Meeting Abstract
In this study, we investigate the evolution of innate immunity signaling components among hemichordates and other underrepresented, and/or non-model, metazoans using a hidden Markov model (HMM)-based approach. Previous studies have shown that although the core innate immunity signaling pathways possess deep roots within Metazoa, the receptors responsible for host-pathogen interfacing exhibit dynamic diversification events within several bilaterian lineages such as annelids, bivalves, and echinoids. Like many signaling pathways, innate immunity-associated proteins fundamentally rely on domains of discrete characteristics – such as hydrophobic ligand binding, transmembrane helices, or catabolic activity. The identification and classification of any given protein’s domain architecture is integral for inferring functional conservation/diversification among related proteins, particularly when investigating understudied, non-model taxa. In this study, we investigate three vital innate immunity protein families: Toll-like receptors, NOD-like receptors, and RIG-1-like receptors. The bioinformatic pipeline established here also principally addresses issues raised by database bias towards classic biomedical model systems (e.g., mouse, fly, and human). We show that HMM-based approaches, such as the one used in this study, provide a powerful alternative to similarity-based searches (e.g., BLAST); furthermore, the pipeline developed here can be applied to a large variety of protein families and taxa dependent upon the user’s target protein and phylogenetic depth.
