Emergence of Plant RNA Viruses
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.
Further reading: Recent Advances in Plant Virology | Virology Publications
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.
Further reading: Recent Advances in Plant Virology | Virology Publications
Viral Suppressors of RNA Silencing
Mechanism of Action of Viral Suppressors of RNA Silencing
from József Burgyán writing in Recent Advances in Plant Virology
RNA silencing is an evolutionarily conserved sequence-specific gene-inactivation system that also functions as an antiviral mechanism in higher plants and insects. To overcome this defence system, viruses encode suppressors of RNA silencing, which can counteract the host silencing-based antiviral process. More than 50 individual viral suppressors have been identified from almost all plant virus genera, underlining their crucial role in successful virus infection. Viral suppressors are considered to be of recent evolution, and they are surprisingly diverse within and across kingdoms, exhibiting no obvious sequence similarity. Virus-encoded silencing suppressors can target several key components in the silencing machinery, such as silencing-related RNA structures and essential effector proteins and complexes. There has been much recent progress in our understanding of the mechanism and function of viral suppressors of antiviral RNA silencing in plants.
Further reading: Recent Advances in Plant Virology | Virology Publications | RNA and the Regulation of Gene Expression
from József Burgyán writing in Recent Advances in Plant Virology
RNA silencing is an evolutionarily conserved sequence-specific gene-inactivation system that also functions as an antiviral mechanism in higher plants and insects. To overcome this defence system, viruses encode suppressors of RNA silencing, which can counteract the host silencing-based antiviral process. More than 50 individual viral suppressors have been identified from almost all plant virus genera, underlining their crucial role in successful virus infection. Viral suppressors are considered to be of recent evolution, and they are surprisingly diverse within and across kingdoms, exhibiting no obvious sequence similarity. Virus-encoded silencing suppressors can target several key components in the silencing machinery, such as silencing-related RNA structures and essential effector proteins and complexes. There has been much recent progress in our understanding of the mechanism and function of viral suppressors of antiviral RNA silencing in plants.
Further reading: Recent Advances in Plant Virology | Virology Publications | RNA and the Regulation of Gene Expression
miRNAs in Mammalian Antiviral Immune Responses
Virus-encoded Suppressors of RNA Silencing and the Role of Cellular miRNAs in Mammalian Antiviral Immune Responses
from Joost Haasnoot and Ben Berkhout writing in RNA Interference and Viruses
Small RNA-directed silencing mechanisms play important roles in the regulation of eukaryotic gene expression. In plants, insects, nematodes and fungi RNA silencing mechanisms are also involved in innate antiviral defence responses. To counter antiviral RNA silencing, viruses from plants, insects and fungi encode RNA silencing suppressors (RSSs). Recent studies suggest that RNA silencing in mammals, or RNA interference (RNAi), is also involved in antiviral responses. In particular, there is increasing evidence that cellular regulatory microRNAs (miRNAs) have a function in restricting virus replication in mammalian cells. Similar to plant and insect viruses, several mammalian viruses encode RSS factors that inhibit the RNAi mechanism. Several of these suppressors are multifunctional proteins that were previously shown to block innate antiviral immune responses involving the interferon (IFN) pathway.
Further reading: Recent Advances in Plant Virology | RNA Interference and Viruses | RNA and the Regulation of Gene Expression
from Joost Haasnoot and Ben Berkhout writing in RNA Interference and Viruses
Small RNA-directed silencing mechanisms play important roles in the regulation of eukaryotic gene expression. In plants, insects, nematodes and fungi RNA silencing mechanisms are also involved in innate antiviral defence responses. To counter antiviral RNA silencing, viruses from plants, insects and fungi encode RNA silencing suppressors (RSSs). Recent studies suggest that RNA silencing in mammals, or RNA interference (RNAi), is also involved in antiviral responses. In particular, there is increasing evidence that cellular regulatory microRNAs (miRNAs) have a function in restricting virus replication in mammalian cells. Similar to plant and insect viruses, several mammalian viruses encode RSS factors that inhibit the RNAi mechanism. Several of these suppressors are multifunctional proteins that were previously shown to block innate antiviral immune responses involving the interferon (IFN) pathway.
Further reading: Recent Advances in Plant Virology | RNA Interference and Viruses | RNA and the Regulation of Gene Expression
RNA Silencing in Plants and Viral Suppressors
RNA Silencing in Plants and the Role of Viral Suppressors
from Ana Giner, Juan Jose Lopez-Moya and Lorant Lakatos writing in RNA Interference and Viruses
The term RNA silencing refers to several pathways present in eukaryotic organisms that lead to the sequence specific elimination or functional blocking of RNAs with homology to double stranded RNAs (dsRNAs) that have previously triggered the mechanism. Besides playing important roles in developmental control, RNA silencing forms part of the defence against viruses in plants, acting as a potent antiviral mechanism. To escape from the RNA silencing-based defence, most plant viruses make use of different strategies, the most common relying in the action of viral proteins with the capacity to suppress RNA silencing. The characterization of these viral suppressors is providing useful insights to understand how RNA silencing works, revealing components and steps in the silencing pathways.
Further reading: Recent Advances in Plant Virology | RNA Interference and Viruses | RNA and the Regulation of Gene Expression
from Ana Giner, Juan Jose Lopez-Moya and Lorant Lakatos writing in RNA Interference and Viruses
The term RNA silencing refers to several pathways present in eukaryotic organisms that lead to the sequence specific elimination or functional blocking of RNAs with homology to double stranded RNAs (dsRNAs) that have previously triggered the mechanism. Besides playing important roles in developmental control, RNA silencing forms part of the defence against viruses in plants, acting as a potent antiviral mechanism. To escape from the RNA silencing-based defence, most plant viruses make use of different strategies, the most common relying in the action of viral proteins with the capacity to suppress RNA silencing. The characterization of these viral suppressors is providing useful insights to understand how RNA silencing works, revealing components and steps in the silencing pathways.
Further reading: Recent Advances in Plant Virology | RNA Interference and Viruses | RNA and the Regulation of Gene Expression
RNA Silencing and the Interplay Between Plants and Viruses
RNA Silencing and the Interplay Between Plants and Viruses
from Lourdes Fernández-Calvino, Livia Donaire and César Llave writing in Recent Advances in Plant Virology
In eukaryotes, RNA silencing controls gene expression to regulate development, genome stability and stress-induced responses. In plants, this process is also recognized as a major immune system targeted against plant viruses. Plant viruses stimulate RNA silencing responses though formation of viral RNA with double-stranded features that are subsequently processed into functional small RNAs (sRNAs). Recent studies highlight the complexity of the viral sRNA populations and their potential to associate with multiple silencing effector complexes. This fact has profound implications in the cross-talk interactions between plants and viruses since both virus genomes and host genes are putative targets of viral sRNAs. The concept of RNA silencing is an elegant natural antiviral mechanism in plants. Viral sRNA-mediated regulation of gene expression is important in the frame of compatible interactions between plants and viruses.
Further reading: Recent Advances in Plant Virology | Virology Publications | RNA and the Regulation of Gene Expression
from Lourdes Fernández-Calvino, Livia Donaire and César Llave writing in Recent Advances in Plant Virology
In eukaryotes, RNA silencing controls gene expression to regulate development, genome stability and stress-induced responses. In plants, this process is also recognized as a major immune system targeted against plant viruses. Plant viruses stimulate RNA silencing responses though formation of viral RNA with double-stranded features that are subsequently processed into functional small RNAs (sRNAs). Recent studies highlight the complexity of the viral sRNA populations and their potential to associate with multiple silencing effector complexes. This fact has profound implications in the cross-talk interactions between plants and viruses since both virus genomes and host genes are putative targets of viral sRNAs. The concept of RNA silencing is an elegant natural antiviral mechanism in plants. Viral sRNA-mediated regulation of gene expression is important in the frame of compatible interactions between plants and viruses.
Further reading: Recent Advances in Plant Virology | Virology Publications | RNA and the Regulation of Gene Expression
Plant RNA Viruses
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 host¹s 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.
Further reading: Recent Advances in Plant Virology | Virology Publications | RNA and the Regulation of Gene Expression
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 host¹s 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.
Further reading: Recent Advances in Plant Virology | Virology Publications | RNA and the Regulation of Gene Expression
Translation of Viral RNAs
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.
Further reading: Recent Advances in Plant Virology | Virology Publications
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.
Further reading: Recent Advances in Plant Virology | Virology Publications
Small RNAs of Salmonella
The small RNAs of Salmonella
from Sridhar Javayel, Kai Papenfort and Jörg Vogel writing in Salmonella: From Genome to Function
To date, close to one hundred distinct small noncoding RNAs (sRNAs) have been identified in Salmonella by a variety of biocomputational or wet-lab approaches including RNA sequencing. The function of more than twenty of these sRNAs is known from studies in Salmonella itself or can be inferred from conserved homologs in E. coli Many of these sRNAs act in conjunction with the RNA-chaperone Hfq to post-transcriptionally repress or activate trans-encoded target genes, but cis-antisense RNAs and regulators of protein activity are also abundantly present. In addition to a large number of sRNAs conserved in other enteric bacteria, Salmonella also expresses a set of sRNAs specific to this genus. Interestingly, such regulators have been shown to control the expression of conserved genes encoded on the "core" Salmonella genome. Conversely, conserved sRNA can act as regulators of recently acquired Salmonella-specific genes, indicating significant cross-talk of conserved and horizontally acquired elements at the RNA level. A recent review covers strategies for the identification of sRNAs as well as their characterized functional roles in Salmonella.
Further reading: Salmonella: From Genome to Function | RNA and the Regulation of Gene Expression
from Sridhar Javayel, Kai Papenfort and Jörg Vogel writing in Salmonella: From Genome to Function
To date, close to one hundred distinct small noncoding RNAs (sRNAs) have been identified in Salmonella by a variety of biocomputational or wet-lab approaches including RNA sequencing. The function of more than twenty of these sRNAs is known from studies in Salmonella itself or can be inferred from conserved homologs in E. coli Many of these sRNAs act in conjunction with the RNA-chaperone Hfq to post-transcriptionally repress or activate trans-encoded target genes, but cis-antisense RNAs and regulators of protein activity are also abundantly present. In addition to a large number of sRNAs conserved in other enteric bacteria, Salmonella also expresses a set of sRNAs specific to this genus. Interestingly, such regulators have been shown to control the expression of conserved genes encoded on the "core" Salmonella genome. Conversely, conserved sRNA can act as regulators of recently acquired Salmonella-specific genes, indicating significant cross-talk of conserved and horizontally acquired elements at the RNA level. A recent review covers strategies for the identification of sRNAs as well as their characterized functional roles in Salmonella.
Further reading: Salmonella: From Genome to Function | RNA and the Regulation of Gene Expression