Large scale comparative codon-pair context analysis unveils general rules that fine-tune evolution of mRNA primary structure.
BACKGROUND: Codon usage and codon-pair context are important gene primary structure features that influence mRNA decoding fidelity. In order to identify general rules that shape codon-pair context and minimize mRNA decoding error, we have carried out a large scale comparative codon-pair context anal...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2007-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC1952141?pdf=render |
| _version_ | 1819127970598486016 |
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| author | Gabriela Moura Miguel Pinheiro Joel Arrais Ana Cristina Gomes Laura Carreto Adelaide Freitas José L Oliveira Manuel A S Santos |
| author_facet | Gabriela Moura Miguel Pinheiro Joel Arrais Ana Cristina Gomes Laura Carreto Adelaide Freitas José L Oliveira Manuel A S Santos |
| author_sort | Gabriela Moura |
| collection | DOAJ |
| description | BACKGROUND: Codon usage and codon-pair context are important gene primary structure features that influence mRNA decoding fidelity. In order to identify general rules that shape codon-pair context and minimize mRNA decoding error, we have carried out a large scale comparative codon-pair context analysis of 119 fully sequenced genomes. METHODOLOGIES/PRINCIPAL FINDINGS: We have developed mathematical and software tools for large scale comparative codon-pair context analysis. These methodologies unveiled general and species specific codon-pair context rules that govern evolution of mRNAs in the 3 domains of life. We show that evolution of bacterial and archeal mRNA primary structure is mainly dependent on constraints imposed by the translational machinery, while in eukaryotes DNA methylation and tri-nucleotide repeats impose strong biases on codon-pair context. CONCLUSIONS: The data highlight fundamental differences between prokaryotic and eukaryotic mRNA decoding rules, which are partially independent of codon usage. |
| first_indexed | 2024-12-22T08:20:23Z |
| format | Article |
| id | doaj.art-01c10da5a75245a682d996c3320cf377 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-22T08:20:23Z |
| publishDate | 2007-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-01c10da5a75245a682d996c3320cf3772022-12-21T18:32:46ZengPublic Library of Science (PLoS)PLoS ONE1932-62032007-01-0129e84710.1371/journal.pone.0000847Large scale comparative codon-pair context analysis unveils general rules that fine-tune evolution of mRNA primary structure.Gabriela MouraMiguel PinheiroJoel ArraisAna Cristina GomesLaura CarretoAdelaide FreitasJosé L OliveiraManuel A S SantosBACKGROUND: Codon usage and codon-pair context are important gene primary structure features that influence mRNA decoding fidelity. In order to identify general rules that shape codon-pair context and minimize mRNA decoding error, we have carried out a large scale comparative codon-pair context analysis of 119 fully sequenced genomes. METHODOLOGIES/PRINCIPAL FINDINGS: We have developed mathematical and software tools for large scale comparative codon-pair context analysis. These methodologies unveiled general and species specific codon-pair context rules that govern evolution of mRNAs in the 3 domains of life. We show that evolution of bacterial and archeal mRNA primary structure is mainly dependent on constraints imposed by the translational machinery, while in eukaryotes DNA methylation and tri-nucleotide repeats impose strong biases on codon-pair context. CONCLUSIONS: The data highlight fundamental differences between prokaryotic and eukaryotic mRNA decoding rules, which are partially independent of codon usage.http://europepmc.org/articles/PMC1952141?pdf=render |
| spellingShingle | Gabriela Moura Miguel Pinheiro Joel Arrais Ana Cristina Gomes Laura Carreto Adelaide Freitas José L Oliveira Manuel A S Santos Large scale comparative codon-pair context analysis unveils general rules that fine-tune evolution of mRNA primary structure. PLoS ONE |
| title | Large scale comparative codon-pair context analysis unveils general rules that fine-tune evolution of mRNA primary structure. |
| title_full | Large scale comparative codon-pair context analysis unveils general rules that fine-tune evolution of mRNA primary structure. |
| title_fullStr | Large scale comparative codon-pair context analysis unveils general rules that fine-tune evolution of mRNA primary structure. |
| title_full_unstemmed | Large scale comparative codon-pair context analysis unveils general rules that fine-tune evolution of mRNA primary structure. |
| title_short | Large scale comparative codon-pair context analysis unveils general rules that fine-tune evolution of mRNA primary structure. |
| title_sort | large scale comparative codon pair context analysis unveils general rules that fine tune evolution of mrna primary structure |
| url | http://europepmc.org/articles/PMC1952141?pdf=render |
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