Abstract
Key message
LRRop-1, induced by DOF6 transcription factor, negatively regulates abiotic stress responses during Arabidopsis seed germination. The lrrop-1 mutant has reduced ABA signaling, which is part of the underlying stress-remediation mechanism.
Abstract
The large family of leucine-rich repeat (LRR) proteins plays a role in plant immune responses. Most LRR proteins have multiple functional domains, but a subfamily is known to possess only the LRR domain. The roles of these LRR-only proteins in Arabidopsis remain largely uncharacterized. In the present study, we have identified 44 LRR-only proteins in Arabidopsis and phylogenetically classified them into nine sub-groups. We characterized the function of LRRop-1, belonging to sub-group V. LRRop-1 encodes a predominantly ER-localized LRR domain-containing protein that is highly expressed in seeds and rosette leaves. Promoter motif analysis revealed an enrichment in binding sites for several GA-responsive and stress-responsive transcription factors. The lrrop-1 mutant seeds showed enhanced seed germination on medium containing abscisic acid (ABA), paclobutrazol and NaCl compared to the wild type (WT), demonstrating higher abiotic stress tolerance. Also, the lrrop-1 mutant seeds have lower levels of endogenous ABA, but higher levels of gibberellic acid (GA) and jasmonic acid-Ile (JA-Ile) compared to the WT. Furthermore, lrrop-1 mutant seeds imbibed with ABA exhibited reduced expression of ABA-responsive genes compared to similarly treated WT seeds, suggesting suppressed ABA signaling events in the mutant. Furthermore, chromatin immunoprecipitation (ChIP) data showed that DNA BINDING1 ZINC FINGER6 (DOF6), a negative regulator of seed germination, could directly bind to the LRRop-1 promoter and up-regulate its expression. Thus, our results show that LRRop-1 regulates ABA-mediated abiotic stress responses during Arabidopsis seed germination.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Abe H, Urao T, Ito T, Seki M, Shinozaki K, Yamaguchi-Shinozaki K (2003) Arabidopsis AtMYC2 (bHLH) and AtMYB2 (MYB) function as transcriptional activators in abscisic acid signaling. Plant Cell 15:63–78
Afzal AJ, Wood AJ, Lightfoot DA (2008) Plant receptor-like serine threonine kinases: roles in signaling and plant defense. Mol Plant Microbe Interact 21:507–517. https://doi.org/10.1094/MPMI-21-5-0507
Bailey TL, Elkan C (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2:28–36
Baumberger N, Steiner M, Ryser U, Keller B, Ringli C (2003) Synergistic interaction of the two paralogous Arabidopsis genes LRX1 and LRX2 in cell wall formation during root hair development. Plant J 35:71–81
Cai X, Zhang C, Shu W, Ye Z, Li H, Zhang Y (2016) The transcription factor SlDof22 involved in ascorbate accumulation and salinity stress in tomato. Biochem Biophys Res Commun 474:736–741. https://doi.org/10.1016/j.bbrc.2016.04.148
Chen H, Lai Z, Shi J, Xiao Y, Chen Z, Xu X (2010) Roles of Arabidopsis WRKY18, WRKY40 and WRKY60 transcription factors in plant responses to abscisic acid and abiotic stress. BMC Plant Biol 10:281. https://doi.org/10.1186/1471-2229-10-281
Corrales AR et al (2017) Multifaceted role of cycling DOF factor 3 (CDF3) in the regulation of flowering time and abiotic stress responses in Arabidopsis. Plant Cell Environ 40:748–764. https://doi.org/10.1111/pce.12894
Davuluri RV, Sun H, Palaniswamy SK, Matthews N, Molina C, Kurtz M, Grotewold E (2003) AGRIS: Arabidopsis gene regulatory information server, an information resource of Arabidopsis cis-regulatory elements and transcription factors. BMC Bioinform 4:25. https://doi.org/10.1186/1471-2105-4-25
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 53:28–37. https://doi.org/10.1093/pcp/pcr113
DeYoung BJ, Innes RW (2006) Plant NBS-LRR proteins in pathogen sensing and host defense. Nat Immunol 7:1243–1249. https://doi.org/10.1038/ni1410
Dievart A, Clark SE (2004) LRR-containing receptors regulating plant development and defense. Development 131:251–261. https://doi.org/10.1242/dev.00998
Draeger C et al (2015) Arabidopsis leucine-rich repeat extensin (LRX) proteins modify cell wall composition and influence plant growth. BMC Plant Biol 15:155. https://doi.org/10.1186/s12870-015-0548-8
Dubey N, Singh K (2018) Role of NBS-LRR proteins in plant defense. Molecular aspects of plant-pathogen interaction. Springer, Berlin, pp 115–138
Fabrice TN et al (2018) LRX proteins play a crucial role in pollen grain and pollen tube cell wall development. Plant Physiol 176:1981–1992
Felsenstein J (1985) Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783–791. https://doi.org/10.1111/j.1558-5646.1985.tb00420.x
Fujita M et al (2004) A dehydration-induced NAC protein, RD26, is involved in a novel ABA-dependent stress-signaling pathway. Plant J 39:863–876. https://doi.org/10.1111/j.1365-313X.2004.02171.x
Geng Y et al (2013) A spatio-temporal understanding of growth regulation during the salt stress response in Arabidopsis. Plant Cell 25:2132–2154. https://doi.org/10.1105/tpc.113.112896
Higo K, Ugawa Y, Iwamoto M, Korenaga T (1999) Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res 27:297–300. https://doi.org/10.1093/nar/27.1.297
Hong SW, Jon JH, Kwak JM, Nam HG (1997) Identification of a receptor-like protein kinase gene rapidly induced by abscisic acid, dehydration, high salt, and cold treatments in Arabidopsis thaliana. Plant Physiol 113:1203–1212. https://doi.org/10.1104/pp.113.4.1203
Huang E, Yang L, Chowdhary R, Kassim A, Bajic VB (2005) An algorithm for ab-initio DNA motif detection. Information processing and living systems. World Scientific, New York, pp 611–614
Jiang Y, Deyholos MK (2006) Comprehensive transcriptional profiling of NaCl-stressed Arabidopsis roots reveals novel classes of responsive genes. BMC Plant Biol 6:25. https://doi.org/10.1186/1471-2229-6-25
Kalunke RM, Tundo S, Benedetti M, Cervone F, De Lorenzo G, D'Ovidio R (2015) An update on polygalacturonase-inhibiting protein (PGIP), a leucine-rich repeat protein that protects crop plants against pathogens. Front Plant Sci 6:146. https://doi.org/10.3389/fpls.2015.00146
Kaufmann K, Muino JM, Osteras M, Farinelli L, Krajewski P, Angenent GC (2010) Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP). Nat Protoc 5:457–472. https://doi.org/10.1038/nprot.2009.244
Kazan K (2015) Diverse roles of jasmonates and ethylene in abiotic stress tolerance. Trends Plant Sci 20:219–229. https://doi.org/10.1016/j.tplants.2015.02.001
Letunic I, Doerks T, Bork P (2009) SMART 6: recent updates and new developments. Nucleic Acids Res 37:D229–232. https://doi.org/10.1093/nar/gkn808
Li X (2011) Infiltration of Nicotiana benthamiana protocol for transient expression via Agrobacterium. Bio Protoc 1:e95. https://doi.org/10.21769/BioProtoc.95
Liu PL, Du L, Huang Y, Gao SM, Yu M (2017) Origin and diversification of leucine-rich repeat receptor-like protein kinase (LRR-RLK) genes in plants. BMC Evol Biol 17:47. https://doi.org/10.1186/s12862-017-0891-5
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 32:317–328
Matsushima N, Miyashita H (2012) Leucine-Rich Repeat (LRR) domains containing intervening motifs in plants. Biomolecules 2:288–311. https://doi.org/10.3390/biom2020288
Matys V et al (2003) TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res 31:374–378. https://doi.org/10.1093/nar/gkg108
Mir MA, John R, Alyemeni MN, Alam P, Ahmad P (2018) Jasmonic acid ameliorates alkaline stress by improving growth performance, ascorbate glutathione cycle and glyoxylase system in maize seedlings. Sci Rep 8:2831. https://doi.org/10.1038/s41598-018-21097-3
Msanne J, Lin J, Stone JM, Awada T (2011) Characterization of abiotic stress-responsive Arabidopsis thaliana RD29A and RD29B genes and evaluation of transgenes. Planta 234:97–107. https://doi.org/10.1007/s00425-011-1387-y
Nelson B, Cai X, Nebenführ A (2007) A multi-color set of in vivo organelle markers for colocalization studies in Arabidopsis and other plants. Plant J 51:1126–1136
Osakabe Y, Maruyama K, Seki M, Satou M, Shinozaki K, Yamaguchi-Shinozaki K (2005) Leucine-rich repeat receptor-like kinase1 is a key membrane-bound regulator of abscisic acid early signaling in Arabidopsis. Plant Cell 17:1105–1119. https://doi.org/10.1105/tpc.104.027474
Osakabe Y et al (2010) Overproduction of the membrane-bound receptor-like protein kinase 1, RPK1, enhances abiotic stress tolerance in Arabidopsis. J Biol Chem 285:9190–9201. https://doi.org/10.1074/jbc.M109.051938
Ravindran P, Verma V, Stamm P, Kumar PP (2017) A novel RGL2-DOF6 complex contributes to primary seed dormancy in Arabidopsis thaliana by regulating a GATA transcription factor. Mol Plant 10:1307–1320. https://doi.org/10.1016/j.molp.2017.09.004
Rueda-Romero P, Barrero-Sicilia C, Gomez-Cadenas A, Carbonero P, Onate-Sanchez L (2012) Arabidopsis thaliana DOF6 negatively affects germination in non-after-ripened seeds and interacts with TCP14. J Exp Bot 63:1937–1949. https://doi.org/10.1093/jxb/err388
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425. https://doi.org/10.1093/oxfordjournals.molbev.a040454
Seo M, Jikumaru Y, Kamiya Y (2011) Profiling of hormones and related metabolites in seed dormancy and germination studies. Seed dormancy. Springer, Berlin, pp 99–111
Shanmugam V (2005) Role of extracytoplasmic leucine rich repeat proteins in plant defence mechanisms. Microbiol Res 160:83–94. https://doi.org/10.1016/j.micres.2004.09.014
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 7:1884. https://doi.org/10.3389/fpls.2016.01884
Su Y, Liang W, Liu Z, Wang Y, Zhao Y, Ijaz B, Hua J (2017) Overexpression of GhDof1 improved salt and cold tolerance and seed oil content in Gossypium hirsutum. J Plant Physiol 218:222–234. https://doi.org/10.1016/j.jplph.2017.07.017
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739. https://doi.org/10.1093/molbev/msr121
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729. https://doi.org/10.1093/molbev/mst197
Urbach JM, Ausubel FM (2017) The NBS-LRR architectures of plant R-proteins and metazoan NLRs evolved in independent events. Proc Natl Acad Sci USA 114:1063–1068. https://doi.org/10.1073/pnas.1619730114
Verma V, Ravindran P, Kumar PP (2016) Plant hormone-mediated regulation of stress responses. BMC Plant Biol 16:86. https://doi.org/10.1186/s12870-016-0771-y
Wang J, Liu S, Li C, Wang T, Zhang P, Chen K (2017a) PnLRR-RLK27, a novel leucine-rich repeats receptor-like protein kinase from the Antarctic moss Pohlia nutans, positively regulates salinity and oxidation-stress tolerance. PLoS ONE 12:e0172869. https://doi.org/10.1371/journal.pone.0172869
Wang M, Wang B, Liu M, Jiang K, Wang L (2019) A novel LRR-only protein mediates bacterial proliferation in hemolymph through regulating expression of antimicrobial peptides in mollusk Chlamys farreri. Dev Comp Immunol 92:223–229
Wang M, Wang L, Jia Z, Wang X, Yi Q, Zhao L, Song L (2017b) The versatile functions of LRR-only proteins in mollusk Chlamys farreri. Dev Comp Immunol 77:188–199. https://doi.org/10.1016/j.dci.2017.08.005
Wang M et al (2016) Two novel LRR-only proteins in Chlamys farreri: Similar in structure, yet different in expression profile and pattern recognition. Dev Comp Immunol 59:99–109. https://doi.org/10.1016/j.dci.2016.01.013
Wu Y et al (2016) Genome-wide expression pattern analyses of the Arabidopsis Leucine-rich Repeat Receptor-Like Kinases. Mol Plant 9:289–300. https://doi.org/10.1016/j.molp.2015.12.011
Xu A-L (2015) Amphioxus immunity: tracing the origins of human immunity. Elsevier, New York
Yanagisawa S (2004) Dof domain proteins: plant-specific transcription factors associated with diverse phenomena unique to plants. Plant Cell Physiol 45:386–391. https://doi.org/10.1093/pcp/pch055
Yoo S-D, Cho Y-H, Sheen J (2007) Arabidopsis mesophyll protoplasts: a versatile cell system for transient gene expression analysis. Nature Protoc 2:1565–1572
Zhang X, Henriques R, Lin SS, Niu QW, Chua NH (2006) Agrobacterium-mediated transformation of Arabidopsis thaliana using the floral dip method. Nat Protoc 1:641–646. https://doi.org/10.1038/nprot.2006.97
Zhao C et al (2018) Leucine-rich repeat extensin proteins regulate plant salt tolerance in Arabidopsis. Proc Natl Acad Sci USA 115:13123–13128
Acknowledgements
Shi Yin Yong is a recipient of research scholarship from the National University of Singapore, Singapore. We thank Dr. Luis Oñate-Sánchez for supplying the ioexDOF6 seeds.
Funding
Research in the PI’s laboratory was supported by a grant from the Singapore National Research Foundation under its Environment and Water Research Programme and administered by PUB, Singapore’s National Water Agency, Singapore.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare no competing interests.
Consent for publication
All authors agreed with the content and all gave explicit consent to submit data for publication.
Availability of data and material
The datasets generated and/or analyzed during the current study are available from the corresponding author on reasonable request.
Additional information
Communicated by Prakash Lakshmanan.
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Ravindran, P., Yong, S.Y., Mohanty, B. et al. An LRR-only protein regulates abscisic acid-mediated abiotic stress responses during Arabidopsis seed germination. Plant Cell Rep 39, 909–920 (2020). https://doi.org/10.1007/s00299-020-02538-8
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00299-020-02538-8