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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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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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The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
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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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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.
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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...
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Genome-wide Quantification of Translation in Budding Yeast by Ribosome Profiling
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Ribosome Fate during Decoding of UGA-Sec Codons.

Paul R Copeland1, Michael T Howard2

  • 1Department of Biochemistry and Molecular Biology, Rutgers-Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA.

International Journal of Molecular Sciences
|December 24, 2021
PubMed
Summary

Genetic recoding allows UGA codons to encode selenocysteine, the 21st amino acid, during protein synthesis. This review explores the mechanisms of this UGA recoding and the fate of ribosomes during selenoprotein translation.

Keywords:
SECISSECIS-binding proteinnonsense-mediated decayrecodingribosome rescueselenocysteineselenoproteintranslation termination

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Area of Science:

  • Molecular Biology
  • Genetics
  • Biochemistry

Background:

  • Translation typically follows universal genetic code rules.
  • Specific mRNA signals can alter standard codon assignments.
  • Selenoprotein synthesis involves a unique recoding event.

Purpose of the Study:

  • To review the mechanisms of UGA recoding.
  • To discuss the incorporation of selenocysteine.
  • To examine ribosome behavior during selenoprotein translation.

Main Methods:

  • Literature review of existing research on mRNA recoding.
  • Analysis of mechanisms governing UGA codon reassignment.
  • Investigation of selenoprotein synthesis pathways.

Main Results:

  • UGA codons are recoded to selenocysteine in selenoprotein mRNAs.
  • Specific sequences and factors facilitate this recoding.
  • Ribosomes may stall or terminate if selenocysteine incorporation fails.

Conclusions:

  • mRNA recoding provides a mechanism for expanding the proteome.
  • Understanding UGA recoding is crucial for selenoprotein biology.
  • Ribosome fate after failed recoding impacts protein production.