Viroids, small circular non-coding RNAs, act as infectious pathogens in higher plants, demonstrating high stability despite consisting solely of naked RNA. Their dependence of replication on host machinery poses the question of whether RNA modifications play a role in viroid biology. Here, we explore RNA modifications in the avocado sunblotch viroid (ASBVd) and the citrus exocortis viroid (CEVd), representative members of viroids replicating in chloroplasts and the nucleus, respectively, using LC - MS and Oxford Nanopore Technology (ONT) direct RNA sequencing. Although no modification was detected in ASBVd, CEVd contained approximately one m6A per RNA molecule. ONT sequencing predicted three m6A positions. Employing orthogonal SELECT method, we confirmed m6A in two positions A353 and A360, which are highly conserved among CEVd variants. These positions are located in the left terminal region of the CEVd rod-like structure where likely RNA Pol II and and TFIIIA-7ZF bind, thus suggesting potential biological role of methylation in viroid replication.
- Klíčová slova
- 6-methyladenosine, LC-MS, m6A SELECT, RNA modification, Viroid, direct RNA-seq,
- MeSH
- konformace nukleové kyseliny MeSH
- kruhová RNA * genetika metabolismus MeSH
- nemoci rostlin virologie MeSH
- posttranskripční úpravy RNA * MeSH
- replikace viru MeSH
- RNA virová * genetika metabolismus chemie MeSH
- sekvenční analýza RNA MeSH
- viroidy * genetika MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- kruhová RNA * MeSH
- RNA virová * MeSH
Fungi harbor a vast diversity of mobile genetic elements (MGEs). Recently, novel fungal MGEs, tentatively referred to as 'ambiviruses,' were described. 'Ambiviruses' have single-stranded RNA genomes of about 4-5 kb in length that contain at least two open reading frames (ORFs) in non-overlapping ambisense orientation. Both ORFs are conserved among all currently known 'ambiviruses,' and one of them encodes a distinct viral RNA-directed RNA polymerase (RdRP), the hallmark gene of ribovirian kingdom Orthornavirae. However, 'ambivirus' genomes are circular and predicted to replicate via a rolling-circle mechanism. Their genomes are also predicted to form rod-like structures and contain ribozymes in various combinations in both sense and antisense orientations-features reminiscent of viroids, virusoids, ribozyvirian kolmiovirids, and yet-unclassified MGEs (such as 'epsilonviruses,' 'zetaviruses,' and some 'obelisks'). As a first step toward the formal classification of 'ambiviruses,' the International Committee on Taxonomy of Viruses (ICTV) recently approved the establishment of a novel ribovirian phylum, Ambiviricota, to accommodate an initial set of 20 members with well-annotated genome sequences.
- Klíčová slova
- Ambiviricota, Ascomycota, Basidiomycota, ICTV, International Committee on Taxonomy of Viruses, Riboviria, ambiviricot, ambivirus, deltavirus, fungi, fungus, hairpin, hammerhead, phylum, ribozyme, twister, viroid, virus classification, virus nomenclature, virus taxonomy,
- MeSH
- fylogeneze MeSH
- genom virový * MeSH
- houby genetika virologie MeSH
- mykoviry genetika klasifikace izolace a purifikace MeSH
- otevřené čtecí rámce * MeSH
- RNA virová genetika MeSH
- RNA-dependentní RNA-polymerasa genetika MeSH
- RNA-viry genetika klasifikace MeSH
- viroidy * genetika klasifikace MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- RNA virová MeSH
- RNA-dependentní RNA-polymerasa MeSH
Grafting cultivars onto rootstocks is a widely used practice by the apple industry predominantly aimed at faster fruit bearing. Using high-throughput sequencing, we revealed the presence of recently described viral agents, namely apple hammerhead viroid (AHVd), apple luteovirus 1 (ALV-1), and citrus concave gum-associated virus (CCGaV), in germplasm collections and production orchards in the Czech Republic and Hungary. The HTS results were validated with RT-(q)PCR, and Northern blotting techniques. To obtain further insight about the presence of these agents, RT-PCR based surveys were carried out and showed their widespread presence alone or in mixed infections. The pathogens were present both in production areas and in feral samples. In addition, rootstock-to-scion transmission of ALV-1 and CCGaV was confirmed using commercial rootstock materials. Phylogenetic relationships based on partial sequences of distinct variants were also investigated. Furthermore, the rosy apple aphid was found to be ALV-1-positive, suggesting that it might be a potential vector of the virus.
- Klíčová slova
- HTS, aphid, apple, rootstock, transmission, viroid, virus,
- MeSH
- Citrus * MeSH
- fylogeneze MeSH
- Luteovirus * MeSH
- satelitní viry MeSH
- viroidy * genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Česká republika MeSH
- Maďarsko MeSH
Viroids are small, non-coding, pathogenic RNAs with a significant ability of adaptation to several basic cellular processes in plants. TFIIIA-7ZF, a splicing variant of transcription factor IIIA, is involved in replication of nuclear-replicating viroids by DNA-dependent polymerase II. We overexpressed NbTFIIIA-7ZF from Nicotiana benthamiana in tobacco (Nicotiana tabacum) where it caused morphological and physiological deviations like plant stunting, splitting of leaf petioles, pistils or apexes, irregular branching of shoots, formation of double-blade leaves, deformation of main stems, and modification of glandular trichomes. Plant aging and senescence was dramatically delayed in transgenic lines. Factors potentially involved in viroid degradation and elimination in pollen were transiently depressed in transgenic leaves. This depressed "degradome" in young plants involved NtTudor S-like nuclease, dicers, argonoute 5, and pollen extracellular nuclease I showing expression in tobacco anthers and leaves. Analysis of the "degradome" in tobacco leaves transformed with either of two hop viroids confirmed modifications of the "degradome" and TFIIIA expression. Thus, the regulatory network connected to TFIIIA-7ZF could be involved in plant pathogenesis as well as in viroid adaptation to avoid its degradation. These results support the hypothesis on a significant impact of limited TFIIIA-7ZF on viroid elimination in pollen.
- Klíčová slova
- Nicotiana tabacum, nucleolytic enzymes, plant aging, plant morphology changes, plant transformation, transcription factors, viroid,
- MeSH
- malá nekódující RNA * MeSH
- pyl genetika MeSH
- tabák genetika MeSH
- transkripční faktor TFIIIA MeSH
- užívání tabáku MeSH
- viroidy * genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- malá nekódující RNA * MeSH
- transkripční faktor TFIIIA MeSH
Long non-coding RNAs (lncRNAs) are a highly heterogeneous class of non-protein-encoding transcripts that play an essential regulatory role in diverse biological processes, including stress responses. The severe stunting disease caused by Citrus bark cracking viroid (CBCVd) poses a major threat to the production of Humulus lupulus (hop) plants. In this study, we systematically investigate the characteristics of the lncRNAs in hop and their role in CBCVd-infection using RNA-sequencing data. Following a stringent filtration criterion, a total of 3598 putative lncRNAs were identified with a high degree of certainty, of which 19% (684) of the lncRNAs were significantly differentially expressed (DE) in CBCVd-infected hop, which were predicted to be mainly involved in plant-pathogen interactions, kinase cascades, secondary metabolism and phytohormone signal transduction. Besides, several lncRNAs and CBCVd-responsive lncRNAs were identified as the precursor of microRNAs and predicted as endogenous target mimics (eTMs) for hop microRNAs involved in CBCVd-infection.
- Klíčová slova
- Citrus bark cracking viroid, Genomics, Humulus lupulus, Long non-coding RNAs, Plant defense, RNA-sequencing,
- MeSH
- Citrus * genetika MeSH
- Humulus * genetika MeSH
- kůra rostlin MeSH
- nemoci rostlin genetika MeSH
- RNA dlouhá nekódující * genetika MeSH
- stanovení celkové genové exprese MeSH
- viroidy * genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- RNA dlouhá nekódující * MeSH
Members of the family Pospiviroidae have single-stranded circular RNA genomes that adopt a rod-like or a quasi-rod-like conformation. These genomes contain a central conserved region that is involved in replication in the nucleus through an asymmetric RNA-RNA rolling-circle mechanism. Members of the family Pospiviroidae lack the hammerhead ribozymes that are typical of viroids classified in the family Avsunviroidae. The family Pospiviroidae includes the genera Apscaviroid, Cocadviroid, Coleviroid, Hostuviroid and Pospiviroid, with >25 species. This is a summary of the ICTV Report on the family Pospiviroidae, which is available at ictv.global/report/pospiviroidae.
- Klíčová slova
- ICTV Report, Pospiviroidae, taxonomy,
- MeSH
- genom virový MeSH
- kruhová RNA MeSH
- replikace viru * MeSH
- RNA katalytická genetika MeSH
- RNA virová genetika MeSH
- RNA genetika MeSH
- viroidy klasifikace genetika fyziologie MeSH
- Publikační typ
- časopisecké články MeSH
- Research Support, N.I.H., Extramural MeSH
- Názvy látek
- hammerhead ribozyme MeSH Prohlížeč
- kruhová RNA MeSH
- RNA katalytická MeSH
- RNA virová MeSH
- RNA MeSH
The mediator (MED) represents a large, conserved, multi-subunit protein complex that regulates gene expression through interactions with RNA polymerase II and enhancer-bound transcription factors. Expanding research accomplishments suggest the predominant role of plant MED subunits in the regulation of various physiological and developmental processes, including the biotic stress response against bacterial and fungal pathogens. However, the involvement of MED subunits in virus/viroid pathogenesis remains elusive. In this study, we investigated for the first time the gene expression modulation of selected MED subunits in response to five viroid species (Apple fruit crinkle viroid (AFCVd), Citrus bark cracking viroid (CBCVd), Hop latent viroid (HLVd), Hop stunt viroid (HSVd), and Potato spindle tuber viroid (PSTVd)) in two model plant species (Nicotiana tabacum and N. benthamiana) and a commercially important hop (Humulus lupulus) cultivar. Our results showed a differential expression pattern of MED subunits in response to a viroid infection. The individual plant MED subunits displayed a differential and tailored expression pattern in response to different viroid species, suggesting that the MED expression is viroid- and plant species-dependent. The explicit evidence obtained from our results warrants further investigation into the association of the MED subunit with symptom development. Together, we provide a comprehensive portrait of MED subunit expression in response to viroid infection and a plausible involvement of MED subunits in fine-tuning transcriptional reprogramming in response to viroid infection, suggesting them as a potential candidate for rewiring the defense response network in plants against pathogens.
- Klíčová slova
- Nicotiana benthamiana, Nicotiana tabacum, differential expression, hop, mediator complex, pathogen, quantitative reverse transcription PCR, viroid,
- MeSH
- druhová specificita MeSH
- Humulus genetika virologie MeSH
- listy rostlin genetika mikrobiologie MeSH
- mediátorový komplex genetika MeSH
- regulace genové exprese u rostlin MeSH
- rostlinné proteiny genetika MeSH
- rostlinné viry MeSH
- stanovení celkové genové exprese MeSH
- tabák genetika virologie MeSH
- viroidy genetika patogenita MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- mediátorový komplex MeSH
- rostlinné proteiny MeSH
Transcription factors (TFs) play a major role in controlling gene expression by intricately regulating diverse biological processes such as growth and development, the response to external stimuli and the activation of defense responses. The systematic identification and classification of TF genes are essential to gain insight into their evolutionary history, biological roles, and regulatory networks. In this study, we performed a global mining and characterization of hop TFs and their involvement in Citrus bark cracking viroid CBCVd infection by employing a digital gene expression analysis. Our systematic analysis resulted in the identification of a total of 3,818 putative hop TFs that were classified into 99 families based on their conserved domains. A phylogenetic analysis classified the hop TFs into several subgroups based on a phylogenetic comparison with reference TF proteins from Arabidopsis thaliana providing glimpses of their evolutionary history. Members of the same subfamily and subgroup shared conserved motif compositions. The putative functions of the CBCVd-responsive hop TFs were predicted using their orthologous counterparts in A. thaliana. The analysis of the expression profiling of the CBCVd-responsive hop TFs revealed a massive differential modulation, and the expression of the selected TFs was validated using qRT-PCR. Together, the comprehensive integrated analysis in this study provides better insights into the TF regulatory networks associated with CBCVd infections in the hop, and also offers candidate TF genes for improving the resistance in hop against viroids.
- Klíčová slova
- hop stunt disease, management, transcriptional reprogramming, viroid pathogenesis,
- MeSH
- fylogeneze MeSH
- Humulus klasifikace genetika imunologie virologie MeSH
- kůra rostlin imunologie virologie MeSH
- nemoci rostlin genetika imunologie virologie MeSH
- rostlinné proteiny genetika imunologie MeSH
- stanovení celkové genové exprese MeSH
- transkripční faktory genetika imunologie MeSH
- viroidy genetika fyziologie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- rostlinné proteiny MeSH
- transkripční faktory MeSH
Viroids are smallest known pathogen that consist of non-capsidated, single-stranded non-coding RNA replicons and they exploits host factors for their replication and propagation. The severe stunting disease caused by Citrus bark cracking viroid (CBCVd) is a serious threat, which spreads rapidly within hop gardens. In this study, we employed comprehensive transcriptome analyses to dissect host-viroid interactions and identify gene expression changes that are associated with disease development in hop. Our analysis revealed that CBCVd-infection resulted in the massive modulation of activity of over 2000 genes. Expression of genes associated with plant immune responses (protein kinase and mitogen-activated protein kinase), hypersensitive responses, phytohormone signaling pathways, photosynthesis, pigment metabolism, protein metabolism, sugar metabolism, and modification, and others were altered, which could be attributed to systemic symptom development upon CBCVd-infection in hop. In addition, genes encoding RNA-dependent RNA polymerase, pathogenesis-related protein, chitinase, as well as those related to basal defense responses were up-regulated. The expression levels of several genes identified from RNA sequencing analysis were confirmed by qRT-PCR. Our systematic comprehensive CBCVd-responsive transcriptome analysis provides a better understanding and insights into complex viroid-hop plant interaction. This information will assist further in the development of future measures for the prevention of CBCVd spread in hop fields.
- Klíčová slova
- Citrus bark cracking viroid, differentially expressed genes, hop, pathogen, transcriptome analysis, viroids,
- MeSH
- Humulus genetika metabolismus virologie MeSH
- listy rostlin genetika metabolismus virologie MeSH
- nemoci rostlin genetika virologie MeSH
- regulace genové exprese u rostlin MeSH
- rostlinné proteiny genetika metabolismus MeSH
- rostlinné viry genetika izolace a purifikace fyziologie MeSH
- stanovení celkové genové exprese MeSH
- viroidy klasifikace genetika izolace a purifikace fyziologie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- rostlinné proteiny MeSH
Members of the family Avsunviroidae have a single-stranded circular RNA genome that adopts a rod-like or branched conformation and can form, in the strands of either polarity, hammerhead ribozymes involved in their replication in plastids through a symmetrical RNA-RNA rolling-circle mechanism. These viroids lack the central conserved region typical of members of the family Pospiviroidae. The family Avsunviroidae includes three genera, Avsunviroid, Pelamoviroid and Elaviroid, with a total of four species. This is a summary of the ICTV Report on the taxonomy of the family Avsunviroidae, which is available at http://www.ictv.global/report/avsunviroidae.
- Klíčová slova
- Avsunviroidae, ICTV, avocado sunblotch viroid, eggplant latent viroid, peach latent mosaic viroid, taxonomy, viroid,
- MeSH
- genom virový MeSH
- kruhová RNA MeSH
- replikace DNA MeSH
- replikace viru * MeSH
- RNA katalytická genetika MeSH
- RNA virová genetika MeSH
- RNA genetika MeSH
- viroidy klasifikace genetika fyziologie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- hammerhead ribozyme MeSH Prohlížeč
- kruhová RNA MeSH
- RNA katalytická MeSH
- RNA virová MeSH
- RNA MeSH
