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Related Concept Videos

Initiation of Translation02:33

Initiation of Translation

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...
Initiation of Translation02:33

Initiation of Translation

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...
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...
From DNA to Protein03:06

From DNA to Protein

The flow of genetic information in cells from DNA to mRNA to protein is described by the central dogma, which states that genes specify the sequence of mRNAs, which in turn specify the sequence of amino acids making up all proteins. The decoding of one molecule to another is performed by specific proteins and RNAs. Because the information stored in DNA is so central to cellular function, it makes intuitive sense that the cell would make mRNA copies of this information for protein synthesis...
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...
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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Related Experiment Video

Updated: May 10, 2026

Toeprinting Analysis of Translation Initiation Complex Formation on Mammalian mRNAs
10:37

Toeprinting Analysis of Translation Initiation Complex Formation on Mammalian mRNAs

Published on: May 10, 2018

Efficient translation initiation dictates codon usage at gene start.

Kajetan Bentele1, Paul Saffert, Robert Rauscher

  • 1Institute for Theoretical Biology, Humboldt Universität zu Berlin, Berlin, Germany.

Molecular Systems Biology
|June 19, 2013
PubMed
Summary
This summary is machine-generated.

Bacterial gene translation rates are primarily influenced by mRNA structure near the start codon, not codon usage. Selection favors codons that reduce mRNA folding, optimizing translation initiation.

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Last Updated: May 10, 2026

Toeprinting Analysis of Translation Initiation Complex Formation on Mammalian mRNAs
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Area of Science:

  • Evolutionary genetics
  • Molecular biology
  • Genomics

Background:

  • The genetic code's degeneracy means protein evolution doesn't dictate DNA sequence.
  • Unusual codon usage at the start of bacterial genes is debated: slowed elongation vs. efficient initiation.
  • Reduced mRNA folding near translation start sites suggests selection for efficient initiation.

Purpose of the Study:

  • To differentiate between selection for slowed elongation and selection for reduced mRNA structure at gene start sites.
  • To determine the primary driver of unusual codon usage in bacterial gene translation initiation.

Main Methods:

  • Genome-wide analysis of codon usage and mRNA folding in bacterial genes.
  • Experimental validation of the role of mRNA structure versus codon usage in translation rate.

Main Results:

  • Bacterial selection favors codons that minimize mRNA folding around the translation start site.
  • This preference for reduced mRNA structure holds true for both frequent and rare codons.
  • Experimental results confirm mRNA structure, not codon usage, dictates translation rate at gene beginnings.

Conclusions:

  • Selection for reduced mRNA folding at the translation start is the dominant force shaping initial codon choice in bacteria.
  • Unusual codon usage is likely a consequence of selection for optimal mRNA structure, not a direct selection for specific codon frequencies.