Appl Microbiol Biotechnol (2004) 65: 74–83 DOI 10.1007/s00253-004-1608-4 GENOMICS AND PROTEOMICS Hiroshi Maeda . Motoaki Sano . Yutaka Maruyama . Takeki Tanno . Takeshi Akao . Yoshiteru Totsuka . Misako Endo . Rumi Sakurada . Youhei Yamagata . Masayuki Machida . Osamu Akita . Fumihiko Hasegawa . Keietsu Abe . Katsuya Gomi . Tasuku Nakajima . Yasutaka Iguchi Transcriptional analysis of genes for energy catabolism and hydrolytic enzymes in the filamentous fungus Aspergillus oryzae using cDNA microarrays and expressed sequence tags Received: 3 December 2003 / Revised: 23 February 2004 / Accepted: 5 March 2004 / Published online: 20 May 2004 # Springer-Verlag 2004 Abstract Aspergillus oryzae is a fungus used extensively in the fermentation industry. We constructed cDNA microarrays comprising 2,070 highly expressed cDNAs selected from the ∼6,000 non-redundant expressed se- quence tags (ESTs) in the A. oryzae EST database (http:// www.aist.go.jp/RIODB/ffdb/index.html). Using the cDNA microarrays, we analyzed the gene expression profiles of A. oryzae cells grown under the glucose-rich (AC) and glucose-depleted (AN) liquid culture conditions used during the construction of the EST database. The sets of genes identified by the cDNA microarray as highly expressed under each culture condition agreed well with the highly redundant ESTs obtained under the same conditions. In particular, transcription levels of most catabolic genes of the glycolytic pathway (EMP) and tricarboxylic acid (TCA) cycle were higher under AC than AN conditions, suggesting that A. oryzae uses both EMP and TCA for glucose metabolism under AC conditions. We further studied the expression of genes encoding hydrolytic enzymes and enzymes involved in energy catabolism by using three industrial solid-phase biomass media, including wheat-bran. The wheat-bran culture gave the richest gene expression profile of hydrolytic enzymes and the lowest expression levels of catabolic genes (EMP, TCA) among the three media tested. The low expression levels of catabolic genes in the wheat-bran culture may release catabolite repression, consequently leading to the rich expression profiles of the hydrolytic enzymes. Introduction The Aspergillus section flavi complex consists of myco- toxin producers such as A. flavus and A. parasiticus and the non-toxigenic industrial species A. oryzae and A. sojae (Yu et al. 2004; Takahashi et al. 2002). A. flavus and A. parasiticus contaminate post-harvest crops (corn, peanut, cotton, etc.) in low latitudes, and thus agribusiness is often overwhelmed by fungal contamination (Yu et al. 2004; Takahashi et al. 2002). In contrast, A. oryzae and A. sojae, so-called koji molds, have been used extensively for indigenous Japanese fermentation products such as sake (rice wine), shochu (spirits), shoyu (soy sauce), and miso (soybean paste) for more than 1,000 years (Yu et al. 2004; Machida 2003). The long history of extensive use in food industries prompted the United States Food and Drug Administration to place A. oryzae on the list of generally regarded as safe (GRAS) organisms. The safety of A. oryzae is also supported by the World Health Organization (Barbesgaard et al. 1992; Tailor and Richardson 1979; Machida 2003). In another current application, koji molds are used as host cells for enzyme production using DNA H. Maeda . Y. Maruyama . T. Tanno . Y. Totsuka . Y. Yamagata . K. Abe (*) . K. Gomi . T. Nakajima Department of Molecular and Cell Biology, Graduate School of Agricultural Science, Tohoku University, 1-1 Amamiya, Tsutsumi-dori, Sendai, 981-8555, Japan e-mail: kabe@biochem.tohoku.ac.jp Tel.: +81-22-7178777 Fax: +81-22-7178778 H. Maeda . Y. Maruyama . Y. Yamagata . F. Hasegawa . K. Abe . K. Gomi . T. Nakajima . Y. Iguchi The New Industry Creation Hatchery Center, Tohoku University, Sendai, 980-8579, Japan H. Maeda Tohoku Technoarch Co. Ltd, Sendai, 981-0845, Japan M. Sano . M. Machida Research Center for Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, 305-8566, Japan T. Akao . O. Akita National Research Institute of Brewing, Higashi-Hiroshima, 739-0046, Japan M. Endo . R. Sakurada Industrial Technology Institute, Miyagi Prefectural Government, Sendai, 981-3206, Japan