1
|
Gu T, Hu J, Yu L. Evolution and conservation genetics of pangolins. Integr Zool 2024; 19:426-441. [PMID: 38146613 DOI: 10.1111/1749-4877.12796] [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] [Indexed: 12/27/2023]
Abstract
Pangolins (Pholidota, Manidae) are classified as an evolutionarily distinct and globally endangered mammal due to their unique morphology (nail-like scales and a myrmecophagous diet) and being the victim of heavy poaching and worldwide trafficking. As such, pangolins serve as a textbook example for studying the special phenotypic evolutionary adaptations and conservation genetics of an endangered species. Recent years have demonstrated significant advancements in the fields of molecular genetics and genomics, which have translated to a series of important research achievements and breakthroughs concerning the evolution and conservation genetics of pangolins. This review comprehensively presents the hitherto advances in phylogeny, adaptive evolution, conservation genetics, and conservation genomics that are related to pangolins, which will provide an ample understanding of their diversity, molecular adaptation mechanisms, and evolutionary potentials. In addition, we highlight the priority of investigating species/population diversity among pangolins and suggest several avenues of research that are highly relevant for future pangolin conservation.
Collapse
Affiliation(s)
- Tongtong Gu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Jingyang Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| |
Collapse
|
2
|
Deng S, Tian X, Belshaw R, Zhou J, Zhang S, Yang Y, Huang C, Chen W, Qiu H, Choo SW. An RNA-Seq analysis of coronavirus in the skin of the Pangolin. Sci Rep 2024; 14:910. [PMID: 38195813 PMCID: PMC10776870 DOI: 10.1038/s41598-024-51261-x] [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: 10/26/2023] [Accepted: 01/02/2024] [Indexed: 01/11/2024] Open
Abstract
Protection of the Critically Endangered East Asian Pangolin species is hampered by the vulnerability of captive individuals to infection. Studies have previously shown the pangolin to have a unique pseudogenisation of many immunity genes (including IFNE, IFIH1, cGAS, STING, TLR5, and TLR11), and we suspected that these losses could account for this vulnerability. Here we used RNA-Seq data to show the effect of these gene losses on the transcriptional response to a viral skin infection in a deceased pangolin. This virus is very closely related to the one causing the current COVID-19 pandemic in the human population (SARS-CoV2), and we found the most upregulated pathway was the same one previously identified in the lungs of SARS-CoV2-infected humans. As predicted, we found that the pathways downstream of the lost genes were not upregulated. For example, the pseudogenised interferon epsilon (IFNE) is known to be particularly important in epithelial immunity, and we show that interferon-related responses were not upregulated in the infected pangolin skin. We suggest that the pangolin's innate gene pseudogenisation is indeed likely to be responsible for the animal's vulnerability to infection.
Collapse
Affiliation(s)
- Siwei Deng
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang, 325060, China
| | - Xuechen Tian
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang, 325060, China
- Zhejiang Bioinformatics International Science and Technology Cooperation Centre, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang, 325060, China
- Wenzhou Municipal Key Laboratory for Applied Biomedical and Biopharmaceutical Informatics, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang, 325060, China
| | - Robert Belshaw
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang, 325060, China
| | - Jinfeng Zhou
- China Biodiversity Conservation and Green Development Foundation (CBCGDF), Empark International Apartment, No. 69, Banding Road, Haidian District, Beijing, China
| | - Siyuan Zhang
- China Biodiversity Conservation and Green Development Foundation (CBCGDF), Empark International Apartment, No. 69, Banding Road, Haidian District, Beijing, China
| | - Yixin Yang
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang, 325060, China
- Zhejiang Bioinformatics International Science and Technology Cooperation Centre, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang, 325060, China
- Wenzhou Municipal Key Laboratory for Applied Biomedical and Biopharmaceutical Informatics, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang, 325060, China
- Dorothy and George Hennings College of Science, Mathematics and Technology, Kean University, 1000 Morris Ave, Union, NJ, 07083, USA
| | - Chang Huang
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang, 325060, China
| | - Weikang Chen
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang, 325060, China
| | - Hailu Qiu
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang, 325060, China
| | - Siew Woh Choo
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang, 325060, China.
- Zhejiang Bioinformatics International Science and Technology Cooperation Centre, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang, 325060, China.
- Wenzhou Municipal Key Laboratory for Applied Biomedical and Biopharmaceutical Informatics, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang, 325060, China.
- Dorothy and George Hennings College of Science, Mathematics and Technology, Kean University, 1000 Morris Ave, Union, NJ, 07083, USA.
| |
Collapse
|
3
|
Pinto B, Valente R, Caramelo F, Ruivo R, Castro LFC. Decay of Skin-Specific Gene Modules in Pangolins. J Mol Evol 2023:10.1007/s00239-023-10118-z. [PMID: 37249590 DOI: 10.1007/s00239-023-10118-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 05/10/2023] [Indexed: 05/31/2023]
Abstract
The mammalian skin exhibits a rich spectrum of evolutionary adaptations. The pilosebaceous unit, composed of the hair shaft, follicle, and the sebaceous gland, is the most striking synapomorphy. The evolutionary diversification of mammals across different ecological niches was paralleled by the appearance of an ample variety of skin modifications. Pangolins, order Pholidota, exhibit keratin-derived scales, one of the most iconic skin appendages. This formidable armor is intended to serve as a deterrent against predators. Surprisingly, while pangolins have hair on their abdomens, the occurrence of sebaceous and sweat glands is contentious. Here, we explore various molecular modules of skin physiology in four pangolin genomes, including that of sebum production. We show that genes driving wax monoester formation, Awat1/2, show patterns of inactivation in the stem pangolin branch, while the triacylglycerol synthesis gene Dgat2l6 seems independently eroded in the African and Asian clades. In contrast, Elovl3 implicated in the formation of specific neutral lipids required for skin barrier function is intact and expressed in the pangolin skin. An extended comparative analysis shows that genes involved in skin pathogen defense and structural integrity of keratinocyte layers also show inactivating mutations: associated with both ancestral and independent pseudogenization events. Finally, we deduce that the suggested absence of sweat glands is not paralleled by the inactivation of the ATP-binding cassette transporter Abcc11, as previously described in Cetacea. Our findings reveal the sophisticated and complex history of gene retention and loss as key mechanisms in the evolution of the highly modified mammalian skin phenotypes.
Collapse
Affiliation(s)
- Bernardo Pinto
- CIMAR/CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto (U. Porto), Rua Do Campo Alegre S/N, 4169-007, Porto, Portugal
| | - Raul Valente
- CIMAR/CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto (U. Porto), Rua Do Campo Alegre S/N, 4169-007, Porto, Portugal
| | - Filipe Caramelo
- CIMAR/CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto (U. Porto), Rua Do Campo Alegre S/N, 4169-007, Porto, Portugal
| | - Raquel Ruivo
- CIMAR/CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal.
| | - L Filipe C Castro
- CIMAR/CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal.
- Department of Biology, Faculty of Sciences, University of Porto (U. Porto), Rua Do Campo Alegre S/N, 4169-007, Porto, Portugal.
| |
Collapse
|
4
|
Eckhart L, Sipos W. Differential Loss of OAS Genes Indicates Diversification of Antiviral Immunity in Mammals. Vaccines (Basel) 2023; 11:vaccines11020419. [PMID: 36851296 PMCID: PMC9964502 DOI: 10.3390/vaccines11020419] [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: 12/31/2022] [Revised: 02/04/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
One of the main mechanisms of inducing an antiviral response depends on 2'-5'-oligoadenylate synthetases (OAS), which sense double-stranded RNA in the cytoplasm and activate RNase L. Mutations leading to the loss of functional OAS1 and OAS2 genes have been identified as important modifiers of the human immune response against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we performed comparative genomics to search for inactivating mutations of OAS genes in other species of mammals and to establish a model for the diversifying evolution of the OAS gene family. We found that a recombination of the OAS and OAS-like (OASL) loci has led to the loss of OAS2 in camelids, which also lack OAS3. Both paralogs of OASL and OAS3 are absent in Asian pangolins. An evolutionarily ancient OAS paralog, which we tentatively name OAS4, has been lost in pangolins, bats and humans. A previously unknown OAS gene, tentatively named OAS5, is present in Yangochiroptera, a suborder of bats. These differences in the OAS gene repertoire may affect innate immune responses to coronaviruses and other RNA viruses.
Collapse
Affiliation(s)
- Leopold Eckhart
- Department of Dermatology, Medical University of Vienna, 1090 Vienna, Austria
- Correspondence:
| | - Wolfgang Sipos
- Clinical Department for Farm Animals and Herd Management, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| |
Collapse
|
5
|
Post-Translational Modifications of cGAS-STING: A Critical Switch for Immune Regulation. Cells 2022; 11:cells11193043. [PMID: 36231006 PMCID: PMC9563579 DOI: 10.3390/cells11193043] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/13/2022] [Accepted: 09/24/2022] [Indexed: 12/02/2022] Open
Abstract
Innate immune mechanisms initiate immune responses via pattern-recognition receptors (PRRs). Cyclic GMP-AMP synthase (cGAS), a member of the PRRs, senses diverse pathogenic or endogenous DNA and activates innate immune signaling pathways, including the expression of stimulator of interferon genes (STING), type I interferon, and other inflammatory cytokines, which, in turn, instructs the adaptive immune response development. This groundbreaking discovery has rapidly advanced research on host defense, cancer biology, and autoimmune disorders. Since cGAS/STING has enormous potential in eliciting an innate immune response, understanding its functional regulation is critical. As the most widespread and efficient regulatory mode of the cGAS-STING pathway, post-translational modifications (PTMs), such as the covalent linkage of functional groups to amino acid chains, are generally considered a regulatory mechanism for protein destruction or renewal. In this review, we discuss cGAS-STING signaling transduction and its mechanism in related diseases and focus on the current different regulatory modalities of PTMs in the control of the cGAS-STING-triggered innate immune and inflammatory responses.
Collapse
|
6
|
Bibo-Verdugo B, Joglekar I, Karadi Giridhar MN, Ramirez ML, Snipas SJ, Clark AC, Poreba M, Salvesen GS. Resurrection of an ancient inflammatory locus reveals switch to caspase-1 specificity on a caspase-4 scaffold. J Biol Chem 2022; 298:101931. [PMID: 35427646 PMCID: PMC9144055 DOI: 10.1016/j.jbc.2022.101931] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 04/05/2022] [Accepted: 04/08/2022] [Indexed: 12/02/2022] Open
Abstract
Pyroptosis is a mechanism of inflammatory cell death mediated by the activation of the prolytic protein gasdermin D by caspase-1, caspase-4, and caspase-5 in human, and caspase-1 and caspase-11 in mouse. In addition, caspase-1 amplifies inflammation by proteolytic activation of cytokine interleukin-1β (IL-1β). Modern mammals of the order Carnivora lack the caspase-1 catalytic domain but express an unusual version of caspase-4 that can activate both gasdermin D and IL-1β. Seeking to understand the evolutionary origin of this caspase, we utilized the large amount of data available in public databases to perform ancestral sequence reconstruction of an inflammatory caspase of a Carnivora ancestor. We expressed the catalytic domain of this putative ancestor in Escherichia coli, purified it, and compared its substrate specificity on synthetic and protein substrates to extant caspases. We demonstrated that it activates gasdermin D but has reduced ability to activate IL-1β. Our reconstruction suggests that caspase-1 was lost in a Carnivora ancestor, perhaps upon a selective pressure for which the generation of biologically active IL-1β by caspase-1 was detrimental. We speculate that later, a Carnivora encountered selective pressures that required the production of IL-1β, and caspase-4 subsequently gained this activity. This hypothesis would explain why extant Carnivora possess an inflammatory caspase with caspase-1 catalytic function placed on a caspase-4 scaffold.
Collapse
Affiliation(s)
| | - Isha Joglekar
- Department of Biology, University of Texas at Arlington, Arlington, Texas, USA
| | | | - Monica L Ramirez
- Department of Pharmacology, University of California San Diego, La Jolla, California, USA
| | - Scott J Snipas
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - A Clay Clark
- Department of Biology, University of Texas at Arlington, Arlington, Texas, USA
| | - Marcin Poreba
- Department of Bioorganic Chemistry, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Guy S Salvesen
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA.
| |
Collapse
|
7
|
Zhao Y, Seluanov A, Gorbunova V. Revelations About Aging and Disease from Unconventional Vertebrate Model Organisms. Annu Rev Genet 2021; 55:135-159. [PMID: 34416119 DOI: 10.1146/annurev-genet-071719-021009] [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: 11/09/2022]
Abstract
Aging is a major risk factor for multiple diseases. Understanding the underlying mechanisms of aging would help to delay and prevent age-associated diseases. Short-lived model organisms have been extensively used to study the mechanisms of aging. However, these short-lived species may be missing the longevity mechanisms that are needed to extend the lifespan of an already long-lived species such as humans. Unconventional long-lived animal species are an excellent resource to uncover novel mechanisms of longevity and disease resistance. Here, we review mechanisms that evolved in nonmodel vertebrate species to counteract age-associated diseases. Some antiaging mechanisms are conserved across species; however, various nonmodel species also evolved unique mechanisms to delay aging and prevent disease. This variety of antiaging mechanisms has evolved due to the remarkably diverse habitats and behaviors of these species. We propose that exploring a wider range of unconventional vertebrates will provide important resources to study antiaging mechanisms that are potentially applicable to humans.
Collapse
Affiliation(s)
- Yang Zhao
- Department of Biology, University of Rochester, Rochester, New York 14627, USA; ,
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, New York 14627, USA; ,
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, New York 14627, USA; ,
| |
Collapse
|
8
|
Salova M, Sipos W, Tschachler E, Eckhart L. NOD2 and reproduction-associated NOD-like receptors have been lost during the evolution of pangolins. Immunogenetics 2021; 74:261-268. [PMID: 34725731 PMCID: PMC8560141 DOI: 10.1007/s00251-021-01230-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 10/20/2021] [Indexed: 12/14/2022]
Abstract
NOD-like receptors (NLRs) are sensors of pathogen-associated molecular patterns with critical roles in the control of immune responses and programmed cell death. Recent studies have revealed inter-species differences in mammalian innate immune genes and a particular degeneration of nucleic acid sensing pathways in pangolins, which are currently investigated as potential hosts for zoonotic pathogens. Here, we used comparative genomics to determine which NLR genes are conserved or lost in pangolins and related mammals. We show that NOD2, which is implicated in sensing bacterial muramyl dipeptide and viral RNA, is a pseudogene in pangolins, but not in any other mammalian species investigated. NLRC4 and NAIP are absent in pangolins and canine carnivorans, suggesting convergent loss of cytoplasmic sensing of bacterial flagellin in these taxa. Among NLR family pyrin domain containing proteins (NLRPs), skin barrier-related NLRP10 has been lost in pangolins after the evolutionary divergence from Carnivora. Strikingly, pangolins lack all NLRPs associated with reproduction (germ cells and embryonic development) in other mammals, i.e., NLRP2, 4, 5, 7, 8, 9, 11, 13, and 14. Taken together, our study shows a massive degeneration of NLR genes in pangolins and suggests that these endangered mammals may have unique adaptations of innate immunity and reproductive cell biology.
Collapse
Affiliation(s)
- Margarita Salova
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Wolfgang Sipos
- Clinical Department for Farm Animals and Herd Management, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Erwin Tschachler
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Leopold Eckhart
- Department of Dermatology, Medical University of Vienna, Vienna, Austria.
| |
Collapse
|
9
|
Verrier ER, Langevin C. Cyclic Guanosine Monophosphate-Adenosine Monophosphate Synthase (cGAS), a Multifaceted Platform of Intracellular DNA Sensing. Front Immunol 2021; 12:637399. [PMID: 33708225 PMCID: PMC7940176 DOI: 10.3389/fimmu.2021.637399] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 01/28/2021] [Indexed: 12/17/2022] Open
Abstract
Innate immune pathways are the first line of cellular defense against pathogen infections ranging from bacteria to Metazoa. These pathways are activated following the recognition of pathogen associated molecular patterns (PAMPs) by membrane and cytosolic pattern recognition receptors. In addition, some of these cellular sensors can also recognize endogenous danger-associated molecular patterns (DAMPs) arising from damaged or dying cells and triggering innate immune responses. Among the cytosolic nucleic acid sensors, the cyclic guanosine monophosphate–adenosine monophosphate (cGAMP) synthase (cGAS) plays an essential role in the activation of the type I interferon (IFNs) response and the production of pro-inflammatory cytokines. Indeed, upon nucleic acid binding, cGAS synthesizes cGAMP, a second messenger mediating the activation of the STING signaling pathway. The functional conservation of the cGAS-STING pathway during evolution highlights its importance in host cellular surveillance against pathogen infections. Apart from their functions in immunity, cGAS and STING also play major roles in nuclear functions and tumor development. Therefore, cGAS-STING is now considered as an attractive target to identify novel biomarkers and design therapeutics for auto-inflammatory and autoimmune disorders as well as infectious diseases and cancer. Here, we review the current knowledge about the structure of cGAS and the evolution from bacteria to Metazoa and present its main functions in defense against pathogens and cancer, in connection with STING. The advantages and limitations of in vivo models relevant for studying the cGAS-STING pathway will be discussed for the notion of species specificity and in the context of their integration into therapeutic screening assays targeting cGAG and/or STING.
Collapse
Affiliation(s)
- Eloi R Verrier
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, Strasbourg, France
| | | |
Collapse
|
10
|
Stegmann UE. Medical toolkit organisms and Covid-19. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2021; 43:14. [PMID: 33528761 PMCID: PMC7851655 DOI: 10.1007/s40656-021-00371-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/15/2021] [Indexed: 06/12/2023]
Abstract
The Covid-19 pandemic has intensified interest in animals with superior antiviral defences. I argue that the role of such animals in biomedical research contrasts with the role of disease models.
Collapse
Affiliation(s)
- Ulrich E Stegmann
- School of Divinity, History and Philosophy, University of Aberdeen, 50-52 College Bounds, Aberdeen, AB24 3DS, UK.
| |
Collapse
|
11
|
Cui H, Zhang L. Key Components of Inflammasome and Pyroptosis Pathways Are Deficient in Canines and Felines, Possibly Affecting Their Response to SARS-CoV-2 Infection. Front Immunol 2021; 11:592622. [PMID: 33584656 PMCID: PMC7876337 DOI: 10.3389/fimmu.2020.592622] [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: 09/02/2020] [Accepted: 12/31/2020] [Indexed: 12/13/2022] Open
Abstract
SARS-CoV-2 causes the ongoing COVID-19 pandemic. Natural SARS-COV-2 infection has been detected in dogs, cats and tigers. However, the symptoms in canines and felines were mild. The underlying mechanisms are unknown. Excessive activation of inflammasome pathways can trigger cytokine storm and severe damage to host. In current study, we performed a comparative genomics study of key components of inflammasome and pyroptosis pathways in dogs, cats and tigers. Cats and tigers do not have AIM2 and NLRP1. Dogs do not contain AIM2, and encode a short form of NLRC4. The activation sites in GSDMB were absent in dogs, cats and tigers, while GSDME activation sites in cats and tigers were abolished. We propose that deficiencies of inflammasome and pyroptosis pathways might provide an evolutionary advantage against SARS-CoV-2 by reducing cytokine storm-induced host damage. Our findings will shed important lights on the mild symptoms in canines and felines infected with SARS-CoV-2.
Collapse
Affiliation(s)
- Haoran Cui
- Institute of Basic Medicine, The First Affiliated Hospital of Shandong First Medical University, Jinan, China.,Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Leiliang Zhang
- Institute of Basic Medicine, The First Affiliated Hospital of Shandong First Medical University, Jinan, China.,Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| |
Collapse
|
12
|
MicroRNAs for Virus Pathogenicity and Host Responses, Identified in SARS-CoV-2 Genomes, May Play Roles in Viral-Host Co-Evolution in Putative Zoonotic Host Species. Viruses 2021; 13:v13010117. [PMID: 33467206 PMCID: PMC7830670 DOI: 10.3390/v13010117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/07/2021] [Accepted: 01/13/2021] [Indexed: 12/12/2022] Open
Abstract
Our recent study identified seven key microRNAs (miR-8066, 5197, 3611, 3934-3p, 1307-3p, 3691-3p, 1468-5p) similar between SARS-CoV-2 and the human genome, pointing at miR-related mechanisms in viral entry and the regulatory effects on host immunity. To identify the putative roles of these miRs in zoonosis, we assessed their conservation, compared with humans, in some key wild and domestic animal carriers of zoonotic viruses, including bat, pangolin, pig, cow, rat, and chicken. Out of the seven miRs under study, miR-3611 was the most strongly conserved across all species; miR-5197 was the most conserved in pangolin, pig, cow, bat, and rat; miR-1307 was most strongly conserved in pangolin, pig, cow, bat, and human; miR-3691-3p in pangolin, cow, and human; miR-3934-3p in pig and cow, followed by pangolin and bat; miR-1468 was most conserved in pangolin, pig, and bat; while miR-8066 was most conserved in pangolin and pig. In humans, miR-3611 and miR-1307 were most conserved, while miR-8066, miR-5197, miR-3334-3p and miR-1468 were least conserved, compared with pangolin, pig, cow, and bat. Furthermore, we identified that changes in the miR-5197 nucleotides between pangolin and human can generate three new miRs, with differing tissue distribution in the brain, lung, intestines, lymph nodes, and muscle, and with different downstream regulatory effects on KEGG pathways. This may be of considerable importance as miR-5197 is localized in the spike protein transcript area of the SARS-CoV-2 genome. Our findings may indicate roles for these miRs in viral–host co-evolution in zoonotic hosts, particularly highlighting pangolin, bat, cow, and pig as putative zoonotic carriers, while highlighting the miRs’ roles in KEGG pathways linked to viral pathogenicity and host responses in humans. This in silico study paves the way for investigations into the roles of miRs in zoonotic disease.
Collapse
|
13
|
Shankar EM, Che KF, Yong YK, Girija ASS, Velu V, Ansari AW, Larsson M. Asymptomatic SARS-CoV-2 infection: is it all about being refractile to innate immune sensing of viral spare-parts?-Clues from exotic animal reservoirs. Pathog Dis 2021; 79:ftaa076. [PMID: 33289808 PMCID: PMC7799061 DOI: 10.1093/femspd/ftaa076] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 12/04/2020] [Indexed: 01/08/2023] Open
Abstract
A vast proportion of coronavirus disease 2019 (COVID-19) individuals remain asymptomatic and can shed severe acute respiratory syndrome (SARS-CoV) type 2 virus to transmit the infection, which also explains the exponential increase in the number of COVID-19 cases globally. Furthermore, the rate of recovery from clinical COVID-19 in certain pockets of the globe is surprisingly high. Based on published reports and available literature, here, we speculated a few immunovirological mechanisms as to why a vast majority of individuals remain asymptomatic similar to exotic animal (bats and pangolins) reservoirs that remain refractile to disease development despite carrying a huge load of diverse insidious viral species, and whether such evolutionary advantage would unveil therapeutic strategies against COVID-19 infection in humans. Understanding the unique mechanisms that exotic animal species employ to achieve viral control, as well as inflammatory regulation, appears to hold key clues to the development of therapeutic versatility against COVID-19.
Collapse
MESH Headings
- Animals
- Animals, Exotic/virology
- Asymptomatic Diseases
- COVID-19/genetics
- COVID-19/immunology
- COVID-19/transmission
- COVID-19/virology
- Chiroptera/virology
- Cytokine Release Syndrome/genetics
- Cytokine Release Syndrome/immunology
- Cytokine Release Syndrome/prevention & control
- Cytokine Release Syndrome/virology
- Disease Reservoirs
- Eutheria/virology
- Gene Expression
- Host Specificity
- Humans
- Immune Tolerance
- Immunity, Innate
- Interferon-beta/deficiency
- Interferon-beta/genetics
- Interferon-beta/immunology
- Killer Cells, Natural/immunology
- Killer Cells, Natural/virology
- Monocytes/immunology
- Monocytes/virology
- NLR Family, Pyrin Domain-Containing 3 Protein/deficiency
- NLR Family, Pyrin Domain-Containing 3 Protein/genetics
- NLR Family, Pyrin Domain-Containing 3 Protein/immunology
- Receptors, KIR/deficiency
- Receptors, KIR/genetics
- Receptors, KIR/immunology
- Receptors, NK Cell Lectin-Like/deficiency
- Receptors, NK Cell Lectin-Like/genetics
- Receptors, NK Cell Lectin-Like/immunology
- SARS-CoV-2/pathogenicity
- Tumor Necrosis Factor-alpha/deficiency
- Tumor Necrosis Factor-alpha/genetics
- Tumor Necrosis Factor-alpha/immunology
- Zoonoses/genetics
- Zoonoses/immunology
- Zoonoses/transmission
- Zoonoses/virology
Collapse
Affiliation(s)
- Esaki M Shankar
- Infection Biology, Department of Life Sciences, Central University of Tamil Nadu, Neelakudi, Thiruvarur 610005, India
| | - Karlhans F Che
- Unit for Lung and Airway Research, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Yean K Yong
- Laboratory Centre, Xiamen University, Sepang, Malaysia
| | - A S Smiline Girija
- Department of Microbiology, Saveetha Dental College and Hospital, Chennai, India
| | - Vijayakumar Velu
- Division of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA USA
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Abdul W Ansari
- Sharjah Institute of Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Marie Larsson
- Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| |
Collapse
|
14
|
Zahid A, Ismail H, Li B, Jin T. Molecular and Structural Basis of DNA Sensors in Antiviral Innate Immunity. Front Immunol 2020; 11:613039. [PMID: 33329609 PMCID: PMC7734173 DOI: 10.3389/fimmu.2020.613039] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 11/02/2020] [Indexed: 12/30/2022] Open
Abstract
DNA viruses are a source of great morbidity and mortality throughout the world by causing many diseases; thus, we need substantial knowledge regarding viral pathogenesis and the host’s antiviral immune responses to devise better preventive and therapeutic strategies. The innate immune system utilizes numerous germ-line encoded receptors called pattern-recognition receptors (PRRs) to detect various pathogen-associated molecular patterns (PAMPs) such as viral nucleic acids, ultimately resulting in antiviral immune responses in the form of proinflammatory cytokines and type I interferons. The immune-stimulatory role of DNA is known for a long time; however, DNA sensing ability of the innate immune system was unraveled only recently. At present, multiple DNA sensors have been proposed, and most of them use STING as a key adaptor protein to exert antiviral immune responses. In this review, we aim to provide molecular and structural underpinnings on endosomal DNA sensor Toll-like receptor 9 (TLR9) and multiple cytosolic DNA sensors including cyclic GMP-AMP synthase (cGAS), interferon-gamma inducible 16 (IFI16), absent in melanoma 2 (AIM2), and DNA-dependent activator of IRFs (DAI) to provide new insights on their signaling mechanisms and physiological relevance. We have also addressed less well-understood DNA sensors such as DEAD-box helicase DDX41, RNA polymerase III (RNA pol III), DNA-dependent protein kinase (DNA-PK), and meiotic recombination 11 homolog A (MRE11). By comprehensive understanding of molecular and structural aspects of DNA-sensing antiviral innate immune signaling pathways, potential new targets for viral and autoimmune diseases can be identified.
Collapse
Affiliation(s)
- Ayesha Zahid
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.,Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Hazrat Ismail
- MOE Key Laboratory for Cellular Dynamics & Anhui Key Laboratory for Chemical Biology, CAS Center for Excellence in Molecular Cell Science, Hefei National Science Center for Physical Sciences at Microscale & University of Science and Technology of China, Hefei, China
| | - Bofeng Li
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.,Department of Medical Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Tengchuan Jin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.,Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.,CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Science, Shanghai, China
| |
Collapse
|
15
|
Wu Y, Li S. Role of Post-Translational Modifications of cGAS in Innate Immunity. Int J Mol Sci 2020; 21:ijms21217842. [PMID: 33105828 PMCID: PMC7660100 DOI: 10.3390/ijms21217842] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/18/2020] [Accepted: 10/20/2020] [Indexed: 12/23/2022] Open
Abstract
Cyclic GMP–AMP synthase (cGAS) is the synthase that generates the second messenger cyclic GMP–AMP (cGAMP) upon DNA binding. cGAS was first discovered as the cytosolic DNA sensor that detects DNA exposed in the cytoplasm either from pathogens or cellular damage. Activated cGAS instigates the signaling cascades to activate type I interferon (IFN) expression, critical for host defense and autoimmune diseases. In addition, cGAS plays a role in senescence, DNA repair, apoptosis, and tumorigenesis. Recently, various post-translational modifications (PTMs) of cGAS have been reported, such as phosphorylation, ubiquitination, acetylation, glutamylation, and sumoylation. These PTMs profoundly affect cGAS functions. Thus, here we review the recent reported PTMs of cGAS and how these PTMs regulate cGAS enzymatic activity, DNA binding, and protein stability, and discuss the potential future directions.
Collapse
Affiliation(s)
| | - Shitao Li
- Correspondence: ; Tel.: +1-504-988-2203
| |
Collapse
|
16
|
Li HM, Liu P, Zhang XJ, Li LM, Jiang HY, Yan H, Hou FH, Chen JP. Combined proteomics and transcriptomics reveal the genetic basis underlying the differentiation of skin appendages and immunity in pangolin. Sci Rep 2020; 10:14566. [PMID: 32884035 PMCID: PMC7471334 DOI: 10.1038/s41598-020-71513-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 08/17/2020] [Indexed: 11/18/2022] Open
Abstract
Pangolin (Mains javanica) is an interesting endangered mammal with special morphological characteristics. Here, we applied proteomics and transcriptomics to explore the differentiation of pangolin skin appendages at two developmental stages and to compare gene expression profiles between abdomen hair and dorsal scale tissues. We identified 4,311 genes and 91 proteins differentially expressed between scale-type and hair-type tissue, of which 6 genes were shared by the transcriptome and proteome. Differentiation altered the abundance of hundreds of proteins and mRNA in the two types of skin appendages, many of which are involved in keratinocyte differentiation, epidermal cell differentiation, and multicellular organism development based on GO enrichment analysis, and FoxO, MAPK, and p53 signalling pathways based on KEGG enrichment analysis. DEGs in scale-type tissues were also significantly enriched in immune-related terms and pathways compared with that in hair-type tissues. Thus, we propose that pangolins have a normal skin innate immune system. Compared with the abdomen, the back skin of pangolins had more genes involved in the regulation of immune function, which may be an adaptive adjustment for the vulnerability of scaly skin to infection and injury. This investigation provides a scientific basis for the study of development and immunity of pangolin skin, which may be helpful in the protection of wild pangolin in China.
Collapse
Affiliation(s)
- Hui-Ming Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, 510260, China
| | - Ping Liu
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, 510260, China
| | - Xiu-Juan Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, 510260, China
| | - Lin-Miao Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, 510260, China
| | - Hai-Ying Jiang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, 510260, China
| | - Hua Yan
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, Guangdong Province, China
| | - Fang-Hui Hou
- Guangdong Provincial Wildlife Rescue Centre, Guangzhou, Guangdong Province, China
| | - Jin-Ping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, 510260, China.
| |
Collapse
|