title: Multilevel comparative analysis of the contributions of genome reduction and heat shock to the Escherichia coli transcriptome.
abstract: BACKGROUND
  Both large deletions in genome and heat shock stress would lead to alterations in the gene expression profile; however, whether there is any potential linkage between these disturbances to the transcriptome have not been discovered. Here, the relationship between the genomic and environmental contributions to the transcriptome was analyzed by comparing the transcriptomes of the bacterium Escherichia coli (strain MG1655 and its extensive genomic deletion derivative, MDS42) grown in regular and transient heat shock conditions.
  
  
  RESULTS
  The transcriptome analysis showed the following: (i) there was a reorganization of the transcriptome in accordance with preferred chromosomal periodicity upon genomic or heat shock perturbation; (ii) there was a considerable overlap between the perturbed regulatory networks and the categories enriched for differentially expressed genes (DEGs) following genome reduction and heat shock; (iii) the genes sensitive to genome reduction tended to be located close to genomic scars, and some were also highly responsive to heat shock; and (iv) the genomic and environmental contributions to the transcriptome displayed not only a positive correlation but also a negatively compensated relationship (i.e., antagonistic epistasis).
  
  
  CONCLUSIONS
  The contributions of genome reduction and heat shock to the Escherichia coli transcriptome were evaluated at multiple levels. The observations of overlapping perturbed networks, directional similarity in transcriptional changes, positive correlation and epistatic nature linked the two contributions and suggest somehow a crosstalk guiding transcriptional reorganization in response to both genetic and environmental disturbances in bacterium E. coli.
authors: Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, Japan.
authors: Bei-Wen
authors: BW
authors: Ying
authors: Shigeto
authors: S
authors: Seno
authors: Fuyuro
authors: F
authors: Kaneko
authors: Hideo
authors: H
authors: Matsuda
authors: Tetsuya
authors: T
authors: Yomo
mesh_terms: D002876:Chromosomes, Bacterial / Q000235:genetics / Q000502:physiology; D004777:Environment; D004843:Epistasis, Genetic / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics* / Q000502:physiology*; D015964:Gene Expression Regulation, Bacterial / Q000235:genetics; D053263:Gene Regulatory Networks / Q000235:genetics; D059647:Gene-Environment Interaction; D005798:Genes, Bacterial / Q000235:genetics; D023281:Genomics; D018869:Heat-Shock Response / Q000235:genetics*; D010507:Periodicity; D013045:Species Specificity; D059467:Transcriptome