Papain-like leader proteases are found in diverse families of human, animal, plant, and fungal positive-strand RNA viruses. In addition to autocatalytic processing, these proteases play a variety of roles in the virus life cycle. In particular, the leader protease (L-Pro) of a prototype member of the Closterovirus genus, Beet yellows...
More than half of the recognized genera of positive strand RNA viruses employ polyprotein processing as one of the strategies for their genome expression. Normally, this processing is mediated by virus-encoded proteinases that belong to the trypsin-like or papain-like family. In particular, papain-like, leader proteinases were found in diverse families...
Beet yellows virus (BYV) is a filamentous, positive-strand RNA virus that belongs to the family Closteroviridae. BYV particles encapsidate a 15.5 kb RNA and posses complex polar architecture. A long virion body is formed by the major capsid protein(CP), whereas the minor capsid protein (CPm) assembles a short tail that...
In this investigation we examined the molecular architecture and functions associated with the virion components of the Beet yellows virus (BYV), family Closteroviridae. The BYV virions are filamentous particles composed of two coat proteins, the major coat protein (CP), which encapsidates the majority of the genome, and the minor coat...
Important progress in understanding replication, interactions with host plants, and evolution of closteroviruses enabled engineering of several vectors for gene expression and virus-induced gene silencing. Due to the broad host range of closteroviruses, these vectors expanded vector applicability to include important woody plants such as citrus and grapevine. Furthermore, large...
Viruses and/or virus-like selfish elements are associated with all cellular life forms and are the most abundant biological entities on Earth, with the number of virus particles in many environments exceeding the number of cells by one to two orders of magnitude. The genetic diversity of viruses is commensurately enormous...
Viruses were defined as one of the two principal types of organisms
in the biosphere, namely, as capsid-encoding organisms in
contrast to ribosome-encoding organisms, i.e., all cellular life
forms. Structurally similar, apparently homologous capsids are
present in a huge variety of icosahedral viruses that infect bacteria,
archaea, and eukaryotes. These...
Plant viruses of the recently recognized family Amalgaviridae have monopartite double-stranded (ds) RNA genomes
and encode two proteins: an RNA-dependent RNA polymerase (RdRp) and a putative capsid protein (CP). Whereas the
RdRp of amalgaviruses has been found to be most closely related to the RdRps of dsRNA viruses of the...
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genomes
Krupovic, M., Dolja, V. V., & Koonin, E. V. (2015). Plant viruses of the
Amalgaviridae family
Viruses and other selfish genetic elements are dominant entities in the biosphere, with respect to both physical abundance and genetic diversity. Various selfish elements parasitize on all cellular life forms. The relative abundances of different classes of viruses are dramatically different between prokaryotes and eukaryotes. In prokaryotes, the great majority...
Using genetic approaches, particle image velocimetry and an inert tracer of cytoplasmic streaming, we have made a mechanistic connection between the motor proteins (myosins XI), cargo transported by these motors (distinct endomembrane compartment defined by membrane-anchored MyoB receptors) and the process of cytoplasmic streaming in plant cells. It is shown...
Plant viruses of the recently recognized family Amalgaviridae have monopartite double-stranded (ds) RNA genomes
and encode two proteins: an RNA-dependent RNA polymerase (RdRp) and a putative capsid protein (CP). Whereas the
RdRp of amalgaviruses has been found to be most closely related to the RdRps of dsRNA viruses of the...
Plant viruses of the recently recognized family Amalgaviridae have monopartite double-stranded (ds) RNA genomes and encode two proteins: an RNA-dependent RNA polymerase (RdRp) and a putative capsid protein (CP). Whereas the RdRp of amalgaviruses has been found to be most closely related to the RdRps of dsRNA viruses of the...
Grapevine red blotch virus (GRBV), the causal agent of red blotch disease (RBD) in grapevine, Vitis vinifera L., is an emerging pathogen of significance to the wine grape industry of Oregon, USA. To address knowledge gaps of GRBV epidemiology, spread of GRBV was evaluated in Oregon vineyards over four years....
The advent of improved DNA sequencing technologies has allowed the analysis of various microbial communities. Bloom-forming freshwater cyanobacteria can produce toxins and taste-and-odor compounds that can negatively affect drinking water supplies. Here, I have employed second- and third-generation sequencing technologies to characterize bloom-forming freshwater cyanobacterial genomes and their associated heterotrophic...
Plant viruses have been instrumental in our understanding of the biophysical properties pertaining to non-enveloped icosahedral virus particles. A substantial amount of research has been performed over five decades on Turnip yellow mosaic virus (TYMV), arguably one of the most extensively studied icosahedral plant viruses and the type-member of the...
Viruses are obligatory parasites that depend on host cellular factors for their replication as well as for their local and systemic
movement to establish infection. Although myosin motors are thought to contribute to plant virus infection, their exact roles
in the specific infection steps have not been addressed. Here we...
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of Tobacco Mosaic Virus
Amari, K., Di Donato, M., Dolja, V. V., Heinlein, M. (2014) Myosins VIII and
Viruses are obligatory parasites that depend on host cellular factors for their replication as well as for their local and systemic
movement to establish infection. Although myosin motors are thought to contribute to plant virus infection, their exact roles
in the specific infection steps have not been addressed. Here we...
Viruses are obligatory parasites that depend on host cellular factors for their replication as well as for their local and systemic movement to establish infection. Although myosin motors are thought to contribute to plant virus infection, their exact roles in the specific infection steps have not been addressed. Here we...
Cooperative behaviors in bacteria are increasingly appreciated for their relevance to microbial ecology and utility as model systems for social evolution. One example is the secretion of siderophores, a structurally diverse group of compounds that chelate extracellular iron. Siderophore production is considered cooperative because the benefits can be shared with...
Acute lymphoblastic leukemia (ALL) encompasses a spectrum of lymphoid progenitors that have undergone malignant transformation and clonal proliferation at various stages of differentiation. Some cases of ALL have been documented to have prenatal origins and in particular neonatal exposure to various environmental pollutants is associated with increased disease risk, including...
Some positive-strand RNA plant viruses possess a transfer RNA-like structure (TLS) at the 3'-terminus of their genomic RNAs. The closest mimicry to tRNA is exhibited by the valylatable TLSs from tymoviruses and furo-like viruses, which are able to interact with key cellular tRNA enzymes: [CTP, ATP]:tRNA nucleotidyltransferase (CCA NTase), valyl-tRNA...
RNA silencing pathways are required for a wide variety of processes in most
eucaryotes. In plants, small-interfering RNA (siRNA) arising from transposons and other
repetitive sequences is associated with heterochromatin formation and maintenance.
MicroRNAs and trans-acting siRNAs encoded at discrete loci function as negative regulators of
gene expression by triggering...
The objective of this study was to characterize an unknown agent associated with decline in black raspberry (Rubus occidentalis) in Oregon. A virus was found consistently associated with decline symptoms of black raspberries and was named Black raspberry decline associated virus (BRDaV). Double stranded RNA extraction from BRDaV-infected black raspberry...
The United States is the third-largest producer of raspberries in the world. Washington
State leads the nation in red raspberry (Rubus idaeus L.) production. 'Meeker', the
most grown red raspberry cultivar in the Pacific Northwest (Washington, Oregon and
British Columbia, Canada) is highly susceptible to Raspberry crumbly fruit, a virusinduced...
Plant hormones regulate progression through the different phases of plant development in response to endogenous and environmental cues. Gene expression studies, as well as genetic and molecular analysis of mutants with altered hormonal responses, are two common approaches to elucidate hormone response pathways. This dissertation compares ovary and fruit development...
In this thesis, I studied the translation of dengue virus RNA using a luciferase reporter gene system in Vero cells. The dengue reporter mRNA construct, which harbors 5´-terminal viral nts and 3´-terminal nts, could be translated efficiently compared to an alpha globin reporter construct. The 5´-cap structure and 3´-untranslated region...
To characterize the mechanism through which myosin XI-K attaches to its principal endomembrane cargo, a yeast two-hybrid library of Arabidopsis thaliana cDNAs was screened using the myosin cargo binding domain as bait. This screen identified two previously uncharacterized transmembrane proteins (hereinafter myosin binding proteins or MyoB1/2) that share a myosin...
The Pacific Northwest (Oregon and Washington in the United States and British Columbia in Canada) is one of the major producers of red raspberry (Rubus idaeus L.) and blueberry (Vaccinium corymbosum L.) in the world. The expansion of growing area with these crops has resulted in the emergence of new...
The improvement of the agricultural and wine-making qualities of the grapevine (Vitis vinifera) is hampered by adherence to traditional varieties, the recalcitrance of this plant to genetic modifications, and public resistance to genetically modified organism (GMO) technologies. To address these challenges, we developed an RNA virus-based vector for the introduction...
Plants possess two myosin classes, VIII and XI. The myosins XI are implicated in organelle transport, filamentous actin
organization, and cell and plant growth. Due to the large size of myosin gene families, knowledge of these molecular motors
remains patchy. Using deep transcriptome sequencing and bioinformatics, we systematically investigated myosin...
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Instructions for Authors (www.plantphysiol.org) is:
ValerianV. Dolja (doljav@science.oregonstate.edu).
[W
Plants possess two myosin classes, VIII and XI. The myosins XI are implicated in organelle transport, filamentous actin
organization, and cell and plant growth. Due to the large size of myosin gene families, knowledge of these molecular motors
remains patchy. Using deep transcriptome sequencing and bioinformatics, we systematically investigated myosin...
Plants possess two myosin classes, VIII and XI. The myosins XI are implicated in organelle transport, filamentous actin
organization, and cell and plant growth. Due to the large size of myosin gene families, knowledge of these molecular motors
remains patchy. Using deep transcriptome sequencing and bioinformatics, we systematically investigated myosin...
RNA silencing is an evolutionarily conserved system that
functions as an antiviral mechanism in higher plants and
insects. To counteract RNA silencing, viruses express
silencing suppressors that interfere with both siRNA- and
microRNA-guided silencing pathways. We used comparative
in vitro and in vivo approaches to analyse the molecular
mechanism of...
Virus-infected plants accumulate abundant, 21–24 nucleotide viral siRNAs which are generated by the evolutionary
conserved RNA interference (RNAi) machinery that regulates gene expression and defends against invasive nucleic acids.
Here we show that, similar to RNA viruses, the entire genome sequences of DNA viruses are densely covered with siRNAs in...
Virus-infected plants accumulate abundant, 21–24 nucleotide viral siRNAs which are generated by the evolutionary
conserved RNA interference (RNAi) machinery that regulates gene expression and defends against invasive nucleic acids.
Here we show that, similar to RNA viruses, the entire genome sequences of DNA viruses are densely covered with siRNAs in...
Virus-infected plants accumulate abundant, 21–24 nucleotide viral siRNAs which are generated by the evolutionary conserved RNA interference (RNAi) machinery that regulates gene expression and defends against invasive nucleic acids. Here we show that, similar to RNA viruses, the entire genome sequences of DNA viruses are densely covered with siRNAs in...
Deep sequencing analysis of an asymptomatic grapevine revealed a virome containing five RNA viruses and a viroid. Of these, Grapevine leafroll-associated virus 7 (GLRaV-7), an unassigned closterovirus, was by far the most prominently represented sequence in the analysis. Graft-inoculation of the infection to another grape variety confirmed the lack of...
Evaluating the relative influences of positive and negative interactions in shaping communities is a major topic in modern ecology. Facilitative interactions between basal species are important in habitats with intense predation pressure or severe abiotic stresses. However, few studies address the potential for positive interactions between trophic levels to influence...
Grapevine leafroll disease (GLD) is one of the most important grapevine viral diseases affecting grapevines worldwide. The impact on vine health, crop yield, and quality is difficult to assess due to a high number of variables, but significant economic losses are consistently reported over the lifespan of a vineyard if...
Two studies used DNA markers to assess their usefulness in germplasm identification and evaluation of genetic stability in four cryopreserved Rubus accessions that were stored for over 10 years in liquid nitrogen. In the first study, 12 robust Simple Sequence Repeat (SSR) markers were developed from two microsatellite-enriched libraries of...
A field study was established to determine the impact of interfering vegetation on survival and growth of Engelmann spruce (Piceaeigelmannii Parry) and lodgepole pine (Pinus contorta var contorta Dougi.) at a site in the high elevation Engelmann spruce-Subalpine fir (ESSF) zone, of south-central British Columbia. The study examined (1) the...
One of the important ‘hallmarks’ of cancer is angiogenesis, which is the process of formation of new blood vessels that are necessary for tumor expansion, invasion and metastasis. Under normal physiological conditions, angiogenesis is well balanced and controlled by endogenous proangiogenic factors and antiangiogenic factors. However, factors produced by cancer...
Lifestyle factors are responsible for a considerable portion of cancer incidence worldwide, but credible estimates from the World Health Organization and the International Agency for Research on Cancer (IARC) suggest that the fraction of cancers attributable to toxic environmental exposures is between 7% and 19%. To explore the hypothesis that...
Intercellular transport of viruses through cytoplasmic connections, termed plasmodesmata (PD), is essential for systemic infection in plants by viruses. Previous genetic and ultrastructural data revealed that the potyvirus cyclindrical inclusion (CI) protein is directly involved in cell-to-cell movement, likely through the formation of conical structures anchored to and extended through...
A genetic complementation system was developed
in which tobacco etch virus (TEV) polymerase (NIb)-
expressing transgenic plants or protoplasts were inoculated
with NIb-defective TEV mutants. A β-glucuronidase (GUS)
reporter gene integrated into the genomes of parental and four
mutant viruses was used to assay RNA amplification. Two
mutants (termed VNN...
The tobacco etch potyvirus (TEV) polyprotein is proteolytically processed by three viral proteinases (NIa,
HC-Pro, and P1). While the NIa and HC-Pro proteinases each provide multiple functions essential for viral
infectivity, the role of the P1 proteinase beyond its autoproteolytic activity is understood poorly. To determine
if P1 is necessary...