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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,...

Frames

Frames

Frames are essential components of various mechanical and structural systems used daily. These structures are known for their stability and ability to bear heavy loads. A frame is constructed using two-force and multi-force members, interconnected using pin joints. In contrast, trusses are made entirely of two-force members.
Frames are versatile and widely used in various applications such as structural supports for beams and columns, automobile chassis construction, and in the construction...

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...

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...

Point and Frameshift Mutations

Point and Frameshift Mutations

Point mutations are genetic alterations involving the change of a single nucleotide base pair in DNA. Depending on how the alteration affects protein synthesis, they can lead to various consequences.Point mutations fall into the following types:Silent mutations occur when a nucleotide change does not alter the amino acid sequence due to the redundancy of the genetic code. For instance, changing ACC to ACA still encodes threonine, leaving the protein function unaffected. This occurs because...

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Related Experiment Video

Updated: Jul 10, 2026

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

Published on: February 18, 2022

A computational model for reading frame maintenance.

L Ponnala¹, D L Bitzer, A Stomp

¹Dept. of Electr. & Comput. Eng., North Carolina State Univ., Raleigh, NC 27695, USA.

Conference Proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference

|October 20, 2007

Summary

This summary is machine-generated.

A weak sinusoidal pattern in translation may encode reading frame information. This study models ribosome frameshifting, showing a link between signal phase and reading frame accuracy during elongation.

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De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

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An In Vitro Single-Molecule Imaging Assay for the Analysis of Cap-Dependent Translation Kinetics

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Published on: September 15, 2020

Area of Science:

Molecular Biology
Bioinformatics
Genetics

Background:

Translation involves ribosome movement along mRNA.
Maintaining the correct reading frame is crucial for accurate protein synthesis.
Frameshifting, or slipping out of the correct reading frame, can lead to non-functional proteins.

Purpose of the Study:

To investigate a hypothesized signal in 16S rRNA-mRNA interactions.
To explore the role of this signal in maintaining the translational reading frame.
To develop and validate a model predicting ribosome in-frame status.

Main Methods:

Analysis of the free energy pattern during 16S rRNA-mRNA interaction.
Investigating the prfB gene in E. coli as a model for frameshifting.
Developing a computational model for ribosome reading frame maintenance.
Validating the model using verified E. coli coding sequences.

Main Results:

A weak sinusoidal pattern (frequency 1/3 cycles/nucleotide) was detected in the free energy of 16S rRNA-mRNA interaction.
A direct relationship was observed between cumulative signal phase and reading frame in the prfB frameshifter.
The developed model shows predictive power for ribosome in-frame status during elongation.

Conclusions:

The identified sinusoidal signal likely plays a role in maintaining the translational reading frame.
The computational model provides a framework for understanding ribosome fidelity during elongation.
This finding contributes to understanding the mechanisms of translational control and accuracy.