MicrobiologyBytes

I recently wrote about the top 10 plant viruses in molecular plant pathology. Well Ed didn’t like that list, so he’s published his own:

1. Tobacco mosaic virus (TMV)
2. Tomato spotted wilt virus (TSWV)
3. Tomato yellow leaf curl virus (TYLCV)
4. Cucumber mosaic virus (CMV)
5. Potato virus Y (PVY)
6. Cauliflower mosaic virus (CaMV)
7. African cassava mosaic virus (ACMV)
8. Plum pox virus (PPV)
9. Brome mosaic virus (BMV)
10. Potato virus X (PVX)

“I see only ONE virus in the major list – African cassava mosaic begomovirus (ACMV) – that infects and causes severe losses in one of the four major food crops grown on this planet: all the rest, excepting viruses infecting the also-ran potato, are pathogens of fruits, vegetables or horticulturally-important plants. Or hardly pathogenic at all, as in the case of BMV – and before anyone argues, I probably have the best collection of African (and other) isolates of the virus in the world, and a lot of experience of it in the field.”

I have a feeling this could go on for some time :-)

Many scientists, if not all, feel that their particular plant virus should appear in any list of the most important plant viruses. However, to our knowledge, no such list exists. The aim of this review was to survey all plant virologists with an association with Molecular Plant Pathology and ask them to nominate which plant viruses they would place in a ‘Top 10′ based on scientific/economic importance. The survey generated more than 250 votes from the international community, and allowed the generation of a Top 10 plant virus list including, in rank order:

• Tobacco mosaic virus
• Tomato spotted wilt virus
• Tomato yellow leaf curl virus
• Cucumber mosaic virus
• Potato virus Y
• Cauliflower mosaic virus
• African cassava mosaic virus
• Plum pox virus
• Brome mosaic virus
• Potato virus X

This review article presents a short review on each virus of the Top 10 list and its importance, with the intent of initiating discussion and debate amongst the plant virology community, as well as laying down a benchmark, as it will be interesting to see in future years how perceptions change and which viruses enter and leave the Top 10.

Top 10 plant viruses in molecular plant pathology. (2011) Mol Plant Pathol. 12(9): 938-954. doi: 10.1111/j.1364-3703.2011.00752.x

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Viruses infecting higher plants are typically small RNA viruses that encode only a few genes. Although small viruses have recently been discovered that infect algae, many viruses infecting eukaryotic algae are huge dsDNA viruses with genomes ranging from 160 to 560 kb with up to 600 protein-encoding genes and are the subject of this review. These large viruses (family Phycodnaviridae), are found in aqueous environments throughout the world and play dynamic, albeit largely undocumented, roles in regulating algal communities such as the termination of massive algal blooms commonly referred to as red and brown tides.

This review focuses on one genus in the Phycodnaviridae, the chloroviruses, which are large, icosahedral, plaque-forming, dsDNA-containing viruses that replicate in certain unicellular, chlorella-like green algae. Their structure, their initial stages of infection, and many of their genes resemble bacteriophages more than viruses that infect eukaryotes – i.e. they are not your everyday plant virus.

Chloroviruses: not your everyday plant virus. Trends Plant Sci. Nov 17 2011
Viruses infecting higher plants are among the smallest viruses known and typically have four to ten protein-encoding genes. By contrast, many viruses that infect algae (classified in the virus family Phycodnaviridae) are among the largest viruses found to date and have up to 600 protein-encoding genes. This brief review focuses on one group of plaque-forming phycodnaviruses that infect unicellular chlorella-like green algae. The prototype chlorovirus PBCV-1 has more than 400 protein-encoding genes and 11 tRNA genes. About 40% of the PBCV-1 encoded proteins resemble proteins of known function including many that are completely unexpected for a virus. In many respects, chlorovirus infection resembles bacterial infection by tailed bacteriophages.

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Eucaryotic organisms depend on networks of gene regulatory pathways. Small RNAs (sRNAs), are key components of these networks. sRNAs are short (21–24 nt in length), endogenously expressed, and are processed from double stranded (ds)RNAs or dsRNA-like precursors. In both plants and animals, sRNAs exert their functions upon incorporation into ribonucleoprotein silencing complexes and through their base-paring capacity. They are implicated in a variety of processes, including post-transcriptional regulation of mRNA, mRNA stability and availability for translation, establishment of heterochromatin and silencing of transposons. Different classes of sRNAs differ in the proteins required in their biogenesis, the constitution of ribonucleoprotein complexes that mediate their regulatory functions, their type of gene regulation, and the biological functions in which they are implicated. Plants display a remarkable diversity of sRNA types and sRNA pathways, likely needed for managing multiple environmental stimuli, including biotic and abiotic stresses. Several lines of evidence suggest that plant sRNAs play critical roles in plant–pathogen interactions. Indeed, upon infection, most plant pathogens can interfere with the expression of endogenous sRNAs, thus altering the expression of specific host factors implicated in the suppression or in the activation of plant defences. Evidence for these phenomena has been reported for bacterial and fungal pathogens.

Viruses are obligate infectious agents, whose life cycle (expression of viral proteins, viral genome replication and virion assembly) is integrated with host cell functions. Plant viruses can both modify the profiles of endogenous sRNAs (in common with bacteria and fungi) and induce the production of additional sRNAs derived from their own genomes (viral sRNAs; vsiRNAs). The latter gives a clear indication of the activation of RNA silencing-based responses of the plant. In some cases, this results in reduction of the titre of the invading virus and, in recovery of upper, non-inoculated leaves. To counteract RNA silencing, many plant viruses have evolved proteins (viral suppressors of RNA silencing: VSR) that target various components of the plant silencing machinery. Viruses can induce specific symptoms resembling developmental anomalies and affecting organs and tissues such as leaves, flowers and fruits. These anomalies are often reconcilable with virus-induced alterations of RNA silencing-based endogenous pathways, due to: i) the direct activity of VSRs on endogenous sRNAs or on silencing related effectors; ii) the abundance of vsiRNAs in competition with endogenous sRNAs; iii) the action of specific vsiRNAs entering into RNA silencing complexes and targeting specific host genes.

This review provides an overview of the major cellular RNA silencing pathways in plants with particular reference to those involved in antiviral functions and highlights examples of the complex interactions between viral molecular processes and host RNA processes.

Viral induction and suppression of RNA silencing in plants. Biochim Biophys Acta. Apr 30 2011
RNA silencing in plants and insects can function as a defence mechanism against invading viruses. RNA silencing-based antiviral defence entails the production of virus-derived small interfering RNAs which guide specific antiviral effector complexes to inactivate viral genomes. As a response to this defence system, viruses have evolved viral suppressors of RNA silencing (VSRs) to overcome the host defence. VSRs can act on various steps of the different silencing pathways. Viral infection can have a profound impact on the host endogenous RNA silencing regulatory pathways; alterations of endogenous short RNA expression profile and gene expression are often associated with viral infections and their symptoms. Here we discuss our current understanding of the main steps of RNA-silencing responses to viral invasion in plants and the effects of VSRs on endogenous pathways. This article is part of a Special Issue entitled: MicroRNAs in viral gene regulation.

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Plant viruses are often accompanied by small parasitic RNAs termed satellite RNAs. Satellite RNAs range in size from ~220 to 1400 nucleotides (nt) in length and depend on their associated viruses (known as the helper virus) for replication, encapsidation, movement and transmission, but share little or no sequence homology to the helper virus itself. Most satellite RNAs do not encode functional proteins, yet can induce disease symptoms which range from chlorosis and necrosis, to total death of the infected plant. How such non-protein-coding RNA pathogens induce disease symptoms has been a longstanding question.

Early studies showed that the pathogenicity of a satellite RNA is determined at the nucleotide level, with one to several nucleotide changes dramatically altering both the virulence and host specificity of disease induction. Subsequent studies demonstrated that satellite RNA replication is associated with the accumulation of high levels of satellite RNA-derived small interfering RNAs (siRNA). These findings led to the suggestion that pathogenic satellite-derived siRNAs might have sequence complementarity to a physiologically important host gene, and that the observed disease symptoms are in fact due to satellite siRNA-directed silencing of the targeted host gene. However, to date, no such host gene has been identified, leaving the satellite RNA-induced disease mechanism unsolved.

This paper explores the sRNA-mediated disease mechanism using the Y-satellite of Cucumber mosaic virus (CMV Y-Sat). The CMV Y-Sat consists of a 369-nt single-stranded RNA genome and induces distinct yellowing symptoms in a number of Nicotiana species including N. tabacum (tobacco). Y-Sat-induced yellowing symptoms result from Y-Sat siRNA-directed silencing of the host chlorophyll biosynthetic gene, CHLI, and Y-Sat-induced symptoms can be prevented by transforming tobacco with a silencing-resistant version of CHLI. The observed species specificity of Y-Sat-induced disease symptoms is due to natural sequence variation within the targeted region of the CHLI transcript.

Viral Small Interfering RNAs Target Host Genes to Mediate Disease Symptoms in Plants. (2011) PLoS Pathog 7(5): e1002022. doi:10.1371/journal.ppat.1002022
The Cucumber mosaic virus (CMV) Y-satellite RNA (Y-Sat) has a small non-protein-coding RNA genome that induces yellowing symptoms in infected Nicotiana tabacum (tobacco). How this RNA pathogen induces such symptoms has been a longstanding question. We show that the yellowing symptoms are a result of small interfering RNA (siRNA)-directed RNA silencing of the chlorophyll biosynthetic gene, CHLI. The CHLI mRNA contains a 22-nucleotide (nt) complementary sequence to the Y-Sat genome, and in Y-Sat-infected plants, CHLI expression is dramatically down-regulated. Small RNA sequencing and 5′ RACE analyses confirmed that this 22-nt sequence was targeted for mRNA cleavage by Y-Sat-derived siRNAs. Transformation of tobacco with a RNA interference (RNAi) vector targeting CHLI induced Y-Sat-like symptoms. In addition, the symptoms of Y-Sat infection can be completely prevented by transforming tobacco with a silencing-resistant variant of the CHLI gene. These results suggest that siRNA-directed silencing of CHLI is solely responsible for the Y-Sat-induced symptoms. Furthermore, we demonstrate that two Nicotiana species, which do not develop yellowing symptoms upon Y-Sat infection, contain a single nucleotide polymorphism within the siRNA-targeted CHLI sequence. This suggests that the previously observed species specificity of Y-Sat-induced symptoms is due to natural sequence variation in the CHLI gene, preventing CHLI silencing in species with a mismatch to the Y-Sat siRNA. Taken together, these findings provide the first demonstration of small RNA-mediated viral disease symptom production and offer an explanation of the species specificity of the viral disease.

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Viroids are the smallest known infectious agents and induce disease in a wide variety of plant hosts, including many crop species. Ranging in size from ca. 250–400 nucleotides (nt) replication of their single-stranded, circular, non-coding RNA genomes is entirely dependent on transcriptional and processing machinery supplied by the host. Their small size and unique molecular structure makes these molecules an attractive system with which to analyze many different aspects of host–pathogen interaction.

Although replication occurs in different subcellular compartments, members of both families of viroids induce RNA silencing and the accumulation of viroid-specific small RNAs following infection. Post-transcriptional gene silencing (RNA silencing) provides a multi-layer defense system which protects plants from invasion by exogenous RNA replicons such as viruses and viroids. Silencing is triggered by conversion of double-stranded or hairpin RNAs to small RNAs whose sizes ranging between 18 and 26 nucleotides. Infected plants contain high levels of viroid-specific small RNAs, but the circular genomic RNAs themselves appear relatively resistant to RNA silencing – raising the possibility that viroid replication may also be resistant. The mechanism underlying this resistance/tolerance is not yet understood, but certain transgenic tomato lines expressing high levels of hairpin RNA-derived small viroid RNAs are resistant to infection. This paper looks at the accumulation pattern and size distribution of viroid-specific small RNAs in infected plants and identifies several potential targets for RNA silencing mediated by small RNAs.

Accumulation of Potato spindle tuber viroid-specific small RNAs is accompanied by specific changes in gene expression in two tomato cultivars. Virology. 24 Feb 2011
To better understand the biogenesis of viroid-specific small RNAs and their possible role in disease induction, we have examined the accumulation of these small RNAs in potato spindle tuber viroid (PSTVd)-infected tomato plants. Large-scale sequence analysis of viroid-specific small RNAs revealed active production from the upper portion of the pathogenicity and central domains, two regions previously thought to be underrepresented. Profiles of small RNA populations derived from PSTVd antigenomic RNA were more variable, with differences between infected Rutgers (severe symptoms) and Moneymaker (mild symptoms) plants pointing to possible cultivar-specific differences in small RNA synthesis and/or stability. Using microarray analysis, we monitored the effects of PSTVd infection on the expression levels of >100 tomato genes containing potential binding sites for PSTVd small RNAs. Of 18 such genes down-regulated early in infection, two genes involved in gibberellin or jasmonic acid biosynthesis contain binding sites for PSTVd small RNAs in their respective ORFs.

Related:

• The Biology of Viroid-Host Interactions
• Resistance to Plant Viruses

The immune system of plants can be unstable in the face of rapidly evolving micro-organisms, and pathogens that can evade recognition can spread with alarming speed through a plant population. In this article in Microbiology Today, Gail Preston and Dawn Arnold ask, what is the reason for this inherent instability, and how can disease control be improved?

Plants, unlike animals, lack an adaptive immune system that allows them to recognize and defend against novel pathogenic micro-organisms. Instead they rely on a heritable, innate immune system in which plant receptors recognize the presence or activity of microbial molecules known as elicitors. Plants exposed to infection can increase the effectiveness of their immune system by increasing the speed and strength of their defence mechanisms. However, pathogens that have the ability to evade recognition can spread rapidly through plant populations. The instability of receptor-dependent resistance in the face of rapid microbial evolution creates one of the most fundamental challenges in plant breeding. In this article we discuss why receptordependent resistance breaks down in the face of pathogen evolution and consider whether knowledge of pathogen evolution can provide insights to improve disease control.

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Related:

• Toxins for microbial attack and plant defence
• Bacteriophages for plant disease control

The filamentous plant viruses of the family Potyviridae include almost a quarter of the known plant viruses. The family includes the genera Potyvirus, Rymovirus, Tritimovirus, Bymovirus, Maclurovirus, Ipomovirus and Brambyvirus. Potyvirid particles are approximately 7500 Å long and 120 Å in diameter and have helical pitches of about 33 Å. Circular dichroism measurements and secondary structure predictions suggest that the coat proteins are about 50% α-helical, similar to the potexviruses, and that the N- and C-termini of the coat proteins are located near the surface of the virions. Little other structural information was available for members of this family until recently. This paper shows that the potyvirids exhibit significant variation in helical symmetry, like the potexviruses and unlike the tobamoviruses.

Architecture of the potyviruses. Virology. Jul 1 2010 doi: 10.1016/j.virol.2010.06.013
X-ray fiber diffraction data were obtained and helical pitch and symmetry were determined for seven members of the family Potyviridae, including representatives from the genera Potyvirus, Rymovirus, and Tritimovirus. The diffraction patterns are similar, as expected. There are, however, significant variations in the symmetries, as previously found among the flexible potexviruses, but not among the rigid tobamoviruses. Wheat streak mosaic virus, the only member of the genus Tritimovirus examined, displayed the largest deviations in diffraction data and helical parameters from the other viruses in the group.

Related:

• Blight ravages European potato crops, but there’s good news from Africa
• Resistance to Plant Viruses

Strategies in modern agriculture aim to enhance harvest yields per acreage and to reduce pre-harvest and post-harvest losses caused by detrimental abiotic and biotic causes. The potential of that reflects an estimate 20–40% reduction of agricultural production worldwide that is taken by pests and diseases. Modern pest management strategies in crop plants include classical and molecular marker-based resistance breeding, genetic engineering of plant immunity and the use of chemicals as pesticides or strengtheners of plant health. While breeding strategies are time-consuming and harbor the problem of ‘linkage drag’ (transfer of undesirable traits that need to be removed after introgression of the desired trait by back-crossing), genetic engineering holds the potential of being reasonably fast and predictable in its consequences because of the targeted introduction of individual, heterologous traits into elite crop lines.

Sequencing of entire plant genomes, systematic plant transcriptome profiling and comprehensive genetic dissection of immune pathways in model plants (Arabidopsis thaliana, rice) has significantly enhanced our understanding of the mechanisms underlying microbial infection and plant immunity. The plant immune system consists of two evolutionarily linked branches. Recognition of invariant microbial surface patterns (pathogen or microbe-associated patterns; PAMP/MAMP) through plant pattern recognition receptors is referred to as PAMP-triggered immunity (PTI) and is the basis for broad-spectrum resistance of plants against host non-adapted microbial pathogens (i.e. all genetic variants of a given microbial species are unable to grow on a given plant species).

Novel insight into plant immunity and disease may now be turned into new tools to engineer durable, broad-spectrum plant disease resistance. This review highlights recent scientific discoveries in plant immunity and discusses their potential for enhancing plant immunity in crop plants with particular emphasis on immunity to bacterial and fungal infection. Saving the world’s food supply constitutes one of the major challenges of the future. As a complement to classical and molecular breeding technologies, novel strategies for biotechnological improvement of plant immunity aim at enhancing host recognition capacities for potential pathogens, at boosting the executive arsenal of plant immunity, and at interfering with virulence strategies employed by microbial pathogens. In addition, chemical and biological priming provides means for triggering plant defenses in a non-transgenic manner. Major advances in our understanding of the molecular basis of plant immunity and of microbial infection strategies have opened new ways for engineering durable disease resistance in crop plants that are highlighted in this review.

Biotechnological concepts for improving plant innate immunity. Curr Opin Biotechnol. Feb 22 2010

Related:

• Toxins for microbial attack and plant defence
• Resistance to Plant Viruses
• Bacteriophages for plant disease control