Post-duplication charge evolution of phosphoglucose isomerases in teleost fishes through weak selection on many amino acid sites
<p>Abstract</p> <p>Background</p> <p>The partitioning of ancestral functions among duplicated genes by neutral evolution, or subfunctionalization, has been considered the primary process for the evolution of novel proteins (neofunctionalization). Nonetheless, how a subf...
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| Format: | Article |
| Language: | English |
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BMC
2007-10-01
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| Series: | BMC Evolutionary Biology |
| Online Access: | http://www.biomedcentral.com/1471-2148/7/204 |
| _version_ | 1818384792561909760 |
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| author | Sato Yukuto Nishida Mutsumi |
| author_facet | Sato Yukuto Nishida Mutsumi |
| author_sort | Sato Yukuto |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>The partitioning of ancestral functions among duplicated genes by neutral evolution, or subfunctionalization, has been considered the primary process for the evolution of novel proteins (neofunctionalization). Nonetheless, how a subfunctionalized protein can evolve into a more adaptive protein is poorly understood, mainly due to the limitations of current analytical methods, which can detect only strong selection for amino acid substitutions involved in adaptive molecular evolution. In this study, we employed a comparative evolutionary approach to this question, focusing on differences in the structural properties of a protein, specifically the electric charge, encoded by fish-specific duplicated phosphoglucose isomerase (<it>Pgi</it>) genes.</p> <p>Results</p> <p>Full-length cDNA cloning, RT-PCR based gene expression analyses, and comparative sequence analyses showed that after subfunctionalization with respect to the expression organ of duplicate <it>Pgi </it>genes, the net electric charge of the PGI-1 protein expressed mainly in internal tissues became more negative, and that of PGI-2 expressed mainly in muscular tissues became more positive. The difference in net protein charge was attributable not to specific amino acid sites but to the sum of various amino acid sites located on the surface of the PGI molecule.</p> <p>Conclusion</p> <p>This finding suggests that the surface charge evolution of PGI proteins was not driven by strong selection on individual amino acid sites leading to permanent fixation of a particular residue, but rather was driven by weak selection on a large number of amino acid sites and consequently by steady directional and/or purifying selection on the overall structural properties of the protein, which is derived from many modifiable sites. The mode of molecular evolution presented here may be relevant to various cases of adaptive modification in proteins, such as hydrophobic properties, molecular size, and electric charge.</p> |
| first_indexed | 2024-12-14T03:27:53Z |
| format | Article |
| id | doaj.art-446005ade16342628d6cbeaff22ef0b3 |
| institution | Directory Open Access Journal |
| issn | 1471-2148 |
| language | English |
| last_indexed | 2024-12-14T03:27:53Z |
| publishDate | 2007-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Evolutionary Biology |
| spelling | doaj.art-446005ade16342628d6cbeaff22ef0b32022-12-21T23:18:50ZengBMCBMC Evolutionary Biology1471-21482007-10-017120410.1186/1471-2148-7-204Post-duplication charge evolution of phosphoglucose isomerases in teleost fishes through weak selection on many amino acid sitesSato YukutoNishida Mutsumi<p>Abstract</p> <p>Background</p> <p>The partitioning of ancestral functions among duplicated genes by neutral evolution, or subfunctionalization, has been considered the primary process for the evolution of novel proteins (neofunctionalization). Nonetheless, how a subfunctionalized protein can evolve into a more adaptive protein is poorly understood, mainly due to the limitations of current analytical methods, which can detect only strong selection for amino acid substitutions involved in adaptive molecular evolution. In this study, we employed a comparative evolutionary approach to this question, focusing on differences in the structural properties of a protein, specifically the electric charge, encoded by fish-specific duplicated phosphoglucose isomerase (<it>Pgi</it>) genes.</p> <p>Results</p> <p>Full-length cDNA cloning, RT-PCR based gene expression analyses, and comparative sequence analyses showed that after subfunctionalization with respect to the expression organ of duplicate <it>Pgi </it>genes, the net electric charge of the PGI-1 protein expressed mainly in internal tissues became more negative, and that of PGI-2 expressed mainly in muscular tissues became more positive. The difference in net protein charge was attributable not to specific amino acid sites but to the sum of various amino acid sites located on the surface of the PGI molecule.</p> <p>Conclusion</p> <p>This finding suggests that the surface charge evolution of PGI proteins was not driven by strong selection on individual amino acid sites leading to permanent fixation of a particular residue, but rather was driven by weak selection on a large number of amino acid sites and consequently by steady directional and/or purifying selection on the overall structural properties of the protein, which is derived from many modifiable sites. The mode of molecular evolution presented here may be relevant to various cases of adaptive modification in proteins, such as hydrophobic properties, molecular size, and electric charge.</p>http://www.biomedcentral.com/1471-2148/7/204 |
| spellingShingle | Sato Yukuto Nishida Mutsumi Post-duplication charge evolution of phosphoglucose isomerases in teleost fishes through weak selection on many amino acid sites BMC Evolutionary Biology |
| title | Post-duplication charge evolution of phosphoglucose isomerases in teleost fishes through weak selection on many amino acid sites |
| title_full | Post-duplication charge evolution of phosphoglucose isomerases in teleost fishes through weak selection on many amino acid sites |
| title_fullStr | Post-duplication charge evolution of phosphoglucose isomerases in teleost fishes through weak selection on many amino acid sites |
| title_full_unstemmed | Post-duplication charge evolution of phosphoglucose isomerases in teleost fishes through weak selection on many amino acid sites |
| title_short | Post-duplication charge evolution of phosphoglucose isomerases in teleost fishes through weak selection on many amino acid sites |
| title_sort | post duplication charge evolution of phosphoglucose isomerases in teleost fishes through weak selection on many amino acid sites |
| url | http://www.biomedcentral.com/1471-2148/7/204 |
| work_keys_str_mv | AT satoyukuto postduplicationchargeevolutionofphosphoglucoseisomerasesinteleostfishesthroughweakselectiononmanyaminoacidsites AT nishidamutsumi postduplicationchargeevolutionofphosphoglucoseisomerasesinteleostfishesthroughweakselectiononmanyaminoacidsites |