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Identification of c-di-GMP-Responsive Riboswitches

  • Johann Peltier
  • Olga SoutourinaEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1657)

Abstract

Bis-(3′-5′)-cyclic dimeric guanosine monophosphate (c-di-GMP) is an important signaling molecule for community behavior control, cell morphogenesis, and virulence in bacteria. In addition to protein effectors, this second messenger binds RNA molecules that act as riboswitches to control target gene expression. In this chapter, we describe a method for experimental validation of the functionality of c-di-GMP-responsive riboswitches and the analysis of c-di-GMP control of target gene expression by qRT-PCR and Northern blot. This procedure can be used for the studies of in silico-predicted riboswitch candidates, as well as a targeted experimental approach for exploring the data from next-generation sequencing. The examples on the analysis of type I and type II c-di-GMP-responsive riboswitches in Clostridium difficile are provided to illustrate the application of the method.

Key words

Riboswitches c-di-GMP Premature termination of transcription Target gene Northern blot qRT-PCR 

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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  1. 1.Laboratoire Pathogenèse des Bactéries AnaérobiesInstitut PasteurParis Cedex 15France
  2. 2.Université Paris Diderot, Sorbonne Paris CitéParis Cedex 15France
  3. 3.Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-SaclayGif-sur-Yvette CedexFrance

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