Melon necrotic spot virus Replication Occurs in Association with Altered Mitochondria

Co-immunoprecipitation-Based Isolation of Double-Stranded RNA-Associated Protein Complexes in Nicotiana benthamiana

Double-stranded RNA (dsRNA) is associated with most viral infections, and is generated in host cells during viral replication. Viral RNA replication occurs within the viral factories called the viral replication complexes (VRCs). In addition to viral genome, viral-derived dsRNA and replicase, the VRCs composition remains largely unexplored. The dsRNA binding domain of the B2 protein from Flock house virus has been reported to be used for detecting viral-derived long dsRNA in plants efficiently. Nicotiana benthamiana is widely used as a model plant for plant-microbe interactions owing to its susceptibility to diverse plant diseases, especially viral diseases. Here, we describe the use of Nicotiana benthamiana stably expressing GFP-tagged dsRNA binding protein (B2: GFP) to pull down dsRNA and associated host and viral proteins from turnip mosaic virus-infected plants. The obtained protein complexes are compatible with functional assays, Western blotting, and mass spectrometry. This system provides a valuable and robust tool to study VRC proteome in N. benthamiana upon plant viral infections.

A viral protein targets mitochondria and chloroplasts by subverting general import pathways and specific receptors

IMPORTANCE

Many plant proteins and some proteins from plant pathogens are dually targeted to chloroplasts and mitochondria, and are supposed to be transported along the general pathways for organellar protein import, but this issue has not been explored yet. Moreover, organellar translocon receptors exist as families of several members whose functional specialization in different cargos is supposed but not thoroughly studied. This article provides novel insights into such topics showing for the first time that an exogenous protein, the melon necrotic spot virus coat protein, exploits the common Toc/Tom import systems to enter both mitochondria and chloroplasts while identifying the involved specific receptors.

A Correlation between 3'-UTR of OXA1 Gene and Yeast Mitochondrial Translation

Mitochondria possess their own DNA (mtDNA) and are capable of carrying out their transcription and translation. Although protein synthesis can take place in mitochondria, the majority of the proteins in mitochondria have nuclear origin. 3' and 5' untranslated regions of mRNAs (3'-UTR and 5'-UTR, respectively) are thought to play key roles in directing and regulating the activity of mitochondria mRNAs. Here we investigate the association between the presence of 3'-UTR from OXA1 gene on a prokaryotic reporter mRNA and mitochondrial translation in yeast. OXA1 is a nuclear gene that codes for mitochondrial inner membrane insertion protein and its 3'-UTR is shown to direct its mRNA toward mitochondria. It is not clear, however, if this mRNA may also be translated by mitochondria. In the current study, using a β-galactosidase reporter gene, we provide genetic evidence for a correlation between the presence of 3'-UTR of OXA1 on an mRNA and mitochondrial translation in yeast.

Manipulation of the Cellular Membrane-Cytoskeleton Network for RNA Virus Replication and Movement in Plants

Viruses infect all cellular life forms and cause various diseases and significant economic losses worldwide. The majority of viruses are positive-sense RNA viruses. A common feature of infection by diverse RNA viruses is to induce the formation of altered membrane structures in infected host cells. Indeed, upon entry into host cells, plant-infecting RNA viruses target preferred organelles of the cellular endomembrane system and remodel organellar membranes to form organelle-like structures for virus genome replication, termed as the viral replication organelle (VRO) or the viral replication complex (VRC). Different viruses may recruit different host factors for membrane modifications. These membrane-enclosed virus-induced replication factories provide an optimum, protective microenvironment to concentrate viral and host components for robust viral replication. Although different viruses prefer specific organelles to build VROs, at least some of them have the ability to exploit alternative organellar membranes for replication. Besides being responsible for viral replication, VROs of some viruses can be mobile to reach plasmodesmata (PD) via the endomembrane system, as well as the cytoskeleton machinery. Viral movement protein (MP) and/or MP-associated viral movement complexes also exploit the endomembrane-cytoskeleton network for trafficking to PD where progeny viruses pass through the cell-wall barrier to enter neighboring cells.

Three-dimensional analysis of membrane structures associated with tomato spotted wilt virus infection

To study viral infection, the direct structural visualization of the viral life cycle consisting of virus attachment, entry, replication, assembly and transport is essential. Although conventional electron microscopy (EM) has been extremely helpful in the investigation of virus-host cell interactions, three-dimensional (3D) EM not only provides important information at the nanometer resolution, but can also create 3D maps of large volumes, even entire virus-infected cells. Here, we determined the ultrastructural details of tomato spotted wilt virus (TSWV)-infected plant cells using focused ion beam scanning EM (FIB-SEM). The viral morphogenesis and dynamic transformation of paired parallel membranes (PPMs) were analyzed. The endoplasmic reticulum (ER) membrane network consisting of tubules and sheets was related to viral intracellular trafficking and virion storage. Abundant lipid-like bodies, clustering mitochondria, cell membrane tubules, and myelin-like bodies were likely associated with viral infection. Additionally, connecting structures between neighboring cells were found only in infected plant tissues and showed the characteristics of tubular structure. These novel connections that formed continuously in the cell wall or were wrapped by the cell membranes of neighboring cells appeared frequently in the large-scale 3D model, suggesting additional strategies for viral trafficking that were difficult to distinguish using conventional EM.

Co-opted membranes, lipids, and host proteins: what have we learned from tombusviruses?

Positive-strand RNA viruses replicate in intracellular membranous structures formed after virus-driven intensive manipulation of subcellular organelles and membranes. These unique structures are called viral-replication organelles (VROs). To build VROs, the replication proteins coded by (+)RNA viruses co-opt host proteins, including membrane-shaping, lipid synthesis, and lipid-modification enzymes to create an optimal microenvironment that (i) concentrates the viral replicase and associated host proteins and the viral RNAs; (ii) regulates enzymatic activities and spatiotemporally the replication process; and (iii) protects the viral RNAs from recognition and degradation by the host innate immune defense. Tomato bushy stunt virus (TBSV), a plant (+)RNA virus, serves as an advanced model to study the interplay among viral components, co-opted host proteins, lipids, and membranes. This review presents our current understanding of the complex interaction between TBSV and host with panviral implications.

Voltage-dependent anion channel proteins associate with dynamic Bamboo mosaic virus-induced complexes

Infection cycles of viruses are highly dependent on membrane-associated host factors. To uncover the infection cycle of Bamboo mosaic virus (BaMV) in detail, we purified the membrane-associated viral complexes from infected Nicotiana benthamiana plants and analyzed the involved host factors. Four isoforms of voltage-dependent anion channel (VDAC) proteins on the outer membrane of mitochondria were identified due to their upregulated expression in the BaMV complex-enriched membranous fraction. Results from loss- and gain-of-function experiments indicated that NbVDAC2, -3, and -4 are essential for efficient BaMV accumulation. During BaMV infection, all NbVDACs concentrated into larger aggregates, which overlapped and trafficked with BaMV virions to the structure designated as the "dynamic BaMV-induced complex." Besides the endoplasmic reticulum and mitochondria, BaMV replicase and double-stranded RNAs were also found in this complex, suggesting the dynamic BaMV-induced complex is a replication complex. Yeast two-hybrid and pull-down assays confirmed that BaMV triple gene block protein 1 (TGBp1) could interact with NbVDACs. Confocal microscopy revealed that TGBp1 is sufficient to induce NbVDAC aggregates, which suggests that TGBp1 may play a pivotal role in the NbVDAC-virion complex. Collectively, these findings indicate that NbVDACs may associate with the dynamic BaMV-induced complex via TGBp1 and NbVDAC2, -3, or -4 and can promote BaMV accumulation. This study reveals the involvement of mitochondrial proteins in a viral complex and virus infection.

Three-dimensional quantitative imaging of Tobacco mosaic virus and Zucchini yellow mosaic virus induced ultrastructural changes

Two-dimensional ultrastructural changes of Tobacco mosaic virus (TMV) and Zucchini yellow mosaic virus (ZYMV) in tobacco and pumpkin plants, respectively, are well studied. To provide 3D data, representative control and infected cells were reconstructed using serial sectioning and transmission electron microscopy. Quantitative data of 3D ultrastructural changes were then extracted from the cytosol and organelles by image analysis. While TMV induced the accumulation of an average of 40 virus inclusion bodies in the cytosol, which covered about 13% of the cell volume, ZYMV caused the accumulation of an average of 1752 cylindrical inclusions in the cytosol, which covered about 2.7% of the total volume of the cell. TMV infection significantly decreased the number and size of mitochondria (- 49 and - 20%) and peroxisomes (- 62 and - 28%) of the reconstructed cell. The reconstructed ZYMV-infected cell contained more (105%) and larger (109%) mitochondria when compared to the control cell. While the reconstructed TMV-infected cell contained larger (20%) and the ZYMV-infected smaller (19%) chloroplasts, both contained less chloroplasts (- 40% for TMV and - 23% for ZYMV). In chloroplasts, the volume of starch and plastoglobules increased (664% and 150% for TMV and 1324% and 1300% for ZYMV) when compared to the control. The latter was correlated with a decrease in the volume of thylakoids in the reconstructed ZYMV-infected cell (- 31%) indicating that degradation products from thylakoids are transported and stored in plastoglobules. Summing up, the data collected in this study give a comprehensive overview of 3D changes induced by TMV and ZYMV in plants.

The mitochondrial and chloroplast dual targeting of a multifunctional plant viral protein modulates chloroplast-to-nucleus communication, RNA silencing suppressor activity, encapsidation, pathogenesis and tissue tropism

Plant defense against melon necrotic spot virus (MNSV) is triggered by the viral auxiliary replicase p29 that is targeted to mitochondrial membranes causing morphological alterations, oxidative burst and necrosis. Here we show that MNSV coat protein (CP) was also targeted to mitochondria and mitochondrial-derived replication complexes [viral replication factories or complex (VRC)], in close association with p29, in addition to chloroplasts. CP import resulted in the cleavage of the R/arm domain previously implicated in genome binding during encapsidation and RNA silencing suppression (RSS). We also show that CP organelle import inhibition enhanced RSS activity, CP accumulation and VRC biogenesis but resulted in inhibition of systemic spreading, indicating that MNSV whole-plant infection requires CP organelle import. We hypothesize that to alleviate the p29 impact on host physiology, MNSV could moderate its replication and p29 accumulation by regulating CP RSS activity through organelle targeting and, consequently, eluding early-triggered antiviral response. Cellular and molecular events also suggested that S/P domains, which correspond to processed CP in chloroplast stroma or mitochondrion matrix, could mitigate host response inhibiting p29-induced necrosis. S/P deletion mainly resulted in a precarious balance between defense and counter-defense responses, generating either cytopathic alterations and MNSV cell-to-cell movement restriction or some degree of local movement. In addition, local necrosis and defense responses were dampened when RSS activity but not S/P organelle targeting was affected. Based on a robust biochemical and cellular analysis, we established that the mitochondrial and chloroplast dual targeting of MNSV CP profoundly impacts the viral infection cycle.

Proteasome and selective autophagy: Brothers-in-arms for organelle quality control

Maintaining the integrity of organelles despite the cellular disturbances that arise during stress is essential for life. To ensure organelle proteostasis (protein homeostasis), plants have evolved multitiered quality control mechanisms that work together to repair or recycle the damaged organelles. Despite recent advances, our understanding of plant organelle quality control mechanisms is far from complete. Especially, the crosstalk between different quality control pathways remains elusive. Here, we highlight recent advances on organelle quality control, focusing on the targeted protein degradation pathways that maintain the homeostasis of the endoplasmic reticulum (ER), chloroplast, and mitochondria. We discuss how plant cells decide to employ different degradation pathways and propose tools that could be used to discover the missing components in organelle quality control.

Ultrastructural Features of Membranous Replication Organelles Induced by Positive-Stranded RNA Viruses

All intracellular pathogens critically depend on host cell organelles and metabolites for successful infection and replication. One hallmark of positive-strand RNA viruses is to induce alterations of the (endo)membrane system in order to shield their double-stranded RNA replication intermediates from detection by the host cell’s surveillance systems. This spatial seclusion also allows for accruing host and viral factors and building blocks required for efficient replication of the genome and prevents access of antiviral effectors. Even though the principle is iterated by almost all positive-strand RNA viruses infecting plants and animals, the specific structure and the organellar source of membranes differs. Here, we discuss the characteristic ultrastructural features of the virus-induced membranous replication organelles in plant and animal cells and the scientific progress gained by advanced microscopy methods.

Gimme shelter: three-dimensional architecture of the endoplasmic reticulum, the replication site of grapevine Pinot gris virus

Grapevine leaf mottling and deformation is a novel grapevine disease that has been associated with grapevine Pinot gris virus (GPGV). The virus was observed exclusively inside membrane-bound structures in the bundle sheath cells of the infected grapevines. As reported widely in the literature, many positive-sense single-stranded RNA viruses modify host-cell membranes to form a variety of deformed organelles, which shelter viral genome replication from host antiviral compounds. Morphologically, the GPGV-associated membranous structures resemble the deformed endoplasmic reticulum described in other virus-host interactions. In this study we investigated the GPGV-induced membranous structures observed in the bundle sheath cells of infected plants. The upregulation of different ER stress-related genes was evidenced by RT-qPCR assays, further confirming the involvement of the ER in grapevine/GPGV interaction. Specific labelling of the membranous structures with an antibody against luminal-binding protein identified them as ER. Double-stranded RNA molecules, which are considered intermediates of viral replication, were localised exclusively in the ER-derived structures and indicated that GPGV exploited this organelle to replicate itself in a shelter niche. Novel analyses using focussed ion-beam scanning electron microscopy (FIB-SEM) were performed in grapevine leaf tissues to detail the three-dimensional organisation of the ER-derived structures and their remodelling due to virus replication.

Imaging Techniques to Study Plant Virus Replication and Vertical Transmission

Plant viruses are obligate parasites that need to usurp plant cell metabolism in order to infect their hosts. Imaging techniques have been used for quite a long time to study plant virus-host interactions, making it possible to have major advances in the knowledge of plant virus infection cycles. The imaging techniques used to study plant-virus interactions have included light microscopy, confocal laser scanning microscopy, and scanning and transmission electron microscopies. Here, we review the use of these techniques in plant virology, illustrating recent advances in the area with examples from plant virus replication and virus plant-to-plant vertical transmission processes.

Three-dimensional reconstruction and comparison of vacuolar membranes in response to viral infection

The vacuole is a unique plant organelle that plays an important role in maintaining cellular homeostasis under various environmental stress conditions. However, the effects of biotic stress on vacuole structure has not been examined using three-dimensional (3D) visualization. Here, we performed 3D electron tomography to compare the ultrastructural changes in the vacuole during infection with different viruses. The 3D models revealed that vacuoles are remodeled in cells infected with cucumber mosaic virus (CMV) or tobacco necrosis virus A Chinese isolate (TNV-AC ), resulting in the formation of spherules at the periphery of the vacuole. These spherules contain neck-like channels that connect their interior with the cytosol. Confocal microscopy of CMV replication proteins 1a and 2a and TNV-AC auxiliary replication protein p23 showed that all of these proteins localize to the tonoplast. Electron microscopy revealed that the expression of these replication proteins alone is sufficient to induce spherule formation on the tonoplast, suggesting that these proteins play prominent roles in inducing vacuolar membrane remodeling. This is the first report of the 3D structures of viral replication factories built on the tonoplasts. These findings contribute to our understanding of vacuole biogenesis under normal conditions and during assembly of plant (+) RNA virus replication complexes.

Intercellular movement of plant RNA viruses: Targeting replication complexes to the plasmodesma for both accuracy and efficiency

Replication and movement are two critical steps in plant virus infection. Recent advances in the understanding of the architecture and subcellular localization of virus-induced inclusions and the interactions between viral replication complex (VRC) and movement proteins (MPs) allow for the dissection of the intrinsic relationship between replication and movement, which has revealed that recruitment of VRCs to the plasmodesma (PD) via direct or indirect MP-VRC interactions is a common strategy used for cell-to-cell movement by most plant RNA viruses. In this review, we summarize the recent advances in the understanding of virus-induced inclusions and their roles in virus replication and cell-to-cell movement, analyze the advantages of such coreplicational movement from a viral point of view and discuss the possible mechanical force by which MPs drive the movement of virions or viral RNAs through the PD. Finally, we highlight the missing pieces of the puzzle of viral movement that are especially worth investigating in the near future.

Ultrastructural Analysis of Cells From Bell Pepper (Capsicum annuum) Infected With Bell Pepper Endornavirus

Endornaviruses include viruses that infect fungi, oomycetes, and plants. The genome of plant endornaviruses consists of linear ssRNA ranging in size from approximately 13-18 kb and lacking capsid protein and cell-to-cell movement capability. Although, plant endornaviruses have not been shown to cause detectable changes in the plant phenotype, they have been associated with alterations of the host physiology. Except for the association of cytoplasmic vesicles with infections by Vicia faba endornavirus, effects on the plant cell ultrastructure caused by endornaviruses have not been reported. Bell pepper endornavirus (BPEV) has been identified in several pepper (Capsicum spp.) species. We conducted ultrastructural analyses of cells from two near-isogenic lines of the bell pepper (C. annuum) cv. Marengo, one infected with BPEV and the other BPEV-free, and found cellular alterations associated with BPEV-infections. Some cells of plants infected with BPEV exhibited alterations of organelles and other cell components. Affected cells were located mainly in the mesophyll and phloem tissues. Altered organelles included mitochondrion, chloroplast, and nucleus. The mitochondria from BPEV-infected plants exhibited low number of cristae and electron-lucent regions. Chloroplasts contained plastoglobules and small vesicles in the surrounding cytoplasm. Translucent regions in thylakoids were observed, as well as hypertrophy of the chloroplast structure. Many membranous vesicles were observed in the stroma along the envelope. The nuclei revealed a dilation of the nuclear envelope with vesicles and perinuclear areas. The organelle changes were accompanied by membranous structure rearrangements, such as paramural bodies and multivesicular bodies. These alterations were not observed in cells from plants of the BPEV-free line. Overall, the observed ultrastructural cell alterations associated with BPEV are similar to those caused by plant viruses and viroids and suggest some degree of parasitic interaction between BPEV and the plant host.

Development of monoclonal antibodies against melon necrotic spot virus and their use for virus detection

Melon necrotic spot virus (MNSV) is endemic in cucurbit crops worldwide, causing epidemic outbreaks from time to time. MNSV is transmitted in nature by a soil-inhabiting fungus and also through seeds, making its detection in seed certification programs a necessity. Polyclonal antisera and RT-PCR-based detection assays have been developed for MNSV, but up to now no monoclonal antibodies (mAbs) have been described for this virus. In this study, we have produced mAbs in BALB/c mice against the MNSV over-expressed coat protein (CP). Titers of the antibodies produced against the recombinant MNSV CP ranged around 10^-3-10^-4 and the IgG yields for each mAb from ascitic fluids ranged from 1.51 to 6 mg/mL. Supernatants from ten hybridoma cell lines were evaluated in Western blot analysis and seven of them efficiently recognized the MNSV CP in crude extracts of MNSV-infected leaf material; the 2D4H4 hybridoma cell line was selected for further purification and characterization. The isotype of the 2D4H4 immunoglobulin class was identified as IgG2a and kappa light-chain. Western-blot analyses showed that mAb 2D4H4 provided sensitive and specific detection of MNSV. A TAS-ELISA protocol was developed for mAb 2D4H4. Using this protocol, limits of detection of 1:20,480 and 1:10,240 (g/mL, w/v) were attained for the homologous isolate and a heterologous MNSV isolate, respectively. Moreover, mAb 2D4H4 was used successfully to localize the MNSV CP in infected cells by immunocytochemistry/transmission electron microscopy, illustrating the usefulness of this mAb for advanced cellular studies.

The viral replication organelles within cells studied by electron microscopy

Transmission electron microscopy (TEM) has been crucial to study viral infections. As a result of recent advances in light and electron microscopy, we are starting to be aware of the variety of structures that viruses assemble inside cells. Viruses often remodel cellular compartments to build their replication factories. Remarkably, viruses are also able to induce new membranes and new organelles. Here we revise the most relevant imaging technologies to study the biogenesis of viral replication organelles. Live cell microscopy, correlative light and electron microscopy, cryo-TEM, and three-dimensional imaging methods are unveiling how viruses manipulate cell organization. In particular, methods for molecular mapping in situ in two and three dimensions are revealing how macromolecular complexes build functional replication complexes inside infected cells. The combination of all these imaging approaches is uncovering the viral life cycle events with a detail never seen before.

In situ hybridization for the localization of two pepino mosaic virus isolates in mixed infections

In situ hybridization (ISH) is an informative and relatively accessible technique for the localization of viral genomes in plant tissue and cells. However, simultaneous visualization of related plant viruses in mixed infections may be limited by the nucleotide similarity in the genomes and the single chromogenic detection over the same sample preparation. To address this issue, we used two Pepino mosaic virus isolates and performed ISH over consecutive serial cross-sections of paraffin-embedded leaf samples of single and mixed infected Nicotiana benthamiana plants. Moreover, the probe design was optimized to reduce cross-hybridisation, and co-localization was based on the overlapping of consecutive cross-sections from mixed infected leaves; thus, our results showed that both Pepino mosaic virus isolates co-localized in the same leaf tissue. In turn, both isolates were localized in the cytoplasm of the same cells. These results provide valuable information for studying mixed infections in plants by using a simple ISH procedure that is accessible to any pathology laboratory.

Electron Microscopy Methods for Virus Diagnosis and High Resolution Analysis of Viruses

The term "virosphere" describes both the space where viruses are found and the space they influence, and can extend to their impact on the environment, highlighting the complexity of the interactions involved. Studying the biology of viruses and the etiology of virus disease is crucial to the prevention of viral disease, efficient and reliable virus diagnosis, and virus control. Electron microscopy (EM) is an essential tool in the detection and analysis of virus replication. New EM methods and ongoing technical improvements offer a broad spectrum of applications, allowing in-depth investigation of viral impact on not only the host but also the environment. Indeed, using the most up-to-date electron cryomicroscopy methods, such investigations are now close to atomic resolution. In combination with bioinformatics, the transition from 2D imaging to 3D remodeling allows structural and functional analyses that extend and augment our knowledge of the astonishing diversity in virus structure and lifestyle. In combination with confocal laser scanning microscopy, EM enables live imaging of cells and tissues with high-resolution analysis. Here, we describe the pivotal role played by EM in the study of viruses, from structural analysis to the biological relevance of the viral metagenome (virome).

Killing two birds with one stone: How do Plant Viruses Break Down Plant Defenses and Manipulate Cellular Processes to Replicate Themselves?

As simple organisms with a parasite nature, viruses have become masters in manipulating and subvert cellular components, including host proteins and organelles, to improve viral replication. Therefore, the understanding of viral strategies to manipulate cell function disrupting plant defenses and enhancing viral infection cycles is fundamental to the production of virus-resistant plant lines. After invading susceptible plants, viruses create conditions that favor local and systemic infections by suppressing multiple layers of innate host defenses while use cellular machinery to own benefit. Viral interference in interlinked essential cellular functions results in phenotypic changes and disease symptoms, which debilitates plants favoring infection establishment. Herein in this review, the novelty it will be the discussion about the strategies used by (+) single strand RNA viruses to affect cellular processes and components to improve viral replication, in parallel to overcome plant defenses, favoring disease establishment by applying in one action using the same viral protein to coordinate viral replication and breaking down plant defense. This focus on plant-virus interaction was never done before, and this knowledge has the potential to help in the development of new strategies to produce resistant plants.

Electron Microscopy Methods for Virus Diagnosis and High Resolution Analysis of Viruses

The term "virosphere" describes both the space where viruses are found and the space they influence, and can extend to their impact on the environment, highlighting the complexity of the interactions involved. Studying the biology of viruses and the etiology of virus disease is crucial to the prevention of viral disease, efficient and reliable virus diagnosis, and virus control. Electron microscopy (EM) is an essential tool in the detection and analysis of virus replication. New EM methods and ongoing technical improvements offer a broad spectrum of applications, allowing in-depth investigation of viral impact on not only the host but also the environment. Indeed, using the most up-to-date electron cryomicroscopy methods, such investigations are now close to atomic resolution. In combination with bioinformatics, the transition from 2D imaging to 3D remodeling allows structural and functional analyses that extend and augment our knowledge of the astonishing diversity in virus structure and lifestyle. In combination with confocal laser scanning microscopy, EM enables live imaging of cells and tissues with high-resolution analysis. Here, we describe the pivotal role played by EM in the study of viruses, from structural analysis to the biological relevance of the viral metagenome (virome).

Three-Dimensional Architecture and Biogenesis of Membrane Structures Associated with Plant Virus Replication

Positive-sense (+) RNA viruses represent the most abundant group of viruses and are dependent on the host cell machinery to replicate. One remarkable feature that occurs after (+) RNA virus entry into cells is the remodeling of host endomembranes, leading to the formation of viral replication factories. Recently, rapid progress in three-dimensional (3D) imaging technologies, such as electron tomography (ET) and focused ion beam-scanning electron microscopy (FIB-SEM), has enabled researchers to visualize the novel membrane structures induced by viruses at high resolution. These 3D imaging technologies provide new mechanistic insights into the viral infection cycle. In this review, we summarize the latest reports on the cellular remodeling that occurs during plant virus infection; in particular, we focus on studies that provide 3D architectural information on viral replication factories. We also outline the mechanisms underlying the formation of these membranous structures and discuss possible future research directions.

Host Factors Involved in the Intracellular Movement of Bamboo mosaic virus

Viruses move intracellularly to their replication compartments, and the newly synthesized viral complexes are transported to neighboring cells through hijacking of the host endomembrane systems. During these processes, numerous interactions occur among viral proteins, host proteins, and the cytoskeleton system. This review mainly focuses on the plant endomembrane network, which may be utilized by Bamboo mosaic virus (BaMV) to move to its replication compartment, and summarizes the host factors that may be directly involved in delivering BaMV cargoes during intracellular movement. Accumulating evidence indicates that plant endomembrane systems are highly similar but exhibit significant variations from those of other eukaryotic cells. Several Nicotiana benthamiana host proteins have recently been identified to participate in the intracellular movement of BaMV. Chloroplast phosphoglycerate kinase, a host protein transported to chloroplasts, binds to BaMV RNAs and facilitates BaMV replication. NbRABG3f is a small GTPase that plays an essential role in vesicle transportation and is also involved in BaMV replication. These two host proteins may deliver BaMV to the replication compartment. Rab GTPase activation protein 1, which switches Rab GTPase to the inactive conformation, participates in the cell-to-cell movement of BaMV, possibly by trafficking BaMV cargo to neighboring cells after replication. By analyzing the host factors involved in the intracellular movement of BaMV and the current knowledge of plant endomembrane systems, a tentative model for BaMV transport to its replication site within plant cells is proposed.

An Update on the Intracellular and Intercellular Trafficking of Carmoviruses

Despite harboring the smallest genomes among plant RNA viruses, carmoviruses have emerged as an ideal model system for studying essential steps of the viral cycle including intracellular and intercellular trafficking. Two small movement proteins, formerly known as double gene block proteins (DGBp1 and DGBp2), have been involved in the movement throughout the plant of some members of carmovirus genera. DGBp1 RNA-binding capability was indispensable for cell-to-cell movement indicating that viral genomes must interact with DGBp1 to be transported. Further investigation on Melon necrotic spot virus (MNSV) DGBp1 subcellular localization and dynamics also supported this idea as this protein showed an actin-dependent movement along microfilaments and accumulated at the cellular periphery. Regarding DGBp2, subcellular localization studies showed that MNSV and Pelargonium flower break virus DGBp2s were inserted into the endoplasmic reticulum (ER) membrane but only MNSV DGBp2 trafficked to plasmodesmata (PD) via the Golgi apparatus through a COPII-dependent pathway. DGBp2 function is still unknown but its localization at PD was a requisite for an efficient cell-to-cell movement. It is also known that MNSV infection can induce a dramatic reorganization of mitochondria resulting in anomalous organelles containing viral RNAs. These putative viral factories were frequently found associated with the ER near the PD leading to the possibility that MNSV movement and replication could be spatially linked. Here, we update the current knowledge of the plant endomembrane system involvement in carmovirus intra- and intercellular movement and the tentative model proposed for MNSV transport within plant cells.

Transcriptomic profiling of Melon necrotic spot virus-infected melon plants revealed virus strain and plant cultivar-specific alterations

Background

Viruses are among the most destructive and difficult to control plant pathogens. Melon (Cucumis melo L.) has become the model species for the agriculturally important Cucurbitaceae family. Approaches that take advantage of recently developed genomic tools in melon have been extremely useful for understanding viral pathogenesis and can contribute to the identification of target genes for breeding new resistant cultivars. In this work, we have used a recently described melon microarray for transcriptome profiling of two melon cultivars infected with two strains of Melon necrotic spot virus (MNSV) that only differ on their 3′-untranslated regions.

Results

Melon plant tissues from the cultivars Tendral or Planters Jumbo were locally infected with either MNSV-Mα5 or MNSV-Mα5/3’264 and analysed in a time-course experiment. Principal component and hierarchical clustering analyses identified treatment (healthy vs. infected) and sampling date (3 vs. 5 dpi) as the primary and secondary variables, respectively. Out of 7566 and 7074 genes deregulated by MNSV-Mα5 and MNSV-Mα5/3’264, 1851 and 1356, respectively, were strain-specific. Likewise, MNSV-Mα5/3’264 specifically deregulated 2925 and 1618 genes in Tendral and Planters Jumbo, respectively. The GO categories that were significantly affected were clearly different for the different virus/host combinations. Grouping genes according to their patterns of expression allowed for the identification of two groups that were specifically deregulated by MNSV-Mα5/3’264 with respect to MNSV-Mα5 in Tendral, and one group that was antagonistically regulated in Planters Jumbo vs. Tendral after MNSV-Mα5/3’264 infection. Genes in these three groups belonged to diverse functional classes, and no obvious regulatory commonalities were identified. When data on MNSV-Mα5/Tendral infections were compared to equivalent data on cucumber mosaic virus or watermelon mosaic virus infections, cytokinin-O-glucosyltransferase2 was identified as the only gene that was deregulated by all three viruses, with infection dynamics correlating with the amplitude of transcriptome remodeling.

Conclusions

Strain-specific changes, as well as cultivar-specific changes, were identified by profiling the transcriptomes of plants from two melon cultivars infected with two MNSV strains. No obvious regulatory features shared among deregulated genes have been identified, pointing toward regulation through differential functional pathways.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2772-5) contains supplementary material, which is available to authorized users.

Virus assembly factories in a lipid world

Many viruses build specialized structures known as viral factories, a protected environment in which viral genome replication and morphogenesis take place. Recent findings show that viruses manipulate lipid flows to assemble these replication platforms. Viruses are thus able to create new membranes by interfering with lipid metabolism, targeting and transport; they make use of specific lipid transfer proteins (LTP) at membrane contact sites, and frequently recruit endoplasmic reticulum (ER), ER export sites, and mitochondria. Some factories, such as those built by plant and certain animal viruses, are motile membranous structures involved in intracellular or intercellular transport of the replicated viral genome. The identification of lipids and LTP subverted by viruses might lead to better understand and fight viral infections.

Cell-Free and Cell-Based Approaches to Explore the Roles of Host Membranes and Lipids in the Formation of Viral Replication Compartment Induced by Tombusviruses

Plant positive strand RNA viruses are intracellular infectious agents that take advantage of cellular lipids and membranes to support replication and protect viral RNA from degradation by host antiviral responses. In this review, we discuss how Tomato bushy stunt virus (TBSV) co-opts lipid transfer proteins and modulates lipid metabolism and transport to facilitate the assembly of the membrane-bound viral replicase complexes within intricate replication compartments. Identification and characterization of the proviral roles of specific lipids and proteins involved in lipid metabolism based on results from yeast (Saccharomyces cerevisiae) model host and cell-free approaches are discussed. The review also highlights the advantage of using liposomes with chemically defined composition to identify specific lipids required for TBSV replication. Remarkably, all the known steps in TBSV replication are dependent on cellular lipids and co-opted membranes.

Morphogenesis of Endoplasmic Reticulum Membrane-Invaginated Vesicles during Beet Black Scorch Virus Infection: Role of Auxiliary Replication Protein and New Implications of Three-Dimensional Architecture

All well-characterized positive-strand RNA viruses[(+)RNA viruses] induce the formation of host membrane-bound viral replication complexes (VRCs), yet the underlying mechanism and machinery for VRC formation remain elusive. We report here the biogenesis and topology of the Beet black scorch virus (BBSV) replication complex. Distinct cytopathological changes typical of endoplasmic reticulum (ER) aggregation and vesiculation were observed in BBSV-infected Nicotiana benthamiana cells. Immunogold labeling of the auxiliary replication protein p23 and double-stranded RNA (dsRNA) revealed that the ER-derived membranous spherules provide the site for BBSV replication. Further studies indicated that p23 plays a crucial role in mediating the ER rearrangement. Three-dimensional electron tomographic analysis revealed the formation of multiple ER-originated vesicle packets. Each vesicle packet enclosed a few to hundreds of independent spherules that were invaginations of the ER membranes into the lumen. Strikingly, these vesicle packets were connected to each other via tubules, a rearrangement event that is rare among other virus-induced membrane reorganizations. Fibrillar contents within the spherules were also reconstructed by electron tomography, which showed diverse structures. Our results provide the first, to our knowledge, three-dimensional ultrastructural analysis of membrane-bound VRCs of a plant (+)RNA virus and should help to achieve a better mechanistic understanding of the organization and microenvironment of plant (+)RNA virus replication complexes.

IMPORTANCE

Assembly of virus replication complexes for all known positive-strand RNA viruses depends on the extensive remodeling of host intracellular membranes. Beet black scorch virus, a necrovirus in the family Tombusviridae, invaginates the endoplasmic reticulum (ER) membranes to form spherules in infected cells. Double-stranded RNAs, the viral replication intermediate, and the viral auxiliary replication protein p23 are all localized within such viral spherules, indicating that these are the sites for generating progeny viral RNAs. Furthermore, the BBSV p23 protein could to some extent reorganize the ER when transiently expressed in N. benthamiana. Electron tomographic analysis resolves the three-dimensional (3D) architecture of such spherules, which are connected to the cytoplasm via a neck-like structure. Strikingly, different numbers of spherules are enclosed in ER-originated vesicle packets that are connected to each other via tubule-like structures. Our results have significant implications for further understanding the mechanisms underlying the replication of positive-strand RNA viruses.