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Djurišić M. Immune receptors and aging brain. Biosci Rep 2024; 44:BSR20222267. [PMID: 38299364 PMCID: PMC10866841 DOI: 10.1042/bsr20222267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 01/08/2024] [Accepted: 01/29/2024] [Indexed: 02/02/2024] Open
Abstract
Aging brings about a myriad of degenerative processes throughout the body. A decrease in cognitive abilities is one of the hallmark phenotypes of aging, underpinned by neuroinflammation and neurodegeneration occurring in the brain. This review focuses on the role of different immune receptors expressed in cells of the central and peripheral nervous systems. We will discuss how immune receptors in the brain act as sentinels and effectors of the age-dependent shift in ligand composition. Within this 'old-age-ligand soup,' some immune receptors contribute directly to excessive synaptic weakening from within the neuronal compartment, while others amplify the damaging inflammatory environment in the brain. Ultimately, chronic inflammation sets up a positive feedback loop that increases the impact of immune ligand-receptor interactions in the brain, leading to permanent synaptic and neuronal loss.
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Affiliation(s)
- Maja Djurišić
- Departments of Biology, Neurobiology, and Bio-X, Stanford University, Stanford, CA 94305, U.S.A
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Wang Y, Liu D, Wei M, Chen J, Li Y, Zhao F, Zhang Z, Ma Y. Genome-wide identification and expression analyses of Toll-like receptors provide new insights on adaptation to intertidal benthic environments in Urechis unicinctus (Annelida, Echiura). AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2023; 260:106594. [PMID: 37263159 DOI: 10.1016/j.aquatox.2023.106594] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/26/2023] [Accepted: 05/27/2023] [Indexed: 06/03/2023]
Abstract
Toll-like receptors (TLR) are an important class of pattern recognition receptors involved in innate immunity that recognize pathogen-associated and damage-associated molecular patterns. Although the role of TLRs in immunity has been extensively studied, a systematic investigation of their function in environmental adaptation is still in its infancy. In this study, a genome-wide search was conducted to systematically investigate TLR family members of Urechis unicinctus, a typical benthic organism in intertidal mudflats. A total of 28 TLR genes were identified in the U. unicinctus genome, and their fundamental physiological and biochemical properties were characterized. Gene copy number analysis among species in different habitats indicated that TLR family gene expansion may be probably related with benthic environmental adaptation. To further investigate the expression patterns of TLR members under environmental stress, transcriptome data was analyzed from different developmental stages and the hindgut under sulfide stress. Transcriptome analysis of different developmental stages showed that most TLR genes were highly expressed during a key period of benthic environment adaptation (worm-shaped larva). Transcriptome analysis of the hindgut under sulfide stress showed that the expression of 12 TLR members was significantly induced under sulfide stress. These results indicate that the regulation of TLR gene expression may be probably involved in the adaptation of U. unicinctus to the benthic intertidal zone environment. Taken together, this study may lay the foundation for future functional analysis of the specific role of TLRs in host immune responses against sulfide exposure and benthic environmental stress in annelid.
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Affiliation(s)
- Yunjian Wang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Danwen Liu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Maokai Wei
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Jiao Chen
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Yunpeng Li
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
| | - Feng Zhao
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Zhifeng Zhang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
| | - Yubin Ma
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
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Fan XL, Song Y, Qin DX, Lin PY. Regulatory Effects of Clock and Bmal1 on Circadian Rhythmic TLR Expression. Int Rev Immunol 2023; 42:101-112. [PMID: 34544330 DOI: 10.1080/08830185.2021.1931170] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Circadian locomotor output cycles kaput (Clock) and brain and muscle ARNT-like 1 (Bmal1) are two core circadian clock genes. They form a heterodimer that can bind to the E-box element in the promoters of Period circadian protein (Per) and Cryptochrome (Cry) genes, thereby inducing the rhythmic expression of circadian clock control genes. Toll-like receptors (TLRs) are type I transmembrane proteins belonging to the pattern recognition receptor (PRR) family. They can recognize a variety of pathogens and play an important role in innate immunity and adaptive immune responses. Recent studies have found that the circadian clock is closely associated with the immune system. TLRs have a certain correlation with the circadian rhythms; Bmal1 seems to be the central mediator connecting the circadian clock and the immune system. Research on Bmal1 and TLRs has made some progress, but the specific relationship between TLRs and Bmal1 remains unclear. Understanding the relationship between TLRs and Clock/Bmal1 genes is increasingly important for basic research and clinical treatment.
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Affiliation(s)
- Xu-Li Fan
- Department of Pharmacology, Zhejiang University of Technology, Hangzhou, Zhejiang, P.R. China
| | - Ying Song
- Department of Pharmacology, Zhejiang University of Technology, Hangzhou, Zhejiang, P.R. China
| | - Dong-Xu Qin
- Department of Pharmacology, Zhejiang University of Technology, Hangzhou, Zhejiang, P.R. China
| | - Pei-Yao Lin
- Department of Pharmacology, Zhejiang University of Technology, Hangzhou, Zhejiang, P.R. China
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Neves F, Muñoz-Mérida A, Machado AM, Almeida T, Gaigher A, Esteves PJ, Castro LFC, Veríssimo A. Uncovering a 500 million year old history and evidence of pseudogenization for TLR15. Front Immunol 2022; 13:1020601. [PMID: 36605191 PMCID: PMC9808068 DOI: 10.3389/fimmu.2022.1020601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/23/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction Toll like receptors (TLRs) are at the front line of pathogen recognition and host immune response. Many TLR genes have been described to date with some being found across metazoans while others are restricted to specific lineages. A cryptic member of the TLR gene family, TLR15, has a unique phylogenetic distribution. Initially described in extant species of birds and reptiles, an ortholog has been reported for cartilaginous fish. Methods Here, we significantly expanded the evolutionary analysis of TLR15 gene evolution, taking advantage of large genomic and transcriptomic resources available from different lineages of vertebrates. Additionally, we objectively search for TLR15 in lobe-finned and ray-finned fish, as well as in cartilaginous fish and jawless vertebrates. Results and discussion We confirm the presence of TLR15 in early branching jawed vertebrates - the cartilaginous fish, as well as in basal Sarcopterygii - in lungfish. However, within cartilaginous fish, the gene is present in Holocephalans (all three families) but not in Elasmobranchs (its sister-lineage). Holocephalans have long TLR15 protein sequences that disrupt the typical TLR structure, and some species display a pseudogene sequence due to the presence of frameshift mutations and early stop codons. Additionally, TLR15 has low expression levels in holocephalans when compared with other TLR genes. In turn, lungfish also have long TLR15 protein sequences but the protein structure is not compromised. Finally, TLR15 presents several sites under negative selection. Overall, these results suggest that TLR15 is an ancient TLR gene and is experiencing ongoing pseudogenization in early-branching vertebrates.
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Affiliation(s)
- Fabiana Neves
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal,*Correspondence: Fabiana Neves,
| | - Antonio Muñoz-Mérida
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - André M. Machado
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal,CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Tereza Almeida
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Arnaud Gaigher
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal,Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany,Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
| | - Pedro J. Esteves
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal,CITS - Center of Investigation in Health Technologies, CESPU, Gandra, Portugal
| | - L. Filipe C. Castro
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal,CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Ana Veríssimo
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
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Redwan EM, Aljadawi AA, Uversky VN. Hepatitis C Virus Infection and Intrinsic Disorder in the Signaling Pathways Induced by Toll-Like Receptors. BIOLOGY 2022; 11:1091. [PMID: 36101469 PMCID: PMC9312352 DOI: 10.3390/biology11071091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/07/2022] [Accepted: 07/19/2022] [Indexed: 11/23/2022]
Abstract
In this study, we examined the interplay between protein intrinsic disorder, hepatitis C virus (HCV) infection, and signaling pathways induced by Toll-like receptors (TLRs). To this end, 10 HCV proteins, 10 human TLRs, and 41 proteins from the TLR-induced downstream pathways were considered from the prevalence of intrinsic disorder. Mapping of the intrinsic disorder to the HCV-TLR interactome and to the TLR-based pathways of human innate immune response to the HCV infection demonstrates that substantial levels of intrinsic disorder are characteristic for proteins involved in the regulation and execution of these innate immunity pathways and in HCV-TLR interaction. Disordered regions, being commonly enriched in sites of various posttranslational modifications, may play important functional roles by promoting protein-protein interactions and support the binding of the analyzed proteins to other partners such as nucleic acids. It seems that this system represents an important illustration of the role of intrinsic disorder in virus-host warfare.
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Affiliation(s)
- Elrashdy M. Redwan
- Biological Science Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; (E.M.R.); (A.A.A.)
- Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City for Scientific Research and Technology Applications, New Borg EL-Arab, Alexandria 21934, Egypt
| | - Abdullah A. Aljadawi
- Biological Science Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; (E.M.R.); (A.A.A.)
| | - Vladimir N. Uversky
- Biological Science Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; (E.M.R.); (A.A.A.)
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
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Zhang L, Liu G, Xia T, Yang X, Sun G, Zhao C, Xu C, Zhang H. Evolution of toll-like receptor gene family in amphibians. Int J Biol Macromol 2022; 208:463-474. [PMID: 35337917 DOI: 10.1016/j.ijbiomac.2022.03.112] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 02/09/2022] [Accepted: 03/17/2022] [Indexed: 12/24/2022]
Abstract
The evolutionary position and lifestyle of amphibians highlights the important roles of the immune system in adaptive radiation and their adaptation to a complex pathogenic environment. Toll-like receptors (TLRs) are membrane-like sensors that recognize and bind conserved molecular motifs in pathogens to initiate downstream immune responses. To understand the evolutionary patterns of TLRs in amphibians, we analyzed TLR genes from the genomes and transcriptomes of 102 amphibian species. Phylogenetic results showed that 578 intact amphibian TLR sequences belonged to 16 TLR genes and were divided into seven subfamilies. The TLR4 subfamily was only identified in the Anura. Purification selection plays a leading role in amphibian TLR evolution and mean ω (dN/dS) values ranged from 0.252 for TLR7 to 0.381 for TLR19. Furthermore, the ω values of different domains were significantly different. We found positive selection patterns for 141 of 12,690 codons (1.1%) in all amphibian TLRs, most of which were located in leucine-rich repeats (LRRs). We also observed low to moderate levels of single-nucleotide polymorphisms (SNPs) in Pelophylax nigromaculatus and Bombina orientalis. This study provided critical primers, meaningful information regarding TLR gene family evolution in amphibians, and insights into the complex evolutionary patterns and implications of TLR polymorphisms.
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Affiliation(s)
- Lei Zhang
- College of Life Science, Qufu Normal University, Qufu, Shandong 273165, China
| | - Guangshuai Liu
- College of Life Science, Qufu Normal University, Qufu, Shandong 273165, China
| | - Tian Xia
- College of Life Science, Qufu Normal University, Qufu, Shandong 273165, China
| | - Xiufeng Yang
- College of Life Science, Qufu Normal University, Qufu, Shandong 273165, China
| | - Guolei Sun
- College of Life Science, Qufu Normal University, Qufu, Shandong 273165, China
| | - Chao Zhao
- College of Life Science, Qufu Normal University, Qufu, Shandong 273165, China
| | - Chunzhu Xu
- College of Life Science, Northeast Agricultural University, Harbin 150030, China.
| | - Honghai Zhang
- College of Life Science, Qufu Normal University, Qufu, Shandong 273165, China.
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Organic UV Filters Induce Toll-like-Receptors and Related Signaling Pathways in Peripheral Blood Mononuclear Cells of Juvenile Loggerhead Sea Turtles (Caretta caretta). Animals (Basel) 2022; 12:ani12050594. [PMID: 35268162 PMCID: PMC8909695 DOI: 10.3390/ani12050594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Emerging environmental contaminants, such as sunscreen agents, have been broadly identified in marine ecosystems. Thus, the present work aims to investigate whether organic UV filters cause immunotoxic effects in juvenile loggerhead sea turtles (Caretta caretta). We found that loggerhead sea turtles showing high circulating levels of organic UV filters manifested increased expression of genes involved in inflammatory responses, probably due to contaminant-induced oxidative damage. Abstract Recent evidence suggests that exposure to organic ultraviolet filters (UV filters) is associated with dysregulated neuroendocrine-immune homeostasis. Marine species are likely to be among the most vulnerable to UV filters due to widespread diffusion of these chemicals in the aquatic environment. In the present study, the effects of UV filter bioaccumulation on toll-like-receptors (TLRs) and related signaling pathways were investigated in peripheral blood mononuclear cells (PBMCs) of juvenile loggerhead sea turtles (Caretta caretta). We found that the expression of both TLR1 and TLR2 was significantly increased in UV-filter exposed turtles compared to control animals. Similarly, the signaling pathway downstream of activated TLRs (i.e., Ras-related C3 botulinum toxin substrate 1 (RAC1), Phosphoinositide 3-kinase (PI3K), serine/threonine-protein kinase (AKT3), and nuclear factor κB (NF-κB)) was significantly up-regulated, leading to an enhanced transcription of pro-inflammatory cytokines. In addition, we demonstrated that high levels of plasma UV filters increased lipid peroxidation in sea turtles’ PBMCs. Our results indicated that UV filters affected the inflammatory responses of PBMCs via modulation of the TLR/NF-κB signaling pathway and provided a new insight into the link between exposure to sunscreen agents and sea turtle health.
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Bezhaeva T, Karper J, Quax PHA, de Vries MR. The Intriguing Role of TLR Accessory Molecules in Cardiovascular Health and Disease. Front Cardiovasc Med 2022; 9:820962. [PMID: 35237675 PMCID: PMC8884272 DOI: 10.3389/fcvm.2022.820962] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/19/2022] [Indexed: 12/12/2022] Open
Abstract
Activation of Toll like receptors (TLR) plays an important role in cardiovascular disease development, progression and outcomes. Complex TLR mediated signaling affects vascular and cardiac function including tissue remodeling and repair. Being central components of both innate and adaptive arms of the immune system, TLRs interact as pattern recognition receptors with a series of exogenous ligands and endogenous molecules or so-called danger associated molecular patterns (DAMPs) that are released upon tissue injury and cellular stress. Besides immune cells, a number of structural cells within the cardiovascular system, including endothelial cells, smooth muscle cells, fibroblasts and cardiac myocytes express TLRs and are able to release or sense DAMPs. Local activation of TLR-mediated signaling cascade induces cardiovascular tissue repair but in a presence of constant stimuli can overshoot and cause chronic inflammation and tissue damage. TLR accessory molecules are essential in guiding and dampening these responses toward an adequate reaction. Furthermore, accessory molecules assure specific and exclusive TLR-mediated signal transduction for distinct cells and pathways involved in the pathogenesis of cardiovascular diseases. Although much has been learned about TLRs activation in cardiovascular remodeling, the exact role of TLR accessory molecules is not entirely understood. Deeper understanding of the role of TLR accessory molecules in cardiovascular system may open therapeutic avenues aiming at manipulation of inflammatory response in cardiovascular disease. The present review outlines accessory molecules for membrane TLRs that are involved in cardiovascular disease progression. We first summarize the up-to-date knowledge on TLR signaling focusing on membrane TLRs and their ligands that play a key role in cardiovascular system. We then survey the current evidence of the contribution of TLRs accessory molecules in vascular and cardiac remodeling including myocardial infarction, heart failure, stroke, atherosclerosis, vein graft disease and arterio-venous fistula failure.
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Affiliation(s)
- Taisiya Bezhaeva
- Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, Netherlands
| | - Jacco Karper
- Department of Cardiology, Wilhelmina Hospital Assen, Assen, Netherlands
| | - Paul H. A. Quax
- Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, Netherlands
| | - Margreet R. de Vries
- Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, Netherlands
- *Correspondence: Margreet R. de Vries
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Sousa C, Fernandes SA, Cardoso JCR, Wang Y, Zhai W, Guerreiro PM, Chen L, Canário AVM, Power DM. Toll-Like Receptor Evolution: Does Temperature Matter? Front Immunol 2022; 13:812890. [PMID: 35237266 PMCID: PMC8882821 DOI: 10.3389/fimmu.2022.812890] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/03/2022] [Indexed: 11/13/2022] Open
Abstract
Toll-like receptors (TLRs) recognize conserved pathogen-associated molecular patterns (PAMPs) and are an ancient and well-conserved group of pattern recognition receptors (PRRs). The isolation of the Antarctic continent and its unique teleost fish and microbiota prompted the present investigation into Tlr evolution. Gene homologues of tlr members in teleosts from temperate regions were present in the genome of Antarctic Nototheniidae and the non-Antarctic sister lineage Bovichtidae. Overall, in Nototheniidae apart from D. mawsoni, no major tlr gene family expansion or contraction occurred. Instead, lineage and species-specific changes in the ectodomain and LRR of Tlrs occurred, particularly in the Tlr11 superfamily that is well represented in fish. Positive selective pressure and associated sequence modifications in the TLR ectodomain and within the leucine-rich repeats (LRR), important for pathogen recognition, occurred in Tlr5, Tlr8, Tlr13, Tlr21, Tlr22, and Tlr23 presumably associated with the unique Antarctic microbiota. Exposure to lipopolysaccharide (Escherichia coli O111:B4) Gram negative bacteria did not modify tlr gene expression in N. rossii head–kidney or anterior intestine, although increased water temperature (+4°C) had a significant effect.
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Affiliation(s)
- Cármen Sousa
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, Faro, Portugal
| | | | - João C. R. Cardoso
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, Faro, Portugal
| | - Ying Wang
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University (SHOU), Shanghai, China
| | - Wanying Zhai
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University (SHOU), Shanghai, China
| | - Pedro M. Guerreiro
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, Faro, Portugal
| | - Liangbiao Chen
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University (SHOU), Shanghai, China
| | - Adelino V. M. Canário
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, Faro, Portugal
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University (SHOU), Shanghai, China
| | - Deborah M. Power
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, Faro, Portugal
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University (SHOU), Shanghai, China
- *Correspondence: Deborah M. Power,
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Tan M, Redmond AK, Dooley H, Nozu R, Sato K, Kuraku S, Koren S, Phillippy AM, Dove ADM, Read T. The whale shark genome reveals patterns of vertebrate gene family evolution. eLife 2021; 10:e65394. [PMID: 34409936 PMCID: PMC8455134 DOI: 10.7554/elife.65394] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 08/18/2021] [Indexed: 02/06/2023] Open
Abstract
Chondrichthyes (cartilaginous fishes) are fundamental for understanding vertebrate evolution, yet their genomes are understudied. We report long-read sequencing of the whale shark genome to generate the best gapless chondrichthyan genome assembly yet with higher contig contiguity than all other cartilaginous fish genomes, and studied vertebrate genomic evolution of ancestral gene families, immunity, and gigantism. We found a major increase in gene families at the origin of gnathostomes (jawed vertebrates) independent of their genome duplication. We studied vertebrate pathogen recognition receptors (PRRs), which are key in initiating innate immune defense, and found diverse patterns of gene family evolution, demonstrating that adaptive immunity in gnathostomes did not fully displace germline-encoded PRR innovation. We also discovered a new toll-like receptor (TLR29) and three NOD1 copies in the whale shark. We found chondrichthyan and giant vertebrate genomes had decreased substitution rates compared to other vertebrates, but gene family expansion rates varied among vertebrate giants, suggesting substitution and expansion rates of gene families are decoupled in vertebrate genomes. Finally, we found gene families that shifted in expansion rate in vertebrate giants were enriched for human cancer-related genes, consistent with gigantism requiring adaptations to suppress cancer.
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Affiliation(s)
- Milton Tan
- Illinois Natural History Survey at University of Illinois Urbana-ChampaignChampaignUnited States
| | | | - Helen Dooley
- University of Maryland School of Medicine, Institute of Marine & Environmental TechnologyBaltimoreUnited States
| | - Ryo Nozu
- Okinawa Churashima Research Center, Okinawa Churashima FoundationOkinawaJapan
| | - Keiichi Sato
- Okinawa Churashima Research Center, Okinawa Churashima FoundationOkinawaJapan
- Okinawa Churaumi Aquarium, MotobuOkinawaJapan
| | - Shigehiro Kuraku
- RIKEN Center for Biosystems Dynamics Research (BDR), RIKENKobeJapan
| | - Sergey Koren
- National Human Genome Research Institute, National Institutes of HealthBethesdaUnited States
| | - Adam M Phillippy
- National Human Genome Research Institute, National Institutes of HealthBethesdaUnited States
| | | | - Timothy Read
- Department of Infectious Diseases, Emory University School of MedicineAtlantaUnited States
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Yang J, Zhou M, Zhong Y, Xu L, Zeng C, Zhao X, Zhang M. Gene duplication and adaptive evolution of Toll-like receptor genes in birds. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 119:103990. [PMID: 33422554 DOI: 10.1016/j.dci.2020.103990] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 12/27/2020] [Accepted: 12/27/2020] [Indexed: 06/12/2023]
Abstract
Toll-like receptors (TLRs) play an important role in innate immune through recognizes pathogens. In order to reveal the evolutionary patterns and adaptive evolution of avian TLRs, we examined 66 representative bird species in 26 orders. Phylogenetic results indicated that TLR1A and TLR1B may have differentiated functionally. Evolutionary analysis showed that the TLR genes in birds under strong Purification selection (0.165-0.4265). A total of 126 common positively selected codons were identified in 10 TLR genes of avian, and most sites were located in the extracellular leucine-rich repeat (LRR) functional domains, and both environment and feeding habits were external factors driving the evolution of avian TLR genes. Environmental pressures had a greater effect on TLR1B, TLR2B, TLR3 and TLR4, while feeding habits were active in affecting TLR2A, TLR2B, TLR15 and TLR21. Our data suggested that TLR genes have been subjected to different selective pressures in the diversification of birds and that these changes enabled them to respond differently to pathogens from diverse sources.
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Affiliation(s)
- Jiandong Yang
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, 611130, China; Key Laboratory of Southwest China Wildlife Rsources Conservation (Ministry of Education), China West Normal University, Nanchong, 637009, PR China.
| | - Ming Zhou
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, 611130, China; Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Yun Zhong
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Liqun Xu
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Changjun Zeng
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaoling Zhao
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ming Zhang
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, 611130, China
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Mielcarska MB, Bossowska-Nowicka M, Toka FN. Cell Surface Expression of Endosomal Toll-Like Receptors-A Necessity or a Superfluous Duplication? Front Immunol 2021; 11:620972. [PMID: 33597952 PMCID: PMC7882679 DOI: 10.3389/fimmu.2020.620972] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 12/11/2020] [Indexed: 12/28/2022] Open
Abstract
Timely and precise delivery of the endosomal Toll-like receptors (TLRs) to the ligand recognition site is a critical event in mounting an effective antimicrobial immune response, however, the same TLRs should maintain the delicate balance of avoiding recognition of self-nucleic acids. Such sensing is widely known to start from endosomal compartments, but recently enough evidence has accumulated supporting the idea that TLR-mediated signaling pathways originating in the cell membrane may be engaged in various cells due to differential expression and distribution of the endosomal TLRs. Therefore, the presence of endosomal TLRs on the cell surface could benefit the host responses in certain cell types and/or organs. Although not fully understood why, TLR3, TLR7, and TLR9 may occur both in the cell membrane and intracellularly, and it seems that activation of the immune response can be initiated concurrently from these two sites in the cell. Furthermore, various forms of endosomal TLRs may be transported to the cell membrane, indicating that this may be a normal process orchestrated by cysteine proteases-cathepsins. Among the endosomal TLRs, TLR3 belongs to the evolutionary distinct group and engages a different protein adapter in the signaling cascade. The differently glycosylated forms of TLR3 are transported by UNC93B1 to the cell membrane, unlike TLR7, TLR8, and TLR9. The aim of this review is to reconcile various views on the cell surface positioning of endosomal TLRs and add perspective to the implication of such receptor localization on their function, with special attention to TLR3. Cell membrane-localized TLR3, TLR7, and TLR9 may contribute to endosomal TLR-mediated inflammatory signaling pathways. Dissecting this signaling axis may serve to better understand mechanisms influencing endosomal TLR-mediated inflammation, thus determine whether it is a necessity for immune response or simply a circumstantial superfluous duplication, with other consequences on immune response.
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Affiliation(s)
- Matylda Barbara Mielcarska
- Division of Immunology, Institute of Veterinary Medicine, Department of Preclinical Sciences, Warsaw University of Life Sciences, Warsaw, Poland
| | - Magdalena Bossowska-Nowicka
- Division of Immunology, Institute of Veterinary Medicine, Department of Preclinical Sciences, Warsaw University of Life Sciences, Warsaw, Poland
| | - Felix Ngosa Toka
- Division of Immunology, Institute of Veterinary Medicine, Department of Preclinical Sciences, Warsaw University of Life Sciences, Warsaw, Poland.,Center for Integrative Mammalian Research, Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
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13
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Priyam M, Gupta SK, Sarkar B, Sharma TR, Pattanayak A. Variation in selection constraints on teleost TLRs with emphasis on their repertoire in the Walking catfish, Clarias batrachus. Sci Rep 2020; 10:21394. [PMID: 33288798 PMCID: PMC7721727 DOI: 10.1038/s41598-020-78347-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 11/24/2020] [Indexed: 11/10/2022] Open
Abstract
The high degree of conservation of toll-like receptors (TLRs), and yet their subtle variations for better adaptation of species in the host–pathogen arms race make them worthy candidates for understanding evolution. We have attempted to track the trend of TLR evolution in the most diverse vertebrate group—teleosts, where Clarias batrachus was given emphasis, considering its traits for terrestrial adaptation. Eleven C. batrachus TLRs (TLR1, 2, 3, 5, 7, 8 9, 13, 22, 25, 26) were identified in this study which clustered in proximity to its Siluriformes relative orthologues in the phylogenetic analysis of 228 TLRs from 25 teleosts. Ten TLRs (TLR1, 2, 3, 5, 7, 8 9, 13, 21, 22) with at least 15 member orthologues for each alignment were processed for selection pressure and coevolutionary analysis. TLR1, 7, 8 and 9 were found to be under positive selection in the alignment-wide test. TLR1 also showed maximum episodic diversification in its clades while the teleost group Eupercaria showed the maximum divergence in their TLR repertoire. Episodic diversification was evident in C. batrachus TLR1 and 7 alignments. These results present a strong evidence of a divergent TLR repertoire in teleosts which may be contributing towards species-specific variation in TLR functions.
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Affiliation(s)
- Manisha Priyam
- School of Molecular Diagnostics and Prophylactics, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, 834 010, India
| | - Sanjay K Gupta
- School of Molecular Diagnostics and Prophylactics, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, 834 010, India.
| | - Biplab Sarkar
- School of Molecular Diagnostics and Prophylactics, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, 834 010, India
| | - T R Sharma
- School of Molecular Diagnostics and Prophylactics, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, 834 010, India
| | - A Pattanayak
- School of Molecular Diagnostics and Prophylactics, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, 834 010, India
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14
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Zapata D, Rivera-Gutierrez HF, Parra JL, Gonzalez-Quevedo C. Low adaptive and neutral genetic diversity in the endangered Antioquia wren (Thryophilus sernai). CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01313-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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15
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Liu G, Zhang H, Zhao C, Zhang H. Evolutionary History of the Toll-Like Receptor Gene Family across Vertebrates. Genome Biol Evol 2020; 12:3615-3634. [PMID: 31800025 PMCID: PMC6946030 DOI: 10.1093/gbe/evz266] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/27/2019] [Indexed: 12/13/2022] Open
Abstract
Adaptation to a wide range of pathogenic environments is a major aspect of the ecological adaptations of vertebrates during evolution. Toll-like receptors (TLRs) are ancient membrane-bound sensors in animals and are best known for their roles in detecting and defense against invading pathogenic microorganisms. To understand the evolutionary history of the vertebrate TLR gene family, we first traced the origin of single-cysteine cluster TLRs that share the same protein architecture with vertebrate TLRs in early-branching animals and then analyzed all members of the TLR family in over 200 species covering all major vertebrate clades. Our results indicate that although the emergence of single-cysteine cluster TLRs predates the separation of bilaterians and cnidarians, most vertebrate TLR members originated shortly after vertebrate emergence. Phylogenetic analyses divided 1,726 vertebrate TLRs into 8 subfamilies, and TLR3 may represent the most ancient subfamily that emerged before the branching of deuterostomes. Our analysis reveals that purifying selection predominated in the evolution of all vertebrate TLRs, with mean dN/dS (ω) values ranging from 0.082 for TLR21 in birds to 0.434 for TLR11 in mammals. However, we did observe patterns of positive selection acting on specific codons (527 of 60,294 codons across all vertebrate TLRs, 8.7‰), which are significantly concentrated in ligand-binding extracellular domains and suggest host–pathogen coevolutionary interactions. Additionally, we found stronger positive selection acting on nonviral compared with viral TLRs, indicating the more essential nonredundant function of viral TLRs in host immunity. Taken together, our findings provide comprehensive insight into the complex evolutionary processes of the vertebrate TLR gene family, involving gene duplication, pseudogenization, purification, and positive selection.
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Affiliation(s)
- Guangshuai Liu
- College of Life Science, Qufu Normal University, Shandong, China
| | - Huanxin Zhang
- College of Marine Life Science, Ocean University of China, Qingdao, Shandong, China
| | - Chao Zhao
- College of Life Science, Qufu Normal University, Shandong, China
| | - Honghai Zhang
- College of Life Science, Qufu Normal University, Shandong, China
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16
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17
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Levy H, Fiddaman SR, Vianna JA, Noll D, Clucas GV, Sidhu JKH, Polito MJ, Bost CA, Phillips RA, Crofts S, Miller GD, Pistorius P, Bonnadonna F, Le Bohec C, Barbosa A, Trathan P, Raya Rey A, Frantz LAF, Hart T, Smith AL. Evidence of Pathogen-Induced Immunogenetic Selection across the Large Geographic Range of a Wild Seabird. Mol Biol Evol 2020; 37:1708-1726. [PMID: 32096861 PMCID: PMC7253215 DOI: 10.1093/molbev/msaa040] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Over evolutionary time, pathogen challenge shapes the immune phenotype of the host to better respond to an incipient threat. The extent and direction of this selection pressure depend on the local pathogen composition, which is in turn determined by biotic and abiotic features of the environment. However, little is known about adaptation to local pathogen threats in wild animals. The Gentoo penguin (Pygoscelis papua) is a species complex that lends itself to the study of immune adaptation because of its circumpolar distribution over a large latitudinal range, with little or no admixture between different clades. In this study, we examine the diversity in a key family of innate immune genes-the Toll-like receptors (TLRs)-across the range of the Gentoo penguin. The three TLRs that we investigated present varying levels of diversity, with TLR4 and TLR5 greatly exceeding the diversity of TLR7. We present evidence of positive selection in TLR4 and TLR5, which points to pathogen-driven adaptation to the local pathogen milieu. Finally, we demonstrate that two positively selected cosegregating sites in TLR5 are sufficient to alter the responsiveness of the receptor to its bacterial ligand, flagellin. Taken together, these results suggest that Gentoo penguins have experienced distinct pathogen-driven selection pressures in different environments, which may be important given the role of the Gentoo penguin as a sentinel species in some of the world's most rapidly changing environments.
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Affiliation(s)
- Hila Levy
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | - Juliana A Vianna
- Departamento de Ecosistemas y Medio Ambiente, Pontificia Universidad Católica de Chile, Macul, Santiago, Chile
| | - Daly Noll
- Departamento de Ecosistemas y Medio Ambiente, Pontificia Universidad Católica de Chile, Macul, Santiago, Chile
- Departamento de Ciencias Ecológicas, Instituto de Ecología y Biodiversidad, Universidad de Chile, Santiago, Chile
| | - Gemma V Clucas
- Cornell Atkinson Center for a Sustainable Future, Cornell University, Ithaca, NY
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY
| | | | - Michael J Polito
- Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, LA
| | - Charles A Bost
- Centre d’Etudes Biologiques de Chizé (CEBC), UMR 7372 du CNRS‐Université de La Rochelle, Villiers‐en‐Bois, France
| | | | - Sarah Crofts
- Falklands Conservation, Stanley, Falkland Islands, United Kingdom
| | - Gary D Miller
- Microbiology and Immunology, PALM, University of Western Australia, Crawley, Western Australia, Australia
| | - Pierre Pistorius
- DST/NRF Centre of Excellence at the Percy FitzPatrick Institute for African Ornithology, Department of Zoology, Nelson Mandela University, Port Elizabeth, South Africa
| | - Francesco Bonnadonna
- CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, Montpellier, France
| | - Céline Le Bohec
- Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg, France
- Département de Biologie Polaire, Centre Scientifique de Monaco, Monaco, Principality of Monaco
| | - Andrés Barbosa
- Museo Nacional de Ciencias Naturales, Departamento de Ecología Evolutiva, CSIC, Madrid, Spain
| | - Phil Trathan
- British Antarctic Survey, Cambridge, United Kingdom
| | - Andrea Raya Rey
- Centro Austral de Investigaciones Científicas – Consejo Nacional de Investigaciones Científicas y Técnicas (CADIC-CONICET), Ushuaia, Tierra del Fuego, Argentina
- Instituto de Ciencias Polares, Ambiente y Recursos Naturales, Universidad Nacional de Tierra del Fuego, Ushuaia, Tierra del Fuego, Argentina
- Wildlife Conservation Society, Buenos Aires, Argentina
| | - Laurent A F Frantz
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Tom Hart
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Adrian L Smith
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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18
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Xu W, Zhou X, Fang W, Chen X. Genetic diversity of toll-like receptor genes in the vulnerable Chinese egret (Egretta eulophotes). PLoS One 2020; 15:e0233714. [PMID: 32469968 PMCID: PMC7259618 DOI: 10.1371/journal.pone.0233714] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 05/11/2020] [Indexed: 01/15/2023] Open
Abstract
Toll-like receptor (TLR) genes have recently been employed to assess genetic diversity, as they can be used to infer both demographic history and adaptation to environments with different pathogen pressure. Here, we sampled 120 individuals of the Chinese egret (Egretta eulophotes), a globally vulnerable species, from four breeding populations across China. We assessed the levels of genetic diversity, selection pressure, and population differentiation at seven TLR loci (TLR1LB, TLR2A, TLR3, TLR4, TLR5, TLR7, and TLR15). Using a variety of metrics (SNPs, heterozygosity, nucleotides, haplotypes), our analyses showed that genetic diversity was lower at 4 of the 7 TLR loci in the vulnerable Chinese egret compared to the more common little egret (Egretta garzetta). The selection test indicated TLRs, except for TLR5, were under purifying selection in TLR evolution, suggesting that low TLR genetic diversity in the Chinese egret may be caused by purifying selection. Moreover, analysis of molecular variance indicated low but significant population differentiation among four populations at all of the TLR loci in this egret. However, some comparisons based on fixation index analyses did not show significant population differentiation, and Bayesian clustering showed admixture. Our finding suggested that these four populations of the Chinese egret in China may be considered a single unit for conservation planning. These results, the new report of TLR genetic diversity in a long-distance migratory vulnerable Ardeid species, will provide fundamental TLR information for further studies on the conservation genetics of the Chinese egret and other Ardeids.
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Affiliation(s)
- Wei Xu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People’s Republic of China
| | - Xiaoping Zhou
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People’s Republic of China
| | - Wenzhen Fang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People’s Republic of China
| | - Xiaolin Chen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People’s Republic of China
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19
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Chen CY, Shih YC, Hung YF, Hsueh YP. Beyond defense: regulation of neuronal morphogenesis and brain functions via Toll-like receptors. J Biomed Sci 2019; 26:90. [PMID: 31684953 PMCID: PMC6827257 DOI: 10.1186/s12929-019-0584-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 10/23/2019] [Indexed: 12/16/2022] Open
Abstract
Toll-like receptors (TLRs) are well known as critical pattern recognition receptors that trigger innate immune responses. In addition, TLRs are expressed in neurons and may act as the gears in the neuronal detection/alarm system for making good connections. As neuronal differentiation and circuit formation take place along with programmed cell death, neurons face the challenge of connecting with appropriate targets while avoiding dying or dead neurons. Activation of neuronal TLR3, TLR7 and TLR8 with nucleic acids negatively modulates neurite outgrowth and alters synapse formation in a cell-autonomous manner. It consequently influences neural connectivity and brain function and leads to deficits related to neuropsychiatric disorders. Importantly, neuronal TLR activation does not simply duplicate the downstream signal pathways and effectors of classical innate immune responses. The differences in spatial and temporal expression of TLRs and their ligands likely account for the diverse signaling pathways of neuronal TLRs. In conclusion, the accumulated evidence strengthens the idea that the innate immune system of neurons serves as an alarm system that responds to exogenous pathogens as well as intrinsic danger signals and fine-tune developmental processes of neurons.
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Affiliation(s)
- Chiung-Ya Chen
- Institute of Molecular Biology, Academia Sinica, 128, Academia Rd., Sec. 2, Taipei, 11529, Taiwan, Republic of China.
| | - Yi-Chun Shih
- Institute of Molecular Biology, Academia Sinica, 128, Academia Rd., Sec. 2, Taipei, 11529, Taiwan, Republic of China
| | - Yun-Fen Hung
- Institute of Molecular Biology, Academia Sinica, 128, Academia Rd., Sec. 2, Taipei, 11529, Taiwan, Republic of China
| | - Yi-Ping Hsueh
- Institute of Molecular Biology, Academia Sinica, 128, Academia Rd., Sec. 2, Taipei, 11529, Taiwan, Republic of China.
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20
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Qi D, Chao Y, Zhang C, Wang Z, Wang W, Chen Q, Zheng Z, Zhang Z. Duplication of toll-like receptor 22 in teleost fishes. FISH & SHELLFISH IMMUNOLOGY 2019; 94:752-760. [PMID: 31580937 DOI: 10.1016/j.fsi.2019.09.067] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/23/2019] [Accepted: 09/29/2019] [Indexed: 06/10/2023]
Abstract
The TLRs of teleost fishes have distinct features and are highly diverse, but the duplication characteristics and expression patterns of the tlr22 gene remain unclear. Here, we identified paralogous tlr22 genes in 13 teleost fishes by screening available fish genomic resources and using molecular cloning. We then conducted comprehensive bioinformatics analyses and investigated spatiotemporal differences in the expression patterns of the tlr22 genes in G. eckloni. The results indicated that more than three paralogous tlr22 genes were possessed by some teleost fishes. Of these, tlr22c is specific to some subfamilies of the Cyprinidae (e.g., Barbinae, Cyprininae, Schizothoracinae, and Leuciscinae). Phylogenetic and syntenic analyses showed that the paralogous tlr22 genes originated from two single-gene duplication events. Molecular clock calculations dated the two gene duplication events at 49.5 and 39.3 MYA, which is before the common carp-specific genome duplication event and well after the fish-specific genome duplication. Gene duplication of tlr22 was followed by gene loss or pseudogene events in certain lineages. Spatiotemporal expression differences between the three duplicated tlr22 genes from G. eckloni suggested that these genes diverged functionally after gene duplication.
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Affiliation(s)
- Delin Qi
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China.
| | - Yan Chao
- Animal Science Department of Agriculture and Animal Husbandry College, Qinghai University, Xining, 810016, China
| | - Cunfang Zhang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China
| | - Zhenji Wang
- Fishery Environmental Monitoring Station of Qinghai Province, Xining, 810012, China
| | - Wei Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China
| | - Qichang Chen
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China
| | - Ziqin Zheng
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China; Animal Science Department of Agriculture and Animal Husbandry College, Qinghai University, Xining, 810016, China
| | - Zhao Zhang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China; Animal Science Department of Agriculture and Animal Husbandry College, Qinghai University, Xining, 810016, China
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21
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Liu T, Han Y, Chen S, Zhao H. Genome-wide identification of Toll-like receptors in the Chinese soft-shelled turtle Pelodiscus sinensis and expression analysis responding to Aeromonas hydrophila infection. FISH & SHELLFISH IMMUNOLOGY 2019; 87:478-489. [PMID: 30716519 DOI: 10.1016/j.fsi.2019.01.052] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/23/2019] [Accepted: 01/30/2019] [Indexed: 06/09/2023]
Abstract
Toll-like receptors (TLRs) recognizing specific pathogen-associated molecular patterns play crucial roles in immune defence against pathogen invasion. Although recent advances in many species have reported the characterization and functional roles of TLRs in innate immunity, systematic knowledge of TLRs is still lacking in the Chinese soft-shelled turtle Pelodiscus sinensis. In this study, a genome-wide search was performed and identified 15 candidate PsTLR family genes in P. sinensis. Protein structure analysis revealed the conserved domain arrangements for these PsTLR proteins. Phylogenetic analysis indicated the evolutionary conservation of TLRs among various species. Additionally, a putative interaction network among PsTLR proteins was proposed and several functional partner proteins involved in TLR signalling pathway were predicted in P. sinensis. Expression profiling showed that these PsTLRs exhibited constitutive expression patterns in different tissues of P. sinensis. Moreover, several genes were highly expressed in the major immune organ spleen. Remarkably, the mRNA levels of PsTLR2-1, PsTLR4 and several TLR signalling molecules were significantly up-regulated in the spleen after Aeromonas hydrophila infection, indicating that PsTLRs and these genes responded to bacterial stress. These results provide rich information for the functional exploration of PsTLRs and will facilitate uncovering the molecular mechanisms underlying immune regulation in P. sinensis.
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Affiliation(s)
- Tengfei Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
| | - Yawen Han
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
| | - Shulin Chen
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
| | - Huiying Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
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22
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Ji J, Ramos-Vicente D, Navas-Pérez E, Herrera-Úbeda C, Lizcano JM, Garcia-Fernàndez J, Escrivà H, Bayés À, Roher N. Characterization of the TLR Family in Branchiostoma lanceolatum and Discovery of a Novel TLR22-Like Involved in dsRNA Recognition in Amphioxus. Front Immunol 2018; 9:2525. [PMID: 30450099 PMCID: PMC6224433 DOI: 10.3389/fimmu.2018.02525] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 10/12/2018] [Indexed: 01/09/2023] Open
Abstract
Toll-like receptors (TLRs) are important for raising innate immune responses in both invertebrates and vertebrates. Amphioxus belongs to an ancient chordate lineage which shares key features with vertebrates. The genomic research on TLR genes in Branchiostoma floridae and Branchiostoma belcheri reveals the expansion of TLRs in amphioxus. However, the repertoire of TLRs in Branchiostoma lanceolatum has not been studied and the functionality of amphioxus TLRs has not been reported. We have identified from transcriptomic data 30 new putative TLRs in B. lanceolatum and all of them are transcribed in adult amphioxus. Phylogenetic analysis showed that the repertoire of TLRs consists of both non-vertebrate and vertebrate-like TLRs. It also indicated a lineage-specific expansion in orthologous clusters of the vertebrate TLR11 family. We did not detect any representatives of the vertebrate TLR1, TLR3, TLR4, TLR5 and TLR7 families. To gain insight into these TLRs, we studied in depth a particular TLR highly similar to a B. belcheri gene annotated as bbtTLR1. The phylogenetic analysis of this novel BlTLR showed that it clusters with the vertebrate TLR11 family and it might be more related to TLR13 subfamily according to similar domain architecture. Transient and stable expression in HEK293 cells showed that the BlTLR localizes on the plasma membrane, but it did not respond to the most common mammalian TLR ligands. However, when the ectodomain of BlTLR is fused to the TIR domain of human TLR2, the chimeric protein could indeed induce NF-κB transactivation in response to the viral ligand Poly I:C, also indicating that in amphioxus, specific accessory proteins are needed for downstream activation. Based on the phylogenetic, subcellular localization and functional analysis, we propose that the novel BlTLR might be classified as an antiviral receptor sharing at least partly the functions performed by vertebrate TLR22. TLR22 is thought to be viral teleost-specific TLR but here we demonstrate that teleosts and amphioxus TLR22-like probably shared a common ancestor. Additional functional studies with other lancelet TLR genes will enrich our understanding of the immune response in amphioxus and will provide a unique perspective on the evolution of the immune system.
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Affiliation(s)
- Jie Ji
- Department of Cell Biology, Animal Physiology and Immunology, Institute of Biotechnology and Biomedicine (IBB), Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - David Ramos-Vicente
- Department of Cell Biology, Animal Physiology and Immunology, Institute of Biotechnology and Biomedicine (IBB), Universitat Autònoma de Barcelona, Bellaterra, Spain.,Molecular Physiology of the Synapse Laboratory, Biomedical Research Institute Sant Pau (IIB Sant Pau), Barcelona, Spain
| | - Enrique Navas-Pérez
- Department of Genetics, School of Biology and Institute of Biomedicine (IBUB), University of Barcelona, Barcelona, Spain
| | - Carlos Herrera-Úbeda
- Department of Genetics, School of Biology and Institute of Biomedicine (IBUB), University of Barcelona, Barcelona, Spain
| | - José Miguel Lizcano
- Department of Biochemistry and Molecular Biology, Institute of Neurosciences, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Jordi Garcia-Fernàndez
- Department of Genetics, School of Biology and Institute of Biomedicine (IBUB), University of Barcelona, Barcelona, Spain
| | - Hector Escrivà
- CNRS, Biologie Intégrative des Organismes Marins, BIOM, Sorbonne Université, Banyuls-sur-Mer, France
| | - Àlex Bayés
- Department of Cell Biology, Animal Physiology and Immunology, Institute of Biotechnology and Biomedicine (IBB), Universitat Autònoma de Barcelona, Bellaterra, Spain.,Molecular Physiology of the Synapse Laboratory, Biomedical Research Institute Sant Pau (IIB Sant Pau), Barcelona, Spain
| | - Nerea Roher
- Department of Cell Biology, Animal Physiology and Immunology, Institute of Biotechnology and Biomedicine (IBB), Universitat Autònoma de Barcelona, Bellaterra, Spain
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23
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Velová H, Gutowska-Ding MW, Burt DW, Vinkler M. Toll-Like Receptor Evolution in Birds: Gene Duplication, Pseudogenization, and Diversifying Selection. Mol Biol Evol 2018; 35:2170-2184. [PMID: 29893911 PMCID: PMC6107061 DOI: 10.1093/molbev/msy119] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Toll-like receptors (TLRs) are key sensor molecules in vertebrates triggering initial phases of immune responses to pathogens. The avian TLR family typically consists of ten receptors, each adapted to distinct ligands. To understand the complex evolutionary history of each avian TLR, we analyzed all members of the TLR family in the whole genome assemblies and target sequence data of 63 bird species covering all major avian clades. Our results indicate that gene duplication events most probably occurred in TLR1 before synapsids diversified from sauropsids. Unlike mammals, ssRNA-recognizing TLR7 has duplicated independently in several avian taxa, while flagellin-sensing TLR5 has pseudogenized multiple times in bird phylogeny. Our analysis revealed stronger positive, diversifying selection acting in TLR5 and the three-domain TLRs (TLR10 [TLR1A], TLR1 [TLR1B], TLR2A, TLR2B, TLR4) that face the extracellular space and bind complex ligands than in single-domain TLR15 and endosomal TLRs (TLR3, TLR7, TLR21). In total, 84 out of 306 positively selected sites were predicted to harbor substitutions dramatically changing the amino acid physicochemical properties. Furthermore, 105 positively selected sites were located in the known functionally relevant TLR regions. We found evidence for convergent evolution acting between birds and mammals at 54 of these sites. Our comparative study provides a comprehensive insight into the evolution of avian TLR genetic variability. Besides describing the history of avian TLR gene gain and gene loss, we also identified candidate positions in the receptors that have been likely shaped by direct molecular host-pathogen coevolutionary interactions and most probably play key functional roles in birds.
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Affiliation(s)
- Hana Velová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Maria W Gutowska-Ding
- Department of Genomics and Genetics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The Roslin Institute Building, University of Edinburgh, Midlothian, United Kingdom
| | - David W Burt
- Office of DVC (Research), University of Queensland, St. Lucia, QLD, Australia
| | - Michal Vinkler
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
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Králová T, Albrecht T, Bryja J, Hořák D, Johnsen A, Lifjeld JT, Novotný M, Sedláček O, Velová H, Vinkler M. Signatures of diversifying selection and convergence acting on passerine Toll-like receptor 4 in an evolutionary context. Mol Ecol 2018; 27:2871-2883. [PMID: 29772096 DOI: 10.1111/mec.14724] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 04/23/2018] [Accepted: 04/24/2018] [Indexed: 12/26/2022]
Abstract
Positive selection acting on Toll-like receptors (TLRs) has been recently investigated to reveal evolutionary mechanisms of host-pathogen molecular co-adaptation. Much of this research, however, has focused mainly on the identification of sites predicted to be under positive selection, bringing little insight into the functional differences and similarities among species and a limited understanding of convergent evolution in the innate immune molecules. In this study, we provide evidence of phenotypic variability in the avian TLR4 ligand-binding region (LBR), the direct interface between host and pathogen molecular structures. We show that 55 passerine species vary substantially in the distribution of electrostatic potential on the surface of the receptor, and based on these distinct patterns, we identified four species clusters. Seven of the 34 evolutionarily nonconservative and positively selected residues correspond topologically to sites previously identified as being important for lipopolysaccharide, lipid IVa or MD-2 binding. Five of these positions codetermine the identity of the charge clusters. Groups of species that host-related communities of pathogens were predicted to cluster based on their TLR4 LBR charge. Despite some evidence for convergence among taxa, there were no clear associations between the TLR4 LBR charge distribution and any of the general ecological characteristics compared (migration, latitudinal distribution and diet). Closely related species, however, mostly belonged to the same surface charge cluster indicating that phylogenetic constraints are key determinants shaping TLR4 adaptive evolution. Our results suggest that host innate immune evolution is consistent with Fahrenholz's rule on the cospeciation of hosts and their parasites.
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Affiliation(s)
- Tereza Králová
- Institute of Vertebrate Biology, The Czech Academy of Sciences, Brno, Czech Republic.,Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Tomáš Albrecht
- Institute of Vertebrate Biology, The Czech Academy of Sciences, Brno, Czech Republic.,Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Josef Bryja
- Institute of Vertebrate Biology, The Czech Academy of Sciences, Brno, Czech Republic.,Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - David Hořák
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Arild Johnsen
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Jan T Lifjeld
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Marian Novotný
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ondřej Sedláček
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Hana Velová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Michal Vinkler
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
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25
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Genomic evidence of gene duplication and adaptive evolution of Toll like receptors (TLR2 and TLR4) in reptiles. Int J Biol Macromol 2018; 109:698-703. [DOI: 10.1016/j.ijbiomac.2017.12.123] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 12/21/2017] [Accepted: 12/21/2017] [Indexed: 12/31/2022]
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26
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Liao Z, Wan Q, Su H, Wu C, Su J. Pattern recognition receptors in grass carp Ctenopharyngodon idella: I. Organization and expression analysis of TLRs and RLRs. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 76:93-104. [PMID: 28559111 DOI: 10.1016/j.dci.2017.05.019] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 05/24/2017] [Accepted: 05/24/2017] [Indexed: 06/07/2023]
Abstract
Pattern recognition receptors (PRRs) play indispensable roles in the immune responses against invading pathogens. In the present study, we systematically identified and characterized Toll-like receptors (TLRs), retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs) as well as their adaptors in grass carp (Ctenopharyngodon idella). A comprehensive analysis of BLAST and other bioinformatics methods showed that C. idella TLR family consist of 21 members and their adaptors contain four members. Phylogenetic analyses confirmed the existence of six TLR subfamilies (TLR1, 3, 4, 5, 7 and 11 subfamily) in C. idella and revealed their homologous relationships with other species. Most C. idella TLRs possess three typical structural features of TLR protein family: LRR, TM and TIR domains. Meanwhile, RLR family consist of three conserved members (RIG-I, MDA5 and LGP2) as well as two adaptors (IPS-1 and STING) in C. idella. mRNA expression analyses of TLRs, RLRs and their adaptors indicated that most members are sustainably expressed in multiple tissues before and after grass carp reovirus (GCRV) or Aeromonas hydrophila infection, while TLR9, TLR20a/b, TLR25, TIRAP, SARM1 and STING are transiently expressed in specific tissues. TLRs are transmembrane receptors with few introns, while RLRs are cytoplasmic receptors with plenty of introns. TLRs and RLRs interact with adaptors to perform their functions via various signaling pathways. In conclusion, this study systematically explores the characteristics of TLRs and RLRs in C. idella and provides evidence for the response patterns after viral and/or bacterial infection in vivo. These results contribute to studying the regulation mechanisms of TLR and RLR signaling pathways, and deeply understanding fish immune responses against pathogen infection.
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Affiliation(s)
- Zhiwei Liao
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Quanyuan Wan
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Hang Su
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Changsong Wu
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Jianguo Su
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
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Zhang J, Wang L, Zhao Y, Kong X, Wu F, Zhao X. Molecular characterization and expression analysis of toll-like receptors 5 and 22 from natural triploid Carassius auratus. FISH & SHELLFISH IMMUNOLOGY 2017; 64:1-13. [PMID: 28259778 DOI: 10.1016/j.fsi.2017.03.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 02/15/2017] [Accepted: 03/01/2017] [Indexed: 06/06/2023]
Abstract
Innate immunity, as the most primitive and universal host defense in fish, constitutes an efficient first line of defense to combat invading microbes. Toll-like receptors (TLRs) play essential roles in the innate immunity, and TLR5 and TLR22 are two important TLRs that can recognize flagellin and double stranded RNA (dsRNA), respectively. In this study, we identified and characterized two TLRs genes of Qihe crucian carp (Carassius auratus) (designated as CaTLR5 and CaTLR22). The full-length cDNA sequence of CaTLR5 was cloned with 2972 bp including a 140 bp 5'-terminal untranslated region (UTR), a 183 bp 3'-UTR, and a 2649 bp open reading frame (ORF) encoding a deduced protein with 882 amino acids. The full-length cDNA of CaTLR22 was identified to be 3613 bp, consisting of a 228 bp 5'-UTR, a 547 bp 3'-UTR, and a 2838 bp ORF encoding a predicted protein of 945 amino acids. A typical TLR structure (an extracellular leucine-rich repeat domain, a transmembrane domain, and an intracellular Toll/IL-1 receptor domain) was found in CaTLR5 and CaTLR22. For either CaTLR5 or CaTLR22 gene, the mRNA expression levels varied in the different periods during the early stages of development. It was suggested that expression changes of gene CaTLR5 and CaTLR22 at mRNA levels were involved in developmental regulation in the early stages, and it was postulated that CaTLR5 and CaTLR22 play the important roles in immune defense in the early development stages of fish. Quantitative Real-Time PCR (qRT-PCR) revealed that CaTLR5 and CaTLR22 were constitutively expressed in all eleven tissues examined, although the mRNA expression level varied considerably among the different tissues. Following exposure to polyI:C, flagellin, and Aeromonas hydrophila, CaTLR5 and CaTLR22 were up-regulated in different tissues, and it was suggested that CaTLR5 and CaTLR22 were involved in the immune response of Qihe crucian carp against pathogenic invasions. The present findings will provide the valuable information for understanding the structure, function, expression, and the immune defense process of CaTLR5 and CaTLR22 in Qihe crucian carp, and provide new insights for developing the new strategies of disease control to protect fish against pathogens infection.
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Affiliation(s)
- Jie Zhang
- College of Fisheries, Henan Normal University, Xinxiang 453007, PR China
| | - Li Wang
- College of Fisheries, Henan Normal University, Xinxiang 453007, PR China; College of Life Science, Henan Normal University, Xinxiang 453007, PR China
| | - Yanjing Zhao
- College of Fisheries, Henan Normal University, Xinxiang 453007, PR China
| | - Xianghui Kong
- College of Fisheries, Henan Normal University, Xinxiang 453007, PR China.
| | - Fan Wu
- College of Fisheries, Henan Normal University, Xinxiang 453007, PR China
| | - Xianliang Zhao
- College of Fisheries, Henan Normal University, Xinxiang 453007, PR China
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