Publications

the infectivities of turnip yellow mosaic virus genomes with altered trna mimicry are not dependent on compensating mutations in the viral replication protein.	five highly infectious turnip yellow mosaic virus (tymv) genomes with sequence changes in their 3'-terminal regions that result in altered aminoacylation and eef1a binding have been studied. these genomes were derived from cloned parental rnas of low infectivity by sequential passaging in plants. three of these genomes that are incapable of aminoacylation have been reported previously (j. b. goodwin, j. m. skuzeski, and t. w. dreher, virology 230:113-124, 1997). we now demonstrate by subcloning ...	2000	10954536
refined structure of desmodium yellow mottle tymovirus at 2.7 a resolution.	desmodium yellow mottle virus is a 28 nm diameter, t=3 icosahedral plant virus of the tymovirus group. its structure has been solved to a resolution of 2.7 a using x-ray diffraction analysis based on molecular replacement and phase extension methods. the final r value was 0.151 (r(free)=0.159) for 134,454 independent reflections. the folding of the polypeptide backbone is nearly identical with that of turnip yellow mosaic virus, as is the arrangement of subunits in the virus capsid. however, a m ...	2000	10966774
cca initiation boxes without unique promoter elements support in vitro transcription by three viral rna-dependent rna polymerases.	it has previously been observed that the only specific requirement for transcriptional initiation on viral rna in vitro by the rna-dependent rna polymerase (rdrp) of turnip yellow mosaic virus is the cca at the 3' end of the genome. we now compare the abilities of this rdrp, turnip crinkle virus rdrp, and qbeta replicase, an enzyme capable of supporting the complete viral replication cycle in vitro, to transcribe rna templates containing multiple cca boxes but lacking specific viral sequences. e ...	2000	10836791
selection of viral rna-derived trna-like structures with improved valylation activities.	the trna-like structure (tls) of turnip yellow mosaic virus (tymv) rna was previously shown to be efficiently charged by yeast valyl-trna synthetase (valrs). this rna has a noncanonical structure at its 3'-terminus but mimics a trna l-shaped fold, including an anticodon loop containing the major identity nucleotides for valylation, and a pseudoknotted amino acid accepting domain. here we describe an in vitro selection experiment aimed (i) to verify the completeness of the valine identity set, (i ...	2000	10821696
tobacco mosaic virus rna as genetic determinant: genesis of a discovery.	it is generally held that the american geneticists alfred hershey and martha chase were the first to elucidate, in 1952, the genetic functions of phage dna. the discovery of the genetic functions of rna in a plant virus (tobacco mosaic virus, tmv) is commonly attributed to the american plant virologist heinz fraenkel-conrat, and to the germans alfred gierer and gerhard schramm, who came to the same conclusion independently in 1956. in reality, the first understandings dated back to about 1940, w ...	2000	11256209
identification and functional analysis of the turnip yellow mosaic tymovirus subgenomic promoter.	most plant viruses rely on the production of subgenomic rnas (sgrnas) for the expression of their genes and survival in the plant. although this is a widely adopted strategy among viruses, the mechanism(s) whereby sgrna production occurs remains poorly defined. turnip yellow mosaic tymovirus (tymv) is a positive-stranded rna virus that produces an sgrna for the expression of its coat protein. here we report that the subgenomic promoter sequence of tymv is located on a 494-nucleotide fragment, co ...	2000	11070002
evaluation of seed transmission of turnip yellow mosaic virus and tobacco mosaic virus in arabidopsis thaliana.	abstract the mechanism of virus transmission through seed was studied in arabidopsis thaliana infected with turnip yellow mosaic virus (tymv) and tobacco mosaic virus (tmv). serological and biological tests were conducted to identify the route by which the viruses reach the seed and subsequently are located in the seed. both tymv and tmv were detected in seed from infected plants, however only tymv was seed-transmitted. this is the first report of transmission of tymv in seed of a. thaliana. est ...	2000	18944425
detection and subcellular localization of the turnip yellow mosaic virus 66k replication protein in infected cells.	turnip yellow mosaic virus (tymv) encodes a 206-kda (206k) polyprotein with domains of methyltransferase, proteinase, ntpase/helicase, and rna-dependent rna polymerase (rdrp). in vitro, the 206k protein has been shown to undergo proteolytic processing, giving rise to the synthesis of 140-kda (140k) and 66-kda (66k) proteins, the latter comprising the rdrp protein domain. antibodies were raised against the 66k protein and were used to detect the corresponding viral protein in infected cells; both ...	2001	11222099
the formation of empty shells upon pressure induced decapsidation of turnip yellow mosaic virus.	the stability of turnip yellow mosaic virus (tymv) was investigated under pressure, using solution neutron small angle scattering. dissociation products were characterized by analytical ultracentrifugation and electron microscopy. at ph 6.0, tymv remained unaffected by pressure, up to 260 megapascals (mpa), the highest pressure reached in these experiments. at ph 8.0, tymv remained unaffected by pressure up to 160 mpa, but decapsidated irreversibly above 200 mpa, giving rise to more and more emp ...	2001	11402855
protonation of non-watson-crick base pairs and encapsidation of turnip yellow mosaic virus rna.	the 5' utr of turnip yellow mosaic virus rna contains two conserved hairpins with internal loops consisting of c.c and c.a mismatches. in this article, evidence is presented indicating that the 5' proximal hairpin functions as an encapsidation initiation signal. extensive mutagenesis studies on this hairpin and sequencing of virus progeny showed a clear preference for c.c and c.a mismatches within the internal loop. the importance of these mismatches lies in their ph-dependent protonation and st ...	2002	12361978
structural variation and functional importance of a d-loop-t-loop interaction in valine-accepting trna-like structures of plant viral rnas.	valine-accepting trna-like structures (tlss) are found at the 3' ends of the genomic rnas of most plant viruses belonging to the genera tymovirus, furovirus, pomovirus and pecluvirus, and of one tobamovirus species. sequence alignment of these tlss suggests the existence of a tertiary d-loop-t-loop interaction consisting of 2 bp, analogous to those in the elbow region of canonical trnas. the conserved g(18).psi(55) pair of regular trnas is found to covary in these tlss between g.u (possibly also ...	2002	12364602
stability in vitro of the 69k movement protein of turnip yellow mosaic virus is regulated by the ubiquitin-mediated proteasome pathway.	plant viruses move to adjacent cells with the use of virus-encoded cell-to-cell movement proteins. using proteins produced by in vitro translation, we present evidence that the '69k' movement protein of turnip yellow mosaic virus (tymv) is recognized as a substrate for the attachment of polyubiquitin chains and for subsequent rapid and selective proteolysis by the proteasome, the atp-dependent proteolytic system present in reticulocyte lysate. truncation of the 69k protein suggests the existence ...	2002	12466497
rna-protein interactions in spherical viruses.	the three-dimensional structure of many non-enveloped spherical rna viruses has been determined in great detail, mainly using x-ray crystallography. great insight in the structure of the protein capsid has been obtained, but much less information is available about the secondary and tertiary structure of the rna in situ, due to a number of methodological problems. in this paper the current knowledge about rna-protein interactions and the folding of the rna is reviewed, with a special emphasis on ...	2002	12491096
entrapping ribosomes for viral translation: trna mimicry as a molecular trojan horse.	turnip yellow mosaic virus (tymv) has a genomic plus-strand rna with a 5' cap followed by overlapping and different reading frames for the movement protein and polyprotein, while the distal coat protein cistron is translated from a subgenomic rna. the 3'-untranslated region harbors a trna-like structure (tls) to which a valine moiety can be added and it is indispensable for virus viability. here, we report about a surprising interaction between tymv-rna-programmed ribosomes and 3'-valylated tls ...	2003	12526799
the 5'-proximal hairpin of turnip yellow mosaic virus rna: its role in translation and encapsidation.	the rna genome of turnip yellow mosaic virus (tymv) consists of more than 6,000 nucleotides. during a study of the roles of the two hairpins located in its 90-nucleotide 5' untranslated region, it was observed that stabilization of the 5'-proximal hairpin leads to a delay in the development of symptoms on plants. this delay in symptom development for both locally and systemically infected leaves was found to be dependent on a change in the free energy of the hairpin caused by introduced mutation ...	2003	12805444
targeting of the turnip yellow mosaic virus 66k replication protein to the chloroplast envelope is mediated by the 140k protein.	turnip yellow mosaic virus (tymv), a positive-strand rna virus in the alphavirus-like superfamily, encodes two replication proteins, 140k and 66k, both being required for its rna genome replication. the 140k protein contains domains indicative of methyltransferase, proteinase, and ntpase/helicase, and the 66k protein encompasses the rna-dependent rna polymerase domain. during viral infection, the 66k protein localizes to virus-induced chloroplastic membrane vesicles, which are closely associated ...	2003	12915529
expression of the two nested overlapping reading frames of turnip yellow mosaic virus rna is enhanced by a 5' cap and by 5' and 3' viral sequences.	the translation efficiency of an mrna molecule is typically determined by its 5'- and/or 3'-untranslated regions (utrs). previously, we have found that the 3'-utr of turnip yellow mosaic virus (tymv) rna enhances translation synergistically with a 5' cap. here, we use a luciferase reporter system in cowpea protoplasts to show that the 5' 217 nucleotides from tymv genomic rna enhance expression relative to a vector-derived 17-nucleotide 5'-utr. maximum expression was observed from rnas with a cap ...	2004	15308727
crystal structure of an empty capsid of turnip yellow mosaic virus.	empty capsids (artificial top component) of turnip yellow mosaic virus were co-crystallized with an encapsidation initiator rna hairpin. no clear density was observed for the rna, but there were clear differences in the conformation of a loop of the coat protein at the opening of the pentameric capsomer (formed by five a-subunits) protruding from the capsid, compared to the corresponding loop in the intact virus. further differences were found at the n terminus of the a-subunit. these difference ...	2004	15321716
single molecule studies of rna secondary structure: afm of tymv viral rna.	nowadays, the development of experimental procedures for the determination of the secondary structure of rna molecules is taking advantage of the novel single-molecule probing and imaging techniques. we report a method for the mapping of the secondary structure of rna molecules spread on a flat surface by means of the atomic force microscope. globular domains comprising groups of rna secondary and tertiary structure elements separated by unstructured domains can be discerned in the micrographs a ...	2004	15630685
the trna-like structure of turnip yellow mosaic virus rna is a 3'-translational enhancer.	many positive stand rna viral genomes lack the poly(a) tail that is characteristic of cellular mrnas and that promotes translation in cis. the 3' untranslated regions (utrs) of such genomes are expected to provide similar translation-enhancing properties as a poly(a) tail, yet the great variety of 3' sequences suggests that this is accomplished in a range of ways. we have identified a translational enhancer present in the 3' utr of turnip yellow mosaic virus (tymv) rna using luciferase reporter ...	2004	15033563
eef1a binding to aminoacylated viral rna represses minus strand synthesis by tymv rna-dependent rna polymerase.	the genomic rna of turnip yellow mosaic virus (tymv) has an 82-nucleotide-long trna-like structure at its 3'-end that can be valylated and then form a stable complex with translation elongation factor eef1a.gtp. transcription of this rna by tymv rna-dependent rna polymerase (rdrp) to yield minus strands has previously been shown to initiate within the 3'-cca sequence. we have now demonstrated that minus strand synthesis is strongly repressed upon the binding of eef1a.gtp to the valylated viral r ...	2004	15033564
two histidines of the coat protein of turnip yellow mosaic virus at the capsid interior are crucial for viability.	rna-coat protein interactions in turnip yellow mosaic virus (tymv) have been shown to involve low pk proton-donating groups. two different types of interaction have been proposed. in the so-called type i interaction, protonated c-residues interact with acidic amino acids at low ph, thereby providing a rationale for the high c-content (38%) of the genomic rna. the type ii interaction involves charged histidines interacting with phosphates of the rna backbone. site-directed mutagenesis of the tymv ...	2004	15048817
viral virulence protein suppresses rna silencing-mediated defense but upregulates the role of microrna in host gene expression.	small interfering rnas (sirnas) and micrornas (mirnas) are processed by the ribonuclease dicer from distinct precursors, double-stranded rna (dsrna) and hairpin rnas, respectively, although either may guide rna silencing via a similar complex. the sirna pathway is antiviral, whereas an emerging role for mirnas is in the control of development. here, we describe a virulence factor encoded by turnip yellow mosaic virus, p69, which suppresses the sirna pathway but promotes the mirna pathway in arab ...	2004	15100397
turnip yellow mosaic virus: transfer rna mimicry, chloroplasts and a c-rich genome.	summary taxonomy: turnip yellow mosaic virus (tymv) is the type species of the genus tymovirus, family tymoviridae. tymv is a positive strand rna virus of the alphavirus-like supergroup. physical properties: virions are non-enveloped 28-nm t = 3 icosahedrons composed of a single 20-kda coat protein that is clustered in 20 hexameric and 12 pentameric subunits. infectious particles and empty capsids coexist in infected tissue. the genomic rna is 6.3 kb long, with a 5'(m7)gpppg cap and a 3' untrans ...	2004	20565613
trna-like structure regulates translation of brome mosaic virus rna.	for various groups of plant viruses, the genomic rnas end with a trna-like structure (tls) instead of the 3' poly(a) tail of common mrnas. the actual function of these tlss has long been enigmatic. recently, however, it became clear that for turnip yellow mosaic virus, a tymovirus, the valylated tls(tymv) of the single genomic rna functions as a bait for host ribosomes and directs them to the internal initiation site of translation (with n-terminal valine) of the second open reading frame for th ...	2004	15047816
assembly of turnip yellow mosaic virus replication complexes: interaction between the proteinase and polymerase domains of the replication proteins.	turnip yellow mosaic virus (tymv), a positive-strand rna virus in the alphavirus-like supergroup, encodes two nonstructural replication proteins (140k and 66k), both of which are required for its rna genome replication. the 140k protein contains domains indicative of methyltransferase, proteinase, and ntpase/helicase activities, while the 66k protein encompasses the rna-dependent rna polymerase domain. recruitment of the 66k protein to the sites of viral replication, located at the periphery of ...	2004	15254167
atomic force microscopy analysis of icosahedral virus rna.	single-stranded genomic rnas from four icosahedral viruses (poliovirus, turnip yellow mosaic virus (tymv), brome mosaic virus (bmv), and satellite tobacco mosaic virus (stmv)) along with the rna from the helical tobacco mosaic virus (tmv) were extracted using phenol/chloroform. the rnas were imaged using atomic force microscopy (afm) under dynamic conditions in which the rna was observed to unfold. rnas from the four icosahedral viruses initially exhibited highly condensed, uniform spherical sha ...	2005	15733916
the rna of turnip yellow mosaic virus exhibits icosahedral order.	difference electron density maps, based on structure factor amplitudes and experimental phases from crystals of wild-type turnip yellow mosaic virus and those of empty capsids prepared by freeze-thawing, show a large portion of the encapsidated rna to have an icosahedral distribution. four unique segments of base-paired, double-helical rna, one to two turns in length, lie between 33-a and 101-a radius and are organized about either 2-fold or 5-fold icosahedral axes. in addition, single-stranded ...	2005	15780874
variation in the coat protein sequence of british isolates of turnip yellow mosaic virus and comparison with previously published isolates. brief report.	isolates of turnip yellow mosaic virus (tymv) were collected from wild cabbage (brassica oleracea) on a 400 m stretch of dorset coastline. the coat protein genes of four isolates showed high homology in nucleotide sequence (0.970-1.000, mean 0.987). lower levels of homology where found to previously published sequences of australian isolates [10] (0.725-0.775, mean 0.741). the amino acid composition of the dorset isolates showed high levels of homology (0.964-1.000, mean 0.986). numerous amino a ...	2005	16052285
atomic force microscopy investigation of turnip yellow mosaic virus capsid disruption and rna extrusion.	turnip yellow mosaic virus (tymv) was subjected to a variety of procedures which disrupted the protein capsids and produced exposure of the ssrna genome. the results of the treatments were visualized by atomic force microscopy (afm). both in situ and ex situ freeze-thawing produced rna emission, though at low efficiency. the rna lost from such particles was evident, in some cases in the process of exiting the virions. more severe disruption of tymv and extrusion of intact rna onto the substrate ...	2006	16730366
phosphorylation of viral rna-dependent rna polymerase and its role in replication of a plus-strand rna virus.	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 ...	2006	16717096
encapsidation of genomic but not subgenomic turnip yellow mosaic virus rna by coat protein provided in trans.	we have studied the encapsidation requirements of turnip yellow mosaic virus (tymv) genomic and subgenomic rna using an "agroinfiltration" procedure involving transient expression of rnas and coat protein (cp) in nicotiana benthamiana leaves. although n. benthamiana is a nonhost, expression of tymv rna in its leaves by agroinfiltration resulted in efficient local infection and production of the expected virions containing genomic and subgenomic rnas together with empty capsids. a nonreplicating ...	2006	16942786
expression of artificial micrornas in transgenic arabidopsis thaliana confers virus resistance.	plant micrornas (mirnas) regulate the abundance of target mrnas by guiding their cleavage at the sequence complementary region. we have modified an arabidopsis thaliana mir159 precursor to express artificial mirnas (amirnas) targeting viral mrna sequences encoding two gene silencing suppressors, p69 of turnip yellow mosaic virus (tymv) and hc-pro of turnip mosaic virus (tumv). production of these amirnas requires a. thaliana dicer-like protein 1. transgenic a. thaliana plants expressing amir-p69 ...	2006	17057702
a turnip yellow mosaic virus infection system in arabidopsis suspension cell culture.	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 demonstrate ...	2007	17222410
turnip yellow mosaic virus as a chemoaddressable bionanoparticle.	viruses and virus-like particles (vlps) have been demonstrated to be robust scaffolds for the construction of nanomaterials. in order to develop new nanoprobes for time-resolved fluoroimmuno assays as well as to investigate the two-dimensional self-assembly of viruses and vlps, the icosahedral turnip yellow mosaic virus (tymv) was investigated as a potential building block in our study. tymv is an icosahedral plant virus with an average diameter of 28 nm that can be isolated inexpensively in gra ...	2007	17428027
genetics and virology: two interdisciplinary branches of biology.	genetics has a tradition that dates back to the ancient greeks. it developed, between insight and contradiction, from the post-renaissance to the mid-1800s, when mendel and darwin gave it the first experimental and conceptual bases. from 1910, genetics became a true experimental discipline of biology thanks to the work of morgan's group. on the contrary, virology is a relatively young discipline which had origin only after the success of the "germ theory" of pasteur and koch, by the hypothesis o ...	2007	17592822
prototype protein assembly as scaffold for time-resolved fluoroimmuno assays.	turnip yellow mosaic virus (tymv) is an icosahedral plant virus with an average diameter of 28 nm and can be isolated in gram quantities from turnip or chinese cabbage inexpensively. in this study, it was selected as a prototype bionanoparticle for time-resolved fluoroimmuno assay (trfia). two types of reactive amino acid residues were employed to anchor luminescent terbium complexes and biotin groups based on orthogonal chemical reactions. while terbium complexes were used as luminescent signal ...	2007	17542581
proteolytic processing of turnip yellow mosaic virus replication proteins and functional impact on infectivity.	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 b ...	2007	17686855
cap- and initiator trna-dependent initiation of tymv polyprotein synthesis by ribosomes: evaluation of the trojan horse model for tymv rna translation.	turnip yellow mosaic virus (tymv) rna directs the translation of two overlapping open reading frames. competing models have been previously published to explain ribosome access to the downstream polyprotein cistron. the trojan horse model, based on cell-free experiments, proposes noncanonical cap-independent initiation in which the 3'-terminal trna-like structure (tls) functionally replaces initiator trna, and the valine bound to the tls becomes cis-incorporated into viral protein. the initiatio ...	2007	17095542
gcn2-dependent phosphorylation of eukaryotic translation initiation factor-2alpha in arabidopsis.	the yeast regulatory protein kinase, general control non-derepressible-2 (gcn2) plays a key role in general amino acid control. gcn2 phosphorylates the alpha subunit of the trimeric eukaryotic translation initiation factor-2 (eif2), bringing about a decrease in the general rate of protein synthesis but an increase in the synthesis of gcn4, a transcription factor that promotes the expression of genes encoding enzymes for amino acid biosynthesis. the present study concerned the phosphorylation of ...	2008	18603615
formation of two-dimensional crystals of icosahedral rna viruses.	the formation of 2d arrays of three small icosahedral rna viruses with known 3d structures (tomato bushy stunt virus, turnip yellow mosaic virus and bromegrass mosaic virus) has been investigated to determine the role of each component of a negative staining solution containing ammonium molybdate and polyethylene glycol. virion association was monitored by dynamic light scattering (dls) and virus array formation was visualised by conventional transmission electron microscopy and cryo-electron mi ...	2008	17466523
complete nucleotide sequence and experimental host range of okra mosaic virus.	okra mosaic virus (okmv) is a tymovirus infecting members of the family malvaceae. early infections in okra (abelmoschus esculentus) lead to yield losses of 12-19.5%. besides intensive biological characterizations of okmv only minor molecular data were available. therefore, we determined the complete nucleotide sequence of a nigerian isolate of okmv. the complete genomic rna (grna) comprises 6,223 nt and its genome organization showed three major orfs coding for a putative movement protein (mp) ...	2008	18049886
efficient virus-induced gene silencing in arabidopsis using a 'one-step' tymv-derived vector.	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 m ...	2008	18643968
the promotion of osteoblastic differentiation of rat bone marrow stromal cells by a polyvalent plant mosaic virus.	to investigate the role that the micro/nano-environment plays on the differentiation pathway of bone marrow stromal cells (bmscs) into osteoblasts, we employed a 2d substrate coated with turnip yellow mosaic virus (tymv) particles. tymv is a non-enveloped icosahedral plant virus which has an average diameter 28 nm and the protein cage structure consists of 180 identical subunits. the temporal effect of tymv coated substrate on the adhesion and differentiation capacity of the bmscs was monitored ...	2008	18649940
replication and encapsidation of recombinant turnip yellow mosaic virus rna.	turnip yellow mosaic virus (tymv) is a positive strand rna virus that infects mainly cruciferae plants. in this study, the tymv genome was modified by inserting an extra subgenomic rna promoter and a multiple cloning site. this modified tymv was introduced into nicotiana benthamiana using a agrobacterium-mediated t-dna transfer system (agroinfiltration). when a gene encoding beta-glucuronidase or green fluorescent protein was expressed using this modified tymv as a vector, replication of the rec ...	2008	18959822
role of 5'-utr hairpins of the turnip yellow mosaic virus rna in replication and systemic movement.	turnip yellow mosaic virus (tymv) rna has two hairpins in its 5' untranslated region (5'-utr). to investigate the role of the hairpins in replication of tymv, mutants lacking one or both of the two hairpins were constructed. the tymv constructs were introduced into chinese cabbage by an agrobacterium-mediated t-dna transfer method, called agroinfiltration. analysis of total rna from agroinfiltrated leaves showed that replication of the mutant tymv rna lacking both hairpins was about 1/100 of wil ...	2008	19017489
role of trna-like structures in controlling plant virus replication.	transfer rna-like structures (tlss) that are sophisticated functional mimics of trnas are found at the 3'-termini of the genomes of a number of plant positive strand rna viruses. three natural aminoacylation identities are represented: valine, histidine, and tyrosine. paralleling this variety in structure, the roles of tlss vary widely between different viruses. for turnip yellow mosaic virus, the tls must be capable of valylation in order to support infectivity, major roles being the provision ...	2009	18638511
comparison and functional implications of the 3d architectures of viral trna-like structures.	rna viruses co-opt the host cell's biological machinery, and their infection strategies often depend on specific structures in the viral genomic rna. examples are trna-like structures (tlss), found at the 3' end of certain plant viral rnas, which can use the cell's aminoacyl trna-synthetases (aarss) to drive addition of an amino acid to the 3' end of the viral rna. tlss are multifunctional rnas involved in processes such as viral replication, translation, and viral rna stability; these functions ...	2009	19144910
occurrence of potato virus x on hybrid dock in czech republic.	hybrid dock of uteush (rumex patientia l. x rumex tianschanicus a. los., the family polygonaceae) is a perspective high productive crop and in the last decade its farming area has continuously grown in czech republic. however, the introduction of this non-native perennial crop into a present plant production creates a new potential reservoir for some plant viruses. also, the hybrid dock could become a host of currently uncommon or insignificant viruses. we screened two dock-farming localities si ...	2009	19301951
interfacial assembly of turnip yellow mosaic virus nanoparticles.	an extensive study of the factors that affect the interfacial assembly of bionanoparticles at the oil/water (o/w) interface is reported. bionanoparticles, such as viruses, have distinctive structural properties due to the unique arrangement of their protein structures. the assembly process of such bionanoparticles at interfaces is governed by factors including the ionic strength and ph of the aqueous layer, concentration of the particles, and nature of the oil phase. this study highlights the im ...	2009	19354217
the 5'-utr of turnip yellow mosaic virus does not include a critical encapsidation signal.	turnip yellow mosaic virus (tymv) rna has two hairpins in the 5' untranslated region (utr) with internal cc and ca mismatches that become protonated and are able to base pair at a ph near 5. the protonatable hairpins have previously been implicated as playing an important role in rna encapsidation. we have examined the role of the 5'-utr in the amplification and packaging of tymv rna using agroinfiltration of chinese cabbage leaves to express various tymv constructs with mutations affecting the ...	2009	19282015
a tymovirus with an atypical 3'-utr illuminates the possibilities for 3'-utr evolution.	we report the complete genome sequence of dulcamara mottle virus (dumv), confirming its membership within the tymovirus genus, which was previously based on physical and pathology evidence. the 5'-untranslated region (utr) and coding region of dumv rna have the typical characteristics of tymoviral rnas. in contrast, the 3'-utr is the longest and most unusual yet reported for a tymovirus, possessing an internal poly(a) tract, lacking a 3'-trna-like structure (tls) and terminating at the 3'-end wi ...	2009	19664793
oligonucleotide-based microarray for detection of plant viruses employing sequence-independent amplification of targets.	the potential of dna microarrays for detection of plant viruses is hampered by underutilization of sequence-independent amplification methods for target nucleic acid enrichment. a microarray system is described for an unbiased detection of plant viruses using both short (30 nt) and long (50 and 70 nt) oligonucleotide probes. the assay involves amplification of target nucleic acid using random primers followed by in vitro transcription whose crna product is labeled chemically, fragmented and used ...	2010	19850081
the pro/hel region is indispensable for packaging non-replicating turnip yellow mosaic virus rna, but not replicating viral rna.	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 agroinfiltr ...	2010	20396967
multi-domain packing in the aminoacylatable 3' end of a plant viral rna.	turnip yellow mosaic virus (tymv) contains a trna-like structure (tls) in its 3' untranslated region (3' utr). this highly structured element induces valylation of the viral rna by host cell enzymes and is important for virus proliferation. directly upstream of the tymv tls is an upstream pseudoknot domain (upd) that has been considered to be structurally distinct from the tls. however, using a combination of functional, biochemical, and biophysical assays, we show that the entire 3' utr of the ...	2010	20398674
chemoselective modification of turnip yellow mosaic virus by cu(i) catalyzed azide-alkyne 1,3-dipolar cycloaddition reaction and its application in cell binding.	turnip yellow mosaic virus (tymv) is an icosahedral plant virus with a diameter of 28-30 nm that can be isolated in gram quantities from turnip or chinese cabbage inexpensively. in this study, tymv combined with spatially addressable surface chemistries was selected as a prototype bionanoparticle for modulating patterns of cell adhesion, morphology, and proliferation. we exploited the chemical reactivity of tymv using the mild conditions of cu(i) catalyzed azide-alkyne cycloaddition (cuaac) reac ...	2010	21166476
new in vitro method for evaluating antiviral activity of acyclic nucleoside phosphonates against plant viruses.	a new method was developed for testing antiviral compounds against plant viruses based on rapidly growing brassicas in vitro on liquid medium. this method enables exchange of media containing tested chemicals in various concentrations and simultaneous evaluation of their phytotoxicity and antiviral activity. while using ribavirin as a standard for comparison, phytotoxicity and ability of the acyclic nucleotide analogues (r)-pmpa, pmea, pmedap, and (s)-hpmpc to eliminate ssrna turnip yellow mosai ...	2010	20933018
the ubiquitin-proteasome system regulates the accumulation of turnip yellow mosaic virus rna-dependent rna polymerase during viral infection.	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 cel ...	2010	20823192
a viral deubiquitylating enzyme targets viral rna-dependent rna polymerase and affects viral infectivity.	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 proce ...	2011	22117220
identification and validation of reference genes for normalization of transcripts from virus-infected arabidopsis thaliana.	real-time quantitative polymerase chain reaction (qpcr) of complementary dna is now a standard method for studies of gene expression. however, qpcr can identify genuine variation only when transcript quantities are accurately normalized to an appropriate reference. to identify the most reliable reference genes for transcript quantification by qpcr, we describe a systematic evaluation of candidate reference genes of arabidopsis thaliana ecotype columbia-0 (col-0). twelve genes were selected for t ...	2011	21091160
in praise of impurity: 30s ribosomal s15 protein-assisted crystallization of turnip yellow mosaic virus proteinase.	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 re ...	2012	22505427
arabidopsis drb4 protein in antiviral defense against turnip yellow mosaic virus infection.	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 indicat ...	2012	21883552
turnip yellow mosaic virus forms infectious particles without the native beta-annulus structure and flexible coat protein n-terminus.	structural studies have implicated the tymv n-terminal amino acids of the coat protein (cp) in both static (virion stabilization) and dynamic (rna encapsidation and disencapsidation) roles. we have deleted residues 2-5, 2-10 and 2-26 from the n-terminus and expressed the mutant cps in e. coli to assess assembly in the absence of genomic rna and in plant infections to assess infectivity and virion properties. in e. coli, the deletion constructs formed virus-like particles, but in decreased yield. ...	2012	22078163
increased density and coverage uniformity of viruses on a sensor surface by using u-type, t-type, and w-type microfluidic devices.	microorganisms, molecules, or viruses in the fluidic environment are usually at considerably low reynolds numbers because of small diameters. the viscous forces of molecules and viruses dominate at considerably low reynolds numbers. this study developed three microfluidic devices, that is, t type, u type, and w type devices, to control the flow movement, which can increase the adhesion density of viruses on the surface of the sensor. the linker 11-mercaptoundecanoic acid (11-mua) and turnip yell ...	2012	22712035
polyvalent display of rgd motifs on turnip yellow mosaic virus for enhanced stem cell adhesion and spreading.	turnip yellow mosaic virus (tymv) is a stable 28 nm icosahedral plant virus that can be isolated in gram quantities. in order to study the polyvalent effect of arg-gly-asp (rgd) clustering on the response of bone marrow stem cells (bmscs), an rgd motif was genetically displayed on the coat protein of the tymv capsid. composite films composed of either wild-type tymv or tymv-rgd44, in combination with poly(allylamine hydrochloride) (pah), were fabricated by a layer-by-layer adsorption of virus an ...	2012	22522012
analysis of the solvent accessibility of cysteine residues on maize rayado fino virus virus-like particles produced in nicotiana benthamiana plants and cross-linking of peptides to vlps.	mimicking and exploiting virus properties and physicochemical and physical characteristics holds promise to provide solutions to some of the world's most pressing challenges. the sheer range and types of viruses coupled with their intriguing properties potentially give endless opportunities for applications in virus-based technologies. viruses have the ability to self- assemble into particles with discrete shape and size, specificity of symmetry, polyvalence, and stable properties under a wide r ...	2013	23439009
crystallization, structural diversity and anisotropy effects in 2d arrays of icosahedral viruses.	we investigate two-dimensional (2d) assembly of the icosahedral turnip yellow mosaic virus (tymv) under cationic lipid monolayers at the aqueous solution–vapor interface. the 2d crystallization of tymv has been achieved by enhancing electrostatically induced interfacial adsorption, an approach recently demonstrated for another virus. in situ x-ray scattering reveals two close-packed 2d crystalline phases of tymv that are distinct from the previously reported hexagonal and centered square (√2 × √ ...	2013	26029772
modification of turnip yellow mosaic virus coat protein and its effect on virion assembly.	turnip yellow mosaic virus (tymv) is a positive strand rna virus. we have modified tymv coat protein (cp) by inserting a c-myc epitope peptide at the n- or c-terminus of the cp, and have examined its effect on assembly. we introduced the recombinant cp constructs into nicotiana benthamiana leaves by agroinfiltration. examination of the leaf extracts by agarose gel electrophoresis and western blot analysis showed that the cp modified at the n-terminus produced a band co-migrating with wild-type v ...	2013	24148770
feasibility study for detection of turnip yellow mosaic virus (tymv) infection of chinese cabbage plants using raman spectroscopy.	raman spectroscopy provides many advantages compared to other common analytical techniques due to its ability of rapid and accurate identification of unknown specimens as well as simple sample preparation. here, we described potential of raman spectroscopic technique as an efficient and high throughput method to detect plants infected by economically important viruses. to enhance the detection sensitivity of raman measurement, surface enhanced raman scattering (sers) was employed. spectra of ext ...	2013	25288935
a protocol for vigs in arabidopsis thaliana using a one-step tymv-derived vector.	virus-induced gene silencing (vigs) is an important tool for the analysis of gene function in plants, which can be adapted for high-throughput functional genomics in model plant species such as arabidopsis thaliana.here we describe the use of the turnip yellow mosaic virus (tymv)-derived vector pty-s that has the ability to induce vigs in arabidopsis thaliana. this vector harbors a cdna copy of the viral genome, in which a unique snabi restriction site has been engineered. this site allows the c ...	2013	23386305
fate of artificial microrna-mediated resistance to plant viruses in mixed infections.	artificial micrornas (amirnas) are the expression products of engineered microrna (mirna) genes that efficiently and specifically downregulate rnas that contain complementary sequences. transgenic plants expressing high levels of one or more amirnas targeting particular sequences in the genomes of some rna viruses have shown specific resistance to the corresponding virus. this is the case of the arabidopsis thaliana transgenic line 12-4 expressing a high level of the amir159-hc-pro targeting 21 ...	2013	23617337
a compact viral processing proteinase/ubiquitin hydrolase from the otu family.	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 ...	2013	23966860
the structural basis of transfer rna mimicry and conformational plasticity by a viral rna.	rna is arguably the most functionally diverse biological macromolecule. in some cases a single discrete rna sequence performs multiple roles, and this can be conferred by a complex three-dimensional structure. such multifunctionality can also be driven or enhanced by the ability of a given rna to assume different conformational (and therefore functional) states. despite its biological importance, a detailed structural understanding of the paradigm of rna structure-driven multifunctionality is la ...	2014	24909993
replication and packaging of turnip yellow mosaic virus rna containing flock house virus rna1 sequence.	turnip yellow mosaic virus (tymv) is a spherical plant virus that has a single 6.3 kb positive strand rna as a genome. in this study, rna1 sequence of flock house virus (fhv) was inserted into the tymv genome to test whether tymv can accommodate and express another viral entity. in the resulting construct, designated ty-fhv, the fhv rna1 sequence was expressed as a tymv subgenomic rna. northern analysis of the nicotiana benthamiana leaves agroinfiltrated with the ty-fhv showed that both genomic ...	2014	24286326
mutational bias of turnip yellow mosaic virus in the context of host anti-viral gene silencing.	plant dicer-like (dcl) enzymes exhibit a gc-preference during anti-viral post-transcriptional gene silencing (ptgs), delivering an evolutionary selection pressure resulting in plant viruses with gc-poor genomes. however, some viruses, e.g. turnip yellow mosaic virus (tymv, genus tymovirus) have gc-rich genomes, raising the question as to whether or not dcl derived selection pressure affects these viruses. in this study we analyzed the virus-derived small interfering rnas from tymv-infected leave ...	2015	26379088
crystallization of mutants of turnip yellow mosaic virus protease/ubiquitin hydrolase designed to prevent protease self-recognition.	processing of the polyprotein of turnip yellow mosaic virus is mediated by the protease pro. pro cleaves at two places, one of which is at the c-terminus of the pro domain of another polyprotein molecule. in addition to this processing activity, pro possesses an ubiquitin hydrolase (dub) activity. the crystal structure of pro has previously been reported in its polyprotein-processing mode with the c-terminus of one pro inserted into the catalytic site of the next pro, generating pro polymers in ...	2015	25849500
finding our roots and celebrating our shoots: plant virology in virology, 1955-1964.	to celebrate the sixtieth anniversary of virology a survey is made of the plant viruses, virologists and their institutions, and tools and technology described in the first decade of plant virus publications in virology. this was a period when plant viruses increasingly became tools of discovery as epistemic objects and plant virology became a discipline discrete from plant pathology and other life sciences.	2015	25842010
a new application of monolithic supports: the separation of viruses from one another.	the emergence of next-generation "deep" sequencing has enabled the study of virus populations with much higher resolutions. this new tool increases the possibility of observing mixed infections caused by combinations of plant viruses, which are likely to occur more frequently than previously thought. the biological impact of co-infecting viruses on their host has yet to be determined and fully understood, and the first step towards reaching this goal is the separation and purification of individ ...	2015	25724100
development of a specific diagnostic system for detecting turnip yellow mosaic virus from chinese cabbage in korea.	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 compare ...	2016	26843703
highly sensitive and practical detection of plant viruses via electrical impedance of droplets on textured silicon-based devices.	early diagnosis of plant virus infections before the disease symptoms appearance may represent a significant benefit in limiting disease spread by a prompt application of appropriate containment steps. we propose a label-free procedure applied on a device structure where the electrical signal transduction is evaluated via impedance spectroscopy techniques. the device consists of a droplet suspension embedding two representative purified plant viruses i.e., tomato mosaic virus and turnip yellow m ...	2016	27869726
turnip yellow mosaic virus p69 interacts with and suppresses glk transcription factors to cause pale-green symptoms in arabidopsis.		2016	27964999