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Related Concept Videos

Initiation of Translation02:33

Initiation of Translation

34.6K
Initiating translation is complex because it involves multiple molecules. Initiator tRNA, ribosomal subunits, and eukaryotic initiation factors (eIFs) are all required to assemble on the initiation codon of mRNA. This process consists of several steps that are mediated by different eIFs.
First, the initiator tRNA must be selected from the pool of elongator tRNAs by eukaryotic initiation factor 2 (eIF2). The initiator tRNA (Met-tRNAi) has conserved sequence elements including modified bases at...
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Leaky Scanning02:28

Leaky Scanning

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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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Cotranslational Protein Translocation01:20

Cotranslational Protein Translocation

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Translocation of proteins across membranes is an ancient process that occurs even in bacteria and archaebacteria. In fact, the components of the translocation machinery are still conserved between prokaryotes and eukaryotes.
Sec61 channel partners for cotranslational translocation
During cotranslational translocation, the Sec61 channel partners with the signal recognition particle (SRP), the signal recognition particle receptor (SR), and the ribosomes to transport the nascent polypeptide chain...
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Improving Translational Accuracy02:07

Improving Translational Accuracy

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Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
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Directing Proteins to the Rough Endoplasmic Reticulum01:34

Directing Proteins to the Rough Endoplasmic Reticulum

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The organelle-specific signaling sequences direct proteins synthesized in the cytosol to their final destination like ER, mitochondria, peroxisomes, etc. Some of the proteins directed to ER are then trafficked via vesicles to other organelles within the cell or the extracellular environment through the Golgi complex. For example, the rough ER synthesizes soluble proteins for transportation to the lysosomes or secretion out of the cell. It can also synthesize transmembrane proteins that can...
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Ribosome Profiling02:24

Ribosome Profiling

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
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Related Experiment Video

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De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
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De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

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A compact viral IRES translates a downstream open reading frame.

Madeline E Sherlock, Katherine E Segar, Jeffrey S Kieft

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    |June 4, 2025
    PubMed
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    Researchers discovered a small Type IV internal ribosome entry site (IRES) in the megrivirus E 3' untranslated region. This RNA structure enables cap-independent translation, but at lower levels than previously known IRESs.

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    Xenopus laevis as a Model to Identify Translation Impairment

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    Area of Science:

    • Virology
    • Molecular Biology
    • Structural Biology

    Background:

    • Hepatitis C virus (HCV) and other RNA viruses utilize Type IV internal ribosome entry sites (IRES) in their 5' untranslated regions (UTRs) for cap-independent translation initiation.
    • These IRES elements form complex tertiary structures that directly engage with the ribosome.

    Purpose of the Study:

    • To identify novel Type IV IRES RNAs in viral genomes using bioinformatic approaches.
    • To characterize a newly discovered, unusually located and sized Type IV IRES in megrivirus E (MeV-E).

    Main Methods:

    • Bioinformatic analysis of viral genomes to detect potential Type IV IRES elements.
    • Determination of the secondary and 3D structures of the MeV-E 3' IRES using cryo-electron microscopy (cryo-EM).
    • Functional assays to assess the translation initiation activity of the MeV-E 3' IRES.

    Main Results:

    • A putative Type IV IRES was identified in the 3' UTR of MeV-E, distinct from typical 5' UTR locations.
    • The MeV-E 3' IRES possesses a reduced size and confirmed secondary structure, interacting with the ribosome.
    • This IRES facilitates translation initiation for a downstream open reading frame, albeit at reduced efficiency compared to the 5' IRES.

    Conclusions:

    • The MeV-E 3' IRES represents a novel, compact Type IV IRES variant, likely adapted for regulated expression of downstream viral proteins.
    • Structural variations in IRES elements allow for precise tuning of translation levels, as demonstrated by the pared-down MeV-E 3' IRES.
    • This discovery provides insights into viral RNA structural diversity and its role in modulating gene expression.