rima-dependent nuclear accumulation of iyo triggers auxin ...feb 21, 2017 · 1 1 research article...

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RESEARCH ARTICLE 1 2 RIMA-dependent nuclear accumulation of IYO triggers auxin-3 irreversible cell differentiation in Arabidopsis 4 5 Alfonso Muñoza, Silvina Manganoa,1,4, Mary Paz González-Garcíaa,4, Ramón 6 Contrerasa, Michael Sauera,2, Bert De Rybelb,3, Dolf Weijersb, José Juan Sánchez-7 Serranoa, Maite Sanmartína,5 and Enrique Rojoa,5 8 9 aCentro Nacional de Biotecnología-CSIC, Cantoblanco, E-28049 Madrid, Spain. 10 bWageningen University, Laboratory of Biochemistry, Dreijenlaan 3, 6703 HA Wageningen. 11 1Current address: Fundación Instituto Leloir, Buenos Aires, Argentina, C1405BWE. 12 2Current address: Department of Plant Physiology, University of Potsdam, 14476 13 Potsdam, Germany. 14 3Current address: Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium and 15 Department of Plant Biotechnology and Bioinformatics, Gent University, B-9052 Ghent, 16 Belgium. 17 4These authors contributed equally to this work 18 5Corresponding Authors: [email protected] or [email protected]; fax: 34915854506 19 20 Short title: RIMA/IYO nuclear differentiation switch 21 22 One-sentence summary: The Arabidopsis RPAP2/RTR1 homologue RIMA interacts with 23 IYO and mediates its nuclear accumulation to activate cell differentiation that cannot be 24 reversed by auxins. 25 26 The authors responsible for distribution of materials integral to the findings presented in 27 this article in accordance with the policy described in the Instructions for Authors 28 (www.plantcell.org) are: Enrique Rojo ([email protected]) and Maite Sanmartín 29 ([email protected]). 30 31 ABSTRACT 32 The transcriptional regulator MINIYO (IYO) is essential and rate-limiting for initiating cell 33 differentiation in Arabidopsis thaliana. Moreover, IYO moves from the cytosol into the 34 nucleus in cells at the meristem periphery, possibly triggering their differentiation. 35 However, the genetic mechanisms controlling IYO nuclear accumulation were unknown 36 and the evidence that increased nuclear IYO levels trigger differentiation remained 37 correlative. Searching for IYO interactors, we have identified RPAP2 IYO Mate (RIMA), a 38 homologue of yeast and human proteins linked to nuclear import of selective cargo. 39 Knockdown of RIMA causes delayed onset of cell differentiation, phenocopying the effects 40 of IYO knock down at the transcriptomic and developmental levels. Moreover, 41 differentiation is completely blocked when IYO and RIMA activities are simultaneously 42 reduced and is synergistically accelerated when IYO and RIMA are concurrently 43 overexpressed, confirming their functional interaction. Indeed, RIMA knockdown reduces 44 the nuclear levels of IYO and prevents its pro-differentiation activity, supporting the 45 conclusion that RIMA-dependent nuclear IYO accumulation triggers cell differentiation in 46 Arabidopsis. Importantly, by analysing the effect of the IYO/RIMA pathway on xylem pole 47 pericycle cells, we provide compelling evidence reinforcing the view that the capacity for 48 de novo organogenesis and regeneration from mature plant tissues can reside in stem cell 49 reservoirs. 50

Plant Cell Advance Publication. Published on February 21, 2017, doi:10.1105/tpc.16.00791

©2017 American Society of Plant Biologists. All Rights Reserved

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INTRODUCTION 52 53 Stem cell progeny may retain pluripotency to renew the stem cell pool or undergo 54 differentiation to acquire specialized functions. This cell fate decision is under strict 55 genetic control to assure proper development of the organism, but the circuitry 56 controlling and executing this choice is still largely unknown (Benfey, 2016). 57 Moreover, in certain organisms this decision may be revoked and differentiated 58 cells can return into a stem cell state (Sugimoto et al., 2011; Sanchez Alvarado 59 and Yamanaka, 2014). Unravelling if and how cells may be reprogrammed into 60 pluripotency is key for understanding processes such as regeneration, wound 61 healing and somatic cloning. Plants in particular have a high capacity for 62 regenerating organs and even the whole organism (Sugimoto et al., 2011; Liu et 63 al., 2014). Moreover, callus cultures of pluripotent stem cells are easily obtained 64 from many plant species by incubating mature tissues in auxin-rich media (Atta et 65 al., 2009; Sugimoto et al., 2010; Ikeuchi et al., 2013). These findings have led to 66 the widely-held hypothesis that plant cells can readily dedifferentiate into 67 pluripotency (Iwase et al., 2011b; Chupeau et al., 2013; Ikeuchi et al., 2013; 68 Ikeuchi et al., 2015; Sugiyama, 2015). However, plants retain reservoirs of 69 undifferentiated cells in adult tissues, such as the stem cell populations in apical 70 meristems that generate post-embryonically most of the organs of the plant 71 (Scheres, 2007; Wolters and Jurgens, 2009). Thus, stem cells present in adult 72 tissues could be the source for callus formation and for organ regeneration, 73 bypassing the need for a dedifferentiation step. Indeed, it has been now 74 convincingly shown that auxin-induced callus cultures derive from xylem pole 75 pericycle and pericycle-like cambium cells (Che et al., 2007; Atta et al., 2009; 76 Sugimoto et al., 2010; Liu et al., 2014), which have meristematic characteristics 77 (Beeckman et al., 2001; Atta et al., 2009; Liu et al., 2014). Moreover, in a root tip 78 regeneration assay, the competence for regeneration was mapped to the root 79 apical meristem cells (Sena et al., 2009). These results suggest that pre-existing 80 stem cells are the source for auxin-induced callus formation and possibly for organ 81 regeneration in plants, but definitive proof of this is lacking. 82

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Cell fate conversions are in essence a matter of altering genome 83 expression. Indeed, the conversion from pluripotency into differentiation implies 84 large changes in genome transcription, to activate cell lineage developmental 85 programs and turn off stem cell self-renewal programs (Sablowski, 2011; Young, 86 2011). In metazoans, the implementation of these mutually exclusive 87 transcriptional states is in large part dependent on regulation at the elongation 88 phase of transcription (Guenther et al., 2007; Stock et al., 2007; Brookes et al., 89 2012). In plants, factors regulating transcriptional elongation also play key roles in 90 development (Sanmartin et al., 2012; Van Lijsebettens and Grasser, 2014). In 91 particular, the Arabidopsis thaliana MINIYO (IYO) gene encodes an RNA 92 polymerase II (Pol II)-interacting factor that sustains transcriptional elongation in 93 developing organs and is essential for initiating cell differentiation throughout the 94 plant. IYO is rate limiting for cell differentiation and accumulates in the nucleus with 95 timing that coincides with the onset of cell differentiation, suggesting that increased 96 nuclear IYO levels may trigger this cell fate transition (Sanmartin et al., 2011). 97 However, the genetic mechanisms that determine the subcellular localization of 98 IYO have remained unknown and we have lacked direct evidence that nuclear 99 accumulation of IYO is required for its pro-differentiation activity. 100 Proteomic studies aimed at characterizing the components of the human 101 transcriptional machinery uncovered a set of four RNA Polymerase II Associated 102 Proteins (RPAPs) that are conserved in all eukaryotic kingdoms (Jeronimo et al., 103 2007). RPAPs form an interaction network that is tightly connected to the Pol II 104 complex in the nuclear compartment (Jeronimo et al., 2007; Boulon et al., 2010; 105 Forget et al., 2010). RPAP1, the human homologue of Arabidopsis IYO, forms part 106 of the functionally active Pol II complex and is thought to directly regulate 107 transcription (Jeronimo et al., 2004). Human RPAP2 and RPAP4/GPN1, and their 108 yeast counterparts RTR1 and NPA3, have been ascribed diverse functions in 109 assembly, nuclear import and regulation of Pol II activity (Forget et al., 2010; 110 Calera et al., 2011; Carre and Shiekhattar, 2011; Staresincic et al., 2011; Egloff et 111 al., 2012; Forget et al., 2013; Minaker et al., 2013; Wani et al., 2014; Gomez-112 Navarro and Estruch, 2015; Niesser et al., 2016). However, very little is known in 113

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yeast and animals about the biological processes in which these RPAP proteins 114 are involved. In yeast, the homologues of RPAP1, RPAP2 and RPAP4 are either 115 essential for viability (Giaever et al., 2002) or cause severe growth defects when 116 mutated (Gibney et al., 2008), supporting the conclusion that they play 117 fundamental, although yet uncharacterized roles in the physiology of these 118 organisms. In animals, siRNA knockdown of RPAP2 and RPAP4 in immortalized 119 cell lines interferes with nuclear import and activity of Pol II (Forget et al., 2010; 120 Calera et al., 2011; Carre and Shiekhattar, 2011; Egloff et al., 2012; Forget et al., 121 2013; Wani et al., 2014), but the physiological in vivo roles of these genes remain 122 unexplored.. 123 Here, in searching for IYO interactors, we identified the RPAP2 homologue 124 RIMA and the RPAP4 homologues GPN1 and GPN2. Arabidopsis T-DNA 125 insertional mutants in GPN1 and GPN2 arrest at the octant/16-cell stage of 126 embryogenesis (Lahmy et al., 2007), which hampers genetic characterization of 127 their developmental roles. Accordingly, we focused our functional analysis on 128 RIMA, which was unexplored to date. The results we present strongly support the 129 conclusion that RIMA is an essential partner of IYO in activating cell differentiation 130 and suggest that this is a process that cannot be reversed. 131 132

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RESULTS 133 134 IYO interactors are conserved from plants to humans 135 136 Identification by mass-spectrometry of proteins co-immunopurifying with a 137 functional IYO-GFP protein (Supplemental Table 1) and confirmation by 138 bimolecular fluorescence complementation (BiFC) and pull down assays (Figure 139 1A and Sanmartin et al., 2011) revealed that IYO interacts with the Pol II subunits 140 RPB2, RPB3, RPB10 and RPB11, and with the RPAP4 homologues GPN1 and 141 GPN2. Interestingly, the human IYO homologue RPAP1 has also been found in a 142 complex with RPB2, RPB3, RPB10, RPB11, RPAP4/GPN1 and GPN2, as well as 143 with an additional RPAP protein, RPAP2 (Boulon et al., 2010). The Arabidopsis 144 genome contains a homologue of RPAP2 encoded by the RPAP2 IYO MATE 145 (RIMA/At5g26760) gene, which was not identified among the proteins co-purifying 146 with IYO-GFP. However, in these experiments IYO-GFP was constitutively 147 expressed under the 35S promoter, which could dilute out the fraction interacting 148 with RIMA, which has a restricted domain of expression (see below), and prevent 149 detection of the interaction. Indeed, we observed BiFC interaction between IYO 150 and RIMA when we co-expressed both proteins in Nicotiana benthamiana leaves 151 (Figure 1B). The BiFC interaction with IYO was abolished by point mutations that 152 disrupt the RIMA zinc finger domain (Figure 1C), which is conserved in RIMA 153 homologues from plants, yeast and mammals (Supplemental Figure 1) and has 154 been proved essential for the in vivo activity of yeast RTR1 (Gibney et al., 2008). 155 To confirm the interaction between IYO and RIMA, we raised specific antibodies 156 against RIMA (Supplemental Figure 2). We observed co-purification of HA-tagged 157 IYO when we immunopurified the endogenous RIMA (Figure 1D), indicating that 158 the two proteins interact in vivo. Together, these results show that the IYO/RPAP1 159 interactome is conserved from plants to animals and includes a Pol II subcomplex, 160 GPN GTPases and RIMA. 161 162

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RIMA is expressed in meristems where it shuttles through the cytosol and 163 the nucleus 164 To determine the expression profile of RIMA, we analyzed plants expressing GUS 165 under the control of the RIMA promoter (ProRIMA:GUS). In the aerial part of the 166 plant, ProRIMA:GUS expression was highest in the shoot apical meristem (SAM), 167 in leaf and flower primordia, in ovules and in developing embryos (Figure 2A). In 168 the root, strong ProRIMA:GUS signal was observed in the root apical meristem 169 (RAM), in the transition zone and in lateral root primordia (Figure 2B). This 170 promoter activity domain largely overlaps with that of the IYO promoter (Sanmartin 171 et al., 2011), and is in agreement with high degree of co-expression between the 172 IYO and RIMA transcripts (Pearson correlation coefficient of 0.62) found using the 173 ACT tool (Jen et al., 2006). To characterize the subcellular distribution of RIMA, we 174 used as a proxy a functional ProRIMA:RIMA-GFP construct that complements all 175 rima mutant phenotypes (see below). In roots of ProRIMA:RIMA-GFP rima-1 176 plants, strong GFP fluorescence was observed in the RAM, in the transition zone 177 and in lateral root primordia (Figure 2C), matching the activity profile of the 178 ProRIMA:GUS plants. The fluorescence was primarily cytosolic, but it was also 179 detectable in the nucleus (Figure 2D-E). Similarly, fluorescence was largely 180 cytosolic in N. benthamiana leaves transiently transformed with Pro35S:RIMA-GFP 181 (Figure 2F). The yeast and human homologues RTR1 and RPAP2 are also 182 localized at steady state primarily in the cytosol, but they redistribute to the nucleus 183 upon inhibition of the XPO1 nuclear export receptor with Leptomycin B (LMB) 184 (Gibney et al., 2008; Forget et al., 2013), which also blocks the Arabidopsis XPO1 185 receptor (Haasen et al., 1999). Treatment with LMB resulted in higher nuclear 186 levels of RIMA-GFP (Figure 2F-G), confirming that RIMA shuttles between the 187 cytosol and the nucleus in plants. 188 189 RIMA activity is required for cell differentiation 190 To analyze the in vivo function of RIMA, we characterized two T-DNA insertional 191 lines from the SALK collection, rima-1 (SALK_012339) and rima-2 (SALK_11576). 192 Homozygous plants for the rima-1 allele, containing a T-DNA insertion in the first 193

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exon of the gene, could not be recovered. In siliques from rima-1/RIMA 194 heterozygous plants, the growth of 26% of the seeds (n=472) was abnormal and 195 eventually ceased. Analysis of the arrested seeds showed that rima-1 embryos 196 develop aberrantly, retaining a globular morphology lacking any discernible 197 cotyledon, hypocotyl or root structures, and eventually aborting at mature stage 198 (Figure 3A). Notably, these defects in embryonic organogenesis are similar to 199 those observed in strong iyo alleles (Sanmartin et al., 2011). By contrast, plants 200 homozygous for the rima-2 allele, which contains a T-DNA insertion in the third 201 intron of the gene, were viable and fertile but developed abnormally, displaying 202 similar alterations as the iyo-1 knockdown mutant (Sanmartin et al., 2011). The 203 rima-2 plants showed delayed leaf emergence, altered phyllotaxis and perturbed 204 leaf morphology (Figure 3B). Moreover, the SAM was enlarged, splitting into 205 several meristems, and generating highly fasciated stems (Figure 3C-D). Splitting 206 of flower meristems was also observed in rima-2 plants, which gave rise to 207 compound flowers and siliques (Figure 3D). These alterations suggest that RIMA is 208 required for proper cell differentiation and organogenesis in the SAM. Likewise, 209 differentiation was delayed and defective in the protoderm of rima-2 cotyledons 210 (Figure 3E), which are organs of embryonic origin. At a stage when the wild-type 211 (Wt) cotyledon epidermis was fully differentiated, the rima-2 epidermis still retained 212 small protoderm-like cells expressing the ProTMM:TMM-GFP stem cell marker. We 213 also observed developmental alterations indicative of defective differentiation in the 214 rima-2 RAM. In the proximal side, ectopic periclinal divisions of ground tissue cells 215 broadened the meristem (Figure 3F), while in the distal side, differentiating 216 columella cells abnormally retained expression of a stem cell marker (Figure 3G). 217 These developmental alterations are shared with the iyo-1 mutant (Sanmartin et 218 al., 2011) and demonstrate that RIMA is required for proper cell differentiation 219 throughout the plant. 220

Expression analysis revealed that rima-2 plants accumulate much reduced 221 levels of the full-length transcript and the corresponding protein, besides 222 accumulating a shorter RIMA transcript encoding a truncated protein (Figure 3H 223 and Supplemental Figure 2A). This suggests that the intron containing the T-DNA 224

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in rima-2 is spliced out with low efficiency, causing an acute reduction in the 225 expression of the full-length protein. The rima-2 allele was fully recessive and 226 developmental perturbations were worsened in trans-heterozygous rima-1/rima-2 227 plants, which showed further delay in leaf emergence, larger meristems and 228 increased shoot fasciation relative to the rima-2 homozygous mutant (Figure 3I). 229 Moreover, all phenotypes of rima-1 and rima-2 mutants were complemented by 230 transformation with a genomic RIMA sequence, which demonstrated that they were 231 due to the disruption of the RIMA gene. From these results, we conclude that rima-232 1 is a null allele that provokes a complete block in organogenesis and is embryo 233 lethal, while rima-2 is a knockdown allele with reduced expression of full-length 234 RIMA that causes defective cell and organ differentiation throughout an otherwise 235 viable plant. RIMA fused to GFP under the control of the RIMA promoter 236 (ProRIMA:RIMA-GFP) also complemented the rima mutants (Figure 3J, note 237 rescue of plant death and of the irregular pattern of leaf emergence in 238 ProRIMA:RIMA-GFP rima-1 plants), indicating that the ProRIMA:RIMA-GFP 239 construct fully recapitulates the expression and activity of the endogenous RIMA 240 gene. Transformation with Pro35S:RIMA-GFP also rescued rima-1 lethality (Figure 241 3J), but a zinc-finger mutant version (Pro35S:RIMAC94A/C98A-GFP) failed to 242 complement it, indicating that this domain is essential for RIMA function. Notably, 243 complementation in the Pro35S:RIMA-GFP rima-1 plants was partial, and the 244 plants phenocopied the adult phenotype of rima-2 knock down mutants, including 245 delayed leaf emergence (Figure 3J). This partial complementation corresponded 246 with lower expression of the transgene than in the fully complemented 247 ProRIMA:RIMA-GFP rima-1 lines (Figure 3J). Interestingly, twin embryos 248 developed frequently in Pro35S:RIMA-GFP rima-1 seeds (Figure 3K), implying that 249 when RIMA activity is insufficient, ectopic totipotent stem cells are retained. 250 Together, these phenotypes indicate that RIMA is required for initiating cell 251 differentiation throughout the plant. 252

253 The iyo-1 and rima-2 mutants have matching transcriptomic fingerprints 254

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Qualitatively, the developmental phenotypes of rima and iyo mutants are very 255 similar (Sanmartin et al., 2011), consistent with RIMA and IYO regulating common 256 downstream processes. To gain a quantitative measure of their phenotypic identity, 257 we compared the transcriptome alterations in inflorescences (consisting of the 258 SAM and developing flowers) of the iyo-1 and rima-2 mutants relative to those of 259 Wt plants. This analysis revealed a striking similarity between the mutants. The 260 overlap between the sets of genes that were most strongly down-regulated (top 261 400 genes by fold-change) in each mutant to Wt comparison (genes that require 262 IYO and RIMA for full expression) was 31-fold higher than expected at random (p-263 value=1.57e-295, hypergeometric test, Figure 4A) and 12-fold higher (p-264 value=3.45e-66, hypergeometric test) for the genes most strongly up-regulated in 265 both mutants. In all, 372 out of the 400 most down-regulated genes in iyo-1 were 266 also down-regulated in rima-2 (Figure 4B) and 352 out of the 400 most up-267 regulated genes in iyo-1 were up-regulated in rima-2. Geneset enrichment analysis 268 (GSEA) showed that pathways related to morphogenesis and flower 269 organogenesis were enriched among the down-regulated genes in inflorescences 270 from both mutants (Figure 4C). These common down-regulated genes included all 271 floral organ identity genes (Supplemental Table 2), which act as master regulators 272 for differentiation and organogenesis in inflorescence meristems (Sablowski, 273 2015). These results indicate that IYO and RIMA are required for activating 274 common genetic programs related with organogenesis. 275 276 IYO and RIMA cooperate genetically to activate differentiation 277 The remarkable degree of gene co-regulation in the mutants provides robust 278 quantitative support for the hypothesis that IYO and RIMA function in the same 279 developmental pathway. To further explore this hypothesis, we tested for their 280 genetic interaction. We first analyzed the effect of a simultaneous reduction in the 281 activity of both genes by crossing the iyo-1 and rima-2 knockdown mutants. The 282 iyo-1 rima-2 double mutant seedlings failed to develop proper organs, and 283 eventually developed into a friable callus-like mass of cells that could be 284 propagated in vitro without external addition of hormones (Figure 5A-B). The 285

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majority of the cells in those calli had either 2C or 4C DNA content (Figure 5C), 286 demonstrating that they consisted mainly of mitotically active cells. The synergistic 287 inhibition of cell differentiation when combining the iyo-1 and rima-2 mutations is 288 consistent with RIMA and IYO cooperating in a function that is essential for cells to 289 differentiate. To confirm this genetic interaction, we analyzed the effect of 290 concurrent overexpression of IYO and RIMA. We reported previously that 291 overexpression of HA-tagged IYO under the constitutive 35S promoter 292 (Pro35S:IYO-HA lines) causes premature onset of cell differentiation and 293 eventually, meristem termination (Sanmartin et al., 2011). Although expression of 294 RIMA tagged with HA, Flag or GFP under the same 35S promoter did not produce 295 any evident developmental phenotype on its own, when combined with the 296 Pro35S:IYO-HA transgene, a synergistic acceleration of SAM termination was 297 observed (Figure 5D), indicating that IYO and RIMA cooperatively activate cell 298 differentiation. 299 300 RIMA mediates IYO nuclear accumulation to activate cell differentiation 301 Considering that RIMA and IYO interact physically, we presumed that their genetic 302 cooperation reflected cross activation at the protein level. Based on the reported 303 function of RPAP2 and RTR1 in nuclear import in mammals and yeast, we 304 hypothesized that RIMA could activate IYO by mediating its nuclear accumulation. 305 Thus, we compared the localization of ProIYO:IYO-GFP in Wt and rima-2 mutant 306 plants. As previously reported (Sanmartin et al., 2011), ProIYO:IYO-GFP 307 fluorescence in Wt roots showed a diffuse cytosolic distribution in cells at the 308 meristem core, but concentrated in the nucleus of cells at the meristem periphery 309 (Figure 6A). In rima-2 roots there was a strong reduction in IYO-GFP nuclear 310 accumulation across the root, which was coupled to increased cytosolic levels 311 (Figure 6A). Moreover, nuclear IYO-GFP accumulation was restored when rima-2 312 plants were incubated in the presence of LMB, demonstrating that reduced RIMA 313 activity impairs nuclear targeting of IYO-GFP and not its expression. This role in 314 transport of IYO into the nucleus is consistent with the steady-state localization of 315 RIMA in the cytosol and its redistribution to the nucleus when irreversibly linked to 316

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IYO in the BiFC complex (Figure 1B). Moreover, co-expression with IYO-HA in N. 317 benthamiana leaves increased the nuclear RIMA-GFP levels relative to plants 318 expressing RIMA-GFP alone (Figure 6B), consistent with RIMA escorting IYO 319 during transport into the nucleus. We reasoned from these results that if nuclear 320 accumulation were required for IYO pro-differentiation function, then the rima-2 321 mutation should be epistatic on IYO activity. To check this, we introgressed 322 Pro35S:IYO-HA into the rima-2 mutant background. The rima-2 mutation 323 suppressed meristem termination caused by IYO-HA overexpression (Figure 6C, 324 note the indeterminate SAM growth of Pro35S:IYO-HA rima-2 plants), indicating 325 that IYO requires RIMA to activate differentiation. To exclude the possibility that the 326 suppression of the phenotype was due to silencing of the IYO-HA transgene, we 327 analyzed its expression. The levels of IYO-HA were actually increased in the rima-328 2 background (Figure 6C), demonstrating that RIMA activity is required for IYO 329 overexpression to induce premature differentiation and suggesting that a 330 compensatory mechanism increases IYO protein accumulation when RIMA activity 331 is compromised. All together, these genetic analyses support the conclusion that 332 RIMA mediates nuclear IYO accumulation to activate cell differentiation. 333 334 Forced differentiation of xylem pole pericycle cells blocks lateral root 335 formation and callus growth. 336 It is still disputed whether lateral root formation, callus growth and subsequent 337 plant regeneration involves a process of dedifferentiation or rather results from the 338 expansion of undifferentiated cells present in the starting tissue (Atta et al., 2009; 339 Sugimoto et al., 2010; Iwase et al., 2011b; Iwase et al., 2011a; Chupeau et al., 340 2013; Ikeuchi et al., 2013; Liu et al., 2014; Sanchez Alvarado and Yamanaka, 341 2014; Sugiyama, 2015). Lateral roots and calli derive from xylem pole pericycle 342 cells and pericycle-like cambium cells (Dubrovsky et al., 2000; Beeckman et al., 343 2001; Che et al., 2007; Atta et al., 2009; Sugimoto et al., 2010; Liu et al., 2014). 344 Although their actual differentiation status remains unknown, it has been shown 345 that they retain certain meristematic properties (Beeckman et al., 2001; Atta et al., 346 2009; Liu et al., 2014). In this regard, a hallmark of undifferentiated cells in apical 347

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meristems is the exclusion of IYO-GFP from the nucleus (Sanmartin et al., 2011). 348 To determine if this is also the case in xylem pole pericycle cells, we analyzed the 349 localization of IYO-GFP in the mature zone of the root, using as control the nuclear 350 marker RPB10-GFP expressed under the same 35S promoter. Both RPB10-GFP 351 and IYO-GFP were found to accumulate in the nuclei of cells from the epidermis, 352 the cortex, the endodermis and the vasculature. By contrast, only RPB10-GFP was 353 detectable in the nucleus of xylem pole pericycle cells (Figure 7A and 354 Supplemental Figure 3; Pro35S:RPB10-GFP roots: 4-6 GFP positive xylem pole 355 pericycle nuclei per field of view; Pro35S:IYO-GFP: 0 GFP positive xylem pole 356 pericycle nuclei per field). Incubation with auxins induces proliferation of xylem pole 357 pericycle cells, which undergo periclinal divisions to form a multilayer tissue that 358 eventually develops into a callus. RPB10-GFP labelled the nuclei of the auxin-359 induced multilayer xylem pole pericycle, but IYO-GFP was conspicuously absent 360 from their nuclei (Figure 7B). Likewise, in the mature zone of the root ProIYO:IYO-361 GFP was expressed specifically in xylem pole pericycle cells, but it did not 362 accumulate in the nucleus (Supplemental Figure 4). These results support that 363 xylem pole pericycle cells specifically exclude IYO from the nucleus to remain 364 undifferentiated, similarly to cells in apical meristems. It follows from this premise 365 that increasing the expression of IYO and RIMA may cause their differentiation and 366 possibly result in defects in lateral root formation and callus generation. In 367 agreement with this, plants overexpressing IYO and RIMA rarely formed lateral 368 root primordia, which ceased growth prior to or shortly after emergence, causing a 369 "solitary root" phenotype (Figure 7C). Moreover, in contrast to the widespread 370 proliferation of xylem pole pericycle cells that is induced in Wt roots incubated in 371 auxin-rich media, overexpression of IYO caused more discrete foci of pericycle cell 372 proliferation and reduced callus formation, and over expression of IYO and RIMA 373 severely impaired xylem pole pericycle proliferation and callus formation (Figure 374 7D-E). These results indicate that auxin-treatment alone does not revert 375 differentiation triggered by IYO and RIMA. Moreover, these findings support the 376 emerging paradigm that pre-existing stem cells are necessary for auxin-induced 377 callus formation and lateral root development in plants. However, we cannot 378

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exclude that a step of dedifferentiation, blocked by overexpression of IYO and 379 RIMA, may be involved in these processes. 380 381 DISCUSSION 382 383 Regulation of the IYO/RIMA cell differentiation switch 384 Our results identify RIMA as an essential partner of IYO for inducing cell 385 differentiation in Arabidopsis. Although the two partners are co-regulated at the 386 transcriptional level, there is evidence of differential post-translational regulation of 387 their localization and activities. Whereas RIMA has a uniform and primarily 388 cytosolic distribution across the root tip, IYO localization changes markedly from 389 the meristem core to the periphery, where it accumulates in the nucleus coinciding 390 with the onset of cell differentiation (Sanmartin et al., 2011). Furthermore, we did 391 not observe any effect when RIMA was overexpressed on its own, while IYO 392 overexpression activated premature differentiation. These data support the 393 conclusion that RIMA activity is constitutive and sufficient for differentiation, 394 whereas IYO activity is highly regulated and rate limiting for differentiation. In fact, 395 RIMA becomes limiting for differentiation in the context of IYO overexpression, 396 which is fully consistent with a role in mediating nuclear IYO accumulation. In 397 agreement with a constitutive RIMA activity, RIMA knockdown causes lower levels 398 of nuclear IYO accumulation both in meristematic cells, where IYO-GFP becomes 399 totally excluded from the nucleus, and in transition cells, where only weak nuclear 400 accumulation is observed. Constitutive activity of RIMA throughout the meristem 401 may allow meristematic cells to rapidly enter differentiation, or, alternatively, it may 402 reflect additional roles of RIMA in undifferentiated cells. The observation that 403 RIMA-dependent nuclear IYO import is operative, albeit at low rate, in meristematic 404 cells explains how IYO overexpression can induce their premature differentiation 405 and why this is blocked when RIMA activity is knocked down. These data also 406 suggest that RIMA is required but not responsible for generating the gradient of 407 IYO nuclear accumulation. Conditional post-translational modifications of IYO or 408 additional partners could differentially modulate the interaction of IYO with the 409

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constitutively active RIMA to regulate the rate of import and generate the nuclear 410 abundance gradient. Considering that GPN proteins are conserved partners of IYO 411 and RIMA that have been implicated in nuclear import in yeast and humans (Forget 412 et al., 2010; Calera et al., 2011; Carre and Shiekhattar, 2011; Staresincic et al., 413 2011), it will be worth exploring their role in RIMA-dependent IYO transport. 414 Moreover, RPAP2 and RTR1 have been assigned nuclear functions independent 415 of their roles in protein import. A number of reports suggest that RPAP2/RTR1 are 416 responsible for dephosphorylating Pol II during transcriptional elongation (Mosley 417 et al., 2009; Egloff et al., 2012; Hsu et al., 2014; Ni et al., 2014; Hunter et al., 418 2016), a striking link to IYO nuclear function. Although it has been questioned 419 whether RTR1 had intrinsic phosphatase activity (Xiang et al., 2012), a recent 420 structural analysis revealed a putative active site in RTR1 and identified several 421 residues important for phosphatase activity (Irani et al., 2016). Those residues are 422 conserved in RIMA, which accordingly may also have Pol II phosphatase activity. It 423 is thus possible that IYO and RIMA maintain their cooperation after import into the 424 nucleus to regulate Pol II transcriptional activity, an intriguing hypothesis to pursue. 425 426 Stem cell reservoirs for regeneration in plants 427 Although dedifferentiation is a widely-documented phenomenon in plants (Iwase et 428 al., 2011b; Chupeau et al., 2013; Ikeuchi et al., 2013; Ikeuchi et al., 2015; 429 Sugiyama, 2015), recent studies have questioned its general involvement in de 430 novo organogenesis and regeneration (Sugimoto et al., 2011; Gaillochet and 431 Lohmann, 2015). Detailed morphological analysis in Arabidopsis has shown that 432 lateral roots and calli derive from root xylem pole pericycle cells or leaf pericycle-433 like cambium cells (Dubrovsky et al., 2000; Beeckman et al., 2001; Atta et al., 434 2009; Sugimoto et al., 2010; Liu et al., 2014). Moreover, callus formation in roots is 435 severely impaired when xylem pole pericycle cells are ablated through specific 436 expression of diphteria toxin chain A (Che et al., 2007), supporting the idea that 437 they are the unique source for callus growth in roots. Although the actual 438 differentiation status of xylem pole pericycle cells is unknown, they have 439 meristematic characteristics that distinguish them from the surrounding cell layers 440

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in the mature root: they retain diploidy, express cell-cycle genes, rapidly re-enter 441 mitosis to form lateral root primordia (Beeckman et al., 2001; Atta et al., 2009; Liu 442 et al., 2014) and exclude IYO from the nucleus (this work). By forcing differentiation 443 throughout the plant, we have now provided conclusive evidence suggesting that 444 xylem pole pericycle cells are indeed stem cells that need to remain 445 undifferentiated to generate lateral roots during normal development, and callus in 446 auxin-rich media. Thus, our results support the emerging view that stem cell 447 reservoirs present in the adult tissues can be the source for de novo 448 organogenesis, auxin-induced callus formation and subsequent regeneration in 449 plants (Gaillochet and Lohmann, 2015). This paradigm shift means that to 450 understand these processes we need to focus on studying how plants regulate the 451 fate of stem cell reservoirs in adult plant tissues. Auxins and cytokinins are likely to 452 play a key role in their regulation, given their central function in lateral root 453 development, callus formation and regeneration (Fukaki et al., 2007; Ikeuchi et al., 454 2013; Perianez-Rodriguez et al., 2014; Su and Zhang, 2014). In addition, very-455 long-chain fatty acids and, not surprisingly, tissue aging have recently been shown 456 to restrict regeneration potential in Arabidopsis (Zhang et al., 2015; Shang et al., 457 2016). Moreover, several genes required for lateral root development and callus 458 formation, apart from IYO and RIMA, have been characterized: the cell cycle 459 regulator KRP2 (Sanz et al., 2011; Cheng et al., 2015), the regulators of auxin 460 signalling genes ARF7, ARF19 and SLR1 (Fukaki et al., 2002; Okushima et al., 461 2007; Fan et al., 2012; Shang et al., 2016), the transcription factors LBD16, 462 LBD17, LBD18, LBD29 (Okushima et al., 2007; Lee et al., 2009; Fan et al., 2012) 463 and the plant-specific ALF4 gene (DiDonato et al., 2004; Sugimoto et al., 2010). A 464 key challenge for the future will be to unravel how these genetic networks integrate 465 hormonal and metabolic signals to regulate the fate of stem cell reservoirs in adult 466 tissues during development and in response to environmental cues. 467

468 METHODS 469 Plant Materials and Growth Conditions 470

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The T-DNA insertion lines in the Col-0 background rima-1 (SALK_012339) and 471 rima-2 (SALK_11576) were obtained from the Arabidopsis Stock Center and 472 genotyped using specific primers (Supplemental Table 3). The iyo-1 mutant and 473 the ProSTM:GUS, ProTMM:TMM-GFP, J2341, Pro35S:RPB10-GFP, Pro35S:IYO-474 GFP, ProIYO:IYO-GFP and Pro35S:IYO-HA lines used were previously described 475 (Sanmartin et al., 2011). Plants were grown on soil in the greenhouse under 476 natural light, supplemented with Osram HQL 400w sodium lamps when illuminance 477 fell below 5000 lx, and a 16h light/8h dark cycle at a temperature range between 478 22ºC maximum/18ºC minimum. For in vitro culture, plants were grown at 22ºC 479 under 6000 luxs of illuminance in a 16h light/8 h dark cycle. 480 481 Constructs 482 RIMA coding sequence, promoter and genomic DNA were PCR amplified using 483 primers listed on Supplemental Table 3 and cloned into pDONR207 vector for 484 Gateway recombination-based subcloning (Invitrogen). The following destination 485 vectors were used: pGWB3 (for ProRIMA:GUS), pGWB4 (for ProRIMA:RIMA-GFP, 486 and pGWB5 (for Pro35S:RIMA-GFP). For bimolecular fluorescence 487 complementation, RIMA, GPN and IYO coding sequences were amplified with 488 primers shown in Supplemental Table 3, cloned into pDONR207 vector for 489 Gateway recombination-based cloning in pBIFP vectors and agroinfiltrated into 490 leaves of Nicotiana benthamiana as described (Sanmartin et al., 2011). 491 492 Chemicals and treatments 493 For in vitro culture, plants were grown in medium containing Murashige and Skoog 494 salts and 1% sucrose, with (solid MS) or without (liquid MS) 0.7% agar. For 495 Leptomycin B treatments, agroinfiltrated N. benthamiana leaves or Arabidopsis 496 thaliana seedlings were incubated in liquid MS containing 0.9 μM Leptomycin B 497 before imaging by confocal microscopy. For callus induction assays, sections from 498 the mature zone of roots were cultured in solid MS medium containing 2% sucrose 499 and 1 mg/l 2,4-D. 500 501

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Site-Directed mutagenesis 502 PCR-based site mutagenesis was carried out using as template the amplified 503 coding sequence of RIMA in the pDONR207 vector. Primers (Supplemental Table 504 3) were phosphorylated in a reaction with T4 polynucleotide kinase enzyme. For 505 PCR reaction, we used Phusion ® High-Fidelity DNA Polymerase (Thermo) 506 following the manufacturer’s protocol. The purified PCR product was ligated and 507 transformed into DH5a E. coli. 508 509 Protein production for immunization 510 The RIMA coding sequence in the pDONR207 vector was used as template for 511 inverse PCR with primers Flag F and RIMAc R (Supplemental Table 3) to obtain 512 the N-terminal part of RIMA (amino acids 1-305) fused to Flag epitope tag in the 513 pDONR207 vector. This construct was used for Gateway recombination-based 514 cloning into the pDEST17 destination vector and transformed into E. coli strain 515 BL21-CodonPlus. Cells were induced for protein expression overnight at 18ºC by 516 adding 0.1 mM IPTG in LB culture medium supplemented with 100 mg/l 517 carbenicillin and 2g/l glucose after reaching OD600=0.6. The cells were harvested 518 at 3200 x g for 20 min at 4ºC, resuspended in 200 gl/l sucrose and frozen at -20ºC 519 until use. The defrosted suspension was supplemented to reach a final 520 concentration of 50 mM Tris-HCl (pH 7.5), 150 mM NaCl and protease inhibitors 521 (Roche). Cells were disrupted by passing through a French Press and the 522 suspension centrifuged at 20000 x g to remove cell debris. The supernatant was 523 loaded onto a Ni-NTA (Clontech) column that was washed with 50 mM Tris-HCl 524 (pH 7.5), 5% (v/v) glycerol, 150 mM NaCl, and eluted with the same buffer 525 supplemented with 250 mM imidazole. The eluted fraction was passed through an 526 anti-Flag resin (Sigma) column, and this was washed with the former wash buffer 527 and eluted in the same buffer supplemented with 0.2 g/l Flag peptide. The soluble 528 purified protein was used to immunize rabbits for antiserum production by Pineda 529 Antibody-Services (Germany). 530 531 Co-immunoprecipitation 532

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Plant material was ground in 4 ml extraction buffer (50 mM Tris-HCl, pH 7.5; 5% 533 glycerol; 150 mM NaCl; 0.1% Triton X-100; 100 μM ZnSO4; 2 mM DTT; 1 mM 534 PMSF and protease inhibitors [Roche]) per gram of material and centrifuged at 535 20000 x g for 30 min. Protein concentration was adjusted using the Bradford 536 method (Bio-rad). Co-immunoprecipitation mixtures were made containing the 537 same amounts of total protein in the same volume. For immunoprecipitation protein 538 G Dynabeads (Life Technologies) were used. 539 540 Microscopy analyses 541 For Nomarski microscopy, tissues were cleared in chloral hydrate and imaged with 542 a Zeiss Axioskop microscope. For confocal microscopy, plants were monitored 543 using a Leica TCS SP5 laser scanning confocal microscope with propidium iodide 544 as counterstain. For GFP fluorescence quantification, single optical sections from 545 roots of ProRIMA:RIMA-GFP rima-1 plants were acquired with identical settings 546 under sequential scanning to prevent signal bleed-through. The fields imaged were 547 125 μm x 125 μm (1024 x 1024 pixels). In cells of the elongation zone, nuclei were 548 unequivocally distinguished from vacuoles by the weak propidium iodide labelling 549 of the nucleolus. Mean GFP intensity per pixel within the nuclei, cytosol and 550 vacuoles was measured using the FIJI software package. 551 552 Identification of IYO-interacting proteins using IP/MS-MS 553 Immunoprecipitation (IP) experiments were performed as described previously 554 (Kaufmann et al., 2010) using 3 g of Pro35S:IYO-GFP or Wt seedlings for each 555 sample. Interacting proteins were isolated by applying total protein extracts to anti-556 GFP coupled magnetic beads (Milteny Biotech). Three biological replicates of 557 Pro35S:IYO-GFP were compared to three replicates of Wt controls (see 558 Supplemental Table 1). Tandem mass spectrometry (MS) and statistical analysis 559 using MaxQuant and Perseus software was performed as described previously 560 (Lee and Young, 2013; Pijnappel et al., 2013). 561 562 Microarray analysis 563

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For microarray analysis, seeds were sown in soil, vernalized for 2 days at 4ºC and 564 grown in a growth chamber under a 14 h light: 10 h dark photoperiod for 32 days. 565 Inflorescence shoot apices from 11 plants of each genotype were pooled in each 566 experiment. Total RNA was extracted using Trizol (Invitrogen) and 4 biological 567 replicates with pooled RNA from 3 independent experiments (12 independent 568 experiments in total) were obtained for each genotype. Microarray profiles were 569 obtained as described (Sanmartin et al., 2011). For co-expression analysis, we 570 used the ACT tool that analyzes 322 ATH1 microarray hybridizations from the 571 NASC/GARNet dataset covering a wide range of biological processes and 572 conditions (Jen et al., 2006). 573 574 575 Flow Cytometry Analysis 576 Leaves from Wt and the callus-like rima-2 iyo-1 plants were chopped with a razor 577 blade in Galbraith’s buffer (45 mM MgCl2, 30 mM sodium citrate, 20 mM MOPS, 578 0.1% TritonX-100) (Galbraith et al., 1983) and filtered through a 30-μm nylon filter 579 to remove tissue debris. DNA was stained with propidium iodide (50 mg/l) at 37ºC 580 in darkness for 20 min prior to nuclear DNA content measurements in a Coulter 581 Cytomics FC500 cytometer. 582 583 Accession numbers 584 Sequence data from this article can be found in the Arabidopsis Genome Initiative 585 of GenBank/EMBL databases under the following accession numbers: RIMA: 586 At5g26760; IYO: At4g38440; GPN1: At4g21800; GPN2: At5g22370. Microarray 587 data from this article has been deposited at MIAMEXPRESS (GSE60169). 588 589 Supplemental Data 590 591 Supplemental Figure 1. Alignment of the zinc-finger domains from 592 Arabidopsis RIMA, human RPAP2 and budding yeast RTR1. 593

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Supplemental Figure 2. Characterization of antibodies against RIMA. 594 Supplemental Figure 3. IYO-GFP is excluded from nuclei of xylem pole 595 pericycle cells. 596 Supplemental Figure 4. ProIYO:IYO-GFP is expressed in xylem pole pericycle 597 cells but does not accumulate in the nucleus. 598 Supplemental Table 1. Overview of the IP-MS results. 599 Supplemental Table 2. Microarray expression data for a selected list of 600 genes. 601 Supplemental Table 3. Primers used in this work 602 603 Acknowledgements 604 We thank P. Paredes for excellent technical assistance. This work was supported 605 by the Spanish Ministry of Economy & Competitivity and FEDER funds (BIO2015-606 69582-P MINECO/FEDER to ER, MS and JJSS), by the Netherlands Organization 607 for Scientific Research (NWO VIDI 864.13.001 to BDR and ERA-CAPS project 608 EURO-PEC; 849.13.006 to DW), the Research Foundation Flanders (FWO 609 G0D0515N and 12D1815 to BDR) and the European Research Council (Starting 610 Grant “CELLPATTERN”, Contract no. 281573 to DW). 611 612 Author Contributions 613 A.M, S.M, M.P. G-G, R. C., Mi. S, B. DeR., D. W., M.S and E.R performed614 research; J.J. S-S, M.S and E.R designed the research; M.S and E.R wrote the 615 manuscript. 616 617 REFERENCES 618 619 Atta, R., Laurens, L., Boucheron-Dubuisson, E., Guivarc'h, A., Carnero, E., 620

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FIGURE LEGENDS 861 862 Figure 1. IYO interacts with GPN proteins and RIMA. (A) BiFC assay with the N-863 terminal half of YFP fused to IYO (N-IYO) and the C-terminal half of YFP fused to 864 GPN1 (GPN1-C) or GPN2 (GPN2-C). (B) BiFC assay with the C-terminal half of 865 YFP fused to IYO (C-IYO) and the N-terminal half of YFP fused to RIMA (N-RIMA). 866 (C) BiFC assay with the C-terminal half of YFP fused to IYO (C-IYO) and the N-867 terminal half of YFP fused to Wt RIMA (N-RIMA) or to the C56A/C61A (N-56/61) or 868 C94A/C98A (N-94/98) RIMA mutant construct. Immunoblotting verified expression 869 of all constructs in the assays. The arrowhead marks the position of C-IYO and the 870 arrow the position of N-RIMA, N-56/61 and N-94/98. Scale bar: 25 μm. (D) Total 871 protein sample from 12-day-old Pro35S:IYO-HA transgenic seedlings (Input) was 872 immunoprecipitated with anti-RIMA antibodies (a-RIMA) or preimmune serum from 873 the same rabbit (Preimm) and aliquots were analyzed by immunoblots with anti-HA 874 and anti-RIMA antibodies (low exposure image on top to show RIMA specifically 875 immunopurified with the immune serum and long exposure image below to show 876 RIMA in the input). Coomassie staining of the blots showed lack of contamination 877 with Rubisco in the immunopurified fractions. Scale bars: 25 μm. 878 879 Figure 2. RIMA is expressed in meristems and organ primordia. (A-B) β-880 glucuronidase activity in the aerial organs (A) and roots (B) of ProRIMA:GUS 881 plants. Scale bar: 1 mm (top-left panel), 50 μm (additional panels). (C) Confocal 882 images of roots from a rima-1 mutant complemented with ProRIMA:RIMA-GFP. 883 Green signal: GFP; Red signal: propidium iodide. Scale bar: 50 μm. (D) Confocal 884 images of epidermal cells from the meristematic (top panel) and the elongation 885 zone (bottom panel) of a root from a ProRIMA:RIMA-GFP rima-1 plant. Scale bar: 886 10 μm. (E) Mean GFP fluorescence intensity in the cytosol and in the nucleus of 887 epidermal cells from the elongation zone of primary roots from ProRIMA:RIMA-888 GFP rima-1 plants. The average local background signal (measured in vacuoles 889 from the same cells) was subtracted from the values. a. u.: artificial units. The 890 standard deviation (error bars) and the p-values (unpaired t-test for the null 891

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hypothesis that fluorescence is not above background levels) are shown above the 892 graphs. (F) Confocal image of Nicotiana benthamiana leaf epidermal cells 893 transiently transformed with Pro35S:RIMA-GFP and mock treated (-LMB) or 894 incubated with 0.9 μM Leptomycin B (+LMB) for 2 h. Arrowhead marks a nucleus 895 with low internal fluorescence and arrow a nucleus with high internal fluorescence. 896 Scale bar: 25 μm. (G) Confocal images of roots from ProRIMA:RIMA-GFP plants 897 mock treated (-LMB) or incubated with 0.9 μM LMB for 2.5 hours (+LMB). Insets 898 show details of nuclei from the roots shown on the left. Scale bar: 10 μm. 899 900 Figure 3. RIMA is required for cell differentiation. (A) Nomarski images of 901 cleared seeds from siliques of heterozygous rima-1/RIMA plants. The rima-1 902 mutant embryos and the corresponding Wt or heterozygous sibling (Wt) from the 903 same silique at torpedo stage (left panels) and mature stage (right panels) are 904 shown. Scale bar: 25 μm. (B) Images of 10-day-old (upper panels) and 30-day-old 905 (lower panels) Wt and rima-2 plants. Scale bar: 1 mm. (C) Expression of the 906 ProSTM:GUS shoot meristem marker in 5-day-old seedlings. Scale bar: 100 μm. 907 (D) Images of the primary stem from a rima-2 plant. All rima-2 plants developed 908 fasciated meristems with split primary SAMs. Scale bar: 1 mm. Upper inset shows 909 enlarged image of a duplicated flower and lower inset shows a duplicated silique 910 from a rima-2 plant (on average there were more than one duplicated flower per 911 plant, n=150 plants). (E) Images of the cotyledon epidermis from 6-day-old 912 seedlings. The rima-2 mutant retains small protoderm-like cells that express the 913 ProTMM: TMM-GFP marker. Scale bar: 25 μm. Inset shows cluster of stomata in 914 cotyledons of 10-day-old rima-2 plants. Scale bar: 12.5 μm. (F) Images of cleared 915 root apical meristems from 5-day-old Wt and rima-2 plants. Cell tracings of the files 916 marked with the brackets are shown to highlight the ectopic periclinal divisions in 917 the mutant. Arrow: quiescent center. Scale bar: 25 μm. (G) Expression of the 918 J2341 columella initials marker in 5-day-old seedlings. Arrow: quiescent center. 919 Scale bar: 20 μm. (H) Northern analysis of RNA samples from inflorescences of Wt 920 and rima-2 plants. The arrowhead marks the full-length RIMA transcript and the 921 asterisk marks a truncated transcript that accumulates in the mutant. rRNA is 922

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shown as a loading control. (I) Images of 14-day-old (upper panels) and 60-day-old 923 (lower panels) rima-2 and rima-1/rima-2 plants. Scale bar: 1 mm. (J) Aerial view of 924 a 12-day-old Wt plant, a rima-2 mutant, and two representative lines of rima-1 925 transformed with ProRIMA:RIMA-GFP or Pro35S:RIMA-GFP. In the lower panel, 926 the expression level of the transgenes in each of the genotypes from the top panel 927 was determined by immunoblot with anti-GFP antibodies. (K) Two examples of twin 928 globular embryos formed in seeds from a representative line of rima-1 transformed 929 with Pro35S:RIMA-GFP (5% of seeds had twin embryos, n=162). Scale bar: 25 930 μm. 931 932 Figure 4. IYO and RIMA activate transcription of common developmental 933 programs. (A) Venn diagram analysis of the overlap between the sets of 400 934 genes most down-regulated in iyo-1/Wt (down iyo-1) and rima-2/Wt (down rima-2) 935 inflorescences. The p-value (Hypergeometric test) for the observed level of overlap 936 is shown above the graphs. (B) Graphical display of microarray expression data 937 (log2 of the expression ratio) in Wt versus iyo-1 (Wt/iyo-1) and Wt versus rima-2 938 (Wt/rima-2) of the 400 genes most highly down-regulated in iyo-1 inflorescences 939 (Sanmartin et al., 2011). (C) GSEA analysis of gene sets significantly down-940 regulated in iyo-1/Wt and rima-2/Wt inflorescence apices. 941 942 Figure 5. IYO and RIMA interact genetically to activate differentiation. (A) 943 Images of 10-day-old plants (genotypes as indicated in the panels). A 944 magnification of the framed iyo-1 rima-2 seedling is shown on the right panel. 945 Scale bar: 0.5 mm. (B) 80-day-old iyo-1 rima-2 plant. Scale bar: 2 mm. (C) Flow 946 cytometry analysis of nuclear DNA content in 45-day-old iyo-1 rima-2 mutants. The 947 DNA content of the first pair of leaves from 18-day-old wild-type plants is shown for 948 comparison. (D) Images from 11-day-old plants (genotypes as indicated in the 949 panels). Scale bar: 1mm. 950 951 Figure 6. RIMA is required for IYO nuclear accumulation and for its pro-952 differentiation activity. (A) Confocal images of roots from a ProIYO:IYO-GFP line 953

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in a Wt background or introgressed into a rima-2 mutant background (rima-2) mock 954 treated (-LMB) or incubated with 0.9 μM LMB for 2.5 hours (+LMB). Scale bar: 50 955 μm. (B) Confocal images of N. benthamiana leaf epidermal cells transiently 956 transformed with Pro35S:RIMA-GFP alone or together with Pro35S:IYO-HA. 957 Arrowheads mark nuclei with low internal fluorescence and arrows nuclei with high 958 internal fluorescence. Scale bar: 25 μm. (C) Images of 14-day-old rima-2, 959 Pro35S:IYO-HA, and Pro35S:IYO-HA rima-2 plants. Scale bar: 1 mm. In the lower 960 panel, IYO-HA expression in plants from the genotypes shown was determined by 961 immunoblotting with anti-HA antibodies. 962 963 Figure 7. Overexpression of IYO and RIMA blocks callus formation (A-B) 964 Confocal images of Pro35S:IYO-GFP and Pro35S:RPB10-GFP plants. Note that 965 root development and RAM size in the transgenic Pro35S:IYO-GFP line was 966 indistinguishable from Pro35S:RPB10-GFP and Wt plants. (A) Single confocal 967 longitudinal sections at the equatorial plane containing the two xylem poles of roots 968 from 5-day-old plants (top panels). Orthogonal views of the roots reconstructed 969 from serial sections are shown in the bottom panels. The positions of the 970 orthogonal sections are marked on the top panels. Asterisks mark GFP positive 971 nuclei from the xylem pole pericycle. Nuclei from other cell layers are identified by 972 the letters. ep: epidermis; c: cortex; e: endodermis; v: vasculature; Scale bar: 25 973 μm. (B) Confocal images from roots of 6-day-old plants treated for 3 days in liquid 974 MS medium containing 300 ng/ml of 2,4D. Scale bar: 50 μm. (C-E) Images from 975 Pro35S:RIMA-GFP, Pro35S:IYO-HA and Pro35S:RIMA-GFP Pro35S:IYO-HA 976 double transgenic plants. Note that Wt plants were indistinguishable from 977 Pro35S:RIMA-GFP plants and are not shown. (C) Roots from 14-day-old plants. 978 Scale bar: 1 mm. Inset shows a Nomarski image of the only root primordia 979 emerged in a Pro35S:RIMA-GFP Pro35S:IYO-HA plant. Scale bar: 50 μm (D) 980 Nomarski images of sections from the mature zone of the root from 24-day-old 981 plants cultured for 5 days in callus-inducing medium. Red bars mark pericycle 982 domains where periclinal divisions have taken place. Scale bar: 25 μm. (E) Images 983

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of sections from the mature zone of the root from 24-day-old plants cultured for 41 984 days in callus-inducing medium. Scale bar: 1 mm. 985 986

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DOI 10.1105/tpc.16.00791; originally published online February 21, 2017;Plant Cell

De Rybel, Dolf Weijers, José J. Sánchez-Serrano, Maite Sanmartín and Enrique RojoAlfonso Muñoz, Silvina Mangano, Mary Paz González-García, Ramón Contreras, Michael B Sauer, Bert

ArabidopsisRIMA-dependent nuclear accumulation of IYO triggers auxin-irreversible cell differentiation in

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rima-dependent nuclear accumulation of iyo triggers auxin ...feb 21, 2017 · 1 1 research article...

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