Evolution of intrinsic disorder in the structural domains of viral and cellular proteomes
Abstract Intrinsically disordered regions are flexible regions that complement the typical structured regions of proteins. Little is known however about their evolution. Here we leverage a comparative and evolutionary genomics approach to analyze intrinsic disorder in the structural domains of thous...
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Nature Portfolio
2025-01-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-025-86045-4 |
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| author | Fizza Mughal Gustavo Caetano-Anollés |
| author_facet | Fizza Mughal Gustavo Caetano-Anollés |
| author_sort | Fizza Mughal |
| collection | DOAJ |
| description | Abstract Intrinsically disordered regions are flexible regions that complement the typical structured regions of proteins. Little is known however about their evolution. Here we leverage a comparative and evolutionary genomics approach to analyze intrinsic disorder in the structural domains of thousands of proteomes. Our analysis revealed that viral and cellular proteomes employ similar strategies to increase disorder but achieve different goals. Viral proteomes evolve disorder for economy of genomic material and multifunctionality. On the other hand, cellular proteomes evolve disorder to advance functionality with increasing genomic complexity. Remarkably, phylogenomic analysis of intrinsic disorder showed that ancient domains were ordered and that disorder evolved as a benefit acquired later in evolution. Evolutionary chronologies of domains indexed with disorder levels and distributions across Archaea, Bacteria, Eukarya and viruses revealed six evolutionary phases, the oldest two harboring only ordered and moderate disorder domains. A biphasic spectrum of disorder versus proteome makeup captured the dichotomy in the evolutionary trajectories of viral and cellular ancestors, one following reductive evolution driven by viral spread of molecular wealth and the other following expansive evolutionary trends to advance functionality through massive domain-forming co-option of disordered loop regions. |
| format | Article |
| id | doaj-art-13cf8b0881d14e80bf1af2958e276e0a |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
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| series | Scientific Reports |
| spelling | doaj-art-13cf8b0881d14e80bf1af2958e276e0a2025-01-26T12:33:52ZengNature PortfolioScientific Reports2045-23222025-01-0115111910.1038/s41598-025-86045-4Evolution of intrinsic disorder in the structural domains of viral and cellular proteomesFizza Mughal0Gustavo Caetano-Anollés1Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of IllinoisEvolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of IllinoisAbstract Intrinsically disordered regions are flexible regions that complement the typical structured regions of proteins. Little is known however about their evolution. Here we leverage a comparative and evolutionary genomics approach to analyze intrinsic disorder in the structural domains of thousands of proteomes. Our analysis revealed that viral and cellular proteomes employ similar strategies to increase disorder but achieve different goals. Viral proteomes evolve disorder for economy of genomic material and multifunctionality. On the other hand, cellular proteomes evolve disorder to advance functionality with increasing genomic complexity. Remarkably, phylogenomic analysis of intrinsic disorder showed that ancient domains were ordered and that disorder evolved as a benefit acquired later in evolution. Evolutionary chronologies of domains indexed with disorder levels and distributions across Archaea, Bacteria, Eukarya and viruses revealed six evolutionary phases, the oldest two harboring only ordered and moderate disorder domains. A biphasic spectrum of disorder versus proteome makeup captured the dichotomy in the evolutionary trajectories of viral and cellular ancestors, one following reductive evolution driven by viral spread of molecular wealth and the other following expansive evolutionary trends to advance functionality through massive domain-forming co-option of disordered loop regions.https://doi.org/10.1038/s41598-025-86045-4 |
| spellingShingle | Fizza Mughal Gustavo Caetano-Anollés Evolution of intrinsic disorder in the structural domains of viral and cellular proteomes Scientific Reports |
| title | Evolution of intrinsic disorder in the structural domains of viral and cellular proteomes |
| title_full | Evolution of intrinsic disorder in the structural domains of viral and cellular proteomes |
| title_fullStr | Evolution of intrinsic disorder in the structural domains of viral and cellular proteomes |
| title_full_unstemmed | Evolution of intrinsic disorder in the structural domains of viral and cellular proteomes |
| title_short | Evolution of intrinsic disorder in the structural domains of viral and cellular proteomes |
| title_sort | evolution of intrinsic disorder in the structural domains of viral and cellular proteomes |
| url | https://doi.org/10.1038/s41598-025-86045-4 |
| work_keys_str_mv | AT fizzamughal evolutionofintrinsicdisorderinthestructuraldomainsofviralandcellularproteomes AT gustavocaetanoanolles evolutionofintrinsicdisorderinthestructuraldomainsofviralandcellularproteomes |