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Yaman Y, Aymaz R, Keleş M, Bay V, Ün C, Heaton MP. Association of TLR2 haplotypes encoding Q650 with reduced susceptibility to ovine Johne's disease in Turkish sheep. Sci Rep 2021; 11:7088. [PMID: 33782507 PMCID: PMC8007707 DOI: 10.1038/s41598-021-86605-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 03/18/2021] [Indexed: 02/06/2023] Open
Abstract
Ovine Johne’s disease (OJD) is caused by Mycobacterium avium subsp. paratuberculosis (MAP) and carries a potential zoonotic risk for humans. Selective breeding strategies for reduced OJD susceptibility would be welcome tools in disease eradication efforts, if available. The Toll-like receptor 2 gene (TLR2) plays an important signaling role in immune response to MAP, and missense variants are associated with mycobacterial infections in mammals. Our aim was to identify and evaluate ovine TLR2 missense variants for association with OJD in Turkish sheep. Eleven TLR2 missense variants and 17 haplotype configurations were identified in genomic sequences of 221 sheep from 61 globally-distributed breeds. The five most frequent haplotypes were tested for OJD association in 102 matched pairs of infected and uninfected ewes identified in 2257 Turkish sheep. Ewes with one or two copies of TLR2 haplotypes encoding glutamine (Q) at position 650 (Q650) in the Tir domain were 6.6-fold more likely to be uninfected compared to ewes with arginine (R650) at that position (CI95 = 2.6 to 16.9, p-value = 3.7 × 10–6). The protective TLR2 Q650 allele was present in at least 25% of breeds tested and thus may facilitate selective breeding for sheep with reduced susceptibility to OJD.
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Affiliation(s)
- Yalçın Yaman
- Department of Biometry and Genetics, Sheep Breeding and Research Institute, 10200, Bandırma, Balıkesir, Turkey.
| | - Ramazan Aymaz
- Department of Biometry and Genetics, Sheep Breeding and Research Institute, 10200, Bandırma, Balıkesir, Turkey
| | - Murat Keleş
- Department of Biometry and Genetics, Sheep Breeding and Research Institute, 10200, Bandırma, Balıkesir, Turkey
| | - Veysel Bay
- Department of Biometry and Genetics, Sheep Breeding and Research Institute, 10200, Bandırma, Balıkesir, Turkey
| | - Cemal Ün
- Department of Biology, Faculty of Science, Ege University, 35000, İzmir, Turkey
| | - Michael P Heaton
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
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Purifying selection shaping the evolution of the Toll-like receptor 2 TIR domain in brown hares (Lepus europaeus) from Europe and the Middle East. Mol Biol Rep 2020; 47:2975-2984. [PMID: 32236892 DOI: 10.1007/s11033-020-05382-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 03/19/2020] [Indexed: 10/24/2022]
Abstract
Toll-like receptors (TLRs) are transmembrane proteins of the innate immune system, composed of the ectodomain involved in pathogen recognition and the intracellular Toll/interleukin-1 receptor (TIR) domain important for downstream signal transduction. Here, we analyze the genetic variability of TIR nucleotide and amino-acid sequences of the TLR2 gene in 243 brown hares from Europe and the Middle East and tested for the presence of selection signals and spatial structuring. TLR2 TIR domain sequences were PCR amplified and sequenced, while genotyping was performed by phasing. Genetic diversity indices were calculated in DnaSP and Arlequin, while presence of selection signals was tested using MEGA and the Datamonkey web server. The presence of spatial patterns in TIR sequence distribution was tested by spatial Principal Component Analysis (sPCA) in adegenet. A total of 13 haplotypes were revealed with haplotype diversity of 0.424, and nucleotide diversity (π) of 0.00138. Two spatial clusters were revealed: "Anatolia/Middle East" and "Europe". In Anatolia the two most prevalent amino-acid variants, A and B (the latter being the most ancestral) were maintained at similar frequencies; but in Europe a shift in genotype frequencies was observed as well as a higher number of nonsynonymous substitutions giving rise to novel amino-acid protein variants originating from the evolutionarily younger protein variant. Molecular diversity (haplotype and nucleotide diversity) indices were significantly higher in the "Anatolia/Middle East" cluster. A signal of purifying selection was detected acting on the TIR sequences.
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Neves F, Águeda-Pinto A, Pinheiro A, Abrantes J, Esteves PJ. Strong selection of the TLR2 coding region among the Lagomorpha suggests an evolutionary history that differs from other mammals. Immunogenetics 2019; 71:437-443. [PMID: 30874861 DOI: 10.1007/s00251-019-01110-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 02/15/2019] [Indexed: 12/13/2022]
Abstract
Toll-like receptors (TLRs) are one of the first lines of defense against pathogens and are crucial for triggering an appropriate immune response. Among TLRs, TLR2 is functional in all vertebrates and has high ability in detecting bacterial and viral pathogen ligands. The mammals' phylogenetic tree of TLR2 showed longer branches for the Lagomorpha clade, raising the hypothesis that lagomorphs experienced an acceleration of the mutation rate. This hypothesis was confirmed by (i) Tajima's test of neutrality that revealed different evolutionary rates between lagomorphs and the remaining mammals with lagomorphs presenting higher nucleotide diversity; (ii) genetic distances were similar among lagomorphs and between lagomorphs and other mammals; and (iii) branch models reinforced the existence of an acceleration of the mutation rate in lagomorphs. These results suggest that the lagomorph TLR2 has been strongly involved in pathogen recognition, which probably caused a host-pathogen arms race that led to the observed acceleration of the mutation rate.
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Affiliation(s)
- Fabiana Neves
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, nr.7, 4485-661, Vairão, Portugal
| | - Ana Águeda-Pinto
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, nr.7, 4485-661, Vairão, Portugal
| | - Ana Pinheiro
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, nr.7, 4485-661, Vairão, Portugal
| | - Joana Abrantes
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, nr.7, 4485-661, Vairão, Portugal
| | - Pedro J Esteves
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, nr.7, 4485-661, Vairão, Portugal. .,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal. .,CITS - Centro de Investigação em Tecnologias de Saúde, CESPU, Gandra, Portugal.
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Xu S, Tian R, Lin Y, Yu Z, Zhang Z, Niu X, Wang X, Yang G. Widespread positive selection on cetacean TLR extracellular domain. Mol Immunol 2018; 106:135-142. [PMID: 30597475 DOI: 10.1016/j.molimm.2018.12.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 12/04/2018] [Accepted: 12/20/2018] [Indexed: 12/20/2022]
Abstract
Toll like receptors (TLRs), key members of innate immune system, can recognize a wide diversity of pathogens and initiate both innate and adaptive immune responses in vertebrate. Cetaceans must have faced new challenges of pathogens when their terrestrial relatives transitioned from the terrestrial to aquatic environment. Here, we sequenced the extracellular domain (ECD) of 10 TLRs in cetacean lineages because this region involved in the recognition of pathogens. A total of 148 sites ranging between 5-26 codons (0.01%-4.83%) were identified to be robust candidates of positive selection at the ECD of 10 TLRs. In addition, the majority (90.54%) of these positively selected codons were found to have radical amino acid changes, which strengthen the evidence of positive selection. Importantly, more radical amino acid changes in selected sites were enriched in the period of early evolutionary transition from land to semi-aquatic and from semi-aquatic to full-aquatic habitat, which might endow cetaceans with a faster adaptation to new pathogens as they transitioned into novel habitat. Interestingly, similar selective intensity was detected in both viral and non-viral TLRs in cetaceans, which was not in line with previous studies on primates and birds that reported stronger positive selection in non-viral TLRs than in viral TLRs. This result may be explained by the fact that cetaceans might have faced diversity of bacteria and viruses during its transitions from terrestrial to aquatic environment whereas both primates and birds probably being affected by only a restricted number of related viruses due to their homogeneous habitat.
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Affiliation(s)
- Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China.
| | - Ran Tian
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China.
| | - Yurui Lin
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China.
| | - Zhenpeng Yu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China.
| | - Zepeng Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China.
| | - Xu Niu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China.
| | - Xiaohong Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China.
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China.
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Awadi A, Ben Slimen H, Smith S, Kahlen J, Makni M, Suchentrunk F. Genetic diversity of the toll-like receptor 2 (TLR2) in hare (Lepus capensis) populations from Tunisia. C R Biol 2018; 341:315-324. [PMID: 30032779 DOI: 10.1016/j.crvi.2018.06.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 06/14/2018] [Accepted: 06/15/2018] [Indexed: 10/28/2022]
Abstract
Toll-like receptors (TLRs) are a major group of proteins that recognize molecular components of infectious agents, known as pathogen associated molecular patterns (PAMPs). The structure of these genes is similar and characterized by the presence of an ectodomain, a signal transmembrane segment and a highly conserved cytoplasmic domain. The latter domain is homologous to the human interleukin-1 receptor (IL1R) and human IL-18 receptor (IL-18R) and designated TIR domain. The latter domain of the TLR genes was suggested to be very conservative and its evolution is driven by purifying selection. Variability and evolution of the TIR sequences of TLR2 gene were studied in three hare populations from Tunisia with different ecological characteristics (NT-North Tunisia with Mediterranean, CT-Central Tunisia with semi-arid, and ST-South Tunisia with arid climate). Sequencing of a 372bp fragment of TIR2 revealed 25 alleles among 110 hares. Twenty variable nucleotide positions were detected, of which 7 were non-synonymous. The highest variability was observed in CT, with 16 polymorphic positions. In ST, only 4 polymorphic nucleotide positions were detected with all diversity values lower than those recorded for the other two populations. By using several approaches, no positive selection was detected. However, evidence of purifying selection was found at two positions. The logistic models of the most common TIR2 protein variant that we run to examine whether its occurrence was affected by climatic variation independent of the geographic sample location suggested only a longitudinal effect. Finally, the mapping of the non-synonymous mutations to the inferred tertiary protein structure showed that they were all localized in the different loop regions. Among all non-synonymous substitutions, three were suggested to be deleterious as evidenced by PROVEAN analysis. The observed patterns of variability characterized by low genetic diversity in ST might suggest that the TIR region was more affected, than other markers, by genetic drift or/and that these patterns were shaped by different selective pressures under different ecological conditions. Notably, this low diversity was not detected by other (putatively neutral) microsatellite markers analysed in the course of other studies. But low diversity was also found for two MHC class II adaptive immune genes. As expected from functionally important regions, the evolution of the TIR2 domain is mainly driven by purifying selection. However, the occurrence of deleterious non-synonymous substitutions might highlight the flexible evolution of the TIR genes and/or their interactions with other proteins.
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Affiliation(s)
- Asma Awadi
- UR Génomique des insectes ravageurs des cultures d'intérêt agronomique (GIRC), Université de Tunis El-Manar, 2092 El Manar, Tunis, Tunisia.
| | - Hichem Ben Slimen
- UR Génomique des insectes ravageurs des cultures d'intérêt agronomique (GIRC), Université de Tunis El-Manar, 2092 El Manar, Tunis, Tunisia; Institut supérieur de biotechnologie de Béja, Beja 9000, University of Jendouba, Tunisia
| | - Steve Smith
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Savoyenstrasse 1, 1160 Vienna, Austria
| | - Jonas Kahlen
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Savoyenstrasse 1, 1160 Vienna, Austria
| | - Mohamed Makni
- UR Génomique des insectes ravageurs des cultures d'intérêt agronomique (GIRC), Université de Tunis El-Manar, 2092 El Manar, Tunis, Tunisia
| | - Franz Suchentrunk
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Savoyenstrasse 1, 1160 Vienna, Austria
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Quéméré E, Galan M, Cosson JF, Klein F, Aulagnier S, Gilot-Fromont E, Merlet J, Bonhomme M, Hewison AJM, Charbonnel N. Immunogenetic heterogeneity in a widespread ungulate: the European roe deer (Capreolus capreolus). Mol Ecol 2015; 24:3873-87. [PMID: 26120040 DOI: 10.1111/mec.13292] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Revised: 06/18/2015] [Accepted: 06/24/2015] [Indexed: 12/25/2022]
Abstract
Understanding how immune genetic variation is shaped by selective and neutral processes in wild populations is of prime importance in both evolutionary biology and epidemiology. The European roe deer (Capreolus capreolus) has considerably expanded its distribution range these last decades, notably by colonizing agricultural landscapes. This range shift is likely to have led to bottlenecks and increased roe deer exposure to a new range of pathogens that until recently predominantly infected humans and domestic fauna. We therefore investigated the historical and contemporary forces that have shaped variability in a panel of genes involved in innate and acquired immunity in roe deer, including Mhc-Drb and genes encoding cytokines or toll-like receptors (TLRs). Together, our results suggest that genetic drift is the main contemporary evolutionary force shaping immunogenetic variation within populations. However, in contrast to the classical view, we found that some innate immune genes involved in micropathogen recognition (e.g. Tlrs) continue to evolve dynamically in roe deer in response to pathogen-mediated positive selection. Most studied Tlrs (Tlr2, Tlr4 and Tlr5) had similarly high levels of amino acid diversity in the three studied populations including one recently established in southwestern France that showed a clear signature of genetic bottleneck. Tlr2 implicated in the recognition of Gram-positive bacteria in domestic ungulates, showed strong evidence of balancing selection. The high immunogenetic variation revealed here implies that roe deer are able to cope with a wide spectrum of pathogens and to respond rapidly to emerging infectious diseases.
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Affiliation(s)
- Erwan Quéméré
- Laboratoire Comportement et Ecologie de la Faune Sauvage (CEFS), INRA UR35, B.P. 52627, 31326, Castanet-Tolosan, France
| | - Maxime Galan
- INRA, UMR CBGP, (INRA/IRD/Cirad/Montpellier SupAgro), Campus International de Baillarguet CS 30016, 34988, Montferrier-sur-Lez Cedex, France
| | - Jean-François Cosson
- INRA, UMR CBGP, (INRA/IRD/Cirad/Montpellier SupAgro), Campus International de Baillarguet CS 30016, 34988, Montferrier-sur-Lez Cedex, France
| | - François Klein
- ONCFS, CNERA Cervidés-Sanglier, 1 Place Exelmans, F-55000, Bar-le-Duc, France
| | - Stéphane Aulagnier
- Laboratoire Comportement et Ecologie de la Faune Sauvage (CEFS), INRA UR35, B.P. 52627, 31326, Castanet-Tolosan, France
| | - Emmanuelle Gilot-Fromont
- Université de Lyon, Université Lyon 1, UMR CNRS, 5558, Villeurbanne, France.,Université de Lyon, VetAgro Sup, Marcy l'Etoile, France
| | - Joël Merlet
- Laboratoire Comportement et Ecologie de la Faune Sauvage (CEFS), INRA UR35, B.P. 52627, 31326, Castanet-Tolosan, France
| | - Maxime Bonhomme
- Laboratoire de Recherches en Sciences Végétales, Université de Toulouse UPS, CNRS UMR5546, Castanet-Tolosan, France
| | - A J Mark Hewison
- Laboratoire Comportement et Ecologie de la Faune Sauvage (CEFS), INRA UR35, B.P. 52627, 31326, Castanet-Tolosan, France
| | - Nathalie Charbonnel
- INRA, UMR CBGP, (INRA/IRD/Cirad/Montpellier SupAgro), Campus International de Baillarguet CS 30016, 34988, Montferrier-sur-Lez Cedex, France
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