Evolution of RNA sensing receptors in birds

Magor, Katharine E.

doi:10.1007/s00251-021-01238-1

Cited by 11 publications

(15 citation statements)

References 187 publications

(256 reference statements)

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“…Several PRRs are involved in viral RNA recognition in birds [ 3 ]. Most importantly, RNA-sensing PRRs include RIG-I-like receptors (RLRs), which are cytosolic RNA sensors responsible for the detection of viral or other atypical RNA [ 4 , 5 ].…”

Section: Introductionmentioning

confidence: 99%

Dynamic Evolution of Avian RNA Virus Sensors: Repeated Loss of RIG-I and RIPLET

Krchlíková

Hron

Těšický

et al. 2022

Viruses

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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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Section: Introductionmentioning

confidence: 99%

Dynamic Evolution of Avian RNA Virus Sensors: Repeated Loss of RIG-I and RIPLET

Krchlíková

Hron

Těšický

et al. 2022

Viruses

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“…Poly:IC is an analog of viral RNA; this analog has been used in many studies to stimulate the RLR and Toll-like receptor (TLR) pathways [ 20 , 22 – 25 ]. MDA5 , LGP2 , and TLR3 are important sensors for virus recognition to stimulate innate immune responses in chickens [ 23 , 26 ]. This study focused on whether or not organoids containing neural-like cells recognize poly:IC through the RLR family.…”

Section: Resultsmentioning

confidence: 99%

“…In addition to MDA5 and LGP2 , IL-6 , IL-1 beta , and Mx1 expression also increased after 6 h of exposure to poly:IC. These genes are stimulated by RLR-derived signals [ 23 ]. Based on these results, we concluded that organoids containing neural-like cells respond to poly:IC through MDA5 and LGP2 .…”

Section: Discussionmentioning

confidence: 99%

Organoids containing neural-like cells derived from chicken iPSCs respond to poly:IC through the RLR family

et al. 2023

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There is still much room for development in pluripotent stem cell research on avian species compared to human stem cell studies. Neural cells are useful for the evaluation of risk assessment of infectious diseases since several avian species die of encephalitis derived from infectious diseases. In this study, we attempted to develop induced pluripotent stem cells (iPSCs) technology for avian species by forming organoids containing neural-like cells. In our previous study, we established two types iPSCs from chicken somatic cells, the first is iPSCs with PB-R6F reprogramming vector and the second is iPSCs with PB-TAD-7F reprogramming vector. In this study, we first compared the nature of these two cell types using RNA-seq analysis. The total gene expression of iPSCs with PB-TAD-7F was closer to that of chicken ESCs than that of iPSCs with PB-R6F; therefore, we used iPSCs with PB-TAD-7F to form organoids containing neural-like cells. We successfully established organoids containing neural-like cells from iPSCs using PB-TAD-7F. Furthermore, our organoids responded to poly:IC through the RIG-I-like receptor (RLR) family. In this study, we developed iPSCs technology for avian species via organoid formation. In the future, organoids containing neural-like cells from avian iPSCs can develop as a new evaluation tool for infectious disease risk in avian species, including endangered avian species.

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“…We also genotyped a sample of individuals from five further duck species ( Anas crecca, Anas penelope, Anas americana, Aythya ferina, Aythya fuligula ). As waterfowl are important hosts of the AIV, which can be detected by different classes of PRRs, including TLRs and RLRs ( Evseev and Magor 2019 ; Magor 2022 ), we included genes across the TLR, RIG-I, and Influenza A signaling pathways and additional genes (interferon-induced transmembrane protein 3 [IFITM3] and β-defensins) that have been studied in mallards previously ( supplementary table S1, Supplementary Material online). The sequenced regions added up to approximately 1.77 Mbp, with individual genes ranging from 90 bp to 100 kbp in size including both introns and exons.…”

Section: Resultsmentioning

confidence: 99%

Comparative Genomics of the Waterfowl Innate Immune System

Jax

Franchini

Sekar

et al. 2022

Molecular Biology and Evolution

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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 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 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. 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 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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Evolution of RNA sensing receptors in birds

Cited by 11 publications

References 187 publications

Dynamic Evolution of Avian RNA Virus Sensors: Repeated Loss of RIG-I and RIPLET

Dynamic Evolution of Avian RNA Virus Sensors: Repeated Loss of RIG-I and RIPLET

Organoids containing neural-like cells derived from chicken iPSCs respond to poly:IC through the RLR family

Comparative Genomics of the Waterfowl Innate Immune System

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