Abstract
Key message
OsJAZ2 protein has a propensity to form condensates, possibly by multivalent interactions, and can be used to construct artificial compartments in plant cells.
Abstract
Eukaryotic cells contain various membraneless organelles, which are compartments consisting of proteinaceous condensates formed by phase separation. Such compartments are attractive for bioengineering and synthetic biology, because they can modify cellular function by the enrichment of molecules of interest and providing an orthogonal reaction system. This study reports that Oryza sativa JAZ2 protein (OsJAZ2) is an atypical jasmonate signalling regulator that can form large condensates in both the nucleus and cytosol of O. sativa cells. TIFY and Jas domains and low-complexity regions contribute to JAZ2 condensation, possibly by multivalent interaction. Fluorescence recovery after photobleaching (FRAP) analysis suggests that JAZ2 condensates form mostly gel-like or solid compartments, but can also be in a liquid-like state. Deletion of the N-terminal region or the TIFY domain of JAZ2 causes an increase in the mobile fraction of JAZ2 condensates, moderately. Moreover, JAZ2 can also form liquid-like condensates when expressed in Nicotiana benthamiana cells. The recombinant JAZ2 fused to the green fluorescent protein (GFP) forms condensate in vitro, suggesting that the intermolecular interaction of JAZ2 molecules is a driving force for condensation. These results suggest the potential use of JAZ2 condensates to construct artificial membraneless organelles in plant cells.
Similar content being viewed by others
Data availability
The datasets generated during and/or analysed during the current study are available from the corresponding author on reasonable request.
References
Alberti S, Hyman AA (2021) Biomolecular condensates at the nexus of cellular stress, protein aggregation disease and ageing. Nat Rev Mol Cell Biol 22:196–213. https://doi.org/10.1038/s41580-020-00326-6
Alberti S, Gladfelter A, Mittag T (2019) Considerations and challenges in studying liquid–liquid phase separation and biomolecular condensates. Cell 176:419–434. https://doi.org/10.1016/j.cell.2018.12.035
Asai S, Ohta K, Yoshioka H (2008) MAPK signaling regulates nitric oxide and NADPH oxidase-dependent oxidative bursts in Nicotiana benthamiana. Plant Cell 20:1390–1406
Balbirnie M, Grothe R, Eisenberg DS (2001) An amyloid-forming peptide from the yeast prion Sup35 reveals a dehydrated beta-sheet structure for amyloid. Proc Natl Acad Sci USA 98:2375–2380. https://doi.org/10.1073/pnas.041617698
Banani SF, Lee HO, Hyman AA et al (2017) Biomolecular condensates: organizers of cellular biochemistry. Nat Rev Mol Cell Biol 18:285–298
Bauer MT, Gilmore KA, Petty SA (2011) Formation of β-sheets in glutamine and alanine tripeptides. Biochem Biophys Res Commun 406:348–352. https://doi.org/10.1016/j.bbrc.2011.02.041
Boke E, Ruer M, Wühr M et al (2016) Amyloid-like self-assembly of a cellular compartment. Cell 166:637–650. https://doi.org/10.1016/j.cell.2016.06.051
Bose M, Lampe M, Mahamid J et al (2022) Liquid-to-solid phase transition of oskar ribonucleoprotein granules is essential for their function in Drosophila embryonic development. Cell 185:1308–1324. https://doi.org/10.1016/j.cell.2022.02.022
Chini A, Fonseca S, Chico JM et al (2009) The ZIM domain mediates homo- and heteromeric interactions between Arabidopsis JAZ proteins. Plant J 59:77–87
Chini A, Gimenez-Ibanez S, Goossens A et al (2016) Redundancy and specificity in jasmonate signalling. Curr Opin Plant Biol 33:147–156. https://doi.org/10.1016/j.pbi.2016.07.005
Courchaine EM, Lu A, Neugebauer KM (2016) Droplet organelles? EMBO J 35:1603–1612. https://doi.org/10.15252/embj.201593517
Fang X, Wang L, Ishikawa R et al (2019) Arabidopsis FLL2 promotes liquid–liquid phase separation of polyadenylation complexes. Nature 569:265–269. https://doi.org/10.1038/s41586-019-1165-8
Franzmann TM, Jahnel M, Pozniakovsky A et al (2018) Phase separation of a yeast prion protein promotes cellular fitness. Science 359:eaao05654. https://doi.org/10.1126/science.aao5654
Garabedian MV, Wang W, Dabdoub JB et al (2021) Designer membraneless organelles sequester native factors for control of cell behavior. Nat Chem Biol 17:998–1007. https://doi.org/10.1038/s41589-021-00840-4
Garbuzynskiy SO, Lobanov MY, Galzitskaya OV (2010) FoldAmyloid: a method of prediction of amyloidogenic regions from protein sequence. Bioinformatics 26:326–332. https://doi.org/10.1093/bioinformatics/btp691
Gomes E, Shorter J (2019) The molecular language of membraneless organelles. J Biol Chem 294:7115–7127. https://doi.org/10.1074/jbc.TM118.001192
Hastings RL, Boeynaems S (2021) Designer condensates: a toolkit for the biomolecular architect. J Mol Biol 433:166837
Hellens RP, Edwards EA, Leyland NR et al (2000) pGreen: a versatile and flexible binary Ti vector for Agrobacterium-mediated plant transformation. Plant Mol Biol 42:819–832. https://doi.org/10.1023/a:1006496308160 (PMID: 10890530)
Hennig S, Kong G, Mannen T et al (2015) Prion-like domains in RNA binding proteins are essential for building subnuclear paraspeckles. J Cell Biol 210:529–539. https://doi.org/10.1083/jcb.201504117
Hori Y, Kurotani K, Toda Y et al (2014) Overexpression of the JAZ factors with mutated Jas domains causes pleiotropic defects in rice spikelet development. Plant Signal Behav 9:e970414. https://doi.org/10.4161/15592316.2014.970414
Howe GA, Major IT, Koo AJ (2018) Modularity in jasmonate signaling for multistress resilience. Annu Rev Plant Biol 69:387–415. https://doi.org/10.1146/annurev-arplant-042817-040047
Huang H, Liu B, Liu L et al (2017) Jasmonate action in plant growth and development. J Exp Bot 68:1349–1359. https://doi.org/10.1093/jxb/erw495
Hughes MP, Sawaya MR, Boyer DR et al (2018) Atomic structures of low-complexity protein segments reveal kinked β sheets that assemble networks. Science 359:698–701. https://doi.org/10.1126/science.aan6398
Jumper J, Evans R, Pritzel A et al (2021) Highly accurate protein structure prediction with AlphaFold. Nature 596:583–589. https://doi.org/10.1038/s41586-021-03819-2
Kato M, Han TW, Xie S et al (2012) Cell-free formation of RNA granules: low complexity sequence domains form dynamic fibers within hydrogels. Cell 149:753–767
Kroschwald S, Maharana S, Mateju D et al (2015) Promiscuous interactions and protein disaggregates determine the material state of stress-inducible RNP granules. Elife 4:e06807. https://doi.org/10.7554/eLife.06807
Kroschwald S, Maharana S, Alberti S (2017) Hexanediol: a chemical probe to investigate the material properties of membrane-less compartments. Matters. https://doi.org/10.19185/matters.201702000010
Kurotani K, Hayashi K, Hatanaka S et al (2015) Elevated levels of CYP94 family gene expression alleviate the jasmonate response and enhance salt tolerance in rice. Plant Cell Physiol 56:779–789. https://doi.org/10.1093/pcp/pcv006
Laporte D, Salin B, Daignan-Fornier B et al (2008) Reversible cytoplasmic localization of the proteasome in quiescent yeast cells. J Cell Biol 181:737–745. https://doi.org/10.1083/jcb.200711154
Lin Y, Protter DS, Rosen MK et al (2015) Formation and maturation of phase-separated liquiddroplets by RNA-binding proteins. Mol Cell 60:208–219. https://doi.org/10.1016/j.molcel.2015.08.018
Lundberg KM, Stenland CJ, Cohen FE et al (1997) Kinetics and mechanism of amyloid formation by the prion protein H1 peptide as determined by time-dependent ESR. Chem Biol 4:345–355. https://doi.org/10.1016/S1074-5521(97)90125-3
Mirdita M, Schütze K, Moriwaki Y et al (2021) ColabFold—making protein folding accessible to all. bioRxiv. https://doi.org/10.1101/2021.08.15.456425
Molliex A, Temirov J, Lee J et al (2015) Phase separation by low complexity domains promotes stress granule assembly and drives pathological fibrillization. Cell 163:123–133
Motohashi K (2015) A simple and efficient seamless DNA cloning method using SLiCE from Escherichia coli laboratory strains and its application to SLiP site-directed mutagenesis. BMC Biotechnol 15:47. https://doi.org/10.1186/s12896-015-0162-8
Nelson R, Sawaya MR, Balbirnie M et al (2005) Structure of the cross-beta spine of amyloid-like fibrils. Nature 435:773–778. https://doi.org/10.1038/nature03680
Niepel M, Gallie DR (1999) Identification and characterization of the functional elements within the tobacco etch virus 5’ leader required for cap-independent translation. J Virol 73:9080–9088. https://doi.org/10.1128/JVI.73.11.9080-9088.1999
Ogawa D, Suzuki Y, Yokoo T et al (2021) Acetic-acid-induced jasmonate signaling in root enhances drought avoidance in rice. Sci Rep 11:6280. https://doi.org/10.1038/s41598-021-85355-7
Ohira K, Ojima K, Fujiwara A (1973) Studies on the nutrition of rice cell culture I. A simple, defined medium for rapid growth in suspension culture. Plant Cell Physiol 14:1113–1121. https://doi.org/10.1093/oxfordjournals.pcp.a074950
Pancsa R, Schad E, Tantos A et al (2019) Emergent functions of proteins in non-stoichiometric supramolecular assemblies. Biochim Biophys Acta Proteins Proteom 1867:970–979. https://doi.org/10.1016/j.bbapap.2019.02.007
Patel A, Lee HO, Jawerth L et al (2015) A liquid-to-solid phase transition of the ALS protein FUS accelerated by disease mutation. Cell 162:1066–1077
Peran I, Mittag T (2020) Molecular structure in biomolecular condensates. Curr Opin Struct Biol 60:17–26. https://doi.org/10.1016/j.sbi.2019.09.007
Reinkemeier CD, Girona GE, Lemke EA (2019) Designer membraneless organelles enable codon reassignment of selected mRNAs in eukaryotes. Science 363:eaaw2644. https://doi.org/10.1126/science.aaw2644
Saad S, Cereghetti G, Feng Y et al (2017) Reversible protein aggregation is a protective mechanism to ensure cell cycle restart after stress. Nat Cell Biol 19:1202–1213. https://doi.org/10.1038/ncb3600
Segami S, Makino S, Miyake A et al (2014) Dynamics of vacuoles and H+-pyrophosphatase visualized by monomeric green fluorescent protein in Arabidopsis: artifactual bulbs and native intravacuolar spherical structures. Plant Cell 26:3416–3434. https://doi.org/10.1105/tpc.114.127571
Shin Y, Brangwynne CP (2017) Liquid phase condensation in cell physiology and disease. Science 357:eaaf4382
Shyu C, Figueroa P, Depew CL et al (2012) JAZ8 lacks a canonical degron and has an EAR motif that mediates transcriptional repression of jasmonate responses in Arabidopsis. Plant Cell 24:536–550. https://doi.org/10.1105/tpc.111.093005
Toda Y, Tanaka M, Ogawa D et al (2013) RICE SALT SENSITIVE3 forms a ternary complex with JAZ and class-C bHLH factors and regulates jasmonate-induced gene expression and root cell elongation. Plant Cell 25:1709–1725. https://doi.org/10.1105/tpc.113.112052
Tuttle MD, Comellas G, Nieuwkoop AJ et al (2016) Solid-state NMR structure of a pathogenic fibril of full-length human α-synuclein. Nat Chem Biol 23:409–415
Uversky VN (2017) Protein intrinsic disorder-based liquid-liquid phase transitions in biological systems: complex coacervates and membrane-less organelles. Adv Colloid Interface Sci 239:97–114. https://doi.org/10.1016/j.cis.2016.05.012
Wälti MA, Ravotti F, Arai H et al (2016) Atomic-resolution structure of a disease-relevant Aβ(1–42) amyloid fibril. Proc Natl Acad Sci USA 113:E4976–E4984. https://doi.org/10.1073/pnas.1600749113
Wang J, Choi J-M, Holehouse AS et al (2018) A molecular grammar governing the driving forces for phase separation of prion-like RNA binding proteins. Cell 174:688–699. https://doi.org/10.1016/j.cell.2018.06.006
Wasternack C, Hause B (2013) Jasmonates: biosynthesis, perception, signal transduction and action in plant stress response, growth and development. An update to the 2007 review in Annals of Botany. Ann Bot 111:1021–1058. https://doi.org/10.1093/aob/mct067
Withers J, Yao J, Mecey C et al (2012) Transcription factor-dependent nuclear localization of a transcriptional repressor in jasmonate hormone signaling. Proc Natl Acad Sci USA 109:20148–20153. https://doi.org/10.1073/pnas.1210054109
Woodruff JB, Ferreira Gomes B, Widlund PO et al (2017) The centrosome is a selective condensate that nucleates microtubules by concentrating tubulin. Cell 169:1066–1077. https://doi.org/10.1016/j.cell.2017.05.028
Woodruff JB, Hyman AA, Boke E (2018) Organization and function of non-dynamic biomolecular condensates. Trends Biochem Sci 43:81–94. https://doi.org/10.1016/j.tibs.2017.11.005
Wu H, Ye H, Yao R et al (2015) OsJAZ9 acts as a transcriptional regulator in jasmonate signaling and modulates salt stress tolerance in rice. Plant Sci 232:1–12. https://doi.org/10.1016/j.plantsci.2014.12.010
Yang P, Mathieu C, Kolaitis RM et al (2020) G3BP1 is a tunable switch that triggers phase separation to assemble stress granules. Cell 181:325–345. https://doi.org/10.1016/j.cell.2020.03.046
Zacharias DA, Violin JD, Newton AC et al (2002) Partitioning of lipid-modified monomeric GFPs into membrane microdomains of live cells. Science 296:913–916. https://doi.org/10.1126/science.1068539
Acknowledgements
We thank Drs. M. Matsuoka and H. Yoshioka for their helpful suggestions in transient assays using rice protoplasts and N. benthamiana, respectively, H. Shibata and T. Kojima for useful suggestions on FRAP and SLiCE techniques, respectively, T. Nakagawa, C. Dean, and Y. Habu for the gifts of their plasmids used for the preparation of the Gateway-based vectors pUGW42 and pUGW45, the pETL8 based plasmids, carrying MBP–GFP, MBP–GFP–FCA–RRM and MBP–GFP–FCA–PrLD, and pGFP–Ex–ENS, respectively, C. Ueguchi in Nagoya University for helpful discussion, and Editage (www.editage.com) for English language editing.
Funding
This work was partially supported by the Japan Society for the Promotion of Science (JSPS) KAKENHI (JP16K08140 and JP22K05427) and Nagoya University–National Institute of Advanced Industrial Science and Technology (NU–AIST) alliance project. YK was supported by the Japan Science and Technology Agency (JST) SPRING (JPMJSP2125) and “Graduate Program of Transformative Chem-Bio Research” in Nagoya University, supported by The Ministry of Education, Culture, Sports, Science and Technology (MEXT) (WISE Program).
Author information
Authors and Affiliations
Contributions
All authors contributed to the study conception and/or design. Material preparation, data collection, and analysis were performed by YK, YJ, TA, YY, HG, NH, and HK. OsJAZ2 condensation in Oryza sativa cells was first reported by HK. Data interpretation was performed by TH and ST in addition to the authors described above. The first draft of the manuscript was written by YK and ST and improved by the other authors’ suggestions. All authors read and approved the final manuscript.
Corresponding author
Ethics declarations
Conflict of interest
The authors have no relevant financial or non-financial interests to disclose.
Additional information
Communicated by Attila Feher.
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Koja, Y., Joshima, Y., Yoritaka, Y. et al. Formation of subcellular compartments by condensation-prone protein OsJAZ2 in Oryza sativa and Nicotiana benthamiana leaf cells. Plant Cell Rep 42, 269–286 (2023). https://doi.org/10.1007/s00299-022-02955-x
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00299-022-02955-x