The nitrogen-fixing gene (nifH) of Rhodopseudomonas palustris: A case of lateral gene transfer?

Microbiology

Volumn 150, Issue 7, 2004, Pages 2237-2246

  Cantera, Jose Jason L ^a,b   Kawasaki, Hiroko ^a   Seki, Tatsuji ^a  

^a OSAKA UNIVERSITY   (Japan)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; GUANINE; NITROGEN; RNA 16S;

ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BRADYRHIZOBIUM JAPONICUM; CONTROLLED STUDY; GENETIC ASSOCIATION; GENETIC VARIABILITY; GRAM NEGATIVE BACTERIUM; HORIZONTAL GENE TRANSFER; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; MOLECULAR WEIGHT; NITROGEN FIXATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHOTOSYNTHESIS; PHOTOTROPHIC BACTERIUM; PRIORITY JOURNAL; RHODOBACTER; RHODOBACTER SPHAEROIDES; RHODOPSEUDOMONAS PALUSTRIS; RHODOSPIRILLUM RUBRUM; SEQUENCE ALIGNMENT; UNINDEXED SEQUENCE;

ALPHAPROTEOBACTERIA; BRADYRHIZOBIUM; BRADYRHIZOBIUM JAPONICUM; BRADYRHIZOBIUM JAPONICUM USDA 110; PHOTOBACTERIA; PROTEOBACTERIA; RHODOBACTER; RHODOBACTER SPHAEROIDES; RHODOBACTER SPHAEROIDES 2.4.1; RHODOPSEUDOMONAS PALUSTRIS; RHODOSPIRILLUM; RHODOSPIRILLUM RUBRUM; RHODOVULUM;

EID: 4344560389     PISSN: 13500872     EISSN: None     Source Type: Journal    
DOI: 10.1099/mic.0.26940-0     Document Type: Article

References (39)

1. Adachi, J. & Hasegawa, M. (1996). MOLPHY: Programs for Molecular Phylogeny, Version 2.3. Tokyo: Institute of Statistical Mathematics.
2. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25, 3389-3402.
3. Ausubel, F. M., Brent, R., Kingston, R. E., Moore, D. D., Seidman, J. G., Smith, J. A. & Struhl, K. (1995). Current Protocols in Molecular Biology, vol. I. New York Wiley.
4. Cantera, J. J. L., Kawasaki, H. & Seki, T. (2002). Evolutionary relationship of phototrophic bacteria in the α-Proteobacteria based on farnesyl diphosphate synthase. Microbiology 148, 1923-1929.
5. 2-fixing Rhizobium: characteristics. In Nitrogen Fixation: Achievements and Objectives, pp. 805-811. Edited by P. M. Gresshoff, L. E. Roth, G. Stacey & W. L. Newton. London: Chapman & Hall.
6. Eardly, B. D., Young, J. P. W. & Selander, R. K. (1992). Phylogenetic position of Rhizobium sp. strain Or 191, a symbiont of both Medicago sativa and Phaseolus vulgaris, based on partial sequences of the 16S rRNA and nifH genes. Appl Environ Microbiol 58, 1809-1815.
7. Fleischman, D. E., Evans, W. R. & Miller, I. M. (1995). Bacteriochlorophyll-containing Rhizobium species. Adv Photosynth 2, 123-126.
8. Haukka, K., Lindström, K. & Young, J. P. W. (1998). Three phylogenetic groups of nodA and nifH genes in Sinorhizobium and Mesorhizobium isolates from leguminous trees growing in Africa and Latin America. Appl Environ Microbiol 64, 419-426.
9. Hennecke, H., Kaluza, K., Thöny, B., Fuhrmann, M., Ludwig, W. & Stackebrandt, E. (1985). Concurrent evolution of nitrogenase genes and 16S rRNA in Rhizobium species and other nitrogen-fixing bacteria. Arch Microbiol 142, 342-348.
10. Hirsch, A. M., McKhann, H. I., Reddy, A., Liao, J., Fang, Y. & Marshall, C. R. (1995). Assessing horizontal transfer of nifHDK genes in eubacteria: nucleotide sequence of nifK from Frankia strain HFPCc13. Mol Biol Evol 12, 16-27.
11. Hurek, T., Egener, T. & Reinhold-Hurek, B. (1997). Divergence in nitrogenases of Azoarcus spp., Proteobacteria of the β subclass. J Bacteriol 179, 4172-4178.
12. Igarashi, N., Harada, J., Nagashima, S., Matsuura, K., Shimada, K. & Nagashima, K. V. P. (2001). Horizontal transfer of the photosynthesis gene cluster and operon rearrangement in purple bacteria. J Mol Evol 52, 333-341.
13. Imhoff, J. F., Trüper, H. G. & Pfennig, N. (1984). Rearrangement of the species and genera of the phototrophic "purple nonsulfur bacteria". Int J Syst Bacteriol 34, 340-343.
14. Inui, M., Roh, J. H., Zahn, K. & Yukawa, H. (2001). Sequence analysis of the cryptic plasmid pMG101 from Rhodopseudomonas palustris and construction of stable cloning vectors. Appl Environ Microbiol 66, 54-63.
15. Jeanmougin, F., Thompson, J. D., Gouy, M., Higgins, D. G. & Gibson, T. J. (1998). Multiple sequence alignment with Clustal X. Trends Biochem Sci 23, 403-405.
16. Kawasaki, H., Hoshino, Y. & Yamasato, K. (1993). Phylogenetic diversity of phototrophic purple non-sulfur bacteria in the Proteobacteria α group. FEMS Microbiol Lett 112, 61-66.
17. Ladha, J. K. & So, R. B. (1994). Numerical taxonomy of photosynthetic rhizobia nodulating Aeschynomene species. Int J Syst Bacteriol 44, 62-73.
18. Lisdiyanti, P., Kawasaki, H., Seki, T., Yamada, Y., Uchimura, T. & Komagata, K. (2000). Systematic study of the genus Acetobacter with descriptions of Acetobacter indonesiensis sp. nov., Acetobacter tropicalis sp. nov., Acetobacter orleanensis (Hannenberg 1906) comb. nov., Acetobacter lovaniensis (Frateur 1950) comb. nov., and Acetobacter estunensis (Carr 1958) comb. nov. J Gen Appl Microbiol 46, 147-165.
19. Meyer, J., Kelley, B. C. & Vignais, P. M. (1978). Effect of light nitrogenase function and synthesis in Rhodopseudomonas capsulata. J Bacteriol 136, 201-208.
20. Nagashima, K. V. P., Hiraishi, A., Shimada, K. & Matsuura, K. (1997). Horizontal transfer of genes coding for the photosynthetic reaction centers of purple bacteria. J Mol Evol 45, 131-136.
21. Normand, P. & Bousquet, J. (1989). Phylogeny of nitrogenase sequences in Frankia and other nitrogen-fixing microorganisms. J Mol Evol 29, 436-444.
22. Ohkuma, M., Noda, S., Usami, R., Horikoshi, K. & Kudo, T. (1996). Diversity of nitrogen fixation genes in the symbiotic intestinal microflora of the termite Reticulitermes speratus. Appl Environ Microbiol 62, 2747-2752.
23. Ohkuma, M., Noda, S. & Kudo, T. (1999). Phylogenetic diversity of nitrogen fixation genes in the symbiotic microbial community in the gut of diverse termites. Appl Environ Microbiol 65, 4926-4934.
24. Page, R. D. M. (1996). TREEVIEW: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12, 357-358.
25. Perrière, G. & Gouy, M. (1996). WWW-Query: an on-line retrieval system for biological sequence banks. Biochimie 78, 364-369.
26. Ruvkum, G. B. & Ausubel, F. M. (1980). Interspecies homology of nitrogenase genes. Proc Natl Acad Sci U S A 77, 191-195.
27. Saitoh, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
28. Sanger, F., Nicklen, S. & Coulson, A. R. (1977). DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74, 5463-5467.
29. Stackebrandt, E., Rainey, F. A. & Ward-Rainey, N. (1996). Anoxygenic phototrophy across the phylogenetic spectrum: current understanding and future perspectives. Arch Microbiol 166, 211-223.
30. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. (1997). The ClustalX Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24, 4876-4882.
31. Torok, I. & Kondorosi, A. (1981). Nucleotide sequence of the R. meliloti nitrogenase reductase (nifH) gene. Nucleic Acids Res 9, 5711-5723.
32. 2-fixing bacterial diversity detected in rice roots by molecular evolutionary analysis of nifH gene sequences. J Bacteriol 177, 1414-1417.
33. Widmer, R., Shaffer, B. T., Porteous, L. A. & Seidler, J. (1999). Analysis of nifH gene pool complexity in soil and litter at a Douglas fir forest site in the Oregon cascade mountain range. Appl Environ Microbiol 65, 374-380.
34. Woese, C. R. (1987). Bacterial evolution. Microbiol Rev 51, 221-271.
35. Woese, C. R., Stackebrandt, E., Weisburg, W. G. & 8 other authors (1984). Phylogeny of purple bacteria: the alpha subdivision. Syst Appl Microbiol 5, 315-326.
36. Wong, F. Y. K., Stackebrandt, E., Ladha, J. K., Fleischman, D. E., Date, R. A. & Fuerst, J. A. (1994). Phylogenetic analysis of Bradyrhizobium japonicum and photosynthetic stem-nodulating bacteria from Aeschynomene species grown in separated geographical regions. Appl Environ Microbiol 60, 940-946.
37. Xiong, J., Inoue, K. & Bauer, C. E. (1998). Tracking molecular evolution of photosynthesis by characterization of a major photosynthesis gene cluster from Heliobacillus mobilis. Proc Natl Acad Sci U S A 95, 14851-14856.
38. 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.
39. Young, J. P., Downer, H. L. & Eardly, B. D. (1991). Phylogeny of phototrophic Rhizobium strain BTAi1 by polymerase chain reaction-based sequencing of a 16S rRNA segment. J Bacteriol 173, 2271-2277.