Global Gene Expression in Bradyrhizobium japonicum Cultured with Vanillin, Vanillate, 4-Hydroxybenzoate and Protocatechuate

Microbes and Environments

Volumn 21, Issue 4, 2006, Pages 240-250

  Ito, Naofumi ^a   Itakura, Manabu ^a   Eda, Shima ^a   Saeki, Kazuhiko ^b   Oomori, Hirofumi ^c   Yokoyama, Tadashi ^d   Kaneko, Takakazu ^e   Tabata, Satoshi ^e   Ohwada, Takuji ^f   Tajima, Shigeyuki ^g   Uchiumi, Toshiki ^h   Masai, Eiji ⁱ   Tsuda, Masataka ^a   Mitsui, Hisayuki ^a   Minamisawa, Kiwamu ^a  

^a TOHOKU UNIVERSITY   (Japan)

^b NARA WOMEN'S UNIVERSITY   (Japan)

^c OSAKA UNIVERSITY   (Japan)

^d TOKYO UNIVERSITY OF AGRICULTURE AND TECHNOLOGY   (Japan)

^e KAZUSA DNA RESEARCH INSTITUTE   (Japan)

^f OBIHIRO UNIVERSITY OF AGRICULTURE AND VETERINARY MEDICINE   (Japan)

^g KAGAWA UNIVERSITY   (Japan)

^h KAGOSHIMA UNIVERSITY   (Japan)

ⁱ NAGAOKA UNIVERSITY OF TECHNOLOGY   (Japan)

Author keywords

aromatic degradation; Bradyrhizobium japonicum; C1 metabolism; transcriptome

Indexed keywords

EID: 60749122881     PISSN: 13426311     EISSN: 13474405     Source Type: Journal    
DOI: 10.1264/jsme2.21.240     Document Type: Article

References (35)

1. Altschul, S.F., T.L. Madden, A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller and D.J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search program. Nucleic Acids Res. 25: 3389–3402.
2. Cohen-Bazire, G., W.R. Sistrom and R.Y. Stanier. 1957. Kinetic studies of pigment synthesis by non-sulfur purple bacteria. J. Cell Comp. Physiol. 49: 25–68.
3. Conway, T. and G.K. Schoolnik. 2003. Microarray expression profiling: capturing a genome-wide portrait of the transcriptome. Mol. Microbiol. 47: 879–889.
4. Crist, D.K., R.E. Wyza, K.K. Millis, W.D. Bauer and W.R. Evans. 1984. Preservation of Rhizobium viability and symbiotic infectivity by suspension in water. Appl. Environ. Microbiol. 47: 895–900.
5. Denef, V.D., J. Park, T.V. Tsoi, J.M. Rouillard, H. Zhang, J.A. Wibbenmeyer, W. Verstraete, E. Glulari, S.A. Hashsham and J.M. Tiedje. 2004. Biphenyl and benzoate metabolism in a genomic context: Outlining genome-wide metabolic networks in Burkholderia xenovorans LB400. Appl. Environ. Microbiol. 70: 4961–4970.
6. Denef, V.D., M.A. Patrauchan, C. Florizone, J. Park, T.V. Tsoi, W. Verstraete, J.M. Tiedje and L.D. Eltis. 2005. Growth substrate- and phase-specific expression of biphenyl, benzoate, and C1 metabolic pathways in Burkholderia xenovorans LB400. J. Bacteriol. 187: 7996–8005.
7. Gottfert, M., H. Hennecke and S. Tabata. 2005. Facets of the Bradyrhizobium japonicum 110 genome. pp. 99–111. In R. Palacios and W.E. Newton (ed.), Genomes and genomics of nitrogen-fixing organisms. Springer, Dordrecht, The Netherlands.
8. Gupta, K.G., J.C. Aggarwal and N.S. Makkar. 1973. Sensitivity of rhizobia to vanillin. Folia Microbiol. 19: 317–321.
9. Harms, N., W.N.M. Reijnders, S. Koning and R.J.M. van Spanning. 2001. Two component system that regulates methanol and formaldehyde oxidation in Paracoccus denitrificans. J. Bacteriol. 183: 664–670.
10. Harwood, C.S. and R.E. Parales. 1996. The β-ketoadipate pathway and the biology of self-identity. Annu. Rev. Microbiol. 50: 553–590.
11. Iwaki, H., H. Saji, K. Abe and Y. Hasegawa. 2005. Cloning and sequence analysis of the 4-hydroxybenzoate 3-hydroxylase gene from a cyclohexanecarboxylate-degrading Gram-positive bacterium, “Corynebacterium cyclohexanicum” strain ATCC 51369. Microbes Environ. 20: 144–150.
12. Kaneko, T., Y. Nakamura, S. Sato, K. Minamisawa, T. Uchiumi, S. Sasamoto, A. Watanabe, K. Idesawa, M. Iriguchi, K. Kawa-shima, 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: 189–197.
13. Kimbara, K. 2005. Recent developments in the study of microbial aerobic degradation of polychlorinated biphenyls. Microbes Environ. 20: 127–134.
14. Lorite, M.J., J. Sanjuan, L. Velasco, J. Olivares and E.J. Bedmar. 1998. Characterization of Bradyrhizobium japonicum pcaBDC genes involved in 4-hydroxybenzoate degradation. Biochim. Biophys. Acta 1397: 257–261.
15. MacLean, A.M., G. MacPherson, P. Aneji and T.M. Finan. 2006. Characterization of the β-ketoadipate pathway in Sinorhizobium meliloti. Appl. Environ. Microbiol. 72: 5403–5413.
16. Minamisawa, K. and H. Mitsui. 2000. Genetic ecology of soybean bradyrhizobia. pp. 349–377. In J. Bollag and G. Stotzky (ed.), Soil Biochemistry Vol. 10. Marcel Dekker Inc., New York, N.Y.
17. 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.
18. Morimoto, S., K. Togami, N. Ogawa, A. Hasebe and T. Fujii. 2005. Analysis of a bacterial community in 3-chlorobenzoate-contaminated soil by PCR-DGGE targeting the 16S rRNA gene and benzoate 1,2-dioxygenase gene (benA). Microbes Environ. 20: 151–159.
19. 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.
20. Nukui, N., K. Minamisawa, S. Ayabe and T. Aoki. 2006. Expression of 1-aminocyclopropane-1-carboxylic acid deaminase gene requires symbiotic nitrogen-fixing regulator gene nifA2 in Mesorhizobium loti MAFF303099. Appl. Environ. Microbiol. 72: 4964–4969.
21. Okazaki, S., N. Nukui, M. Sugawara and K. Minamisawa. 2004. Rhizobial strategies to enhance symbiotic interaction: rhizobitox-ine and 1-aminocyclopropane-1-carboxylate deaminase. Microbes Environ. 19: 99–111.
22. Parke, D. 1997. Acquisition, recognition, and merger of genes: novel management of the β-ketoadipate pathway in Agrobacterium tumefaciens. FEMS Microbiol. Lett. 146: 3–12.
23. Parke, D. and L.N. Ornston. 1984. Nutritional diversity of Rhizo-biaceae revealed by auxanography. J. Gen. Microbiol. 130: 1743–1750.
24. Parke, D. and L.N. Ornston. 1986. Enzymes of the β-ketoadipate pathway are inducible in Rhizobium and Agrobacterium spp. and constitutive in Bradyrhizobium spp., J. Bacteriol. 165: 288–292.
25. Parke, D. and L.N. Ornston. 2003. Hydroxycinnamate (hca) catabolic genes from Acinetobacter sp. Strain ADP1 are repressed by HcaR and are induced by hydroxycinnamol-coenzyme A thioesters. Appl. Environ. Microbiol. 69: 5398–5409.
26. Priefert, H., J. Rabenhorst and A. Steinbuchel. 1997. Molecular characterization of genes of Pseudomonas sp. Strain HR199 involved in bioconversion of vanillin to protocatechuate. J. Bacteriol. 179: 2595–2607.
27. Rudolph, G., H. Hennecke and H. Fisher. 2006. Beyond the Fur paradigm: iron-controlled gene expression in rhizobia. FEMS Microbiol. Rev. 30: 613–648.
28. Saito, A. and K. Minamisawa. 2006. Evaluation of nitrogen fixation capability of endophytic clostridia by acetylene reduction and reverse transcription-PCR targeted to nifH transcript and ribosomal RNA. Microbes Environ. 21: 23–35.
29. Sameshima-Sato, R., K. Chiba, J. Hirayama, M. Itakura, H. Mitsui, S. Eda and K. Minamisawa. 2006. Symbiotic Bradyrhizobium japonicum reduces N2O surrounding the soybean root system via nitrous oxide reductase. Appl. Environ. Microbiol. 72: 2526–2532.
30. Sameshima, 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. Shen, X., Y. Huang and S. Liu. 2005. Genomic analysis and identification of catabolic pathways for aromatic compounds in Corynebacterium glutamicum. Microbes Environ. 20: 160–167.
32. Uchiumi, T., T. Ohwada, M. Itakura, H. Mitsui, N. Nukui, P. Dawadi, T. Kaneko, S. Tabata, T. 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.
33. Vorhold, J.A. 2002. Cofactor-dependent pathways of formaldehyde oxidation in methylotrophic bacteria. Arch Microbiol. 178: 239–249.
34. You, M., T. Nishiguchi, A. Saito, T. Isawa, H. Mitsui and K. Minamisawa. 2005. Expression of the nifH gene of a Herbaspirillum endophyte in wild rice species: daily rhythm during the light-dark cycle. Appl. Environ. Microbiol. 71: 8183–8190.
35. Zhou, J., D.K. Thompson, Y. Xu and J.M. Tiedje. 2004. Microbial functional genomics. A John Wiley & Sons, Inc., Hoboken, New Jersey.