Genome-wide identification and characterization of toll-like receptor 5 (TLR5) in fishes

Abstract

Toll-like receptors 5 (TLR5), a member of the toll-like receptors (TLRs) family, is a class of pattern recognition receptors (PRRs) that recognize pathogen-associated molecular patterns (PAMPs). It responds to vertebrate recognition of bacterial flagellin and participates in innate immune responses. However, genome-wide identification and characterization of TLR5 in fishes have not been investigated. Here, three TLR5M isotypes (TLR5Ma, TLR5Mb1, and TLR5Mb2) and a TLR5S are all extracted from fish genomes on the basis of phylogenetic and synteny analyses. We confirmed that the non-teleost fishes have one TLR5M gene, as well as additional TLR5 genes (TLR5M and TLR5S) in teleost fishes. In addition, some special teleost fishes possess two to three TLR5 genes, which have undergone the fourth whole-genome duplication (WGD). According to our results, we inferred that the diversity of TLR5 genes in fishes seems to be the result of combinations of WGD and gene loss. Furthermore, TLR5 isoforms displayed differences at the flagellin interaction sites and viral binding sites, and showed lineage-specific, which indicated that TLR5 duplicates may generate functional divergence. Bacterial experiments also supported the idea that CiTLR5Ma and CiTLR5Mb are subfunctionalized to sense bacterial flagellin. In summary, our present comparative genomic survey will benefit for further functional investigations of TLR5 genes in fish.

Keywords: TLR5; adaptive evolution; fish; gene loss; whole-genome duplications.

FIGURE 1

Phylogenetic relationships among various fish TLR5s. Representative TLR5 genes were categorized into three main clades (L1, L2, and L3). Furthermore, diploid teleost TLR5 genes were classified into two subgroups (diploid teleost TLR5S and TLR5M). TLR5 genes in Salmonidae were clustered into three different clades (salmonidae TLR5S, TLR5Mb, and TLR5Mb). TLR5 genes in Cyprinidae were divided into two subgroups (cyprinidae TLR5Ma and TLR5Mb/b1/b2). Detailed abbreviation of each species is available in Table 1.

FIGURE 2

Synteny analyses of the chromosome loci harboring TLR5 genes in fishes. Different colored rectangles represent different gene loci. Some gene loci near TLR5 present conserved synteny in these examined fishes. Detailed abbreviation of each species is available in Table 1.

FIGURE 3

The domain features of TLR5 genes among fishes. Detailed abbreviation of each species is available in Table 1.

FIGURE 4

The expression patterns of CiTLR5Ma and CiTLR5Mb on transcription level in tissues of liver, spleen and head kidney, after infected with A. hydrophila. The expression level of CiTLR5Ma and CiTLR5Mb on 0 h was used as the baseline calibrator. The significance levels were obtained by comparing with corresponding 0 h (*p < 0.05, **p < 0.01).

FIGURE 5

All teleost fishes undergone at least three whole-genome duplication (WGD) events, the two earlier rounds of vertebrate genome duplication (1R and 2R) that occurred before the di-vergence of lamprey and hagfish from the jawed vertebrates, and the third teleost-specific WGD (3R) at the base of the teleosts 320 million years ago (MYA). Atlantic salmon and river trout share the salmonid-specific WGD (4R 1) that occurred in the common ancestor of salmonids 80 MYA. Common carp and goldfish share the fourth WGD (4R) that occurred approximately 14 MYA in their common ancestor. Atlantic salmon and river trout share the salmonid-specific WGD (4R 1) that occurred in the common ancestor of salmonids 80 MYA. Common and goldfish share the fourth WGD (4R 2) that occurred approximately 14 MYA in their common ancestor. The TLR5 isoform is given in parentheses.