Caister Academic Press

Plant Viruses

Brewing Microbiology: Current Research, Omics and Microbial Ecology
Edited by: Nicholas A. Bokulich and Charles W. Bamforth
Recent discoveries in brewing microbiology with an emphasis on omics techniques and other modern technologies.
Carole Caranta et al, from "Recent Advances in Plant Virology" Eds: Carole Caranta, Miguel A. Aranda, Mark Tepfer and J.J. Lopez-Moya (2011) Caister Academic Press.
The translation and replication of viral RNA, viral movement within and between plants, plant responses to viral infection, antiviral control measures, virus evolution, newly emerging plant viruses and the biotechnological applications of plant viruses.

Plant Viruses

Full details at Recent Advances in Plant Virology

Viruses that infect plants are responsible for reduction in both yield and quality of crops around the world, and are thus of great economic importance. This has provided the impetus for the extensive research into the molecular and cellular biology of these pathogens and into their interaction with their plant hosts and their vectors. However interest in plant viruses extends beyond their ability to damage crops. Many plant viruses, for example tobacco mosaic virus, have been used as model systems to provide basic understanding of how viruses express genes and replicate. Others permitted the elucidation of the processes underlying RNA silencing, now recognised as a core epigenetic mechanism underpinning numerous areas of biology.

Roles of Cis-acting Elements in Translation of Viral RNAs
from W. Allen Miller, Jelena Kraft, Zhaohui Wang and Qiuling Fan writing in Recent Advances in Plant Virology
Cis-acting signals regulate translation of viral RNAs to produce viral proteins at the appropriate levels and timing to maximize virus replication. A recent review describes the cis-acting sequences that achieve this translational control via processes such as cap-dependent translation, leaky scanning to initiate translation at more than one start codon, ribosomal shunting, cap-independent translation initiation controlled from the 5' and/or 3' untranslated region, poly(A) tail-independent translation initiation, stop codon readthrough, and ribosomal frameshifting. Secondary structures and, in some cases, tertiary structures of the RNA sequences control these events and translation events facilitated by the cis-acting signals mesh with the overall replication strategies of the diverse viruses that employ these mechanisms.

Replication of Plant RNA viruses
from Peter D. Nagy and Judit Pogany writing in Recent Advances in Plant Virology
Among plant viruses, the positive-stranded RNA [(+)RNA] viruses are the largest group, and the most widespread. The central step in the infection cycle of (+)RNA viruses is RNA replication, which is carried out by virus-specific replicase complexes consisting of viral RNA-dependent RNA polymerase, one or more auxiliary viral replication proteins, and a number of co-opted host factors. Viral replicase complexes assemble in specialized membranous compartments in infected cells. Sequestering the replicase complexes is not only helpful for rapid production of a large number of viral (+)RNA progeny, but it also facilitates avoiding recognition by the host's anti-viral surveillance system, and it provides protection from degradation of the viral RNA. Successful viral replication is followed by cell-to-cell and long-distance movement throughout the plant, as well as encapsidation of the (+)RNA progeny to facilitate transmission to new plants. A recent review provides an overview of our current understanding of the molecular mechanisms in plant (+)RNA virus replication. Recent significant progress in this research area is based on development of powerful in vivo and in vitro methods, including replicase assays, reverse genetic approaches, intracellular localization studies, genome-wide screens for co-opted host factors and the use of plant or yeast model hosts.

Plasmodesmata as Active Conduits for Virus Cell-to-Cell Movement
from Lourdes Fernandez-Calvino, Christine Faulkner and Andy Maule writing in Recent Advances in Plant Virology
It has been known for many decades that viruses need to exploit plasmodesmata as channels of cytoplasmic connectivity through plant cell walls. However, we do not yet understand the molecular mechanisms involved in moving a single infectious entity from cell to cell, although it is clear that virus-encoded movement proteins play a central role. Major progress has been made in identifying movement proteins, their associations with subcellular structures/organelles, and their biochemical properties with respect to nucleic acid-binding and physical associations with host and other viral proteins. These studies reveal a specificity in functional evolution where viruses share some similarities in their movement strategies with near and far phylogenetic groups but show few examples of processes that might apply to all or many individual viruses. Plasmodesmata also provide channels for cellular communication essential for plant growth, development and defense. As such, there is increasing attention aimed at resolving their constituent components necessary for structure and function. With the limited success of genetic screens, proteomic analysis of biochemically-enriched plasmodesmal fractions has also been pursued. Through the identification of plasmodesmal proteins we will have the opportunity to understand how movement proteins bring about the massive changes in the physical behaviour of plasmodesmata that result in the translocation of the macromolecular complexes responsible for virus infectivity.

Systemic Movement of Viruses Via the Plant Phloem
from Vicente Pallás, Ainhoa Genovés, M. Amelia Sánchez-Pina and José Antonio Navarro writing in Recent Advances in Plant Virology
The incorporation of non invasive techniques has allowed remarkable progress in our understanding of the vascular transport of plant viruses. Indeed, approximately seventy-five percent of reports about this topic have been published after the first use of the jellyfish green fluorescent protein (GFP) in plant virology. In the last two decades, a very detailed picture of the viral determinants involved in phloem transport of plant viruses has been obtained. However, we realize that most virus-host interactions are pathosystem-specific and, consequently, the identification of common host factors involved in phloem transport of plant viruses is the exception rather than the rule. In addition, we are still far from obtaining a clear picture of how environmental factors influence the vascular invasion of plants by these pathogens. A recent publication reviews the progress made in understanding the viral determinants involved in vascular transport of viruses and the pathways followed by viruses during systemic movement, and focuses on host and environmental conditions that influence the final distribution of viruses in the plant.

Functions of Virus and Host Factors During Vector-mediated Transmission
from Stéphane Blanc and Martin Drucker writing in Recent Advances in Plant Virology
Most plant viruses are transmitted by living vectors that transport viruses to a new host plant. One discriminates between circulative transmission, where viruses must pass through the vector interior and are usually inoculated with the saliva on a healthy plant, and non-circulative transmission, where viruses do not need to pass through the vector interior but are directly inoculated from the mouth parts into a new host. Especially transmission of non-circulative viruses has been regarded as a simple process where a vector more or less accidentally transports the virus. However, it becomes more and more evident that this scenario is unlikely, because transmission constitutes a dramatic bottleneck of the virus life cycle, where only very few viral genomes pass to a new host, and where a given virus must do everything to ensure successful transmission. Viruses, also in non-circulative transmission, deliberately manipulate their hosts and vectors in often very unexpected ways to optimise their transmission.

NB-LRR Immune Receptors in Plant Virus Defense
from Patrick Cournoyer and Savithramma P. Dinesh-Kumar writing in Recent Advances in Plant Virology
Resistance genes protect plants from infection by viruses and many other classes of pathogens. The dominant, anti-viral R genes that have been cloned thus far encode NB-LRR immune receptors that detect a single viral protein and trigger defense. Many different types of viral proteins are known to elicit defense by corresponding NB-LRRs. Defense often results in a type of localized programmed cell death at the site of attempted pathogen infection known as the hypersensitive response (HR-PCD), but some NB-LRRs confer resistance to viruses without HR-PCD. The activation of NB-LRRs triggers manifold signaling events including reactive oxygen species (ROS) production, nitric oxide (NO) production, calcium (Ca2+) influx, activation of mitogen activated protein kinases (MAPKs), and production of the plant hormones salicylic acid (SA), jasmonic acid (JA), and ethylene. After a successful NB-LRR-mediated defense event, the plant exhibits heightened resistance to future pathogen challenge in a state called systemic acquired resistance.

Plant Resistance to Viruses Mediated by Translation Initiation Factors
from Olivier Le Gall, Miguel A. Aranda and Carole Caranta writing in Recent Advances in Plant Virology
Host resistance to viruses can show dominant or recessive inheritance. Remarkably, recessive resistance genes are much more common for viruses than for other plant pathogens. Recessive resistances to viruses are especially well documented within the dicotyledons, and have been described for various viruses that belong to very different viral genera, although clearly they predominate among viruses belonging to the genus Potyvirus. The elucidation of the molecular nature of this particular class of resistance genes is recent, but has so far only revealed a group of proteins linked to the translation machinery, chiefly the eukaryotic translation initiation factors (eIF) 4E and 4G. There are specific features and mechanisms of eIF4E- and 4G-mediated resistances to potyviruses and viruses belonging to other genera, such as carmoviruses.

Advanced Breeding for Virus Resistance in Plants
from Alain Palloix and Frank Ordon writing in Recent Advances in Plant Virology
Breeding for virus resistance was successful in the past years using conventional breeding methods since many virus resistant cultivars have been delivered for a wide range of crops. Genome mapping provided molecular markers for many resistance loci (i.e., major genes or Quantitative Trait Loci) that were introgressed into cultivars e.g., through backcross breeding schemes. Molecular mapping also delivered much information on the genomic architecture of polygenic and quantitative resistances. However, marker assisted selection for such complex traits is difficult so that the combination of quantitative resistance factors from multiallelic origins commonly relies on sophisticated phenotyping procedures. The cloning of resistance genes and the rapid development of high throughput molecular technologies increased the access to functional markers and multiallelic markers, promoting the applicability of marker assisted selection for complex traits at the whole genome scale in the near future. In parallel, the advances in the identification of molecular determinants of plant/virus interactions and in genetics and evolution of virus populations provide new selection criteria for breeders to choose the most durable resistance genes and gene combinations, so that breeding for durable virus resistance becomes an accessible quest.

Sustainable Management of Plant Resistance to Viruses
from Benoit Moury, Alberto Fereres, Fernando Garcia-Arenal and Herve Lecoq writing in Recent Advances in Plant Virology
Although viruses are among the parasites which induce the most severe damages on cultivated plants, few control methods have been developed against them. Notably, no curative methods can be applied against virus diseases in crops. In view of this major economic problem, the development of resistant cultivars has become a critical factor of competitiveness for breeders. However, plant - virus interactions are highly dynamic and the selective pressure exerted by plant resistance frequently favours the emergence of adapted virus populations. Given the scarcity of resistance genes, there is consequently an urgent need to increase the sustainability of these genetic resources. A recent publication reviews the biological mechanisms which allow the emergence of virus populations adapted to plant resistances and how we can use this knowledge to explain the relative durability of different resistance genes, to built predictors of resistance durability and to combine the use of resistances with other control methods to increase their sustainability.

Integrated Control Measures Against Viruses and Their Vectors
from Alberto Fereres and Aranzazu Moreno writing in Recent Advances in Plant Virology
Viruses and their vectors produce severe damage to crops worldwide. Of importance are the strategies and tactics used to manage vectors of plant viruses, with special attention to insects, by far the most important type of vector. The philosophy and principles of Integrated Pest Management (IPM) developed long ago can still provide an effective and sustainable way to manage insect vectors of virus diseases of plants. Preventive strategies such as the development of models that forecast virus disease outbreaks together with host plant resistance, cultural and physical tactics are the most effective ways to control nonpersistently-transmitted viruses. A reduction in vector numbers using conventional systemic insecticides or innundative biological control agents can also provide effective control of persistently-transmitted viruses. Recent advances on understanding of the mode of transmission of plant viruses are also a very promising way to develop molecules to block putative virus binding sites within the vector and to avoid virus retention and transmission. Also, the characterization of aphid's salivary components that is underway may facilitate the development of new tools to interfere with the process of transmission of plant viruses.

Population Dynamics and Genetics of Plant Infection by Viruses
from Fernando Garcia-Arenal and Aurora Fraile writing in Recent Advances in Plant Virology
During the last thirty years, progress in understanding the mechanistic aspects of virus-plant interactions has been remarkable, notably in aspects such as genome replication, movement within the infected host or pathogenesis and resistance. Progress in understanding the population dynamics and genetics of plant infection by viruses has not been as great. However, understanding the kinetics of plant colonisation and the genetic structure of the within-host virus population is necessary for addressing many issues of plant-virus interaction and of virus evolution. The quantitative aspects of plant infection and colonisation by viruses were mostly addressed during the early period of plant virology, when many detailed studies were published that often incorporated mathematical modelling. These issues have not been thoroughly re-examined using molecular techniques. Recent work has focussed on the description of the genetic structure of the virus population at the organ and the plant level. Data suggest that in spite of huge fecundity, the effective numbers of the within-host virus population may be small due to severe population bottlenecks at each stage of plant infection and colonisation, which results in a spatially structured population.

Evolutionary Constraints on Emergence of Plant RNA Viruses
from Santiago F. Elena writing in Recent Advances in Plant Virology
Over the recent years, agricultural activity in many regions has been compromised by a succession of devastating epidemics caused by new viruses that switched host species, or by new variants of classic viruses that acquired new virulence factors or changed their epidemiological patterns. Although viral emergence has been classically associated with ecological change or with agronomical practices that brought in contact reservoirs and crop species, it has become obvious that the picture is much more complex, and results from an evolutionary process in which the main players are the changes in ecological factors, the tremendous genetic plasticity of viruses, the several host factors required for virus replication, and a strong stochastic component. A recent review puts the emergence of RNA viruses into the framework of evolutionary genetics and reviews the basic notions necessary to understand emergence, stressing that viral emergence begins with a stochastic process that involves the transmission of a pre-existing viral strain with the right genetic background into a new host species, followed by adaptation to the new host during the early stages of infection.

Emergence of Begomovirus Diseases
from Enrique Moriones, Jesus Navas-Castillo and Juan-Antonio Díaz-Pendón writing in Recent Advances in Plant Virology
Begomoviruses (genus Begomovirus, family Geminiviridae) rank among the top of the most important plant viruses causing disease of severe consequences in economically and socially relevant crops. From the early 1990s, a rapid emergence and geographic expansion of begomoviruses has occurred worldwide. As a result, these viruses have become the most destructive group of plant viruses in tropical and subtropical regions of the world. Their emergence is associated with the emergence of populations of the insect vector, the whitefly Bemisia tabaci, probably due to increased plant trading between distantly separated geographical regions and changes in agricultural practices. Human activity seems to have been a major factor promoting emergence of begomoviruses. Other factors also drive emergence.

Genomic Approaches to Discovery of Viral Species Diversity of Non-cultivated Plants
from Ulrich Melcher and Veenita Grover writing in Recent Advances in Plant Virology
Outbreaks of newly emerging and re-emerging animal and plant viruses pose a constant threat to public health and food security and emphasize the need to develop efficient methods for viral detection and identification. Ongoing studies for discovery of viral species in non-cultivated plants utilize genomic approaches for systematic unbiased searches for viruses related to known viruses. Genomic approaches use various combinations of methods for sampling the environment, enriching samples for content of viral genomes, amplifying nucleic acids, and detecting virus-related sequences among the amplified nucleic acids. These methods include particularly array hybridization to macroarrays and microarrays, and various megasequencing approaches. In all cases, relatives of known viruses are discovered. However, the identification of a novel plant virus completely unrelated to known ones remains a challenge. Despite a growing list of viruses infecting wild plants, virus infections in wild plant communities are often underestimated relative to cultivated systems, since viruses in wild plants are generally considered not to harm the host. Viruses may not be explicitly damaging wild plants, but their biodiversity and abundance suggest an important role of these viruses in ecosystems. These roles should not be under-rated just because they are under-researched.

Endogenous Viral Sequences in Plant Genomes
from Pierre-Yves Teycheney and Andrew D.W. Geering writing in Recent Advances in Plant Virology
Endogenous viral sequences from members of two virus families, the Caulimoviridae and Geminiviridae, have been discovered in several monocotyledonous and dicotyledonous plant species. For the most part, these sequences are replication-defective but those capable of causing infection have been discovered in tobacco (Nicotiana edwardsonii), petunia (Petunia hybrida) and banana and plantain (Musa spp.). Activation of endogenous caulimovirid sequences is one of the major impediments to international banana and plantain breeding efforts. Research on endogenous viral sequences in plants is still in its infancy, with little known about the contributions of these sequences to host and virus evolution, nor even a classification system adopted. On a practical note, problems still exist with differentially detecting viral genomic DNA in a host genetic background containing endogenous viral sequences, and a solution to the problem of activation of endogenous viral sequences in banana is still far away.

Virus Particles and the Uses of Such Particles in Bio- and Nanotechnology
from George P. Lomonossoff writing in Recent Advances in Plant Virology
The capsids of most plant viruses are simple and robust structures consisting of multiple copies of one or a few types of protein subunit arranged with either icosahedral or helical symmetry. The capsids can be produced in large quantities either by the infection of plants or by the expression of the subunit(s) in a variety of heterologous systems. In view of their relative simplicity and ease of production, plant virus particles or virus-like particles (VLPs) have attracted much interest over the past 20 years for applications in both bio- and nanotechnology. As result, plant virus particles have been subjected to both genetic and chemical modification, have been used to encapsulate foreign material and have, themselves, been incorporated into supramolecular structures.

Plant Viral Vectors for Protein Expression
from Yuri Y. Gleba and Anatoli Giritch writing in Recent Advances in Plant Virology
Plant-virus-driven transient expression of heterologous proteins is the basis of several mature manufacturing processes that are currently being used for the production of multiple proteins including vaccine antigens and antibodies. Viral vectors have also become useful tools for research. In recent years, advances have been made both in the development of first-generation vectors (those that employ the 'full virus' strategy) as well as second-generation vectors designed using the 'deconstructed virus' approach. This second strategy relies on Agrobacterium as a vector to deliver DNA copies of one or more viral RNA replicons. Among the most often used viral backbones are those of Tobacco mosaic virus, Potato virus X, and Cowpea mosaic virus. Prototypes of industrial processes that provide for high-yield, rapid scale-up, and fast manufacturing have been recently developed using viral vectors, with several manufacturing facilities compliant with good manufacturing practices (GMP) in place, and a number of pharmaceutical proteins currently in pre-clinical and clinical trials.

Further reading