title: Growth rate-coordinated transcriptome reorganization in bacteria.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.forename: Yuki
authors.initials: Y
authors.lastname: Matsumoto
authors.forename: Yoshie
authors.initials: Y
authors.lastname: Murakami
authors.forename: Saburo
authors.initials: S
authors.lastname: Tsuru
authors.forename: Bei-Wen
authors.initials: BW
authors.lastname: Ying
authors.affiliation: Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan. yomo@ist.osaka-u.ac.jp.
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Yomo
mesh_terms: D004926:Escherichia coli / Q000235:genetics / Q000254:growth & development* / Q000378:metabolism; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial / Q000235:genetics*; D059647:Gene-Environment Interaction; D016680:Genome, Bacterial; D009997:Osmotic Pressure; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D013696:Temperature
chemical_list: D012333:RNA, Messenger