Abstract
Legume-rhizobium symbiosis requires the expression of a series of plant genes playing roles in nodulation signaling that leads to the formation of functional nodules. A few plant-specific GRAS proteins have been shown to be involved in early nodulation signaling. Here, we isolated a novel SCARECROW-like GRAS protein gene, MtSymSCL1, from the model legume Medicago truncatula. MtSymSCL1 has unique gene and protein domain structures, and its homologs are identified from various plant species. Phylogenetic analysis showed that MtSymSCL1 could be classified into a novel subclass in the GRAS protein family. MtSymSCL1 transcript accumulated highly in nodulated roots at 14 days after inoculation of Sinorhizobium meliloti. Translationally fused MtSymSCL1-GFP expressed from a viral or the native promoter was co-localized with nuclear localization signal-fused RFP in leaf mesophyll protoplasts, Agrobacterium rhizogenes-transformed hairy root cells, and epidermal cells of nodules that developed on the transformed roots. Unlike SCARECROW of Arabidopsis, however, RNA silencing of MtsymSCL1 did not affect root growth, nor root hair curling and infection thread growth. Nevertheless, MtSymSCL1-silenced roots developed significantly fewer nodules than GUS-silenced roots, as shown by replicated nodulation assay with pot- or agar plate-grown plants. The structure of MtSymSCL1-silenced root nodules appeared similar to that of the wild type, as shown by sectioned nodules stained with green fluorescent dye. Together, these results suggest that MtSymSCL1 plays a role in regulating nodule number during legume-rhizobium symbiosis.
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Arrighi JF, Barre A, Ben Amor B, Bersoult A, Soriano LC, Mirabella R, de Carvalho-Niebel F, Journet EP, Gherardi M, Huguet T, Geurts R, Denarie J, Rouge P, Gough C (2006) The Medicago truncatula lysin [corrected] motif-receptor-like kinase gene family includes NFP and new nodule-expressed genes. Plant Physiol 142:265–279
Bapaume L, Reinhardt D (2012) How membranes shape plant symbioses: signaling and transport in nodulation and arbuscular mycorrhiza. Front Plant Sci 3: Article 22
Benedito VA, Torres-Jerez I, Murray JD, Andriankaja A, Allen S, Kakar K, Wandrey M, Verdier J, Zuber H, Ott T et al (2008) A gene expression atlas of the model legume Medicago truncatula. Plant J 55:504–513
Boisson-Dernier A, Chabaud M, Garcia F, Becard G, Rosenberg C, Barker DG (2001) Hairy roots of Medicago truncatula as tools for studying nitrogen-fixing and endomycorrhizal symbioses. Mol Plant Microbe Interact 14:695–700
Boivin C, Camut S, Malpica CA, Truchet G, Rosenberg C (1990) Rhizobium meliloti genes encoding catabolism of trigonelline are induced under symbiotic condition. Plant Cell 2:1157–1170
Bolle C (2004) The role of GRAS proteins in plant signal transduction and development. Planta 218:683–692
Broghammer A, Krusell L, Blaise M, Sauer J, Sullivan JT, Maolanon N, Vinther M, Lorentzen A, Madsen EB, Jensen KJ, Roepstorff P, Thirup S, Ronson CW, Thygesen MB, Stougaard J (2012) Legume receptors perceive the rhizobial lipochitin oligosaccharide signal molecules by direct binding. Proc Natl Acad Sci USA 109:13859–13864
Catford JG, Staehelin C, Lerat S, Piche Y, Vierheilig H (2003) Suppression of arbuscular mycorrhizal colonization and nodulation in split-root systems of alfalfa after pre-inoculation and treatment with Nod factors. J Exp Bot 54:1481–1487
Cerri MR, Frances L, Laloum T, Auriac MC, Niebel A, Oldroyd GE, Barker DG, Fournier J, de Carvalho-Niebel F (2012) Medicago truncatula ERN transcription factors: regulatory interplay with NSP1/NSP2 GRAS factors and expression dynamics throughout rhizobial infection. Plant Physiol 160:2155–2172
Chang S, Puryear J, Cairney J (1993) A simple and efficient method for isolating RNA from pine trees. Plant Mol Biol Rep 11:113–116
Combier JP, Frugier F, de Billy F, Boualem A, El-Yahyaoui F, Moreau S, Vernie T, Ott T, Gamas P, Crespi M, Niebel A (2006) MtHAP2-1 is a key transcriptional regulator of symbiotic nodule development regulated by microRNA169 in Medicago truncatula. Genes Dev 20:3084–3088
Cui H, Levesque MP, Vernoux T, Jung JW, Paquette AJ, Gallagher KL, Wang JY, Blilou I, Scheres B, Benfey PN (2007) An evolutionarily conserved mechanism delimiting SHR movement defines a single layer of endodermis in plants. Science 316:421–425
de Lucas M, Daviere JM, Rodriguez-Falcon M, Pontin M, Iglesias-Pedraz JM, Lorrain S, Fankhauser C, Blazquez MA, Titarenko E, Prat S (2008) A molecular framework for light and gibberellin control of cell elongation. Nature 451:480–484
Den Herder G, Parniske M (2009) The unbearable naivety of legumes in symbiosis. Curr Opin Plant Biol 12:491–499
Di Laurenzio L, WysockaDiller J, Malamy JE, Pysh L, Helariutta Y, Freshour G, Hahn MG, Feldmann KA, Benfey PN (1996) The SCARECROW gene regulates an asymmetric cell division that is essential for generating the radial organization of the Arabidopsis root. Cell 86:423–433
Ehrhardt DW, Atkinson EM, Long SR (1992) Depolarization of alfalfa root hair membrane potential by Rhizobium meliloti Nod factors. Science 256:998–1000
Engstrom EM (2011) Phylogenetic analysis of GRAS proteins from moss, lycophyte and vascular plant lineages reveals that GRAS genes arose and underwent substantial diversification in the ancestral lineage common to bryophytes and vascular plants. Plant Signal Behav 6:850–854
Fehlberg V, Vieweg MF, Dohmann EM, Hohnjec N, Puhler A, Perlick AM, Kuster H (2005) The promoter of the leghaemoglobin gene VfLb29: functional analysis and identification of modules necessary for its activation in the infected cells of root nodules and in the arbuscule-containing cells of mycorrhizal roots. J Exp Bot 56:799–806
Fournier J, Timmers AC, Sieberer BJ, Jauneau A, Chabaud M, Barker DG (2008) Mechanism of infection thread elongation in root hairs of Medicago truncatula and dynamic interplay with associated rhizobial colonization. Plant Physiol 148:1985–1995
Gobbato E, Marsh JF, Vernie T, Wang E, Maillet F, Kim J, Miller JB, Sun J, Bano SA, Ratet P, Mysore KS, Denarie J, Schultze M, Oldroyd GE (2012) A GRAS-type transcription factor with a specific function in mycorrhizal signaling. Curr Biol 22:2236–2241
Gomez SK, Javot H, Deewatthanawong P, Torres-Jerez I, Tang Y, Blancaflor EB, Udvardi MK, Harrison MJ (2009) Medicago truncatula and Glomus intraradices gene expression in cortical cells harboring arbuscules in the arbuscular mycorrhizal symbiosis. BMC Plant Biol 9:10
Goujon M, McWilliam H, Li W, Valentin F, Squizzato S, Paern J, Lopez R (2010) A new bioinformatics analysis tools framework at EMBL-EBI. Nucleic Acids Res 38:W695–W699
Grebenok RJ, Pierson E, Lambert GM, Gong FC, Afonso CL, HaldemanCahill R, Carrington JC, Galbraith DW (1997) Green-fluorescent protein fusions for efficient characterization of nuclear targeting. Plant J 11:573–586
Griffiths J, Murase K, Rieu I, Zentella R, Zhang ZL, Powers SJ, Gong F, Phillips AL, Hedden P, Sun TP, Thomas SG (2006) Genetic characterization and functional analysis of the GID1 gibberellin receptors in Arabidopsis. Plant Cell 18:3399–3414
Haynes JG, Cyzmmek KJ, Carlson CA, Veereshlingam H, Dickstein R, Sherrier DJ (2004) A novel method for rapid analysis of legume root nodule development using confocal microscopy. New Phytol 163:661–668
Higo K, Ugawa Y, Iwamoto M, Korenaga T (1999) Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res 27:297–300
Hirsch S, Oldroyd GED (2009) GRAS-domain transcription factors that regulate plant development. Plant Signal Behav 4:698–700
Hirsch S, Kim J, Munoz A, Heckmann AB, Downie JA, Oldroyd GED (2009) GRAS proteins form a DNA binding complex to induce gene expression during nodulation signaling in Medicago truncatula. Plant Cell 21:545–557
Hogekamp C, Arndt D, Pereira PA, Becker JD, Hohnjec N, Kuster H (2011) Laser microdissection unravels cell-type-specific transcription in arbuscular mycorrhizal roots, including CAAT-box transcription factor gene expression correlating with fungal contact and spread. Plant Physiol 157:2023–2043
Hogg BV, Cullimore JV, Ranjeva R, Bono JJ (2006) The DMI1 and DMI2 early symbiotic genes of Medicago truncatula are required for a high-affinity nodulation factor-binding site associated to a particulate fraction of roots. Plant Physiol 140:365–373
Jefferson RA, Kavanagh TA, Bevan MW (1987) GUS fusions: β-glucuronidase as a sensitive and versatile gene fusion marker in higher plants. EMBO J 6:3901–3907
Johannesson H, Wang Y, Engstrom P (2001) DNA-binding and dimerization preferences of Arabidopsis homeodomain-leucine zipper transcription factors in vitro. Plant Mol Biol 45:63–73
Journet EP, El-Gachtouli N, Vernoud V, de Billy F, Pichon M, Dedieu A, Arnould C, Morandi D, Barker DG, Gianinazzi-Pearson V (2001) Medicago truncatula ENOD11: a novel RPRP-encoding early nodulin gene expressed during mycorrhization in arbuscule-containing cells. Mol Plant Microbe Interact 14:737–748
Kakar K, Wandrey M, Czechowski T, Gaertner T, Scheible WR, Stitt M, Torres-Jerez I, Xiao Y, Redman JC, Wu HC, Cheung F, Town CD, Udvardi MK (2008) A community resource for high-throughput quantitative RT-PCR analysis of transcription factor gene expression in Medicago truncatula. Plant Methods 4:18
Kalo P, Gleason C, Edwards A, Marsh J, Mitra RM, Hirsch S, Jakab J, Sims S, Long SR, Rogers J, Kiss GB, Downie JA, Oldroyd GE (2005) Nodulation signaling in legumes requires NSP2, a member of the GRAS family of transcriptional regulators. Science 308:1786–1789
Karimi M, Inzé D, Depicker A (2002) GATEWAY vectors for Agrobacterium-mediated plant transformation. Trends Plant Sci 7:193–195
Karimi M, Bleys A, Vanderhaeghen R, Hilson P (2007) Building blocks for plant gene assembly. Plant Physiol 145:1183–1191
Kim GB, Nam YW (2012) Isolation and characterization of Medicago truncatula U6 promoters for the construction of small hairpin RNA-mediated gene silencing vectors. Plant Mol Biol Rep. doi:10.1007/s11105-012-0528-1
Kim GB, Nam YW (2013) A novel Δ1-pyrroline-5-carboxylate synthetase gene of Medicago truncatula plays a predominant role in stress-induced proline accumulation during symbiotic nitrogen fixation. J Plant Physiol 170:291–302
Kim GB, Bae JH, An CS, Nam YW (2013) Single or multiple gene silencing directed by U6 promoter-based shRNA vectors facilitates efficient functional genome analysis in Medicago truncatula. Plant Mol Biol Rep. doi:10.1007/s11105-013-0562-7
Lee MH, Kim B, Song SK, Heo JO, Yu NI, Lee SA, Kim M, Kim DG, Sohn SO, Lim CE, Chang KS, Lee MM, Lim J (2008) Large-scale analysis of the GRAS gene family in Arabidopsis thaliana. Plant Mol Biol 67:659–670
Lefebvre B, Timmers T, Mbengue M, Moreau S, Herve C, Toth K, Bittencourt-Silvestre J, Klaus D, Deslandes L, Godiard L et al (2010) A remorin protein interacts with symbiotic receptors and regulates bacterial infection. Proc Natl Acad Sci USA 107:2343–2348
Leong SA, Williams PH, Ditta GS (1985) Analysis of the 5′ regulatory region of the gene for delta-aminolevulinic acid synthetase of Rhizobium meliloti. Nucleic Acids Res 13:5965–5976
Lévy J, Bres C, Geurts R, Chalhoub B, Kulikova O, Duc G, Journet EP, Ané JM, Lauber E, Bisseling T, Dénarié J, Rosenberg C, Debellé F (2004) A putative Ca2+ and calmodulin-dependent protein kinase required for bacterial and fungal symbioses. Science 303:1361–1364
Limpens E, Ramos J, Franken C, Raz V, Compaan B, Franssen H, Bisseling T, Geurts R (2004) RNA interference in Agrobacterium rhizogenes-transformed roots of Arabidopsis and Medicago truncatula. J Exp Bot 55:983–992
Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods 25:402–408
Madsen EB, Madsen LH, Radutoiu S, Olbryt M, Rakwalska M, Szczyglowski K, Sato S, Kaneko T, Tabata S, Sandal N, Stougaard J (2003) A receptor kinase gene of the LysM type is involved in legume perception of rhizobial signals. Nature 425:637–640
Maekawa T, Maekawa-Yoshikawa M, Takeda N, Imaizumi-Anraku H, Murooka Y, Hayashi M (2009) Gibberellin controls the nodulation signaling pathway in Lotus japonicus. Plant J 58:183–194
Marsh JF, Rakocevic A, Mitra RM, Brocard L, Sun J, Eschstruth A, Long SR, Schultze M, Ratet P, Oldroyd GE (2007) Medicago truncatula NIN is essential for rhizobial-independent nodule organogenesis induced by autoactive calcium/calmodulin-dependent protein kinase. Plant Physiol 144:324–335
Middleton PH, Jakab J, Penmetsa RV, Starker CG, Doll J, Kalo P, Prabhu R, Marsh JF, Mitra RM, Kereszt A, Dudas B, VandenBosch K, Long SR, Cook DR, Kiss GB, Oldroyd GE (2007) An ERF transcription factor in Medicago truncatula that is essential for Nod factor signal transduction. Plant Cell 19:1221–1234
Mitra RM, Shaw SL, Long SR (2004) Six nonnodulating plant mutants defective for Nod factor-induced transcriptional changes associated with the legume-rhizobia symbiosis. Proc Natl Acad Sci USA 101:10217–10222
Murakami Y, Miwa H, Imaizumi-Anraku H, Kouchi H, Downie JA, Kawaguchi M, Kawasaki S (2006) Positional cloning identifies Lotus japonicus NSP2, a putative transcription factor of the GRAS family, required for NIN and ENOD40 gene expression in nodule initiation. DNA Res 13:255–265
Oldroyd GE, Long SR (2003) Identification and characterization of nodulation-signaling pathway 2, a gene of Medicago truncatula involved in Nod factor signaling. Plant Physiol 131:1027–1032
Oldroyd GE, Murray JD, Poole PS, Downie JA (2011) The rules of engagement in the legume-rhizobial symbiosis. Annu Rev Genet 45:119–144
Park HC, Kim ML, Lee SM, Bahk JD, Yun DJ, Lim CO, Hong JC, Lee SY, Cho MJ, Chung WS (2007) Pathogen-induced binding of the soybean zinc finger homeodomain proteins GmZF-HD1 and GmZF-HD2 to two repeats of ATTA homeodomain binding site in the calmodulin isoform 4 (GmCaM4) promoter. Nucleic Acids Res 35:3612–3623
Popp C, Ott T (2011) Regulation of signal transduction and bacterial infection during root nodule symbiosis. Curr Opin Plant Biol 14:458–467
Pysh LD, Wysocka-Diller JW, Camilleri C, Bouchez D, Benfey PN (1999) The GRAS gene family in Arabidopsis: sequence characterization and basic expression analysis of the SCARECROW-LIKE genes. Plant J 18:111–119
Quandt HJ, Pühler A, Broer I (1993) Transgenic root nodules of Vicia hirsuta: a fast and efficient system for the study of gene expression in indeterminate-type nodules. Mol Plant Microbe Interact 6:699–706
Radutoiu S, Madsen LH, Madsen EB, Felle HH, Umehara Y, Grønlund M, Sato S, Nakamura Y, Tabata S, Sandal N, Stougaard J (2003) Plant recognition of symbiotic bacteria requires two LysM receptor-like kinases. Nature 425:585–592
Sbabou L, Bucciarelli B, Miller S, Liu J, Berhada F, Filali-Maltouf A, Allan D, Vance C (2010) Molecular analysis of SCARECROW genes expressed in white lupin cluster roots. J Exp Bot 61:1351–1363
Scheres B, Di Laurenzio L, Willemsen V, Hauser MT, Janmaat K, Weisbeek P, Benfey PN (1995) Mutations affecting the radial organisation of the Arabidopsis root display specific defects throughout the embryonic axis. Development 121:53–62
Smit P, Raedts J, Portyanko V, Debelle F, Gough C, Bisseling T, Geurts R (2005) NSP1 of the GRAS protein family is essential for rhizobial Nod factor induced transcription. Science 308:1789–1791
Stougaard J, Jorgensen JE, Christensen T, Kuhle A, Marcker KA (1990) Interdependence and nodule specificity of cis-acting regulatory elements in the soybean leghemoglobin lbc3 and N23 gene promoters. Mol Gen Genet 220:353–360
Sun X, Xue B, Jones WT, Rikkerink E, Dunker AK, Uversky VN (2011) A functionally required unfoldome from the plant kingdom: intrinsically disordered N-terminal domains of GRAS proteins are involved in molecular recognition during plant development. Plant Mol Biol 77:205–223
Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680
Tian CG, Wan P, Sun SH, Li JY, Chen MS (2004) Genome-wide analysis of the GRAS gene family in rice and Arabidopsis. Plant Mol Biol 54:519–532
Toth K, Stratil TF, Madsen EB, Ye J, Popp C, Antolin-Llovera M, Grossmann C, Jensen ON, Schussler A, Parniske M, Ott T (2012) Functional domain analysis of the remorin protein LjSYMREM1 in Lotus japonicus. PLoS One 7:e30817
Veereshlingam H, Haynes JG, Penmetsa RV, Cook DR, Sherrier DJ, Dickstein R (2004) nip, a symbiotic Medicago truncatula mutant that forms root nodules with aberrant infection threads and plant defense-like response. Plant Physiol 136:3692–3702
Vernié T, Moreau S, de Billy F, Plet J, Combier JP et al (2008) EFD Is an ERF transcription factor involved in the control of nodule number and differentiation in Medicago truncatula. Plant Cell 20:2696–2713
Zhang Q, Blaylock LA, Harrison MJ (2010) Two Medicago truncatula half-ABC transporters are essential for arbuscule development in arbuscular mycorrhizal symbiosis. Plant Cell 22:1483–1497
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Kim, GB., Nam, YW. A novel GRAS protein gene MtSymSCL1 plays a role in regulating nodule number in Medicago truncatula . Plant Growth Regul 71, 77–92 (2013). https://doi.org/10.1007/s10725-013-9814-7
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DOI: https://doi.org/10.1007/s10725-013-9814-7