Identification of a basic helix-loop-helix-type transcription regulator gene in Aspergillus oryzae by systematically deleting large chromosomal segments

Applied and Environmental Microbiology

Volumn 75, Issue 18, 2009, Pages 5943-5951

  Feng, Jie Jin ^a   Takahashi, Tadashi ^a   Machida, Masayuki ^b   Koyama, Yasuji ^a  

^a Noda Institute for Scientific Research   (Japan)

^b NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ASPERGILLUS ORYZAE; BASIC HELIX LOOP HELIXES; BINDING PROTEINS; CHROMOSOMAL DELETIONS; CONIDIATION; DELETION ANALYSIS; DELETION MUTANTS; DNA SEGMENTS; FUNCTIONAL GENES; MUTANT PHENOTYPE; PHENOTYPIC CHANGES; TYPE METHODS;

GENES; INDUSTRIAL APPLICATIONS; NUCLEIC ACIDS; TRANSCRIPTION FACTORS;

TRANSCRIPTION;

HELIX LOOP HELIX PROTEIN;

CHROMOSOME; FUNGUS; GENE EXPRESSION; GENETIC ENGINEERING; IDENTIFICATION METHOD; PHENOTYPE;

ARTICLE; ASPERGILLUS ORYZAE; CHROMOSOME 7; CHROMOSOME DELETION; FUNGUS GROWTH; GENE IDENTIFICATION; NONHUMAN;

AMINO ACID SEQUENCE; ASPERGILLUS ORYZAE; CHROMOSOMES, FUNGAL; DNA, FUNGAL; GENES, FUNGAL; GENES, REGULATOR; HELIX-LOOP-HELIX MOTIFS; MOLECULAR SEQUENCE DATA; SEQUENCE ALIGNMENT; SEQUENCE DELETION; SPORES, FUNGAL; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

ASPERGILLUS ORYZAE;

EID: 70149106165     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.00975-09     Document Type: Article

References (24)

1. Boylan, M. T., P. M. Mirabito, C. E. Willett, C. R. Zimmerman, and W. E. Timberlake. 1987. Isolation and physical characterization of three essential conidiation genes from Aspergillus nidulans. Mol. Cell. Biol. 7:3113-3118.
2. DeFazio, L. G., R. M. Stansel, J. D. Griffith, and G. Chu. 2002. Synapsis of DNA ends by DNA-dependent protein kinase. EMBO J. 21:3192-3200.
3. Giaever, G., A. M. Chu, L. Ni, C. Connelly, L. Riles, S. Véronneau, S. Dow, A. Lucau-Danila, K. Anderson, B. André, A. P. Arkin, A. Astromoff, M. El Bakkoury, R. Bangham, R. Benito, S. Brachat, S. Campanaro, M. Curtiss, K. Davis, A. Deutschbauer, K.-D. Entian, P. Flaherty, F. Foury, D. J. Garfinkel, M. Gerstein, D. Gotte, U. Güldener, J. H. Hegemann, S. Hempel, Z. Herman, D. F. Jaramillo, D. E. Kelly, S. L. Kelly, P. Kötter, D. LaBonte, D. C. Lamb, N. Lan, H. Liang, H. Liao, L. Liu, C. Luo, M. Lussier, R. Mao, P. Menard, S. L. Ooi, J. L. Revuelta, C. J. Roberts, M. Rose, P. Ross-Macdonald, B. Scherens, G. Schimmack, B. Shafer, D. D. Shoemaker, S. Sookhai-Mahadeo, R. K. Storms, J. N. Strathern, G. Valle, M. Voet, G. Volckaert, C.-Y. Wang, T. R. Ward, J. Wilhelmy, E. A. Winzeler, Y. Yang, G. Yen, E. Youngman, K. Yu, H. Bussey, J. D. Boeke, M. Snyder, P. Philippsen, R. W. Davis, and M. Johnston. 2002. Functional profiling of the Saccharomyces cerevisiae genome. Nature 418:387-391.
4. Jin, F. J., J. Maruyama, P. R. Juvvadi, M. Arioka, and K. Kitamoto. 2004. Development of a novel quadruple auxotrophic host transformation system by argB gene disruption using adeA gene and exploiting adenine auxotrophy in Aspergillus oryzae. FEMS Microbiol. Lett. 239:79-85.
5. Jones, J. M., M. Gellert, and W. Yang. 2001. A Ku bridge over broken DNA. Structure 9:881-884.
6. Kamath, R. S., A. G. Fraser, Y. Dong, G. Poulin, R. Durbin, M. Gotta, A. Kanapin, N. Le Bot, S. Moreno, M. Sohrmann, D. P. Welchman, P. Zipperlen, and J. Ahringer. 2003. Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421:231-237.
7. Kim, S. K., J. Lund, M. Kiraly, K. Duke, M. Jiang, J. M. Stuart, A. Eizinger, B. N. Wylie, and G. S. Davidson. 2001. A gene expression map for Caenorhabditis elegans. Science 293:2087-2092.
8. Kitamoto, K. 2002. Molecular biology of the Koji molds. Adv. Appl. Microbiol. 51:129-153.
9. Kobayashi, K., S. D. Ehrlich, A. Albertini, G. Amati, K. K. Andersen, M. Arnaud, K. Asai, S. Ashikaga, S. Aymerich, P. Bessieres, F. Boland, S. C. Brignell, S. Bron, K. Bunai, J. Chapuis, L. C. Christiansen, A. Danchin, M. Débarbouille, E. Dervyn, E. Deuerling, K. Devine, S. K. Devine, O. Dreesen, J. Errington, S. Fillinger, S. J. Foster, Y. Fujita, A. Galizzi, R. Gardan, C. Eschevins, T. Fukushima, K. Haga, C. R. Harwood, M. Hecker, D. Hosoya, M. F. Hullo, H. Kakeshita, D. Karamata, Y. Kasahara, F. Kawamura, K. Koga, P. Koski, R. Kuwana, D. Imamura, M. Ishimaru, S. Ishikawa, I. Ishio, D. Le Coq, A. Masson, C. Mauël, R. Meima, R. P. Mellado, A. Moir, S. Moriya, E. Nagakawa, H. Nanamiya, S. Nakai, P. Nygaard, M. Ogura, T. Ohanan, M. O'Reilly, M. O'Rourke, Z. Pragai, H. M. Pooley, G. Rapoport, J. P. Rawlins, L. A. Rivas, C. Rivolta, A. Sadaie, Y. Sadaie, M. Sarvas, T. Sato, H. H. Saxild, E. Scanlan, W. Schumann, J. F. Seegers, J. Sekiguchi, A. Sekowska, S. J. Séror, M. Simon, P. Stragier, R. Studer, H. Takamatsu, T. Tanaka, M. Takeuchi, H. B. Thomaides, V. Vagner, J. M. van Dijl, K. Watabe, A. Wipat, H. Yamamoto, M. Yamamoto, Y. Yamamoto, K. Yamane, K. Yata, K. Yoshida, H. Yoshikawa, U. Zuber, and N. Ogasawara. 2003. Essential Bacillus subtilis genes. Proc. Natl. Acad. Sci. USA 100:4678-4683.
10. Kobayashi, T., K. Abe, K. Asai, K. Gomi, P. R. Juvvadi, M. Kato, K. Kitamoto, M. Takeuchi, and M. Machida. 2007. Genomics of Aspergillus oryzae. Biosci. Biotechnol. Biochem. 71:646-670.
11. Li, X., X. Duan, H. Jiang, Y. Sun, Y. Tang, Z. Yuan, J. Guo, W. Liang, L. Chen, J. Yin, H. Ma, J. Wang, and D. Zhang. 2006. Genome-wide analysis of basic/helix-loop-helix transcription factor family in rice and Arabidopsis. Plant Physiol. 141:1167-1184. (Pubitemid 44223270)
12. Machida, M., K. Asai, M. Sano, T. Tanaka, T. Kumagai, G. Terai, K. Kusumoto, T. Arima, O. Akita, Y. Kashiwagi, K. Abe, K. Gomi, H. Horiuchi, K. Kitamoto, T. Kobayashi, M. Takeuchi, D. W. Denning, J. E. Galagan, W. C. Nierman, J. Yu, D. B. Archer, J. W. Bennett, D. Bhatnagar, T. E. Cleveland, N. D. Fedorova, O. Gotoh, H. Horikawa, A. Hosoyama, M. Ichinomiya, R. Igarashi, K. Iwashita, P. R. Juvvadi, M. Kato, Y. Kato, T. Kin, A. Kokubun, H. Maeda, N. Maeyama, J. Maruyama, H. Nagasaki, T. Nakajima, K. Oda, K. Okada, I. Paulsen, K. Sakamoto, T. Sawano, M. Takahashi, K. Takase, Y. Terabayashi, J. R. Wortman, O. Yamada, Y. Yamagata, H. Anazawa, Y. Hata, Y. Koide, T. Komori, Y. Koyama, T. Minetoki, S. Suharnan, A. Tanaka, K. Isono, S. Kuhara, N. Ogasawara, and H. Kikuchi. 2005. Genome sequencing and analysis of Aspergillus oryzae. Nature 438:1157-1161.
13. Murakami, K., E. Tao, Y. Ito, M. Sugiyama, Y. Kaneko, S. Harashima, T. Sumiya, A. Nakamura, and M. Nishizawa. 2007. Large scale deletions in the Saccharomyces cerevisiae genome create strains with altered regulation of carbon metabolism. Appl. Microbiol. Biotechnol. 75:589-597.
14. Ninomiya, Y., K. Suzuki, C. Ishii, and H. Inoue. 2004. Highly efficient gene replacements in Neurospora strains deficient for nonhomologous end-joining. Proc. Natl. Acad. Sci. USA 101:12248-12253.
15. Sun, X., and D. Baltimore. 1991. An inhibitory domain of E12 transcription factor prevents DNA binding in E12 homodimers but not in E12 heterodimers. Cell 64:459-467. (Pubitemid 121001269)
16. Takahashi, T., F. J. Jin, M. Sunagawa, M. Machida, and Y. Koyama. 2008. Generation of large chromosomal deletions in koji molds Aspergillus oryzae and Aspergillus sojae via a loop-out recombination. Appl. Environ. Microbiol. 74:7684-7693.
17. Takahashi, T., F. J. Jin, and Y. Koyama. Nonhomologous end-joining deficiency allows large chromosomal deletions to be produced by replacement-type recombination in Aspergillus oryzae. Fungal Genet. Biol., in press.
18. Takahashi, T., O. Hatamoto, Y. Koyama, and K. Abe. 2004. Efficient gene disruption in the koji-mold Aspergillus sojae using a novel variation of the positive-negative method. Mol. Genet. Genomics 272:344-352.
19. Takahashi, T., T. Masuda, and Y. Koyama. 2006. Enhanced gene targeting frequency in ku70 and ku80 disruption mutants of Aspergillus sojae and Aspergillus oryzae. Mol. Genet. Genomics 275:460-470. (Pubitemid 43725263)
20. Tamano, K., M. Sano, N. Yamane, Y. Terabayashi, T. Toda, M. Sunagawa, H. Koike, O. Hatamoto, G. Umitsuki, T. Takahashi, Y. Koyama, R. Asai, K. Abe, and M. Machida. 2008. Transcriptional regulation of genes on the non-syntenic blocks of Aspergillus oryzae and its functional relationship to solid-state cultivation. Fungal Genet. Biol. 45:139-151.
21. Toledo-Ortiz, G., E. Huq, and P. H. Quail. 2003. The Arabidopsis basic/helix-loop-helix transcription factor family. Plant Cell 15:1749-1770. (Pubitemid 37078332)
22. Winzeler, E. A., D. D. Shoemaker, A. Astromoff, H. Liang, K. Anderson, B. Andre, R. Bangham, R. Benito, J. D. Boeke, H. Bussey, A. M. Chu, C. Connelly, K. Davis, F. Dietrich, S. W. Dow, M. El Bakkoury, F. Foury, S. H. Friend, E. Gentalen, G. Giaever, J. H. Hegemann, T. Jones, M. Laub, H. Liao, N. Liebundguth, D. J. Lockhart, A. Lucau-Danila, M. Lussier, N. M'Rabet, P. Menard, M. Mittmann, C. Pai, C. Rebischung, J. L. Revuelta, L. Riles, C. J. Roberts, P. Ross-MacDonald, B. Scherens, M. Snyder, S. Sookhai-Mahadeo, R. K. Storms, S. Véronneau, M. Voet, G. Volckaert, T. R. Ward, R. Wysocki, G. S. Yen, K. Yu, K. Zimmermann, P. Philippsen, M. Johnston, and R. W. Davis. 1999. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285:901-906.
23. Yamada, O., B. R. Lee, K. Gomi, and Y. Iimura. 1999. Cloning and functional analysis of the Aspergillus oryzae conidiation regulator gene brlA by its disruption and misscheduled expression. J. Biosci. Bioeng. 87:424-429.
24. Yu, B. J., B. H. Sung, M. D. Koob, C. H. Lee, J. H. Lee, W. S. Lee, M. S. Kim, and S. C. Kim. 2002. Minimization of the Escherichia coli genome using a Tn5-targeted Cre/loxP excision system. Nat. Biotechnol. 20:1018-1023.