Ectodomain Architecture Affects Sequence and Functional Evolution of Vertebrate Toll-like Receptors.

Jinlan Wang,Jing Zhao,Jing Liu,Zheng Zhang,Deling Yin

doi:10.1038/srep26705

Abstract

Toll-like receptors (TLRs) are crucial components of innate immunity that specifically recognize diverse pathogen-associated molecular patterns from pathogens. The continuous hydrogen-bond network (asparagine ladder) formed among the asparagine residues on the concave surfaces of neighboring leucine-rich repeat modules assists in stabilizing the overall shape of TLR ectodomains responsible for ligand recognition. Analysis of 28 types of vertebrate TLRs showed that their ectodomains possessed three types of architectures: a single-domain architecture with an intact asparagine ladder, a three-domain architecture with the ladder interrupted in the middle, and a trans-three-domain architecture with the ladder broken in both termini. Based on a phylogenetic analysis, the three vertebrate TLR architectures arose during early evolution. The 1428 vertebrate TLRs can be divided into eight families based on sequence and structural differences. TLRs ligand specificities are affected by their ectodomain architectures. Three-domain TLRs bind hydrophobic ligands, whereas single-domain and trans-three-domain TLRs mainly recognize hydrophilic ligands. Analysis of 39 vertebrate genomes suggested that the number of single-domain TLR genes in terrestrial vertebrate genomes decreased by half compared to aquatic vertebrate genomes. Single-domain TLR genes underwent stronger purifying selective pressures than three-domain TLR genes in mammals. Overall, ectodomain architecture influences the sequence and functional evolution of vertebrate TLRs.

Highlights

Gene duplications are believed to the primary driving force of evolutionary innovation
The conserved asparagines (Asn) in the concave surface are important for maintaining the shape of the entire ectodomain because they form a continuous hydrogen-bond network with backbone carbonyl oxygens of neighboring leucine-rich repeat (LRR) modules; they are visually defined as an asparagine ladder[20,21]
Analysis of the known Toll-like receptors (TLRs)-ECD crystal structures showed that the ectodomains of TLR3/5/8/9/13 possessed complete asparagine ladders; they were designated as possessing single-domain architecture (SD TLRs)

Summary

Introduction

Gene duplications are believed to the primary driving force of evolutionary innovation. Several crystal structures of TLR ectodomains in complex with agonistic ligands have been determined (TLR1-TLR2-lipopeptide, TLR2-TLR6-lipopeptide, TLR3-dsRNA, TLR4-MD-2-LPS, TLR5-flagellin, TLR8-ssRNA, TLR9-CpG DNA, and TLR13-ssRNA)[12,13,14,15,16,17,18,19]. Based on comparative analyses of a large amount of sequence and structural information, we tried to reveal structural divergences, phylogenetic relationships, ligand preferences, and distribution characteristics in the vertebrate genomes among the different types of ectodomain architectures to provide a full-scale perspective of TLR evolution among the three levels of sequence, structure, and function

Methods

Results

Conclusion