Publications

small rna analysis of potato spindle tuber viroid infected phelipanche ramosa.	plants defend themselves against virus/viroid infection by induction of a mechanism of viral rna degradation or translation inhibition. this is achieved by the production of small rnas referred to as small interfering rnas and microrna, the key molecules in establishment of rna directed silencing. potato spindle tuber viroid (pstvd) was the first viroid species to be identified as naturally infecting potato, and it was found to infect many other crop species, wild and ornamental plants. recently ...	2014	24326144
distribution of potato spindle tuber viroid in reproductive organs of petunia during its developmental stages.	embryo infection is important for efficient seed transmission of viroids. to identify the major pattern of seed transmission of viroids, we used in situ hybridization to histochemically analyze the distribution of potato spindle tuber viroid (pstvd) in each developmental stage of petunia (flowering to mature seed stages). in floral organs, pstvd was present in the reproductive tissues of infected female × infected male and infected female × healthy male but not of healthy female × infected male ...	2014	25116641
comparing mirnas and viroids; highly conserved molecular mechanisms for the transmission of genetic information.		2014	24600348
expression of sant/hth myb mrna, a plant morphogenesis-regulating transcription factor, changes due to viroid infection.	potato spindle tuber viroid (pstvd) belongs to plant-pathogenic, circular, non-coding rnas. its propagation is accompanied by (mis)regulation of host genes and induction of pathogenesis symptoms including changes of leaf morphogenesis depending on the strength of viroid variant. we found strong genotype-dependent suppression of tomato morphogenesis-regulating transcription factor sant/hth-myb (slmyb) due to viroid pathogenesis. its relative mrna level was found to be significantly decreased in p ...	2015	26118459
analysis of small rna production patterns among the two potato spindle tuber viroid variants in tomato plants.	in order to analyze the production of small rna (srna) by viroids upon infecting the plants, the tomato plants (solanum lycopersicum cultivar rutgers) were inoculated with the variants of potato spindle tuber viroid (pstvd). after 21-days of postinoculation, total rna was extracted and subjected for deep-sequencing using illumina hiseq platform. the primers were trimmed and only 21- to 24-nt long srnas were filtered after quality check of the raw data. the filtered srna population was then mappe ...	2015	26697336
rnai mediated inhibition of viroid infection in transgenic plants expressing viroid-specific small rnas derived from various functional domains.	previous attempts to develop rnai-mediated viroid-resistant transgenic plants using nearly full-length potato spindle tuber viroid (pstvd) hairpin rna (hprna) were successful; however unusual phenotypes resembling viroid infection occurred. therefore, in the present work, transgenic nicotiana benthamiana lines expressing both partial and truncated versions of pstvd hprna were developed. specifically, seven partial or truncated versions of pstvd sequences were selected according to the hotspots o ...	2015	26656294
small rna derived from the virulence modulating region of the potato spindle tuber viroid silences callose synthase genes of tomato plants.	the tomato (solanum lycopersicum) callose synthase genes cals11-like and cals12-like encode proteins that are essential for the formation of callose, a major component of pollen mother cell walls; these enzymes also function in callose formation during pathogen infection. this article describes the targeting of these callose synthase mrnas by a small rna derived from the virulence modulating region of two potato spindle tuber viroid variants. more specifically, viroid infection of tomato plants ...	2015	26290537
viroid rna turnover: characterization of the subgenomic rnas of potato spindle tuber viroid accumulating in infected tissues provides insights into decay pathways operating in vivo.	while biogenesis of viroid rnas is well-known, how they decay is restricted to data involving host rna silencing. here we report an alternative degradation pathway operating on potato spindle tuber viroid (pstvd), the type species of nuclear-replicating viroids (family pospiviroidae). northern-blot hybridizations with full- and partial-length probes revealed a set of pstvd (+) subgenomic (sg)rnas in early-infected eggplant, some partially overlapping and reaching levels comparable to those of th ...	2015	25662219
quantitation and localization of pospiviroids in aphids.	in this paper, the potential role of aphids in viroid transmission was explored. apterous aphids were fed on pospiviroid-infected plants and viroid targets in the aphids were consequently quantified through rt-qpcr and localized within the aphid body using fluorescence in situ hybridization (fish). based on the analytical sensitivity test, the limit of detection (lod) was estimated at 1.69×10(6) viroid copies per individual aphid body. to localize the viroids in the aphids, a pospiviroid-generic ...	2015	25455904
analysis and application of viroid-specific small rnas generated by viroid-inducing rna silencing.	viroids are noncoding rna pathogens inducing severe to mild disease symptoms on agriculturally important crop plants. viroid replication is entirely dependent on host transcription machinery, and their replication/accumulation in the infected cells can activate rna silencing-a host defense mechanism that targets the viroid itself. rna silencing produces in the cell large amounts of viroid-specific small rnas of 21-24-nucleotides by cleaving (or "dicing") entire molecules of viroid rna. however, ...	2015	25287502
evaluation of disinfectants to prevent mechanical transmission of viruses and a viroid in greenhouse tomato production.	in recent years, a number of serious disease outbreaks caused by viruses and viroids on greenhouse tomatoes in north america have resulted in significant economic losses to growers. the objectives of this study were to evaluate the effectiveness of commercial disinfectants against mechanical transmission of these pathogens, and to select disinfectants with broad spectrum reactivity to control general virus and viroid diseases in greenhouse tomato production.	2015	25623384
detection of potato spindle tuber viroid and other related viroids by a dig labelled rna probe.	viroids can cause diseases of considerable economic importance; in europe the main concern is with pospiviroids that may affect the tomato and potato industries. methods for detection are required that are both sensitive and robust. the detection method described here is a probe hybridization method with a commercially available digoxigenin (dig) labelled full-length potato spindle tuber viroid (pstvd) rna probe. this method detects pstvd and all other known pospiviroids.	2015	25981260
shining a light on lamp assays--a comparison of lamp visualization methods including the novel use of berberine.	the need for simple and effective assays for detecting nucleic acids by isothermal amplification reactions has led to a great variety of end point and real-time monitoring methods. here we tested direct and indirect methods to visualize the amplification of potato spindle tuber viroid (pstvd) by loop-mediated isothermal amplification (lamp) and compared features important for one-pot in-field applications. we compared the performance of magnesium pyrophosphate, hydroxynaphthol blue (hnb), calcei ...	2015	25861931
replicating potato spindle tuber viroid mediates de novo methylation of an intronic viroid sequence but no cleavage of the corresponding pre-mrna.	in plants, potato spindle tuber viroid (pstvd) replication triggers post-transcriptional gene silencing (ptgs) and rna-directed dna methylation (rddm) of homologous rna and dna sequences, respectively. ptgs predominantly occurs in the cytoplasm, but nuclear ptgs has been also reported. in this study, we investigated whether the nuclear replicating pstvd is able to trigger nuclear ptgs. transgenic tobacco plants carrying cytoplasmic and nuclear ptgs sensor constructs were pstvd-infected resulting ...	2015	25826660
rna-directed dna methylation efficiency depends on trigger and target sequence identity.	rna-directed dna methylation (rddm) in plants has been extensively studied, but the rna molecules guiding the rddm machinery to their targets are still to be characterized. it is unclear whether these molecules require full complementarity with their target. in this study, we have generated nicotiana tabacum (nt) plants carrying an infectious tomato apical stunt viroid (tasvd) transgene (nt-tasvd) and a non-infectious potato spindle tuber viroid (pstvd) transgene (nt-sb2). the two viroid sequenc ...	2016	27121647
a land plant-specific transcription factor directly enhances transcription of a pathogenic noncoding rna template by dna-dependent rna polymerase ii.	some dna-dependent rna polymerases (ddrps) possess rna-dependent rna polymerase activity, as was first discovered in the replication of potato spindle tuber viroid (pstvd) rna genome in tomato (solanum lycopersicum). recent studies revealed that this activity in bacteria and mammals is important for transcriptional and posttranscriptional regulatory mechanisms. here, we used pstvd as a model to uncover auxiliary factors essential for rna-templated transcription by ddrp pstvd replication in the n ...	2016	27113774
artificial micrornas and synthetic trans-acting small interfering rnas interfere with viroid infection.	artificial micrornas (amirnas) and synthetic trans-acting small interfering rnas (syn-tasirnas) are two classes of artificial small rnas (srnas) engineered to silence endogenous transcripts as well as viral rnas in plants. here, we explore the possibility of using amirnas and syn-tasirnas to specifically interfere with infections by viroids, small (250-400-nucleotide) non-coding circular rnas with compact secondary structure infecting a wide range of plant species. the combined use of recent hig ...	2016	28026103
replication of a pathogenic non-coding rna increases dna methylation in plants associated with a bromodomain-containing viroid-binding protein.	viroids are plant-pathogenic molecules made up of single-stranded circular non-coding rnas. how replicating viroids interfere with host silencing remains largely unknown. in this study, we investigated the effects of a nuclear-replicating potato spindle tuber viroid (pstvd) on interference with plant rna silencing. using transient induction of silencing in gfp transgenic nicotiana benthamiana plants (line 16c), we found that pstvd replication accelerated gfp silencing and increased virp1 mrna, w ...	2016	27767195
a nuclear-replicating viroid antagonizes infectivity and accumulation of a geminivirus by upregulating methylation-related genes and inducing hypermethylation of viral dna.	dna methylation and post-transcriptional gene silencing play critical roles in controlling infection of single-stranded (ss) dna geminiviruses and ssrna viroids, respectively, but both pathogens can counteract these host defense mechanisms and promote their infectivity. moreover, a specific role of dna methylation in viroid-host interactions is not yet confirmed. here, using an experimental system where two nuclear-replicating agents, the geminivirus tomato yellow leaf curl sardinia virus (tylcs ...	2016	27739453
dissecting the secondary structure of the circular rna of a nuclear viroid in vivo: a "naked" rod-like conformation similar but not identical to that observed in vitro.	with a minimal (250-400 nt), non-protein-coding, circular rna genome, viroids rely on sequence/structural motifs for replication and colonization of their host plants. these motifs are embedded in a compact secondary structure whose elucidation is crucial to understand how they function. viroid rna structure has been tackled in silico with algorithms searching for the conformation of minimal free energy, and in vitro by probing in solution with rnases, dimethyl sulphate and bisulphite, and with ...	2016	27574720
effects of potato spindle tuber viroid infection on tomato metabolic profile.	viroids are the smallest plant pathogens consisting of a single stranded circular rna molecule with a strong secondary structure, lacking a coat protein or any other proteins. the mechanism of viroid pathogenicity has remained unclear. recent advances in instrumentation and data mining have made it possible to study the effects of various stresses on primary and secondary metabolisms. here, we have utilized metabolic profiling approach to show how pstvd infection alters tomato metabolic profile ...	2016	27393919
insight on genes affecting tuber development in potato upon potato spindle tuber viroid (pstvd) infection.	potato (solanum tuberosum l) is a natural host of potato spindle tuber viroid (pstvd) which can cause characteristic symptoms on developing plants including stunting phenotype and distortion of leaves and tubers. pstvd is the type species of the family pospiviroidae, and can replicate in the nucleus and move systemically throughout the plant. it is not well understood how the viroid can affect host genes for successful invasion and which genes show altered expression levels upon infection. our p ...	2016	26937634
molecular dissection of a dahlia isolate of potato spindle tuber viroid inciting a mild symptoms in tomato.	the dahlia isolate of potato spindle tuber viroid (pstvd) accumulates slowly and induces mild disease symptoms in tomato (solanum lycopersicum, cv. rutgers) plants in contrast to the intermediate isolate (pstvd-i). the dahlia isolate (pstvd-d) differs from pstvd-i in eight locations: 42 and 43 in the terminal left (tl); 64/65, 311, and 312/313 in the pathogenicity (p); 118 and 126 in the variable (v); and 201 in the terminal right (tr) domains. to investigate the molecular determinants in the ps ...	2016	26732488
combined activity of dcl2 and dcl3 is crucial in the defense against potato spindle tuber viroid.	viroids are self replicating non-coding rnas capable of infecting a wide range of plant hosts. they do not encode any proteins, thus the mechanism by which they escape plant defenses remains unclear. rnai silencing is a major defense mechanism against virus infections, with the four dcl proteins being principal components of the pathway. we have used nicotiana benthamiana as a model to study potato spindle tuber viroid infection. this viroid is a member of the pospiviroidae family and replicates ...	2016	27732664
plant-specific 4/1 polypeptide interacts with an endoplasmic reticulum protein related to human bap31.	the plant-specific 4/1 protein interacts, both in yeast two-hybrid system and in vitro, and co-localizes in plant cells with plant bap-like protein, the orthologue of human protein bap31. in yeast two-hybrid system, we identified a number of nicotiana benthamiana protein interactors of nt-4/1, the protein known to affect systemic transport of potato spindle tuber viroid. for one of these interactors, an orthologue of human b-cell receptor-associated protein 31 (bap31) termed plant bap-like prote ...	2017	27714454
viroid quasispecies revealed by deep sequencing.	viroids are non-coding single-stranded circular rna molecules that replicate autonomously in infected host plants causing mild to lethal symptoms. their genomes contain about 250-400 nucleotides, depending on viroid species. members of the family pospiviroidae, like the potato spindle tuber viroid (pstvd), replicate via an asymmetric rolling-circle mechanism using the host dna-dependent rna-polymerase ii in the nucleus, while members of avsunviroidae are replicated in a symmetric rolling-circle ...	2017	28027000
comprehensive transcriptome analyses reveal that potato spindle tuber viroid triggers genome-wide changes in alternative splicing, inducible trans-acting activity of phasirnas and immune responses.	many pathogens express non-coding 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 of pathogenic ncrnas have been implicated in regulating gene expression, 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, usi ...	2017	28331096
functional analysis of a viroid rna motif mediating cell-to-cell movement in nicotiana benthamiana.	cell-to-cell trafficking through different cellular layers is a key process for various rnas including those of plant viruses and viroids, but the regulatory mechanisms involved are still not fully elucidated and good model systems are important. here, we analyse the function of a simple rna motif (termed 'loop19') in potato spindle tuber viroid (pstvd) which is required for trafficking in nicotiana benthamiana leaves. northern blotting, reverse transcriptase pcr (rt-pcr) and in situ hybridizati ...	2017	27902342
phylogenetic and functional analyses of a plant protein related to human b-cell receptor-associated proteins.	human b-cell receptor-associated protein bap31 (hsbap31) is the endoplasmic reticulum-resident protein involved in protein sorting and transport as well as pro-apoptotic signaling. plant orthologs of hsbap31 termed 'plant bap-like proteins' (pbl proteins) have thus far remained unstudied. recently, the pbl protein from nicotiana tabacum (ntpbl) was identified as an interactor of nt-4/1, a plant protein known to interact with plant virus movement proteins and affect the long-distance transport of ...	2017	27770627