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

BMC Genomics

Research Article

Shigeto Seno¹  Bei-Wen Ying¹  Hideo Matsuda¹  Fuyuro Kaneko¹  Tetsuya Yomo² 

[1] Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, 565-0871, Suita, Osaka, Japan;Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, 565-0871, Suita, Osaka, Japan;Graduate School of Frontier Biosciences, Osaka University, 1-5 Yamadaoka, 565-0871, Suita, Osaka, Japan;Exploratory Research for Advanced Technology (ERATO), Japan Science and Technology Agency (JST), 565-0871, Suita, Osaka, Japan;

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

DOI  :  10.1186/1471-2164-14-25

 received in 2012-07-15, accepted in 2012-12-29,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundBoth 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.ResultsThe 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).ConclusionThe 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.

【 授权许可】

Unknown   
© Ying et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.