Techniques to Analyze sRNA Protein Cofactor Self-Assembly In Vitro

  • David Partouche
  • Antoine Malabirade
  • Thomas Bizien
  • Marisela Velez
  • Sylvain Trépout
  • Sergio Marco
  • Valeria Militello
  • Christophe Sandt
  • Frank Wien
  • Véronique Arluison
Part of the Methods in Molecular Biology book series (MIMB, volume 1737)


Post-transcriptional control of gene expression by small regulatory noncoding RNA (sRNA) needs protein accomplices to occur. Past research mainly focused on the RNA chaperone Hfq as cofactor. Nevertheless, recent studies indicated that other proteins might be involved in sRNA-based regulations. As some of these proteins have been shown to self-assemble, we describe in this chapter protocols to analyze the nano-assemblies formed. Precisely, we focus our analysis on Escherichia coli Hfq as a model, but the protocols presented here can be applied to analyze any polymer of proteins. This chapter thus provides a guideline to develop commonly used approaches to detect prokaryotic protein self-assembly, with a special focus on the detection of amyloidogenic polymers.


Protein self-assembly Noncoding RNA cofactor Functional amyloid 



Atomic force microscopy


Curve fitting


Fourier transform infrared spectroscopy


Small angle X-ray scattering


Synchrotron radiation circular dichroism


Transmission electron microscopy


Thioflavin T



This work was supported by Université Paris Diderot, CNRS, CEA, and Synchrotron SOLEIL. We gratefully acknowledge help to MV from the French Embassy for their program for scientific and university cooperation. We are indebted to F. Gobeaux (CEA Saclay, Gif-sur-Yvette, France) and A. Deniset-Besseau (LCP, Université Paris-Sud, France) for many fruitful discussions. We thank Kimberly Stanek (University of Virginia) for her careful and critical reading of our manuscript.


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Copyright information

© Springer Science+Business Media, LLC 2018

Authors and Affiliations

  • David Partouche
    • 1
    • 2
  • Antoine Malabirade
    • 2
  • Thomas Bizien
    • 1
  • Marisela Velez
    • 3
  • Sylvain Trépout
    • 4
    • 5
  • Sergio Marco
    • 4
    • 5
  • Valeria Militello
    • 6
  • Christophe Sandt
    • 1
  • Frank Wien
    • 1
  • Véronique Arluison
    • 7
  1. 1.Synchrotron SOLEIL, L’Orme des Merisiers Saint AubinGif-sur-YvetteFrance
  2. 2.Université Paris Diderot-Paris 7, Sorbonne Paris CitéParisFrance
  3. 3.Instituto de Catálisis y Petroleoquímica, CSICMadridSpain
  4. 4.INSERM, U1196, Université Paris Sud, Université Paris-SaclayOrsayFrance
  5. 5.Institut Curie, PSL Research University, CNRS, UMR 91873348OrsayFrance
  6. 6.Department of Physics and ChemistryUniversity of PalermoPalermoItaly
  7. 7.Université Paris Diderot & LLB/CEA/CNRSGif-sur-YvetteFrance

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