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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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2
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Erdemci-Evin S, Bosso M, Krchlikova V, Bayer W, Regensburger K, Mayer M, Dittmer U, Sauter D, Kmiec D, Kirchhoff F. A Variety of Mouse PYHIN Proteins Restrict Murine and Human Retroviruses. Viruses 2024; 16:493. [PMID: 38675836 PMCID: PMC11054388 DOI: 10.3390/v16040493] [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: 02/14/2024] [Revised: 03/15/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
PYHIN proteins are only found in mammals and play key roles in the defense against bacterial and viral pathogens. The corresponding gene locus shows variable deletion and expansion ranging from 0 genes in bats, over 1 in cows, and 4 in humans to a maximum of 13 in mice. While initially thought to act as cytosolic immune sensors that recognize foreign DNA, increasing evidence suggests that PYHIN proteins also inhibit viral pathogens by more direct mechanisms. Here, we examined the ability of all 13 murine PYHIN proteins to inhibit HIV-1 and murine leukemia virus (MLV). We show that overexpression of p203, p204, p205, p208, p209, p210, p211, and p212 strongly inhibits production of infectious HIV-1; p202, p207, and p213 had no significant effects, while p206 and p214 showed intermediate phenotypes. The inhibitory effects on infectious HIV-1 production correlated significantly with the suppression of reporter gene expression by a proviral Moloney MLV-eGFP construct and HIV-1 and Friend MLV LTR luciferase reporter constructs. Altogether, our data show that the antiretroviral activity of PYHIN proteins is conserved between men and mice and further support the key role of nuclear PYHIN proteins in innate antiviral immunity.
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Affiliation(s)
- Sümeyye Erdemci-Evin
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; (S.E.-E.); (M.B.); (K.R.); (M.M.); (D.K.)
| | - Matteo Bosso
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; (S.E.-E.); (M.B.); (K.R.); (M.M.); (D.K.)
| | - Veronika Krchlikova
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, 72076 Tübingen, Germany; (V.K.)
| | - Wibke Bayer
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany; (W.B.); (U.D.)
| | - Kerstin Regensburger
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; (S.E.-E.); (M.B.); (K.R.); (M.M.); (D.K.)
| | - Martha Mayer
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; (S.E.-E.); (M.B.); (K.R.); (M.M.); (D.K.)
| | - Ulf Dittmer
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany; (W.B.); (U.D.)
| | - Daniel Sauter
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, 72076 Tübingen, Germany; (V.K.)
| | - Dorota Kmiec
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; (S.E.-E.); (M.B.); (K.R.); (M.M.); (D.K.)
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; (S.E.-E.); (M.B.); (K.R.); (M.M.); (D.K.)
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3
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Silva RCMC, Gomes FM. Evolution of the Major Components of Innate Immunity in Animals. J Mol Evol 2024; 92:3-20. [PMID: 38281163 DOI: 10.1007/s00239-024-10155-2] [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: 10/28/2023] [Accepted: 01/11/2024] [Indexed: 01/30/2024]
Abstract
Innate immunity is present in all animals. In this review, we explore the main conserved mechanisms of recognition and innate immune responses among animals. In this sense, we discuss the receptors, critical for binding to pathogen-associated molecular patterns (PAMPs) or danger-associated molecular patterns (DAMPs); the downstream signaling proteins; and transcription factors that govern immune responses. We also highlight conserved inflammatory mediators that are induced after the recognition of DAMPs and PAMPs. At last, we discuss the mechanisms that are involved in the regulation and/or generation of reactive oxygen species (ROS), influencing immune responses, like heme-oxygenases (HOs).
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Affiliation(s)
- Rafael Cardoso Maciel Costa Silva
- Laboratory of Immunoreceptors and Signaling, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Fábio Mendonça Gomes
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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4
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Bukhari SIA, Truesdell SS, Datta C, Choudhury P, Wu KQ, Shrestha J, Maharjan R, Plotsker E, Elased R, Laisa S, Bhambhani V, Lin Y, Kreuzer J, Morris R, Koh SB, Ellisen LW, Haas W, Ly A, Vasudevan S. Regulation of RNA methylation by therapy treatment, promotes tumor survival. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.19.540602. [PMID: 37292633 PMCID: PMC10245743 DOI: 10.1101/2023.05.19.540602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Our data previously revealed that chemosurviving cancer cells translate specific genes. Here, we find that the m6A-RNA-methyltransferase, METTL3, increases transiently in chemotherapy-treated breast cancer and leukemic cells in vitro and in vivo. Consistently, m6A increases on RNA from chemo-treated cells, and is needed for chemosurvival. This is regulated by eIF2α phosphorylation and mTOR inhibition upon therapy treatment. METTL3 mRNA purification reveals that eIF3 promotes METTL3 translation that is reduced by mutating a 5'UTR m6A-motif or depleting METTL3. METTL3 increase is transient after therapy treatment, as metabolic enzymes that control methylation and thus m6A levels on METTL3 RNA, are altered over time after therapy. Increased METTL3 reduces proliferation and anti-viral immune response genes, and enhances invasion genes, which promote tumor survival. Consistently, overriding phospho-eIF2α prevents METTL3 elevation, and reduces chemosurvival and immune-cell migration. These data reveal that therapy-induced stress signals transiently upregulate METTL3 translation, to alter gene expression for tumor survival.
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Affiliation(s)
- Syed IA Bukhari
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Brigham and Harvard Medical School, Boston, MA 02114
| | - Samuel S Truesdell
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Brigham and Harvard Medical School, Boston, MA 02114
| | - Chandreyee Datta
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Brigham and Harvard Medical School, Boston, MA 02114
| | - Pritha Choudhury
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Brigham and Harvard Medical School, Boston, MA 02114
| | - Keith Q Wu
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Brigham and Harvard Medical School, Boston, MA 02114
| | - Jitendra Shrestha
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Brigham and Harvard Medical School, Boston, MA 02114
| | - Ruby Maharjan
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Brigham and Harvard Medical School, Boston, MA 02114
| | - Ethan Plotsker
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Brigham and Harvard Medical School, Boston, MA 02114
| | - Ramzi Elased
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Brigham and Harvard Medical School, Boston, MA 02114
| | - Sadia Laisa
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Brigham and Harvard Medical School, Boston, MA 02114
| | - Vijeta Bhambhani
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Brigham and Harvard Medical School, Boston, MA 02114
| | - Yue Lin
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Brigham and Harvard Medical School, Boston, MA 02114
| | - Johannes Kreuzer
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Brigham and Harvard Medical School, Boston, MA 02114
| | - Robert Morris
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Brigham and Harvard Medical School, Boston, MA 02114
| | - Siang-Boon Koh
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Brigham and Harvard Medical School, Boston, MA 02114
| | - Leif W. Ellisen
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Brigham and Harvard Medical School, Boston, MA 02114
| | - Wilhelm Haas
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Brigham and Harvard Medical School, Boston, MA 02114
| | - Amy Ly
- Department of Pathology, Massachusetts General Hospital, Massachusetts General Brigham and Harvard Medical School, Boston, MA 02114
| | - Shobha Vasudevan
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Brigham and Harvard Medical School, Boston, MA 02114
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5
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Zhang P, Zhu Y, Guo Q, Li J, Zhan X, Yu H, Xie N, Tan H, Lundholm N, Garcia-Cuetos L, Martin MD, Subirats MA, Su YH, Ruiz-Trillo I, Martindale MQ, Yu JK, Gilbert MTP, Zhang G, Li Q. On the origin and evolution of RNA editing in metazoans. Cell Rep 2023; 42:112112. [PMID: 36795564 PMCID: PMC9989829 DOI: 10.1016/j.celrep.2023.112112] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 11/28/2022] [Accepted: 01/30/2023] [Indexed: 02/16/2023] Open
Abstract
Extensive adenosine-to-inosine (A-to-I) editing of nuclear-transcribed mRNAs is the hallmark of metazoan transcriptional regulation. Here, by profiling the RNA editomes of 22 species that cover major groups of Holozoa, we provide substantial evidence supporting A-to-I mRNA editing as a regulatory innovation originating in the last common ancestor of extant metazoans. This ancient biochemistry process is preserved in most extant metazoan phyla and primarily targets endogenous double-stranded RNA (dsRNA) formed by evolutionarily young repeats. We also find intermolecular pairing of sense-antisense transcripts as an important mechanism for forming dsRNA substrates for A-to-I editing in some but not all lineages. Likewise, recoding editing is rarely shared across lineages but preferentially targets genes involved in neural and cytoskeleton systems in bilaterians. We conclude that metazoan A-to-I editing might first emerge as a safeguard mechanism against repeat-derived dsRNA and was later co-opted into diverse biological processes due to its mutagenic nature.
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Affiliation(s)
- Pei Zhang
- BGI-Shenzhen, Shenzhen 518083, China; Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | | | - Qunfei Guo
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ji Li
- BGI Research-Wuhan, BGI, Wuhan 430074, China
| | | | - Hao Yu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Nianxia Xie
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Nina Lundholm
- Natural History Museum of Denmark, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Lydia Garcia-Cuetos
- Natural History Museum of Denmark, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway; Center for Theoretical Evolutionary Genomics, Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | | | - Yi-Hsien Su
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Iñaki Ruiz-Trillo
- Institute of Evolutionary Biology, UPF-CSIC Barcelona, 08003 Barcelona, Spain; ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Catalonia, Spain; Departament de Genètica, Microbiologia i Estadística, Facultat de Bilogia, Universitat de Barcelona (UB), 08028 Barcelona, Spain
| | - Mark Q Martindale
- The Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan; Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan 26242, Taiwan
| | - M Thomas P Gilbert
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway; Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Guojie Zhang
- Center of Evolutionary and Organismal Biology, & Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark.
| | - Qiye Li
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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6
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Haridevamuthu B, Guru A, Velayutham M, Snega Priya P, Arshad A, Arockiaraj J. Long non‐coding RNA, a supreme post‐transcriptional immune regulator of bacterial or virus‐driven immune evolution in teleost. REVIEWS IN AQUACULTURE 2023; 15:163-178. [DOI: 10.1111/raq.12709] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/18/2022] [Indexed: 10/16/2023]
Abstract
AbstractThe global aquaculture boom, fuelled by a reduction in wild population and detection of novel viruses, has created a demanding market, hence, there is a pressing need to investigate the immune system of fish, further. As the most diverse community of vertebrates and a central contributor to the progressing global aquaculture market, teleost continues to draw vast scientific interest. Recent breakthroughs in multi‐omics technologies have provided a platform to understand the role of long non‐coding RNA (lncRNA) in the host immune system during infection. Emerging evidence shows that teleost lncRNA might have a regulatory role in immune responses, mostly through lncRNA–microRNA (miRNA) sponging. Teleost lncRNA shares a functionally active short sequence complement to target the miRNA which is conserved among the several fish species. Recent report suggests that rhabdovirus exploits a lncRNA in teleost and, to dodge the host immune mechanism and negatively regulate the immune system. This observation reveals the essentiality of lncRNA in pathogen‐driven immunity in teleost. Reports available on the function of teleost lncRNA are still in early stages and experimental verifications are a limiting factor. Unravelling the lncRNA‐mediated immune regulation in fishes could be used against the invading pathogens to strengthen the aquaculture production. This review elaborates on the experimentally identified and functionally characterized lncRNA and its regulatory role in the teleost immune response during infection and pathogen‐driven host immune evolution, which could eventually lead to achieving high standards in aquaculture productivity.
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Affiliation(s)
- B. Haridevamuthu
- Department of Biotechnology, College of Science and Humanities SRM Institute of Science and Technology Chennai Tamil Nadu India
| | - Ajay Guru
- Department of Biotechnology, College of Science and Humanities SRM Institute of Science and Technology Chennai Tamil Nadu India
| | - Manikandan Velayutham
- Department of Biotechnology, College of Science and Humanities SRM Institute of Science and Technology Chennai Tamil Nadu India
| | - P. Snega Priya
- Department of Biotechnology, College of Science and Humanities SRM Institute of Science and Technology Chennai Tamil Nadu India
| | - Aziz Arshad
- International Institute of Aquaculture and Aquatic Sciences (I‐AQUAS) Universiti Putra Malaysia Port Dickson Malaysia
| | - Jesu Arockiaraj
- Department of Biotechnology, College of Science and Humanities SRM Institute of Science and Technology Chennai Tamil Nadu India
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7
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Brownsword MJ, Locker N. A little less aggregation a little more replication: Viral manipulation of stress granules. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1741. [PMID: 35709333 PMCID: PMC10078398 DOI: 10.1002/wrna.1741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/29/2022] [Accepted: 05/05/2022] [Indexed: 01/31/2023]
Abstract
Recent exciting studies have uncovered how membrane-less organelles, also known as biocondensates, are providing cells with rapid response pathways, allowing them to re-organize their cellular contents and adapt to stressful conditions. Their assembly is driven by the phase separation of their RNAs and intrinsically disordered protein components into condensed foci. Among these, stress granules (SGs) are dynamic cytoplasmic biocondensates that form in response to many stresses, including activation of the integrated stress response or viral infections. SGs sit at the crossroads between antiviral signaling and translation because they concentrate signaling proteins and components of the innate immune response, in addition to translation machinery and stalled mRNAs. Consequently, they have been proposed to contribute to antiviral activities, and therefore are targeted by viral countermeasures. Equally, SGs components can be commandeered by viruses for their own efficient replication. Phase separation processes are an important component of the viral life cycle, for example, driving the assembly of replication factories or inclusion bodies. Therefore, in this review, we will outline the recent understanding of this complex interplay and tug of war between viruses, SGs, and their components. This article is categorized under: RNA in Disease and Development > RNA in Disease Translation > Regulation RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Matthew J. Brownsword
- Faculty of Health and Medical Sciences, School of Biosciences and MedicineUniversity of SurreyGuildfordSurreyUK
| | - Nicolas Locker
- Faculty of Health and Medical Sciences, School of Biosciences and MedicineUniversity of SurreyGuildfordSurreyUK
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8
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Justice JL, Cristea IM. Nuclear antiviral innate responses at the intersection of DNA sensing and DNA repair. Trends Microbiol 2022; 30:1056-1071. [PMID: 35641341 PMCID: PMC9560981 DOI: 10.1016/j.tim.2022.05.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 01/13/2023]
Abstract
The coevolution of vertebrate and mammalian hosts with DNA viruses has driven the ability of host cells to distinguish viral from cellular DNA in the nucleus to induce intrinsic immune responses. Concomitant viral mechanisms have arisen to inhibit DNA sensing. At this virus-host interface, emerging evidence links cytokine responses and cellular homeostasis pathways, particularly the DNA damage response (DDR). Nuclear DNA sensors, such as the interferon (IFN)-γ inducible protein 16 (IFI16), functionally intersect with the DDR regulators ataxia telangiectasia mutated (ATM) and DNA-dependent protein kinase (DNA-PK). Here, we discuss accumulating knowledge for the DDR-innate immunity signaling axis. Through the lens of this infection-driven signaling axis, we present host and viral molecular strategies acquired to regulate autoinflammation and antiviral responses.
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Affiliation(s)
- Joshua L Justice
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA.
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9
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Juretić D. Designed Multifunctional Peptides for Intracellular Targets. Antibiotics (Basel) 2022; 11:antibiotics11091196. [PMID: 36139975 PMCID: PMC9495127 DOI: 10.3390/antibiotics11091196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/25/2022] [Accepted: 08/29/2022] [Indexed: 11/25/2022] Open
Abstract
Nature’s way for bioactive peptides is to provide them with several related functions and the ability to cooperate in performing their job. Natural cell-penetrating peptides (CPP), such as penetratins, inspired the design of multifunctional constructs with CPP ability. This review focuses on known and novel peptides that can easily reach intracellular targets with little or no toxicity to mammalian cells. All peptide candidates were evaluated and ranked according to the predictions of low toxicity to mammalian cells and broad-spectrum activity. The final set of the 20 best peptide candidates contains the peptides optimized for cell-penetrating, antimicrobial, anticancer, antiviral, antifungal, and anti-inflammatory activity. Their predicted features are intrinsic disorder and the ability to acquire an amphipathic structure upon contact with membranes or nucleic acids. In conclusion, the review argues for exploring wide-spectrum multifunctionality for novel nontoxic hybrids with cell-penetrating peptides.
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Affiliation(s)
- Davor Juretić
- Mediterranean Institute for Life Sciences, 21000 Split, Croatia;
- Faculty of Science, University of Split, 21000 Split, Croatia;
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10
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Haley PJ. From bats to pangolins: new insights into species differences in the structure and function of the immune system. Innate Immun 2022; 28:107-121. [PMID: 35506564 PMCID: PMC9136466 DOI: 10.1177/17534259221093120] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Species differences in the structure and function of the immune system of laboratory animals are known to exist and have been reviewed extensively. However, the number and diversity of wild and exotic species, along with their associated viruses, that come into contact with humans has increased worldwide sometimes with lethal consequences. Far less is known about the immunobiology of these exotic and wild species. Data suggest that species differences of the mechanisms of inflammation, innate immunity and adaptive immunity are all involved in the establishment and maintenance of viral infections across reservoir hosts. The current review attempts to collect relevant data concerning the basics of innate and adaptive immune functions of exotic and wild species followed by identification of those differences that may play a role in the maintenance of viral infections in reservoir hosts.
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Affiliation(s)
- Patrick J Haley
- Haley Tox/Path Consulting LLC, 104 Cypress Springs Way, 78633, Georgetown Texas, United States
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11
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Wang JF, Cai W, Qiu FS, Yu CH. Pathogenic roles of m6A modification in viral infection and virus-driven carcinogenesis. Endocr Metab Immune Disord Drug Targets 2022; 22:1009-1017. [PMID: 35418293 DOI: 10.2174/2772432817666220412112759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 01/06/2022] [Accepted: 01/17/2022] [Indexed: 11/22/2022]
Abstract
N6-methyladenosine (m6A) is a prevalent modification of RNA in eukaryotes, bacteria, and viruses. It is highly conserved and can affect the structure, localization, and biology functions of RNA. In recent years, multiple m6A methylation sites have been identified in the viral RNA genome and transcripts of DNA viruses. This modification occurs commonly during the primary infection and is dynamically regulated by a methyltransferase (writers), demethylase (eraser) and m6A-binding proteins (readers) within the host cells. The abnormal m6A modification not only affects the replication of pathogenic viruses and host immune response but also contributes to the pathogenesis of virus-induced cancers. In this review, we highlight recent advances on the mechanism of m6A modification on viral replication, host immune response and carcinogenesis to provide a novel insight for epigenetic prevention of viral infection and virus-driven carcinogenesis.
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Affiliation(s)
- Jia-Feng Wang
- Zhejiang Provincial Laboratory of Experimental Animal's & Nonclinical Laboratory Studies, Hangzhou Medical College, Hangzhou, China
| | - Wei Cai
- Department of traditional Chinese Medicine, Zhejiang Pharmaceutical College, Ningbo, China
| | - Fen-Sheng Qiu
- Zhejiang Provincial Laboratory of Experimental Animal's & Nonclinical Laboratory Studies, Hangzhou Medical College, Hangzhou, China
| | - Chen-Huan Yu
- Zhejiang Provincial Laboratory of Experimental Animal's & Nonclinical Laboratory Studies, Hangzhou Medical College, Hangzhou, China
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12
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Divergences of the RLR Gene Families across Lophotrochozoans: Domain Grafting, Exon-Intron Structure, Expression, and Positive Selection. Int J Mol Sci 2022; 23:ijms23073415. [PMID: 35408776 PMCID: PMC8998645 DOI: 10.3390/ijms23073415] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/06/2022] [Accepted: 03/10/2022] [Indexed: 02/04/2023] Open
Abstract
Invertebrates do not possess adaptive immunity but have evolved a variety of unique repertoires of innate immune sensors. In this study, we explored the immune diversity and specificity of invertebrates based on the lophotrochozoan RLRs, a major component in antiviral immune recognition. By annotating RLRs in the genomes of 58 representative species across metazoan evolution, we explored the gene expansion of RLRs in Lophotrochozoa. Of note, the N-terminal domains of lophotrochozoan RLRs showed the most striking diversity which evolved independently by domain grafting. Exon–intron structures were revealed to be prevalent in the domain grafting of lophotrochozoan RLRs based on an analysis of sibling paralogs and orthologs. In more than half of the cases, the mechanism of ‘exonization/pseudoexonization’ led to the generation of non-canonical N-terminal domains. Transcriptomic studies revealed that many non-canonical RLRs display immune-related expression patterns. Two of these RLRs showed obvious evidence of positive selection, which may be the result of host defense selection pressure. Overall, our study suggests that the complex and unique domain arrangement of lophotrochozoan RLRs might result from domain grafting, exon–intron divergence, expression diversification, and positive selection, which may have led to functionally distinct lophotrochozoan RLRs.
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Ramana CV, Das B. Profiling transcription factor sub-networks in type I interferon signaling and in response to SARS-CoV-2 infection. COMPUTATIONAL AND MATHEMATICAL BIOPHYSICS 2021. [DOI: 10.1515/cmb-2020-0128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Type I interferons (IFN α/β) play a central role in innate immunity to respiratory viruses, including coronaviruses. In this study, transcription factor profiling in the transcriptome was used to gain novel insights into the role of inducible transcription factors in response to type I interferon signaling in immune cells and in lung epithelial cells after SARS-CoV-2 infection. Modeling the interferon-inducible transcription factor mRNA data in terms of distinct sub-networks based on biological functions such as antiviral response, immune modulation, and cell growth revealed enrichment of specific transcription factors in mouse and human immune cells. Interrogation of multiple microarray datasets revealed that SARS-CoV-2 induced high levels of IFN-beta and interferon-inducible transcription factor mRNA in human lung epithelial cells. Transcription factor mRNA of the three sub-networks were differentially regulated in human lung epithelial cell lines after SARS-CoV-2 infection and in COVID-19 patients. A subset of type I interferon-inducible transcription factors and inflammatory mediators were specifically enriched in the lungs and neutrophils of Covid-19 patients. The emerging complex picture of type I IFN transcriptional regulation consists of a rapid transcriptional switch mediated by the Jak-Stat cascade and a graded output of the inducible transcription factor activation that enables temporal regulation of gene expression.
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Affiliation(s)
- Chilakamarti V. Ramana
- Department of Medicine, Dartmouth-Hitchcock Medical Center, Lebanon , NH 03766, USA ; Department of Stem Cell and Infectious Diseases , KaviKrishna Laboratory , Guwahati Biotech Park, Indian Institute of Technology , Guwahati , India ; Thoreau Laboratory for Global Health , University of Massachusetts , Lowell, MA 01854, USA
| | - Bikul Das
- Department of Stem Cell and Infectious Diseases , KaviKrishna Laboratory, Guwahati Biotech Park, Indian Institute of Technology , Guwahati , India ; Thoreau Laboratory for Global Health , University of Massachusetts , Lowell, MA 01854, USA
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Capozza P, Pratelli A, Camero M, Lanave G, Greco G, Pellegrini F, Tempesta M. Feline Coronavirus and Alpha-Herpesvirus Infections: Innate Immune Response and Immune Escape Mechanisms. Animals (Basel) 2021; 11:ani11123548. [PMID: 34944324 PMCID: PMC8698202 DOI: 10.3390/ani11123548] [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: 10/24/2021] [Revised: 12/11/2021] [Accepted: 12/12/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Feline coronavirus (FCoV) and feline herpesvirus-1 (FeHV-1) can induce infections that are difficult to prevent and to treat due to the involvement of host genetic factors and immune mechanisms. These two viruses areimportant examples of viral immune evasion of the host’s innate immune response. The innate immune system provides an early form of host protection from infectious diseases without pre-exposure and plays an essential role in determining the outcome of viral infections. The mechanisms that the innate immune system utilizes to counteract infections are based on therecognition of a relatively limited set of molecular structures that are either products of microbes (virus, bacteria, fungi, parasites) or expressed by injured or dead host cells. This review provides a brief overview of the main mechanisms achieved by host’s innate immunity, focusing primarily on the immune escape mechanisms developed and carried out by FCoV and FeHV-1 during infection. Abstract Over time, feline viruses have acquired elaborateopportunistic properties, making their infections particularly difficult to prevent and treat. Feline coronavirus (FCoV) and feline herpesvirus-1 (FeHV-1), due to the involvement of host genetic factors and immune mechanisms in the development of the disease and more severe forms, are important examples of immune evasion of the host’s innate immune response by feline viruses.It is widely accepted that the innate immune system, which providesan initial universal form of the mammalian host protection from infectious diseases without pre-exposure, plays an essential role in determining the outcome of viral infection.The main components of this immune systembranchare represented by the internal sensors of the host cells that are able to perceive the presence of viral component, including nucleic acids, to start and trigger the production of first type interferon and to activate the cytotoxicity by Natural Killercells, often exploited by viruses for immune evasion.In this brief review, we providea general overview of the principal tools of innate immunity, focusing on the immunologic escape implemented byFCoVand FeHV-1 duringinfection.
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Abstract
One of the first layers of protection that metazoans put in place to defend themselves against viruses rely on the use of proteins containing DExD/H-box helicase domains. These members of the duplex RNA–activated ATPase (DRA) family act as sensors of double-stranded RNA (dsRNA) molecules, a universal marker of viral infections. DRAs can be classified into 2 subgroups based on their mode of action: They can either act directly on the dsRNA, or they can trigger a signaling cascade. In the first group, the type III ribonuclease Dicer plays a key role to activate the antiviral RNA interference (RNAi) pathway by cleaving the viral dsRNA into small interfering RNAs (siRNAs). This represents the main innate antiviral immune mechanism in arthropods and nematodes. Even though Dicer is present and functional in mammals, the second group of DRAs, containing the RIG-I-like RNA helicases, appears to have functionally replaced RNAi and activate type I interferon (IFN) response upon dsRNA sensing. However, recent findings tend to blur the frontier between these 2 mechanisms, thereby highlighting the crucial and diverse roles played by RNA helicases in antiviral innate immunity. Here, we will review our current knowledge of the importance of these key proteins in viral infection, with a special focus on the interplay between the 2 main types of response that are activated by dsRNA.
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Affiliation(s)
- Morgane Baldaccini
- Université de Strasbourg, Architecture et Réactivité de l’ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France
| | - Sébastien Pfeffer
- Université de Strasbourg, Architecture et Réactivité de l’ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France
- * E-mail:
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Le Roux M, Ollivier A, Kervoaze G, Beke T, Gillet L, Pichavant M, Gosset P. IL-20 Cytokines Are Involved in Epithelial Lesions Associated with Virus-Induced COPD Exacerbation in Mice. Biomedicines 2021; 9:biomedicines9121838. [PMID: 34944654 PMCID: PMC8699027 DOI: 10.3390/biomedicines9121838] [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] [Received: 11/01/2021] [Revised: 11/26/2021] [Accepted: 12/02/2021] [Indexed: 12/24/2022] Open
Abstract
(1) Background: viral infections are a frequent cause of chronic obstructive pulmonary disease (COPD) exacerbations, which are responsible for disease progression and mortality. Previous reports showed that IL-20 cytokines facilitate bacterial lung infection, but their production and their role in COPD and viral infection has not yet been investigated. (2) Methods: C57BL/6 WT and IL-20 Rb KO mice were chronically exposed to air or cigarette smoke (CS) to mimic COPD. Cytokine production, antiviral response, inflammation and tissue damages were analyzed after PVM infection. (3) Results: CS exposure was associated with an increase in viral burden and antiviral response. PVM infection in CS mice enhanced IFN-γ, inflammation and tissue damage compared to Air mice. PVM infection and CS exposure induced, in an additive manner, IL-20 cytokines expression and the deletion of IL-20 Rb subunit decreased the expression of interferon-stimulated genes and the production of IFN-λ2/3, without an impact on PVM replication. Epithelial cell damages and inflammation were also reduced in IL-20 Rb-/- mice, and this was associated with reduced lung permeability and the maintenance of intercellular junctions. (4) Conclusions: PVM infection and CS exposure additively upregulates the IL-20 pathway, leading to the promotion of epithelial damages. Our data in our model of viral exacerbation of COPD identify IL-20 cytokine as a potential therapeutic target.
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Affiliation(s)
- Mélina Le Roux
- CIIL-Center for Infection and Immunity of Lille, CHRU Lille, Institute Pasteur de Lille, University Lille, CNRS UMR9017, Inserm U1019, 59000 Lille, France; (M.L.R.); (A.O.); (G.K.); (T.B.); (M.P.)
| | - Anaïs Ollivier
- CIIL-Center for Infection and Immunity of Lille, CHRU Lille, Institute Pasteur de Lille, University Lille, CNRS UMR9017, Inserm U1019, 59000 Lille, France; (M.L.R.); (A.O.); (G.K.); (T.B.); (M.P.)
| | - Gwenola Kervoaze
- CIIL-Center for Infection and Immunity of Lille, CHRU Lille, Institute Pasteur de Lille, University Lille, CNRS UMR9017, Inserm U1019, 59000 Lille, France; (M.L.R.); (A.O.); (G.K.); (T.B.); (M.P.)
| | - Timothé Beke
- CIIL-Center for Infection and Immunity of Lille, CHRU Lille, Institute Pasteur de Lille, University Lille, CNRS UMR9017, Inserm U1019, 59000 Lille, France; (M.L.R.); (A.O.); (G.K.); (T.B.); (M.P.)
| | - Laurent Gillet
- Immunology-Vaccinology Laboratory, Department of Infection and Parasitic Diseases, FARAH, University of Liege, 4000 Liege, Belgium;
| | - Muriel Pichavant
- CIIL-Center for Infection and Immunity of Lille, CHRU Lille, Institute Pasteur de Lille, University Lille, CNRS UMR9017, Inserm U1019, 59000 Lille, France; (M.L.R.); (A.O.); (G.K.); (T.B.); (M.P.)
| | - Philippe Gosset
- CIIL-Center for Infection and Immunity of Lille, CHRU Lille, Institute Pasteur de Lille, University Lille, CNRS UMR9017, Inserm U1019, 59000 Lille, France; (M.L.R.); (A.O.); (G.K.); (T.B.); (M.P.)
- Correspondence: ; Tel.: +33-320-877-965
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Gregori J, Cortese MF, Piñana M, Campos C, Garcia-Cehic D, Andrés C, Abril JF, Codina MG, Rando A, Esperalba J, Sulleiro E, Joseph J, Saubí N, Colomer-Castell S, Martin MC, Castillo C, Esteban JI, Pumarola T, Rodriguez-Frias F, Antón A, Quer J. Host-dependent editing of SARS-CoV-2 in COVID-19 patients. Emerg Microbes Infect 2021; 10:1777-1789. [PMID: 34402744 PMCID: PMC8425778 DOI: 10.1080/22221751.2021.1969868] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A common trait among RNA viruses is their high capability to acquire genetic variability due to viral and host mechanisms. Next-generation sequencing (NGS) analysis enables the deep study of the viral quasispecies in samples from infected individuals. In this study, the viral quasispecies complexity and single nucleotide polymorphisms of the SARS-CoV-2 spike gene of coronavirus disease 2019 (COVID-19) patients with mild or severe disease were investigated using next-generation sequencing (Illumina platform). SARS-CoV-2 spike variability was higher in patients with long-lasting infection. Most substitutions found were present at frequencies lower than 1%, and had an A → G or T → C pattern, consistent with variants caused by adenosine deaminase acting on RNA-1 (ADAR1). ADAR1 affected a small fraction of replicating genomes, but produced multiple, mainly non-synonymous mutations. ADAR1 editing during replication rather than the RNA-dependent RNA polymerase (nsp12) was the predominant mechanism generating SARS-CoV-2 genetic variability. However, the mutations produced are not fixed in the infected human population, suggesting that ADAR1 may have an antiviral role, whereas nsp12-induced mutations occurring in patients with high viremia and persistent infection are the main source of new SARS-CoV-2 variants.
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Affiliation(s)
- Josep Gregori
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Roche Diagnostics SL, Barcelona, Spain
| | - Maria Francesca Cortese
- Biochemistry and Microbiology Departments, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Maria Piñana
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Carolina Campos
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Damir Garcia-Cehic
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Cristina Andrés
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Josep Francesc Abril
- Computational Genomics Lab, Genetics, Microbiology and Statistics Department, Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Spain
| | - Maria Gema Codina
- Microbiology Department, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Ariadna Rando
- Microbiology Department, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Juliana Esperalba
- Microbiology Department, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Elena Sulleiro
- Microbiology Department, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Joan Joseph
- Microbiology Department, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Narcís Saubí
- Biochemistry and Microbiology Departments, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Sergi Colomer-Castell
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Mari Carmen Martin
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Carla Castillo
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Juan Ignacio Esteban
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Tomas Pumarola
- Microbiology Department, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Francisco Rodriguez-Frias
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Biochemistry and Microbiology Departments, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Andrés Antón
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Universitat Autònoma de Barcelona, Bellaterra, Spain
- Andrés Antón Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Pg Vall d’Hebron 119-129, Barcelona08035, Spain
| | - Josep Quer
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Josep Quer , Virus Translational Research Unit, Liver Diseases, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, Barcelona08035, Spain
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18
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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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19
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Duan W, Cen Y, Lin C, Ouyang H, Du K, Kumar A, Wang B, Avolio J, Grasemann H, Moraes TJ. Inflammatory epithelial cytokines after in vitro respiratory syncytial viral infection are associated with reduced lung function. ERJ Open Res 2021; 7:00365-2021. [PMID: 34527729 PMCID: PMC8435810 DOI: 10.1183/23120541.00365-2021] [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] [Received: 06/02/2021] [Accepted: 06/11/2021] [Indexed: 11/27/2022] Open
Abstract
Respiratory syncytial virus (RSV) infections in early life predispose children with cystic fibrosis (CF) to more severe lung function decline in later life. The mechanisms explaining the associations between RSV and progression of CF lung disease are not clear. In this study, a human bronchial epithelial cell line and primary human nasal epithelial cells (PNECs) from individuals with CF and healthy control donors were infected with RSV. Real-time PCR, plaque assay, cytokine detection, immunofluorescence and Western blot analyses were performed. RSV is replicated to a higher degree in CF epithelial cells as compared to control cells; however, no defects in innate immune pathways were identified in CF cells. Rather, primary p.Phe508del cystic fibrosis transmembrane conductance regulator PNECs produced more cytokines after RSV infection than control cells. Moreover, interleukin-8 and tumour necrosis factor-α production post RSV negatively correlated with lung function (% predicted forced expiratory volume in 1 s) in the individuals who donated the cells. These data suggest that CF epithelium has a dysfunctional response to RSV allowing for enhanced viral replication and an exaggerated inflammatory response that ultimately may predispose to greater airway inflammation and reduced lung function. This work demonstrates an association between epithelial inflammatory cytokines after in vitro viral infection and lung function in cystic fibrosis, and reinforces the importance of studying innate immune epithelial cell function in cystic fibrosishttps://bit.ly/3gDNwwo
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Affiliation(s)
- Wenming Duan
- Program in Translational Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Yuchen Cen
- Program in Translational Medicine, Hospital for Sick Children, Toronto, ON, Canada.,Dept of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Cindy Lin
- Program in Translational Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Hong Ouyang
- Program in Translational Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Kai Du
- Program in Molecular Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Anushree Kumar
- Program in Translational Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Borui Wang
- Program in Translational Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Julie Avolio
- Program in Translational Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Hartmut Grasemann
- Program in Translational Medicine, Hospital for Sick Children, Toronto, ON, Canada.,Division of Respiratory Medicine, Dept of Pediatrics, Hospital for Sick Children, Toronto, ON, Canada
| | - Theo J Moraes
- Program in Translational Medicine, Hospital for Sick Children, Toronto, ON, Canada.,Dept of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Division of Respiratory Medicine, Dept of Pediatrics, Hospital for Sick Children, Toronto, ON, Canada
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20
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Borkenhagen LK, Allen MW, Runstadler JA. Influenza virus genotype to phenotype predictions through machine learning: a systematic review. Emerg Microbes Infect 2021; 10:1896-1907. [PMID: 34498543 PMCID: PMC8462836 DOI: 10.1080/22221751.2021.1978824] [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: 11/22/2022]
Abstract
Background: There is great interest in understanding the viral genomic predictors of phenotypic traits that allow influenza A viruses to adapt to or become more virulent in different hosts. Machine learning techniques have demonstrated promise in addressing this critical need for other pathogens because the underlying algorithms are especially well equipped to uncover complex patterns in large datasets and produce generalizable predictions for new data. As the body of research where these techniques are applied for influenza A virus phenotype prediction continues to grow, it is useful to consider the strengths and weaknesses of these approaches to understand what has prevented these models from seeing widespread use by surveillance laboratories and to identify gaps that are underexplored with this technology. Methods and Results: We present a systematic review of English literature published through 15 April 2021 of studies employing machine learning methods to generate predictions of influenza A virus phenotypes from genomic or proteomic input. Forty-nine studies were included in this review, spanning the topics of host discrimination, human adaptability, subtype and clade assignment, pandemic lineage assignment, characteristics of infection, and antiviral drug resistance. Conclusions: Our findings suggest that biases in model design and a dearth of wet laboratory follow-up may explain why these models often go underused. We, therefore, offer guidance to overcome these limitations, aid in improving predictive models of previously studied influenza A virus phenotypes, and extend those models to unexplored phenotypes in the ultimate pursuit of tools to enable the characterization of virus isolates across surveillance laboratories.
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Affiliation(s)
- Laura K Borkenhagen
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, USA
| | - Martin W Allen
- Department of Computer Science, School of Engineering, Tufts University, Medford, MA, USA
| | - Jonathan A Runstadler
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, USA
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21
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Girardi E, Pfeffer S, Baumert TF, Majzoub K. Roadblocks and fast tracks: How RNA binding proteins affect the viral RNA journey in the cell. Semin Cell Dev Biol 2021; 111:86-100. [PMID: 32847707 PMCID: PMC7443355 DOI: 10.1016/j.semcdb.2020.08.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/14/2020] [Accepted: 08/14/2020] [Indexed: 12/12/2022]
Abstract
As obligate intracellular parasites with limited coding capacity, RNA viruses rely on host cells to complete their multiplication cycle. Viral RNAs (vRNAs) are central to infection. They carry all the necessary information for a virus to synthesize its proteins, replicate and spread and could also play essential non-coding roles. Regardless of its origin or tropism, vRNA has by definition evolved in the presence of host RNA Binding Proteins (RBPs), which resulted in intricate and complicated interactions with these factors. While on one hand some host RBPs recognize vRNA as non-self and mobilize host antiviral defenses, vRNA must also co-opt other host RBPs to promote viral infection. Focusing on pathogenic RNA viruses, we will review important scenarios of RBP-vRNA interactions during which host RBPs recognize, modify or degrade vRNAs. We will then focus on how vRNA hijacks the largest ribonucleoprotein complex (RNP) in the cell, the ribosome, to selectively promote the synthesis of its proteins. We will finally reflect on how novel technologies are helping in deepening our understanding of vRNA-host RBPs interactions, which can be ultimately leveraged to combat everlasting viral threats.
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Affiliation(s)
- Erika Girardi
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France
| | - Sebastien Pfeffer
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France
| | - Thomas F Baumert
- Inserm, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Université de Strasbourg, 67000, Strasbourg, France; Pole Hépatodigestif, Institut Hopitalo-universitaire, Hopitaux Universitaires de Strasbourg, 67000 Strasbourg, France
| | - Karim Majzoub
- Inserm, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Université de Strasbourg, 67000, Strasbourg, France.
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22
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Nganso BT, Sela N, Soroker V. A genome-wide screening for RNAi pathway proteins in Acari. BMC Genomics 2020; 21:791. [PMID: 33183236 PMCID: PMC7659050 DOI: 10.1186/s12864-020-07162-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 10/19/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND RNA interference (RNAi) is a highly conserved, sequence-specific gene silencing mechanism present in Eukaryotes. Three RNAi pathways are known, namely micro-RNA (miRNA), piwi-interacting RNA (piRNA) and short interfering RNA (siRNA). However, little knowledge exists about the proteins involved in these pathways in Acari. Moreover, variable successes has been obtained in gene knockdown via siRNA pathway in their functional genomics and management. We hypothesized that the clue may be in the variability of the composition and the efficacy of siRNA machinery among Acari. RESULTS Both comparative genomic analyses and domain annotation suggest that all the analyzed species have homologs of putative core proteins that mediate cleaving of targeted genes via the three RNAi pathways. We identified putative homologs of Caenorhabditis elegans RNA-dependent RNA polymerase (RdRP) protein in all species though no secondary Argonaute homologs that operate with this protein in siRNA amplification mechanism were found, suggesting that the siRNA amplification mechanism present in Acari may be distinct from that described in C. elegans. Moreover, the genomes of these species do not encode homologs of C. elegans systemic RNAi defective-1 (Sid-1) protein that mediate silencing of the mRNA target throughout the treated organisms suggesting that the phenomena of systemic RNAi that has been reported in some Acari species probably occur through a different mechanism. However, homologs of putative RNAi spreading defective-3 (Rsd-3) protein and scavenger receptors namely Eater and SR-CI that mediate endocytosis cellular update of dsRNA in C. elegans and Drosophila melanogaster were found in Acari genomes. This result suggests that cellular dsRNA uptake in Acari is endocytosis-dependent. Detailed phylogenetic analyses of core RNAi pathway proteins in the studied species revealed that their evolution is compatible with the proposed monophyletic evolution of this group. CONCLUSIONS Our analyses have revealed the potential activity of all three pathways in Acari. Still, much experimental work remains to be done to confirm the mechanisms behind these pathways in particular those that govern systemic/parental RNAi and siRNA amplification in Acari. Disclosure of these mechanisms will facilitate the development of new and specific management tools for the harmful species and enrichment of the beneficial species.
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Affiliation(s)
- Beatrice T Nganso
- Institute of Plant Protection, Agricultural Research Organization, the Volcani Center, P.O.B 15159, 7505101, Rishon leZion, Israel
| | - Noa Sela
- Institute of Plant Protection, Agricultural Research Organization, the Volcani Center, P.O.B 15159, 7505101, Rishon leZion, Israel
| | - Victoria Soroker
- Institute of Plant Protection, Agricultural Research Organization, the Volcani Center, P.O.B 15159, 7505101, Rishon leZion, Israel.
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Fois A, Boucher-Lafleur AM, Thompson Legault J, Renaud C, Morin C, Des Rosiers C, Coderre L, Laprise C, Lesage S. Humoral responses to the measles, mumps and rubella vaccine are impaired in Leigh Syndrome French Canadian patients. PLoS One 2020; 15:e0239860. [PMID: 33085679 PMCID: PMC7577467 DOI: 10.1371/journal.pone.0239860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 09/14/2020] [Indexed: 12/21/2022] Open
Abstract
Leigh Syndrome French Canadian (LSFC) is a rare autosomal recessive metabolic disorder characterized by severe lactic acidosis crises and early mortality. LSFC patients carry mutations in the Leucine Rich Pentatricopeptide Repeat Containing (LRPPRC) gene, which lead to defects in the respiratory chain complexes and mitochondrial dysfunction. Mitochondrial respiration modulates cellular metabolic activity, which impacts many cell types including the differentiation and function of immune cells. Hence, we postulated that, in addition to neurological and metabolic disorders, LSFC patients may show impaired immune activity. To gain insight into the quality of the immune response in LSFC patients, we examined the response to the measles, mumps and rubella (MMR) vaccine by measuring antibody titers to MMR in the plasma. In a cohort of eight LSFC patients, the response to the MMR vaccine was variable, with some individuals showing antibodies to all three viruses, while others had antibodies to two or fewer viruses. These results suggest that the mutations in the LRPPRC gene present in LSFC patients may affect the immune response to vaccines. Monitoring vaccine response in this fragile population should be considered to ensure full protection against pathogens.
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Affiliation(s)
- Adrien Fois
- Immunology-oncology Section, Maisonneuve-Rosemont Hospital Research Center, Montréal, Québec, Canada
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Québec, Canada
| | | | | | - Christian Renaud
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Québec, Canada
| | | | | | - Lise Coderre
- Immunology-oncology Section, Maisonneuve-Rosemont Hospital Research Center, Montréal, Québec, Canada
| | - Catherine Laprise
- Centre intersectoriel en santé durable, Université du Québec à Chicoutimi, Saguenay, Québec, Canada
| | - Sylvie Lesage
- Immunology-oncology Section, Maisonneuve-Rosemont Hospital Research Center, Montréal, Québec, Canada
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Québec, Canada
- * E-mail:
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Eiermann N, Haneke K, Sun Z, Stoecklin G, Ruggieri A. Dance with the Devil: Stress Granules and Signaling in Antiviral Responses. Viruses 2020; 12:v12090984. [PMID: 32899736 PMCID: PMC7552005 DOI: 10.3390/v12090984] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/31/2020] [Accepted: 08/31/2020] [Indexed: 02/07/2023] Open
Abstract
Cells have evolved highly specialized sentinels that detect viral infection and elicit an antiviral response. Among these, the stress-sensing protein kinase R, which is activated by double-stranded RNA, mediates suppression of the host translation machinery as a strategy to limit viral replication. Non-translating mRNAs rapidly condensate by phase separation into cytosolic stress granules, together with numerous RNA-binding proteins and components of signal transduction pathways. Growing evidence suggests that the integrated stress response, and stress granules in particular, contribute to antiviral defense. This review summarizes the current understanding of how stress and innate immune signaling act in concert to mount an effective response against virus infection, with a particular focus on the potential role of stress granules in the coordination of antiviral signaling cascades.
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Affiliation(s)
- Nina Eiermann
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany; (N.E.); (K.H.); (G.S.)
| | - Katharina Haneke
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany; (N.E.); (K.H.); (G.S.)
| | - Zhaozhi Sun
- Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research (CIID), University of Heidelberg, 69120 Heidelberg, Germany;
| | - Georg Stoecklin
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany; (N.E.); (K.H.); (G.S.)
| | - Alessia Ruggieri
- Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research (CIID), University of Heidelberg, 69120 Heidelberg, Germany;
- Correspondence:
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Fan S, Wu K, Luo C, Li X, Zhao M, Song D, Ma S, Zhu E, Chen Y, Ding H, Yi L, Li J, Zhao M, Chen J. Dual NDP52 Function in Persistent CSFV Infection. Front Microbiol 2020; 10:2962. [PMID: 31969869 PMCID: PMC6960106 DOI: 10.3389/fmicb.2019.02962] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 12/09/2019] [Indexed: 12/16/2022] Open
Abstract
Viruses have evolved many mechanisms to escape host antiviral responses. Previously, we found that classical swine fever virus (CSFV) infection induces autophagy using the autophagosome as a self-replication site, thereby evading the host immune response and promoting long-term infection. However, the underlying mechanisms used by CSFV to enter autophagosomes and the mechanism by which autophagy promotes viral replication remain unclear. We found that CSFV infection inhibited autophagy receptor nuclear dot protein 52 kDa (NDP52) expression, ubiquitination, and SUMO2-4 modification. Further analyses revealed that CSFV mediated ubiquitination and SUMOylation of NDP52 via Pten-induced kinase 1 (PINK1)-Parkin. Moreover, NDP52 inhibition also inhibited CSFV replication and the induction of mitophagy marker proteins expression. Inhibition of NDP52 reduced CD63 expression and binding to CSFV E2 protein, which has an essential role in persistent CSFV infection. As NDP52 has a close relationship with the NF-κB innate immunity pathway and plays an important role in the antiviral response, we investigated whether NDP52 inhibited CSFV replication through the release of immune factors and antivirus signals. Our results showed that inhibiting NDP52 boosted interferon and TNF release and promoted NF-κB pathway activation. In summary, we found that NDP52 inhibition not only reduces CSFV binding and entry into autophagic vesicles, but also inhibits CSFV replication by active NF-κB antiviral immune pathways. Our data reveal a novel mechanism by which NDP52, an autophagy receptor, mediates CSFV infection, and provide new avenues for the development of antiviral strategies.
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Affiliation(s)
- Shuangqi Fan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Keke Wu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Chaowei Luo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xin Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Mengpo Zhao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Dan Song
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Shengming Ma
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Erpeng Zhu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yuming Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Hongxing Ding
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Lin Yi
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jun Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Mingqiu Zhao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jinding Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
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Special Issue "IFN-Independent ISG Expression and its Role in Antiviral Cell-Intrinsic Innate Immunity". Viruses 2019; 11:v11110981. [PMID: 31653097 PMCID: PMC6893697 DOI: 10.3390/v11110981] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 10/23/2019] [Indexed: 02/07/2023] Open
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