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Nucleic Acids Res. 2013 Oct;41(18):8726-37. doi: 10.1093/nar/gkt651. Epub 2013 Jul 27.

Synthetic tolerance: three noncoding small RNAs, DsrA, ArcZ and RprA, acting supra-additively against acid stress.

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Department Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711, USA, Molecular Biotechnology Laboratory, Department of Chemical and Biomolecular Engineering, The Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA, Department of Biological Sciences, University of Delaware, Newark, DE 19711, USA and Department of Biology, Sultan Qaboos University, Muscat, 123, Oman.


Synthetic acid tolerance, especially during active cell growth, is a desirable phenotype for many biotechnological applications. Natively, acid resistance in Escherichia coli is largely a stationary-phase phenotype attributable to mechanisms mostly under the control of the stationary-phase sigma factor RpoS. We show that simultaneous overexpression of noncoding small RNAs (sRNAs), DsrA, RprA and ArcZ, which are translational RpoS activators, increased acid tolerance (based on a low-pH survival assay) supra-additively up to 8500-fold during active cell growth, and provided protection against carboxylic acid and oxidative stress. Overexpression of rpoS without its regulatory 5'-UTR resulted in inferior acid tolerance. The supra-additive effect of overexpressing the three sRNAs results from the impact their expression has on RpoS-protein levels, and the beneficial perturbation of the interconnected RpoS and H-NS networks, thus leading to superior tolerance during active growth. Unlike the overexpression of proteins, overexpression of sRNAs imposes hardly any metabolic burden on cells, and constitutes a more effective strain engineering strategy.

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