Viral and nonviral elements in potexvirus replication and movement and in antiviral responses

Differential expression of microRNAs in response to Papaya ringspot virus infection in differentially responding genotypes of papaya (Carica papaya L.) and its wild relative

Papaya ringspot virus (PRSV) is one of the most devastating viruses of papaya that has significantly hampered papaya production across the globe. Although PRSV resistance is known in some of its wild relatives, such as Vasconcellea cauliflora and in some of the improved papaya genotypes, the molecular basis of this resistance mechanism has not been studied and understood. Plant microRNAs are an important class of small RNAs that regulate the gene expression in several plant species against the invading plant pathogens. These miRNAs are known to manifest the expression of genes involved in resistance against plant pathogens, through modulation of the plant's biochemistry and physiology. In this study we made an attempt to study the overall expression pattern of small RNAs and more specifically the miRNAs in different papaya genotypes from India, that exhibit varying levels of tolerance or resistance to PRSV. Our study found that the expression of some of the miRNAs was differentially regulated in these papaya genotypes and they had entirely different miRNA expression profile in healthy and PRSV infected symptomatic plants. This data may help in improvement of papaya cultivars for resistance against PRSV through new breeding initiatives or biotechnological approaches such as genome editing.

Role of Plant Virus Movement Proteins in Suppression of Host RNAi Defense

One of the systems of plant defense against viral infection is RNA silencing, or RNA interference (RNAi), in which small RNAs derived from viral genomic RNAs and/or mRNAs serve as guides to target an Argonaute nuclease (AGO) to virus-specific RNAs. Complementary base pairing between the small interfering RNA incorporated into the AGO-based protein complex and viral RNA results in the target cleavage or translational repression. As a counter-defensive strategy, viruses have evolved to acquire viral silencing suppressors (VSRs) to inhibit the host plant RNAi pathway. Plant virus VSR proteins use multiple mechanisms to inhibit silencing. VSRs are often multifunctional proteins that perform additional functions in the virus infection cycle, particularly, cell-to-cell movement, genome encapsidation, or replication. This paper summarizes the available data on the proteins with dual VSR/movement protein activity used by plant viruses of nine orders to override the protective silencing response and reviews the different molecular mechanisms employed by these proteins to suppress RNAi.

Plantago asiatica mosaic virus: An emerging plant virus causing necrosis in lilies and a new model RNA virus for molecular research

TAXONOMY

Plantago asiatica mosaic virus belongs to the genus Potexvirus in the family Alphaflexiviridae of the order Tymovirales.

VIRION AND GENOME PROPERTIES

Plantago asiatica mosaic virus (PlAMV) has flexuous virions of approximately 490-530 nm in length and 10-15 nm in width. The genome of PlAMV consists of a single-stranded, positive-sense RNA of approximately 6.13 kb. It contains five open reading frames (ORFs 1-5), encoding a putative viral polymerase (RdRp), movement proteins (triple gene block proteins, TGBp1-3), and coat protein (CP), respectively.

HOST RANGE

PlAMV has an exceptionally wide host range and has been isolated from various wild plants, including Plantago asiatica, Nandina domestica, Rehmannia glutinosa, and other weed plants. Experimentally PlAMV can infect many plant species including Nicotiana benthamiana and Arabidopsis thaliana. It also infects ornamental lilies and frequently causes severe necrotic symptoms. However, host range varies depending on isolates, which show significant biological diversity within the species.

GENOME DIVERSITY

PlAMV can be separated into five clades based on phylogenetic analyses; nucleotide identities are significantly low between isolates in the different clades.

TRANSMISSION

PlAMV is not reported to be transmitted by biological vectors. Virions of PlAMV are quite stable and it can be transmitted efficiently by mechanical contact.

DISEASE SYMPTOMS

PlAMV causes red-rusted systemic necrosis in ornamental lilies, but it shows much weaker, if any, symptoms in wild plants such as P. asiatica.

CONTROL

Control of the disease caused by PlAMV is based mainly on rapid diagnosis and elimination of the infected bulbs or plants.

Maf/ham1-like pyrophosphatases of non-canonical nucleotides are host-specific partners of viral RNA-dependent RNA polymerases

Cassava brown streak disease (CBSD), dubbed the “Ebola of plants”, is a serious threat to food security in Africa caused by two viruses of the family Potyviridae: cassava brown streak virus (CBSV) and Ugandan (U)CBSV. Intriguingly, U/CBSV, along with another member of this family and one secoviridae, are the only known RNA viruses encoding a protein of the Maf/ham1-like family, a group of widespread pyrophosphatase of non-canonical nucleotides (ITPase) expressed by all living organisms. Despite the socio-economic impact of CDSD, the relevance and role of this atypical viral factor has not been yet established. Here, using an infectious cDNA clone and reverse genetics, we demonstrate that UCBSV requires the ITPase activity for infectivity in cassava, but not in the model plant Nicotiana benthamiana. HPLC-MS/MS experiments showed that, quite likely, this host-specific constraint is due to an unexpected high concentration of non-canonical nucleotides in cassava. Finally, protein analyses and experimental evolution of mutant viruses indicated that keeping a fraction of the yielded UCBSV ITPase covalently bound to the viral RNA-dependent RNA polymerase (RdRP) optimizes viral fitness, and this seems to be a feature shared by the other members of the Potyviridae family expressing Maf/ham1-like proteins. All in all, our work (i) reveals that the over-accumulation of non-canonical nucleotides in the host might have a key role in antiviral defense, and (ii) provides the first example of an RdRP-ITPase partnership, reinforcing the idea that RNA viruses are incredibly versatile at adaptation to different host setups.

Cassava is one the most important staple food around the world in term of caloric intake. The cassava brown streak disease, caused by cassava brown streak virus (CBSV) and Ugandan (U)CBSV–Ipomovirus genus, Potyviridae family-, produces massive losses in cassava production. Curiously, these two viruses, unlike the vast majority of members of the family, encode a Maf1/ham1-like pyrophosphatase (HAM1) of non-canonical nucleotides with unknown relevance and function in viruses. This study aims to fill this gap in our knowledge by using reverse genetics, biochemistry, metabolomics and directed virus evolution. Hence, we found that HAM1 is required for UCBSV to infect cassava, where its pyrophosphatase activity resulted critical, but not to propagate in the model plant Nicotiana benthamiana. In addition, we demonstrated that HAM1 works in partnership with the viral RdRP during infection. Unexpected high levels of ITP/XTP non-canonical nucleotides found in cassava, and the known flexibility of RNA viruses to incorporate additional factors when required, supports the idea that the high concentration of ITP/XTP worked as a selection pressure to promote the acquisition of HAM1 into the virus in order to promote a successful infection.

Second generation of pepino mosaic virus vectors: improved stability in tomato and a wide range of reporter genes

BACKGROUND

Vectors based on plant viruses are important tools for functional genomics, cellular biology, plant genome engineering and molecular farming. We previously reported on the construction of PepGFP2a, a viral vector based on pepino mosaic virus (PepMV) which expressed GFP efficiently and stably in plants of its experimental host Nicotiana benthamiana, but not in its natural host tomato. We have prepared a new set of PepMV-based vectors with improved stability that are able to express a wide range of reporter genes, useful for both N. benthamiana and tomato.

RESULTS

We first tested PepGFPm1 and PepGFPm2, two variants of PepGFP2a in which we progressively reduced a duplication of nucleotides encoding the N-terminal region of the coat protein. The new vectors had improved GFP expression levels and stability in N. benthamiana but not in tomato plants. Next, we replaced GFP by DsRed or mCherry in the new vectors PepDsRed and PepmCherry, respectively; while PepmCherry behaved similarly to PepGFPm2, PepDsRed expressed the reporter gene efficiently also in tomato plants. We then used PepGFPm2 and PepDsRed to study the PepMV localization in both N. benthamiana and tomato cells. Using confocal laser scanning microscopy (CLSM), we observed characteristic fluorescent bodies in PepMV-infected cells; these bodies had a cytoplasmic localization and appeared in close proximity to the cell nucleus. Already at 3 days post-agroinoculation there were fluorescent bodies in almost every cell of agroinoculated tissues of both hosts, and always one body per cell. When markers for the endoplasmic reticulum or the Golgi apparatus were co-expressed with PepGFPm2 or PepDsRed, a reorganisation of these organelles was observed, with images suggesting that both are intimately related but not the main constituents of the PepMV bodies. Altogether, this set of data suggested that the PepMV bodies are similar to the potato virus X (PVX) "X-bodies", which have been described as the PVX viral replication complexes (VRCs). To complete the set of PepMV-based vectors, we constructed a vector expressing the BAR herbicide resistance gene, useful for massive susceptibility screenings.

CONCLUSIONS

We have significantly expanded the PepMV tool box by producing a set of new vectors with improved stability and efficiency in both N. benthamiana and tomato plants. By using two of these vectors, we have described characteristic cellular bodies induced by PepMV infection; these bodies are likely the PepMV VRCs.

A thioredoxin NbTRXh2 from Nicotiana benthamiana negatively regulates the movement of Bamboo mosaic virus

An up-regulated gene derived from Bamboo mosaic virus (BaMV)-infected Nicotiana benthamiana plants was cloned and characterized in this study. BaMV is a single-stranded, positive-sense RNA virus. This gene product, designated as NbTRXh2, was matched with sequences of thioredoxin h proteins, a group of small proteins with a conserved active-site motif WCXPC conferring disulfide reductase activity. To examine how NbTRXh2 is involved in the infection cycle of BaMV, we used the virus-induced gene silencing technique to knock down NbTRXh2 expression in N. benthamiana and inoculated the plants with BaMV. We observed that, compared with control plants, BaMV coat protein accumulation increased in knockdown plants at 5 days post-inoculation (dpi). Furthermore, BaMV coat protein accumulation did not differ significantly between NbTRXh2-knockdown and control protoplasts at 24 hpi. The BaMV infection foci in NbTRXh2-knockdown plants were larger than those in control plants. In addition, BaMV coat protein accumulation decreased when NbTRXh2 was transiently expressed in plants. These results suggest that NbTRXh2 plays a role in restricting BaMV accumulation. Moreover, confocal microscopy results showed that NbTRXh2-OFP (NbTRXh2 fused with orange fluorescent protein) localized at the plasma membrane, similar to AtTRXh9, a homologue in Arabidopsis. The expression of the mutant that did not target the substrates failed to reduce BaMV accumulation. Co-immunoprecipitation experiments revealed that the viral movement protein TGBp2 could be the target of NbTRXh2. Overall, the functional role of NbTRXh2 in reducing the disulfide bonds of targeting factors, encoded either by the host or virus (TGBp2), is crucial in restricting BaMV movement.

Plasma membrane-associated cation-binding protein 1-like protein negatively regulates intercellular movement of BaMV

To establish a successful infection, a virus needs to replicate and move cell-to-cell efficiently. We investigated whether one of the genes upregulated in Nicotiana benthamiana after Bamboo mosaic virus (BaMV) inoculation was involved in regulating virus movement. We revealed the gene to be a plasma membrane-associated cation-binding protein 1-like protein, designated NbPCaP1L. The expression of NbPCaP1L in N. benthamiana was knocked down using Tobacco rattle virus-based gene silencing and consequently the accumulation of BaMV increased significantly to that of control plants. Further analysis indicated no significant difference in the accumulation of BaMV in NbPCaP1L knockdown and control protoplasts, suggesting NbPCaP1L may affect cell-to-cell movement of BaMV. Using a viral vector expressing green fluorescent protein in the knockdown plants, the mean area of viral focus, as determined by fluorescence, was found to be larger in NbPCaP1L knockdown plants. Orange fluorescence protein (OFP)-fused NbPCaP1L, NbPCaP1L-OFP, was expressed in N. benthamiana and reduced the accumulation of BaMV to 46%. To reveal the possible interaction of viral protein with NbPCaP1L, we performed yeast two-hybrid and co-immunoprecipitation experiments. The results indicated that NbPCaP1L interacted with BaMV replicase. The results also suggested that NbPCaP1L could trap the BaMV movement RNP complex via interaction with the viral replicase in the complex and so restricted viral cell-to-cell movement.

Gut microbiota modulate the immune effect against hepatitis B virus infection

The immunological mechanisms by which hepatitis B virus (HBV) initiates and maintains acute or chronic infection, even the formation of cirrhosis and hepatocellular carcinoma, are still undefined. An increasing number of studies have shown that intestinal flora regulate immune homeostasis, and, thus, protect the immunologic function against hepatitis virus infection. In this article, we discuss gut microbiota and its potential immune effects against HBV infection. It may provide a novel insight into the pathogenesis of HBV infection, as well as a potential therapeutic target to HBV-related disease.

Double Subgenomic Promoter Control for a Target Gene Superexpression by a Plant Viral Vector

Several new deconstructed vectors based on a potexvirus genome sequence for efficient expression of heterologous proteins in plants were designed. The first obtained vector (AltMV-single), based on the Alternanthera mosaic virus (AltMV) strain MU genome, bears a typical architecture for deconstructed plant viral vectors, i.e. a triple gene block was deleted from the viral genome and the model gene of interest was placed under control of the first viral subgenomic promoter. To enhance the efficiency of expression, maintained by the AltMV-single, another vector (AltMV-double) was designed. In AltMV-double, the gene of interest was controlled by two viral subgenomic promoters located sequentially without a gap upstream of the target gene. It was found that AltMV-double provided a significantly higher level of accumulation of the target protein in plants than AltMV-single. Moreover, our data clearly show the requirement of the presence and functioning of both the subgenomic promoters for demonstrated high level of target protein expression by AltMV-double. Taken together, our results describe an additional possible way to enhance the efficiency of transient protein expression maintained in plants by a plant viral vector.

Cis-acting RNA elements in positive-strand RNA plant virus genomes

Positive-strand RNA viruses are the most common type of plant virus. Many aspects of the reproductive cycle of this group of viruses have been studied over the years and this has led to the accumulation of a significant amount of insightful information. In particular, the identification and characterization of cis-acting RNA elements within these viral genomes have revealed important roles in many fundamental viral processes such as virus disassembly, translation, genome replication, subgenomic mRNA transcription, and packaging. These functional cis-acting RNA elements include primary sequences, secondary and tertiary structures, as well as long-range RNA-RNA interactions, and they typically function by interacting with viral or host proteins. This review provides a general overview and update on some of the many roles played by cis-acting RNA elements in positive-strand RNA plant viruses.

Role of the Pepino mosaic virus 3'-untranslated region elements in negative-strand RNA synthesis in vitro

Pepino mosaic virus (PepMV) is a mechanically-transmitted positive-strand RNA potexvirus, with a 6410 nt long single-stranded (ss) RNA genome flanked by a 5'-methylguanosine cap and a 3' poly-A tail. Computer-assisted folding of the 64 nt long PepMV 3'-untranslated region (UTR) resulted in the prediction of three stem-loop structures (hp1, hp2, and hp3 in the 3'-5' direction). The importance of these structures and/or sequences for promotion of negative-strand RNA synthesis and binding to the RNA dependent RNA polymerase (RdRp) was tested in vitro using a specific RdRp assay. Hp1, which is highly variable among different PepMV isolates, appeared dispensable for negative-strand synthesis. Hp2, which is characterized by a large U-rich loop, tolerated base-pair changes in its stem as long as they maintained the stem integrity but was very sensitive to changes in the U-rich loop. Hp3, which harbours the conserved potexvirus ACUUAA hexamer motif, was essential for template activity. Template-RNA polymerase binding competition experiments showed that the ACUUAA sequence represents a high-affinity RdRp binding element.

Understanding the intracellular trafficking and intercellular transport of potexviruses in their host plants

The movement of potexviruses through the cytoplasm to plasmodesmata (PD) and through PD to adjacent cells depends on the viral and host cellular proteins. Potexviruses encode three movement proteins [referred to as the triple gene block (TGB1-3)]. TGB1 protein moves cell-to-cell through PD and requires TGB2 and TGB3, which are endoplasmic reticulum (ER)-located proteins. TGB3 protein directs the movement of the ER-derived vesicles induced by TGB2 protein from the perinuclear ER to the cortical ER. TGB2 protein physically interacts with TGB3 protein in a membrane-associated form and also interacts with either coat protein (CP) or TGB1 protein at the ER network. Recent studies indicate that potexvirus movement involves the interaction between TGB proteins and CP with host proteins including membrane rafts. A group of host cellular membrane raft proteins, remorins, can serve as a counteracting membrane platform for viral ribonucleoprotein (RNP) docking and can thereby inhibit viral movement. The CP, which is a component of the RNP movement complex, is also critical for viral cell-to-cell movement through the PD. Interactions between TGB1 protein and/or the CP subunit with the 5'-terminus of genomic RNA [viral RNA (vRNA)] form RNP movement complexes and direct the movement of vRNAs through the PD. Recent studies show that tobacco proteins such as NbMPB2C or NbDnaJ-like proteins interact with the stem-loop 1 RNA located at the 5'-terminus of Potato virus X vRNA and regulate intracellular as well as intercellular movement. Although several host proteins that interact with vRNAs or viral proteins and that are crucial for vRNA transport have been screened and characterized, additional host proteins and details of viral movement remain to be characterized. In this review, we describe recent progress in understanding potexvirus movement within and between cells and how such movement is affected by interactions between vRNA/proteins and host proteins.