Golgi-localized cyclophilin 21 proteins negatively regulate ABA signalling via the peptidyl prolyl isomerase activity during early seedling development

  • Haemyeong Jung
  • Seung Hee Jo
  • Hyun Ji Park
  • Areum Lee
  • Hyun-Soon Kim
  • Hyo-Jun Lee
  • Hye Sun ChoEmail author


Key message

Plant possesses particular Golgi-resident cyclophilin 21 proteins (CYP21s) and the catalytic isomerase activities have a negative effect on ABA signalling gene expression during early seedling development.


Cyclophilins (CYPs) are essential for diverse cellular process, as these catalyse a rate-limiting step in protein folding. Although Golgi proteomics in Arabidopsis thaliana suggests the existence of several CYPs in the Golgi apparatus, only one putative Golgi-resident CYP protein has been reported in rice (Oryza sativa L.; OsCYP21-4). Here, we identified the Golgi-resident CYP21 family genes and analysed their molecular characteristics in Arabidopsis and rice. The CYP family genes (CYP21-1, CYP21-2, CYP21-3, and CYP21-4) are plant-specific, and their appearance and copy numbers differ among plant species. CYP21-1 and CYP21-4 are common to all angiosperms, whereas CYP21-2 and CYP21-3 evolved in the Malvidae subclass. Furthermore, all CYP21 proteins localize to cis-Golgi, trans-Golgi or both cis- and trans-Golgi membranes in plant cells. Additionally, based on the structure, enzymatic function, and topological orientation in Golgi membranes, CYP21 proteins are divided into two groups. Genetic analysis revealed that Group I proteins (CYP21-1 and CYP21-2) exhibit peptidyl prolyl cis–trans isomerase (PPIase) activity and regulate seed germination and seedling growth and development by affecting the expression levels of abscisic acid signalling genes. Thus, we identified the Golgi-resident CYPs and demonstrated that their PPIase activities are required for early seedling growth and development in higher plants.


ABA signalling Cyclophilin 21 proteins Golgi apparatus Peptidyl prolyl isomerase Seed germination Seedling development 



We thank Dr. An Gynheung (Kyung Hee University, Korea) for kindly providing us with the T-DNA insertion mutant of OsCYP21-1. This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korean government (Grant No. 2019R1A2C2002295) and Korea Research Institute of Bioscience and Biotechnology Research Initiative Programs (Grant Nos. KGM5371911 and KGM9481913) to H.S.C.

Author contributions

HSC designed the research. HJ performed the most of experiments. SHJ performed a part of qRT-PCR analysis. HJP and AL helped in cell biology experiments. H-SK and H-JL contributed to the biological interpretation. HJ and HSC analysed all data and wrote the paper.

Compliance with ethical standards

Conflict of interest

The authors declare no conflict of interest.

Supplementary material

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  1. Ahn JC, Kim DW, You YN, Seok MS, Park JM, Hwang H, Kim BG, Luan S, Park HS, Cho HS (2010) Classification of rice (Oryza sativa L. Japonica nipponbare) immunophilins (FKBPs, CYPs) and expression patterns under water stress. BMC Plant Biol 10:253PubMedPubMedCentralCrossRefGoogle Scholar
  2. Barbosa Dos Santos I, Park SW (2019) Versatility of cyclophilins in plant growth and survival: a case study in Arabidopsis. Biomolecules 9:20PubMedCentralCrossRefGoogle Scholar
  3. Bewley JD (1997) Seed germination and dormancy. Plant Cell 9:1055–1066PubMedPubMedCentralCrossRefGoogle Scholar
  4. Breiman A, Fawcett TW, Ghirardi ML, Mattoo AK (1992) Plant organelles contain distinct peptidylprolyl cis, trans-isomerases. J Biol Chem 267:21293–21296PubMedGoogle Scholar
  5. Carles C, Bies-Etheve N, Aspart L, Leon-Kloosterziel KM, Koornneef M, Echeverria M, Delseny M (2002) Regulation of Arabidopsis thaliana Em genes: role of ABI5. Plant J 30:373–383PubMedCrossRefGoogle Scholar
  6. Che P, Bussell JD, Zhou W, Estavillo GM, Pogson BJ, Smith SM (2010) Signaling from the endoplasmic reticulum activates brassinosteroid signaling and promotes acclimation to stress in Arabidopsis. Sci Signal 3:ra69PubMedCrossRefGoogle Scholar
  7. Chen X, Andrews PC, Wang Y (2012) Quantitative analysis of liver Golgi proteome in the cell cycle. Methods Mol Biol 909:125–140PubMedPubMedCentralGoogle Scholar
  8. Daskalova SM, Pah AR, Baluch DP, Lopez LC (2009) The Arabidopsis thaliana putative sialyltransferase resides in the Golgi apparatus but lacks the ability to transfer sialic acid. Plant Biol (Stuttg) 11:284–299CrossRefGoogle Scholar
  9. Dave A, Vaistij FE, Gilday AD, Penfield SD, Graham IA (2016) Regulation of Arabidopsis thaliana seed dormancy and germination by 12-oxo-phytodienoic acid. J Exp Bot 67:2277–2284PubMedPubMedCentralCrossRefGoogle Scholar
  10. Dekkers BJ, Willems L, Bassel GW, van Bolderen-Veldkamp RP, Ligterink W, Hilhorst HW, Bentsink L (2012) Identification of reference genes for RT-qPCR expression analysis in Arabidopsis and tomato seeds. Plant Cell Physiol 53:28–37PubMedCrossRefGoogle Scholar
  11. Finch-Savage WE, Leubner-Metzger G (2006) Seed dormancy and the control of germination. New Phytol 171:501–523PubMedCrossRefGoogle Scholar
  12. Finkelstein RR, Lynch TJ (2000) Abscisic acid inhibition of radicle emergence but not seedling growth is suppressed by sugars. Plant Physiol 122:1179–1186PubMedPubMedCentralCrossRefGoogle Scholar
  13. Finkkelstein R (2013) The Arabidopsis bookGoogle Scholar
  14. Fischer G, Bang H, Mech C (1984) Determination of enzymatic catalysis for the cis-trans-isomerization of peptide binding in proline-containing peptides. Biomed Biochim Acta 43:1101–1111PubMedGoogle Scholar
  15. Graeber K, Nakabayashi K, Miatton E, Leubner-Metzger G, Soppe WJ (2012) Molecular mechanisms of seed dormancy. Plant, Cell Environ 35:1769–1786CrossRefGoogle Scholar
  16. Hawes A, Osterrieder A, Sparkes I (2008) The Golgi apparatus. Springer, ViennaGoogle Scholar
  17. He Z, Li L, Luan S (2004) Immunophilins and parvulins. Superfamily of peptidyl prolyl isomerases in Arabidopsis. Plant Physiol 134:1248–1267PubMedPubMedCentralCrossRefGoogle Scholar
  18. Heijne G (1986) The distribution of positively charged residues in bacterial inner membrane proteins correlates with the trans-membrane topology. EMBO J 5:3021–3027PubMedPubMedCentralCrossRefGoogle Scholar
  19. Hirayama T, Shinozaki K (2007) Perception and transduction of abscisic acid signals: keys to the function of the versatile plant hormone ABA. Trends Plant Sci 12:343–351PubMedCrossRefGoogle Scholar
  20. Holdsworth MJ, Bentsink L, Soppe WJ (2008) Molecular networks regulating Arabidopsis seed maturation, after-ripening, dormancy and germination. New Phytol 179:33–54PubMedCrossRefGoogle Scholar
  21. Hubbard KE, Nishimura N, Hitomi K, Getzoff ED, Schroeder JI (2010) Early abscisic acid signal transduction mechanisms: newly discovered components and newly emerging questions. Genes Dev 24:1695–1708PubMedPubMedCentralCrossRefGoogle Scholar
  22. Ingelsson B, Shapiguzov A, Kieselbach T, Vener AV (2009) Peptidyl-prolyl isomerase activity in chloroplast thylakoid lumen is a dispensable function of immunophilins in Arabidopsis thaliana. Plant Cell Physiol 50:1801–1814PubMedCrossRefGoogle Scholar
  23. Ito Y, Uemura T, Nakano A (2014) Formation and maintenance of the Golgi apparatus in plant cells. Int Rev Cell Mol Biol 310:221–287PubMedCrossRefGoogle Scholar
  24. Kim H, Hwang H, Hong JW, Lee YN, Ahn IP, Yoon IS, Yoo SD, Lee S, Lee SC, Kim BG (2012) A rice orthologue of the ABA receptor, OsPYL/RCAR5, is a positive regulator of the ABA signal transduction pathway in seed germination and early seedling growth. J Exp Bot 63:1013–1024PubMedCrossRefGoogle Scholar
  25. Koornneef M, Bentsink L, Hilhorst H (2002) Seed dormancy and germination. Curr Opin Plant Biol 5:33–36PubMedCrossRefGoogle Scholar
  26. Korves TM, Bergelson J (2003) A developmental response to pathogen infection in Arabidopsis. Plant Physiol 133:339–347PubMedPubMedCentralCrossRefGoogle Scholar
  27. Lee SS, Park HJ, Jung WY, Lee A, Yoon DH, You YN, Kim HS, Kim BG, Ahn JC, Cho HS (2015) OsCYP21-4, a novel Golgi-resident cyclophilin, increases oxidative stress tolerance in rice. Front Plant Sci 6:797PubMedPubMedCentralGoogle Scholar
  28. Leung J, Giraudat J (1998) Abscisic acid signal transduction. Annu Rev Plant Physiol Plant Mol Biol 49:199–222PubMedCrossRefGoogle Scholar
  29. Liu JX, Howell SH (2010) Endoplasmic reticulum protein quality control and its relationship to environmental stress responses in plants. Plant Cell 22:2930–2942PubMedPubMedCentralCrossRefGoogle Scholar
  30. Lopez-Molina L, Mongrand S, Chua NH (2001) A postgermination developmental arrest checkpoint is mediated by abscisic acid and requires the ABI5 transcription factor in Arabidopsis. Proc Natl Acad Sci USA 98:4782–4787PubMedCrossRefGoogle Scholar
  31. Lopez-Molina L, Mongrand S, McLachlin DT, Chait BT, Chua NH (2002) ABI5 acts downstream of ABI3 to execute an ABA-dependent growth arrest during germination. Plant J 32:317–328PubMedCrossRefGoogle Scholar
  32. Magwa RA, Zhao H, Xing Y (2016) Genome-wide association mapping revealed a diverse genetic basis of seed dormancy across subpopulations in rice (Oryza sativa L.). BMC Genet 17:28PubMedPubMedCentralCrossRefGoogle Scholar
  33. Mayr C, Richter K, Lilie H, Buchner J (2000) Cpr6 and Cpr7, two closely related Hsp90-associated immunophilins from Saccharomyces cerevisiae, differ in their functional properties. J Biol Chem 275:34140–34146PubMedCrossRefGoogle Scholar
  34. McCourt P, Creelman R (2008) The ABA receptors—we report you decide. Curr Opin Plant Biol 11:474–478PubMedCrossRefGoogle Scholar
  35. Min MK, Jang M, Lee M, Lee J, Song K, Lee Y, Choi KY, Robinson DG, Hwang I (2013) Recruitment of Arf1-GDP to Golgi by Glo3p-type ArfGAPs is crucial for golgi maintenance and plant growth. Plant Physiol 161:676–691PubMedCrossRefGoogle Scholar
  36. Mowbrey K, Dacks JB (2009) Evolution and diversity of the Golgi body. FEBS Lett 583:3738–3745PubMedCrossRefGoogle Scholar
  37. Nakamura S, Toyama T (2001) Isolation of a VP1 homologue from wheat and analysis of its expression in embryos of dormant and non-dormant cultivars. J Exp Bot 52:875–876PubMedCrossRefGoogle Scholar
  38. Nakamura S, Abe F, Kawahigashi H, Nakazono K, Tagiri A, Matsumoto T, Utsugi S, Ogawa T, Handa H, Ishida H, Mori M, Kawaura K, Ogihara Y, Miura H (2011) A wheat homolog of MOTHER OF FT AND TFL1 acts in the regulation of germination. Plant Cell 23:3215–3229PubMedPubMedCentralCrossRefGoogle Scholar
  39. Nakano RT, Yamada K, Bednarek P, Nishimura M, Hara-Nishimura I (2014) ER bodies in plants of the Brassicales order: biogenesis and association with innate immunity. Front Plant Sci 5:73PubMedPubMedCentralGoogle Scholar
  40. Nebenfuhr A, Staehelin LA (2001) Mobile factories: Golgi dynamics in plant cells. Trends Plant Sci 6:160–167PubMedCrossRefGoogle Scholar
  41. Nelson BK, Cai X, Nebenfuhr A (2007) A multicolored set of in vivo organelle markers for co-localization studies in Arabidopsis and other plants. Plant J 51:1126–1136PubMedCrossRefGoogle Scholar
  42. Nikolovski N, Rubtsov D, Segura MP, Miles GP, Stevens TJ, Dunkley TP, Munro S, Lilley KS, Dupree P (2012) Putative glycosyltransferases and other plant Golgi apparatus proteins are revealed by LOPIT proteomics. Plant Physiol 160:1037–1051PubMedPubMedCentralCrossRefGoogle Scholar
  43. Nikolovski N, Shliaha PV, Gatto L, Dupree P, Lilley KS (2014) Label-free protein quantification for plant Golgi protein localization and abundance. Plant Physiol 166:1033–1043PubMedPubMedCentralCrossRefGoogle Scholar
  44. Ohnishi T, Sugahara S, Yamada T, Kikuchi K, Yoshiba Y, Hirano HY, Tsutsumi N (2005) OsNAC6, a member of the NAC gene family, is induced by various stresses in rice. Genes Genet Syst 80:135–139PubMedCrossRefGoogle Scholar
  45. Okekeogbu IO, Pattathil S, Gonzalez Fernandez-Nino SM, Aryal UK, Penning BW, Lao J, Heazlewood JL, Hahn MG, McCann MC, Carpita NC (2019) Glycome and proteome components of Golgi membranes are common between two angiosperms with distinct cell-wall structures. Plant Cell 31:1094–1112PubMedCrossRefGoogle Scholar
  46. Opat AS, van Vliet C, Gleeson PA (2001) Trafficking and localisation of resident Golgi glycosylation enzymes. Biochimie 83:763–773PubMedCrossRefGoogle Scholar
  47. Park HJ, Lee A, Lee SS, An DJ, Moon KB, Ahn JC, Kim HS, Cho HS (2017) Overexpression of Golgi protein CYP21-4 s improves crop productivity in potato and rice by increasing the abundance of mannosidic glycoproteins. Front Plant Sci 8:1250PubMedPubMedCentralCrossRefGoogle Scholar
  48. Parsons HT, Christiansen K, Knierim B, Carroll A, Ito J, Batth TS, Smith-Moritz AM, Morrison S, McInerney P, Hadi MZ, Auer M, Mukhopadhyay A, Petzold CJ, Scheller HV, Loque D, Heazlewood JL (2012a) Isolation and proteomic characterization of the Arabidopsis Golgi defines functional and novel components involved in plant cell wall biosynthesis. Plant Physiol 159:12–26PubMedPubMedCentralCrossRefGoogle Scholar
  49. Parsons HT, Drakakaki G, Heazlewood JL (2012b) Proteomic dissection of the Arabidopsis Golgi and trans-Golgi network. Front Plant Sci 3:298PubMedGoogle Scholar
  50. Raghavendra AS, Gonugunta VK, Christmann A, Grill E (2010) ABA perception and signalling. Trends Plant Sci 15:395–401PubMedCrossRefGoogle Scholar
  51. Rapoport TA, Goder V, Heinrich SU, Matlack KE (2004) Membrane-protein integration and the role of the translocation channel. Trends Cell Biol 14:568–575PubMedCrossRefGoogle Scholar
  52. Rock C (2000) Pathways to abscisic acid-regulated gene expression. New Phytol 148:357–396CrossRefGoogle Scholar
  53. Rodriguez-Gacio Mdel C, Matilla-Vazquez MA, Matilla AJ (2009) Seed dormancy and ABA signaling: the breakthrough goes on. Plant Signal Behav 4:1035–1049PubMedCrossRefGoogle Scholar
  54. Shu K, Liu XD, Xie Q, He ZH (2016) Two faces of one seed: hormonal regulation of dormancy and germination. Mol Plant 9:34–45PubMedCrossRefGoogle Scholar
  55. Skubacz A, Daszkowska-Golec A, Szarejko I (2016) The role and regulation of ABI5 (ABA-Insensitive 5) in plant development, abiotic stress responses and phytohormone crosstalk. Front Plant Sci 7:1884PubMedPubMedCentralCrossRefGoogle Scholar
  56. Sperotto RA, Ricachenevsky FK, Duarte GL, Boff T, Lopes KL, Sperb ER, Grusak MA, Fett JP (2009) Identification of up-regulated genes in flag leaves during rice grain filling and characterization of OsNAC5, a new ABA-dependent transcription factor. Planta 230:985–1002PubMedCrossRefGoogle Scholar
  57. Sprenger J, Lynn Fink J, Karunaratne S, Hanson K, Hamilton NA, Teasdale RD (2008) LOCATE: a mammalian protein subcellular localization database. Nucleic Acids Res 36:D230–D233PubMedCrossRefGoogle Scholar
  58. Tu L, Banfield DK (2010) Localization of Golgi-resident glycosyltransferases. Cell Mol Life Sci 67:29–41PubMedCrossRefGoogle Scholar
  59. Wang P, Heitman J (2005) The cyclophilins. Genome Biol 6:226PubMedPubMedCentralCrossRefGoogle Scholar
  60. Wei JH, Seemann J (2010) Unraveling the Golgi ribbon. Traffic 11:1391–1400PubMedPubMedCentralCrossRefGoogle Scholar
  61. Weiergraber OH, Eckhoff A, Granzin J (2006) Crystal structure of a plant immunophilin domain involved in regulation of MDR-type ABC transporters. FEBS Lett 580:251–255PubMedCrossRefGoogle Scholar
  62. Weitbrecht K, Muller K, Leubner-Metzger G (2011) First off the mark: early seed germination. J Exp Bot 62:3289–3309PubMedCrossRefGoogle Scholar
  63. Wilson RL, Kim H, Bakshi A, Binder BM (2014) The ethylene receptors ETHYLENE RESPONSE1 and ETHYLENE RESPONSE2 have contrasting roles in seed germination of Arabidopsis during salt stress. Plant Physiol 165:1353–1366PubMedPubMedCentralCrossRefGoogle Scholar
  64. Yamada K, Hara-Nishimura I, Nishimura M (2011) Unique defense strategy by the endoplasmic reticulum body in plants. Plant Cell Physiol 52:2039–2049PubMedCrossRefGoogle Scholar
  65. Yan A, Wu M, Yan L, Hu R, Ali I, Gan Y (2014) AtEXP2 is involved in seed germination and abiotic stress response in Arabidopsis. PLoS ONE 9:e85208PubMedPubMedCentralCrossRefGoogle Scholar
  66. Yang X, Yang YN, Xue LJ, Zou MJ, Liu JY, Chen F, Xue HW (2011) Rice ABI5-Like1 regulates abscisic acid and auxin responses by affecting the expression of ABRE-containing genes. Plant Physiol 156:1397–1409PubMedPubMedCentralCrossRefGoogle Scholar
  67. Yoon DH, Lee SS, Park HJ, Lyu JI, Chong WS, Liu JR, Kim BG, Ahn JC, Cho HS (2016) Overexpression of OsCYP19-4 increases tolerance to cold stress and enhances grain yield in rice (Oryza sativa). J Exp Bot 67:69–82PubMedCrossRefGoogle Scholar
  68. Yu Y, Wang J, Shi H, Gu J, Dong J, Deng XW, Huang R (2016) Salt stress and ethylene antagonistically regulate nucleocytoplasmic partitioning of COP1 to control seed germination. Plant Physiol 170:2340–2350PubMedPubMedCentralCrossRefGoogle Scholar
  69. Zhang XC, Wang WD, Wang JS, Pan JC (2013) PPIase independent chaperone-like function of recombinant human Cyclophilin A during arginine kinase refolding. FEBS Lett 587:666–672PubMedCrossRefGoogle Scholar
  70. Zong W, Tang N, Yang J, Peng L, Ma S, Xu Y, Li G, Xiong L (2016) Feedback regulation of ABA signaling and biosynthesis by a bZIP transcription factor targets drought-resistance-related genes. Plant Physiol 171:2810–2825PubMedPubMedCentralGoogle Scholar

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© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Plant Systems Engineering Research CenterKorea Research Institute of Bioscience and Biotechnology (KRIBB)DaejeonSouth Korea
  2. 2.Department of Biosystems and Bioengineering, KRIBB School of BiotechnologyKorea University of Science and Technology (UST)DaejeonSouth Korea

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