References
- Vierstra RD. Proteolysis in plants: mechanisms and functions. Plant Mol Biol. 1996;32(1–2):1–17. doi:https://doi.org/10.1007/BF00039386.
- Smalle J, Vierstra RD. The ubiquitin 26S proteasome proteolytic pathway. Annu Rev Plant Biol. 2004;55(1):555–590. doi:https://doi.org/10.1146/annurev.arplant.55.031903.141801.
- Klionsky DJ. The molecular machinery of autophagy: unanswered questions. J Cell Sci. 2005;118(1):7–18. doi:https://doi.org/10.1242/jcs.01620.
- Mizushima N. Autophagy: process and function. Genes Dev. 2007;21(22):2861–2873. doi:https://doi.org/10.1101/gad.1599207.
- Marshall, Richard S, Vierstra,Richard D. Autophagy: the master of bulk and selective recycling. Annu Rev Plant Biol. 2018;69:173–208. doi:https://doi.org/10.1146/annurev-arplant-042817-040606.
- Li F, Vierstra RD. Autophagy: a multifaceted intracellular system for bulk and selective recycling. Trends Plant Sci. 2012;17(9):526–537. doi:https://doi.org/10.1016/j.tplants.2012.05.006.
- Lamb CA, Yoshimori T, Tooze SA. The autophagosome: origins unknown, biogenesis complex. Nat Rev Mol Cell Biol. 2013;14(12):759–774. doi:https://doi.org/10.1038/nrm3696.
- Yin Z, Pascual C, Klionsky DJ. Autophagy: machinery and regulation. Microb Cell. 2016;3(12):588–596. doi:https://doi.org/10.15698/mic2016.12.546.
- Takeshige K, Baba M, Tsuboi S, Ohsumi NY. Autophagy in yeast demonstrated with proteinase-deficient mutants and conditions for its induction. J Cell Biol. 1992;119(2):301–311. doi:https://doi.org/10.1083/jcb.119.2.301.
- Baba M, Takeshige K, Ohsumi BY. Ultrastructural analysis of the autophagic process in yeast: detection of autophagosomes and their characterization. J Cell Biol. 1994;124(6):903–913. doi:https://doi.org/10.1083/jcb.124.6.903.
- Tsukada M, Ohsumi Y. Isolation and characterization of autophagy-defective mutants of Saccharomyces cerevisiae. FEBS Lett. 1993;333(1–2):169–174. doi:https://doi.org/10.1016/0014-5793(93)80398-e.
- Thumm M, Egner R, Koch B, Schlumpberger M, Straub M, Veenhuis M, Wolf DH. Isolation of autophagocytosis mutants of Saccharomyces cerevisiae. FEBS Lett. 1994;349(2):275–280. doi:https://doi.org/10.1016/0014-5793(94)00672-5.
- Harding TM. Isolation and characterization of yeast mutants in the cytoplasm to vacuole protein targeting pathway. J Cell Biol. 1995;131(3):591–602. doi:https://doi.org/10.1083/jcb.131.3.591.
- Klionsky DJ, Cregg JM, Dunn WA, Emr SD, Ohsumi Y. A unified nomenclature for yeast autophagy-related genes. Dev Cell. 2003;5(4):539–545. doi:https://doi.org/10.1016/s1534-5807(03)00296-x.
- Feng Y, He D, Yao Z, Klionsky DJ. The machinery of macroautophagy. Cell Res. 2014;24(1):24–41. doi:https://doi.org/10.1038/cr.2013.168.
- Hurley JH, Young LN. Mechanisms of autophagy initiation. Annu Rev Biochem. 2017;86:225–244. doi:https://doi.org/10.1146/annurev-biochem-061516-044820.
- Mizushima N, Yoshimori T, Ohsumi Y. The role of Atg proteins in autophagosome formation. Annu Rev Cell Dev Biol. 2011;27:107–132. doi:https://doi.org/10.1146/annurev-cellbio-092910-154005.
- Bassham DC, Laporte M, Marty F, Moriyasu Y, Ohsumi Y, Olsen LJ, Yoshimoto K. Autophagy in development and stress responses of plants. Autophagy. 2006;2(1):2–11. doi:https://doi.org/10.4161/auto.2092.
- Hanaoka H, Noda T, Shirano Y, Kato T, Hayashi H, Shibata D, Tabata S, Ohsumi Y. Leaf senescence and starvation-induced chlorosis are accelerated by the disruption of an Arabidopsis autophagy gene. Plant Physiol. 2002;129(3):1181–1193. doi:https://doi.org/10.1104/pp.011024.
- Suttangkakul A, Li F, Chung T, Vierstra RD. The ATG1/ATG13 protein kinase complex is both a regulator and a target of autophagic recycling in Arabidopsis. Plant Cell. 2011;23(10):3761–3779. doi:https://doi.org/10.1105/tpc.111.090993.
- Avin-Wittenberg T, Honig A, Galili G. Variations on a theme: plant autophagy in comparison to yeast and mammals. Protoplasma. 2012;249(2):285–299. doi:https://doi.org/10.1007/s00709-011-0296-z.
- Mizushima N, Levine B. Autophagy in mammalian development and differentiation. Nat Cell Biol. 2010;12(9):823–830. doi:https://doi.org/10.1038/ncb0910-823.
- Yang C, Luo M, Zhuang X, Li F, Gao C. Transcriptional and epigenetic regulation of autophagy in plants. Trends Genet. 2020;36(9):676–688. doi:https://doi.org/10.1016/j.tig.2020.06.013.
- Cao JJ, Liu CX, Shao SJ, Zhou J. Molecular mechanisms of autophagy regulation in plants and their applications in agriculture. Front Plant Sci. 2021;11:618944. doi:https://doi.org/10.3389/fpls.2020.618944.
- Lai Z, Wang F, Zheng Z, Fan B, Chen Z. A critical role of autophagy in plant resistance to necrotrophic fungal pathogens. Plant J. 2011;66(6):953–968. doi:https://doi.org/10.1111/j.1365-313X.2011.04553.x.
- Yang C, Shen W, Yang L, Sun Y, Li X, Lai M, Wei J, Wang C, Xu Y, Li F, et al. HY5-HDA9 module transcriptionally regulates plant autophagy in response to light-to-dark conversion and nitrogen starvation. Mol Plant. 2020;13(3):515–531. doi:https://doi.org/10.1016/j.molp.2020.02.011.
- Wang Y, Cai S, Yin L, Shi K, Xia X, Zhou Y, Yu J, Zhou J. Tomato HsfA1a plays a critical role in plant drought tolerance by activating ATG genes and inducing autophagy. Autophagy. 2015;11(11):2033–2047. doi:https://doi.org/10.1080/15548627.2015.1098798.
- Zhu T, Zou L, Li Y, Yao X, Xu F, Deng X, Zhang D, Lin H. Mitochondrial alternative oxidase-dependent autophagy involved in ethylene-mediated drought tolerance in Solanum lycopersicum. Plant Biotechnol J. 2018;16(12):2063–2076. doi:https://doi.org/10.1111/pbi.12939.
- Wang Y, Cao JJ, Wang KX, Xia XJ, Shi K, Zhou YH, Yu JQ, Zhou J. BZR1 mediates brassinosteroid-induced autophagy and nitrogen starvation in tomato. Plant Physiol. 2019;179(2):671–685. doi:https://doi.org/10.1104/pp.18.01028.
- Wang P, Nolan TM, Yin Y, Bassham DC. Identification of transcription factors that regulate ATG8 expression and autophagy in Arabidopsis. Autophagy. 2020;16(1):123–139. doi:https://doi.org/10.1080/15548627.2019.1598753.
- Wang P, Mugume Y, Bassham DC. New advances in autophagy in plants: regulation, selectivity and function. Semin Cell Dev Biol. 2018;80:113–122. doi:https://doi.org/10.1016/j.semcdb.2017.07.018.
- Soto-Burgos J, Zhuang X, Jiang L, Bassham DC. Dynamics of autophagosome formation. Plant Physiol. 2018;176(1):219–229. doi:https://doi.org/10.1104/pp.17.01236.
- Sugden C, Crawford RM, Halford NG. Regulation of spinach SNF1-related (SnRK1) kinases by protein kinases and phosphatases is associated with phosphorylation of the T loop and is regulated by 5ʹ-AMP. Plant J. 1999;19(4):433–439. doi:https://doi.org/10.1046/j.1365-313x.1999.00532.x.
- Crozet P, Margalha L, Confraria A, Rodrigues A, Martinho C, Adamo M, Elias CA, Baena-González E. Mechanisms of regulation of SNF1/AMPK/SnRK1 protein kinases. Front Plant Sci. 2014;5:190. doi:https://doi.org/10.3389/fpls.2014.00190.
- Polge C, Thomas M. SNF1/AMPK/SnRK1 kinases, global regulators at the heart of energy control? Trends Plant Sci. 2007;12(1):20–28. doi:https://doi.org/10.1016/j.tplants.2006.11.005.
- Emanuelle S, Hossain MI, Moller IE, Pedersen HL, van de Meene AM, Doblin MS, Koay A, Oakhill JS, Scott JW, Willats WG, et al. SnRK1 from Arabidopsis thaliana is an atypical AMPK. Plant J. 2015;82(2):183–192. doi:https://doi.org/10.1111/tpj.12813.
- Baena-Gonzalez E, Rolland F, Thevelein JM, Sheen J. A central integrator of transcription networks in plant stress and energy signalling. Nature. 2007;448(7156):938–942. doi:https://doi.org/10.1038/nature06069.
- Chen L, Su ZZ, Huang L, Xia FN, Qi H, Xie LJ, Xiao S, Chen QF. The AMP-activated protein kinase KIN10 is involved in the regulation of autophagy in Arabidopsis. Front Plant Sci. 2017;8:1201. doi:https://doi.org/10.3389/fpls.2017.01201.
- Hardie DG. AMP-activated protein kinase: an energy sensor that regulates all aspects of cell function. Genes Dev. 2011;25(18):1895–1908. doi:https://doi.org/10.1101/gad.17420111.
- Carroll B, Dunlop EA. The lysosome: a crucial hub for AMPK and mTORC1 signalling. Biochem J. 2017;474(9):1453–1466. doi:https://doi.org/10.1042/BCJ20160780.
- Lee JW, Park S, Takahashi Y, Wang HG. The association of AMPK with ULK1 regulates autophagy. PloS One. 2010;5(11):e15394. doi:https://doi.org/10.1371/journal.pone.0015394.
- Galluzzi L, Baehrecke EH, Ballabio A, Boya P, Bravo-San Pedro JM, Cecconi F, Choi AM, Chu CT, Codogno P, Colombo MI, et al. Molecular definitions of autophagy and related processes. EMBO J. 2017;36(13):1811–1836. doi:https://doi.org/10.15252/embj.201796697.
- Dobrenel T, Caldana C, Hanson J, Robaglia C, Vincentz M, Veit B, Meyer C. TOR signaling and nutrient sensing. Annu Rev Plant Biol. 2016;67:261–285. doi:https://doi.org/10.1146/annurev-arplant-043014-114648.
- Li F, Chung T, Vierstra RD. AUTOPHAGY-RELATED11 plays a critical role in general autophagy- and senescence-induced mitophagy in Arabidopsis. Plant Cell. 2014;26(2):788–807. doi:https://doi.org/10.1105/tpc.113.120014.
- Menand B, Desnos T, Nussaume L, Berger F, Bouchez D, Meyer C, Robaglia C. Expression and disruption of the Arabidopsis TOR (target of rapamycin) gene. Proc Natl Acad Sci U S A. 2002;99(9):6422–6427. doi:https://doi.org/10.1073/pnas.092141899.
- Deprost D, Yao L, Sormani R, Moreau M, Leterreux G, Nicolai M, Bedu M, Robaglia C, Meyer C. The Arabidopsis TOR kinase links plant growth, yield, stress resistance and mRNA translation. EMBO Rep. 2007;8(9):864–870. doi:https://doi.org/10.1038/sj.embor.7401043.
- Liu Y, Bassham DCTOR. Is a negative regulator of autophagy in Arabidopsis thaliana. PloS One. 2010;5(7):e11883. doi:https://doi.org/10.1371/journal.pone.0011883.
- Pu Y, Luo X, Bassham DC. TOR-dependent and -independent pathways regulate autophagy in Arabidopsis thaliana. Front Plant Sci. 2017;8:1204. doi:https://doi.org/10.3389/fpls.2017.01204.
- Huang X, Zheng C, Liu F, Yang C, Zheng P, Lu X, Tian J, Chung T, Otegui MS, Xiao S, et al. Genetic analyses of the Arabidopsis ATG1 kinase complex reveal both kinase-dependent and independent autophagic routes during fixed-carbon starvation. Plant Cell. 2019;31(12):2973–2995. doi:https://doi.org/10.1105/tpc.19.00066.
- Lin Y, Zeng Y, Zhu Y, Shen J, Ye H, Jiang L. Plant Rho GTPase signaling promotes autophagy. Mol Plant. 2021;14(6):905–920. doi:https://doi.org/10.1016/j.molp.2021.03.021.
- Xiong Y, Contento AL, Bassham DC. AtATG18a is required for the formation of autophagosomes during nutrient stress and senescence in Arabidopsis thaliana. Plant J. 2005;42(4):535–546. doi:https://doi.org/10.1111/j.1365-313X.2005.02397.x.
- Zhuang X, Chung KP, Yong C, Lin W, Jiang L. ATG9 regulates autophagosome progression from the endoplasmic reticulum in Arabidopsis. Proc Natl Acad Sci U S A. 2017;114(3):E426–E435. doi:https://doi.org/10.1073/pnas.1616299114.
- Yamamoto H, Kakuta S, Watanabe TM, Kitamura A, Sekito T, Kondo-Kakuta C, Ichikawa R, Kinjo M, Ohsumi Y. Atg9 vesicles are an important membrane source during early steps of autophagosome formation. J Cell Biol. 2012;198(2):219–233. doi:https://doi.org/10.1083/jcb.201202061.
- Lai LTF, Yu C, Wong JSK, Lo HS, Benlekbir S, Jiang L, Lau WCY. Subnanometer resolution cryo-EM structure of Arabidopsis thalianaATG9. Autophagy. 2020;16(3):575–583. doi:https://doi.org/10.1080/15548627.2019.1639300.
- LiuF, Hu W, Li F, Marshall RS, Zarza X, Munnik T, Vierstra RD. AUTOPHAGY-RELATED14 and its associated phosphatidylinositol 3-kinase complex promote autophagy inArabidopsis. Plant Cell. 2020;32(12):3939–3960. doi:https://doi.org/10.1105/tpc.20.00285.
- Lee HN, Zarza X, Kim JH, Yoon MJ, Kim SH, Lee JH, Paris N, Munnik T, Otegui MS, Chung T. Vacuolar trafficking protein VPS38 is dispensable for autophagy. Plant Physiol. 2018;176(2):1559–1572. doi:https://doi.org/10.1104/pp.17.01297.
- Xu N, Gao XQ, Zhao XY, Zhu DZ, Zhou LZ, Zhang XS. Arabidopsis AtVPS15 is essential for pollen development and germination through modulating phosphatidylinositol 3-phosphate formation. Plant Mol Biol. 2011;77(3):251–260. doi:https://doi.org/10.1007/s11103-011-9806-9.
- Lee Y, Kim ES, Choi Y, Hwang I, Staiger CJ, Chung YY, Lee Y. The Arabidopsis phosphatidylinositol 3-kinase is important for pollen development. Plant Physiol. 2008;147(4):1886–1897. doi:https://doi.org/10.1104/pp.108.121590.
- Kang S, Shin KD, Kim JH, Chung T. Autophagy-related (ATG) 11, ATG9 and the phosphatidylinositol 3-kinase control ATG2-mediated formation of autophagosomes in Arabidopsis. Plant Cell Rep. 2018;37(4):653–664. doi:https://doi.org/10.1007/s00299-018-2258-9.
- Ohsumi Y. Molecular dissection of autophagy: two ubiquitin-like systems. Nat Rev Mol Cell Biol. 2001;2(3):211–216. doi:https://doi.org/10.1038/35056522.
- Yoshimoto K, Hanaoka H, Sato S, Kato T, Tabata S, Noda T, Ohsumi Y. Processing of ATG8s, ubiquitin-like proteins, and their deconjugation by ATG4s are essential for plant autophagy. Plant Cell. 2004;16(11):2967–2983. doi:https://doi.org/10.1105/tpc.104.025395.
- Ichimura Y, Kirisako T, Takao T, Satomi Y, Shimonishi Y, Ishihara N, Mizushima N, Tanida I, Kominami E, Ohsumi M. A ubiquitin-like system mediates protein lipidation. Nature. 2000;408(6811):488–492. doi:https://doi.org/10.1038/35044114.
- Mizushima N, Noda T, Ohsumi Y. Apg16p is required for the function of the Apg12p–Apg5p conjugate in the yeast autophagy pathway. EMBO J. 1999;18(14):3888–3896. doi:https://doi.org/10.1093/emboj/18.14.3888.
- Suzuki K, Kirisako T, Kamada Y, Mizushima N, Noda T, Ohsumi Y. The pre-autophagosomal structure organized by concerted functions of APG genes is essential for autophagosome formation. EMBO J. 2001;20(21):5971–5981. doi:https://doi.org/10.1093/emboj/20.21.5971.
- Kuma A. Formation of the 350-kDa Apg12-Apg5·Apg16 multimeric complex, mediated by Apg16 oligomerization, is essential for autophagy in yeast. J Biol Chem. 2002;277(21):18619–18625. doi:https://doi.org/10.1074/jbc.M111889200.
- Le Bars R, Marion J, Le Borgne R, Satiat-Jeunemaitre B, Bianchi MW. ATG5 defines a phagophore domain connected to the endoplasmic reticulum during autophagosome formation in plants. Nat Commun. 2014;5(10):4121. doi:https://doi.org/10.1038/ncomms5121.
- Zhuang X, Wang H, Lam SK, Gao C, Wang X, Cai Y, Jiang L. A BAR-domain protein SH3P2, which binds to phosphatidylinositol 3-phosphate and ATG8, regulates autophagosome formation in Arabidopsis. Plant Cell. 2013;25(11):4596–4615. doi:https://doi.org/10.1105/tpc.113.118307.
- Zhuang X, Chung KP, Luo M, Jiang L. Autophagosome biogenesis and the endoplasmic reticulum: a plant perspective. Trends Plant Sci. 2018;23(8):677–692. doi:https://doi.org/10.1016/j.tplants.2018.05.002.
- Kirisako T, Ichimura Y, Okada H, Kabeya Y, Ohsumi Y. The reversible modification regulates the membrane-binding state of Apg8/Aut7 essential for autophagy and the cytoplasm to vacuole targeting pathway. J Cell Biol. 2000;151(2):263–276. doi:https://doi.org/10.1083/jcb.151.2.263.
- Ketelaar T, Voss C, Dimmock SA, Thumm M, Hussey PJ. Arabidopsis homologues of the autophagy protein Atg8 are a novel family of microtubule binding proteins. FEBS Lett. 2004;567(2–3):302–306. doi:https://doi.org/10.1016/j.febslet.2004.04.088.
- Zientara-Rytter K, Sirko A. Selective autophagy receptor Joka2 co-localizes with cytoskeleton in plant cells. Plant Signal Behav. 2014;9(3):e28523. doi:https://doi.org/10.4161/psb.28523.
- Wang Y, Zheng X, Yu B, Han S, Guo J, Tang H, Yu AY, Deng H, Hong Y, Liu Y. Disruption of microtubules in plants suppresses macroautophagy and triggers starch excess-associated chloroplast autophagy. Autophagy. 2015;11(12):2259–2274. doi:https://doi.org/10.1080/15548627.2015.1113365.
- Machesky LM, Insall RH. Scar1 and the related Wiskott-Aldrich syndrome protein, WASP, regulate the actin cytoskeleton through the Arp2/3 complex. Curr Biol. 1998;8(25):1347–1356. doi:https://doi.org/10.1016/s0960-9822(98)00015-3.
- Pollard TD, Beltzner CC. Structure and function of the Arp2/3 complex. Curr Opin Struct Biol. 2002;12(6):768–774. doi:https://doi.org/10.1016/s0959-440x(02)00396-2.
- Deeks MJ, Hussey PJ. Arp2/3 and SCAR: plants move to the fore. Nat Rev Mol Cell Biol. 2005;6(12):954–964. doi:https://doi.org/10.1038/nrm1765.
- Szymanski D. Breaking the WAVE complex: the point of Arabidopsis trichomes. Curr Opin Plant Biol. 2005;8(1):103–112. doi:https://doi.org/10.1016/j.pbi.2004.11.004.
- Dyachok J, Shao MR, Vaughn K, Bowling A, Facette M, Djakovic S, Clark L, Smith L. Plasma membrane-associated SCAR complex subunits promote cortical F-actin accumulation and normal growth characteristics in Arabidopsis roots. Mol Plant. 2008;1(6):990–1006. doi:https://doi.org/10.1093/mp/ssn059.
- Wang P, Richardson C, Hawes C, Hussey PJ. Arabidopsis NAP1 regulates the formation of autophagosomes. Curr Biol. 2016;26(15):2060–2069. doi:https://doi.org/10.1016/j.cub.2016.06.008.
- Zheng X, Wu M, Li X, Cao J, Li J, Wang J, Huang S, Liu Y, Wang Y. Actin filaments are dispensable for bulk autophagy in plants. Autophagy. 2019;15(12):2126–2141. doi:https://doi.org/10.1080/15548627.2019.1596496.
- Lin Y, Guo R, Ji C, Zhou J, Jiang L. New insights into AtNBR1 as a selective autophagy cargo receptor in Arabidopsis. Plant Signal Behav. 2021;16(1):1839226. doi:https://doi.org/10.1080/15592324.2020.1839226.
- Henne WM, Buchkovich NJ, Emr SD. The ESCRT pathway. Dev Cell. 2011;21(1):77–91. doi:https://doi.org/10.1016/j.devcel.2011.05.015.
- Winter V, Hauser MT. Exploring the ESCRTing machinery in eukaryotes. Trends Plant Sci. 2006;11(3):115–123. doi:https://doi.org/10.1016/j.tplants.2006.01.008.
- Gao C. Dual roles of an Arabidopsis ESCRT component FREE1 in regulating vacuolar protein transport and autophagic degradation. Proc Natl Acad Sci U S A. 2015;112(112):1886–1891. doi:https://doi.org/10.1073/pnas.1421271112.
- Kolb C, Nagel MK, Kalinowska K, Hagmann J, Ichikawa M, Anzenberger F, Alkofer A, Sato MH, Braun P, Isono E. FYVE1 is essential for vacuole biogenesis and intracellular trafficking in Arabidopsis. Plant Physiol. 2015;167(4):1361–1373. doi:https://doi.org/10.1104/pp.114.253377.
- Katsiarimpa A, Kalinowska K, Anzenberger F, Weis C, Ostertag M, Tsutsumi C, Schwechheimer C, Brunner F, Huckelhoven R, Isono E. The deubiquitinating enzyme AMSH1 and the ESCRT-III subunit VPS2.1 are required for autophagic degradation in Arabidopsis. Plant Cell. 2013;25(6):2236–2252. doi:https://doi.org/10.1105/tpc.113.113399.
- Sutipatanasomboon A, Herberth S, Alwood EG, Haweker H, Muller B, Shahriari M, Zienert AY, Marin B, Robatzek S, Praefcke GJK, et al. Disruption of the plant-specific CFS1 gene impairs autophagosome turnover and triggers EDS1-dependent cell death. Sci Rep. 2017;7(1):8677. doi:https://doi.org/10.1038/s41598-017-08577-8.
- Isono E, Katsiarimpa A, Muller IK, Anzenberger F, Stierhof YD, Geldner N, Chory J, Schwechheimer C. The deubiquitinating enzyme AMSH3 is required for intracellular trafficking and vacuole biogenesis in Arabidopsis thaliana. Plant Cell. 2010;22(6):1826–1837. doi:https://doi.org/10.1105/tpc.110.075952.
- Kulich I, Pecenkova T, Sekeres J, Smetana O, Fendrych M, Foissner I, Hoftberger M, Zarsky V. Arabidopsis exocyst subcomplex containing subunit EXO70B1 is involved in autophagy-related transport to the vacuole. Traffic. 2013;14(11):1155–1165. doi:https://doi.org/10.1111/tra.12101.
- Surpin M, Zheng H, Morita MT, Saito C, Avila E, Blakeslee JJ, Bandyopadhyay A, Kovaleva V, Carter D, Murphy A, et al. The VTI family of SNARE proteins is necessary for plant viability and mediates different protein transport pathways. Plant Cell. 2003;15(12):2885–2899. doi:https://doi.org/10.1105/tpc.016121.
- Zouhar J, Rojo E, Bassham DC. AtVPS45 is a positive regulator of the SYP41/SYP61/VTI12 SNARE complex involved in trafficking of vacuolar cargo. Plant Physiol. 2009;149(4):1668–1678. doi:https://doi.org/10.1104/pp.108.134361.
- Hyttinen JM, Niittykoski M, Salminen A, Kaarniranta K. Maturation of autophagosomes and endosomes: a key role for Rab7. Biochim Biophys Acta. 2013;1833(3):503–510. doi:https://doi.org/10.1016/j.bbamcr.2012.11.018.
- Gutierrez MG. Rab7 is required for the normal progression of the autophagic pathway in mammalian cells. J Cell Sci. 2004;117(13):2687–2697. doi:https://doi.org/10.1242/jcs.01114.
- Balderhaar HJK, Arlt H, Ostrowicz C, Brocker C, Sundermann F, Brandt R, Babst M, Ungermann C. The Rab GTPase Ypt7 is linked to retromer-mediated receptor recycling and fusion at the yeast late endosome. J Cell Sci. 2010;123(23):4085–4094. doi:https://doi.org/10.1242/jcs.071977.
- Kwon SI, Cho HJ, Jung JH, Yoshimoto K, Shirasu K, Park OK. The Rab GTPase RabG3b functions in autophagy and contributes to tracheary element differentiation in Arabidopsis. Plant J. 2010;64(1):151–164. doi:https://doi.org/10.1111/j.1365-313X.2010.04315.x.
- Kwon SI, Cho HJ, Kim SR, Park OK. The Rab GTPase RabG3b positively regulates autophagy and immunity-associated hypersensitive cell death in Arabidopsis. Plant Physiol. 2013;161(4):1722–1736. doi:https://doi.org/10.1104/pp.112.208108.
- Zeng Y, Li B, Ji C, Feng L, Niu F, Deng C, Chen S, Lin Y, Cheung KCP, Shen J, et al. A unique AtSar1D-AtRabD2a nexus modulates autophagosome biogenesis in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2021;118(17):e2021293118. doi:https://doi.org/10.1073/pnas.2021293118.
- Zeng Y, Jiang L. A unique COPII population in plant autophagy. Autophagy. 2021:1–3. doi:https://doi.org/10.1080/15548627.2021.1933298.
- Yang X, Bassham DC. New insight into the mechanism and function of autophagy in plant cells. Int Rev Cell Mol Biol. 2015;320:1–40. doi:https://doi.org/10.1016/bs.ircmb.2015.07.005.
- Rojo E, Zouhar J, Carter C, Kovaleva V, Raikhel NV. A unique mechanism for protein processing and degradation in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2003;100(12):7389–7394. doi:https://doi.org/10.1073/pnas.1230987100.
- Sze H. Energization of plant cell membranes by H+-Pumping ATPases: regulation and biosynthesis. Plant Cell. 1999;11(4):677–689. doi:https://doi.org/10.1105/tpc.11.4.677.
- Kriegel A, Andres Z, Medzihradszky A, Kruger F, Scholl S, Delang S, Patir-Nebioglu MG, Gute G, Yang H, Murphy AS, et al. Job sharing in the endomembrane system: vacuolar acidification requires the combined activity of V-ATPase and V-PPase. Plant Cell. 2015;27(12):3383–3396. doi:https://doi.org/10.1105/tpc.15.00733.
- Thompson AR, Doelling JH, Suttangkakul A, Vierstra RD. Autophagic nutrient recycling in Arabidopsis directed by the ATG8 and ATG12 conjugation pathways. Plant Physiol. 2005;138(4):2097–2110. doi:https://doi.org/10.1104/pp.105.060673.
- Yu J, Zhou J. Vacuolar accumulation and colocalization is not a proper criterion for cytoplasmic soluble proteins undergoing selective autophagy. Plant Signal Behav. 2021;16(10):1932319. doi:https://doi.org/10.1080/15592324.2021.1932319.
- Slavikova S, Shy G, Yao Y, Glozman R, Levanony H, Pietrokovski S, Elazar Z, Galili G. The autophagy-associated Atg8 gene family operates both under favourable growth conditions and under starvation stresses in Arabidopsis plants. J Exp Bot. 2005;56(421):2839–2849. doi:https://doi.org/10.1093/jxb/eri276.
- Inoue Y, Suzuki T, Hattori M, Yoshimoto K, Ohsumi Y, Moriyasu Y. AtATG genes, homologs of yeast autophagy genes, are involved in constitutive autophagy in Arabidopsis root tip cells. Plant Cell Physiol. 2006;47(12):1641–1652. doi:https://doi.org/10.1093/pcp/pcl031.
- Liu Y, Xiong Y, Bassham DC. Autophagy is required for tolerance of drought and salt stress in plants. Autophagy. 2009;5(7):954–963. doi:https://doi.org/10.4161/auto.5.7.9290.
- Hayward AP, Dinesh-Kumar SP. What can plant autophagy do for an innate immune response? Annu Rev Phytopathol. 2011;49:557–576. doi:https://doi.org/10.1146/annurev-phyto-072910-095333.
- Breeze E, Harrison E, McHattie S, Hughes L, Hickman R, Hill C, Kiddle S, Kim YS, Penfold CA, Jenkins D, et al. High-resolution temporal profiling of transcripts during Arabidopsis leaf senescence reveals a distinct chronology of processes and regulation. Plant Cell. 2011;23(3):873–894. doi:https://doi.org/10.1105/tpc.111.083345.
- Ren C, Liu J, Gong Q. Functions of autophagy in plant carbon and nitrogen metabolism. Front Plant Sci. 2014;5:301. doi:https://doi.org/10.3389/fpls.2014.00301.
- Yang C, Luo M, Zhuang X, Li F, Gao C. Transcriptional and epigenetic regulation of autophagy in plants. Trends Genet. 2020;36(9):676–688. doi:https://doi.org/10.1016/j.tig.2020.06.013.
- Smith AM, Stitt M. Coordination of carbon supply and plant growth. Plant Cell Environ. 2007;30(9):1126–1149. doi:https://doi.org/10.1111/j.1365-3040.2007.01708.x.
- Wang Y, Yu B, Zhao J, Guo J, Li Y, Han S, Huang L, Du Y, Hong Y, Tang D, et al. Autophagy contributes to leaf starch degradation. Plant Cell. 2013;25(4):1383–1399. doi:https://doi.org/10.1105/tpc.112.108993.
- Izumi M, Hidema J, Makino A, Ishida H. Autophagy contributes to nighttime energy availability for growth in Arabidopsis. Plant Physiol. 2013;161(4):1682–1693. doi:https://doi.org/10.1104/pp.113.215632.
- Araujo WL, Tohge T, Ishizaki K, Leaver CJ, Fernie AR. Protein degradation - an alternative respiratory substrate for stressed plants. Trends Plant Sci. 2011;16(9):489–498. doi:https://doi.org/10.1016/j.tplants.2011.05.008.
- Kurusu T, Koyano T, Hanamata S, Kubo T, Noguchi Y, Yagi C, Nagata N, Yamamoto T, Ohnishi T, Okazaki Y, et al. OsATG7 is required for autophagy-dependent lipid metabolism in rice postmeiotic anther development. Autophagy. 2014;10(5):878–888. doi:https://doi.org/10.4161/auto.28279.
- Fan J, Yu L, Xu C. Dual role for autophagy in lipid metabolism in Arabidopsis. Plant Cell. 2019;31(7):1598–1613. doi:https://doi.org/10.1105/tpc.19.00170.
- Barros JAS, Magen S, Lapidot-Cohen T, Rosental L, Brotman Y, Araujo WL, Avin-Wittenberg T. Autophagy is required for lipid homeostasis during dark-induced senescence. Plant Physiol. 2021;185(4):1542–1558. doi:https://doi.org/10.1093/plphys/kiaa120.
- Izumi M, Hidema J, Ishida H. Deficiency of autophagy leads to significant changes of metabolic profiles in Arabidopsis. Plant Signal Behav. 2013;8(8):e25023. doi:https://doi.org/10.4161/psb.25023.
- Avin-Wittenberg T, Bajdzienko K, Wittenberg G, Alseekh S, Tohge T, Bock R, Giavalisco P, Fernie AR. Global analysis of the role of autophagy in cellular metabolism and energy homeostasis in Arabidopsis seedlings under carbon starvation. Plant Cell. 2015;27(2):306–322. doi:https://doi.org/10.1105/tpc.114.134205.
- Thirumalaikumar VP, Wagner M, Balazadeh S, Skirycz A. Autophagy is responsible for the accumulation of proteogenic dipeptides in response to heat stress in Arabidopsis thaliana. FEBS J. 2021;288(1):281–292. doi:https://doi.org/10.1111/febs.15336.
- McLoughlin F, Augustine RC, Marshall RS, Li F, Kirkpatrick LD, Otegui MS, Vierstra RD. Maize multi-omics reveal roles for autophagic recycling in proteome remodelling and lipid turnover. Nat Plants. 2018;4(12):1056–1070. doi:https://doi.org/10.1038/s41477-018-0299-2.
- McLoughlin F, Marshall RS, Ding X, Chatt EC, Kirkpatrick LD, Augustine RC, Li F, Otegui MS, Vierstra RD. Autophagy plays prominent roles in amino acid, nucleotide, and carbohydrate metabolism during fixed-carbon starvation in maize. Plant Cell. 2020;32(9):2699–2724. doi:https://doi.org/10.1105/tpc.20.00226.
- Osmond MB. Effects of nitrogen nutrition on nitrogen partitioning between chloroplasts and mitochondria in pea and wheat. Plant Physiol. 1991;96(2):355–362. doi:https://doi.org/10.1104/pp.96.2.355.
- Guiboileau A, Yoshimoto K, Soulay F, Bataille MP, Avice JC, Masclaux-Daubresse C. Autophagy machinery controls nitrogen remobilization at the whole-plant level under both limiting and ample nitrate conditions in Arabidopsis. New Phytol. 2012;194(3):732–740. doi:https://doi.org/10.1111/j.1469-8137.2012.04084.x.
- Guiboileau A, Avila-Ospina L, Yoshimoto K, Soulay F, Azzopardi M, Marmagne A, Lothier J, Masclaux-Daubresse C. Physiological and metabolic consequences of autophagy deficiency for the management of nitrogen and protein resources in Arabidopsis leaves depending on nitrate availability. New Phytol. 2013;199(3):683–694. doi:https://doi.org/10.1111/nph.12307.
- Wada S, Hayashida Y, Izumi M, Kurusu T, Hanamata S, Kanno K, Kojima S, Yamaya T, Kuchitsu K, Makino A, et al. Autophagy supports biomass production and nitrogen use efficiency at the vegetative stage in rice. Plant Physiol. 2015;168(1):60–73. doi:https://doi.org/10.1104/pp.15.00242.
- Xia T, Xiao D, Liu D, Chai W, Gong Q, Wang NN. Heterologous expression of ATG8c from soybean confers tolerance to nitrogen deficiency and increases yield in Arabidopsis. PloS One. 2012;7(5):e37217. doi:https://doi.org/10.1371/journal.pone.0037217.
- Chen Q, Soulay F, Saudemont B, Elmayan T, Marmagne A, Masclaux-Daubresse CL. Overexpression of ATG8 in Arabidopsis stimulates autophagic activity and increases nitrogen remobilization efficiency and grain filling. Plant Cell Physiol. 2019;60(2):343–352. doi:https://doi.org/10.1093/pcp/pcy214.
- Phillips AR, Suttangkakul A, Vierstra RD. The ATG12-conjugating enzyme ATG10 is essential for autophagic vesicle formation in Arabidopsis thaliana. Genetics. 2008;178(3):1339–1353. doi:https://doi.org/10.1534/genetics.107.086199.
- Doelling JH, Walker JM, Friedman EM, Thompson AR, Vierstra RD. The APG8/12-activating enzyme APG7 is required for proper nutrient recycling and senescence in Arabidopsis thaliana. J Biol Chem. 2002;277(36):33105–33114. doi:https://doi.org/10.1074/jbc.M204630200.
- Masclaux-Daubresse C, Clement G, Anne P, Routaboul JM, Guiboileau A, Soulay F, Shirasu K, Yoshimoto K. Stitching together the multiple dimensions of autophagy using metabolomics and transcriptomics reveals impacts on metabolism, development, and plant responses to the environment in Arabidopsis. Plant Cell. 2014;26(5):1857–1877. doi:https://doi.org/10.1105/tpc.114.124677.
- Tegeder M, Rentsch D. Uptake and partitioning of amino acids and peptides. Mol Plant. 2010;3(6):997–1011. doi:https://doi.org/10.1093/mp/ssq047.
- Hillmer S, Movafeghi A, Robinson DG, Hinz G. Vacuolar storage proteins are sorted in the cis-cisternae of the pea cotyledon Golgi apparatus. J Cell Biol. 2001;152(1):41–50. doi:https://doi.org/10.1083/jcb.152.1.41.
- Ibl V, Stoger E. The formation, function and fate of protein storage compartments in seeds. Protoplasma. 2012;249(2):379–392. doi:https://doi.org/10.1007/s00709-011-0288-z.
- Chrispeels MJ, Herman EM. Endoplasmic reticulum-derived compartments function in storage and as mediators of vacuolar remodeling via a new type of organelle, precursor protease vesicles. Plant Physiol. 2000;123(4):1227–1233. doi:https://doi.org/10.1104/pp.123.4.1227.
- Bassham DC. Golgi-independent trafficking of macromolecules to the plant vacuole. Adv Bot Res. 2002;38:65–92. doi:https://doi.org/10.1016/S0065-2296(02)38028-5.
- Angelovici R, Fait A, Zhu X, Szymanski J, Feldmesser E, Fernie AR, Galili G. Deciphering transcriptional and metabolic networks associated with lysine metabolism during Arabidopsis seed development. Plant Physiol. 2009;151(4):2058–2072. doi:https://doi.org/10.1104/pp.109.145631.
- Di Berardino J, Marmagne A, Berger A, Yoshimoto K, Cueff G, Chardon F, Masclaux-Daubresse C, Reisdorf-Cren M. Autophagy controls resource allocation and protein storage accumulation in Arabidopsis seeds. J Exp Bot. 2018;69(6):1403–1414. doi:https://doi.org/10.1093/jxb/ery012.
- Chung T, Suttangkakul A, Vierstra RD. The ATG autophagic conjugation system in maize: ATG transcripts and abundance of the ATG8-lipid adduct are regulated by development and nutrient availability. Plant Physiol. 2009;149(1):220–234. doi:https://doi.org/10.1104/pp.108.126714.
- Li F, Chung T, Pennington JG, Federico ML, Kaeppler HF, Kaeppler SM, Otegui MS, Vierstra RD. Autophagic recycling plays a central role in maize nitrogen remobilization. Plant Cell. 2015;27(5):1389–1408. doi:https://doi.org/10.1105/tpc.15.00158.
- Honig A, Avin-Wittenberg T, Ufaz S, Galili G. A new type of compartment, defined by plant-specific Atg8-interacting proteins, is induced upon exposure of Arabidopsis plants to carbon starvation. Plant Cell. 2012;24(1):288–303. doi:https://doi.org/10.1105/tpc.111.093112.
- Xiong Y, Contento AL, Bassham DC. AtATG18a is required for the formation of autophagosomes during nutrient stress and senescence in Arabidopsis thaliana. Plant J. 2005;42(4):535–546. doi:https://doi.org/10.1111/j.1365-313X.2005.02397.x.
- Lee TA, Vande Wetering SW, Brusslan JA. Stromal protein degradation is incomplete in Arabidopsis thaliana autophagy mutants undergoing natural senescence. BMC Res Notes. 2013;6:17. doi:https://doi.org/10.1186/1756-0500-6-17.
- Kwon SI, Cho HJ, Park OK. Role of Arabidopsis RabG3b and autophagy in tracheary element differentiation. Autophagy. 2010;6(8):1187–1189. doi:https://doi.org/10.4161/auto.6.8.13429.
- Huang L, Yu LJ, Zhang X, Fan B, Wang FZ, Dai YS, Qi H, Zhou Y, Xie LJ, Xiao S. Autophagy regulates glucose-mediated root meristem activity by modulating ROS production in Arabidopsis. Autophagy. 2019;15(3):407–422. doi:https://doi.org/10.1080/15548627.2018.1520547.
- Zhang Y, Li S, Zhou LZ, Fox E, Pao J, Sun W, Zhou C, McCormick S. Overexpression of Arabidopsis thaliana PTEN caused accumulation of autophagic bodies in pollen tubes by disrupting phosphatidylinositol 3-phosphate dynamics. Plant J. 2011;68(6):1081–1092. doi:https://doi.org/10.1111/j.1365-313X.2011.04761.x.
- Fujiki Y, Yoshimoto K, Ohsumi Y. An Arabidopsis homolog of yeast ATG6/VPS30 is essential for pollen germination. Plant Physiol. 2007;143(3):1132–1139. doi:https://doi.org/10.1104/pp.106.093864.
- Harrison-Lowe NJ, Olsen LJ. Autophagy protein 6 (ATG6) is required for pollen germination in Arabidopsis thaliana. Autophagy. 2008;4(3):339–348. doi:https://doi.org/10.4161/auto.5629.
- Wang WY, Zhang L, Xing S, Ma Z, Liu J, Gu H, Qin G, Qu LJ. Arabidopsis AtVPS15 plays essential roles in pollen germination possibly by interacting with AtVPS34. J Genet Genomics. 2012;39(2):81–92. doi:https://doi.org/10.1016/j.jgg.2012.01.002.
- Qin G, Ma Z, Zhang L, Xing S, Hou X, Deng J, Liu J, Chen Z, Qu LJ, Gu H. Arabidopsis AtBECLIN 1/AtAtg6/AtVps30 is essential for pollen germination and plant development. Cell Res. 2007;17(3):249–263. doi:https://doi.org/10.1038/cr.2007.7.
- Hanamata S, Sawada J, Ono S, Ogawa K, Fukunaga T, Nonomura KI, Kimura S, Kurusu T, Kuchitsu K. Impact of autophagy on gene expression and tapetal programmed cell death during pollen development in rice. Front Plant Sci. 2020;11:172. doi:https://doi.org/10.3389/fpls.2020.00172.
- Dundar G, Shao Z, Higashitani N, Kikuta M, Izumi M, Higashitani A. Autophagy mitigates high-temperature injury in pollen development of Arabidopsis thaliana. Dev Biol. 2019;456(2):190–200. doi:https://doi.org/10.1016/j.ydbio.2019.08.018.
- Zhao P, Zhou XM, Zhao LL, Cheung AY, Sun MX. Autophagy-mediated compartmental cytoplasmic deletion is essential for tobacco pollen germination and male fertility. Autophagy. 2020;16(12):2180–2192. doi:https://doi.org/10.1080/15548627.2020.1719722.
- Hanamata S, Kurusu T, Kuchitsu K. Roles of autophagy in male reproductive development in plants. Front Plant Sci. 2014;5:457. doi:https://doi.org/10.3389/fpls.2014.00457.
- Norizuki T, Minamino N, Ueda T. Role of autophagy in male reproductive processes in land plants. Front Plant Sci. 2020;11:756. doi:https://doi.org/10.3389/fpls.2020.00756.
- Jones JDG, Dangl JL. The plant immune system. Nature. 2006;444(7117):323–329. doi:https://doi.org/10.1038/nature05286.
- Dodds PN, Rathjen JP. Plant immunity: towards an integrated view of plant–pathogen interactions. Nat Rev Genet. 2010;11(8):539–548. doi:https://doi.org/10.1038/nrg2812.
- Liu Y, Bassham DC. Autophagy: pathways for self-eating in plant cells. Annu Rev Plant Biol. 2012;63:215–237. doi:https://doi.org/10.1146/annurev-arplant-042811-105441.
- Liu Y, Schiff M, Czymmek K, Talloczy Z, Levine B, Dinesh-Kumar SP. Autophagy regulates programmed cell death during the plant innate immune response. Cell. 2005;121(4):567–577. doi:https://doi.org/10.1016/j.cell.2005.03.007.
- Patel S, Dinesh-Kumar SP. Arabidopsis ATG6 is required to limit the pathogen-associated cell death response. Autophagy. 2008;4(1):20–27. doi:https://doi.org/10.4161/auto.5056.
- Hofius D, Schultz-Larsen T, Joensen J, Tsitsigiannis DI, Petersen NH, Mattsson O, Jorgensen LB, Jones JD, Mundy J, Petersen M. Autophagic components contribute to hypersensitive cell death in Arabidopsis. Cell. 2009;137(4):773–783. doi:https://doi.org/10.1016/j.cell.2009.02.036.
- Hofius D, Mundy J, Petersen M. Self-consuming innate immunity in Arabidopsis. Autophagy. 2009;5(8):1206–1207. doi:https://doi.org/10.4161/auto.5.8.9892.
- Lenz HD, Haller E, Melzer E, Kober K, Wurster K, Stahl M, Bassham DC, Vierstra RD, Parker JE, Bautor J, et al. Autophagy differentially controls plant basal immunity to biotrophic and necrotrophic pathogens. Plant J. 2011;66(5):818–830. doi:https://doi.org/10.1111/j.1365-313X.2011.04546.x.
- Lenz HD, Vierstra RD, Nürnberger T, Gust AA. ATG7 contributes to plant basal immunity towards fungal infection. Plant Signal Behav. 2011;6(7):1040–1042. doi:https://doi.org/10.4161/psb.6.7.15605.
- Li Y, Kabbage M, Liu W, Dickman MB. Aspartyl protease-mediated cleavage of BAG6 is necessary for autophagy and fungal resistance in plants. Plant Cell. 2016;28(1):233–247. doi:https://doi.org/10.1105/tpc.15.00626.
- Henry E, Fung N, Liu J, Drakakaki G, Coaker G. Beyond glycolysis: gAPDHs are multi-functional enzymes involved in regulation of ROS, autophagy, and plant immune responses. PLoS Genet. 2015;11(4):e1005199. doi:https://doi.org/10.1371/journal.pgen.1005199.
- Han S, Wang Y, Zheng X, Jia Q, Zhao J, Bai F, Hong Y, Liu Y. Cytoplastic glyceraldehyde-3-phosphate dehydrogenases interact with ATG3 to negatively regulate autophagy and immunity in Nicotiana benthamiana. Plant Cell. 2015;27(4):1316–1331. doi:https://doi.org/10.1105/tpc.114.134692.
- Zhang B, Shao L, Wang J, Zhang Y, Guo X, Peng Y, Cao Y, Lai Z. Phosphorylation of ATG18a by BAK1 suppresses autophagy and attenuates plant resistance against necrotrophic pathogens. Autophagy. 2020;1–18. doi:https://doi.org/10.1080/15548627.2020.1810426.
- Brillada C, Teh OK, Ditengou FA, Lee CW, Klecker T, Saeed B, Furlan G, Zietz M, Hause G, Eschen-Lippold L, et al. Exocyst subunit Exo70B2 is linked to immune signaling and autophagy. Plant Cell. 2021;33(2):404–419. doi:https://doi.org/10.1093/plcell/koaa022.
- Koornneef A, Pieterse CM. Cross talk in defense signaling. Plant Physiol. 2008;146(3):839–844. doi:https://doi.org/10.1104/pp.107.112029.
- Spoel SH, Dong X. Making sense of hormone crosstalk during plant immune responses. Cell Host Microbe. 2008;3(6):348–351. doi:https://doi.org/10.1016/j.chom.2008.05.009.
- De Vleesschauwer D, Xu J, Hofte M. Making sense of hormone-mediated defense networking: from rice to Arabidopsis. Front Plant Sci. 2014;5:611. doi:https://doi.org/10.3389/fpls.2014.00611.
- Yoshimoto K, Jikumaru Y, Kamiya Y, Kusano M, Consonni C, Panstruga R, Ohsumi Y, Shirasu K. Autophagy negatively regulates cell death by controlling NPR1-dependent salicylic acid signaling during senescence and the innate immune response in Arabidopsis. Plant Cell. 2009;21(9):2914–2927. doi:https://doi.org/10.1105/tpc.109.068635.
- Wang Y, Nishimura MT, Zhao T, Tang D. ATG2, an autophagy-related protein, negatively affects powdery mildew resistance and mildew-induced cell death in Arabidopsis. Plant J. 2011;68(1):74–87. doi:https://doi.org/10.1111/j.1365-313X.2011.04669.x.
- Hofius D, Munch D, Bressendorff S, Mundy J, Petersen M. Role of autophagy in disease resistance and hypersensitive response-associated cell death. Cell Death Differ. 2011;18(8):1257–1262. doi:https://doi.org/10.1038/cdd.2011.43.
- Kim SH, Kwon C, Lee JH, Chung T. Genes for plant autophagy: functions and interactions. Mol Cells. 2012;34(5):413–423. doi:https://doi.org/10.1007/s10059-012-0098-y.
- Lal NK, Thanasuwat B, Chan B, Dinesh-Kumar SP. Pathogens manipulate host autophagy through injected effector proteins. Autophagy. 2020;16(12):2301–2302. doi:https://doi.org/10.1080/15548627.2020.1831816.
- Lal NK, Thanasuwat B, Huang P-j, Cavanaugh KA, Carter A, Michelmore RW, Dinesh-Kumar SP. Phytopathogen effectors use multiple mechanisms to manipulate plant autophagy. Cell Host Microbe. 2020;28(4):558–571.e556. doi:https://doi.org/10.1016/j.chom.2020.07.010.
- Dagdas YF, Khaoula B, Abbas M, Angela CG, Pooja P, Benjamin P, Nadra T, Neftaly CM, Hughes RK, Jan S. An effector of the Irish potato famine pathogen antagonizes a host autophagy cargo receptor. eLife. 2016;14(5):e10856. doi:https://doi.org/10.7554/eLife.10856.
- Maqbool A, Hughes RK, Dagdas YF, Tregidgo N, Zess E, Belhaj K, Round A, Bozkurt TO, Kamoun S, Banfield MJ. Structural basis of host autophagy-related protein 8 (ATG8) binding by the Irish potato famine pathogen effector protein PexRD54. J Biol Chem. 2016;291(38):20270–20282. doi:https://doi.org/10.1074/jbc.M116.744995.
- Yang M, Ismayil A, Liu Y. Autophagy in plant-virus interactions. Annual Review of Virology. 2020;7(1):1–17. doi:https://doi.org/10.1146/annurev-virology-010220-054709.
- Choi Y, Bowman JW, Jung JU. Autophagy during viral infection - a double-edged sword. Nat Rev Microbiol. 2018;16(6):341–354. doi:https://doi.org/10.1038/s41579-018-0003-6.
- Gorovits R, Moshe A, Ghanim M, Czosnek H. Degradation mechanisms of the Tomato yellow leaf curl virus coat protein following inoculation of tomato plants by the whitefly Bemisia tabaci. Pest Manag Sci. 2014;70(10):1632–1639. doi:https://doi.org/10.1002/ps.3737.
- Gorovits R, Fridman L, Kolot M, Rotem O, Ghanim M, Shriki O, Czosnek H. Tomato yellow leaf curl virus confronts host degradation by sheltering in small/midsized protein aggregates. Virus Res. 2016;213:304–313. doi:https://doi.org/10.1016/j.virusres.2015.11.020.
- Haxim Y, Ismayil A, Qi J, Yan W, Liu Y. Autophagy functions as an antiviral mechanism against geminiviruses in plants. eLife. 2017;6:e23897. doi:https://doi.org/10.7554/eLife.23897.
- Hafrén A, Macia JL, Love AJ, Milner JJ, Drucker M, Hofius D. Selective autophagy limits cauliflower mosaic virus infection by NBR1-mediated targeting of viral capsid protein and particles. Proc Natl Acad Sci U S A. 2017;114(10):E2026–E2035. doi:https://doi.org/10.1073/pnas.1610687114.
- Li F, Zhang M, Zhang C, Zhou X. Nuclear autophagy degrades a geminivirus nuclear protein to restrict viral infection in solanaceous plants. New Phytol. 2020;225(4):1746–1761. doi:https://doi.org/10.1111/nph.16268.
- Yang M, Zhang Y, Xie X, Yue N, Li J, Wang XB, Han C, Yu J, Liu Y, Li D. Barley stripe mosaic virus γb protein subverts autophagy to promote viral infection by disrupting the ATG7-ATG8 interaction. Plant Cell. 2018;30(7):1582–1595. doi:https://doi.org/10.1105/tpc.18.00122.
- Hafren A, Ustun S, Hochmuth A, Svenning S, Johansen T, Hofius D. Turnip mosaic virus counteracts selective autophagy of the viral silencing suppressor HCpro. Plant Physiol. 2018;176(1):649–662. doi:https://doi.org/10.1104/pp.17.01198.
- Li F, Zhang C, Li Y, Wu G, Hou X, Zhou X, Wang A. Beclin1 restricts RNA virus infection in plants through suppression and degradation of the viral polymerase. Nat Commun. 2018;9(1):1268. doi:https://doi.org/10.1038/s41467-018-03658-2.
- Fu S, Xu Y, Li C, Li Y, Wu J, Zhou X. Rice stripe virus interferes with S-acylation of remorin and induces its autophagic degradation to facilitate virus infection. Mol Plant. 2018;11(2):269–287. doi:https://doi.org/10.1016/j.molp.2017.11.011.
- Xiong Y, Contento AL, Nguyen PQ, Bassham DC. Degradation of oxidized proteins by autophagy during oxidative stress in Arabidopsis. Plant Physiol. 2007;143(1):291–299. doi:https://doi.org/10.1104/pp.106.092106.
- Zhou J, Wang J, Cheng Y, Chi YJ, Fan B, Yu JQ, Chen Z. NBR1-mediated selective autophagy targets insoluble ubiquitinated protein aggregates in plant stress responses. PLoS Genet. 2013;9(1):e1003196. doi:https://doi.org/10.1371/journal.pgen.1003196.
- Gassmann W, Zhou J, Zhang Y, Qi J, Chi Y, Fan B, Yu JQ, Chen Z. E3 ubiquitin ligase CHIP and NBR1-mediated selective autophagy protect additively against proteotoxicity in plant stress responses. PLoS Genet. 2014;10(1):e1004116. doi:https://doi.org/10.1371/journal.pgen.1004116.
- Kuzuoglu-Ozturk D, Cebeci Yalcinkaya O, Akpinar BA, Mitou G, Korkmaz G, Gozuacik D, Budak H. Autophagy-related gene, TdAtg8, in wild emmer wheat plays a role in drought and osmotic stress response. Planta. 2012;236(4):1081–1092. doi:https://doi.org/10.1007/s00425-012-1657-3.
- Pei D, Zhang W, Sun H, Wei X, Yue J, Wang H. 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. Plant Cell Rep. 2014;33(10):1697–1710. doi:https://doi.org/10.1007/s00299-014-1648-x.
- Mahajan S, Tuteja N. Cold, salinity and drought stresses: an overview. Arch Biochem Biophys. 2005;444(2):139–158. doi:https://doi.org/10.1016/j.abb.2005.10.018.
- Leshem Y, Seri L, Levine A. Induction of phosphatidylinositol 3-kinase-mediated endocytosis by salt stress leads to intracellular production of reactive oxygen species and salt tolerance. Plant J. 2007;51(2):185–197. doi:https://doi.org/10.1111/j.1365-313X.2007.03134.x.
- Slavikova S, Ufaz S, Avin-Wittenberg T, Levanony H, Galili G. An autophagy-associated Atg8 protein is involved in the responses of Arabidopsis seedlings to hormonal controls and abiotic stresses. J Exp Bot. 2008;59(14):4029–4043. doi:https://doi.org/10.1093/jxb/ern244.
- Shin JH, Yoshimoto K, Ohsumi Y, Jeon JS, An G. OsATG10b, an autophagosome component, is needed for cell survival against oxidative stresses in rice. Mol Cells. 2009;27(1):67–74. doi:https://doi.org/10.1007/s10059-009-0006-2.
- Luo L, Zhang P, Zhu R, Fu J, Su J, Zheng J, Wang Z, Wang D, Gong Q. Autophagy is rapidly induced by salt stress and is required for salt tolerance in Arabidopsis. Front Plant Sci. 2017;8:1459. doi:https://doi.org/10.3389/fpls.2017.01459.
- Sung DY, Kaplan F, Lee KJ, Guy CL. Acquired tolerance to temperature extremes. Trends Plant Sci. 2003;8(4):179–187. doi:https://doi.org/10.1016/s1360-1385(.03)00047-5.
- Zhou J, Wang J, Yu JQ, Chen Z. Role and regulation of autophagy in heat stress responses of tomato plants. Front Plant Sci. 2014;5:174. doi:https://doi.org/10.3389/fpls.2014.00174.
- Sedaghatmehr M, Thirumalaikumar VP, Kamranfar I, Marmagne A, Masclaux-Daubresse C, Balazadeh S. A regulatory role of autophagy for resetting the memory of heat stress in plants. Plant Cell Environ. 2019;42(3):1054–1064. doi:https://doi.org/10.1111/pce.13426.
- Jiang Z, Zhu L, Wang Q, Hou X. Autophagy-related 2 regulates chlorophyll degradation under abiotic stress conditions in Arabidopsis. Int J Mol Sci. 2020;21(12):4515. doi:https://doi.org/10.3390/ijms21124515.
- Zhang Y, Min H, Shi C, Xia G, Lai Z. Transcriptome analysis of the role of autophagy in plant response to heat stress. PLoS One. 2021;16(2):e0247783. doi:https://doi.org/10.1371/journal.pone.0247783.
- Ron D, Walter P. Signal integration in the endoplasmic reticulum unfolded protein response. Nat Rev Mol Cell Biol. 2007;8(7):519–529. doi:https://doi.org/10.1038/nrm2199.
- Minina EA, Moschou PN, Vetukuri RR, Sanchez-Vera V, Cardoso C, Liu Q, Elander PH, Dalman K, Beganovic M, Lindberg Yilmaz J, et al. Transcriptional stimulation of rate-limiting components of the autophagic pathway improves plant fitness. J Exp Bot. 2018;69(6):1415–1432. doi:https://doi.org/10.1093/jxb/ery010.
- Kroemer G, Marino G, Levine B. Autophagy and the integrated stress response. Mol Cell. 2010;40(2):280–293. doi:https://doi.org/10.1016/j.molcel.2010.09.023.
- Chen L, Liao B, Qi H, Xie LJ, Huang L, Tan WJ, Zhai N, Yuan LB, Zhou Y, Yu LJ, et al. Autophagy contributes to regulation of the hypoxia response during submergence in Arabidopsis thaliana. Autophagy. 2015;11(12):2233–2246. doi:https://doi.org/10.1080/15548627.2015.1112483.
- Yamauchi S, Mano S, Oikawa K, Hikino K, Teshima KM, Kimori Y, Nishimura M, Shimazaki KI, Takemiya A. Autophagy controls reactive oxygen species homeostasis in guard cells that is essential for stomatal opening. Proc Natl Acad Sci U S A. 2019;116(38):19187–19192. doi:https://doi.org/10.1073/pnas.1910886116.
- Luo S, Li X, Zhang Y, Fu Y, Fan B, Zhu C, Chen Z. Cargo recognition and function of selective autophagy receptors in plants. Int J Mol Sci. 2021;22(3):1013. doi:https://doi.org/10.3390/ijms22031013.
- Noda NN, Ohsumi Y, Inagaki F. Atg8-family interacting motif crucial for selective autophagy. FEBS Lett. 2010;584(7):1379–1385. doi:https://doi.org/10.1016/j.febslet.2010.01.018.
- Marshall RS, Li F, Gemperline DC, Book AJ, Vierstra RD. Autophagic degradation of the 26s proteasome is mediated by the dual ATG8/ubiquitin receptor RPN10 in Arabidopsis. Mol Cell. 2015;58(6):1053–1066. doi:https://doi.org/10.1016/j.molcel.2015.04.023.
- Marshall RS, Hua Z, Mali S, McLoughlin F, Vierstra RD. ATG8-binding UIM proteins define a new class of autophagy adaptors and receptors. Cell. 2019;177(3):766–781. doi:https://doi.org/10.1016/j.cell.2019.02.009.
- Li X, Liu Q, Feng H, Deng J, Zhang R, Wen J, Dong J, Wang T. Dehydrin MtCAS31 promotes autophagic degradation under drought stress. Autophagy. 2019;16(5):862–877. doi:https://doi.org/10.1080/15548627.2019.1643656.
- Bao Y, Song WM, Wang P, Yu X, Bassham DC. COST1 regulates autophagy to control plant drought tolerance. Proc Natl Acad Sci U S A. 2020;117(13):7482–7493. doi:https://doi.org/10.1073/pnas.1918539117.
- Nolan TM, Brennan B, Yang M, Chen J, Zhang M, Li Z, Wang X, Bassham DC, Walley J, Yin Y. Selective autophagy of BES1 mediated by DSK2 balances plant growth and survival. Dev Cell. 2017;41(1):33–46. doi:https://doi.org/10.1016/j.devcel.2017.03.013.
- Guillaumot D, Guillon S, Deplanque T, Vanhee C, Gumy C, Masquelier D, Morsomme P, Batoko H. The Arabidopsis TSPO-related protein is a stress and abscisic acid-regulated, endoplasmic reticulum-Golgi-localized membrane protein. Plant J. 2009;60(2):242–256. doi:https://doi.org/10.1111/j.1365-313X.2009.03950.x.
- Balsemão-Pires E, Jaillais Y, Olson BJ, Andrade LR, Umen JG, Chory J, Sachetto-Martins G. The Arabidopsis translocator protein (AtTSPO) is regulated at multiple levels in response to salt stress and perturbations in tetrapyrrole metabolism. BMC Plant Biol. 2011;11(1):1–17. doi:https://doi.org/10.1186/1471-2229-11-108.
- Vanhee C, Zapotoczny G, Masquelier D, Ghislain M, Batoko H. The Arabidopsis multistress regulator TSPO is a heme binding membrane protein and a potential scavenger of porphyrins via an autophagy-dependent degradation mechanism. Plant Cell. 2011;23(2):785–805. doi:https://doi.org/10.1105/tpc.110.081570.
- Michaeli S, Honig A, Levanony H, Peled-Zehavi H, Galili G. Arabidopsis ATG8-INTERACTING PROTEIN1 is involved in autophagy-dependent vesicular trafficking of plastid proteins to the vacuole. Plant Cell. 2014;26(10):4084–4101. doi:https://doi.org/10.1105/tpc.114.129999.
- Zhou J, Wang Z, Wang X, Li X, Zhang Z, Fan B, Zhu C, Chen Z. Dicot-specific ATG8-interacting ATI3 proteins interact with conserved UBAC2 proteins and play critical roles in plant stress responses. Autophagy. 2018;14(3):487–504. doi:https://doi.org/10.1080/15548627.2017.1422856.
- Thirumalaikumar VP, Gorka M, Schulz K, Masclaux-Daubresse C, Sampathkumar A, Skirycz A, Vierstra RD, Balazadeh S. Selective autophagy regulates heat stress memory in Arabidopsis by NBR1-mediated targeting of HSP90 and ROF1. Autophagy. 2020;1–16. doi:https://doi.org/10.1080/15548627.2020.1820778. Online ahead of print.
- Chi C, Li X, Fang P, Xia X, Shi K, Zhou Y, Zhou J, Yu J. Brassinosteroids act as a positive regulator of NBR1-dependent selective autophagy in response to chilling stress in tomato. J Exp Bot. 2020;71(3):1092–1106. doi:https://doi.org/10.1093/jxb/erz466.
- Su W, Bao Y, Lu Y, He F, Liu C. Poplar autophagy receptor NBR1 enhances salt stress tolerance by regulating selective autophagy and antioxidant system. Front Plant Sci. 2021;11:568411. doi:https://doi.org/10.3389/fpls.2020.568411.
- Zhang Y, Chen Z. Broad and complex roles of NBR1-mediated selective autophagy in plant stress responses. Cells. 2020;9(12):2562. doi:https://doi.org/10.3390/cells9122562.
- Luo S, Li X, Zhang Y, Fu Y, Fan B, Zhu C, Chen Z. Cargo recognition and function of selective autophagy receptors in plants. Int J Mol Sci. 2021;22(3):1013. doi:https://doi.org/10.3390/ijms22031013.
- Qi H, Xia FN, Xiao S. Autophagy in plants: physiological roles and post-translational regulation. J Integr Plant Biol. 2021;63(1):161–179. doi:https://doi.org/10.1111/jipb.12941.