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. 2013 Feb 17;82(1):68–76. doi: 10.1134/S0026261713010062

Search for the new potential RNA thermometers in the genome of Salmonella enterica

O Yu Limanskaya 1,2,✉, L A Murtazaeva 3, A P Limanskii 1
PMCID: PMC7089039  PMID: 32214462

Abstract

Currently, a number of structurally and functionally different temperature-sensitive elements such as RNA thermometers which control a variety of biological processes in bacteria, including virulence, are known. Based on computer and thermodynamic analysis of completely sequenced genomes of 25 Salmonella enterica isolates, the algorithm and criteria for the search of potential RNA thermometers were developed. It will make it possible to carry out the search for potential riboswitches in the genome of other socially important pathogens. For S. enterica, apart from the known 4U RNA thermometer, four hairpin-loop structures were identified which may probably act as additional RNA thermometers. They satisfy the necessary and sufficient conditions for formation of RNA thermometers and are highly conservative uncanonical structures, since these highly conservative structures were found in the genome of all 25 isolates of S. enterica. The hairpins forming a cruciform structure in the supercoiled pUC8 DNA were visualized by atomic force microscopy.

Keywords: RNA thermometer, Shine-Dalgarno sequence, hairpin structure, Salmonella enterica, AFM, atomic force microscopy

Footnotes

Original Russian Text © O.Yu. Limanskaya, L.A. Murtazaeva, A.P. Limanskii, 2013, published in Mikrobiologiya, 2013, Vol. 82, No. 1, pp. 69–78.

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