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Related Concept Videos

Termination of Translation01:44

Termination of Translation

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The large ribosomal subunit has several important structures essential to translation. These include the peptidyl transferase center (PTC) - which is the site where the peptide bond is formed - and a large, internal, water-filled tube through which the nascent polypeptide moves. This latter structure is called the Peptide Exit Tunnel, and it begins at the PTC and spans the body of the large ribosomal subunit. During translation, as the nascent polypeptide chain is synthesized, it passes through...
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Leaky Scanning02:28

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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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Initiation of Translation02:33

Initiation of Translation

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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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Initiation of Translation02:33

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Improving Translational Accuracy02:07

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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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Analysis of Termination of Transcription Using BrUTP-strand-specific Transcription Run-on TRO Approach
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Structural basis for ArfA-RF2-mediated translation termination on mRNAs lacking stop codons.

Paul Huter1, Claudia Müller1, Bertrand Beckert1,2

  • 1Gene Center, Department of Biochemistry and Center for integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.

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|December 2, 2016
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Summary

Alternative rescue factor A (ArfA) rescues bacterial ribosomes stalled on truncated mRNAs. This study reveals ArfA

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Area of Science:

  • Bacterial translation termination
  • Ribosome rescue mechanisms
  • Molecular cryo-electron microscopy

Background:

  • Bacteria utilize tmRNA, ArfA, or ArfB to rescue ribosomes stalled on truncated mRNAs lacking stop codons.
  • Previous structural studies elucidated tmRNA-ribosome and ArfB-ribosome complexes, but ArfA's mechanism remained unclear.

Purpose of the Study:

  • To elucidate the structural mechanism by which ArfA recognizes truncated mRNAs and recruits release factor 2 (RF2) for ribosome rescue.
  • To determine the structure of the Escherichia coli 70S ribosome stalled on a truncated mRNA in complex with ArfA and RF2.

Main Methods:

  • Cryo-electron microscopy (cryo-EM) reconstruction of the 70S ribosome stalled on a truncated mRNA with ArfA and RF2.
  • Structural analysis of molecular interactions between ArfA, RF2, and the ribosome.

Main Results:

  • The C-terminus of ArfA binds the mRNA entry channel of the small ribosomal subunit, enabling discrimination between truncated and full-length mRNAs.
  • The N-terminus of ArfA interacts with the decoding domain of RF2, facilitating RF2 recruitment to the stalled ribosome.
  • ArfA stabilizes an active conformation of RF2, mimicking canonical termination by positioning the GGQ motif at the peptidyl-transferase center.

Conclusions:

  • The structure reveals how ArfA recruits RF2 to stalled ribosomes.
  • ArfA promotes an active RF2 conformation, enabling translation termination even without a stop codon.
  • This provides a molecular understanding of the ArfA-mediated ribosome rescue pathway.