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RNA recognition by double-stranded RNA binding domains: a matter of shape and sequence

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Abstract

The double-stranded RNA binding domain (dsRBD) is a small protein domain of 65–70 amino acids adopting an αβββα fold, whose central property is to bind to double-stranded RNA (dsRNA). This domain is present in proteins implicated in many aspects of cellular life, including antiviral response, RNA editing, RNA processing, RNA transport and, last but not least, RNA silencing. Even though proteins containing dsRBDs can bind to very specific dsRNA targets in vivo, the binding of dsRBDs to dsRNA is commonly believed to be shape-dependent rather than sequence-specific. Interestingly, recent structural information on dsRNA recognition by dsRBDs opens the possibility that this domain performs a direct readout of RNA sequence in the minor groove, allowing a global reconsideration of the principles describing dsRNA recognition by dsRBDs. We review in this article the current structural and molecular knowledge on dsRBDs, emphasizing the intricate relationship between the amino acid sequence, the structure of the domain and its RNA recognition capacity. We especially focus on the molecular determinants of dsRNA recognition and describe how sequence discrimination can be achieved by this type of domain.

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Abbreviations

ADAR:

Adenosine deaminase acting on RNA

DGCR8:

DiGeorge syndrome critical region 8

dsRBD:

Double-stranded RNA binding domain

dsRNA:

Double-stranded RNA

HYL1:

HYPONASTIC LEAVES1

ILF3:

Interleukin enhancer binding factor 3

PACT:

PKR activator

PKR:

Protein kinase RNA-activated

RHA:

RNA helicase A

SPNR:

Spindle perinuclear protein

TRBP:

HIV transactivation response RNA binding protein

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Acknowledgments

We sincerely apologize to the colleagues whose important work is not cited because of space limitation, or unfortunately because of our negligence. This work was supported by the Swiss National Science Foundation Nr. 31003AB-133134 and 310030E-131031, the SNF-NCCR structural biology and a KTI Grant 11329.1 PFLS-LS. G.M. was supported by grant from the “Fondation pour la Recherche Médicale”. P.B. was supported by the Postdoctoral ETH Fellowship Program.

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  1. Institute of Molecular Biology and Biophysics, ETH Zurich, Schafmattstrasse 20, 8093, Zürich, Switzerland

    Grégoire Masliah, Pierre Barraud & Frédéric H. -T. Allain

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  1. Grégoire Masliah
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  2. Pierre Barraud
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  3. Frédéric H. -T. Allain
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Correspondence to Frédéric H. -T. Allain.

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G. Masliah and P. Barraud contributed equally to this work.

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Masliah, G., Barraud, P. & Allain, F.H.T. RNA recognition by double-stranded RNA binding domains: a matter of shape and sequence. Cell. Mol. Life Sci. 70, 1875–1895 (2013). https://doi.org/10.1007/s00018-012-1119-x

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  • DOI: https://doi.org/10.1007/s00018-012-1119-x

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