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Nucleic Acids Research, 2001, Vol. 29, No. 3 683-692
© 2001 Oxford University Press

Combined transcriptome and proteome analysis as a powerful approach to study genes under glucose repression in Bacillus subtilis

Ken-ichi Yoshida, Kazuo Kobayashi1, Yasuhiko Miwa, Choong-Min Kang, Masayuki Matsunaga, Hirotake Yamaguchi, Shigeo Tojo, Mami Yamamoto, Ryoko Nishi2, Naotake Ogasawara1, Tatsuo Nakayama2 and Yasutaro Fujita*

Faculty of Engineering, Fukuyama University, Fukuyama 729-0292, Japan, 1Advanced Institute of Science and Technology, Nara, Ikoma 630-0101, Japan and 2Department of Biochemistry, Miyazaki Medical College, Miyazaki 889-1692, Japan

We used 2D protein gel electrophoresis and DNA microarray technologies to systematically analyze genes under glucose repression in Bacillus subtilis. In particular, we focused on genes expressed after the shift from glycolytic to gluconeogenic at the middle logarithmic phase of growth in a nutrient sporulation medium, which remained repressed by the addition of glucose. We also examined whether or not glucose repression of these genes was mediated by CcpA, the catabolite control protein of this bacterium. The wild-type and ccpA1 cells were grown with and without glucose, and their proteomes and transcriptomes were compared. 2D gel electrophoresis allowed us to identify 11 proteins, the synthesis of which was under glucose repression. Of these proteins, the synthesis of four (IolA, I, S and PckA) was under CcpA-independent control. Microarray analysis enabled us to detect 66 glucose-repressive genes, 22 of which (glmS, acoA, C, yisS, speD, gapB, pckA, yvdR, yxeF, iolA, B, C, D, E, F, G, H, I, J, R, S and yxbF ) were at least partially under CcpA-independent control. Furthermore, we found that CcpA and IolR, a repressor of the iol divergon, were involved in the glucose repression of the synthesis of inositol dehydrogenase encoded by iolG included in the above list. The CcpA-independent glucose repression of the iol genes appeared to be explained by inducer exclusion.

* To whom correspondence should be addressed at: Department of Biotechnology, Faculty of Engineering, Fukuyama University, 985 Sanzo, Higashimura-cho, Fukuyama-shi, Hiroshima 729-0292, Japan. Tel: +81 849 36 2111; Fax: +81 849 36 2459; Email: yfujita{at}bt.fubt.fukuyama-u.ac.jp Present address:Choong-Min Kang, Faculty of Life Science and Engineering, Youngdong University, Youngdong, South Korea The authors wish it to be known that, in their opinion, the first three authors should be regarded as joint First Authors


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