title: Bacterial transcriptome reorganization in thermal adaptive evolution.
abstract: BACKGROUND
  Evolution optimizes a living system at both the genome and transcriptome levels. Few studies have investigated transcriptome evolution, whereas many studies have explored genome evolution in experimentally evolved cells. However, a comprehensive understanding of evolutionary mechanisms requires knowledge of how evolution shapes gene expression. Here, we analyzed Escherichia coli strains acquired during long-term thermal adaptive evolution.
  
  
  RESULTS
  Evolved and ancestor Escherichia coli cells were exponentially grown under normal and high temperatures for subsequent transcriptome analysis. We found that both the ancestor and evolved cells had comparable magnitudes of transcriptional change in response to heat shock, although the evolutionary progression of their expression patterns during exponential growth was different at either normal or high temperatures. We also identified inverse transcriptional changes that were mediated by differences in growth temperatures and genotypes, as well as negative epistasis between genotype-and heat shock-induced transcriptional changes. Principal component analysis revealed that transcriptome evolution neither approached the responsive state at the high temperature nor returned to the steady state at the regular temperature. We propose that the molecular mechanisms of thermal adaptive evolution involve the optimization of steady-state transcriptomes at high temperatures without disturbing the heat shock response.
  
  
  CONCLUSIONS
  Our results suggest that transcriptome evolution works to maintain steady-state gene expression during constrained differentiation at various evolutionary stages, while also maintaining responsiveness to environmental stimuli and transcriptome homeostasis.
authors.affiliation: Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, 305-8572, Japan. ying.beiwen.gf@u.tsukuba.ac.jp.
authors.forename: Bei-Wen
authors.initials: BW
authors.lastname: Ying
authors.affiliation: Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, 305-8572, Japan. yuki.matsumoto@riken.jp.|Present address: IMS, RIKEN, Kanagawa, 230-0045, Japan. yuki.matsumoto@riken.jp.
authors.forename: Yuki
authors.initials: Y
authors.lastname: Matsumoto
authors.affiliation: Graduate School of Information Science and Technology, Osaka University, Osaka, 565-0871, Japan. hakuhaku11kkam18@hotmail.co.jp.
authors.forename: Kazuki
authors.initials: K
authors.lastname: Kitahara
authors.affiliation: QBiC, RIKEN, Osaka, 565-0874, Japan. ssuzuki@riken.jp.
authors.forename: Shingo
authors.initials: S
authors.lastname: Suzuki
authors.affiliation: Graduate School of Information Science, Nara Institute of Science and Technology, Nara, 630-0192, Japan. nono@is.naist.jp.
authors.forename: Naoaki
authors.initials: N
authors.lastname: Ono
authors.affiliation: Graduate School of Information Science and Technology, Osaka University, Osaka, 565-0871, Japan. chikara.furusawa@riken.jp.|QBiC, RIKEN, Osaka, 565-0874, Japan. chikara.furusawa@riken.jp.
authors.forename: Chikara
authors.initials: C
authors.lastname: Furusawa
authors.affiliation: Faculty of Science, Toho University, Chiba, 274-8510, Japan. kisimoto@biomol.sci.toho-u.ac.jp.
authors.forename: Toshihiko
authors.initials: T
authors.lastname: Kishimoto
authors.affiliation: Graduate School of Information Science and Technology, Osaka University, Osaka, 565-0871, Japan. yomo@ist.osaka-u.ac.jp.|Graduate School of Frontier Biosciences, Osaka University, Osaka, 565-0871, Japan. yomo@ist.osaka-u.ac.jp.|Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Tokyo, 102-0076, Japan. yomo@ist.osaka-u.ac.jp.
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Yomo
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D004926:Escherichia coli / Q000235:genetics* / Q000502:physiology; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D018869:Heat-Shock Response / Q000235:genetics*; D006358:Hot Temperature; D059467:Transcriptome / Q000235:genetics*