Vacuolar Processing Enzymes in Plant Programmed Cell Death: Comparison
View Latest Version
Please note this is a comparison between Version 3 by Jessie Wu and Version 2 by Jessie Wu.

Vacuolar processing enzymes (VPEs), which can also be named asparaginyl endopeptidases (AEPs), legumains, or colloquially, plant caspases, as they perform caspase-1-like/YVADase activity, are widespread in the plant kingdom. Their occurrence has been found in lower and higher plants. VPEs are plant cysteine proteases that are subjected to autoactivation in an acidic pH. It is presumed that VPEs, by activating other vacuolar hydrolases, are in control of tonoplast rupture during programmed cell death (PCD). Involvement of VPEs has been indicated in various types of plant PCD related to development, senescence, and environmental stress responses. 

  • protease
  • vacuole
  • autophagy

1. Classification of Vacuolar Processing Enzymes

Analysis of the Arabidopsis thaliana genome has revealed four vacuolar processing enzymes (VPEs) (αVPE, βVPE, γVPE, and δVPE) that were previously divided into three subfamilies based on the homology and expression pattern: seed-type (βVPE), vegetative-type (αVPE, γVPE), and uncharacterized-type (δVPE) [1]. However, this initial classification of VPEs was not without discrepancies; for example, it was reported that although βVPE plays the main role in the processing of storage proteins in Arabidopsis thaliana, vegetative VPEs can also be expressed in the embryo during seed maturation [2]. The new classification is based on an analysis of the phylogenetic tree of VPE proteins, as different clades are characterized by the occurrence of different isoforms. The simplified classification is as follows: in angiosperms, there are two major types, γVPE and βVPE, whereas in gymnosperms the distinction between these two types of VPEs does not occur. These two types of VPEs are also found in monocots and basal eudicots. Subsequent clades belonging to core eudicots are characterized by the occurrence of δVPE. The occurrence of αVPE has only been confirmed in plants belonging to the Brassicaceae family. This phylogenetic classification is not perfect, however, as some data are missing [3]. Nevertheless, it can be recognized that four Arabidopsis thaliana genes of VPEs have been generated by three gene duplication events, which started with the evolution of angiosperms from gymnosperms. The first gene replication event has been well studied in the most recent common ancestor of the living flowering plant Amborella trichopoda [4]. Based on the genome-wide identification of VPE genes, it can be assumed that their number is not constant among species. The genome of the model plant Arabidopsis thaliana contains four VPE genes [5][6], the pear (Pyrus) genome contains eight VPE genes (named from PbrVPE1 to PbrVPE8) [7], and the apple (Malus) genome contains twenty VPE genes (MdVPE) [8].

2. Functions of Vacuolar Processing Enzymes

VPEs are regulators of various critical processes in the plant life cycle. Primarily, it has been found that VPEs are responsible for the maturation of seed storage proteins such as 2S albumin and 12S globulin [9]. Now it is known that they participate in other developmental processes [10][11][12][13][14][15], senescence [16][17][18], and environmental stress responses [17][19][20][21]. During development, senescence, and plant responses to environmental stimuli, both autophagy [22] and programmed cell death (PCD) can be initiated [23]. Upregulation of VPEs occurs in various types of PCD. VPE involvement has been widely demonstrated during developmental PCD (dPCD), including seed coat formation in angiosperms [10], xylogenesis [12], development of the root velamen radicum in the epiphytic orchid Cymbidium tracyanum [14], development of pollen and tapetal cell degradation in Arabidopsis thaliana [13][15], leaf morphogenesis of the lace plant (Aponogeton madagascariensis) [24], and degradation of aleurone layers in rice (Oryza sativa) [11][19]. One of the best-known types of PCD regulated by VPEs is the hypersensitive response (HR), which was first observed in VPE-silenced Nicotiana benthamiana infected with tobacco mosaic virus (TMV) [25]. Furthermore, they take part in PCD induced by various abiotic stresses [8][17][19][26][27][28][29] and are even called executors of plant PCD. On the other hand, their role in the late stages of autophagy, i.e., degradation of autophagic bodies, is only presumed. Nevertheless, new data on the involvement of autophagy in PCD have appeared recently, and VPEs are considered an important part of this relationship [14][21].
Besides protease activity, the ligase activity of VPEs has also been observed [3][30]. The protein ligation activity of VPEs has been studied on the two-chain hybrid form of γVPE (AtLEGγ). It contains the C-terminal pro-domain LSAM (legumain stabilization and activity modulation), which modulates its activity and provides stability at neutral pH. Under such conditions, ligase activity rather than protease activity is favored [31]. Meanwhile, some VPEs preferably exhibit ligase or protease activity regardless of pH. VPEs isolated from Clitoria ternatea, named butelase 1 and butelase 2, perform predominantly ligase activity at a mildly acidic pH and protease activity at neutral pH, respectively [30]. The ligase activity allows VPEs to form cyclic peptides [3][32][33][34]. It has been observed that some VPEs may perform greater protein cyclization activity than others. Among four VPEs (PxAEP1, 2, 3a, and 3b) found in petunia (Petunia), PxAEP3b has been characterized with the most efficient ability to produce cyclic peptide kalata B1 (kB1). PxAFP3a was found to be significantly less effective in kB1 cyclic formation despite having a sequence very similar to that of PxAFP3b [35].

3. Role of Vacuolar Processing Enzymes in Programmed Cell Death under Biotic Stress

Local PCD, also called the hypersensitive response (HR), is a radical but effective plant method to combat various biotic stressors such as viruses, bacteria, and fungi. Rapid death of cells at the site of pathogen infection prevents it from spreading in the host plant [36]. HR mediated by VPEs was first observed on VPE-silenced Nicotiana benthamiana infected with TMV. In VPE-non-silenced plants, pathogen attack was related to increased expression and translation of VPEs in the infected leaves. Moreover, ultrastructural images showed disintegration of the tonoplast in the cells of VPE-non-silenced plants, whereas in cells of VPE-silenced plants, vacuole morphology remained unchanged. These ultrastructural analyses have shown the contribution of VPEs to vacuole collapse during PCD [25]. Further research has shown that VPEs are involved in plant defense against such pathogens as the bacterium Erwinia amylovora [37], nematode Heterodera filipjevi [38], the oomycetes Hyaloperonospora arabidopsidis [39] and Phytophthora parasitica [40], and the fungi Phaeoisariopsis personata [41], Fusarium oxysporum (FocTR4) [42] and Botryosphaeria dothidea [43].

4. Role of Vacuolar Processing Enzymes in Programmed Cell Death Induced by Abiotic Stress

VPEs have been found to mediate ePCD induced by several abiotic stresses. Genome-wide analysis of the apple (Malus) genome has shown the presence of twenty genes coding for VPEs (MdVPEs), which have been distinguished into four groups based on Arabidopsis thaliana types: MdαVPEs, MdβVPEs, MdγVPEs, and MdδVPEs. Expression patterns of eighteen MdVPEs were examined under abiotic stresses such as salinity, cadmium treatment, low temperature, and drought. Each of the above-mentioned stresses increased the expression of some MdVPEs; however, during salinity, eighteen examined MdVPEs were up-regulated. It has also been shown that different groups respond specifically to different stresses, as three of five MdγVPEs were more sensitive to drought and salinity than cadmium and low temperature [8]. On the other hand, genome-wide analysis of upland cotton (Gossypium hirsutum) showed the presence of thirteen genes coding for VPEs (GhVPEs). Three of these showed increased expression under waterlogging and salinity. In detail, VPEs of upland cotton whose expression increased during these abiotic stresses were γ- and δVPE-like [29]. Salinity-induced PCD has also been studied in rice (Oryza sativa), in which four genes of VPEs (OsVPEs) were found. In particular, OsVPE3 mediated salinity-induced PCD, as its silencing increases plant tolerance to this kind of stress. Moreover, it has been demonstrated that PCD prevention by silencing OsVPE3 is related to the suppression of tonoplast rupture [27]. Salinity also increased the expression of γVPE in alfalfa (Medicago sativa) root meristem. Interestingly, melatonin treatment reduced ROS formation and decreased γVPE gene expression, which prevented salinity-induced ePCD. The pro-survival mechanism of melatonin is thought to be related to upregulation of uncoupling proteins 1 and 2 (UCP1 and UCP2) and Bax inhibitor-1 (BI-1) genes. UCPs probably mediate a decrease in electron leakage and ROS formation in plant mitochondria, whereas BI-1 (inhibitor of pro-apoptotic Bax protein) regulates Ca2+ homeostasis [28]. Both ROS and Ca2+ are signal messengers that can participate in the MPK activation cascade. MPK6 was found to positively regulate γVPE expression in Arabidopsis thaliana seedlings during abiotic stress [26]. Therefore, melatonin may contribute to the initiation of a molecular cascade that leads to a decreased expression of γVPE. ePCD can also be induced by low or high temperatures. In Arabidopsis thaliana, increased gene expression and enzyme activity of γVPE were observed after heat shock induction. Silencing γVPE, as in the case of rice, also contributed to suppression of tonoplast rupture. Moreover, a relation between γVPE and mitogen-activated protein kinase (MPK6) was demonstrated. The application of MPK6 inhibitor during heat shock contributed to a decrease in gene expression and enzyme activity of γVPE. Similar relations have been observed with mutants lacking MPK6. Additionally, Arabidopsis mutants overexpressing MPK6 showed an increase in γVPE gene expression and enzyme activity resulting in a significant decrease in seedling fresh weight in comparison to the wild type. Therefore, MPK6 may be considered as a positive regulator of γVPE [26]. The members of the NAC family, transcription factors of PCD, also regulate the expression of VPEs. GmNAC30/GmNAC81 from soybean (Glycine max) affected the expression of VPEs by directly activating their promoters under ER- and osmotic stress-induced PCD [44]. Molecular manipulation of GmNAC81 altered the plant response to stress. Overexpression of GmNAC81, through the mediation of VPEs, increased the sensitivity of plants to drought [17]. VPEs have also been found to execute sugar starvation-induced ePCD in tobacco BY-2 cells. Moreover, in this case for the first time, it was observed that VPEs are translocated from the ER to the vacuole through autophagosomes [21].

References

  1. Yamada, K.; Shimada, T.; Nishimura, M.; Hara-Nishimura, I. A VPE Family Supporting Various Vacuolar Functions in Plants. Physiol. Plant. 2005, 123, 369–375.
  2. Shimada, T.; Yamada, K.; Kataoka, M.; Nakaune, S.; Koumoto, Y.; Kuroyanagi, M.; Tabata, S.; Kato, T.; Shinozaki, K.; Seki, M.; et al. Vacuolar Processing Enzymes Are Essential for Proper Processing of Seed Storage Proteins in Arabidopsis Thaliana. J. Biol. Chem. 2003, 278, 32292–32299.
  3. Yamada, K.; Basak, A.; Goto, S.; Tarnawska-Glatt, K.; Hara-Nishimura, I. Vacuolar Processing Enzymes in the Plant Life Cycle. New Phytol. 2019, 226, 21–31.
  4. Poncet, V.; Scutt, C.; Tournebize, R.; Villegente, M.; Cueff, G.; Rajjou, L.; Balliau, T.; Zivy, M.; Fogliani, B.; Job, C.; et al. The Amborella Vacuolar Processing Enzyme Family. Front. Plant Sci. 2015, 6, 618.
  5. Vorster, B.; Cullis, C.; Kunert, K. Plant Vacuolar Processing Enzymes. Front. Plant Sci. 2019, 10, 479.
  6. Wang, B.; Li, N.; Huang, S.; Hu, J.; Wang, Q.; Tang, Y.; Yang, T.; Asmutola, P.; Wang, J.; Yu, Q. Enhanced Soluble Sugar Content in Tomato Fruit Using CRISPR/Cas9-Mediated SlINVINH1 and SlVPE5 Gene Editing. PeerJ 2021, 9, 12478.
  7. Zhang, H.; Tao, X.; Zhang, F. Genome-Wide Identification and Expression Analysis of the Vacuolar Processing Enzyme (VPE) Family Genes in Pear. J. Hortic. Sci. Biotechnol. 2021, 96, 469–478.
  8. Song, J.; Yang, F.; Xun, M.; Xu, L.; Tian, X.; Zhang, W.; Yang, H. Genome-Wide Identification and Characterization of Vacuolar Processing Enzyme Gene Family and Diverse Expression Under Stress in Apple (Malus × Domestic). Front. Plant Sci. 2020, 11, 626.
  9. Hara-Nishimura, I.; Shimada, T.; Hiraiwa, N.; Nishimura, M. Vacuolar Processing Enzyme Responsible for Maturation of Seed Proteins. J. Plant Physiol. 1995, 145, 632–640.
  10. Nakaune, S.; Yamada, K.; Kondo, M.; Kato, T.; Tabata, S.; Nishimura, M.; Hara-Nishimura, I. A Vacuolar Processing Enzyme, δVPE, Is Involved in Seed Coat Formation at the Early Stage of Seed Development. Plant Cell 2005, 17, 876–887.
  11. Zheng, Y.; Zhang, H.; Deng, X.; Liu, J.; Chen, H. The Relationship between Vacuolation and Initiation of PCD in Rice (Oryza Sativa) Aleurone Cells. Sci. Rep. 2017, 7, 41245.
  12. Cheng, Z.; Zhang, J.; Yin, B.; Liu, Y.; Wang, B.; Li, H.; Lu, H. γVPE Plays an Important Role in Programmed Cell Death for Xylem Fiber Cells by Activating Protease CEP1 Maturation in Arabidopsis thaliana. Int. J. Biol. Macromol. 2019, 137, 703–711.
  13. Cheng, Z.; Guo, X.; Zhang, J.; Liu, Y.; Wang, B.; Li, H.; Lu, H. ΒVPE Is Involved in Tapetal Degradation and Pollen Development by Activating Proprotease Maturation in Arabidopsis Thaliana. J. Exp. Bot. 2020, 71, 1943–1955.
  14. Li, J.-W.; Zhang, S.-B.; Xi, H.-P.; Bradshaw, C.J.A.; Zhang, J.-L. Processes Controlling Programmed Cell Death of Root Velamen Radicum in an Epiphytic Orchid. Ann. Bot. 2020, 126, 261–275.
  15. Guo, X.; Li, L.; Liu, X.; Zhang, C.; Yao, X.; Xun, Z.; Zhao, Z.; Yan, W.; Zou, Y.; Liu, D.; et al. MYB2 Is Important for Tapetal PCD and Pollen Development by Directly Activating Protease Expression in Arabidopsis. Int. J. Mol. Sci. 2022, 23, 3563.
  16. Jiang, J.; Hu, J.; Tan, R.; Han, Y.; Li, Z. Expression of IbVPE1 from Sweet Potato in Arabidopsis Affects Leaf Development, Flowering Time and Chlorophyll Catabolism. BMC Plant Biol. 2019, 19, 184.
  17. Ferreira, D.O.; Fraga, O.T.; Pimenta, M.R.; Caetano, H.D.N.; Machado, J.P.B.; Carpinetti, P.A.; Brustolini, O.J.B.; Quadros, I.P.S.; Reis, P.A.B.; Fontes, E.P.B. GmNAC81 Inversely Modulates Leaf Senescence and Drought Tolerance. Front Genet 2020, 11, 601876.
  18. Fraga, O.T.; de Melo, B.P.; Quadros, I.P.S.; Reis, P.A.B.; Fontes, E.P.B. Senescence-Associated Glycine Max (Gm)NAC Genes: Integration of Natural and Stress-Induced Leaf Senescence. Int. J. Mol. Sci. 2021, 22, 8287.
  19. Zhang, H.; Xiao, Y.; Deng, X.; Feng, H.; Li, Z.; Zhang, L.; Chen, H. OsVPE3 Mediates GA-Induced Programmed Cell Death in Rice Aleurone Layers via Interacting with Actin Microfilaments. Rice 2020, 13, 22.
  20. Quadros, I.; Madeira, N.; Loriato, V.; Fillietaz Saia, T.; Coutinho Silva, J.; Soares, F.; Carvalho, J.; Reis, P.A.; Fontes, E.; Clarindo, W.; et al. Cadmium-mediated Toxicity in Plant Cells Is Associated with the DCD / NRP -mediated Cell Death Response. Plant Cell Environ. 2021, 45, 556–571.
  21. Teper-Bamnolker, P.; Danieli, R.; Peled-Zehavi, H.; Belausov, E.; Abu-Abied, M.; Avin-Wittenberg, T.; Sadot, E.; Eshel, D. Vacuolar Processing Enzyme Translocates to the Vacuole through the Autophagy Pathway to Induce Programmed Cell Death. Autophagy 2021, 17, 3109–3123.
  22. Stefaniak, S.; Wojtyla, Ł.; Pietrowska-Borek, M.; Borek, S. Molecular Sciences Completing Autophagy: Formation and Degradation of the Autophagic Body and Metabolite Salvage in Plants. Int. J. Mol. Sci. 2020, 21, 2205.
  23. Sychta, K.; Słomka, A.; Kuta, E. Insights into Plant Programmed Cell Death Induced by Heavy Metals—Discovering a Terra Incognita. Cells 2021, 10, 65.
  24. Rantong, G.; Gunawardena, A.H.L.A.N. Vacuolar Processing Enzymes, AmVPE1 and AmVPE2, as Potential Executors of Ethylene Regulated Programmed Cell Death in the Lace Plant (Aponogeton Madagascariensis). Botany 2018, 96, 235–247.
  25. Hatsugai, N.; Kuroyanagi, M.; Yamada, K.; Meshi, T.; Tsuda, S.; Kondo, M.; Nishimura, M.; Hara-Nishimura, I. A Plant Vacuolar Protease, VPE, Mediates Virus-Induced Hypersensitive Cell Death. Science 2004, 305, 855–858.
  26. Li, Z.; Yue, H.; Xing, D. MAP Kinase 6-Mediated Activation of Vacuolar Processing Enzyme Modulates Heat Shock-Induced Programmed Cell Death in Arabidopsis. New Phytol. 2012, 195, 85–96.
  27. Lu, W.; Deng, M.; Guo, F.; Wang, M.; Zeng, Z.; Han, N.; Yang, Y.; Zhu, M.; Bian, H. Suppression of OsVPE3 Enhances Salt Tolerance by Attenuating Vacuole Rupture during Programmed Cell Death and Affects Stomata Development in Rice. Rice 2016, 9, 65.
  28. Jalili, S.; Ehsanpour, A.A.; Javadirad, S.M. The Role of Melatonin on Caspase-3-like Activity and Expression of the Genes Involved in Programmed Cell Death (PCD) Induced by in Vitro Salt Stress in Alfalfa (Medicago Sativa L.) Roots. Bot. Stud. 2022, 63, 19.
  29. Zhu, L.; Wang, X.; Tian, J.; Zhang, X.; Yu, T.; Li, Y.; Li, D. Genome-Wide Analysis of VPE Family in Four Gossypium Species and Transcriptional Expression of VPEs in the Upland Cotton Seedlings under Abiotic Stresses. Funct. Integr. Genomics 2022, 22, 179–192.
  30. Hemu, X.; El Sahili, A.; Hu, S.; Wong, K.; Chen, Y.; Wong, Y.H.; Zhang, X.; Serra, A.; Goh, B.C.; Darwis, D.A.; et al. Structural Determinants for Peptide-Bond Formation by Asparaginyl Ligases. Proc. Natl. Acad. Sci. USA 2019, 116, 11737–11746.
  31. Zauner, F.B.; Dall, E.; Regl, C.; Grassi, L.; Huber, C.G.; Cabrele, C.; Brandstetter, H. Crystal Structure of Plant Legumain Reveals a Unique Two-Chain State with PH-Dependent Activity Regulation. Plant Cell 2018, 30, 686–699.
  32. Shafee, T.; Harris, K.; Anderson, M. Chapter Eight—Biosynthesis of Cyclotides. In Advances in Botanical Research; Craik, D.J., Ed.; Academic Press: Cambridge, MA, USA, 2015; Volume 76, pp. 227–269.
  33. Poon, S.; Harris, K.S.; Jackson, M.A.; McCorkelle, O.C.; Gilding, E.K.; Durek, T.; van der Weerden, N.L.; Craik, D.J.; Anderson, M.A. Co-Expression of a Cyclizing Asparaginyl Endopeptidase Enables Efficient Production of Cyclic Peptides in Planta. J. Exp. Bot. 2018, 69, 633–641.
  34. James, A.M.; Haywood, J.; Mylne, J.S. Macrocyclization by Asparaginyl Endopeptidases. New Phytol. 2018, 218, 923–928.
  35. Jackson, M.A.; Gilding, E.K.; Shafee, T.; Harris, K.S.; Kaas, Q.; Poon, S.; Yap, K.; Jia, H.; Guarino, R.; Chan, L.Y.; et al. Molecular Basis for the Production of Cyclic Peptides by Plant Asparaginyl Endopeptidases. Nat. Commun. 2018, 9, 2411.
  36. Balint-Kurti, P. The Plant Hypersensitive Response: Concepts, Control and Consequences. Mol. Plant Pathol. 2019, 20, 1163–1178.
  37. Iakimova, E.T.; Sobiczewski, P.; Michalczuk, L.; Węgrzynowicz-Lesiak, E.; Mikiciński, A.; Woltering, E.J. Morphological and Biochemical Characterization of Erwinia Amylovora-Induced Hypersensitive Cell Death in Apple Leaves. Plant Physiol. Biochem. 2013, 63, 292–305.
  38. Labudda, M.; Różańska, E.; Prabucka, B.; Muszyńska, E.; Marecka, D.; Kozak, M.; Dababat, A.A.; Sobczak, M. Activity Profiling of Barley Vacuolar Processing Enzymes Provides New Insights into the Plant and Cyst Nematode Interaction. Mol. Plant Pathol. 2019, 21, 38–52.
  39. Misas-Villamil, J.C.; Toenges, G.; Kolodziejek, I.; Sadaghiani, A.M.; Kaschani, F.; Colby, T.; Bogyo, M.; van der Hoorn, R.A.L. Activity Profiling of Vacuolar Processing Enzymes Reveals a Role for VPE during Oomycete Infection. Plant J. 2013, 73, 689–700.
  40. Gao, X.; Tang, Y.; Shi, Q.; Wei, Y.; Wang, X.; Shan, W.; Qiang, X. Vacuolar Processing Enzyme Positively Modulates Plant Resistance and Cell Death in Response to Phytophthora Parasitica Infection. J. Integr. Agric. 2022. In Press, Journal Pre-proof.
  41. Kumar, D.; Rampuria, S.; Singh, N.K.; Shukla, P.; Kirti, P.B. Characterization of a Vacuolar Processing Enzyme Expressed in Arachis Diogoi in Resistance Responses against Late Leaf Spot Pathogen, Phaeoisariopsis Personata. Plant Mol. Biol. 2015, 88, 177–191.
  42. Wan Abdullah, W.M.A.N.; Saidi, N.B.; Yusof, M.T.; Wee, C.-Y.; Loh, H.-S.; Ong-Abdullah, J.; Lai, K.-S. Vacuolar Processing Enzymes Modulating Susceptibility Response to Fusarium Oxysporum f. Sp. Cubense Tropical Race 4 Infections in Banana. Front. Plant Sci. 2022, 12, 769855.
  43. Dong, C.; Li, R.; Wang, N.; Liu, Y.; Zhang, Y.; Bai, S. Apple Vacuolar Processing Enzyme 4 Is Regulated by Cysteine Protease Inhibitor and Modulates Fruit Disease Resistance. J. Exp. Bot. 2022, 73, 3758–3773.
  44. Mendes, G.C.; Reis, P.A.B.; Calil, I.P.; Carvalho, H.H.; Aragão, F.J.L.; Fontes, E.P.B. GmNAC30 and GmNAC81 Integrate the Endoplasmic Reticulum Stress- and Osmotic Stress-Induced Cell Death Responses through a Vacuolar Processing Enzyme. Proc. Natl. Acad. Sci. USA 2013, 110, 19627–19632.
More
© Text is available under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/)
Video Production Service
Feedback