In eubacteria, unlike eukaryotes, there is no evidence for selection favouring fail-safe 3' additional stop codons

Area of Science:

• Genetics
• Molecular Biology
• Evolutionary Biology

Background:

• Gene expression errors can be harmful, leading to selection for mechanisms that mitigate their effects.
• Additional stop codons (ASCs) are in-frame sequences downstream of the primary stop codon, potentially preventing deleterious consequences of translational read-through.
• While ASCs are found in eukaryotes, their role in prokaryotes, specifically eubacteria, remains largely unexplored despite high read-through rates.

Purpose of the Study:

• To systematically investigate the hypothesis that ASCs function as a fail-safe mechanism in eubacteria.
• To compare the presence and selection patterns of ASCs in eubacteria with existing evidence from eukaryotes.

Main Methods:

• Analysis of ASCs in eubacterial genomes, focusing on their frequency and distribution downstream of primary stop codons.
• Examination of substitution patterns in 3' sequences, including in-frame and out-of-frame changes affecting stop codons.
• Correlation analysis between gene expression levels and the presence of ASCs.
• Investigation of primary stop codon usage (TGA vs. TAA) in highly and lowly expressed genes in relation to ASC enrichment.

Main Results:

• Contrary to expectations, a paucity, not an enrichment, of ASCs was observed downstream of primary stop codons in eubacteria.
• Substitutions that degrade stop codons were more frequent in-frame than out-of-frame in the 3' sequence.
• Highly expressed genes showed no greater likelihood of possessing ASCs compared to lowly expressed genes.
• The usage of the leaky stop codon TGA in highly expressed genes did not predict ASC enrichment, even when compared to the non-leaky stop codon TAA in lowly expressed genes.

Conclusions:

• There is no compelling evidence to support the selection of ASCs as a protective mechanism in eubacteria.
• This finding highlights an intriguing divergence in error-correction strategies between eukaryotes and prokaryotes, despite a shared potential error (read-through).
• Possible explanations include the absence of nonsense-mediated decay in bacteria, leading to gene truncation for error resolution, and distinct mechanisms in eukaryotes.