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Open Access Highly Accessed Research article

Multilevel comparative analysis of the contributions of genome reduction and heat shock to the Escherichia coli transcriptome

Bei-Wen Ying1, Shigeto Seno1, Fuyuro Kaneko1, Hideo Matsuda1 and Tetsuya Yomo123*

Author Affiliations

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

2 Graduate School of Frontier Biosciences, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan

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

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BMC Genomics 2013, 14:25  doi:10.1186/1471-2164-14-25

Published: 16 January 2013

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).

Conclusion

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.

Keywords:
Transcriptome; Negative epistasis; Genome reduction; Chromosomal periodicity; Regulatory network; Transcriptional change; Genomic interruption; Environmental perturbation; Heat shock; Directionality