EvoProDom: evolutionary modeling of protein families by assessing translocations of protein domains

• Published in: FEBS open bio Vol. 11; no. 9; pp. 2507 - 2524
• Main Authors: Carmi, Gon, Gorohovski, Alessandro, Frenkel‐Morgenstern, Milana
• Format: Journal Article
• Language: English
• Published: England John Wiley & Sons, Inc 01.09.2021; John Wiley and Sons Inc; Wiley
• Subjects: Algorithms; Annotations; Bacteria; Chromosome translocations; Computational Biology - methods; Databases, Protein; Datasets; Evolution; Genes; Genomes; genomics; Humans; Models, Molecular; Molecular Sequence Annotation; Organisms; protein domains; protein evolution; Protein families; Protein Interaction Domains and Motifs; Protein Transport; Proteins; Proteins - chemistry; Proteins - metabolism; Proteomics; Proteomics - methods; Software; trans-splicing; translocations; Workflow; protein evolution; translocations; protein domains
• ISSN: 2211-5463; 2211-5463
• DOI: 10.1002/2211-5463.13245

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. The evolutionary model of protein domains builds new proteins. It is based on the ‘mix and merge’ of protein domains by means of chromosomal translocations, insertions, deletions, or duplication events in organisms during evolution. The changes have been identified in orthologous protein families using preserved, gained, and/or missing protein domains that appeared on evolutionary conserved chromosomal regions.