1
|
Motorina DM, Galimova YA, Battulina NV, Omelina ES. Systems for Targeted Silencing of Gene Expression and Their Application in Plants and Animals. Int J Mol Sci 2024; 25:5231. [PMID: 38791270 PMCID: PMC11121118 DOI: 10.3390/ijms25105231] [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: 04/15/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
At present, there are a variety of different approaches to the targeted regulation of gene expression. However, most approaches are devoted to the activation of gene transcription, and the methods for gene silencing are much fewer in number. In this review, we describe the main systems used for the targeted suppression of gene expression (including RNA interference (RNAi), chimeric transcription factors, chimeric zinc finger proteins, transcription activator-like effectors (TALEs)-based repressors, optogenetic tools, and CRISPR/Cas-based repressors) and their application in eukaryotes-plants and animals. We consider the advantages and disadvantages of each approach, compare their effectiveness, and discuss the peculiarities of their usage in plant and animal organisms. This review will be useful for researchers in the field of gene transcription suppression and will allow them to choose the optimal method for suppressing the expression of the gene of interest depending on the research object.
Collapse
Affiliation(s)
| | | | | | - Evgeniya S. Omelina
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| |
Collapse
|
2
|
Wang Y, Liu H, Wang Z, Guo Y, Hu T, Zhou X. P25 and P37 proteins encoded by firespike leafroll-associated virus are viral suppressors of RNA silencing. Front Microbiol 2022; 13:964156. [PMID: 36051767 PMCID: PMC9424829 DOI: 10.3389/fmicb.2022.964156] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
Firespike leafroll-associated virus (FLRaV) is a major pathogen associated with firespike (Odontonema tubaeforme) leafroll disease. Phylogenetic analysis showed that FLRaV possesses typical traits of subgroup II members of ampeloviruses, but encodes two additional proteins, P25 and P37. Here, we determined the microfilament localization of P25 protein. Posttranscriptional gene silencing (PTGS) assay showed that both FLRaV P25 and P37 were able to suppress the local and systemic PTGS and FLRaV P25 was capable of suppressing the green fluorescent protein (GFP) gene silencing triggered by both sense RNA-induced PTGS (S-PTGS) and inverted repeat RNA-induced PTGS (IR-PTGS). In contrast, FLRaV P37 was only able to inhibit the GFP silencing triggered by the S-PTGS but not the IR-PTGS. In the transcriptional gene silencing (TGS) assay, only FLRaV P25 was found to be able to reverse established TGS-mediated silencing of GFP in 16-TGS plants. We also found that FLRaV P25 could aggravate the disease symptom and viral titer of potato virus X in N. benthamiana. These results suggest that FLRaV P25 and P37 may have crucial roles in overcoming host RNA silencing, which provides key insights into our understanding of the molecular mechanisms underlying FLRaV infection.
Collapse
Affiliation(s)
- Yaqin Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Hui Liu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Zhanqi Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, China
| | - Yushuang Guo
- Key Laboratory of Molecular Genetics, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Tao Hu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
- *Correspondence: Tao Hu,
| | - Xueping Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Xueping Zhou,
| |
Collapse
|
3
|
Ghavami S, Zamani M, Ahmadi M, Erfani M, Dastghaib S, Darbandi M, Darbandi S, Vakili O, Siri M, Grabarek BO, Boroń D, Zarghooni M, Wiechec E, Mokarram P. Epigenetic regulation of autophagy in gastrointestinal cancers. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166512. [PMID: 35931405 DOI: 10.1016/j.bbadis.2022.166512] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 07/11/2022] [Accepted: 07/28/2022] [Indexed: 11/09/2022]
Abstract
The development of novel therapeutic approaches is necessary to manage gastrointestinal cancers (GICs). Considering the effective molecular mechanisms involved in tumor growth, the therapeutic response is pivotal in this process. Autophagy is a highly conserved catabolic process that acts as a double-edged sword in tumorigenesis and tumor inhibition in a context-dependent manner. Depending on the stage of malignancy and cellular origin of the tumor, autophagy might result in cancer cell survival or death during the GICs' progression. Moreover, autophagy can prevent the progression of GIC in the early stages but leads to chemoresistance in advanced stages. Therefore, targeting specific arms of autophagy could be a promising strategy in the prevention of chemoresistance and treatment of GIC. It has been revealed that autophagy is a cytoplasmic event that is subject to transcriptional and epigenetic regulation inside the nucleus. The effect of epigenetic regulation (including DNA methylation, histone modification, and expression of non-coding RNAs (ncRNAs) in cellular fate is still not completely understood. Recent findings have indicated that epigenetic alterations can modify several genes and modulators, eventually leading to inhibition or promotion of autophagy in different cancer stages, and mediating chemoresistance or chemosensitivity. The current review focuses on the links between autophagy and epigenetics in GICs and discusses: 1) How autophagy and epigenetics are linked in GICs, by considering different epigenetic mechanisms; 2) how epigenetics may be involved in the alteration of cancer-related phenotypes, including cell proliferation, invasion, and migration; and 3) how epidrugs modulate autophagy in GICs to overcome chemoresistance.
Collapse
Affiliation(s)
- Saeid Ghavami
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada; Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Research Institute of Hematology and Oncology, Cancer Care Manitoba, Winnipeg, MB R3E 0V9, Canada; Faculty of Medicine in Zabrze, University of Technology in Katowice, Academia of Silesia, 41-800 Zabrze, Poland.
| | - Mozhdeh Zamani
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mazaher Ahmadi
- Department of Analytical Chemistry, Faculty of Chemistry, Bu-Ali Sina University, Hamedan, Iran
| | - Mehran Erfani
- Department of Biochemistry, School of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Sanaz Dastghaib
- Endocrinology and Metabolism Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mahsa Darbandi
- Fetal Health Research Center, Hope Generation Foundation, Tehran, Iran; Gene Therapy and Regenerative Medicine Research Center, Hope Generation Foundation, Tehran, Iran
| | - Sara Darbandi
- Fetal Health Research Center, Hope Generation Foundation, Tehran, Iran; Gene Therapy and Regenerative Medicine Research Center, Hope Generation Foundation, Tehran, Iran
| | - Omid Vakili
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Morvarid Siri
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Beniamin Oskar Grabarek
- Department of Histology, Cytophysiology, and Embryology in Zabrze, Faculty of Medicine in Zabrze, University of Technology in Katowice, Academia of Silesia, 41-800 Zabrze, Poland; Department of Gynecology and Obstetrics in Zabrze, Faculty of Medicine in Zabrze, University of Technology in Katowice, Academia of Silesia, 41-800 Zabrze, Poland
| | - Dariusz Boroń
- Department of Histology, Cytophysiology, and Embryology in Zabrze, Faculty of Medicine in Zabrze, University of Technology in Katowice, Academia of Silesia, 41-800 Zabrze, Poland; Department of Gynecology and Obstetrics in Zabrze, Faculty of Medicine in Zabrze, University of Technology in Katowice, Academia of Silesia, 41-800 Zabrze, Poland
| | - Maryam Zarghooni
- Department of Laboratory Medicine and Pathobiology, University of Toronto Alumni, Toronto, Canada
| | - Emilia Wiechec
- Division of Cell Biology, Department of Biomedical and Clinical Sciences, Linköping University, 58185 Linköping, Sweden
| | - Pooneh Mokarram
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
| |
Collapse
|
4
|
Annacondia ML, Martinez G. Reprogramming of RNA silencing triggered by cucumber mosaic virus infection in Arabidopsis. Genome Biol 2021; 22:340. [PMID: 34911561 PMCID: PMC8672585 DOI: 10.1186/s13059-021-02564-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 12/02/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND RNA silencing has an important role mediating sequence-specific virus resistance in plants. The complex interaction of viruses with RNA silencing involves the loading of viral small interfering RNAs (vsiRNAs) into its host ARGONAUTE (AGO) proteins. As a side effect of their antiviral activity, vsiRNAs loading into AGO proteins can also mediate the silencing of endogenous genes. Here, we analyze at the genome-wide level both aspects of the interference of cucumber mosaic virus (CMV) with the RNA silencing machinery of Arabidopsis thaliana. RESULTS We observe CMV-derived vsiRNAs affect the levels of endogenous sRNA classes. Furthermore, we analyze the incorporation of vsiRNAs into AGO proteins with a described antiviral role and the viral suppressor of RNA silencing (VSR) 2b, by combining protein immunoprecipitation with sRNA high-throughput sequencing. Interestingly, vsiRNAs represent a substantial percentage of AGO-loaded sRNAs and displace other endogenous sRNAs. As a countermeasure, the VSR 2b loaded vsiRNAs and mRNA-derived siRNAs, which affect the expression of the genes they derive from. Additionally, we analyze how vsiRNAs incorporate into the endogenous RNA silencing pathways by exploring their target mRNAs using parallel analysis of RNA end (PARE) sequencing, which allow us to identify vsiRNA-targeted genes genome-wide. CONCLUSIONS This work exemplifies the complex relationship of RNA viruses with the endogenous RNA silencing machinery and the multiple aspects of virus resistance and virulence that this interaction induces.
Collapse
Affiliation(s)
- Maria Luz Annacondia
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - German Martinez
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden.
| |
Collapse
|
5
|
Tarquini G, Pagliari L, Ermacora P, Musetti R, Firrao G. Trigger and Suppression of Antiviral Defenses by Grapevine Pinot Gris Virus (GPGV): Novel Insights into Virus-Host Interaction. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1010-1023. [PMID: 33983824 DOI: 10.1094/mpmi-04-21-0078-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Grapevine Pinot gris virus (GPGV) is an emerging trichovirus that has been putatively associated with a novel grapevine disease known as grapevine leaf mottling and deformation (GLMD). Yet the role of GPGV in GLMD disease is poorly understood, since it has been detected both in symptomatic and symptomless grapevines. We exploited a recently constructed GPGV infectious clone (pRI::GPGV-vir) to induce an antiviral response in Nicotiana benthamiana plants. In silico prediction of virus-derived small interfering RNAs and gene expression analyses revealed the involvement of DCL4, AGO5, and RDR6 genes during GPGV infection, suggesting the activation of the posttranscriptional gene-silencing (PTGS) pathway as a plant antiviral defense. PTGS suppression assays in transgenic N. benthamiana 16c plants revealed the ability of the GPGV coat protein to suppress RNA silencing. This work provides novel insights on the interaction between GPGV and its host, revealing the ability of the virus to trigger and suppress antiviral RNA silencing.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Collapse
Affiliation(s)
- Giulia Tarquini
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, Udine I-33100, Italy
| | - Laura Pagliari
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, Udine I-33100, Italy
| | - Paolo Ermacora
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, Udine I-33100, Italy
| | - Rita Musetti
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, Udine I-33100, Italy
| | - Giuseppe Firrao
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, Udine I-33100, Italy
| |
Collapse
|
6
|
HTS-Based Diagnostics of Sugarcane Viruses: Seasonal Variation and Its Implications for Accurate Detection. Viruses 2021; 13:v13081627. [PMID: 34452491 PMCID: PMC8402784 DOI: 10.3390/v13081627] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/09/2021] [Accepted: 08/13/2021] [Indexed: 01/26/2023] Open
Abstract
Rapid global germplasm trade has increased concern about the spread of plant pathogens and pests across borders that could become established, affecting agriculture and environment systems. Viral pathogens are of particular concern due to their difficulty to control once established. A comprehensive diagnostic platform that accurately detects both known and unknown virus species, as well as unreported variants, is playing a pivotal role across plant germplasm quarantine programs. Here we propose the addition of high-throughput sequencing (HTS) from total RNA to the routine quarantine diagnostic workflow of sugarcane viruses. We evaluated the impact of sequencing depth needed for the HTS-based identification of seven regulated sugarcane RNA/DNA viruses across two different growing seasons (spring and fall). Our HTS analysis revealed that viral normalized read counts (RPKM) was up to 23-times higher in spring than in the fall season for six out of the seven viruses. Random read subsampling analyses suggested that the minimum number of reads required for reliable detection of RNA viruses was 0.5 million, with a viral genome coverage of at least 92%. Using an HTS-based total RNA metagenomics approach, we identified all targeted viruses independent of the time of the year, highlighting that higher sequencing depth is needed for the identification of DNA viruses.
Collapse
|
7
|
Wang J, Zhang Q, You X, Hou X. Transcriptome and Small RNA Combined Sequencing Analysis of Cold Tolerance in Non-heading Chinese Cabbage. Front Genet 2021; 12:605292. [PMID: 34367230 PMCID: PMC8334874 DOI: 10.3389/fgene.2021.605292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 03/29/2021] [Indexed: 12/03/2022] Open
Abstract
Background Non-heading Chinese cabbage (Brassica rapa ssp. chinensis) is an important leaf vegetable grown worldwide. However, there has currently been not enough transcriptome and small RNA combined sequencing analysis of cold tolerance, which hinders further functional genomics research. Results In this study, 63.43 Gb of clean data was obtained from the transcriptome analysis. The clean data of each sample reached 6.99 Gb, and the basic percentage of Q30 was 93.68% and above. The clean reads of each sample were sequence aligned with the designated reference genome (Brassica rapa, IVFCAASv1), and the efficiency of the alignment varied from 81.54 to 87.24%. According to the comparison results, 1,860 new genes were discovered in Pak-choi, of which 1,613 were functionally annotated. Among them, 13 common differentially expressed genes were detected in all materials, including seven upregulated and six downregulated. At the same time, we used quantitative real-time PCR to confirm the changes of these gene expression levels. In addition, we sequenced miRNA of the same material. Our findings revealed a total of 34,182,333 small RNA reads, 88,604,604 kinds of small RNAs, among which the most common size was 24 nt. In all materials, the number of common differential miRNAs is eight. According to the corresponding relationship between miRNA and its target genes, we carried out Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis on the set of target genes on each group of differentially expressed miRNAs. Through the analysis, it is found that the distributions of candidate target genes in different materials are different. We not only used transcriptome sequencing and small RNA sequencing but also used experiments to prove the expression levels of differentially expressed genes that were obtained by sequencing. Sequencing combined with experiments proved the mechanism of some differential gene expression levels after low-temperature treatment. Conclusion In all, this study provides a resource for genetic and genomic research under abiotic stress in Pak-choi.
Collapse
Affiliation(s)
- Jin Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture/Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education, Nanjing Agricultural University, Nanjing, China.,School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Qinxue Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture/Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Xiong You
- College of Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xilin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture/Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| |
Collapse
|
8
|
Liu X, Shen L, Han B, Yao H. Involvement of noncoding RNA in blood-brain barrier integrity in central nervous system disease. Noncoding RNA Res 2021; 6:130-138. [PMID: 34377876 PMCID: PMC8327137 DOI: 10.1016/j.ncrna.2021.06.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 06/27/2021] [Accepted: 06/28/2021] [Indexed: 02/06/2023] Open
Abstract
Given the important role of the blood-brain barrier (BBB) in the central nervous system (CNS), increasing studies have been carried out to determine how the structural and functional integrity of the BBB impacts the pathogenesis of CNS diseases such as stroke, traumatic brain injuries (TBIs), and gliomas. Emerging studies have revealed that noncoding RNAs (ncRNAs) help to maintain the integrity and permeability of the BBB, thereby mediating CNS homeostasis. This review summarizes recent studies that focus on the effects of ncRNAs on the BBB in CNS diseases, including regulating the biological processes of inflammation, necrosis, and apoptosis of cells, affecting the translational dysfunction of proteins and regulating tight junctions (TJs). A comprehensive and detailed understanding of the interaction between ncRNAs and the BBB will lay a solid foundation for the development of early diagnostic methods and effective treatments for CNS diseases.
Collapse
Affiliation(s)
- Xi Liu
- School of Medicine, Southeast University, Nanjing, 210009, Jiangsu, China
| | - Ling Shen
- School of Medicine, Southeast University, Nanjing, 210009, Jiangsu, China
| | - Bing Han
- School of Medicine, Southeast University, Nanjing, 210009, Jiangsu, China
| | - Honghong Yao
- School of Medicine, Southeast University, Nanjing, 210009, Jiangsu, China
| |
Collapse
|
9
|
Structure and dsRNA-binding activity of the Birnavirus Drosophila X Virus VP3 protein. J Virol 2021; 95:JVI.02166-20. [PMID: 33239452 PMCID: PMC7851550 DOI: 10.1128/jvi.02166-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Birnavirus multifunctional protein VP3 plays an essential role coordinating the virus life cycle, interacting with the capsid protein VP2, with the RNA-dependent RNA polymerase VP1 and with the dsRNA genome. Furthermore, the role of this protein in controlling host cell responses triggered by dsRNA and preventing gene silencing has been recently demonstrated. Here we report the X-ray structure and dsRNA-binding activity of the N-terminal domain of Drosophila X virus (DXV) VP3. The domain folds in a bundle of three α-helices and arranges as a dimer, exposing to the surface a well-defined cluster of basic residues. Site directed mutagenesis combined with Electrophoretic Mobility Shift Assays (EMSA) and Surface Plasmon Resonance (SPR) revealed that this cluster, as well as a flexible and positively charged region linking the first and second globular domains of DXV VP3, are essential for dsRNA-binding. Also, RNA silencing studies performed in insect cell cultures confirmed the crucial role of this VP3 domain for the silencing suppression activity of the protein.IMPORTANCE The Birnavirus moonlighting protein VP3 plays crucial roles interacting with the dsRNA genome segments to form stable ribonucleoprotein complexes and controlling host cell immune responses, presumably by binding to and shielding the dsRNA from recognition by the host silencing machinery. The structural, biophysical and functional data presented in this work has identified the N-terminal domain of VP3 as responsible for the dsRNA-binding and silencing suppression activities of the protein in Drosophila X virus.
Collapse
|
10
|
Mao K, Breen P, Ruvkun G. Mitochondrial dysfunction induces RNA interference in C. elegans through a pathway homologous to the mammalian RIG-I antiviral response. PLoS Biol 2020; 18:e3000996. [PMID: 33264285 PMCID: PMC7735679 DOI: 10.1371/journal.pbio.3000996] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 12/14/2020] [Accepted: 11/09/2020] [Indexed: 12/27/2022] Open
Abstract
RNA interference (RNAi) is an antiviral pathway common to many eukaryotes that detects and cleaves foreign nucleic acids. In mammals, mitochondrially localized proteins such as mitochondrial antiviral signaling (MAVS), retinoic acid-inducible gene I (RIG-I), and melanoma differentiation-associated protein 5 (MDA5) mediate antiviral responses. Here, we report that mitochondrial dysfunction in Caenorhabditis elegans activates RNAi-directed silencing via induction of a pathway homologous to the mammalian RIG-I helicase viral response pathway. The induction of RNAi also requires the conserved RNA decapping enzyme EOL-1/DXO. The transcriptional induction of eol-1 requires DRH-1 as well as the mitochondrial unfolded protein response (UPRmt). Upon mitochondrial dysfunction, EOL-1 is concentrated into foci that depend on the transcription of mitochondrial RNAs that may form double-stranded RNA (dsRNA), as has been observed in mammalian antiviral responses. Enhanced RNAi triggered by mitochondrial dysfunction is necessary for the increase in longevity that is induced by mitochondrial dysfunction. Surveillance of mitochondrial dysfunction in the nematode Caenorhabditis elegans triggers the activation of an RNA interference pathway to mediate antiviral defense, in a manner homologous to the mammalian RIG-I helicase viral response pathway.
Collapse
Affiliation(s)
- Kai Mao
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Peter Breen
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Gary Ruvkun
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
11
|
Plant Virus Genome Is Shaped by Specific Dinucleotide Restrictions That Influence Viral Infection. mBio 2020; 11:mBio.02818-19. [PMID: 32071264 PMCID: PMC7029135 DOI: 10.1128/mbio.02818-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The presence of CpG and UpA dinucleotides is restricted in the genomes of animal RNA viruses to avoid specific host defenses. We wondered whether a similar phenomenon exists in nonanimal RNA viruses. Here, we show that these two dinucleotides, especially UpA, are underrepresented in the family Potyviridae, the most important group of plant RNA viruses. Using plum pox virus (PPV; Potyviridae family) as a model, we show that an increase in UpA frequency strongly diminishes virus accumulation. Remarkably, unlike previous observations in animal viruses, PPV variants harboring CpG-rich fragments display just faint (or no) attenuation. The anticorrelation between UpA frequency and viral fitness additionally demonstrates the relevance of this particular dinucleotide: UpA-high mutants are attenuated in a dose-dependent manner, whereas a UpA-low variant displays better fitness than its parental control. Using high-throughput sequencing, we also show that UpA-rich PPV variants are genetically stable, without apparent changes in sequence that revert and/or compensate for the dinucleotide modification despite its attenuation. In addition, we also demonstrate here that the PPV restriction of UpA-rich variants works independently of the classical RNA silencing pathway. Finally, we show that the anticorrelation between UpA frequency and RNA accumulation applies to mRNA-like fragments produced by the host RNA polymerase II. Together, our results inform us about a dinucleotide-based system in plant cells that controls diverse RNAs, including RNA viruses.IMPORTANCE Dinucleotides (combinations of two consecutive nucleotides) are not randomly present in RNA viruses; in fact, the presence of CpG and UpA is significantly repressed in their genomes. Although the meaning of this phenomenon remains obscure, recent studies with animal-infecting viruses have revealed that their low CpG/UpA frequency prevents virus restriction via a host antiviral system that recognizes, and promotes the degradation of, CpG/UpA-rich RNAs. Whether similar systems act in organisms from other life kingdoms has been unknown. To fill this gap in our knowledge, we built several synthetic variants of a plant RNA virus with deoptimized dinucleotide frequencies and analyzed their viral fitness and genome adaptation. In brief, our results inform us for the first time about an effective dinucleotide-based system that acts in plants against viruses. Remarkably, this viral restriction in plants is reminiscent of, but not identical to, the equivalent antiviral response in animals.
Collapse
|
12
|
Jing C, Li P, Zhang J, Wang R, Wu G, Li M, Xie L, Qing L. The Malvastrum Yellow Vein Virus C4 Protein Promotes Disease Symptom Development and Enhances Virus Accumulation in Plants. Front Microbiol 2019; 10:2425. [PMID: 31708897 PMCID: PMC6823909 DOI: 10.3389/fmicb.2019.02425] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 10/08/2019] [Indexed: 01/06/2023] Open
Abstract
The begomovirus C4 protein is required for disease symptom development during virus infection in host plants. It can reprogram the cell cycle process for more efficient virus accumulation. In this study, we showed that the Malvastrum yellow vein virus (MaYVV) C4 protein could cause leaf up-ward curling and flower malformation, and increase virus accumulation in plants using PVX-based transient expression technology. We also demonstrated that, in the presence of its cognate betasatellite DNA (MaYVB), a mutant MaYVV, defective in producing the C4 protein (MaYVVΔC4), caused and alleviated infection in Nicotiana benthamiana. Transgenic plants expressing the MaYVV C4 protein showed upward leaf curling and uneven leaf lamina growth. Microscopic analysis showed that the epidermal cells of the C4 transgenic leaves were much smaller than those in the wild type (WT) leaves, and the mesophyll cells size and arrangement of transgenic plants was significantly altered. Inoculation of C4 transgenic plants with MaYVV or MaYVVΔC4 alone or associated with MaYVB showed that the transgenic C4 protein could promote viral and betasatellite accumulation and rescue the accumulation defect of MaYVVΔC4. Other transient expression assays also confirmed that the MaYVV C4 protein could suppress silencing of a GFP gene. In summary, our results indicate that the MaYVV C4 protein is a determinant of disease symptom and viral DNA accumulation. This protein can also function as a suppressor of RNA silencing and alter cell division and expansion.
Collapse
Affiliation(s)
- Chenchen Jing
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, China
| | - Pengbai Li
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, China
| | - Jiayuan Zhang
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, China
| | - Rui Wang
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, China
| | - Gentu Wu
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, China
| | - Mingjun Li
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, China
| | - Li Xie
- Analysis Center of Agrobiology and Environmental Sciences, Zhejiang University, Hangzhou, China
| | - Ling Qing
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, China
| |
Collapse
|
13
|
Jay F, Vitel M, Brioudes F, Louis M, Knobloch T, Voinnet O. Chemical enhancers of posttranscriptional gene silencing in Arabidopsis. RNA (NEW YORK, N.Y.) 2019; 25:1078-1090. [PMID: 31164480 PMCID: PMC6800516 DOI: 10.1261/rna.068627.118] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 06/02/2019] [Indexed: 05/24/2023]
Abstract
RNAi mediated by small-interfering RNAs (siRNAs) operates via transcriptional (TGS) and posttranscriptional gene silencing (PTGS). In Arabidopsis thaliana, TGS relies on DICER-LIKE-3 (DCL3)-dependent 24-nt siRNAs loaded into AGO4-clade ARGONAUTE effector proteins. PTGS operates via DCL4-dependent 21-nt siRNAs loaded into AGO1-clade proteins. We set up and validated a medium-throughput, semi-automatized procedure enabling chemical screening, in a 96-well in vitro format, of Arabidopsis transgenic seedlings expressing an inverted-repeat construct from the phloem companion cells. The ensuing quantitative PTGS phenotype was exploited to identify molecules, which, upon topical application, either inhibit or enhance siRNA biogenesis/activities. The vast majority of identified modifiers were enhancers, among which Sortin1, Isoxazolone, and [5-(3,4-dichlorophenyl)furan-2-yl]-piperidine-1-ylmethanethione (DFPM) provided the most robust and consistent results, including upon their application onto soil-grown plants in which their effect was nonautonomous and long lasting. The three molecules increased the RNAi potency of the inverted-repeat construct, in large part by enhancing 21-nt siRNA accumulation and loading into AGO1, and concomitantly reducing AGO4 and DCL3 levels in planta. A similar, albeit not identical effect, was observed on 22-nt siRNAs produced from a naturally occurring inverted-repeat locus, demonstrating that the molecules also enhance endogenous PTGS. In standardized assays conducted in seedling extracts, the three enhancers selectively increased DCL4-mediated processing of in vitro-synthesized double-stranded RNAs, indicating the targeting of a hitherto unknown PTGS component probably independent of the DCL4-cofactor DOUBLE-STRANDED RNA-BINDING 4 (DRB4). This study establishes the proof-of-concept that RNAi efficacy can be modulated by chemicals in a whole organism. Their potential applications and the associated future research are discussed.
Collapse
Affiliation(s)
- Florence Jay
- Department of Biology, Swiss Federal Institute of Technology (ETH Zürich), 8092 Zürich, Switzerland
| | - Maxime Vitel
- Bayer S.A.S., Biochemistry and New Technology, 69263 Lyon Cedex 09, France
| | - Florian Brioudes
- Department of Biology, Swiss Federal Institute of Technology (ETH Zürich), 8092 Zürich, Switzerland
| | - Mélissa Louis
- Bayer S.A.S., Biochemistry and New Technology, 69263 Lyon Cedex 09, France
| | - Thomas Knobloch
- Bayer S.A.S., Biochemistry and New Technology, 69263 Lyon Cedex 09, France
| | - Olivier Voinnet
- Department of Biology, Swiss Federal Institute of Technology (ETH Zürich), 8092 Zürich, Switzerland
| |
Collapse
|
14
|
Gebert D, Jehn J, Rosenkranz D. Widespread selection for extremely high and low levels of secondary structure in coding sequences across all domains of life. Open Biol 2019; 9:190020. [PMID: 31138098 PMCID: PMC6544989 DOI: 10.1098/rsob.190020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Codon composition, GC content and local RNA secondary structures can have a profound effect on gene expression, and mutations affecting these parameters, even though they do not alter the protein sequence, are not neutral in terms of selection. Although evidence exists that, in some cases, selection favours more stable RNA secondary structures, we currently lack a concrete idea of how many genes are affected within a species, and whether this is a universal phenomenon in nature. We searched for signs of structural selection in a global manner, analysing a set of 1 million coding sequences from 73 species representing all domains of life, as well as viruses, by means of our newly developed software PACKEIS. We show that codon composition and amino acid identity are main determinants of RNA secondary structure. In addition, we show that the arrangement of synonymous codons within coding sequences is non-random, yielding extremely high, but also extremely low, RNA structuredness significantly more often than expected by chance. Taken together, we demonstrate that selection for high and low levels of secondary structure is a widespread phenomenon. Our results provide another line of evidence that synonymous mutations are less neutral than commonly thought, which is of importance for many evolutionary models.
Collapse
Affiliation(s)
- Daniel Gebert
- Institute of Organismic and Molecular Evolution iOME, Anthropology, Johannes Gutenberg University Mainz , Anselm-Franz-von-Bentzel-Weg 7, 55099 Mainz , Germany
| | - Julia Jehn
- Institute of Organismic and Molecular Evolution iOME, Anthropology, Johannes Gutenberg University Mainz , Anselm-Franz-von-Bentzel-Weg 7, 55099 Mainz , Germany
| | - David Rosenkranz
- Institute of Organismic and Molecular Evolution iOME, Anthropology, Johannes Gutenberg University Mainz , Anselm-Franz-von-Bentzel-Weg 7, 55099 Mainz , Germany
| |
Collapse
|
15
|
Kang SH, Sun YD, Atallah OO, Huguet-Tapia JC, Noble JD, Folimonova SY. A Long Non-Coding RNA of Citrus tristeza virus: Role in the Virus Interplay with the Host Immunity. Viruses 2019; 11:E436. [PMID: 31091710 PMCID: PMC6563247 DOI: 10.3390/v11050436] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 05/08/2019] [Accepted: 05/11/2019] [Indexed: 01/01/2023] Open
Abstract
During infection, Citrus tristeza virus (CTV) produces a non-coding subgenomic RNA referred to as low-molecular-weight tristeza 1 (LMT1), which for a long time has been considered as a by-product of the complex CTV replication machinery. In this study, we investigated the role of LMT1 in the virus infection cycle using a CTV variant that does not produce LMT1 (CTV-LMT1d). We showed that lack of LMT1 did not halt virus ability to replicate or form proper virions. However, the mutant virus demonstrated significantly reduced invasiveness and systemic spread in Nicotiana benthamiana as well as an inability to establish infection in citrus. Introduction of CTV-LMT1d into the herbaceous host resulted in elevation of the levels of salicylic acid (SA) and SA-responsive pathogenesis-related genes beyond those upon inoculation with wild-type (WT) virus (CTV-WT). Further analysis showed that the LMT1 RNA produced by CTV-WT or via ectopic expression in the N. benthamiana leaves suppressed SA accumulation and up-regulated an alternative oxidase gene, which appeared to mitigate the accumulation of reactive oxygen species. To the best of our knowledge, this is the first report of a plant viral long non-coding RNA being involved in counter-acting host response by subverting the SA-mediated plant defense.
Collapse
Affiliation(s)
- Sung-Hwan Kang
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA.
| | - Yong-Duo Sun
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA.
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA.
| | - Osama O Atallah
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA.
| | | | - Jerald D Noble
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA.
| | - Svetlana Y Folimonova
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA.
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA.
| |
Collapse
|
16
|
Cross ST, Michalski D, Miller MR, Wilusz J. RNA regulatory processes in RNA virus biology. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1536. [PMID: 31034160 PMCID: PMC6697219 DOI: 10.1002/wrna.1536] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 04/02/2019] [Indexed: 12/13/2022]
Abstract
Numerous post‐transcriptional RNA processes play a major role in regulating the quantity, quality and diversity of gene expression in the cell. These include RNA processing events such as capping, splicing, polyadenylation and modification, but also aspects such as RNA localization, decay, translation, and non‐coding RNA‐associated regulation. The interface between the transcripts of RNA viruses and the various RNA regulatory processes in the cell, therefore, has high potential to significantly impact virus gene expression, regulation, cytopathology and pathogenesis. Furthermore, understanding RNA biology from the perspective of an RNA virus can shed considerable light on the broad impact of these post‐transcriptional processes in cell biology. Thus the goal of this article is to provide an overview of the richness of cellular RNA biology and how RNA viruses use, usurp and/or avoid the associated machinery to impact the outcome of infection. This article is categorized under:RNA in Disease and Development > RNA in Disease
Collapse
Affiliation(s)
- Shaun T Cross
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
| | - Daniel Michalski
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
| | - Megan R Miller
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
| |
Collapse
|
17
|
Nayak A, Kim DY, Trnka MJ, Kerr CH, Lidsky PV, Stanley DJ, Rivera BM, Li KH, Burlingame AL, Jan E, Frydman J, Gross JD, Andino R. A Viral Protein Restricts Drosophila RNAi Immunity by Regulating Argonaute Activity and Stability. Cell Host Microbe 2018; 24:542-557.e9. [PMID: 30308158 PMCID: PMC6450077 DOI: 10.1016/j.chom.2018.09.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 07/13/2018] [Accepted: 09/10/2018] [Indexed: 11/30/2022]
Abstract
The dicistrovirus, Cricket paralysis virus (CrPV) encodes an RNA interference (RNAi) suppressor, 1A, which modulates viral virulence. Using the Drosophila model, we combined structural, biochemical, and virological approaches to elucidate the strategies by which CrPV-1A restricts RNAi immunity. The atomic resolution structure of CrPV-1A uncovered a flexible loop that interacts with Argonaute 2 (Ago-2), thereby inhibiting Ago-2 endonuclease-dependent immunity. Mutations disrupting Ago-2 binding attenuates viral pathogenesis in wild-type but not Ago-2-deficient flies. CrPV-1A also contains a BC-box motif that enables the virus to hijack a host Cul2-Rbx1-EloBC ubiquitin ligase complex, which promotes Ago-2 degradation and virus replication. Our study uncovers a viral-based dual regulatory program that restricts antiviral immunity by direct interaction with and modulation of host proteins. While the direct inhibition of Ago-2 activity provides an efficient mechanism to establish infection, the recruitment of a ubiquitin ligase complex enables CrPV-1A to amplify Ago-2 inactivation to restrict further antiviral RNAi immunity.
Collapse
Affiliation(s)
- Arabinda Nayak
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94158, USA; Department of Biology and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Dong Young Kim
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA; College of Pharmacy, Yeungnam University, Gyeongsan, Gyeongbuk 38541, South Korea
| | - Michael J Trnka
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Craig H Kerr
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Peter V Lidsky
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94158, USA
| | - David J Stanley
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Brianna Monique Rivera
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Kathy H Li
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Eric Jan
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Judith Frydman
- Department of Biology and Genetics, Stanford University, Stanford, CA 94305, USA
| | - John D Gross
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Raul Andino
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94158, USA.
| |
Collapse
|
18
|
Fay EJ, Langlois RA. MicroRNA-Attenuated Virus Vaccines. Noncoding RNA 2018; 4:E25. [PMID: 30279330 PMCID: PMC6316615 DOI: 10.3390/ncrna4040025] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 09/25/2018] [Accepted: 09/28/2018] [Indexed: 12/18/2022] Open
Abstract
Live-attenuated vaccines are the most effective way to establish robust, long-lasting immunity against viruses. However, the possibility of reversion to wild type replication and pathogenicity raises concerns over the safety of these vaccines. The use of host-derived microRNAs (miRNAs) to attenuate viruses has been accomplished in an array of biological contexts. The broad assortment of effective tissue- and species-specific miRNAs, and the ability to target a virus with multiple miRNAs, allow for targeting to be tailored to the virus of interest. While escape is always a concern, effective strategies have been developed to improve the safety and stability of miRNA-attenuated viruses. In this review, we discuss the various approaches that have been used to engineer miRNA-attenuated viruses, the steps that have been taken to improve their safety, and the potential use of these viruses as vaccines.
Collapse
Affiliation(s)
- Elizabeth J Fay
- Biochemistry, Molecular Biology, and Biophysics Graduate Program, University of Minnesota, Minneapolis, MN 55455, USA.
- Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Ryan A Langlois
- Biochemistry, Molecular Biology, and Biophysics Graduate Program, University of Minnesota, Minneapolis, MN 55455, USA.
- Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA.
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455, USA.
| |
Collapse
|
19
|
Carluccio AV, Prigigallo MI, Rosas-Diaz T, Lozano-Duran R, Stavolone L. S-acylation mediates Mungbean yellow mosaic virus AC4 localization to the plasma membrane and in turns gene silencing suppression. PLoS Pathog 2018; 14:e1007207. [PMID: 30067843 PMCID: PMC6089456 DOI: 10.1371/journal.ppat.1007207] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 08/13/2018] [Accepted: 07/11/2018] [Indexed: 11/19/2022] Open
Abstract
RNA silencing plays a critical role in plant resistance against viruses. To counteract host defense, plant viruses encode viral suppressors of RNA silencing (VSRs) that interfere with the cellular silencing machinery through various mechanisms not always well understood. We examined the role of Mungbean yellow mosaic virus (MYMV) AC4 and showed that it is essential for infectivity but not for virus replication. It acts as a determinant of pathogenicity and counteracts virus induced gene silencing by strongly suppressing the systemic phase of silencing whereas it does not interfere with local production of siRNA. We demonstrate the ability of AC4 to bind native 21-25 nt siRNAs in vitro by electrophoretic mobility shift assay. While most of the known VSRs have cytoplasmic localization, we observed that despite its hydrophilic nature and the absence of trans-membrane domain, MYMV AC4 specifically accumulates to the plasma membrane (PM). We show that AC4 binds to PM via S-palmitoylation, a process of post-translational modification regulating membrane-protein interactions, not known for plant viral protein before. When localized to the PM, AC4 strongly suppresses systemic silencing whereas its delocalization impairs VSR activity of the protein. We also show that AC4 interacts with the receptor-like kinase (RLK) BARELY ANY MERISTEM 1 (BAM1), a positive regulator of the cell-to-cell movement of RNAi. The absolute requirement of PM localization for direct silencing suppression activity of AC4 is novel and intriguing. We discuss a possible model of action: palmitoylated AC4 anchors to the PM by means of palmitate to acquire the optimal conformation to bind siRNAs, hinder their systemic movement and hence suppress the spread of the PTGS signal in the plant.
Collapse
Affiliation(s)
- Anna Vittoria Carluccio
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle ricerche, Bari, Italia
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Maria Isabella Prigigallo
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle ricerche, Bari, Italia
| | - Tabata Rosas-Diaz
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Rosa Lozano-Duran
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
- Chinese Academy of Sciences–John Innes Centre Center of Excellence for Plant and Microbial Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Livia Stavolone
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle ricerche, Bari, Italia
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| |
Collapse
|
20
|
Waldron FM, Stone GN, Obbard DJ. Metagenomic sequencing suggests a diversity of RNA interference-like responses to viruses across multicellular eukaryotes. PLoS Genet 2018; 14:e1007533. [PMID: 30059538 PMCID: PMC6085071 DOI: 10.1371/journal.pgen.1007533] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 08/09/2018] [Accepted: 07/04/2018] [Indexed: 11/24/2022] Open
Abstract
RNA interference (RNAi)-related pathways target viruses and transposable element (TE) transcripts in plants, fungi, and ecdysozoans (nematodes and arthropods), giving protection against infection and transmission. In each case, this produces abundant TE and virus-derived 20-30nt small RNAs, which provide a characteristic signature of RNAi-mediated defence. The broad phylogenetic distribution of the Argonaute and Dicer-family genes that mediate these pathways suggests that defensive RNAi is ancient, and probably shared by most animal (metazoan) phyla. Indeed, while vertebrates had been thought an exception, it has recently been argued that mammals also possess an antiviral RNAi pathway, although its immunological relevance is currently uncertain and the viral small RNAs (viRNAs) are not easily detectable. Here we use a metagenomic approach to test for the presence of viRNAs in five species from divergent animal phyla (Porifera, Cnidaria, Echinodermata, Mollusca, and Annelida), and in a brown alga-which represents an independent origin of multicellularity from plants, fungi, and animals. We use metagenomic RNA sequencing to identify around 80 virus-like contigs in these lineages, and small RNA sequencing to identify viRNAs derived from those viruses. We identified 21U small RNAs derived from an RNA virus in the brown alga, reminiscent of plant and fungal viRNAs, despite the deep divergence between these lineages. However, contrary to our expectations, we were unable to identify canonical (i.e. Drosophila- or nematode-like) viRNAs in any of the animals, despite the widespread presence of abundant micro-RNAs, and somatic transposon-derived piwi-interacting RNAs. We did identify a distinctive group of small RNAs derived from RNA viruses in the mollusc. However, unlike ecdysozoan viRNAs, these had a piRNA-like length distribution but lacked key signatures of piRNA biogenesis. We also identified primary piRNAs derived from putatively endogenous copies of DNA viruses in the cnidarian and the echinoderm, and an endogenous RNA virus in the mollusc. The absence of canonical virus-derived small RNAs from our samples may suggest that the majority of animal phyla lack an antiviral RNAi response. Alternatively, these phyla could possess an antiviral RNAi response resembling that reported for vertebrates, with cryptic viRNAs not detectable through simple metagenomic sequencing of wild-type individuals. In either case, our findings show that the antiviral RNAi responses of arthropods and nematodes, which are highly divergent from each other and from that of plants and fungi, are also highly diverged from the most likely ancestral metazoan state.
Collapse
Affiliation(s)
- Fergal M. Waldron
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh, United Kingdom
| | - Graham N. Stone
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh, United Kingdom
| | - Darren J. Obbard
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh, United Kingdom
- Centre for Immunity Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Edinburgh, United Kingdom
| |
Collapse
|
21
|
Tomato Spotted Wilt Virus NSs Protein Supports Infection and Systemic Movement of a Potyvirus and Is a Symptom Determinant. Viruses 2018. [PMID: 29538326 PMCID: PMC5869522 DOI: 10.3390/v10030129] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Plant viruses are inducers and targets of antiviral RNA silencing. To condition susceptibility, most plant viruses encode silencing suppressor proteins that interfere with antiviral RNA silencing. The NSs protein is an RNA silencing suppressor in orthotospoviruses, such as the tomato spotted wilt virus (TSWV). The mechanism of RNA silencing suppression by NSs and its role in virus infection and movement are poorly understood. Here, we cloned and tagged TSWV NSs and expressed it from a GFP-tagged turnip mosaic virus (TuMV-GFP) carrying either a wild-type or suppressor-deficient (AS9) helper component proteinase (HC-Pro). When expressed in cis, NSs restored pathogenicity and promoted systemic infection of suppressor-deficient TuMV-AS9-GFP in Nicotiana benthamiana and Arabidopsis thaliana. Inactivating mutations were introduced in NSs RNA-binding domain one. A genetic analysis with active and suppressor-deficient NSs, in combination with wild-type and mutant plants lacking essential components of the RNA silencing machinery, showed that the NSs insert is stable when expressed from a potyvirus. NSs can functionally replace potyviral HC-Pro, condition virus susceptibility, and promote systemic infection and symptom development by suppressing antiviral RNA silencing through a mechanism that partially overlaps that of potyviral HC-Pro. The results presented provide new insight into the mechanism of silencing suppression by NSs and its effect on virus infection.
Collapse
|
22
|
von Born P, Bernardo-Faura M, Rubio-Somoza I. An artificial miRNA system reveals that relative contribution of translational inhibition to miRNA-mediated regulation depends on environmental and developmental factors in Arabidopsis thaliana. PLoS One 2018; 13:e0192984. [PMID: 29451902 PMCID: PMC5815599 DOI: 10.1371/journal.pone.0192984] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 02/01/2018] [Indexed: 11/24/2022] Open
Abstract
Development and fitness of any organism rely on properly controlled gene expression. This is especially true for plants, as their development is determined by both internal and external cues. MicroRNAs (miRNAs) are embedded in the genetic cascades that integrate and translate those cues into developmental programs. miRNAs negatively regulate their target genes mainly post-transcriptionally through two co-existing mechanisms; mRNA cleavage and translational inhibition. Despite our increasing knowledge about the genetic and biochemical processes involved in those concurrent mechanisms, little is known about their relative contributions to the overall miRNA-mediated regulation. Here we show that co-existence of cleavage and translational inhibition is dependent on growth temperature and developmental stage. We found that efficiency of an artificial miRNA-mediated (amiRNA) gene silencing declines with age during vegetative development in a temperature-dependent manner. That decline is mainly due to a reduction on the contribution from translational inhibition. Both, temperature and developmental stage were also found to affect mature amiRNA accumulation and the expression patterns of the core players involved in miRNA biogenesis and action. Therefore, that suggests that each miRNA family specifically regulates their respective targets, while temperature and growth might influence the performance of miRNA-dependent regulation in a more general way.
Collapse
Affiliation(s)
- Patrick von Born
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | | | - Ignacio Rubio-Somoza
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
- Molecular Reprogramming and Evolution Laboratory. Centre for Research in Agricultural Genomics, Barcelona, Spain
- * E-mail:
| |
Collapse
|
23
|
Kumar S, Tanti B, Patil BL, Mukherjee SK, Sahoo L. RNAi-derived transgenic resistance to Mungbean yellow mosaic India virus in cowpea. PLoS One 2017; 12:e0186786. [PMID: 29077738 PMCID: PMC5659608 DOI: 10.1371/journal.pone.0186786] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/06/2017] [Indexed: 11/21/2022] Open
Abstract
Cowpea is an important grain legume crop of Africa, Latin America, and Southeast Asia. Leaf curl and golden mosaic diseases caused by Mungbean yellow mosaic India virus (MYMIV) have emerged as most devastating viral diseases of cowpea in Southeast Asia. In this study, we employed RNA interference (RNAi) strategy to control cowpea-infecting MYMIV. For this, we generated transgenic cowpea plants harbouring three different intron hairpin RNAi constructs, containing the AC2, AC4 and fusion of AC2 and AC4 (AC2+AC4) of seven cowpea-infecting begomoviruses. The T0 and T1 transgenic cowpea lines of all the three constructs accumulated transgene-specific siRNAs. Transgenic plants were further assayed up to T1 generations, for resistance to MYMIV using agro-infectious clones. Nearly 100% resistance against MYMIV infection was observed in transgenic lines, expressing AC2-hp and AC2+AC4-hp RNA, when compared with untransformed controls and plants transformed with empty vectors, which developed severe viral disease symptoms within 3 weeks. The AC4-hp RNA expressing lines displayed appearance of milder symptoms after 5 weeks of MYMIV-inoculation. Northern blots revealed a positive correlation between the level of transgene-specific siRNAs accumulation and virus resistance. The MYMIV-resistant transgenic lines accumulated nearly zero or very low titres of viral DNA. The transgenic cowpea plants had normal phenotype with no yield penalty in greenhouse conditions. This is the first demonstration of RNAi-derived resistance to MYMIV in cowpea.
Collapse
Affiliation(s)
- Sanjeev Kumar
- Department of Bioscience and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
- Department of Botany, Gauhati University, Guwahati, Assam, India
| | - Bhaben Tanti
- Department of Botany, Gauhati University, Guwahati, Assam, India
| | - Basavaprabhu L. Patil
- ICAR-National Research Centre on Plant Biotechnology, LBS Centre, IARI, Pusa Campus, New Delhi, India
| | - Sunil Kumar Mukherjee
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | - Lingaraj Sahoo
- Department of Bioscience and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
- * E-mail:
| |
Collapse
|
24
|
Jeyaraj A, Liu S, Zhang X, Zhang R, Shangguan M, Wei C. Genome-wide identification of microRNAs responsive to Ectropis oblique feeding in tea plant (Camellia sinensis L.). Sci Rep 2017; 7:13634. [PMID: 29051614 PMCID: PMC5648755 DOI: 10.1038/s41598-017-13692-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 09/29/2017] [Indexed: 12/02/2022] Open
Abstract
The tea plant (Camellia sinensis L.) is vulnerable to the geometrid Ectropis oblique; although microRNAs (miRNAs) are important for plant growth, development and stress response, the function of miRNAs in the response of C. sinensis to stress from E. oblique is unclear. To identify E. oblique stress-responsive miRNAs and their target genes in tea plant, three small RNA libraries were constructed from leaves subjected to mechanical wounding (MW), geometrid attack (GA) and from healthy control (CK) leaves. Using high-throughput sequencing, 130 known miRNAs and 512 novel miRNAs were identified; of these, differential expression under GA stress was observed for 36 known and 139 novel miRNAs. Furthermore, 169 GA-responsive and 173 MW-responsive miRNAs were detected by miRNA microarray. The expression patterns of six GA-responsive miRNAs were validated by qRT-PCR. Several target genes for these miRNAs encode various transcription factors, including ethylene-responsive transcription factors and squamosa promoter-binding-like proteins, which suggests that these miRNAs may regulate stress-responsive transcriptional processes in tea plant. The present findings provide novel insights into miRNA-mediated regulatory mechanisms underlying the response to GA stress, and also offer valuable information for development of pest resistance using RNA interference-based strategies in tea plants.
Collapse
Affiliation(s)
- Anburaj Jeyaraj
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, P.R. China
| | - Shengrui Liu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, P.R. China
| | - Xiao Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, P.R. China
| | - Ran Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, P.R. China
| | - Mingzhu Shangguan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, P.R. China
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, P.R. China.
| |
Collapse
|
25
|
The evolution of animal Argonautes: evidence for the absence of antiviral AGO Argonautes in vertebrates. Sci Rep 2017; 7:9230. [PMID: 28835645 PMCID: PMC5569025 DOI: 10.1038/s41598-017-08043-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 06/21/2017] [Indexed: 12/17/2022] Open
Abstract
In addition to mediating regulation of endogenous gene expression, RNA interference (RNAi) in plants and invertebrates plays a crucial role in defense against viruses via virus-specific siRNAs. Different studies have demonstrated that the functional diversity of RNAi in animals is linked to the diversification of the Argonaute superfamily, central components of RISCs (RNA induced silencing complexes). The animal Argonaute superfamily is traditionally grouped into AGO and PIWI Argonautes. Yet, by performing phylogenetic analyses and determining the selective evolutionary pressure in the metazoan Argonaute superfamily, we provide evidence for the existence of three conserved Argonaute lineages between basal metazoans and protostomes, namely siRNA-class AGO, miRNA-class AGO and PIWI Argonautes. In addition, it shown that the siRNA-class AGO lineage is characterized by high rates of molecular evolution, suggesting a role in the arms race with viruses, while the miRNA-class AGOs display strong sequence conservation. Interestingly, we also demonstrate that vertebrates lack siRNA-class AGO proteins and that vertebrate AGOs display low rates of molecular evolution. In this way, we provide supportive evidence for the loss of the antiviral siRNA-class AGO group in vertebrates and discuss the consequence hereof on antiviral immunity and the use of RNAi as a loss of function tool in these animals.
Collapse
|
26
|
Kovalev N, Inaba JI, Li Z, Nagy PD. The role of co-opted ESCRT proteins and lipid factors in protection of tombusviral double-stranded RNA replication intermediate against reconstituted RNAi in yeast. PLoS Pathog 2017; 13:e1006520. [PMID: 28759634 PMCID: PMC5552349 DOI: 10.1371/journal.ppat.1006520] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 08/10/2017] [Accepted: 07/07/2017] [Indexed: 01/28/2023] Open
Abstract
Reconstituted antiviral defense pathway in surrogate host yeast is used as an intracellular probe to further our understanding of virus-host interactions and the role of co-opted host factors in formation of membrane-bound viral replicase complexes in protection of the viral RNA against ribonucleases. The inhibitory effect of the RNA interference (RNAi) machinery of S. castellii, which only consists of the two-component DCR1 and AGO1 genes, was measured against tomato bushy stunt virus (TBSV) in wild type and mutant yeasts. We show that deletion of the co-opted ESCRT-I (endosomal sorting complexes required for transport I) or ESCRT-III factors makes TBSV replication more sensitive to the RNAi machinery in yeast. Moreover, the lack of these pro-viral cellular factors in cell-free extracts (CFEs) used for in vitro assembly of the TBSV replicase results in destruction of dsRNA replication intermediate by a ribonuclease at the 60 min time point when the CFE from wt yeast has provided protection for dsRNA. In addition, we demonstrate that co-opted oxysterol-binding proteins and membrane contact sites, which are involved in enrichment of sterols within the tombusvirus replication compartment, are required for protection of viral dsRNA. We also show that phosphatidylethanolamine level influences the formation of RNAi-resistant replication compartment. In the absence of peroxisomes in pex3Δ yeast, TBSV subverts the ER membranes, which provide as good protection for TBSV dsRNA against RNAi or ribonucleases as the peroxisomal membranes in wt yeast. Altogether, these results demonstrate that co-opted protein factors and usurped lipids are exploited by tombusviruses to build protective subcellular environment against the RNAi machinery and possibly other cellular ribonucleases. Positive-strand RNA viruses build membranous replication compartment to support their replication in the infected hosts. One of the proposed functions of the usurped subcellular membranes is to protect the viral RNA from recognition and destruction by various cellular RNA sensors and ribonucleases. To answer this fundamental question on the putative role of co-opted host factors and membranes in protecting the viral double-stranded RNA replication intermediate during replication, the authors took advantage of yeast (Saccharomyces cerevisiae), which lacks the conserved RNAi machinery, as a surrogate host for TBSV. The reconstituted RNAi machinery from S. castellii in S. cerevisiae was used as an intracellular probe to study the effect of various co-opted cellular proteins and lipids on the formation of RNAi-insensitive replication compartment. Overall, the authors demonstrate the interaction between the RNAi machinery and the viral replicase complex, and the essential roles of usurped host factors in protecting the viral dsRNA replication intermediate from RNAi-based degradation.
Collapse
Affiliation(s)
- Nikolay Kovalev
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, United States of America
| | - Jun-ichi Inaba
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, United States of America
| | - Zhenghe Li
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, United States of America
- Institute of Biotechnology, State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, P. R. China
| | - Peter D. Nagy
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, United States of America
- * E-mail:
| |
Collapse
|
27
|
Gammon DB, Ishidate T, Li L, Gu W, Silverman N, Mello CC. The Antiviral RNA Interference Response Provides Resistance to Lethal Arbovirus Infection and Vertical Transmission in Caenorhabditis elegans. Curr Biol 2017; 27:795-806. [PMID: 28262484 DOI: 10.1016/j.cub.2017.02.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 01/18/2017] [Accepted: 02/01/2017] [Indexed: 11/18/2022]
Abstract
The recent discovery of the positive-sense single-stranded RNA (ssRNA) Orsay virus (OV) as a natural pathogen of the nematode Caenorhabditis elegans has stimulated interest in exploring virus-nematode interactions. However, OV infection is restricted to a small number of intestinal cells, even in nematodes defective in their antiviral RNA interference (RNAi) response, and is neither lethal nor vertically transmitted. Using a fluorescent reporter strain of the negative-sense ssRNA vesicular stomatitis virus (VSV), we show that microinjection of VSV particles leads to a dose-dependent, muscle tissue-tropic, lethal infection in C. elegans. Furthermore, we find nematodes deficient for components of the antiviral RNAi pathway, such as Dicer-related helicase 1 (DRH-1), to display hypersusceptibility to VSV infection as evidenced by elevated infection rates, virus replication in multiple tissue types, and earlier mortality. Strikingly, infection of oocytes and embryos could also be observed in drh-1 mutants. Our results suggest that the antiviral RNAi response not only inhibits vertical VSV transmission but also promotes transgenerational inheritance of antiviral immunity. Our study introduces a new, in vivo virus-host model system for exploring arbovirus pathogenesis and provides the first evidence for vertical pathogen transmission in C. elegans.
Collapse
Affiliation(s)
- Don B Gammon
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| | - Takao Ishidate
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Lichao Li
- Department of Cell Biology and Neuroscience, University of California, Riverside, Riverside, CA 92521, USA
| | - Weifeng Gu
- Department of Cell Biology and Neuroscience, University of California, Riverside, Riverside, CA 92521, USA
| | - Neal Silverman
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Craig C Mello
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| |
Collapse
|
28
|
Calil IP, Fontes EPB. Plant immunity against viruses: antiviral immune receptors in focus. ANNALS OF BOTANY 2017; 119:711-723. [PMID: 27780814 PMCID: PMC5604577 DOI: 10.1093/aob/mcw200] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 08/05/2016] [Indexed: 05/07/2023]
Abstract
BACKGROUND Among the environmental limitations that affect plant growth, viruses cause major crop losses worldwide and represent serious threats to food security. Significant advances in the field of plant-virus interactions have led to an expansion of potential strategies for genetically engineered resistance in crops during recent years. Nevertheless, the evolution of viral virulence represents a constant challenge in agriculture that has led to a continuing interest in the molecular mechanisms of plant-virus interactions that affect disease or resistance. SCOPE AND CONCLUSION This review summarizes the molecular mechanisms of the antiviral immune system in plants and the latest breakthroughs reported in plant defence against viruses. Particular attention is given to the immune receptors and transduction pathways in antiviral innate immunity. Plants counteract viral infection with a sophisticated innate immune system that resembles the non-viral pathogenic system, which is broadly divided into pathogen-associated molecular pattern (PAMP)-triggered immunity and effector-triggered immunity. An additional recently uncovered virus-specific defence mechanism relies on host translation suppression mediated by a transmembrane immune receptor. In all cases, the recognition of the virus by the plant during infection is central for the activation of these innate defences, and, conversely, the detection of host plants enables the virus to activate virulence strategies. Plants also circumvent viral infection through RNA interference mechanisms by utilizing small RNAs, which are often suppressed by co-evolving virus suppressors. Additionally, plants defend themselves against viruses through hormone-mediated defences and activation of the ubiquitin-26S proteasome system (UPS), which alternatively impairs and facilitates viral infection. Therefore, plant defence and virulence strategies co-evolve and co-exist; hence, disease development is largely dependent on the extent and rate at which these opposing signals emerge in host and non-host interactions. A deeper understanding of plant antiviral immunity may facilitate innovative biotechnological, genetic and breeding approaches for crop protection and improvement.
Collapse
Affiliation(s)
- Iara P. Calil
- Departamento de Bioquímica e Biologia Molecular/National Institute of Science and Technology in Plant–Pest Interactions/Bioagro, Universidade Federal de Viçosa, 36570.000, Viçosa, MG, Brazil
| | - Elizabeth P. B. Fontes
- Departamento de Bioquímica e Biologia Molecular/National Institute of Science and Technology in Plant–Pest Interactions/Bioagro, Universidade Federal de Viçosa, 36570.000, Viçosa, MG, Brazil
- For correspondence. E-mail
| |
Collapse
|
29
|
Machado JPB, Calil IP, Santos AA, Fontes EPB. Translational control in plant antiviral immunity. Genet Mol Biol 2017; 40:292-304. [PMID: 28199446 PMCID: PMC5452134 DOI: 10.1590/1678-4685-gmb-2016-0092] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 09/27/2016] [Indexed: 01/11/2023] Open
Abstract
Due to the limited coding capacity of viral genomes, plant viruses depend extensively on the host cell machinery to support the viral life cycle and, thereby, interact with a large number of host proteins during infection. Within this context, as plant viruses do not harbor translation-required components, they have developed several strategies to subvert the host protein synthesis machinery to produce rapidly and efficiently the viral proteins. As a countermeasure against infection, plants have evolved defense mechanisms that impair viral infections. Among them, the host-mediated translational suppression has been characterized as an efficient mean to restrict infection. To specifically suppress translation of viral mRNAs, plants can deploy susceptible recessive resistance genes, which encode translation initiation factors from the eIF4E and eIF4G family and are required for viral mRNA translation and multiplication. Additionally, recent evidence has demonstrated that, alternatively to the cleavage of viral RNA targets, host cells can suppress viral protein translation to silence viral RNA. Finally, a novel strategy of plant antiviral defense based on suppression of host global translation, which is mediated by the transmembrane immune receptor NIK1 (nuclear shuttle protein (NSP)-Interacting Kinase1), is discussed in this review.
Collapse
Affiliation(s)
- João Paulo B Machado
- Department of Biochemistry and Molecular Biology, BIOAGRO, National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, 36571.000, Viçosa, MG, Brazil
| | - Iara P Calil
- Department of Biochemistry and Molecular Biology, BIOAGRO, National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, 36571.000, Viçosa, MG, Brazil
| | - Anésia A Santos
- Department of General Biology, Universidade Federal de Viçosa, 36571.000, Viçosa, MG, Brazil
| | - Elizabeth P B Fontes
- Department of Biochemistry and Molecular Biology, BIOAGRO, National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, 36571.000, Viçosa, MG, Brazil
| |
Collapse
|
30
|
Koonin EV. Evolution of RNA- and DNA-guided antivirus defense systems in prokaryotes and eukaryotes: common ancestry vs convergence. Biol Direct 2017; 12:5. [PMID: 28187792 PMCID: PMC5303251 DOI: 10.1186/s13062-017-0177-2] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 02/06/2017] [Indexed: 12/18/2022] Open
Abstract
Abstract Complementarity between nucleic acid molecules is central to biological information transfer processes. Apart from the basal processes of replication, transcription and translation, complementarity is also employed by multiple defense and regulatory systems. All cellular life forms possess defense systems against viruses and mobile genetic elements, and in most of them some of the defense mechanisms involve small guide RNAs or DNAs that recognize parasite genomes and trigger their inactivation. The nucleic acid-guided defense systems include prokaryotic Argonaute (pAgo)-centered innate immunity and CRISPR-Cas adaptive immunity as well as diverse branches of RNA interference (RNAi) in eukaryotes. The archaeal pAgo machinery is the direct ancestor of eukaryotic RNAi that, however, acquired additional components, such as Dicer, and enormously diversified through multiple duplications. In contrast, eukaryotes lack any heritage of the CRISPR-Cas systems, conceivably, due to the cellular toxicity of some Cas proteins that would get activated as a result of operon disruption in eukaryotes. The adaptive immunity function in eukaryotes is taken over partly by the PIWI RNA branch of RNAi and partly by protein-based immunity. In this review, I briefly discuss the interplay between homology and analogy in the evolution of RNA- and DNA-guided immunity, and attempt to formulate some general evolutionary principles for this ancient class of defense systems. Reviewers This article was reviewed by Mikhail Gelfand and Bojan Zagrovic.
Collapse
Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA.
| |
Collapse
|
31
|
Romay G, Bragard C. Antiviral Defenses in Plants through Genome Editing. Front Microbiol 2017; 8:47. [PMID: 28167937 PMCID: PMC5253358 DOI: 10.3389/fmicb.2017.00047] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 01/06/2017] [Indexed: 01/29/2023] Open
Abstract
Plant-virus interactions based-studies have contributed to increase our understanding on plant resistance mechanisms, providing new tools for crop improvement. In the last two decades, RNA interference, a post-transcriptional gene silencing approach, has been used to induce antiviral defenses in plants with the help of genetic engineering technologies. More recently, the new genome editing systems (GES) are revolutionizing the scope of tools available to confer virus resistance in plants. The most explored GES are zinc finger nucleases, transcription activator-like effector nucleases, and clustered regularly interspaced short palindromic repeats/Cas9 endonuclease. GES are engineered to target and introduce mutations, which can be deleterious, via double-strand breaks at specific DNA sequences by the error-prone non-homologous recombination end-joining pathway. Although GES have been engineered to target DNA, recent discoveries of GES targeting ssRNA molecules, including virus genomes, pave the way for further studies programming plant defense against RNA viruses. Most of plant virus species have an RNA genome and at least 784 species have positive ssRNA. Here, we provide a summary of the latest progress in plant antiviral defenses mediated by GES. In addition, we also discuss briefly the GES perspectives in light of the rebooted debate on genetic modified organisms (GMOs) and the current regulatory frame for agricultural products involving the use of such engineering technologies.
Collapse
Affiliation(s)
- Gustavo Romay
- Applied Microbiology – Phytopathology, Earth and Life Institute, Université catholique de LouvainLouvain-la-Neuve, Belgium
| | - Claude Bragard
- Applied Microbiology – Phytopathology, Earth and Life Institute, Université catholique de LouvainLouvain-la-Neuve, Belgium
| |
Collapse
|
32
|
Abstract
ARGONAUTEs (AGOs) are the effector proteins in eukaryotic small RNA (sRNA)-based gene silencing pathways controlling gene expression and transposon activity. In plants, AGOs regulate key biological processes such as development, response to stress, genome structure and integrity, and pathogen defense. Canonical functions of plant AGO-sRNA complexes include the endonucleolytic cleavage or translational inhibition of target RNAs and the methylation of target DNAs. Here, I provide a brief update on the major features, molecular functions, and biological roles of plant AGOs. A special focus is given to the more recent discoveries related to emerging molecular or biological functions of plant AGOs, as well as to the major unknowns in the plant AGO field.
Collapse
Affiliation(s)
- Alberto Carbonell
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia), Valencia, 46022, Spain.
| |
Collapse
|
33
|
Li J, Zheng H, Zhang C, Han K, Wang S, Peng J, Lu Y, Zhao J, Xu P, Wu X, Li G, Chen J, Yan F. Different Virus-Derived siRNAs Profiles between Leaves and Fruits in Cucumber Green Mottle Mosaic Virus-Infected Lagenaria siceraria Plants. Front Microbiol 2016; 7:1797. [PMID: 27881977 PMCID: PMC5101232 DOI: 10.3389/fmicb.2016.01797] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 10/25/2016] [Indexed: 01/24/2023] Open
Abstract
RNA silencing is an evolutionarily conserved antiviral mechanism, through which virus-derived small interfering RNAs (vsiRNAs) playing roles in host antiviral defense are produced in virus-infected plant. Deep sequencing technology has revolutionized the study on the interaction between virus and plant host through the analysis of vsiRNAs profile. However, comparison of vsiRNA profiles in different tissues from a same host plant has been rarely reported. In this study, the profiles of vsiRNAs from leaves and fruits of Lagenaria siceraria plants infected with Cucumber green mottle mosaic virus (CGMMV) were comprehensively characterized and compared. Many more vsiRNAs were present in infected leaves than in fruits. vsiRNAs from both leaves and fruits were mostly 21- and 22-nt in size as previously described in other virus-infected plants. Interestingly, vsiRNAs were predominantly produced from the viral positive strand RNAs in infected leaves, whereas in infected fruits they were derived equally from the positive and negative strands. Many leaf-specific positive vsiRNAs with lengths of 21-nt (2058) or 22-nt (3996) were identified but only six (21-nt) and one (22-nt) positive vsiRNAs were found to be specific to fruits. vsiRNAs hotspots were only present in the 5'-terminal and 3'-terminal of viral positive strand in fruits, while multiple hotspots were identified in leaves. Differences in GC content and 5'-terminal nucleotide of vsiRNAs were also observed in the two organs. To our knowledge, this provides the first high-resolution comparison of vsiRNA profiles between different tissues of the same host plant.
Collapse
Affiliation(s)
- Junmin Li
- State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural SciencesHangzhou, China
- Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Hongying Zheng
- State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural SciencesHangzhou, China
- Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Chenhua Zhang
- State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural SciencesHangzhou, China
- College of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Kelei Han
- State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural SciencesHangzhou, China
- Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Shu Wang
- State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Jiejun Peng
- State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural SciencesHangzhou, China
- Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Yuwen Lu
- State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural SciencesHangzhou, China
- Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Jinping Zhao
- State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural SciencesHangzhou, China
- Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Pei Xu
- State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural SciencesHangzhou, China
- Institute of Vegetable, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Xiaohua Wu
- State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural SciencesHangzhou, China
- Institute of Vegetable, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Guojing Li
- State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural SciencesHangzhou, China
- Institute of Vegetable, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Jianping Chen
- State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural SciencesHangzhou, China
- Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural SciencesHangzhou, China
- College of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Fei Yan
- State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural SciencesHangzhou, China
- Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural SciencesHangzhou, China
| |
Collapse
|
34
|
Wang L, Du H, Wuyun TN. Genome-Wide Identification of MicroRNAs and Their Targets in the Leaves and Fruits of Eucommia ulmoides Using High-Throughput Sequencing. FRONTIERS IN PLANT SCIENCE 2016; 7:1632. [PMID: 27877179 PMCID: PMC5099690 DOI: 10.3389/fpls.2016.01632] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 10/17/2016] [Indexed: 05/03/2023]
Abstract
MicroRNAs (miRNAs), a group of endogenous small non-coding RNAs, play important roles in plant growth, development, and stress response processes. Eucommia ulmoides Oliver (hardy rubber tree) is one of the few woody plants capable of producing trans-1, 4-polyisoprene (TPI), also known as Eu-rubber, which has been utilized as an industrial raw material and is extensively cultivated in China. However, the mechanism of TPI biosynthesis has not been identified in E. ulmoides. To characterize small RNAs and their targets with potential biological roles involved in the TPI biosynthesis in E. ulmoides, in the present study, eight small RNA libraries were constructed and sequenced from young and mature leaves and fruits of E. ulmoides. Further analysis identified 34 conserved miRNAs belonging to 20 families (two unclassified families), and 115 novel miRNAs seemed to be specific to E. ulmoides. Among these miRNAs, fourteen conserved miRNAs and 49 novel miRNAs were significantly differentially expressed and identified as Eu-rubber accumulation related miRNAs. Based on the E. ulmoides genomic data, 202 and 306 potential target genes were predicted for 33 conserved and 92 novel miRNAs, respectively; the predicted targets are mostly transcription factors and functional genes, which were enriched in metabolic pathways and biosynthesis of secondary metabolites. Noticeably, based on the expression patterns of miRNAs and their target genes in combination with the Eu-rubber accumulation, the negative correlation of expression of six miRNAs (Eu-miR14, Eu-miR91, miR162a, miR166a, miR172c, and miR396a) and their predicted targets serving as potential regulators in Eu-rubber accumulation. This study is the first to detect conserved and novel miRNAs and their potential targets in E. ulmoides and identify several candidate genes potentially controlling rubber accumulation, and thus provide molecular evidence for understanding the roles of miRNAs in regulating the TPI biosynthesis in E. ulmoides.
Collapse
Affiliation(s)
- Lin Wang
- Non-timber Forest Research and Development Center, Chinese Academy of ForestryZhengzhou, China
- The Eucommia Engineering Research Center of State Forestry AdministrationZhengzhou, China
| | - Hongyan Du
- Non-timber Forest Research and Development Center, Chinese Academy of ForestryZhengzhou, China
- The Eucommia Engineering Research Center of State Forestry AdministrationZhengzhou, China
| | - Ta-na Wuyun
- Non-timber Forest Research and Development Center, Chinese Academy of ForestryZhengzhou, China
- The Eucommia Engineering Research Center of State Forestry AdministrationZhengzhou, China
| |
Collapse
|
35
|
Kontra L, Csorba T, Tavazza M, Lucioli A, Tavazza R, Moxon S, Tisza V, Medzihradszky A, Turina M, Burgyán J. Distinct Effects of p19 RNA Silencing Suppressor on Small RNA Mediated Pathways in Plants. PLoS Pathog 2016; 12:e1005935. [PMID: 27711201 PMCID: PMC5053613 DOI: 10.1371/journal.ppat.1005935] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 09/13/2016] [Indexed: 12/30/2022] Open
Abstract
RNA silencing is one of the main defense mechanisms employed by plants to fight viruses. In change, viruses have evolved silencing suppressor proteins to neutralize antiviral silencing. Since the endogenous and antiviral functions of RNA silencing pathway rely on common components, it was suggested that viral suppressors interfere with endogenous silencing pathway contributing to viral symptom development. In this work, we aimed to understand the effects of the tombusviral p19 suppressor on endogenous and antiviral silencing during genuine virus infection. We showed that ectopically expressed p19 sequesters endogenous small RNAs (sRNAs) in the absence, but not in the presence of virus infection. Our presented data question the generalized model in which the sequestration of endogenous sRNAs by the viral suppressor contributes to the viral symptom development. We further showed that p19 preferentially binds the perfectly paired ds-viral small interfering RNAs (vsiRNAs) but does not select based on their sequence or the type of the 5' nucleotide. Finally, co-immunoprecipitation of sRNAs with AGO1 or AGO2 from virus-infected plants revealed that p19 specifically impairs vsiRNA loading into AGO1 but not AGO2. Our findings, coupled with the fact that p19-expressing wild type Cymbidium ringspot virus (CymRSV) overcomes the Nicotiana benthamiana silencing based defense killing the host, suggest that AGO1 is the main effector of antiviral silencing in this host-virus combination.
Collapse
Affiliation(s)
- Levente Kontra
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Gödöllő, Hungary
- Szent István University, Gödöllő, Hungary
| | - Tibor Csorba
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Gödöllő, Hungary
| | - Mario Tavazza
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), C.R. Casaccia, Rome, Italy
| | - Alessandra Lucioli
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), C.R. Casaccia, Rome, Italy
| | - Raffaela Tavazza
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), C.R. Casaccia, Rome, Italy
| | - Simon Moxon
- School of Biological Sciences, University of East Anglia, Norwich, Norfolk, United Kingdom
| | - Viktória Tisza
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Gödöllő, Hungary
| | - Anna Medzihradszky
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Gödöllő, Hungary
| | - Massimo Turina
- National Research Council, Institute for Sustainable Plant Protection, Torino, Italy
| | - József Burgyán
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Gödöllő, Hungary
| |
Collapse
|
36
|
Niehl A, Wyrsch I, Boller T, Heinlein M. Double-stranded RNAs induce a pattern-triggered immune signaling pathway in plants. THE NEW PHYTOLOGIST 2016; 211:1008-19. [PMID: 27030513 DOI: 10.1111/nph.13944] [Citation(s) in RCA: 135] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 02/24/2016] [Indexed: 05/20/2023]
Abstract
Pattern-triggered immunity (PTI) is a plant defense response that relies on the perception of conserved microbe- or pathogen-associated molecular patterns (MAMPs or PAMPs, respectively). Recently, it has been recognized that PTI restricts virus infection in plants; however, the nature of the viral or infection-induced PTI elicitors and the underlying signaling pathways are still unknown. As double-stranded RNAs (dsRNAs) are conserved molecular patterns associated with virus replication, we applied dsRNAs or synthetic dsRNA analogs to Arabidopsis thaliana and investigated PTI responses. We show that in vitro-generated dsRNAs, dsRNAs purified from virus-infected plants and the dsRNA analog polyinosinic-polycytidylic acid (poly(I:C)) induce typical PTI responses dependent on the co-receptor SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE 1 (SERK1), but independent of dicer-like (DCL) proteins in Arabidopsis. Moreover, dsRNA treatment of Arabidopsis induces SERK1-dependent antiviral resistance. Screening of Arabidopsis wild accessions demonstrates natural variability in dsRNA sensitivity. Our findings suggest that dsRNAs represent genuine PAMPs in plants, which induce a signaling cascade involving SERK1 and a specific dsRNA receptor. The dependence of dsRNA-mediated PTI on SERK1, but not on DCLs, implies that dsRNA-mediated PTI involves membrane-associated processes and operates independently of RNA silencing. dsRNA sensitivity may represent a useful trait to increase antiviral resistance in cultivated plants.
Collapse
Affiliation(s)
- Annette Niehl
- Botany, Department of Environmental Sciences, University of Basel, Basel, CH-4056, Switzerland
| | - Ines Wyrsch
- Botany, Department of Environmental Sciences, University of Basel, Basel, CH-4056, Switzerland
| | - Thomas Boller
- Botany, Department of Environmental Sciences, University of Basel, Basel, CH-4056, Switzerland
| | - Manfred Heinlein
- Botany, Department of Environmental Sciences, University of Basel, Basel, CH-4056, Switzerland
- Institut de Biologie Moléculaire des Plantes, CNRS UPR 2357, Strasbourg, 67000, France
| |
Collapse
|
37
|
Abstract
Eukaryotic gene expression is extensively controlled at the level of mRNA stability and the mechanisms underlying this regulation are markedly different from their archaeal and bacterial counterparts. We propose that two such mechanisms, nonsense‐mediated decay (NMD) and motif‐specific transcript destabilization by CCCH‐type zinc finger RNA‐binding proteins, originated as a part of cellular defense against RNA pathogens. These branches of the mRNA turnover pathway might have been used by primeval eukaryotes alongside RNA interference to distinguish their own messages from those of RNA viruses and retrotransposable elements. We further hypothesize that the subsequent advent of “professional” innate and adaptive immunity systems allowed NMD and the motif‐triggered mechanisms to be efficiently repurposed for regulation of endogenous cellular transcripts. This scenario explains the rapid emergence of archetypical mRNA destabilization pathways in eukaryotes and argues that other aspects of post‐transcriptional gene regulation in this lineage might have been derived through a similar exaptation route.
Collapse
Affiliation(s)
- Fursham M Hamid
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Eugene V Makeyev
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,Centre for Developmental Neurobiology, King's College London, London, UK
| |
Collapse
|
38
|
Li ML, Weng KF, Shih SR, Brewer G. The evolving world of small RNAs from RNA viruses. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:575-88. [PMID: 27046163 DOI: 10.1002/wrna.1351] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/29/2016] [Accepted: 03/03/2016] [Indexed: 11/10/2022]
Abstract
RNA virus infection in plants and invertebrates can produce virus-derived small RNAs. These RNAs share features with host endogenous small interfering RNAs (siRNAs). They can potentially mediate RNA interference (RNAi) and related RNA silencing pathways, resulting in specific antiviral defense. Although most RNA silencing components such as Dicer, Ago2, and RISC are conserved among eukaryotic hosts, whether RNA virus infection in mammals can generate functional small RNAs that act in antiviral defense remains under discussion. Here, we review recent studies on the molecular and biochemical features of viral siRNAs and other virus-derived small RNAs from infected plants, arthropods, nematodes, and vertebrates and discuss the genetic pathways for their biogenesis and their roles in antiviral activity. WIREs RNA 2016, 7:575-588. doi: 10.1002/wrna.1351 For further resources related to this article, please visit the WIREs website.
Collapse
Affiliation(s)
- Mei-Ling Li
- Department of Biochemistry & Molecular Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Kuo-Feng Weng
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Shin-Ru Shih
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Clinical Virology Laboratory, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Gary Brewer
- Department of Biochemistry & Molecular Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA
| |
Collapse
|
39
|
An Interferon Regulated MicroRNA Provides Broad Cell-Intrinsic Antiviral Immunity through Multihit Host-Directed Targeting of the Sterol Pathway. PLoS Biol 2016; 14:e1002364. [PMID: 26938778 PMCID: PMC4777525 DOI: 10.1371/journal.pbio.1002364] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 12/22/2015] [Indexed: 12/11/2022] Open
Abstract
In invertebrates, small interfering RNAs are at the vanguard of cell-autonomous antiviral immunity. In contrast, antiviral mechanisms initiated by interferon (IFN) signaling predominate in mammals. Whilst mammalian IFN-induced miRNA are known to inhibit specific viruses, it is not known whether host-directed microRNAs, downstream of IFN-signaling, have a role in mediating broad antiviral resistance. By performing an integrative, systematic, global analysis of RNA turnover utilizing 4-thiouridine labeling of newly transcribed RNA and pri/pre-miRNA in IFN-activated macrophages, we identify a new post-transcriptional viral defense mechanism mediated by miR-342-5p. On the basis of ChIP and site-directed promoter mutagenesis experiments, we find the synthesis of miR-342-5p is coupled to the antiviral IFN response via the IFN-induced transcription factor, IRF1. Strikingly, we find miR-342-5p targets mevalonate-sterol biosynthesis using a multihit mechanism suppressing the pathway at different functional levels: transcriptionally via SREBF2, post-transcriptionally via miR-33, and enzymatically via IDI1 and SC4MOL. Mass spectrometry-based lipidomics and enzymatic assays demonstrate the targeting mechanisms reduce intermediate sterol pathway metabolites and total cholesterol in macrophages. These results reveal a previously unrecognized mechanism by which IFN regulates the sterol pathway. The sterol pathway is known to be an integral part of the macrophage IFN antiviral response, and we show that miR-342-5p exerts broad antiviral effects against multiple, unrelated pathogenic viruses such Cytomegalovirus and Influenza A (H1N1). Metabolic rescue experiments confirm the specificity of these effects and demonstrate that unrelated viruses have differential mevalonate and sterol pathway requirements for their replication. This study, therefore, advances the general concept of broad antiviral defense through multihit targeting of a single host pathway.
Collapse
|
40
|
Qian X, Hamid FM, El Sahili A, Darwis DA, Wong YH, Bhushan S, Makeyev EV, Lescar J. Functional Evolution in Orthologous Cell-encoded RNA-dependent RNA Polymerases. J Biol Chem 2016; 291:9295-309. [PMID: 26907693 PMCID: PMC4861493 DOI: 10.1074/jbc.m115.685933] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Indexed: 12/15/2022] Open
Abstract
Many eukaryotic organisms encode more than one RNA-dependent RNA polymerase (RdRP) that probably emerged as a result of gene duplication. Such RdRP paralogs often participate in distinct RNA silencing pathways and show characteristic repertoires of enzymatic activities in vitro However, to what extent members of individual paralogous groups can undergo functional changes during speciation remains an open question. We show that orthologs of QDE-1, an RdRP component of the quelling pathway in Neurospora crassa, have rapidly diverged in evolution at the amino acid sequence level. Analyses of purified QDE-1 polymerases from N. crassa (QDE-1(Ncr)) and related fungi, Thielavia terrestris (QDE-1(Tte)) and Myceliophthora thermophila (QDE-1(Mth)), show that all three enzymes can synthesize RNA, but the precise modes of their action differ considerably. Unlike their QDE-1(Ncr) counterpart favoring processive RNA synthesis, QDE-1(Tte) and QDE-1(Mth) produce predominantly short RNA copies via primer-independent initiation. Surprisingly, a 3.19 Å resolution crystal structure of QDE-1(Tte) reveals a quasisymmetric dimer similar to QDE-1(Ncr) Further electron microscopy analyses confirm that QDE-1(Tte) occurs as a dimer in solution and retains this status upon interaction with a template. We conclude that divergence of orthologous RdRPs can result in functional innovation while retaining overall protein fold and quaternary structure.
Collapse
Affiliation(s)
- Xinlei Qian
- From the Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 138673 Singapore, Singapore
| | - Fursham M Hamid
- From the Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 138673 Singapore, Singapore
| | - Abbas El Sahili
- From the Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 138673 Singapore, Singapore
| | - Dina Amallia Darwis
- From the Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 138673 Singapore, Singapore
| | - Yee Hwa Wong
- From the Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 138673 Singapore, Singapore
| | - Shashi Bhushan
- From the Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 138673 Singapore, Singapore
| | - Eugene V Makeyev
- From the Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 138673 Singapore, Singapore, the Medical Research Council Centre for Developmental Neurobiology, King's College, London SE1 1UL, United Kingdom, and
| | - Julien Lescar
- From the Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 138673 Singapore, Singapore, UPMC UMRS CR7-CNRS ERL 8255-INSERM U1135 Centre d' Immunologie et des Maladies Infectieuses, Faculté de Médecine Pierre et Marie Curie, Centre Hospitalier Universitaire Pitié-Salpêtrière, 75031 Paris, France
| |
Collapse
|
41
|
Hombach S, Kretz M. Non-coding RNAs: Classification, Biology and Functioning. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 937:3-17. [PMID: 27573892 DOI: 10.1007/978-3-319-42059-2_1] [Citation(s) in RCA: 539] [Impact Index Per Article: 67.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
One of the long-standing principles of molecular biology is that DNA acts as a template for transcription of messenger RNAs, which serve as blueprints for protein translation. A rapidly growing number of exceptions to this rule have been reported over the past decades: they include long known classes of RNAs involved in translation such as transfer RNAs and ribosomal RNAs, small nuclear RNAs involved in splicing events, and small nucleolar RNAs mainly involved in the modification of other small RNAs, such as ribosomal RNAs and transfer RNAs. More recently, several classes of short regulatory non-coding RNAs, including piwi-associated RNAs, endogenous short-interfering RNAs and microRNAs have been discovered in mammals, which act as key regulators of gene expression in many different cellular pathways and systems. Additionally, the human genome encodes several thousand long non-protein coding RNAs >200 nucleotides in length, some of which play crucial roles in a variety of biological processes such as epigenetic control of chromatin, promoter-specific gene regulation, mRNA stability, X-chromosome inactivation and imprinting. In this chapter, we will introduce several classes of short and long non-coding RNAs, describe their diverse roles in mammalian gene regulation and give examples for known modes of action.
Collapse
Affiliation(s)
- Sonja Hombach
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany.
| | - Markus Kretz
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany
| |
Collapse
|
42
|
Baksa I, Nagy T, Barta E, Havelda Z, Várallyay É, Silhavy D, Burgyán J, Szittya G. Identification of Nicotiana benthamiana microRNAs and their targets using high throughput sequencing and degradome analysis. BMC Genomics 2015; 16:1025. [PMID: 26626050 PMCID: PMC4667520 DOI: 10.1186/s12864-015-2209-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 11/12/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Nicotiana benthamiana is a widely used model plant species for research on plant-pathogen interactions as well as other areas of plant science. It can be easily transformed or agroinfiltrated, therefore it is commonly used in studies requiring protein localization, interaction, or plant-based systems for protein expression and purification. To discover and characterize the miRNAs and their cleaved target mRNAs in N. benthamiana, we sequenced small RNA transcriptomes and degradomes of two N. benthamiana accessions and validated them by Northern blots. RESULTS We used a comprehensive molecular approach to detect and to experimentally validate N. benthamiana miRNAs and their target mRNAs from various tissues. We identified 40 conserved miRNA families and 18 novel microRNA candidates and validated their target mRNAs with a genomic scale approach. The accumulation of thirteen novel miRNAs was confirmed by Northern blot analysis. The conserved and novel miRNA targets were found to be involved in various biological processes including transcription, RNA binding, DNA modification, signal transduction, stress response and metabolic process. Among the novel miRNA targets we found the mRNA of REPRESSOR OF SILENCING (ROS1). Regulation of ROS1 by a miRNA provides a new regulatory layer to reinforce transcriptional gene silencing by a post-transcriptional repression of ROS1 activity. CONCLUSIONS The identified conserved and novel miRNAs along with their target mRNAs also provides a tissue specific atlas of known and new miRNA expression and their cleaved target mRNAs of N. benthamiana. Thus this study will serve as a valuable resource to the plant research community that will be beneficial well into the future.
Collapse
Affiliation(s)
- Ivett Baksa
- Institute of Plant Biotechnology, National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Szent-Györgyi Albert ut 4, H-2100, Gödöllő, Hungary.
| | - Tibor Nagy
- Institute of Plant Biotechnology, National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Szent-Györgyi Albert ut 4, H-2100, Gödöllő, Hungary.
| | - Endre Barta
- Institute of Plant Biotechnology, National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Szent-Györgyi Albert ut 4, H-2100, Gödöllő, Hungary.
| | - Zoltán Havelda
- Institute of Plant Biotechnology, National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Szent-Györgyi Albert ut 4, H-2100, Gödöllő, Hungary.
| | - Éva Várallyay
- Institute of Plant Biotechnology, National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Szent-Györgyi Albert ut 4, H-2100, Gödöllő, Hungary.
| | - Dániel Silhavy
- Institute of Plant Biotechnology, National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Szent-Györgyi Albert ut 4, H-2100, Gödöllő, Hungary.
| | - József Burgyán
- Institute of Plant Biotechnology, National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Szent-Györgyi Albert ut 4, H-2100, Gödöllő, Hungary.
| | - György Szittya
- Institute of Plant Biotechnology, National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Szent-Györgyi Albert ut 4, H-2100, Gödöllő, Hungary.
| |
Collapse
|
43
|
Zhang C, Wu Z, Li Y, Wu J. Biogenesis, Function, and Applications of Virus-Derived Small RNAs in Plants. Front Microbiol 2015; 6:1237. [PMID: 26617580 PMCID: PMC4637412 DOI: 10.3389/fmicb.2015.01237] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/26/2015] [Indexed: 11/13/2022] Open
Abstract
RNA silencing, an evolutionarily conserved and sequence-specific gene-inactivation system, has a pivotal role in antiviral defense in most eukaryotic organisms. In plants, a class of exogenous small RNAs (sRNAs) originating from the infecting virus called virus-derived small interfering RNAs (vsiRNAs) are predominantly responsible for RNA silencing-mediated antiviral immunity. Nowadays, the process of vsiRNA formation and the role of vsiRNAs in plant viral defense have been revealed through deep sequencing of sRNAs and diverse genetic analysis. The biogenesis of vsiRNAs is analogous to that of endogenous sRNAs, which require diverse essential components including dicer-like (DCL), argonaute (AGO), and RNA-dependent RNA polymerase (RDR) proteins. vsiRNAs trigger antiviral defense through post-transcriptional gene silencing (PTGS) or transcriptional gene silencing (TGS) of viral RNA, and they hijack the host RNA silencing system to target complementary host transcripts. Additionally, several applications that take advantage of the current knowledge of vsiRNAs research are being used, such as breeding antiviral plants through genetic engineering technology, reconstructing of viral genomes, and surveying viral ecology and populations. Here, we will provide an overview of vsiRNA pathways, with a primary focus on the advances in vsiRNA biogenesis and function, and discuss their potential applications as well as the future challenges in vsiRNAs research.
Collapse
Affiliation(s)
- Chao Zhang
- Key Laboratory of Plant Virology of Fujian Province, Institute of Plant Virology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Zujian Wu
- Key Laboratory of Plant Virology of Fujian Province, Institute of Plant Virology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Yi Li
- Peking-Yale Joint Center for Plant Molecular Genetics and Agrobiotechnology, The National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University Beijing, China
| | - Jianguo Wu
- Key Laboratory of Plant Virology of Fujian Province, Institute of Plant Virology, Fujian Agriculture and Forestry University Fuzhou, China ; Peking-Yale Joint Center for Plant Molecular Genetics and Agrobiotechnology, The National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University Beijing, China
| |
Collapse
|
44
|
Moon SL, Dodd BJT, Brackney DE, Wilusz CJ, Ebel GD, Wilusz J. Flavivirus sfRNA suppresses antiviral RNA interference in cultured cells and mosquitoes and directly interacts with the RNAi machinery. Virology 2015; 485:322-9. [PMID: 26331679 DOI: 10.1016/j.virol.2015.08.009] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 08/07/2015] [Accepted: 08/09/2015] [Indexed: 10/23/2022]
Abstract
Productive arbovirus infections require mechanisms to suppress or circumvent the cellular RNA interference (RNAi) pathway, a major antiviral response in mosquitoes. In this study, we demonstrate that two flaviviruses, Dengue virus and Kunjin virus, significantly repress siRNA-mediated RNAi in infected human cells as well as during infection of the mosquito vector Culex quinquefasciatus. Arthropod-borne flaviviruses generate a small structured non-coding RNA from the viral 3' UTR referred to as sfRNA. Analysis of infections with a mutant Kunjin virus that is unable to generate appreciable amounts of the major sfRNA species indicated that RNAi suppression was associated with the generation of the non-coding sfRNA. Co-immunoprecipitation of sfRNA with RNAi mediators Dicer and Ago2 suggest a model for RNAi suppression. Collectively, these data help to establish a clear role for sfRNA in RNAi suppression and adds to the emerging impact of viral long non-coding RNAs in modulating aspects of anti-viral immune processes.
Collapse
Affiliation(s)
- Stephanie L Moon
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Benjamin J T Dodd
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Doug E Brackney
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Carol J Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Gregory D Ebel
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA.
| |
Collapse
|
45
|
Garcia-Ruiz H, Carbonell A, Hoyer JS, Fahlgren N, Gilbert KB, Takeda A, Giampetruzzi A, Garcia Ruiz MT, McGinn MG, Lowery N, Martinez Baladejo MT, Carrington JC. Roles and programming of Arabidopsis ARGONAUTE proteins during Turnip mosaic virus infection. PLoS Pathog 2015; 11:e1004755. [PMID: 25806948 PMCID: PMC4373807 DOI: 10.1371/journal.ppat.1004755] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 02/19/2015] [Indexed: 11/24/2022] Open
Abstract
In eukaryotes, ARGONAUTE proteins (AGOs) associate with microRNAs (miRNAs), short interfering RNAs (siRNAs), and other classes of small RNAs to regulate target RNA or target loci. Viral infection in plants induces a potent and highly specific antiviral RNA silencing response characterized by the formation of virus-derived siRNAs. Arabidopsis thaliana has ten AGO genes of which AGO1, AGO2, and AGO7 have been shown to play roles in antiviral defense. A genetic analysis was used to identify and characterize the roles of AGO proteins in antiviral defense against Turnip mosaic virus (TuMV) in Arabidopsis. AGO1, AGO2 and AGO10 promoted anti-TuMV defense in a modular way in various organs, with AGO2 providing a prominent antiviral role in leaves. AGO5, AGO7 and AGO10 had minor effects in leaves. AGO1 and AGO10 had overlapping antiviral functions in inflorescence tissues after systemic movement of the virus, although the roles of AGO1 and AGO10 accounted for only a minor amount of the overall antiviral activity. By combining AGO protein immunoprecipitation with high-throughput sequencing of associated small RNAs, AGO2, AGO10, and to a lesser extent AGO1 were shown to associate with siRNAs derived from silencing suppressor (HC-Pro)-deficient TuMV-AS9, but not with siRNAs derived from wild-type TuMV. Co-immunoprecipitation and small RNA sequencing revealed that viral siRNAs broadly associated with wild-type HC-Pro during TuMV infection. These results support the hypothesis that suppression of antiviral silencing during TuMV infection, at least in part, occurs through sequestration of virus-derived siRNAs away from antiviral AGO proteins by HC-Pro. These findings indicate that distinct AGO proteins function as antiviral modules, and provide a molecular explanation for the silencing suppressor activity of HC-Pro. RNA silencing is a primary, adaptive defense system against viruses in plants. Viruses have evolved counter-defensive mechanisms that inhibit RNA silencing through the activity of silencing suppressor proteins. Understanding how antiviral silencing is controlled, and how suppressor proteins function, is essential for understanding how plants normally resist viruses, why some viruses are highly virulent in different hosts, and how sustainable antiviral resistance strategies can be deployed in agricultural settings. We used a mutant version of Turnip mosaic virus lacking a functional silencing suppressor (HC-Pro) to understand the genetic requirements for resistance in the model plant Arabidopsis thaliana. We focused on ARGONAUTE proteins, which have long been hypothesized to bind short interfering RNAs (siRNAs) derived from virus genomes for use as sequence-specific guides to recognize and target viral RNA for degradation or repression. We demonstrated specialized antiviral roles for specific ARGONAUTES and showed that several can bind viral siRNAs from across the entire viral genome. However, ARGONAUTE proteins are only loaded with virus-derived siRNAs in the absence of HC-Pro, which we showed binds siRNAs from the viral genome. This indicates that several AGO proteins, which collectively are necessary for full anti-TuMV defense, need to properly load virus-derived siRNAs to execute their antiviral roles.
Collapse
Affiliation(s)
- Hernan Garcia-Ruiz
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
- Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Alberto Carbonell
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
- Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - J. Steen Hoyer
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
- Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
- Computational and Systems Biology Program, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Noah Fahlgren
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
- Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Kerrigan B. Gilbert
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Atsushi Takeda
- Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Annalisa Giampetruzzi
- Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Mayra T. Garcia Ruiz
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Michaela G. McGinn
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Nicholas Lowery
- Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | | | - James C. Carrington
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
- Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
- * E-mail:
| |
Collapse
|
46
|
Activation of Tomato Bushy Stunt Virus RNA-Dependent RNA Polymerase by Cellular Heat Shock Protein 70 Is Enhanced by Phospholipids In Vitro. J Virol 2015; 89:5714-23. [PMID: 25762742 DOI: 10.1128/jvi.03711-14] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Accepted: 03/08/2015] [Indexed: 01/12/2023] Open
Abstract
UNLABELLED Similar to other positive-strand RNA viruses, tombusviruses are replicated by the membrane-bound viral replicase complex (VRC). The VRC consists of the p92 virus-coded RNA-dependent RNA polymerase (RdRp), the viral p33 RNA chaperone, and several co-opted host proteins. In order to become a functional RdRp after its translation, the p92 replication protein should be incorporated into the VRC, followed by its activation. We have previously shown in a cell-free yeast extract-based assay that the activation of the Tomato bushy stunt virus (TBSV) RdRp requires a soluble host factor(s). In this article, we identify the cellular heat shock protein 70 (Hsp70) as the co-opted host factor required for the activation of an N-terminally truncated recombinant TBSV RdRp. In addition, small-molecule-based blocking of Hsp70 function inhibits RNA synthesis by the tombusvirus RdRp in vitro. Furthermore, we show that neutral phospholipids, namely, phosphatidylethanolamine (PE) and phosphatidylcholine (PC), enhance RdRp activation in vitro. In contrast, phosphatidylglycerol (PG) shows a strong and dominant inhibitory effect on in vitro RdRp activation. We also demonstrate that PE and PC stimulate RdRp-viral plus-strand RNA [(+)RNA] interaction, while PG inhibits the binding of the viral RNA to the RdRp. Based on the stimulatory versus inhibitory roles of various phospholipids in tombusvirus RdRp activation, we propose that the lipid composition of targeted subcellular membranes might be utilized by tombusviruses to regulate new VRC assembly during the course of infection. IMPORTANCE The virus-coded RNA-dependent RNA polymerase (RdRp), which is responsible for synthesizing the viral RNA progeny in infected cells of several positive-strand RNA viruses, is initially inactive. This strategy is likely to avoid viral RNA synthesis in the cytosol that would rapidly lead to induction of RNA-triggered cellular antiviral responses. During the assembly of the membrane-bound replicase complex, the viral RdRp becomes activated through an incompletely understood process that makes the RdRp capable of RNA synthesis. By using TBSV RdRp, we show that the co-opted cellular Hsp70 chaperone and neutral phospholipids facilitate RdRp activation in vitro. In contrast, phosphatidylglycerol (PG) has a dominant inhibitory effect on in vitro RdRp activation and RdRp-viral RNA interaction, suggesting that the membranous microdomain surrounding the RdRp greatly affects its ability for RNA synthesis. Thus, the activation of the viral RdRp likely depends on multiple host components in infected cells.
Collapse
|
47
|
Rigby RE, Rehwinkel J. RNA degradation in antiviral immunity and autoimmunity. Trends Immunol 2015; 36:179-88. [PMID: 25709093 PMCID: PMC4358841 DOI: 10.1016/j.it.2015.02.001] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 02/02/2015] [Accepted: 02/02/2015] [Indexed: 01/09/2023]
Abstract
The nonsense-mediated decay (NMD) pathway defends cells against RNA virus invasion. NMD targets viral RNAs for degradation, including by the RNA exosome. Genetic deficiencies in NMD and RNA exosome components cause autoimmunity. NMD and the RNA exosome prevent aberrant activation of innate immune responses.
Post-transcriptional control determines the fate of cellular RNA molecules. Nonsense-mediated decay (NMD) provides quality control of mRNA, targeting faulty cellular transcripts for degradation by multiple nucleases including the RNA exosome. Recent findings have revealed a role for NMD in targeting viral RNA molecules, thereby restricting virus infection. Interestingly, NMD is also linked to immune responses at another level: mutations affecting the NMD or RNA exosome machineries cause chronic activation of defence programmes, resulting in autoimmune phenotypes. Here we place these observations in the context of other links between innate antiviral immunity and type I interferon mediated disease and examine two models: one in which expression or function of pathogen sensors is perturbed and one wherein host-derived RNA molecules with a propensity to activate such sensors accumulate.
Collapse
Affiliation(s)
- Rachel E Rigby
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Jan Rehwinkel
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK.
| |
Collapse
|
48
|
Chuang C, Prasanth KR, Nagy PD. Coordinated function of cellular DEAD-box helicases in suppression of viral RNA recombination and maintenance of viral genome integrity. PLoS Pathog 2015; 11:e1004680. [PMID: 25693185 PMCID: PMC4333740 DOI: 10.1371/journal.ppat.1004680] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Accepted: 01/12/2015] [Indexed: 12/16/2022] Open
Abstract
The intricate interactions between viruses and hosts include an evolutionary arms race and adaptation that is facilitated by the ability of RNA viruses to evolve rapidly due to high frequency mutations and genetic RNA recombination. In this paper, we show evidence that the co-opted cellular DDX3-like Ded1 DEAD-box helicase suppresses tombusviral RNA recombination in yeast model host, and the orthologous RH20 helicase functions in a similar way in plants. In vitro replication and recombination assays confirm the direct role of the ATPase function of Ded1p in suppression of viral recombination. We also present data supporting a role for Ded1 in facilitating the switch from minus- to plus-strand synthesis. Interestingly, another co-opted cellular helicase, the eIF4AIII-like AtRH2, enhances TBSV recombination in the absence of Ded1/RH20, suggesting that the coordinated actions of these helicases control viral RNA recombination events. Altogether, these helicases are the first co-opted cellular factors in the viral replicase complex that directly affect viral RNA recombination. Ded1 helicase seems to be a key factor maintaining viral genome integrity by promoting the replication of viral RNAs with correct termini, but inhibiting the replication of defective RNAs lacking correct 5' end sequences. Altogether, a co-opted cellular DEAD-box helicase facilitates the maintenance of full-length viral genome and suppresses viral recombination, thus limiting the appearance of defective viral RNAs during replication.
Collapse
Affiliation(s)
- Chingkai Chuang
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, United States of America
| | - K. Reddisiva Prasanth
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, United States of America
| | - Peter D. Nagy
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, United States of America
| |
Collapse
|
49
|
van Cleef KWR, van Mierlo JT, Miesen P, Overheul GJ, Fros JJ, Schuster S, Marklewitz M, Pijlman GP, Junglen S, van Rij RP. Mosquito and Drosophila entomobirnaviruses suppress dsRNA- and siRNA-induced RNAi. Nucleic Acids Res 2014; 42:8732-44. [PMID: 24939903 PMCID: PMC4117760 DOI: 10.1093/nar/gku528] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
RNA interference (RNAi) is a crucial antiviral defense mechanism in insects, including the major mosquito species that transmit important human viruses. To counteract the potent antiviral RNAi pathway, insect viruses encode RNAi suppressors. However, whether mosquito-specific viruses suppress RNAi remains unclear. We therefore set out to study RNAi suppression by Culex Y virus (CYV), a mosquito-specific virus of the Birnaviridae family that was recently isolated from Culex pipiens mosquitoes. We found that the Culex RNAi machinery processes CYV double-stranded RNA (dsRNA) into viral small interfering RNAs (vsiRNAs). Furthermore, we show that RNAi is suppressed in CYV-infected cells and that the viral VP3 protein is responsible for RNAi antagonism. We demonstrate that VP3 can functionally replace B2, the well-characterized RNAi suppressor of Flock House virus. VP3 was found to bind long dsRNA as well as siRNAs and interfered with Dicer-2-mediated cleavage of long dsRNA into siRNAs. Slicing of target RNAs by pre-assembled RNA-induced silencing complexes was not affected by VP3. Finally, we show that the RNAi-suppressive activity of VP3 is conserved in Drosophila X virus, a birnavirus that persistently infects Drosophila cell cultures. Together, our data indicate that mosquito-specific viruses may encode RNAi antagonists to suppress antiviral RNAi.
Collapse
Affiliation(s)
- Koen W R van Cleef
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Joël T van Mierlo
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Pascal Miesen
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Gijs J Overheul
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Jelke J Fros
- Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Susan Schuster
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Marco Marklewitz
- Institute of Virology, University of Bonn Medical Centre, Sigmund Freud Str. 25, 53127 Bonn, Germany
| | - Gorben P Pijlman
- Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Sandra Junglen
- Institute of Virology, University of Bonn Medical Centre, Sigmund Freud Str. 25, 53127 Bonn, Germany
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| |
Collapse
|
50
|
Mouse knockout models for HIV-1 restriction factors. Cell Mol Life Sci 2014; 71:3749-66. [PMID: 24854580 PMCID: PMC4160573 DOI: 10.1007/s00018-014-1646-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/24/2014] [Accepted: 05/05/2014] [Indexed: 12/21/2022]
Abstract
Infection of cells with human immunodeficiency virus 1 (HIV-1) is controlled by restriction factors, host proteins that counteract a variety of steps in the life cycle of this lentivirus. These include SAMHD1, APOBEC3G and tetherin, which block reverse transcription, hypermutate viral DNA and prevent progeny virus release, respectively. These and other HIV-1 restriction factors are conserved and have clear orthologues in the mouse. This review summarises studies in knockout mice lacking HIV-1 restriction factors. In vivo experiments in such animals have not only validated in vitro data obtained from cultured cells, but have also revealed new findings about the biology of these proteins. Indeed, genetic ablation of HIV-1 restriction factors in the mouse has provided evidence that restriction factors control retroviruses and other viruses in vivo and has led to new insights into the mechanisms by which these proteins counteract infection. For example, in vivo experiments in knockout mice demonstrate that virus control exerted by restriction factors can shape adaptive immune responses. Moreover, the availability of animals lacking restriction factors opens the possibility to study the function of these proteins in other contexts such as autoimmunity and cancer. Further in vivo studies of more recently identified HIV-1 restriction factors in gene targeted mice are, therefore, justified.
Collapse
|