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Predicted Functional RNAs within Coding Regions Constrain Evolutionary Rates of Yeast Proteins
- Source :
- PLoS ONE, PLoS ONE, Vol 3, Iss 2, p e1559 (2008)
- Publication Year :
- 2008
- Publisher :
- Public Library of Science, 2008.
-
Abstract
- Functional RNAs (fRNAs) are being recognized as an important regulatory component in biological processes. Interestingly, recent computational studies suggest that the number and biological significance of functional RNAs within coding regions (coding fRNAs) may have been underestimated. We hypothesized that such coding fRNAs will impose additional constraint on sequence evolution because the DNA primary sequence has to simultaneously code for functional RNA secondary structures on the messenger RNA in addition to the amino acid codons for the protein sequence. To test this prediction, we first utilized computational methods to predict conserved fRNA secondary structures within multiple species alignments of Saccharomyces sensu strico genomes. We predict that as much as 5% of the genes in the yeast genome contain at least one functional RNA secondary structure within their protein-coding region. We then analyzed the impact of coding fRNAs on the evolutionary rate of protein-coding genes because a decrease in evolutionary rate implies constraint due to biological functionality. We found that our predicted coding fRNAs have a significant influence on evolutionary rates (especially at synonymous sites), independent of other functional measures. Thus, coding fRNA may play a role on sequence evolution. Given that coding regions of humans and flies contain many more predicted coding fRNAs than yeast, the impact of coding fRNAs on sequence evolution may be substantial in genomes of higher eukaryotes.
- Subjects :
- Genome evolution
lcsh:Medicine
Sequence alignment
Computational biology
Biology
Genome
Evolution, Molecular
Fungal Proteins
Molecular evolution
Coding region
lcsh:Science
Evolutionary Biology/Genomics
Gene
Genetics
Multidisciplinary
Evolutionary Biology/Evolutionary and Comparative Genetics
Base Sequence
Human evolutionary genetics
lcsh:R
Computational Biology
RNA, Fungal
Sequence Analysis, DNA
Non-coding RNA
lcsh:Q
Genetics and Genomics/Comparative Genomics
Genome, Fungal
Sequence Alignment
Research Article
Subjects
Details
- Language :
- English
- ISSN :
- 19326203
- Volume :
- 3
- Issue :
- 2
- Database :
- OpenAIRE
- Journal :
- PLoS ONE
- Accession number :
- edsair.doi.dedup.....8a593c5ac01a7453f3a12757bedcd6a2