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Plos Biology : Conserved and Variable Functions of the Re Stress Response in Related Genomes, Volume 4

By Eisen, Jonathan A.

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Book Id: WPLBN0003925347
Format Type: PDF eBook :
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Reproduction Date: 2015

Title: Plos Biology : Conserved and Variable Functions of the Re Stress Response in Related Genomes, Volume 4  
Author: Eisen, Jonathan A.
Volume: Volume 4
Language: English
Subject: Journals, Science, Biology
Collections: Periodicals: Journal and Magazine Collection, PLoS Biology
Publication Date:
Publisher: Plos


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Eisen, J. A. (n.d.). Plos Biology : Conserved and Variable Functions of the Re Stress Response in Related Genomes, Volume 4. Retrieved from

Description : Bacteria often cope with environmental stress by inducing alternative sigma (r) factors, which direct RNA polymerase to specific promoters, thereby inducing a set of genes called a regulon to combat the stress. To understand the conserved and organism-specific functions of each r, it is necessary to be able to predict their promoters, so that their regulons can be followed across species. However, the variability of promoter sequences and motif spacing makes their prediction difficult. We developed and validated an accurate promoter prediction model for Escherichia coli rE, which enabled us to predict a total of 89 unique rE-controlled transcription units in E. coli K-12 and eight related genomes. rE controls the envelope stress response in E. coli K-12. The portion of the regulon conserved across genomes is functionally coherent, ensuring the synthesis, assembly, and homeostasis of lipopolysaccharide and outer membrane porins, the key constituents of the outer membrane of Gram-negative bacteria. The larger variable portion is predicted to perform pathogenesis-associated functions, suggesting that rE provides organism-specific functions necessary for optimal host interaction. The success of our promoter prediction model for rE suggests that it will be applicable for the prediction of promoter elements for many alternative r factors.


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