The genome-scale interplay amongst xenogene silencing, stress response and chromosome architecture in Escherichia coli

Srinivasan, Rajalakshmi and Scolari, Vittore Ferdinando (2015) The genome-scale interplay amongst xenogene silencing, stress response and chromosome architecture in Escherichia coli. Nucleic Acids Research Advance Access, 43 (1). pp. 1-14.

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Abstract

The gene expression state of exponentially growing Escherichia coli cells is manifested by high expression of essential and growth-associated genes and low levels of stress-related and horizontally acquired genes. An important player in maintaining this homeostasis is the H-NS-StpA gene silencing system. A Ahns-stpA deletion mutant results in high expression of otherwise-silent horizontally acquired genes, many located in the terminus-half of the chromosome, and an indirect downregulation of many highly expressed genes. The Ahns-stpA double mutant displays slow growth. Using laboratory evolution we address the evolutionary strategies that E. coli would adopt to redress this gene expression imbalance. We show that two global gene regulatory mutations-(i) point mutations inactivating the stress-responsive sigma factor RpoS or 0"38 and (ii) an amplification of "'40% of the chromosome centred around the origin of replication-converge in partially reversing the global gene expression imbalance caused by AbnsstpA. Transcriptome data of these mutants further show a three-way link amongst the global gene regulatory networks of H-NS and 0"38, as well as chromosome architecture. Increasing gene expression around the terminus of replication results in a decrease in the expression of genes around the origin and vice versa; this appears to be a persistent phenomenon observed as an association across "'300 publicly-available gene expression data sets for E. coli. These global suppressor effects are transient and rapidly give way to more specific mutations, whose roles in reversing the growth defect of H-NS mutations remain to be understood.

Item Type: Article
Subjects: Research > Research Center - Health Sciences
Depositing User: KMC Manipal
Date Deposited: 24 Apr 2015 06:05
Last Modified: 24 Apr 2015 06:05
URI: http://eprints.manipal.edu/id/eprint/142507

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