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<small>1</small>Department of Plant Molecular Genetics, Centro Nacional de Biotecnologı´a (CNB-CSIC), Darwin 3, Campus de Cantoblanco, 28049 Madrid, Spain
<small>2</small>Department of Biochemistry, Plant Molecular and Cellular Biology, Estacio´n Experimental del Zaidı´n-CSIC, Profesor Albareda 1, 18008 Granada, Spain
<small>3</small>These authors contributed equally to this work
<small>4</small>Present address: CBGP (UPM-INIA), Parque Cientı´fico y Tecnolo´gico, UPM, Campus de Montegancedo, Ctra M40 Km 38, 28223 Pozuelo de Alarco´n, Madrid, Spain
<small>5</small>Present address: Departamento de Ecologia Funcional, Instituto de Ecologı´a, Universidad Nacional Autono´ma de Me´xico, Ciudad Universitaria, circuito exterior. Coyoaca´n 04510 DF Me´xico
*Correspondence: DOI10.1016/j.devcel.2012.04.008
Figure 1. BR Alters Actin Filament Organization and PIN2 Localization in Wild-Type Roots
(A) Confocal analysis of actin configuration in 5-day-old plants grown on vertical LN-MS plates and transferred to liquid media. Plants were untreated (Col-0) or treated with 5 nM eBL (2 hr, Col-0 eBL) or 50mM IAA (1 hr, Col-0 IAA). Bar = 10 mm.
(B) Quantification of actin filament displacement in untreated wild-type plants (eBL 0 nM) or plants treated with 5, 10, or 20 nM eBL (3 hr). Error bars represent SD. (C) Actin filament configuration in untreated wild-type plants (eBL 0 nM) or treated with 5, 10, or 20 nM eBL (3 hr).
(D) Percentage of mobile filaments (PMF; left) and skewness (right) (seeExperimental Procedures) in 5-day-old wild-type plants grown on vertical plates and transferred to liquid medium, alone or with 10 nM eBL (2 hr). Error bars indicate SD.
(E) Localization of PIN2 transporters in epidermal cells in untreated plants (Col-0) or plants treated with 5 nM eBL (2 hr, Col-0 eBL) or 50mM IAA (1 hr, Col-0 IAA). Arrows indicate PIN2 depolarization. Bar = 5mm. Asterisks in (B) and (D) indicate significant differences relative to untreated Col-0 plants (eBL 0 nM) (p < 0.05, Student’s t test).
See alsoMovies S1andS2.
</div><span class="text_page_counter">Trang 3</span><div class="page_container" data-page="3">Figure 2. Phenotypic Characterization of the wavy1-1 Mutant
<i>(A) Root-growth phenotype of Col-0 and wavy1-1 plants,</i>
grown 5 days on vertical plates alone or with 5 nM eBL.
<i>(B) Root wave-number quantification in Col-0 and wavy1-1</i>
seedlings grown 5 days on vertical plates alone or with different eBL concentrations. Error bars show SD. *Significant differences relative to Col-0 plants in each treatment; Student’s t test, p < 0.05.
<i>(C) wavy1-1 bending phenotype in stems and siliques,</i>
rosette leaves, flower organs, and cauline leaves.
<i>(D) Root-growth phenotypes of wild-type (Col-0), act2T-DNA null allele (act2-TDNA), bzr1-1D, and act2-5 plants</i>
grown 5 days on vertical plates. See alsoFigure S1.
Figure 3. act2-5/Col-0 and act2-5/act2-TDNA Interallelic Interaction
<i>(A) Analysis of the wavy-root phenotype in Col-0, act2-5</i>
and in the inducible overexpressor lines expressing act2-5 on the Col-0 background (oxact2-5;Col-0). Plants were grown on vertical plates alone ( Est) or with 10 mM estradiol (+Est).
<i>(B) Analysis of the wavy-root phenotype in the act2 T-DNAnull allele mutant (act2-TDNA) and the act2-5 inducible</i>
overexpressor line on the <i>act2-TDNA</i> background
<i>(oxact2-5;act2-TDNA). Plants were grown on vertical</i>
plates alone ( Est) or with 10mM estradiol (+Est).
<i>(C) Quantification of root waves in TDNA in two act2-5-inducible overexpressor lines on the act2-TDNA back-ground (oxact2-5;act2-TDNA, lines 1 and 2) and in theact2-5 mutant alone ( Est) or with 10</i>mM estradiol (+Est). Error bars indicate SD. *Significant differences relative to
<i>act2-TDNA in each treatment; Student’s t test, p < 0.05.</i>
See alsoFigure S2.
</div><span class="text_page_counter">Trang 5</span><div class="page_container" data-page="5">Figure 4. Wavy-Root Phenotype Correlates with Altered Actin Configuration and PIN2 Localization Images at left show actin configuration and those at right show PIN2 localization.
(A) Confocal analysis of actin filament configuration and PIN2 polar localization in 5-day-old seedlings of Col-0,
<i>act2-5, bzr1-1D and act2 T-DNA null (act2-TDNA) grown</i>
on vertical plates. Arrows indicate PIN2 depolarization. Scale bar = 10mm for actin; 5 mm for PIN2 panels. (B and C) PMF (B) and skewness (C) in 5-day-old wild-type plants grown on vertical plates. Error bars represent SD. Asterisks in (B) and (C) indicate significant differences relative to Col-0 plants; Student’s t test, p < 0.05. See
Figure S3andMovies S3andS4.
Figure 5. eBL Stimulation of Gravitropic Response and Lateral Root Number Are Activated inact2-5
(A) Time course measurement of the gravitropic
<i>response in Col-0, act2-5, and act2-TDNA plants,</i>
untreated or treated with 10 nM eBL. Error bars show SD.
(B) Wavy-root phenotype in 5-day-old Col-0,
<i>act2-5, and act2-TDNA plants grown on vertical</i>
plates alone or at various eBL concentrations. (C) Quantification of wave number per cm of the
<i>main root in Col-0, act2-5, and act2-TDNA alone</i>
( eBL) or at distinct eBL concentrations. Error bars indicate SD.
(D) Quantification of emerged lateral roots per cm of main root (see Experimental Procedures) in
<i>Col-0, act2-5, and act2-TDNA alone ( eBL-IAA) or</i>
treated with 2 nM eBL, 50 nM IAA, or both. Error bars indicate SD. Asterisks in (C) and (D) indicate significant differences relative to Col-0 plants in each treatment; Student’s t test, p < 0.05. SeeMovies S4andS5.
Figure 6. BR Signaling is Constitutively Activated inact2-5
<i>(A) Gene expression analysis of auxin:BR-responsive genes. Relative expression of IAA5, IAA6, IAA19, BEE1, and BAS1 in wild-type, act2-5, and act2-TDNA</i>
plants in response to IAA or IAA and eBL. Plants were grown for 5 days on vertical plates and transferred to liquid medium for treatment with 1mM IAA (IAA), or 1mM IAA and 1 mM eBL (IAA+eBL) (30 min) before RNA extraction. Error bars represent SD.
<i>(B) Analysis of microarray data. Genes with significant expression in act2-5 versus Col-0 plants were compared to BZR1 target genes (</i>Sun et al., 2010) or genes significantly up- or downregulated (>23) by eBL or IAA (seeYu et al., 2011; Nemhauser et al., 2004). Table includes the size of observed overlap and expected size in case of random distribution. Significant overlaps are highlighted in bold (c<small>2</small>
test, p < 0.05).
<i>(C) qRT-PCR of BZR1 target genes in act2-TDNA and act2-5 mutants, and in the inducible overexpressor line oxact2-5;act2-TDNA, alone ( Est) or with estradiol</i>
(+Est). Plants were grown for 5 days on vertical plates and transferred to liquid medium for estradiol treatment (10mM, 3 hr). Data were normalized to untreated
<i>act2-TDNA conditions. Error bars show SD.</i>
(D) Western blot analysis of 5-day-old BZR1-CFP seedlings grown in darkness in LN-MS medium supplemented with 1mM brassinazole. Seedlings were placed in liquid medium alone ( eBL) or treated with 1mM eBL (+eBL) for 2 hr prior to harvest. Ribulose-1,5-bisphosphate carboxylase oxygenase (RuB) was used as a loading control.
See alsoTable S1.
</div><span class="text_page_counter">Trang 8</span><div class="page_container" data-page="8">EXPERIMENTAL PROCEDURES Plant Material and Growth Conditions
<i>All Arabidopsis thaliana plants used in this study, including mutants and </i>
trans-genic plants, were on the Columbia (Col-0) background. We used seeds of
<i>previ-ously termed act2-3 (</i>Nishimura et al., 2003<i>), BZR1-CFP (</i>Wang et al., 2002),
Scheres, 2005<i>). Homozygous lines of ABD2:GFP, PIN2:GFP, and BZR1:CFPon the act2-5, act2-TDNA, and bzr1-1D backgrounds were obtained by</i>
crosses and selection. Growth conditions were as described (Catarecha et al., 2007), except for darkness treatment. Root-growth phenotypes were observed in 5 day plants grown on vertical plates in modified Murashige and Skoog medium (Murashige and Skoog, 1962) with reduced nitrate content (LN-MS), in which 95% KNO<small>3</small>was replaced with 95% K<small>2</small>SO<small>4</small>and 0.5% sucrose. For specific experiments, auxin (IAA) and brassinosteroid (eBL) concentrations are indicated.
Plasmid Construction and Plant Transformation
<i>A Gateway-compatible fragment bearing the ACT2 or act2-5 ORF was PCR-amplified from cDNA from wild-type or act2-5 mutant plants, respectively,</i>
using primers Act2F, ggggacaagtttgtacaaaaaagcaggctcaatggctgaggctgat gatattc, and Act2R, ggggaccactttgtacaagaaagctgggtcttagaaacattttctgtgaa. PCR products were purified and cloned by LR recombination, according to manufacturer’s recommendations (Invitrogen, Paisley, Scotland), into the binary vector pMDC7, which has the CaMV 35S promoter and a human estrogen receptor regulatory region (Zuo et al., 2000). Prior to transformation of Agrobacterium, the expression construct was sequenced. A binary vector
<i>containing the ACT2 or act2-5 ORF was introduced into Agrobacteriumtumefaciens strain C58C1. A. thaliana Col-0 and the mutants act2-5 andact2-TDNA were transformed by dipping the flowers in MS medium with Silwet</i>
L77 (Bechtold et al., 1993). Transgenic seedlings were selected on medium containing 30 mg/l hygromycin. For further analyses, T1 segregation ratios were analyzed to select transformants with one T-DNA insertion and to isolate T3-homozygous plants. Other standard procedures were as described (Sambrook et al., 1989), except where indicated.
Confocal Microscopy, Image Analysis, and Quantification
For static images, maximum projections of 12 z-stacks with a fixed 2mm z-distance were generated on a Leica SP5 microscope with a 633 1.2 NA
water immersion objective (zoom 1.0, field 246 3 246 mm scanned at 10243 1024 pixels). Pinhole was set to 1.4 Airy units, and laser and PMT settings were adjusted to avoid under-/overexposed pixels; signal-to-noise ratio was increased by averaging eight times (line-averaging mode). Settings were identical for all samples. For time-lapse imaging, laser and PMT settings were identical; pinhole was set to 3.5 Airy units to allow tracking of filaments moving out of the direct confocal plane and to alleviate potential slight focus drift. A 5123 512 pixel field was scanned at zoom 2.0 (123 3 123 mm field. T was 60 s, line average 4, and 23 frames were captured per movie.
All image analyses were performed in FIJI distribution of ImageJ 1.46a ( For actin displacement measurements, we used a modification of the method ofVan Bruaene et al. (2004). Two 3D stacks (x, y, z at 0.5mm intervals) from single cells were acquired at 1 min intervals and maximum projections analyzed by image subtraction using Volocity (Improvision, Coventry, UK), to yield the filament displacement distance. For analysis of skewness, we used an approach similar to that ofHigaki et al. (2010); maximum projections of static image stacks were generated, Gaussian blur at 1.7 px radius applied and skeletonized with the ThinLine function of the Kbi_2d-filter package plugin ( KbiFilter2d). Skewness parameters were obtained by the line features function of the package for the entire frame, comprising four cells. At least 60 cells/ sample were measured. For PMF, we used the preprocessing stage of the Kbi_Flow analysis plugin (Ueda et al., 2010), which sectorizes a time-lapse stack and detects changes due to motion in each sector. The plugin returns number of mobile and static image sectors; the percentage of mobile sectors was calculated. Only parts with clearly visible filaments were analyzed by adequate masking. Each stack normally corresponds to three cells with clearly visible filament areas; at least 30 areas/sample were measured.
Root Measurements
Plants were cultured for 5 days on vertical LN-MS plates before transfer to the same medium supplemented with 50 nM IAA, 2 nM eBL, or both. After 3 days culture, apparent rootlets and root buds were counted with the aid of a dissect-ing microscope essentially as described (Bao et al., 2004). Root waving was analyzed using ImageJ in plants sown on LN-MS vertical plates, alone or
<i>sup-plemented with 2 or 5 nM eBL. To avoid root wave disturbance, DR5:GUS lines</i>
were<i>b-glucuronidase (GUS)-stained (</i>Catarecha et al., 2007) in the plates in which plants were grown. Gravitropic response was analyzed in 5-day-old plants sown on vertical plates and covered with a layer of medium to prevent root bending. Plants were grown for 5 days, alone or supplemented with 10 nM eBL; they were then turned 90<sup></sup>, and the curvature angle of the main root was measured with ImageJ after 3, 9, and 24 hr.
Identification and Positional Cloning of theact2-5 Mutation
<i>An Arabidopsis EMS-mutagenized population from Lehle’s collection wasscreened on vertical plates and wavy1-1 was selected. Mutant homozygous</i>
plants were backcrossed three times to wild-type Col-0 plants. Seeds from
<i>the last self-pollinated progeny were crossed to Landsberg erecta (Ler)</i>
ecotype, and 100 7-day-old F2 individuals screened for wavy phenotype in vertical plates. Genomic DNA was extracted (Dellaporta et al., 1983) from selected mutant F2 individuals and mapped using cleaved amplified poly-morphic sequence, simple sequence length polymorphism markers (Bell and Ecker, 1994; Konieczny and Ausubel, 1993), and other PCR-based markers from the Monsanto Arabidopsis Polymorphism and Ler Sequence Collections ( The construct used for complementation of the mutation was described byRingli et al. (2002).
Microarray Studies
Transcriptomic analyses were performed using the Affymetrix ATH1 platform.
<i>Three replicates of wild-type and act2-5 seedlings were grown on 0.5</i>3 MS medium (8 days) before harvest and storage at 80<sup></sup>C. RNA was isolated with TriReagent and Plant RNA Isolation Aid (Ambion, Austin, TX, USA), fol-lowed by cleanup with the RNeasy Mini Kit (QIAGEN, Venlo, The Netherlands). Biotin-labeled cRNA was synthesized using One-Cycle target labeling and control reagents (Affymetrix, Shanghai, China), and fragmented into 35–200
<i>bases. Each replicate was hybridized independently to the Arabidopsis</i>
ATH1 genome array (Affymetrix). Microarrays were washed and stained with
</div><span class="text_page_counter">Trang 9</span><div class="page_container" data-page="9">streptavidin-phycoerythrin and scanned at 2.5mm resolution in a GeneChip Scanner 3000 7G System (Affymetrix). Data were analyzed using GeneChip Operating Software and the affylmGUIR package (Wettenhall et al., 2006). The Robust Multi-Array Analysis algorithm was used for background correc-tion, normalizacorrec-tion, and expression-level summarization (Irizarry et al., 2003).
<i>Differential expression analysis was performed with the Bayes t-statistics</i>
from the linear models for microarray data (limma). p values were corrected for multiple-testing using the Benjamini-Hochberg method (false discovery rate) (Reiner et al., 2003). Data discussed here are deposited in the NCBI Gene Expression Omnibus (Edgar et al., 2002), accessible through GEO Series Accession No. GSE27077.
Gene Expression Analysis
<i>RNA was isolated from A. thaliana using TRIzol (Invitrogen). For cDNA</i>
synthesis, we used 2 mg RNA with the High-Capacity cDNA Archive Kit (Applied Biosystems, Foster City, CA, USA). Quantitative PCR (qRT-PCR) reactions were performed in the Applied Biosystems 7300 real-time PCR system using FastStart Universal SYBR Green Master-Rox (Roche, Basel, Switzerland); three biological replicates were analyzed in each case. C<small>T</small>values were obtained with 7300 Systems SDS software v.1.4 (Applied Biosystems). Relative expression changes were calculated by the comparative C<small>T</small>method;
difference between the C<small>T</small>value and the C<small>T</small>value of EF1a. DDC<small>T</small>was the difference betweenDC<small>T</small>and the C<small>T</small>value of the calibrator. Primers used in quantitative PCR reactions are shown in the Supplemental Experimental Procedures.
Protein Extraction and Western Blot Analysis
Protein extraction and western blot analysis of whole seedlings were as described (Stavang et al., 2009). Five-day-old seedlings were homogenized in nondenaturing buffer (100 mM Tris-HCl, pH 7.5, 150 mM NaCl, 0.2% NP40, 1 mM PMSF, protease inhibitor cocktail tablets (Roche)). After two centrifugations (10,0003 g, 10 min, 4<small></small><sub>C), supernatant was collected and total</sub>
protein content measured using a Bradford protein assay kit (Bio-Rad Labora-tories, Hercules, CA, USA). Samples were resolved in 10% SDS-polyacryl-amide gels, transferred to PVDF membranes, incubated with anti-GFP antibody (632460, Clontech, Mountain View, CA, USA; overnight at 4<sup></sup>C), followed by HRP-conjugated secondary antibodies (A1949, Sigma-Aldrich, St. Louis, MO, USA; 1 hr, room temperature). Detection was with ECL reagent (PerkinElmer, Waltham, MA, USA).
SUPPLEMENTAL INFORMATION
Supplemental information includes four figures, one table, Supplemental Experimental Procedures, and five movies and can be found with this article online atdoi:10.1016/j.devcel.2012.04.008.
We thank Salome´ Prat, Roberto Solano, Pablo Vera, Carlos Alonso-Blanco, and Carmen L. Tora´n for critical reading of the manuscript. We are very grateful
<i>to Andrew Meagher and Beat Keller for providing the construct of the ACTIN2gene promoter fused to the ACTIN2 cDNA, Frantisek Baluska for theABD2:GFP expression line, Joan Chory for the BZR1-1D:CFP expressionline, and Juan Carlos del Pozo for the DR5:GUS- and PIN2:GFP-expressing</i>
lines. We also thank Sylvia Gutie´rrez for her help with confocal microscopy studies, Jose´ Manuel Franco and the CNB Genomics Facility for microarray hybridization and analysis, Luis Caldero´n for technical assistance, and Cather-ine Mark for editorial assistance. This work was supported by fellowships from the Spanish Ministry of Science and Innovation (MICINN) (to M.L., B.G.-P., P.C., and E.S.-B.) and La-Caixa/CNB International PhD program (to M.T.C.), as well as research grants (BIO2004-03759, BIO2007-66104, BIO2011-25306, CSD2007-00057, and EUI2009-03993) from MICINN.
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