Aerobic vanillate degradation and C1 compound metabolism in Bradyrhizobium japonicum

Applied and Environmental Microbiology

Volumn 75, Issue 15, 2009, Pages 5012-5017

  Sudtachat, Nirinya ^a   Ito, Naofumi ^a   Itakura, Manabu ^a   Masuda, Sachiko ^a   Eda, Shima ^a   Mitsui, Hisayuki ^a   Kawaharada, Yasuyuki ^a   Minamisawa, Kiwamu ^a  

^a TOHOKU UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BRADYRHIZOBIUM JAPONICUM; ENERGY SOURCE; GLUTATHIONE; LIGNIN MONOMER; LOW CONCENTRATIONS; METABOLIC CAPABILITIES; METHANOL OXIDATION; MULTIPLE GENES; NODULATION; PATHWAY GENES; PROTOCATECHUATE; SOIL BACTERIUM; TRANSCRIPTOME ANALYSIS; VANILLATE; WILD TYPES; WILD-TYPE STRAIN;

BIOCHEMISTRY; CELL MEMBRANES; DEGRADATION; GENES; GROWTH KINETICS; METABOLISM; METHANOL; NITROGEN FIXATION;

CELL GROWTH;

AMPICILLIN; GLUTATHIONE; KANAMYCIN; METHANOL; NITROGEN; OXYGENASE; POLYMYXIN B; PROTOCATECHUIC ACID; SPECTINOMYCIN; STREPTOMYCIN; TETRACYCLINE; VANILLIC ACID;

ALCOHOL; BIODEGRADATION; GENE EXPRESSION; GENETIC ANALYSIS; LIGNIN; METABOLISM; METHANOL; MUTATION; NODULATION; OXIC CONDITIONS; RHIZOBACTERIUM; SOIL MICROORGANISM;

AEROBIC METABOLISM; ANTIBIOTIC RESISTANCE; ARTICLE; BACTERIAL CELL; BACTERIAL GENE; BACTERIAL METABOLISM; BACTERIAL STRAIN; BRADYRHIZOBIUM JAPONICUM; CELL GROWTH; CONTROLLED STUDY; CULTURE MEDIUM; GENE EXPRESSION; GENE FUNCTION; GENE MUTATION; METHYLOTROPHIC BACTERIUM; MICROBIAL DEGRADATION; MODULATION; MUTANT; NONHUMAN; OXIDATION; PHENOTYPE; RHIZOBIACEAE; SOYBEAN; UPREGULATION; WILD TYPE;

BACTERIAL PROTEINS; BRADYRHIZOBIUM; CARBON; CULTURE MEDIA; GENE DELETION; GENE EXPRESSION PROFILING; HYDROXYBENZOIC ACIDS; METABOLIC NETWORKS AND PATHWAYS; METHANOL; MODELS, BIOLOGICAL; NITROGEN FIXATION; OXIDATION-REDUCTION; PLANT ROOT NODULATION; SOYBEANS; VANILLIC ACID;

BACTERIA (MICROORGANISMS); BRADYRHIZOBIUM JAPONICUM; GLYCINE MAX;

EID: 67651247621     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.00755-09     Document Type: Article

References (36)

1. 1-transfer modules: from genomics to ecology. ASM News 71:521-528.
2. Cole, M. A., and G. H. Elkan. 1973. Transmissible resistance to penicillin G, neomycin, and chloramphenicol in Rhizobium japonicum. Antimicrob. Agents Chemother. 4:248-253.
3. Dao, T. V., M. Nomura, R. Hamaguchi, K. Kato, M. Itakura, K. Minamisawa, S. Sinsuwongwat, H. T. Le, T. Kaneko, S. Tabata, and S. Tajima. 2008. NAD-malic enzyme affects nitrogen fixing activity of Bradyrhizobium japonicum USDA 110 bacteroids in soybean nodules. Microbes Environ. 23:215-220.
4. 1 metabolic pathways in Burkholderia xenovorans LB400. J. Bacteriol. 187:7996-8005.
5. Ferdman, M. Y. 1973. Reaction of nucleic acids and nucleoproteins with formaldehyde. Prog. Nucleic Acid Res. Mol. Biol. 13:1-49.
6. Figurski, D. H., and D. R. Helinski. 1979. Replication of an origin-containing derivative of plasmid RK2 dependent on a plasmid function provided in trans. Proc. Natl. Acad. Sci. USA 76:1648-1652.
7. Giraud, E., L. Moulin, D. Vallenet, V. Barbe, E. Cytryn, J. C. Avarre, M. Jaubert, D. Simon, F. Cartieaux, Y. Prin, G. Bena, L. Hannibal, J. Fardoux, M. Kojadinovic, L. Vuillet, A. Lajus, S. Cruveiller, Z. Rouy, S. Mangenot, B. Segurens, C. Dossat, W. L. Franck, W. S. Chang, E. Saunders, D. Bruce, P. Richardson, P. Normand, B. Dreyfus, D. Pignol, G. Stacey, D. Emerich, A. Verméglio, C. Médigue, and M. Sadowsky. 2007. Legumes symbioses: absence of Nod genes in photosynthetic bradyrhizobia. Science 316:1307-1312.
8. Harwood, C. S., and R. E. Parales. 1996. The β-ketoadipate pathway and the biology of self-identity. Annu. Rev. Microbiol. 50:553-590.
9. 54 regulon, and identification of a ferredoxin gene (fdxN) for symbiotic nitrogen fixation. Mol. Genet. Genomics 278:255-271.
10. Hibi, M., T. Sonoki, and H. Mori. 2005. Functional coupling between vanillate-O-demethylase and formaldehyde detoxification pathway. FEMS Microbiol. Lett. 253:237-242.
11. Itakura, M., K. Saeki, H. Omori, T. Yokoyama, T. Kaneko, S. Tabata, T. Ohwada, S. Tajima, T. Uchiumi, K. Honnma, K. Fujita, H. Iwata, Y. Saeki, Y. Hara, S. Ikeda, S. Eda, H. Mitsui, and K. Minamisawa. 2009. Genomic comparison of Bradyrhizobium japonicum strains with different symbiotic nitrogen-fixing capabilities and other Bradyrhizobiaceae members. ISME J. 3:326-339.
12. Ito, N., M. Itakura, S. Eda, K. Saeki, H. Oomori, T. Yokoyama, T. Kaneko, S. Tabata, T. Ohwada, S. Tajima, T. Uchiumi, E. Masai, M. Tsuda, H. Mitsui, and K. Minamisawa. 2006. Global gene expression in Bradyrhizobium japonicum cultured with vanillin, vanillate, 4-hydroxybenzoate and protocatechuate. Microbes Environ. 21:240-250.
13. Jourand, P., A. Renier, S. Rapior, S. M. de Faria, Y. Prin, A. Galiana, E. Giraud, and B. Dreyfus. 2005. Role of methylotrophy during symbiosis between Methylobacterium nodulans and Crotalaria pedocarpa. Mol. Plant-Microbe Interact. 18:1061-1068.
14. Kaneko, T., Y. Nakamura, S. Sato, K. Minamisawa, T. Uchiumi, S. Sasamoto, A. Watanabe, K. Idesawa, M. Iriguchi, K. Kawashima, M. Kohara, M. Matsumoto, S. Shimpo, H. Tsuruoka, T. Wada, M. Yamada, and S. Tabata. 2002. Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110. DNA Res. 9:225-256.
15. Levipan, H. A., R. A. Quiñones, H. E. Johansson, and H. Urrutia. 2007. Methylotrophic methanogens in the water column of an upwelling zone with a strong oxygen gradient off central Chile. Microbes Environ. 22:268-278.
16. Martinez, A. T., M. Speranza, F. J., Ruiz-Duenas, P. Ferreria, S. Camarero, F. Guillen, M. J. Martinez, A. Gutierrez, and J. C. del Rio. 2005. Biodegradation of lignocellulosics: microbial, chemical, and enzymatic aspects of the fungal attack of lignin. Int. Microbiol. 8:195-204.
17. McDonald, I. R., and J. C. Murrell. 1997. The methanol dehydrogenase structural gene mxaF and its use as a functional gene probe for methanotrophs and methylotrophs. Appl. Environ. Microbiol. 63:3218-3224.
18. Mitsui, R., Y. Kusano, H. Yurimoto, Y. Sakai, N. Kato, and M. Tanaka. 2003. Formaldehyde fixation contributes to detoxification for growth of a nonmethylotroph, Burkholderia cepacia TM1, on vanillic acid. Appl. Environ. Microbiol. 69:6128-6132.
19. Morawski, B., A. Segura, and L. N. Ornston. 2000. Substrate range and genetic analysis of Acinetobacter vanillate demethylase. J. Bacteriol. 182: 1383-1389.
20. Mou, X., S. Sun, R. A. Edwards, R. E. Hodson, and M. A. Moran. 2008. Bacterial carbon processing by generalist species in the coastal ocean. Nature 451:708-711.
21. Nardi, S., D. Pizzeghello, L. Bragazza, and R. Gerdol. 2003. Low-molecular-weight organic acids and hormone-like activity of dissolved organic matter in two forest soils in N Italy. J. Chem. Ecol. 29:1549-1563.
22. Nemecek-Marshall, M., R. C. MacDonald, J. J. Franzen, C. L. Wojciechowski, and R. Fall. 1995. Methanol emission from leaves. Plant Physiol. 108:1359-1368.
23. Okazaki, S., M. Sugawara, K. Yuhashi, and K. Minamisawa. 2007. Rhizobitoxine-induced chlorosis occurs in coincidence with methionine deficiency in soybeans. Ann. Bot. 100:55-59.
24. Parke, D., and L. N. Ornston. 1984. Nutritional diversity of Rhizobiaceae revealed by auxanography. J. Gen. Microbiol. 130:1743-1750.
25. Prentki, P., and H. M. Krisch. 1984. In vitro insertional mutagenesis with a selectable DNA fragment. Gene 29:303-313.
26. Sadowsky, M. J., and B. B. Bohool. 1986. Growth of fast- and slow-growing rhizobia on ethanol. Appl. Environ. Microbiol. 52:951-953.
27. Saito, A., S. Ikeda, H. Ezura, and K. Minamisawa. 2007. Microbial community analysis of the phytosphere using culture-independent methodologies. Microbes Environ. 22:93-105.
28. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
29. 2O surrounding the soybean root system via nitrous oxide reductase. Appl. Environ. Microbiol. 72:2526-2532.
30. Sameshima-Saito, R., K. Chiba, and K. Minamisawa. 2006. Correlation of denitrifying capability with the existence of nap, nir, nor and nos genes in diverse strains of soybean bradyrhizobia. Microbes Environ. 21:174-184.
31. Schäfer, A., A. Tauch, W. Jäger, J. Kalinowski, G. Thierbach, and A. Pühler. 1994. Small mobilizable multi-purpose cloning vectors derived from the Escherichia coli plasmids pK18 and pK19: selection of defined deletions in the chromosome of Corynebacterium glutamicum. Gene 145:69-73.
32. Segura, A., P. V. Bünz, D. A. D'Argenio, and L. N. Ornston. 1999. Genetic analysis of a chromosomal region containing vanA and vanB, genes required for conversion of either ferulate or vanillate to protocatechuate in Acinetobacter. J. Bacteriol. 181:3494-3504.
33. Sy, A., A. C. J. Timmers, C. Knief, and J. A. Vorholt. 2005. Methylotropic metabolism is advantageous for Methylobacterium extorquens during colonization of Medicago truncatula under competitive conditions. Appl. Environ. Microbiol. 71:7245-7252.
34. Uchiumi, T., T. Ohwada, M. Itakura, H. Mitsui, N. Nukui, P. Dawadi, T. Kaneko, S. Tabata, Y. Yokoyama, K. Tejima, K. Saeki, H. Omori, M. Hayashi, T. Maekawa, R. Sriprang, Y. Murooka, S. Tajima, K. Simomura, M. Nomura, A. Suzuki, Y. Shimoda, K. Sioya, M. Abe, and K. Minamisawa. 2004. Expression islands clustered on the symbiosis island of the Mesorhizobium loti genome. J. Bacteriol. 186:2439-2448.
35. Vorholt, J. A. 2002. Cofactor-dependent pathway of formaldehyde oxidation in methylotrophic bacteria. Arch. Microbiol. 178:239-249.
36. Zhang, M., and M. E. Lidstrom. 2003. Promoters and transcripts for genes involved in methanol oxidation in Methylobacterium extorquens AM1. Microbiology 149:1033-1040.