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Applied and Environmental Microbiology, April 2004, p. 2354-2366, Vol. 70, No. 4
0099-2240/04/$08.00+0     DOI: 10.1128/AEM.70.4.2354-2366.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

Analysis of Gene Expression in Escherichia coli in Response to Changes of Growth-Limiting Nutrient in Chemostat Cultures

Qiang Hua,1 Chen Yang,1 Taku Oshima,2 Hirotada Mori,1,2 and Kazuyuki Shimizu1,3*

Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017,1 Research and Education Center for Genetic Information, Nara Institute of Science and Technology, Ikoma 630-0101,2 Department of Biochemical Engineering and Science, Kyushu Institute of Technology, Iizuka 820-8502, Japan3

Received 11 August 2003/ Accepted 13 January 2004

Studies of steady-state metabolic fluxes in Escherichia coli grown in nutrient-limited chemostat cultures suggest remarkable flux alterations in response to changes of growth-limiting nutrient in the medium (Hua et al., J. Bacteriol. 185:7053-7067, 2003). To elucidate the physiological adaptation of cells to the nutrient condition through the flux change and understand the molecular mechanisms underlying the change in the flux, information on gene expression is of great importance. DNA microarray analysis was performed to investigate the global transcriptional responses of steady-state cells grown in chemostat cultures with limited glucose or ammonia while other environmental conditions and the growth rate were kept constant. In slow-growing cells (specific growth rate of 0.10 h–1), 9.8% of a total of 4,071 genes investigated, especially those involved in amino acid metabolism, central carbon and energy metabolism, transport system and cell envelope, were observed to be differentially expressed between the two nutrient-limited cultures. One important characteristic of E. coli grown under nutrient limitation was its capacity to scavenge carbon or nitrogen from the medium through elevating the expression of the corresponding transport and assimilation genes. The number of differentially expressed genes in faster-growing cells (specific growth rate of 0.55 h–1), however, decreased to below half of that in slow-growing cells, which could be explained by diverse transcriptional responses to the growth rate under different nutrient limitations. Independent of the growth rate, 92 genes were identified as being differentially expressed. Genes tightly related to the culture conditions were highlighted, some of which may be used to characterize nutrient-limited growth.

* Corresponding author. Mailing address: Department of Biochemical Engineering and Science, Kyusha Institute of Technology, Iizuka 820-8502, Japan. Phone: 81-948-29-7817. Fax: 81-948-29-7801. E-mail: shimi{at}bse.kyutech.ac.jp.

Applied and Environmental Microbiology, April 2004, p. 2354-2366, Vol. 70, No. 4
0099-2240/04/$08.00+0     DOI: 10.1128/AEM.70.4.2354-2366.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.



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