Synonymous codon usage influences the local protein structure observed
Translation of mRNA into protein is a unidirectional information flow process. Analysing the input (mRNA) and output (protein) of translation, we find that local protein structure information is encoded in the mRNA nucleotide sequence. The Coding Sequence and Structure (CSandS) database developed in...
| Main Authors: | , |
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| Format: | Journal article |
| Language: | English |
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Oxford University Press
2010
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| _version_ | 1826270782143070208 |
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| author | Saunders, R Deane, C |
| author_facet | Saunders, R Deane, C |
| author_sort | Saunders, R |
| collection | OXFORD |
| description | Translation of mRNA into protein is a unidirectional information flow process. Analysing the input (mRNA) and output (protein) of translation, we find that local protein structure information is encoded in the mRNA nucleotide sequence. The Coding Sequence and Structure (CSandS) database developed in this work provides a detailed mapping between over 4000 solved protein structures and their mRNA. CSandS facilitates a comprehensive analysis of codon usage over many organisms. In assigning translation speed, we find that relative codon usage is less informative than tRNA concentration. For all speed measures, no evidence was found that domain boundaries are enriched with slow codons. In fact, genes seemingly avoid slow codons around structurally defined domain boundaries. Translation speed, however, does decrease at the transition into secondary structure. Codons are identified that have structural preferences significantly different from the amino acid they encode. However, each organism has its own set of 'significant codons'. Our results support the premise that codons encode more information than merely amino acids and give insight into the role of translation in protein folding. |
| first_indexed | 2024-03-06T21:46:13Z |
| format | Journal article |
| id | oxford-uuid:49b17980-6e6e-4d15-a977-7bc78a063824 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-06T21:46:13Z |
| publishDate | 2010 |
| publisher | Oxford University Press |
| record_format | dspace |
| spelling | oxford-uuid:49b17980-6e6e-4d15-a977-7bc78a0638242022-03-26T15:33:03ZSynonymous codon usage influences the local protein structure observedJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:49b17980-6e6e-4d15-a977-7bc78a063824Statistics (see also social sciences)EnglishOxford University Research Archive - ValetOxford University Press2010Saunders, RDeane, CTranslation of mRNA into protein is a unidirectional information flow process. Analysing the input (mRNA) and output (protein) of translation, we find that local protein structure information is encoded in the mRNA nucleotide sequence. The Coding Sequence and Structure (CSandS) database developed in this work provides a detailed mapping between over 4000 solved protein structures and their mRNA. CSandS facilitates a comprehensive analysis of codon usage over many organisms. In assigning translation speed, we find that relative codon usage is less informative than tRNA concentration. For all speed measures, no evidence was found that domain boundaries are enriched with slow codons. In fact, genes seemingly avoid slow codons around structurally defined domain boundaries. Translation speed, however, does decrease at the transition into secondary structure. Codons are identified that have structural preferences significantly different from the amino acid they encode. However, each organism has its own set of 'significant codons'. Our results support the premise that codons encode more information than merely amino acids and give insight into the role of translation in protein folding. |
| spellingShingle | Statistics (see also social sciences) Saunders, R Deane, C Synonymous codon usage influences the local protein structure observed |
| title | Synonymous codon usage influences the local protein structure observed |
| title_full | Synonymous codon usage influences the local protein structure observed |
| title_fullStr | Synonymous codon usage influences the local protein structure observed |
| title_full_unstemmed | Synonymous codon usage influences the local protein structure observed |
| title_short | Synonymous codon usage influences the local protein structure observed |
| title_sort | synonymous codon usage influences the local protein structure observed |
| topic | Statistics (see also social sciences) |
| work_keys_str_mv | AT saundersr synonymouscodonusageinfluencesthelocalproteinstructureobserved AT deanec synonymouscodonusageinfluencesthelocalproteinstructureobserved |