Analysis of Stop Codons within Prokaryotic Protein-Coding Genes Suggests Frequent Readthrough Events
| Autor: | Igor B. Rogozin, Vyacheslav Yurchenko, Eugenia Poliakov, Ishan Ganguly, Frida Belinky |
|---|---|
| Rok vydání: | 2021 |
| Předmět: |
0301 basic medicine
short-term evolution media_common.quotation_subject Pseudogene Nonsense Nonsense mutation Biology Article Catalysis Conserved sequence Evolution Molecular lcsh:Chemistry Inorganic Chemistry Open Reading Frames 03 medical and health sciences Negative selection 0302 clinical medicine Bacterial Proteins Sequence Homology Nucleic Acid expression Point Mutation population polymorphism Selection Genetic Physical and Theoretical Chemistry lcsh:QH301-705.5 Molecular Biology Gene Phylogeny Spectroscopy media_common Genetics Bacteria Base Sequence Models Genetic Organic Chemistry negative selection General Medicine Stop codon Computer Science Applications 030104 developmental biology Prokaryotic Cells lcsh:Biology (General) lcsh:QD1-999 Codon Nonsense Codon Terminator Rate of evolution in-fame stop codon Pseudogenes 030217 neurology & neurosurgery |
| Zdroj: | International Journal of Molecular Sciences, Vol 22, Iss 1876, p 1876 (2021) International Journal of Molecular Sciences Volume 22 Issue 4 |
| ISSN: | 1422-0067 |
| DOI: | 10.3390/ijms22041876 |
| Popis: | Nonsense mutations turn a coding (sense) codon into an in-frame stop codon that is assumed to result in a truncated protein product. Thus, nonsense substitutions are the hallmark of pseudogenes and are used to identify them. Here we show that in-frame stop codons within bacterial protein-coding genes are widespread. Their evolutionary conservation suggests that many of them are not pseudogenes, since they maintain dN/dS values (ratios of substitution rates at non-synonymous and synonymous sites) significantly lower than 1 (this is a signature of purifying selection in protein-coding regions). We also found that double substitutions in codons—where an intermediate step is a nonsense substitution—show a higher rate of evolution compared to null models, indicating that a stop codon was introduced and then changed back to sense via positive selection. This further supports the notion that nonsense substitutions in bacteria are relatively common and do not necessarily cause pseudogenization. In-frame stop codons may be an important mechanism of regulation: Such codons are likely to cause a substantial decrease of protein expression levels. |
| Databáze: | OpenAIRE |
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