages 2251-2262

  Desnoues, Nicole ^a   Lin, Min ^b   Guo, Xianwu ^a,c,e   Ma, Luyan ^a,f   Carreño Lopez, Ricardo ^a,g   Elmerich, Claudine ^a,d  

^a INSTITUT PASTEUR   (France)

^b INSTITUTE OF PLANT PROTECTION   (China)

^c INSTITUTO DE CIENCIAS FÍSICAS   (Mexico)

^d INSTITUT DES SCIENCES DU VÉGÉTAL   (France)

^e HUAZHONG AGRICULTURAL UNIVERSITY   (China)

^f CHINA AGRICULTURAL UNIVERSITY   (China)

^g BENEMÉRITA UNIVERSIDAD AUTÓNOMA DE PUEBLA   (Mexico)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; GENE PRODUCT; HYBRID PROTEIN; NITROGENASE;

AZOTOBACTER VINELANDII; BACTERIAL COLONIZATION; BACTERIAL GENE; BACTERIAL GENETICS; BACTERIAL STRAIN; CHROMOSOME; CONTROLLED STUDY; ELECTRON TRANSPORT; GENE EXPRESSION; GENE INSERTION; GENETIC REGULATION; MUTAGENESIS; NITROGEN FIXATION; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PRIORITY JOURNAL; PROMOTER REGION; PSEUDOMONAS STUTZERI; REVIEW; RHODOBACTER CAPSULATUS; RICE; STRAIN DIFFERENCE;

ALCALIGENES; ALCALIGENES FAECALIS; AZOTOBACTER; AZOTOBACTER VINELANDII; BACTERIA (MICROORGANISMS); INSERTION SEQUENCES; NEGIBACTERIA; PSEUDOMONAS; PSEUDOMONAS STUTZERI; RHODOBACTER; RHODOBACTER CAPSULATUS; RHODOPSEUDOMONAS;

EID: 0041923849     PISSN: 13500872     EISSN: None     Source Type: Journal    
DOI: 10.1099/mic.0.26270-0     Document Type: Review

References (62)

1. Allen, L. N. & Hanson, R. S. (1985). Construction of broad-host-range cosmid cloning vectors: identification of genes necessary for growth of Methylobacterium organophilum on methanol. J Bacteriol 161, 955-962.
2. Alvarez-Morales, A., Dixon, R. & Merrick, M. (1984). Positive and negative control of the glnA ntrBC regulon in Klebsiella pneumoniae. EMBO J 3, 501-507.
3. Arnold, W., Rump, A., Klipp, W., Priefer, U. B. & Pühler, A. (1988). Nucleotide sequence of a 24,206-base-pair DNA fragment carrying the entire nitrogen fixation gene cluster of Klebsiella pneumoniae. J Mol Biol 203, 715-738.
4. 54-dependent promoter sequences. Nucleic Acids Res 27, 4305-4313.
5. Bergersen, F. J. (1991). Physiological control of nitrogenase and uptake hydrogenase. In Biology and Biochemistry of Nitrogen Fixation, pp. 76-102. Edited by M. J. Dilworth & A. R. Glenn. Amsterdam: Elsevier.
6. Blanco, G., Drummond, M., Woodley, P. & Kennedy, C. (1993). Sequence and molecular analysis of the nifL gene of Azotobacter vinelandii. Mol Microbiol 9, 869-879.
7. Bozouklian, H., Fogher, C. & Elmerich, C. (1986). Cloning and characterization of the glnA gene of Azospirillum brasilense Sp7. Ann Inst Pasteur 137B, 3-18.
8. Carlton, J. M., Anguioli, S. V., Suh, B. & 41 other authors (2002). Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature 419, 512-519.
9. 2-fixing pseudomonads and related soil bacteria. FEMS Microbiol Rev 13, 95-118.
10. Dean, D. R. & Jacobson, M. R. (1992). Biochemical genetics of nitrogenase. In Biological Nitrogen Fixation, pp. 763-834. Edited by G. Stacey, R. H. Burris & H. J. Evans. New York: Chapman & Hall.
11. de Zamaroczy, M., Delorme, F. & Elmerich, C. (1989). Regulation of transcription and promoter mapping of the structural genes for nitrogenase (nifHDK) of Azospirillum brasilense Sp7. Mol Gen Genet 220, 88-94.
12. Ditta, G., Schmidhauser, T., Yakobson, E., Lu, P., Liang, X. W., Finlay, D. R., Guiney, D. & Helinski, D. R. (1985). Plasmids related to the broad host range vector, pRK290, useful for gene cloning and for monitoring gene expression. Plasmid 13, 149-153.
13. 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.
14. 2 fixation and nitrogenase "switch-off" of Azoarcus sp. strain BH72. J Bacteriol 183, 3752-3760.
15. Egener, T., Sarkar, A., Martin, D. E. & Reinhold-Hurek, B. (2002). Identification of a NifL-like protein in a diazotroph of the β-subgroup of the Proteobacteria, Azoarcus sp. strain BH72. Microbiology 148, 3203-3212.
16. Elmerich, C. (1991). Genetics and regulation of Mo-nitrogenase. In Biology and Biochemistry of Nitrogen Fixation, pp. 103-141. Edited by M. J. Dilworth & A. R. Glenn. Amsterdam: Elsevier.
17. Fallik, E., Chan, Y. K. & Robson, R. L. (1991). Detection of alternative nitrogenases in aerobic Gram-negative nitrogen-fixing bacteria. J Bacteriol 173, 365-371.
18. Fischer, H. M. (1994). Genetic regulation of nitrogen fixation in rhizobia. Microbiol Rev 58, 352-386.
19. Galimand, M., Perroud, B., Delorme, F., Paquelin, A., Vieille, C., Bozouklian, H. & Elmerich, C. (1989). Identification of DNA regions homologous to nitrogen fixation genes nifE, nifUS and fixABC in Azospirillum brasilense Sp7. J Gen Microbiol 135, 1047-1059.
20. Hallmann, J., Quadt-Hallmann, A., Mahaffee, W. F. & Kloepper, J. W. (1997). Bacterial endophytes in agricultural crops. Can J Microbiol 43, 895-914.
21. Häse, C. & Mekalanos, J. J. (1999). Effects of changes in membrane sodium flux on virulence gene expression in Vibrio cholerae. Proc Natl Acad Sci U S A 96, 3183-3187.
22. Hübner, P., Masepohl, B., Klipp, W. & Bickle, T. A. (1993). nif gene expression studies in Rhodobacter capsulatus: ntrC-independent repression by high ammonium concentrations. Mol Microbiol 10, 123-132.
23. Jacobson, M. R., Brigle, K. V., Bennett, L. T., Setterquist, R. A., Wilson, M. S., Cash, V. L., Beynon, J., Newton, W. E. & Dean, D. R. (1989). Physical and genetic map of the major nif gene cluster from Azotobacter vinelandii. J Bacteriol 171, 1017-1027.
24. Joerger, R. D. & Bishop, P. E. (1988). Nucleotide sequence and genetic analysis of the nifB-nifQ region from Azotobacter vinelandii. J Bacteriol 170, 1475-1487.
25. Jouanneau, Y., Jeong, H. S., Hugo, N., Meyer, C. & Willison, J. C. (1998). Overexpression in Escherichia coli of the rnf genes from Rhodobacter capsulatus: characterization of two membrane-bound iron-sulphur proteins. Eur J Biochem 251, 54-64.
26. Knauf, V. C. & Nester, E. W. (1982). Wide host range cloning vectors: a cosmid clone bank of an Agrobacterium Ti plasmid. Plasmid 8, 45-54.
27. Kokotek, W. & Lotz, W. (1989). Construction of a lacZ-kanamycin-resistance cassette, useful for site-directed mutagenesis and as a promoter probe. Gene 84, 467-471.
28. Krotkzy, A. & Werner, D. (1987). Nitrogen fixation in Pseudomonas stutzeri. Arch Microbiol 147, 48-57.
29. Kumagai, H., Fujiwara, T., Matsubara, H. & Saeki, K. (1997). Membrane localization, topology, and mutual stabilization of the rnfABC gene products in Rhodobacter capsulatus and implications for a new family of energy-coupling NADH oxidoreductases. Biochemistry 36, 5509-5521.
30. Lee, S., Reth, A., Meletzus, D., Sevilla, M. & Kennedy, C. (2000). Characterization of a major cluster of nif, fix and associated genes in a sugarcane endophyte, Acetobacter diazotrophicus. J Bacteriol 182, 7088-7091.
31. Liang, Y. Y., Kaminski, P. A. & Elmerich, C. (1991). Identification of a nifA-like regulatory gene of Azospirillum brasilense Sp-7 expressed under conditions of nitrogen fixation and in the presence of air and ammonia. Mol Microbiol 5, 2735-2744.
32. Liang, Y. Y., Arsène, F. & Elmerich, C. (1993). Characterization of the ntrBC genes of Azospirillum brasilense Sp7: their involvement in the regulation of nitrogenase synthesis and activity. Mol Gen Genet 240, 188-196.
33. Lin, M., Smalla, K., Heuer, H. & van Elsas, J. D. (2000). Effect of an Alcaligenes faecalis inoculant strain on bacterial communities in flooded microcosms planted with rice seedlings. Appl Soil Ecol 15, 211-225.
34. Loveless, T. M. & Bishop, P. E. (1999). Identification of genes unique to Mo-independent nitrogenase systems in diverse diazotrophs. Can J Microbiol 45, 312-317.
35. Lovell, C. R., Piceno, Y. M., Quattro, J. M. & Bagwell, C. E. (2000). Molecular analysis of diazotroph diversity in the rhizosphere of the smooth cordgrass, Spartina alterniflora. Appl Environ Microbiol 66, 3814-3822.
36. Ludden, P. W. (1994). Reversible ADP-ribosylation as a mechanism of enzyme regulation in procaryotes. Mol Cell Biochem 138, 123-129.
37. Mandon, K., Michel-Reydellet, N., Encarnacion, S., Kaminski, A., Leija, A., Cevallos, M., Elmerich, C. & Mora, J. (1998). Poly-β-hydroxybutyrate turnover in Azorhizobium caulinodans is required for growth and controls nifA expression. J Bacteriol 180, 5070-5076.
38. Mavingui, P., Flores, M., Guo, X., Davilla, G., Perret, X., Broughton, W. J. & Palacios, R. (2002). Dynamics of genome architecture in Rhizobium sp. NGR234. J Bacteriol 184, 171-176.
39. Merrick, M. J. (1992). Regulation of nitrogen fixation genes in free-living and symbiotic bacteria. In Biological Nitrogen Fixation, pp. 835-876. Edited by G. Stacey, R. H. Burris & H. J. Evans. New York: Chapman and Hall.
40. Miller, J. (1972). Assay for β-galactosidase. In Experiments in Molecular Genetics, pp. 352-355. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
41. Reyes-Ramirez, F., Little, R. & Dixon, R. (2001). Role of Escherichia coli nitrogen regulatory genes in the nitrogen response of the Azotobacter vinelandii NifL-NifA complex. J Bacteriol 183, 3076-3082.
42. Rodrigue, A., Quentin, Y., Lazdunski, A., Méjean, V. & Foglino, M. (2000). Two-component systems in Pseudomonas aeruginosa: why so many? Trends Microbiol 8, 498-504.
43. Roth, J. R., Lawrence, J. G. & Bobik, T. A. (1996). Cobalamin (coenzyme B12) : synthesis and biological significance. Annu Rev Microbiol 50, 137-181.
44. Rubio, L. M., Rangaraj, P., Homers, M. J., Roberts, G. P. & Ludden, P. W. (2002). Cloning and mutational analysis of the γ gene from Azotobacter vinelandii defines a new family of proteins capable of metallocluster binding and protein stabilization. J Biol Chem 277, 14299-14305.
45. Rudnick, P., Kunz, C., Gunatilaka, M. K., Hines, E. R. & Kennedy, C. (2002). Role of GlnK in NifL-mediated regulation of NifA activity in Azotobacter vinelandii. J Bacteriol 184, 812-820.
46. Saez, L. P., Garcia, P., Martinez-Luque, M., Klipp, W., Blasco, R. & Castillo, F. (2001). Role of draTG and rnf genes in reduction of 2,4-dinitrophenol by Rhodobacter capsulatus. J Bacteriol 183, 1780-1783.
47. Sambrook, J., Fritsch, E. F. & Maniatis, T. (1989). Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
48. Schmel, M., Jahn, A., Meyer zu Vilsendorf, A., Hennecke, S., Masepohl, B., Schuppler, M., Marxer, M., Oelze, J. & Klipp, W. (1993 . Identification of a new class of nitrogen fixation genes in Rhodobacter capsulatus: a putative membrane complex involved in electron transport to nitrogenase. Mol Gen Genet 241, 602-615.
49. Schmidhauser, T. J., Ditta, G. & Helinski, D. R. (1988). Broad-host-range plasmid cloning vectors for gram-negative bacteria. Biotechnology 10, 287-332.
50. Siddavattam, D., Steibl, H. D., Kreutzer, R. & Klingmuller, W. (1995). Regulation of nif gene expression in Enterobacter agglomerans: nucleotide sequence of the nifLA operon and influence of temperature and ammonium on its transcription. Mol Gen Genet 249, 629-636.
51. Sikorski, J., Rosello-Mora, R. & Lorenz, M. G. (1999). Analysis of genotypic diversity and relationships among Pseudomonas stutzeri strains by PCR-based genomic fingerprinting and multilocus enzyme electrophoresis. Syst Appl Microbiol 22, 393-402.
52. Simon, R., Priefer, U. & Pühler, A. (1983). A broad host range mobilization system for in vivo genetic engineering: transposon mutagenesis in Gram-negative bacteria. Biotechnology 1, 784-791.
53. Toukdarian, A. & Kennedy, C. (1986). Regulation of nitrogen metabolism in Azotobacter vinelandii: isolation of ntr and glnA genes and construction of ntr mutants. EMBO J 5, 399-407.
54. 2-fixing bacteria associated with rice roots. Can J Microbiol 41, 235-240.
55. Vermeiren, H., Hai, W. L. & Vanderleyden, J. (1998). Colonization and nifH expression on rice roots by Alcaligenes faecalis A15. In Nitrogen Fixation with Non-Legumes, pp. 167-177. Edited by K. A. Malik, M. S. Mirza & J. K. Ladha. Dordrecht: Kluwer.
56. Vermeiren, H., Willems, A., Schoofs, G., de Mot, R., Keijers, V., Hai, W. & Vanderleyden, J. (1999). The rice inoculant strain A15 is a nitrogen-fixing Pseudomonas stutzeri strain. Syst Appl Microbiol 22, 215-224.
57. You, C. & Zhou, F (1989). Non-nodular endorhizospheric nitrogen fixation in wetland rice. Can J Microbiol 35, 403-408.
58. You, C. B., Song, H. X., Wang, J. P., Lin, M. & Hai, W. L. (1991). Association of Alcaligenes faecalis with wetland rice. Plant Soil 137, 81-85.
59. Young, J. P. W. (1992). Phylogenetic classification of nitrogen-fixing organisms. In Biological Nitrogen Fixation, pp. 43-86. Edited by G. Stacey, R. H. Burris & H. J. Evans. New York: Chapman & Hall.
60. Zehr, J. & McReynolds, L. A. (1989). Use of degenerate oligonucleotides for amplification of the nifH gene from the marine cyanobacterium Trichodesmium thiebautii. Appl Environ Microbiol 55, 2522-2526.
61. Zhang, Y., Pohlmann, E. L., Ludden, P. W. & Roberts, G. P. (2000). Mutagenesis and functional characterization of the glnB, glnA, and nifA genes from the photosynthetic bacterium Rhodospirillum rubrum. J Bacteriol 182, 983-992.
62. Zhulin, I. B., Taylor, B. L. & Dixon, R. (1997). PAS domain S-boxes in Archaea, Bacteria and sensors for oxygen and redox. Trends Biochem Sci 22, 331-333.