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Shekhar MS, Karthic K, Kumar KV, Kumar JA, Swathi A, Hauton C, Peruzza L, Vijayan KK. Comparative analysis of shrimp (Penaeus vannamei) miRNAs expression profiles during WSSV infection under experimental conditions and in pond culture. FISH & SHELLFISH IMMUNOLOGY 2019; 93:288-295. [PMID: 31330255 DOI: 10.1016/j.fsi.2019.07.057] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 06/17/2019] [Accepted: 07/19/2019] [Indexed: 06/10/2023]
Abstract
In recent years, the importance of viral and host microRNAs (miRNAs) in mediating viral replication and control of host cellular machinery, has been realised and increasing efforts have been taken in order to understand the interactions of miRNAs from host and pathogen during infection. However, all existing studies has thus far been conducted in controlled experimental conditions and the veracity of these data for field conditions are yet to be established. In this framework, small RNA sequencing was performed to identify the miRNAs involved in shrimp (Penaeus vannamei) immune responses under two different WSSV infection conditions of natural infection and experimentally challenged conditions. The expression profiles of miRNAs of shrimp infected with WSSV under two contrasting conditions were compared and as a result, 23365 known miRNAs and 481 novel miRNAs were identified. Amongst the most abundantly expressed miRNAs, the hypoxia related miR-210 and immune pathway related miR-29b were expressed only in infected shrimps of both conditions. miR-8-5p, having a functional role in modulation of chitin biosynthesis was exclusively represented in higher numbers in the WSSV -infected shrimps under natural conditions whilst four of the miRNAs (mja-miR-6493-5p, mja-miR-6492, mmu-miR-3968, tcf-miR-9b-5p) identified from shrimps collected from pond culture targeted chitinase, an important enzyme involved in growth and moulting in shrimps, indicating an interaction between WSSV infection and moult cycle under culture conditions. Some of the miRNAs (tca-miR-87b-3p, cte-miR-277a) and miRNAs belonging to class miR-9, miR-981 that were identified only in WSSV infected shrimps under experimental conditions, are known to respond against WSSV infection in shrimps. Moreover, the miRNA target prediction revealed several immune-related gene targets such as cathepsin, c-type lectin, haemocyanin and ubiquitin protein ligase were commonly identified under both the conditions. However, the miRNAs identified from challenge experiment had wide number of gene targets as compared to the miRNAs of natural infection. The shrimp miRNA mja-miR-6489-3p, was also found to target early virus gene wsv001 of WSSV. Our study, therefore, provides the comparative analysis of miRNA expression from shrimp during WSSV infection in two different conditions.
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Affiliation(s)
- M S Shekhar
- Genetics and Biotechnology Unit, Central Institute of Brackishwater Aquaculture, 75 Santhome High Road, R.A Puram, Chennai, India.
| | - K Karthic
- Genetics and Biotechnology Unit, Central Institute of Brackishwater Aquaculture, 75 Santhome High Road, R.A Puram, Chennai, India
| | - K Vinaya Kumar
- Genetics and Biotechnology Unit, Central Institute of Brackishwater Aquaculture, 75 Santhome High Road, R.A Puram, Chennai, India
| | - J Ashok Kumar
- Genetics and Biotechnology Unit, Central Institute of Brackishwater Aquaculture, 75 Santhome High Road, R.A Puram, Chennai, India
| | - A Swathi
- Genetics and Biotechnology Unit, Central Institute of Brackishwater Aquaculture, 75 Santhome High Road, R.A Puram, Chennai, India
| | - Chris Hauton
- School of Ocean and Earth Science, University of Southampton, Hampshire, SO14 3ZH, United Kingdom
| | - L Peruzza
- School of Ocean and Earth Science, University of Southampton, Hampshire, SO14 3ZH, United Kingdom
| | - K K Vijayan
- Genetics and Biotechnology Unit, Central Institute of Brackishwater Aquaculture, 75 Santhome High Road, R.A Puram, Chennai, India
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Rosen A, Casciola-Rosen L. Autoantigens as Partners in Initiation and Propagation of Autoimmune Rheumatic Diseases. Annu Rev Immunol 2016; 34:395-420. [PMID: 26907212 DOI: 10.1146/annurev-immunol-032414-112205] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Systemic autoimmune diseases are characterized by specific targeting of a limited group of ubiquitously expressed autoantigens by the immune system. This review examines the mechanisms underlying their selection as immune targets. Initiation of autoimmune responses likely reflects the presentation of antigens with a distinct structure not previously encountered by the immune system, in a proimmune context (injury, malignancy, or infection). Causes of modified structure include somatic mutation and posttranslational modifications (including citrullination and proteolysis). Many autoantigens are components of multimolecular complexes, and some of the other components may provide adjuvant activity. Propagation of autoimmune responses appears to reflect a bidirectional interaction between the immune response and the target tissues in a mutually reinforcing cycle: Immune effector pathways generate additional autoantigen, which feeds further immune response. We propose that this resonance may be a critical principle underlying disease propagation, with specific autoantigens functioning as the hubs around which amplification occurs.
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Affiliation(s)
- Antony Rosen
- Division of Rheumatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21224; ,
| | - Livia Casciola-Rosen
- Division of Rheumatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21224; ,
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Petrova EK, Dmitrieva AA, Trifonova EA, Nikitin NA, Karpova OV. The key role of rubella virus glycoproteins in the formation of immune response, and perspectives on their use in the development of new recombinant vaccines. Vaccine 2016; 34:1006-11. [PMID: 26776468 DOI: 10.1016/j.vaccine.2016.01.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 12/29/2015] [Accepted: 01/05/2016] [Indexed: 12/23/2022]
Abstract
Rubella is a highly contagious viral disease which is mostly threatens to women of reproductive age. Existent live attenuated vaccines are effective enough, but have some drawbacks and are unusable for a certain group of people, including pregnant women and people with AIDS and other immunodeficiency. Thereby the development of alternative non-replicating, recombinant vaccines undoubtedly is needed. This review discusses the protein E1 and E2 role in formation of immune response and perspectives in development of new generation recombinant vaccines using them.
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Affiliation(s)
- Ekaterina K Petrova
- Faculty of Biology, Department of Virology, Lomonosov Moscow State University, 1/12 Leninskie Gory, Moscow 119234, Russia.
| | - Anastasia A Dmitrieva
- Faculty of Biology, Department of Virology, Lomonosov Moscow State University, 1/12 Leninskie Gory, Moscow 119234, Russia
| | - Ekaterina A Trifonova
- Faculty of Biology, Department of Virology, Lomonosov Moscow State University, 1/12 Leninskie Gory, Moscow 119234, Russia
| | - Nikolai A Nikitin
- Faculty of Biology, Department of Virology, Lomonosov Moscow State University, 1/12 Leninskie Gory, Moscow 119234, Russia
| | - Olga V Karpova
- Faculty of Biology, Department of Virology, Lomonosov Moscow State University, 1/12 Leninskie Gory, Moscow 119234, Russia
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Reddy MS, Kanakala S, Srinivas KP, Hema M, Malathi VG, Sreenivasulu P. Complete genome sequence of a new begomovirus associated with yellow mosaic disease of Hemidesmus indicus in India. Arch Virol 2013; 159:1223-8. [PMID: 24276235 DOI: 10.1007/s00705-013-1811-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 06/27/2013] [Indexed: 11/30/2022]
Abstract
The complete DNA A genome of a virus isolate associated with yellow mosaic disease of a medicinal plant, Hemidesmus indicus, from India was cloned and sequenced. The length of DNA A was 2825 nucleotides, 35 nucleotides longer than the unit genome of monopartite begomoviruses. Comparison of the nucleotide sequence of DNA A of the virus isolate with those of other begomoviruses showed maximum sequence identity of 69 % to DNA A of ageratum yellow vein China virus (AYVCNV; AJ558120) and 68 % with tomato yellow leaf curl virus- LBa4 (TYLCV; EF185318), and it formed a distinct clade in phylogenetic analysis. The genome organization of the present virus isolate was found to be similar to that of Old World monopartite begomoviruses. The genome was considered to be monopartite, because association of DNA B and β satellite DNA components was not detected. Based on its sequence identity (<70 %) to all other begomoviruses known to date and ICTV (International Committee on Taxonomy of Viruses) species demarcating criteria (<89 % identity), it is considered a member of a novel begomovirus species, and the tentative name "Hemidesmus yellow mosaic virus" (HeYMV) is proposed.
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Affiliation(s)
- M Sreekanth Reddy
- Sri Venkateswara University, Tirupati, Andhra Pradesh, 517 502, India
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Khadka S, Vangeloff AD, Zhang C, Siddavatam P, Heaton NS, Wang L, Sengupta R, Sahasrabudhe S, Randall G, Gribskov M, Kuhn RJ, Perera R, LaCount DJ. A physical interaction network of dengue virus and human proteins. Mol Cell Proteomics 2011; 10:M111.012187. [PMID: 21911577 DOI: 10.1074/mcp.m111.012187] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Dengue virus (DENV), an emerging mosquito-transmitted pathogen capable of causing severe disease in humans, interacts with host cell factors to create a more favorable environment for replication. However, few interactions between DENV and human proteins have been reported to date. To identify DENV-human protein interactions, we used high-throughput yeast two-hybrid assays to screen the 10 DENV proteins against a human liver activation domain library. From 45 DNA-binding domain clones containing either full-length viral genes or partially overlapping gene fragments, we identified 139 interactions between DENV and human proteins, the vast majority of which are novel. These interactions involved 105 human proteins, including six previously implicated in DENV infection and 45 linked to the replication of other viruses. Human proteins with functions related to the complement and coagulation cascade, the centrosome, and the cytoskeleton were enriched among the DENV interaction partners. To determine if the cellular proteins were required for DENV infection, we used small interfering RNAs to inhibit their expression. Six of 12 proteins targeted (CALR, DDX3X, ERC1, GOLGA2, TRIP11, and UBE2I) caused a significant decrease in the replication of a DENV replicon. We further showed that calreticulin colocalized with viral dsRNA and with the viral NS3 and NS5 proteins in DENV-infected cells, consistent with a direct role for calreticulin in DENV replication. Human proteins that interacted with DENV had significantly higher average degree and betweenness than expected by chance, which provides additional support for the hypothesis that viruses preferentially target cellular proteins that occupy central position in the human protein interaction network. This study provides a valuable starting point for additional investigations into the roles of human proteins in DENV infection.
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Affiliation(s)
- Sudip Khadka
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
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McLaughlin M, Vandenbroeck K. The endoplasmic reticulum protein folding factory and its chaperones: new targets for drug discovery? Br J Pharmacol 2011; 162:328-45. [PMID: 20942857 DOI: 10.1111/j.1476-5381.2010.01064.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Cytosolic heat shock proteins have received significant attention as emerging therapeutic targets. Much of this excitement has been triggered by the discovery that HSP90 plays a central role in the maintenance and stability of multifarious oncogenic membrane receptors and their resultant tyrosine kinase activity. Numerous studies have dealt with the effects of small molecules on chaperone- and stress-related pathways of the endoplasmic reticulum (ER). However, unlike cytosolic chaperones, relatively little emphasis has been placed upon translational avenues towards targeting of the ER for inhibition of folding/secretion of disease-promoting proteins. Here, we summarise existing small molecule inhibitors and potential future targets of ER chaperone-mediated inhibition. Client proteins of translational relevance in disease treatment are outlined, alongside putative future disease treatment modalities based on ER-centric targeted therapies. Particular attention is paid to cancer and autoimmune disorders via the effects of the GRP94 inhibitor geldanamycin and its population of client proteins, overloading of the unfolded protein response, and inhibition of members of the IL-12 family of cytokines by celecoxib and non-coxib analogues.
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Li G, Scull C, Ozcan L, Tabas I. NADPH oxidase links endoplasmic reticulum stress, oxidative stress, and PKR activation to induce apoptosis. Crit Rev Microbiol 2010; 41:150-64. [PMID: 25168431 PMCID: PMC7113905 DOI: 10.3109/1040841x.2013.813899] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The endoplasmic reticulum (ER) is a cellular membrane organelle that plays important roles in virus replication and maturation. Accumulating evidence indicates that virus infection often disturbs ER homeostasis and leads to ER stress, which is associated with a variety of prevalent diseases. To cope with the deleterious effects of virus-induced ER stress, cells activate critical signaling pathways including the unfolded protein response (UPR) and intrinsic mitochondrial apoptosis, which have complex effects on virus replication and pathogenesis. In this review, we present a comprehensive summary of recent research in this field, which revealed that about 36 viruses trigger ER stress and differentially activate ER stress-related signaling pathways. We also highlight the strategies evolved by viruses to modulate ER stress-related signaling networks including immune responses in order to ensure their survival and pathogenesis. Together, the knowledge gained from this field will shed light on unveiling the mechanisms of virus replication and pathogenesis and provide insight for future research as well as antiviral development.
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Affiliation(s)
- Gang Li
- Department of Medicine, Columbia University, New York, NY 10032, USA
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Galluzzi L, Kepp O, Morselli E, Vitale I, Senovilla L, Pinti M, Zitvogel L, Kroemer G. Viral strategies for the evasion of immunogenic cell death. J Intern Med 2010; 267:526-42. [PMID: 20433579 DOI: 10.1111/j.1365-2796.2010.02223.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Viral strategies for the evasion of immunogenic cell death (Symposium). J Intern Med 2010; 267: 526-542. Driven by co-evolutionary forces, viruses have refined a wide arsenal of strategies to interfere with the host defences. On one hand, viruses can block/retard programmed cell death in infected cells, thereby suppressing one of the most ancient mechanisms against viral dissemination. On the other hand, multiple viral factors can efficiently trigger the death of infected cells and uninfected cells from the immune system, which favours viral spreading and prevents/limits an active antiviral response, respectively. Moreover, several viruses are able to inhibit the molecular machinery that drives the translocation of calreticulin to the surface of dying cells. Thereby, viruses block the exposure of an engulfment signal that is required for the efficient uptake of dying cells by dendritic cells and for the induction of the immune response. In this review, we discuss a variety of mechanisms by which viruses interfere with the cell death machinery and, in particular, by which they subvert immunogenic cell death.
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Zhou Y, Frey TK, Yang JJ. Viral calciomics: interplays between Ca2+ and virus. Cell Calcium 2009; 46:1-17. [PMID: 19535138 PMCID: PMC3449087 DOI: 10.1016/j.ceca.2009.05.005] [Citation(s) in RCA: 206] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2008] [Revised: 05/15/2009] [Accepted: 05/18/2009] [Indexed: 12/23/2022]
Abstract
Ca2+ is one of the most universal and versatile signaling molecules and is involved in almost every aspect of cellular processes. Viruses are adept at utilizing the universal Ca2+ signal to create a tailored cellular environment that meets their own demands. This review summarizes most of the known mechanisms by which viruses perturb Ca2+ homeostasis and utilize Ca2+ and cellular Ca2+-binding proteins to their benefit in their replication cycles. Ca2+ plays important roles in virion structure formation, virus entry, viral gene expression, posttranslational processing of viral proteins and virion maturation and release. As part of the review, we introduce an algorithm to identify linear “EF-hand” Ca2+-binding motifs which resulted in the prediction of a total of 93 previously unrecognized Ca2+-binding motifs in virus proteins. Many of these proteins are nonstructural proteins, a class of proteins among which Ca2+ interactions had not been formerly appreciated. The presence of linear Ca2+-binding motifs in viral proteins enlarges the spectrum of Ca2+–virus interplay and expands the total scenario of viral calciomics.
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Affiliation(s)
- Yubin Zhou
- Department of Chemistry, Georgia State University, 50 Decatur St., Atlanta, GA 30303 USA
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Lodes MJ, Suciu D, Elliott M, Stover AG, Ross M, Caraballo M, Dix K, Crye J, Webby RJ, Lyon WJ, Danley DL, McShea A. Use of semiconductor-based oligonucleotide microarrays for influenza a virus subtype identification and sequencing. J Clin Microbiol 2006; 44:1209-18. [PMID: 16597840 PMCID: PMC1448669 DOI: 10.1128/jcm.44.4.1209-1218.2006] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the face of concerns over an influenza pandemic, identification of virulent influenza A virus isolates must be obtained quickly for effective responses. Rapid subtype identification, however, is difficult even in well-equipped virology laboratories or is unobtainable in the field under more austere conditions. Here we describe a genome assay and microarray design that can be used to rapidly identify influenza A virus hemagglutinin subtypes 1 through 15 and neuraminidase subtypes 1 through 9. Also described is an array-based enzymatic assay that can be used to sequence portions of both genes or any other sequence of interest.
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Affiliation(s)
- Michael J Lodes
- CombiMatrix Corporation, 6500 Harbour Heights Parkway, Suite 301, Mukilteo, WA 98275, USA.
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Tanaka Y, Kato J, Kohara M, Galinski MS. Antiviral effects of glycosylation and glucose trimming inhibitors on human parainfluenza virus type 3. Antiviral Res 2006; 72:1-9. [PMID: 16730076 DOI: 10.1016/j.antiviral.2006.03.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2005] [Revised: 03/04/2006] [Accepted: 03/04/2006] [Indexed: 10/24/2022]
Abstract
Endoplasmic reticulum (ER) alpha-glucosidase inhibitors block the trimming of N-linked glycosylation and thus prevent the production of several viruses. The present study investigates the antiviral effects of the alpha-glucosidase and alpha-mannosidase inhibitors (castanospermine, 1-deoxynojirimycin, bromoconduritol, deoxymannojirimycin and swainsonine) on human parainfluenza virus type 3 (HPIV3). The alpha-glucosidase inhibitors (castanospermine, 1-deoxynojirimycin) in recombinant expression systems reduced the surface and intracellular expression of both HPIV3 F and HN proteins. On the other hand, alpha-mannosidase inhibitors prevented processing of the oligosaccharides on HPIV3 glycoproteins into the complex form. Consequently, alpha-glycosidase inhibitors (castanospermine and 1-deoxynojirimycin) significantly inhibited viral fusion activity. We demonstrated that the alpha-glucosidase inhibitors (castanospermine and 1-deoxynojirimycin) reduced the infectivity of newly released viral particles. We postulate that alpha-glucosidase inhibitors can prevent the first steps of HPIV3 envelope glycoprotein processing and that the inhibition of glucose trimming has antiviral effects.
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Affiliation(s)
- Yoshikazu Tanaka
- Department of Veterinary Hygiene, Veterinary School, Nippon Veterinary & Life Science University, 1-7-1 Kyounan, Musashino, Tokyo 180-8602, Japan.
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Ramanujam M, Hofmann J, Nakhasi HL, Atreya CD. Effect of site-directed asparagine to isoleucine substitutions at the N-linked E1 glycosylation sites on rubella virus viability. Virus Res 2001; 81:151-6. [PMID: 11682134 DOI: 10.1016/s0168-1702(01)00374-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The role of three N-linked glycosylation sites in rubella virus (RV) E1 protein on virion release was analyzed by transfecting Vero 76 cells with infectious RV RNA (Robo302WT) containing isoleucine substitutions at N76, N177, and N209 (individually and in combinations). RV RNAs were detected and found to retain substitutions in the transfected cells, but RV capsid indicative of infection was undetectable, except for in Robo302WT and Robo302-N177I transfected cells. Only culture supernatants of Robo302WT and Robo302-N177I RNA transfected cells were positive for RV, suggestive of the virion release into the culture medium. Further, detection of intracellular RV E1 and newly released virion-associated E1 was possible only from cells previously incubated with Robo302-N177I and Robo302WT culture supernatants, suggesting that N177I substituted virus retained infectivity. These results suggest that while glycosylation at N177 is not critical, N76I and N209I mutations are lethal to RV viability.
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Affiliation(s)
- M Ramanujam
- Center for Biologics Evaluation and Research (CBER), Food and Drug Administration, Bethesda, MD 20892, USA
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