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Riboproteomic Approaches to Understanding IRES Elements

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Book cover Biophysical approaches to translational control of gene expression

Part of the book series: Biophysics for the Life Sciences ((BIOPHYS,volume 1))

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Abstract

Initiation of translation is a key step of protein synthesis. Two basic mechanisms govern translation initiation in eukaryotic mRNAs, the cap-dependent initiation mechanism that operates in the vast majority of mRNAs and the internal ribosome entry site (IRES)-dependent mechanism. IRES elements, first discovered in picornaviruses, are cis-acting RNA sequences that form secondary and tertiary structures and recruit the translation machinery using a 5′ end-independent mechanism, usually assisted by a subset of translation initiation factors and various RNA-binding proteins termed IRES transacting factors (ITAFs). RNA-binding proteins are pivotal regulators of gene expression, including internal initiation of translation, in response to numerous stresses. This chapter discusses recent advances on riboproteomic approaches aimed to identify ITAFs and the relationship between RNA–protein interaction and IRES activity.

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Abbreviations

CBV3:

Coxsackie B3 virus

DHX9:

DEAH-box polypeptide 9

DRBP76:

Double-stranded RNA-binding protein 76

Ebp1:

erbB-3-binding protein 1

eIFs:

Translation initiation factors

EMCV:

Encephalomyocarditis virus

FBP2:

Binding protein 2

FMDV:

Foot-and-mouth disease virus

FUSE:

Far upstream element

G3BP:

Ras-GTPase-activating protein

HCV:

Hepatitis C virus

HIV-1:

Human immunodeficiency virus

hnRNPs:

Heterogeneous ribonucleoproteins

HRV:

Human rhinovirus

IGF2BP1:

Insulin-like growth factor II mRNA-binding protein 1

IRES:

Internal ribosome entry site

ITAFs:

IRES transacting factors

LEF-1:

Lymphoid enhancer factor

NF45:

Nuclear factor of activated T cells

PABP1:

Poly(A) binding protein

PCBP1-2:

Poly(rC) binding protein

PTB:

Polypyrimidine tract-binding protein

PV:

Poliovirus

RRM:

RNA recognition motif

SILAC:

Stable isotopic labeling with amino acid in cell culture

Unr:

Upstream of N-ras

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Acknowledgments

This work was supported by grant BFU2011-25437, CSD2009-00080, and by an Institutional grant from Fundación Ramón Areces.

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Authors and Affiliations

  1. Encarnacion Martinez-Salas, Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049, Madrid, Spain

    Encarnacion Martinez-Salas, David Piñeiro & Noemi Fernandez

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  1. Encarnacion Martinez-Salas
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  2. David Piñeiro
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  3. Noemi Fernandez
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Correspondence to Encarnacion Martinez-Salas .

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  1. College Park, Cell Biology and Molecular Genetics, University of Maryland, Rm. 2135 Microbiology Building, College Park, 20742-4451, Maryland, USA

    Jonathan D. Dinman

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Martinez-Salas, E., Piñeiro, D., Fernandez, N. (2012). Riboproteomic Approaches to Understanding IRES Elements. In: Dinman, J. (eds) Biophysical approaches to translational control of gene expression. Biophysics for the Life Sciences, vol 1. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-3991-2_6

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