Abstract
Members of the family Suidae have diverged over extended evolutionary periods in diverse environments, suggesting that adaptation in response to endemic infectious agents may have occurred. Toll-like receptors (TLRs) comprise a multigene family that acts as the first line of defense against infectious microbes at the host-environment interface. We hypothesized that across the Suidae, positive selection mediated by infectious agents has contributed to the evolution of TLR diversity. Thus, we analyzed Sus scrofa, Sus barbatus, Sus verrucosus, Sus celebensis, Sus scebifrons, Babyrousa babyrussa, Potamochoerus larvatus, Potamochoerus porcus and Phacochoerus africanus genomes. Specifically, analyses were performed to identify evidence of positive selection using Maximum likelihood (ML) methods within a phylogenetic framework for bacterial and viral sensing Suidae TLR extracellular domains. Our analyses did not reveal evidence of positive selection for TLR3 and TLR7, suggesting strong functional conservation among these two genes for members of the Suidae. Positive selection was inferred for Suidae TLR1, TLR2, TLR6 and TLR8 evolution. ML methods identified amino acid sites of the bacterial sensing TLR1, TLR2, TLR6 and the viral sensing TLR8 to be under persistent positive selection. Some of these sites are in close proximity to functionally relevant sites, further strengthening the case for pathogen mediated selection for these sites. The branch leading to the genus Sus demonstrated evidence of episodic positive selection for TLR1, indicating selection mediated by infectious agents encountered within the specific geographic origin of the Sus. These results indicate that species of the Suidae have positively selected residues within functional domains of TLRs reflective of prior infections. Thus, TLR genes represent candidates for experimental validation to determine their functional role in antibacterial and antiviral activity within members of the Suidae.
Highlights
Bacterial and viral infectious diseases constitute a significant threat to host survival
Cell surface expressed Toll-like receptors (TLRs) (TLR1, TLR2, TLR4, TLR5 and TLR6) recognize predominantly bacterial ligands and several fungal and parasite ligands while TLR3, TLR7 and TLR8 are expressed within the endosome and recognize single and double-stranded viral RNA [9]
The length of the extracellular domains in terms of number of nucleotides of the TLRs ranged from 1668 bases for TLR1 to 2445 bases for TLR7
Summary
Bacterial and viral infectious diseases constitute a significant threat to host survival. With respect to vertebrate immune-related genes, studies on adaptive evolution have mainly focused on the major histocompatibility complex (MHC), cell surface glycoproteins of the acquired immune system that mediate presentation of peptides to T-cell receptors [3]. It has been shown that half of the genetic variability in immune response to infections is accounted for by non-MHC genes [4] Most of these non-MHC genes seem to belong to the innate immune system [5], indicating that such genes may be under adaptive evolution. Phagocytic cells such as monocytes, macrophages and dendritic cells mediate the recognition of pathogens by the innate immune system through germline encoded receptors known as pattern recognition receptors (PRRs). TLRs are type I transmembrane glycoproteins composed of an extracellular domain characterized by a leucine-rich repeat (LRR) motif responsible for binding infectious agents ligands, a transmembrane domain and an intracellular signaling domain
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