The Experts below are selected from a list of 666 Experts worldwide ranked by ideXlab platform
Andrew K White - One of the best experts on this subject based on the ideXlab platform.
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pelarspovirus a proposed new genus in the family Tombusviridae
Archives of Virology, 2015Co-Authors: Kay Scheets, Andrew K White, Ramon Jordan, Carmen HernándezAbstract:Currently, the family Tombusviridae encompasses thirteen viral genera that contain single-stranded, positive-sense RNA genomes and isometric virions; the exception being the genus Umbravirus, whose members do not encode a coat protein (CP). A new genus, tentatively named Pelarspovirus, is proposed to be added to this family and would include five members, with Pelargonium line pattern virus recommended as the type species. Viruses assigned to this proposed genus have monopartite genomes encoding five open reading frames (ORFs) that include two 5′-proximal replication proteins, two centrally located movement proteins (MP1 and MP2) and a 3′-proximal CP that, at least for pelargonium line pattern virus (PLPV), has been shown to act also as suppressor of RNA silencing. Distinguishing characteristics of these viruses include i) production of a single, tricistronic subgenomic RNA for expression of MP and CP genes, ii) presence of a non-AUG start codon (CUG or GUG) initiating the MP2 ORF, iii) absence of AUG codons in any frame between the AUG initiation codons of MP1 and CP genes, and iv) sequence-based phylogenetic clustering of all encoded proteins in separate clades from those of other family members.
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structure and prevalence of replication silencer 3 terminus rna interactions in Tombusviridae
Virology, 2006Co-Authors: Hong Na, Andrew K WhiteAbstract:Abstract Tombusviridae is a large positive-strand RNA virus family. Tomato bushy stunt virus (TBSV), the type virus of this family, has a genome ending with AGCCC −OH , termed the 3′-complementary silencer sequence (3′CSS). The 3′CSS is able to base pair with a complementary internally-located sequence, 5′GGGCU, called the replication silencer element (RSE). In TBSV, previous compensatory mutational analysis of the RSE–3′CSS interaction showed it to be functionally important for viral RNA synthesis both in vitro and in vivo. However, these investigations also revealed that the RSE and 3′CSS are very sensitive to nucleotide changes, even when base pairing potential between the two elements is maintained. Consequently, an alternative investigative approach was used in this study where the wild-type sequences of these elements were preserved and their surrounding contexts were modified. Results from these analyses, using a TBSV DI RNA, revealed important new structural requirements necessary for the RSE and 3′CSS to operate in vivo. Collectively, the data suggest that accessibility of the elements and their proximity to adjoining stem structures are important functional parameters. Based on these findings, a working structural model for the TBSV RSE–3′CSS interaction is proposed that involves coaxial stacking of adjacent helices at either end of the RSE–3′CSS interaction. Components of this structural model are extendable to potential RSE–3′CSS interactions that were identified throughout Tombusviridae by comparative sequence analysis. This survey also revealed a significant level of diversity and modularity with respect to RSEs, 3′CSSs and their structural contexts and, moreover, suggests that RSE–3′CSS interactions are prevalent in Tombusviridae and related viruses.
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5 3 rna rna interaction facilitates cap and poly a tail independent translation of tomato bushy stunt virus mrna a potential common mechanism for Tombusviridae
Journal of Biological Chemistry, 2004Co-Authors: Marc R Fabian, Andrew K WhiteAbstract:Abstract Tomato bushy stunt virus (TBSV) is the prototypical member of the genus Tombusvirus in the family Tombusviridae. The (+)-strand RNA genome of TBSV lacks both a 5′ cap and a 3′ poly(A) tail and instead contains a 3′-terminal RNA sequence that acts as a cap-independent translational enhancer (3′ CITE). In this study, we have determined the RNA secondary structure of the translation-specific central segment of the 3′ CITE, termed region 3.5 (R3.5). MFOLD structural modeling combined with solution structure mapping and comparative sequence analysis indicate that R3.5 adopts a branched structure that contains three major helices. Deletion and substitution studies revealed that two of these extended stem-loop (SL) structures are essential for 3′ CITE activity in vivo. In particular, the terminal loop of one of these SLs, SL-B, was found to be critical for translation. Compensatory mutational analysis showed that SL-B functions by base pairing with another SL, SL3, in the 5′ untranslated region of the TBSV genome. Thus, efficient translation of TBSV mRNA in vivo requires a 5′-3′ RNA-RNA interaction that effectively circularizes the message. Similar types of interactions are also predicted to occur in TBSV subgenomic mRNAs between their 5′ untranslated regions and the 3′ CITE, and both genomic and subgenomic 5′-3′ interactions are well conserved in all members of the genus Tombusvirus. In addition, a survey of other genera in Tombusviridae revealed the potential for similar 5′-3′ RNA-RNA-based interactions in their viral mRNAs, suggesting that this mechanism extends throughout this large virus family.
Jae Sun Moon - One of the best experts on this subject based on the ideXlab platform.
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Complete genome sequence of a tentative new umbravirus isolated from Patrinia scabiosaefolia.
Archives of Virology, 2019Co-Authors: Jae Sun MoonAbstract:The complete genomic RNA sequence of a tentative new umbravirus from Patrinia scabiosaefolia, tentatively named “patrinia mild mottle virus” (PatMMoV), was determined. The genome of PatMMoV consists of 4,214 nucleotides and has a typical umbravirus genome organization with four open reading frames. BLAST searches showed that the complete nucleotide sequence of PatMMoV had the highest identity (72%; 50% query coverage) to Ixeridium yellow mottle-associated virus 2 (IxYMaV-2; an unclassified umbravirus). In addition, phylogenetic analysis and pairwise comparisons showed that PatMMoV and IxYMaV-2 were the most closely related and placed in the same clade within a group of umbraviruses. These results suggest that PatMMoV is a putative new member of the genus Umbravirus in the family Tombusviridae.
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complete genome sequence of rice virus a a new member of the family Tombusviridae
Archives of Virology, 2017Co-Authors: Fumei Zhao, Dasom Baek, Davaajargal Igori, Jieun Ra, Ki Do Park, Jae Sun MoonAbstract:An evaluation of the virus population in rice plants using next-generation sequencing technologies resulted in the discovery of a new RNA virus, tentatively named rice virus A (RVA). The complete RVA genome sequence was determined and analyzed, revealing a genome organization resembling that of viruses classified in the genera Aureusvirus, Tombusvirus and Zeavirus within the family Tombusviridae. With 4,832 nucleotides, the RVA genome may be the largest monopartite genome sequenced to date in the family Tombusviridae. The 453-amino acid RVA coat protein shares the highest identity with the gp3 protein of an unclassified carascovirus, SF1 (GenBank accession no. KF510027) isolated from San Francisco wastewater, rather than the coat protein of any known member of the family Tombusviridae. These novel characteristics represent a significant divergence from the genomes of viruses belonging to the sixteen existing genera of the family Tombusviridae, demonstrating that RVA is likely a new family member.
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First Report of Soybean yellow mottle mosaic virus in Soybean in North America
Plant Disease, 2009Co-Authors: Shuxian Li, Jae Sun Moon, Leslie L. DomierAbstract:Soybean yellow mottle mosaic virus (SYMMV) is a soybean-infecting virus recently discovered in Korea that initially induces bright yellow mosaic on leaves followed by stunting and reduced growth of older leaves (1). Nucleotide sequence analysis of genomic RNA of the Korean SYMMV isolate suggested that the virus is a new member of the genus Carmovirus in the family Tombusviridae. To determine whether SYMMV is present in the United States, single leaflets were collected without regard for symptoms from 7 to 10 plants in each of 136 plots in August 2008 from a research field in Stoneville, MS that contained 16 plant introductions (including five from Korea) and ‘Williams 82’. Samples were grouped into 10 pools of 100 leaves from which total RNA was extracted with the Qiagen RNeasy Plant Mini Kit (Germantown, MD), reverse transcribed, and amplified with SuperScript III Platinum SYBR Green One-Step Quantitative Real-time Reverse Transcriptase-PCR Kit (Invitrogen, Carlsbad, CA) and two pairs of oligonucleotide ...
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Nucleotide sequence and genomic organization of a newly identified member of the genus Carmovirus, soybean yellow mottle mosaic virus, from soybean
Archives of Virology, 2009Co-Authors: Leslie L. Domier, Jung Kyung Moon, Hong Soo Choi, Jae Sun MoonAbstract:The viral genome of soybean yellow mottle mosaic virus (SYMMV) from infected soybean ( Glycine max ) in Korea was cloned and sequenced. The complete monopartite single-stranded RNA genome of SYMMV consists of 4009 base pairs with six putative open reading frames and includes 5′- and 3′-untranslated regions of 39 and 229 nucleotides, respectively. The nucleotide and coat protein sequences of SYMMV share the highest sequence identity with those of cowpea mottle virus. Based on its genomic organization, its predicted amino acid sequence, and its phylogenetic relatedness to known carmoviruses, we report that SYMMV is a new member of the genus Carmovirus in the family Tombusviridae .
K A White - One of the best experts on this subject based on the ideXlab platform.
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Intragenomic Long-Distance RNA-RNA Interactions in Plus-Strand RNA Plant Viruses.
Frontiers in Microbiology, 2018Co-Authors: T Chkuaseli, K A WhiteAbstract:Plant viruses that contain positive-strand RNA genomes represent an important class of pathogen. The genomes of these viruses harbor RNA sequences and higher-order RNA structures that are essential for the regulation of viral processes during infections. In recent years, it has become increasingly evident that, in addition to locally positioned RNA structures, long-distance intragenomic interactions, involving nucleotide base pairing over large distances, also contribute significantly to the control of various viral events. Viral processes that are modulated by such interactions include genome replication, translation initiation, translational recoding, and subgenomic mRNA transcription. Here, we review the structure and function of different types of long-distance RNA-RNA interactions, herein termed LDRIs, present in members of the family Tombusviridae and other plus-strand RNA plant viruses.
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internal rna replication elements are prevalent in Tombusviridae
Frontiers in Microbiology, 2012Co-Authors: Beth L Nicholson, K A WhiteAbstract:Internal replication elements (IREs) are RNA structures that are present at internal positions in the genomes of different types of plus-strand RNA viruses. Members of the genus Tombusvirus (family Tombusviridae) contain an IRE within the polymerase coding region of their genomes and this RNA element participates in both genome targeting to sites of replication and replicase complex assembly. Here we propose that other members of the virus family Tombusviridae also possess comparable IREs. Through sequence and structural analyses, candidate IREs in several genera of this family were identified, including aureusviruses, necroviruses, carmoviruses and pelarspoviruses. The results from subsequent mutational analysis of selected proposed IREs were consistent with a critical role for these structures in viral genome accumulation during infections. Our study supports the existence of IREs in several genera in Tombusviridae and points to previously unappreciated similarities in genome replication strategies between members of this virus family.
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subgenomic mrna transcription in Tombusviridae
RNA Biology, 2011Co-Authors: S D Jiwan, K A WhiteAbstract:Members of the large virus family Tombusviridae are plus-strand RNA viruses that infect a wide variety of plant hosts. As part of their gene expression strategy, these viruses transcribe viral subgenomic (sg) mRNAs during infections. These short viral messages are synthesized so as to allow for efficient translation of a subset of viral genes. Over the past decade, evidence has been mounting that different members of this virus family utilize a premature termination mechanism for transcription of their sg mRNAs. Here, we describe what is currently known about this unique transcriptional process as gleaned from studies on members of Tombusviridae.
K. Andrew White - One of the best experts on this subject based on the ideXlab platform.
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Construction and characterization of an aureusvirus defective RNA.
Virology, 2014Co-Authors: K. Andrew WhiteAbstract:Abstract Defective RNAs (D RNAs) are small RNA replicons derived from viral RNA genomes. No D RNAs have been found associated with members of the plus-strand RNA virus genus Aureusvirus (family Tombusviridae). Accordingly, we sought to construct a D RNA for the aureusvirus Cucumber leaf spot virus (CLSV) using the known structure of tombusvirus defective interfering RNAs as a guide. An efficiently accumulating CLSV D RNA was generated that contained four non-contiguous regions of the viral genome and this replicon was used as a tool to studying viral cis -acting RNA elements. The results of structural and functional analyses indicated that CLSV contains counterparts for several of the major RNA elements found in tombusviruses. However, although similar, the CLSV D RNA and its components are distinct and provide insights into RNA-based specificity and mechanisms of function.
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Translational readthrough in Tobacco necrosis virus-D.
Virology, 2014Co-Authors: Laura R Newburn, Beth L Nicholson, Michael Yosefi, Peter A Cimino, K. Andrew WhiteAbstract:The plus-strand RNA genome of Tobacco necrosis virus-D (TNV-D) expresses its polymerase via translational readthrough. The RNA signals involved in this readthrough process were characterized in vitro using a wheat germ extract translation system and in vivo via protoplast infections. The results indicate that (i) TNV-D requires a long-range RNA-RNA interaction between an extended stem-loop (SL) structure proximal to the readthrough site and a sequence in the 3'-untranslated region of its genome; (ii) stability of the extended SL structure is important for its function; (iii) TNV-D readthrough elements are compatible with UAG and UGA, but not UAA; (iv) a readthrough defect can be rescued by a heterologous readthrough element in vitro, but not in vivo; and (v) readthrough elements can also mediate translational frameshifting. These results provide new information on determinants of readthrough in TNV-D and further support the concept of a common general mechanism for readthrough in Tombusviridae.
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Subgenomic mRNA transcription in tobacco necrosis virus.
Virology, 2011Co-Authors: S D Jiwan, Baodong Wu, K. Andrew WhiteAbstract:Abstract Tobacco necrosis virus-D (TNV-D), a positive-strand RNA Necrovirus in the family Tombusviridae , transcribes two subgenomic (sg) mRNAs during infections. We have investigated the strategy used by TNV-D in this process and uncovered evidence that it employs a premature termination (PT) mechanism for the transcription of its sg mRNAs. Structural and mutational analysis of the TNV-D genome identified local RNA structures upstream from transcriptional initiation sites that functioned in the plus-strand as attenuation structures and mediated the production of sg mRNA-sized minus-strands. Other evidence in support of a PT mechanism included the ability to uncouple minus-strand sg RNA production from plus-strand sg mRNA synthesis and the sequence similarities observed between the sg mRNA promoter and that for the viral genome. Accordingly, our results indicate that the necrovirus TNV-D, like several other genera in the family Tombusviridae , uses a PT mechanism for transcription of its sg mRNAs.
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Subgenomic mRNA transcription in an aureusvirus: down-regulation of transcription and evolution of regulatory RNA elements.
Virology, 2007Co-Authors: Wei Xu, K. Andrew WhiteAbstract:Abstract The genus Aureusvirus is composed of a group of positive-strand RNA plant viruses that belong to the family Tombusviridae . Expression of certain aureusvirus genes requires the transcription of two subgenomic (sg) mRNAs. Interestingly, the level of sg mRNA2 accumulation in aureusvirus infections is considerably lower than that of sg mRNA1. The nature of this difference was investigated using the aureusvirus Cucumber leaf spot virus (CLSV). Analysis of sg mRNA2 transcription indicated that it is synthesized by a premature termination mechanism. The results also implicated the transcriptional promoter, the attenuation signal, and global RNA folding of the viral genome as mediators of sg mRNA2 suppression. Additionally, evaluation of the transcriptional regulatory RNA elements in aureusviruses and related tombusviruses revealed alternative strategies for building functionally-equivalent stem-loop structures and showed that sequences encoding a critical and invariant amino acid can be successfully incorporated into essential long-distance tertiary RNA–RNA interactions.
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Long-Distance RNA-RNA Interactions in Plant Virus Gene Expression and Replication
Annual Review of Phytopathology, 2006Co-Authors: W. Allen Miller, K. Andrew WhiteAbstract:The vast majority of plant and animal viruses have RNA genomes. Viral gene expression and replication are controlled by cis-acting elements in the viral genome, which have been viewed conventionally as localized structures. However, recent research has altered this perception and provided compelling evidence for cooperative activity involving distantly positioned RNA elements. This chapter focuses on viral RNA elements that interact across hundreds or thousands of intervening nucleotides to control translation, genomic RNA synthesis, and subgenomic mRNA transcription. We discuss evidence supporting the existence and function of the interactions, and speculate on the regulatory roles that such long-distance interactions play in the virus life cycle. We emphasize viruses in the Tombusviridae and Luteoviridae families in which long-distance interactions are best characterized, but similar phenomena in other viruses are also discussed. Many more examples likely remain undiscovered.
D'ann Rochon - One of the best experts on this subject based on the ideXlab platform.
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Current Protocols in Microbiology - Fungal transmission of plant viruses.
Current protocols in microbiology, 2020Co-Authors: D'ann RochonAbstract:Fungal zoospores of Olpidium species transmit several viruses in the family Tombusviridae as well as in the Ophio- and Varicosavirus genera. This unit describes procedures for virus transmission by Olpidium sp. The method is useful for assessing fungal transmissibility of a given virus as well as for further studies on molecular and biological aspects of virus/vector interaction. Curr. Protoc. Microbiol. 12:16B.4.1-16B.4.17. © 2009 by John Wiley & Sons, Inc. Keywords: Olpidium bornovanus; Olpidium brassicae; fungus transmission
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Fungal transmission of plant viruses.
Current protocols in microbiology, 2020Co-Authors: D'ann RochonAbstract:Fungal zoospores of Olpidium species transmit several viruses in the family Tombusviridae as well as in the Ophio- and Varicosavirus genera. This unit describes procedures for virus transmission by Olpidium sp. The method is useful for assessing fungal transmissibility of a given virus as well as for further studies on molecular and biological aspects of virus/vector interaction.
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Near-Atomic-Resolution Cryo-Electron Microscopy Structures of Cucumber Leaf Spot Virus and Red Clover Necrotic Mosaic Virus: Evolutionary Divergence at the Icosahedral Three-Fold Axes.
Journal of Virology, 2020Co-Authors: Michael B. Sherman, Richard Guenther, Ron Reade, D'ann Rochon, Thomas J. SmithAbstract:Members of the Tombusviridae family have highly similar structures, and yet there are important differences among them in host, transmission, and capsid stabilities. Viruses in the Tombusviridae family have single-stranded RNA (ssRNA) genomes with T=3 icosahedral protein shells with a maximum diameter of approximately 340 A. Each capsid protein is comprised of three domains: R (RNA binding), S (shell), and P (protruding). Between the R domain and S domain is the "arm" region that studies have shown to play a critical role in assembly. To better understand how the details of structural differences and similarities influence the Tombusviridae viral life cycles, the structures of cucumber leaf spot virus (CLSV; genus Aureusvirus) and red clover necrotic mosaic virus (RCNMV; genus Dianthovirus) were determined to resolutions of 3.2 A and 2.9 A, respectively, with cryo-electron microscopy and image reconstruction methods. While the shell domains had homologous structures, the stabilizing interactions at the icosahedral 3-fold axes and the R domains differed greatly. The heterogeneity in the R domains among the members of the Tombusviridae family is likely correlated with differences in the sizes and characteristics of the corresponding genomes. We propose that the changes in the R domain/RNA interactions evolved different arm domain interactions at the beta-annuli. For example, RCNMV has the largest genome and it appears to have created the necessary space in the capsid by evolving the shortest R domain. The resulting loss in RNA/R domain interactions may have been compensated for by increased intersubunit beta-strand interactions at the icosahedral 3-fold axes. Therefore, the R and arm domains may have coevolved to package different genomes within the conserved and rigid shell.IMPORTANCE Members of the Tombusviridae family have nearly identical shells, and yet they package genomes that range from 4.6 kb (monopartite) to 5.3 kb (bipartite) in size. To understand how this genome flexibility occurs within a rigidly conserved shell, we determined the high-resolution cryo-electron microscopy (cryo-EM) structures of cucumber leaf spot virus and red clover necrotic mosaic virus. In response to genomic size differences, it appears that the ssRNA binding (R) domain of the capsid diverged evolutionarily in order to recognize the different genomes. The next region, the "arm," seems to have also coevolved with the R domain to allow particle assembly via interactions at the icosahedral 3-fold axes. In addition, there are differences at the icosahedral 3-fold axes with regard to metal binding that are likely important for transmission and the viral life cycle.
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The Cucumber leaf spot virus p25 auxiliary replicase protein binds and modifies the endoplasmic reticulum via N-terminal transmembrane domains
Virology, 2014Co-Authors: Kankana Ghoshal, Ron Reade, J. Theilmann, Hélène Sanfaçon, D'ann RochonAbstract:Cucumber leaf spot virus (CLSV) is a member of the Aureusvirus genus, family Tombusviridae. The auxiliary replicase of Tombusvirids has been found to localize to endoplasmic reticulum (ER), peroxisomes or mitochondria; however, localization of the auxiliary replicase of aureusviruses has not been determined. We have found that the auxiliary replicase of CLSV (p25) fused to GFP colocalizes with ER and that three predicted transmembrane domains (TMDs) at the N-terminus of p25 are sufficient for targeting, although the second and third TMDs play the most prominent roles. Confocal analysis of CLSV infected 16C plants shows that the ER becomes modified including the formation of punctae at connections between ER tubules and in association with the nucleus. Ultrastructural analysis shows that the cytoplasm contains numerous vesicles which are also found between the perinuclear ER and nuclear membrane. It is proposed that these vesicles correspond to modified ER used as sites for CLSV replication.
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genome structure of cucumber leaf spot virus sequence analysis suggests it belongs to a distinct species within the Tombusviridae
Virus Research, 1997Co-Authors: J S Miller, Ron Reade, H Damude, M A Robbins, D'ann RochonAbstract:Abstract The complete nucleotide sequence of cucumber leaf spot virus (CLSV) has been determined and the sizes and locations of predicted viral proteins deduced. The genome consists of 4432 nucleotides and contains five long ORFs. The 5′ proximal ORF encodes a 25 kDa product that terminates in an amber codon which may be readthrough to produce an 84 kDa protein (ORF 2). ORF 3 codes for the 41 kDa coat protein (CP). ORFs 4 and 5 are completely overlapping at the 3′ terminus and code for 27 and 17 kDa products, respectively. The CLSV genome structure is similar to that of tombusviruses and nearly identical to pothos latent virus (PoLV), a newly proposed, atypical, member of the Tombusviridae. It is proposed that CLSV and PoLV be considered strains of a new tombusvirus species. Amino acid sequence comparisons of the CLSV CP and the CPs of several small spherical plant viruses suggest that CLSV is most closely related to melon necrotic spot carmovirus (MNSV), red clover necrotic mosaic dianthovirus (RCNMV) and cucumber necrosis tombusvirus (CNV). These viruses, like CLSV, are transmitted by the soil inhabiting fungus, Olpidium bornovanus .
