Autophagy functions as an antiviral mechanism against geminiviruses in plants

Microbial Effector Proteins - A Journey through the Proteolytic Landscape

In the evolutionary arms race between pathogens and plants, pathogens evolved effector molecules that they secrete into the host to subvert plant cellular responses in a process termed the effector-targeted pathway (ETP). During recent years the repertoire of ETPs has increased and mounting evidence indicates that the proteasome and autophagy pathways are central hubs of microbial effectors. Both degradation pathways are implicated in a broad array of cellular responses and thus constitute an attractive target for effector proteins to have a broader impact on the host. In this article we first summarize recent findings on how effectors from various pathogens modulate proteolytic pathways and then provide a network analysis of established effector targets implicated in proteolytic degradation machineries. With this network we emphasize the idea that effectors targeting proteolytic degradation pathways will affect the protein synthesis-transport and degradation triangle. We put in perspective that, in utilizing the effector diversity of microbes, we produce excellent tools to study diverse cellular pathways and their possible interplay with each other.

Cotton leaf curl Multan virus βC1 Protein Induces Autophagy by Disrupting the Interaction of Autophagy-Related Protein 3 with Glyceraldehyde-3-Phosphate Dehydrogenases

Autophagy plays an important role in plant-pathogen interactions. Several pathogens including viruses induce autophagy in plants, but the underpinning mechanism remains largely unclear. Furthermore, in virus-plant interactions, viral factor(s) that induce autophagy have yet to be identified. Here, we report that the βC1 protein of Cotton leaf curl Multan betasatellite (CLCuMuB) interacts with cytosolic glyceraldehyde-3-phosphate dehydrogenase (GAPC), a negative autophagic regulator, to induce autophagy in Nicotiana benthamiana CLCuMuB βC1 bound to GAPCs and disrupted the interaction between GAPCs and autophagy-related protein 3 (ATG3). A mutant βC1 protein (βC13A) in which I45, Y48, and I53 were all substituted with Ala (A), had a dramatically reduced binding capacity with GAPCs, failed to disrupt the GAPCs-ATG3 interactions and failed to induce autophagy. Furthermore, mutant virus carrying βC13A showed increased symptoms and viral DNA accumulation associated with decreased autophagy in plants. These results suggest that CLCuMuB βC1 activates autophagy by disrupting GAPCs-ATG3 interactions.

Combating stress: the interplay between hormone signaling and autophagy in plants

Autophagy is a conserved recycling process in which cellular components are delivered to and degraded in the vacuole/lysosome for reuse. In plants, it assists in responding to dynamic environmental conditions and maintaining metabolite homeostasis under normal or stress conditions. Under stress, autophagy is activated to remove damaged components and to recycle nutrients for survival, and the energy sensor kinases target of rapamycin (TOR) and SNF-related kinase 1 (SnRK1) are key to this activation. Here, we discuss accumulating evidence that hormone signaling plays critical roles in regulating autophagy and plant stress responses, although the molecular mechanisms by which this occurs are often not clear. Several hormones have been shown to regulate TOR activity during stress, in turn controlling autophagy. Hormone signaling can also regulate autophagy gene expression, while, reciprocally, autophagy can regulate hormone synthesis and signaling pathways. We highlight how the interplay between major energy sensors, plant hormones, and autophagy under abiotic and biotic stress conditions can assist in plant stress tolerance.

Remorin interacting with PCaP1 impairs Turnip mosaic virus intercellular movement but is antagonised by VPg

Group 1 Remorins (REMs) are extensively involved in virus trafficking through plasmodesmata (PD). However, their roles in Potyvirus cell-to-cell movement are not known. The plasma membrane (PM)-associated Ca²⁺ binding protein 1 (PCaP1) interacts with the P3N-PIPO of Turnip mosaic virus (TuMV) and is required for TuMV cell-to-cell movement, but the underlying mechanism remains elusive. The mutant plants with overexpression or knockout of REM1.2 were used to investigate its role in TuMV cell-to-cell movement. Arabidopsis thaliana complementary mutants of pcap1 were used to investigate the role of PCaP1 in TuMV cell-to-cell movement. Yeast-two-hybrid, bimolecular fluorescence complementation, co-immunoprecipitation and RT-qPCR assays were employed to investigate the underlying molecular mechanism. The results show that TuMV-P3N-PIPO recruits PCaP1 to PD and the actin filament-severing activity of PCaP1 is required for TuMV intercellular movement. REM1.2 negatively regulates the cell-to-cell movement of TuMV via competition with PCaP1 for binding actin filaments. As a counteractive response, TuMV mediates REM1.2 degradation via both 26S ubiquitin-proteasome and autophagy pathways through the interaction of VPg with REM1.2 to establish systemic infection in Arabidopsis. This work unveils the actin cytoskeleton and PM nanodomain-associated molecular events underlying the cell-to-cell movement of potyviruses.

How autophagy can restore proteostasis defects in multiple diseases?

Cellular evolution develops several conserved mechanisms by which cells can tolerate various difficult conditions and overall maintain homeostasis. Autophagy is a well-developed and evolutionarily conserved mechanism of catabolism, which endorses the degradation of foreign and endogenous materials via autolysosome. To decrease the burden of the ubiquitin-proteasome system (UPS), autophagy also promotes the selective degradation of proteins in a tightly regulated way to improve the physiological balance of cellular proteostasis that may get perturbed due to the accumulation of misfolded proteins. However, the diverse as well as selective clearance of unwanted materials and regulations of several cellular mechanisms via autophagy is still a critical mystery. Also, the failure of autophagy causes an increase in the accumulation of harmful protein aggregates that may lead to neurodegeneration. Therefore, it is necessary to address this multifactorial threat for in-depth research and develop more effective therapeutic strategies against lethal autophagy alterations. In this paper, we discuss the most relevant and recent reports on autophagy modulations and their impact on neurodegeneration and other complex disorders. We have summarized various pharmacological findings linked with the induction and suppression of autophagy mechanism and their promising preclinical and clinical applications to provide therapeutic solutions against neurodegeneration. The conclusion, key questions, and future prospectives sections summarize fundamental challenges and their possible feasible solutions linked with autophagy mechanism to potentially design an impactful therapeutic niche to treat neurodegenerative diseases and imperfect aging.

Nuclear autophagy degrades a geminivirus nuclear protein to restrict viral infection in solanaceous plants

Autophagy is an evolutionarily conserved degradation pathway in the cytoplasm and has emerged as a key defense mechanism against invading pathogens. However, there is no evidence showing nuclear autophagy in plants. Here, we show that a geminivirus nuclear protein, C1 of tomato leaf curl Yunnan virus (TLCYnV) induces autophagy and interacts directly with the core autophagy-related protein ATG8h. The interaction between ATG8h and C1 leads to the translocation of the C1 protein from the nucleus to the cytoplasm and the decreased protein accumulation of C1, which is dependent on the exportin1-mediated nuclear export pathway. The degradation of C1 is blocked by autophagy inhibitors and compromised when the autophagy-related genes (ATGs) ATG8h, ATG5, or ATG7 are knocked down. Similarly, silencing of these ATGs also promotes TLCYnV infection in Nicotiana benthamiana and Solanum lycopersicum plants. The mutation of a potential ATG8 interacting motif (AIM) in C1 abolishes its interaction with ATG8h in the cytoplasm but favors its interaction with Fibrillarin1 in the nucleolus. TLCYnV carrying the AIM mutation displays enhanced pathogenicity in solanaceous plants. Taken together, these data suggest that a new type of nuclear autophagy-mediated degradation of viral proteins through an exportin1-dependent nuclear export pathway restricts virus infection in plants.

The RNA-Dependent RNA Polymerase NIb of Potyviruses Plays Multifunctional, Contrasting Roles during Viral Infection

Potyviruses represent the largest group of known plant RNA viruses and include many agriculturally important viruses, such as Plum pox virus, Soybean mosaic virus, Turnip mosaic virus, and Potato virus Y. Potyviruses adopt polyprotein processing as their genome expression strategy. Among the 11 known viral proteins, the nuclear inclusion protein b (NIb) is the RNA-dependent RNA polymerase responsible for viral genome replication. Beyond its principal role as an RNA replicase, NIb has been shown to play key roles in diverse virus–host interactions. NIb recruits several host proteins into the viral replication complexes (VRCs), which are essential for the formation of functional VRCs for virus multiplication, and interacts with the sumoylation pathway proteins to suppress NPR1-mediated immunity response. On the other hand, NIb serves as a target of selective autophagy as well as an elicitor of effector-triggered immunity, resulting in attenuated virus infection. These contrasting roles of NIb provide an excellent example of the complex co-evolutionary arms race between plant hosts and potyviruses. This review highlights the current knowledge about the multifunctional roles of NIb in potyvirus infection, and discusses future research directions.

Coordination and Crosstalk between Autophagosome and Multivesicular Body Pathways in Plant Stress Responses

In eukaryotic cells, autophagosomes and multivesicular bodies (MVBs) are two closely related partners in the lysosomal/vacuolar protein degradation system. Autophagosomes are double membrane-bound organelles that transport cytoplasmic components, including proteins and organelles for autophagic degradation in the lysosomes/vacuoles. MVBs are single-membrane organelles in the endocytic pathway that contain intraluminal vesicles whose content is either degraded in the lysosomes/vacuoles or recycled to the cell surface. In plants, both autophagosome and MVB pathways play important roles in plant responses to biotic and abiotic stresses. More recent studies have revealed that autophagosomes and MVBs also act together in plant stress responses in a variety of processes, including deployment of defense-related molecules, regulation of cell death, trafficking and degradation of membrane and soluble constituents, and modulation of plant hormone metabolism and signaling. In this review, we discuss these recent findings on the coordination and crosstalk between autophagosome and MVB pathways that contribute to the complex network of plant stress responses.

Cell Biology During Infection of Plant Viruses in Insect Vectors and Plant Hosts

Plant viruses typically cause severe pathogenicity in plants, even resulting in the death of plants. Many pathogenic plant viruses are transmitted in a persistent manner via insect vectors. Interestingly, unlike in the plant hosts, persistent viruses are either nonpathogenic or show limited pathogenicity in their insect vectors, while taking advantage of the cellular machinery of insect vectors for completing their life cycles. This review discusses why persistent plant viruses are nonpathogenic or have limited pathogenicity to their insect vectors while being pathogenic to plants hosts. Current advances in cell biology of virus-insect vector interactions are summarized, including virus-induced inclusion bodies, changes of insect cellular ultrastructure, and immune response of insects to the viruses, especially autophagy and apoptosis. The corresponding findings of virus-plant interactions are compared. An integrated view of the balance strategy achieved by the interaction between viral attack and the immune response of insect is presented. Finally, we outline progress gaps between virus-insect and virus-plant interactions, thus highlighting the contributions of cultured cells to the cell biology of virus-insect interactions. Furthermore, future prospects of studying the cell biology of virus-vector interactions are presented.

Arabidopsis cargo receptor NBR1 mediates selective autophagy of defective proteins

Aggrephagy, a type of selective autophagy that sequesters protein aggregates for degradation in the vacuole, is an important protein quality control mechanism, particularly during cell stress. In mammalian cells, aggrephagy and several other forms of selective autophagy are mediated by dedicated cargo receptors such as NEIGHBOR OF BRCA1 (NBR1). Although plant NBR1 homologs have been linked to selective autophagy during biotic stress, it remains unclear how they impact selective autophagy under non-stressed and abiotic stress conditions. Through microscopic and biochemical analysis of nbr1 mutants expressing autophagy markers and an aggregation-prone reporter, we tested the connection between NBR1 and aggrephagy in Arabidopsis. Although NBR1 is not essential for general autophagy, or for the selective clearance of peroxisomes, mitochondria, or the ER, we found that NBR1 is required for the heat-induced formation of autophagic vesicles. Moreover, cytoplasmic puncta containing aggregation-prone proteins, which were rarely observed in wild-type plants, were found to accumulate in nbr1 mutants under both control and heat stress conditions. Given that NBR1 co-localizes with these cytoplasmic puncta, we propose that Arabidopsis NBR1 is a plant aggrephagy receptor essential for maintaining proteostasis under both heat stress and non-stress conditions.

A 7-Amino-Acid Motif of Rep Protein Essential for Virulence Is Critical for Triggering Host Defense Against Sri Lankan Cassava Mosaic Virus

Geminiviruses cause severe damage to agriculture worldwide. The replication (Rep) protein is the indispensable viral protein for viral replication. Although various functional domains of Rep protein in Geminivirus spp. have been characterized, the most carboxyl terminus of Rep protein was not available. We have reported the first cassava-infecting geminivirus, Sri Lankan cassava mosaic virus (SLCMV-HN7 strain), in China. In this study, we reported the second Chinese SLCMV strain, SLCMV-Col, and conducted comparative genomic analysis between these two SLCMV strains. The virulence of SLCMV-Col is much stronger than SLCMV-HN7, indicated by the higher virus titer, more severe symptoms, and more extent host defense. We functionally characterized that Rep protein, a 7-amino-acid motif at the most carboxyl terminus, is essential for Rep protein accumulation and virulence of SLCMV. We also provided evidence suggesting that the motif could also enhance triggering of salicylic acid (SA) defense against SLCMV infection in Nicotiana benthamiana. The significance of the balance between virulence and host SA defense responses in expanding invasions of SLCMV is also discussed.

βC1, pathogenicity determinant encoded by Cotton leaf curl Multan betasatellite, interacts with calmodulin-like protein 11 (Gh-CML11) in Gossypium hirsutum

Begomoviruses interfere with host plant machinery to evade host defense mechanism by interacting with plant proteins. In the old world, this group of viruses are usually associated with betasatellite that induces severe disease symptoms by encoding a protein, βC1, which is a pathogenicity determinant. Here, we show that βC1 encoded by Cotton leaf curl Multan betasatellite (CLCuMB) requires Gossypium hirsutum calmodulin-like protein 11 (Gh-CML11) to infect cotton. First, we used the in silico approach to predict the interaction of CLCuMB-βC1 with Gh-CML11. A number of sequence- and structure-based in-silico interaction prediction techniques suggested a strong putative binding of CLCuMB-βC1 with Gh-CML11 in a Ca+2-dependent manner. In-silico interaction prediction was then confirmed by three different experimental approaches: The Gh-CML11 interaction was confirmed using CLCuMB-βC1 in a yeast two hybrid system and pull down assay. These results were further validated using bimolecular fluorescence complementation system showing the interaction in cytoplasmic veins of Nicotiana benthamiana. Bioinformatics and molecular studies suggested that CLCuMB-βC1 induces the overexpression of Gh-CML11 protein and ultimately provides calcium as a nutrient source for virus movement and transmission. This is the first comprehensive study on the interaction between CLCuMB-βC1 and Gh-CML11 proteins which provided insights into our understating of the role of βC1 in cotton leaf curl disease.

Tailoring the cell: a glimpse of how plant viruses manipulate their hosts

Viruses are intracellular parasites that completely rely on the molecular machinery of the infected host to complete their cycle. Upon invasion of a susceptible cell, viruses dramatically reshape the intracellular environment to suit their needs, in a complex process that requires the fine manipulation of multiple aspects of the host cell biology, including those enabling replication of the viral genome, facilitating suppression or avoidance of anti-viral plant defence mechanisms, and supporting precise intra-cellular and inter-cellular trafficking of viral components. This tailoring of the cell to fit viral functions occurs through the coordinated action of fast-evolving, multifunctional viral proteins, which efficiently target host factors. In this review, we intend to offer a glimpse of how plant viruses manipulate their hosts from a cell biology perspective, focusing on recent advances covering three specific aspects of the viral infection: viral manipulation of organelle function; virus-induced formation of viral replication complexes through membrane remodelling; and viral evasion of autophagy.

Actin filaments are dispensable for bulk autophagy in plants

Actin filament, also known as microfilament, is one of two major cytoskeletal elements in plants and plays important roles in various biological processes. Like in animal cells, actin filaments have been thought to participate in autophagy in plants. However, surprisingly, in this study we found that actin filaments are dispensable for the occurrence of autophagy in plants. Disruption of actin filaments by short term treatment with actin polymerization inhibitors, cytochalasin D and latrunculin B, or transient overexpression of Profilin 3 in Nicotiana benthamiana had no effect on basal autophagy as well as the upregulation of nocturnal autophagy and salt stress-induced autophagy. Furthermore, anti-microfilament drug treatment affected neither basal nor salt stress-induced autophagy in Arabidopsis. In addition, prolonged perturbation of actin filaments by silencing Actin7 or 24-h treatment with microfilament-disrupting agents in N. benthamiana caused endoplasmic reticulum (ER) disorganization and subsequent degradation via autophagy involving ATG2, 3, 5, 6 and 7. Our findings reveal that, unlike mammalian cells, actin filaments are unnecessary for bulk autophagy in plants.Abbreviations: ATG: autophagy-related; CD: cytochalasin D; Cvt pathway: cytoplasm to vacuole targeting pathway; DMSO: dimethyl sulfoxide; ER: endoplasmic reticulum; LatB: latrunculin B; Nb: Nicotiana benthamiana; PAS: phagophore assembly site; PRF3: Profilin 3; RER: rough ER; SER: smooth ER; TEM: transmission electron microscopy; TRV: Tobacco rattle virus; VIGS: virus-induced gene silencing; wpi: weeks post-agroinfiltration.

Contrasting and emerging roles of autophagy in plant immunity

Autophagy is a conserved eukaryotic process that mediates degradation and relocation of cellular material to maintain homeostasis and cope with cellular stress. Remarkably, this ancient catabolic machinery has been co-opted to eliminate invading pathogens in a variety of ways. Plant autophagy not only mediates selective destruction of viruses but also limits infection by extracellular bacterial and filamentous pathogens. The emerging paradigm is that autophagy adaptors, responsible for selective cargo sorting, have been appointed to counteract pathogen infection, while adapted pathogens have evolved to subvert the immune functions of the autophagic machinery. In this review, we discuss recent findings that contribute to understanding the role of autophagy in plant immunity and highlight key questions to address in the field moving forward.

Journey of begomovirus betasatellite molecules: from satellites to indispensable partners

Betasatellites are a group of circular, single-stranded DNA molecules that are frequently found to be associated with monopartite begomoviruses of the family Geminiviridae. Betasatellites require their helper viruses for replication, movement, and encapsidation and they are often essential for induction of typical disease symptoms. The βC1 protein encoded by betasatellites is multifunctional that participates in diverse cellular events. It interferes with several cellular processes like normal development, chloroplasts, and innate immune system of plants. Recent research has indicated βC1 protein interaction with cellular proteins and its involvement in modulation of the host's cell cycle and symptom determination. This article focuses on the functional mechanisms of βC1 and its interactions with other viral and host proteins.

Host factors against plant viruses

Plant virus genome replication and movement is dependent on host resources and factors. However, plants respond to virus infection through several mechanisms, such as autophagy, ubiquitination, mRNA decay and gene silencing, that target viral components. Viral factors work in synchrony with pro-viral host factors during the infection cycle and are targeted by antiviral responses. Accordingly, establishment of virus infection is genetically determined by the availability of the pro-viral factors necessary for genome replication and movement, and by the balance between plant defence and viral suppression of defence responses. Sequential requirement of pro-viral factors and the antagonistic activity of antiviral factors suggest a two-step model to explain plant-virus interactions. At each step of the infection process, host factors with antiviral activity have been identified. Here we review our current understanding of host factors with antiviral activity against plant viruses.

The viral F-box protein P0 induces an ER-derived autophagy degradation pathway for the clearance of membrane-bound AGO1

The viral suppressor of RNA silencing P0 is known to target plant antiviral ARGONAUTE (AGO) proteins for degradation via an autophagy-related process. Here we utilized P0 to gain insight into the cellular degradation dynamics of AGO1, the major plant effector of RNA silencing. We revealed that P0 targets endoplasmic reticulum (ER)-associated AGO1 by inducing the formation of ER-related bodies that are delivered to the vacuole with both P0 and AGO1 as cargos. This process involves ATG8-interacting proteins 1 and 2 (ATI1 and ATI2) that interact with AGO1 and negatively regulate its transgene-silencing activity. Together, our results reveal a layer of ER-bound AGO1 posttranslational regulation that is manipulated by P0 to subvert plant antiviral defense.

RNA silencing is a major antiviral defense mechanism in plants and invertebrates. Plant ARGONAUTE1 (AGO1) is pivotal in RNA silencing, and hence is a major target for counteracting viral suppressors of RNA-silencing proteins (VSRs). P0 from Turnip yellows virus (TuYV) is a VSR that was previously shown to trigger AGO1 degradation via an autophagy-like process. However, the identity of host proteins involved and the cellular site at which AGO1 and P0 interact were unknown. Here we report that P0 and AGO1 associate on the endoplasmic reticulum (ER), resulting in their loading into ER-associated vesicles that are mobilized to the vacuole in an ATG5- and ATG7-dependent manner. We further identified ATG8-Interacting proteins 1 and 2 (ATI1 and ATI2) as proteins that associate with P0 and interact with AGO1 on the ER up to the vacuole. Notably, ATI1 and ATI2 belong to an endogenous degradation pathway of ER-associated AGO1 that is significantly induced following P0 expression. Accordingly, ATI1 and ATI2 deficiency causes a significant increase in posttranscriptional gene silencing (PTGS) activity. Collectively, we identify ATI1 and ATI2 as components of an ER-associated AGO1 turnover and proper PTGS maintenance and further show how the VSR P0 manipulates this pathway.

Autophagy-virus interplay in plants: from antiviral recognition to proviral manipulation

Autophagy is a conserved self-cleaning and renewal system required for cellular homeostasis and stress tolerance. Autophagic processes are also implicated in the response to 'non-self' such as viral pathogens, yet the functions and mechanisms of autophagy during plant virus infection have only recently started to be revealed. Compelling evidence now indicates that autophagy is an integral part of antiviral immunity in plants. It can promote the hypersensitive cell death response upon incompatible viral infections or mediate the selective elimination of entire particles and individual proteins from compatible viruses in a pathway similar to xenophagy in animals. Several viruses, however, have evolved measures to antagonize xenophagic degradation or utilize autophagy to suppress disease-associated cell death and other defence pathways like RNA silencing. Here, we highlight the current advances and gaps in our understanding of the complex autophagy-virus interplay and its consequences for host immunity and viral pathogenesis in plants.

Shedding light on autophagy coordinating with cell wall integrity signaling to govern pathogenicity of Magnaporthe oryzae

Cells are faced with various stresses during their growth and development, and autophagy is a degradative process in which cells can break down their own components to recycle macromolecules and provide energy under these stresses. For pathogenic fungi that utilize cell wall as the first barrier against external stress, the cell wall integrity (CWI) pathway also provides an essential role in responding to these stresses. However, the specific connection between autophagy and CWI remains elusive in either the model fungi including budding yeast Saccharomyces cerevisiae or the rice blast fungus Magnaporthe oryzae. Here, we provided evidence that the endoplasmic reticulum (ER) stress is highly induced during M. oryzae infection and that CWI MAP kinase kinase MoMkk1 (S. cerevisiae Mkk1/2 homolog) was subject to phosphorylation regulation by MoAtg1, the only identified kinase in the core autophagy machinery. We also identified MoMkk1 serine 115 as the MoAtg1-dependent phosphorylation site and this phosphorylation could activate CWI, similar to that by the conserved MAP kinase kinase kinase MoMck1 (S. cerevisiae Bck1 homolog). Together with the first report of MoMkk1 subjects to phosphorylation regulation by MoAtg1, we revealed a new mechanism by which autophagy coordinates with CWI signaling under ER stress, and this MoAtg1-dependent MoMkk1 phosphorylation is essential for the pathogenicity of M. oryzae.Abbreviations: A/Ala: alanine; Atg: autophagy-related; Bck1: bypass of C kinase 1; co-IP: co-immunoprecipitation; CWI: cell wall integrity;DTT: dithiothreitol; ER: endoplasmic reticulum; GFP: green fluorescent protein; Mo: Magnaporthe oryzae; MAPK: mitogen-activated protein kinase; Mkk1: mitogen-activated protein kinase-kinase 1; MS: mass spectrometry; PAS: phagophore assembly site; RFP: red fluorescent protein; RT: room temperature; S/Ser: serine; Slt2: suppressor of the lytic phenotype 2; T/Thr: threonine; UPR: unfolded protein response; Y2H: yeast two-hybrid screen.

Proximity-dependent biotinylation screening identifies NbHYPK as a novel interacting partner of ATG8 in plants

BACKGROUND

Autophagy is a conserved, highly-regulated catabolic process that plays important roles in growth, development and innate immunity in plants. In this study, we compared the rate of autophagy induction in Nicotiana benthamiana plants infected with Tobacco mosaic virus or the TMV 24A + UPD mutant variant, which replicates at a faster rate and induces more severe symptoms. Using a BirA* tag and proximity-dependent biotin identification (BioID) analysis, we identified host proteins that interact with the core autophagy protein, ATG8 in TMV 24A + UPD infected plants. By combining the use of a fast replicating TMV mutant and an in vivo protein-protein screening technique, we were able to gain functional insight into the role of autophagy in a compatible virus-host interaction.

RESULTS

Our study revealed an increased autophagic flux induced by TMV 24A + UPD, as compared to TMV in N. benthamiana. Analysis of the functional proteome associated with ATG8 revealed a total of 67 proteins, 16 of which are known to interact with ATG8 or its orthologs in mammalian and yeast systems. The interacting proteins were categorized into four functional groups: immune system process, response to ROS, sulphur amino acid metabolism and calcium signalling. Due to the presence of an ubiquitin-associated (UBA) domain, which is demonstrated to interact with ATG8, the Huntingtin-interacting protein K-like (HYPK) was selected for validation of the physical interaction and function. We used yeast two hybrid (Y2H), bimolecular fluorescence complementation (BiFC) and subcellular localization to validate the ATG8-HYPK interaction. Subsequent down-regulation of ATG8 by virus-induced gene silencing (VIGS) showed enhanced TMV symptoms, suggesting a protective role for autophagy during TMV 24A + UPD infection.

CONCLUSION

This study presents the use of BioID as a suitable method for screening ATG8 interacting proteins in planta. We have identified many putative binding partners of ATG8 during TMV 24A + UPD infection in N. benthamiana plants. In addition, we have verified that NbHYPK is an interacting partner of ATG8. We infer that autophagy plays a protective role in TMV 24A + UPD infected plants.

CpATG8, a Homolog of Yeast Autophagy Protein ATG8, Is Required for Pathogenesis and Hypovirus Accumulation in the Chest Blight Fungus

Autophagy is a degradation system in the cell, involved in the turnover of cellular components, development, differentiation, immune responses, protection against pathogens, and cell death. Autophagy is induced by nutrient starvation, in which cytoplasmic components and organelles are digested via vacuoles/lysosomes. In this study, by using electron microscopy, we observed that hypovirus CHV1-EP713 infection of Cryphonectria parasitica, the causative agent of chestnut blight disease, caused proliferation of autophagic-like vesicles. This phenomenon could be mimicked by treating the wild-type strain of the fungus EP155 with the autophagy induction drug rapamycin. Some of the hypovirulence-associated traits, including reduced pigmentation and conidiation, were also observed in the rapamycin-treated EP155. Quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) revealed that genes involved in autophagy were up-regulated in expression. Deletion of cpatg8, a gene encoding a homolog of ATG8 in Saccharomyces cerevisiae, resulted in attenuation of virulence and reduction in sporulation, as well as accumulation of the double-stranded viral RNA. Furthermore, virus-encoded p29 protein was found to co-localize with CpATG8, implying that the viral protein may interfere with the function of CpATG8. Taken together, these findings show that cpatg8 can be regulated by the hypovirus and is required for virulence and development of the fungus and accumulation of viral dsRNA in chestnut blight fungus.

Ubiquitin Extension Protein UEP1 Modulates Cell Death and Resistance to Various Pathogens in Tobacco

Ubiquitin (Ub) extension proteins (UEPs) are fusion proteins of a Ub at the N terminus to a ribosomal protein. They are the main source of Ub and the only source of extension ribosomal protein. Although important roles of the Ub-26S proteasome system in various biological processes have been well established, direct evidence for the role of UEP genes in plant defense is rarely reported. In this study, we cloned a Ub-S27a-type UEP gene (NbUEP1) from Nicotiana benthamiana and demonstrated its function in cell death and disease resistance. Virus-induced gene silencing of NbUEP1 led to intensive cell death, culminating in whole-seedling withering. Transient RNA interference (RNAi) of NbUEP1 caused strong cell death in infiltrated areas, while stable NbUEP1-RNAi tobacco plants constitutively formed necrotic lesions in leaves. NbUEP1-RNAi plants exhibited increased resistance to the oomycete Pythium aphanidermatum and viruses Tobacco mosaic virus and Cucumber mosaic virus while displaying decreased resistance to the nematode Meloidogyne incognita compared with non-RNAi control plants. Transcription profiling analysis indicated that jasmonate and ethylene pathways, lipid metabolism, copper amine oxidase-mediated active species generation, glycine-rich proteins, vacuolar processing enzyme- and RD21-mediated cell death and defense regulation, and autophagy might be associated with NbUEP1-mediated cell death and resistance. Our results provided evidence for the important roles of plant UEPs in modulating plant cell death and disease resistance.

A geminivirus betasatellite encoded βC1 protein interacts with PsbP and subverts PsbP-mediated antiviral defence in plants

Geminivirus disease complexes potentially interfere with plants physiology and cause disastrous effects on a wide range of economically important crops throughout the world. Diverse geminivirus betasatellite associations exacerbate the epidemic threat for global food security. Our previous study showed that βC1, the pathogenicity determinant of geminivirus betasatellites induce symptom development by disrupting the ultrastructure and function of chloroplasts. Here we explored the betasatellite-virus-chloroplast interaction in the scope of viral pathogenesis as well as plant defence responses, using Nicotiana benthamiana-Radish leaf curl betasatellite (RaLCB) as the model system. We have shown an interaction between RaLCB-encoded βC1 and one of the extrinsic subunit proteins of oxygen-evolving complex of photosystem II both in vitro and in vivo. Further, we demonstrate a novel function of the Nicotiana benthamiana oxygen-evolving enhancer protein 2 (PsbP), in that it binds DNA, including geminivirus DNA. Transient silencing of PsbP in N. benthamiana plants enhances pathogenicity and viral DNA accumulation. Overexpression of PsbP impedes disease development during the early phase of infection, suggesting that PsbP is involved in generation of defence response during geminivirus infection. In addition, βC1-PsbP interaction hampers non-specific binding of PsbP to the geminivirus DNA. Our findings suggest that betasatellite-encoded βC1 protein accomplishes counter-defence by physical interaction with PsbP reducing the ability of PsbP to bind geminivirus DNA to establish infection.

Multifaceted role of geminivirus associated betasatellite in pathogenesis

Begomoviruses have emerged as a group of plant pathogens that cause devastating diseases in a wide range of crops in tropical and subtropical regions of the world. Betasatellites, the circular single-stranded DNA molecules with the size of almost half of that of the associated helper begomoviruses, are often essential for the production of typical disease symptoms in several virus-host systems. Association of betasatellites with begomoviruses results in more severe symptoms in the plants and affects the yield of numerous crops leading to huge agroeconomic losses. βC1, the only protein encoded by betasatellites, plays a multifaceted role in the successful establishment of infection. This protein counteracts the innate defence mechanisms of the host, like RNA silencing, ubiquitin-proteasome system and defence responsive hormones. In the last two decades, the molecular aspect of betasatellite pathogenesis has attracted much attention from the researchers worldwide, and reports have shown that βC1 protein aggravates the helper begomovirus disease complex by modulating specific host factors. This review discusses the molecular aspects of the pathogenesis of betasatellites, including various βC1-host factor interactions and their effects on the suppression of defence responses of the plants.

Diverse plant viruses: a toolbox for dissection of cellular pathways

Research in virology has usually focused on one selected host-virus pathosystem to examine the mechanisms underlying a particular disease. However, as exemplified by the mechanistically versatile suppression of antiviral RNA silencing by plant viruses, there may be functionally convergent evolution. Assuming this is a widespread feature, we propose that effector proteins from diverse plant viruses can be a powerful resource for discovering new regulatory mechanisms of distinct cellular pathways. The efficiency of this approach will depend on how deeply and widely the studied pathway is integrated into viral infections. Beyond this, comparative studies using broad virus diversity should increase our global understanding of plant-virus interactions.

Plant Antiviral Immunity Against Geminiviruses and Viral Counter-Defense for Survival

The family Geminiviridae includes plant-infecting viruses whose genomes are composed of one or two circular non-enveloped ssDNAs(+) of about 2.5-5.2 kb each in size. These insect-transmissible geminiviruses cause significant crop losses across continents and pose a serious threat to food security. Under the control of promoters generally located within the intergenic region, their genomes encode five to eight ORFs from overlapping viral transcripts. Most proteins encoded by geminiviruses perform multiple functions, such as suppressing defense responses, hijacking ubiquitin-proteasomal pathways, altering hormonal responses, manipulating cell cycle regulation, and exploiting protein-signaling cascades. Geminiviruses establish complex but coordinated interactions with several host elements to spread and facilitate successful infection cycles. Consequently, plants have evolved several multilayered defense strategies against geminivirus infection and distribution. Recent studies on the evasion of host-mediated resistance factors by various geminivirus proteins through novel mechanisms have provided new insights into the development of antiviral strategies against geminiviruses. This review summarizes the current knowledge concerning virus movement within and between cells, as well as the recent advances in our understanding of the biological roles of virus-encoded proteins in manipulating host-mediated responses and insect transmission. This review also highlights unexplored areas that may increase our understanding of the biology of geminiviruses and how to combat these important plant pathogens.

Geminivirus-Associated Betasatellites: Exploiting Chinks in the Antiviral Arsenal of Plants

Betasatellites are a diverse group of circular single-stranded DNA satellites frequently associated with begomoviruses belonging to the family Geminiviridae. Challenged with a geminivirus-betasatellite infection, plants have employed sophisticated defense mechanisms to protect themselves. Betasatellites, in turn, employ mechanisms to antagonize these plant antiviral pathways. In this review, we focus on the anti-geminiviral immune pathways present both in plants and whiteflies. We also outline the counter-defensive strategies deployed by betasatellites to overcome the host defenses and initiate a successful infection. Finally, we discuss the outcomes of the opposing forces of plant immunity and betasatellite-mediated antagonism in the context of an evolutionary arms race. Understanding of the molecular dialog between plants and betasatellites will likely allow for the development of novel antiviral strategies.

Interaction between Brassica yellows virus silencing suppressor P0 and plant SKP1 facilitates stability of P0 in vivo against degradation by proteasome and autophagy pathways

P0 protein of some polerovirus members can target ARGONAUTE1 (AGO1) to suppress RNA silencing. Although P0 harbors an F-box-like motif reported to be essential for interaction with S phase kinase-associated protein 1 (SKP1) and RNA silencing suppression, it is the autophagy pathway that was shown to contribute to AGO1 degradation. Therefore, the role of P0-SKP1 interaction in silencing suppression remains unclear. We conducted global mutagenesis and comparative functional analysis of P0 encoded by Brassica yellows virus (BrYV) (P0Br ). We found that several residues within P0Br are required for local and systemic silencing suppression activities. Remarkably, the F-box-like motif mutant of P0Br , which failed to interact with SKP1, is destabilized in vivo. Both the 26S proteasome system and autophagy pathway play a role in destabilization of the mutant protein. Furthermore, silencing of a Nicotiana benthamiana SKP1 ortholog leads to the destabilization of P0Br . Genetic analyses indicated that the P0Br -SKP1 interaction is not directly required for silencing suppression activity of P0Br , but it facilitates stability of P0Br to ensure efficient RNA silencing suppression. Consistent with these findings, efficient systemic infection of BrYV requires P0Br . Our results reveal a novel strategy used by BrYV for facilitating viral suppressors of RNA silencing stability against degradation by plant cells.

Protein and RNA Quality Control by Autophagy in Plant Cells

Eukaryotic cells use conserved quality control mechanisms to repair or degrade defective proteins, which are synthesized at a high rate during proteotoxic stress. Quality control mechanisms include molecular chaperones, the ubiquitin-proteasome system, and autophagic machinery. Recent research reveals that during autophagy, membrane-bound organelles are selectively sequestered and degraded. Selective autophagy is also critical for the clearance of excess or damaged protein complexes (e.g., proteasomes and ribosomes) and membrane-less compartments (e.g., protein aggregates and ribonucleoprotein granules). As sessile organisms, plants rely on quality control mechanisms for their adaptation to fluctuating environments. In this mini-review, we highlight recent work elucidating the roles of selective autophagy in the quality control of proteins and RNA in plant cells. Emphasis will be placed on selective degradation of membrane-less compartments and protein complexes in the cytoplasm. We also propose possible mechanisms by which defective proteins are selectively recognized by autophagic machinery.

Geminiviral V2 Protein Suppresses Transcriptional Gene Silencing through Interaction with AGO4

In plants, RNA-directed DNA methylation (RdDM)-mediated transcriptional gene silencing (TGS) is a natural antiviral defense against geminiviruses. Several geminiviral proteins have been shown to target the enzymes related to the methyl cycle or histone modification; however, it remains largely unknown whether and by which mechanism geminiviruses directly inhibit RdDM-mediated TGS. In this study, we showed that Cotton leaf curl Multan virus (CLCuMuV) V2 directly interacts with Nicotiana benthamiana AGO4 (NbAGO4) and that the L76S mutation in V2 (V2L76S) abolishes such interaction. We further showed that V2, but not V2L76S, can suppresses RdDM and TGS. Silencing of NbAGO4 inhibits TGS, reduces the viral methylation level, and enhances CLCuMuV DNA accumulation. In contrast, the V2L76S substitution mutant attenuates CLCuMuV infection and enhances the viral methylation level. These findings reveal that CLCuMuV V2 contributes to viral infection by interaction with NbAGO4 to suppress RdDM-mediated TGS in plants.IMPORTANCE In plants, the RNA-directed DNA methylation (RdDM) pathway is a natural antiviral defense mechanism against geminiviruses. However, how geminiviruses counter RdDM-mediated defense is largely unknown. Our findings reveal that Cotton leaf curl Multan virus V2 contributes to viral infection by interaction with NbAGO4 to suppress RNA-directed DNA methylation-mediated transcriptional gene silencing in plants. Our work provides the first evidence that a geminiviral protein is able to directly target core RdDM components to counter RdDM-mediated TGS antiviral defense in plants, which extends our current understanding of viral counters to host antiviral defense.

Homology modeling and docking analysis of ßC1 protein encoded by Cotton leaf curl Multan betasatellite with different plant flavonoids

Cotton leaf curl Multan virus (CLCuMuV) belonging to begomoviruses (Family Geminiviridae) can infect cotton and many other agricultural crops. Betasatellite associated with CLCuMuV i.e., cotton leaf curl Multan betasatellite (CLCuMuB) is a small circular single-stranded deoxyribose nucleic acid (ssDNA) molecule that is essential for CLCuMuV to induce disease symptoms. Betasatellite molecule contains a ßC1 gene encoding for a pathogenicity determinant multifunctional protein, which extensively interacts with host plant machinery to cause virus infection. In this study the interaction of ßC1 with selected plant flavonoids has been studied. The study was focused on sequence analysis, three-dimensional structural modeling and docking analysis of ßC1 protein of CLCuMuB. Sequence analysis and physicochemical properties showed that ßC1 is negatively charged protein having more hydrophilic regions and is not very stable. Three-dimensional model of this protein revealed three helical, four beta pleated sheets and four coiled regions. The score of docking experiments using flavonoids as ligand indicated that plant flavonoids robinetinidol-(4alpha,8)-gallocatechin, quercetin 7-O-beta-D-glucoside, swertianolin, 3',4',5-trihydroxy-3-methoxyflavon-7-olate, agathisflavone, catiguanin B, 3',4',5,6-tetrahydroxy-3,7-dimethoxyflavone, quercetin-7-O-[alpha-L-rhamnopyranosyl(1->6)-beta-D-galactopyranoside], prunin 6″-O-gallate and luteolin 7-O-beta-D-glucosiduronic acid have strong binding with active site of ßC1 protein. The results obtained from this study clearly indicate that flavonoids are involved in defense against the virus infection, as these molecules binds to the active site of ßC1 protein. This information might be interesting to study plant defense mechanism based on the special compounds produced by the plants.

The Tug-of-War between Plants and Viruses: Great Progress and Many Remaining Questions

Plants are persistently challenged by various phytopathogens. To protect themselves, plants have evolved multilayered surveillance against all pathogens. For intracellular parasitic viruses, plants have developed innate immunity, RNA silencing, translation repression, ubiquitination-mediated and autophagy-mediated protein degradation, and other dominant resistance gene-mediated defenses. Plant viruses have also acquired diverse strategies to suppress and even exploit host defense machinery to ensure their survival. A better understanding of the defense and counter-defense between plants and viruses will obviously benefit from the development of efficient and broad-spectrum virus resistance for sustainable agriculture. In this review, we summarize the cutting edge of knowledge concerning the defense and counter-defense between plants and viruses, and highlight the unexploited areas that are especially worth investigating in the near future.

Manipulating Cellular Factors to Combat Viruses: A Case Study From the Plant Eukaryotic Translation Initiation Factors eIF4

Genes conferring resistance to plant viruses fall in two categories; the dominant genes that mostly code for proteins with a nucleotide binding site and leucine rich repeats (NBS-LRR), and that directly or indirectly, recognize viral avirulence factors (Avr), and the recessive genes. The latter provide a so-called recessive resistance. They represent roughly half of the known resistance genes and are alleles of genes that play an important role in the virus life cycle. Conversely, all cellular genes critical for the viral infection virtually represent recessive resistance genes. Based on the well-documented case of recessive resistance mediated by eukaryotic translation initiation factors of the 4E/4G family, this review is intended to summarize the possible approaches to control viruses via their host interactors. Classically, resistant crops have been developed through introgression of natural variants of the susceptibility factor from compatible relatives or by random mutagenesis and screening. Transgenic methods have also been applied to engineer improved crops by overexpressing the translation factor either in its natural form or after directed mutagenesis. More recently, innovative approaches like silencing or genome editing have proven their great potential in model and crop plants. The advantages and limits of these different strategies are discussed. This example illustrates the need to identify and characterize more host factors involved in virus multiplication and to assess their application potential in the control of viral diseases.

A Plant Immune Receptor Degraded by Selective Autophagy

Plants recycle non-activated immune receptors to maintain a functional immune system. The Arabidopsis immune receptor kinase FLAGELLIN-SENSING 2 (FLS2) recognizes bacterial flagellin. However, the molecular mechanisms by which non-activated FLS2 and other non-activated plant PRRs are recycled remain not well understood. Here, we provide evidence showing that Arabidopsis orosomucoid (ORM) proteins, which have been known to be negative regulators of sphingolipid biosynthesis, act as selective autophagy receptors to mediate the degradation of FLS2. Arabidopsis plants overexpressing ORM1 or ORM2 have undetectable or greatly diminished FLS2 accumulation, nearly lack FLS2 signaling, and are more susceptible to the bacterial pathogen Pseudomonas syringae. On the other hand, ORM1/2 RNAi plants and orm1 or orm2 mutants generated by the CRISPR/Cas9-mediated gene editing have increased FLS2 accumulation and enhanced FLS2 signaling, and are more resistant to P. syringae. ORM proteins interact with FLS2 and the autophagy-related protein ATG8. Interestingly, overexpression of ORM1 or ORM2 in autophagy-defective mutants showed FLS2 abundance that is comparable to that in wild-type plants. Moreover, FLS2 levels were not decreased in Arabidopsis plants overexpressing ORM1/2 derivatives that do not interact with ATG8. Taken together, these results suggest that selective autophagy functions in maintaining the homeostasis of a plant immune receptor and that beyond sphingolipid metabolic regulation ORM proteins can also act as selective autophagy receptors.

Autophagy in Plant Immunity

The highly conserved catabolic process of autophagy delivers unwanted proteins or damaged organelles to vacuoles for degradation and recycling. This is essential for the regulation of cellular homeostasis, stress adaptation, and programmed cell death in eukaryotes. In particular, emerging evidence indicates that autophagy plays a multifunctional regulatory role in plant innate immunity during plant-pathogen interactions. In this review, we highlight existing knowledge regarding the involvement of autophagy in plant immunity, mechanisms functioning in the induction of autophagy upon pathogen infection, and possible directions for future research.

Autophagy in crop plants: what's new beyond Arabidopsis?

Autophagy is a major degradation and recycling pathway in plants. It functions to maintain cellular homeostasis and is induced by environmental cues and developmental stimuli. Over the past decade, the study of autophagy has expanded from model plants to crop species. Many features of the core machinery and physiological functions of autophagy are conserved among diverse organisms. However, several novel functions and regulators of autophagy have been characterized in individual plant species. In light of its critical role in development and stress responses, a better understanding of autophagy in crop plants may eventually lead to beneficial agricultural applications. Here, we review recent progress on understanding autophagy in crops and discuss potential future research directions.

Exploring the Diversity of Mechanisms Associated With Plant Tolerance to Virus Infection

Tolerance is defined as an interaction in which viruses accumulate to some degree without causing significant loss of vigor or fitness to their hosts. Tolerance can be described as a stable equilibrium between the virus and its host, an interaction in which each partner not only accommodate trade-offs for survival but also receive some benefits (e.g., protection of the plant against super-infection by virulent viruses; virus invasion of meristem tissues allowing vertical transmission). This equilibrium, which would be associated with little selective pressure for the emergence of severe viral strains, is common in wild ecosystems and has important implications for the management of viral diseases in the field. Plant viruses are obligatory intracellular parasites that divert the host cellular machinery to complete their infection cycle. Highjacking/modification of plant factors can affect plant vigor and fitness. In addition, the toxic effects of viral proteins and the deployment of plant defense responses contribute to the induction of symptoms ranging in severity from tissue discoloration to malformation or tissue necrosis. The impact of viral infection is also influenced by the virulence of the specific virus strain (or strains for mixed infections), the host genotype and environmental conditions. Although plant resistance mechanisms that restrict virus accumulation or movement have received much attention, molecular mechanisms associated with tolerance are less well-understood. We review the experimental evidence that supports the concept that tolerance can be achieved by reaching the proper balance between plant defense responses and virus counter-defenses. We also discuss plant translation repression mechanisms, plant protein degradation or modification pathways and viral self-attenuation strategies that regulate the accumulation or activity of viral proteins to mitigate their impact on the host. Finally, we discuss current progress and future opportunities toward the application of various tolerance mechanisms in the field.

Cotton Leaf Curl Multan virus C4 protein suppresses both transcriptional and post-transcriptional gene silencing by interacting with SAM synthetase

Gene silencing is a natural antiviral defense mechanism in plants. For effective infection, plant viruses encode viral silencing suppressors to counter this plant antiviral response. The geminivirus-encoded C4 protein has been identified as a gene silencing suppressor, but the underlying mechanism of action has not been characterized. Here, we report that Cotton Leaf Curl Multan virus (CLCuMuV) C4 protein interacts with S-adenosyl methionine synthetase (SAMS), a core enzyme in the methyl cycle, and inhibits SAMS enzymatic activity. By contrast, an R13A mutation in C4 abolished its capacity to interact with SAMS and to suppress SAMS enzymatic activity. Overexpression of wild-type C4, but not mutant C4R13A, suppresses both transcriptional gene silencing (TGS) and post-transcriptional gene silencing (PTGS). Plants infected with CLCuMuV carrying C4R13A show decreased levels of symptoms and viral DNA accumulation associated with enhanced viral DNA methylation. Furthermore, silencing of NbSAMS2 reduces both TGS and PTGS, but enhanced plant susceptibility to two geminiviruses CLCuMuV and Tomato yellow leaf curl China virus. These data suggest that CLCuMuV C4 suppresses both TGS and PTGS by inhibiting SAMS activity to enhance CLCuMuV infection in plants.

Barley stripe mosaic virus γb Protein Subverts Autophagy to Promote Viral Infection by Disrupting the ATG7-ATG8 Interaction

Autophagy is a conserved defense strategy against viral infection. However, little is known about the counterdefense strategies of plant viruses involving interference with autophagy. Here, we show that γb protein from Barley stripe mosaic virus (BSMV), a positive single-stranded RNA virus, directly interacts with AUTOPHAGY PROTEIN7 (ATG7). BSMV infection suppresses autophagy, and overexpression of γb protein is sufficient to inhibit autophagy. Furthermore, silencing of autophagy-related gene ATG5 and ATG7 in Nicotiana benthamiana plants enhanced BSMV accumulation and viral symptoms, indicating that autophagy plays an antiviral role in BSMV infection. Molecular analyses indicated that γb interferes with the interaction of ATG7 with ATG8 in a competitive manner, whereas a single point mutation in γb, Tyr29Ala (Y29A), made this protein deficient in the interaction with ATG7, which was correlated with the abolishment of autophagy inhibition. Consistently, the mutant BSMVY29A virus showed reduced symptom severity and viral accumulation. Taken together, our findings reveal that BSMV γb protein subverts autophagy-mediated antiviral defense by disrupting the ATG7-ATG8 interaction to promote plant RNA virus infection, and they provide evidence that ATG7 is a target of pathogen effectors that functions in the ongoing arms race of plant defense and viral counterdefense.

Molecular identification of GAPDHs in cassava highlights the antagonism of MeGAPCs and MeATG8s in plant disease resistance against cassava bacterial blight

KEY MESSAGE

MeGAPCs were identified as negative regulators of plant disease resistance, and the interaction of MeGAPCs and MeATG8s was highlighted in plant defense response. As an important enzyme of glycolysis metabolic pathway, glyceraldehyde-3-P dehydrogenase (GAPDH) plays important roles in plant development, abiotic stress and immune responses. Cassava (Manihot esculenta) is most important tropical crop and one of the major food crops, however, no information is available about GAPDH gene family in cassava. In this study, 14 MeGAPDHs including 6 cytosol GAPDHs (MeGAPCs) were identified from cassava, and the transcripts of 14 MeGAPDHs in response to Xanthomonas axonopodis pv manihotis (Xam) indicated their possible involvement in immune responses. Further investigation showed that MeGAPCs are negative regulators of disease resistance against Xam. Through transient expression in Nicotiana benthamiana, we found that overexpression of MeGAPCs led to decreased disease resistance against Xam. On the contrary, MeGAPCs-silenced cassava plants through virus-induced gene silencing (VIGS) conferred improved disease resistance. Notably, MeGAPCs physically interacted with autophagy-related protein 8b (MeATG8b) and MeATG8e and inhibited autophagic activity. Moreover, MeATG8b and MeATG8e negatively regulated the activities of NAD-dependent MeGAPDHs, and are involved in MeGAPCs-mediated disease resistance. Taken together, this study highlights the involvement of MeGAPCs in plant disease resistance, through interacting with MeATG8b and MeATG8e.

Autophagy: The Master of Bulk and Selective Recycling

Plants have evolved sophisticated mechanisms to recycle intracellular constituents, which are essential for developmental and metabolic transitions; for efficient nutrient reuse; and for the proper disposal of proteins, protein complexes, and even entire organelles that become obsolete or dysfunctional. One major route is autophagy, which employs specialized vesicles to encapsulate and deliver cytoplasmic material to the vacuole for breakdown. In the past decade, the mechanics of autophagy and the scores of components involved in autophagic vesicle assembly have been documented. Now emerging is the importance of dedicated receptors that help recruit appropriate cargo, which in many cases exploit ubiquitylation as a signal. Although operating at a low constitutive level in all plant cells, autophagy is upregulated during senescence and various environmental challenges and is essential for proper nutrient allocation. Its importance to plant metabolism and energy balance in particular places autophagy at the nexus of robust crop performance, especially under suboptimal conditions.

Beclin1 restricts RNA virus infection in plants through suppression and degradation of the viral polymerase

Autophagy emerges as an essential immunity defense against intracellular pathogens. Here we report that turnip mosaic virus (TuMV) infection activates autophagy in plants and that Beclin1 (ATG6), a core component of autophagy, inhibits virus replication. Beclin1 interacts with NIb, the RNA-dependent RNA polymerase (RdRp) of TuMV, via the highly conserved GDD motif and the interaction complex is targeted for autophagic degradation likely through the adaptor protein ATG8a. Beclin1-mediated NIb degradation is inhibited by autophagy inhibitors. Deficiency of Beclin1 or ATG8a enhances NIb accumulation and promotes viral infection and vice versa. These data suggest that Beclin1 may be a selective autophagy receptor. Overexpression of a Beclin1 truncation mutant that binds to NIb but lacks the ability to mediate NIb degradation also inhibits virus replication. The Beclin1-RdRp interaction further extends to several RNA viruses. Thus Beclin1 restricts viral infection through suppression and also likely autophagic degradation of the viral RdRp.

Modulation of plant autophagy during pathogen attack

In plants, the highly conserved catabolic process of autophagy has long been known as a means of maintaining cellular homeostasis and coping with abiotic stress conditions. Accumulating evidence has linked autophagy to immunity against invading pathogens, regulating plant cell death, and antimicrobial defences. In turn, it appears that phytopathogens have evolved ways not only to evade autophagic clearance but also to modulate and co-opt autophagy for their own benefit. In this review, we summarize and discuss the emerging discoveries concerning how pathogens modulate both host and self-autophagy machineries to colonize their host plants, delving into the arms race that determines the fate of interorganismal interaction.

Autophagy-related approaches for improving nutrient use efficiency and crop yield protection

Autophagy is a eukaryotic catabolic pathway essential for growth and development. In plants, it is activated in response to environmental cues or developmental stimuli. However, in contrast to other eukaryotic systems, we know relatively little regarding the molecular players involved in autophagy and the regulation of this complex pathway. In the framework of the COST (European Cooperation in Science and Technology) action TRANSAUTOPHAGY (2016-2020), we decided to review our current knowledge of autophagy responses in higher plants, with emphasis on knowledge gaps. We also assess here the potential of translating the acquired knowledge to improve crop plant growth and development in a context of growing social and environmental challenges for agriculture in the near future.

Bacteria Exploit Autophagy for Proteasome Degradation and Enhanced Virulence in Plants

Autophagy and the ubiquitin-proteasome system (UPS) are two major protein degradation pathways implicated in the response to microbial infections in eukaryotes. In animals, the contribution of autophagy and the UPS to antibacterial immunity is well documented and several bacteria have evolved measures to target and exploit these systems to the benefit of infection. In plants, the UPS has been established as a hub for immune responses and is targeted by bacteria to enhance virulence. However, the role of autophagy during plant-bacterial interactions is less understood. Here, we have identified both pro- and antibacterial functions of autophagy mechanisms upon infection of Arabidopsis thaliana with virulent Pseudomonas syringae pv tomato DC3000 (Pst). We show that Pst activates autophagy in a type III effector (T3E)-dependent manner and stimulates the autophagic removal of proteasomes (proteaphagy) to support bacterial proliferation. We further identify the T3E Hrp outer protein M1 (HopM1) as a principle mediator of autophagy-inducing activities during infection. In contrast to the probacterial effects of Pst-induced proteaphagy, NEIGHBOR OF BRCA1-dependent selective autophagy counteracts disease progression and limits the formation of HopM1-mediated water-soaked lesions. Together, we demonstrate that distinct autophagy pathways contribute to host immunity and bacterial pathogenesis during Pst infection and provide evidence for an intimate crosstalk between proteasome and autophagy in plant-bacterial interactions.

Turnip Mosaic Virus Counteracts Selective Autophagy of the Viral Silencing Suppressor HCpro

Autophagy is a conserved intracellular degradation pathway and has emerged as a key mechanism of antiviral immunity in metazoans, including the selective elimination of viral components. In turn, some animal viruses are able to escape and modulate autophagy for enhanced pathogenicity. Whether host autophagic responses and viral countermeasures play similar roles in plant-virus interactions is not well understood. Here, we have identified selective autophagy as antiviral pathway during plant infection with turnip mosaic virus (TuMV), a positive-stranded RNA potyvirus. We show that the autophagy cargo receptor NBR1 suppresses viral accumulation by targeting the viral RNA silencing suppressor helper-component proteinase (HCpro), presumably in association with virus-induced RNA granules. Intriguingly, TuMV seems to antagonize NBR1-dependent autophagy during infection by the activity of distinct viral proteins, thereby limiting its antiviral capacity. We also found that NBR1-independent bulk autophagy prevents premature plant death, thus extending the lifespan of virus reservoirs and particle production. Together, our study highlights a conserved role of selective autophagy in antiviral immunity and suggests the evolvement of viral protein functions to inhibit autophagy processes, despite a potential trade-off in host survival.

Understanding and exploiting autophagy signaling in plants

Autophagy is an essential catabolic pathway and is activated by various endogenous and exogenous stimuli. In particular, autophagy is required to allow sessile organisms such as plants to cope with biotic or abiotic stress conditions. It is thought that these various environmental signaling pathways are somehow integrated with autophagy signaling. However, the molecular mechanisms of plant autophagy signaling are not well understood, leaving a big gap of knowledge as a barrier to being able to manipulate this important pathway to improve plant growth and development. In this review, we discuss possible regulatory mechanisms at the core of plant autophagy signaling.