Autophagy as an emerging arena for plant-pathogen interactions

Physiological and autophagy evaluation of different pear varieties (Pyrus spp.) in response to Botryosphaeria dothidea infection

Ring rot disease is one of the most common diseases in pear orchards. To better understand the physiology, biochemistry and autophagic changes of different pear varieties after Botryosphaeria dothidea (B.dothidea) infection, we evaluated eight different pear varieties for B. dothidea resistance. The susceptible varieties had larger spot diameters, lower chlorophyll contents and higher malondialdehyde contents than the resistant varieties. In disease-resistant varieties, reactive oxygen species (ROS) levels were relatively lower, while the ROS metabolism (antioxidant enzyme activities and the ascorbic acid-glutathione cycle) was also maintained at higher levels, and it induced a significant upregulation of related gene expression. In addition, autophagy, as an important evaluation index, was found to have more autophagic activity in disease-resistant varieties than in susceptible varieties, suggesting that pathogen infestation drives plants to increase autophagy to defend against pathogens. In summary, the results of this study reveal that different resistant pear varieties enhance plant resistance to the disease through a series of physio-biochemical changes and autophagic activity after inoculation with B. dothidea. This study provides clear physiological and biochemical traits for pear disease resistance selection, potential genetic resources and material basis for pear disease control and disease resistance, breeding and points out the direction for research on the mechanism of pear resistance to B. dothidea.

Antifungal effects of carvacrol, the main volatile compound in Origanum vulgare L. essential oil, against Aspergillus flavus in postharvest wheat

Plant volatile organic compounds (VOCs) with antimicrobial activity could potentially be extremely useful fumigants to prevent and control the fungal decay of agricultural products postharvest. In this study, antifungal effects of volatile compounds in essential oils extracted from Origanum vulgare L. against Aspergillus flavus growth were investigated using transcriptomic and biochemical analyses. Carvacrol was identified as the major volatile constituent of the Origanum vulgare L. essential oil, accounting for 66.01 % of the total content. The minimum inhibitory concentrations of carvacrol were 0.071 and 0.18 μL/mL in gas-phase fumigation and liquid contact, respectively. Fumigation with 0.60 μL/mL of carvacrol could completely inhibit A. flavus proliferation in wheat grains with 20 % moisture, showing its potential as a biofumigant. Scanning electron microscopy revealed that carvacrol treatment caused morphological deformation of A. flavus mycelia, and the resulting increased electrolyte leakage indicates damage to the plasma membrane. Confocal laser scanning microscopy confirmed that the carvacrol treatment caused a decrease in mitochondrial membrane potential, reactive oxygen species accumulation, and DNA damage. Transcriptome analysis revealed that differentially expressed genes were mainly associated with fatty acid degradation, autophagy, peroxisomes, the tricarboxylic acid cycle, oxidative phosphorylation, and DNA replication in A. flavus mycelia exposed to carvacrol. Biochemical analyses of hydrogen peroxide and superoxide anion content, and catalase, superoxide dismutase, and glutathione S-transferase activities showed that carvacrol induced oxidative stress in A. flavus, which agreed with the transcriptome results. In summary, this study provides an experimental basis for the use of carvacrol as a promising biofumigant for the prevention of A. flavus contamination during postharvest grain storage.

PlAtg8-mediated autophagy regulates vegetative growth, sporangial cleavage, and pathogenesis in Peronophythora litchii

IMPORTANCE

Peronophythora litchii is the pathogen of litchi downy blight, which is the most serious disease in litchi. Autophagy is an evolutionarily conserved catabolic process in eukaryotes. Atg8 is a core protein of the autophagic pathway, which modulates growth and pathogenicity in the oomycete P. litchii. In P. litchii, CRISPR/Cas9-mediated knockout of the PlATG8 impaired autophagosome formation. PlATG8 knockout mutants exhibited attenuated colony expansion, sporangia production, zoospore discharge, and virulence on litchi leaves and fruits. The reduction in zoospore release was likely underpinned by impaired sporangial cleavage. Thus, in addition to governing autophagic flux, PlAtg8 is indispensable for vegetative growth and infection of P. litchii.

Silencing GmATG7 Leads to Accelerated Senescence and Enhanced Disease Resistance in Soybean

Autophagy plays a critical role in nutrient recycling/re-utilizing under nutrient deprivation conditions. However, the role of autophagy in soybeans has not been intensively investigated. In this study, the Autophay-related gene 7 (ATG7) gene in soybeans (referred to as GmATG7) was silenced using a virus-induced gene silencing approach mediated by Bean pod mottle virus (BPMV). Our results showed that ATG8 proteins were highly accumulated in the dark-treated leaves of the GmATG7-silenced plants relative to the vector control leaves (BPMV-0), which is indicative of an impaired autophagy pathway. Consistent with the impaired autophagy, the dark-treated GmATG7-silenced leaves displayed an accelerated senescence phenotype, which was not seen on the dark-treated BPMV-0 leaves. In addition, the accumulation levels of both H2O2 and salicylic acid (SA) were significantly induced in the GmATG7-silenced plants compared with the BPMV-0 plants, indicating an activated immunity. Consistently, the GmATG7-silenced plants were more resistant against both Pseudomonas syringae pv. glycinea (Psg) and Soybean mosaic virus (SMV) compared with the BPMV-0 plants. However, the activated immunity in the GmATG7-silenced plant was not dependent upon the activation of MPK3/MPK6. Collectively, our results demonstrated that the function of GmATG7 is indispensable for autophagy in soybeans, and the activated immunity in the GmATG7-silenced plant is a result of impaired autophagy.

"Order from disordered": Potential role of intrinsically disordered regions in phytopathogenic oomycete intracellular effector proteins

There is a continuous arms race between pathogens and their host plants. However, successful pathogens, such as phytopathogenic oomycetes, secrete effector proteins to manipulate host defense responses for disease development. Structural analyses of these effector proteins reveal the existence of regions that fail to fold into three-dimensional structures, intrinsically disordered regions (IDRs). Because of their flexibility, these regions are involved in important biological functions of effector proteins, such as effector-host protein interactions that perturb host immune responses. Despite their significance, the role of IDRs in phytopathogenic oomycete effector-host protein interactions is not clear. This review, therefore, searched the literature for functionally characterized oomycete intracellular effectors with known host interactors. We further classify regions that mediate effector-host protein interactions into globular or disordered binding sites in these proteins. To fully appreciate the potential role of IDRs, five effector proteins encoding potential disordered binding sites were used as case studies. We also propose a pipeline that can be used to identify, classify as well as characterize potential binding regions in effector proteins. Understanding the role of IDRs in these effector proteins can aid in the development of new disease-control strategies.

An effector of 'Candidatus Liberibacter asiaticus' manipulates autophagy to promote bacterial infection

Autophagy functions in plant host immunity responses to pathogen infection. The molecular mechanisms and functions used by the citrus Huanglongbing (HLB)-associated intracellular bacterium 'Candidatus Liberibacter asiaticus' (CLas) to manipulate autophagy are unknown. We identified a CLas effector, SDE4405 (CLIBASIA_04405), which contributes to HLB progression. 'Wanjincheng' orange (Citrus sinensis) transgenic plants expressing SDE4405 promotes CLas proliferation and symptom expression via suppressing host immunity responses. SDE4405 interacts with the ATG8-family of proteins (ATG8s), and their interactions activate autophagy in Nicotiana benthamiana. The occurrence of autophagy is also significantly enhanced in SDE4405-transgenic citrus plants. Interrupting NbATG8s-SDE4405 interaction by silencing of NbATG8c reduces Pseudomonas syringae pv. tomato strain DC3000ΔhopQ1-1 (Pst DC3000ΔhopQ1-1) proliferation in N. benthamiana, and transient overexpression of CsATG8c and SDE4405 in citrus promotes Xanthomonas citri subsp. citri (Xcc) multiplication, suggesting that SDE4405-ATG8s interaction negatively regulates plant defense. These results demonstrate the role of the CLas effector protein in manipulating autophagy, and provide new molecular insights into the interaction between CLas and citrus hosts.

Autophagy promotes jasmonate-mediated defense against nematodes

Autophagy, as an intracellular degradation system, plays a critical role in plant immunity. However, the involvement of autophagy in the plant immune system and its function in plant nematode resistance are largely unknown. Here, we show that root-knot nematode (RKN; Meloidogyne incognita) infection induces autophagy in tomato (Solanum lycopersicum) and different atg mutants exhibit high sensitivity to RKNs. The jasmonate (JA) signaling negative regulators JASMONATE-ASSOCIATED MYC2-LIKE 1 (JAM1), JAM2 and JAM3 interact with ATG8s via an ATG8-interacting motif (AIM), and JAM1 is degraded by autophagy during RKN infection. JAM1 impairs the formation of a transcriptional activation complex between ETHYLENE RESPONSE FACTOR 1 (ERF1) and MEDIATOR 25 (MED25) and interferes with transcriptional regulation of JA-mediated defense-related genes by ERF1. Furthermore, ERF1 acts in a positive feedback loop and regulates autophagy activity by transcriptionally activating ATG expression in response to RKN infection. Therefore, autophagy promotes JA-mediated defense against RKNs via forming a positive feedback circuit in the degradation of JAMs and transcriptional activation by ERF1.

A tripartite rheostat controls self-regulated host plant resistance to insects

Plants deploy receptor-like kinases and nucleotide-binding leucine-rich repeat receptors to confer host plant resistance (HPR) to herbivores¹. These gene-for-gene interactions between insects and their hosts have been proposed for more than 50 years². However, the molecular and cellular mechanisms that underlie HPR have been elusive, as the identity and sensing mechanisms of insect avirulence effectors have remained unknown. Here we identify an insect salivary protein perceived by a plant immune receptor. The BPH14-interacting salivary protein (BISP) from the brown planthopper (Nilaparvata lugens Stål) is secreted into rice (Oryza sativa) during feeding. In susceptible plants, BISP targets O. satvia RLCK185 (OsRLCK185; hereafter Os is used to denote O. satvia-related proteins or genes) to suppress basal defences. In resistant plants, the nucleotide-binding leucine-rich repeat receptor BPH14 directly binds BISP to activate HPR. Constitutive activation of Bph14-mediated immunity is detrimental to plant growth and productivity. The fine-tuning of Bph14-mediated HPR is achieved through direct binding of BISP and BPH14 to the selective autophagy cargo receptor OsNBR1, which delivers BISP to OsATG8 for degradation. Autophagy therefore controls BISP levels. In Bph14 plants, autophagy restores cellular homeostasis by downregulating HPR when feeding by brown planthoppers ceases. We identify an insect saliva protein sensed by a plant immune receptor and discover a three-way interaction system that offers opportunities for developing high-yield, insect-resistant crops.

Barley yellow dwarf Virus-GAV movement protein activating wheat TaATG6-Mediated antiviral autophagy pathway

Barley yellow dwarf virus-GAV (BYDV-GAV) is a highly destructive virus that is transmitted by aphids and can cause substantial yield losses in crops such as wheat (Triticum aestivum), barley (Hordeum vulgare) and oat (Avena sativa). Autophagy is an evolutionarily conserved degradation process that eliminates damaged or harmful intracellular substances during stress conditions or specific developmental processes. However, the mechanism of autophagy involved in disease resistance in wheat remains unknown. In this study, we demonstrate that BYDV-GAV infection could induces the upregulation of genes related to the autophagy pathway in wheat, accompanied by the production of autophagosomes. Furthermore, we confirmed the direct interaction between the viral movement protein (MP) and wheat autophagy-related gene 6 (TaATG6) both in vivo and in vitro. Through yeast function complementation experiments, we determined that TaATG6 can restore the autophagy function in a yeast mutant, atg6. Additionally, we identified the interaction between TaATG6 and TaATG8, core factors of the autophagic pathway, using the yeast two-hybrid system. TaATG6 and TaATG8-silenced wheat plants exhibited a high viral content. Overall, our findings suggest that wheat can recognize BYDV-GAV infection and activate the MP-TaATG6-TaATG8 regulatory network of defense responses through the induction of the autophagy pathway.

Geminiviral C2 proteins inhibit active autophagy to facilitate virus infection by impairing the interaction of ATG7 and ATG8

Autophagy is a conserved intracellular degradation process that plays an active role in plant response to virus infections. Here we report that geminiviruses counteract activated autophagy-mediated antiviral defense in plant cells through the C2 proteins they encode. We found that, in Nicotiana benthamiana plants, tomato leaf curl Yunnan virus (TLCYnV) infection upregulated the transcription levels of autophagy-related genes (ATGs). Overexpression of NbATG5, NbATG7, or NbATG8a in N. benthamiana plants decreased TLCYnV accumulation and attenuated viral symptoms. Interestingly, transgenic overexpression of NbATG7 promoted the growth of N. benthamiana plants and enhanced plant resistance to TLCYnV. We further revealed that the C2 protein encoded by TLCYnV directly interacted with the ubiquitin-activating domain of ATG7. This interaction competitively disrupted the ATG7-ATG8 binding in N. benthamiana and Solanum lycopersicum plants, thereby inhibiting autophagy activity. Furthermore, we uncovered that the C2-mediated autophagy inhibition mechanism was conserved in three other geminiviruses. In summary, we discovered a novel counter-defensive strategy employed by geminiviruses that enlists their C2 proteins as disrupters of ATG7-ATG8 interactions to defeat antiviral autophagy.

Autophagy and its mediated mitochondrial quality control maintain pollen tube growth and male fertility in Arabidopsis

Macroautophagy/autophagy, a major catabolic pathway in eukaryotes, participates in plant sexual reproduction including the processes of male gametogenesis and the self-incompatibility response. Rapid pollen tube growth is another essential reproductive process that is metabolically highly demanding to drive the vigorous cell growth for delivery of male gametes for fertilization in angiosperms. Whether and how autophagy operates to maintain the homeostasis of pollen tubes remains unknown. Here, we provide evidence that autophagy is elevated in growing pollen tubes and critically required during pollen tube growth and male fertility in Arabidopsis. We demonstrate that SH3P2, a critical non-ATG regulator of plant autophagy, colocalizes with representative ATG proteins during autophagosome biogenesis in growing pollen tubes. Downregulation of SH3P2 expression significantly disrupts Arabidopsis pollen germination and pollen tube growth. Further analysis of organelle dynamics reveals crosstalk between autophagosomes and prevacuolar compartments following the inhibition of phosphatidylinositol 3-kinase. In addition, time-lapse imaging and tracking of ATG8e-labeled autophagosomes and depolarized mitochondria demonstrate that they interact specifically via the ATG8-family interacting motif (AIM)-docking site to mediate mitophagy. Ultrastructural identification of mitophagosomes and two additional forms of autophagosomes imply that multiple types of autophagy are likely to function simultaneously within pollen tubes. Altogether, our results suggest that autophagy is functionally crucial for mediating mitochondrial quality control and canonical cytoplasm recycling during pollen tube growth.Abbreviations: AIM: ATG8-family interacting motif; ATG8: autophagy related 8; ATG5: autophagy related 5; ATG7: autophagy related 7; BTH: acibenzolar-S-methyl; DEX: dexamethasone; DNP: 2,4-dinitrophenol; GFP: green fluorescent protein; YFP: yellow fluorescent protein; PtdIns3K: phosphatidylinositol 3-kinase; PtdIns3P: phosphatidylinositol-3-phosphate; PVC: prevacuolar compartment; SH3P2: SH3 domain-containing protein 2.

Ferric Chloride Controls Citrus Anthracnose by Inducing the Autophagy Activity of Colletotrichum gloeosporioides

Colletotrichum gloeosporioides causes citrus anthracnose, which seriously endangers the pre-harvest production and post-harvest storage of citrus due to its devastating effects on fruit quality, shelf life, and profits. However, although some chemical agents have been proven to effectively control this plant disease, little to no efforts have been made to identify effective and safe anti-anthracnose alternatives. Therefore, this study assessed and verified the inhibitory effect of ferric chloride (FeCl₃) against C. gloeosporioides. Our findings demonstrated that FeCl₃ could effectively inhibit C. gloeosporioides spore germination. After FeCl₃ treatment, the germination rate of the spores in the minimum inhibitory concentration (MIC) and minimum fungicidal concentration (MFC) groups decreased by 84.04% and 89.0%, respectively. Additionally, FeCl₃ could effectively inhibit the pathogenicity of C. gloeosporioides in vivo. Optical microscopy (OM) and scanning electron microscopy (SEM) analyses demonstrated the occurrence of wrinkled and atrophic mycelia. Moreover, FeCl₃ induced autophagosome formation in the test pathogen, as confirmed by transmission electron microscopy (TEM) and monodansylcadaverine (MDC) staining. Additionally, a positive correlation was identified between the FeCl₃ concentration and the damage rate of the fungal sporophyte cell membrane, as the staining rates of the control (untreated), 1/2 MIC, and MIC FeCl₃ treatment groups were 1.87%, 6.52%, and 18.15%, respectively. Furthermore, the ROS content in sporophyte cells increased by 3.6%, 29.27%, and 52.33% in the control, 1/2 MIC, and MIC FeCl₃ groups, respectively. Therefore, FeCl₃ could reduce the virulence and pathogenicity of C. gloeosporioides. Finally, FeCl₃-handled citrus fruit exhibited similar physiological qualities to water-handled fruit. The results show that FeCl₃ may prove to be a good substitute for the treatment of citrus anthracnose in the future.

A key virulence effector from cyst nematodes targets host autophagy to promote nematode parasitism

Autophagy, an intracellular degradation system conserved in eukaryotes, has been increasingly recognized as a key battlefield in plant-pathogen interactions. However, the role of plant autophagy in nematode parasitism is mostly unknown. We report here the identification of a novel and conserved effector, Nematode Manipulator of Autophagy System 1 (NMAS1), from plant-parasitic cyst nematodes (Heterodera and Globodera spp.). We used molecular and genetic analyses to demonstrate that NMAS1 is required for nematode parasitism. The NMAS1 effectors are potent suppressors of reactive oxygen species (ROS) induced by flg22 and cell death mediated by immune receptors in Nicotiana benthamiana, suggesting a key role of NMAS1 effectors in nematode virulence. Arabidopsis atg mutants defective in autophagy showed reduced susceptibility to nematode infection. The NMAS1 effectors contain predicted AuTophaGy-related protein 8 (ATG8)-interacting motif (AIM) sequences. In planta protein-protein interaction assays further demonstrated that NMAS1 effectors specifically interact with host plant ATG8 proteins. Interestingly, mutation in AIM2 of GrNMAS1 from the potato cyst nematode Globodera rostochiensis abolishes its interaction with potato StATG8 proteins and its activity in ROS suppression. Collectively, our results reveal for the first time that cyst nematodes employ a conserved AIM-containing virulence effector capable of targeting a key component of host autophagy to promote disease.

Rice stripe virus p2 protein interacts with ATG5 and is targeted for degradation by autophagy

Autophagy can be induced by viral infection and plays antiviral roles in plants, but the underlying mechanism is not well understood. In our previous reports, we have demonstrated that the plant ATG5 plays an essential role in activating autophagy in rice stripe virus (RSV)-infected plants. We also showed that eIF4A, a negative factor of autophagy, interacts with and inhibits ATG5. We here found that RSV p2 protein interacts with ATG5 and can be targeted by autophagy for degradation. Expression of p2 protein induced autophagy and p2 protein was shown to interfere with the interaction between ATG5 and eIF4A, while eIF4A had no effect on the interaction between ATG5 and p2. These results indicate an additional information on the induction of autophagy in RSV-infected plants.

Comparative transcriptomics and genomic analyses reveal differential gene expression related to Colletotrichum brevisporum resistance in papaya (Carica papaya L.)

Colletotrichum brevisporum is an important causal pathogen of anthracnose that seriously affects the fruit quality and yield of papaya (Carica papaya L.). Although many genes and biological processes involved in anthracnose resistance have been reported in other species, the molecular mechanisms involved in the response or resistance to anthracnose in post-harvest papaya fruits remain unclear. In this study, we compared transcriptome changes in the post-harvest fruits of the anthracnose-susceptible papaya cultivar Y61 and the anthracnose-resistant cultivar G20 following C. brevisporum inoculation. More differentially expressed genes (DEGs) and differentially expressed long non-coding RNAs (DElnRNAs) were identified in G20 than in Y61, especially at 24 h post-inoculation (hpi), suggesting a prompt activation of defense responses in G20 in the first 24 h after C. brevisporum inoculation. These DEGs were mainly enriched in plant-pathogen interaction, phenylpropanoid biosynthesis/metabolism, and peroxisome and flavonoid biosynthesis pathways in both cultivars. However, in the first 24 hpi, the number of DEGs related to anthracnose resistance was greater in G20 than in Y61, and changes in their expression levels were faster in G20 than in Y61. We also identified a candidate anthracnose-resistant gene cluster, which consisted of 12 genes, 11 in G20 and Y61, in response to C. brevisporum inoculation. Moreover, 529 resistance gene analogs were identified in papaya genome, most of which responded to C. brevisporum inoculation and were genetically different between papaya cultivars and wild-type populations. The total expression dose of the resistance gene analogs may help papaya resist C. brevisporum infection. This study revealed the mechanisms underlying different anthracnose resistance between the anthracnose-resistant and anthracnose-susceptible cultivars based on gene expression, and identified some potential anthracnose resistance-related candidate genes/major regulatory factors. Our findings provided potential targets for developing novel genetic strategies to overcome anthracnose in papaya.

Cucumber Mosaic Virus-Induced Systemic Necrosis in Arabidopsis thaliana: Determinants and Role in Plant Defense

Effector-triggered immunity (ETI) is one of the most studied mechanisms of plant resistance to viruses. During ETI, viral proteins are recognized by specific plant R proteins, which most often trigger a hypersensitive response (HR) involving programmed cell death (PCD) and a restriction of infection in the initially infected sites. However, in some plant-virus interactions, ETI leads to a response in which PCD and virus multiplication are not restricted to the entry sites and spread throughout the plant, leading to systemic necrosis. The host and virus genetic determinants, and the consequences of this response in plant-virus coevolution, are still poorly understood. Here, we identified an allelic version of RCY1-an R protein-as the host genetic determinant of broad-spectrum systemic necrosis induced by cucumber mosaic virus (CMV) infection in the Arabidopsis thaliana Co-1 ecotype. Systemic necrosis reduced virus fitness by shortening the infectious period and limiting virus multiplication; thus, this phenotype could be adaptive for the plant population as a defense against CMV. However, the low frequency (less than 1%) of this phenotype in A. thaliana wild populations argues against this hypothesis. These results expand current knowledge on the resistance mechanisms to virus infections associated with ETI in plants.

The Gain-of-Function Mutation, OsSpl26, Positively Regulates Plant Immunity in Rice

Rice spotted-leaf mutants are ideal materials to study the molecular mechanism underlying programmed cell death and disease resistance in plants. LOC_Os07g04820 has previously been identified as the candidate gene responsible for the spotted-leaf phenotype in rice Spotted-leaf 26 (Spl26) mutant. Here, we cloned and validated that LOC_Os07g04820 is the locus controlling the spotted-leaf phenotype of Spl26 by reverse functional complementation and CRISPR/Cas9-mediated knockout of the mutant allele. The recessive wild-type spl26 allele (Oryza sativa spotted-leaf 26, Osspl26) is highly conservative in grass species and encodes a putative G-type lectin S-receptor-like serine/threonine protein kinase with 444 amino acid residuals. OsSPL26 localizes to the plasma membrane and can be detected constitutively in roots, stems, leaves, sheaths and panicles. The single base substitution from T to A at position 293 leads to phenylalanine/tyrosine replacement at position 98 in the encoded protein in the mutant and induces excessive accumulation of H₂O₂, leading to oxidative damage to cells, and finally, formation of the spotted-leaf phenotype in Spl26. The formation of lesions not only affects the growth and development of the plants but also activates the defense response and enhances the resistance to the bacterial blight pathogen, Xanthomonas oryzae pv. oryzae. Our results indicate that the gain-of-function by the mutant allele OsSpl26 positively regulates cell death and immunity in rice.

Autophagy in the Lifetime of Plants: From Seed to Seed

Autophagy is a highly conserved self-degradation mechanism in eukaryotes. Excess or harmful intracellular content can be encapsulated by double-membrane autophagic vacuoles and transferred to vacuoles for degradation in plants. Current research shows three types of autophagy in plants, with macroautophagy being the most important autophagic degradation pathway. Until now, more than 40 autophagy-related (ATG) proteins have been identified in plants that are involved in macroautophagy, and these proteins play an important role in plant growth regulation and stress responses. In this review, we mainly introduce the research progress of autophagy in plant vegetative growth (roots and leaves), reproductive growth (pollen), and resistance to biotic (viruses, bacteria, and fungi) and abiotic stresses (nutrients, drought, salt, cold, and heat stress), and we discuss the application direction of plant autophagy in the future.

Roles of Species-Specific Legumains in Pathogenicity of the Pinewood Nematode Bursaphelenchus xylophilus

Peptidases are very important to parasites, which have central roles in parasite biology and pathogenesis. In this study, by comparative genome analysis, genome-wide peptidase diversities among plant-parasitic nematodes are estimated. We find that genes encoding cysteine peptidases in family C13 (legumain) are significantly abundant in pine wood nematodes Bursaphelenchus genomes, compared to those in other plant-parasitic nematodes. By phylogenetic analysis, a clade of B. xylophilus-specific legumain is identified. RT-qPCR detection shows that these genes are highly expressed at early stage during the nematode infection process. Utilizing transgene technology, cDNAs of three species-specific legumain were introduced into the Arabidopsis γvpe mutant. Functional complementation assay shows that these B. xylophilus legumains can fully complement the activity of Arabidopsis γVPE to mediate plant cell death triggered by the fungal toxin FB1. Secretory activities of these legumains are experimentally validated. By comparative transcriptome analysis, genes involved in plant cell death mediated by legumains are identified, which enrich in GO terms related to ubiquitin protein transferase activity in category molecular function, and response to stimuli in category biological process. Our results suggest that B. xylophilu-specific legumains have potential as effectors to be involved in nematode-plant interaction and can be related to host cell death.

Network and Evolutionary Analysis Reveals Candidate Genes of Membrane Trafficking Involved in Maize Seed Development and Immune Response

The plant membrane-trafficking system plays a crucial role in maintaining proper cellular functions and responding to various developmental and environmental cues. Thus far, our knowledge of the maize membrane-trafficking system is still limited. In this study, we systematically identified 479 membrane-trafficking genes from the maize genome using orthology search and studied their functions by integrating transcriptome and evolution analyses. These genes encode the components of coated vesicles, AP complexes, autophagy, ESCRTs, retromers, Rab GTPases, tethering factors, and SNAREs. The maize genes exhibited diverse but coordinated expression patterns, with 249 genes showing elevated expression in reproductive tissues. Further WGCNA analysis revealed that five COPII components and four Rab GTPases had high connectivity with protein biosynthesis during endosperm development and that eight components of autophagy, ESCRT, Rab, and SNARE were strongly co-upregulated with defense-related genes and/or with secondary metabolic processes to confer basal resistance to Fusarium graminearum. In addition, we identified 39 membrane-trafficking genes with strong selection signals during maize domestication and/or improvement. Among them, ZmSec23a and ZmVPS37A were selected for kernel oil production during improvement and pathogen resistance during domestication, respectively. In summary, these findings will provide important hints for future appreciation of the functions of membrane-trafficking genes in maize.

Autophagy modulates the metabolism and growth of tomato fruit during development

Although autophagy is a conserved mechanism operating across eukaryotes, its effects on crops and especially their metabolism has received relatively little attention. Indeed, whilst a few recent studies have used systems biology tools to look at the consequences of lack of autophagy in maize these focused on leaf tissues rather than the kernels. Here we utilized RNA interference (RNAi) to generate tomato plants that were deficient in the autophagy-regulating protease ATG4. Plants displayed an early senescence phenotype yet relatively mild changes in the foliar metabolome and were characterized by a reduced fruit yield phenotype. Metabolite profiling indicated that metabolites of ATG4-RNAi tomato leaves just exhibited minor alterations while that of fruit displayed bigger difference compared to the WT. In detail, many primary metabolites exhibited decreases in the ATG4-RNAi lines, such as proline, tryptophan and phenylalanine, while the representative secondary metabolites (quinic acid and 3-trans-caffeoylquinic acid) were present at substantially higher levels in ATG4-RNAi green fruits than in WT. Moreover, transcriptome analysis indicated that the most prominent differences were in the significant upregulation of organelle degradation genes involved in the proteasome or chloroplast vesiculation pathways, which was further confirmed by the reduced levels of chloroplastic proteins in the proteomics data. Furthermore, integration analysis of the metabolome, transcriptome and proteome data indicated that ATG4 significantly affected the lipid metabolism, chlorophyll binding proteins and chloroplast biosynthesis. These data collectively lead us to propose a more sophisticated model to explain the cellular co-ordination of the process of autophagy.

Exogenous Melatonin Improves Pear Resistance to Botryosphaeria dothidea by Increasing Autophagic Activity and Sugar/Organic Acid Levels

Pear is an important fruit tree worldwide, but it is often infected by the pathogen Botryosphaeria dothidea, which causes pear ring rot disease. To explore the effect of exogenous melatonin on the disease resistance of pear, we treated inoculated pear fruits with different concentrations of melatonin. The results showed that 100 μΜ of melatonin had the most significant effect with resistance to B. dothidea. In addition, melatonin treatment significantly reduced the diameter of disease lesions and enhanced the endogenous melatonin content in pears inoculated with B. dothidea. Compared with the control treatment, melatonin treatment suppressed increases in reactive oxygen species (ROS) and activated ROS-scavenging enzymes. Treatment with exogenous melatonin maintained ascorbic acid-glutathione at more reductive status. The expression levels of core autophagic genes and autophagosome formation were elevated by melatonin treatment in pear fruits. Silencing of PbrATG5 in Pyrus pyrifolia conferred sensitivity to inoculation that was only slightly attenuated by melatonin treatment. After inoculation with B. dothidea, exogenous melatonin treatment led to higher levels of soluble sugars and organic acids in pear fruits than H₂O treatment. Overall, our results demonstrate that melatonin enhances resistance to B. dothidea by increasing autophagic activity and soluble sugar/organic acid accumulation.

Salicylic acid and the viral virulence factor 2b regulate the divergent roles of autophagy during cucumber mosaic virus infection

Macroautophagy/autophagy is a conserved intracellular degradation pathway that has recently emerged as an integral part of plant responses to virus infection. The known mechanisms of autophagy range from the selective degradation of viral components to a more general attenuation of disease symptoms. In addition, several viruses are able to manipulate the autophagy machinery and counteract autophagy-dependent resistance. Despite these findings, the complex interplay of autophagy activities, viral pathogenicity factors, and host defense pathways in disease development remains poorly understood. In the current study, we analyzed the interaction between autophagy and cucumber mosaic virus (CMV) in Arabidopsis thaliana. We show that autophagy is induced during CMV infection and promotes the turnover of the major virulence protein and RNA silencing suppressor 2b. Intriguingly, autophagy induction is mediated by salicylic acid (SA) and dampened by the CMV virulence factor 2b. In accordance with 2b degradation, we found that autophagy provides resistance against CMV by reducing viral RNA accumulation in an RNA silencing-dependent manner. Moreover, autophagy and RNA silencing attenuate while SA promotes CMV disease symptoms, and epistasis analysis suggests that autophagy-dependent disease and resistance are uncoupled. We propose that autophagy counteracts CMV virulence via both 2b degradation and reduced SA-responses, thereby increasing plant fitness with the viral trade-off arising from increased RNA silencing-mediated resistance.

Linking Autophagy to Potential Agronomic Trait Improvement in Crops

Autophagy is an evolutionarily conserved catabolic process in eukaryotic cells, by which the superfluous or damaged cytoplasmic components can be delivered into vacuoles or lysosomes for degradation and recycling. Two decades of autophagy research in plants uncovers the important roles of autophagy during diverse biological processes, including development, metabolism, and various stress responses. Additionally, molecular machineries contributing to plant autophagy onset and regulation have also gradually come into people’s sights. With the advancement of our knowledge of autophagy from model plants, autophagy research has expanded to include crops in recent years, for a better understanding of autophagy engagement in crop biology and its potentials in improving agricultural performance. In this review, we summarize the current research progress of autophagy in crops and discuss the autophagy-related approaches for potential agronomic trait improvement in crop plants.

Identification and Characterization of Rice Circular RNAs Responding to Xanthomonas oryzae pv. oryzae Invasion

Emerging roles of circular RNAs (circRNAs) in various biological processes have advanced our knowledge of transcriptional and posttranscriptional gene regulation. To date, no research has been conducted to explore their roles in the rice-Xanthomonas oryzae pv. oryzae interaction. Therefore, we identified 3,517 circRNAs from rice leaves infected with the highly virulent X. oryzae pv. oryzae strain PXO99^A by using rRNA depleted RNA sequencing technique coupled with the CIRI2 and CIRCexplorer2 pipeline. Characterization analyses showed that these circRNAs were distributed across the whole genome of rice, and most circRNAs arose from exons (85.13%), ranged from 200 to 1,000 bp, and were with a noncanonical GT/AG (including CT/AC equivalent) splicing signal. Functional annotation and enrichment analysis of the host genes that produced the differentially expressed circRNAs (DEcircRNAs) suggested that these identified circRNAs might play an important role in reprogramming rice responses to PXO99^A invasion, mainly by mediating photorespiration and chloroplast, peroxisome, and diterpenoid biosynthesis. Moreover, 31 DEcircRNAs were predicted to act as microRNA decoys in rice. The expression profile of four DEcircRNAs were validated by quantitative real-time PCR with divergent primers, and the back-splicing sites of seven DEcircRNAs were verified by PCR analysis and Sanger sequencing. Collectively, these results inferred a potential functional role of circRNAs in the regulation of rice immunity and provide novel clues about the molecular mechanisms of rice-PXO99^A interaction.

Light-Engineering Technology for Enhancing Plant Disease Resistance

Insect vector-borne diseases are a major constraint to a wide variety of crops. Plants integrate environmental light and internal signalings to defend dual stresses both from the vector insects and vector-transmitted pathogens. In this review, we highlight a studies that demonstrate how light regulates plants deploying mechanisms against vector-borne diseases. Four major host defensive pathways involved in the host defense network against multiple biotic stresses are reviewed: innate immunity, phytohormone signaling, RNA interference, and protein degradation. The potential with light-engineering technology with light emitting diodes (LEDs) and genome engineering technology for fine-tuning crop defense and yield are also discussed.

ATG8-Interacting Motif: Evolution and Function in Selective Autophagy of Targeting Biological Processes

Autophagy is an evolutionarily conserved vacuolar process functioning in the degradation of cellular components for reuse. In plants, autophagy is generally activated upon stress and its regulation is executed by numbers of AuTophaGy-related genes (ATGs), of which the ATG8 plays a dual role in both biogenesis of autophagosomes and recruitment of ATG8-interacting motif (AIM) anchored selective autophagy receptors (SARs). Such motif is either termed as AIM or ubiquitin-interacting motif (UIM), corresponding to the LC3-interacting region (LIR)/AIM docking site (LDS) or the UIM docking site (UDS) of ATG8, respectively. To date, dozens of AIM or UIM containing SARs have been characterized. However, the knowledge of these motifs is still obscured. In this review, we intend to summarize the current understanding of SAR proteins and discuss the conservation and diversification of the AIMs/UIMs, expectantly providing new insights into the evolution of them in various biological processes in plants.

Autophagy regulates whitefly-symbiont metabolic interactions

Nutritional symbionts are restricted to specialized host cells called bacteriocytes in various insect orders. These symbionts can provide essential nutrients to the host. However, the cellular mechanisms underlying the regulation of these insect-symbiont metabolic associations remain largely unclear. The whitefly, Bemisia tabaci MEAM1, hosts Portiera and Hamiltonella bacteria in the same bacteriocyte. In this study, the induction of autophagy by chemical treatment and gene silencing decreased symbiont titers, and essential amino acid (EAA) and B vitamin contents. In contrast, the repression of autophagy in bacteriocytes via Atg8 silencing increased symbiont titers, and amino acid and B vitamin contents. Furthermore, dietary supplementation with non-EAAs or B vitamins alleviated autophagy in whitefly bacteriocytes, elevated TOR (target of rapamycin) expression and increased symbiont titers. TOR silencing restored symbiont titers in whiteflies after dietary supplementation with B vitamins. These data suggest that Portiera and Hamiltonella evade autophagy of the whitefly bacteriocytes by activating the TOR pathway via providing essential nutrients. Taken together, we demonstrated that autophagy plays a critical role in regulating the metabolic interactions between the whitefly and two intracellular symbionts. Therefore, this study reveals that autophagy is an important cellular basis for bacteriocyte evolution and symbiosis persistence in whiteflies. The whitefly symbiosis unravels the interactions between cellular and metabolic functions of bacteriocytes. Importance Nutritional symbionts, which are restricted to specialized host cells called bacteriocytes, can provide essential nutrients for many hosts. However, the cellular mechanisms of regulation of animal-symbiont metabolic associations have been largely unexplored. Here, using the whitefly-Portiera/Hamiltonella endosymbiosis, we demonstrate autophagy regulates the symbiont titers, and thereby alters the essential amino acid and B vitamin contents. For persistence in the whitefly bacteriocytes, Portiera and Hamiltonella alleviate autophagy by activating the TOR (target of rapamycin) pathway through providing essential nutrients. Therefore, we demonstrate that autophagy plays a critical role in regulating the metabolic interactions between the whitefly and two intracellular symbionts. This study also provides insight into the cellular basis of bacteriocyte evolution and symbiosis persistence in the whitefly. The mechanisms underlying the role of autophagy in whitefly symbiosis could be widespread in many insect nutritional symbioses. These findings provide new avenue for whitefly control via regulating autophagy in the future.

Silencing Autophagy-Related Gene 2 (ATG2) Results in Accelerated Senescence and Enhanced Immunity in Soybean

Autophagy plays a critical role in nutrient recycling and stress adaptations. However, the role of autophagy has not been extensively investigated in crop plants. In this study, soybean autophagy-related gene 2 (GmATG2) was silenced, using virus-induced silencing (VIGS) mediated by Bean pod mottle virus (BPMV). An accelerated senescence phenotype was exclusively observed for the GmATG2-silenced plants under dark conditions. In addition, significantly increased accumulation of both ROS and SA as well as a significantly induced expression of the pathogenesis-related gene 1 (PR1) were also observed on the leaves of the GmATG2-silenced plants, indicating an activated immune response. Consistent with this, GmATG2-silenced plants exhibited a significantly enhanced resistance to Pseudomonas syringae pv. glycinea (Psg) relative to empty vector control plants (BPMV-0). Notably, the activated immunity of the GmATG2-silenced plants was independent of the MAPK signaling pathway. The fact that the accumulation levels of ATG8 protein and poly-ubiquitinated proteins were significantly increased in the dark-treated GmATG2-silenced plants relative to the BPMV-0 plants indicated that the autophagic degradation is compromised in the GmATG2-silenced plants. Together, our results indicated that silencing GmATG2 compromises the autophagy pathway, and the autophagy pathway is conserved in different plant species.

SsATG8 and SsNBR1 mediated-autophagy is required for fungal development, proteasomal stress response and virulence in Sclerotinia sclerotiorum

Autophagy plays vital roles in the interaction between the necrotrophic fungal pathogen Sclerotinia sclerotiorum and its hosts. However, so far, only little is known about the impacts of autophagy machinery in S. sclerotiorum per se on the fungal morphogenesis and pathogenesis. Here, through functional genomic approaches, we showed that SsATG8, one of the core components of the autophagy machinery, and its interactor SsNBR1, an autophagy cargo receptor, are important for vegetative growth, sclerotial formation, oxalic acid (OA) production, compound appressoria development, and virulence of S. sclerotiorum. Complementation assays with chimeric fusion constructs revealed that both LDS [AIM (ATG8 interacting motif) / LIR (LC3-interacting region) docking site] and UDS [UIM (ubiquitin-interacting motif) docking site] sites of the SsATG8 are required for its functions in autophagy and pathogenesis. Importantly, ΔSsatg8 and ΔSsnbr1 mutants showed enhanced sensitivity to the exogenous treatment with the proteasome inhibitors bortezomib and carfilzomib, and ΔSsnbr1 mutant had decreased expression of SsATG8 under the proteasomal stress conditions, suggesting that a cross-talk exists between ubiquitin-proteasome and selective autophagy pathways, which enables downstream protein degradation to proceed properly during diverse biological processes. Collectively, our data indicate that SsATG8- and SsNBR1-mediated autophagy is crucial for S. sclerotiorum development, proteasomal stress response and virulence.

eIF4A, a target of siRNA derived from rice stripe virus, negatively regulates antiviral autophagy by interacting with ATG5 in Nicotiana benthamiana

Autophagy is induced by viral infection and has antiviral functions in plants, but the underlying mechanism is poorly understood. We previously identified a viral small interfering RNA (vsiRNA) derived from rice stripe virus (RSV) RNA4 that contributes to the leaf-twisting and stunting symptoms caused by this virus by targeting the host eukaryotic translation initiation factor 4A (eIF4A) mRNA for silencing. In addition, autophagy plays antiviral roles by degrading RSV p3 protein, a suppressor of RNA silencing. Here, we demonstrate that eIF4A acts as a negative regulator of autophagy in Nicotiana benthamiana. Silencing of NbeIF4A activated autophagy and inhibited RSV infection by facilitating autophagic degradation of p3. Further analysis showed that NbeIF4A interacts with NbATG5 and interferes with its interaction with ATG12. Overexpression of NbeIF4A suppressed NbATG5-activated autophagy. Moreover, expression of vsiRNA-4A, which targets NbeIF4A mRNA for cleavage, induced autophagy by silencing NbeIF4A. Finally, we demonstrate that eIF4A from rice, the natural host of RSV, also interacts with OsATG5 and suppresses OsATG5-activated autophagy, pointing to the conserved function of eIF4A as a negative regulator of antiviral autophagy. Taken together, these results reveal that eIF4A negatively regulates antiviral autophagy by interacting with ATG5 and that its mRNA is recognized by a virus-derived siRNA, resulting in its silencing, which induces autophagy against viral infection.

Research Advances in Potyviruses: From the Laboratory Bench to the Field

Potyviruses (viruses in the genus Potyvirus, family Potyviridae) constitute the largest group of known plant-infecting RNA viruses and include many agriculturally important viruses that cause devastating epidemics and significant yield losses in many crops worldwide. Several potyviruses are recognized as the most economically important viral pathogens. Therefore, potyviruses are more studied than other groups of plant viruses. In the past decade, a large amount of knowledge has been generated to better understand potyviruses and their infection process. In this review, we list the top 10 economically important potyviruses and present a brief profile of each. We highlight recent exciting findings on the novel genome expression strategy and the biological functions of potyviral proteins and discuss recent advances in molecular plant-potyvirus interactions, particularly regarding the coevolutionary arms race. Finally, we summarize current disease control strategies, with a focus on biotechnology-based genetic resistance, and point out future research directions.

Understanding In Vitro Tissue Culture-Induced Variation Phenomenon in Microspore System

In vitro tissue culture plant regeneration is a complicated process that requires stressful conditions affecting the cell functioning at multiple levels, including signaling pathways, transcriptome functioning, the interaction between cellular organelles (retro-, anterograde), compounds methylation, biochemical cycles, and DNA mutations. Unfortunately, the network linking all these aspects is not well understood, and the available knowledge is not systemized. Moreover, some aspects of the phenomenon are poorly studied. The present review attempts to present a broad range of aspects involved in the tissue culture-induced variation and hopefully would stimulate further investigations allowing a better understanding of the phenomenon and the cell functioning.

Activation of microlipophagy during early infection of insect hosts by Metarhizium robertsii

The requirement of macroautophagic/autophagic machinery for filamentous fungal development and pathogenicity has been recognized, but the underlying effects and mechanisms remain elusive. The insect pathogenic fungus Metarhizium robertsii infects hosts by cuticular penetration through the formation of the infection structure appressoria. Here, we show that autophagic fluxes were highly activated during the appressorial formation of M. robertsii. Genome-wide deletion of the autophagy-related genes and insect bioassays identified 10 of 23 encoded MrATG genes with requirements for topical fungal infection of insect hosts. Besides the defect in forming appressoria on insects (two null mutants), these virulence-reduced mutants were largely impaired in penetrating cellophane membrane and insect cuticles, suggesting their failures in generating proper appressorium turgor. We found that the conidial storage of lipid droplets (LDs) had no obvious difference between strains, but autophagic LD degradation was impaired in different mutants. After induction of cell autophagy by nitrogen starvation, we found that LD entry into vacuoles was unaffected in the selected mutant cells with potential failures in forming autophagosomes. The finding therefore reveals a microlipophagy machinery employed in this fungus and that the direct engulfment of LDs occurs without inhibition by the downstream defective lipolysis. Our data first unveil the activation and contribution of microlipophagy to fungal infection biology. The obtained technique may benefit future detection of microlipophagy in different organisms by examining vacuolar or lysosomal engulfment of LDs in core autophagic gene deletion mutants.

Abscisic Acid-Induced Stomatal Closure: An Important Component of Plant Defense Against Abiotic and Biotic Stress

Abscisic acid (ABA) is a stress hormone that accumulates under different abiotic and biotic stresses. A typical effect of ABA on leaves is to reduce transpirational water loss by closing stomata and parallelly defend against microbes by restricting their entry through stomatal pores. ABA can also promote the accumulation of polyamines, sphingolipids, and even proline. Stomatal closure by compounds other than ABA also helps plant defense against both abiotic and biotic stress factors. Further, ABA can interact with other hormones, such as methyl jasmonate (MJ) and salicylic acid (SA). Such cross-talk can be an additional factor in plant adaptations against environmental stresses and microbial pathogens. The present review highlights the recent progress in understanding ABA's multifaceted role under stress conditions, particularly stomatal closure. We point out the importance of reactive oxygen species (ROS), reactive carbonyl species (RCS), nitric oxide (NO), and Ca²⁺ in guard cells as key signaling components during the ABA-mediated short-term plant defense reactions. The rise in ROS, RCS, NO, and intracellular Ca²⁺ triggered by ABA can promote additional events involved in long-term adaptive measures, including gene expression, accumulation of compatible solutes to protect the cell, hypersensitive response (HR), and programmed cell death (PCD). Several pathogens can counteract and try to reopen stomata. Similarly, pathogens attempt to trigger PCD of host tissue to their benefit. Yet, ABA-induced effects independent of stomatal closure can delay the pathogen spread and infection within leaves. Stomatal closure and other ABA influences can be among the early steps of defense and a crucial component of plants' innate immunity response. Stomatal guard cells are quite sensitive to environmental stress and are considered good model systems for signal transduction studies. Further research on the ABA-induced stomatal closure mechanism can help us design strategies for plant/crop adaptations to stress.

The plant protein NbP3IP directs degradation of Rice stripe virus p3 silencing suppressor protein to limit virus infection through interaction with the autophagy-related protein NbATG8

In plants, autophagy is involved in responses to viral infection. However, the role of host factors in mediating autophagy to suppress viruses is poorly understood. A previously uncharacterized plant protein, NbP3IP, was shown to interact with p3, an RNA-silencing suppressor protein encoded by Rice stripe virus (RSV), a negative-strand RNA virus. The potential roles of NbP3IP in RSV infection were examined. NbP3IP degraded p3 through the autophagy pathway, thereby affecting the silencing suppression activity of p3. Transgenic overexpression of NbP3IP conferred resistance to RSV infection in Nicotiana benthamiana. RSV infection was promoted in ATG5- or ATG7-silenced plants and was inhibited in GAPC-silenced plants where autophagy was activated, confirming the role of autophagy in suppressing RSV infection. NbP3IP interacted with NbATG8f, indicating a potential selective autophagosomal cargo receptor role for P3IP. Additionally, the rice NbP3IP homolog (OsP3IP) also mediated p3 degradation and interacted with OsATG8b and p3. Through identification of the involvement of P3IP in the autophagy-mediated degradation of RSV p3, we reveal a new mechanism to antagonize the infection of RSV, and thereby provide the first evidence that autophagy can play an antiviral role against negative-strand RNA viruses.

Transcriptomic and functional analyses reveal an antiviral role of autophagy during pepper mild mottle virus infection

BACKGROUND

Pepper mild mottle virus (PMMoV) is a member in the genus Tobamovirus and infects mainly solanaceous plants. However, the mechanism of virus-host interactions remains unclear. To explore the responses of pepper plants to PMMoV infection, we analyzed the transcriptomic changes in pepper plants after PMMoV infection using a high-throughput RNA sequencing approach and explored the roles of host autophagy in regulating PMMoV infection.

RESULTS

A total of 197 differentially expressed genes (DEGs) were obtained after PMMoV infection, including 172 significantly up-regulated genes and 25 down-regulated genes. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that most up-regulated DEGs were involved in plant abiotic and biotic stresses. Further analyses showed the expressions of multiple autophagy-related genes (ATGs) were increased after PMMoV infection in pepper and Nicotiana benthamiana plants. Through confocal microscopy and transmission electron microscopy, we have found that PMMoV infection in plant can induce autophagy, evidenced by the increased number of GFP-ATG8a fluorescent punctate and the appearance of double membrane autophagic structures in cells of N. benthamiana. Additionally, inhibition of autophagy significantly increased PMMoV RNA accumulation and aggravated systemic PMMoV symptoms through autophagy inhibitor (3-MA and E64d) treatment and silencing of NbATG expressions by a Tobacco rattle virus-induced gene silencing assays. These results indicated that autophagy played a positive role in plant resistance to PMMoV infection.

CONCLUSIONS

Taken together, our results provide a transcriptomic insight into pepper responding to PMMoV infection and reveal that autophagy induced by PMMoV infection has an antiviral role in regulating PMMoV infection. These results also help us to better understand the mechanism controlling PMMoV infection in plants and to develop better strategies for breeding projects for virus-resistant crops.

Exogenous Calcium Improved Resistance to Botryosphaeria dothidea by Increasing Autophagy Activity and Salicylic Acid Level in Pear

Pear ring rot, caused by Botryosphaeria dothidea, is one of the most serious diseases in pear. Calcium (Ca²⁺) was reported to play a key role in the plant defense response. Here, we found that exogenous calcium could enhance resistance to B. dothidea in pear leaves. Less H₂O₂ and O₂^- but more activated reactive oxygen species scavenge enzymes accumulated in calcium-treated leaves than in H₂O-treated leaves. Moreover, the increased level of more ascorbic acid-glutathione was maintained by Ca²⁺ treatment under pathogen infection. The expression of core autophagy-related genes and autophagosome formations were enhanced in Ca²⁺-treated leaves. Silencing of PbrATG5 in Pyrus betulaefolia conferred sensitivity to inoculation, which was only slightly recovered by Ca²⁺ treatment. Moreover, the salicylic acid (SA) level and SA-related gene expression were induced more strongly by B. dothidea in Ca²⁺-treated leaves than in H₂O-treated leaves. Taken together, these results demonstrated that exogenous Ca²⁺ enhanced resistance to B. dothidea by increasing autophagic activity and SA accumulation. Our findings reveal a new mechanism of Ca²⁺ in increasing the tolerance of pear to B. dothidea infection.

UvAtg8-Mediated Autophagy Regulates Fungal Growth, Stress Responses, Conidiation, and Pathogenesis in Ustilaginoidea virens

BACKGROUND

Ustilaginoidea virens has become one of the most devastating rice pathogens in China, as well as other rice-growing areas. Autophagy is an important process in normal cell differentiation and development among various organisms. To date, there has been no optimized experimental system introduced for the study of autophagy in U. virens. In addition, the function of autophagy in pathogenesis remains unknown in U. virens. Therefore, the functional analyses of UvAtg8 may potentially shed some light on the regulatory mechanism and function of autophagy in U. virens.

RESULTS

In this study, we characterized the functions of UvAtg8, which is a homolog of Saccharomyces cerevisiae ScAtg8, in the rice false smut fungus U. virens. The results showed that UvATG8 is essential for autophagy in U. virens. Also, the GFP-UvATG8 strain, which could serve as an appropriate marker for monitoring autophagy in U. virens, was generated. Furthermore, this study found that the ΔUvatg8 mutant was defective in the vegetative growth, conidiation, adaption to oxidative, hyperosmotic, cell wall stresses, and production of toxic compounds. Pathogenicity assays indicated that deletion of UvATG8 resulted in significant reduction in virulence of U. virens. Further microscopic examinations of the infection processes revealed that the severe virulence defects in the ∆Uvatg8 were mainly caused by the highly reduced conidiation and secondary spore formation.

CONCLUSIONS

Our results indicated that the UvAtg8 is necessary for the fungal growth, stresses responses, conidiation, secondary spore formation, and pathogenicity of U. virens. Moreover, our research finding will potentially assist in further clarifying the molecular mechanism of U. virens infection, as well as provide a good marker for autophagy in U. virens and a good reference value for the further development of effective fungicides based on gene targeting.

ATG4 Mediated Psm ES4326/AvrRpt2-Induced Autophagy Dependent on Salicylic Acid in Arabidopsis Thaliana

Psm ES4326/AvrRpt2 (AvrRpt2) was widely used as the reaction system of hypersensitive response (HR) in Arabidopsis. The study showed that in npr1 (GFP-ATG8a), AvrRpt2 was more effective at inducing the production of autophagosome and autophagy flux than that in GFP-ATG8a. The mRNA expression of ATG1, ATG6 and ATG8a were more in npr1 during the early HR. Based on transcriptome data analysis, enhanced disease susceptibility 1 (EDS1) was up-regulated in wild-type (WT) but was not induced in atg4a4b (ATG4 deletion mutant) during AvrRpt2 infection. Compared with WT, atg4a4b had higher expression of salicylic acid glucosyltransferase 1 (SGT1) and isochorismate synthase 1 (ICS1); but less salicylic acid (SA) in normal condition and the same level of free SA during AvrRpt2 infection. These results suggested that the consumption of free SA should be occurred in atg4a4b. AvrRpt2 may trigger the activation of Toll/Interleukin-1 receptor (TIR)-nucleotide binding site (NB)-leucine rich repeat (LRR)—TIR-NB-LRR—to induce autophagy via EDS1, which was inhibited by nonexpressor of PR genes 1 (NPR1). Moreover, high expression of NPR3 in atg4a4b may accelerate the degradation of NPR1 during AvrRpt2 infection.

Cell Death in Plant Immunity

Pathogen recognition by the plant immune system leads to defense responses that are often accompanied by a form of regulated cell death known as the hypersensitive response (HR). HR shares some features with regulated necrosis observed in animals. Genetically, HR can be uncoupled from local defense responses at the site of infection and its role in immunity may be to activate systemic responses in distal parts of the organism. Recent advances in the field reveal conserved cell death-specific signaling modules that are assembled by immune receptors in response to pathogen-derived effectors. The structural elucidation of the plant resistosome-an inflammasome-like structure that may attach to the plasma membrane on activation-opens the possibility that HR cell death is mediated by the formation of pores at the plasma membrane. Necrotrophic pathogens that feed on dead tissue have evolved strategies to trigger the HR cell death pathway as a survival strategy. Ectopic activation of immunomodulators during autoimmune reactions can also promote HR cell death. In this perspective, we discuss the role and regulation of HR in these different contexts.

Plant Cells under Attack: Unconventional Endomembrane Trafficking during Plant Defense

Since plants lack specialized immune cells, each cell has to defend itself independently against a plethora of different pathogens. Therefore, successful plant defense strongly relies on precise and efficient regulation of intracellular processes in every single cell. Smooth trafficking within the plant endomembrane is a prerequisite for a diverse set of immune responses. Pathogen recognition, signaling into the nucleus, cell wall enforcement, secretion of antimicrobial proteins and compounds, as well as generation of reactive oxygen species, all heavily depend on vesicle transport. In contrast, pathogens have developed a variety of different means to manipulate vesicle trafficking to prevent detection or to inhibit specific plant responses. Intriguingly, the plant endomembrane system exhibits remarkable plasticity upon pathogen attack. Unconventional trafficking pathways such as the formation of endoplasmic reticulum (ER) bodies or fusion of the vacuole with the plasma membrane are initiated and enforced as the counteraction. Here, we review the recent findings on unconventional and defense-induced trafficking pathways as the plant´s measures in response to pathogen attack. In addition, we describe the endomembrane system manipulations by different pathogens, with a focus on tethering and fusion events during vesicle trafficking.

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.

Nitrated Nucleotides: New Players in Signaling Pathways of Reactive Nitrogen and Oxygen Species in Plants

Nitration of diverse biomolecules, including proteins, lipids and nucleic acid, by reactive nitrogen species represents one of the key mechanisms mediating nitric oxide (NO) biological activity across all types of organisms. 8-nitroguanosine 3'5'-cyclic monophosphate (8-nitro-cGMP) has been described as a unique electrophilic intermediate involved in intracellular redox signaling. In animal cells, 8-nitro-cGMP is formed from guanosine-5'-triphosphate by a combined action of reactive nitrogen (RNS) and oxygen species (ROS) and guanylate cyclase. As demonstrated originally in animal models, 8-nitro-cGMP shows certain biological activities closely resembling its analog cGMP; however, its regulatory functions are mediated mainly by its electrophilic properties and chemical interactions with protein thiols resulting in a novel protein post-translational modification termed S-guanylation. In Arabidopsis thaliana, 8-nitro-cGMP was reported to mediate NO-dependent signaling pathways controlling abscisic acid (ABA)-induced stomatal closure, however, its derivative 8-mercapto-cGMP (8-SH-cGMP) was later shown as the active component of hydrogen sulfide (H₂S)-mediated guard cell signaling. Here we present a survey of current knowledge on biosynthesis, metabolism and biological activities of nitrated nucleotides with special attention to described and proposed functions of 8-nitro-cGMP and its metabolites in plant physiology and stress responses.

The PTI to ETI Continuum in Phytophthora-Plant Interactions

Phytophthora species are notorious pathogens of several economically important crop plants. Several general elicitors, commonly referred to as Pathogen-Associated Molecular Patterns (PAMPs), from Phytophthora spp. have been identified that are recognized by the plant receptors to trigger induced defense responses in a process termed PAMP-triggered Immunity (PTI). Adapted Phytophthora pathogens have evolved multiple strategies to evade PTI. They can either modify or suppress their elicitors to avoid recognition by host and modulate host defense responses by deploying hundreds of effectors, which suppress host defense and physiological processes by modulating components involved in calcium and MAPK signaling, alternative splicing, RNA interference, vesicle trafficking, cell-to-cell trafficking, proteolysis and phytohormone signaling pathways. In incompatible interactions, resistant host plants perceive effector-induced modulations through resistance proteins and activate downstream components of defense responses in a quicker and more robust manner called effector-triggered-immunity (ETI). When pathogens overcome PTI-usually through effectors in the absence of R proteins-effectors-triggered susceptibility (ETS) ensues. Qualitatively, many of the downstream defense responses overlap between PTI and ETI. In general, these multiple phases of Phytophthora-plant interactions follow the PTI-ETS-ETI paradigm, initially proposed in the zigzag model of plant immunity. However, based on several examples, in Phytophthora-plant interactions, boundaries between these phases are not distinct but are rather blended pointing to a PTI-ETI continuum.

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.

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.

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.

Alternative responses to fungal attack on a metalliferous soil: Phytohormone levels and structural changes in Silene paradoxa L. growing under copper stress

In this work, a non-metallicolous and a metallicolous population of S. paradoxa were exposed to copper excess and fungal elicitation, and investigated for phytohormone production and cytological alterations. Under the stress applied separately and in combination, S. paradoxa plants varied phytohormone concentration in a population-specific way, suggesting a different signalling in response to biotic and abiotic stimuli according to the environment of origin. Generally, the stress responses consisted in increased levels of salicylic acid, auxin, and gibberellin in the non-metallicolous population, and of jasmonic and abscisic acid in the metallicolous one. Interestingly, the metallicolous population increased the level of such phytohormones following exposure to the fungal elicitor only in the presence of copper. This alternative hormonal signalling could derive from the incompatibility between the ordinary ROS-mediated response to pathogens and the acquired mechanisms that prevent oxidative stress in the population from the metal-rich soil. Furthermore, stress-induced autophagic phenomena were more evident in the non-metallicolous plants than in the metallicolous ones, suggesting that the adaptation to the metalliferous environment has also affected autophagy intensity and signalling in response to copper excess and fungal elicitation.