the GSK3/SHAGGY-like kinase OsGSK3 to modulate brassinosteroid signaling. *Plant Cell*. 2019b:31(5):1077-1093. https://doi.org/10.1105/tpc.18.00836

García-Lorenzo M, Sjödin A, Jansson S, Funk C. Protease gene families in Populus and Arabidopsis. BMC Plant Biol. 2006:6:30. https://doi.org/10.1186/1471-2229-6-30

Garcia-Leon M, Cuyas L, El Moneim DA, Rodriguez L, Belda-Palazon B, Sanchez-Quant E, Fernandez Y, Roux B, Zamarreno AM, Garcia-Mina JM, et al. Arabidopsis ALIX regulates stomatal aperture and turnover of abscisic acid receptors. *Plant Cell*. 2019: 31(10):2411-2429. https://doi.org/10.1105/tpc.19.00399

Garcia-Molina A, Pastor V. Systemic analysis of metabolome reconfiguration in Arabidopsis after abiotic stressors uncovers metabolites that modulate defense against pathogens. *Plant Comm.* 2023:5(1):100645. https://doi.org/10.1016/j.xplc.2023.100645

Garland T. Trade-offs. Curr Biol. 2014:24(2):R60-R61. https://doi.org/10.1016/j.cub.2013.11.036

Garzón M, Eifler K, Faust A, Scheel H, Hofmann K, Koncz C, Yephremov A, Bachmair A. PRT6/At5g02310 encodes an Arabidopsis ubiquitin ligase of the N-end rule pathway with arginine specificity and is not the CER3 locus. FEBS Lett. 2007:581(17): 3189-3196. https://doi.org/10.1016/j.febslet.2007.06.005

Genschik P, Marrocco K, Bach L, Noir S, Criqui MC. Selective protein degradation: a rheostat to modulate cell-cycle phase transitions. *J Exp Bot*. 2014:65(10):2603-2615. https://doi.org/10.1093/jxb/ert426

Gentric N, Masoud K, Journot RP, Cognat V, Chabouté ME, Noir S, Genschik P. The f-box-like protein FBL17 is a regulator of DNA-damage response and colocalizes with RETINOBLASTOMA RELATED1 at DNA lesion sites. *Plant Physiol.* 2020:183(3): 1295-1305. https://doi.org/10.1104/pp.20.00188

Ghifari AS, Huang S, Murcha MW. The peptidases involved in plant mitochondrial protein import. *J Exp Bot*. 2019:70(21):6005-6018. https://doi.org/10.1093/jxb/erz365

Ghifari AS, Ivanova A, Berkowitz O, Whelan J, Murcha MW. FTSH PROTEASE 3 facilitates complex I degradation through a direct interaction with the complex I subunit PSST. *Plant Cell*. 2023a:35(8): 3092-3108. https://doi.org/10.1093/plcell/koad128

Ghifari AS, Murcha MW. Proteolytic regulation of mitochondrial oxidative phosphorylation components in plants. *Biochem Soci Trans.* 2022:50(3):1119-1132. https://doi.org/10.1042/BST20220195

Ghifari AS, Saha S, Murcha MW. The biogenesis and regulation of the plant oxidative phosphorylation system. *Plant Physiol.* 2023b:192(2):728-747. https://doi.org/10.1093/plphys/kiad108

Ghifari AS, Teixeira PF, Kmiec B, Pružinská A, Glaser E, Murcha MW. A mitochondrial prolyl aminopeptidase PAP2 releases N-terminal proline and regulates proline homeostasis during stress response. *Plant J*. 2020:104(5):1182-1194. https://doi.org/10.1111/tpj.14987

Ghorbani S, Hoogewijs K, Pečenková T, Fernandez A, Inzé A, Eeckhout D, Kawa D, De Jaeger G, Beeckman T, Madder A, et al. The SBT6.1 subtilase processes the GOLVEN1 peptide controlling cell elongation. *J Exp Bot*. 2016:67(16):4877-4887. https://doi.org/10.1093/jxb/erw241

Gibbs DJ. Emerging functions for N-terminal protein acetylation in plants. *Trends Plant Sci.* 2015:20(10):599-601. https://doi.org/10.1016/j.tplants.2015.08.008

Gibbs DJ, Bacardit J, Bachmair A, Holdsworth MJ. The eukaryotic N-end rule pathway: conserved mechanisms and diverse functions. *Trends Cell Biol.* 2014:24(10):603-611. https://doi.org/10.1016/j.tcb.2014.05.001

Gibbs DJ, Bailey M, Etherington RD. A stable start: cotranslational Nt-acetylation promotes proteome stability across kingdoms.

Trends Cell Biol. 2022:32(5):374-376. https://doi.org/10.1016/j.tcb.2022.02.004

Gibbs DJ, Lee SC, Isa NM, Gramuglia S, Fukao T, Bassel GW, Correia CS, Corbineau F, Theodoulou FL, Bailey-Serres J, et al. Homeostatic response to hypoxia is regulated by the N-end rule pathway in plants. *Nature*. 2011:479(7373):415-418. https://doi.org/10.1038/nature10534

Gibbs DJ, Tedds HM, Labandera AM, Bailey M, White MD, Hartman S, Sprigg C, Mogg SL, Osborne R, Dambire C, et al. Oxygen-dependent proteolysis regulates the stability of angiosperm polycomb repressive complex 2 subunit VERNALIZATION 2. *Nat Commun.* 2018:9(1):5438. https://doi.org/10.1038/s41467-018-07875-7

Giglione C, Meinnel T. Evolution-driven versatility of N terminal acetylation in photoautotrophs. *Trends Plant Sci.* 2021:26(4):375-391. https://doi.org/10.1016/j.tplants.2020.11.012

Gilkerson R, De La Torre P, St. Vallier S. Mitochondrial OMA1 and OPA1 as gatekeepers of organellar structure/function and cellular stress response. *Frontiers Cell Devel Biol.* 2021:9:626117. https://doi.org/10.3389/fcell.2021.626117

Ginzburg DN, Bossi F, Rhee SY. Uncoupling differential water usage from drought resistance in a dwarf Arabidopsis mutant. *Plant Physiol.* 2022:190(4):2115-2121. https://doi.org/10.1093/plphys/kiac411

Gladman NP, Marshall RS, Lee K-H, Vierstra RD. The proteasome stress regulon is controlled by a pair of NAC transcription factors in Arabidopsis. *Plant Cell*. 2016:28(6):1279-1296. https://doi.org/10.1105/tpc.15.01022

Glaser E, Eriksson A, Sjöling S, Sjoling S, Sjöling S. Bifunctional role of the bc₁ complex in plants. Mitochondrial bc1 complex catalyses both electron transport and protein processing. *FEBS Lett.* 1994:346(1):83-87. https://doi.org/10.1016/0014-5793(94)00312-2

Gomes F, Palma FR, Barros MH, Tsuchida ET, Turano HG, Alegria TGP, Demasi M, Netto LES. Proteolytic cleavage by the inner membrane peptidase (IMP) complex or Oct1 peptidase controls the localization of the yeast peroxiredoxin Prx1 to distinct mitochondrial compartments. *J Biol Chem.* 2017:292(41):17011-17024. https://doi.org/10.1074/jbc.M117.788588

Gomez-Roldan V, Fermas S, Brewer PB, Puech-Pagès V, Dun EA, Pillot JP, Letisse F, Matusova R, Danoun S, Portais JC, et al. Strigolactone inhibition of shoot branching. *Nature*. 2008:455(7210):189-194. https://doi.org/10.1038/nature07271

Gong X, Huang Y, Liang Y, Yuan Y, Liu Y, Han T, Li S, Gao H, Lv B, Huang X, et al. OsHYPK-mediated protein N-terminal acetylation coordinates plant development and abiotic stress responses in rice. *Mol Plant*. 2022:15(4):740-754. https://doi.org/10.1016/j.molp.2022.03.001

Goslin K, Eschen-Lippold L, Naumann C, Linster E, Sorel M, Klecker M, de Marchi R, Kind A, Wirtz M, Lee J, et al. Differential N-end rule degradation of RIN4/NOI fragments generated by the AvrRpt2 effector protease. *Plant Physiol.* 2019:180(4):2272-2289. https://doi.org/10.1104/pp.19.00251

Graciet E, Mesiti F, Wellmer F. Structure and evolutionary conservation of the plant N-end rule pathway. *Plant J.* 2010:61(5):741-751. https://doi.org/10.1111/j.1365-313X.2009.04099.x

Grimmer J, Helm S, Dobritsch D, Hause G, Shema G, Zahedi RP. Baginsky S mild proteasomal stress improves photosynthetic performance in Arabidopsis chloroplasts. *Nat Commun.* 2020:11(1): 1662. https://doi.org/10.1038/s41467-020-15539-8

Guedes JP, Boyer JB, Elurbide J, Carte B, Redeker V, Sago L, Meinnel T, Côrte-Real M, Giglione C, Aldabe R. NatB-dependent acetylation protects procaspase-8 from UBR4-mediated degradation and is 2 required for full induction of the extrinsic apoptosis pathway.
bioRxiv. 2023. https://doi.org/10.1101/2023.09.25.559278, pre-
print: not peer reviewed.

Guercio AM, Palayam M, Shabek N. Strigolactones: diversity, percep-
tion, and hydrolysis. *Phytochem Rev.* 2023;22(2):339–359. https://
doi.org/10.1007/s11101-023-09853-4

Gully K, Pelletier S, Guillou M-C, Ferrand M, Aligon S, Pokotylo I, Perrin A, Vergne E, Fagard M, Ruelland E, et al. The SCOOP12 peptide regulates defense response and root elongation in *Arabidopsis thaliana*. *J Exp Bot.* 2019;70(4):1349–1365. https://doi.org/10.1093/jxb/ery454

Guo H, Ecker JR. Plant responses to ethylene gas are mediated by SCFEBF1/EBF2-dependent proteolysis of EIN3 transcription factor. *Cell*. 2003;115(6):667–677. https://doi.org/10.1016/S0092-8674(03)00969-3

Gusti A, Baumberger N, Nowack M, Pusch S, Eisler H, Potuschak T, De Veylder L, Schnittger A, Genschik P. The Arabidopsis thaliana F-box protein FBL17 is essential for progression through the second mitosis during pollen development. *PLoS One*. 2009;4(3):e4780. https://doi.org/10.1371/journal.pone.0004780

Gutjahr C, Gobbato E, Choi J, Riemann M, Johnston MG, Summers W, Carbonnel S, Mansfield C, Yang SY, Nadal M, et al. Rice perception of symbiotic arbuscular mycorrhizal fungi requires the karrikin receptor complex. *Science*. 2015;350(6267):1521–1524. https://doi.org/10.1126/science.aac9715

Guzman UH, Aksnes H, Ree R, Krogh N, Jakobsson ME, Jensen LJ, Arnesen T, Olsen JV. Loss of N-terminal acetyltransferase A activity induces thermally unstable ribosomal proteins and increases their turnover in Saccharomyces cerevisiae. *Nat Commun.* 2023;14(1):4517. https://doi.org/10.1038/s41467-023-40224-x

Hachez C, Veljanovski V, Reinhardt H, Guillaumot D, Vanhee C, Chaumont F, Batoko H. The Arabidopsis abiotic stress-induced TSPO-related protein reduces cell-surface expression of the aquaporin PIP2; 7 through protein-protein interactions and auto-phagic degradation. *Plant Cell*. 2014;26(12):4974–4990. https://doi.org/10.1105/tpc.114.134080

Hamiaux C, Drummond RSM, Janssen BJ, Ledger SE, Cooney JM, Newcomb RD, Snowden KC. DAD2 is an α/β hydrolase likely to be involved in the perception of the plant branching hormone, strigolactone. *Curr Biol*. 2012;22(21):2032–2036. https://doi.org/10.1016/j.cub.2012.08.007

Han Y, Watanabe S, Shimada H, Sakamoto A. Dynamics of the leaf endoplasmic reticulum modulate b-glucosidase-mediated stress-activated ABA production from its glucosyl ester. *J Exp Bot.* 2020;71(6):2058–2071. https://doi.org/10.1093/jxb/erz528

Han YF, Zhang CZ, Sha HJ, Wang XJ, Yu Y, Liu J, Zhao GX, Wang JY, Qiu GK, Xu XJ, et al. Ubiquitin-conjugating enzyme affects the development of roots via auxin pathway. *Rice*. 2023;16(1):9. https://doi.org/10.1186/s12284-023-00626-3

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. https://doi.org/10.1104/pp.011024

Harashima H, Dissmeyer N, Schnittger A. Cell cycle control across the eukaryotic kingdom. *Trends Cell Biol.* 2013;23(7):345–356. https://doi.org/10.1016/j.tcb.2013.03.002

Hartung F, Suer S, Knoll A, Wurz-Wildersinn R, Puchta H. Topoisomerase 3alpha and RMI1 suppress somatic crossovers and are essential for resolution of meiotic recombination intermediates in Arabidopsis thaliana. *PLoS Genet.* 2008;4(12):e1000285. https://doi.org/10.1371/journal.pgen.1000285

Hatsugai N, Iwasaki S, Tamura K, Kondo M, Fuji K, Ogasawara K, Nishimura M, Hara-Nishimura I. A novel membrane fusion-

mediated plant immunity against bacterial pathogens. *Genes Dev.* 2009;23(21):2496–2506. https://doi.org/10.1101/gad.1825209

Heidorn-Czarna M, Domanski D, Kwasniak-Owczarek M, Janska H. Targeted proteomics approach toward understanding the role of the mitochondrial protease FTSH4 in the biogenesis of OXPHOS during arabidopsis seed germination. *Front Plant Sci.* 2018;9:1–22. https://doi.org/10.3389/fpls.2018.00821

Heidorn-Czarna M, Maziak A, Janska H. Protein processing in plant mitochondria compared to yeast and mammals. *Front Plant Sci.* 2022;13:824080. https://doi.org/10.3389/fpls.2022.824080

Heo AJ, Ji CH, Kwon YT. The Cys/N-degron pathway in the ubiquitin-proteasome system and autophagy. *Trends Cell Biol.* 2023;33(3):247–259. https://doi.org/10.1016/j.tcb.2022.07.005

Hohl M, Stintzi A, Schaller A. A novel subtilase inhibitor in plants shows structural and functional similarities to protease propeptides. *J Biol Chem.* 2017;292(15):6389–6401. https://doi.org/10.1074/jbc.M117.775445

Holdsworth MJ, Vicente J, Sharma G, Abbas M, Zubrycka A. The plant N-degron pathways of ubiquitin-mediated proteolysis. *J Integr Plant Biol.* 2020;62(1):70–89. https://doi.org/10.1111/jipb.12882

Homma F, Huang J, van der Hoon RAL. AlphaFold-multimer predicts cross-kingdom interactions at the plant-pathogen interface. *Nat Commun.* 2023;14(1):6040. https://doi.org/10.1038/s41467-023-41721-9

Hruz T, Laule O, Szabo G, Wessendorp F, Bleuler S, Oertle L, Widmayer P, Gruissem W, Zimmermann P. Genevestigator v3: a reference expression database for the meta-analysis of transcriptomes. *Adv Bioinformatics.* 2008;2008:420747. https://doi.org/10.1155/2008/420747

Hu Q, He Y, Wang L, Liu S, Meng X, Liu G, Jing Y, Chen M, Song X, Jiang L, et al. DWARF14, a receptor covalently linked with the active form of strigolactones, undergoes strigolactone-dependent degradation in rice. *Front Plant Sci.* 2017;8:1935. https://doi.org/10.3389/fpls.2017.01935

Hu XH, Shen S, Wu JL, Liu J, Wang H, He JX, Yao ZL, Bai YF, Zhang X, Zhu Y, et al. A natural allele of proteasome maturation factor improves rice resistance to multiple pathogens. *Nat Plants.* 2023;9(2):228–237. https://doi.org/10.1038/s41477-022-01327-3

Huang L, Yu L-J, Zhang X, Fan B, Wang F-Z, Dai Y-S, Qi H, Zhou Y, Xie L-J, Xiao S. Autophagy regulates glucose-mediated root meristem activity by modulating ROS production in Arabidopsis. *Autophagy.* 2018;15(3):407–422. https://doi.org/10.1080/15548627.2018.1520547

Huang S, Nelson CJ, Li L, Taylor NL, Ströher E, Petereit J, Millar AH. Intermediate cleavage peptidase 55 modifies enzyme amino termini and alters protein stability in Arabidopsis mitochondria. *Plant Physiol.* 2015;168(2):415–427. https://doi.org/10.1104/pp.15.00300

Huang X, Ouyang X, Yang P, Lau OS, Chen L, Wei N, Deng XW. Conversion from CUL4-based COP1-SPA E3 apparatus to UVR8-COP1-SPA complexes underlies a distinct biochemical function of COP1 under UV-B. *Proc Natl Acad Sci U S A.* 2013;110(41):16669–16674. https://doi.org/10.1073/pnas.1316622110

Huang X, Yang P, Ouyang X, Chen L, Deng XW. Photoactivated UVR8-COP1 module determines photomorphogenic UV-B signaling output in Arabidopsis. *PLoS Genet.* 2014;10(3):e1004218. https://doi.org/10.1371/journal.pgen.1004218

Huber M, Armbruster L, Etherington RD, De La Torre C, Hawkesford MJ, Sticht C, Gibbs DJ, Hell R, Wirtz M. Disruption of the N(alpha)-acetyltransferase NatB causes sensitivity to reductive stress in Arabidopsis thaliana. *Front Plant Sci.* 2021;12:799954. https://doi.org/10.3389/fpls.2021.799954
Huber M, Bienvenut WV, Linster E, Stephan I, Armbruster L, Sticht C, Layer D, Lapouge K, Meinnel T, Sinning I, et al. NatB-mediated N-terminal acetylation affects growth and biotic stress responses. *Plant Physiol.* 2020;182(2):792–806. https://doi.org/10.1104/pp.19.00792

Hugosson M, Andreu D, Boman HG, Glaser E. Antibacterial peptides and mitochondrial presequences affect mitochondrial coupling, respiration and protein import. *Eur J Biochem.* 1994;223(3): 1027–1033. https://doi.org/10.1111/j.1432-1033.1994.tb19081.x

Humbard MA, Surkov S, De Donatis GM, Jenkins LM, Maurizi MR. The N-degradome of Escherichia coli: limited proteolysis in vivo generates a large pool of proteins bearing N-degrons. *J Biol Chem.* 2013;288(40):28913–28924. https://doi.org/10.1074/jbc.M113.492108

Hunter T. The age of crosstalk: phosphorylation, ubiquitination, and beyond. *Mol Cell.* 2007;28(5):730–738. https://doi.org/10.1016/j.molcel.2007.11.019

Huot B, Yao J, Montgomery BL, He SY. Growth-defense tradeoffs in plants: a balancing act to optimize fitness. *Mol Plant.* 2014;7(8): 1267–1287. https://doi.org/10.1093/mp/ssu049

Hwang CS, Shemorry A, Auerbach D, Varshavsky A. The N-end rule pathway is mediated by a complex of the RING-type Ubr1 and HECT-type Ufd4 ubiquitin ligases. *Nat Cell Biol.* 2010;12(12): 1177–1185. https://doi.org/10.1038/ncb2121

Iconomou M, Saunders DN. Systematic approaches to identify E3 ligase substrates. *Biochem J.* 2016;473(22):4083–4101. https://doi.org/10.1042/BCJ20160719

Irigoyen ML, Iniesto E, Rodriguez L, Puga MI, Yanagawa Y, Pick E, Strickland E, Paz-Ares J, Wei N, De Jaeger G, et al. Targeted degradation of abscisic acid receptors is mediated by the ubiquitin ligase substrate adaptor DDA1 in Arabidopsis. *Plant Cell.* 2014;26(2):712–728. https://doi.org/10.1105/tpc.113.122234

Ivanova A, Ghifari AS, Berkowitz O, Whelan J, Murcha MW. The mitochondrial AAA protease FTSH3 regulates complex I abundance by promoting its disassembly. *Plant Physiol.* 2021;186(1):599–610. https://doi.org/10.1093/plphys/kiab074

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. https://doi.org/10.1104/pp.113.215632

Izumi M, Ishida H, Nakamura S, Hidema J. Entire photodamaged chloroplasts are transported to the central vacuole by autophagy. *Plant Cell.* 2017;29(2):377–394. https://doi.org/10.1105/tpc.16.00637

Jamsheer KM, Kumar M, Srivastava V, Lunn J. SNF1-related protein kinase 1: the many-faced signaling hub regulating developmental plasticity in plants. *J Exp Bot.* 2021;72(17):6042–6065. https://doi.org/10.1093/jxb/erab079

Jang IC, Henriques R, Seo HS, Nagatani A, Chua NH. Arabidopsis PHYTOCHROME INTERACTING FACTOR proteins promote phytochrome B polyubiquitination by COP1 E3 ligase in the nucleus. *Plant Cell.* 2010;22(7):2370–2383. https://doi.org/10.1105/tpc.109.072520

Janse van Rensburg HC, Van den Ende W, Signorelli S. Autophagy in plants: both a puppet and a puppet master of sugars. *Front Plant Sci.* 2019;10:14. https://doi.org/10.3389/fpls.2019.00014

Janska H, Piechota J, Kwasniak M. ATP-dependent proteases in biogenesis and maintenance of plant mitochondria. *Biochim Biophys Acta.* 2010;1797(6-7):1071–1075. https://doi.org/10.1016/j.babio.2010.02.027

Janzik I, Macheroux P, Amrhein N, Schaller A. LeSBT1, a subtilase from tomato plants. Overexpression in insect cells, purification

and characterization. *J Biol Chem.* 2000;275(7):5193–5199. https://doi.org/10.1074/jbc.275.7.5193

Jarvis P, López-Juez E. Biogenesis and homeostasis of chloroplasts and other plastids. *Nature Reviews Molec Cell Biol.* 2013;14(12): 787–802. https://doi.org/10.1038/nrm3702

Jeong DE, Lee HS, Ku B, Kim CH, Kim SJ, Shin HC. Insights into the recognition mechanism in the UBR box of UBR4 for its specific substrates. *Commun Biol.* 2023;6(1):1214. https://doi.org/10.1038/s42003-023-05602-7

Jia X, Jia X, Li T, Wang Y, Sun X, Huo L, Wang P, Che R, Gong X, Ma F. MdATG5a induces drought tolerance by improving the antioxidant defenses and promoting starch degradation in apple. *Plant Sci.* 2021;312:111052. https://doi.org/10.1016/j.plantsci.2021.111052

Jiang L, Liu X, Xiong G, Liu H, Chen F, Wang L, Meng X, Liu G, Yu H, Yuan Y, et al. DWARF 53 acts as a repressor of strigolactone signalling in rice. *Nature*. 2013;504(7480):401–405. https://doi.org/10.1038/nature12870

Jin H, Kim R, Bhaya D. Deciphering proteolysis pathways for the error-prone DNA polymerase in cyanobacteria. *Environ Microbiol.* 2021;2(2):559–571. https://doi.org/10.1111/1462-2920.14911

Julian J, Coego A, Lozano-Juste J, Lechner E, Wu Q, Zhang X, Merilo E, Belda-Palazon B, Park SY, Cutler SR, et al. The MATH-BTB BPM3 and BPM5 subunits of Cullin3-RING E3 ubiquitin ligases target PP2CA and other clade A PP2Cs for degradation. *Proc Natl Acad Sci U S A.* 2019;116(31):15725–15734. https://doi.org/10.1073/pnas.1908677116

Jurado-Flores A, Aroca A, Romero LC, Gotor C. Sulfide promotes tolerance to drought through protein persulfidation in Arabidopsis. *J Exp Bot.* 2023;74(15):4654–4669. https://doi.org/10.1093/jxb/erad165

Juretschke T, Beli P. Causes and consequences of DNA damage-induced autophagy. *Matrix Biol.* 2021;100:39–53. https://doi.org/10.1016/j.matbio.2021.02.004

Kabbage M, Kessens R, Bartholomay LC, Williams B. The life and death of a plant cell. *Annu Rev Plant Biol.* 2017;68(1):375–404. https://doi.org/10.1146/annurev-arplant-043015-111655

Kagiyama M, Hirano Y, Mori T, Kim SY, Kyozuka J, Seto Y, Yamaguchi S, Hakoshima T. Structures of D14 and D14L in the strigolactone and karrikin signaling pathways. *Genes Cells.* 2013;18(2):147–160. https://doi.org/10.1111/gtc.12025

Kats I, Khmelinskii A, Kschonsak M, Huber F, Knieß RA, Bartosik A, Knop M. Mapping degradation signals and pathways in a eukaryotic N-terminome. *Mol Cell.* 2018;70(3):488–501e5. https://doi.org/10.1016/j.molcel.2018.03.033

Kendrick RE, Kronenberg GHM. *Photomorphogenesis* in plants. Dordrecht-Boston-London: Hluwer Academic Publishers; 1994.

Kessler F, Schnell D. Chloroplast biogenesis: diversity and regulation of the protein import apparatus. *Curr Opin Cell Biol.* 2009;21(4): 494–500. https://doi.org/10.1016/j.ceb.2009.03.004

Kim HJ, Oh SA, Brownfield L, Hong SH, Ryu H, Hwang I, Twell D, Nam HG. Control of plant germline proliferation by SCFFBL17 degradation of cell cycle inhibitors. *Nature*. 2008;455(7216):1134–1137. https://doi.org/10.1038/nature07289

Kim L, Heo J, Kwon DH, Shin JS, Jang SH, Park ZY, Song HK. Structural basis for the N-degron specificity of ClpS1 from Arabidopsis thaliana. *Protein Sci.* 2021;30(3):700–708. https://doi.org/10.1002/pro.4018

Kim S, Fei X, Sauer RT, Baker TA. AAA+ protease-adaptor structures reveal altered conformations and ring specialization. *Nat Struct Mol Biol.* 2022;29(11):1068–1079. https://doi.org/10.1038/s41594-022-00850-3
Kmiec B, Branca RMM, Berkowitz O, Li L, Wang Y, Murcha MW, Whelan J, Lehtiö J, Glaser E, Teixeira PF. Accumulation of endogenous peptides triggers a pathogen stress response in *Arabidopsis thaliana*. *Plant J.* 2018a:96(4):705–715. https://doi.org/10.1111/tpj.14100

Kmiec B, Branca RMM, Murcha MW, Lehtiö J, Glaser E, Teixeira PF. A common peptidolytic mechanism for targeting peptide degradation in mitochondria and chloroplasts. *Molec Plant*. 2018b:11(2): 342–345. https://doi.org/10.1016/j.molp.2017.11.008

Kmiec B, Teixeira PF, Berntsson RP, Murcha MW, Branca RM, Radomiljac JD, Regberg J, Svensson LM, Bakali A, Langel U, et al. Organellar oligopeptidase (OOP) provides a complementary pathway for targeting peptide degradation in mitochondria and chloroplasts. *Proc Natl Acad Sci U S A.* 2013:110(40):E3761–E3769. https://doi.org/10.1073/pnas.1307637110

Kmiec B, Teixeira PF, Glaser E. Phenotypical consequences of expressing the dually targeted presequence protease, AtPreP, exclusively in mitochondria. *Biochimie*. 2014:100:167–170. https://doi.org/10.1016/j.biochi.2013.12.012

Kohler A, Carlströ A, Nolte H, Berndtsson J, Langer T, Correspondence MO, Kohler V, Jung S-J, Sridhara S, Tatsuta T, et al. Early fate decision for mitochondrially encoded proteins by a molecular triage. *Mol Cell*. 2023:83(19):3470–3484. https://doi.org/10.1016/j.molcel.2023.09.001

Kolodziejczak M, Gibala M, Urantowka A, Janska H. The significance of Arabidopsis AAA proteases for activity and assembly/stability of mitochondrial OXPHOS complexes. *Physiol Plant*. 2007:129(1): 135–142. https://doi.org/10.1111/j.1399-3054.2006.00835.x

Kolodziejczak M, Skibior-Blaszczyk R, Janska H. m-AAA Complexes are not crucial for the survival of arabidopsis under optimal growth conditions despite their importance for mitochondrial translation. *Plant Cell Physiol.* 2018:59(5):1006–1016. https://doi.org/10.1093/pcp/pcy041

Kong L, Cheng J, Zhu Y, Ding Y, Meng J, Chen Z, Xie Q, Guo Y, Li J, Yang S, et al. Degradation of the ABA co-receptor ABI1 by PUB12/13 U-box E3 ligases. *Nat Commun.* 2015:6(1):8630. https://doi.org/10.1038/ncomms9630

Koornneef M, Rolff E, Spruit CJP. Genetic control of light-inhibited hypocotyl elongation in *Arabidopsis thaliana* (L.) Heynh. *Z fur Pflanzenphysiologie*. 1980:100(2):147–160. https://doi.org/10.1016/S0044-328X(80)80208-X

Kozlic A, Winter N, Telser T, Reimann J, Rose K, Nehlin L, Berckhan S, Sharma G, Dambire C, Boeckx T, et al. A yeast-based functional assay to study plant N-degron—N-recognin interactions. *Front Plant Sci.* 2022:12:806129. https://doi.org/10.3389/fpls.2021.806129

Kumar N, Harashima H, Kalve S, Bramsiepe J, Wang K, Sizani BL, Bertrand LL, Johnson MC, Faulk C, Dale R, et al. Functional conservation in the SIAMESE-RELATED family of cyclin-dependent kinase inhibitors in land plants. *Plant Cell*. 2015:27(11): 3065–3080. https://doi.org/10.1105/tpc.15.00489

Kumaran G, Pathak PK, Quandoh E, Mursalimov S, Devi J, Alkalaituvia S, Leong JX, Schenstnyi K, Levin E, Üstün S, et al. Autophagy restricts tomato fruit ripening via a general role in ethylene repression. *bioRxiv*. 2023. https://doi.org/10.1101/2023.12.20.572633

Kurepa J, Wang S, Li Y, Smalle J. Proteasome regulation, plant growth and stress tolerance. *Plant Signal Behav.* 2009:4(10):924–927. https://doi.org/10.4161/psb.4.10.9469

Laloum D, Magen S, Soroka Y, Avin-Wittenberg T. Exploring the contribution of autophagy to the excess-sucrose response in *Arabidopsis thaliana*. *Int J Mol Sci.* 2022:23(7):3891. https://doi.org/10.3390/ijms23073891

Langin G, González-fuente M, Üstün S. The plant ubiquitin—proteasome system as a target for microbial manipulation. *Ann Rev Phytopathol.* 2023a:61(1):351–372. https://doi.org/10.1146/annurev-phyto-021622-110443

Langin G, Gouguet P, Üstün S. Microbial effector proteins—a journey through the proteolytic landscape. *Trends Microbiol.* 2020:28(7): 523–535. https://doi.org/10.1016/j.tim.2020.02.010

Langin G, Raffeiner M, Biermann D, Franz-Wachtel M, Spinti D, Börnke F, Macek B, Üstün S. ER-anchored protein sorting controls the fate of two proteasome activators for intracellular organelle communication during proteotoxic stress. *bioRxiv:*571118. https://doi.org/10.1101/2023.12.11.571118, 12 December 2023b, preprint: not peer reviewed.

Lau K, Podolec R, Chappuis R, Ulm R, Hothorn M. Plant photoreceptors and their signaling components compete for COP 1 binding via VP peptide motifs. *EMBO J.* 2019:38(18):e102140. https://doi.org/10.15252/embj.2019102140

Laureano-Marín AM, Aroca Á, Pérez-Pérez ME, Yruela I, Jurado-Flores A, Moreno I, Crespo JL, Romero LC, Gotor C. Abscisic acid-triggered persulfidation of the Cys protease ATG4 mediates regulation of autophagy by sulfide. *Plant Cell.* 2020: 32(12):3902–3920. https://doi.org/10.1105/tpc.20.00766

Law SR, Chrobok D, Juvany M, Delhomme N, Lindén P, Brouwer B, Ahad A, Moritz T, Jansson S, Gardeström P, et al. Darkened leaves use different metabolic strategies for senescence and survival. *Plant Physiol.* 2018:177(1):132–150. https://doi.org/10.1104/pp.18.00062

Lee D-H, Choi I, Park SJ, Kim S, Choi M-S, Lee H-S, Pai H-S. Three consecutive cytosolic glycolysis enzymes modulate autophagic flux. *Plant Physiol.* 2023:193(3):1797–1815. https://doi.org/10.1093/plphys/kiad439

Lee DW, Kim SJ, Oh YJ, Choi B, Lee J, Hwang I. Arabidopsis BAG1 functions as a cofactor in Hsc70-mediated proteasomal degradation of unimported plastid proteins. *Mol Plant*. 2016:9(10):1428–1431. https://doi.org/10.1016/j.molp.2016.06.005

Lee S, Lee DW, Lee Y, Mayer U, Stierhof YD, Lee S, Jürgens G, Hwang I. Heat shock protein cognate 70-4 and an E3 ubiquitin ligase, CHIP, mediate plastid-destined precursor degradation through the ubiquitin-26S proteasome system in *Arabidopsis*. *Plant Cell.* 2009:21(12):3984–4001. https://doi.org/10.1105/tpc.109.071548

Li B, Liu G, Wang Y, Wei Y, Shi H. Overexpression of banana ATG8f modulates drought stress resistance in *Arabidopsis*. *Biomolecules.* 2019:9(12):814. https://doi.org/10.3390/biom9120814

Li H-m, Chiu C-C. Protein transport into chloroplasts. *Ann Rev Plant Biol.* 2010:61(1):157–180. https://doi.org/10.1146/annurev-arplant-042809-112222

Li J, Zhang BL, Duan PG, Yan L, Yu HY, Zhang LM, Li N, Zheng LY, Chai TY, Xu R, et al. An endoplasmic reticulum-associated degradation-related E2-E3 enzyme pair controls grain size and weight through the brassinosteroid signaling pathway in rice. *Plant Cell.* 2023a:35(3):1076–1091. https://doi.org/10.1093/plcell/koac364

Li L, Nelson C, Fenske R, Trösch J, Pružinská A, Millar AH, Huang S. Changes in specific protein degradation rates in *Arabidopsis thaliana* reveal multiple roles of Lon1 in mitochondrial protein homeostasis. *Plant J.* 2017:89(3):458–471. https://doi.org/10.1111/tpj.13392

Li L, Wang K, Zhou Y, Liu X. Review: a silent concert in developing plants: dynamic assembly of cullin-RING ubiquitin ligases. *Plant Sci.* 2023b:330:111662. https://doi.org/10.1016/j.plantsci.2023.111662

Li M, Kim C. Chloroplast ROS and stress signaling. *Plant Commun.* 2022:3(1):100264. https://doi.org/10.1016/j.xplc.2021.100264
Li W, Chen M, Zhong L, Liu J, Xu Z, Li L, Zhou Y-B, Guo C-H, Ma Y-Z. Overexpression of the autophagy-related gene SiATG8a from foxtail millet (Setaria italica L.) confers tolerance to both nitrogen starvation and drought stress in Arabidopsis. *Biochem Biophys Res Commun.* 2015:468(4):800–806. https://doi.org/10.1016/j.bbrc. 2015.11.035

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*. 2020a:16(5):862–877. https://doi.org/10.1080/ 15548627.2019.1643656

Li Z, Dogra V, Lee KP, Li R, Li M, Li M, Kim C. N-terminal acetylation stabilizes SIGMA FACTOR BINDING PROTEIN1 involved in salicylic acid-primed cell death. *Plant Physiol.* 2020b:183(1):358–370. https://doi.org/10.1104/pp.19.01417

Lian HL, He SB, Zhang YC, Zhu DM, Zhang JY, Jia KP, Sun SX, Li L, Yang HQ. Blue-light-dependent interaction of cryptochrome 1 with SPA1 defines a dynamic signaling mechanism. *Genes Dev.* 2011:25(10):1023–1028. https://doi.org/10.1101/gad.2025111

Liao C-Y, Wang P, Yin Y, Bassham DC. Interactions between autophagy and phytohormone signaling pathways in plants. *FEBS Lett.* 2022:596(17):2198–2214. https://doi.org/10.1002/1873-3468.14355

Licausi F, Kosmacz M, Weits DA, Giuntoli B, Giorgi FM, Voesenek LA, Perata P, van Dongen JT. Oxygen sensing in plants is mediated by an N-end rule pathway for protein destabilization. *Nature*. 2011:479(7373):419–422. https://doi.org/10.1038/nature10536

Lin CC, Chao YT, Chen WC, Ho HY, Chou MY, Li YR, Wu YL, Yang HA, Hsieh H, Lin CS, et al. Regulatory cascade involving transcriptional and N-end rule pathways in rice under submergence. *Proc Natl Acad Sci U S A.* 2019:116(8):3300–3309. https://doi.org/10.1073/ pnas.1818507116

Lin Z, Li Y, Wang Y, Liu X, Ma L, Zhang Z, Mu C, Zhang Y, Peng L, Xie S, et al. Initiation and amplification of SnRK2 activation in abscisic acid signaling. *Nat Commun.* 2021:12(1):2456. https://doi.org/10. 1038/s41467-021-22812-x

Ling JJ, Li J, Zhu D, Deng XW. Noncanonical role of Arabidopsis COP1/SPA complex in repressing BIN2-mediated PIF3 phosphorylation and degradation in darkness. *Proc Natl Acad Sci U S A.* 2017:114- (13):3539–3544. https://doi.org/10.1073/pnas.1700850114

Ling Q, Broad W, Trösch R, Töpel M, Demiral Sert T, Lymperopoulos P, Baldwin A, Jarvis RP. Ubiquitin-dependent chloroplast-associated protein degradation in plants. *Science*. 2019: 363(6429):eaav4467. https://doi.org/10.1126/science.aav4467

Ling Q, Huang W, Baldwin A, Jarvis P. Chloroplast biogenesis is regulated by direct action of the ubiquitin-proteasome system. *Science*. 2012:338(6107):655–659. https://doi.org/10.1126/science. 1225053

Ling Q, Jarvis P. Regulation of chloroplast protein import by the ubiquitin E3 ligase SP1 is important for stress tolerance in plants. *Curr Biol.* 2015;25(19):2527–2534. https://doi.org/10.1016/j.cub.2015.08. 015

Ling Q, Sadali NM, Soufi Z, Zhou Y, Huang B, Zeng Y, Rodriguez-Concepcion M, Jarvis RP. The chloroplast-associated protein degradation pathway controls chromoplast development and fruit ripening in tomato. *Nat Plants*. 2021:7(5):655–666. https:// doi.org/10.1038/s41477-021-00916-y

Linster E, Forero Ruiz FL, Miklankova P, Ruppert T, Mueller J, Armbruster L, Gong X, Serino G, Mann M, Hell R, et al. Cotranslational N-degron masking by acetylation promotes proteome stability in plants. *Nat Commun.* 2022:13(1):810. https://doi. org/10.1038/s41467-022-28414-5

Linster E, Stephan I, Bienvenut WV, Maple-Grodem J, Myklebust LM, Huber M, Reichelt M, Sticht C, Moller SG, Meinnel T, et al. Downregulation of N-terminal acetylation triggers

ABA-mediated drought responses in Arabidopsis. *Nat Commun.* 2015:6(1):7640. https://doi.org/10.1038/ncomms8640

Lister R, Carrie C, Duncan O, Ho LHM, Howell KA, Murcha MW, Whelan J. Functional definition of outer membrane proteins involved in preprotein import into mitochondria. *Plant Cell.* 2007: 19(11):3739–3759. https://doi.org/10.1105/tpc.107.050534

Liu B, Jiang Y, Tang H, Tong S, Lou S, Shao C, Zhang J, Song Y, Chen N, Bi H, et al. The ubiquitin E3 ligase SR1 modulates the submergence response by degrading phosphorylated WRKY33 in Arabidopsis. *Plant Cell.* 2021:33(5):1771–1789. https://doi.org/10. 1093/plcell/koab062

Liu J-X, Howell SH. Managing the protein folding demands in the endoplasmic reticulum of plants. *New Phytol.* 2016:211(2):418–428. https://doi.org/10.1111/nph.13915

Liu M, Zeng T, Zhang X, Liu C, Wu Z, Yao L, Xie C, Xia H, Lin Q, Xie L, et al. ATR/chk1 signaling induces autophagy through sumoylated RhoB-mediated lysosomal translocation of TSC2 after DNA damage. *Nature Comm.* 2018b:9(1):4139. https://doi.org/10.1038/ s41467-018-06556-9

Liu G, Pfeifer J, de Brito Francisco R, Emonet A, Stirnemann M, Gübeli C, Hutter O, Sasse J, Mattheyer C, Stelzer E, et al. Changes in the allocation of endogenous strigolactone improve plant biomass production on phosphate-poor soils. *New Phytol.* 2018a:217(2): 784–798. https://doi.org/10.1111/nph.14847

Liu Y, Xiong Y, Bassham DC. Autophagy is required for tolerance of drought and salt stress in plants. *Autophagy*. 2009:5(7):954–963. https://doi.org/10.4161/auto.5.7.9290

Liu YD, Li JM. Endoplasmic reticulum-mediated protein quality control in *Front Plant Sci.* 2014:5:162. https://doi.org/10.3389/fpls. 2014.00162

López-Bucio J, de La Vega OM, Guevara-García A, Herrera-Estrella L. Enhanced phosphorus uptake in transgenic tobacco plants that overproduce citrate. *Nat Biotechnol.* 2000:18(4):450–453. https:// doi.org/10.1038/74531

Lopez-Juez E, Pyke K. Plastids unleashed: their development and their integration in plant development. *Int J Dev Biol.* 2005: 49(5-6):557–577. https://doi.org/10.1387/ijdb.051997el

López-Vidal O, Olmedilla A, Sandalio LM, Sevilla F, Jiménez A. Is autophagy involved in pepper fruit ripening? *Cells*. 2020:9(1):106. https://doi.org/10.3390/cells9010106

Lozano-Durán R, Macho AP, Boutrot F, Segonzac C, Somssich IE, Zipfel C. The transcriptional regulator BZR1 mediates trade-off between plant innate immunity and growth. *Elife.* 2013:2: e00983. https://doi.org/10.7554/eLife.00983

Lu XD, Zhou CM, Xu PB, Luo Q, Lian HL, Yang HQ. Red-light-dependent interaction of phyB with SPA1 promotes COP1-SPA1 dissociation and photomorphogenic development in arabidopsis. *Mol Plant.* 2015:8(3):467–478. https://doi.org/10. 1016/j.molp.2014.11.025

Lv F, Zhou J, Zeng L, Xing D. β-Cyclocitral upregulates salicylic acid signalling to enhance excess light acclimation in Arabidopsis. *J Exp Bot.* 2015:66(15):4719–4732. https://doi.org/10.1093/jxb/erv231

Ma L, Li X, Zhao Z, Hao Y, Shang R, Zeng D, Liu H. Light-response Bric-A-Brack/Tramtrack/Broad proteins mediate cryptochrome 2 degradation in response to low ambient temperature. *Plant Cell.* 2021:33(12):3610–3620. https://doi.org/10.1093/plcell/koab219

Majsec K, Bhuiyan NH, Sun Q, Kumari S, Kumar V, Ware D, van Wijk KJ. The plastid and mitochondrial peptidase network in *Arabidopsis thaliana*: a foundation for testing genetic interactions and functions in organellar proteostasis. *Plant Cell.* 2017:29(11): 2687–2710. https://doi.org/10.1105/tpc.17.00481
Maldonado M, Guo F, Letts JA. Atomic structures of respiratory com-
plex III2, complex IV, and supercomplex III2-IV from vascular
plants. *Elife*. 2021:10:e62047. https://doi.org/10.7554/eLife.62047

Margalha L, Confraria A, Baena-González E. SnRK1 and TOR: modu-
lating growth-defense trade-offs in plant stress responses. *J Exp
Bot*. 2019;70(8):2261-2274. https://doi.org/10.1093/jxb/erz066

Marshall RS, Vierstra RD. Autophagy: the master of bulk and selec-
tive recycling. *Ann/Rev Plant Biol*. 2018:69(1):173-208. https://doi.
org/10.1146/annurev-arplant-042817-040606

Marshall RS, Vierstra RD. Dynamic regulation of the 26S proteasome: from synthesis to degradation. *Front Mol Biosci*. 2019:6:40. https://doi.org/10.3389/fmolb.2019.00040

Marzec M, Brewer P. Binding or hydrolysis? How does the strigolac-
tone receptor work? *Trends Plant Sci*. 2019;24(7):571-574. https://
doi.org/10.1016/j.tplants.2019.05.001

Masclaux-Daubresse C, Clement G, Anne P, Routaboul JM,
Guiboileau A, Soulay F, Shirasu K, Yoshimoto K. Stitching togeth-
er the multiple dimensions of autophagy using metabolomics
and transcriptomics reveals impacts on metabolism, develop-
ment, and plant responses to the environment in Arabidopsis.
*Plant Cell*. 2014;26(5):1857-1877. https://doi.org/10.1105/tpc.114.
124677

Maziak A, Heidorn-Czarna M, Weremczuk A, Janska H. FTSH4 and OMA1 mitochondrial proteases reduce moderate heat stress-induced protein aggregation. *Plant Physiol.* 2021;187(2): 1-18. https://doi.org/10.1093/plphys/kiab296

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. 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 me-
tabolism during fixed-carbon starvation in maize. *Plant Cell*.
2020;32(9):2699-2724. https://doi.org/10.1105/tpc.20.00226

Meijer AJ, Codogno P. Regulation and role of autophagy in mamma-
lian cells. *Intl J Biochem Cell Biol*. 2004;36(12):2445-2462. https://doi.
org/10.1016/j.biocel.2004.02.002

Menges M, Hennig L, Gruissem W, Murray JAH. Genome-wide gene expression in an Arabidopsis cell suspension. *Plant Mol Biol*. 2003;53(4):423-442. https://doi.org/10.1023/B:PLAN.0000019059.56489.ca

Metzger MB, Pruneda JN, Klevit RE, Weissman AM. RING-type E3 ligases: master manipulators of E2 ubiquitin-conjugating enzymes and ubiquitination. *Biochim Biophys Acta*. 2014;1843(1):47-60. https://doi.org/10.1016/j.bbamcr.2013.05.026

Meyer M, Leptihn S, Welz M, Schaller A. Functional characterization of propeptides in plant subtilases as intramolecular chaperones and inhibitors of the mature protease. *J Biol Chem*. 2016;291(37): 19449-19461. https://doi.org/10.1074/jbc.M116.744151

Miao L, Zhao J, Yang G, Xu P, Cao X, Du S, Xu F, Jiang L, Zhang S, Wei X, et al. Arabidopsis cryptochrome 1 undergoes COP1 and LRBs-dependent degradation in response to high blue light. *New Phytol*. 2022;234(4):1347-1362. https://doi.org/10.1111/nph.17695

Migdal I, Skibior-Blaszczyk R, Heidorn-Czarna M, Kolodziejczak M, Garbiec A, Janska H. AtOMA1 affects the OXPHOS system and plant growth in contrast to other newly identified ATP-independent proteases in Arabidopsis mitochondria. *Front Plant Sci*. 2017:8:1-16. https://doi.org/10.3389/fpls.2017.01543

Miklankova P, Linster E, Boyer JB, Weidenhausen J, Mueller J, Armbruster L, Lapouge K, De La Torre C, Bienvenut W, Sticht C, et al. HYPK promotes the activity of the N(alpha)-

acetyltransferase A complex to determine proteostasis of
nonAc-X(2)/N-degron-containing proteins. *Sci Adv.* 2022:8(24):
eabn6153. https://doi.org/10.1126/sciadv.abn6153

Minina EA, Moschou PN, Vetukuri RR, Sanchez-Vera V, Cardoso C, Liu Q, Elander PH, Dalman K, Beganovic M, Yilmaz JL, et al. Transcriptional stimulation of rate-limiting components of the autophagic pathway improves plant fitness. *J Exp Bot.* 2018;69(6):1415-1432. https://doi.org/10.1093/jxb/ery010

Mocciaro A, Rape M. Emerging regulatory mechanisms in ubiquitin-
dependent cell cycle control. *J Cell Sci.* 2012;125(2):255-263.
https://doi.org/10.1242/jcs.091199

Mohd Ali S, Li N, Soufi Z, Yao J, Johnson E, Ling Q, Jarvis RP. Multiple ubiquitin E3 ligase genes antagonistically regulate chloroplast-associated protein degradation. *Curr Biol*. 2023;33(6):1138-1146.e1135. https://doi.org/10.1016/j.cub.2023.01.060

Montandon C, Dougan DA, van Wijk KJ. N-Degron specificity of chlor-
elast ClpS1 in plants. FEBS Lett. 2019a:593(9):962-970. https://
doi.org/10.1002/1873-3468.13378

Montandon C, Friso G, Liao JR, Choi J, van Wijk KJ. In vivo trapping of proteins interacting with the chloroplast CLPC1 chaperone: potential substrates and adaptors. *J Proteome Res.* 2019b:18(6): 2585-2600. https://doi.org/10.1021/acs.jproteome.9b00112

Morelli L, Torres-Montilla S, Glauser G, Shanmugabalaji V, Kessler F, Rodriguez-Concepcion M. Novel insights into the contribution of plastoglobules and reactive oxygen species to chromoplast differentiation. *New Phytol.* 2023;237(5):1696-1710. https://doi.org/10.1111/nph.18585

Mot AC, Prell E, Klecker M, Naumann C, Faden F, Westermann B, Dissmeyer N. Real-time detection of N-end rule-mediated ubiquitination via fluorescently labeled substrate probes. *New Phytol.* 2018;217(2):613-624. https://doi.org/10.1111/nph.14497

Mueller F, Friese A, Pathe C, da Silva RC, Rodriguez KB, Musacchio A, Bange T. Overlap of NatA and IAP substrates implicates N-terminal acetylation in protein stabilization. *Sci Adv.* 2021;7(3):eabc8590. https://doi.org/10.1126/sciadv.abc8590

Mugume Y, Kazibwe Z, Bassham DC. Target of rapamycin in control of autophagy: puppet master and signal integrator. *Int J Mol Sci.* 2020;21(21):8259. https://doi.org/10.3390/ijms21218259

Nathan JA, Kim HT, Ting L, Gygi SP, Goldberg AL. Why do cellular proteins linked to K63-polyubiquitin chains not associate with proteasomes. *EMBO J.* 2013;32(4):552-565. https://doi.org/10.1038/emboj.2012.354

Nellaepalli S, Lau AS, Jarvis RP. Chloroplast protein translocation pathways and ubiquitin-dependent regulation at a glance. *J Cell Sci.* 2023;136(18):jcs241125. https://doi.org/10.1242/jcs.241125

Nguyen KT, Mun SH, Lee CS, Hwang CS. Control of protein degrada-
tion by N-terminal acetylation and the N-end rule pathway. *Exp
Mol Med.* 2018;50(7):1-8. https://doi.org/10.1038/s12276-018-0097-y

Ni W, Xu SL, Tepperman JM, Stanley DJ, Maltby DA, Gross JD, Burlingame AL, Wang ZY, Quail PH. A mutually assured destruction mechanism attenuates light signaling in Arabidopsis. *Science*. 2014;344(6188):1160-1164. https://doi.org/10.1126/science.1250778

Nishimura K, Apitz J, Friso G, Kim J, Ponnala L, Grimm B, van Wijk KJ. Discovery of a unique Clp component, ClpF, in chloroplasts: a proposed binary ClpF-ClpS1 adaptor complex functions in substrate recognition and delivery. *Plant Cell*. 2015:27:2677-2691. https://doi.org/10.1105/tpc.15.00574

Nishimura K, Asakura Y, Friso G, Kim J, Oh SH, Rutschow H, Ponnala L, van Wijk KJ. Clps1 is a conserved substrate selector for the chloroplast Clp protease system in Arabidopsis. *Plant Cell*. 2013;25(6):2276-2301. https://doi.org/10.1105/tpc.113.112557
Nishimura K, van Wijk KJ. Organization, function and substrates of the essential Clp protease system in plastids. *Biochim Biophys Acta*. 2015;1847(9):915-930. https://doi.org/10.1016/j.bbabio. 2014.11.012

Noir S, Marrocco K, Masoud K, Thomann A, Gusti A, Bitrian M, Schnittger A, Genschik P. The control of Arabidopsis thaliana growth by cell proliferation and endreplication requires the F-box protein FBL17. *Plant Cell*. 2015;27(5):1461-1476. https://doi. org/10.1105/tpc.114.135301

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.e7. https://doi.org/10.1016/j.devcel.2017.03.013

Nowack MK, Harashima H, Dissmeyer N, Zhao X, Bouyer D, Weimer AK, De Winter F, Yang F, Schnittger A. Genetic framework of cyclin-dependent kinase function in Arabidopsis. *Dev Cell*. 2012;22(5):1030-1040. https://doi.org/10.1016/j.devcel.2012.02. 015

Nukarinen E, Nägele T, Pedrotti L, Wurzinger B, Mair A, Landgraf R, Börnke F, Hanson J, Teige M, Baena-Gonzalez E, et al. Quantitative phosphoproteomics reveals the role of the AMPK plant ortholog SnRK1 as a metabolic master regulator under energy deprivation. *Sci Rep*. 2016;6(1):31697. https://doi.org/10.1038/ srep31697

Ogita N, Okushima Y, Tokizawa M, Yamamoto YY, Tanaka M, Seki M, Makita Y, Matsui M, Okamoto-Yoshiyama K, Sakamoto T, et al. Identifying the target genes of SUPPRESSOR OF GAMMA RESPONSE 1, a master transcription factor controlling DNA damage response in Arabidopsis. *Plant J*. 2018;94(3):439-453. https:// doi.org/10.1111/tpj.13866

Oh J, Park E, Song K, Bae G, Choi G. PHYTOCHROME INTERACTING FACTOR8 inhibits phytochrome A-mediated far-red light responses in Arabidopsis. *Plant Cell*. 2020a:32(1):186-205. https:// doi.org/10.1105/tpc.19.00515

Oh JH, Hyun JY, Chen SJ, Varshavsky A. Five enzymes of the Arg/N-degron pathway form a targeting complex: the concept of superchanneling. *Proc Natl Acad Sci U S A*. 2020b:117(20): 10778-10788. https://doi.org/10.1073/pnas.2003043117

Opalińska M, Parys K, Jańska H. Identification of physiological substrates and binding partners of the plant mitochondrial protease FTSH4 by the trapping approach. *Internat J Molec Sci*. 2017:18(11): 2455. https://doi.org/10.3390/ijms18112455

Opalinska M, Parys K, Murcha MW, Janska H. The plant i-AAA protease controls the turnover of an essential mitochondrial protein import component. *J Cell Sci*. 2018:131(2):jcs200733. https://doi. org/10.1242/jcs.200733

Oravecza A, Baumann A, Máté Z, Brzezinska A, Molinier J, Oakeley EJ, Ádám É, Schäfer E, Nagy F, Ulm R. CONSTITUTIVELY PHOTOMORPHOGENIC1 is required for the UV-B response in Arabidopsis. *Plant Cell*. 2006;18(8):1975-1990. https://doi.org/10. 1105/tpc.105.040097

Oreb M, Zoryan M, Vojta A, Maier UG, Eichacker LA, Schleiff E. Phospho-mimicry mutant of atToc33 affects early development of Arabidopsis thaliana. FEBS Lett. 2007;581(30):5945-5951. https://doi.org/10.1016/j.febslet.2007.11.071

Orosa-Puente B, Spoel SH. Harnessing the ubiquitin code to respond to environmental cues. *Essays Biochem*. 2022:66(2):111-121. https://doi.org/10.1042/EBC20210094

Ottmann C, Rose R, Huttenlocher F, Cedzich A, Hauske P, Kaiser M, Huber R, Schaller A. Structural basis for Ca²⁺-independence and activation by homodimerization of tomato subtilase 3. *Proc Natl Acad Sci U S A*. 2009:106(40):17223-17228. https://doi.org/10. 1073/pnas.0907587106

Pan M, Zheng Q, Wang T, Liang L, Mao J, Zuo C, Ding R, Ai H, Xie Y, Si D, et al. Structural insights into Ubr1-mediated N-degron polyubiquitination. *Nature*. 2021a:600(7888):334-338. https://doi.org/ 10.1038/s41586-021-04097-8

Pan T, Gao S, Cui X, Wang L, Yan S. APC/CCDC20 targets SCFFBL17 to activate replication stress responses in Arabidopsis. *Plant Cell*. 2023:35(2):910-923. https://doi.org/10.1093/plcell/koac360

Pan T, Qin Q, Nong C, Gao S, Wang L, Cai B, Zhang M, Wu C, Chen H, Li T, et al. A novel WEE1 pathway for replication stress responses. *Nat Plants*. 2021b:7(2):209-218. https://doi.org/10.1038/s41477- 021-00855-8

Pan W, Lin B, Yang X, Liu L, Xia R, Li J, Wu Y, Xie Q. The UBC27-AIRP3 ubiquitination complex modulates ABA signaling by promoting the degradation of ABI1 in Arabidopsis. *Proc Natl Acad Sci U S A*. 2020:117(44):27694-27702. https://doi.org/10. 1073/pnas.2007366117

Papci D, Pérez-Salamó I, Joseph MP, Giuntoli B, Bögre L, Koncz C, Szabados L. The low oxygen, oxidative and osmotic stress responses synergistically act through the ethylene response factor VII genes RAP2.12, RAP2.2 and RAP2.3. *Plant J*. 2015:82(5):772-784. https://doi.org/10.1111/tpj.12848

Park JH, Kang CH, Nawkar GM, Lee ES, Paeng SK, Chae HB, Chi YH, Kim WY, Yun DJ, Lee SY. EMR, a cytosolic-abundant ring finger E3 ligase, mediates ER-associated protein degradation in Arabidopsis. *New Phytol*. 2018:220(1):163-177. https://doi.org/10. 1111/nph.15279

Park SE, Kim JM, Seok OH, Cho H, Wadas B, Kim SY, Varshavsky A, Hwang CS. Control of mammalian G protein signaling by N-terminal acetylation and the N-end rule pathway. *Science*. 2015:347(6227):1249-1252. https://doi.org/10.1126/science. aaa3844

Paulus JK, Kourelis J, Ramasubramanian S, Homma F, Godson A, Hörger AC, Hong TN, Krahn D, Ossorio Carballo L, Wang S, et al. Extracellular proteolytic cascade in tomato activates immune protease Rcr3. *Proc Natl Acad Sci U S A*. 2020:117(29): 17409-17417. https://doi.org/10.1073/pnas.1921101117

Pedreschi R, Lurie S. Advances and current challenges in understanding postharvest abiotic stresses in perishables. *Postharvest Biol Technol*. 2015:107:77-89. https://doi.org/10.1016/j. postharvbio.2015.05.004

Peirats-Llobet M, Han SK, Gonzalez-Guzman M, Jeong CW, Rodriguez L, Belda-Palazon B, Wagner D, Rodriguez PL. A direct link between abscisic acid sensing and the chromatin-remodeling ATPase BRAHMA via core ABA signaling pathway components. *Mol Plant*. 2016:9(1):136-147. https://doi.org/10.1016/j.molp.2015.10. 003

Perotti MF, Posé D, Martín-Pizarro C. Non-climacteric fruit development and ripening regulation: 'the phytohormones show'. *J Exp Bot*. 2023:74(20):6237-6253. https://doi.org/10.1093/jxb/erad271

Perrar A, Dissmeyer N, Huesgen PF. New beginnings and new ends: methods for large-scale characterization of protein termini and their use in plant biology. *J Exp Bot*. 2019:70(7):2021-2038. https://doi.org/10.1093/jxb/erz104

Pesin JA, Orr-Weaver TL. Regulation of APC/C activators in mitosis and meiosis. *Annu Rev Cell Dev Biol*. 2008:24(1):475-499. https:// doi.org/10.1146/annurev.cellbio.041408.115949

Petereit J, Duncan O, Murcha MW, Fenske R, Cincu E, Cahn J, Pružinská A, Ivanova A, Kollipara L, Wortelkamp S, et al. Mitochondrial CLPP2 assists coordination and homeostasis of respiratory complexes. *Plant Physiol*. 2020:184(1):148-164. https://doi.org/10.1104/pp.20.00136

Pfanner N, Warscheid B, Wiedemann N. Mitochondrial proteins: from biogenesis to functional networks. *Nature Rev Molec Cell*
Biol. 2019:20(5):267-284. https://doi.org/10.1038/s41580-018-0092-0

Pham VN, Kathare PK, Huq E. Dynamic regulation of PIF5 by COP1-SPA complex to optimize photomorphogenesis in Arabidopsis. *Plant J.* 2018:96(2):260-273. https://doi.org/10.1111/tpj.14074

Pierce NW, Kleiger G, Shan SO, Deshaies RJ. Detection of sequential polyubiquitylation on a millisecond timescale. *Nature*. 2009: 462(7273):615-619. https://doi.org/10.1038/nature08595

Polyn S, Willems A, De Veylder L. Cell cycle entry, maintenance, and exit during plant development. *Curr Opin Plant Biol.* 2015:23:1-7. https://doi.org/10.1016/j.pbi.2014.09.012

Ponnu J, Hoecker U. Illuminating the COP1/SPA ubiquitin ligase: fresh insights into its structure and functions during plant photomorphogenesis. *Front Plant Sci.* 2021:12:662793. https://doi.org/10.3389/fpls.2021.662793

Ponnu J, Riedel T, Penner E, Schrader A, Hoecker U. Cryptochrome 2 competes with COP1 substrates to repress COP1 ubiquitin ligase activity during Arabidopsis photomorphogenesis. *Proc Natl Acad Sci U S A.* 2019:116(52):27133-27141. https://doi.org/10.1073/pnas.1909181116

Porat R, Lichter A, Terry LA, Harker R, Buzby J. Postharvest losses of fruit and vegetables during retail and in consumers' homes: quantifications, causes, and means of prevention. *Postharvest Biol Technol.* 2018:139:135-149. https://doi.org/10.1016/j.postharvbio.2017.11.019

Postiglione AE, Muday GK. Abscisic acid increases hydrogen peroxide in mitochondria to facilitate stomatal closure. *Plant Physiol.* 2023:192(1):469-487. https://doi.org/10.1093/plphys/kiac601

Potuschak T, Lechner E, Parmentier Y, Yanagisawa S, Grava S, Koncz C, Genschik P. EIN3-dependent regulation of plant ethylene hormone signaling by two Arabidopsis F box proteins: EBF1 and EBF2. *Cell.* 2003:115(6):679-689. https://doi.org/10.1016/S0092-8674(03)00968-1

Potuschak T, Stary S, Schlögelhofer P, Becker F, Nejinskaia V, Bachmair A. PRT1 of *Arabidopsis thaliana* encodes a component of the plant N-end rule pathway. *Proc Natl Acad Sci U S A.* 1998: 95(14):7904-7908. https://doi.org/10.1073/pnas.95.14.7904

Prusky D, Romanazzi G. Induced resistance in fruit and vegetables: a host physiological response limiting postharvest disease development. *Ann Rev Phytopathol.* 2023:61(1):279-300. https://doi.org/10.1146/annurev-phyto-021722-035135

Pu Y, Luo X, Bassham DC. TOR-dependent and -independent pathways regulate autophagy in Arabidopsis thaliana. *Front Plant Sci.* 2017:8:1204. https://doi.org/10.3389/fpls.2017.01204

Puchades C, Ding B, Song A, Wiseman RL, Lander GC, Glynn SE. Unique structural features of the mitochondrial AAA+ protease afg312 reveal the molecular basis for activity in health and disease. *Molec Cell.* 2019:75:1073-1085.e6. https://doi.org/10.1016/j.molcel.2019.06.016

Puchades C, Rampello AJ, Shin M, Giuliano CJ, Wiseman RL, Glynn SE, Lander GC. Structure of the mitochondrial inner membrane AAA+ protease YME1 gives insight into substrate processing. *Science.* 2017:358(6363):eaa00464. https://doi.org/10.1126/science.aao0464

Puchades C, Sandate CR, Lander GC. The molecular principles governing the activity and functional diversity of AAA+ proteins. *Nature Rev Molec Cell Biol.* 2020:21(1):43-58. https://doi.org/10.1038/s41580-019-0183-6

Qin N, Xu D, Li J, Deng XW. COP9 signalosome: discovery, conservation, activity, and function. *J Integr Plant Biol.* 2020:62(1):90-103. https://doi.org/10.1111/jipb.12903

Raffeiner M, Zhu S, González-Fuente M, Üstün S. Interplay between autophagy and proteasome during protein turnover. *Trends Plant Sci.* 2023:28(6):698-714. https://doi.org/10.1016/j.tplants.2023.01.013

Rampello AJ, Glynn SE. Identification of a degradation signal sequence within substrates of the mitochondrial i-AAA protease. *J Molec Biol.* 2017:429(6):873-885. https://doi.org/10.1016/j.jmb.2017.02.009

Rawlings ND, Barrett AJ, Thomas PD, Huang X, Bateman A, Finn RD. The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database. *Nucleic Acids Res.* 2018:46(D1):D624-D632. https://doi.org/10.1093/nar/gkx1134

Rée R, Varland S, Arnesen T. Spotlight on protein N-terminal acetylation. *Exp Mol Med.* 2018:50(7):1-13. https://doi.org/10.1038/s12276-018-0116-z

Reichardt S, Piepho H-P, Stintzi A, Schaller A. Peptide signaling for drought-induced tomato flower drop. *Science.* 2020:367(6485): 1482-1485. https://doi.org/10.1126/science.aaz5641

Reichardt S, Repper D, Tuzhikov AI, Galiullina RA, Planas-Marques M, Chichkova NV, Vartapetian AB, Stintzi A, Schaller A. The tomato subtilase family includes several cell death-related proteins with caspase specificity. *Sci Rep.* 2018:8(1):10531. https://doi.org/10.1038/s41598-018-28769-0

Rei Liao JY, Friso G, Forsythe ES, Michel EJS, Williams AM, Boguraev SS, Ponnala L, Sloan DB, van Wijk KJ. Proteomics, phylogenetics, and coexpression analyses indicate novel interactions in the plastid CLP chaperone-protease system. *J Biol Chem.* 2022:298(3): 101609. https://doi.org/10.1016/j.jbc.2022.101609

Rei Liao JY, van Wijk KJ. Discovery of AAA+ protease substrates through trapping approaches. *Trends Biochem Sci.* 2019:44(6): 528-545. https://doi.org/10.1016/j.tibs.2018.12.006

Reyes-Prieto A, Weber APM, Bhattacharya D. The origin and establishment of the plastid in algae and plants. *Ann Rev Genet.* 2007:41(1):147-168. https://doi.org/10.1146/annurev.genet.41.110306.130134

Richter AS, Banse C, Grimm B. The GluTR-binding protein is the heme-binding factor for feedback control of glutamyl-tRNA reductase. *Elife.* 2019:8:e46300. https://doi.org/10.7554/eLife.46300

Rizzini L, Favory JJ, Cloix C, Faggionato D, O'Hara A, Kaiserli E, Baumeister R, Schäfer E, Nagy F, Jenkins GI, et al. Perception of UV-B by the arabidopsis UVR8 protein. *Science.* 2011:332(6025): 103-106. https://doi.org/10.1126/science.1200660

Roberts D, Pedmale UV, Morrow J, Sachdev S, Lechner E, Tang X, Zheng N, Hannink M, Genschik P, Liscum E. Modulation of phototropic responsiveness in arabidopsis through ubiquitination of phototropin 1 by the CUL3-ring E3 ubiquitin ligase CRL3NPH3. *Plant Cell.* 2011:23(10):3627-3640. https://doi.org/10.1105/tpc.111.087999

Rodriguez E, Rodriguez E, Chevalier J, Olsen J, Ansbøl J, Kapousidou V, Zuo Z, Svenning S, Loefke C, Koemeda S, et al. Autophagy mediates temporary reprogramming and dedifferentiation in plant somatic cells. *EMBO J.* 2020:39(4):e103315. https://doi.org/10.15252/embj.2019103315

Roesler K, Lu C, Thomas J, Xu Q, Vance P, Hou Z, Williams RW, Liu L, Owens MA, Habben JE. Arabidopsis carboxylesterase 20 binds strigolactone and increases branches and tillers when ectopically expressed in Arabidopsis and maize. *Front Plant Sci.* 2021:12: 639401. https://doi.org/10.3389/fpls.2021.639401

Romisch K. Endoplasmic reticulum-associated degradation. *Annu Rev Cell Dev Biol.* 2005:21(1):435-456. https://doi.org/10.1146/annurev.cellbio.21.012704.133250

Rowland E, Kim J, Bhuiyan NH, van Wijk KJ. The Arabidopsis chloroplast stromal N-terminome: complexities of amino-terminal
protein maturation and stability. *Plant Physiol.* 2015:169(3): 1881-1896. https://doi.org/10.1104/pp.15.01214

Rowland E, Kim J, Friso G, Poliakov A, Ponnala L, Sun Q, van Wijk KJ. The CLP and PREP protease systems coordinate maturation and degradation of the chloroplast proteome in Arabidopsis thaliana. *New Phytol.* 2022:236(4):1339-1357. https://doi.org/10.1111/nph.18426

Royek S, Bayer M, Pfannstiel J, Pleiss J, Ingram G, Stintzi A, Schaller A. Processing of a plant peptide hormone precursor facilitated by posttranslational tyrosine sulfation. *Proc Natl Acad Sci U S A.* 2022: 119(16):e2201195119. https://doi.org/10.1073/pnas.2201195119

Ruyter-Spira C, Al-Babili S, van der Krol S, Bouwmeester H. The biology of strigolactones. *Trends Plant Sci.* 2013:18(2):72-83. https://doi.org/10.1016/j.tplants.2012.10.003

Saeed B, Deligne F, Brillada C, Dunser K, Ditengou FA, Turek I, Allahham A, Grujic N, Dagdas Y, Ott T, et al. K63-linked ubiquitin chains are a global signal for endocytosis and contribute to selective autophagy in plants. *Curr Biol.* 2023:33(7):1337-1345. https://doi.org/10.1016/j.cub.2023.02.024

Saeed W, Naseem S, Ali Z. Strigolactones biosynthesis and their role in abiotic stress resilience in plants: a critical review. *Front Plant Sci.* 2017:8:1487. https://doi.org/10.3389/fpls.2017.01487

Saijo Y, Zhu D, Li J, Rubio V, Zhou Z, Shen Y, Hoecker U, Wang H, Deng XW. Arabidopsis COP1/SPA1 complex and FHY1/FHY3 associate with distinct phosphorylated forms of phytochrome A in balancing light signaling. *Mol Cell.* 2008:31(4):607-613. https://doi.org/10.1016/j.molcel.2008.08.003

Sánchez-Sevilla JF, Botella MA, Valpuesta V, Sanchez-Vera V. Autophagy is required for strawberry fruit ripening. *Front Plant Sci.* 2021:12:688481. https://doi.org/10.3389/fpls.2021.688481

Saxena H, Negi H, Sharma B. Role of F-box E3-ubiquitin ligases in plant development and stress responses. *Plant Cell Rep.* 2023:42(7): 1133-1146. https://doi.org/10.1007/s00299-023-03023-8

Schaller A, Stintzi A, Rivas S, Serrano I, Chichkova NV, Vartapetian AB, Martínez D, Guiamét JJ, Sueldo DJ, van der Hoorn RAL, et al. From structure to function—a family portrait of plant subtilases. *New Phytol.* 2018:218(3):901-915. https://doi.org/10.1111/nph.14582

Schardon K, Hohl M, Graff L, Schulze W, Pfannstiel J, Stintzi A, Schaller A. Precursor processing for plant peptide hormone maturation by subtilisin-like serine proteinases. *Science.* 2016:354-357. https://doi.org/10.1126/science.aai8550

Schlame M. Protein crowding in the inner mitochondrial membrane. *Biochim Biophys Acta Bioenerg.* 2021:1862(1):148305. https://doi.org/10.1016/j.bbabio.2020.148305

Schwechheimer C, Serino G, Callis J, Crosby WL, Lyapina S, Deshaies RJ, Gray WM, Estelle M, Deng X-W. Interactions of the COP9 signalosome with the E3 ubiquitin ligase SCFT1R1 in mediating auxin response. *Science.* 2001:292(5520):1379-1382. https://doi.org/10.1126/science.1059776

Seller CA, Schroeder JI. Distinct guard cell-specific remodeling of chromatin accessibility during abscisic acid- and CO₂-dependent stomatal regulation. *Proc Natl Acad Sci U S A.* 2023:120(52):e2310670120. https://doi.org/10.1073/pnas.2310670120

Seo HS, Watanabe E, Tokutomi S, Nagatani A, Chua NH. Photoreceptor ubiquitination by COP1 E3 ligase desensitizes phytochrome A signaling. *Genes Dev.* 2004:18(6):617-622. https://doi.org/10.1101/gad.1187804

Seto Y, Yasui R, Kameoka H, Tamiru M, Cao M, Terauchi R, Sakurada A, Hirano R, Kisugi T, Hanada A, et al. Strigolactone perception and deactivation by a hydrolase receptor DWARF14. *Nature Comm.* 2019:10(1):191-191. https://doi.org/10.1038/s41467-018-08124-7

Shabek N, Ticchiarelli F, Mao H, Hinds TR, Leyser O, Zheng N. Structural plasticity of D3-D14 ubiquitin ligase in strigolactone signalling. *Nature.* 2018:563(7733):652-656. https://doi.org/10.1038/s41586-018-0743-5

Sheerin DJ, Menon C, Zur Oven-Krockhaus S, Enderle B, Zhu L, Johnen P, Schleifenbaum F, Stierhof YD, Huq E, Hiltbrunner A. Light-activated phytochrome A and B interact with members of the SPA family to promote photomorphogenesis in arabidopsis by reorganizing the COP1/SPA complex. *Plant Cell.* 2015:27(1):189-201. https://doi.org/10.1105/tpc.114.134775

Shemorry A, Hwang CS, Varshavsky A. Control of protein quality and stoichiometries by N-terminal acetylation and the N-end rule pathway. *Mol Cell.* 2013:50(4):540-551. https://doi.org/10.1016/j.molcel.2013.03.018

Sheng X, Wei Q, Jiang L, Li X, Gao Y, Wang L. Different degree in proteasome malfunction has various effects on root growth possibly through preventing cell division and promoting autophagic vacuolization. *PLoS One.* 2012:7(9):e45673. https://doi.org/10.1371/journal.pone.0045673

Sherpa D, Christowicz J, Schulman BA. How the ends signal the end: regulation by E3 ubiquitin ligases recognizing protein termini. *Mol Cell.* 2022:82(8):1424-1438. https://doi.org/10.1016/j.molcel.2022.02.004

Shi H, Shen X, Liu R, Xue C, Wei N, Deng XW, Zhong S. The red light receptor phytochrome B directly enhances substrate-E3 ligase interactions to attenuate ethylene responses. *Dev Cell.* 2016:39(5):597-610. https://doi.org/10.1016/j.devcel.2016.10.020

Shi L-X, Theg SM. The chloroplast protein import system: from algae to trees. *Biochim Biophys Acta.* 2013:1833(2):314-331. https://doi.org/10.1016/j.bbamcr.2012.10.002

Singh AP, Salvatori R, Aftab W, Aufschnaiter A, Carlström A, Forne I, Imhof A, Ott M. Molecular connectivity of mitochondrial gene expression and OXPHOS biogenesis. *Molec Cell.* 2020:79:1051-1065.e10. https://doi.org/10.1016/j.molcel.2020.07.024

Sirko A, Wawrzynska A, Brzywczy J, Sienko M. Control of ABA signaling and crosstalk with other hormones by the selective degradation of pathway components. *Int J Mol Sci.* 2021:22(9):4638. https://doi.org/10.3390/ijms22094638

Smith SM, Li J. Signalling and responses to strigolactones and karrikins. *Curr Opin Plant Biol.* 2014:21:23-29. https://doi.org/10.1016/j.pbi.2014.06.003

Song C, Zhao J, Guichard M, Shi D, Grossmann G, Schmitt C, Jouannet V, Greb T. Strigo-D2—a bio-sensor for monitoring spatiotemporal strigolactone signaling patterns in intact plants. *Plant Physiol.* 2021:188(1):97-110. https://doi.org/10.1093/plphys/kiab504

Song L, Liu J, Cao BL, Liu B, Zhang XP, Chen ZY, Dong CQ, Liu XQ, Zhang ZH, Wang WX, et al. Reducing brassinosteroid signalling enhances grain yield in semi-dwarf wheat. *Nature.* 2023:617(7959):118-124. https://doi.org/10.1038/s41586-023-06023-6

Soto-Burgos J, Bassham DC. SnRK1 activates autophagy via the TOR signaling pathway in Arabidopsis thaliana. *PLoS One.* 2017:12(8):e0182591. https://doi.org/10.1371/journal.pone.0182591

Spinelli JB, Haigis MC. The multifaceted contributions of mitochondria to cellular metabolism. *Nat Cell Biol.* 2018:20(7):745-754. https://doi.org/10.1038/s41556-018-0124-1

Ståhl A, Nilsson S, Lundberg P, Bhushan S, Biverståhl H, Moberg P, Morisset M, Vener A, Måler L, Langel U, et al. Two novel targeting peptide degrading proteases, PrePs, in mitochondria and chloroplasts, so similar and still different. *J Molec Biol.* 2005:349(4):847-860. https://doi.org/10.1016/j.jmb.2005.04.023
Starostina NG, Kipreos ET. Multiple degradation pathways regulate versatile CIP/KIP CDK inhibitors. *Trends Cell Biol.* 2012;22(1): 33-41. https://doi.org/10.1016/j.tcb.2011.10.004

Stary S, Yin XJ, Potuschak T, Schlögelhofer P, Nizhynska V, Bachmaier A. PRT1 of Arabidopsis is a ubiquitin protein ligase of the plant N-end rule pathway with specificity for aromatic amino-terminal residues. *Plant Physiol.* 2003;133(3):1360-1366. https://doi.org/10.1104/pp.103.029272

Stefan CJ, Henne WM, Emr SD. Vacuoles. In: Lennarz WJ, Lane MD, editors. *Encyclopedia of biological chemistry*. 2nd ed. London: Academic Press; 2013. p. 502-508.

Stintzi A, Schaller A. Biogenesis of post-translationally modified peptide signals for plant reproductive development. *Curr Opin Plant Biol.* 2022;69:102274. https://doi.org/10.1016/j.pbi.2022.102274

Stirnberg P, Furner IJ, Leyser HMO. MAX2 participates in an SCF complex which acts locally at the node to suppress shoot branching. *Plant J.* 2007;50(1):80-94. https://doi.org/10.1111/j.1365-313X.2007.03032.x

Stone SL. Role of the ubiquitin proteasome system in plant response to abiotic stress. *Int Rev Cell Mol Biol.* 2019;343:65-110. https://doi.org/10.1016/bs.ircmb.2018.05.012

Stührwohldt N, Ehinger A, Thellmann K, Schaller A. Processing and formation of bioactive CLE40 peptide are controlled by posttranslational proline hydroxylation. *Plant Physiol.* 2020;184(3): 1573-1584. https://doi.org/10.1104/pp.20.00528

Stührwohldt N, Schaller A. Regulation of plant peptide hormones and growth factors by post-translational modification. *Plant Biol.* 2019;21(S1):49-63. https://doi.org/10.1111/plb.12881

Stührwohldt N, Scholl S, Lang L, Katzenberger J, Schumacher K, Schaller A. The biogenesis of CLEL peptides involves several processing events in consecutive compartments of the secretory pathway. *Elife*. 2020;6:e55580. https://doi.org/10.7554/eLife.55580

Su T, Li X, Yang M, Shao Q, Zhao Y, Ma C, Wang P. Autophagy: an intracellular degradation pathway regulating plant survival and stress response. *Front Plant Sci.* 2020;11:164. https://doi.org/10.3389/fpls.2020.00164

Su T, Yang M, Wang P, Zhao Y, Ma C. Interplay between the ubiquitin proteasome system and ubiquitin-mediated autophagy in plants. *Cells*. 2020;9(10):2219. https://doi.org/10.3390/cells9102219

Sun G, Wase N, Shu S, Jenkins J, Zhou B, Torres-Rodriguez JV, Chen C, Sandor L, Plott C, Yoshinga Y, et al. Genome of Paspalum vaginatum and the role of trehalose mediated autophagy in increasing maize biomass. *Nat Commun.* 2022;13(1):7731. https://doi.org/10.1038/s41467-022-35507-8

Sun X, Wang P, Jia X, Huo L, Che R, Ma F. Improvement of drought tolerance by overexpressing MdATG18a is mediated by modified antioxidant system and activated autophagy in transgenic apple. *Plant Biotechnol J.* 2018;16(2):545-557. https://doi.org/10.1111/pbi.12794

Sun Y, Jarvis RP. Chloroplast proteostasis: import, sorting, ubiquitination, and proteolysis. *Ann Rev Plant Biol.* 2023;74(1):259-283. https://doi.org/10.1146/annurev-arplant-070122-032532

Sutterlüty H, Chatelain E, Marti A, Wirbelauer C, Senften M, Müller U, Krek W. p45SKP2promotes p27Kip1degradation and induces S phase in quiescent cells. *Nat Cell Biol.* 1999;1(4):207-214. https://doi.org/10.1038/12027

Szczepanowska K, Senft K, Heidler J, Herholz M, Kukat A, Höhne MN, Hofsetz E, Becker C, Kaspar S, Giese H, et al. A salvage pathway maintains highly functional respiratory complex I. *Nat Comm.* 2020;11(1):1643. https://doi.org/10.1038/s41467-020-15467-7

Szurman-Zubrzycka M, Jędrzejek P, Szarejko I. How do plants cope with DNA damage? A concise review on the DDR pathway in

plants. *Int J Mol Sci.* 2023;24(3):2404. https://doi.org/10.3390/ijms24032404

Tahjib-Ul-Arif M, Zahan MI, Karim MM, Imran S, Hunter CT, Islam MS, Mia MA, Hannan MA, Rhaman MS, Hossain MA, et al. Citric acid-mediated abiotic stress tolerance in plants. *Int J Mol Sci.* 2021;22(13):7235. https://doi.org/10.3390/ijms22137235

Takeshige K, Baba M, Tsuboi S, Noda T, Ohsumi Y. Autophagy in yeast demonstrated with proteinase-deficient mutants and conditions for its induction. *J Cell Biol.* 1992;119(2):301-311. https://doi.org/10.1083/jcb.119.2.301

Tal L, Gil MXA, Guercio AM, Shabek N. Structural aspects of plant hormone signal perception and regulation by ubiquitin ligases. *Plant Physiol.* 2020;182(4):1537-1544. https://doi.org/10.1104/pp.19.01282

Tal L, Palayam M, Ron M, Young A, Britt A, Shabek N. A conformational switch in the SCF-D3/MAX2 ubiquitin ligase facilitates stri-golactone signalling. *Nat Plants.* 2022;8(5):561-573. https://doi.org/10.1038/s41477-022-01145-7

Tan JM, Wong ESP, Kirkpatrick DS, Pletnikova O, Ko HS, Tay S-P, Ho MWL, Troncoso J, Gygi SP, Lee MK, et al. Lysine 63-linked ubiquitination promotes the formation and autophagic clearance of protein inclusions associated with neurodegenerative diseases. *Hum Mol Genet.* 2008;17(3):431-439. https://doi.org/10.1093/hmg/ddm320

Tang J, Bassham DC. Autophagy in crop plants: what's new beyond Arabidopsis? *Open Biol.* 2018;8(12):180162. https://doi.org/10.1098/rsob.180162

Tang J, Bassham DC. Autophagy during drought: function, regulation, and potential application. *Plant J.* 2022;109(2):390-401. https://doi.org/10.1111/tpj.15481

Tang S, Zhao ZY, Liu XT, Sui Y, Zhang DD, Zhi H, Gao YZ, Zhang H, Zhang LL, Wang YN, et al. An E2-E3 pair contributes to seed size control in grain crops. *Nat Commun.* 2023;14(1):3091. https://doi.org/10.1038/s41467-023-38812-y

Tasaki T, Mulder LC, Iwamatsu A, Lee MJ, Davydov IV, Varshavsky A, Muesing M, Kwon YT. A family of mammalian E3 ubiquitin ligases that contain the UBR box motif and recognize N-degrons. *Mol Cell Biol.* 2005;25(16):7120-7136. https://doi.org/10.1128/MCB.25.16.7120-7136.2005

Taylor A, Qiu Y-L. Evolutionary history of subtilases in land plants and their involvement in symbiotic interactions. *Mol Plant Microbe Int.* 2017;30(6):489-501. https://doi.org/10.1094/MPMI-10-16-0218-R

Tedesco D, Lukas J, Reed SI. The pRb-related protein p130 is regulated by phosphorylation-dependent proteolysis via the protein-ubiquitin ligase SCFSkp2. *Genes Dev.* 2002;16(22):2946-2957. https://doi.org/10.1101/gad.1011202

Till CJ, Vicente J, Zhang H, Oszvald M, Deery MJ, Pastor V, Lilley KS, Ray RV, Theodoulou FL, Holdsworth MJ. The *Arabidopsis thaliana* N-recognin E3 ligase PROTEOLYSIS1 influences the immune response. *Plant Direct.* 2019;3(12):e00194. https://doi.org/10.1002/pld3.194

Torii S, Yoshida T, Arakawa S, Honda S, Nakanishi A, Shimizu S. Identification of PPM1D as an essential Ulk1 phosphatase for gen-otoxic stress-induced autophagy. *EMBO Rep.* 2016;17(11): 1552-1564. https://doi.org/10.15252/embr.201642565

Trolet A, Baldrich P, Criqui M-C, Dubois M, Clavel M, Meyers BC, Genschik P. Cell cycle-dependent regulation and function of ARGONAUTE1 in plants. *Plant Cell.* 2019;31(8):1734-1750. https://doi.org/10.1105/tpc.19.00069

Trusova SV, Teplova AD, Golyshev SA, Galiullina RA, Morozova EA, Chichkova NV, Vartapetian AB. Clathrin-mediated endocytosis
delivers proteolytically active phytaspases into plant cells. *Front Plant Sci.* 2019:10:873. https://doi.org/10.3389/fpls.2019.00873

Umehara M, Hanada A, Yoshida S, Akiyama K, Arite T, Takeda-Kamiya N, Magome H, Kamiya Y, Shirasu K, Yoneyama K, et al. Inhibition of shoot branching by new terpenoid plant hormones. *Nature*. 2008;455(7210):195–200. https://doi.org/10.1038/nature07272

Üstün S, Hafrén A, Hofius D. Autophagy as a mediator of life and death in plants. *Curr Opin Plant Biol.* 2017:40:122–130. https://doi.org/10.1016/j.pbi.2017.08.011

Üstün S, Sheikh A, Gimenez-ibanez S, Jones A, Ntoukakis V, Börnke F. The proteasome acts as a hub for plant immunity and is targeted by Pseudomonas type III effectors. *Plant Physiol.* 2016:172(3): 1941–1958. https://doi.org/10.1104/pp.16.00808

Valencia JP, Goodman K, Otegui MS. Endocytosis and endosomal trafficking in plants. *Ann Rev Plant Biol.* 2016:67(1):309–335. https://doi.org/10.1146/annurev-arplant-043015-112242

van de Kooij B, de Vries E, Rooswinkel RW, Janssen GMC, Kok FK, van Veelen PA, Borst J. N-terminal acetylation can stabilize proteins independent of their ubiquitination. *Sci Rep.* 2023:13(1):5333. https://doi.org/10.1038/s41598-023-32380-3

Van der Hoorn RAL. Plant proteases: from phenotypes to molecular mechanisms. *Annu Rev Plant Biol.* 2008:59(1):191–223. https://doi.org/10.1146/annurev.arplant.59.032607.092835

Van Leene J, Hollunder J, Eeckhout D, Persiau G, Van De Slijke E, Stals H, Van Isterdael G, Verkest A, Neirynck S, Buffel Y, et al. Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana. *Mol Syst Biol.* 2010:6(1):397. https://doi.org/10.1038/msb.2010.53

van Wijk KJ. Protein maturation and proteolysis in plant plastids, mitochondria, and peroxisomes. *Ann Rev Plant Biol.* 2015:66(1): 75–111. https://doi.org/10.1146/annurev-arplant-043014-115547

Varland S, Silva RD, Kjosas I, Faustino A, Bogaert A, Billmann M, Boukhatmi H, Kellen B, Costanzo M, Drazic A, et al. N-Terminal acetylation shields proteins from degradation and promotes age-dependent motility and longevity. *Nat Commun.* 2023:14(1):6774. https://doi.org/10.1038/s41467-023-42342-y

Varshavsky A. N-degron and C-degron pathways of protein degradation. *Proc Natl Acad Sci U S A.* 2019:116(2):358–366. https://doi.org/10.1073/pnas.1816596116

Vazquez-Calvo C, Suhm T, Büttner S, Ott M. The basic machineries for mitochondrial protein quality control. *Mitochondrion.* 2020:50:121–131. https://doi.org/10.1016/j.mito.2019.10.003

Vercellino I, Sazanov LA. The assembly, regulation and function of the mitochondrial respiratory chain. *Nature Rev Molec Cell Biol.* 2022:23(2):141–161. https://doi.org/10.1038/s41580-021-00415-0

Verkest A, Manes C-L, Vercruysse S, Maes S, Van Der Schueren E, Beeckman T, Genschik P, Kuiper M, Inze D, De Veylder L, et al. The cyclin-dependent kinase inhibitor KRP2 controls the onset of the endoreduplication cycle during arabidopsis leaf development through inhibition of mitotic CDKA; 1 kinase complexes. *Plant Cell.* 2005a:17(6):1723–1736. https://doi.org/10.1105/tpc.105.032383

Verkest A, Weinl C, Inzé D, De Veylder L, Schnittger A. Switching the cell cycle. Kip-related proteins in plant cell cycle control. *Plant Physiol.* 2005b:139(3):1099–1106. https://doi.org/10.1104/pp.105.069906

Vicente J, Mendiondo GM, Pauwels J, Pastor V, Izquierdo Y, Naumann C, Movahedi M, Rooney D, Gibbs DJ, Smart K, et al. Distinct branches of the N-end rule pathway modulate the plant immune response. *New Phytol.* 2019:221(2):988–1000. https://doi.org/10.1111/nph.15387

Waditee-Sirisattha R, Shibato J, Rakwal R, Sirisattha S, Hattori A, Nakano T, Takabe T, Tsujimoto M. The Arabidopsis aminopeptidase LAP2 regulates plant growth, leaf longevity and stress response. *New Phytol.* 2011:191(4):958–969. https://doi.org/10.1111/j.1469-8137.2011.03758.x

Wang G, Guo L, Guo Z, Guan SL, Zhu N, Qi K, Gu C, Zhang S. The involvement of Ein3-binding F-box protein PbrEBF3 in regulating ethylene signaling during Cuiguan pear fruit ripening. *Plant Sci.* 2023a:329:111600. https://doi.org/10.1016/j.plantsci.2023.111600

Wang L, Wang B, Jiang L, Liu X, Li X, Lu Z, Meng X, Wang Y, Smith SM, Lia J. Strigolactone signaling in Arabidopsis regulates shoot development by targeting D53-like SMXL repressor proteins for ubiquitination and degradation. *Plant Cell.* 2015:27(11):3128–3142. https://doi.org/10.1105/tpc.15.00605

Wang P, Xue L, Batelli G, Lee S, Hou Y-J, Van Oosten MJ, Zhang H, Tao WA, Zhu J-K. Quantitative phosphoproteomics identifies SnRK2 protein kinase substrates and reveals the effectors of abscisic acid action. *Proc Natl Acad Sci U S A.* 2013a:110(27):11205–11210. https://doi.org/10.1073/pnas.1308974110

Wang Q, Yu FF, Xie Q. Balancing growth and adaptation to stress: crosstalk between brassinosteroid and abscisic acid signaling. *Plant Cell Environ.* 2020:43(10):2325–2335. https://doi.org/10.1111/pce.13846

Wang Y, Carrie C, Giraud E, Elhafez D, Narsai R, Duncan O, Whelan J, Murcha MW. Dual location of the mitochondrial preprotein transporters B14.7 and Tim23-2 in complex I and the TIM17:23 complex in Arabidopsis links mitochondrial activity and biogenesis. *Plant Cell.* 2012:24(6):2675–2695. https://doi.org/10.1105/tpc.112.098731

Wang Y, Wang L, Guan Z, Chang H, Ma L, Shen C, Qiu L, Yan J, Zhang D, Li J, et al. Structural insight into UV-B-activated UVR8 bound to COP1. *Sci Adv.* 2022:8(16):eabn3337. https://doi.org/10.1126/sciadv.abn3337

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.* 2013b:25(4):1383–1399. https://doi.org/10.1105/tpc.112.108993

Wang Y, Yue JL, Yang N, Zheng C, Zheng YN, Wu X, Yang J, Zhang HW, Liu LJ, Ning YS, et al. An ERAD-related ubiquitin-conjugating enzyme boosts broad-spectrum disease resistance and yield in rice. *Nat Food.* 2023b:4(9):774–787. https://doi.org/10.1038/s43016-023-00820-y

Wang Y, Zheng C, Peng YL, Chen Q. DGS1 improves rice disease resistance by elevating pathogen-associated molecular pattern-triggered immunity. *aBIOTECH.* 2024:5(1):46–51. https://doi.org/10.1007/s42994-024-00137-9

Watson SJ, Li N, Ye Y, Wu F, Ling Q, Jarvis RP. Crosstalk between the chloroplast protein import and SUMO systems revealed through genetic and molecular investigation in Arabidopsis. *eLife.* 2021:10: e60960. https://doi.org/10.7554/eLife.06906

Weaver LM, Amasino RM. Senescence is induced in individually darkened Arabidopsis leaves, but inhibited in whole darkened plants. *Plant Physiol.* 2001:127(3):876–886. https://doi.org/10.1104/pp.010312

Wei N, Deng XW. COP9: a new genetic locus involved in light-regulated development and gene expression in Arabidopsis. *Plant Cell.* 1992:4(12):1507–1518. https://doi.org/10.1105/tpc.4.12.1507

Weimer AK, Biedermann S, Harashima H, Roodbarkelari F, Takahashi N, Foreman J, Guan Y, Pochon G, Heese M, Van Damme D, et al. The plant-specific CDKB1-CYCB1 complex mediates homologous recombination repair in Arabidopsis. *EMBO J.* 2016:35(19):2068–2086. https://doi.org/10.15252/embj.201593083
Weits DA, Giuntoli B, Kosmacz M, Parlanti S, Hubberten HM, Riegler H, Hoefgen R, Perata P, van Dongen JT, Licausi F. Plant cysteine oxidases control the oxygen-dependent branch of the N-end-rule pathway. *Nat Commun.* 2014;5(1):3425. https://doi.org/10.1038/ncomms4425

Weits DA, Kunkowska AB, Kamps NCW, Portz KMS, Packbier NK, Nemec Venza Z, Gaillochet C, Lohmann JU, Pedersen O, van Dongen JT, et al. An apical hypoxic niche sets the pace of shoot meristem activity. *Nature.* 2019;569(7758):714–717. https://doi.org/10.1038/s41586-019-1203-6

Weits DA, van Dongen JT, Licausi F. Molecular oxygen as a signaling component in plant development. *New Phytol.* 2021;229(1):24–35. https://doi.org/10.1111/nph.16424

White MD, Klecker M, Hopkinson RJ, Weits DA, Mueller C, Naumann C, O'Neill R, Wickens J, Yang J, Brooks-Bartlett JC, et al. Plant cysteine oxidases are dioxygenases that directly enable arginyl transferase-catalysed arginylation of N-end rule targets. *Nat Commun.* 2017;8(1):14690. https://doi.org/10.1038/ncomms14690

Willems A, De Veylder L. The plant anaphase-promoting complex/cyclosome. *Annu Rev Cell Dev Biol.* 2022;38(1):25–48. https://doi.org/10.1146/annurev-cellbio-120420-092421

Williams B, Njaci I, Moghaddam L, Long H, Dickman MB, Zhang X, Mundree S. Trehalose accumulation triggers autophagy during plant desiccation. *PLoS Genet.* 2015;11(12):e1005705. https://doi.org/10.1371/journal.pgen.1005705

Wu J, Zhang X, Zhang L, Wu CY, Rezaeian AH, Chan CH, Li JM, Wang J, Gao Y, Han F, et al. Skp2 E3 ligase integrates ATM activation and homologous recombination repair by ubiquitinating NBS1. *Mol Cell.* 2012;46(3):351–361. https://doi.org/10.1016/j.molcel.2012.02.018

Wu Q, Zhang X, Peirats-Llobet M, Belda-Palazon B, Wang X, Cui S, Yu X, Rodriguez PL, An C. Ubiquitin ligases RGLG1 and RGLG5 regulate abscisic acid signaling by controlling the turnover of phosphatase PP2CA. *Plant Cell.* 2016;28(9):2178–2196. https://doi.org/10.1105/tpc.16.00364

Xu D, Lin F, Jiang Y, Ling J, Hettiarachchi C, Tellgren-Roth C, Holm M, Wei N, Deng XW. Arabidopsis COP1 SUPPRESSOR 2 represses COP1 E3 ubiquitin ligase activity through their coiled-coil domains association. *PLoS Genet.* 2015a:11(12):e1005747. https://doi.org/10.1371/journal.pgen.1005747

Xu E, Chai L, Zhang S, Yu R, Zhang X, Xu C, Hu Y. Catabolism of stri-golactones by a carboxylesterase. *Nat Plants.* 2021;7(11): 1495–1504. https://doi.org/10.1038/s41477-021-01011-y

Xu F, Huang Y, Li L, Gannon P, Linster E, Huber M, Kapos P, Bienvenut W, Polevoda B, Meinnel T, et al. Two N-terminal acetyltransferases antagonistically regulate the stability of a nod-like receptor in Arabidopsis. *Plant Cell.* 2015b:27(5):1547–1562. https://doi.org/10.1105/tpc.15.00173

Xu G, Yuan M, Ai C, Liu L, Zhuang E, Karapetyan S, Wang S, Dong X. UORF-mediated translation allows engineered plant disease resistance without fitness costs. *Nature.* 2017;545(7655):491–494. https://doi.org/10.1038/nature22372

Xu Y, Wang S, Li L, Sahu SK, Petersen M, Liu X, Melkonian M, Zhang G, Liu H. Molecular evidence for origin, diversification and ancient gene duplication of plant subtilases (SBTs). *Sci Rep.* 2019;9(1): 12485. https://doi.org/10.1038/s41598-019-48664-6

Yamauchi S, Mano S, Oikawa K, Hikino K, Teshima KM, Kimori Y, Nishimura M, Shimazaki K-I, Takemiya A. Autophagy controls re-active oxygen species homeostasis in guard cells that is essential for stomatal opening. *Proc Natl Acad Sci U S A.* 2019;116(38): 19187–19192. https://doi.org/10.1073/pnas.1910886116

Yang H, Kim X, Jan S, Aubourg S, Sancho Andrés G, Stah E, Guillou M-C, Gigli-Bisceglia N, Tran Van Canh L, Bender KW, et al.

Subtilase-mediated biogenesis of the expanded family of SERINE RICH ENDOGENOUS PEPTIDES. *Nat Plants.* 2023;10(1): 118–130. https://doi.org/10.1038/s41477-023-01567-x

Yang Y, Wu Y, Pirrello J, Regad F, Bouzayen M, Deng W, Li Z. Silencing Sl-EBF1 and Sl-EBF2 expression causes constitutive ethylene response phenotype, accelerated plant senescence, and fruit ripening in tomato. *J Exp Bot.* 2010;61(3):697–708. https://doi.org/10.1093/jxb/erp332

Yao R, Ming Z, Yan L, Li S, Wang F, Ma S, Yu C, Yang M, Chen L, Chen L, et al. DWARF14 is a non-canonical hormone receptor for strigolactone. *Nature.* 2016;536(7617):469–473. https://doi.org/10.1038/nature19073

Yi D, Alvim Kamei CL, Cools T, Vanderauwera S, Takahashi N, Okushima Y, Eekhout T, Yoshiyama KO, Larkin J, Van den Daele H, et al. The Arabidopsis SIAMESE-RELATED cyclin-dependent kinase inhibitors SMR5 and SMR7 regulate the DNA damage checkpoint in response to reactive oxygen species. *Plant Cell.* 2014;26(1):296–309. https://doi.org/10.1105/tpc.113.118943

Yoneyama K, Awad AA, Xie X, Yoneyama K, Takeuchi Y. Strigolactones as germination stimulants for root parasitic plants. *Plant Cell Physiol.* 2010;51(7):1095–1103. https://doi.org/10.1093/pcp/pcq055

Yoshiyama K, Conklin PA, Huefner ND, Britt AB. Suppressor of gamma response 1 (SOG1) encodes a putative transcription factor governing multiple responses to DNA damage. *Proc Natl Acad Sci USA.* 2009;106(31):12843–12848. https://doi.org/10.1073/pnas.0810304106

Yu F, Lou L, Tian M, Li Q, Ding Y, Cao X, Wu Y, Belda-Palazon B, Rodriguez PL, Yang S, et al. ESCRT-I component VPS23A affects ABA signaling by recognizing ABA receptors for endosomal degradation. *Mol Plant.* 2016;9(12):1570–1582. https://doi.org/10.1016/j.molp.2016.11.002

Yu F, Xie Q. Non-26S proteasome endomembrane trafficking pathways in ABA signaling. *Trends Plant Sci.* 2017;22(11):976–985. https://doi.org/10.1016/j.tplants.2017.08.009

Yu F, Xie Q. ER-associated ubiquitin-conjugating enzyme: a key regulator of grain yield and stress resistance in crops. *Trends Plant Sci.* 2024;29(3):286–289. https://doi.org/10.1016/j.tplants.2023.11.025

Yu Z, Zhang D, Xu Y, Jin S, Zhang L, Zhang S, Yang G, Huang J, Yan K, Wu C, et al. CEPR2 phosphorylates and accelerates the degradation of PYR/PYLs in Arabidopsis. *J Exp Bot.* 2019;70(19): 5457–5469. https://doi.org/10.1093/jxb/erz302

Yue W, Zhang H, Sun X, Su N, Zhao Q, Yan Z, Weining S, Yue H. The landscape of autophagy-related (ATG) genes and functional characterization of TaVAMP727 to autophagy in wheat. *Int J Mol Sci.* 2022;23(2):891. https://doi.org/10.3390/ijms23020891

Zardeneta G, Horowitz PM. Analysis of the perturbation of phospholipid model membranes by rhodanese and its presequence. *J Biol Chem.* 1992;267(34):24193–24198. https://doi.org/10.1016/S0021-9258(18)35749-1

Zhang B, Holmlund M, Lorrain S, Norberg M, Bakó LS, Fankhauser C, Nilsson O. BLADE-ON-PETIOLE proteins act in an E3 ubiquitin ligase complex to regulate PHYTOCHROME INTERACTING FACTOR 4 abundance. *Elife.* 2017;6:e26759. https://doi.org/10.7554/eLife.26759

Zhang H, Rundle C, Winter N, Miricescu A, Mooney BC, Bachmair A, Graciet E, Theodoulou FL. BIG enhances Arg/N-degron pathway-mediated protein degradation to regulate Arabidopsis hypoxia responses and suberin deposition. *Plant Cell.* 2024a:36(9):3177–3200. https://doi.org/10.1093/plcell/koae117

Zhang H, Zhu J, Gong Z, Zhu J-K. Abiotic stress responses in plants. *Nat Rev Genet.* 2022;23(2):104–119. https://doi.org/10.1038/s41576-021-00413-0
Zhang L, Xing J, Lin J. At the intersection of exocytosis and endocytosis in plants. *New Phytol*. 2019a:224(4):1479-1489. https://doi.org/10.1111/nph.16018

Zhang L, Yu Z, Xu Y, Yu M, Ren Y, Zhang S, Yang G, Huang J, Yan K, Zheng C, et al. Regulation of the stability and ABA import activity of NRT1.2/NPF4.6 by CEPR2-mediated phosphorylation in Arabidopsis. *Mol Plant*. 2021:14(4):633-646. https://doi.org/10.1016/j.molp.2021.01.009

Zhang R, Chen H, Duan M, Zhu F, Wen J, Dong J, Wang T. Medicago falcata MfSTMIR, an E3 ligase of endoplasmic reticulum-associated degradation, is involved in salt stress response. *Plant J*. 2019b:98(4):680-696. https://doi.org/10.1111/tpj.14265

Zhang W, Planas-Marquès M, Mazier M, Šimkovicová M, Mantz M, Huesgen P, Takken F, Stintzi A, Schaller A, Sánchez-Coll N, et al. The tomato P69 subtilase family is involved in resistance to bacterial wilt. *Plant J*. 2024b:118(2):388-404. https://doi.org/10.1111/tpj.16613

Zhao XA, Harashima H, Dissmeyer N, Pusch S, Weimer AK, Bramsiepe J, Bouyer D, Rademacher S, Nowack MK, Novak B, et al. A general G1/S-phase cell-cycle control module in the flowing plant Arabidopsis Thaliana. *PLoS Genet*. 2012:8(8):e1002847. https://doi.org/10.1371/journal.pgen.1002847

Zhong R, Thompson J, Ottesen E, Lamppa GK. A forward genetic screen to explore chloroplast protein import in vivo identifies Moco sulfurase, pivotal for ABA and IAA biosynthesis and purine turnover. *Plant J*. 2010:63(1):44-59. https://doi.org/10.1111/j.1365-313X.2010.04220.x

Zhou F, Lin Q, Zhu L, Ren Y, Zhou K, Shabek N, Wu F, Mao H, Dong W, Gan L, et al. D14-SCF D3-dependent degradation of D53 regulates strigolactone signalling. *Nature*. 2013a:504(7480):406-410. https://doi.org/10.1038/nature12878

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*. 2013b:9(1): e1003196. https://doi.org/10.1371/journal.pgen.1003196

Zhu C, Huang Z, Sun Z, Feng S, Wang S, Wang T, Yuan X, Zhong L, Cheng Y, Bao M, et al. The mutual regulation between DcEBF1/2 and DcEIL3-1 is involved in ethylene induced petal senescence in carnation (Dianthus caryophyllus L.). *Plant J*. 2023:114(3): 636-650. https://doi.org/10.1111/tpj.16158

Zhu L, Bu Q, Xu X, Paik I, Huang X, Hoecker U, Deng XW, Huq E. CUL4 forms an E3 ligase with COP1 and SPA to promote light-induced degradation of PIF1. *Nat Commun*. 2015:6(1):7245. https://doi.org/10.1038/ncomms8245

Zhuang X, Cui Y, Gao C, Jiang L. Endocytic and autophagic pathways crosstalk in plants. *Curr Opin Plant Biol*. 2015:28:39-47. https://doi.org/10.1016/j.pbi.2015.08.010

Zimmermann D, Gomez-Barrera JA, Pasule C, Brack-Frick UB, Sieferer E, Nicholson TM, Pfannstiel J, Stintzi A, Schaller A. Cell death control by matrix metalloproteinases. *Plant Physiol*. 2016:171(2):1456-1469. https://doi.org/10.1104/pp.16.00513

Zubrzycki A, Dambire C, Dalle Carbonare L, Sharma G, Boeckx T, Swarup K, Sturrock CJ, Atkinson BS, Swarup R, Corbineau F, et al. ERFVII action and modulation through oxygen-sensing in *Arabidopsis thaliana*. *Nat Commun*. 2023:4:4665. https://doi.org/10.1038/s41467-023-40366-y

Zufferey M, Montandon C, Douet V, Demarsy E, Agne B, Baginsky S, Kessler F. The novel chloroplast outer membrane kinase KOC1 is a required component of the plastid protein import machinery. *J Biol Chem*. 2017:292(17):6952-6964. https://doi.org/10.1074/jbc.M117.776468

Zuo Z, Liu H, Liu B, Liu X, Lin C. Blue light-dependent interaction of CRY2 with SPA1 regulates COP1 activity and floral initiation in arabidopsis. *Curr Biol*. 2011:21(10):841-847. https://doi.org/10.1016/j.cub.2011.03.048