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Related Concept Videos

Inhibitors of Viral Protein Synthesis01:30

Inhibitors of Viral Protein Synthesis

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Protein synthesis is indispensable for viral replication, as viruses lack the cellular machinery required for this process and must hijack the host's translational apparatus. In response, host cells deploy a critical innate immune defense involving interferons, specialized cytokines that play a central role in inhibiting viral propagation.Upon viral detection, infected cells release interferons that bind to receptors on adjacent uninfected cells, activating the JAK-STAT signaling pathway and...
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During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
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Inositol-requiring kinase one or IRE1 is the most conserved eukaryotic unfolded protein response (UPR) receptor. It is a type I transmembrane protein kinase receptor with a distinctive site-specific RNase activity. As the binding mechanics of the misfolded proteins with the N-terminal domain of IRE-1 are unclear, three binding models — direct, indirect, and allosteric -- are proposed for receptor activation. Nevertheless, it is known that once a misfolded protein associates with IRE1, it...
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Related Experiment Video

Updated: Apr 7, 2026

Electrophoretic Mobility Shift Assay EMSA for the Study of RNA-Protein Interactions: The IRE/IRP Example
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RNA-protein interaction methods to study viral IRES elements.

Rosario Francisco-Velilla1, Javier Fernandez-Chamorro1, Gloria Lozano1

  • 1Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid, Nicolas Cabrera 1, 28049 Madrid, Spain.

Methods (San Diego, Calif.)
|July 6, 2015
PubMed
Summary

This review details methods for identifying RNA-binding proteins and studying RNA structures that influence internal ribosome entry site (IRES) elements. Understanding these interactions is crucial for viral protein synthesis and translation control.

Keywords:
IRES elementsRNA structureRNA virusRNA-binding proteinsTranslation control

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Area of Science:

  • Molecular Biology
  • Virology
  • Biochemistry

Background:

  • Translation regulation is critical for cellular processes and is often mediated by RNA-binding proteins (RBPs) interacting with mRNA untranslated regions.
  • Internal ribosome entry site (IRES) elements are key cis-acting RNA regulators that facilitate cap-independent translation initiation, a strategy employed by many positive-strand RNA viruses for efficient protein synthesis.
  • Viral IRES elements exhibit diversity in sequence, secondary structure, and cofactor requirements, necessitating detailed investigation into their functional mechanisms.

Purpose of the Study:

  • To describe methodologies for isolating and identifying RBPs essential for IRES activity.
  • To outline approaches for investigating the impact of RNA structure and RBP interactions on IRES-mediated translation.
  • To enhance understanding of the functional diversity among viral IRES elements.

Main Methods:

  • Isolation and identification of RBPs associated with IRES elements.
  • Structural analysis of IRES RNA secondary structures.
  • Functional assays to assess the impact of RNA-protein interactions on IRES activity.

Main Results:

  • Established methods for identifying key RBPs involved in IRES function.
  • Demonstrated techniques to analyze how RNA structure influences IRES activity.
  • Provided a framework for studying diverse viral IRES mechanisms.

Conclusions:

  • Effective methods exist to dissect the roles of RBPs and RNA structure in IRES-mediated translation.
  • Further research into viral IRES elements is vital for understanding viral replication strategies.
  • This review offers valuable insights for researchers studying translation control and viral pathogenesis.