Abstract
Cell-to-cell communication, principally mediated by short- or long-range mobile signals, is involved in many plant developmental processes. In root nodule symbiosis, a mutual relationship between leguminous plants and nitrogen-fixing rhizobia, the mechanism for the autoregulation of nodulation (AON) plays a key role in preventing the production of an excess number of nodules. AON is based on long-distance cell-to-cell communication between roots and shoots. In Lotus japonicus, two CLAVATA3/ESR-related (CLE) peptides, encoded by CLE-ROOT SIGNAL 1 (CLE-RS1) and -RS2, act as putative root-derived signals that transmit signals inhibiting further nodule development through interaction with a shoot-acting receptor-like kinase HYPERNODULATION ABERRANT ROOT FORMATION 1 (HAR1). Here, an in silico search and subsequent expression analyses enabled us to identify two new L. japonicus CLE genes that are potentially involved in nodulation, designated as CLE-RS3 and LjCLE40. Time-course expression patterns showed that CLE-RS1/2/3 and LjCLE40 expression is induced during nodulation with different activation patterns. Furthermore, constitutive expression of CLE-RS3 significantly suppressed nodule formation in a HAR1-dependent manner. TOO MUCH LOVE, a root-acting regulator of AON, is also required for the CLE-RS3 action. These results suggest that CLE-RS3 is a new component of AON in L. japonicus that may act as a potential root-derived signal through interaction with HAR1. Because CLE-RS2, CLE-RS3 and LjCLE40 are located in tandem in the genome and their expression is induced not only by rhizobial infection but also by nitrate, these genes may have duplicated from a common gene.
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References
Araya T, Miyamoto M, Wibowo J, Suzuki A, Kojima S, Tsuchiya YN, Sawa S, Fukuda H, von Wirén N, Takahashi H (2014) CLE-CLAVATA1 peptide-receptor signaling module regulates the expansion of plant root systems in a nitrogen-dependent manner. Proc Natl Acad Sci USA 111:2029–2034
Bidadi H, Matsuoka K, Sage-Ono K, Fukushima J, Pitaksaringkarn W, Asahina M, Yamaguchi S, Sawa S, Fukuda H, Matsubayashi Y, Ono M, Satoh S (2014) CLE6 expression recovers gibberellin deficiency to promote shoot growth in Arabidopsis. Plant J 78:241–252
Brand U, Fletcher JC, Hobe M, Meyerowitz EM, Simon R (2000) Dependence of stem cell fate in Arabidopsis on a feedback loop regulated by CLV3 activity. Science 289:617–619
Caetano-Anolles G, Gresshoff PM (1991) Plant genetic control of nodulation. Annu Rev Microbiol 45:345–382
Clark SE, Williams RW, Meyerowitz EM (1997) The CLAVATA1 gene encodes a putative receptor kinase that controls shoot and floral meristem size in Arabidopsis. Cell 89:575–585
Cock JM, McCormick S (2001) A large family of genes that share homology with CLAVATA3. Plant Physiol 126:939–942
Daum G, Medzihradszky A, Suzaki T, Lohmann JU (2014) A mechanistic framework for noncell autonomous stem cell induction in Arabidopsis. Proc Natl Acad Sci USA 111:14619–14624
Djordjevic MA, Mohd-Radzman NA, Imin N (2015) Small-peptide signals that control root nodule number, development, and symbiosis. J Exp Bot 66:5171–5181
Endo S, Betsuyaku S, Fukuda H (2014) Endogenous peptide ligand-receptor systems for diverse signaling networks in plants. Curr Opin Plant Biol 21:140–146
Fisher K, Turner S (2007) PXY, a receptor-like kinase essential for maintaining polarity during plant vascular-tissue development. Curr Biol 17:1061–1066
Fletcher JC, Brand U, Running MP, Simon R, Meyerowitz EM (1999) Signaling of cell fate decisions by CLAVATA3 in Arabidopsis shoot meristems. Science 283:1911–1914
Haecker A, Groß-Hardt R, Geiges B, Sarkar A, Breuninger H, Herrmann M, Laux T (2004) Expression dynamics of WOX genes mark cell fate decisions during early embryonic patterning in Arabidopsis thaliana. Development 131:657–668
Handa Y, Nishide H, Takeda N, Suzuki Y, Kawaguchi M, Saito K (2015) RNA-seq transcriptional profiling of an arbuscular mycorrhiza provides insights into regulated and coordinated gene expression in Lotus japonicus and Rhizophagus irregularis. Plant Cell Physiol 56:1490–1511
Hirakawa Y, Shinohara H, Kondo Y, Inoue A, Nakanomyo I, Ogawa M, Sawa S, Ohashi-Ito K, Matsubayashi Y, Fukuda H (2008) Non-cell-autonomous control of vascular stem cell fate by a CLE peptide/receptor system. Proc Natl Acad Sci USA 105:15208–15213
Hirakawa Y, Kondo Y, Fukuda H (2010) TDIF peptide signaling regulates vascular stem cell proliferation via the WOX4 homeobox gene in Arabidopsis. Plant Cell 22:2618–2629
Ito Y, Nakanomyo I, Motose H, Iwamoto K, Sawa S, Dohmae N, Fukuda H (2006) Dodeca-CLE peptides as suppressors of plant stem cell differentiation. Science 313:842–845
Karimi M, Inzé D, Depicker A (2002) GATEWAY™ vectors for Agrobacterium-mediated plant transformation. Trends Plant Sci 7:193–195
Kawaguchi M (2000) Lotus japonicus ‘Miyakojima’ MG-20: an early-flowering accession suitable for indoor handling. J Plant Res 113:507–509
Krusell L, Madsen LH, Sato S, Aubert G, Genua A, Szczyglowski K, Duc G, Kaneko T, Tabata S, de Bruijn F, Pajuelo E, Sandal N, Stougaard J (2002) Shoot control of root development and nodulation is mediated by a receptor-like kinase. Nature 420:422–426
Magori S, Oka-Kira E, Shibata S, Umehara Y, Kouchi H, Hase Y, Tanaka A, Sato S, Tabata S, Kawaguchi M (2009) TOO MUCH LOVE, a root regulator associated with the long-distance control of nodulation in Lotus japonicus. Mol Plant Microbe Interact 22:259–268
Mayer KFX, Schoof H, Haecker A, Lenhard M, Jürgens G, Laux T (1998) Role of WUSCHEL in regulating stem cell fate in the Arabidopsis shoot meristem. Cell 95:805–815
Miyawaki K, Tabata R, Sawa S (2013) Evolutionarily conserved CLE peptide signaling in plant development, symbiosis, and parasitism. Curr Opin Plant Biol 16:598–606
Miyazawa H, Oka-Kira E, Sato N, Takahashi H, Wu GJ, Sato S, Hayashi M, Betsuyaku S, Nakazono M, Tabata S, Harada K, Sawa S, Fukuda H, Kawaguchi M (2010) The receptor-like kinase KLAVIER mediates systemic regulation of nodulation and non-symbiotic shoot development in Lotus japonicus. Development 137:4317–4325
Mortier V, Den Herder G, Whitford R, Van de Velde W, Rombauts S, D’Haeseleer K, Holsters M, Goormachtig S (2010) CLE peptides control Medicago truncatula nodulation locally and systemically. Plant Physiol 153:222–237
Mortier V, De Wever E, Vuylsteke M, Holsters M, Goormachtig S (2012) Nodule numbers are governed by interaction between CLE peptides and cytokinin signaling. Plant J 70:367–376
Nishimura R, Hayashi M, Wu GJ, Kouchi H, Imaizumi-Anraku H, Murakami Y, Kawasaki S, Akao S, Ohmori M, Nagasawa M, Harada K, Kawaguchi M (2002) HAR1 mediates systemic regulation of symbiotic organ development. Nature 420:426–429
Ogawa M, Shinohara H, Sakagami Y, Matsubayashi Y (2008) Arabidopsis CLV3 peptide directly binds CLV1 ectodomain. Science 319:294
Oka-Kira E, Kawaguchi M (2006) Long-distance signaling to control root nodule number. Curr Opin Plant Biol 9:496–502
Oka-Kira E, Tateno K, K-i Miura, Haga T, Hayashi M, Harada K, Sato S, Tabata S, Shikazono N, Tanaka A, Watanabe Y, Fukuhara I, Nagata T, Kawaguchi M (2005) klavier (klv), a novel hypernodulation mutant of Lotus japonicus affected in vascular tissue organization and floral induction. Plant J 44:505–515
Okamoto S, Ohnishi E, Sato S, Takahashi H, Nakazono M, Tabata S, Kawaguchi M (2009) Nod factor/nitrate-induced CLE genes that drive HAR1-mediated systemic regulation of nodulation. Plant Cell Physiol 50:67–77
Okamoto S, Shinohara H, Mori T, Matsubayashi Y, Kawaguchi M (2013) Root-derived CLE glycopeptides control nodulation by direct binding to HAR1 receptor kinase. Nat Commun 4:2191
Okamoto S, Suzuki T, Kawaguchi M, Higashiyama T, Matsubayashi Y (2015) A comprehensive strategy for identifying long-distance mobile peptides in xylem sap. Plant J 84:611–620
Reid DE, Ferguson BJ, Gresshoff PM (2011) Inoculation- and nitrate-induced CLE peptides of soybean control NARK-dependent nodule formation. Mol Plant Microbe Interact 24:606–618
Reid DE, Li D, Ferguson BJ, Gresshoff PM (2013) Structure–function analysis of the GmRIC1 signal peptide and CLE domain required for nodulation control in soybean. J Exp Bot 64:1575–1585
Sasaki T, Suzaki T, Soyano T, Kojima M, Sakakibara H, Kawaguchi M (2014) Shoot-derived cytokinins systemically regulate root nodulation. Nat Commun 5:4983
Sato S, Nakamura Y, Kaneko T, Asamizu E, Kato T, Nakao M, Sasamoto S, Watanabe A, Ono A, Kawashima K, Fujishiro T, Katoh M, Kohara M, Kishida Y, Minami C, Nakayama S, Nakazaki N, Shimizu Y, Shinpo S, Takahashi C, Wada T, Yamada M, Ohmido N, Hayashi M, Fukui K, Baba T, Nakamichi T, Mori H, Tabata S (2008) Genome structure of the legume, Lotus japonicus. DNA Res 15:227–239
Schauser L, Roussis A, Stiller J, Stougaard J (1999) A plant regulator controlling development of symbiotic root nodules. Nature 402:191–195
Schoof H, Lenhard M, Haecker A, Mayer KFX, Jürgens G, Laux T (2000) The stem cell population of Arabidopsis shoot meristems is maintained by a regulatory loop between the CLAVATA and WUSCHEL genes. Cell 100:635–644
Searle IR, Men AE, Laniya TS, Buzas DM, Iturbe-Ormaetxe I, Carroll BJ, Gresshoff PM (2003) Long-distance signaling in nodulation directed by a CLAVATA1-like receptor kinase. Science 299:109–112
Soyano T, Hirakawa H, Sato S, Hayashi M, Kawaguchi M (2014) NODULE INCEPTION creates a long-distance negative feedback loop involved in homeostatic regulation of nodule organ production. Proc Natl Acad Sci USA 111:14607–14612
Stahl Y, Wink RH, Ingram GC, Simon R (2009) A signaling module controlling the stem cell niche in Arabidopsis root meristems. Curr Biol 19:909–914
Stahl Y, Grabowski S, Bleckmann A, Kühnemuth R, Weidtkamp-Peters S, Pinto KG, Kirschner Gwendolyn K, Schmid JB, Wink RH, Hülsewede A, Felekyan S, Seidel CAM, Simon R (2013) Moderation of Arabidopsis root stemness by CLAVATA1 and ARABIDOPSIS CRINKLY4 receptor kinase complexes. Curr Biol 23:362–371
Suzaki T, Toriba T, Fujimoto M, Tsutsumi N, Kitano H, Hirano H-Y (2006) Conservation and diversification of meristem maintenance mechanism in Oryza sativa: function of the FLORAL ORGAN NUMBER2 gene. Plant Cell Physiol 47:1591–1602
Suzaki T, Yano K, Ito M, Umehara Y, Suganuma N, Kawaguchi M (2012) Positive and negative regulation of cortical cell division during root nodule development in Lotus japonicus is accompanied by auxin response. Development 139:3997–4006
Suzaki T, Kim CS, Takeda N, Szczyglowski K, Kawaguchi M (2013) TRICOT encodes an AMP1-related carboxypeptidase that regulates root nodule development and shoot apical meristem maintenance in Lotus japonicus. Development 140:353–361
Suzaki T, Ito M, Yoro E, Sato S, Hirakawa H, Takeda N, Kawaguchi M (2014) Endoreduplication-mediated initiation of symbiotic organ development in Lotus japonicus. Development 141:2441–2445
Suzaki T, Yoro E, Kawaguchi M (2015) Leguminous plants: inventors of root nodules to accommodate symbiotic bacteria. Int Rev Cell Mol Biol 316:111–158
Suzuki A, Hara H, Kinoue T, Abe M, Uchiumi T, K-i Kucho, Higashi S, Hirsch AM, Arima S (2008) Split-root study of autoregulation of nodulation in the model legume Lotus japonicus. J Plant Res 121:245–249
Tabata R, Sumida K, Yoshii T, Ohyama K, Shinohara H, Matsubayashi Y (2014) Perception of root-derived peptides by shoot LRR-RKs mediates systemic N-demand signaling. Science 346:343–346
Takahara M, Magori S, Soyano T, Okamoto S, Yoshida C, Yano K, Sato S, Tabata S, Yamaguchi K, Shigenobu S, Takeda N, Suzaki T, Kawaguchi M (2013) TOO MUCH LOVE, a novel Kelch repeat-containing F-box protein, functions in the long-distance regulation of the legume-Rhizobium symbiosis. Plant Cell Physiol 54:433–447
Wang Y, Wang L, Zou Y, Chen L, Cai Z, Zhang S, Zhao F, Tian Y, Jiang Q, Ferguson BJ, Gresshoff PM, Li X (2014) Soybean miR172c targets the repressive AP2 transcription factor NNC1 to activate ENOD40 expression and regulate nodule initiation. Plant Cell 26:4782–4801
Wopereis J, Pajuelo E, Dazzo FB, Jiang Q, Gresshoff PM, De Bruijn FJ, Stougaard J, Szczyglowski K (2000) Short root mutant of Lotus japonicus with a dramatically altered symbiotic phenotype. Plant J 23:97–114
Yadav RK, Perales M, Gruel J, Girke T, Jönsson H, Reddy GV (2011) WUSCHEL protein movement mediates stem cell homeostasis in the Arabidopsis shoot apex. Genes Dev 25:2025–2030
Acknowledgments
We thank Makoto Hayashi for providing M. loti MAFF303099 expressing DsRED. We also thank Satoru Okamoto for providing the p35S::CLE-RS1, p35S::CLE-RS2 and p35S::GUS plasmids. This work was supported by the National Institute for Basic Biology (NIBB) Core Research Facilities, the NIBB Model Plant Research Facility and by MEXT/JSPS KAKENHI, Japan (16H01457 to T.S. and 25291066 to M.K.).
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10265_2016_842_MOESM3_ESM.tif
Fig. S2 Real-time RT-PCR analysis of CLE-RS3 (a), LjCLE40 (b), CLE-RS1 (c), CLE-RS2 (d), LjCLE39 (e), LjCLE41 (f) and LjCLE42 (g) expression in wild-type. Each cDNA sample was prepared from total RNA derived from the flower, leaf, stem, shoot apex, non-inoculated (-) and 1 dai (+) roots. The expression patterns of CLE-RS1 and CLE-RS2 in the organs other than inoculated roots are shown as inset (c, d). LjUBQ was used to assess the relative expression of each gene. Error bars indicate SE (n = 3 independent pools of respective organs) (TIFF 210 kb)
10265_2016_842_MOESM4_ESM.tif
Fig. S3 Real-time RT-PCR analysis of LjCLE39 (a), LjCLE41 (b) and LjCLE42 (c) expression in wild-type non-inoculated roots (0) and 1, 3, 5, 7 and 14 dai. Each cDNA was prepared from total RNA derived from the entire root. LjUBQ was used to assess the relative expression of each gene. Error bars indicate SE (n = 3–4 independent pools of roots) (TIFF 172 kb)
10265_2016_842_MOESM5_ESM.tif
Fig. S4 Real-time RT-PCR analysis of CLE-RS3 expression in stably transformed L. japonicus transgenic plants that were constitutively expressing CLE-RS3 or GUS. Each cDNA was prepared from total RNA derived from the entire root. LjUBQ was used to assess the relative expression of each gene. Error bars indicate SE (n = 3 independent pools of roots) (TIFF 80 kb)
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Nishida, H., Handa, Y., Tanaka, S. et al. Expression of the CLE-RS3 gene suppresses root nodulation in Lotus japonicus . J Plant Res 129, 909–919 (2016). https://doi.org/10.1007/s10265-016-0842-z
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DOI: https://doi.org/10.1007/s10265-016-0842-z