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Edwards SV, Cloutier A, Cockburn G, Driver R, Grayson P, Katoh K, Baldwin MW, Sackton TB, Baker AJ. A nuclear genome assembly of an extinct flightless bird, the little bush moa. SCIENCE ADVANCES 2024; 10:eadj6823. [PMID: 38781323 DOI: 10.1126/sciadv.adj6823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 04/17/2024] [Indexed: 05/25/2024]
Abstract
We present a draft genome of the little bush moa (Anomalopteryx didiformis)-one of approximately nine species of extinct flightless birds from Aotearoa, New Zealand-using ancient DNA recovered from a fossil bone from the South Island. We recover a complete mitochondrial genome at 249.9× depth of coverage and almost 900 megabases of a male moa nuclear genome at ~4 to 5× coverage, with sequence contiguity sufficient to identify more than 85% of avian universal single-copy orthologs. We describe a diverse landscape of transposable elements and satellite repeats, estimate a long-term effective population size of ~240,000, identify a diverse suite of olfactory receptor genes and an opsin repertoire with sensitivity in the ultraviolet range, show that the wingless moa phenotype is likely not attributable to gene loss or pseudogenization, and identify potential function-altering coding sequence variants in moa that could be synthesized for future functional assays. This genomic resource should support further studies of avian evolution and morphological divergence.
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Affiliation(s)
- Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Alison Cloutier
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Glenn Cockburn
- Evolution of Sensory Systems Research Group, Max Planck Institute for Biological Intelligence, 82319 Seewiesen, Germany
| | - Robert Driver
- Department of Biology, East Carolina University, E 5th Street, Greenville, NC 27605, USA
| | - Phil Grayson
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Kazutaka Katoh
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
| | - Maude W Baldwin
- Evolution of Sensory Systems Research Group, Max Planck Institute for Biological Intelligence, 82319 Seewiesen, Germany
| | - Timothy B Sackton
- Informatics Group, Harvard University, 38 Oxford Street, Cambridge, MA 02138, USA
| | - Allan J Baker
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcox Street, Toronto, ON M5S 3B2, Canada
- Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, ON M5S 2C6, Canada
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2
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Melepat B, Li T, Vinkler M. Natural selection directing molecular evolution in vertebrate viral sensors. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 154:105147. [PMID: 38325501 DOI: 10.1016/j.dci.2024.105147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 12/30/2023] [Accepted: 02/03/2024] [Indexed: 02/09/2024]
Abstract
Diseases caused by pathogens contribute to molecular adaptations in host immunity. Variety of viral pathogens challenging animal immunity can drive positive selection diversifying receptors recognising the infections. However, whether distinct virus sensing systems differ across animals in their evolutionary modes remains unclear. Our review provides a comparative overview of natural selection shaping molecular evolution in vertebrate viral-binding pattern recognition receptors (PRRs). Despite prevailing negative selection arising from the functional constraints, multiple lines of evidence now suggest diversifying selection in the Toll-like receptors (TLRs), NOD-like receptors (NLRs), RIG-I-like receptors (RLRs) and oligoadenylate synthetases (OASs). In several cases, location of the positively selected sites in the ligand-binding regions suggests effects on viral detection although experimental support is lacking. Unfortunately, in most other PRR families including the AIM2-like receptor family, C-type lectin receptors (CLRs), and cyclic GMP-AMP synthetase studies characterising their molecular evolution are rare, preventing comparative insight. We indicate shared characteristics of the viral sensor evolution and highlight priorities for future research.
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Affiliation(s)
- Balraj Melepat
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, 128 43, Prague, EU, Czech Republic
| | - Tao Li
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, 128 43, Prague, EU, Czech Republic
| | - Michal Vinkler
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, 128 43, Prague, EU, Czech Republic.
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3
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Su Q, Chen Y, He H. Molecular evolution of Toll-like receptors in rodents. Integr Zool 2024; 19:371-386. [PMID: 37403417 DOI: 10.1111/1749-4877.12746] [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] [Indexed: 07/06/2023]
Abstract
Toll-like receptors (TLRs), the key sensor molecules in vertebrates, trigger the innate immunity and prime the adaptive immune system. The TLR family of rodents, the largest order of mammals, typically contains 13 TLR genes. However, a clear picture of the evolution of the rodent TLR family has not yet emerged and the TLR evolutionary patterns are unclear in rodent clades. Here, we analyzed the natural variation and the evolutionary processes acting on the TLR family in rodents at both the interspecific and population levels. Our results showed that rodent TLRs were dominated by purifying selection, but a series of positively selected sites (PSSs) primarily located in the ligand-binding domain was also identified. The numbers of PSSs differed among TLRs, and nonviral-sensing TLRs had more PSSs than those in viral-sensing TLRs. Gene-conversion events were found between TLR1 and TLR6 in most rodent species. Population genetic analyses showed that TLR2, TLR8, and TLR12 were under positive selection in Rattus norvegicus and R. tanezumi, whereas positive selection also acted on TLR5 and TLR9 in the former species, as well as TLR1 and TLR7 in the latter species. Moreover, we found that the proportion of polymorphisms with potentially functional change was much lower in viral-sensing TLRs than in nonviral-sensing TLRs in both of these rat species. Our findings revealed the first thorough insight into the evolution of the rodent TLR genetic variability and provided important novel insights into the evolutionary history of TLRs over long and short timescales.
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Affiliation(s)
- Qianqian Su
- College of Forestry, Central South University of Forestry and Technology, Changsha, China
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yi Chen
- College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Hongxuan He
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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4
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Stejskalova K, Janova E, Splichalova P, Futas J, Oppelt J, Vodicka R, Horin P. Twelve toll-like receptor (TLR) genes in the family Equidae - comparative genomics, selection and evolution. Vet Res Commun 2024; 48:725-741. [PMID: 37874499 PMCID: PMC10998774 DOI: 10.1007/s11259-023-10245-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/18/2023] [Indexed: 10/25/2023]
Abstract
Toll-like receptors (TLRs) represent an important part of the innate immune system. While human and murine TLRs have been intensively studied, little is known about TLRs in non-model species. The order Perissodactyla comprises a variety of free-living and domesticated species exposed to different pathogens in different habitats and is therefore suitable for analyzing the diversity and evolution of immunity-related genes. We analyzed TLR genes in the order Perissodactyla with a focus on the family Equidae. Twelve TLRs were identified by bioinformatic analyses of online genomic resources; their sequences were confirmed in equids by genomic DNA re-sequencing of a panel of nine species. The expression of TLR11 and TLR12 was confirmed in the domestic horse by cDNA sequencing. Phylogenetic reconstruction of the TLR gene family in Perissodactyla identified six sub-families. TLR4 clustered together with TLR5; the TLR1-6-10 subfamily showed a high degree of sequence identity. The average estimated evolutionary divergence of all twelve TLRs studied was 0.3% among the Equidae; the most divergent CDS were those of Equus caballus and Equus hemionus kulan (1.34%) in the TLR3, and Equus africanus somaliensis and Equus quagga antiquorum (2.1%) in the TLR1 protein. In each TLR gene, there were haplotypes shared between equid species, most extensively in TLR3 and TLR9 CDS, and TLR6 amino acid sequence. All twelve TLR genes were under strong negative overall selection. Signatures of diversifying selection in specific codon sites were detected in all TLRs except TLR8. Differences in the selection patterns between virus-sensing and non-viral TLRs were observed.
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Affiliation(s)
- K Stejskalova
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, 61242, Czech Republic
| | - E Janova
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, 61242, Czech Republic
- RG Animal Immunogenomics, CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - P Splichalova
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, 61242, Czech Republic
| | - J Futas
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, 61242, Czech Republic
- RG Animal Immunogenomics, CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - J Oppelt
- RG Animal Immunogenomics, CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czech Republic
| | | | - P Horin
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, 61242, Czech Republic.
- RG Animal Immunogenomics, CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czech Republic.
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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 S, Wang D, Bai Y, Zheng G, Han Y, Wang L, Hu J, Zhu H, Bai Y. Expression of Toll-like receptors and host defence peptides in the cecum of chicken challenged with Eimeria tenella. Parasite Immunol 2024; 46:e13022. [PMID: 38384176 DOI: 10.1111/pim.13022] [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: 09/23/2023] [Revised: 01/05/2024] [Accepted: 01/05/2024] [Indexed: 02/23/2024]
Abstract
Chicken coccidiosis, caused by Eimeria protozoa, affects poultry farming. Toll-like receptors (TLRs) and host defence peptides (HDPs) help host innate immune responses to eliminate invading pathogens, but their roles in Eimeria tenella infection remain poorly understood. Herein, 14-day-old chickens were treated orally with 50,000 E. tenella oocysts and the cecum was dissected at different timepoints. mRNA expression of 10 chicken TLRs (chTLRs) and five HDPs was measured by quantitative real-time PCR. chTLR7 and chTLR15 were upregulated significantly at 3 h post-infection while other chTLRs were downregulated (p < .05). chTLR1a, chTLR1b, chTLR2b and chTLR4 peaked at 36 h post-infection, chTLR3, chTLR5 and chTLR15 peaked at 72 h post-infection and chTLR21 expression was highest among chTLRs, peaking at 48 h post-infection (p < 0.05). For HDPs, cathelicidin (CATH) 1 to 3 and B1 peaked at 48 h post-infection, liver-expressed antimicrobial peptide 2 peaked at 96 h post-infection, and CATH 2 expression was highest among HDPs. CATH2 and CATH3 were markedly upregulated at 3 h post-infection (p < .05). The results provide insight into innate immune molecules during E. tenella infection in chicken, and indicate that innate immune responses may mediate resistance to chicken coccidiosis.
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Affiliation(s)
- Song Wang
- Postdoctoral Research Base, Henan Institute of Science and Technology, Xinxiang, China
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, China
| | - Danni Wang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, China
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou, China
| | - Yilin Bai
- School of Agricultural Science, Zhengzhou University, Zhengzhou, China
| | - Guijie Zheng
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, China
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou, China
| | - Yanhui Han
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, China
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou, China
| | - Lei Wang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, China
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou, China
| | - Jianhe Hu
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, China
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou, China
| | - Huili Zhu
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, China
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou, China
| | - Yueyu Bai
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, China
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou, China
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Mahapatra S, Ganguly B, Pani S, Saha A, Samanta M. A comprehensive review on the dynamic role of toll-like receptors (TLRs) in frontier aquaculture research and as a promising avenue for fish disease management. Int J Biol Macromol 2023; 253:126541. [PMID: 37648127 DOI: 10.1016/j.ijbiomac.2023.126541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/01/2023]
Abstract
Toll-like receptors (TLRs) represent a conserved group of germline-encoded pattern recognition receptors (PRRs) that recognize pathogen-associated molecular patterns (PAMPs) and play a crucial role in inducing the broadly acting innate immune response against pathogens. In recent years, the detection of 21 different TLR types in various fish species has sparked interest in exploring the potential of TLRs as targets for boosting immunity and disease resistance in fish. This comprehensive review offers the latest insights into the diverse facets of fish TLRs, highlighting their history, classification, architectural insights through 3D modelling, ligands recognition, signalling pathways, crosstalk, and expression patterns at various developmental stages. It provides an exhaustive account of the distinct TLRs induced during the invasion of specific pathogens in various fish species and delves into the disparities between fish TLRs and their mammalian counterparts, highlighting the specific contribution of TLRs to the immune response in fish. Although various facets of TLRs in some fish, shellfish, and molluscs have been described, the role of TLRs in several other aquatic organisms still remained as potential gaps. Overall, this article outlines frontier aquaculture research in advancing the knowledge of fish immune systems for the proper management of piscine maladies.
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Affiliation(s)
- Smruti Mahapatra
- Immunology Laboratory, Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture (ICAR-CIFA), Kausalyaganga, Bhubaneswar 751002, Odisha, India
| | - Bristy Ganguly
- Immunology Laboratory, Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture (ICAR-CIFA), Kausalyaganga, Bhubaneswar 751002, Odisha, India
| | - Saswati Pani
- Immunology Laboratory, Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture (ICAR-CIFA), Kausalyaganga, Bhubaneswar 751002, Odisha, India
| | - Ashis Saha
- Reproductive Biology and Endocrinology Laboratory, Fish Nutrition and Physiology Division, ICAR-Central Institute of Freshwater Aquaculture (ICAR-CIFA), Kausalyaganga, Bhubaneswar 751002, Odisha, India
| | - Mrinal Samanta
- Immunology Laboratory, Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture (ICAR-CIFA), Kausalyaganga, Bhubaneswar 751002, Odisha, India.
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Minias P, Podlaszczuk P, Indykiewicz P, Ledwoń M, Nowakowski J, Chyb A, Janiszewski T. Genetic variation at innate and adaptive immune genes - contrasting patterns of differentiation and local adaptation in a wild gull. Heredity (Edinb) 2023; 131:282-291. [PMID: 37553491 PMCID: PMC10539538 DOI: 10.1038/s41437-023-00645-2] [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: 05/04/2023] [Revised: 07/15/2023] [Accepted: 07/30/2023] [Indexed: 08/10/2023] Open
Abstract
Immunogenetic variation in natural vertebrate populations is expected to respond to spatial and temporal fluctuations in pathogen assemblages. While spatial heterogeneity in pathogen-driven selection enhances local immunogenetic adaptations and population divergence, different immune genes may yield contrasting responses to the environment. Here, we investigated population differentiation at the key pathogen recognition genes of the innate and adaptive immune system in a colonial bird species, the black-headed gull Chroicocephalus ridibundus. We assessed genetic variation at three toll-like receptor (TLR) genes (innate immunity) and the major histocompatibility complex (MHC) class I and II genes (adaptive immunity) in gulls from seven colonies scattered across Poland. As expected, we found much greater polymorphism at the MHC than TLRs. Population differentiation at the MHC class II, but not MHC-I, was significantly stronger than at neutral microsatellite loci, suggesting local adaptation. This could reflect spatial variation in the composition of extracellular parasite communities (e.g., helminths), possibly driven by sharp differences in habitat structure between colonies. Despite contrasting patterns of population differentiation, both MHC classes showed similar regimes of diversifying selection. Some significant population differentiation was also observed at TLRs, suggesting that innate immune receptors may respond to fine-scale spatial variation in pathogen pressure, although this pattern could have been enhanced by drift. Our results suggested that local adaptation at the pathogen recognition immune genes can be maintained at relatively small or moderate spatial scales in species with high dispersal potential and they highlighted the complexity of immunogenetic responses of animals to heterogeneous environments.
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Affiliation(s)
- Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237, Łódź, Poland.
| | - Patrycja Podlaszczuk
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237, Łódź, Poland
| | - Piotr Indykiewicz
- Department of Biology and Animal Environment, Faculty of Animal Breeding and Biology, Bydgoszcz University of Science and Technology, Mazowiecka 28, 85-084, Bydgoszcz, Poland
| | - Mateusz Ledwoń
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016, Kraków, Poland
| | - Jacek Nowakowski
- Department of Ecology and Environmental Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Plac Łódzki 3, 10-727, Olsztyn, Poland
| | - Amelia Chyb
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237, Łódź, Poland
| | - Tomasz Janiszewski
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237, Łódź, Poland
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9
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Włodarczyk R, Těšický M, Vinkler M, Novotný M, Remisiewicz M, Janiszewski T, Minias P. Divergent evolution drives high diversity of toll-like receptors (TLRs) in passerine birds: Buntings and finches. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 144:104704. [PMID: 37019350 DOI: 10.1016/j.dci.2023.104704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/29/2023] [Accepted: 03/29/2023] [Indexed: 06/05/2023]
Abstract
Toll-like receptors (TLRs) form a key component of animal innate immunity, being responsible for recognition of conserved microbial structures. As such, TLRs may be subject to diversifying and balancing selection, which maintains allelic variation both within and between populations. However, most research on TLRs in non-model avian species is focused on bottlenecked populations with depleted genetic variation. Here, we assessed variation at the extracellular domains of three TLR genes (TLR1LA, TLR3, TLR4) across eleven species from two passerine families of buntings (Emberizidae) and finches (Fringillidae), all having large breeding population sizes (millions of individuals). We found extraordinary TLR polymorphism in our study taxa, with >100 alleles detected at TLR1LA and TLR4 across species and high haplotype diversity (>0.75) in several species. Despite recent species divergence, no nucleotide allelic variants were shared between species, suggesting rapid TLR evolution. Higher variation at TLR1LA and TLR4 than TLR3 was associated with a stronger signal of diversifying selection, as measured with nucleotide substitutions rates and the number of positively selected sites (PSS). Structural protein modelling of TLRs showed that some PSS detected within TLR1LA and TLR4 were previously recognized as functionally important sites or were located in their proximity, possibly affecting ligand recognition. Furthermore, we identified PSS responsible for major surface electrostatic charge clustering, which may indicate their adaptive importance. Our study provides compelling evidence for the divergent evolution of TLR genes in buntings and finches and indicates that high TLR variation may be adaptively maintained via diversifying selection acting on functional ligand binding sites.
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Affiliation(s)
- Radosław Włodarczyk
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237, Łódź, Poland.
| | - Martin Těšický
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, 128 43, Prague, Czech Republic
| | - Michal Vinkler
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, 128 43, Prague, Czech Republic
| | - Marian Novotný
- Charles University, Faculty of Science, Department of Cell Biology, Viničná 7, 128 43, Prague, Czech Republic
| | - Magdalena Remisiewicz
- Bird Migration Research Station, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308, Gdańsk, Poland
| | - Tomasz Janiszewski
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237, Łódź, Poland
| | - Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237, Łódź, Poland.
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10
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Vinkler M, Fiddaman SR, Těšický M, O'Connor EA, Savage AE, Lenz TL, Smith AL, Kaufman J, Bolnick DI, Davies CS, Dedić N, Flies AS, Samblás MMG, Henschen AE, Novák K, Palomar G, Raven N, Samaké K, Slade J, Veetil NK, Voukali E, Höglund J, Richardson DS, Westerdahl H. Understanding the evolution of immune genes in jawed vertebrates. J Evol Biol 2023; 36:847-873. [PMID: 37255207 PMCID: PMC10247546 DOI: 10.1111/jeb.14181] [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: 09/23/2022] [Revised: 04/23/2023] [Accepted: 04/26/2023] [Indexed: 06/01/2023]
Abstract
Driven by co-evolution with pathogens, host immunity continuously adapts to optimize defence against pathogens within a given environment. Recent advances in genetics, genomics and transcriptomics have enabled a more detailed investigation into how immunogenetic variation shapes the diversity of immune responses seen across domestic and wild animal species. However, a deeper understanding of the diverse molecular mechanisms that shape immunity within and among species is still needed to gain insight into-and generate evolutionary hypotheses on-the ultimate drivers of immunological differences. Here, we discuss current advances in our understanding of molecular evolution underpinning jawed vertebrate immunity. First, we introduce the immunome concept, a framework for characterizing genes involved in immune defence from a comparative perspective, then we outline how immune genes of interest can be identified. Second, we focus on how different selection modes are observed acting across groups of immune genes and propose hypotheses to explain these differences. We then provide an overview of the approaches used so far to study the evolutionary heterogeneity of immune genes on macro and microevolutionary scales. Finally, we discuss some of the current evidence as to how specific pathogens affect the evolution of different groups of immune genes. This review results from the collective discussion on the current key challenges in evolutionary immunology conducted at the ESEB 2021 Online Satellite Symposium: Molecular evolution of the vertebrate immune system, from the lab to natural populations.
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Affiliation(s)
- Michal Vinkler
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Martin Těšický
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Anna E. Savage
- Department of BiologyUniversity of Central FloridaFloridaOrlandoUSA
| | - Tobias L. Lenz
- Research Unit for Evolutionary ImmunogenomicsDepartment of BiologyUniversity of HamburgHamburgGermany
| | | | - Jim Kaufman
- Institute for Immunology and Infection ResearchUniversity of EdinburghEdinburghUK
- Department of Veterinary MedicineUniversity of CambridgeCambridgeUK
| | - Daniel I. Bolnick
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
| | | | - Neira Dedić
- Department of Botany and ZoologyMasaryk UniversityBrnoCzech Republic
| | - Andrew S. Flies
- Menzies Institute for Medical ResearchUniversity of TasmaniaHobartTasmaniaAustralia
| | - M. Mercedes Gómez Samblás
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
- Department of ParasitologyUniversity of GranadaGranadaSpain
| | | | - Karel Novák
- Department of Genetics and BreedingInstitute of Animal SciencePragueUhříněvesCzech Republic
| | - Gemma Palomar
- Faculty of BiologyInstitute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | - Nynke Raven
- Department of ScienceEngineering and Build EnvironmentDeakin UniversityVictoriaWaurn PondsAustralia
| | - Kalifa Samaké
- Department of Genetics and MicrobiologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Joel Slade
- Department of BiologyCalifornia State UniversityFresnoCaliforniaUSA
| | | | - Eleni Voukali
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Jacob Höglund
- Department of Ecology and GeneticsUppsala UniversitetUppsalaSweden
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Gamboa M, Kitamura N, Miura K, Noda S, Kaminuma O. Evolutionary mechanisms underlying the diversification of nuclear factor of activated T cells across vertebrates. Sci Rep 2023; 13:6468. [PMID: 37156933 PMCID: PMC10167247 DOI: 10.1038/s41598-023-33751-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 04/18/2023] [Indexed: 05/10/2023] Open
Abstract
The mechanisms of immunity linked to biological evolution are crucial for understanding animal morphogenesis, organogenesis, and biodiversity. The nuclear factor of activated T cells (NFAT) family consists of five members (NFATc1-c4, 5) with different functions in the immune system. However, the evolutionary dynamics of NFATs in vertebrates has not been explored. Herein, we investigated the origin and mechanisms underlying the diversification of NFATs by comparing the gene, transcript and protein sequences, and chromosome information. We defined an ancestral origin of NFATs during the bilaterian development, dated approximately 650 million years ago, where NFAT5 and NFATc1-c4 were derived independently. The conserved parallel evolution of NFATs in multiple species was probably attributed to their innate nature. Conversely, frequent gene duplications and chromosomal rearrangements in the recently evolved taxa have suggested their roles in the adaptive immune evolution. A significant correlation was observed between the chromosome rearrangements with gene duplications and the structural fixation changes in vertebrate NFATs, suggesting their role in NFAT diversification. Remarkably, a conserved gene structure around NFAT genes with vertebrate evolutionary-related breaking points indicated the inheritance of NFATs with their neighboring genes as a unit. The close relationship between NFAT diversification and vertebrate immune evolution was suggested.
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Affiliation(s)
- Maribet Gamboa
- Department of Disease Model, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, 734-8553, Japan.
- Department of Ecology, Faculty of Sciences, Universidad Católica de la Santísima Concepción, 4090541, Concepción, Chile.
| | - Noriko Kitamura
- Neurovirology Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan
| | - Kento Miura
- Department of Disease Model, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, 734-8553, Japan
| | - Satoko Noda
- Graduate School of Science and Engineering, Ibaraki University, Ibaraki, 310-8512, Japan
| | - Osamu Kaminuma
- Department of Disease Model, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, 734-8553, Japan.
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12
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Pergolizzi S, Fumia A, D'Angelo R, Mangano A, Lombardo GP, Giliberti A, Messina E, Alesci A, Lauriano ER. Expression and function of toll-like receptor 2 in vertebrate. Acta Histochem 2023; 125:152028. [PMID: 37075649 DOI: 10.1016/j.acthis.2023.152028] [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: 03/08/2023] [Revised: 04/13/2023] [Accepted: 04/13/2023] [Indexed: 04/21/2023]
Abstract
Toll-like receptors (TLRs) are essential for identifying and detecting pathogen-associated molecular patterns (PAMPs) produced by a variety of pathogens, including viruses and bacteria. Since TLR2 is the only TLR capable of creating functional heterodimers with more than two other TLR types, it is very important for vertebrate immunity. TLR2 not only broadens the variety of PAMPs that it can recognize but has also the potential to diversify the subsequent signaling cascades. TLR2 is ubiquitous, which is consistent with the wide variety of tasks and functions it serves. Immune cells, endothelial cells, and epithelial cells have all been found to express TLR2. This review aims to gather currently available information about the preservation of this intriguing immunological molecule in the phylum of vertebrates.
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Affiliation(s)
- Simona Pergolizzi
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, 98166 Messina, Italy
| | - Angelo Fumia
- Department of Clinical and Experimental Medicine, University of Messina, Padiglione C, A. O. U. Policlinico "G. Martino", 98124 Messina, Italy
| | - Roberta D'Angelo
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, 98166 Messina, Italy
| | - Angelica Mangano
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, 98166 Messina, Italy
| | - Giorgia Pia Lombardo
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, 98166 Messina, Italy
| | - Angelo Giliberti
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, 98166 Messina, Italy
| | - Emmanuele Messina
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, 98166 Messina, Italy
| | - Alessio Alesci
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, 98166 Messina, Italy.
| | - Eugenia Rita Lauriano
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, 98166 Messina, Italy
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13
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Ducatelle R, Goossens E, Eeckhaut V, Van Immerseel F. Poultry gut health and beyond. ANIMAL NUTRITION 2023; 13:240-248. [PMID: 37168453 PMCID: PMC10164775 DOI: 10.1016/j.aninu.2023.03.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/15/2023] [Accepted: 03/21/2023] [Indexed: 04/07/2023]
Abstract
Intestinal health is critically important for the digestion and absorption of nutrients and thus is a key factor in determining performance. Intestinal health issues are very common in high performing poultry lines due to the high feed intake, which puts pressure on the physiology of the digestive system. Excess nutrients which are not digested and absorbed in the small intestine may trigger dysbiosis, i.e. a shift in the microbiota composition in the intestinal tract. Dysbiosis as well as other stressors elicit an inflammatory response and loss of integrity of the tight junctions between the epithelial cells, leading to gut leakage. In this paper, key factors determining intestinal health and the most important nutritional tools which are available to support intestinal health are reviewed.
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14
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Martínez Sosa F, Pilot M. Molecular Mechanisms Underlying Vertebrate Adaptive Evolution: A Systematic Review. Genes (Basel) 2023; 14:416. [PMID: 36833343 PMCID: PMC9957108 DOI: 10.3390/genes14020416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/24/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023] Open
Abstract
Adaptive evolution is a process in which variation that confers an evolutionary advantage in a specific environmental context arises and is propagated through a population. When investigating this process, researchers have mainly focused on describing advantageous phenotypes or putative advantageous genotypes. A recent increase in molecular data accessibility and technological advances has allowed researchers to go beyond description and to make inferences about the mechanisms underlying adaptive evolution. In this systematic review, we discuss articles from 2016 to 2022 that investigated or reviewed the molecular mechanisms underlying adaptive evolution in vertebrates in response to environmental variation. Regulatory elements within the genome and regulatory proteins involved in either gene expression or cellular pathways have been shown to play key roles in adaptive evolution in response to most of the discussed environmental factors. Gene losses were suggested to be associated with an adaptive response in some contexts. Future adaptive evolution research could benefit from more investigations focused on noncoding regions of the genome, gene regulation mechanisms, and gene losses potentially yielding advantageous phenotypes. Investigating how novel advantageous genotypes are conserved could also contribute to our knowledge of adaptive evolution.
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Affiliation(s)
| | - Małgorzata Pilot
- Museum and Institute of Zoology, Polish Academy of Sciences, 80-680 Gdańsk, Poland
- Faculty of Biology, University of Gdańsk, 80-308 Gdańsk, Poland
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15
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Karawita AC, Cheng Y, Chew KY, Challagulla A, Kraus R, Mueller RC, Tong MZW, Hulme KD, Bielefeldt-Ohmann H, Steele LE, Wu M, Sng J, Noye E, Bruxner TJ, Au GG, Lowther S, Blommaert J, Suh A, McCauley AJ, Kaur P, Dudchenko O, Aiden E, Fedrigo O, Formenti G, Mountcastle J, Chow W, Martin FJ, Ogeh DN, Thiaud-Nissen F, Howe K, Tracey A, Smith J, Kuo RI, Renfree MB, Kimura T, Sakoda Y, McDougall M, Spencer HG, Pyne M, Tolf C, Waldenström J, Jarvis ED, Baker ML, Burt DW, Short KR. The swan genome and transcriptome, it is not all black and white. Genome Biol 2023; 24:13. [PMID: 36683094 PMCID: PMC9867998 DOI: 10.1186/s13059-022-02838-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 12/12/2022] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND The Australian black swan (Cygnus atratus) is an iconic species with contrasting plumage to that of the closely related northern hemisphere white swans. The relative geographic isolation of the black swan may have resulted in a limited immune repertoire and increased susceptibility to infectious diseases, notably infectious diseases from which Australia has been largely shielded. Unlike mallard ducks and the mute swan (Cygnus olor), the black swan is extremely sensitive to highly pathogenic avian influenza. Understanding this susceptibility has been impaired by the absence of any available swan genome and transcriptome information. RESULTS Here, we generate the first chromosome-length black and mute swan genomes annotated with transcriptome data, all using long-read based pipelines generated for vertebrate species. We use these genomes and transcriptomes to show that unlike other wild waterfowl, black swans lack an expanded immune gene repertoire, lack a key viral pattern-recognition receptor in endothelial cells and mount a poorly controlled inflammatory response to highly pathogenic avian influenza. We also implicate genetic differences in SLC45A2 gene in the iconic plumage of the black swan. CONCLUSION Together, these data suggest that the immune system of the black swan is such that should any avian viral infection become established in its native habitat, the black swan would be in a significant peril.
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Affiliation(s)
- Anjana C Karawita
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia
- Commonwealth Scientific and Industrial Research Organisation, Australian Centre for Disease Preparedness, 5 Portarlington Road, Geelong, VIC, 3220, Australia
| | - Yuanyuan Cheng
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Keng Yih Chew
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Arjun Challagulla
- Commonwealth Scientific and Industrial Research Organisation, Australian Centre for Disease Preparedness, 5 Portarlington Road, Geelong, VIC, 3220, Australia
| | - Robert Kraus
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, 78315, Germany
- Department of Biology, University of Konstanz, Konstanz, 78457, Germany
| | - Ralf C Mueller
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, 78315, Germany
- Department of Biology, University of Konstanz, Konstanz, 78457, Germany
| | - Marcus Z W Tong
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Katina D Hulme
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Helle Bielefeldt-Ohmann
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Lauren E Steele
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Melanie Wu
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Julian Sng
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Ellesandra Noye
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Timothy J Bruxner
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Gough G Au
- Commonwealth Scientific and Industrial Research Organisation, Australian Centre for Disease Preparedness, 5 Portarlington Road, Geelong, VIC, 3220, Australia
| | - Suzanne Lowther
- Commonwealth Scientific and Industrial Research Organisation, Australian Centre for Disease Preparedness, 5 Portarlington Road, Geelong, VIC, 3220, Australia
| | - Julie Blommaert
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Uppsala University, Science for Life Laboratory, Uppsala, 752 36, Sweden
- The New Zealand Institute for Plant & Food Research Ltd, Nelson, 7010, New Zealand
| | - Alexander Suh
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Uppsala University, Science for Life Laboratory, Uppsala, 752 36, Sweden
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, UK
| | - Alexander J McCauley
- Commonwealth Scientific and Industrial Research Organisation, Australian Centre for Disease Preparedness, 5 Portarlington Road, Geelong, VIC, 3220, Australia
| | - Parwinder Kaur
- School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6009, Australia
| | - Olga Dudchenko
- The Centre for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Centre for Theoretical Biological Physics and Department of Computer Science, Rice University, Houston, TX, 77030, USA
| | - Erez Aiden
- School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6009, Australia
- The Centre for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Centre for Theoretical Biological Physics and Department of Computer Science, Rice University, Houston, TX, 77030, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02139, USA
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong, 201210, China
| | - Olivier Fedrigo
- The Vertebrate Genome Laboratory, The Rockefeller University, NY, 10065, USA
| | - Giulio Formenti
- The Vertebrate Genome Laboratory, The Rockefeller University, NY, 10065, USA
| | | | - William Chow
- Tree of Life, Welcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Denye N Ogeh
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Françoise Thiaud-Nissen
- National Centre for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Kerstin Howe
- Tree of Life, Welcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Alan Tracey
- Tree of Life, Welcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Jacqueline Smith
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Richard I Kuo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Marilyn B Renfree
- School of Biosciences, The University of Melbourne, Melbourne, VIC, 3052, Australia
| | - Takashi Kimura
- Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido, 060-0818, Japan
| | - Yoshihiro Sakoda
- Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido, 060-0818, Japan
| | - Mathew McDougall
- New Zealand Fish & Game - Eastern Region, Rotorua, 3046, New Zealand
| | - Hamish G Spencer
- Department of Zoology, University of Otago, Dunedin, 9054, New Zealand
| | - Michael Pyne
- Currumbin Wildlife Sanctuary, Currumbin, QLD, 4223, Australia
| | - Conny Tolf
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, SE-391 82, Sweden
| | - Jonas Waldenström
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, SE-391 82, Sweden
| | - Erich D Jarvis
- The Vertebrate Genome Laboratory, The Rockefeller University, NY, 10065, USA
| | - Michelle L Baker
- Commonwealth Scientific and Industrial Research Organisation, Australian Centre for Disease Preparedness, 5 Portarlington Road, Geelong, VIC, 3220, Australia
| | - David W Burt
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Kirsty R Short
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia.
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16
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Vlček J, Miláček M, Vinkler M, Štefka J. Effect of population size and selection on Toll-like receptor diversity in populations of Galápagos mockingbirds. J Evol Biol 2023; 36:109-120. [PMID: 36398499 DOI: 10.1111/jeb.14121] [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: 12/09/2021] [Revised: 08/25/2022] [Accepted: 09/10/2022] [Indexed: 11/19/2022]
Abstract
The interactions of evolutionary forces are difficult to analyse in free-living populations. However, when properly understood, they provide valuable insights into evolutionary biology and conservation genetics. This is particularly important for the interplay of genetic drift and natural selection in immune genes that confer resistance to disease. The Galápagos Islands are inhabited by four closely related species of mockingbirds (Mimus spp.). We used 12 different-sized populations of Galápagos mockingbirds and one population of their continental relative northern mockingbird (Mimus polyglottos) to study the effects of genetic drift on the molecular evolution of immune genes, the Toll-like receptors (TLRs: TLR1B, TLR4 and TLR15). We found that neutral genetic diversity was positively correlated with island size, indicating an important effect of genetic drift. However, for TLR1B and TLR4, there was little correlation between functional (e.g., protein) diversity and island size, and protein structural properties were largely conserved, indicating only a limited effect of genetic drift on molecular phenotype. By contrast, TLR15 was less conserved and even its putative functional polymorphism correlated with island size. The patterns observed for the three genes suggest that genetic drift does not necessarily dominate selection even in relatively small populations, but that the final outcome depends on the degree of selection constraint that is specific for each TLR locus.
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Affiliation(s)
- Jakub Vlček
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic.,Department of Zoology, University of South Bohemia in České Budějovice Faculty of Science, České Budějovice, Czech Republic.,Department of Botany, Charles University Faculty of Science, Prague, Czech Republic
| | - Matěj Miláček
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic.,Department of Zoology, University of South Bohemia in České Budějovice Faculty of Science, České Budějovice, Czech Republic
| | - Michal Vinkler
- Department of Zoology, Charles University Faculty of Science, Prague, Czech Republic
| | - Jan Štefka
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic.,Department of Zoology, University of South Bohemia in České Budějovice Faculty of Science, České Budějovice, Czech Republic
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17
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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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18
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Krchlíková V, Hron T, Těšický M, Li T, Ungrová L, Hejnar J, Vinkler M, Elleder D. Dynamic Evolution of Avian RNA Virus Sensors: Repeated Loss of RIG-I and RIPLET. Viruses 2022; 15:3. [PMID: 36680044 PMCID: PMC9861763 DOI: 10.3390/v15010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/05/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Retinoic acid-inducible gene I (RIG-I) and melanoma differentiation-associated protein 5 (MDA5) are key RNA virus sensors belonging to the RIG-I-like receptor (RLR) family. The activation of the RLR inflammasome leads to the establishment of antiviral state, mainly through interferon-mediated signaling. The evolutionary dynamics of RLRs has been studied mainly in mammals, where rare cases of RLR gene losses were described. By in silico screening of avian genomes, we previously described two independent disruptions of MDA5 in two bird orders. Here, we extend this analysis to approximately 150 avian genomes and report 16 independent evolutionary events of RIG-I inactivation. Interestingly, in almost all cases, these inactivations are coupled with genetic disruptions of RIPLET/RNF135, an ubiquitin ligase RIG-I regulator. Complete absence of any detectable RIG-I sequences is unique to several galliform species, including the domestic chicken (Gallus gallus). We further aimed to determine compensatory evolution of MDA5 in RIG-I-deficient species. While we were unable to show any specific global pattern of adaptive evolution in RIG-I-deficient species, in galliforms, the analyses of positive selection and surface charge distribution support the hypothesis of some compensatory evolution in MDA5 after RIG-I loss. This work highlights the dynamic nature of evolution in bird RNA virus sensors.
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Affiliation(s)
- Veronika Krchlíková
- Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Tomáš Hron
- Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Martin Těšický
- Department of Zoology, Faculty of Science, Charles University, 12843 Prague, Czech Republic
| | - Tao Li
- Department of Zoology, Faculty of Science, Charles University, 12843 Prague, Czech Republic
| | - Lenka Ungrová
- Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Jiří Hejnar
- Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Michal Vinkler
- Department of Zoology, Faculty of Science, Charles University, 12843 Prague, Czech Republic
| | - Daniel Elleder
- Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic
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19
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Miao X, Liu L, Liu L, Hu G, Wu G, Wang Y, Zhao Y, Yang J, Li X. Regulation of mRNA and miRNA in the response to Salmonella enterica serovar Enteritidis infection in chicken cecum. BMC Vet Res 2022; 18:437. [PMID: 36514049 PMCID: PMC9749161 DOI: 10.1186/s12917-022-03522-y] [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: 06/01/2022] [Accepted: 11/18/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Salmonella enterica, serovar Enteritidis (SE) is a food-borne pathogen, which can cause great threat to human health through consumption of the contaminated poultry products. Chicken is the main host of SE. The mRNA and microRNA (miRNA) expression profiles were analyzed on cecum of Shouguang chicken via next-generation sequencing and bioinformatics approaches. The treated group was inoculated SE, and the control group was inoculated with phosphate buffer saline (PBS). RESULTS There were 1760 differentially expressed mRNAs in the SE-infected group, of which 1046 were up-regulated mRNA, and 714 were down-regulated mRNA. In addition, a total of 821 miRNAs were identified, and 174 miRNAs were differentially expressed, of which 100 were up-regulated and 74 were down-regulated. Functional enrichment of differentially expressed mRNAs was similar to miRNA target genes. The functional analysis results of differentially expressed mRNAs and miRNAs were performed. Immune-related processes and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways were enriched by up-regulated mRNA. The down-regulated mRNAs were enriched in tissue development and metabolic-related KEGG pathways. The functional analysis of up-regulated miRNA target genes was similar to the down-regulated mRNAs. The down-regulated miRNA target genes were enriched in metabolic-related GO (Gene Ontology) -BP (Biological process) terms and KEGG pathways. The overlap of the up-regulated mRNA and the up-regulated miRNA target genes (class I) was 325, and the overlap of the down-regulated miRNA target genes (class II) was 169. The class I enriched in the immune-related GO-BP terms and KEGG pathways. The class II mainly enriched in metabolic-related GO-BP terms and KEGG pathways. Then we detected the expression of mRNA and miRNA through qRT-PCR. The results shown that the expression of HHIP, PGM1, HTR2B, ITGB5, RELN, SFRP1, TCF7L2, SCNN1A, NEK7, miR-20b-5p, miR-1662, miR-15a, miR-16-1-3p was significantly different between two groups. Dual-luciferase reporter assay was used to detect the relationship between miR-20b-5p and SCNN1A. The result indicated that miR-20b-5p regulate immune or metabolic responses after SE infection in Shouguang chickens by directly targeting SCNN1A. CONCLUSIONS The findings here contribute to the further analysis of the mechanism of mRNA and miRNA defense against SE infection, and provide a theoretical foundation for the molecular disease-resistant breeding of chickens.
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Affiliation(s)
- Xiuxiu Miao
- grid.440622.60000 0000 9482 4676College of Animal Science and Technology, Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai’an, 271018 China
| | - Lewen Liu
- grid.440622.60000 0000 9482 4676College of Animal Science and Technology, Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai’an, 271018 China
| | - Liying Liu
- grid.440622.60000 0000 9482 4676College of Life Sciences, Shandong Agricultural University, Tai’an, 271018 China
| | - Geng Hu
- grid.440622.60000 0000 9482 4676College of Animal Science and Technology, Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai’an, 271018 China
| | - Guixian Wu
- grid.440622.60000 0000 9482 4676College of Animal Science and Technology, Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai’an, 271018 China
| | - Yuanmei Wang
- grid.440622.60000 0000 9482 4676College of Animal Science and Technology, Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai’an, 271018 China
| | - Yanan Zhao
- grid.440622.60000 0000 9482 4676College of Animal Science and Technology, Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai’an, 271018 China
| | - Jingchao Yang
- Shandong Animal Husbandry General Station, Jinan, 250010 China
| | - Xianyao Li
- grid.440622.60000 0000 9482 4676College of Animal Science and Technology, Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai’an, 271018 China
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20
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Divín D, Goméz Samblas M, Kuttiyarthu Veetil N, Voukali E, Świderská Z, Krajzingrová T, Těšický M, Beneš V, Elleder D, Bartoš O, Vinkler M. Cannabinoid receptor 2 evolutionary gene loss makes parrots more susceptible to neuroinflammation. Proc Biol Sci 2022; 289:20221941. [PMID: 36475439 PMCID: PMC9727682 DOI: 10.1098/rspb.2022.1941] [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] [Indexed: 12/13/2022] Open
Abstract
In vertebrates, cannabinoids modulate neuroimmune interactions through two cannabinoid receptors (CNRs) conservatively expressed in the brain (CNR1, syn. CB1) and in the periphery (CNR2, syn. CB2). Our comparative genomic analysis indicates several evolutionary losses in the CNR2 gene that is involved in immune regulation. Notably, we show that the CNR2 gene pseudogenized in all parrots (Psittaciformes). This CNR2 gene loss occurred because of chromosomal rearrangements. Our positive selection analysis suggests the absence of any specific molecular adaptations in parrot CNR1 that would compensate for the CNR2 loss in the modulation of the neuroimmune interactions. Using transcriptomic data from the brains of birds with experimentally induced sterile inflammation we highlight possible functional effects of such a CNR2 gene loss. We compare the expression patterns of CNR and neuroinflammatory markers in CNR2-deficient parrots (represented by the budgerigar, Melopsittacus undulatus and five other parrot species) with CNR2-intact passerines (represented by the zebra finch, Taeniopygia guttata). Unlike in passerines, stimulation with lipopolysaccharide resulted in neuroinflammation in the parrots linked with a significant upregulation of expression in proinflammatory cytokines (including interleukin 1 beta (IL1B) and 6 (IL6)) in the brain. Our results indicate the functional importance of the CNR2 gene loss for increased sensitivity to brain inflammation.
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Affiliation(s)
- Daniel Divín
- Faculty of Science, Department of Zoology, Charles University, Viničná 7, Prague 128 44, Czech Republic
| | - Mercedes Goméz Samblas
- Faculty of Science, Department of Zoology, Charles University, Viničná 7, Prague 128 44, Czech Republic
| | - Nithya Kuttiyarthu Veetil
- Faculty of Science, Department of Zoology, Charles University, Viničná 7, Prague 128 44, Czech Republic
| | - Eleni Voukali
- Faculty of Science, Department of Zoology, Charles University, Viničná 7, Prague 128 44, Czech Republic
| | - Zuzana Świderská
- Faculty of Science, Department of Zoology, Charles University, Viničná 7, Prague 128 44, Czech Republic
| | - Tereza Krajzingrová
- Faculty of Science, Department of Zoology, Charles University, Viničná 7, Prague 128 44, Czech Republic
| | - Martin Těšický
- Faculty of Science, Department of Zoology, Charles University, Viničná 7, Prague 128 44, Czech Republic
| | - Vladimír Beneš
- Genomics Core Facility, European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Daniel Elleder
- Institute of Molecular Genetics, Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Oldřich Bartoš
- Military Health Institute, Military Medical Agency, Tychonova 1, 160 01 Prague 6, Czech Republic
| | - Michal Vinkler
- Faculty of Science, Department of Zoology, Charles University, Viničná 7, Prague 128 44, Czech Republic
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21
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Wu X, Chen J, Wang X, Shang Y, Wei Q, Zhang H. Evolutionary Impacts of Pattern Recognition Receptor Genes on Carnivora Complex Habitat Stress Adaptation. Animals (Basel) 2022; 12:ani12233331. [PMID: 36496853 PMCID: PMC9739989 DOI: 10.3390/ani12233331] [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: 10/19/2022] [Revised: 11/22/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022] Open
Abstract
Many mammals develop specific immune responses owing to the changes in their ecological niche and diet that are essential for animal survival. However, pattern recognition receptors (PRRs) serve as the first line of defense in innate immunity and generate immune responses in the host. However, the evolutionary impacts on PRR genes in Carnivora are not well studied. Herein, we explored the evolution of 946 PRR gene sequences in 43 Carnivora species to elucidate the molecular mechanisms of carnivore adaptation to complex habitats. We found that the PRRs were relatively conserved, and different gene families showed different evolutionary patterns. PRRs were highly purified based on their overall roles in Carnivora species but interspersed with positive-selection patterns during evolution. Different niche types may have jointly driven the evolution of PRR genes. In particular, the selection pressure of toll-like receptor (TLR) 10 was relaxed in seven species with pseudogenes, which may have emerged during recent evolutionary events. We speculated that a "functional compensation" mechanism may exist for genes with overlapping functions in the TLR gene family. Additionally, TLR2, TLR4, NLRC5, and DECTIN1 were subject to positive selection in semi-aquatic species, and the adaptive evolution of these genes may have been related to the adaptation to semi-aquatic environments. In summary, our findings offer valuable insights into the molecular and functional evolution of PRR genes, which are important for immune adaptations in Carnivora.
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Affiliation(s)
- Xiaoyang Wu
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Jun Chen
- College of Marine Life Sciences, Ocean University of China, Qingdao 266005, China
| | - Xibao Wang
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Yongquan Shang
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Qinguo Wei
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Honghai Zhang
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
- Correspondence:
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22
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Effects of Acute Cold Stress after Intermittent Cold Stimulation on Immune-Related Molecules, Intestinal Barrier Genes, and Heat Shock Proteins in Broiler Ileum. Animals (Basel) 2022; 12:ani12233260. [PMID: 36496781 PMCID: PMC9739716 DOI: 10.3390/ani12233260] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/19/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022] Open
Abstract
Cold stress will have a negative impact on animal welfare and health. In order to explore the effect of intermittent cold stimulation training on the cold resistance of broilers. Immune-related and intestinal barrier genes were detected before and after acute cold stress (ACS), aiming to find an optimal cold stimulation training method. A total of 240 1-day-old Ross broilers (Gallus) were divided into three groups (G1, G2, and G3), each with 5 replicates (16 chickens each replicate). The broilers of G1 were raised at normal temperature, while the broilers of G2 and G3 were treated with cold stimulation at 3 °C lower than the G1 for 3 h and 6 h from 15 to 35 d, respectively, at one-day intervals. At 50 d, the ambient temperature for all groups was reduced to 10 °C for six hours. The results demonstrated that before ACS, IL6, IL17, TLR21, and HSP40 mRNA levels in G3 were apparently down-regulated (p < 0.05), while IL8 and Claudin-1 mRNA levels were significantly up-regulated compared with G1 (p < 0.05). After ACS, IL2, IL6, and IL8 expression levels in G3 were lower than those in G2 (p < 0.05). Compared to G2, Claudin-1, HSP90 mRNA levels, HSP40, and HSP70 protein levels were increased in G3 (p < 0.05). The mRNA levels of TLR5, Mucin2, and Claudin-1 in G2 and IL6, IL8, and TLR4 in G3 were down-regulated after ACS, while IL2, IL6, and IL17 mRNA levels in G2 and HSP40 protein levels in G3 were up-regulated after ACS (p < 0.05). Comprehensive investigation shows that cold stimulation at 3 °C lower than the normal feeding temperature for six hours at one day intervals can enhanced immune function and maintain the stability of intestinal barrier function to lessen the adverse effects on ACS in broilers.
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23
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Jax E, Franchini P, Sekar V, Ottenburghs J, Monné Parera D, Kellenberger RT, Magor KE, Müller I, Wikelski M, Kraus RHS. Comparative genomics of the waterfowl innate immune system. Mol Biol Evol 2022; 39:6649919. [PMID: 35880574 PMCID: PMC9356732 DOI: 10.1093/molbev/msac160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Animal species differ considerably in their ability to fight off infections. Finding the genetic basis of these differences is not easy, as the immune response is comprised of a complex network of proteins that interact with one another to defend the body against infection. Here, we used population- and comparative genomics to study the evolutionary forces acting on the innate immune system in natural hosts of the avian influenza virus (AIV). For this purpose, we used a combination of hybrid capture, next- generation sequencing and published genomes to examine genetic diversity, divergence, and signatures of selection in 127 innate immune genes at a micro- and macroevolutionary time scale in 26 species of waterfowl. We show across multiple immune pathways (AIV-, toll-like-, and RIG-I -like receptors signalling pathways) that genes involved genes in pathogen detection (i.e., toll-like receptors) and direct pathogen inhibition (i.e., antimicrobial peptides and interferon-stimulated genes), as well as host proteins targeted by viral antagonist proteins (i.e., mitochondrial antiviral-signaling protein, [MAVS]) are more likely to be polymorphic, genetically divergent, and under positive selection than other innate immune genes. Our results demonstrate that selective forces vary across innate immune signaling signalling pathways in waterfowl, and we present candidate genes that may contribute to differences in susceptibility and resistance to infectious diseases in wild birds, and that may be manipulated by viruses. Our findings improve our understanding of the interplay between host genetics and pathogens, and offer the opportunity for new insights into pathogenesis and potential drug targets.
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Affiliation(s)
- Elinor Jax
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany.,Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Paolo Franchini
- Department of Biology, University of Konstanz, Konstanz, Germany.,Department of Biology and Biotechnologies "Charles Darwin", Sapienza University, Rome, Italy
| | - Vaishnovi Sekar
- Department of Biology, Lund University, Lund, Sweden.,Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
| | - Jente Ottenburghs
- Wildlife Ecology and Conservation Group, Wageningen University, Wageningen, The Netherlands.,Forest Ecology and Forest Management Group, Wageningen University, Wageningen, The Netherlands
| | | | - Roman T Kellenberger
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Katharine E Magor
- Department of Biological Sciences and Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Canada
| | - Inge Müller
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Martin Wikelski
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany.,Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, Germany
| | - Robert H S Kraus
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany
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24
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Genomic insights into the secondary aquatic transition of penguins. Nat Commun 2022; 13:3912. [PMID: 35853876 PMCID: PMC9296559 DOI: 10.1038/s41467-022-31508-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 06/17/2022] [Indexed: 11/21/2022] Open
Abstract
Penguins lost the ability to fly more than 60 million years ago, subsequently evolving a hyper-specialized marine body plan. Within the framework of a genome-scale, fossil-inclusive phylogeny, we identify key geological events that shaped penguin diversification and genomic signatures consistent with widespread refugia/recolonization during major climate oscillations. We further identify a suite of genes potentially underpinning adaptations related to thermoregulation, oxygenation, diving, vision, diet, immunity and body size, which might have facilitated their remarkable secondary transition to an aquatic ecology. Our analyses indicate that penguins and their sister group (Procellariiformes) have the lowest evolutionary rates yet detected in birds. Together, these findings help improve our understanding of how penguins have transitioned to the marine environment, successfully colonizing some of the most extreme environments on Earth. This study examines the tempo and drivers of penguin diversification by combining genomes from all extant and recently extinct penguin lineages, stratigraphic data from fossil penguins and morphological and biogeographic data from all extant and extinct species. Together, these datasets provide new insights into the genetic basis and evolution of adaptations in penguins.
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25
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Sharp C, Foster KR. Host control and the evolution of cooperation in host microbiomes. Nat Commun 2022; 13:3567. [PMID: 35732630 PMCID: PMC9218092 DOI: 10.1038/s41467-022-30971-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 05/27/2022] [Indexed: 12/14/2022] Open
Abstract
Humans, and many other species, are host to diverse symbionts. It is often suggested that the mutual benefits of host-microbe relationships can alone explain cooperative evolution. Here, we evaluate this hypothesis with evolutionary modelling. Our model predicts that mutual benefits are insufficient to drive cooperation in systems like the human microbiome, because of competition between symbionts. However, cooperation can emerge if hosts can exert control over symbionts, so long as there are constraints that limit symbiont counter evolution. We test our model with genomic data of two bacterial traits monitored by animal immune systems. In both cases, bacteria have evolved as predicted under host control, tending to lose flagella and maintain butyrate production when host-associated. Moreover, an analysis of bacteria that retain flagella supports the evolution of host control, via toll-like receptor 5, which limits symbiont counter evolution. Our work puts host control mechanisms, including the immune system, at the centre of microbiome evolution.
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Affiliation(s)
- Connor Sharp
- Department of Zoology, University of Oxford, Oxford, UK.
- Department of Biochemistry, University of Oxford, Oxford, UK.
| | - Kevin R Foster
- Department of Zoology, University of Oxford, Oxford, UK.
- Department of Biochemistry, University of Oxford, Oxford, UK.
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26
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Magid M, Wold JR, Moraga R, Cubrinovska I, Houston DM, Gartrell BD, Steeves TE. Leveraging an existing whole genome resequencing population dataset to characterize toll‐like receptor gene diversity in a threatened bird. Mol Ecol Resour 2022; 22:2810-2825. [PMID: 35635119 PMCID: PMC9543821 DOI: 10.1111/1755-0998.13656] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/29/2022] [Accepted: 05/26/2022] [Indexed: 11/27/2022]
Abstract
Species recovery programs are increasingly using genomic data to measure neutral genetic diversity and calculate metrics like relatedness. While these measures can inform conservation management, determining the mechanisms underlying inbreeding depression requires information about functional genes associated with adaptive or maladaptive traits. Toll‐like receptors (TLRs) are one family of functional genes, which play a crucial role in recognition of pathogens and activation of the immune system. Previously, these genes have been analysed using species‐specific primers and PCR. Here, we leverage an existing short‐read reference genome, whole‐genome resequencing population data set, and bioinformatic tools to characterize TLR gene diversity in captive and wild tchūriwat’/tūturuatu/shore plover (Thinornis novaeseelandiae), a threatened bird endemic to Aotearoa New Zealand. Our results show that TLR gene diversity in tchūriwat’/tūturuatu is low, and forms two distinct captive and wild genetic clusters. The bioinformatic approach presented here has broad applicability to other threatened species with existing genomic resources in Aotearoa New Zealand and beyond.
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Affiliation(s)
- Molly Magid
- University of Canterbury School of Biological Sciences Christchurch NZ
| | - Jana R. Wold
- University of Canterbury School of Biological Sciences Christchurch NZ
| | - Roger Moraga
- Tea Break Bioinformatics, Ltd Palmerston North NZ
| | - Ilina Cubrinovska
- University of Canterbury School of Biological Sciences Christchurch NZ
| | | | - Brett D. Gartrell
- Wildbase Massey University Institute of Veterinary, Animal, and Biomedical Sciences, Palmerston North, Manawatu NZ
| | - Tammy E. Steeves
- University of Canterbury School of Biological Sciences Christchurch NZ
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27
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Minias P, Vinkler M. Selection balancing at innate immune genes: adaptive polymorphism maintenance in Toll-like receptors. Mol Biol Evol 2022; 39:6586215. [PMID: 35574644 PMCID: PMC9132207 DOI: 10.1093/molbev/msac102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Balancing selection is a classic mechanism for maintaining variability in immune genes involved in host–pathogen interactions. However, it remains unclear how widespread the mechanism is across immune genes other than the major histocompatibility complex (MHC). Although occasional reports suggest that balancing selection (heterozygote advantage, negative frequency-dependent selection, and fluctuating selection) may act on other immune genes, the current understanding of the phenomenon in non-MHC immune genes is far from solid. In this review, we focus on Toll-like receptors (TLRs), innate immune genes directly involved in pathogen recognition and immune response activation, as there is a growing body of research testing the assumptions of balancing selection in these genes. After reviewing infection- and fitness-based evidence, along with evidence based on population allelic frequencies and heterozygosity levels, we conclude that balancing selection maintains variation in TLRs, though it tends to occur under specific conditions in certain evolutionary lineages rather than being universal and ubiquitous. Our review also identifies key gaps in current knowledge and proposes promising areas for future research. Improving our understanding of host–pathogen interactions and balancing selection in innate immune genes are increasingly important, particularly regarding threats from emerging zoonotic diseases.
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28
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Liu C, Zhou S, Bai W, Shi L, Li X. Protective effect of food derived nutrients on cisplatin nephrotoxicity and its mechanism. Food Funct 2022; 13:4839-4860. [PMID: 35416186 DOI: 10.1039/d1fo04391a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Platinum-based metal complexes, especially cisplatin (cis-diamminedichloroplatinum II, CDDP), possess strong anticancer properties and a broad anticancer spectrum. However, the clinical application of CDDP has been limited by its side effects including nephrotoxicity, ototoxicity, and neurotoxicity. Furthermore, the therapeutic effects of current clinical protocols are imperfect. Accordingly, it is essential to identify key targets and effective clinical protocols to restrict CDDP-induced nephrotoxicity. Herein, we first analyzed the relevant molecular mechanisms during the process of CDDP-induced nephrotoxicity including oxidative stress, apoptosis, and inflammation. Evidence from current studies was collected and potential targets and clinical protocols are summarized. The evidence indicates an efficacious role of nutrition-based substances in CDDP-induced renal injury.
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Affiliation(s)
- Chaofan Liu
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, PR China.
| | - Sajin Zhou
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, PR China.
| | - Weibin Bai
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, PR China.
| | - Lei Shi
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, PR China.
| | - Xiaoling Li
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, PR China.
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29
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TLR7 and TLR8 evolution in lagomorphs: different patterns in the different lineages. Immunogenetics 2022; 74:475-485. [PMID: 35419618 DOI: 10.1007/s00251-022-01262-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/30/2022] [Indexed: 11/05/2022]
Abstract
Toll-like receptors (TLRs) are one of the most ancient and widely studied innate immune receptors responsible for host defense against invading pathogens. Among the known TLRs, TLR7 and TLR8 sense and recognize single-stranded (ss) RNAs with a dynamic evolutionary history. While TLR8 was lost in birds and duplicated in turtles and crocodiles, TLR7 is duplicated in some birds, but in other tetrapods, there is only one copy. In mammals, with the exception of lagomorphs, TLR7 and TLR8 are highly conserved. Here, we aim to study the evolution of TLR7 and TLR8 in mammals, with a special focus in the order Lagomorpha. By searching public sequence databases, conducting evolutionary analysis, and evaluating gene expression, we were able to confirm that TLR8 is absent in hares but widely expressed in the European rabbit. In contrast, TLR7 is absent in the European rabbit and quite divergent in hares. Our results suggest that, in lagomorphs, more in particular in leporids, TLR7 and TLR8 genes have evolved faster than in any other mammalian group. The long history of interaction with viruses and their location in highly dynamic telomeric regions might explain the pattern observed.
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30
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Immunity and lifespan: answering long-standing questions with comparative genomics. Trends Genet 2022; 38:650-661. [DOI: 10.1016/j.tig.2022.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/14/2022] [Accepted: 02/28/2022] [Indexed: 10/18/2022]
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31
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Han F, Zhang Y, Xu A, Wang X, He Y, Song N, Gao T. Genome-wide identification and characterization of Toll-like receptor genes in black rockfish (Sebastes schlegelii) and their response mechanisms following poly (I:C) injection. Comp Biochem Physiol C Toxicol Pharmacol 2022; 254:109277. [PMID: 35085815 DOI: 10.1016/j.cbpc.2022.109277] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 01/10/2022] [Accepted: 01/19/2022] [Indexed: 12/13/2022]
Abstract
Toll-like receptors (TLRs) are canonical transmembrane receptors that play an important role in defending against invading pathogens. In this study, we identified a total of 12 TLR genes in black rockfish (Sebastes schlegelii) with an analysis of their sequence characterizations. The phylogenetic analysis suggested that 12 distinct TLRs were grouped into five subfamilies (i.e., TLR1, TLR3, TLR5, TLR7, and TLR11 subfamilies), and each SsTLR gene respectively corresponded to the orthologs genes of other species. The protein domain analysis indicated that TLRs are type I transmembrane proteins, including an extracellular leucine-rich repeat (LRR), a transmembrane region (TM) domain and an intracellular Toll/IL-1 receptor (TIR) domain. The evolutionary ratios indicted that 12 SsTLRs were under purifying selection. qRT-PCR assays exhibited diverse TLRs molecular expression patterns in the heart, brain, head kidney, kidney, liver, intestine, and spleen of 3 black rockfish, and the expression levels were high in some immune tissues (e.g., head kidney, kidney, and spleen). Subsequently, 30 fish were equally divided into 2 groups i.e., poly (I:C)-treated and PBS-Control groups. After poly (I:C) injection, eight SsTLRs, i.e., SsTLR2, SsTLR2-1, SsTLR2-2, SsTLR3, SsTLR5S, SsTLR7, SsTLR8 and SsTLR22, were dramatically increased. Altogether these results contribute to understanding how SsTLRs respond to immune defense after poly (I:C) injection and provide researchers with comprehensive TLR gene family data of black rockfish.
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Affiliation(s)
- Fei Han
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China
| | - Yuan Zhang
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China
| | - Anle Xu
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China
| | - Xiaoyan Wang
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China
| | - Yan He
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong 266003, China
| | - Na Song
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China
| | - Tianxiang Gao
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China.
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Abstract
Birds are important hosts for many RNA viruses, including influenza A virus, Newcastle disease virus, West Nile virus and coronaviruses. Innate defense against RNA viruses in birds involves detection of viral RNA by pattern recognition receptors. Several receptors of different classes are involved, such as endosomal toll-like receptors and cytoplasmic retinoic acid-inducible gene I-like receptors, and their downstream adaptor proteins. The function of these receptors and their antagonism by viruses is well established in mammals; however, this has received less attention in birds. These receptors have been characterized in a few bird species, and the completion of avian genomes will permit study of their evolution. For each receptor, functional work has established ligand specificity and activation by viral infection. Engagement of adaptors, regulation by modulators and the supramolecular organization of proteins required for activation are incompletely understood in both mammals and birds. These receptors bind conserved nucleic acid agonists such as single- or double-stranded RNA and generally show purifying selection, particularly the ligand binding regions. However, in birds, these receptors and adaptors differ between species, and between individuals, suggesting that they are under selection for diversification over time. Avian receptors and signalling pathways, like their mammalian counterparts, are targets for antagonism by a variety of viruses, intent on escape from innate immune responses.
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Li X, Li Q, Ruan W. Identification of Avian Toll-Like Receptor 3 and 7 and Analysis of Gene Variation Sites. BRAZILIAN JOURNAL OF POULTRY SCIENCE 2022. [DOI: 10.1590/1806-9061-2020-1431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Affiliation(s)
- X Li
- Beijing University of Agriculture, China
| | - Q Li
- Beijing University of Agriculture, China
| | - W Ruan
- Beijing University of Agriculture, China
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34
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Fiddaman SR, Vinkler M, Spiro SG, Levy H, Emerling CA, Boyd AC, Dimopoulos EA, Vianna JA, Cole TL, Pan H, Fang M, Zhang G, Hart T, Frantz LAF, Smith AL. Adaptation and cryptic pseudogenization in penguin Toll-like Receptors. Mol Biol Evol 2021; 39:6460345. [PMID: 34897511 PMCID: PMC8788240 DOI: 10.1093/molbev/msab354] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Penguins (Sphenisciformes) are an iconic order of flightless, diving seabirds distributed across a large latitudinal range in the Southern Hemisphere. The extensive area over which penguins are endemic is likely to have fostered variation in pathogen pressure, which in turn will have imposed differential selective pressures on the penguin immune system. At the front line of pathogen detection and response, the Toll-like receptors (TLRs) provide insight into host evolution in the face of microbial challenge. TLRs respond to conserved pathogen-associated molecular patterns and are frequently found to be under positive selection, despite retaining specificity for defined agonist classes. We undertook a comparative immunogenetics analysis of TLRs for all penguin species and found evidence of adaptive evolution that was largely restricted to the cell surface-expressed TLRs, with evidence of positive selection at, or near, key agonist-binding sites in TLR1B, TLR4, and TLR5. Intriguingly, TLR15, which is activated by fungal products, appeared to have been pseudogenized multiple times in the Eudyptes spp., but a full-length form was present as a rare haplotype at the population level. However, in vitro analysis revealed that even the full-length form of Eudyptes TLR15 was nonfunctional, indicating an ancestral cryptic pseudogenization prior to its eventual disruption multiple times in the Eudyptes lineage. This unusual pseudogenization event could provide an insight into immune adaptation to fungal pathogens such as Aspergillus, which is responsible for significant mortality in wild and captive bird populations.
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Affiliation(s)
- Steven R Fiddaman
- Department of Zoology, University of Oxford South Parks Road, Oxford, OX1 3PS, UK
| | - Michal Vinkler
- Department of Zoology, Faculty of Science, Charles University Prague, Czech Republic
| | - Simon G Spiro
- Wildlife Health Services, Zoological Society of London Regent's Park, London, UK
| | - Hila Levy
- Department of Zoology, University of Oxford South Parks Road, Oxford, OX1 3PS, UK
| | | | - Amy C Boyd
- Jenner Institute, University of Oxford Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Evangelos A Dimopoulos
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford Oxford, UK
| | - Juliana A Vianna
- Pontificia Universidad Católica de Chile, Facultad de Agronomía e Ingeniería Forestal, Departamento de Ecosistemas y Medio Ambiente Vicuña Mackenna 4860, Macul, Santiago, Chile
| | - Theresa L Cole
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen DK2100, Copenhagen, Denmark
| | - Hailin Pan
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District Shenzhen 518083, China
| | - Miaoquan Fang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District Shenzhen 518083, China
| | - Guojie Zhang
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen DK2100, Copenhagen, Denmark.,BGI-Shenzhen, Beishan Industrial Zone, Yantian District Shenzhen 518083, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
| | - Tom Hart
- Department of Zoology, University of Oxford South Parks Road, Oxford, OX1 3PS, UK
| | - Laurent A F Frantz
- School of Biological and Chemical Sciences, Fogg Building, Queen Mary University of London Mile End Rd, Bethnal Green, London E1 4DQ, UK.,Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Faculty of Veterinary Medicine, Ludwig Maximilian University of Munich, Germany
| | - Adrian L Smith
- Department of Zoology, University of Oxford South Parks Road, Oxford, OX1 3PS, UK
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35
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Repeated MDA5 Gene Loss in Birds: An Evolutionary Perspective. Viruses 2021; 13:v13112131. [PMID: 34834938 PMCID: PMC8619217 DOI: 10.3390/v13112131] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 11/17/2022] Open
Abstract
Two key cytosolic receptors belonging to the retinoic acid-inducible gene I (RIG-I)-like receptor (RLR) family sense the viral RNA-derived danger signals: RIG-I and melanoma differentiation-associated protein 5 (MDA5). Their activation establishes an antiviral state by downstream signaling that ultimately activates interferon-stimulated genes (ISGs). While in rare cases RIG-I gene loss has been detected in mammalian and avian species, most notably in the chicken, MDA5 pseudogenization has only been detected once in mammals. We have screened over a hundred publicly available avian genome sequences and describe an independent disruption of MDA5 in two unrelated avian lineages, the storks (Ciconiiformes) and the rallids (Gruiformes). The results of our RELAX analysis confirmed the absence of negative selection in the MDA5 pseudogene. In contrast to our prediction, we have shown, using multiple dN/dS-based approaches, that the MDA5 loss does not appear to have resulted in any compensatory evolution in the RIG-I gene, which may partially share its ligand-binding specificity. Together, our results indicate that the MDA5 pseudogenization may have important functional effects on immune responsiveness in these two avian clades.
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36
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Boyd RJ, Denommé MR, Grieves LA, MacDougall-Shackleton EA. Stronger population differentiation at infection-sensing than infection-clearing innate immune loci in songbirds: Different selective regimes for different defenses. Evolution 2021; 75:2736-2746. [PMID: 34596241 DOI: 10.1111/evo.14368] [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: 12/31/2020] [Revised: 08/30/2021] [Accepted: 09/14/2021] [Indexed: 10/20/2022]
Abstract
Parasite-mediated selection is widespread at loci involved in immune defense, but different defenses may experience different selective regimes. For defenses involved in clearing infections, purifying selection favoring a single most efficacious allele likely predominates. However, for defenses involved in sensing and recognizing infections, evolutionary arms races may make positive selection particularly important. This could manifest primarily within populations (e.g., balancing selection maintaining variation) or among them (e.g., spatially varying selection enhancing population differences in allele frequencies). We genotyped three toll-like receptors (TLR; involved in sensing infections) and three avian beta-defensins (involved in clearing infections) in 96 song sparrows (Melospiza melodia) from three breeding populations that differ in disease resistance. Variation-based indicators of selection (proportion of variable sites, proportion of nonsynonymous SNPs, proportion of sites bearing signatures of positive or purifying selection, rare allele frequencies) did not differ appreciably between the two locus types. However, differentiation was generally higher at infection-sensing than infection-clearing loci. Allele frequencies differed markedly at TLR3, driven by a variant predicted to alter protein function. Geographically structured variants at infection-sensing loci may reflect local adaptation to spatially heterogeneous parasite communities. Selective regimes experienced by infection-sensing versus infection-clearing loci may differ primarily due to parasite-mediated population differentiation.
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Affiliation(s)
- Rachel J Boyd
- Department of Biology, University of Western Ontario, London, Ontario, N6A 5B7, Canada.,McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205
| | - Melanie R Denommé
- Department of Biology, University of Western Ontario, London, Ontario, N6A 5B7, Canada.,Department of Biological Sciences, Brock University Faculty of Mathematics & Science, St. Catherines, Ontario, L2S 3A1, Canada
| | - Leanne A Grieves
- Department of Biology, University of Western Ontario, London, Ontario, N6A 5B7, Canada.,Department of Psychology, Neuroscience and Behaviour, McMaster University, Hamilton, Ontario, L8S 4M4, Canada
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37
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Minias P, Drzewińska-Chańko J, Włodarczyk R. Evolution of innate and adaptive immune genes in a non-model waterbird, the common tern. INFECTION GENETICS AND EVOLUTION 2021; 95:105069. [PMID: 34487864 DOI: 10.1016/j.meegid.2021.105069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 08/28/2021] [Accepted: 09/01/2021] [Indexed: 11/25/2022]
Abstract
Toll-like receptors (TLRs) and the Major Histocompatibility Complex (MHC) are the key pathogen-recognition genes of vertebrate immune system and they have a crucial role in the initiation of innate and adaptive immune response, respectively. Recent advancements in sequencing technology sparked research on highly duplicated MHC genes in non-model species, but TLR variation in natural vertebrate populations has remained little studied and comparisons of polymorphism across both TLRs and MHC are scarce. Here, we aimed to compare variation across innate (four TLR loci) and adaptive (MHC class I and class II) immune genes in a non-model avian species, the common tern Sterna hirundo. We detected relatively high allelic richness at TLR genes (9-48 alleles per locus), which was similar to or even higher than the estimated per locus allelic richness at the MHC (24-30 alleles at class I and 13-16 alleles at class II under uniform sample sizes). Despite this, the total number of MHC alleles across all duplicated loci (four class I and three class II) was much higher and MHC alleles showed greater sequence divergence than TLRs. Positive selection targeted relatively more sites at the MHC than TLRs, but the strength of selection (dN/dS ratios) at TLRs was higher when compared to MHC class I. There were also differences in the signature of positive selection and recombination (gene conversion) between MHC class I and II (stronger signature at class II), suggesting that mechanisms maintaining variation at the MHC may vary between both classes. Our study indicates that allelic richness of both innate and adaptive immune receptors may be maintained at relatively high levels in viable avian populations and we recommend a transition from the traditional gene-specific to multi-gene approach in studying molecular evolution of vertebrate immune system.
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Affiliation(s)
- Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237 Łódź, Poland.
| | - Joanna Drzewińska-Chańko
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237 Łódź, Poland
| | - Radosław Włodarczyk
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237 Łódź, Poland
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38
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Mahesh KC, Ngunjiri JM, Ghorbani A, Abundo MEC, Wilbanks KQ, Lee K, Lee CW. Assessment of TLR3 and MDA5-Mediated Immune Responses Using Knockout Quail Fibroblast Cells. Avian Dis 2021; 65:419-428. [PMID: 34427417 DOI: 10.1637/0005-2086-65.3.419] [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: 01/15/2021] [Accepted: 06/21/2021] [Indexed: 11/05/2022]
Abstract
Toll-like receptor 3 (TLR3) and melanoma differentiation-associated gene 5 (MDA5) are double-stranded RNA (dsRNA)-recognizing receptors that mediate innate immune responses to virus infection. However, the roles played by these receptors in the pathogenesis of avian viruses are poorly understood. In this study, we generated TLR3 and MDA5 single knockout (SKO) and TLR3-MDA5 double knockout (DKO) quail fibroblast cells and examined dsRNA receptor-mediated innate immune responses in vitro. The knockout cells were then stimulated with a synthetic dsRNA ligand polyinosinic:polycytidylic acid [poly(I:C)] or influenza A virus. Endosomal stimulation of TLR3 by adding poly(I:C) in cell culture media or cytoplasmic stimulation of MDA5 by transfecting poly(I:C) resulted in significant increases of TLR3, MDA5, interferon (IFN) β, and interleukin 8 gene expression levels in wild type (WT) cells. Endosomal poly(I:C) treatment induced a higher level expression of most of the genes tested in MDA5 SKO cells compared with WT cells, but not in TLR3 SKO and DKO cells. Cytoplasmic transfection of poly(I:C) led to significant upregulation of all four genes in WT, TLR3 SKO, and MDA5 SKO cells at 8 hr posttransfection and negligible gene expression changes in TLR3-MDA5 DKO cells. Upon infection with a strain of influenza virus with compromised IFN antagonistic capability, WT cells produced the highest amount of biologically active type I IFN followed by TLR3 SKO and MDA5 SKO cells. DKO cells did not produce detectable amounts of type I IFN. However, the IFN did not induce an antiviral state fast enough to block virus replication, even in WT cells under the experimental conditions employed. In summary, our data demonstrate that TLR3 and MDA5 are the key functional dsRNA receptors in quail and imply their coordinated roles in the induction of innate immune responses upon virus infection.
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Affiliation(s)
- K C Mahesh
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691.,Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210
| | - John M Ngunjiri
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691
| | - Amir Ghorbani
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691.,Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210
| | - Michael E C Abundo
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691
| | | | - Kichoon Lee
- Department of Animal Sciences, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Columbus, OH 43210
| | - Chang-Won Lee
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691, .,Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210
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39
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Vrtílek M, Bolnick DI. Macroevolutionary foundations of a recently evolved innate immune defense. Evolution 2021; 75:2600-2612. [PMID: 34347301 PMCID: PMC8488947 DOI: 10.1111/evo.14316] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 07/06/2021] [Accepted: 07/20/2021] [Indexed: 01/13/2023]
Abstract
Antagonistic interactions between hosts and parasites may drive the evolution of novel host defenses, or new parasite strategies. Host immunity is therefore one of the fastest evolving traits. But where do the novel immune traits come from? Here, we test for phylogenetic conservation in a rapidly evolving immune trait—peritoneal fibrosis. Peritoneal fibrosis is a costly defense against a specialist tapeworm, Schistocephalus solidus (Cestoda), expressed in some freshwater populations of threespine stickleback fish (Gasterosteus aculeatus, Perciformes). We asked whether stickleback fibrosis is a derived species‐specific trait or an ancestral immune response that was widely distributed across ray‐finned fish (Actinopterygii) only to be employed by threespine stickleback against the specialist parasite. We combined literature review on peritoneal fibrosis with a comparative experiment using either parasite‐specific, or nonspecific, immune challenge in deliberately selected species across fish tree of life. We show that ray‐finned fish are broadly, but not universally, able to induce peritoneal fibrosis when challenged with a generic stimulus (Alum adjuvant). The experimental species were, however, largely indifferent to the tapeworm antigen homogenate. Peritoneal fibrosis, thus, appears to be a common and deeply conserved fish immune response that was co‐opted by stickleback to adapt to a new selective challenge.
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Affiliation(s)
- Milan Vrtílek
- Institute of Vertebrate Biology, The Czech Academy of Sciences, Brno, 603 65, Czech Republic
| | - Daniel I Bolnick
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, 06269
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40
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Wang KL, Chen SN, Huo HJ, Nie P. Identification and expression analysis of sixteen Toll-like receptor genes, TLR1, TLR2a, TLR2b, TLR3, TLR5M, TLR5S, TLR7-9, TLR13a-c, TLR14, TLR21-23 in mandarin fish Siniperca chuatsi. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 121:104100. [PMID: 33862097 DOI: 10.1016/j.dci.2021.104100] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 04/06/2021] [Accepted: 04/07/2021] [Indexed: 06/12/2023]
Abstract
Toll-like receptors (TLRs), as a family of pattern recognition receptors (PRRs), possess specific pathogen-related molecular pattern (PAMP) recognition spectrum in inducing immune responses. In this study, sixteen TLRs were identified and characterized in mandarin fish (Siniperca chuatsi). All these TLRs consist of leucine-rich repeats (LRRs), a transmembrane domain and a Toll/interleukin-I receptor (TIR) domain, with the exception of TLR5S which lacks TIR domain, and they can be clustered into five branches, i.e. TLR1 subfamily, TLR3 subfamily, TLR5 subfamily, TLR7 subfamily and TLR11 subfamily in phylogenetic tree. These TLR genes were expressed in all tested tissues and had high expression levels in immune-related tissues such as head-kidney and spleen or mucosa-related tissues such as intestine and pyloric caecum. The transcripts of TLR2a, TLR2b, TLR3, TLR13a, TLR14, TLR22 and TLR23 were all significantly up-regulated after stimulation with poly(I:C); TLR1, TLR2a, TLR2b, TLR3, TLR5M, TLR5S, TLR13a and TLR13b transcripts were all significantly up-regulated after stimulation with PGN; and TLR2a, TLR2b, TLR5M, TLR5S, TLR7, TLR8, TLR9, TLR13c, TLR14 and TLR22 transcripts were all significantly up-regulated after stimulation with LPS in isolated head kidney lymphocytes of mandarin fish. The findings in this study may provide a valuable basis for functional study on TLR genes in mandarin fish.
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Affiliation(s)
- Kai Lun Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, And Key Laboratory of Aquaculture Disease Control, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China; The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
| | - Shan Nan Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, And Key Laboratory of Aquaculture Disease Control, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China; The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.
| | - Hui Jun Huo
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, Shandong Province, 266237, China; School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong Province, 266109, China.
| | - Pin Nie
- State Key Laboratory of Freshwater Ecology and Biotechnology, And Key Laboratory of Aquaculture Disease Control, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China; The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, Shandong Province, 266237, China; School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong Province, 266109, China.
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41
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Coelacanth SERINC2 Inhibits HIV-1 Infectivity and Is Counteracted by Envelope Glycoprotein from Foamy Virus. J Virol 2021; 95:e0022921. [PMID: 33883219 PMCID: PMC8316019 DOI: 10.1128/jvi.00229-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
SERINC5 restricts nef-defective HIV-1 by affecting early steps of the virus life cycle. Distantly related retroviruses with a wide host range encode virulent factors in response to challenge by SERINC5. However, the evolutionary origins of this antiretroviral activity, its prevalence among the paralogs, and its ability to target retroviruses remain understudied. In agreement with previous studies, we found that four human SERINC paralogs inhibit nef-defective HIV-1, with SERINC2 being an exception. Here, we demonstrate that this lack of activity in human SERINC2 is associated with its post-whole-genome duplication (post-WGD) divergence, as evidenced by the ability of pre-WGD orthologs from Saccharomyces cerevisiae and flies and a post-WGD-proximate SERINC2 from coelacanths to inhibit the virus. Intriguingly, Nef is unable to counter coelacanth SERINC2, indicating that such activity was directed toward other retroviruses found in coelacanths (like foamy viruses). However, foamy virus-derived vectors are intrinsically resistant to the action of SERINC2, and we show that the foamy virus envelope confers this resistance by affecting its steady-state levels. Our study highlights an ancient origin of antiretroviral activity in SERINCs and a hitherto-unknown interaction with a foamy virus. IMPORTANCESERINC5 constitutes a critical barrier to the propagation of retroviruses, as highlighted by parallel emergence of anti-SERINC5 activities among distant retroviral lineages. Therefore, understanding the origin and evolution of these host factors will provide key information about virus-host relationships that can be exploited for future drug development. Here, we show that SERINC5-mediated nef-defective HIV-1 infection inhibition is evolutionarily conserved. SERINC2 from coelacanth restricts HIV-1, and it was functionally adapted to target foamy viruses. Our findings provide insights into the evolutionary origin of antiretroviral activity in the SERINC gene family and uncover the role of SERINCs in shaping the long-term conflicts between retroviruses and their hosts.
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42
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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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43
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Davies CS, Taylor MI, Hammers M, Burke T, Komdeur J, Dugdale HL, Richardson DS. Contemporary evolution of the innate immune receptor gene TLR3 in an isolated vertebrate population. Mol Ecol 2021; 30:2528-2542. [PMID: 33949028 DOI: 10.1111/mec.15914] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 03/24/2021] [Accepted: 03/26/2021] [Indexed: 12/15/2022]
Abstract
Understanding where genetic variation exists, and how it influences fitness within populations is important from an evolutionary and conservation perspective. Signatures of past selection suggest that pathogen-mediated balancing selection is a key driver of immunogenetic variation, but studies tracking contemporary evolution are needed to help resolve the evolutionary forces and mechanism at play. Previous work in a bottlenecked population of Seychelles warblers (Acrocephalus sechellensis) show that functional variation has been maintained at the viral-sensing Toll-like receptor 3 (TLR3) gene, including one nonsynonymous SNP, resulting in two alleles. Here, we characterise evolution at this TLR3 locus over a 25-year period within the original remnant population of the Seychelles warbler, and in four other derived, populations. Results show a significant and consistent temporal decline in the frequency of the TLR3C allele in the original population, and that similar declines in the TLR3C allele frequency occurred in all the derived populations. Individuals (of both sexes) with the TLR3CC genotype had lower survival, and males - but not females - that carry the TLR3C allele had significantly lower lifetime reproductive success than those with only the TLR3A allele. These results indicate that positive selection on the TLR3A allele, caused by an as yet unknown agent, is driving TLR3 evolution in the Seychelles warbler. No evidence of heterozygote advantage was detected. However, whether the positive selection observed is part of a longer-term pattern of balancing selection (through fluctuating selection or rare-allele advantage) cannot be resolved without tracking the TLR3C allele over an extended time period.
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Affiliation(s)
- Charli S Davies
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, UK
| | - Martin I Taylor
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, UK
| | - Martijn Hammers
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Terry Burke
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Jan Komdeur
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Hannah L Dugdale
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands.,Faculty of Biological Sciences, School of Biology, University of Leeds, Leeds, UK
| | - David S Richardson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, UK.,Nature Seychelles, Roche Caiman, Mahé, Republic of Seychelles
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44
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Sharma V, Hecker N, Walther F, Stuckas H, Hiller M. Convergent Losses of TLR5 Suggest Altered Extracellular Flagellin Detection in Four Mammalian Lineages. Mol Biol Evol 2021; 37:1847-1854. [PMID: 32145026 DOI: 10.1093/molbev/msaa058] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Toll-like receptors (TLRs) play an important role for the innate immune system by detecting pathogen-associated molecular patterns. TLR5 encodes the major extracellular receptor for bacterial flagellin and frequently evolves under positive selection, consistent with coevolutionary arms races between the host and pathogens. Furthermore, TLR5 is inactivated in several vertebrates and a TLR5 stop codon polymorphism is widespread in human populations. Here, we analyzed the genomes of 120 mammals and discovered that TLR5 is convergently lost in four independent lineages, comprising guinea pigs, Yangtze river dolphin, pinnipeds, and pangolins. Validated inactivating mutations, absence of protein-coding transcript expression, and relaxed selection on the TLR5 remnants confirm these losses. PCR analysis further confirmed the loss of TLR5 in the pinniped stem lineage. Finally, we show that TLR11, encoding a second extracellular flagellin receptor, is also absent in these four lineages. Independent losses of TLR5 and TLR11 suggest that a major pathway for detecting flagellated bacteria is not essential for different mammals and predicts an impaired capacity to sense extracellular flagellin.
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Affiliation(s)
- Virag Sharma
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany.,CRTD-DFG Center for Regenerative Therapies Dresden, Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Dresden; Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at University Hospital Carl Gustav Carus and Faculty of Medicine, Technische Universität Dresden, Dresden; German Center for Diabetes Research (DZD), Munich, Neuherberg, Germany
| | - Nikolai Hecker
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany
| | - Felix Walther
- Senckenberg Natural History Collections Dresden, Senckenberg - Leibniz Institution for Biodiversity and Earth System Research, Dresden, Germany
| | - Heiko Stuckas
- Senckenberg Natural History Collections Dresden, Senckenberg - Leibniz Institution for Biodiversity and Earth System Research, Dresden, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany
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45
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Tian R, Geng Y, Yang Y, Seim I, Yang G. Oxidative stress drives divergent evolution of the glutathione peroxidase (GPX) gene family in mammals. Integr Zool 2021; 16:696-711. [PMID: 33417299 DOI: 10.1111/1749-4877.12521] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The molecular basis for adaptations to extreme environments can now be understood by interrogating the ever-increasing number of sequenced genomes. Mammals such as cetaceans, bats, and highland species can protect themselves from oxidative stress, a disruption in the balance of reactive oxygen species, which results in oxidative injury and cell damage. Here, we consider the evolution of the glutathione peroxidase (GPX) family of antioxidant enzymes by interrogating publicly available genome data from 70 mammalian species from all major clades. We identified 8 GPX subclasses ubiquitous to all mammalian groups. Mammalian GPX gene families resolved into the GPX4/7/8 and GPX1/2/3/5/6 groups and are characterized by several instances of gene duplication and loss, indicating a dynamic process of gene birth and death in mammals. Seven of the eight GPX subfamilies (all but GPX7) were under positive selection, with the residues under selection located at or close to active sites or at the dimer interface. We also reveal evidence of a correlation between ecological niches (e.g. high oxidative stress) and the divergent selection and gene copy number of GPX subclasses. Notably, a convergent expansion of GPX1 was observed in several independent lineages of mammals under oxidative stress and may be important for avoiding oxidative damage. Collectively, this study suggests that the GPX gene family has shaped the adaption of mammals to stressful environments.
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Affiliation(s)
- Ran Tian
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China.,Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Yuepan Geng
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Ying Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China.,School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
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46
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Xu W, Zhou X, Fang W, Chen X. Primer development of toll-like receptor genes in the vulnerable Chinese egret (Egretta eulophotes) and its applicability in Ardeidae. CONSERV GENET RESOUR 2020. [DOI: 10.1007/s12686-020-01179-z] [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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47
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Chuang YC, Tseng JC, Yang JX, Liu YL, Yeh DW, Lai CY, Yu GY, Hsu LC, Huang CM, Chuang TH. Toll-Like Receptor 21 of Chicken and Duck Recognize a Broad Array of Immunostimulatory CpG-oligodeoxynucleotide Sequences. Vaccines (Basel) 2020; 8:vaccines8040639. [PMID: 33147756 PMCID: PMC7712946 DOI: 10.3390/vaccines8040639] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/15/2020] [Accepted: 10/29/2020] [Indexed: 12/20/2022] Open
Abstract
CpG-oligodeoxynucleotides (CpG-ODNs) mimicking the function of microbial CpG-dideoxynucleotides containing DNA (CpG-DNA) are potent immune stimuli. The immunostimulatory activity and the species-specific activities of a CpG-ODN depend on its nucleotide sequence properties, including CpG-hexamer motif types, spacing between motifs, nucleotide sequence, and length. Toll-like receptor (TLR) 9 is the cellular receptor for CpG-ODNs in mammalian species, while TLR21 is the receptor in avian species. Mammalian cells lack TLR21, and avian cells lack TLR9; however, both TLRs are expressed in fish cells. While nucleotide sequence properties required for a CpG-ODN to strongly activate mammalian TLR9 and its species-specific activities to different mammalian TLR9s are better studied, CpG-ODN activation of TLR21 is not yet well investigated. Here we characterized chicken and duck TLR21s and investigated their activation by CpG-ODNs. Chicken and duck TLR21s contain 972 and 976 amino acid residues, respectively, and differ from TLR9s as they do not have an undefined region in their ectodomain. Cell-based TLR21 activation assays were established to investigate TLR21 activation by different CpG-ODNs. Unlike grouper TLR21, which was preferentially activated by CpG-ODN with a GTCGTT hexamer motif, chicken and duck TLR21s do not distinguish among different CpG-hexamer motifs. Additionally, these two poultry TLR21s were activated by CpG-ODNs with lengths ranging from 15 to 31 nucleotides and with different spacing between CpG-hexamer motifs. These suggested that compared to mammalian TLR9 and grouper TLR21, chicken and duck TLR21s have a broad CpG-ODN sequence recognition profile. Thus, they could also recognize a wide array of DNA-associated molecular patterns from microbes. Moreover, CpG-ODNs are being investigated as antimicrobial agents and as vaccine adjuvants for different species. This study revealed that there are more optimized CpG-ODNs that can be used in poultry farming as anti-infection agents compared to CpG-ODN choices available for other species.
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Affiliation(s)
- Yu-Chen Chuang
- Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli 35053, Taiwan; (Y.-C.C.); (J.-C.T.); (J.-X.Y.); (Y.-L.L.); (D.-W.Y.)
| | - Jen-Chih Tseng
- Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli 35053, Taiwan; (Y.-C.C.); (J.-C.T.); (J.-X.Y.); (Y.-L.L.); (D.-W.Y.)
| | - Jing-Xing Yang
- Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli 35053, Taiwan; (Y.-C.C.); (J.-C.T.); (J.-X.Y.); (Y.-L.L.); (D.-W.Y.)
| | - Yi-Ling Liu
- Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli 35053, Taiwan; (Y.-C.C.); (J.-C.T.); (J.-X.Y.); (Y.-L.L.); (D.-W.Y.)
| | - Da-Wei Yeh
- Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli 35053, Taiwan; (Y.-C.C.); (J.-C.T.); (J.-X.Y.); (Y.-L.L.); (D.-W.Y.)
| | - Chao-Yang Lai
- Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung 41354, Taiwan;
| | - Guann-Yi Yu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli 35053, Taiwan;
| | - Li-Chung Hsu
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei 10002, Taiwan;
| | - Chun-Ming Huang
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan 32001, Taiwan;
| | - Tsung-Hsien Chuang
- Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli 35053, Taiwan; (Y.-C.C.); (J.-C.T.); (J.-X.Y.); (Y.-L.L.); (D.-W.Y.)
- Program in Environmental and Occupational Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Correspondence: ; Tel.: +886-37-246166 (ext. 37611); Fax: +886-37-568642
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48
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Nandakumar M, Ishtiaq F. Genetic drift and bottleneck do not influence diversity in Toll-like receptor genes at a small spatial scale in a Himalayan passerine. Ecol Evol 2020; 10:12246-12263. [PMID: 33209285 PMCID: PMC7663051 DOI: 10.1002/ece3.6855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/14/2020] [Accepted: 07/29/2020] [Indexed: 12/15/2022] Open
Abstract
Genetic diversity is important for long-term viability of a population. Low genetic diversity reduces persistence and survival of populations and increases susceptibility to diseases. Comparisons of the neutral markers with functional loci such as immune genes [Toll-like receptors; TLR] can provide useful insights into evolutionary potential of a species and how the diversity of pathogens and selection pressures on their hosts are directly linked to their environment. In this study, we compare genetic diversity in neutral (eleven microsatellite loci) and adaptive (seven TLR loci) loci to determine genetic variation in a nonmigratory western Himalayan passerine, the black-throated tit (Aegithalos concinnus), distributed across an elevation gradient with varying degree of pathogen-mediated selection pressure. We further compare the diversity in TLR loci with a high-elevation sister species, the white-throated tit (Aegithalos niveogularis). Our results indicate a lack of population genetic structure in the black-throated tit and signatures of a past bottleneck. In contrast, we found high diversity in TLR loci and locus-specific (TLR7) signatures of pathogen-mediated selection, which was comparable to diversity in the white-throated tit. Levels of diversity at TLR5 locus corresponded very closely with neutral microsatellite variation. We found evidence of positive selection in TLR1LA, TLR5, and TLR7 loci highlighting the importance in pathogen recognition. Our finding demonstrates that reduction in neutral variation does not necessarily lead to reduction in functional genetic diversity and probably helps in revival of population in a widespread species.
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Affiliation(s)
- Mridula Nandakumar
- Centre for Ecological SciencesIndian Institute of ScienceBangaloreIndia
- Present address:
Department of BiologyLund UniversityLundSweden
| | - Farah Ishtiaq
- Centre for Ecological SciencesIndian Institute of ScienceBangaloreIndia
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49
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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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50
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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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