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Tselika M, Belmezos N, Kallemi P, Andronis C, Chiumenti M, Navarro B, Lavigne M, Di Serio F, Kalantidis K, Katsarou K. PSTVd infection in Nicotiana benthamiana plants has a minor yet detectable effect on CG methylation. FRONTIERS IN PLANT SCIENCE 2023; 14:1258023. [PMID: 38023875 PMCID: PMC10645062 DOI: 10.3389/fpls.2023.1258023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/13/2023] [Indexed: 12/01/2023]
Abstract
Viroids are small circular RNAs infecting a wide range of plants. They do not code for any protein or peptide and therefore rely on their structure for their biological cycle. Observed phenotypes of viroid infected plants are thought to occur through changes at the transcriptional/translational level of the host. A mechanism involved in such changes is RNA-directed DNA methylation (RdDM). Till today, there are contradictory works about viroids interference of RdDM. In this study, we investigated the epigenetic effect of viroid infection in Nicotiana benthamiana plants. Using potato spindle tuber viroid (PSTVd) as the triggering pathogen and via bioinformatic analyses, we identified endogenous gene promoters and transposable elements targeted by 24 nt host siRNAs that differentially accumulated in PSTVd-infected and healthy plants. The methylation status of these targets was evaluated following digestion with methylation-sensitive restriction enzymes coupled with PCR amplification, and bisulfite sequencing. In addition, we used Methylation Sensitive Amplification Polymorphism (MSAP) followed by sequencing (MSAP-seq) to study genomic DNA methylation of 5-methylcytosine (5mC) in CG sites upon viroid infection. In this study we identified a limited number of target loci differentially methylated upon PSTVd infection. These results enhance our understanding of the epigenetic host changes as a result of pospiviroid infection.
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Affiliation(s)
- Martha Tselika
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | | | - Paraskevi Kallemi
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Christos Andronis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Michela Chiumenti
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Beatriz Navarro
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Matthieu Lavigne
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Kriton Kalantidis
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Konstantina Katsarou
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
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2
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Chaudhary S, Selvaraj V, Awasthi P, Bhuria S, Purohit R, Kumar S, Hallan V. Small Heat Shock Protein (sHsp22.98) from Trialeurodes vaporariorum Plays Important Role in Apple Scar Skin Viroid Transmission. Viruses 2023; 15:2069. [PMID: 37896846 PMCID: PMC10611230 DOI: 10.3390/v15102069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/11/2023] [Accepted: 09/16/2023] [Indexed: 10/29/2023] Open
Abstract
Trialeurodes vaporariorum, commonly known as the greenhouse whitefly, severely infests important crops and serves as a vector for apple scar skin viroid (ASSVd). This vector-mediated transmission may cause the spread of infection to other herbaceous crops. For effective management of ASSVd, it is important to explore the whitefly's proteins, which interact with ASSVd RNA and are thereby involved in its transmission. In this study, it was found that a small heat shock protein (sHsp) from T. vaporariorum, which is expressed under stress, binds to ASSVd RNA. The sHsp gene is 606 bp in length and encodes for 202 amino acids, with a molecular weight of 22.98 kDa and an isoelectric point of 8.95. Intermolecular interaction was confirmed through in silico analysis, using electrophoretic mobility shift assays (EMSAs) and northwestern assays. The sHsp22.98 protein was found to exist in both monomeric and dimeric forms, and both forms showed strong binding to ASSVd RNA. To investigate the role of sHsp22.98 during ASSVd infection, transient silencing of sHsp22.98 was conducted, using a tobacco rattle virus (TRV)-based virus-induced gene silencing system. The sHsp22.98-silenced whiteflies showed an approximate 50% decrease in ASSVd transmission. These results suggest that sHsp22.98 from T. vaporariorum is associated with viroid RNA and plays a significant role in transmission.
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Affiliation(s)
- Savita Chaudhary
- Plant Virology Laboratory, Division of Biotechnology, CSIR—Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India (R.P.)
| | - Vijayanandraj Selvaraj
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India (R.P.)
- Plant Molecular Virology Laboratory, Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow 226001, Uttar Pradesh, India
| | - Preshika Awasthi
- Plant Virology Laboratory, Division of Biotechnology, CSIR—Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India
| | - Swati Bhuria
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India (R.P.)
- Plant Molecular Virology Laboratory, Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow 226001, Uttar Pradesh, India
| | - Rituraj Purohit
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India (R.P.)
- Bioinformatics Lab, Division of Biotechnology, CSIR—Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India
| | - Surender Kumar
- Plant Virology Laboratory, Division of Biotechnology, CSIR—Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India
| | - Vipin Hallan
- Plant Virology Laboratory, Division of Biotechnology, CSIR—Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India (R.P.)
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3
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Márquez-Molins J, Villalba-Bermell P, Corell-Sierra J, Pallás V, Gomez G. Integrative time-scale and multi-omics analysis of host responses to viroid infection. PLANT, CELL & ENVIRONMENT 2023. [PMID: 37378473 DOI: 10.1111/pce.14647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/18/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023]
Abstract
Viroids are circular RNAs of minimal complexity compelled to subvert plant-regulatory networks to accomplish their infectious process. Studies focused on the response to viroid-infection have mostly addressed specific regulatory levels and considered specifics infection-times. Thus, much remains to be done to understand the temporal evolution and complex nature of viroid-host interactions. Here we present an integrative analysis of the temporal evolution of the genome-wide alterations in cucumber plants infected with hop stunt viroid (HSVd) by integrating differential host transcriptome, sRNAnome and methylome. Our results support that HSVd promotes the redesign of the cucumber regulatory-pathways predominantly affecting specific regulatory layers at different infection-phases. The initial response was characterised by a reconfiguration of the host-transcriptome by differential exon-usage, followed by a progressive transcriptional downregulation modulated by epigenetic changes. Regarding endogenous small RNAs, the alterations were limited and mainly occurred at the late stage. Significant host-alterations were predominantly related to the downregulation of transcripts involved in plant-defence mechanisms, the restriction of pathogen-movement and the systemic spreading of defence signals. We expect that these data constituting the first comprehensive temporal-map of the plant-regulatory alterations associated with HSVd infection could contribute to elucidate the molecular basis of the yet poorly known host-response to viroid-induced pathogenesis.
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Affiliation(s)
- Joan Márquez-Molins
- Department of Molecular Interactions and Regulation, Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC), Universitat de València (UV), Parc Científic, Paterna, Spain
- Department of Virologia Molecular y Evolutiva de Plantas, Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, Valencia, Spain
| | - Pascual Villalba-Bermell
- Department of Molecular Interactions and Regulation, Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC), Universitat de València (UV), Parc Científic, Paterna, Spain
| | - Julia Corell-Sierra
- Department of Molecular Interactions and Regulation, Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC), Universitat de València (UV), Parc Científic, Paterna, Spain
| | - Vicente Pallás
- Department of Virologia Molecular y Evolutiva de Plantas, Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, Valencia, Spain
| | - Gustavo Gomez
- Department of Molecular Interactions and Regulation, Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC), Universitat de València (UV), Parc Científic, Paterna, Spain
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4
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Ortolá B, Daròs JA. Viroids: Non-Coding Circular RNAs Able to Autonomously Replicate and Infect Higher Plants. BIOLOGY 2023; 12:biology12020172. [PMID: 36829451 PMCID: PMC9952643 DOI: 10.3390/biology12020172] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/24/2023]
Abstract
Viroids are a unique type of infectious agent, exclusively composed of a relatively small (246-430 nt), highly base-paired, circular, non-coding RNA. Despite the small size and non-coding nature, the more-than-thirty currently known viroid species infectious of higher plants are able to autonomously replicate and move systemically through the host, thereby inducing disease in some plants. After recalling viroid discovery back in the late 60s and early 70s of last century and discussing current hypotheses about their evolutionary origin, this article reviews our current knowledge about these peculiar infectious agents. We describe the highly base-paired viroid molecules that fold in rod-like or branched structures and viroid taxonomic classification in two families, Pospiviroidae and Avsunviroidae, likely gathering nuclear and chloroplastic viroids, respectively. We review current knowledge about viroid replication through RNA-to-RNA rolling-circle mechanisms in which host factors, notably RNA transporters, RNA polymerases, RNases, and RNA ligases, are involved. Systemic movement through the infected plant, plant-to-plant transmission and host range are also discussed. Finally, we focus on the mechanisms of viroid pathogenesis, in which RNA silencing has acquired remarkable importance, and also for the initiation of potential biotechnological applications of viroid molecules.
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5
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Di Serio F, Owens RA, Navarro B, Serra P, Martínez de Alba ÁE, Delgado S, Carbonell A, Gago-Zachert S. Role of RNA silencing in plant-viroid interactions and in viroid pathogenesis. Virus Res 2023; 323:198964. [PMID: 36223861 PMCID: PMC10194176 DOI: 10.1016/j.virusres.2022.198964] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 10/04/2022] [Accepted: 10/07/2022] [Indexed: 11/05/2022]
Abstract
Viroids are small, single-stranded, non-protein coding and circular RNAs able to infect host plants in the absence of any helper virus. They may elicit symptoms in their hosts, but the underlying molecular pathways are only partially known. Here we address the role of post-transcriptional RNA silencing in plant-viroid-interplay, with major emphasis on the involvement of this sequence-specific RNA degradation mechanism in both plant antiviroid defence and viroid pathogenesis. This review is a tribute to the memory of Dr. Ricardo Flores, who largely contributed to elucidate this and other molecular mechanisms involved in plant-viroid interactions.
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Affiliation(s)
- Francesco Di Serio
- Institute for Sustainable Plant Protection, National Research Council, Bari 70122, Italy.
| | - Robert A Owens
- Molecular Plant Pathology Laboratory, US Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA
| | - Beatriz Navarro
- Institute for Sustainable Plant Protection, National Research Council, Bari 70122, Italy
| | - Pedro Serra
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València), Valencia 46022, Spain
| | - Ángel Emilio Martínez de Alba
- Institute for Agribiotechnology Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Villamayor 37185, Salamanca, Spain
| | - Sonia Delgado
- Instituto Agroforestal Mediterráneo (IAM-UPV), Camino de Vera, s/n 46022, Valencia, Spain
| | - Alberto Carbonell
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València), Valencia 46022, Spain
| | - Selma Gago-Zachert
- Institute of Biochemistry and Biotechnology, Section Microbial Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale 06120, Germany
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6
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Gómez G, Marquez-Molins J, Martinez G, Pallas V. Plant epigenome alterations: an emergent player in viroid-host interactions. Virus Res 2022; 318:198844. [DOI: 10.1016/j.virusres.2022.198844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/31/2022] [Accepted: 06/05/2022] [Indexed: 10/18/2022]
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Mycoviroids: Fungi as Hosts and Vectors of Viroids. Cells 2022; 11:cells11081335. [PMID: 35456014 PMCID: PMC9027725 DOI: 10.3390/cells11081335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 02/05/2023] Open
Abstract
Viroids were discovered by the American plant pathologist Theodor O [...]
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Ma J, Mudiyanselage SDD, Wang Y. Emerging value of the viroid model in molecular biology and beyond. Virus Res 2022; 313:198730. [PMID: 35263622 PMCID: PMC8976779 DOI: 10.1016/j.virusres.2022.198730] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 02/25/2022] [Accepted: 03/05/2022] [Indexed: 01/21/2023]
Abstract
Viroids are single-stranded circular noncoding RNAs that infect plants. Research in the past five decades has deciphered the viroid genome structures, viroid replication cycles, numerous host factors for viroid infection, viroid motifs for intracellular and intercellular trafficking, interactions with host defense machinery, etc. In this review, we mainly focus on some significant questions that remain to be tackled, centered around (1) how the RNA polymerase II machinery performs transcription on RNA templates of nuclear-replicating viroids, (2) how viroid RNAs coordinate multiple structural elements for diverse functions, and (3) how viroid RNAs activate plant immunity. Research on viroids has led to seminal discoveries in biology, and we expect the research directions outlined in this review to continue providing key knowledge inspiring other areas of biology.
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Werghi S, Herrero FA, Fakhfakh H, Gorsane F. Auxin drives tomato spotted wilt virus (TSWV) resistance through epigenetic regulation of auxin response factor ARF8 expression in tomato. Gene 2021; 804:145905. [PMID: 34411646 DOI: 10.1016/j.gene.2021.145905] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/11/2021] [Accepted: 08/13/2021] [Indexed: 11/26/2022]
Abstract
Tomato spotted wilt virus (TSWV) causes severe losses of tomato crops worldwide. To cope dynamically with such a threat, plants deploy strategies acting at the molecular and the epigenetic levels. We found that tomato symptoms progress in a specific-genotype-manner upon TSWV infection. Susceptible genotypes showed within the Auxin Response Factor (ARF8) promoter coupled to enhanced expression of miRNA167a, reduced ARF8 gene and decreased levels of the hormone auxin. This constitutes a deliberate attempt of TSWV to disrupt plant growth to promote spread in sensitive cultivars. Epigenetic regulation through the level of cytosine methylation and the miR167a-ARF8 module are part of a complex network modulating auxin-triggered synthesis and shaping tomato responses to TSWV. Furthermore, modulation of miR167a-ARF8 regulatory module could be applied in tomato-resistance breeding programs.
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Affiliation(s)
- Sirine Werghi
- Laboratory of Molecular Genetics, Immunology and Biotechnology, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis 2092, Tunisia
| | - Frederic Aparicio Herrero
- Institute of Molecular and Cellular Biology of Plants (UPV-CSIC), Valencia 46022, Spain; Dept of Biotechnology, ETSIAMN, Universidad Politécnica de Valencia, 46002, Spain
| | - Hatem Fakhfakh
- Laboratory of Molecular Genetics, Immunology and Biotechnology, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis 2092, Tunisia; Faculty of Sciences of Bizerte, Zarzouna 702, University of Carthage, Tunisia
| | - Faten Gorsane
- Laboratory of Molecular Genetics, Immunology and Biotechnology, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis 2092, Tunisia; Faculty of Sciences of Bizerte, Zarzouna 702, University of Carthage, Tunisia.
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Abstract
Viroids are small, single-stranded, circular RNAs infecting plants. Composed of only a few hundred nucleotides and being unable to code for proteins, viroids represent the lowest level of complexity for an infectious agent, even below that of the smallest known viruses. Despite the relatively small size, viroids contain RNA structural elements embracing all the information needed to interact with host factors involved in their infectious cycle, thus providing models for studying structure-function relationships of RNA. Viroids are specifically targeted to nuclei (family Pospiviroidae) or chloroplasts (family Avsunviroidae), where replication based on rolling-circle mechanisms takes place. They move locally and systemically through plasmodesmata and phloem, respectively, and may elicit symptoms in the infected host, with pathogenic pathways linked to RNA silencing and other plant defense responses. In this review, recent advances in the dissection of the complex interplay between viroids and plants are presented, highlighting knowledge gaps and perspectives for future research. Expected final online publication date for the Annual Review of Virology, Volume 8 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Beatriz Navarro
- Institute for Sustainable Plant Protection, National Research Council of Italy; I-70126 Bari, Italy;
| | - Ricardo Flores
- Institute of Molecular and Cellular Biology of Plants (UPV-CSIC), Polytechnic University of Valencia, 46022 Valencia, Spain
| | - Francesco Di Serio
- Institute for Sustainable Plant Protection, National Research Council of Italy; I-70126 Bari, Italy;
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Symptom Severity, Infection Progression and Plant Responses in Solanum Plants Caused by Three Pospiviroids Vary with the Inoculation Procedure. Int J Mol Sci 2021; 22:ijms22126189. [PMID: 34201240 PMCID: PMC8273692 DOI: 10.3390/ijms22126189] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 05/31/2021] [Accepted: 06/02/2021] [Indexed: 11/17/2022] Open
Abstract
Infectious viroid clones consist of dimeric cDNAs used to generate transcripts which mimic the longer-than-unit replication intermediates. These transcripts can be either generated in vitro or produced in vivo by agro-inoculation. We have designed a new plasmid, which allows both inoculation methods, and we have compared them by infecting Solanum lycopersicum and Solanum melongena with clones of Citrus exocortis virod (CEVd), Tomato chlorotic dwarf viroid (TCDVd), and Potato spindle tuber viroid (PSTVd). Our results showed more uniform and severe symptoms in agro-inoculated plants. Viroid accumulation and the proportion of circular and linear forms were different depending on the host and the inoculation method and did not correlate with the symptoms, which correlated with an increase in PR1 induction, accumulation of the defensive signal molecules salicylic (SA) and gentisic (GA) acids, and ribosomal stress in tomato plants. The alteration in ribosome biogenesis was evidenced by both the upregulation of the tomato ribosomal stress marker SlNAC082 and the impairment in 18S rRNA processing, pointing out ribosomal stress as a novel signature of the pathogenesis of nuclear-replicating viroids. In conclusion, this updated binary vector has turned out to be an efficient and reproducible method that will facilitate the studies of viroid–host interactions.
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Navarro B, Gisel A, Serra P, Chiumenti M, Di Serio F, Flores R. Degradome Analysis of Tomato and Nicotiana benthamiana Plants Infected with Potato Spindle Tuber Viroid. Int J Mol Sci 2021; 22:3725. [PMID: 33918424 PMCID: PMC8038209 DOI: 10.3390/ijms22073725] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/30/2021] [Accepted: 03/30/2021] [Indexed: 11/16/2022] Open
Abstract
Viroids are infectious non-coding RNAs that infect plants. During infection, viroid RNAs are targeted by Dicer-like proteins, generating viroid-derived small RNAs (vd-sRNAs) that can guide the sequence specific cleavage of cognate host mRNAs via an RNA silencing mechanism. To assess the involvement of these pathways in pathogenesis associated with nuclear-replicating viroids, high-throughput sequencing of sRNAs and degradome analysis were carried out on tomato and Nicotiana benthamiana plants infected by potato spindle tuber viroid (PSTVd). Both hosts develop similar stunting and leaf curling symptoms when infected by PSTVd, thus allowing comparative analyses. About one hundred tomato mRNAs potentially targeted for degradation by vd-sRNAs were initially identified. However, data from biological replicates and comparisons between mock and infected samples reduced the number of bona fide targets-i.e., those identified with high confidence in two infected biological replicates but not in the mock controls-to only eight mRNAs that encode proteins involved in development, transcription or defense. Somewhat surprisingly, results of RT-qPCR assays revealed that the accumulation of only four of these mRNAs was inhibited in the PSTVd-infected tomato. When these analyses were extended to mock inoculated and PSTVd-infected N. benthamiana plants, a completely different set of potential mRNA targets was identified. The failure to identify homologous mRNA(s) targeted by PSTVd-sRNA suggests that different pathways could be involved in the elicitation of similar symptoms in these two species. Moreover, no significant modifications in the accumulation of miRNAs and in the cleavage of their targeted mRNAs were detected in the infected tomato plants with respect to the mock controls. Taken together, these data suggest that stunting and leaf curling symptoms induced by PSTVd are elicited by a complex plant response involving multiple mechanisms, with RNA silencing being only one of the possible components.
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Affiliation(s)
- Beatriz Navarro
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy; (B.N.); (M.C.)
| | - Andreas Gisel
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy;
- International Institute of Tropical Agriculture, Ibadan 200001, Nigeria
| | - Pedro Serra
- Istituto de Biología Molecular y Celular de Plantas (CSIC-UPV), 46022 Valencia, Spain; (P.S.); (R.F.)
| | - Michela Chiumenti
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy; (B.N.); (M.C.)
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy; (B.N.); (M.C.)
| | - Ricardo Flores
- Istituto de Biología Molecular y Celular de Plantas (CSIC-UPV), 46022 Valencia, Spain; (P.S.); (R.F.)
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Marquez‐Molins J, Gomez G, Pallas V. Hop stunt viroid: A polyphagous pathogenic RNA that has shed light on viroid-host interactions. MOLECULAR PLANT PATHOLOGY 2021; 22:153-162. [PMID: 33305492 PMCID: PMC7814962 DOI: 10.1111/mpp.13022] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/03/2020] [Accepted: 11/03/2020] [Indexed: 06/12/2023]
Abstract
TAXONOMY Hop stunt viroid (HSVd) is the type species of the genus Hostuviroid (family Pospiviroidae). The other species of this genus is Dahlia latent viroid, which presents an identical central conserved region (CCR) but lacks other structural hallmarks present in Hop stunt viroid. HSVd replication occurs in the nucleus through an asymmetric rolling-circle model as in the other members of the family Pospiviroidae, which also includes the genera Pospiviroid, Cocadviroid, Apscaviroid, and Coleoviroid. PHYSICAL PROPERTIES Hop stunt viroid consists of a single-stranded, circular RNA of 295-303 nucleotides depending on isolates and sequence variants. The most stable secondary structure is a rod-like or quasi-rod-like conformation with two characteristic domains: a CCR and a terminal conserved hairpin similar to that of cocadviroids. HSVd lacks a terminal conserved region. HOSTS AND SYMPTOMS HSVd infects a very broad range of natural hosts and has been reported to be the causal agent of five different diseases (citrus cachexia, cucumber pale fruit, peach and plum apple apricot distortion, and hop stunt). It is distributed worldwide. TRANSMISSION HSVd is transmitted mechanically and by seed.
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Affiliation(s)
- Joan Marquez‐Molins
- Institute for Integrative Systems Biology (I2SysBio)Consejo Superior de Investigaciones Científicas, Universitat de ValènciaPaternaSpain
- Instituto de Biología Molecular y Celular de PlantasConsejo Superior de Investigaciones Científicas, Universitat Politècnica de ValènciaValenciaSpain
| | - Gustavo Gomez
- Institute for Integrative Systems Biology (I2SysBio)Consejo Superior de Investigaciones Científicas, Universitat de ValènciaPaternaSpain
| | - Vicente Pallas
- Instituto de Biología Molecular y Celular de PlantasConsejo Superior de Investigaciones Científicas, Universitat Politècnica de ValènciaValenciaSpain
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Ramesh SV, Yogindran S, Gnanasekaran P, Chakraborty S, Winter S, Pappu HR. Virus and Viroid-Derived Small RNAs as Modulators of Host Gene Expression: Molecular Insights Into Pathogenesis. Front Microbiol 2021; 11:614231. [PMID: 33584579 PMCID: PMC7874048 DOI: 10.3389/fmicb.2020.614231] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 11/19/2020] [Indexed: 02/01/2023] Open
Abstract
Virus-derived siRNAs (vsiRNAs) generated by the host RNA silencing mechanism are effectors of plant’s defense response and act by targeting the viral RNA and DNA in post-transcriptional gene silencing (PTGS) and transcriptional gene silencing (TGS) pathways, respectively. Contrarily, viral suppressors of RNA silencing (VSRs) compromise the host RNA silencing pathways and also cause disease-associated symptoms. In this backdrop, reports describing the modulation of plant gene(s) expression by vsiRNAs via sequence complementarity between viral small RNAs (sRNAs) and host mRNAs have emerged. In some cases, silencing of host mRNAs by vsiRNAs has been implicated to cause characteristic symptoms of the viral diseases. Similarly, viroid infection results in generation of sRNAs, originating from viroid genomic RNAs, that potentially target host mRNAs causing typical disease-associated symptoms. Pathogen-derived sRNAs have been demonstrated to have the propensity to target wide range of genes including host defense-related genes, genes involved in flowering and reproductive pathways. Recent evidence indicates that vsiRNAs inhibit host RNA silencing to promote viral infection by acting as decoy sRNAs. Nevertheless, it remains unclear if the silencing of host transcripts by viral genome-derived sRNAs are inadvertent effects due to fortuitous pairing between vsiRNA and host mRNA or the result of genuine counter-defense strategy employed by viruses to enhance its survival inside the plant cell. In this review, we analyze the instances of such cross reaction between pathogen-derived vsiRNAs and host mRNAs and discuss the molecular insights regarding the process of pathogenesis.
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Affiliation(s)
- S V Ramesh
- ICAR-Central Plantation Crops Research Institute, Kasaragod, India
| | - Sneha Yogindran
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Prabu Gnanasekaran
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | | | - Stephan Winter
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany
| | - Hanu R Pappu
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
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Hashemi L, Golparvar AR, Nasr-Esfahani M, Golabadi M. Expression analysis of defense-related genes in cucumber (Cucumis sativus L.) against Phytophthora melonis. Mol Biol Rep 2020; 47:4933-4944. [DOI: 10.1007/s11033-020-05520-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 05/14/2020] [Indexed: 11/30/2022]
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16
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Hashemi L, Golparvar AR, Nasr Esfahani M, Golabadi M. Correlation between cucumber genotype and resistance to damping-off disease caused by Phytophthora melonis. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1675535] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Affiliation(s)
- Lida Hashemi
- Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan (Khorasgan) Branch, Islamic Azad University, Isfahan, Iran
| | - Ahmad Reza Golparvar
- Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan (Khorasgan) Branch, Islamic Azad University, Isfahan, Iran
| | - Mehdi Nasr Esfahani
- Plant Protection Research Department, Isfahan Agriculture and Natural Resource Research and Education Center (AREEO), Isfahan, Iran
| | - Maryam Golabadi
- Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan (Khorasgan) Branch, Islamic Azad University, Isfahan, Iran
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Jiang J, Ma J, Liu B, Wang Y. Combining a Simple Method for DNA/RNA/Protein Co-Purification and Arabidopsis Protoplast Assay to Facilitate Viroid Research. Viruses 2019; 11:v11040324. [PMID: 30987196 PMCID: PMC6521142 DOI: 10.3390/v11040324] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 03/29/2019] [Accepted: 04/01/2019] [Indexed: 12/12/2022] Open
Abstract
Plant–viroid interactions represent a valuable model for delineating structure–function relationships of noncoding RNAs. For various functional studies, it is desirable to minimize sample variations by using DNA, RNA, and proteins co-purified from the same samples. Currently, most of the co-purification protocols rely on TRI Reagent (Trizol as a common representative) and require protein precipitation and dissolving steps, which render difficulties in experimental handling and high-throughput analyses. Here, we established a simple and robust method to minimize the precipitation steps and yield ready-to-use RNA and protein in solutions. This method can be applied to samples in small quantities, such as protoplasts. Given the ease and the robustness of this new method, it will have broad applications in virology and other disciplines in molecular biology.
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Affiliation(s)
- Jian Jiang
- Department of Biological Sciences, Mississippi State University, Starkville, MS 39762, USA.
| | - Junfei Ma
- Department of Biological Sciences, Mississippi State University, Starkville, MS 39762, USA.
| | - Bin Liu
- Department of Biological Sciences, Mississippi State University, Starkville, MS 39762, USA.
| | - Ying Wang
- Department of Biological Sciences, Mississippi State University, Starkville, MS 39762, USA.
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18
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Annacondia ML, Magerøy MH, Martinez G. Stress response regulation by epigenetic mechanisms: changing of the guards. PHYSIOLOGIA PLANTARUM 2018; 162:239-250. [PMID: 29080251 DOI: 10.1111/ppl.12662] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 09/25/2017] [Accepted: 10/25/2017] [Indexed: 05/23/2023]
Abstract
Plants are sessile organisms that lack a specialized immune system to cope with biotic and abiotic stress. Instead, plants have complex regulatory networks that determine the appropriate distribution of resources between the developmental and the defense programs. In the last years, epigenetic regulation of repeats and gene expression has evolved as an important player in the transcriptional regulation of stress-related genes. Here, we review the current knowledge about how different stresses interact with different levels of epigenetic control of the genome. Moreover, we analyze the different examples of transgenerational epigenetic inheritance and connect them with the known features of genome epigenetic regulation. Although yet to be explored, the interplay between epigenetics and stress resistance seems to be a relevant and dynamic player of the interaction of plants with their environments.
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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
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19
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Matoušek J, Siglová K, Jakše J, Radišek S, Brass JRJ, Tsushima T, Guček T, Duraisamy GS, Sano T, Steger G. Propagation and some physiological effects of Citrus bark cracking viroid and Apple fruit crinkle viroid in multiple infected hop (Humulus lupulus L.). JOURNAL OF PLANT PHYSIOLOGY 2017; 213:166-177. [PMID: 28395198 DOI: 10.1016/j.jplph.2017.02.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 02/28/2017] [Accepted: 02/28/2017] [Indexed: 06/07/2023]
Abstract
The hop metabolome important for the brewing industry and for medical purposes is endangered worldwide due to multiple viroid infections affecting hop physiology. Combinatorial biolistic hop inoculation with Citrus bark cracking viroid (CBCVd), Apple fruit crinkle viroid (AFCVd), Hop latent viroid, and Hop stunt viroid (HSVd) showed a low CBCVd compatibility with HSVd, while all other viroid combinations were highly compatible. Unlike to other viroids, single CBCVd propagation showed a significant excess of (-) over (+) strands in hop, tomato, and Nicotiana benthamiana, but not in citruses. Inoculation of hop with all viroids led to multiple infections with unstable viroid levels in individual plants in the pre- and post-dormancy periods, and to high plant mortality and morphological disorders. Hop isolates of CBCVd and AFCVd were highly stable, only minor quasispecies were detected. CBCVd caused a strong suppression of some crucial mRNAs related to the hop prenylflavonoid biosynthesis pathway, while AFCVd-caused effects were moderate. According to mRNA degradome analysis, this suppression was not caused by a direct viroid-specific small RNA-mediated degradation. CBCVd infection led to a strong induction of two hop transcription factors from WRKY family and to a disbalance of WRKY/WDR1 complexes important for activation of lupulin genes.
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Affiliation(s)
- J Matoušek
- Biology Centre ASCR v.v.i, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice 370 05, Czech Republic
| | - K Siglová
- Biology Centre ASCR v.v.i, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice 370 05, Czech Republic; University of South Bohemia, Faculty of Science, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - J Jakše
- University of Ljubljana, Biotechnical Faculty, Department of Agronomy, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - S Radišek
- Slovenian Institute of Hop Research and Brewing, Cesta Žalskega tabora 2, SI-3310 Žalec, Slovenia
| | - Joseph R J Brass
- Institute of Physical Biology, Heinrich-Heine-Universität Düsseldorf, D-40204 Düsseldorf, Germany
| | - T Tsushima
- Faculty of Agriculture and Life Science, Hirosaki University, Bubkyo-cho, Hirosaki 036-8561, Japan
| | - T Guček
- Slovenian Institute of Hop Research and Brewing, Cesta Žalskega tabora 2, SI-3310 Žalec, Slovenia
| | - G S Duraisamy
- Biology Centre ASCR v.v.i, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice 370 05, Czech Republic
| | - T Sano
- Faculty of Agriculture and Life Science, Hirosaki University, Bubkyo-cho, Hirosaki 036-8561, Japan
| | - G Steger
- Institute of Physical Biology, Heinrich-Heine-Universität Düsseldorf, D-40204 Düsseldorf, Germany.
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Comprehensive Transcriptome Analyses Reveal that Potato Spindle Tuber Viroid Triggers Genome-Wide Changes in Alternative Splicing, Inducible trans-Acting Activity of Phased Secondary Small Interfering RNAs, and Immune Responses. J Virol 2017; 91:JVI.00247-17. [PMID: 28331096 DOI: 10.1128/jvi.00247-17] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 03/16/2017] [Indexed: 11/20/2022] Open
Abstract
Many pathogens express noncoding RNAs (ncRNAs) during infection processes. In the most extreme case, pathogenic ncRNAs alone (such as viroids) can infect eukaryotic organisms, leading to diseases. While a few pathogenic ncRNAs have been implicated in regulating gene expression, the functions of most pathogenic ncRNAs in host-pathogen interactions remain unclear. Here, we employ potato spindle tuber viroid (PSTVd) infecting tomato as a system to dissect host interactions with pathogenic ncRNAs, using comprehensive transcriptome analyses. We uncover various new activities in regulating gene expression during PSTVd infection, such as genome-wide alteration in alternative splicing of host protein-coding genes, enhanced guided-cleavage activities of a host microRNA, and induction of the trans-acting function of phased secondary small interfering RNAs. Furthermore, we reveal that PSTVd infection massively activates genes involved in plant immune responses, mainly those in the calcium-dependent protein kinase and mitogen-activated protein kinase cascades, as well as prominent genes involved in hypersensitive responses, cell wall fortification, and hormone signaling. Intriguingly, our data support a notion that plant immune systems can respond to pathogenic ncRNAs, which has broad implications for providing new opportunities for understanding the complexity of immune systems in differentiating "self" and "nonself," as well as lay the foundation for resolving the long-standing question regarding the pathogenesis mechanisms of viroids and perhaps other infectious RNAs.IMPORTANCE Numerous pathogens, including viruses, express pathogenic noncoding transcripts during infection. In the most extreme case, pathogenic noncoding RNAs alone (i.e., viroids) can cause disease in plants. While some work has demonstrated that pathogenic noncoding RNAs interact with host factors for function, the biological significance of pathogenic noncoding RNAs in host-pathogen interactions remains largely unclear. Here, we apply comprehensive genome-wide analyses of plant-viroid interactions and discover several novel molecular activities underlying nuclear-replicating viroid infection processes in plants, including effects on the expression and function of host noncoding transcripts, as well as the alternative splicing of host protein-coding genes. Importantly, we show that plant immunity is activated upon infection of a nuclear-replicating viroid, which is a new concept that helps to understand viroid-based pathogenesis. Our finding has broad implications for understanding the complexity of host immune systems and the diverse functions of noncoding RNAs.
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Castellano M, Martinez G, Marques MC, Moreno-Romero J, Köhler C, Pallas V, Gomez G. Changes in the DNA methylation pattern of the host male gametophyte of viroid-infected cucumber plants. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:5857-5868. [PMID: 27697787 PMCID: PMC5066502 DOI: 10.1093/jxb/erw353] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Eukaryotic organisms exposed to adverse conditions are required to show a certain degree of transcriptional plasticity in order to cope successfully with stress. Epigenetic regulation of the genome is a key regulatory mechanism allowing dynamic changes of the transcriptional status of the plant in response to stress. The Hop stunt viroid (HSVd) induces the demethylation of ribosomal RNA (rRNA) in cucumber (Cucumis sativus) leaves, leading to increasing transcription rates of rRNA. In addition to the clear alterations observed in vegetative tissues, HSVd infection is also associated with drastic changes in gametophyte development. To examine the basis of viroid-induced alterations in reproductive tissues, we analysed the cellular and molecular consequences of HSVd infection in the male gametophyte of cucumber plants. Our results indicate that in the pollen grain, accumulation of HSVd RNA induces a decondensation of the generative nucleus that correlates with a dynamic demethylation of repetitive regions in the cucumber genome that include rRNA genes and transposable elements (TEs). We therefore propose that HSVd infection impairs the epigenetic control of rRNA genes and TEs in gametic cells of cucumber, a phenomenon thus far unknown to occur in this reproductive tissue as a consequence of pathogen infection.
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Affiliation(s)
- Mayte Castellano
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Politecnica de Valencia (UPV), CPI, Edificio 8 E, Av. de los Naranjos s/n, 46022 Valencia, Spain
| | - German Martinez
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-750 07 Uppsala, Sweden
| | - Maria Carmen Marques
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Politecnica de Valencia (UPV), CPI, Edificio 8 E, Av. de los Naranjos s/n, 46022 Valencia, Spain
| | - Jordi Moreno-Romero
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-750 07 Uppsala, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-750 07 Uppsala, Sweden
| | - Vicente Pallas
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Politecnica de Valencia (UPV), CPI, Edificio 8 E, Av. de los Naranjos s/n, 46022 Valencia, Spain
| | - Gustavo Gomez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Politecnica de Valencia (UPV), CPI, Edificio 8 E, Av. de los Naranjos s/n, 46022 Valencia, Spain
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