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Title:Evolutionary analysis of Suidae TLR signaling pathway
Author(s):Darfour-Oduro, Kwame Asante
Director of Research:Schook, Lawrence B.
Doctoral Committee Chair(s):Schook, Lawrence B.
Doctoral Committee Member(s):White, Bryan A.; Roca, Alfred L.; Ma, Jian
Department / Program:Animal Sciences
Discipline:Animal Sciences
Degree Granting Institution:University of Illinois at Urbana-Champaign
Degree:Ph.D.
Genre:Dissertation
Subject(s):Suidae
Toll-like receptors
Abstract:The innate immune system represents the first line of host defense against pathogens. Toll-like receptors (TLRs) are the best characterized pathogen recognition receptors (PRRs) of the innate immune system. TLRs detect distinct pathogen associated molecules and engage downstream intracellular signaling cascades eventually leading to an innate immune response. Thus, the TLR signaling pathway is under selective pressure from pathogens and is essential for host survival. The family Suidae (domestic pigs and their wild relatives) has diverged over extended evolutionary periods in diverse environments, suggesting that adaptation in response to endemic infectious agents may have occurred. It is therefore expected that the TLR signaling pathway might have played a crucial role in the survival of members of the family Suidae. However, the extent to which pathogen mediated selection pressures have influenced the evolution of family Suidae TLR signaling pathway genes is not well understood. Investigating the role of pathogens in the genetic variation within the TLR signaling pathway genes will indicate the critical role of these genes in host defense against prior and present infections. In this dissertation I first determined whether members of the family Suidae TLRs have evolved adaptively at the interspecies level. To this end, coding sequences of bacterial sensing TLR (TLR1, TLR2 and TLR6) and viral sensing TLR (TLR3, TLR7 and TLR8) were retrieved from resequencing libraries of one animal representing each of the following members of the family Suidae: Sus scrofa from Europe, Sus scrofa from Asia, Potamochoerus larvatus, Potamochoerus porcus and Phacochoerus africanus of sub Saharan African origin and Sus verrucosus, Sus celebensis, Sus scebifrons, Sus barbatus and Babyrousa babyrussa from island Southeast Asia. Evolutionary analyses of the aligned TLR sequences were done using Maximum likelihood (ML) approaches in a phylogenetic framework. These analyses indicated that persistent positive selection pressures have acted on amino acid residues across the family Suidae in both bacterial and viral sensing TLRs. There were more amino acid sites under positive selection in bacterial sensing TLRs than their viral sensing counterparts. Lineage specific positive selective events, where positive selective were inferred for particular family Suidae species were suggestive of species specific pathogens that are acting as selection pressures. Some of the amino acid residues under positive selective pressure were involved in radical amino acid substitutions and were also within or in close proximity to functionally important domains of the TLR proteins. Thus, such residues may have disease resistance implications for the family Suidae. Adaptive evolution was also investigated at the intraspecies level. The European Sus scrofa (wild boars and domestic pigs) diverged from their Asian counterparts over 1million years ago. Distinct pathogen mediated selective pressures might have acted on these geographically separated groups leading to signatures of adaptation in host genes. To investigate whether positive selection pressures have acted on TLRs of Sus scrofa of European and Asian origins, coding sequences of bacterial sensing TLR (TLR1, TLR2 and TLR6) and viral sensing TLR (TLR3, TLR7 and TLR8) were retrieved from resequencing libraries of 15 wild boars and 25 domestic pigs of European origin and 5 wild boars and 22 domestic pigs of Asian origin. Within and between populations analyses of positive selection indicated that the TLR2 gene was under positive selective pressure in European Sus scrofa but not in the Asian Sus scrofa. Specifically, the derived allele (nucleotide: A; Amino acid: Threonine) of TLR2 SNP A376G (Alanine 126 Threonine) was under positive selection. The frequency of the derived allele was 83.33% within European wild boars, 98.00% within domestic pig breeds of European origin, 40.00% within Asian wild boars and 11.36% within Asian domestic pigs. The age of the derived allele was 163,000 years which roughly coincided with a time of Sus scrofa population expansion. This population expansion might have created an environment for pathogen transmission providing the selective force for adaptation at host genes. Three dimensional crystal structure of the TLR2 protein indicated the derived allele under positive selection was located within the N-terminal domain of the extracellular domain where single amino acid substitutions are likely to affect protein function. TLRs act in concert with other genes in the signaling pathway to elicit innate immune response to invading pathogens. A key question in molecular evolution is whether parameters of signaling pathways have an influence on how genes evolve. The evolution of the entire TLR signaling pathway in the context of parameters of the pathway was therefore investigated. In particular, I investigated whether gene position within TLR signaling pathway of the family Suidae have an effect on evolutionary rate of genes. The goal here was to determine whether genes upstream and downstream have distinct selection pressures acting on them and the factors responsible for such a polarity. To do this, genes within the TLR signaling pathway as indicated in the KEGG database were retrieved from resequencing libraries of Sus scrofa from Europe, Sus scrofa from Asia, Potamochoerus larvatus, Potamochoerus porcus and Phacochoerus africanus of sub Saharan African origin and Sus verrucosus, Sus celebensis, Sus scebifrons, Sus barbatus and Babyrousa babyrussa from island Southeast Asia. After screening sequences for suitability for evolutionary analyses, 33 genes remained. Gene position, the number of protein-protein interactions (connectivity), protein length, length of 3’ untranslated region and codon bias measured as Effective Number of Codons (ENC) were estimated for each gene sequence alignment. Gene position was significantly negatively correlated with evolutionary parameters ω (dn/ds) and dn suggesting that downstream genes in the pathway were more selectively constrained than upstream genes. Protein length and connectivity were also significantly correlated with evolutionary parameters ω (dn/ds) and dn such that downstream genes had shorter protein lengths and were connected to more proteins. As gene position was also significantly correlated with protein length and connectivity, the polarity in evolutionary rate along the TLR signaling pathway is due to differences in protein length and connectivity between upstream and downstream genes within TLR signaling pathway of the family Suidae.
Issue Date:2015-04-15
Type:Thesis
URI:http://hdl.handle.net/2142/78382
Rights Information:Copyright 2015 Kwame Darfour-Oduro
Date Available in IDEALS:2015-07-22
Date Deposited:May 2015


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