title: Classification and Lineage Tracing of SH2 Domains Throughout Eukaryotes.
abstract: Today there exists a rapidly expanding number of sequenced genomes. Cataloging protein interaction domains such as the Src Homology 2 (SH2) domain across these various genomes can be accomplished with ease due to existing algorithms and predictions models. An evolutionary analysis of SH2 domains provides a step towards understanding how SH2 proteins integrated with existing signaling networks to position phosphotyrosine signaling as a crucial driver of robust cellular communication networks in metazoans. However organizing and tracing SH2 domain across organisms and understanding their evolutionary trajectory remains a challenge. This chapter describes several methodologies towards analyzing the evolutionary trajectory of SH2 domains including a global SH2 domain classification system, which facilitates annotation of new SH2 sequences essential for tracing the lineage of SH2 domains throughout eukaryote evolution. This classification utilizes a combination of sequence homology, protein domain architecture and the boundary positions between introns and exons within the SH2 domain or genes encoding these domains. Discrete SH2 families can then be traced across various genomes to provide insight into its origins. Furthermore, additional methods for examining potential mechanisms for divergence of SH2 domains from structural changes to alterations in the protein domain content and genome duplication will be discussed. Therefore a better understanding of SH2 domain evolution may enhance our insight into the emergence of phosphotyrosine signaling and the expansion of protein interaction domains.
authors.affiliation: Broad Institute of Harvard and MIT, 415 Main St., 5175 JJ, Cambridge, MA, USA. baliu@broadinstitute.org.
authors.forename: Bernard A
authors.initials: BA
authors.lastname: Liu
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D056890:Eukaryota / Q000235:genetics / Q000378:metabolism*; D019143:Evolution, Molecular; D023281:Genomics / Q000379:methods; D006801:Humans; D008390:Markov Chains; D008958:Models, Molecular; D010766:Phosphorylation; D019000:Phosphotyrosine / Q000378:metabolism; D010802:Phylogeny; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D011505:Protein-Tyrosine Kinases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D011506:Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D012326:RNA Splicing; D017422:Sequence Analysis, DNA; D015398:Signal Transduction; D012984:Software; D013329:Structure-Activity Relationship; D064878:Web Browser; D018909:src Homology Domains
chemical_list: D011506:Proteins; D019000:Phosphotyrosine; D011505:Protein-Tyrosine Kinases
keywords: Domain shuffling; Evolution; Gene duplication; Phosphotyrosine; Protein tyrosine kinase; SH2 domain; Sequence alignment; Structure alignments