April 1, 2015


Takeshi FUJII


Environmental Biofunction Division

Current research topics

  1. Study of regulation mechanisms for gene expression of chitinase genes in Streptomyces
  2. Study of gene expression of bacteria in soil environment
  3. Metatranscriptome analysis of soil bacteria


Tel: +81-29-838-8262
E-mail: ftakeshi@affrc.go.jp

Research results

(Articles available in English)

  1. Suzuki, K., Noguchi, M. T., Shinozaki, Y., Koitabashi, M., Yamashita, Y. S., Yoshida, S., Fujii, T., Kitamoto, H. K. (2014) Purification, characterization, and cloning of the gene for a biodegradable plastic-degrading enzyme from Paraphoma-related fungal strain B47-9. Appl. Microbiol. Biotechnol., 98, (10): 4457-4465
  2. Sakai, Y., Ogawa, N., Shimomura, Y. and Fujii, T. (2014) A 2,4-dichlorophenoxyacetic acid degradation plasmid pM7012 discloses distribution of an unclassified megaplasmid group across bacterial species, Microbiology-SGM, 160:525-536
  3. Watanabe, T., Shinozaki, Y., Yoshida, S., Koitabashi, M., Yamashita, S. Y., T. Fujii, Fukuoka, T. and Kitamoto, H. K. (2014) Xylose induces the phyllosphere yeast Pseudozyma antarctica to produce a cutinase-like enzyme which efficiently degrades biodegradable plastics, J. Biosci. Bioeng., 117(3), 325-329
  4. Suzuki, K., Sakamoto, H., Shinozaki, Y., Tabata, J., Watanabe, T., Mochizuki, A., Koitabashi, M., Fujii, T. , Tsushima, S., and Kitamoto K. H. (2013) Affinity purification and characterization of a biodegradable plastic-degrading enzyme from a yeast isolated from the larval midgut of a stag beetle, Aegus laevicollis, Appl. Microbiol. Biotechnol. 97(17): 7679-7688
  5. Shinozaki, Y., Morita, T., Cao, X. H., Yoshida, S., Koitabashi, M., Watanabe, T., Suzuki, K., Yamashita, S. Y., Kambe N. T., Fujii, T., and Kitamoto, K. H. (2013) Biodegradable plastic-degrading enzyme from Pseudozyma antarctica: Cloning, sequencing, and characterization. Appl. Microbiol. Biotechnol. 97:2951-2959
  6. Saito, A., Ebise, H., Orihara, Y., Murakami, S., Sano, Y., Sugiyama, Y., Ando, A., Fujii, T. , and Miyashita, K. (2013) Enzymatic and genetic characterization of the DasD protein possessing N-acetyl--D-glucosaminidase activity in Streptomyces coelicolor A3(2), FEMS Microbiol. Lett. 340: 33-40
  7. Nazari, B., Kobayashi, M., Saito, A., Hassaninasab, A., Miyashita, K., and Fujii, T. (2013) Chitin-induced gene expression involved in secondary metabolic pathways in Streptomyces coelicolor A3(2) grown in soil. Appl. Environ. Microbiol. 79(2): 707-713
  8. Wang, Y., Nagaoka, K., Hayatsu M., Sakai Y., Tago K., Asakawa S., and Fujii, T. (2012) A novel method for RNA extraction from Andosols using casein and its application to amoA gene expression study in soil, Appl. Microbiol. Biotechnol. 96(3): 793-802
  9. Iino, T., Wang, Y., Miyauchi, K., Kasai, D., Masai, E., Fujii, T., Ogawa, N., and Fukuda M. (2012) Specific gene responses of Rhodococcus jostii RHA1 during growth in soil. Appl. Environ. Microbiol., 78(19): 6954-6962
  10. Wang, Y., Hayatsu, M. and Fujii, T. (2012) Extraction of Bacterial RNA from Soil: Challenges and Solutions. Microbes. Environ., 27: 111-121
  11. Wang, Y., Morimoto, S., Ogawa, N., and Fujii, T. (2011) A survey of the cellular responses in Pseudomonas putida KT2440 growing in sterilized soil by microarray analysis. FEMS Microbiol Ecol., 78: 220-232
  12. Yamamoto-Tamura, K., Ohno M., Fujii, T. , Kataoka, S., Numata, S., Nakajima, M., Hasebe A. and Akutsu K. (2011) Assessment of the effects of genetically modified Pseudomonas spp. expressing chitinase on the soil microbial community in the cucumber rhizosphere. JARQ-Jpn. Agr. Res. Q., 45(4):377-383.
  13. Nazari, B., Kobayashi, M., Miyashita, K., Saito, A., Wang, Y. and Fujii, T. (2011) High expression levels of chitinase genes in Streptomyces coelicolorA3(2) grown in soil. FEMS Microbiol. Ecol., 77: 623-635
  14. Wang, Y., and Fujii, T. (2011) Evaluation of Methods for Determining Humic Acids in the Nucleic Acids Samples for Molecular Biological Analysis. Biosci. Biotechnol. Biochem., 75(2): 355-357
  15. Ohno, M., Kataoka, S., Numata, S., Yamamoto-Tamura, K., Fujii, T. , Nakajima, M., Katsumi Akutsu, K. and Hasebe, A. (2011) Biological control of Rhizoctonia damping-off of cucumber by a transformed Pseudomonas putida strain expressing a chitinase from a marine bacterium. JARQ, 45(1): 91-98
  16. Chu, H., Morimoto, S., Fujii, T. , Yagi, K., and Nishimura, S. (2009) Soil ammonia-oxidizing bacterial communities in paddy rice fields as affected by upland conversion history. Soil Sci. Soc. Am. J. 73(6): 2026-2031
  17. Wang, Y., Morimoto, S., Ogawa, N., Ohmori, T., and Fujii, T. (2009) An improved method to extract RNA from soil with efficient removal of humic acids.J. Appl. Microbiol. 107:1168-1177
  18. Morimoto, S. and Fujii, T. (2009) A new approach to retrieve full lengths of functional genes from soil by PCR-DGGE and metagenome walking. Appl. Microbiol. Biotechnol. 83(2): 389-396
  19. Yoshida, S., Ogawa, N., Fujii, T. , and T., Seiya (2009) Enhanced biofilm formation and 3-chlorobenzoate degrading activity by the bacterial consortium of Burkholderia sp. NK8 and Pseudomonas aeruginosa PAO1. J. Appl. Microbiol. 106:790-800 (doi:10.1111/j.1365-2672.2008.04027.x)
  20. Morimoto, S., Ogawa, N., Hasebe, A., and Fujii, T. (2008) Isolation of Effective 3-Chlorobenzoate- Degraders in Soil using Community Analyses by PCR-DGGE. Microbes. Environ., 23(4):285-292 (doi:10.1264/jsme2.ME08526)
  21. Saito, A., Fujii, T. , Shinya, T., Shibuya, N., Ando, A., and Miyashita. K. (2008) The msiK gene, encoding the ATP-hydrolyzing component of N,Nf-diacetylchitobiose ABC transporters, is essential for induction of chitinase production inStreptomyces coelicolor A3(2) Microbiology-SGM 154:3358-3365
  22. Chu, H., Fujii, T. , Morimoto, S., Lin, X., and Yagi., K. (2008) Population size and specific nitrification potential of soil ammonia-oxidizing bacteria under long-term fertilizer management Soil Biol. Biochem., 40(7):1960-1963 (doi:10.1016/j.soilbio.2008.01.006)
  23. Wang, Y., Shimodaira, J., Miyasaka, T., Morimoto, S., Ohmori, T., Ogawa, N., Fukuda M., and Fujii, T. (2008) Detection ofbphAa gene expression of Rhodococcus sp. strain RHA1 in soil using a new method for RNA preparation from soil. Biosci. Biotechnol. Biochem., 72:694-701 (doi:10.1271/bbb.70493)
  24. Chu, H, Lin, X., Fujii, T. , Morimoto. S., Yagi, K., Hu, J., Zhang, J. (2007) Soil microbial biomass, dehydrogenase activity, bacterial community structure in response to long-term fertilizer management. Soil Biol. Biochem., 39:2971-2976 (doi: 10.1016/j.soilbio.2007.05.031)
  25. Chu, H., Lin, X., Zhang, J., Lin, X., Rui, Y., Xie, Z., Cao, Z., and Fujii, T. (2007) Short-term decomposition of 14C-labelled glucose in a fluvo-aquic soil as affected by lanthanum amendment. Biol. Fertil. Soils, 43:811-814 (doi:)
  26. Sakai, Y., Ogawa, N., Fujii, T. , Sugahara, K., Miyashita, K., and Hasebe, A. (2007) 2,4-Dichrolophenoxyacetic acid-degrading genes from bacteria isolated from soil in Japan: Spread of Burkholderia cepacia RASK-type degrading genes harbored on Large Plasmids. Microbes. Environ., 22:145-156
  27. Saito, A., Shinya, T., Miyamoto, K., Yokoyama T., Kaku H., Minami, E., Shibuya, N., Tsujibo, H., Nagata, Y., Ando, A., Fujii, T. , and Miyashita. K., (2007) The dasABC gene cluster adjacent 1 to dasR encodes a novel ABC transporter for the uptake of N,N' -diacetylchitobiose in Streptomyces coelicolor A3(2). Appl. Environ. Microbiol., 73:3000-3008
  28. Chu, H., Fujii, T. , Morimoto S., Lin, X., Yagi, K., Hu, J., and Zhang, J. (2007) Community structure of ammonia-oxidizing bacteria under long-term application of mineral fertilizer and organic manure in a sandy loam soil. Appl. Environ. Microbiol., 73:485-491 (doi: 10.1128/AEM. 01536-06)
  29. Kawase, T., Yokokawa, S., Saito, A., Fujii, T. , Nikaidou, N., Miyashita, K. and Watanabe, T. (2006) Comparison of the enzymatic and antifunbal properties between family18 and 19 chitinase from S. coelicolor A3(2) Biosci. Biotechnol. Biochem., 70:988-998
  30. Saito, A., Kaku, H., Minami, E., Fujii, T. , Ando, A., Nagata, Y., Schrempf, H. and Miyashitra, K. (2006) An enzyme-linked immunosorbent assay (ELISA) to determine the specificity of the sugar-binding protein NgcE, a component of the ABC transporter for N-acetylglucosamine in Streptomyces olivaceoviridis. Biosci. Biotechnol. Biochem., 70:237-242
  31. Morimoto. S., Togami, K., Ogawa, N., Hasebe, A. and Fujii, T. (2005) Analysis of a Bacterial Community in 3-Chlorobenzoate-Contaminated Soil by PCR-DGGE Targeting 16S rDNA and the Benzoate 1,2-Dioxygenase Gene (benA).Microbes. Environ., 20:151-159
  32. Fujii, T. , Miyashita, K., Ohtomo, R. and Saito, A. (2005) DNA-Binding Protein Involved in the Regulation of Chitinase Production in Streptomyces lividans. Biosci. Biotechnol. Biochem., 69:790-799
  33. Lang, G, Ogawa, N., Tanaka, Y, Fujii, T. , Fulthope, R. R., Fukuda, M., and Miyashita, K. (2005) Two kinds of chlorochatechol 1,2-dioxygenase from 2,4-dichlorophenoxyacetate- degrading Sphingomonas sp. strain TFD44. Biochem. Biophysi. Res. Comm., 332:941-948
  34. Oomori, T., Morimoto, S., Watanabe, T., Fujii, T. , and Hasebe, A. (2005) Bioaugumentation efficiency in two different6 3-chlorobenzoate-contaminated soils (in Japaness). Soil Microorganisms, 59:21-25
  35. Kawase,T., Saito, A., Sato, T., Kanai, R., Fujii, T. , Nikaidou, N., Miyashita, K. and Watanabe, T. (2004) Distribution and phylogenetic analysis of family 19 chitinases in Actinobacteria. Appl. Environ. Microbiol., 70:1135-1144
  36. Saito, A., Fujii, T. and Miyashita, K. (2003) Distribution and evolution of chitinase genes in Streptomyces spieces: involvement of gene-duplication and domain-deletion. Antonie van Leeuwenhoek, 84:7-16
  37. Kong, H., Shimosaka, M., Ando, Y., Nishiyama, K., Fujii, T. and Miyashita, K. (2001) Species-specific distribution of a modular family 19 chitinase gene in Burkholderia gladioli. FEMS. Microb. Ecol., 37:135-141
  38. Saito, A., Ishizaka, M., Fujii, T. , Francisco, P.B.Jr. and Miyashita, K. (2000) Transcriptional co-regulation of five chitinase genes scattered on the Streptomyces coelicolor A3(2)chromosome. Microbiology, 146:2937-2946
  39. Miyashita, K., Fujii, T. and Saito A. (2000)Induction and repression of a Streptomyces lividans chitinase gene promoter in response to various carbon sources. Biosci. Biotechnol. Biochem. 64:39-43
  40. Saito, A., Fujii, T. , Yoneyama, T., Redenbach, M., Ohno, T., Watanabe, T. and Miyashita, K.(1999)High-multiplicity of chitinase genes in Streptomyces coeliclor A3(2). Biosci. Biotechnol. Biochem., 63:710-718
  41. Saito A., Fujii, T. and Miyashita,K. (1999) Chitinase system in Streptomyces. Actinomycetologica, 13:1-10
  42. Saito, A., Fujii, T. , Yoneyama, T. and Miyashita, K. (1998) glkA is involved in glucose repression of chitinase production inStreptomyces lividans. J. Bacteriol., 180:911-2914
  43. Miyashita, K., Fujii, T. . Watanabe, A and Ueno H. (1997) Nucleotide sequence and expression of a gene (chiB) for a chitinase from Streptomyces lividans. J. Ferment. Bioeng., 83:26-31
  44. Fujii, T. , Ogawa, N. and Miyashita, K. (1997) Biological contained Pseudomonas putida that degrade chlorobenzoate. In: The biosafety results of field test of genetically modified plants and microorganisms, JIRCAS Report., 311-313
  45. Fujii, T. , Gramajo, H., Takano, E. and Bibb. M. J. (1996) redD and actII-ORF4, pathway-specific regulatory genes for antibiotic production in Streptomyces coerlicolor A3(2), are transcribed in vitro by an RNA polymerase holoenzyme containing shrdD. J. Bacteriol., 178:3402-3405
  46. FFujii, T. and Miyashita, K. (1993) Multiple domain structure in a chitinase gene (chiC) of Streptomyces lividans. J. Gen. Microbiol., 139:677-686
  47. Miyashita, K. and Fujii, T. (1993) Nucleotide sequence and analysis of a gene (chiA) for a chitinase from Strptomyces lividans 66. Biosci.Biotechnol. Biochem., 57:1691-1698
  48. Watanabe, T., Kobori, K., Miyashita, K., Fujii, T. , Sakai, H., Uchida, M. and Tanak, H. (1993)Identification of glutamic acid 204 and asparatic acid 200 in chitinase A1 of Bacillus circulans WL-12 as essential residues for chitinase activity. J. Biol. Chem. 268. 18567-18572
  49. Miyashita, K., Fujii, T. . and Sawada, Y. (1991) Molecular cloning and characterization of chitinase genes from Streptomyces lividans 66. J. Gen. Microbiol., 137:2065-2072
  50. Fujii, T. ., Kudou, A. and Seto, H. (1989) Genetic transformation in a synchronous culture of Streptococcus pneumoniae.Agric. Biol. Chem., 53:917-922
  51. Fujii, T. , Sekimori, Y., Ishii, Y. and Seto, H. (1988) Isolation and characterization of a transformation deficient mutant of Streptococcus pneumoniae. Agric. Biol. Chem., 52:489-494
  52. Fujii, T. ., Naka, D., Toyoda, N. and Seto, H. (1987) LiCl treatment releases a nickase implicated in genetic transformation of Streptococcus pneumoniae. J. Bacteriol., 169:4901-4906