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Related Concept Videos

Ribosomal RNA Synthesis02:53

Ribosomal RNA Synthesis

Ribosome synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
Improving Translational Accuracy02:07

Improving Translational Accuracy

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...
Leaky Scanning02:28

Leaky Scanning

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 stands for...
Ribosome Profiling02:24

Ribosome Profiling

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.
The technique helps...
Ribosomal RNA Synthesis02:53

Ribosomal RNA Synthesis

Ribosome synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
Improving Translational Accuracy02:07

Improving Translational Accuracy

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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RIBO-seq in Bacteria: a Sample Collection and Library Preparation Protocol for NGS Sequencing
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Published on: August 7, 2021

Predicting ribosomal frameshifting efficiency.

Song Cao1, Shi-Jie Chen

  • 1Department of Physics and Department of Biochemistry, University of Missouri-Columbia, Columbia, MO 65211, USA.

Physical Biology
|March 28, 2008
PubMed
Summary
This summary is machine-generated.

Researchers explored the free energy landscape of -1 ribosomal frameshifting in retroviruses. This analysis revealed a quantitative link between frameshifting efficiency and tension forces during codon-anticodon complex movement.

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Area of Science:

  • Molecular Biology
  • Virology
  • Biophysics

Background:

  • Retroviruses utilize -1 ribosomal frameshifting for translational control of viral protein synthesis.
  • Accurate prediction of frameshifting efficiency is vital for understanding viral gene expression.

Purpose of the Study:

  • To investigate the free energy landscape of the minimal -1 programmed ribosomal frameshifting machinery.
  • To establish a quantitative relationship between frameshifting efficiency and physical forces involved.

Main Methods:

  • Analysis of the free energy landscape.
  • Inclusion of codon-anticodon base pairs at the slippery site.
  • Consideration of downstream messenger RNA structure and spacer length.

Main Results:

  • A quantitative relationship was identified between frameshifting efficiency and tension force during codon-anticodon complex movement.
  • No consistent correlation was found between frameshifting efficiency and the global stability of downstream mRNA structures.

Conclusions:

  • Tension forces during ribosome movement are key determinants of -1 frameshifting efficiency.
  • Downstream mRNA structure stability is not a primary driver of frameshifting efficiency.