The Roslin Institute

Genetics and Genomics

Evolutionary and functional analysis of the avian Toll-like receptor genes

An important group of genes central to innate immunity is the Toll-like receptor (TLR) family. We have already identified ten TLR genes in chicken and in turkey and propose to identify the equivalent genes in duck and goose. It is important that we can study the duck TLR genes alongside other avian species (chicken, turkey, goose and the soon-to-be-available zebra finch sequence), as this will give us an insight into some fundamental differences which seem to exist between the immune systems of different species. The cloning, sequencing and mapping of the duck TLR genes will fill an important gap in comparative and evolutionary research, and identification and functional analysis of duck innate immune genes will provide vital information for the study of disease resistance in birds. 

Specific Objectives:

  1. Identification of the TLR repertoire in chicken, duck, turkey, goose and zebra finch
  2. Assignment of the duck genes to genetic and physical maps
  3. An expression profile of TLR genes in duck and goose
  4. An understanding of the evolutionary history and rates of mutation of the TLR genes/proteins across avian species
  5. Identification of the ligands for TLR3, and possibly other TLR’s
  6. Discovery of genetic similarities/differences in these genes across species, which may ultimately be involved in differences in disease resistance between species.

Figure 1

Fig. 1: ML tree of the TLR1 subfamily based on vertebrate N-terminal amino acid sequences. The tree is rooted with Danio rerio. The bootstrap values of 1,000 pseudo-replicates are shown as percentages at nodes. The clades of avian TLR1A/B, mammalian TLR1/6 /10 are in red, orange, green, purple and blue, respectively. The branches of avian TLR1A and mammalian TLR10 are in a pink background. The branches of avian TLR1B and mammalian TLR1/TLR6 are in a lilac background.

Figure 2

Fig. 2: Distribution of co-evolving amino acids residues mapped onto the surface of TLR2 family protein structures. The protein structures are from Jin et al. (2007) and Kang et al. (2009). Co-evolving amino acids are shown as either network diagrams (displayed using Cytoscape) or mapped onto tertiary structures of protein domains (using PyMOL) for A: human TLR1/TLR2 and B: mouse TLR6/TLR2 complexes. In the network diagrams the TLR1/TLR6 and TLR2 amino acids are depicted by ellipse and rectangle shapes, respectively. Cyan, pale green and pink amino acid residues represent the ligand binding domain, α helices near the ligand binding domain and the extracellular domain, respectively. The color of lines in A(i) and B(i) represents the correlation coefficients of co-evolving amino acids. In the tertiary structures the peptide fragments from TLR1/TLR6 and TLR2 are in pale green and yellow, respectively. Amino acids joined by the same color of the broken lines are clustered to the one evolutionary group.