Beginning to understand autophagy, an intracellular self-degradation system in plants

The Role of Brassinosteroids in Plant Cold Stress Response

Temperature affects plant growth and geographical distribution. Cold stress occurs when temperatures fall below the physiologically optimal range for plants, causing permanent and irreversible damage to plant growth, development, and production. Brassinosteroids (BRs) are steroid hormones that play an important role in plant growth and various stress responses. Recent studies have shown that low temperatures affect BR biosynthesis in many plant species and that BR signaling is involved in the regulation of plant tolerance to low temperatures, both in the CBF-dependent and CBF-independent pathways. These two regulatory pathways correspond to transient and acclimation responses of low temperature, respectively. The crosstalk between BRs and other hormones is a significant factor in low-temperature tolerance. We provide an overview of recent developments in our knowledge of BRs' function in plant responses to cold stress and how they interact with other plant hormones in this review.

Maize Autophagy-Related Protein ZmATG3 Confers Tolerance to Multiple Abiotic Stresses

Abiotic stresses pose a major increasing problem for the cultivation of maize. Autophagy plays a vital role in recycling and re-utilizing nutrients and adapting to stress. However, the role of autophagy in the response to abiotic stress in maize has not yet been investigated. Here, ZmATG3, which is essential for ATG8-PE conjugation, was isolated from the maize inbred line B73. The ATG3 sequence was conserved, including the C-terminal domains with HPC and FLKF motifs and the catalytic domain in different species. The promoter of the ZmATG3 gene contained a number of elements involved in responses to environmental stresses or hormones. Heterologous expression of ZmATG3 in yeast promoted the growth of strain under salt, mannitol, and low-nitrogen stress. The expression of ZmATG3 could be altered by various types of abiotic stress (200 mM NaCl, 200 mM mannitol, low N) and exogenous hormones (500 µM ABA). GUS staining analysis of ZmATG3-GUS transgenic Arabidopsis revealed that GUS gene activity increased after abiotic treatment. ZmATG3-overexpressing Arabidopsis plants had higher osmotic and salinity stress tolerance than wild-type plants. Overexpression of ZmATG3 up-regulated the expression of other AtATGs (AtATG3, AtATG5, and AtATG8b) under NaCl, mannitol and LN stress. These findings demonstrate that overexpression of ZmATG3 can improve tolerance to multiple abiotic stresses.

Autophagy maintains endosperm quality during seed storage to preserve germination ability in Arabidopsis

To preserve germination ability, plant seeds must be protected from environmental stresses during the storage period. Here, we demonstrate that autophagy, an intracellular degradation system, maintains seed germination ability in Arabidopsis thaliana. The germination ability of long-term (>5 years) stored dry seeds of autophagy-defective (atg) mutant and wild-type (WT) plants was compared. Long-term stored (old) seeds of atg mutants showed lower germination ability than WT seeds, although short-term stored (new) seeds of atg mutants did not show such a phenotype. After removal of the seed coat and endosperm from old atg mutant seeds, the embryos developed into seedlings. Autophagic flux was maintained in endosperm cells during the storage period, and autophagy defect resulted in the accumulation of oxidized proteins and accelerated endosperm cell death. Consistent with these findings, the transcripts of genes, ENDO-β-MANNANASE 7 and EXPANSIN 2, which are responsible for degradation/remodeling of the endosperm cell wall during germination, were reduced in old atg mutant seeds. We conclude that autophagy maintains endosperm quality during seed storage by suppressing aging-dependent oxidative damage and cell death, which allows the endosperm to perform optimal functions during germination, i.e., cell wall degradation/remodeling, even after long-term storage.

A detailed molecular network map and model of the NLRP3 inflammasome

The NLRP3 inflammasome is a key regulator of inflammation that responds to a broad range of stimuli. The exact mechanism of activation has not been determined, but there is a consensus on cellular potassium efflux as a major common denominator. Once NLRP3 is activated, it forms high-order complexes together with NEK7 that trigger aggregation of ASC into specks. Typically, there is only one speck per cell, consistent with the proposal that specks form - or end up at - the centrosome. ASC polymerisation in turn triggers caspase-1 activation, leading to maturation and release of IL-1β and pyroptosis, i.e., highly inflammatory cell death. Several gain-of-function mutations in the NLRP3 inflammasome have been suggested to induce spontaneous activation of NLRP3 and hence contribute to development and disease severity in numerous autoinflammatory and autoimmune diseases. Consequently, the NLRP3 inflammasome is of significant clinical interest, and recent attention has drastically improved our insight in the range of involved triggers and mechanisms of signal transduction. However, despite recent progress in knowledge, a clear and comprehensive overview of how these mechanisms interplay to shape the system level function is missing from the literature. Here, we provide such an overview as a resource to researchers working in or entering the field, as well as a computational model that allows for evaluating and explaining the function of the NLRP3 inflammasome system from the current molecular knowledge. We present a detailed reconstruction of the molecular network surrounding the NLRP3 inflammasome, which account for each specific reaction and the known regulatory constraints on each event as well as the mechanisms of drug action and impact of genetics when known. Furthermore, an executable model from this network reconstruction is generated with the aim to be used to explain NLRP3 activation from priming and activation to the maturation and release of IL-1β and IL-18. Finally, we test this detailed mechanistic model against data on the effect of different modes of inhibition of NLRP3 assembly. While the exact mechanisms of NLRP3 activation remains elusive, the literature indicates that the different stimuli converge on a single activation mechanism that is additionally controlled by distinct (positive or negative) priming and licensing events through covalent modifications of the NLRP3 molecule. Taken together, we present a compilation of the literature knowledge on the molecular mechanisms on NLRP3 activation, a detailed mechanistic model of NLRP3 activation, and explore the convergence of diverse NLRP3 activation stimuli into a single input mechanism.

Autophagy-Mediated Phosphate Homeostasis in Arabidopsis Involves Modulation of Phosphate Transporters

Autophagy in plants is regulated by diverse signaling cascades in response to environmental changes. Fine-tuning of its activity is critical for the maintenance of cellular homeostasis under basal and stressed conditions. In this study, we compared the Arabidopsis autophagy-related (ATG) system transcriptionally under inorganic phosphate (Pi) deficiency versus nitrogen deficiency and showed that most ATG genes are only moderately upregulated by Pi starvation, with relatively stronger induction of AtATG8f and AtATG8h among the AtATG8 family. We found that Pi shortage increased the formation of GFP-ATG8f-labeled autophagic structures and the autophagic flux in the differential zone of the Arabidopsis root. However, the proteolytic cleavage of GFP-ATG8f and the vacuolar degradation of endogenous ATG8 proteins indicated that Pi limitation does not drastically alter the autophagic flux in the whole roots, implying a cell type-dependent regulation of autophagic activities. At the organismal level, the Arabidopsis atg mutants exhibited decreased shoot Pi concentrations and smaller meristem sizes under Pi sufficiency. Under Pi limitation, these mutants showed enhanced Pi uptake and impaired root cell division and expansion. Despite a reduced steady-state level of several PHOSPHATE TRANSPORTER 1s (PHT1s) in the atg root, cycloheximide treatment analysis suggested that the protein stability of PHT1;1/2/3 is comparable in the Pi-replete wild type and atg5-1. By contrast, the degradation of PHT1;1/2/3 is enhanced in the Pi-deplete atg5-1. Our findings reveal that both basal autophagy and Pi starvation-induced autophagy are required for the maintenance of Pi homeostasis and may modulate the expression of PHT1s through different mechanisms.

The role of Atg16 in autophagy, anthocyanin biosynthesis, and programmed cell death in leaves of the lace plant (Aponogeton madagascariensis)

Aponogeton madagascariensis, commonly known as the lace plant, produces leaves that form perforations by programmed cell death (PCD). Leaf development is divided into several stages beginning with "pre-perforation" furled leaves enriched with red pigmentation from anthocyanins. The leaf blade is characterized by a series of grids known as areoles bounded by veins. As leaves develop into the "window stage", anthocyanins recede from the center of the areole towards the vasculature creating a gradient of pigmentation and cell death. Cells in the middle of the areole that lack anthocyanins undergo PCD (PCD cells), while cells that retain anthocyanins (non-PCD cells) maintain homeostasis and persist in the mature leaf. Autophagy has reported roles in survival or PCD promotion across different plant cell types. However, the direct involvement of autophagy in PCD and anthocyanin levels during lace plant leaf development has not been determined. Previous RNA sequencing analysis revealed the upregulation of autophagy-related gene Atg16 transcripts in pre-perforation and window stage leaves, but how Atg16 affects PCD in lace plant leaf development is unknown. In this study, we investigated the levels of Atg16 in lace plant PCD by treating whole plants with either an autophagy promoter rapamycin or inhibitors concanamycin A (ConA) or wortmannin. Following treatments, window and mature stage leaves were harvested and analyzed using microscopy, spectrophotometry, and western blotting. Western blotting showed significantly higher Atg16 levels in rapamycin-treated window leaves, coupled with lower anthocyanin levels. Wortmannin-treated leaves had significantly lower Atg16 protein and higher anthocyanin levels compared to the control. Mature leaves from rapamycin-treated plants generated significantly fewer perforations compared to control, while wortmannin had the opposite effect. However, ConA treatment did not significantly change Atg16 levels, nor the number of perforations compared to the control, but anthocyanin levels did increase significantly in window leaves. We propose autophagy plays a dual role in promoting cell survival in NPCD cells by maintaining optimal anthocyanin levels and mediating a timely cell death in PCD cells in developing lace plant leaves. How autophagy specifically affects anthocyanin levels remained unexplained.

Killing me softly - Programmed cell death in plant reproduction from sporogenesis to fertilization

Regulated or programmed cell death (RCD or PCD) is a fundamental biological principle integral to a considerable variety of functions in multicellular organisms. In plants, different PCD processes are part of biotic and abiotic stress responses, but also occur as an essential aspect of unperturbed plant development. PCD is particularly abundant during plant reproduction, eliminating unwanted or no longer needed cells, tissues, or organs in a precisely controlled manner. Failure in reproductive PCD can have detrimental consequences for plant reproduction. Here we shed a light on the latest research into PCD mechanisms in plant reproduction from sex determination over sporogenesis to pollination and fertilization.

Integrative analysis of transcriptome and miRNAome reveals molecular mechanisms regulating pericarp thickness in sweet corn during kernel development

Pericarp thickness affects the edible quality of sweet corn (Zea mays L. saccharata Sturt.). Therefore, breeding varieties with a thin pericarp is important for the quality breeding of sweet corn. However, the molecular mechanisms underlying the pericarp development remain largely unclear. We performed an integrative analysis of mRNA and miRNA sequencing to elucidate the genetic mechanism regulating pericarp thickness during kernel development (at 15 days, 19 days, and 23 days after pollination) of two sweet corn inbred lines with different pericarp thicknesses (M03, with a thinner pericarp and M08, with a thicker pericarp). A total of 2,443 and 1,409 differentially expressed genes (DEGs) were identified in M03 and M08, respectively. Our results indicate that phytohormone-mediated programmed cell death (PCD) may play a critical role in determining pericarp thickness in sweet corn. Auxin (AUX), gibberellin (GA), and brassinosteroid (BR) signal transduction may indirectly mediate PCD to regulate pericarp thickness in M03 (the thin pericarp variety). In contrast, abscisic acid (ABA), cytokinin (CK), and ethylene (ETH) signaling may be the key regulators of pericarp PCD in M08 (the thick pericarp variety). Furthermore, 110 differentially expressed microRNAs (DEMIs) and 478 differentially expressed target genes were identified. miRNA164-, miRNA167-, and miRNA156-mediated miRNA-mRNA pairs may participate in regulating pericarp thickness. The expression results of DEGs were validated by quantitative real-time PCR. These findings provide insights into the molecular mechanisms regulating pericarp thickness and propose the objective of breeding sweet corn varieties with a thin pericarp.

Links between autophagy and lipid droplet dynamics

Autophagy is a catabolic process in which cytoplasmic components are delivered to vacuoles or lysosomes for degradation and nutrient recycling. Autophagy-mediated degradation of membrane lipids provides a source of fatty acids for the synthesis of energy-rich, storage lipid esters such as triacylglycerol (TAG). In eukaryotes, storage lipids are packaged into dynamic subcellular organelles, lipid droplets. In times of energy scarcity, lipid droplets can be degraded via autophagy in a process termed lipophagy to release fatty acids for energy production via fatty acid β-oxidation. On the other hand, emerging evidence suggests that lipid droplets are required for the efficient execution of autophagic processes. Here, we review recent advances in our understanding of metabolic interactions between autophagy and TAG storage, and discuss mechanisms of lipophagy. Free fatty acids are cytotoxic due to their detergent-like properties and their incorporation into lipid intermediates that are toxic at high levels. Thus, we also discuss how cells manage lipotoxic stresses during autophagy-mediated mobilization of fatty acids from lipid droplets and organellar membranes for energy generation.

Identification of New ATG8s-Binding Proteins with Canonical LC3-Interacting Region in Autophagosomes of Barley Callus

Autophagy is essential to maintain cellular homeostasis for normal cell growth and development. In selective autophagy, ATG8 plays a crucial role in cargo target recognition by binding to various adaptors and receptors with the ATG8-interacting motif, also known as the LC3-interacting region (LIR). However, the process of autophagy in the callus, as a proliferating cell type, is largely unknown. In this study, we overexpressed green fluorescent protein (GFP)-ATG8a and GFP-ATG8b transgenic barley callus and checked their autophagic activities. We identified five new ATG8 candidate interactors containing the canonical LIR motif by using immunoprecipitation coupled with mass spectrometry: RPP3, COPE, NCLN, RAE1, and CTSL. The binding activities between these candidate interactors and ATG8 were further demonstrated in the punctate structure. Notably, RPP3 was colocalized in ATG8-labeled autophagosomes under tunicamycin-induced ER stress. GST pull-down assays showed that the interaction between RPP3 and ATG8 could be prevented by mutating the LIRs region of RPP3 or the LIR docking site (LDS) of ATG8, suggesting that RPP3 directly interacted with ATG8 in an LIR-dependent manner via the LDS. Our findings would provide the basis for further investigations on novel receptors and functions of autophagy in plants, especially in the physiological state of cell de-differentiation.

Plant susceptible responses: the underestimated side of plant-pathogen interactions

Plant susceptibility to pathogens is usually considered from the perspective of the loss of resistance. However, susceptibility cannot be equated with plant passivity since active host cooperation may be required for the pathogen to propagate and cause disease. This cooperation consists of the induction of reactions called susceptible responses that transform a plant from an autonomous biological unit into a component of a pathosystem. Induced susceptibility is scarcely discussed in the literature (at least compared to induced resistance) although this phenomenon has a fundamental impact on plant-pathogen interactions and disease progression. This review aims to summarize current knowledge on plant susceptible responses and their regulation. We highlight two main categories of susceptible responses according to their consequences and indicate the relevance of susceptible response-related studies to agricultural practice. We hope that this review will generate interest in this underestimated aspect of plant-pathogen interactions.

Optimal Distribution of Iron to Sink Organs via Autophagy Is Important for Tolerance to Excess Zinc in Arabidopsis

Zinc (Zn) is nutritionally an essential metal element, but excess Zn in the environment is toxic to plants. Autophagy is a major pathway responsible for intracellular degradation. Here, we demonstrate the important role of autophagy in adaptation to excess Zn stress. We found that autophagy-defective Arabidopsis thaliana (atg2 and atg5) exhibited marked excess Zn-induced chlorosis and growth defects relative to wild-type (WT). Imaging and biochemical analyses revealed that autophagic activity was elevated under excess Zn. Interestingly, the excess Zn symptoms of atg5 were alleviated by supplementation of high levels of iron (Fe) to the media. Under excess Zn, in atg5, Fe starvation was especially severe in juvenile true leaves. Consistent with this, accumulation levels of Fe3+ near the shoot apical meristem remarkably reduced in atg5. Furthermore, excision of cotyledons induced severe excess Zn symptoms in WT, similar to those observed in atg5.Our data suggest that Fe3+ supplied from source leaves (cotyledons) via autophagy is distributed to sink leaves (true leaves) to promote healthy growth under excess Zn, revealing a new dimension, the importance of heavy-metal stress responses by the intracellular recycling.

Genome-wide identification, characterization, and expression analysis of tea plant autophagy-related genes (CsARGs) demonstrates that they play diverse roles during development and under abiotic stress

Background

Autophagy, meaning ‘self-eating’, is required for the degradation and recycling of cytoplasmic constituents under stressful and non-stressful conditions, which helps to maintain cellular homeostasis and delay aging and longevity in eukaryotes. To date, the functions of autophagy have been heavily studied in yeast, mammals and model plants, but few studies have focused on economically important crops, especially tea plants (Camellia sinensis). The roles played by autophagy in coping with various environmental stimuli have not been fully elucidated to date. Therefore, investigating the functions of autophagy-related genes in tea plants may help to elucidate the mechanism governing autophagy in response to stresses in woody plants.

Results

In this study, we identified 35 C. sinensis autophagy-related genes (CsARGs). Each CsARG is highly conserved with its homologues from other plant species, except for CsATG14. Tissue-specific expression analysis demonstrated that the abundances of CsARGs varied across different tissues, but CsATG8c/i showed a degree of tissue specificity. Under hormone and abiotic stress conditions, most CsARGs were upregulated at different time points during the treatment. In addition, the expression levels of 10 CsARGs were higher in the cold-resistant cultivar ‘Longjing43’ than in the cold-susceptible cultivar ‘Damianbai’ during the CA period; however, the expression of CsATG101 showed the opposite tendency.

Conclusions

We performed a comprehensive bioinformatic and physiological analysis of CsARGs in tea plants, and these results may help to establish a foundation for further research investigating the molecular mechanisms governing autophagy in tea plant growth, development and response to stress. Meanwhile, some CsARGs could serve as putative molecular markers for the breeding of cold-resistant tea plants in future research.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07419-2.

Ammonium stress increases microautophagic activity while impairing macroautophagic flux in Arabidopsis roots

Plant responses to NH₄⁺ stress are complex, and multiple mechanisms underlying NH₄⁺ sensitivity and tolerance in plants may be involved. Here, we demonstrate that macro- and microautophagic activities are oppositely affected in plants grown under NH₄⁺ toxicity conditions. When grown under NH₄⁺ stress conditions, macroautophagic activity was impaired in roots. Root cells accumulated autophagosomes in the cytoplasm, but showed less autophagic flux, indicating that late steps of the macroautophagy process are affected under NH₄⁺ stress conditions. Under this scenario, we also found that the CCZ1-MON1 complex, a critical factor for vacuole delivery pathways, functions in the late step of the macroautophagic pathway in Arabidopsis. In contrast, an accumulation of tonoplast-derived vesicles was observed in vacuolar lumens of root cells of NH₄⁺ -stressed plants, suggesting the induction of a microautophagy-like process. In this sense, some SYP22-, but mainly VAMP711-positive vesicles were observed inside vacuole in roots of NH₄⁺ -stressed plants. Consistent with the increased tonoplast degradation and the reduced membrane flow to the vacuole due to the impaired macroautophagic flux, the vacuoles of root cells of NH₄⁺ -stressed plants showed a simplified structure and lower tonoplast content. Taken together, this study presents evidence that postulates late steps of the macroautophagic process as a relevant physiological mechanism underlying the NH₄⁺ sensitivity response in Arabidopsis, and additionally provides insights into the molecular tools for studying microautophagy in plants.

Mutual regulation of ROS accumulation and cell autophagy in wheat roots under hypoxia stress

Here, we explored the mutual regulation of radical oxygen species (ROS) and autophagy in wheat (Triticum aestivum L.) roots under hypoxia stress. We also analyzed differences between the responses of the stele and the cortex in the two wheat cultivars Huamai 8 (waterlogging-tolerant) and Huamai 9 (waterlogging-sensitive) to hypoxia stress. In situ detection and ultracytochemical localization analysis in wheat roots showed that hypoxia stress caused greater increases in ROS levels and the expression levels of alternative oxidase (AOX) and antioxidant enzymes in the stele than in the cortex. The analysis of exogenous ROS addition and the inhibition of its production revealed the pivotal roles played by ROS in autophagy. Moreover, transmission electron microscopy and qRT-PCR analysis indicated that the stele had a higher level of autophagy than the cortex and that the two wheat cultivars primarily differed in the type and number of autophagosomes. Additional research revealed that autophagy could remove excess ROS, as pre-treatment with the autophagy inhibitor 3-methyladenine increased ROS levels in roots and the addition of the autophagy inducer rapamycin reduced root ROS levels. In conclusion, hypoxia stress induced ROS accumulation in wheat roots where ROS acted as an autophagy signal. Furthermore, higher levels of autophagy and antioxidant enzyme expression in the stele facilitated the elimination of oxidative damage caused by excessive ROS and thereby increased cell survival; in the cortex, a large number of cells died and formed aerenchyma.

Recent Advances in Carbon and Nitrogen Metabolism in C3 Plants

C and N are the most important essential elements constituting organic compounds in plants. The shoots and roots depend on each other by exchanging C and N through the xylem and phloem transport systems. Complex mechanisms regulate C and N metabolism to optimize plant growth, agricultural crop production, and maintenance of the agroecosystem. In this paper, we cover the recent advances in understanding C and N metabolism, regulation, and transport in plants, as well as their underlying molecular mechanisms. Special emphasis is given to the mechanisms of starch metabolism in plastids and the changes in responses to environmental stress that were previously overlooked, since these changes provide an essential store of C that fuels plant metabolism and growth. We present general insights into the system biology approaches that have expanded our understanding of core biological questions related to C and N metabolism. Finally, this review synthesizes recent advances in our understanding of the trade-off concept that links C and N status to the plant's response to microorganisms.

Autophagy contributes to resistance to the oxidative stress induced by pine reactive oxygen species metabolism, promoting infection by Bursaphelenchus xylophilus

BACKGROUND

Autophagy plays an important role in eukaryotes. We investigated its role in the pine wood nematode (PWN), Bursaphelenchus xylophilus, the causative agent of pine wilt disease (PWD), to find promising control strategies against PWD.

RESULTS

We analysed the expression levels of PtRBOH1 and PtRBOH2, which regulate reactive oxygen species (ROS) metabolism, in Pinus thunbergii and the expression of three autophagy genes, BxATG5, BxATG9 and BxATG16, in PWN by quantitative reverse transcription-polymerase chain reaction (qRT-PCR), and measured the content of H₂ O₂ , the main product of ROS metabolism, in pine stem. There was a correlation between the expression of autophagy genes in PWN and pine ROS metabolism during early infection. We also found that oxidative stress induces autophagy in PWN according to qRT-PCR, transmission electron microscopy and Western blot analyses. Inhibition of autophagy by 3-methyladenine or silencing of the autophagy genes BxATG9 and BxATG16 in PWN showed that autophagy is essential for feeding, fecundity, egg hatching and survival of PWN under oxidative stress, confirming the importance of autophagy in the antioxidant defences of PWN. Similarly, we demonstrated that autophagy contributes to the virulence of PWN. Moreover, PWN likely ameliorates oxidative damage by enhancing the activities of the peroxidase and catalase antioxidant pathways when autophagy is inhibited.

CONCLUSION

Autophagy contributes to resistance to the oxidative stress induced by pine ROS metabolism, thus promoting infection by PWN. Our findings clarify the defence mechanisms of PWN and the pathogenesis of PWD, and provide promising hints for control of PWD by blocking autophagy. © 2020 Society of Chemical Industry.

Friend or Enemy: A Dual Role of Autophagy in Plant Virus Infection

Autophagy is a primary protective process that involves removing damaged organelles or dysfunctional proteins in eukaryotes. The autophagy pathway not only maintains cellular homeostasis, but also modulates the host's cellular response to pathogen infection. Several studies proved that autophagy plays a dominant role in plant fitness and immunity. As intracellular parasites, the replication and spread of viruses entirely rely upon the molecular machinery of the host cell, including the autophagy process. Plant viruses severely affect crop yields and quality. During infection, complex interactions occur between viral proteins and host factors in relation to plant defense and virus counter-defense. An increasing number of studies demonstrated that plants use autophagy to eliminate and inhibit viruses; some viruses were shown to manipulate the process of autophagy to promote their own replication and survival in plant cells. In this review, we summarize recent advances in plant autophagy, with an emphasis on the role of autophagy in plant virus infection.

Microautophagy in Plants: Consideration of Its Molecular Mechanism

Microautophagy is a type of autophagy. It is characterized by direct enclosing with the vacuolar/lysosomal membrane, which completes the isolation and uptake of cell components in the vacuole. Several publications present evidence that plants exhibit microautophagy. Plant microautophagy is involved in anthocyanin accumulation in the vacuole, eliminating damaged chloroplasts and degrading cellular components during starvation. However, information on the molecular mechanism of microautophagy is less available than that on the general macroautophagy, because the research focusing on microautophagy has not been widely reported. In yeast and animals, it is suggested that microautophagy can be classified into several types depending on morphology and the requirements of autophagy-related (ATG) genes. This review summarizes the studies on plant microautophagy and discusses possible techniques for a future study in this field while taking into account the information on microautophagy obtained from yeast and animals.

Brassinosteroids act as a positive regulator of NBR1-dependent selective autophagy in response to chilling stress in tomato

Autophagy is a highly conserved and regulated catabolic process involved in the degradation of protein aggregates, which plays critical roles in eukaryotes. In plants, multiple molecular processes can induce or suppress autophagy but the mechanism of its regulation by phytohormones is poorly understood. Brassinosteroids (BRs) are steroid phytohormones that play crucial roles in plant response to stresses. Here, we investigate the role of BRs in NBR1-dependent selective autophagy in response to chilling stress in tomato. BRs and their signaling element BZR1 can induce autophagy and accumulation of the selective autophagy receptor NBR1 in tomato under chilling stress. Cold increased the stability of BZR1, which was promoted by BRs. Cold- and BR-induced increased BZR1 stability activated the transcription of several autophagy-related genes (ATGs) and NBR1 genes by directly binding to their promoters, which resulted in selective autophagy. Furthermore, silencing of these ATGs or NBR1 genes resulted in a decreased accumulation of several functional proteins and an increased accumulation of ubiquitinated proteins, subsequently compromising BR-induced cold tolerance. These results strongly suggest that BRs regulate NBR1-dependent selective autophagy in a BZR1-dependent manner in response to chilling stress in tomato.

Algal Autophagy Is Necessary for the Regulation of Carbon Metabolism Under Nutrient Deficiency

Autophagy is a mechanism to recycle intracellular constituents such as amino acids and other carbon- and nitrogen (N)-containing compounds. Although autophagy-related (ATG) genes required for autophagy are encoded by many algal genomes, their functional importance in microalgae in nutrient-deficiency has not been appraised using ATG-defective mutants. Recently, by characterization of an insertional mutant of the ATG8 encoding a ubiquitin-like protein indispensable for autophagosome formation in a green alga Chlamydomonas reinhardtii, we have provided evidence that supports the following notions. ATG8 protein is required for the degradation of lipid droplets and triacylglycerol (TAG) triggered by resupply of N to cell culture in N-deficient conditions. ATG8 protein is also necessary for starch accumulation under phosphorus-deficient conditions. Algal autophagy is not necessary for inheritance of chloroplast and mitochondrial genomes. In this review, we discuss the physiological roles of algal autophagy associated with nutrient deficiency revealed by the genetic and biochemical analyses using disruption mutants and reagents that inhibit the fatty acid biosynthesis and vacuolar H⁺-ATPase.

Role of Autophagy in Male Reproductive Processes in Land Plants

Autophagy is a highly conserved system for degrading and recycling cytoplasmic components. The identification of autophagy-related (ATG) genes, required for autophagosome formation, has led to numerous studies using atg mutants. These studies have revealed the physiological significance of autophagy in various functions of diverse organisms. In land plants, autophagy is required for higher-order functions such as stress responses and development. Although defective autophagy does not result in any marked defect in the reproductive processes of Arabidopsis thaliana under laboratory conditions, several studies have shown that autophagy plays a pivotal role in male reproduction in several land plants. In this review, we aim to summarize information on the role of autophagy in male reproductive processes in land plants.

A Rice Autophagy Gene OsATG8b Is Involved in Nitrogen Remobilization and Control of Grain Quality

Enhancing nitrogen (N) use efficiency is a potential way to reduce excessive nitrogen application and increase yield. Autophagy is a conserved degradation system in the evolution of eukaryotic cells and plays an important role in plant development and stress response. Autophagic cores have two conjugation pathways that attach the product of autophagy-related gene 8 (ATG8) to phosphatidylethanolamine (PE) and ATG5 to ATG12, respectively, which then help with vesicle elongation and enclosure. Rice has six ATG8 genes, which have not been functionally confirmed so far. We identified the rice gene OsATG8b and characterized its role in N remobilization to affect grain quality by generating transgenic plants with its over-expression and knockdown. Our study confirmed the autophagy activity of OsATG8b through the complementation of the yeast autophagy-defective mutant scatg8 and by observation of autophagosome formation in rice. The autophagy activity is higher in OsATG8b-OE lines and lower in OsATG8b-RNAi than that in wild type (ZH11). ¹⁵N pulse-chase analysis revealed that OsATG8b-OE plants conferred higher N recycling efficiency to grains, while OsATG8b-RNAi transgenic plants exhibited lower N recycling efficiency and poorer grain quality. The autophagic role of OsATG8b was experimentally confirmed, and it was concluded that OsATG8b-mediated autophagy is involved in N recycling to grains and contributes to the grain quality, indicating that OsATG8b may be a potential gene for molecular breeding and cultivation of rice.

Impact of Autophagy on Gene Expression and Tapetal Programmed Cell Death During Pollen Development in Rice

Autophagy has recently been shown to be required for tapetal programmed cell death (PCD) and pollen maturation in rice. A transcriptional regulatory network is also known to play a key role in the progression of tapetal PCD. However, the relationship between the gene regulatory network and autophagy in rice anther development is mostly unknown. Here, we comprehensively analyzed the effect of autophagy disruption on gene expression profile during the tapetal PCD in rice anther development using high-throughput RNA sequencing. Expression of thousands of genes, including specific transcription factors and several proteases required for tapetal degradation, fluctuated synchronously at specific stages during tapetal PCD progression in the wild-type anthers, while this fluctuation showed significant delay in the autophagy-deficient mutant Osatg7-1. Moreover, gene ontology enrichment analysis in combination with self-organizing map clustering as well as pathway analysis revealed that the expression patterns of a variety of organelle-related genes as well as genes involved in carbohydrate/lipid metabolism were affected in the Osatg7-1 mutant during pollen maturation. These results suggest that autophagy is required for proper regulation of gene expression and quality control of organelles and timely progression of tapetal PCD during rice pollen development.

Essential roles of autophagy in metabolic regulation in endosperm development during rice seed maturation

Autophagy plays crucial roles in the recycling of metabolites, and is involved in many developmental processes. Rice mutants defective in autophagy are male sterile due to immature pollens, indicating its critical role in pollen development. However, physiological roles of autophagy during seed maturation had remained unknown. We here found that seeds of the rice autophagy-deficient mutant Osatg7-1, that produces seeds at a very low frequency in paddy fields, are smaller and show chalky appearance and lower starch content in the endosperm at the mature stage under normal growth condition. We comprehensively analyzed the effects of disruption of autophagy on biochemical properties, proteome and seed quality, and found an abnormal activation of starch degradation pathways including accumulation of α-amylases in the endosperm during seed maturation in Osatg7-1. These results indicate critical involvement of autophagy in metabolic regulation in the endosperm of rice, and provide insights into novel autophagy-mediated regulation of starch metabolism during seed maturation.

Sucrose Starvation Induces Microautophagy in Plant Root Cells

Autophagy is an essential system for degrading and recycling cellular components for survival during starvation conditions. Under sucrose starvation, application of a papain protease inhibitor E-64d to the Arabidopsis root and tobacco BY-2 cells induced the accumulation of vesicles, labeled with a fluorescent membrane marker FM4-64. The E-64d-induced vesicle accumulation was reduced in the mutant defective in autophagy-related genes ATG2, ATG5, and ATG7, suggesting autophagy is involved in the formation of these vesicles. To clarify the formation of these vesicles in detail, we monitored time-dependent changes of tonoplast, and vesicle accumulation in sucrose-starved cells. We found that these vesicles were derived from the tonoplast and produced by microautophagic process. The tonoplast proteins were excluded from the vesicles, suggesting that the vesicles are generated from specific membrane domains. Concanamycin A treatment in GFP-ATG8a transgenic plants showed that not all FM4-64-labeled vesicles, which were derived from the tonoplast, contained the ATG8a-containing structure. These results suggest that ATG8a may not always be necessary for microautophagy.

Occurrence of autophagy during pioneer root and stem development in Populus trichocarpa

Autophagy is involved in developmentally programmed cell death and is identified during the early development of phloem, as well as xylem with a dual role, as both an inducer and executioner of cell death. The regulation of primary and secondary development of roots and stems is important for the establishment of root systems and for the overall survival of trees. The molecular and cellular basis of the autophagic processes, which are used at distinct moments during the growth of both organs, is crucial to understand the regulation of their development. To address this, we use Populus trichocarpa seedlings grown in a rhizotron system to examine the autophagy processes involved in root and stem development. To monitor the visual aspects of autophagy, transmission electron microscopy (TEM) and immunolocalization of AuTophaGy-related protein (ATG8) enabled observations of the phenomenon at a structural level. To gain further insight into the autophagy process at the protein and molecular level, we evaluated the expression of ATG gene transcripts and ATG protein levels. Alternations in the expression level of specific ATG genes and localization of ATG8 proteins were observed during the course of root or stem primary and secondary development. Specifically, ATG8 was present in the cells exhibiting autophagy, during the differentiation and early development of xylem and phloem tissues, including both xylary and extraxylary fibers. Ultrastructural observations revealed tonoplast invagination with the formation of autophagic-like bodies. Additionally, the accumulation of autophagosomes was identifiable during the differentiation of xylem in both organs, long before the commencement of cell death. Taken together, these results provide evidence in support of the dual role of autophagy in developmental PCD. A specific role of the controller of cell death, which is a committed step with the release of hydrolytic enzymes from the vacuole and final digestion of protoplast, from which there is no return once initiated, is only attributed to mega-autophagy.

Selective Autophagy of Peroxisomes in Plants: From Housekeeping to Development and Stress Responses

Peroxisomes are dynamic organelles involved in multiple functions, including oxygen and nitrogen reactive species metabolism. In plants, these organelles have a close relationship with chloroplasts and mitochondria, characterized by intense metabolic activity and signal transduction. Peroxisomes undergo rapid changes in size, morphology, and abundance depending on the plant development stage and environmental conditions. As peroxisomes are essential not only for redox homeostasis but also for sensing stress, signaling transduction, and cell survival, their formation and degradation need to be rigorously regulated. In this review, new insights into the regulation of plant peroxisomes are briefly described, with a particular emphasis on pexophagy components and their regulation.

Autophagy and vacuolar biogenesis during the nectary development

Different autophagy pathways are a driver of vacuolar biogenesis and are development stage specific during the extrafloral nectary development in Citharexylum myrianthum. Plant autophagy plays an important role in various developmental processes such as seed germination, pollen maturation and leaf senescence. However, studies that address the evidence of autophagy and its role in the development of plant glands are scarce and largely restricted to laticifers. Regarding nectary, studies have repeatedly pointed to signs of degradation associated with the end of the secretory cycle, without exploring autophagy. Likewise, the relationship between autophagy and biogenesis of vacuoles remains an unexplored issue. In this study, using conventional and microwave fixation in association with ultracytochemical methods for transmission electron microscopy, we investigated the occurrence of autophagy and its implication in the differentiation of extrafloral nectary in Citharexylum myrianthum (Verbenaceae) under natural conditions, focusing on the vacuole biogenesis. We described a variety of vacuole types associated with the stage of nectary epidermis development, which differs with respect to origin, function and nature of the products to be stored. Three distinct autophagy pathways were detected: macroautophagy, microautophagy (both restricted to the undifferentiated epidermal cells, at the presecretory stage) and megaautophagy (circumscribed to the differentiated epidermal cells, at the postsecretory stage). Our study clearly demonstrated that the vacuole variety and autophagy processes in the nectary epidermal cells are development specific. This study highlights the role of autophagy in vacuole biogenesis and its implications for the development of nectary and opens new venues for future studies on regulation mechanisms for autophagy in plant secretory structures under normal conditions.

Ultrastructural patterns of photoacclimation and photodamage to photosynthetic algae cell under environmental stress

In oxygenic phototrophs including unicellular algae, acclimation to and damage by diverse environmental stresses induce profound changes in the ultrastructural organization of the cell. These alterations reflect acclimation of the photosynthetic apparatus to unfavorable conditions (mainly reduction of the chloroplast and its membranal system) and rewiring of the photo-fixed carbon fluxes in the cell. These changes, eventually pursuing mitigation of the photooxidative damage risk, are manifested by the formation of diverse carbon-rich inclusions. Although the physiological and molecular basis of these processes are well understood, the ultrastructural manifestations of the stress responses are often fragmented and frequently controversial. This minireview attempts to generalize on the ultrastructural patterns accompanying stresses in the photosynthetic cell, involving the concerted rearrangements of its assimilatory and storage compartments. The changes characteristic of normal functioning and emergency reduction of the chloroplast thylakoids under harsh stress are also addressed. Special attention is paid to the manifestations of the engagement of photoprotection via active (energy-dependent non-photochemical quenching) and passive mechanisms (e.g. optical shielding by secondary carotenoids). We also underline the potentially important role of autophagy-like processes and provide a more integral view of ultrastructural rearrangements under stress.

A facile forward-genetic screen for Arabidopsis autophagy mutants reveals twenty-one loss-of-function mutations disrupting six ATG genes

Macroautophagy is a process through which eukaryotic cells degrade large substrates including organelles, protein aggregates, and invading pathogens. Over 40 autophagy-related (ATG) genes have been identified through forward-genetic screens in yeast. Although homology-based analyses have identified conserved ATG genes in plants, only a few atg mutants have emerged from forward-genetic screens in Arabidopsis thaliana. We developed a screen that consistently recovers Arabidopsis atg mutations by exploiting mutants with defective LON2/At5g47040, a protease implicated in peroxisomal quality control. Arabidopsis lon2 mutants exhibit reduced responsiveness to the peroxisomally-metabolized auxin precursor indole-3-butyric acid (IBA), heightened degradation of several peroxisomal matrix proteins, and impaired processing of proteins harboring N-terminal peroxisomal targeting signals; these defects are ameliorated by preventing autophagy. We optimized a lon2 suppressor screen to expedite recovery of additional atg mutants. After screening mutagenized lon2-2 seedlings for restored IBA responsiveness, we evaluated stabilization and processing of peroxisomal proteins, levels of several ATG proteins, and levels of the selective autophagy receptor NBR1/At4g24690, which accumulates when autophagy is impaired. We recovered 21 alleles disrupting 6 ATG genes: ATG2/At3g19190, ATG3/At5g61500, ATG5/At5g17290, ATG7/At5g45900, ATG16/At5g50230, and ATG18a/At3g62770. Twenty alleles were novel, and 3 of the mutated genes lack T-DNA insertional alleles in publicly available repositories. We also demonstrate that an insertional atg11/At4g30790 allele incompletely suppresses lon2 defects. Finally, we show that NBR1 is not necessary for autophagy of lon2 peroxisomes and that NBR1 overexpression is not sufficient to trigger autophagy of seedling peroxisomes, indicating that Arabidopsis can use an NBR1-independent mechanism to target peroxisomes for autophagic degradation.

Abbreviations: ATG: autophagy-related; ATI: ATG8-interacting protein; Col-0: Columbia-0; DSK2: dominant suppressor of KAR2; EMS: ethyl methanesulfonate; GFP: green fluorescent protein; IAA: indole-3-acetic acid; IBA: indole-3-butyric acid; ICL: isocitrate lyase; MLS: malate synthase; NBR1: Next to BRCA1 gene 1; PEX: peroxin; PMDH: peroxisomal malate dehydrogenase; PTS: peroxisomal targeting signal; thiolase: 3-ketoacyl-CoA thiolase; UBA: ubiquitin-associated; WT: wild type

Autophagy is essential for optimal translocation of iron to seeds in Arabidopsis

Micronutrient deficiencies affect a large part of the world's population. These deficiencies are mostly due to the consumption of grains with insufficient content of iron (Fe) or zinc (Zn). Both de novo uptake by roots and recycling from leaves may provide seeds with nutrients. Autophagy, which is a conserved mechanism for nutrient recycling in eukaryotes, was shown to be involved in nitrogen remobilization to seeds. Here, we have investigated the role of this mechanism in micronutrient translocation to seeds. We found that Arabidopsis thaliana plants impaired in autophagy display defects in nutrient remobilization to seeds. In the atg5-1 mutant, which is completely defective in autophagy, the efficiency of Fe translocation from vegetative organs to seeds was severely decreased even when Fe was provided during seed formation. Combining atg5-1 with the sid2 mutation that counteracts premature senescence associated with autophagy deficiency and using 57Fe pulse labeling, we propose a two-step mechanism in which Fe taken up de novo during seed formation is first accumulated in vegetative organs and subsequently remobilized to seeds. Finally, we show that translocation of Zn and manganese (Mn) to seeds is also dependent on autophagy. Fine-tuning autophagy during seed formation opens up new possibilities to improve micronutrient remobilization to seeds.

Autophagy in Plants: Both a Puppet and a Puppet Master of Sugars

Autophagy is a major pathway that recycles cellular components in eukaryotic cells both under stressed and non-stressed conditions. Sugars participate both metabolically and as signaling molecules in development and response to various environmental and nutritional conditions. It is therefore essential to maintain metabolic homeostasis of sugars during non-stressed conditions in cells, not only to provide energy, but also to ensure effective signaling when exposed to stress. In both plants and animals, autophagy is activated by the energy sensor SnRK1/AMPK and inhibited by TOR kinase. SnRK1/AMPK and TOR kinases are both important regulators of cellular metabolism and are controlled to a large extent by the availability of sugars and sugar-phosphates in plants whereas in animals AMP/ATP indirectly translate sugar status. In plants, during nutrient and sugar deficiency, SnRK1 is activated, and TOR is inhibited to allow activation of autophagy which in turn recycles cellular components in an attempt to provide stress relief. Autophagy is thus indirectly regulated by the nutrient/sugar status of cells, but also regulates the level of nutrients/sugars by recycling cellular components. In both plants and animals sugars such as trehalose induce autophagy and in animals this is independent of the TOR pathway. The glucose-activated G-protein signaling pathway has also been demonstrated to activate autophagy, although the exact mechanism is not completely clear. This mini-review will focus on the interplay between sugar signaling and autophagy.

Investigation of Morphological Features of Autophagy During Plant Programmed Cell Death

The investigation of autophagy particularly when observed during programmed cell death (PCD) is strongly based on the morphological features recorded with transmission electron microscope (TEM). Here we describe methods to induce and to inhibit autophagy in plants. Also some tips for obtaining better preservation of biological membranes, crucial for the investigation of autophagy, are provided together with information about plant autophagic mutants, use of antibodies and methods for 3D reconstruction of large membrane-bound objects that are commonly formed during autophagic processes leading to PCD in plants.

Isolation and Characterization of Chlamydomonas Autophagy-Related Mutants in Nutrient-Deficient Conditions

Autophagy is a recycling system for amino acids and carbon- and nitrogen (N)-containing compounds. To date, the functional importance of autophagy in microalgae in nutrient-deficient conditions has not been evaluated by using autophagy-defective mutants. Here, we provide evidence which supports the following notions by characterizing an insertional mutant of the autophagy-related gene ATG8, encoding a ubiquitin-like protein necessary for the formation of the autophagosome in the green alga, Chlamydomonas reinhardtii. First, ATG8 is required for maintenance of cell survival and Chl content in N-, sulfur- and phosphate-deficient conditions. Secondly, ATG8 supports the degradation of triacylglycerol and lipid droplets after the resupply of N to cells cultured in N-limiting conditions. Thirdly, ATG8 is also necessary for accumulation of starch in phosphate-deficient conditions. Additionally, autophagy is not essential for maternal inheritance of the organelle genomes in gametogenesis.

Stress-induced changes in the ultrastructure of the photosynthetic apparatus of green microalgae

In photosynthetic organisms including unicellular algae, acclimation to and damage by environmental stresses are readily apparent at the level of the photosynthetic apparatus. Phenotypic manifestations of the stress responses include rapid and dramatic reduction of photosynthetic activity and pigment content aimed at mitigating the risk of photooxidative damage. Although the physiological and molecular mechanisms of these events are well known, the ultrastructural picture of the stress responses is often elusive and frequently controversial. We analyzed an extensive set of transmission electron microscopy images of the microalgal cells obtained across species of Chlorophyta and in a wide range of growth conditions. The results of the analysis allowed us to pinpoint distinct ultrastructural changes typical of normal functioning and emergency reduction of the chloroplast membrane system under high light exposure and/or mineral nutrient starvation. We demonstrate the patterns of the stress-related ultrastructural changes including peculiar thylakoid rearrangements and autophagy-like processes and provide an outlook on their significance for implementation of the stress responses.

Autophagy counteracts instantaneous cell death during seasonal senescence of the fine roots and leaves in Populus trichocarpa

BACKGROUND

Senescence, despite its destructive character, is a process that is precisely-regulated. The control of senescence is required to achieve remobilization of resources, a principle aspect of senescence. Remobilization allows plants to recapture valuable resources that would otherwise be lost to the environment with the senescing organ. Autophagy is one of the critical processes that is switched on during senescence. This evolutionarily conserved process plays dual, antagonistic roles. On the one hand, it counteracts instantaneous cell death and allows the process of remobilization to be set in motion, while on the other hand, it participates in the degradation of cellular components. Autophagy has been demonstrated to occur in many plant species during the senescence of leaves and flower petals. Little is known, however, about the senescence process in other ephemeral organs, such as fine roots, whose lifespan is also relatively short. We hypothesized that, like the case of seasonal leaf senescence, autophagy also plays a role in the senescence of fine roots, and that both processes are synchronized in their timing.

RESULTS

We evaluated which morphological and cytological symptoms are universal or unique in the senescence of fine roots and leaves. The results of our study confirmed that autophagy plays a key role in the senescence of fine roots, and is associated also with the process of cellular components degradation. In both organs, structures related to autophagy were observed, such as autophagic bodies and autophagosomes. The role of autophagy in the senescence of these plant organs was further confirmed by an analysis of ATG gene expression and protein detection.

CONCLUSIONS

The present study is the first one to examine molecular mechanisms associated with the senescence of fine roots, and provide evidence that can be used to determine whether senescence of fine roots can be treated as another example of developmentally programmed cell death (dPCD). Our results indicate that there is a strong similarity between the senescence of fine roots and other ephemeral organs, suggesting that this process occurs by the same autophagy-related mechanisms in all plant ephemeral organs.

Examining Autophagy in Plant by Transmission Electron Microscopy (TEM)

In plants, macroautophagy, here referred as autophagy, is a degradation pathway during which the double-membrane structure named autophagosome engulfs the cargo and then fuses with vacuole for material recycling. To investigate the process of autophagy, transmission electron microscopy (TEM) was used to monitor the ultrastructure of autophagic structures and identify the cargo during this process due to its high resolution. Compared to other autophagy examination methods including biochemical assays and confocal microscopy, TEM is the only method that indicates the morphology of autophagic structures in nanoscale, which is considered to be one of the best ways to illustrate the morphology of autophagic intermediates and the substrate of autophagy. Here, we describe the autophagy examination assay using TEM in Nicotianabenthamiana leaf cells.

Vacuolar Protein Degradation via Autophagy Provides Substrates to Amino Acid Catabolic Pathways as an Adaptive Response to Sugar Starvation in Arabidopsis thaliana

The vacuolar lytic degradation of proteins releases free amino acids that plants can use instead of sugars for respiratory energy production. Autophagy is a major cellular process leading to the transport of proteins into the vacuole for degradation. Here, we examine the contribution of autophagy to the amino acid metabolism response to sugar starvation in mature leaves of Arabidopsis thaliana. During sugar starvation arising from the exposure of wild-type (WT) plants to darkness, autophagic transport of chloroplast stroma, which contains most of the proteins in a leaf, into the vacuolar lumen was induced within 2 d. During this time, the level of soluble proteins, primarily Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase), decreased and the amount of free amino acid increased. In dark-treated autophagy-defective (atg) mutants, the decrease of soluble proteins was suppressed, which resulted in the compromised release of basic amino acids, branched-chain amino acids (BCAAs) and aromatic amino acids. The impairment of BCAA catabolic pathways in the knockout mutants of the electron transfer flavoprotein (ETF)/ETF:ubiquinone oxidoreductase (etfqo) complex and the electron donor protein isovaleryl-CoA dehydrogenase (ivdh) caused a reduced tolerance to dark treatment similar to that in the atg mutants. The enhanced accumulation of BCAAs in the ivdh and etfqo mutants during the dark treatment was reduced by additional autophagy deficiency. These results indicate that vacuolar protein degradation via autophagy serves as an adaptive response to disrupted photosynthesis by providing substrates to amino acid catabolic pathways, including BCAA catabolism mediated by IVDH and ETFQO.

Autophagy mediates hydrotropic response in Arabidopsis thaliana roots

This work shows that autophagy plays a key role in the hydrotropic curvature of Arabidopsis thaliana roots. An analysis of GFP-ATG8a transgenic plants showed that autophagosomes accumulated in the root curvature 2 h after the transfer of seedlings to Normal Medium-Water Stress Medium (NM-WSM). Autophagy flux was required for root bending. Remarkably, several atg mutants did not show hydrotropic curvature in NM-WSM or the splitting-agar system. Hyper, an H₂O₂ sensor showed that H₂O₂ preferentially accumulated in the root curvature at a similar rate as the autophagosomes did during hydrotropic response. Peroxidase and ROBH activity inhibition affected, negatively or positively root curvature. This data suggested H₂O₂ balance was required for root bending. Malondialdehyde, a metabolite used as an indicator of oxidative stress, accumulated at the same rate during the development of the curvature in NM-WSM. These results suggest that autophagy is required for the hydrotropic response in NM-WSM. We discuss the possible regulatory role of H₂O₂ on autophagy during the hydrotropic response that might relieve oxidative stress provoked by water stress. NM-WSM is water stress system suitable for studying hydrotropic responses on a short-term basis.

Regulation of Chlorophagy during Photoinhibition and Senescence: Lessons from Mitophagy

Light energy is essential for photosynthetic energy production and plant growth. Chloroplasts in green tissues convert energy from sunlight into chemical energy via the electron transport chain. When the level of light energy exceeds the capacity of the photosynthetic apparatus, chloroplasts undergo a process known as photoinhibition. Since photoinhibition leads to the overaccumulation of reactive oxygen species (ROS) and the spreading of cell death, plants have developed multiple systems to protect chloroplasts from strong light. Recent studies have shown that autophagy, a system that functions in eukaryotes for the intracellular degradation of cytoplasmic components, participates in the removal of damaged chloroplasts. Previous findings also demonstrated an important role for autophagy in chloroplast turnover during leaf senescence. In this review, we describe the turnover of whole chloroplasts, which occurs via a type of autophagy termed chlorophagy. We discuss a possible regulatory mechanism for the induction of chlorophagy based on current knowledge of photoinhibition, leaf senescence and mitophagy-the autophagic turnover of mitochondria in yeast and mammals.

Autophagy in turnover of lipid stores: trans-kingdom comparison

Lipids and their cellular utilization are essential for life. Not only are lipids energy storage molecules, but their diverse structural and physical properties underlie various aspects of eukaryotic biology, such as membrane structure, signalling, and trafficking. In the ever-changing environment of cells, lipids, like other cellular components, are regularly recycled to uphold the housekeeping processes required for cell survival and organism longevity. The ways in which lipids are recycled, however, vary between different phyla. For example, animals and plants have evolved distinct lipid degradation pathways. The major cell recycling system, autophagy, has been shown to be instrumental for both differentiation of specialized fat storing-cells, adipocytes, and fat degradation in animals. Does plant autophagy play a similar role in storage and degradation of lipids? In this review, we discuss and compare implications of bulk autophagy and its selective route, lipophagy, in the turnover of lipid stores in animals, fungi, and plants.

Autophagy-mediated regulation of phytohormone metabolism during rice anther development

Autophagy has recently been shown to be required for postmeiotic anther development including anther dehiscence, programmed cell death-mediated degradation of the tapetum and pollen maturation in rice. Several phytohormones are known to play essential roles during male reproductive development including pollen maturation. However, the relationship between phytohormone metabolism and autophagy in plant reproductive development is unknown. We here comprehensively analyzed the effect of autophagy disruption on phytohormone contents in rice anthers at the flowering stage, and found that endogenous levels of active-forms of gibberellins (GAs) and cytokinin, trans-zeatin, were significantly lower in the autophagy-defective mutant, Osatg7-1, than in the wild type. Treatment with GA₄ partially recovered maturation of the mutant pollens, but did not recover the limited anther dehiscence as well as sterility phenotype. These results suggest that autophagy affects metabolism and endogenous levels of GAs and cytokinin in rice anthers. Reduction in bioactive GAs in the autophagy-deficient mutant may partially explain the defects in pollen maturation of the autophagy-deficient mutant, but tapetal autophagy also plays other specific roles in fertilization.

New advances in autophagy in plants: Regulation, selectivity and function

Autophagy is a major and conserved pathway for delivering unwanted proteins or damaged organelles to the vacuole for degradation and recycling. In plants, it functions as a housekeeping process to maintain cellular homeostasis under normal conditions and is induced by stress and senescence; it thus plays important roles in development, stress tolerance and metabolism. Autophagy can both execute bulk degradation and be highly selective in targeting cargos under specific environmental conditions or during certain developmental processes. Here, we review recent research on autophagy in plants, and discuss new insights into its core mechanism, regulation, selectivity and physiological roles. Potential future directions are also highlighted.