Related Experiment Video
Updated: Feb 11, 2026
11:26
Sequencing of mRNA from Whole Blood using Nanopore Sequencing
Published on: June 3, 2019
14.8K
Deciphering mRNA Sequence Determinants of Protein Production Rate
Juraj Szavits-Nossan1, Luca Ciandrini2, M Carmen Romano3
1SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom.
Physical Review Letters
|April 26, 2018
Summary
We developed a new analytic method to understand how DNA sequences control protein production rates. The first few codons and initiation rate significantly influence protein output, offering insights into evolutionary codon choice.
Area of Science:
- Biophysics
- Computational Biology
- Molecular Biology
Background:
- Understanding how coding sequences influence translation rates is crucial for predicting protein production.
- Biophysical models of translation are essential for deciphering these regulatory mechanisms.
Purpose of the Study:
- To develop an analytic method for solving translation models.
- To identify key nucleotide sequence features that determine protein production rates.
Main Methods:
- Utilized an inhomogeneous totally asymmetric simple exclusion process model.
- Employed an analytic solution validated against genome-wide simulations of S. cerevisiae transcript sequences.
Main Results:
- The study identified simple design principles of nucleotide sequences affecting protein production.
- The first 10 codons (ribosome footprint) and initiation rate are key determinants of protein production under physiological conditions.
Conclusions:
- The analytic method accurately predicts translation rates and protein production.
- Codon choice plays an evolutionary role in regulating translation rates and ribosome densities.
Related Concept Videos
03:08Rate-Determining Steps
37.5K
Relating Reaction Mechanisms
In a multistep reaction mechanism, one of the elementary steps progresses significantly slower than the others. This slowest step is called the rate-limiting step (or rate-determining step). A reaction cannot proceed faster than its slowest step, and hence, the rate-determining step limits the overall reaction rate.
The concept of rate-determining step can be understood from the analogy of a 4-lane freeway with a short-stretch of traffic-bottleneck caused due to...
In a multistep reaction mechanism, one of the elementary steps progresses significantly slower than the others. This slowest step is called the rate-limiting step (or rate-determining step). A reaction cannot proceed faster than its slowest step, and hence, the rate-determining step limits the overall reaction rate.
The concept of rate-determining step can be understood from the analogy of a 4-lane freeway with a short-stretch of traffic-bottleneck caused due to...
37.5K
02:22Regulated mRNA Transport
7.0K
In eukaryotes, transcription and translation are compartmentalized; an mRNA is first synthesized in the nucleus and then selectively transported to the cytoplasm for protein synthesis. Before transport, a pre-mRNA undergoes several steps of post-transcriptional modifications including splicing, 5' capping, and the addition of a poly-adenine tail. Various proteins bind to the pre-mRNA during these modifications. The mRNA transport takes place with the help of multiple proteins playing...
7.0K
02:01pre-mRNA Processing
57.6K
In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
Once about 20-40 ribonucleotides have been joined together by RNA polymerase, a group of enzymes adds a “cap” to the 5’ end of the growing transcript. In this process, a 5’ phosphate is replaced by modified guanosine that has a methyl group attached to it (7-Methyl...
Once about 20-40 ribonucleotides have been joined together by RNA polymerase, a group of enzymes adds a “cap” to the 5’ end of the growing transcript. In this process, a 5’ phosphate is replaced by modified guanosine that has a methyl group attached to it (7-Methyl...
57.6K
02:31Nuclear Export of mRNA
8.8K
Before mRNAs are exported to the cytoplasm, it is crucial to check each mRNA for structural and functional integrity. Eukaryotic cells use several different mechanisms, collectively known as mRNA surveillance, to look for irregularities in mRNAs. Irregular or aberrant mRNA are rapidly degraded by various enzymes. If a defective mRNA escapes the surveillance, it would be translated into a protein which would either be non-functional or not function properly. One of the primary irregularities in...
8.8K
02:27Nonsense-mediated mRNA Decay
11.9K
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,...
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...
11.9K
02:51mRNA Stability and Gene Expression
6.7K
The structure and stability of mRNA molecules regulates gene expression, as mRNAs are a key step in the pathway from gene to protein. In eukaryotes, the half-life of mRNA varies from a few minutes up to several days. mRNA stability is essential in growth and development. The absence of the proteins regulating its stability, such as tristetraprolin in mice, can cause systemic issues, including bone marrow overgrowth, inflammation, and autoimmunity.
Cis-acting Elements involved in mRNA stability
Cis-acting Elements involved in mRNA stability
6.7K