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Related Concept Videos

Transcription Elongation Factors02:35

Transcription Elongation Factors

Transcription elongation is a dynamic process that alters depending upon the sequence heterogeneity of the DNA being transcribed. Hence, it is not surprising that the elongation complex's composition also varies along the way while transcribing a gene.
The transcription elongation is regulated via pausing of RNA polymerase on several occasions during transcription. In bacteria, these halts are necessary because the transcription of DNA into mRNA is coupled to the translation of that mRNA into a...
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...
Stringent Response in E. coli01:23

Stringent Response in E. coli

Bacterial growth is closely tied to nutrient availability, with cells proliferating exponentially under favorable conditions and entering a stationary phase when resources become scarce. This transition is mediated by a regulatory mechanism known as the stringent response, which allows bacteria to adapt to nutrient deprivation by modulating gene expression and metabolic activity.During nutrient scarcity, intracellular amino acid levels decline. It results in the accumulation of uncharged tRNAs...
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...
Lagging Strand Synthesis01:59

Lagging Strand Synthesis

During replication, the complementary strands in double-stranded DNA are synthesized at different rates. Replication first begins on the leading strand. Replication starts later, occurs more slowly, and proceeds discontinuously on the lagging strand.
There are several major differences between synthesis of the leading strand and synthesis of the lagging strand. 1) Leading strand synthesis happens in the direction of replication fork opening, whereas lagging strand synthesis happens in the...

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Artificial RNA Polymerase II Elongation Complexes for Dissecting Co-transcriptional RNA Processing Events
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Published on: May 13, 2019

Quantifying elongation rhythm during full-length protein synthesis.

Gabriel Rosenblum1, Chunlai Chen, Jaskiran Kaur

  • 1Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA.

Journal of the American Chemical Society
|July 5, 2013
PubMed
Summary

Ribosomal pauses control protein synthesis rhythm. Single-molecule Förster resonance energy transfer (smFRET) reveals how transfer RNA (tRNA) selection influences protein synthesis speed and rhythm, impacting protein folding and modification.

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Isolation of Ribosome Bound Nascent Polypeptides in vitro to Identify Translational Pause Sites Along mRNA

Published on: July 6, 2012

Area of Science:

  • Molecular Biology
  • Biophysics
  • Genetics

Background:

  • Ribosomal pauses are critical for regulating protein synthesis and ensuring proper protein formation.
  • Mutations affecting these pauses can lead to misfolded proteins and human diseases.
  • Traditional ensemble methods struggle to analyze subtle pauses, necessitating advanced single-molecule techniques.

Purpose of the Study:

  • To investigate the role of codon and transfer RNA (tRNA) usage in modulating protein synthesis elongation rates.
  • To quantitatively assess the impact of tRNA abundance on protein synthesis dynamics.
  • To explore the influence of tRNA selection on co-translational processes like protein folding and modification.

Main Methods:

  • Utilized single-molecule Förster resonance energy transfer (smFRET) to monitor real-time protein expression.
  • Studied the synthesis of a full-length protein, specifically the Emerald Green Fluorescent Protein (GFP) variant.
  • Correlated measured elongation rates with codon usage and isoacceptor tRNA availability.

Main Results:

  • Demonstrated significant correlations between protein elongation rates and the usage of specific codons and their cognate tRNAs.
  • Quantitatively estimated the effect of substituting abundant tRNA-recognizing codons with synonymous, rarer tRNA codons on elongation rate.
  • Provided evidence for tRNA selection as a key modulator of protein synthesis rates and rhythms.

Conclusions:

  • tRNA selection is a crucial factor in regulating the speed and rhythm of protein synthesis.
  • These findings suggest that tRNA availability can influence simultaneous co-translational events, including protein folding and chemical modifications.
  • Single-molecule approaches are effective for characterizing subtle pauses in protein synthesis that impact cellular function and disease.