Techniques to Study Autophagy in Plants

Autophagy (or self eating), a cellular recycling mechanism, became the center of interest and subject of intensive research in recent years. Development of new molecular techniques allowed the study of this biological phenomenon in various model organisms ranging from yeast to plants and mammals. Accumulating data provide evidence that autophagy is involved in a spectrum of biological mechanisms including plant growth, development, response to stress, and defense against pathogens. In this review, we briefly summarize general and plant-related autophagy studies, and explain techniques commonly used to study autophagy. We also try to extrapolate how autophagy techniques used in other organisms may be adapted to plant studies.

• Publication year

  2009

• Venue

  International Journal of Plant Genomics

• Publication date

  2009-08-27

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1155/2009/451357PMID 19730746PMCID 2734941
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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  2009cited by this paper
• Two Beclin 1-binding proteins, Atg14L and Rubicon, reciprocally regulate autophagy at different stages

  2009cited by this paper
• High-throughput functional screening for autophagy-related genes and identification of TM9SF1 as an autophagosome-inducing gene

  2009cited by this paper
• Hypoxia-activated autophagy accelerates degradation of SQSTM1/p62

  2009cited by this paper
• Mobilization of Rubisco and Stroma-Localized Fluorescent Proteins of Chloroplasts to the Vacuole by an ATG Gene-Dependent Autophagic Process1[W][OA]

  2008cited by this paper
• The N-terminus and Phe52 residue of LC3 recruit p62/SQSTM1 into autophagosomes

  2008cited by this paper
• Autophagy regulated by day length determines the number of fertile florets in wheat.

  2008cited by this paper
• Loss of Pten, a tumor suppressor, causes the strong inhibition of autophagy without affecting LC3 lipidation

  2008cited by this paper
• The ATG Autophagic Conjugation System in Maize: ATG Transcripts and Abundance of the ATG8-Lipid Adduct Are Regulated by Development and Nutrient Availability1[W][OA]

  2008cited by this paper
• Autophagy activation by rapamycin eliminates mouse Mallory‐Denk bodies and blocks their proteasome inhibitor‐mediated formation

  2008cited by this paper
• Utilizing flow cytometry to monitor autophagy in living mammalian cells

  2008cited by this paper
• Autophagy protein 6 (ATG6) is required for pollen germination in Arabidopsis thaliana

  2008cited by this paper
• The ATG12-Conjugating Enzyme ATG10 Is Essential for Autophagic Vesicle Formation in Arabidopsis thaliana

  2008cited by this paper
• Kinase-Inactivated ULK Proteins Inhibit Autophagy via Their Conserved C-Terminal Domains Using an Atg13-Independent Mechanism

  2008cited by this paper
• Quantitation of autophagy by luciferase release assay

  2008cited by this paper
• Mitophagy in Yeast Occurs through a Selective Mechanism*

  2008cited by this paper
• FIP200, a ULK-interacting protein, is required for autophagosome formation in mammalian cells

  2008cited by this paper
• Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes

  2008cited by this paper
• The role of TOR in autophagy regulation from yeast to plants and mammals

  2008cited by this paper
• To be or not to be? Examples of incorrect identification of autophagic compartments in conventional transmission electron microscopy of mammalian cells

  2008cited by this paper
• Chloroplasts are partially mobilized to the vacuole by autophagy

  2008cited by this paper
• An autophagy-associated Atg8 protein is involved in the responses of Arabidopsis seedlings to hormonal controls and abiotic stresses

  2008cited by this paper
• In Vitro Reconstitution of Plant Atg8 and Atg12 Conjugation Systems Essential for Autophagy*

  2008cited by this paper
• Arabidopsis ATG6 is required to limit the pathogen-associated cell death response

  2008cited by this paper
• LC3-I conversion to LC3-II does not necessarily result in complete autophagy.

  2008cited by this paper
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  2008cited by this paper
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  2007cited by this paper
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  2007cited by this paper
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  2007cited by this paper
• A Novel type of Autophagy Occurs together with Vacuole Genesis in Miniprotoplasts Prepared from Tobacco Culture Cells

  2007cited by this paper
• Implications of 15N‐metabolic labeling for automated peptide identification in Arabidopsis thaliana

  2007cited by this paper
• p62/SQSTM1 Binds Directly to Atg8/LC3 to Facilitate Degradation of Ubiquitinated Protein Aggregates by Autophagy*

  2007cited by this paper
• Quantitative immunoelectron microscopy: alternative ways of assessing subcellular patterns of gold labeling.

  2007cited by this paper
• Listeria monocytogenes Evades Killing by Autophagy During Colonization of Host Cells

  2007cited by this paper
• Identification of amino acid residues involved in substrate specificity of plant acyl-ACP thioesterases using a bioinformatics-guided approach

  2007cited by this paper
• Monitoring autophagy in yeast: the Pho8Delta60 assay.

  2007influential reference
• Ultrastructural evidence for a dual function of the phloem and programmed cell death in the floral nectary of Digitalis purpurea.

  2007cited by this paper
• Autophagosome formation: core machinery and adaptations

  2007cited by this paper
• Human WIPI‐1 puncta‐formation: A novel assay to assess mammalian autophagy

  2007cited by this paper
• An Arabidopsis Homolog of Yeast ATG6/VPS30 Is Essential for Pollen Germination1[W]

  2007cited by this paper
• Disruption of Autophagy Results in Constitutive Oxidative Stress in Arabidopsis

  2007cited by this paper
• Temporal responses of transcripts, enzyme activities and metabolites after adding sucrose to carbon-deprived Arabidopsis seedlings.

  2007cited by this paper
• Identification of a carboxylesterase expressed in protoplasts using fluorescence-activated cell sorting.

  2007cited by this paper
• Autophagy: from phenomenology to molecular understanding in less than a decade

  2007cited by this paper
• Plant autophagy--more than a starvation response.

  2007cited by this paper
• ATG1, an autophagy regulator, inhibits cell growth by negatively regulating S6 kinase

  2007cited by this paper
• Chaperone-mediated autophagy in aging and disease.

  2006cited by this paper
• Autophagic programmed cell death by selective catalase degradation.

  2006cited by this paper
• Metabolic labeling of plant cell cultures with K15NO3 as a tool for quantitative analysis of proteins and metabolites

  2006cited by this paper
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  2006cited by this paper
• Autophagy in Development and Stress Responses of Plants

  2006cited by this paper
• A Role for Intercellular Antigen Transfer in the Recognition of EBV-Transformed B Cell Lines by EBV Nuclear Antigen-Specific CD4+ T Cells1

  2006cited by this paper
• Transcription Analysis of Arabidopsis Membrane Transporters and Hormone Pathways during Developmental and Induced Leaf Senescence1[W]

  2006cited by this paper
• Identification and characterization of two rice autophagy associated genes, OsAtg8 and OsAtg4

  2006cited by this paper
• Function of the Dictyostelium discoideum Atg1 Kinase during Autophagy and Development

  2006cited by this paper
• AtATG genes, homologs of yeast autophagy genes, are involved in constitutive autophagy in Arabidopsis root tip cells.

  2006cited by this paper
• Starvation‐induced expression of autophagy‐related genes in Arabidopsis

  2006cited by this paper
• Autophagy and plant innate immunity

  2006cited by this paper
• The amino acid sensitive TOR pathway from yeast to mammals

  2006cited by this paper
• Degradation of Oxidized Proteins by Autophagy during Oxidative Stress in Arabidopsis1[W][OA]

  2006cited by this paper
• A role for caleosin in degradation of oil-body storage lipid during seed germination.

  2006cited by this paper
• Protein Aggregates are Transported to Vacuoles by Macroautophagic Mechanism in Nutrient-Starved Plant Cells

  2006cited by this paper
• Autophagy regulates programmed cell death during the plant innate immune response.

  2005cited by this paper
• Functions of SNAREs in intracellular membrane fusion and lipid bilayer mixing

  2005cited by this paper
• Autophagic Nutrient Recycling in Arabidopsis Directed by the ATG8 and ATG12 Conjugation Pathways1

  2005cited by this paper
• The Crystal Structure of Plant ATG12 and its Biological Implication in Autophagy

  2005cited by this paper
• Pexophagy: The Selective Autophagy of Peroxisomes

  2005cited by this paper
• Autophagic recycling: lessons from yeast help define the process in plants.

  2005cited by this paper
• AtATG18a is required for the formation of autophagosomes during nutrient stress and senescence in Arabidopsis thaliana.

  2005cited by this paper
• Stable Isotope Labeling of Arabidopsis thaliana Cells and Quantitative Proteomics by Mass Spectrometry*S

  2005cited by this paper
• Many ways to exit? Cell death categories in plants.

  2005cited by this paper
• p62/SQSTM1 forms protein aggregates degraded by autophagy and has a protective effect on huntingtin-induced cell death

  2005cited by this paper
• Bcl-2 antiapoptotic proteins inhibit Beclin 1-dependent autophagy.

  2005cited by this paper
• The molecular machinery of autophagy: unanswered questions

  2005cited by this paper
• The Dynamics of Autophagy Visualised in Live Cells: from Autophagosome Formation to Fusion with Endo/lysosomes

  2005cited by this paper
• Visualization of autophagy in Arabidopsis using the fluorescent dye monodansylcadaverine and a GFP-AtATG8e fusion protein.

  2005cited by this paper
• Internalisation of cell-penetrating peptides into tobacco protoplasts.

  2005cited by this paper
• The autophagy-associated Atg8 gene family operates both under favourable growth conditions and under starvation stresses in Arabidopsis plants.

  2005influential reference
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  2004cited by this paper
• Inhibition of platelet-derived growth factor signalling induces autophagy in malignant glioma cells

  2004cited by this paper
• The mitochondrion--an organelle commonly involved in programmed cell death in Arabidopsis thaliana.

  2004cited by this paper
• 3-methyladenine inhibits autophagy in tobacco culture cells under sucrose starvation conditions.

  2004cited by this paper
• Transcriptome Profiling of the Response of Arabidopsis Suspension Culture Cells to Suc Starvation1[w]

  2004cited by this paper
• Controlled cell death, plant survival and development

  2004cited by this paper
• Autophagy is a defense mechanism inhibiting BCG and Mycobacterium tuberculosis survival in infected macrophages.

  2004cited by this paper
• Methods for monitoring autophagy.

  2004cited by this paper
• Autophagy as a cell death and tumor suppressor mechanism

  2004cited by this paper
• WIPI-1α (WIPI49), a member of the novel 7-bladed WIPI protein family, is aberrantly expressed in human cancer and is linked to starvation-induced autophagy

  2004cited by this paper
• Processing of ATG8s, Ubiquitin-Like Proteins, and Their Deconjugation by ATG4s Are Essential for Plant Autophagy

  2004influential reference
• Les gènes ATG et la macro-autophagie

  2004cited by this paper
• Disposal of chloroplasts with abnormal function into the vacuole in Arabidopsis thaliana cotyledon cells

  2004cited by this paper
• Amino Acids and Insulin Control Autophagic Proteolysis through Different Signaling Pathways in Relation to mTOR in Isolated Rat Hepatocytes*

  2004cited by this paper
• Arabidopsis homologues of the autophagy protein Atg8 are a novel family of microtubule binding proteins

  2004cited by this paper
• The Atg1-Atg13 complex regulates Atg9 and Atg23 retrieval transport from the pre-autophagosomal structure.

  2004cited by this paper
• Role of mitochondrial permeability transition pores in mitochondrial autophagy.

  2004cited by this paper
• Process for the integrated extraction, identification and quantification of metabolites, proteins and RNA to reveal their co‐regulation in biochemical networks

  2004cited by this paper
• Alpha tonoplast intrinsic protein is specifically associated with vacuole membrane involved in an autophagic process.

  2003cited by this paper
• Chemical genetic analysis of Apg1 reveals a non-kinase role in the induction of autophagy.

  2003cited by this paper
• Mouse Apg16L, a novel WD-repeat protein, targets to the autophagic isolation membrane with the Apg12-Apg5 conjugate

  2003cited by this paper

• Investigating Penthiopyrad's Potential Toxicity on Male Reproductive Health via In Vitro Models and Computational Network Toxicology and Docking Studies.

  2025cites this paper
• Microscopy-based methods for characterizing autophagy and understanding its dynamics in resin secretion.

  2025cites this paper
• Bacillus amyloliquefaciens modulate autophagy pathways to control Rhizoctonia solani infection in rice.

  2024cites this paper
• Autophagy functions as a cytoprotective mechanism by regulating programmed cell death during desiccation in Syntrichia caninervis.

  2024cites this paper
• ER‐to‐lysosome‐associated degradation in a nutshell: mammalian, yeast, and plant ER‐phagy as induced by misfolded proteins

  2023cites this paper
• The role of Atg16 in autophagy, anthocyanin biosynthesis, and programmed cell death in leaves of the lace plant (Aponogeton madagascariensis)

  2023cites this paper
• GhROP6 GTPase promotes cell-specific GhPIN3a degradation in cotton fibers by regulating GhPIN3a localization.

  2022cites this paper
• A molecular link between autophagy and circadian rhythm in plants.

  2022cites this paper
• Carbon starvation, senescence and specific mitochondrial stresses, but not nitrogen starvation and general stresses, are major triggers for mitophagy in Arabidopsis

  2022influential citation
• Influence of the Drying Method on the Volatile Component Profile of Hypericum perforatum Herb: A HS-SPME-GC/MS Study

  2022cites this paper
• UR-144, synthetic cannabinoid receptor agonist, induced cardiomyoblast toxicity mechanism comprises cytoplasmic Ca2+ and DAPK1 related autophagy and necrosis

  2022cites this paper
• Cytoskeletal diversification across 1 billion years: What red algae can teach us about the cytoskeleton, and vice versa

  2021cites this paper
• Metabolic patterns in Septoria canker resistant and susceptible Populus trichocarpa genotypes 24 hours post-inoculation.

  2021cites this paper
• Overexpression of the Selective Autophagy Cargo Receptor NBR1 Modifies Plant Response to Sulfur Deficit

  2020cites this paper
• RNA-Seq and secondary metabolite analyses reveal a putative defence-transcriptome in Norway spruce (Picea abies) against needle bladder rust (Chrysomyxa rhododendri) infection

  2020cites this paper
• Autophagy and vacuolar biogenesis during the nectary development

  2019cites this paper
• The Assessment of in Vitro Cardiotoxic Potentials for Synthetic Cannabinoid, AM-2201

  2019cites this paper
• Nitric oxide and ROS mediate autophagy and regulate Alternaria alternata toxin-induced cell death in tobacco BY-2 cells

  2019cites this paper
• Role of cerium oxide nanoparticle-induced autophagy as a safeguard to exogenous H2O2-mediated DNA damage in tobacco BY-2 cells

  2018cites this paper
• Autophagic Induction Greatly Enhances Leishmania major Intracellular Survival Compared to Leishmania amazonensis in CBA/j-Infected Macrophages

  2018cites this paper
• Detection of autophagy processes during the development of nonarticulated laticifers in Euphorbia kansui Liou

  2018influential citation
• Wheat Gene TaATG8j Contributes to Stripe Rust Resistance

  2018cites this paper
• Monitoring autophagy in wheat living cells by visualization of fluorescence protein-tagged ATG8

  2018cites this paper
• Plant Bax Inhibitor-1 interacts with ATG6 to regulate autophagy and programmed cell death

  2017cites this paper
• Biochemical Methods to Monitor Autophagic Responses in Plants.

  2017cites this paper
• Quantitative live cell imaging of autophagic flux and roles of autophagy in reproductive development in plants

  2016cites this paper
• Allyl isothiocyanate depletes glutathione and upregulates expression of glutathione S-transferases in Arabidopsis thaliana

  2015cites this paper
• Cytoplastic Glyceraldehyde-3-Phosphate Dehydrogenases Interact with ATG3 to Negatively Regulate Autophagy and Immunity in Nicotiana benthamiana

  2015cites this paper
• Autophagy and Endocytosis

  2014cites this paper
• Autophagy, senescence and nitrogen remobilization in barley

  2014influential citation
• Autofagia celular em processos patológicos Cellular autophagy in pathological processes

  2014cites this paper
• Identification of autophagy-related genes ATG4 and ATG8 from wheat (Triticum aestivum L.) and profiling of their expression patterns responding to biotic and abiotic stresses

  2014cites this paper
• In vivo imaging and quantitative monitoring of autophagic flux in tobacco BY-2 cells

  2012cites this paper
• Autophagy-related gene, TdAtg8, in wild emmer wheat plays a role in drought and osmotic stress response

  2012cites this paper
• [Autophagic processes in plants: mechanisms, regulation and function].

  2012cites this paper
• Different Degree in Proteasome Malfunction Has Various Effects on Root Growth Possibly through Preventing Cell Division and Promoting Autophagic Vacuolization

  2012cites this paper
• Programmed cell death in the moss Physcomitrella patens : Studying the role of metacaspases in archegonia development through gene knockout by homologous recombination

  2012cites this paper
• Plant abiotic stress signaling

  2012cites this paper
• In vivo and in vitro Leishmania amazonensis infection induces autophagy in macrophages.

  2012cites this paper
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  2012cites this paper
• Genes for plant Autophagy: Functions and interactions

  2012cites this paper
• The Botanical Dance of Death: Programmed Cell Death in Plants

  2011cites this paper
• See How I Eat My Greens—Autophagy in Plant Cells

  2011cites this paper
• Identification and functional analysis of Joka2, a tobacco member of the family of selective autophagy cargo receptors

  2011cites this paper
• The ABA-regulated Arabidopsis TSPO is an ER/Golgi localized heme binding membrane protein and a potential scavenger of porphyrins via an autophagy-dependent degradation mechanism

  2011cites this paper
• Analysis of paternal plastid inheritance in Arabidopsis thaliana and its impact on biosafety of gene-modified plants

  2011influential citation
• The plant orthologue of p 62 / SQSTM 1 links response to nutrients deprivation with the process of selective autophagy

  2010cites this paper