Directional divergence of Ep300 duplicates in teleosts and its implications
Abstract Background EP300 is a conserved protein in vertebrates, which serves as a key mediator of cellular homeostasis. Mutations and dysregulation of EP300 give rise to severe human developmental disorders and malignancy. Danio rerio is a promising model organism to study EP300 related diseases an...
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| Format: | Article |
| Language: | English |
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BMC
2020-10-01
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| Series: | BMC Evolutionary Biology |
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| Online Access: | http://link.springer.com/article/10.1186/s12862-020-01712-6 |
| _version_ | 1818583561300606976 |
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| author | Xianzong Wang Junli Yan |
| author_facet | Xianzong Wang Junli Yan |
| author_sort | Xianzong Wang |
| collection | DOAJ |
| description | Abstract Background EP300 is a conserved protein in vertebrates, which serves as a key mediator of cellular homeostasis. Mutations and dysregulation of EP300 give rise to severe human developmental disorders and malignancy. Danio rerio is a promising model organism to study EP300 related diseases and drugs; however, the effect of EP300 duplicates derived from teleost-specific whole genome duplication should not just be neglected. Results In this study, we obtained EP300 protein sequences of representative teleosts, mammals and sauropsids, with which we inferred a highly supported maximum likelihood tree. We observed that Ep300 duplicates (Ep300a and Ep300b) were widely retained in teleosts and universally expressed in a variety of tissues. Consensus sequences of Ep300a and Ep300b had exactly the same distribution of conserved domains, suggesting that their functions should still be largely overlapped. We analyzed the molecular evolution of Ep300 duplicates in teleosts, using branch-site models, clade models and site models. The results showed that both duplicates were subject to strong positive selection; however, for an extant species, generally at most one copy was under positive selection. At the clade level, there were evident positive correlations between evolutionary rates, the number of positively selected sites and gene expression levels. In Ostariophysi, Ep300a were under stronger positive selection than Ep300b; in Neoteleostei, another species-rich teleost clade, the contrary was the case. We also modeled 3D structures of zf-TAZ domain and its flanking regions of Ep300a and Ep300b of D. rerio and Oryzias latipes and found that in either species the faster evolving copy had more short helixes. Conclusions Collectively, the two copies of Ep300 have undoubtedly experienced directional divergence in main teleost clades. The divergence of EP300 between teleosts and mammals should be greater than the divergence between different teleost clades. Further studies are needed to clarify to what extent the EP300 involved regulatory network has diverged between teleosts and mammals, which would also help explain the huge success of teleosts. |
| first_indexed | 2024-12-16T08:07:14Z |
| format | Article |
| id | doaj.art-ebe9c543aa724a399eb4e6cfbda98a4c |
| institution | Directory Open Access Journal |
| issn | 1471-2148 |
| language | English |
| last_indexed | 2024-12-16T08:07:14Z |
| publishDate | 2020-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Evolutionary Biology |
| spelling | doaj.art-ebe9c543aa724a399eb4e6cfbda98a4c2022-12-21T22:38:27ZengBMCBMC Evolutionary Biology1471-21482020-10-0120111210.1186/s12862-020-01712-6Directional divergence of Ep300 duplicates in teleosts and its implicationsXianzong Wang0Junli Yan1College of Animal Science, Shanxi Agricultural UniversityCollege of Urban and Rural Construction, Shanxi Agricultural UniversityAbstract Background EP300 is a conserved protein in vertebrates, which serves as a key mediator of cellular homeostasis. Mutations and dysregulation of EP300 give rise to severe human developmental disorders and malignancy. Danio rerio is a promising model organism to study EP300 related diseases and drugs; however, the effect of EP300 duplicates derived from teleost-specific whole genome duplication should not just be neglected. Results In this study, we obtained EP300 protein sequences of representative teleosts, mammals and sauropsids, with which we inferred a highly supported maximum likelihood tree. We observed that Ep300 duplicates (Ep300a and Ep300b) were widely retained in teleosts and universally expressed in a variety of tissues. Consensus sequences of Ep300a and Ep300b had exactly the same distribution of conserved domains, suggesting that their functions should still be largely overlapped. We analyzed the molecular evolution of Ep300 duplicates in teleosts, using branch-site models, clade models and site models. The results showed that both duplicates were subject to strong positive selection; however, for an extant species, generally at most one copy was under positive selection. At the clade level, there were evident positive correlations between evolutionary rates, the number of positively selected sites and gene expression levels. In Ostariophysi, Ep300a were under stronger positive selection than Ep300b; in Neoteleostei, another species-rich teleost clade, the contrary was the case. We also modeled 3D structures of zf-TAZ domain and its flanking regions of Ep300a and Ep300b of D. rerio and Oryzias latipes and found that in either species the faster evolving copy had more short helixes. Conclusions Collectively, the two copies of Ep300 have undoubtedly experienced directional divergence in main teleost clades. The divergence of EP300 between teleosts and mammals should be greater than the divergence between different teleost clades. Further studies are needed to clarify to what extent the EP300 involved regulatory network has diverged between teleosts and mammals, which would also help explain the huge success of teleosts.http://link.springer.com/article/10.1186/s12862-020-01712-6EP300Lysine acetyltransferaseTeleostWhole genome duplicationDivergent evolutionPositive selection |
| spellingShingle | Xianzong Wang Junli Yan Directional divergence of Ep300 duplicates in teleosts and its implications BMC Evolutionary Biology EP300 Lysine acetyltransferase Teleost Whole genome duplication Divergent evolution Positive selection |
| title | Directional divergence of Ep300 duplicates in teleosts and its implications |
| title_full | Directional divergence of Ep300 duplicates in teleosts and its implications |
| title_fullStr | Directional divergence of Ep300 duplicates in teleosts and its implications |
| title_full_unstemmed | Directional divergence of Ep300 duplicates in teleosts and its implications |
| title_short | Directional divergence of Ep300 duplicates in teleosts and its implications |
| title_sort | directional divergence of ep300 duplicates in teleosts and its implications |
| topic | EP300 Lysine acetyltransferase Teleost Whole genome duplication Divergent evolution Positive selection |
| url | http://link.springer.com/article/10.1186/s12862-020-01712-6 |
| work_keys_str_mv | AT xianzongwang directionaldivergenceofep300duplicatesinteleostsanditsimplications AT junliyan directionaldivergenceofep300duplicatesinteleostsanditsimplications |