Most cited article - PubMed ID 26283656
Hidden genes in birds
BACKGROUND: Interferon regulatory factors (IRFs) are a family of transcription factors with important functions in immunity. The genomes of most vertebrates encode ten IRF genes. IRF3 and IRF9 have key roles in interferon (IFN) induction and signaling. Most of our knowledge about the IFN pathways originates from the study of the mammalian IFN system, and the description of the corresponding avian components is not as complete. Both IRF3 and IRF9 were considered missing from the chicken genome and from the genomes of other avian species. RESULTS: Here we describe multiple avian IRF3 and IRF9 genes, all with difficult GC-rich sequence context that prevented their earlier characterization. IRF3 orthologs are narrowly distributed and are present in the avian infraclass Palaeognathae. In contrast, IRF9 orthologs were found in most avian species, with the exception of the order Galliformes. In about half of the avian orders, IRF9 was located in noncanonical chromosomal positions, indicating past translocations. Phylogenetic analysis confirmed the correct orthology of all newly described IRFs. We further performed experiments using duck IRF9, confirming its role in the IFN pathway. IRF9 knockout in duck fibroblasts decreases the induction of IFN-stimulated genes (ISGs). Full induction of ISGs in duck cells requires both an intact IRF9 and a canonical IFN-stimulated response element. Lastly, intact IRF9 is needed for IFN-mediated protection of duck cells against the vesicular stomatitis virus-induced cytopathicity. CONCLUSIONS: The identification of avian IRFs fills an important gap in our understanding of avian immunology and brings new questions related to the evolution of the IRF family.
- Keywords
- Avian genome, Gene loss, Interferon regulatory factors, Interferon signaling,
- MeSH
- Phylogeny MeSH
- Interferon Regulatory Factors * genetics metabolism MeSH
- Interferon Regulatory Factor-3 * genetics metabolism MeSH
- Interferon-Stimulated Gene Factor 3, gamma Subunit * genetics metabolism MeSH
- Ducks genetics MeSH
- Chickens genetics MeSH
- Avian Proteins * genetics metabolism MeSH
- Birds * genetics MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
- Names of Substances
- Interferon Regulatory Factors * MeSH
- Interferon Regulatory Factor-3 * MeSH
- Interferon-Stimulated Gene Factor 3, gamma Subunit * MeSH
- Avian Proteins * MeSH
Linker for activation of T cells (LAT) plays a key role in T-cell antigenic signaling in mammals. Accordingly, LAT orthologues were identified in the majority of vertebrates. However, LAT orthologues were not identified in most birds. In this study, we show that LAT gene is present in genomes of multiple extant birds. It was not properly assembled previously because of its GC-rich content. LAT expression is enriched in lymphoid organs in chicken. The analysis of the coding sequences revealed a strong conservation of key signaling motifs in LAT between chicken and human. Overall, our data indicate that mammalian and avian LAT genes are functional homologues with a common role in T-cell signaling.
- MeSH
- Adaptor Proteins, Signal Transducing * genetics MeSH
- Phosphoproteins metabolism MeSH
- Genome MeSH
- Chickens genetics metabolism MeSH
- Humans MeSH
- Membrane Proteins * genetics MeSH
- Mammals genetics MeSH
- T-Lymphocytes metabolism MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Names of Substances
- Adaptor Proteins, Signal Transducing * MeSH
- Phosphoproteins MeSH
- Membrane Proteins * MeSH
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.
- Keywords
- avian genome, gene loss, innate immunity, viral sensors,
- MeSH
- Antiviral Agents MeSH
- DEAD Box Protein 58 genetics metabolism MeSH
- Immunity, Innate MeSH
- Birds virology MeSH
- RNA Helicases MeSH
- RNA Viruses * physiology MeSH
- RNA * MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Names of Substances
- Antiviral Agents MeSH
- DEAD Box Protein 58 MeSH
- RNA Helicases MeSH
- RNA * MeSH
Tetherin/BST-2 is an antiviral protein that blocks the release of enveloped viral particles by linking them to the membrane of producing cells. At first, BST-2 genes were described only in humans and other mammals. Recent work identified BST-2 orthologs in nonmammalian vertebrates, including birds. Here, we identify the BST-2 sequence in domestic chicken (Gallus gallus) for the first time and demonstrate its activity against avian sarcoma and leukosis virus (ASLV). We generated a BST-2 knockout in chicken cells and showed that BST-2 is a major determinant of an interferon-induced block of ASLV release. Ectopic expression of chicken BST-2 blocks the release of ASLV in chicken cells and of human immunodeficiency virus type 1 (HIV-1) in human cells. Using metabolic labeling and pulse-chase analysis of HIV-1 Gag proteins, we verified that chicken BST-2 blocks the virus at the release stage. Furthermore, we describe BST-2 orthologs in multiple avian species from 12 avian orders. Previously, some of these species were reported to lack BST-2, highlighting the difficulty of identifying sequences of this extremely variable gene. We analyzed BST-2 genes in the avian orders Galliformes and Passeriformes and showed that they evolve under positive selection. This indicates that avian BST-2 is involved in host-virus evolutionary arms races and suggests that BST-2 antagonists exist in some avian viruses. In summary, we show that chicken BST-2 has the potential to act as a restriction factor against ASLV. Characterizing the interaction of avian BST-2 with avian viruses is important in understanding innate antiviral defenses in birds.IMPORTANCE Birds are important hosts of viruses that have the potential to cause zoonotic infections in humans. However, only a few antiviral genes (called viral restriction factors) have been described in birds, mostly because birds lack counterparts of highly studied mammalian restriction factors. Tetherin/BST-2 is a restriction factor, originally described in humans, that blocks the release of newly formed virus particles from infected cells. Recent work identified BST-2 in nonmammalian vertebrate species, including birds. Here, we report the BST-2 sequence in domestic chicken and describe its antiviral activity against a prototypical avian retrovirus, avian sarcoma and leukosis virus (ASLV). We also identify BST-2 genes in multiple avian species and show that they evolve rapidly in birds, which is an important indication of their relevance for antiviral defense. Analysis of avian BST-2 genes will shed light on defense mechanisms against avian viral pathogens.
- Keywords
- avian retrovirus, chicken, restriction factor, tetherin,
- MeSH
- Bone Marrow Stromal Antigen 2 genetics immunology MeSH
- Cell Line MeSH
- Fibroblasts immunology virology MeSH
- Galliformes genetics immunology virology MeSH
- gag Gene Products, Human Immunodeficiency Virus genetics immunology MeSH
- HEK293 Cells MeSH
- HIV-1 genetics immunology MeSH
- Host-Pathogen Interactions genetics immunology MeSH
- Humans MeSH
- Evolution, Molecular * MeSH
- Passeriformes genetics immunology virology MeSH
- Avian Proteins genetics immunology MeSH
- Sarcoma, Avian genetics immunology virology MeSH
- Gene Expression Regulation MeSH
- Virus Replication MeSH
- Amino Acid Sequence MeSH
- Sequence Homology, Amino Acid MeSH
- Sequence Alignment MeSH
- Selection, Genetic MeSH
- Signal Transduction MeSH
- Virus Release MeSH
- Avian Sarcoma Viruses genetics immunology pathogenicity MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Research Support, N.I.H., Extramural MeSH
- Research Support, N.I.H., Intramural MeSH
- Names of Substances
- Bone Marrow Stromal Antigen 2 MeSH
- gag Gene Products, Human Immunodeficiency Virus MeSH
- Avian Proteins MeSH
It has now been more than two years since we said our last goodbye to Jan Svoboda (14 [...].
Tumor necrosis factor-α (TNF-α) is a pleiotropic cytokine playing critical roles in host defense and acute and chronic inflammation. It has been described in fish, amphibians, and mammals but was considered to be absent in the avian genomes. Here, we report on the identification and functional characterization of the avian ortholog. The chicken TNF-α (chTNF-α) is encoded by a highly GC-rich gene, whose product shares with its mammalian counterpart 45% homology in the extracellular part displaying the characteristic TNF homology domain. Orthologs of chTNF-α were identified in the genomes of 12 additional avian species including Palaeognathae and Neognathae, and the synteny of the closely adjacent loci with mammalian TNF-α orthologs was demonstrated in the crow (Corvus cornix) genome. In addition to chTNF-α, we obtained full sequences for homologs of TNF-α receptors 1 and 2 (TNFR1, TNFR2). chTNF-α mRNA is strongly induced by lipopolysaccharide (LPS) stimulation of monocyte derived, splenic and bone marrow macrophages, and significantly upregulated in splenic tissue in response to i.v. LPS treatment. Activation of T-lymphocytes by TCR crosslinking induces chTNF-α expression in CD4+ but not in CD8+ cells. To gain insights into its biological activity, we generated recombinant chTNF-α in eukaryotic and prokaryotic expression systems. Both, the full-length cytokine and the extracellular domain rapidly induced an NFκB-luciferase reporter in stably transfected CEC-32 reporter cells. Collectively, these data provide strong evidence for the existence of a fully functional TNF-α/TNF-α receptor system in birds thus filling a gap in our understanding of the evolution of cytokine systems.
- Keywords
- avian, biological activity, chicken, missing gene, tumor necrosis factor-α, tumor necrosis factor-α receptors,
- MeSH
- CD4-Positive T-Lymphocytes immunology MeSH
- GC Rich Sequence genetics MeSH
- Cloning, Molecular MeSH
- Cells, Cultured MeSH
- Chickens immunology MeSH
- Humans MeSH
- Macrophages immunology MeSH
- NF-kappa B metabolism MeSH
- Palaeognathae immunology MeSH
- Avian Proteins genetics metabolism MeSH
- Receptors, Tumor Necrosis Factor genetics metabolism MeSH
- Mammals immunology MeSH
- Sequence Alignment MeSH
- Tumor Necrosis Factor-alpha genetics MeSH
- Crows immunology MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Names of Substances
- NF-kappa B MeSH
- Avian Proteins MeSH
- Receptors, Tumor Necrosis Factor MeSH
- Tumor Necrosis Factor-alpha MeSH
