Open Access Research article

Growth rate-coordinated transcriptome reorganization in bacteria

Yuki Matsumoto1, Yoshie Murakami1, Saburo Tsuru1, Bei-Wen Ying12 and Tetsuya Yomo134*

Author Affiliations

1 Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan

2 Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan

3 Graduate School of Frontier Biosciences, Osaka University, Suita, 1-1 Yamadaoka, Suita, Osaka 565-0871, Japan

4 Exploratory Research for Advanced Technology (ERATO), Japan Science and Technology Agency (JST), Suita, Osaka 565-0871, Japan

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BMC Genomics 2013, 14:808  doi:10.1186/1471-2164-14-808

Published: 20 November 2013



Cell growth rate reflects an organism’s physiological state and largely relies on the ability of gene expression to respond to the environment. The relationship between cellular growth rate and gene expression remains unknown.


Growth rate-coordinated changes in gene expression were discovered by analyzing exponentially growing Escherichia coli cells cultured under multiple defined environments, in which osmotic pressure, temperature and starvation status were varied. Gene expression analyses showed that all 3,740 genes in the genome could be simply divided into three clusters (C1, C2 and C3), which were accompanied by a generic trend in the growth rate that was coordinated with transcriptional changes. The direction of transcriptional change in C1 indicated environmental specificity, whereas those in C2 and C3 were correlated negatively and positively with growth rates, respectively. The three clusters exhibited differentiated gene functions and gene regulation task division.


We identified three gene clusters, exhibiting differential gene functions and distinct directions in their correlations with growth rates. Reverses in the direction of the growth rate correlated transcriptional changes and the distinguished duties of the three clusters indicated how transcriptome homeostasis is maintained to balance the total expression cost for sustaining life in new habitats.