Toll-like receptor pathway evolution in deuterostomes

Abstract

Animals have evolved an array of pattern-recognition receptor families essential for recognizing conserved molecular motifs characteristic of pathogenic microbes. One such family is the Toll-like receptors (TLRs). On pathogen binding, TLRs initiate specialized cytokine signaling catered to the class of invading pathogen. This signaling is pivotal for activating adaptive immunity in vertebrates, suggesting a close evolutionary relationship between innate and adaptive immune systems. Despite significant advances toward understanding TLR-facilitated immunity in vertebrates, knowledge of TLR pathway evolution in other deuterostomes is limited. By analyzing genomes and transcriptomes across 37 deuterostome taxa, we shed light on the evolution and diversity of TLR pathway signaling elements. Here, we show that the deuterostome ancestor possessed a molecular toolkit homologous to that which drives canonical MYD88-dependent TLR signaling in contemporary mammalian lineages. We also provide evidence that TLR3-facilitated antiviral signaling predates the origin of its TCAM1 dependence recognized in the vertebrates. SARM1, a negative regulator of TCAM1-dependent pathways in vertebrates, was also found to be present across all major deuterostome lineages despite the apparent absence of TCAM1 in invertebrate deuterostomes. Whether the presence of SARM1 is the result of its role in immunity regulation, neuron physiology, or a function of both is unclear. Additionally, Bayesian phylogenetic analyses corroborate several lineage-specific TLR gene expansions in urchins and cephalochordates. Importantly, our results underscore the need to sample across taxonomic groups to understand evolutionary patterns of the innate immunity foundation on which complex immunological novelties arose.

Keywords: Deuterostomia; Toll-like receptors; immunity evolution; innate immunity; molecular evolution.

Fig. 1.

Diagram of major TLR pathways. Upon ligand binding and receptor dimerization, TLRs interact with a TIR domain-containing adaptor protein. (Left) Canonically, TLR signal transduction occurs through the MYD88-dependent pathway. (Right) In some cases, such as with TLR3 and TLR4, TLRs require other TIR domain-containing adaptors to signal successfully for cytokine expression. SARM1, a TIR domain-containing negative regulator for TCAM1-dependent signaling pathways, is not shown. Red ellipses denote conserved TIR domains.

Fig. 2.

Deuterostome relationships as reported by recent phylogenomic studies (56). Echinoderms and hemichordates comprise the Ambulacraria, the sister group to Chordata.

Fig. S1.

Diagram of the bioinformatic pipeline for homology identification. For details see Materials and Methods in the main text.

Fig. S2.

Matrix containing the number of homologs identified per taxon. Taxa informed by both transcriptomic and genomic data are indicated in bold. Cells lacking values represent missing data for taxa informed solely by transcriptomic evidence. In contrast, gene absence is denoted by “0” only in taxa for which we analyzed genomic data. A cladogram depicting relationships among taxa is shown at the right of the matrix. Blocks/clades are colored by phylum: Hemichordata are green, Echinodermata are blue, and Chordata are red.

Fig. S3.

TAB1/2/3 gene-tree built using RAxML (54) rapid bootstrap analysis (1,000 replicates) and subsequent inference of best-fitting tree topology. Truncated TAB2s identified among invertebrate deuterostomes ally with human, mouse, and Drosophila TAB2/3s. Names in bold are sequences downloaded from public data repositories (Table S1).

Fig. 3.

TLR gene tree from deuterostome taxa reconstructed with ExaBayes. Human and mouse TLRs, as well as Drosophila Toll, are included as positive controls and have been highlighted in red for orientation to known orthology groups. Tips have been removed for ease of interpretation; see Figs. S4 and S5 for more detail. All nodes have ≥95% posterior probability.

Fig. S4.

Detailed Bayesian gene-tree of deuterostome TLRs. Reference sequences from human, mouse, and Drosophila are highlighted in bold red font, and deuterostome sequences derived from genomic data are in bold font. The subtree contains Toll homology group, P. flava TLR expansion, reference TLR groups, the TLR3 homology group, and the B. floridae TLR expansion. Clades are colored as in Fig. 3. Black circles denote nodes with 100% posterior probability. Clades supported by less than 95% posterior probability have been collapsed. Asterisks indicate S. kowalevskii TLRs obtained from the revised S. kowalevskii genome (62).

Fig. S5.

Detailed Bayesian gene-tree of deuterostome TLRs. Reference sequences from human, mouse, and Drosophila are highlighted in bold red font, and deuterostome sequences derived from genomic data are in bold font. The subtree contains the S. purpuratus TLR expansion. Clades are colored as in Fig. 3. Black circles denote nodes with 100% posterior probability. Clades supported by less than 95% posterior probability have been collapsed. Asterisks indicate S. kowalevskii TLRs obtained from the revised S. kowalevskii genome (62).

Fig. S6.

TIR domain-only TLR amino acid trees. Topologies are consistent with those displayed in Fig. 3 and Figs. S4 and S5, although with considerably lower resolution and node support values. (A) Tree produced using RAxML; all nodes have ≥75% bootstrap support. (B) Tree produced using ExaBayes; all nodes have ≥95% posterior probability.