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Bwalya J, Kim KH. The Crucial Role of Chloroplast-Related Proteins in Viral Genome Replication and Host Defense against Positive-Sense Single-Stranded RNA Viruses. THE PLANT PATHOLOGY JOURNAL 2023; 39:28-38. [PMID: 36760047 PMCID: PMC9929168 DOI: 10.5423/ppj.rw.10.2022.0139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/19/2022] [Accepted: 12/22/2022] [Indexed: 06/18/2023]
Abstract
Plant viruses are responsible for worldwide production losses of numerous economically important crops. The most common plant RNA viruses are positivesense single-stranded RNA viruses [(+)ss RNA viruses]. These viruses have small genomes that encode a limited number of proteins. The viruses depend on their host's machinery for the replication of their RNA genome, assembly, movement, and attraction to the vectors for dispersal. Recently researchers have reported that chloroplast proteins are crucial for replicating (+)ss plant RNA viruses. Some chloroplast proteins, including translation initiation factor [eIF(iso)4E] and 75 DEAD-box RNA helicase RH8, help viruses fulfill their infection cycle in plants. In contrast, other chloroplast proteins such as PAP2.1, PSaC, and ATPsyn-α play active roles in plant defense against viruses. This is also consistent with the idea that reactive oxygen species, salicylic acid, jasmonic acid, and abscisic acid are produced in chloroplast. However, knowledge of molecular mechanisms and functions underlying these chloroplast host factors during the virus infection is still scarce and remains largely unknown. Our review briefly summarizes the latest knowledge regarding the possible role of chloroplast in plant virus replication, emphasizing chloroplast-related proteins. We have highlighted current advances regarding chloroplast-related proteins' role in replicating plant (+)ss RNA viruses.
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Affiliation(s)
- John Bwalya
- Department of Agriculture Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
| | - Kook-Hyung Kim
- Department of Agriculture Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826,
Korea
- Research of Institute Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
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2
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Planchais S, Camborde L, Jupin I. Protocols for Studying Protein Stability in an Arabidopsis Protoplast Transient Expression System. Methods Mol Biol 2023; 2581:179-199. [PMID: 36413318 DOI: 10.1007/978-1-0716-2784-6_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Protein stability influences many aspects of biology, and measuring their stability in vivo can provide important insights into biological systems.This chapter describes in detail two methods to assess the stability of a specific protein based on its transient expression in Arabidopsis protoplasts. First, a pulse-chase assay based on radioactive metabolic labeling of cellular proteins, followed by immunoprecipitation of the protein of interest. The decrease in radioactive signal is monitored over time and can be used to determine the protein's half-life.Alternatively, we also present a nonradioactive assay based on the use of reporter proteins, whose ratio can be quantified. This assay can be used to determine the relative stability of a protein of interest under specific conditions.
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Affiliation(s)
- Séverine Planchais
- Laboratoire de Virologie Moléculaire, Institut Jacques Monod, CNRS, UMR 7592, Univ. Paris-Diderot, Sorbonne Paris Cité, Paris, France
- Unité URF5 « Adaptation des Plantes aux Contraintes Environnementales : Réponses Ecophysiologiques et Moléculaires», Univ. Pierre-et-Marie-Curie, Paris, France
| | - Laurent Camborde
- Laboratoire de Virologie Moléculaire, Institut Jacques Monod, CNRS, UMR 7592, Univ. Paris-Diderot, Sorbonne Paris Cité, Paris, France
- Laboratoire de Recherche en Sciences Végétales, CNRS, Univ. Toulouse Paul Sabatier, Toulouse, France
| | - Isabelle Jupin
- Laboratoire de Virologie Moléculaire, Institut Jacques Monod, CNRS, UMR 7592, Univ. Paris-Diderot, Sorbonne Paris Cité, Paris, France.
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3
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Patel A, McBride JAM, Mark BL. The endopeptidase of the maize-affecting Marafivirus type member maize rayado fino virus doubles as a deubiquitinase. J Biol Chem 2021; 297:100957. [PMID: 34265303 PMCID: PMC8348309 DOI: 10.1016/j.jbc.2021.100957] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/05/2021] [Accepted: 07/09/2021] [Indexed: 10/28/2022] Open
Abstract
Marafiviruses are capable of persistent infection in a range of plants that have importance to the agriculture and biofuel industries. Although the genomes of a few of these viruses have been studied in-depth, the composition and processing of the polyproteins produced from their main ORFs have not. The Marafivirus polyprotein consists of essential proteins that form the viral replicase, as well as structural proteins for virus assembly. It has been proposed that Marafiviruses code for cysteine proteases within their polyproteins, which act as endopeptidases to autocatalytically cleave the polyprotein into functional domains. Furthermore, it has also been suggested that Marafivirus endopeptidases may have deubiquitinating activity, which has been shown to enhance viral replication by downregulating viral protein degradation by the ubiquitin (Ub) proteasomal pathway as well as tampering with cell signaling associated with innate antiviral responses in other positive-sense ssRNA viruses. Here, we provide the first evidence of cysteine proteases from six different Marafiviruses that harbor deubiquitinating activity and reveal intragenus differences toward Ub linkage types. We also examine the structural basis of the endopeptidase/deubiquitinase from the Marafivirus type member, maize rayado fino virus. Structures of the enzyme alone and bound to Ub reveal marked structural rearrangements that occur upon binding of Ub and provide insights into substrate specificity and differences that set it apart from other viral cysteine proteases.
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Affiliation(s)
- Ankoor Patel
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | | | - Brian L Mark
- Department of Microbiology, University of Manitoba, Winnipeg, Canada.
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4
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In vitro translation of virally-encoded replication polyproteins to recapitulate polyprotein maturation processes. Protein Expr Purif 2020; 175:105694. [PMID: 32681958 DOI: 10.1016/j.pep.2020.105694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 06/23/2020] [Accepted: 06/25/2020] [Indexed: 11/21/2022]
Abstract
Single-stranded, positive-sense RNA viruses encode essential replication polyproteins which are composed of several domains. They are usually subjected to finely regulated proteolytic maturation processes to generate cleavage intermediates and end-products. Both polyproteins and maturation products play multiple key roles that ultimately allow synthesis of viral genome progeny. Despite the importance of these proteins in the course of viral replication, their structural properties, including the conformational changes regulating their numerous functions, are poorly described at the structural level. This lack of information is mainly due to the extreme difficulty to express large, membrane-bound, multi-domain proteins with criteria suitable for structural biology methods. To tackle this challenge, we have used a wheat-germ cell-free expression system. We firstly establish that this approach allows to synthesize viral polyproteins encoded by two unrelated positive-sense RNA viruses, a human norovirus and a plant tymovirus. Then, we demonstrate that these polyproteins are fully functional and are spontaneously auto-cleaved by their active protease domain, giving rise to natural maturation products. Moreover, we show that introduction of point mutations in polyproteins allows to inhibit the proteolytic maturation process of each virus. This allowed us to express and partially purify the uncleaved full-length norovirus polyprotein and the tymoviral RNA-dependent RNA polymerase. Thus, this study provides a powerful tool to obtain soluble viral polyproteins and their maturation products in order to conduct challenging structural biology projects and therefore solve unanswered questions.
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5
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Rodamilans B, Shan H, Pasin F, García JA. Plant Viral Proteases: Beyond the Role of Peptide Cutters. FRONTIERS IN PLANT SCIENCE 2018; 9:666. [PMID: 29868107 PMCID: PMC5967125 DOI: 10.3389/fpls.2018.00666] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 04/30/2018] [Indexed: 05/23/2023]
Abstract
Almost half of known plant viral species rely on proteolytic cleavages as key co- and post-translational modifications throughout their infection cycle. Most of these viruses encode their own endopeptidases, proteases with high substrate specificity that internally cleave large polyprotein precursors for the release of functional sub-units. Processing of the polyprotein, however, is not an all-or-nothing process in which endopeptidases act as simple peptide cutters. On the contrary, spatial-temporal modulation of these polyprotein cleavage events is crucial for a successful viral infection. In this way, the processing of the polyprotein coordinates viral replication, assembly and movement, and has significant impact on pathogen fitness and virulence. In this mini-review, we give an overview of plant viral proteases emphasizing their importance during viral infections and the varied functionalities that result from their proteolytic activities.
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Affiliation(s)
- Bernardo Rodamilans
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Madrid, Spain
| | - Hongying Shan
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Madrid, Spain
| | - Fabio Pasin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Juan Antonio García
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Madrid, Spain
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6
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Wang P, Li J, Gong P, Wang W, Ai Y, Zhang X. An OTU deubiquitinating enzyme in Eimeria tenella interacts with Eimeria tenella virus RDRP. Parasit Vectors 2018; 11:74. [PMID: 29386062 PMCID: PMC5793433 DOI: 10.1186/s13071-018-2626-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 01/08/2018] [Indexed: 01/09/2023] Open
Abstract
Background Chicken coccidiosis, a disease caused by seven species of Eimeria (Apicomplexa: Coccidia), inflicts severe economic losses on the poultry industry. Eimeria tenella is the one of the most virulent species pathogenic to chickens. Many parasitic protozoans are parasitised by double-stranded (ds) RNA viruses, and the influence of protozoan viruses on parasitic protozoans has been extensively reported. E. tenella RNA virus 1 (Etv) was identified in E. tenella, and the complete genome sequence of Etv was analysed. Here, we screened Etv-RNA-dependent RNA polymerase (RDRP)-interacting host protein E. tenella ovarian tumour (OTU) protein-like cysteine protease (Et-OTU) using a yeast two-hybrid system with pGBKT7-RDRP plasmid serving as bait. A previous study demonstrated that Et-OTU could regulate the telomerase activity of E. tenella, indicating that Et-OTU affects E. tenella proliferation. However, whether Etv-RDRP affects the molecular biological characteristics of E. tenella by interacting with OTU remains unclear. Results We obtained seven positive clones from the initial screen, and six of the seven preys were identified as false-positives. Finally, we identified an RDRP-associated protein predicted to be an E. tenella OTU protein. A α-galactosidase assay showed that the bait vector did not activate the GAL4 reporter gene, indicating no autoactivation activity from the RDRP bait fusion. Pull-down and co-immunoprecipitation assays verified the interaction between Et-OTU and Etv-RDRP both intracellularly and extracellularly. Additionally, Et-OTU was able to deconjugate K48- and K6-linked di-ubiquitin (di-Ub) chains in vitro but not K63-, K11-, K29-, or K33-linked di-Ub chains. The C239A and H351A mutations eliminated the deubiquitinase (DUB) activity of Et-OTU, whereas the D236A mutation did not. Additionally, when combined with RDRP, the DUB activity of Et-OTU towards K48- and K6-linked chains was significantly enhanced. Conclusion Etv-RDRP interacts with Et-OTU both intracellularly and extracellularly. Etv-RDRP enhances the hydrolysis of Et-OTU to K6- or K48-linked ubiquitin chains. This study lays the foundation for further research on the relationship between E. tenella and Etv.
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Affiliation(s)
- Pu Wang
- College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Jianhua Li
- College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Pengtao Gong
- College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Weirong Wang
- College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Yongxing Ai
- College of Animal Science, Jilin University, Changchun, 130062, China.
| | - Xichen Zhang
- College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
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Kumar S, Kumar A, Mamidi P, Tiwari A, Kumar S, Mayavannan A, Mudulli S, Singh AK, Subudhi BB, Chattopadhyay S. Chikungunya virus nsP1 interacts directly with nsP2 and modulates its ATPase activity. Sci Rep 2018; 8:1045. [PMID: 29348627 PMCID: PMC5773547 DOI: 10.1038/s41598-018-19295-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 12/27/2017] [Indexed: 01/29/2023] Open
Abstract
Chikungunya virus (CHIKV) is a mosquito-borne virus, which has created an alarming threat in the world due to unavailability of vaccine and antiviral compounds. The CHIKV nsP2 contains ATPase, RTPase, helicase and protease activities, whereas, nsP1 is a viral capping enzyme. In alphaviruses, the four non-structural proteins form the replication complex in the cytoplasm and this study characterizes the interaction between CHIKV nsP1 and nsP2. It was observed that, both the proteins co-localize in the cytoplasm and interact in the CHIKV infected cells by confocal microscopy and immunoprecipitation assay. Further, it was demonstrated through mutational analysis that, the amino acids 1-95 of nsP2 and 170-288 of nsP1 are responsible for their direct interaction. Additionally, it was noticed that, the ATPase activity of nsP2 is enhanced in the presence of nsP1, indicating the functional significance of this interaction. In silico analysis showed close (≤1.7 Å) polar interaction (hydrogen bond) between Glu4, Arg7, 96, 225 of nsP2 with Lys256, 206, Val367 and Phe312 of nsP1 respectively. Hence, this investigation provides molecular characterization of CHIKV nsP1-nsP2 interaction which might be a useful target for rational designing of antiviral drugs.
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Affiliation(s)
| | | | | | - Atul Tiwari
- Banaras Hindu University, Varanasi, U.P., India
| | | | | | | | | | - Bharat Bhusan Subudhi
- School of Pharmaceutical Sciences, Siksha O Anusandhan University, Bhubaneswar, India
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8
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Jupin I, Ayach M, Jomat L, Fieulaine S, Bressanelli S. A mobile loop near the active site acts as a switch between the dual activities of a viral protease/deubiquitinase. PLoS Pathog 2017; 13:e1006714. [PMID: 29117247 PMCID: PMC5695851 DOI: 10.1371/journal.ppat.1006714] [Citation(s) in RCA: 14] [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: 01/18/2017] [Revised: 11/20/2017] [Accepted: 10/25/2017] [Indexed: 12/21/2022] Open
Abstract
The positive-strand RNA virus Turnip yellow mosaic virus (TYMV) encodes an ovarian tumor (OTU)-like protease/deubiquitinase (PRO/DUB) protein domain involved both in proteolytic processing of the viral polyprotein through its PRO activity, and in removal of ubiquitin chains from ubiquitylated substrates through its DUB activity. Here, the crystal structures of TYMV PRO/DUB mutants and molecular dynamics simulations reveal that an idiosyncratic mobile loop participates in reversibly constricting its unusual catalytic site by adopting "open", "intermediate" or "closed" conformations. The two cis-prolines of the loop form a rigid flap that in the most closed conformation zips up against the other side of the catalytic cleft. The intermediate and closed conformations also correlate with a reordering of the TYMV PRO/DUB catalytic dyad, that then assumes a classical, yet still unusually mobile, OTU DUB alignment. Further structure-based mutants designed to interfere with the loop's mobility were assessed for enzymatic activity in vitro and in vivo, and were shown to display reduced DUB activity while retaining PRO activity. This indicates that control of the switching between the dual PRO/DUB activities resides prominently within this loop next to the active site. Introduction of mutations into the viral genome revealed that the DUB activity contributes to the extent of viral RNA accumulation both in single cells and in whole plants. In addition, the conformation of the mobile flap was also found to influence symptoms severity in planta. Such mutants now provide powerful tools with which to study the specific roles of reversible ubiquitylation in viral infection. Viruses have much smaller genomes than their hosts. Consequently, they often encode proteins which are multifunctional. For instance, some viral proteases have a dual function, being also deubiquitinases, i.e. enzymes capable of removing ubiquitin tags grafted onto proteins and that often target them for destruction. The protease and deubiquitinase activities share a single active site that is used alternately for one function or the other, but how this switch between activities may be regulated is presently unknown. To answer this question, we studied a simple plant virus that is a useful model system for these complex molecular biology phenomena, and that encodes a simplified protease/deubiquitinase. Here, thanks to a combination of structural and functional analyses, we managed to decouple the two activities, killing the deubiquitinase activity while preserving the protease one. This successful decoupling relies on our discovery that a loop inserted next to the active site is mobile, and can thus act as a switch between the two activities. This result allowed us to demonstrate the importance of the specific deubiquinase activity in viral multiplication. In addition, viral symptoms were also severely affected by mutations affecting the loop mobility. Our data provide powerful tools for further studies, that may also be relevant for more complex or medically relevant viruses.
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Affiliation(s)
- Isabelle Jupin
- Institut Jacques Monod, CNRS—Univ Paris-Diderot, Paris, France
- * E-mail: (IJ); (SB)
| | - Maya Ayach
- Institute for Integrative Biology of the Cell, CEA—CNRS—Univ Paris-Saclay, Gif sur Yvette, France
| | - Lucile Jomat
- Institut Jacques Monod, CNRS—Univ Paris-Diderot, Paris, France
| | - Sonia Fieulaine
- Institute for Integrative Biology of the Cell, CEA—CNRS—Univ Paris-Saclay, Gif sur Yvette, France
| | - Stéphane Bressanelli
- Institute for Integrative Biology of the Cell, CEA—CNRS—Univ Paris-Saclay, Gif sur Yvette, France
- * E-mail: (IJ); (SB)
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9
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Huang YW, Hu CC, Tsai CH, Lin NS, Hsu YH. Chloroplast Hsp70 Isoform Is Required for Age-Dependent Tissue Preference of Bamboo mosaic virus in Mature Nicotiana benthamiana Leaves. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:631-645. [PMID: 28459172 DOI: 10.1094/mpmi-01-17-0012-r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Plant viruses may exhibit age-dependent tissue preference in their hosts but the underlying mechanisms are not well understood. In this study, we provide several lines of evidence to reveal the determining role of a protein of the Nicotiana benthamiana chloroplast Hsp70 (NbcpHsp70) family, NbcpHsp70-2, involved in the preference of Bamboo mosaic virus (BaMV) to infect older tissues. NbcpHsp70 family proteins were identified in complexes pulled down with BaMV replicase as the bait. Among the isoforms of NbcpHsp70, only the specific silencing of NbcpHsp70-2 resulted in the significant decrease of BaMV RNA in N. benthamiana protopalsts, indicating that NbcpHsp70-2 is involved in the efficient replication of BaMV RNA. We further identified the age-dependent import regulation signal contained in the transit peptide of NbcpHsp70-2. Deletion, overexpression, and substitution experiments revealed that the signal in the transit peptide of NbcpHsp70-2 is crucial for both the import of NbcpHsp70-2 into older chloroplasts and the preference of BaMV for infecting older leaves of N. benthamiana. Together, these data demonstrated that BaMV may exploit a cellular age-dependent transportation mechanism to target a suitable environment for viral replication.
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Affiliation(s)
- Ying Wen Huang
- 1 Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan; and
| | - Chung Chi Hu
- 1 Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan; and
| | - Ching Hsiu Tsai
- 1 Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan; and
| | - Na Sheng Lin
- 1 Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan; and
- 2 Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Yau Heiu Hsu
- 1 Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan; and
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10
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Moriceau L, Jomat L, Bressanelli S, Alcaide-Loridan C, Jupin I. Identification and Molecular Characterization of the Chloroplast Targeting Domain of Turnip yellow mosaic virus Replication Proteins. FRONTIERS IN PLANT SCIENCE 2017; 8:2138. [PMID: 29312393 PMCID: PMC5742235 DOI: 10.3389/fpls.2017.02138] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 12/04/2017] [Indexed: 05/20/2023]
Abstract
Turnip yellow mosaic virus (TYMV) is a positive-strand RNA virus infecting plants. The TYMV 140K replication protein is a key organizer of viral replication complex (VRC) assembly, being responsible for recruitment of the viral polymerase and for targeting the VRCs to the chloroplast envelope where viral replication takes place. However, the structural requirements determining the subcellular localization and membrane association of this essential viral protein have not yet been defined. In this study, we investigated determinants for the in vivo chloroplast targeting of the TYMV 140K replication protein. Subcellular localization studies of deletion mutants identified a 41-residue internal sequence as the chloroplast targeting domain (CTD) of TYMV 140K; this sequence is sufficient to target GFP to the chloroplast envelope. The CTD appears to be located in the C-terminal extension of the methyltransferase domain-a region shared by 140K and its mature cleavage product 98K, which behaves as an integral membrane protein during infection. We predicted the CTD to fold into two amphipathic α-helices-a folding that was confirmed in vitro by circular dichroism spectroscopy analyses of a synthetic peptide. The importance for subcellular localization of the integrity of these amphipathic helices, and the function of 140K/98K, was demonstrated by performing amino acid substitutions that affected chloroplast targeting, membrane association and viral replication. These results establish a short internal α-helical peptide as an unusual signal for targeting proteins to the chloroplast envelope membrane, and provide new insights into membrane targeting of viral replication proteins-a universal feature of positive-strand RNA viruses.
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Affiliation(s)
- Lucille Moriceau
- Laboratory of Molecular Virology, Institut Jacques Monod, CNRS, Université Paris-Diderot, Paris, France
- Université Paris-Sud – Université Paris-Saclay, Orsay, France
| | - Lucile Jomat
- Laboratory of Molecular Virology, Institut Jacques Monod, CNRS, Université Paris-Diderot, Paris, France
| | - Stéphane Bressanelli
- Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud – Université Paris-Saclay, Gif-sur-Yvette, France
| | - Catherine Alcaide-Loridan
- Laboratory of Molecular Virology, Institut Jacques Monod, CNRS, Université Paris-Diderot, Paris, France
| | - Isabelle Jupin
- Laboratory of Molecular Virology, Institut Jacques Monod, CNRS, Université Paris-Diderot, Paris, France
- *Correspondence: Isabelle Jupin,
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11
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Zhao J, Zhang X, Hong Y, Liu Y. Chloroplast in Plant-Virus Interaction. Front Microbiol 2016; 7:1565. [PMID: 27757106 PMCID: PMC5047884 DOI: 10.3389/fmicb.2016.01565] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 09/20/2016] [Indexed: 11/16/2022] Open
Abstract
In plants, the chloroplast is the organelle that conducts photosynthesis. It has been known that chloroplast is involved in virus infection of plants for approximate 70 years. Recently, the subject of chloroplast-virus interplay is getting more and more attention. In this article we discuss the different aspects of chloroplast-virus interaction into three sections: the effect of virus infection on the structure and function of chloroplast, the role of chloroplast in virus infection cycle, and the function of chloroplast in host defense against viruses. In particular, we focus on the characterization of chloroplast protein-viral protein interactions that underlie the interplay between chloroplast and virus. It can be summarized that chloroplast is a common target of plant viruses for viral pathogenesis or propagation; and conversely, chloroplast and its components also can play active roles in plant defense against viruses. Chloroplast photosynthesis-related genes/proteins (CPRGs/CPRPs) are suggested to play a central role during the complex chloroplast-virus interaction.
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Affiliation(s)
- Jinping Zhao
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua UniversityBeijing, China
- State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Key Laboratory of Biotechnology in Plant Protection, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Xian Zhang
- Research Centre for Plant RNA Signaling, School of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - Yiguo Hong
- Research Centre for Plant RNA Signaling, School of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - Yule Liu
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua UniversityBeijing, China
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12
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Fernández de Castro I, Tenorio R, Risco C. Virus assembly factories in a lipid world. Curr Opin Virol 2016; 18:20-6. [PMID: 26985879 DOI: 10.1016/j.coviro.2016.02.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/11/2016] [Accepted: 02/19/2016] [Indexed: 12/15/2022]
Abstract
Many viruses build specialized structures known as viral factories, a protected environment in which viral genome replication and morphogenesis take place. Recent findings show that viruses manipulate lipid flows to assemble these replication platforms. Viruses are thus able to create new membranes by interfering with lipid metabolism, targeting and transport; they make use of specific lipid transfer proteins (LTP) at membrane contact sites, and frequently recruit endoplasmic reticulum (ER), ER export sites, and mitochondria. Some factories, such as those built by plant and certain animal viruses, are motile membranous structures involved in intracellular or intercellular transport of the replicated viral genome. The identification of lipids and LTP subverted by viruses might lead to better understand and fight viral infections.
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Affiliation(s)
- Isabel Fernández de Castro
- Cell Structure Laboratory, Centro Nacional de Biotecnología, CNB-CSIC, UAM, Campus de Cantoblanco, 28049 Madrid, Spain.
| | - Raquel Tenorio
- Cell Structure Laboratory, Centro Nacional de Biotecnología, CNB-CSIC, UAM, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Cristina Risco
- Cell Structure Laboratory, Centro Nacional de Biotecnología, CNB-CSIC, UAM, Campus de Cantoblanco, 28049 Madrid, Spain.
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13
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Development of a Specific Diagnostic System for Detecting Turnip Yellow Mosaic Virus from Chinese Cabbage in Korea. Indian J Microbiol 2016; 56:103-7. [PMID: 26843703 DOI: 10.1007/s12088-015-0557-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Accepted: 10/23/2015] [Indexed: 10/22/2022] Open
Abstract
Turnip yellow mosaic virus (TYMV) is a plant pathogenic virus transmitted mainly through its host Brassica spp. TYMV is originated from Europe. Its infection cases have been reported in Australia, Brazil, Turkey, and Japan. Symptoms similar to those of TYMV infections were also reported in Korea in 2012. In this study, we developed RT-PCR primer pairs that were highly sensitive for detecting TYMV. The developed RT-PCR primer pairs offered about 10-100 times stronger detection sensitivity compared to primer pairs previously used in Korea. As a result, a 491 bp TYMV-specific band was identified. The specific band was confirmed to be TYMV based on sequencing results and phylogenetic analysis. The RT-PCR primer pairs developed in this study can be used to rapidly and precisely diagnose TYMV in agricultural products such as Chinese cabbage and other crops infected by TYMV.
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Wang QM, Wang L, Zhou Y, Cui J, Wang Y, Zhao C. Leaf patterning of Clivia miniata var. variegata is associated with differential DNA methylation. PLANT CELL REPORTS 2016; 35:167-84. [PMID: 26466593 DOI: 10.1007/s00299-015-1877-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Revised: 09/21/2015] [Accepted: 09/29/2015] [Indexed: 05/15/2023]
Abstract
Leaf patterns (yellow, green and striped) of Clivia miniata var. variegata might be caused by differential DNA methylation in CCGG sites in response to heterogeneous environmental pressure. Clivia miniata is an important ornamental plant.Clivia miniata var. variegata (Cmvv) is a variegated leaf mutant of C. miniata. Typical Cmvv has attractive green and yellow-stripped leaves. The study has revealed that an explant of Cmvv, even a full-green explant, could regenerate plants of three different types: yellow, green, ands triped; normal-appearing chloroplasts were found in guard cells but not in mesophyll cells of all the three types of Cmvv using confocal laser scanning microscopy (CLSM).Thus, we speculated that cells of the three types of Cmvv had an identical mutation and the mutation might disturb mesophyll cell chloroplast biogenesis after symplastic isolation of guard cells. Using CLSM and methylation sensitive amplification polymorphism (MSAP), we found that (a) striped leaves of Cmvv are due to sectorial decreases in chlorophyll levels and the decreases are associated with CG hypermethylation; (b) extent of epigenetic divergence among the three types of Cmvv leaves is positively correlated with intensity of leaf-color difference; and (c) green stripes of two plants are clustered in one group based on the MSAP profiles, but green and yellow stripes of a plant are not. Sequencing analysis indicated that CG hypermethylation in gene bodies of CPSAR1 and ycf2 might lead to gene silencing and yellow leaves/stripes of Cmvv. All together, it is possible that cytosine methylation involved regulating leaf color of Cmvv, also striped pattern of Cmvv might be caused by differential DNA methylation in response to heterogeneous environmental pressure. Furthermore, a novel leaf-color epigenetic hypothesis was proposed in this article.
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Protocols for Studying Protein Stability in an Arabidopsis Protoplast Transient Expression System. Methods Mol Biol 2016; 1450:175-94. [PMID: 27424754 DOI: 10.1007/978-1-4939-3759-2_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Protein stability influences many aspects of biology, and measuring their stability in vivo can provide important insights into biological systems.This chapter describes in details two methods to assess the stability of a specific protein based on its transient expression in Arabidopsis protoplasts. First, a pulse-chase assay based on radioactive metabolic labeling of cellular proteins, followed by immunoprecipitation of the protein of interest. The decrease in radioactive signal is monitored over time and can be used to determine the protein's half-life.Alternatively, we also present a nonradioactive assay based on the use of reporter proteins, whose ratio can be quantified. This assay can be used to determine the relative stability of a protein of interest under specific conditions.
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Abstract
In plants, the chloroplast is the organelle that conducts photosynthesis. It has been known that chloroplast is involved in virus infection of plants for approximate 70 years. Recently, the subject of chloroplast-virus interplay is getting more and more attention. In this article we discuss the different aspects of chloroplast-virus interaction into three sections: the effect of virus infection on the structure and function of chloroplast, the role of chloroplast in virus infection cycle, and the function of chloroplast in host defense against viruses. In particular, we focus on the characterization of chloroplast protein-viral protein interactions that underlie the interplay between chloroplast and virus. It can be summarized that chloroplast is a common target of plant viruses for viral pathogenesis or propagation; and conversely, chloroplast and its components also can play active roles in plant defense against viruses. Chloroplast photosynthesis-related genes/proteins (CPRGs/CPRPs) are suggested to play a central role during the complex chloroplast-virus interaction.
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Affiliation(s)
- Jinping Zhao
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua UniversityBeijing, China; State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Key Laboratory of Biotechnology in Plant Protection, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Xian Zhang
- Research Centre for Plant RNA Signaling, School of Life and Environmental Sciences, Hangzhou Normal University Hangzhou, China
| | - Yiguo Hong
- Research Centre for Plant RNA Signaling, School of Life and Environmental Sciences, Hangzhou Normal University Hangzhou, China
| | - Yule Liu
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University Beijing, China
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On the interaction and localization of the beet necrotic yellow vein virus replicase. Virus Res 2014; 196:94-104. [PMID: 25445349 DOI: 10.1016/j.virusres.2014.11.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 11/02/2014] [Accepted: 11/04/2014] [Indexed: 01/08/2023]
Abstract
Beet necrotic yellow vein virus (BNYVV) is a multipartite positive-strand RNA virus. BNYVV RNA-1 encodes a non-structural p237 polyprotein processed in two proteins (p150 and p66) by a cis-acting protease activity. BNYVV non-structural proteins are closely related to replication proteins of positive strand RNA viruses such as hepeviruses rather to other plant virus replicases. The p237 and dsRNA have been localized by TEM in ER structures of infected leaf cells whereas dsRNA was immunolabeled in infected protoplasts. The p150 contains domains with methyltransferase, protease, helicase and two domains of unknown function whereas p66 encompasses the RNA-dependent RNA-polymerase signature. We report the existing interactions between functional domains of the p150 and p66 proteins and the addressing of the benyvirus replicase to the endoplasmic reticulum. Yeast two-hybrid approach, colocalization with FRET-FLIM analyses and co-immunoprecipitation highlighted existing interactions that suggest the presence of a multimeric complex at the vicinity of the cellular membranous web.
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Govind K, Bakshi A, Savithri HS. Interaction of Sesbania mosaic virus (SeMV) RNA-dependent RNA polymerase (RdRp) with the p10 domain of polyprotein 2a and its implications in SeMV replication. FEBS Open Bio 2014; 4:362-9. [PMID: 24918050 PMCID: PMC4050190 DOI: 10.1016/j.fob.2014.03.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 03/19/2014] [Accepted: 03/19/2014] [Indexed: 01/10/2023] Open
Abstract
SeMV RdRp strongly interacts with p10 domain of polyprotein 2a. C-terminal disordered domain of RdRp is required for interaction with p10. p10 acts as a positive regulator of RdRp activity.
Identification of viral encoded proteins that interact with RNA-dependent RNA polymerase (RdRp) is an important step towards unraveling the mechanism of replication. Sesbania mosaic virus (SeMV) RdRp was shown to interact strongly with p10 domain of polyprotein 2a and moderately with the protease domain. Mutational analysis suggested that the C-terminal disordered domain of RdRp is involved in the interaction with p10. Coexpression of full length RdRp and p10 resulted in formation of RdRp–p10 complex which showed significantly higher polymerase activity than RdRp alone. Interestingly, CΔ43 RdRp also showed a similar increase in activity. Thus, p10 acts as a positive regulator of RdRp by interacting with the C-terminal disordered domain of RdRp.
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Key Words
- 3AT, 3 amino-1,2,4 triazol
- CP, coat protein
- IPTG, isopropyl-1thio-β-d-galactopyranoside
- LB, Luria Bertani broth
- LacZ, β-galactosidase
- MEL1, α-galactosidase
- MP, movement protein
- Ni–NTA, nickel–nitrilo tri-acetic acid
- ONPG, ortho-nitrophenyl-β-galactoside
- PBST, phosphate buffered saline with 0.1% TWEEN 20
- Pro, protease
- Protein-protein interactions
- RNA-dependent RNA polymerase (RdRp)
- RdRp, RNA-dependent RNA polymerase
- Replication
- SD, synthetic dropout
- SeMV, Sesbania mosaic virus
- Sesbania mosaic virus
- Sobemovirus
- VPg, viral protein genome linked
- Y2H, yeast two hybrid
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Affiliation(s)
- Kunduri Govind
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Arindam Bakshi
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
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Lombardi C, Ayach M, Beaurepaire L, Chenon M, Andreani J, Guerois R, Jupin I, Bressanelli S. A compact viral processing proteinase/ubiquitin hydrolase from the OTU family. PLoS Pathog 2013; 9:e1003560. [PMID: 23966860 PMCID: PMC3744425 DOI: 10.1371/journal.ppat.1003560] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2012] [Accepted: 07/02/2013] [Indexed: 01/06/2023] Open
Abstract
Turnip yellow mosaic virus (TYMV) - a member of the alphavirus-like supergroup of viruses - serves as a model system for positive-stranded RNA virus membrane-bound replication. TYMV encodes a precursor replication polyprotein that is processed by the endoproteolytic activity of its internal cysteine proteinase domain (PRO). We recently reported that PRO is actually a multifunctional enzyme with a specific ubiquitin hydrolase (DUB) activity that contributes to viral infectivity. Here, we report the crystal structure of the 150-residue PRO. Strikingly, PRO displays no homology to other processing proteinases from positive-stranded RNA viruses, including that of alphaviruses. Instead, the closest structural homologs of PRO are DUBs from the Ovarian tumor (OTU) family. In the crystal, one molecule's C-terminus inserts into the catalytic cleft of the next, providing a view of the N-terminal product complex in replication polyprotein processing. This allows us to locate the specificity determinants of PRO for its proteinase substrates. In addition to the catalytic cleft, at the exit of which the active site is unusually pared down and solvent-exposed, a key element in molecular recognition by PRO is a lobe N-terminal to the catalytic domain. Docking models and the activities of PRO and PRO mutants in a deubiquitylating assay suggest that this N-terminal lobe is also likely involved in PRO's DUB function. Our data thus establish that DUBs can evolve to specifically hydrolyze both iso- and endopeptide bonds with different sequences. This is achieved by the use of multiple specificity determinants, as recognition of substrate patches distant from the cleavage sites allows a relaxed specificity of PRO at the sites themselves. Our results thus shed light on how such a compact protein achieves a diversity of key functions in viral genome replication and host-pathogen interaction. Positive-stranded RNA viruses are ultimate parasites. In order to replicate their genome, they first need to invade a host cell and, with usually very limited viral genetic material, subvert the host's molecular machinery. Turnip yellow mosaic virus (TYMV) is an excellent model system for studying positive-stranded RNA virus replication. As for many such viruses, TYMV genome replication is dependent on the activity of a viral proteinase (PRO) to properly process the virus' replication molecules. We have recently established that PRO is a multifunctional enzyme and is also used by TYMV to subvert a key host defense against pathogens. We report here the atomic structure of PRO as well as new functional data on PRO's interaction with the host. Our data shed light on how PRO can perform such multiple activities despite its small size, providing TYMV with a Swiss army knife in its ongoing fight with a vastly more complex host.
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Affiliation(s)
- Charlotte Lombardi
- The Laboratoire de Virologie Moléculaire et Structurale, Centre de Recherche de Gif, CNRS (UPR 3296), Gif sur Yvette, France
| | - Maya Ayach
- The Laboratoire de Virologie Moléculaire et Structurale, Centre de Recherche de Gif, CNRS (UPR 3296), Gif sur Yvette, France
| | - Lionel Beaurepaire
- The Laboratoire de Virologie Moléculaire et Structurale, Centre de Recherche de Gif, CNRS (UPR 3296), Gif sur Yvette, France
| | - Mélanie Chenon
- Laboratoire de Virologie Moléculaire, CNRS - Univ Paris Diderot, Sorbonne Paris Cité, Institut Jacques Monod, UMR 7592, Paris, France
| | - Jessica Andreani
- CEA, iBiTecS, Service de Bioénergétique Biologie Structurale et Mécanismes (SB2SM), Laboratoire de Biologie Structurale et Radiobiologie (LBSR), Gif sur Yvette, France
| | - Raphaël Guerois
- CEA, iBiTecS, Service de Bioénergétique Biologie Structurale et Mécanismes (SB2SM), Laboratoire de Biologie Structurale et Radiobiologie (LBSR), Gif sur Yvette, France
| | - Isabelle Jupin
- Laboratoire de Virologie Moléculaire, CNRS - Univ Paris Diderot, Sorbonne Paris Cité, Institut Jacques Monod, UMR 7592, Paris, France
- * E-mail: (IJ); (SB)
| | - Stéphane Bressanelli
- The Laboratoire de Virologie Moléculaire et Structurale, Centre de Recherche de Gif, CNRS (UPR 3296), Gif sur Yvette, France
- * E-mail: (IJ); (SB)
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Cowan GH, Roberts AG, Chapman SN, Ziegler A, Savenkov EI, Torrance L. The potato mop-top virus TGB2 protein and viral RNA associate with chloroplasts and viral infection induces inclusions in the plastids. FRONTIERS IN PLANT SCIENCE 2012; 3:290. [PMID: 23269927 PMCID: PMC3529358 DOI: 10.3389/fpls.2012.00290] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 12/05/2012] [Indexed: 05/27/2023]
Abstract
The potato mop-top virus (PMTV) triple gene block 2 (TGB2) movement proteins fused to monomeric red fluorescent protein (mRFP-TGB2) was expressed under the control of the PMTV subgenomic promoter from a PMTV vector. The subcellular localizations and interactions of mRFP-TGB2 were investigated using confocal imaging [confocal laser-scanning microscope, (CLSM)] and biochemical analysis. The results revealed associations with membranes of the endoplasmic reticulum (ER), mobile granules, small round structures (1-2 μm in diameter), and chloroplasts. Expression of mRFP-TGB2 in epidermal cells enabled cell-to-cell movement of a TGB2 defective PMTV reporter clone, indicating that the mRFP-TGB2 fusion protein was functional and required for cell-to-cell movement. Protein-lipid interaction assays revealed an association between TGB2 and lipids present in chloroplasts, consistent with microscopical observations where the plastid envelope was labeled later in infection. To further investigate the association of PMTV infection with chloroplasts, ultrastructural studies of thin sections of PMTV-infected potato and Nicotiana benthamiana leaves by electron microscopy revealed abnormal chloroplasts with cytoplasmic inclusions and terminal projections. Viral coat protein (CP), genomic RNA and fluorescently-labeled TGB2 were detected in plastid preparations isolated from the infected leaves, and viral RNA was localized to chloroplasts in infected tissues. The results reveal a novel association of TGB2 and vRNA with chloroplasts, and suggest viral replication is associated with chloroplast membranes, and that TGB2 plays a novel role in targeting the virus to chloroplasts.
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Affiliation(s)
| | | | | | - Angelika Ziegler
- Federal Research Centre for Cultivated Plants, Julius Kühn Institute, Institute for Epidemiology and Pathogen DiagnosticsQuedlinburg, Germany
| | - Eugene I. Savenkov
- Department of Plant Biology and Forest Genetics, Swedish University of Agricultural SciencesUppsala, Sweden
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21
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Characterization of a novel tymovirus on tomato plants in Brazil. Virus Genes 2012; 46:190-4. [DOI: 10.1007/s11262-012-0830-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2012] [Accepted: 09/20/2012] [Indexed: 11/25/2022]
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Ibrahim A, Hutchens HM, Berg RH, Loesch-Fries LS. Alfalfa mosaic virus replicase proteins, P1 and P2, localize to the tonoplast in the presence of virus RNA. Virology 2012; 433:449-61. [PMID: 22999257 DOI: 10.1016/j.virol.2012.08.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 08/01/2012] [Accepted: 08/07/2012] [Indexed: 12/25/2022]
Abstract
To identify the virus components important for assembly of the Alfalfa mosaic virus replicase complex, we used live cell imaging of Arabidopsis thaliana protoplasts that expressed various virus cDNAs encoding native and GFP-fusion proteins of P1 and P2 replicase proteins and full-length virus RNAs. Expression of P1-GFP alone resulted in fluorescent vesicle-like bodies in the cytoplasm that colocalized with FM4-64, an endocytic marker, and RFP-AtVSR2, RabF2a/Rha1-mCherry, and RabF2b/Ara7-mCherry, all of which localize to multivesicular bodies (MVBs), which are also called prevacuolar compartments, that mediate traffic to the lytic vacuole. GFP-P2 was driven from the cytosol to MVBs when expressed with P1 indicating that P1 recruited GFP-P2. P1-GFP localized on the tonoplast, which surrounds the vacuole, in the presence of infectious virus RNA, replication competent RNA2, or P2 and replication competent RNA1 or RNA3. This suggests that a functional replication complex containing P1, P2, and a full-length AMV RNA assembles on MVBs to traffic to the tonoplast.
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Affiliation(s)
- Amr Ibrahim
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
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23
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Robin C, Beaurepaire L, Chenon M, Jupin I, Bressanelli S. In praise of impurity: 30S ribosomal S15 protein-assisted crystallization of turnip yellow mosaic virus proteinase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:486-90. [PMID: 22505427 PMCID: PMC3325827 DOI: 10.1107/s1744309112008445] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Accepted: 02/25/2012] [Indexed: 11/10/2022]
Abstract
Turnip yellow mosaic virus is an excellent model for eukaryotic positive-stranded RNA virus replication. Correct processing of the replication polyprotein is dependent on the virally encoded cysteine proteinase (PRO) domain. Crystalline needles obtained from highly pure preparations of the recombinant 17.6 kDa PRO did not diffract. In contrast, small hexagonal prisms that were obtained together with the needles under the same conditions but from a poorly purified preparation diffracted to 2 Å resolution and allowed structure determination by MIRAS. It turned out that the hexagonal crystals contained stoichiometric amounts of PRO and Escherichia coli 30S ribosomal S15, a 10.1 kDa protein commonly co-purified by immobilized metal-affinity chromatography. The solvent content is nearly 70%, with S15 bridging parallel infinite helices of PRO across large solvent channels. With hindsight, this spurious interaction not only yielded diffraction-quality crystals but would also have allowed structure determination by molecular replacement using S15 as a search model and subsequent automatic rebuilding of the asymmetric unit.
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Affiliation(s)
- Charlotte Robin
- Virologie Moléculaire et Structurale, CNRS UPR 3296, INRA USC, Centre de Recherche de Gif, Avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Lionel Beaurepaire
- Virologie Moléculaire et Structurale, CNRS UPR 3296, INRA USC, Centre de Recherche de Gif, Avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Mélanie Chenon
- Virologie Moléculaire, CNRS–Université Paris Diderot, Sorbonne Paris Cité, Institut Jacques Monod, UMR 7592, 15 Rue Hélène Brion, 75205 Paris CEDEX 13, France
| | - Isabelle Jupin
- Virologie Moléculaire, CNRS–Université Paris Diderot, Sorbonne Paris Cité, Institut Jacques Monod, UMR 7592, 15 Rue Hélène Brion, 75205 Paris CEDEX 13, France
| | - Stéphane Bressanelli
- Virologie Moléculaire et Structurale, CNRS UPR 3296, INRA USC, Centre de Recherche de Gif, Avenue de la Terrasse, 91190 Gif-sur-Yvette, France
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Jakubiec A, Yang SW, Chua NH. Arabidopsis DRB4 protein in antiviral defense against Turnip yellow mosaic virus infection. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 69:14-25. [PMID: 21883552 PMCID: PMC3240694 DOI: 10.1111/j.1365-313x.2011.04765.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
RNA silencing is an important antiviral mechanism in diverse eukaryotic organisms. In Arabidopsis DICER-LIKE 4 (DCL4) is the primary antiviral Dicer, required for the production of viral small RNAs from positive-strand RNA viruses. Here, we showed that DCL4 and its interacting partner dsRNA-binding protein 4 (DRB4) participate in the antiviral response to Turnip yellow mosaic virus (TYMV), and that both proteins are required for TYMV-derived small RNA production. In addition, our results indicate that DRB4 has a negative effect on viral coat protein accumulation. Upon infection DRB4 expression was induced and DRB4 protein was recruited from the nucleus to the cytoplasm, where replication and translation of viral RNA occur. DRB4 was associated with viral RNA in vivo and directly interacted in vitro with a TYMV RNA translational enhancer, raising the possibility that DRB4 might repress viral RNA translation. In plants the role of RNA silencing in viral RNA degradation is well established, but its potential function in the regulation of viral protein levels has not yet been explored. We observed that severe infection symptoms are not necessarily correlated with enhanced viral RNA levels, but might be caused by elevated accumulation of viral proteins. Our findings suggest that the control of viral protein as well as RNA levels might be important for mounting an efficient antiviral response.
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Affiliation(s)
- Anna Jakubiec
- Laboratory of Plant Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Seong Wook Yang
- Department of Plant Biology and Biotechnology, Faculty of Life Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Copenhagen, Denmark
| | - Nam-Hai Chua
- Laboratory of Plant Molecular Biology, The Rockefeller University, New York, NY 10065, USA
- To whom correspondence should be addressed. Corresponding author: Nam-Hai Chua , Fax number: 1-212-327-8327, Phone number: 1-212-327-8126
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25
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Chenon M, Camborde L, Cheminant S, Jupin I. A viral deubiquitylating enzyme targets viral RNA-dependent RNA polymerase and affects viral infectivity. EMBO J 2011; 31:741-53. [PMID: 22117220 PMCID: PMC3273391 DOI: 10.1038/emboj.2011.424] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Accepted: 11/03/2011] [Indexed: 01/17/2023] Open
Abstract
Turnip Yellow Mosaic Virus protects its replicative polymerase from degradation by the host cell ubiquitin-proteasome system, employing deubiquitination activity of a processing protease with resemblance to OTU domain DUBs. Selective protein degradation via the ubiquitin-proteasome system (UPS) plays an essential role in many major cellular processes, including host–pathogen interactions. We previously reported that the tightly regulated viral RNA-dependent RNA polymerase (RdRp) of the positive-strand RNA virus Turnip yellow mosaic virus (TYMV) is degraded by the UPS in infected cells, a process that affects viral infectivity. Here, we show that the TYMV 98K replication protein can counteract this degradation process thanks to its proteinase domain. In-vitro assays revealed that the recombinant proteinase domain is a functional ovarian tumour (OTU)-like deubiquitylating enzyme (DUB), as is the 98K produced during viral infection. We also demonstrate that 98K mediates in-vivo deubiquitylation of TYMV RdRp protein—its binding partner within replication complexes—leading to its stabilization. Finally, we show that this DUB activity contributes to viral infectivity in plant cells. The identification of viral RdRp as a specific substrate of the viral DUB enzyme thus reveals the intricate interplay between ubiquitylation, deubiquitylation and the interaction between viral proteins in controlling levels of RdRp and viral infectivity.
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Affiliation(s)
- Mélanie Chenon
- Laboratoire de Virologie Moléculaire, CNRS-Univ Paris Diderot, Institut Jacques Monod, Cell Biology Department, UMR 7592, Paris, France
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Špak J, Holý A, Pavingerová D, Votruba I, Špaková V, Petrzik K. New in vitro method for evaluating antiviral activity of acyclic nucleoside phosphonates against plant viruses. Antiviral Res 2010; 88:296-303. [DOI: 10.1016/j.antiviral.2010.09.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Revised: 09/10/2010] [Accepted: 09/29/2010] [Indexed: 11/29/2022]
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Camborde L, Planchais S, Tournier V, Jakubiec A, Drugeon G, Lacassagne E, Pflieger S, Chenon M, Jupin I. The ubiquitin-proteasome system regulates the accumulation of Turnip yellow mosaic virus RNA-dependent RNA polymerase during viral infection. THE PLANT CELL 2010; 22:3142-52. [PMID: 20823192 PMCID: PMC2965540 DOI: 10.1105/tpc.109.072090] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2009] [Revised: 08/01/2010] [Accepted: 08/22/2010] [Indexed: 05/19/2023]
Abstract
Replication of positive-strand RNA viruses, the largest group of plant viruses, is initiated by viral RNA-dependent RNA polymerase (RdRp). Given its essential function in viral replication, understanding the regulation of RdRp is of great importance. Here, we show that Turnip yellow mosaic virus (TYMV) RdRp (termed 66K) is degraded by the proteasome at late time points during viral infection and that the accumulation level of 66K affects viral RNA replication in infected Arabidopsis thaliana cells. We mapped the cis-determinants responsible for 66K degradation within its N-terminal noncatalytic domain, but we conclude that 66K is not a natural N-end rule substrate. Instead, we show that a proposed PEST sequence within 66K functions as a transferable degradation motif. In addition, several Lys residues that constitute target sites for ubiquitylation were mapped; mutation of these Lys residues leads to stabilization of 66K. Altogether, these results demonstrate that TYMV RdRp is a target of the ubiquitin-proteasome system in plant cells and support the idea that proteasomal degradation may constitute yet another fundamental level of regulation of viral replication.
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28
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Shin HI, Kim HY, Cho TJ. The Pro/Hel region is indispensable for packaging non-replicating turnip yellow mosaic virus RNA, but not replicating viral RNA. Mol Cells 2010; 29:463-9. [PMID: 20396967 DOI: 10.1007/s10059-010-0057-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Revised: 01/12/2010] [Accepted: 01/13/2010] [Indexed: 10/19/2022] Open
Abstract
Turnip yellow mosaic virus (TYMV) is a spherical plant virus that has a single 6.3 kb positive strand RNA. The genomic RNA has a tRNA-like structure (TLS) at the 3'-end. The 3'-TLS and hairpins in the 5'-untranslated region supposedly serve as packaging signals; however, recent studies have shown that they do not play a role in TYMV RNA packaging. In this study, we focused on packaging signals by examining a series of deletion mutants of TYMV. Analysis of encapsidated viral RNA after agroinfiltration of the deletion constructs into Nicotiana benthamiana showed that the mutant RNA lacking the protease (Pro)/helicase (Hel) region was not encapsidated by the coat proteins provided in trans, implicating that a packaging signal lies in the Pro/Hel region. Examination of two Pro(-)Hel(-) mutants showed that protein activity from the Pro/Hel domains was dispensable for the packaging of the non-replicating TYMV RNA. In contrast, the mutant TYMV RNA lacking the Pro/Hel region was efficiently encapsidated when the mutant TYMV was co-introduced with a wild-type TYMV, suggesting that packaging mechanisms might differ depending on whether the virus is replicating or not.
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Affiliation(s)
- Hyun-Il Shin
- Department of Biochemistry, Chungbuk National University, Cheongju, 361-763, Korea
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Pflieger S, Blanchet S, Camborde L, Drugeon G, Rousseau A, Noizet M, Planchais S, Jupin I. Efficient virus-induced gene silencing in Arabidopsis using a 'one-step' TYMV-derived vector. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2008; 56:678-90. [PMID: 18643968 DOI: 10.1111/j.1365-313x.2008.03620.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Virus-induced gene silencing (VIGS) is an important tool for the analysis of gene function in plants. This technique exploits recombinant viral vectors harbouring fragments of plant genes in their genome to generate double-stranded RNAs that initiate homology-dependent silencing of the target gene. Several viral VIGS vectors have already been successfully used in reverse-genetics studies of a variety of processes occurring in plants. Here, we show that a viral vector derived from Turnip yellow mosaic virus (TYMV) has the ability to induce VIGS in Arabidopsis thaliana, accession Col-0, provided that it carries an inverted-repeat fragment of the target gene. Robust and reliable gene silencing was observed when plants were inoculated simply by abrasion with intact plasmid DNA harbouring a cDNA copy of the viral genome, thus precluding the need for in vitro transcription, biolistic or agroinoculation procedures. Our results indicate that a 76 bp fragment is sufficient to cause gene silencing in leaves, stems and flowers, and that the TYMV-derived vector also has the ability to target genes expressed in meristematic tissues. The VIGS vector described here may thus represent an ideal tool for improving high-throughput functional genomics in Arabidopsis.
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Affiliation(s)
- Stéphanie Pflieger
- Laboratoire de Virologie Moléculaire, Institut Jacques Monod, UMR 7592 CNRS-Universités Paris 6-Paris 7, 2 place Jussieu, 75251 Paris Cedex 05, France
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30
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Chisholm J, Zhang G, Wang A, Sanfaçon H. Peripheral association of a polyprotein precursor form of the RNA-dependent RNA polymerase of Tomato ringspot virus with the membrane-bound viral replication complex. Virology 2007; 368:133-44. [PMID: 17658576 DOI: 10.1016/j.virol.2007.06.032] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2007] [Revised: 06/13/2007] [Accepted: 06/29/2007] [Indexed: 11/23/2022]
Abstract
Replication of Tomato ringspot virus (ToRSV) occurs in association with endoplasmic reticulum (ER)-derived membranes. We have previously shown that the putative nucleotide triphosphate-binding protein (NTB) of ToRSV is an ER-targeted protein and that an intermediate polyprotein containing the domains for NTB and for the genome-linked viral protein (VPg) is associated with the replication complex. We now report the detection of a 95-kDa polyprotein that contains the domains for the RNA-dependent RNA polymerase (Pol), the proteinase (Pro) and the VPg. This polyprotein appears to be a truncated version of the full-length 111-kDa VPg-Pro-Pol polyprotein and was termed VPg-Pro-Pol'. A subpopulation of VPg-Pro-Pol' was peripherally associated with ER-derived membranes active in viral replication. However, the VPg, Pro and Pol domains did not target to membranes in the absence of viral infection. We propose a model in which VPg-Pro-Pol' is brought to the site of replication through interaction with a viral membrane protein.
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Affiliation(s)
- Joan Chisholm
- Pacific Agri-Food Research Centre, Agriculture and Agri-Food Canada, P.O. Box 5000, 4200 Highway 97, Summerland, B.C., Canada V0H 1Z0
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31
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Jakubiec A, Drugeon G, Camborde L, Jupin I. Proteolytic processing of turnip yellow mosaic virus replication proteins and functional impact on infectivity. J Virol 2007; 81:11402-12. [PMID: 17686855 PMCID: PMC2045563 DOI: 10.1128/jvi.01428-07] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Turnip yellow mosaic virus (TYMV), a positive-strand RNA virus belonging to the alphavirus-like supergroup, encodes its nonstructural replication proteins as a 206K precursor with domains indicative of methyltransferase (MT), proteinase (PRO), NTPase/helicase (HEL), and polymerase (POL) activities. Subsequent processing of 206K generates a 66K protein encompassing the POL domain and uncharacterized 115K and 85K proteins. Here, we demonstrate that TYMV proteinase mediates an additional cleavage between the PRO and HEL domains of the polyprotein, generating the 115K protein and a 42K protein encompassing the HEL domain that can be detected in plant cells using a specific antiserum. Deletion and substitution mutagenesis experiments and sequence comparisons indicate that the scissile bond is located between residues Ser879 and Gln880. The 85K protein is generated by a host proteinase and is likely to result from nonspecific proteolytic degradation occurring during protein sample extraction or analysis. We also report that TYMV proteinase has the ability to process substrates in trans in vivo. Finally, we examined the processing of the 206K protein containing native, mutated, or shuffled cleavage sites and analyzed the effects of cleavage mutations on viral infectivity and RNA synthesis by performing reverse-genetics experiments. We present evidence that PRO/HEL cleavage is critical for productive virus infection and that the impaired infectivity of PRO/HEL cleavage mutants is due mainly to defective synthesis of positive-strand RNA.
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Affiliation(s)
- Anna Jakubiec
- Institut Jacques Monod, 2 Place Jussieu, 75251 Paris Cedex 05, France
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32
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Jonczyk M, Pathak KB, Sharma M, Nagy PD. Exploiting alternative subcellular location for replication: Tombusvirus replication switches to the endoplasmic reticulum in the absence of peroxisomes. Virology 2007; 362:320-30. [PMID: 17292435 DOI: 10.1016/j.virol.2007.01.004] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2006] [Revised: 11/02/2006] [Accepted: 01/03/2007] [Indexed: 11/16/2022]
Abstract
Plus-strand RNA virus replication takes place on distinct membranous surfaces in infected cells via the assembly of viral replicase complexes involving multiple viral and host proteins. One group of tombusviruses, such as Tomato bushy stunt virus (TBSV), replicate on the surfaces of peroxisomal membranes in plant and yeast cells. Surprisingly, previous genome-wide screen performed in yeast demonstrated that a TBSV replicon RNA replicated as efficiently in yeast defective in peroxisome biogenesis as in the wt yeast (Panavas et al., Proc Natl Acad Sci U S A, 2005). To further test how the lack of peroxisomes could affect tombusvirus replication, we used yeast cells missing either PEX3 or PEX19 genes, which are absolutely essential for peroxisome biogenesis. Confocal microscopy-based approach revealed that the wild-type tombusvirus p33 replication protein accumulated in the endoplasmic reticulum (ER) in pex3Delta or pex19Delta yeast, suggesting that tombusvirus replication could take place on the surface of ER membrane. The activities of the isolated tombusvirus replicase preparations from wt, pex3Delta or pex19Delta yeasts were comparable, demonstrating that the assembly of the replicase was as efficient in the ER as in the authentic subcellular environments. The generation/accumulation of tombusvirus recombinants was similar in wt, pex3Delta and pex19Delta yeasts, suggesting that the rate of mistakes occurring during tombusvirus replication is comparable in the presence or absence of peroxisomes. Overall, this work demonstrates that a tombusvirus, relying on the wt replication proteins, can efficiently replicate on an alternative intracellular membrane. This suggests that RNA viruses might have remarkable flexibility for using various host membranes for their replication.
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Affiliation(s)
- Magdalena Jonczyk
- Department of Plant Pathology, University of Kentucky, 201F Plant Science Building, Lexington, KY 40546-0312, USA
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33
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Camborde L, Tournier V, Noizet M, Jupin I. A Turnip yellow mosaic virus infection system in Arabidopsis suspension cell culture. FEBS Lett 2007; 581:337-41. [PMID: 17222410 DOI: 10.1016/j.febslet.2006.12.045] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2006] [Revised: 11/06/2006] [Accepted: 12/21/2006] [Indexed: 12/11/2022]
Abstract
Turnip yellow mosaic virus (TYMV) is a positive-strand RNA virus able to infect Arabidopsis thaliana. To establish a TYMV infection system in Arabidopsis cell culture, TYMV replicons with the capsid protein gene replaced by a reporter gene expressing the Sh ble protein conferring zeocin resistance were used to transfect Arabidopsis cells. Zeocin-resistant Arabidopsis calli were used to generate a suspension cell culture. Detection of viral proteins and RNAs after 18 months in culture demonstrated persistent replication of the replicon. The Arabidopsis cell culture yielded soluble, active replication complexes, providing a useful tool to study host factors involved in TYMV replication.
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Affiliation(s)
- Laurent Camborde
- Laboratoire de Virologie Moléculaire, Institut Jacques Monod, UMR 7592 CNRS, Universités Paris 6, Paris 7, 2 place Jussieu, 75251 Paris Cedex 05, France
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34
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Zhou F, Wu G, Deng W, Pu Y, Wei C, Li Y. Interaction of rice dwarf virus outer capsid P8 protein with rice glycolate oxidase mediates relocalization of P8. FEBS Lett 2006; 581:34-40. [PMID: 17174956 DOI: 10.1016/j.febslet.2006.11.073] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2006] [Revised: 11/23/2006] [Accepted: 11/28/2006] [Indexed: 11/18/2022]
Abstract
Yeast two-hybrid and coimmunoprecipitation assays indicated that P8, an outer capsid protein of Rice dwarf phytoreovirus (RDV), interacts with rice glycolate oxidase (GOX), a typical enzyme of peroxisomes. Confocal immunofluorescence microscopy revealed that P8 was colocalized with GOX in peroxisomes. Time course analysis demonstrated that the localization of P8 in Spodoptera frugiperda cells changed from diffuse to discrete, punctuate inclusions during expression from 24 to 48 h post inoculation. Coexpression of GOX with P8 may target P8 into peroxisomes, which serve as replication sites for a number of viruses. Therefore, we conclude that the interaction of P8 with the GOX of host cells leads to translocation of P8 into peroxisomes and we further propose that the interaction between P8 and GOX may play important roles in RDV targeting into the replication site of host cells. Our findings have broad significance in studying the mechanisms whereby viruses target appropriate replication sites and begin their replication.
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Affiliation(s)
- Feng Zhou
- 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, PR China
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35
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Osman TAM, Morris J, Coutts RHA, Buck KW. Synthesis of genomic and subgenomic RNAs by a membrane-bound RNA-dependent RNA polymerase isolated from oat plants infected with cereal yellow dwarf virus. Arch Virol 2006; 151:2229-42. [PMID: 16755373 DOI: 10.1007/s00705-006-0789-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2005] [Accepted: 04/19/2006] [Indexed: 11/25/2022]
Abstract
A membrane-bound RNA-dependent RNA polymerase (RdRp) complex was isolated by differential sedimentation from oat plants infected with cereal yellow dwarf virus (CYDV). When incubated with 32P-labelled UTP, unlabelled ATP, CTP and GTP, and Mg2+ ions, the RdRp preparation catalysed the synthesis of double-stranded (ds) RNAs corresponding in size to the virus genomic RNA (5.7 kbp) and two putative subgenomic RNAs (2.8 and 0.7 kbp). Hybridisation using strand-specific hybridization targets showed that the 5.7-kbp dsRNA was labelled mainly in the plus strand, whereas the 2.8- and 0.7-kbp dsRNAs were labelled only in the minus strand. Genomic-length single-stranded, plus-strand RNA of 5.7 kb and single-stranded, plus-strand subgenomic RNAs of 2.8 and 0.7 kbp were detected in RNA isolated from oat plants infected with CYDV. Mapping experiments were consistent with the genomic and subgenomic RNAs having common 3' ends, but different 5' ends, whether produced in vitro or in vivo. The RdRp-encoding region of the CYDV genome was cloned and expressed in Escherichia coli, and the purified protein was used to raise antibodies in a rabbit. In immunoblots, the antibodies detected a protein of about 68 kDa in RdRp preparations from CYDV-infected oat plants, but not from equivalent preparations from healthy oats. As far as we are aware, this is the first report of an in vitro RNA synthesis system for a phloem-limited virus.
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Affiliation(s)
- T A M Osman
- Division of Biology, Faculty of Natural Sciences, Imperial College London, Sir Alexander Fleming Building, London, UK
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36
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Jakubiec A, Tournier V, Drugeon G, Pflieger S, Camborde L, Vinh J, Héricourt F, Redeker V, Jupin I. Phosphorylation of viral RNA-dependent RNA polymerase and its role in replication of a plus-strand RNA virus. J Biol Chem 2006; 281:21236-21249. [PMID: 16717096 DOI: 10.1074/jbc.m600052200] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Central to the process of plus-strand RNA virus genome amplification is the viral RNA-dependent RNA polymerase (RdRp). Understanding its regulation is of great importance given its essential function in viral replication and the common architecture and catalytic mechanism of polymerases. Here we show that Turnip yellow mosaic virus (TYMV) RdRp is phosphorylated, when expressed both individually and in the context of viral infection. Using a comprehensive biochemical approach, including metabolic labeling and mass spectrometry analyses, phosphorylation sites were mapped within an N-terminal PEST sequence and within the highly conserved palm subdomain of RNA polymerases. Systematic mutational analysis of the corresponding residues in a reverse genetic system demonstrated their importance for TYMV infectivity. Upon mutation of the phosphorylation sites, distinct steps of the viral cycle appeared affected, but in contrast to other plus-strand RNA viruses, the interaction between viral replication proteins was unaltered. Our results also highlighted the role of another TYMV-encoded replication protein as an antagonistic protein that may prevent the inhibitory effect of RdRp phosphorylation on viral infectivity. Based on these data, we propose that phosphorylation-dependent regulatory mechanisms are essential for viral RdRp function and virus replication.
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Affiliation(s)
| | | | | | | | | | - Joëlle Vinh
- Ecole Supérieure de Physique et Chimie Industrielles de la Ville de Paris, 75005 Paris, France
| | | | - Virginie Redeker
- Ecole Supérieure de Physique et Chimie Industrielles de la Ville de Paris, 75005 Paris, France
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Villanueva RA, Rouillé Y, Dubuisson J. Interactions between virus proteins and host cell membranes during the viral life cycle. ACTA ACUST UNITED AC 2006; 245:171-244. [PMID: 16125548 PMCID: PMC7112339 DOI: 10.1016/s0074-7696(05)45006-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The structure and function of cells are critically dependent on membranes, which not only separate the interior of the cell from its environment but also define the internal compartments. It is therefore not surprising that the major steps of the life cycle of viruses of animals and plants also depend on cellular membranes. Indeed, interactions of viral proteins with host cell membranes are important for viruses to enter into host cells, replicate their genome, and produce progeny particles. To replicate its genome, a virus first needs to cross the plasma membrane. Some viruses can also modify intracellular membranes of host cells to create a compartment in which genome replication will take place. Finally, some viruses acquire an envelope, which is derived either from the plasma membrane or an internal membrane of the host cell. This paper reviews recent findings on the interactions of viral proteins with host cell membranes during the viral life cycle.
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Affiliation(s)
- Rodrigo A Villanueva
- CNRS-UPR2511, Institut de Biologie de Lille, Institut Pasteur de Lille, 59021 Lille Cedex, France
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38
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Sanfaçon H. Replication of positive-strand RNA viruses in plants: contact points between plant and virus components. ACTA ACUST UNITED AC 2005. [DOI: 10.1139/b05-121] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Positive-strand RNA viruses constitute the largest group of plant viruses and have an important impact on world agriculture. These viruses have small genomes that encode a limited number of proteins and depend on their hosts to complete the various steps of their replication cycle. In this review, the contact points between positive-strand RNA plant viruses and their hosts, which are necessary for the translation and replication of the viral genomes, are discussed. Special emphasis is placed on the description of viral replication complexes that are associated with specific membranous compartments derived from plant intracellular membranes and contain viral RNAs and proteins as well as a variety of host proteins. These complexes are assembled via an intricate network of protein–protein, protein–membrane, and protein–RNA interactions. The role of host factors in regulating the assembly, stability, and activity of viral replication complexes are also discussed.
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Affiliation(s)
- Hélène Sanfaçon
- Agriculture and Agri-Food Canada, Pacific Agri-Food Research Centre, 4200 Highway 97, Summerland, BC V0H 1Z0, Canada (e-mail: )
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Panavas T, Hawkins CM, Panaviene Z, Nagy PD. The role of the p33:p33/p92 interaction domain in RNA replication and intracellular localization of p33 and p92 proteins of Cucumber necrosis tombusvirus. Virology 2005; 338:81-95. [PMID: 15936051 DOI: 10.1016/j.virol.2005.04.025] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2005] [Revised: 03/01/2005] [Accepted: 04/18/2005] [Indexed: 10/25/2022]
Abstract
Replication of plus-stranded RNA viruses is performed by the viral replicase complex, which, together with the viral RNA, must be targeted to intracellular membranes, where replication takes place in membraneous vesicles/spherules. Tombusviruses code for two overlapping replication proteins, the p33 auxiliary protein and the p92 polymerase. Using replication-competent fluorescent protein-tagged p33 of Cucumber necrosis virus (CNV), we determined that two domains affected p33 targeting to peroxisomal membranes in yeast: an N-proximal hydrophobic trans-membrane sequence and the C-proximal p33:p33/p92 interaction domain. On the contrary, only the deletion of the p33:p33/p92 interaction domain, but not the trans-membrane sequence, altered the intracellular targeting of p92 protein in the presence of wt p33 and DI-72(+) RNA. Moreover, unlike p33, p92 lacking the trans-membrane sequence was still functional in supporting the replication of a replicon RNA in yeast, whereas the p33:p33/p92 interaction domain in both p33 and p92 was essential for replication. In addition, p33 was also shown to facilitate the recruitment of the viral RNA to peroxisomal membranes and that p33 is colocalized with (+) and (-)-stranded viral RNAs. Also, FRET and pull-down analyses confirmed that p33 interacts with other p33 molecules in yeast cells. Based on these data, we propose that p33 facilitates the formation of multimolecular complexes, including p33, p92, viral RNA, and unidentified host factors, which are then targeted to the peroxisomal membranes, the sites of CNV replication.
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Affiliation(s)
- Tadas Panavas
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, USA
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