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Nonsense-mediated mRNA Decay

Nonsense-mediated mRNA Decay

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.
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...

Nonsense-mediated mRNA Decay

Nonsense-mediated mRNA Decay

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.
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...

RNA Editing

RNA Editing

RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...

Improving Translational Accuracy

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...

Mismatch Repair

Mismatch Repair

Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
The Mutator Protein Family Plays a Key Role in DNA Mismatch Repair
The human genome has more than 3 billion base pairs of DNA per cell. Prior to cell division, that vast amount of genetic...

Mismatch Repair

Mismatch Repair

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Related Experiment Video

Updated: Jul 6, 2026

ACT1-CUP1 Assays Determine the Substrate-Specific Sensitivities of Spliceosomal Mutants in Budding Yeast

ACT1-CUP1 Assays Determine the Substrate-Specific Sensitivities of Spliceosomal Mutants in Budding Yeast

Published on: June 30, 2022

Eukaryotic wobble uridine modifications promote a functionally redundant decoding system.

Marcus J O Johansson¹, Anders Esberg, Bo Huang

¹Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden.

Molecular and Cellular Biology

|March 12, 2008

Summary

Naturally occurring tRNA modifications, like 5-methoxycarbonylmethyl (mcm(5)) and 5-carbamoylmethyl (ncm(5)) side chains, are crucial for decoding G-ending codons in yeast. Concurrent mcm(5) and 2-thio (s(2)) groups enhance decoding of both A- and G-ending codons.

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Engineering Artificial Factors to Specifically Manipulate Alternative Splicing in Human Cells

Engineering Artificial Factors to Specifically Manipulate Alternative Splicing in Human Cells

Published on: April 26, 2017

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Last Updated: Jul 6, 2026

ACT1-CUP1 Assays Determine the Substrate-Specific Sensitivities of Spliceosomal Mutants in Budding Yeast

ACT1-CUP1 Assays Determine the Substrate-Specific Sensitivities of Spliceosomal Mutants in Budding Yeast

Published on: June 30, 2022

Engineering Artificial Factors to Specifically Manipulate Alternative Splicing in Human Cells

Engineering Artificial Factors to Specifically Manipulate Alternative Splicing in Human Cells

Published on: April 26, 2017

Area of Science:

Molecular Biology
Genetics
Biochemistry

Background:

Transfer RNA (tRNA) nucleoside modifications fine-tune translational decoding.
Uridines at the wobble position (U(34)) in eukaryotic tRNAs commonly feature 5-methoxycarbonylmethyl (mcm(5)) or 5-carbamoylmethyl (ncm(5)) side chains, sometimes with 2-thio (s(2)) or 2'-O-methyl groups.
The in vivo functions of these modifications remain largely undefined.

Purpose of the Study:

To investigate the in vivo roles of tRNA nucleoside modifications at the wobble position.
To test established wobble rules using modification-deficient Saccharomyces cerevisiae cells.

Main Methods:

Utilized recently characterized modification-deficient Saccharomyces cerevisiae (yeast) strains.
Assessed tRNA decoding properties in vivo by analyzing the impact of specific modifications.

Main Results:

mcm(5) and ncm(5) side chains on U(34) promote the decoding of G-ending codons.
The presence of both mcm(5) and s(2) groups enhances the reading of both A- and G-ending codons.
Certain mcm(5)U(34)- and ncm(5)U(34)-containing tRNAs efficiently decode G-ending codons, challenging previous notions.

Conclusions:

Eukaryotic tRNA modifications play a critical role in codon decoding specificity.
The findings challenge the long-held belief that eukaryotes do not employ U-G wobble pairing.
These modifications are essential for accurate and efficient translation in vivo.