EvoProDom: evolutionary modeling of protein families by assessing translocations of protein domains
Here, we introduce a novel ‘evolution of protein domains’ (EvoProDom) model for describing the evolution of proteins based on the ‘mix and merge’ of protein domains. We assembled and integrated genomic and proteomic data comprising protein domain content and orthologous proteins from 109 organisms....
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
| Published: |
Wiley
2021-09-01
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| Series: | FEBS Open Bio |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/2211-5463.13245 |
| _version_ | 1818682456832737280 |
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| author | Gon Carmi Alessandro Gorohovski Milana Frenkel‐Morgenstern |
| author_facet | Gon Carmi Alessandro Gorohovski Milana Frenkel‐Morgenstern |
| author_sort | Gon Carmi |
| collection | DOAJ |
| description | Here, we introduce a novel ‘evolution of protein domains’ (EvoProDom) model for describing the evolution of proteins based on the ‘mix and merge’ of protein domains. We assembled and integrated genomic and proteomic data comprising protein domain content and orthologous proteins from 109 organisms. In EvoProDom, we characterized evolutionary events, particularly, translocations, as reciprocal exchanges of protein domains between orthologous proteins in different organisms. We showed that protein domains that translocate with highly frequency are generated by transcripts enriched in trans‐splicing events, that is, the generation of novel transcripts from the fusion of two distinct genes. In EvoProDom, we describe a general method to collate orthologous protein annotation from KEGG, and protein domain content from protein sequences using tools such as KoFamKOAL and Pfam. To summarize, EvoProDom presents a novel model for protein evolution based on the ‘mix and merge’ of protein domains rather than DNA‐based evolution models. This confers the advantage of considering chromosomal alterations as drivers of protein evolutionary events. |
| first_indexed | 2024-12-17T10:19:08Z |
| format | Article |
| id | doaj.art-14101416221949c08fd47ae8e762b285 |
| institution | Directory Open Access Journal |
| issn | 2211-5463 |
| language | English |
| last_indexed | 2024-12-17T10:19:08Z |
| publishDate | 2021-09-01 |
| publisher | Wiley |
| record_format | Article |
| series | FEBS Open Bio |
| spelling | doaj.art-14101416221949c08fd47ae8e762b2852022-12-21T21:52:50ZengWileyFEBS Open Bio2211-54632021-09-011192507252410.1002/2211-5463.13245EvoProDom: evolutionary modeling of protein families by assessing translocations of protein domainsGon Carmi0Alessandro Gorohovski1Milana Frenkel‐Morgenstern2Cancer Genomics and BioComputing of Complex Diseases Lab The Azrieli Faculty of Medicine Bar‐Ilan University Safed IsraelCancer Genomics and BioComputing of Complex Diseases Lab The Azrieli Faculty of Medicine Bar‐Ilan University Safed IsraelCancer Genomics and BioComputing of Complex Diseases Lab The Azrieli Faculty of Medicine Bar‐Ilan University Safed IsraelHere, we introduce a novel ‘evolution of protein domains’ (EvoProDom) model for describing the evolution of proteins based on the ‘mix and merge’ of protein domains. We assembled and integrated genomic and proteomic data comprising protein domain content and orthologous proteins from 109 organisms. In EvoProDom, we characterized evolutionary events, particularly, translocations, as reciprocal exchanges of protein domains between orthologous proteins in different organisms. We showed that protein domains that translocate with highly frequency are generated by transcripts enriched in trans‐splicing events, that is, the generation of novel transcripts from the fusion of two distinct genes. In EvoProDom, we describe a general method to collate orthologous protein annotation from KEGG, and protein domain content from protein sequences using tools such as KoFamKOAL and Pfam. To summarize, EvoProDom presents a novel model for protein evolution based on the ‘mix and merge’ of protein domains rather than DNA‐based evolution models. This confers the advantage of considering chromosomal alterations as drivers of protein evolutionary events.https://doi.org/10.1002/2211-5463.13245protein domainsprotein evolutiontranslocations |
| spellingShingle | Gon Carmi Alessandro Gorohovski Milana Frenkel‐Morgenstern EvoProDom: evolutionary modeling of protein families by assessing translocations of protein domains FEBS Open Bio protein domains protein evolution translocations |
| title | EvoProDom: evolutionary modeling of protein families by assessing translocations of protein domains |
| title_full | EvoProDom: evolutionary modeling of protein families by assessing translocations of protein domains |
| title_fullStr | EvoProDom: evolutionary modeling of protein families by assessing translocations of protein domains |
| title_full_unstemmed | EvoProDom: evolutionary modeling of protein families by assessing translocations of protein domains |
| title_short | EvoProDom: evolutionary modeling of protein families by assessing translocations of protein domains |
| title_sort | evoprodom evolutionary modeling of protein families by assessing translocations of protein domains |
| topic | protein domains protein evolution translocations |
| url | https://doi.org/10.1002/2211-5463.13245 |
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