Related Experiment Video

Updated: Apr 22, 2026

Identifying Amino Acid Overproducers Using Rare-Codon-Rich Markers
10:41

Identifying Amino Acid Overproducers Using Rare-Codon-Rich Markers

Published on: June 24, 2019

7.9K

Limitations of the 'ambush hypothesis' at the single-gene scale: what codon biases are to blame?

Robert L Bertrand1, Mona Abdel-Hameed, John L Sorensen

  • 1Department of Chemistry, University of Manitoba, Winnipeg, R3T 2N2, Canada, bertrarl@cc.umanitoba.ca.

Molecular Genetics and Genomics : MGG
|October 14, 2014
PubMed

Insights

Ribosomal frameshifting causes errors in protein synthesis. Our study on fungal PKS genes found fewer hidden stop codons than expected, challenging the Ambush Hypothesis.

Area of Science:

  • Molecular Biology
  • Evolutionary Genetics
  • Bioinformatics

Background:

  • Ribosomal frameshifting is a translational error that alters protein sequences, leading to wasted cellular resources and potentially cytotoxic peptides.
  • The Ambush Hypothesis proposes selective pressure favors hidden stop codons to mitigate frameshifting costs.
  • Previous genomic studies supported the Ambush Hypothesis, but its applicability at the single-gene level remained unexplored.

Purpose of the Study:

  • To investigate the prevalence of hidden stop codons in fungal polyketide synthase (PKS) genes.
  • To determine if the Ambush Hypothesis applies to individual genes.
  • To explore potential reasons for deviations from the Ambush Hypothesis in PKS genes.

Main Methods:

  • Analysis of PKS genes across various fungal species.
  • Statistical comparison of observed hidden stop codon frequencies against a neutral evolution model.
  • Bioinformatic assessment of codon usage biases within PKS genes.

Main Results:

  • Fungal PKS genes exhibited significantly fewer hidden stop codons than predicted by a neutral model (p < 0.0005).
  • This finding contradicts the predictions of the Ambush Hypothesis at the single-gene scale.
  • Evidence suggests suppression of hidden stop codon evolution in PKS genes.

Conclusions:

  • The Ambush Hypothesis may not universally apply to all genes, particularly at the single-gene level.
  • Competing codon biases in PKS genes likely override the selective pressure for hidden stop codons.
  • Further research integrating the Ambush Hypothesis with codon bias drivers is needed for a comprehensive genetic theory.

More Related Videos

Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation07:15

Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation

Published on: January 16, 2019

10.2K
Genotyping Single Nucleotide Polymorphisms in the Mitochondrial Genome by Pyrosequencing07:24

Genotyping Single Nucleotide Polymorphisms in the Mitochondrial Genome by Pyrosequencing

Published on: February 10, 2023

2.0K

Related Concept Videos

From DNA to Protein03:06

From DNA to Protein

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...
20.6K
Leaky Scanning02:28

Leaky Scanning

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...
4.5K
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
6.2K
The Central Dogma01:25

The Central Dogma

Overview
116.1K
The Central Dogma01:20

The Central Dogma

The central dogma explains the flow of genetic information from DNA nucleotides to the amino acid sequence of proteins.
RNA is the Missing Link Between DNA and Proteins
In the early 1900s, scientists discovered that DNA stores all the information needed for cellular functions and that proteins perform most of these functions. However, the mechanisms of converting genetic information into functional proteins remained unknown for many years. Initially, it was believed that a single gene is...
21.1K
Genome Copying Errors02:46

Genome Copying Errors

DNA replication is a well-evolved process that copies millions of base pairs with high fidelity during each cell division. Occasionally a wrong base or a long stretch of wrong bases may get added to the daughter strands. If the errors are left unchecked, cells might accumulate several mutations that might endanger their  survival. Therefore, the copying errors are checked and repaired at three levels.
4.2K