Virus-encoded suppressor of posttranscriptional gene silencing targets a maintenance step in the silencing pathway

Straightforward and affordable agroinfiltration with RUBY accelerates RNA silencing research

Transient expression and induction of RNA silencing by agroinfiltration is a fundamental method in plant RNA biology. Here, we introduce a new reporter assay using RUBY, which encodes three key enzymes of the betalain biosynthesis pathway, as a polycistronic mRNA. The red pigmentation conferred by betalains allows visual confirmation of gene expression or silencing levels without tissue disruption, and the silencing levels can be quantitatively measured by absorbance in as little as a few minutes. Infiltration of RUBY in combination with p19, a well-known RNA silencing suppressor, induced a fivefold higher accumulation of betalains at 7 days post infiltration compared to infiltration of RUBY alone. We demonstrated that co-infiltration of RUBY with two RNA silencing inducers, targeting either CYP76AD1 or glycosyltransferase within the RUBY construct, effectively reduces RUBY mRNA and betalain levels, indicating successful RNA silencing. Therefore, compared to conventional reporter assays for RNA silencing, the RUBY-based assay provides a simple and rapid method for quantitative analysis without the need for specialized equipment, making it useful for a wide range of RNA silencing studies.

Membrane-associated NRPM proteins are novel suppressors of stomatal production in Arabidopsis

In Arabidopsis, stomatal development and patterning require tightly regulated cell division and cell-fate differentiation that are controlled by key transcription factors and signaling molecules. To identify new regulators of stomatal development, we assay the transcriptomes of plants bearing enriched stomatal lineage cells that undergo active division. A member of the novel regulators at the plasma membrane (NRPM) family annotated as hydroxyproline-rich glycoproteins was identified to highly express in stomatal lineage cells. Overexpressing each of the four NRPM genes suppressed stomata formation, while the loss-of-function nrpm triple mutants generated severely overproduced stomata and abnormal patterning, mirroring those of the erecta receptor family and MAPKKK yoda null mutants. Manipulation of the subcellular localization of NRPM1 surprisingly revealed its regulatory roles as a peripheral membrane protein instead of a predicted cell wall protein. Further functional characterization suggests that NRPMs function downstream of the EPF1/2 peptide ligands and upstream of the YODA MAPK pathway. Genetic and cell biological analyses reveal that NRPM may promote the localization and function of the ERECTA receptor proteins at the cell surface. Therefore, we identify NRPM as a new class of signaling molecules at the plasma membrane to regulate many aspects of plant growth and development.

Structural features of T-DNA that induce transcriptional gene silencing during agroinfiltration

Agrobacterium tumefaciens (Rhizobium radiobacter) is used for the transient expression of foreign genes by the agroinfiltration method, but the introduction of foreign genes often induces transcriptional and/or post-transcriptional gene silencing (TGS and/or PTGS). In this study, we characterized the structural features of T-DNA that induce TGS during agroinfiltration. When A. tumefaciens cells harboring an empty T-DNA plasmid containing the cauliflower mosaic virus (CaMV) 35S promoter were infiltrated into the leaves of Nicotiana benthamiana line 16c with a GFP gene over-expressed under the control of the same promoter, no small interfering RNAs (siRNAs) were derived from the GFP sequence. However, siRNAs derived from the CaMV 35S promoter were detected, indicating that TGS against the GFP gene was induced. When the GFP gene was inserted into the T-DNA plasmid, PTGS against the GFP gene was induced whereas TGS against the CaMV 35S promoter was suppressed. We also showed the importance of terminator sequences in T-DNA for gene silencing. Therefore, depending on the combination of promoter, terminator and coding sequences on T-DNA and the host nuclear genome, either or both TGS and/or PTGS could be induced by agroinfiltration. Furthermore, we showed the possible involvement of three siRNA-producing Dicers (DCL2, DCL3 and DCL4) in the induction of TGS by the co-agroinfiltration method. Especially, DCL2 was probably the most important among them in the initial step of TGS induction. These results are valuable for controlling gene expression by agroinfiltration.

Crinivirus Tomato Chlorosis Virus Compromises the Control of Tomato Yellow Leaf Curl Virus in Tomato Plants by the Ty-1 Gene

Tomato yellow leaf curl disease (TYLCD) causes severe damage to tomato crops in warm regions of the world, and is associated with infections of several whitefly (Bemisia tabaci)-transmitted single-stranded (ss)DNA begomoviruses (genus Begomovirus, family Geminiviridae). The most widespread begomovirus isolates associated with TYLCD are those of the type strain of the Tomato yellow leaf curl virus species, known as Israel (TYLCV-IL). The Ty-1 gene is widely used in commercial tomato cultivars to control TYLCV-IL damage, providing resistance to the virus by restricting viral accumulation and tolerance to TYLCD by inhibiting disease symptoms. However, several reports suggest that TYLCV-IL-like isolates are adapting to the Ty-1 gene and are causes of concern for possibly overcoming the provided control. This is the case with TYLCV-IL IS76-like recombinants that have a small genome fragment acquired by genetic exchange from an isolate of Tomato yellow leaf curl Sardinia virus, another begomovirus species associated with TYLCD. Here we show that TYLCV-IL IS76-like isolates partially break down the TYLCD-tolerance provided by the Ty-1 gene and that virulence differences might exist between isolates. Interestingly, we demonstrate that mixed infections with an isolate of the crinivirus (genus Crinivirus, family Closteroviridae) species Tomato chlorosis virus (ToCV), an ssRNA virus also transmitted by B. tabaci and emerging worldwide in tomato crops, boosts the breakdown of the TYLCD-tolerance provided by the Ty-1 gene either with TYLCV-IL IS76-like or canonical TYLCV-IL isolates. Moreover, we demonstrate the incorporation of the Ty-2 gene in Ty-1-commercial tomatoes to restrict (no virus or virus traces, no symptoms) systemic infections of recombinant TYLCV-IL IS76-like and canonical TYLCV-IL isolates, even in the presence of ToCV infections, which provides more robust and durable control of TYLCD.

Two mutually exclusive evolutionary scenarios for allexiviruses that overcome host RNA silencing and autophagy by regulating viral CRP expression

The genus Allexivirus currently includes eight virus species that infect allium plants. Previously, we showed that there are two distinct groups of allexiviruses (deletion [D]-type and insertion [I]-type) based on the presence or absence of a 10- to 20-base insert (IS) between the coat protein (CP) and cysteine rich protein (CRP) genes. In the present study of CRPs to analyze their functions, we postulated that evolution of allexiviruses may have been largely directed by CRPs and thus proposed two evolutionary scenarios for allexiviruses based mainly on the presence or absence of IS and determined by how the allexiviruses challenge host resistance mechanisms (RNA silencing and autophagy). We found that both CP and CRP are RNA silencing suppressors (RSS), that they can inhibit each other's RSS activity in the cytoplasm, and that CRP becomes a target of host autophagy in the cytoplasm but not CP. To mitigate CRP interference with CP, and to increase the CP's RSS activity, allexiviruses developed two strategies: confinement of D-type CRP in the nucleus and degradation of I-type CRP by autophagy in the cytoplasm. Here, we demonstrate that viruses of the same genus achieve two completely different evolutionary scenarios by controlling expression and subcellular localization of CRP.

Overexpression of a WRKY transcription factor McWRKY57-like from Mentha canadensis L. enhances drought tolerance in transgenic Arabidopsis

BACKGROUND

Drought has become a major environmental problem affecting crop production. Members of the WRKY family play important roles in plant development and stress responses. However, their roles in mint have been barely explored.

RESULTS

In this study, we isolated a drought-inducible gene McWRKY57-like from mint and investigated its function. The gene encodes a group IIc WRKY transcription factor, McWRKY57-like, which is a nuclear protein with a highly conserved WRKY domain and a C2H2 zinc-finger structure, and has transcription factor activity. Its expression levels were examined in different tissues of mint and under the treatment of mannitol, NaCl, abscisic acid, and methyl jasmonate. We found that McWRKY57-like overexpression in Arabidopsis significantly increased drought tolerance. Further studies showed that under drought stress, McWRKY57-like-overexpressing plants had higher chlorophyll, soluble sugar, soluble protein, and proline contents but lower water loss rate and malondialdehyde content than wild-type plants. Moreover, the activities of antioxidant enzymes catalase, superoxide dismutase, and peroxidase were enhanced in McWRKY57-like transgenic plants. Furthermore, qRT-PCR analysis revealed that the drought-related genes AtRD29A, AtRD29B, AtRD20, AtRAB18, AtCOR15A, AtCOR15B, AtKIN2, and AtDREB1A were upregulated in McWRKY57-like transgenic plants than in wild-type Arabidopsis under simulated drought conditions.

CONCLUSION

These data demonstrated that McWRKY57-like conferred drought tolerance in transgenic Arabidopsis by regulating plant growth, osmolyte accumulation and antioxidant enzyme activities, and the expression of stress-related genes. The study indicates that McWRKY57-like plays a positive role in drought response in plants.

Seed transmission of raspberry bushy dwarf virus is blocked in Nicotiana benthamiana plants by preventing virus entry into the embryo from the infected embryo sac and endosperm

Raspberry bushy dwarf virus (RBDV) is transmitted through seed in infected red raspberry plants after pollination with pollen grains from healthy red raspberry plants. Here, we show that RBDV is not transmitted through seeds in infected Nicotiana benthamiana (Nb) plants after pollination with virus-free Nb pollen grains. Chromogenic in situ hybridization revealed that the virus invades the shoot apical meristem and the ovule, including the embryo sac, of RBDV-infected Nb plants; however, in seeds that developed from infected embryo sacs after fertilization by virus-free sperm cells, RBDV was absent in the embryos and present in the endosperms. When we analyzed seed transmission of RBDV in Nb mutants with mutations in dicer-like enzyme 2 and 4 (NbDCL2&4) or RNA-dependent RNA polymerase 6 (NbRDR6), RBDV was not present in the offspring from seeds with embryos and endosperms that did not express NbDCL2&4 or NbRDR6. These results suggest that seed transmission of RBDV is prevented by evasion of infection by the embryo and that RNA silencing is not essential for preventing seed transmission of RBDV in Nb plants.

Silencing suppressor protein PRT of rice tungro bacilliform virus interacts with the plant RNA silencing-related protein SGS3

BACKGROUND

Rice tungro bacilliform virus (RTBV) is a double stranded DNA containing virus which causes the devastating tungro disease of rice in association with an RNA virus, rice tungro spherical virus. RNA silencing is an evolutionarily conserved antiviral defence pathway in plants as well as in several classes of higher organisms. Many viruses, in turn, encode proteins which are termed Viral Suppressor of RNA Silencing (VSR) because they downregulate or suppress RNA silencing.

RESULTS

Using an RNA silencing suppressor assay we show that RTBV protease (PRT) acts as a mild VSR. A truncated version of PRT gene abolished the silencing suppression activity. We also show in planta interaction of PRT with the SGS3 protein of Solanum tuberosum and Arabidopsis thaliana using bimolecular fluorescence complementation assay (BIFC). Transient expression of PRT in Nicotiana benthamiana caused an increased accumulation of the begomovirus Sri Lankan cassava mosaic virus (SLCMV) DNA-A, which indicated a virulence function imparted on an unrelated virus.

CONCLUSION

The finding supports the idea that PRT acts as suppressor of RNA silencing and this action may be mediated by its interaction with SGS3.

Grapevine red blotch virus C2 and V2 are suppressors of post-transcriptional gene silencing

Grapevine red blotch virus (GRBV) is the causative agent of grapevine red blotch disease (GRBD) which is one of the major threats faced by grapevine industry in the United States. Since its initial identification in 2011, the disease has rapidly spread in the major US grape-growing regions of the Pacific Northwest, causing major economic impacts. Geminiviruses, the largest family of plant viruses, can induce and be targeted by host post-transcriptional gene-silencing (PTGS) anti-viral mechanisms. As a counter-defense mechanism, viruses have evolved viral silencing suppressor proteins to combat PTGS mechanisms and establish a successful infection in host plants. Here we provide characterization of two ORFs of GRBV, C2 and V2 as viral silencing suppressors. In Nicotiana benthamiana line 16c GFP marker plants, synergism or additive effects of C2 and V2 suppressors was observed at the mRNA level when they are expressed together transiently. Additionally, we showed there is no evidence by yeast two-hybrid of self-interaction (dimerization) of C2 or V2 proteins, and no evidence of physical interaction between these two suppressors.

Development of transgenic okra (Abelmoschus esculentus L. Moench) lines having RNA mediated resistance to Yellow vein mosaic virus (Geminiviridae)

Begomovirus Yellow vein mosaic virus causes severe yield losses in okra and even the resistant lines developed through conventional breeding show susceptibility at various levels. This paper describes the development of YVMV resistant lines through RNAi strategy. A universal ihpRNA construct harbouring βC1 ORF from the β-satellite of the begomovirus was designed using pRNAi-LIC plasmid. Complementarity checks in sequence databases had shown no off-target effects by the target region and the success of siRNA in interference was proven using Custom Dicer-Substrate siRNA analysis. The βC1 ORF of the begomovirus was PCR amplified and sequenced using the primer combination designed. The pRNAi-LIC vector, a derivative of pCAMBIA2300 containing duplicated CaMV 35S promoter and Nos terminator from pYL44, was SmaI digested and the amplified sense and antisense strands of the βC1 region were cloned. E. coli transformed with the plasmid were screened for antibiotic resistance, and the plasmids confirmed for the sense and antisense regions through sequencing, were transferred to Agrobacterium tumefaciens strain GV3101. In planta transformation strategy was followed to transform a highly susceptible okra cv. Salkeerthi with ihpRNA-βC1 cassette. Transformation success, confirmed by the amplification of sense strand using the primers VLIC1 and VLIC5, was 11.42 %. Transcription of siRNA from the βC1 ORF in the transgenic lines was confirmed by its PCR amplification from the cDNA, using the stem loop primers designed (68 bp). When the transformed and healthy wild-type plants were co-grown with infected wild-type plants, inside an insect cage released with whiteflies and maintained within a containment facility, three of the four transgenic plants remained completely healthy throughout the crop span.

Strategies for Efficient RNAi-Based Gene Silencing of Viral Genes for Disease Resistance in Plants

RNA interference (RNAi) is an evolutionarily conserved gene silencing mechanism in eukaryotes including fungi, plants, and animals. In plants, gene silencing regulates gene expression, provides genome stability, and protect against invading viruses. During plant virus interaction, viral genome derived siRNAs (vsiRNA) are produced to mediate gene silencing of viral genes to prevent virus multiplication. After the discovery of RNAi phenomenon in eukaryotes, it is used as a powerful tool to engineer plant viral disease resistance against both RNA and DNA viruses. Despite several successful reports on employing RNA silencing methods to engineer plant for viral disease resistance, only a few of them have reached the commercial stage owing to lack of complete protection against the intended virus. Based on the knowledge accumulated over the years on genetic engineering for viral disease resistance, there is scope for effective viral disease control through careful design of RNAi gene construct. The selection of target viral gene(s) for developing the hairpin RNAi (hp-RNAi) construct is very critical for effective protection against the viral disease. Different approaches and bioinformatics tools which can be employed for effective target selection are discussed. The selection of suitable target regions for RNAi vector construction can help to achieve a high level of transgenic virus resistance.

Silencing of StRIK in potato suggests a role in periderm related to RNA processing and stress

BACKGROUND

The periderm is a protective barrier crucial for land plant survival, but little is known about genetic factors involved in its development and regulation. Using a transcriptomic approach in the cork oak (Q. suber) periderm, we previously identified an RS2-INTERACTING KH PROTEIN (RIK) homologue of unknown function containing a K homology (KH)-domain RNA-binding protein, as a regulatory candidate gene in the periderm.

RESULTS

To gain insight into the function of RIK in the periderm, potato (S. tuberosum) tuber periderm was used as a model: the full-length coding sequence of RIK, hereafter referred to as StRIK, was isolated, the transcript profile analyzed and gene silencing in potato performed to analyze the silencing effects on periderm anatomy and transcriptome. The StRIK transcript accumulated in all vegetative tissues studied, including periderm and other suberized tissues such as root and also in wounded tissues. Downregulation of StRIK in potato by RNA interference (StRIK-RNAi) did not show any obvious effects on tuber periderm anatomy but, unlike Wild type, transgenic plants flowered. Global transcript profiling of the StRIK-RNAi periderm did show altered expression of genes associated with RNA metabolism, stress and signaling, mirroring the biological processes found enriched within the in silico co-expression network of the Arabidopsis orthologue.

CONCLUSIONS

The ubiquitous expression of StRIK transcript, the flower associated phenotype and the differential expression of StRIK-RNAi periderm point out to a general regulatory role of StRIK in diverse plant developmental processes. The transcriptome analysis suggests that StRIK might play roles in RNA maturation and stress response in the periderm.

Rice MutLγ, the MLH1-MLH3 heterodimer, participates in the formation of type I crossovers and regulation of embryo sac fertility

The development of embryo sacs is crucial for seed production in plants, but the genetic basis regulating the meiotic crossover formation in the macrospore and microspore mother cells remains largely unclear. Here, we report the characterization of a spontaneous rice female sterile variation 1 mutant (fsv1) that showed severe embryo sacs abortion with low seed-setting rate. Through map-based cloning and functional analyses, we isolated the causal gene of fsv1, OsMLH3 encoding a MutL-homolog 3 protein, an ortholog of HvMLH3 in barley and AtMLH3 in Arabidopsis. OsMLH3 and OsMLH1 (MutL-homolog 1) interact to form a heterodimer (MutLγ) to promote crossover formation in the macrospore and microspore mother cells and development of functional megaspore during meiosis, defective OsMLH3 or OsMLH1 in fsv1 and CRISPR/Cas9-based knockout lines results in reduced type I crossover and bivalent frequency. The fsv1 and OsMLH3-knockout lines are valuable germplasms for development of female sterile restorer lines for mechanized seed production of hybrid rice.

Ribosome stalling caused by the Argonaute-microRNA-SGS3 complex regulates the production of secondary siRNAs in plants

The path of ribosomes on mRNAs can be impeded by various obstacles. One such example is halting of ribosome movement by microRNAs, but the exact mechanism and physiological role remain unclear. Here, we find that ribosome stalling caused by the Argonaute-microRNA-SGS3 complex regulates production of secondary small interfering RNAs (siRNAs) in plants. We show that the double-stranded RNA-binding protein SGS3 interacts directly with the 3' end of the microRNA in an Argonaute protein, resulting in ribosome stalling. Importantly, microRNA-mediated ribosome stalling correlates positively with efficient production of secondary siRNAs from target mRNAs. Our results illustrate a role of paused ribosomes in regulation of small RNA function that may have broad biological implications across the plant kingdom.

Production of active human FGF21 using tobacco mosaic virus-based transient expression system

Fibroblast growth factor (FGF) family has a wide range of metabolic processes. FGF21 exerts critical physiological functions in clinical application. This study aimed to explore a convenient and highly efficient approach for rhFGF21 expression using TMV-TES. Firstly, the vector pTTEV-GFP was constructed, followed by optimisation of the expression parameters in Nicotiana benthamiana. Then, the rhFGF21 encoding gene harbouring vector pTTEV-rhFGF21 was constructed. Agrobacterium-mediated vacuum infiltration was performed with the optimised parameters and the expression of rhFGF21 was confirmed by the immunoblotting analysis. ELISA revealed that the protein accumulation of rhFGF21 accounts for 0.11% of total soluble proteins. The biological activity was evaluated and the results suggested that tobacco-expressed rhFGF21 could stimulate the glucose uptake in swiss 3T3-L1 adipocytes, which was similar to the activity of commercial products, suggesting its native biological activity. Therefore, using TMV-TES to express rhFGF21 will be a feasible approach for the mass production of rhFGF21.

Molecular cloning and functional characterization of GmAAPTs from soybean (Glycine max)

Aminoalcoholphosphotransferase (AAPT) utilizes diacylglycerols and cytidine diphosphate-choline/ethanolamine as substrates for the synthesis of phosphatidylcholine (PC)/phosphatidylethanolamine (PE). Plant AAPTs involved in phospholipid metabolism mediate diverse physiological processes; however, little is known about their functions in triacylglycerol (TAG) metabolism and seed germination. In the present study, we isolated and characterized two AAPTs, GmAAPT1 and GmAAPT2, from soybean (Glycine max). GmAAPT1 and GmAAPT2 exhibited strong similarity in their amino acid contents and expression patterns, and both were found to localize to the endoplasmic reticulum and Golgi apparatus. In vitro enzymatic analyses showed that GmAAPT1 and GmAAPT2 contributed to PC and PE synthesis and exhibited choline/ethanolamine phosphotransferase-like enzymatic properties. The overexpression of GmAAPT1 and GmAAPT2 in Arabidopsis led to reduced levels of seed TAG and polyunsaturated fatty acids and decreased seed germination under freezing stress. Together, these findings suggest that GmAAPTs mediate TAG metabolism and negatively regulate seed freezing tolerance.

A single amino acid substitution in the movement protein enables the mechanical transmission of a geminivirus

Begomoviruses of the Geminiviridae are usually transmitted by whiteflies and rarely by mechanical inoculation. We used tomato leaf curl New Delhi virus (ToLCNDV), a bipartite begomovirus, to address this issue. Most ToLCNDV isolates are not mechanically transmissible to their natural hosts. The ToLCNDV-OM isolate, originally identified from a diseased oriental melon plant, is mechanically transmissible, while the ToLCNDV-CB isolate, from a diseased cucumber plant, is not. Genetic swapping and pathological tests were performed to identify the molecular determinants involved in mechanical transmission. Various viral infectious clones were constructed and successfully introduced into Nicotiana benthamiana, oriental melon, and cucumber plants by Agrobacterium-mediated inoculation. Mechanical transmissibility was assessed via direct rub inoculation with sap prepared from infected N. benthamiana. The presence or absence of viral DNA in plants was validated by PCR, Southern blotting, and in situ hybridization. The results reveal that mechanical transmissibility is associated with the movement protein (MP) of viral DNA-B in ToLCNDV-OM. However, the nuclear shuttle protein of DNA-B plays no role in mechanical transmission. Analyses of infectious clones carrying a single amino acid substitution reveal that the glutamate at amino acid position 19 of MP in ToLCNDV-OM is critical for mechanical transmissibility. The substitution of glutamate with glycine at this position in the MP of ToLCNDV-OM abolishes mechanical transmissibility. In contrast, the substitution of glycine with glutamate at the 19th amino acid position in the MP of ToLCNDV-CB enables mechanical transmission. This is the first time that a specific geminiviral movement protein has been identified as a determinant of mechanical transmissibility.

Rice Stripe Mosaic Virus-Encoded P4 Is a Weak Suppressor of Viral RNA Silencing and Is Required for Disease Symptom Development

Viral suppressors of RNA silencing (VSRs) are a cluster of viral proteins that have evolved to counteract eukaryotic antiviral RNA silencing pathways, thereby contributing to viral pathogenicity. In this study, we revealed that the matrix protein P4 encoded by rice stripe mosaic virus (RSMV), which is an emerging cytoplasmic rhabdovirus, is a weak RNA silencing suppressor. By conducting yeast two-hybrid, bimolecular fluorescence complementation, and subcellular colocalization assays, we proved that P4 interacts with the rice endogenous suppressor of gene silencing 3 (OsSGS3). We also determined that P4 overexpression has no effect on OsSGS3 transcription. However, P4 can promote the degradation of OsSGS3 via ubiquitination and autophagy. Additionally, a potato virus X-based expression system was used to confirm that P4 enhances the development of mosaic symptoms on Nicotiana benthamiana leaves by promoting hydrogen peroxide accumulation but not cell death. To verify whether P4 is a pathogenicity factor in host plants, we generated transgenic P4-overexpressing rice plants that exhibited disease-related developmental defects including decreased plant height and excessive tillering. Our data suggest that RSMV-encoded P4 serves as a weak VSR that inhibits antiviral RNA silencing by targeting OsSGS3.

Trichome regulator SlMIXTA-like directly manipulates primary metabolism in tomato fruit

Trichomes are storage compartments for specialized metabolites in many plant species. In trichome, plant primary metabolism is significantly changed, providing substrates for downstream secondary metabolism. However, little is known of how plants coordinate trichome formation and primary metabolism regulation. In this report, tomato (Solanum lycopersicum) trichome regulator SlMIXTA-like is indicated as a metabolic regulation gene by mGWAS analysis. Overexpression of SlMIXTA-like in tomato fruit enhances trichome formation. In addition, SlMIXTA-like can directly bind to the promoter region of gene encoding 3-deoxy-7-phosphoheptulonate synthase (SlDAHPS) to activate its expression. Induction of SlDAHPS expression enhances shikimate pathway activities and provides substrates for downstream secondary metabolism. Our data provide direct evidence that trichome regulator can directly manipulate primary metabolism, in which way plants can coordinate metabolic regulation and the formation of storage compartments for specialized metabolites. The newly identified SlMIXTA-like can be used for future metabolic engineering.

Overexpression of soybean GmPLDγ enhances seed oil content and modulates fatty acid composition in transgenic Arabidopsis

Phospholipase D (PLD) hydrolyzes the phosphodiester bond of glycerophospholipids to yield phosphatidic acid (PA) and a free headgroup. PLDs are important for plant growth, development, and responses to external stresses. However, their roles in triacylglycerol (TAG) synthesis are still unclear. Here, we report that a soybean (Glycine max) PLDγ (GmPLDγ) is involved in glycerolipid turnover and seed oil production. GmPLDγ was targeted to mitochondria and exhibited PLD activity that was activated by oleate and phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2]. Overexpression of GmPLDγ (abbreviated GmPLDγ-OE) in Arabidopsis thaliana resulted in enhanced seed weight, elevated levels of TAGs with 18-, 20-, and 22-carbon fatty acids (FAs), and altered oil-body morphology. Furthermore, the levels of membrane lipids in vegetative tissues decreased significantly, whereas no overt changes were found in mature seeds except for a decrease in the digalactosyldiacylglycerol (DGDG) level in the GmPLDγ-OE lines. Additionally, the expression of genes involved in glycerolipid metabolism was significantly upregulated in developing siliques in GmPLDγ-OE lines. Together, our data indicate a regulatory role for GmPLDγ in TAG synthesis and fatty-acid remodeling, highlighting the importance of mitochondria-directed glycerophospholipid homeostasis in seed oil accumulation.

Construction of an Infectious Poa semilatent virus cDNA Clone and Comparisons of Hordeivirus Cytopathology and Pathogenicity

Poa semilatent virus (PSLV), Lychnis ringspot virus (LRSV), and Barley stripe mosaic virus (BSMV) are members of the genus Hordeivirus in the family Virgaviridae. However, the biological properties and molecular genetics of PSLV have not been compared with other hordeiviruses. Here, we have constructed an infectious cDNA clone of the PSLV Canadian strain and provided evidence that PSLV differs from BSMV and LRSV. First, unlike the other two hordeiviruses that replicate in chloroplasts, PSLV induces dramatic structural changes in peroxisome during its infection in barley. The αa replication protein also localizes to peroxisomes, suggesting that PSLV replication occurs in peroxisomes. Second, PSLV encodes a γb protein that shares 19 to 23% identity with those of other hordeiviruses, and its activity as a viral suppressor of RNA (VSR) silencing is distinct from those of BSMV and LRSV. Substitution of the BSMV γb protein with that of PSLV or LRSV revealed a negative correlation between VSR activity and symptom severity of the recombinant BSMV derivatives. Intriguingly, the Ser-Lys-Leu (SKL) peroxisome-targeting signals differ among γb proteins of various hordeiviruses, including some BSMV strains. The presence of the C-terminal SKL motif in the γb protein impairs its silencing suppressor activity and influences symptoms. Finally, we developed a PSLV-based virus-induced gene silencing vector that induced strong and effective silencing phenotypes of endogenous genes in barley, wheat, and millet. Our results shed new light on hordeivirus pathogenesis and evolution, and provide an alternative tool for genomics studies of model hosts and economically important monocots.

Suppressors of RNA silencing encoded by geminiviruses and associated DNA satellites

In plants, RNA silencing provides a major line of defence against viruses. This antiviral immunity involves production of virus-derived small interfering RNAs (vsiRNAs) and results in specific silencing of viruses by vsiRNAs-guided effector complexes. As a counterattack against RNA silencing, many plant viruses encode suppressors of RNA silencing called viral suppressors of RNA silencing (VSRs), which interfere with the silencing pathway by various mechanisms. This review describes various methods that are being used to characterize viral proteins for suppressor function, VSRs found in geminiviruses and associated DNA satellites and their mechanisms of action.

The V2 protein encoded by a monopartite begomovirus is a suppressor of both post-transcriptional and transcriptional gene silencing activity

Papaya leaf curl virus (PaLCuV) is a begomovirus (genus Begomovirus; family Geminiviridae) with a monopartite genome that is usually associated with beta- and alphasatellites in plants. Geminiviruses are DNA viruses with small circular genomes that occur as minichromosomes in the nucleus and are susceptible to post-transcriptional gene silencing (PTGS) and transcriptional gene silencing (TGS). Transient expression of the PaLCuV V2 (PV2) protein together with the green fluorescent protein (GFP) in Nicotiana benthamiana resulted in enhanced levels of GFP fluorescence and GFP mRNA, indicative of suppression of PTGS. Expression of PV2 from a Potato virus X vector restored GFP expression in N. benthamiana plants harbouring a transcriptionally silenced GFP transgene, indicative of suppression of TGS. The results show that the PV2 protein encoded by PaLCuV has both suppressor of PTGS and TGS activity and is an important factor in overcoming host RNA-silencing based defenses.

Transgenic and Genome Editing Approaches for Modifying Plant Oils

Vegetable oils are important for human and animal nutrition and as renewable resources for chemical feedstocks. We provide an overview of transgenic and genome editing approaches for modifying plant oils, describing useful model and crop systems and different strategies for transgenic modifications. We also describe new genome editing approaches that are beginning to be applied to oilseed plants and crops. These approaches are illustrated with examples for modifying the nutritional quality of vegetable oils by altering fatty acid desaturation, producing non-native fatty acids in oilseeds, and enhancing the overall accumulation of oil in seeds and leaves.

A cupin domain is involved in α-amylase inhibitory activity

Proteinaceous α-amylase inhibitors have specialized activities that make some strong inhibition of α-amylases. New α-amylase inhibitors continue to be discovered so far. A proteinaceous α-amylase inhibitor CL-AI was isolated and identified from chickpea seeds. CL-AI, encoded by Q9SMJ4, was a storage legumin precursor containing one α-chain and one β-chain, and each chain possessed a same conserved cupin domain. Amino acid mutation and deficiency of cupin domain would lead to loss of α-amylase inhibitory activity, indicating that it was essential for inhibitory activity. CL-AI(α + β) in its single stranded state in vivo had inhibitory activity. After it was processed into one α-chain and one β-chain, the two chains were connected to each other via disulfide bond, which would cover the cupin domains and lead to the loss of inhibitory activity. The CL-AI(α + β), α-chain and β-chain could inhibit various α-amylases and delay the seed germination of wheat, rice and maize as well as the growth and development of potato beetle larva. Two cupin proteins, Glycinin G1 in soybean and Glutelinin in rice were also found to have inhibitory activity. Our results indicated that the cupin domain is involved in α-amylase inhibitory activity and the proteins with a cupin domain may be a new kind of proteinaceous α-amylase inhibitor.

Octapartite negative-sense RNA genome of High Plains wheat mosaic virus encodes two suppressors of RNA silencing

High Plains wheat mosaic virus (HPWMoV, genus Emaravirus; family Fimoviridae), transmitted by the wheat curl mite (Aceria tosichella Keifer), harbors a monocistronic octapartite single-stranded negative-sense RNA genome. In this study, putative proteins encoded by HPWMoV genomic RNAs 2-8 were screened for potential RNA silencing suppression activity by using a green fluorescent protein-based reporter agroinfiltration assay. We found that proteins encoded by RNAs 7 (P7) and 8 (P8) suppressed silencing induced by single- or double-stranded RNAs and efficiently suppressed the transitive pathway of RNA silencing. Additionally, a Wheat streak mosaic virus (WSMV, genus Tritimovirus; family Potyviridae) mutant lacking the suppressor of RNA silencing (ΔP1) but having either P7 or P8 from HPWMoV restored cell-to-cell and long-distance movement in wheat, thus indicating that P7 or P8 rescued silencing suppressor-deficient WSMV. Furthermore, HPWMoV P7 and P8 substantially enhanced the pathogenicity of Potato virus X in Nicotiana benthamiana. Collectively, these data demonstrate that the octapartite genome of HPWMoV encodes two suppressors of RNA silencing.

pTAC10, a Key Subunit of Plastid-Encoded RNA Polymerase, Promotes Chloroplast Development

Regulation of photosynthetic gene expression by plastid-encoded RNA polymerase (PEP) is essential for chloroplast development. The activity of PEP largely relies on at least 12 PEP-associated proteins (PAPs) encoded in the nuclear genome of plant cells. A recent model proposed that these PAPs regulate the establishment of the PEP complex through broad PAP-PEP or PAP-PAP interactions. In this study, we identified the Arabidopsis (Arabidopsis thaliana) seedling-lethal mutant ptac10-1, which has defects in chloroplast development, and found that the mutant phenotype is caused by the suppression of PLASTID S1 RNA-BINDING DOMAIN PROTEIN (pTAC10/PAP3). Analysis of the heterozygous mutant and pTAC10-overexpressing transgenic plants indicated that the expression level of pTAC10 is tightly linked to chloroplast development. Characterization of the interaction of pTAC10 with PAPs revealed that pTAC10 interacts with other PAPs, such as FSD2, FSD3, TrxZ, pTAC7, and pTAC14, but it does not interact with PEP core enzymes, such as rpoA and rpoB. Analysis of pTAC10 interactions using truncated pTAC10 proteins showed that the pTAC10 carboxyl-terminal region downstream of the S1 domain is involved in the pTAC10-PAP interaction. Furthermore, overexpression of truncated pTAC10s lacking the C-terminal regions downstream of the S1 domain could not rescue the ptac10-1 mutant phenotype and induced an abnormal whitening phenotype in Columbia-0 plants. Our observations suggested that these pTAC10-PAP interactions are essential for the formation of the PEP complex and chloroplast development.

Genome characterization, infectivity assays of in vitro and in vivo infectious transcripts of soybean yellow mottle mosaic virus from India reveals a novel short mild genotype

Nucleotide sequence of a distinct soybean yellow mottle mosaic virusisolate from Vignaradiata (mungbean isolate, SYMMV-Mb) from India was determined and compared with othermembers of the family Tombusviridae. The complete monopartite single-stranded RNA genome of SYMMV-Mb consisted of 3974nt with six putative open reading frames and includes 5' and 3' untranslated regions of 35 and 254nt, respectively. SYMMV-Mb genome shared 75% nt sequence identity at complete genome level and 67-92% identity at all ORFs level with SYMMV Korean and USA isolates (soybean isolates) followed by CPMoV, whereas it shared very low identity with other tombusviridae members (5-41%). A full-length infectious cDNA clone of the SYMMV-Mb placed under the control of the T7 RNA polymerase and the CaMV35S promoters was generated and French bean plants on mechanical inoculation with in vitro RNA transcripts, p35SSYMMV-O4 plasmid and agroinoculation with p35SSYMMV-O4 showed symptoms typical of SYMMV-Mb infection. The infection was confirmed by DAC-ELISA, ISEM, RT-PCR and mechanical transmission to new plant species. Further testing of different plant species with agroinoculation of p35SSYMMV-O4 showed delay in symptoms but indistinguishable from mechanical sap inoculation and the infection was confirmed by DAC-ELISA, RT-PCR and mechanical transmission to new plants. The system developed here will be useful for further studies on pathogenecity, viral gene functions, plant-virus-vector interactions of SYMMV-Mb and to utilize it as a gene expression and silencing vector.

Translation Initiation Factor eIF4E and eIFiso4E Are Both Required for Peanut stripe virus Infection in Peanut (Arachis hypogaea L.)

Peanut stripe virus (PStV) belongs to the genus Potyvirus and is the most important viral pathogen of cultivated peanut (Arachis hypogaea L.). The eukaryotic translation initiation factor, eIF4E, and its isoform, eIF(iso)4E, play key roles during virus infection in plants, particularly Potyvirus. In the present study, we cloned the eIF4E and eIF(iso)4E homologs in peanut and named these as PeaeIF4E and PeaeIF(iso)4E, respectively. Quantitative real-time PCR (qRT-PCR) analysis showed that these two genes were expressed during all growth periods and in all peanut organs, but were especially abundant in young leaves and roots. These also had similar expression levels. Yeast two-hybrid analysis showed that PStV multifunctional helper component proteinase (HC-Pro) and viral protein genome-linked (VPg) both interacted with PeaeIF4E and PeaeIF(iso)4E. Bimolecular fluorescence complementation assay showed that there was an interaction between HC-Pro and PeaeIF4E/PeaeIF(iso)4E in the cytoplasm and between VPg and PeaeIF4E/PeaeIF(iso)4E in the nucleus. Silencing either PeaeIF4E or PeaeIF(iso)4E using a virus-induced gene silencing system did not significantly affect PStV accumulation. However, silencing both PeaeIF4E and PeaeIF(iso)4E genes significantly weakened PStV accumulation. The findings of the present study suggest that PeaeIF4E and PeaeIF(iso)4E play important roles in the PStV infection cycle and may potentially contribute to PStV resistance.

Polypeptide Transport-Associated Domains of the Toc75 Channel Protein Are Located in the Intermembrane Space of Chloroplasts

Toc75 is the channel for protein translocation across the chloroplast outer envelope membrane. Toc75 belongs to the Omp85 protein family and consists of three N-terminal polypeptide transport-associated (POTRA) domains that are essential for the functions of Toc75, followed by a membrane-spanning β-barrel domain. In bacteria, POTRA domains of Omp85 family members are located in the periplasm, where they interact with other partner proteins to accomplish protein secretion and outer membrane protein assembly. However, the orientation and therefore the molecular function of chloroplast Toc75 POTRA domains remain a matter of debate. We investigated the topology of Toc75 using bimolecular fluorescence complementation and immunogold electron microscopy. Bimolecular fluorescence complementation analyses showed that in stably transformed plants, Toc75 N terminus is located on the intermembrane space side, not the cytosolic side, of the outer membrane. Immunogold labeling of endogenous Toc75 POTRA domains in pea (Pisum sativum) and Arabidopsis (Arabidopsis thaliana) confirmed that POTRA domains are located in the intermembrane space of the chloroplast envelope.

Time-delayed model of immune response in plants

In the studies of plant infections, the plant immune response is known to play an essential role. In this paper we derive and analyse a new mathematical model of plant immune response with particular account for post-transcriptional gene silencing (PTGS). Besides biologically accurate representation of the PTGS dynamics, the model explicitly includes two time delays to represent the maturation time of the growing plant tissue and the non-instantaneous nature of the PTGS. Through analytical and numerical analysis of stability of the steady states of the model we identify parameter regions associated with recovery and resistant phenotypes, as well as possible chronic infections. Dynamics of the system in these regimes is illustrated by numerical simulations of the model.

P2 of Rice grassy stunt virus (RGSV) and p6 and p9 of Rice ragged stunt virus (RRSV) isolates from Vietnam exert suppressor activity on the RNA silencing pathway

In Vietnam, the two main viruses that cause disease in rice are the Rice grassy stunt virus (RGSV) and the Rice ragged stunt virus (RRSV). Outbreaks of these two viruses have dramatically decreased rice production in Vietnam. Because natural resistance genes are unknown, an RNAi strategy may be an alternative method to develop resistance to RGSV and RRSV. However, this strategy will be efficient only if putative silencing suppressors encoded by the two viruses are neutralized. To identify these suppressors, we used the classical green fluorescent protein (GFP) agroinfiltration method in Nicotiana benthamiana. Then, we investigated the effects of viral candidate proteins on GFP expression and GFP siRNA accumulation and their interference with the short- or long-range signal of silencing. RGSV genes s2gp1, s5gp2, and s6gp1 and RRSV genes s5gp1, s6gp1, s9gp1, and s10gp1 were selected for viral silencing suppressor investigation according to their small molecular weight, the presence of cysteines, or the presence of a GW motif in related protein products. We confirmed that protein p6 of RRSV displays mild silencing suppressor activity and affects long-range silencing by delaying the systemic silencing signal. In addition, we identified two new silencing suppressors that displayed mild activity: p2 of RGSV and p9 of RRSV.

Differential response of diverse solanaceous hosts to tomato leaf curl New Delhi virus infection indicates coordinated action of NBS-LRR and RNAi-mediated host defense

Tomato leaf curl New Delhi virus (ToLCNDV) is a bipartite begomovirus (family Geminiviridae) that infects a wide range of plants. ToLCNDV has emerged as an important pathogen and a serious threat to tomato production in India. A comparative and molecular analysis of ToLCNDV pathogenesis was performed on diverse solanaceous hosts (Capsicum annuum, Nicotiana benthamiana, N. tabacum, and Solanum lycopersicum). N. benthamiana was found to be the most susceptible host, whereas C. annuum showed resistance against an isolate of ToLCNDV collected in New Delhi from tomato (GenBank accession no. U15015 and U15017). S. lycopersicum and N. tabacum developed conspicuous symptoms and allowed virus to accumulate to significantly high titers. The viral DNA level was concurrent with symptom severity. ToLCNDV-specific siRNA levels were directly proportional to the amount of viral DNA. To investigate the basis for the differences in response of these hosts to ToLCNDV, a comparative expression analysis of selected defense-related genes was carried out. The results indicated differences in expression levels of genes involved in the posttranscriptional gene silencing machinery (RDR6, AGO1 and SGS3) as well as basal host defense responses (nucleotide-binding site and leucine-rich repeat [NBS-LRR] proteins and lipid transfer protein [LTP]). Among these, expression of NBS-LRR genes was found to be significantly higher in C. annuum following ToLCNDV infection. Our analyses suggest that the expression of host defense responses determines the level of ToLCNDV accumulation and degree of symptom development.

Functional comparison of RNA silencing suppressor between the p5 protein of rice grassy stunt virus and the p3 protein of rice stripe virus

Rice grassy stunt virus (RGSV) is a member of the genus Tenuivirus, which includes rice stripe virus (RSV), as the type species. A viral suppressor of RNA silencing (VSR) of RGSV has not been identified, whereas the p3 protein of RSV (RSVp3) encoded by the viral-sense (v) strand of RNA3 has been reported to act as a VSR. In this study, we examined the VSR function of the p5 protein of RGSV (RGSVp5), encoded by vRNA5. Expecting it to correspond to the vRNA3 of RSV, we compared the VSR function of RGSVp5 with that of RSVp3. In an Agrobacterium-mediated transient expression assay using a transgenic line of Nicotiana benthamiana that expressed green fluorescent protein and the wild type, RGSVp5 suppressed sense transgene-mediated post-transcriptional gene silencing (S-PTGS), inverted-repeat (IR) transgene-induced PTGS (IR-PTGS), and the systemic spread of GFP silencing, as in the case with RSVp3. By contrast, a gel mobility shift assay revealed that RGSVp5 did not have any distinct binding activity with 21-, 22-, or 24-nucleotide small interfering RNA (siRNA) duplexes, whereas RSVp3 binds to all three sizes of siRNA duplexes. Furthermore, the transiently expressed p5 protein fused with GFP was dispersed mainly in the cytoplasm, whereas the GFP-fused p3 protein of RSV was localized both in the nucleus and in the cytoplasm. Our results suggest that RGSVp5 functions as a VSR but that the suppression mechanism of RNA silencing and the subcellular localization of RGSVp5 differ from those of the analogous VSR, RSVp3, even in the same genus.

Soybean actin-depolymerizing factor 2 interacts with Soybean mosaic virus-encoded P3 protein

Soybean mosaic virus (SMV), a member of the Potyvirus genus, is one of the most prevalent and devastating viral pathogens in soybean-growing regions worldwide. It is generally accepted that symptom development of a viral plant disease results from molecular interactions between the virus and its host plant. P3 protein is the most variable polyprotein in potyviruses, which potentially plays an important role in the process of the evolution of virus type specialization. However, P3 not only plays a major role in virus replication and movement, but it is also responsible for symptom development in SMV-infected plants. This study provides evidence that actin-depolymerizing factor 2 (designated as ADF2) of soybean interacts with SMV P3 via a two-hybrid yeast system by screening a soybean cDNA library. Bimolecular fluorescence complementation assay further confirmed the interaction, which occurred in both the cytomembrane and cytoskeleton of Nicotiana benthamiana cells. The results support the hypothesis that SMV P3 might have a role in virus movement within cells.

microRNA regulation of fruit growth

Growth is a major factor in plant organ morphogenesis and is influenced by exogenous and endogenous signals including hormones. Although recent studies have identified regulatory pathways for the control of growth during vegetative development, there is little mechanistic understanding of how growth is controlled during the reproductive phase. Using Arabidopsis fruit morphogenesis as a platform for our studies, we show that the microRNA miR172 is critical for fruit growth, as the growth of fruit is blocked when miR172 activity is compromised. Furthermore, our data are consistent with the FRUITFULL (FUL) MADS-domain protein and Auxin Response Factors (ARFs) directly activating the expression of a miR172-encoding gene to promote fruit valve growth. We have also revealed that MADS-domain (such as FUL) and ARF proteins directly associate in planta. This study defines a novel and conserved microRNA-dependent regulatory module integrating developmental and hormone signalling pathways in the control of plant growth.

Analysis of geminivirus AL2 and L2 proteins reveals a novel AL2 silencing suppressor activity

Both posttranscriptional and transcriptional gene silencing (PTGS and TGS, respectively) participate in defense against the DNA-containing geminiviruses. As a countermeasure, members of the genus Begomovirus (e.g., Cabbage leaf curl virus) encode an AL2 protein that is both a transcriptional activator and a silencing suppressor. The related L2 protein of Beet curly top virus (genus Curtovirus) lacks transcription activation activity. Previous studies showed that both AL2 and L2 suppress silencing by a mechanism that correlates with adenosine kinase (ADK) inhibition, while AL2 in addition activates transcription of cellular genes that negatively regulate silencing pathways. The goal of this study was to clarify the general means by which these viral proteins inhibit various aspects of silencing. We confirmed that AL2 inhibits systemic silencing spread by a mechanism that requires transcription activation activity. Surprisingly, we also found that reversal of PTGS and TGS by ADK inactivation depended on whether experiments were conducted in vegetative or reproductive Nicotiana benthamiana plants (i.e., before or after the vegetative-to-reproductive transition). While AL2 was able to reverse silencing in both vegetative and reproductive plants, L2 and ADK inhibition were effective only in vegetative plants. This suggests that silencing maintenance mechanisms can change during development or in response to stress. Remarkably, we also observed that AL2 lacking its transcription activation domain could reverse TGS in reproductive plants, revealing a third, previously unsuspected AL2 suppression mechanism that depends on neither ADK inactivation nor transcription activation.

IMPORTANCE

RNA silencing in plants is a multivalent antiviral defense, and viruses respond by elaborating multiple and sometimes multifunctional proteins that inhibit various aspects of silencing. The studies described here add an additional layer of complexity to this interplay. By examining geminivirus AL2 and L2 suppressor activities, we show that L2 is unable to suppress silencing in Nicotiana benthamiana plants that have undergone the vegetative-to-reproductive transition. As L2 was previously shown to be effective in mature Arabidopsis plants, these results illustrate that silencing mechanisms can change during development or in response to stress in ways that may be species specific. The AL2 and L2 proteins are known to share a suppression mechanism that correlates with the ability of both proteins to inhibit ADK, while AL2 in addition can inhibit silencing by transcriptionally activating cellular genes. Here, we also provide evidence for a third AL2 suppression mechanism that depends on neither transcription activation nor ADK inactivation. In addition to revealing the remarkable versatility of AL2, this work highlights the utility of viral suppressors as probes for the analysis of silencing pathways.

Analysis of geminivirus AL2 and L2 proteins reveals a novel AL2 silencing suppressor activity

Both posttranscriptional and transcriptional gene silencing (PTGS and TGS, respectively) participate in defense against the DNA-containing geminiviruses. As a countermeasure, members of the genus Begomovirus (e.g., Cabbage leaf curl virus) encode an AL2 protein that is both a transcriptional activator and a silencing suppressor. The related L2 protein of Beet curly top virus (genus Curtovirus) lacks transcription activation activity. Previous studies showed that both AL2 and L2 suppress silencing by a mechanism that correlates with adenosine kinase (ADK) inhibition, while AL2 in addition activates transcription of cellular genes that negatively regulate silencing pathways. The goal of this study was to clarify the general means by which these viral proteins inhibit various aspects of silencing. We confirmed that AL2 inhibits systemic silencing spread by a mechanism that requires transcription activation activity. Surprisingly, we also found that reversal of PTGS and TGS by ADK inactivation depended on whether experiments were conducted in vegetative or reproductive Nicotiana benthamiana plants (i.e., before or after the vegetative-to-reproductive transition). While AL2 was able to reverse silencing in both vegetative and reproductive plants, L2 and ADK inhibition were effective only in vegetative plants. This suggests that silencing maintenance mechanisms can change during development or in response to stress. Remarkably, we also observed that AL2 lacking its transcription activation domain could reverse TGS in reproductive plants, revealing a third, previously unsuspected AL2 suppression mechanism that depends on neither ADK inactivation nor transcription activation.

IMPORTANCE

RNA silencing in plants is a multivalent antiviral defense, and viruses respond by elaborating multiple and sometimes multifunctional proteins that inhibit various aspects of silencing. The studies described here add an additional layer of complexity to this interplay. By examining geminivirus AL2 and L2 suppressor activities, we show that L2 is unable to suppress silencing in Nicotiana benthamiana plants that have undergone the vegetative-to-reproductive transition. As L2 was previously shown to be effective in mature Arabidopsis plants, these results illustrate that silencing mechanisms can change during development or in response to stress in ways that may be species specific. The AL2 and L2 proteins are known to share a suppression mechanism that correlates with the ability of both proteins to inhibit ADK, while AL2 in addition can inhibit silencing by transcriptionally activating cellular genes. Here, we also provide evidence for a third AL2 suppression mechanism that depends on neither transcription activation nor ADK inactivation. In addition to revealing the remarkable versatility of AL2, this work highlights the utility of viral suppressors as probes for the analysis of silencing pathways.

A functional genomics method for assaying gene function in phytopathogenic fungi through host-induced gene silencing mediated by agroinfiltration

With the rapid growth of genomic information, there is an increasing demand for efficient analysis tools to study the function of predicted genes coded in genomes. Agroinfiltration, the delivery of gene constructs into plant cells by Agrobacterium tumefaciens infiltrated into leaves, is one such versatile, simple, and rapid technique that is increasingly used for transient gene expression assay in plants. In this chapter, we focus on the use of agroinfiltration as a functional genomics research tool in molecular plant pathology. Specifically, we describe in detail its use in expressing phytopathogenic fungal gene sequences in a host plant to induce RNA silencing of corresponding genes inside the pathogen, a method which has been termed host-induced gene silencing (HIGS). We target the fungal pathogen Puccinia triticina which causes leaf rust on its wheat host, but the method is applicable to a variety of pathosystems.

Multifaceted capsid proteins: multiple interactions suggest multiple roles for Pepino mosaic virus capsid protein

Pepino mosaic virus (PepMV) (family Alphaflexiviridae, genus Potexvirus) is a mechanically transmitted tomato pathogen that, over the last decade, has evolved from emerging to endemic worldwide. Here, two heat-shock cognate (Hsc70) isoforms were identified as part of the coat protein (CP)/Hsc70 complex in vivo, following full-length PepMV and CP agroinoculation. PepMV accumulation was severely reduced in Hsp70 virus-induced gene silenced and in quercetin-treated Nicotiana benthamiana plants. Similarly, in vitro-transcribed as well as virion RNA input levels were reduced in quercetin-treated protoplasts, suggesting an essential role for Hsp70 in PepMV replication. As for Potato virus X, the PepMV CP and triple gene-block protein 1 (TGBp1) self-associate and interact with each other in vitro but, unlike in the prototype, both PepMV proteins represent suppressors of transgene-induced RNA silencing with different modes of action; CP is a more efficient suppressor of RNA silencing, sequesters the silencing signal by preventing its spread to neighboring cells and its systemic movement. Here, we provide evidence for additional roles of the PepMV CP and host-encoded Hsp70 in viral infection, the first as a truly multifunctional protein able to specifically bind to a host chaperone and to counterattack an RNA-based defense mechanism, and the latter as an essential factor for PepMV infection.

Silencing suppressor protein VPg of a potyvirus interacts with the plant silencing-related protein SGS3

Viral genome-linked protein (VPg) of potyviruses is involved in multiple steps of the potyvirus infection cycle, including viral multiplication and movement in plants. Recently, we showed that VPg of Potato virus A (PVA; genus Potyvirus) suppresses sense-mediated RNA silencing, which is linked to one or both nuclear or nucleolar localization. Here, we studied interactions between VPg and components of the plant RNA silencing pathway. Results showed that VPg interacts with the SGS3 protein of Solanum tuberosum and Arabidopsis thaliana, as shown by yeast two-hybrid analysis and bimolecular fluorescence complementation assays. VPg-SGS3 interactions co-localized with small cytoplasmic bodies that contained plant RNA-dependent RNA polymerase 6 (RDR6) (likely SGS3/RDR6 bodies). The N-terminal zinc finger (ZF) domain of SGS3 was the main determinant of the VPg interaction. Our data also suggest that the ZF domain controls SGS3 localization. SGS3 homodimerization was controlled by multiple protein regions. The VPg-SGS3 interaction appeared beneficial for PVA, as viral RNA levels correlated positively with sgs3 mRNA levels in the SGS3-silenced and SGS3-overexpressing leaves of Nicotiana benthamiana. The data support the idea that VPg acts as a suppressor of RNA silencing and suggest that an interaction with SGS3 may be important, especially in suppression of sense-mediated RNA silencing.

Ipomovirus--an atypical genus in the family Potyviridae transmitted by whiteflies

Ipomoviruses (genus Ipomovirus) are whitefly-transmitted viruses assigned to the family Potyviridae. They are characterised by filamentous flexible particles and a positive-sense single-stranded RNA (+ssRNA) genome. The viral genome is translated into a polyprotein precursor, which is processed into mature proteins and a short overlapping open reading frame. The genus Ipomovirus contains four accepted species and one unapproved species, and two other tentative members have recently been characterised. Ipomoviruses cause serious economic losses in many important crops, including cassava, sweet potato, cucurbits, tomato and aubergine. These viruses are transmitted by whiteflies in a non-circulative, semi-persistent manner, the virions being retained on the external surface of the vectors' mouthparts for a few days or weeks. Comparison of the available complete genome sequences of different ipomoviruses revealed differences in their genome organisation and a considerable variation in their proteins and conserved motifs that may reflect functional differences. This review summarises the current knowledge of the members within the genus Ipomovirus, focusing on genome organisation, taxonomic classification and the mechanism by which they are transmitted.

Analysis of the A-U rich hairpin from the intergenic region of tospovirus S RNA as target and inducer of RNA silencing

Earlier work indicated that Tomato spotted wilt virus (TSWV) messenger transcripts, and not the (anti)genomic RNAs, are targeted by the RNA silencing machinery. Here, the predicted AU-rich hairpin (HP) structure encoded by the intergenic region (IGR) of the TSWV S RNA, and present at the 3' end of viral mRNAs, was analyzed as a target and inducer for RNA silencing. Virus-derived siRNAs (vsiRNAs) purified from virus infected plants were found to derive from all three genomic RNA segments but predominantly the ambisense M and S RNAs. Further profiling on the S RNA sequence revealed that vsiRNAs were found from almost the entire S RNA sequence, except the IGR from where hardly any vsiRNAs were found. Similar profiles were observed with the distantly related Tomato yellow ring tospovirus (TYRV). Dicer cleavage assays using Drosophila melanogaster (Dm) embryo extracts showed that synthetic transcripts of the IGR-HP region were recognized as substrate for Dicer. Transient agroinfiltration assays of a GFP-sensor construct containing the IGR-HP sequence at its 3' UTR (GFP-HP) did not show more rapid/strong silencing and profiling of the corresponding siRNAs, generated outside the context of a viral infection, still revealed relatively low levels of IGR-HP-derived siRNAs. These data support the idea that the IGR-HP is a weak inducer of RNA silencing and only plays a minor role in the amplification of a strong antiviral RNAi response.

Replication-associated proteins encoded by Wheat dwarf virus act as RNA silencing suppressors

Wheat dwarf virus (WDV) is an economically important and widespread single-stranded DNA virus in the genus Mastrevirus, family Geminiviridae. So far, an RNA silencing suppressor in the genus Mastrevirus has not been reported. In this study, the viral replication-associated proteins of WDV, Rep and RepA proteins, were demonstrated to have RNA silencing suppressor activities when expressed in agro-infiltrated leaves of Nicotiana benthamiana line 16c, by their ability to inhibit posttranscriptional gene silencing (PTGS) of green fluorescent protein (GFP). On the basis of the analysis of GFP expression and siRNA accumulation, we concluded that both Rep and RepA proteins suppressed local silencing induced by either single-stranded GFP (ssGFP) or inverted repeat GFP (dsGFP) constructs, although their activity can be characterized as relatively weak in comparison to HC-Pro of tobacco etch virus.

Optimization and utilization of Agrobacterium-mediated transient protein production in Nicotiana

Agrobacterium-mediated transient protein production in plants is a promising approach to produce vaccine antigens and therapeutic proteins within a short period of time. However, this technology is only just beginning to be applied to large-scale production as many technological obstacles to scale up are now being overcome. Here, we demonstrate a simple and reproducible method for industrial-scale transient protein production based on vacuum infiltration of Nicotiana plants with Agrobacteria carrying launch vectors. Optimization of Agrobacterium cultivation in AB medium allows direct dilution of the bacterial culture in Milli-Q water, simplifying the infiltration process. Among three tested species of Nicotiana, N. excelsiana (N. benthamiana × N. excelsior) was selected as the most promising host due to the ease of infiltration, high level of reporter protein production, and about two-fold higher biomass production under controlled environmental conditions. Induction of Agrobacterium harboring pBID4-GFP (Tobacco mosaic virus-based) using chemicals such as acetosyringone and monosaccharide had no effect on the protein production level. Infiltrating plant under 50 to 100 mbar for 30 or 60 sec resulted in about 95% infiltration of plant leaf tissues. Infiltration with Agrobacterium laboratory strain GV3101 showed the highest protein production compared to Agrobacteria laboratory strains LBA4404 and C58C1 and wild-type Agrobacteria strains at6, at10, at77 and A4. Co-expression of a viral RNA silencing suppressor, p23 or p19, in N. benthamiana resulted in earlier accumulation and increased production (15-25%) of target protein (influenza virus hemagglutinin).

A non-canonical plant microRNA target site

Plant microRNAs (miRNAs) typically form near-perfect duplexes with their targets and mediate mRNA cleavage. Here, we describe an unconventional miRNA target of miR398 in Arabidopsis, an mRNA encoding the blue copper-binding protein (BCBP). BCBP mRNA carries an miR398 complementary site in its 5′-untranslated region (UTR) with a bulge of six nucleotides opposite to the 5′ region of the miRNA. Despite the disruption of a target site region thought to be especially critical for function, BCBP mRNAs are cleaved by ARGONAUTE1 between nucleotides 10th and 11th, opposite to the miRNA, like conventional plant target sites. Levels of BCBP mRNAs are inversely correlated to levels of miR398 in mutants lacking the miRNA, or transgenic plants overexpressing it. Introducing two mutations that disrupt the miRNA complementarity around the cleavage site renders the target cleavage-resistant. The BCBP site functions outside of the context of the BCBP mRNA and does not depend on 5′-UTR location. Reducing the bulge does not interfere with miR398-mediated regulation and completely removing it increases the efficiency of the slicing. Analysis of degradome data and target predictions revealed that the miR398-BCBP interaction seems to be rather unique. Nevertheless, our results imply that functional target sites with non-perfect pairings in the 5′ region of an ancient conserved miRNA exist in plants.