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First published online December 27, 2007; 10.1104/pp.107.110270 Plant Physiology 146:1142-1154 (2008) © 2008 American Society of Plant Biologists GeBP and GeBP-Like Proteins Are Noncanonical Leucine-Zipper Transcription Factors That Regulate Cytokinin Response in Arabidopsis[C],[W]Laboratoire Plastes et Différenciation Cellulaire, CNRS, Université Joseph Fourier, 38041 Grenoble, France
Understanding the role of transcription factors (TFs) is essential in reconstructing developmental regulatory networks. The plant-specific GeBP TF family of Arabidopsis thaliana (Arabidopsis) comprises 21 members, all of unknown function. A subset of four members, the founding member GeBP and GeBP-like proteins (GPL) 1, 2, and 3, shares a conserved C-terminal domain. Here we report that GeBP/GPL genes represent a newly defined class of leucine-zipper (Leu-zipper) TFs and that they play a redundant role in cytokinin hormone pathway regulation. Specifically, we demonstrate using yeast, in vitro, and split-yellow fluorescent protein in planta assays that GeBP/GPL proteins form homo- and heterodimers through a noncanonical Leu-zipper motif located in the C-terminal domain. A triple loss-of-function mutant of the three most closely related genes gebp gpl1 gpl2 shows a reduced sensitivity to exogenous cytokinins in a subset of cytokinin responses such as senescence and growth, whereas root inhibition is not affected. We find that transcript levels of type-A cytokinin response genes, which are involved in the negative feedback regulation of cytokinin signaling, are higher in the triple mutant. Using a GPL version that acts as a constitutive transcriptional activator, we show that the regulation of Arabidopsis response regulators (ARRs) is mediated by at least one additional, as yet unknown, repressor acting genetically downstream in the GeBP/GPL pathway. Our results indicate that GeBP/GPL genes encode a new class of unconventional Leu-zipper TF proteins and suggest that their role in the cytokinin pathway is to antagonize the negative feedback regulation on ARR genes to trigger the cytokinin response.
Transcription factors (TFs) are key regulators of developmental processes and the complexity of living organisms necessitates a large number of TFs. In plants, TFs are often involved in the control of hormone pathways and several recent studies in Arabidopsis (Arabidopsis thaliana) provide new insight into how TFs and phytohormones interact to control plant development (Long and Benfey, 2006
Among these TFs, GeBP and the three GeBP-like (GPL) 1, 2, and 3 proteins form a distinct clad and share an additional C-terminal conserved region of unknown function (Curaba et al., 2003 We show here that the four GeBP/GPL genes encode a newly defined class of unconventional Leu-zipper proteins and are involved in cytokinin response regulation. This regulation is shown by the finding that a triple loss-of-function mutant is less sensitive to exogenous cytokinin and that transcript levels of type-A ARR cytokinin response genes are increased, likely resulting in an increased negative feedback regulation and ultimately cytokinin insensitivity. Conversely, overexpression of a GPL protein with a constitutive transcriptional-activation activity causes a decrease in type-A ARR transcript levels together with an increased sensitivity to cytokinins, indicating that the GeBP/GPL-dependent regulation of ARRs involves additional unknown repressing TFs acting downstream of GeBP/GPLs. Taken together, these results suggest that the role of GeBP/GPL genes in cytokinin signaling is to antagonize the negative feedback regulation by repressing type-A ARRs through the action of one or several repressors that remain to be identified.
GeBP Family Members Form Homo- and Heterodimers
Previous work on GeBP led to the definition of a new GeBP gene family in Arabidopsis with 21 members, all of unknown function (Curaba et al., 2003
The C-Terminal Region of GeBP and GPL Proteins Harbors a Functional Noncanonical Leu-Zipper Motif A series of deletions were made in the AD:GeBP fusion protein to determine which region of the protein was involved in dimer formation. These deletions covered three regions: the DNA-binding domain, a predicted coiled-coil region (often involved in protein-protein interaction), and the C-terminal domain (Fig. 2A ). As expected, the deletion of the DNA-binding domain did not prevent yeast growth. Similarly, deletion of the coiled coil did not prevent yeast growth, indicating that this region is not involved in dimer formation. On the contrary, deletion of the conserved C-terminal region completely abolished yeast growth, indicating that this region is necessary for dimer formation. Conversely, the C-terminal region alone trans-activated yeast reporter genes, showing that this region is sufficient for GeBP dimerization (Fig. 2A). Cotransformation of just the GeBP C-terminal region with full-length GPL1, 2, or 3 also led to yeast growth (Fig. 2B). Therefore the C-terminal region of the GeBP protein is responsible for homo- and heterodimer formation.
A putative partial Leu-zipper motif in the C-terminal domain of GeBP/GPL proteins was described previously (Curaba et al., 2003
To confirm that these interactions occur in plant cells, we tested dimer formation using the bimolecular fluorescence complementation (BiFC) technique, which allows protein-protein interactions to be visualized in situ (Walter et al., 2004
To determine the intracellular localization of the GeBP/GPL proteins, the four corresponding coding sequences were cloned downstream of and in frame with the GFP reporter gene under the control of the constitutive 35S promoter. In transgenic lines of Arabidopsis, the four GFP fusion proteins were localized in nuclei (Fig. 4A ). This is consistent with the presence of at least one nuclear localization signal (NLS) in GeBP, GPL1, and GPL2 (Fig. 4B). The GPL3 protein was also localized in nuclei despite the lack of an obvious NLS in its primary sequence.
Spatial and temporal expression of the GeBP and GPL genes was further examined by generating lines carrying Promoter:GUS (P:GUS) fusions for each gene. During vegetative development, the PGeBP:GUS, PGPL1:GUS, PGPL2:GUS, and PGPL3:GUS reporter lines showed largely overlapping expression patterns with the main expression being in the SAM and young leaf primordia (Fig. 5, A–L ). The strongest staining was observed in GeBP lines and the weakest in the GPL1 lines, these two genes being the two most similar homologs. The vascular tissues of cotyledons and leaves and hydathodes also stained weakly in the GeBP, GPL1, and GPL2 lines (Fig. 5, A–D). No GUS staining was observed in roots of the GeBP, GPL1, and GPL2 reporter lines (Fig. 5, M–O). In contrast, the GPL3 reporter lines showed a strong staining of primary and secondary roots (Fig. 5P) as well as a marked staining of vascular tissues of rosette leaves (Fig. 5D). During reproductive development, the four GeBP/GPL reporter lines still had overlapping expression patterns with GUS staining in the distal part of pedicels that form a vascular bulge at the base of flowers and siliques (Fig. 5, Q, R, and T), except GPL2 lines where the staining was localized in the septum of siliques (Fig. 5S). The paraclades were also frequently stained in all lines analyzed (Fig. 5, U, V, and X), except GPL2 lines for which no staining was observed (Fig. 5W). Overall, we conclude that GeBP/GPL genes have largely overlapping expression patterns and are mainly expressed in the SAM, young leaf primordia, and vascular tissues.
The Triple Mutant gebp-1 gpl1-1 gpl2-2 Shows a Reduced Sensitivity to Exogenous Cytokinins
The overlapping expression patterns of the GeBP/GPL genes and their ability to interact in all combinations at the protein level are suggestive of functional redundancy. To study this redundancy, single mutants corresponding to the three most closely related genes, GeBP, GPL1, and GPL2, were isolated (Supplemental Fig. S1) and crossed to construct all the corresponding double mutants and the triple mutant. Although the double mutants were indistinguishable from wild types, the triple mutant gebp-1 gpl1-1 gpl2-1 was slightly paler than the wild types when grown on Murashige and Skoog (MS) medium (see below). As the founding member GeBP acts downstream of KNOXI genes (Curaba et al., 2003
Because cytokinins play a role in leaf chlorophyll content (Richmond and Lang, 1957
To further investigate the effect of GeBP/GPL mutations on the response of aerial parts of the plant to cytokinins, we measured the effect of cytokinins on detached leaves during the process of dark-induced senescence, which partially mimics senescence processes, including chlorophyll degradation (Ueguchi et al., 2001
Cytokinins normally stimulate cell division and greening of calli. According to microarray databases, at least GeBP and GPL1 are strongly expressed in calli. Therefore, responses of tissue-cultured explants were examined with varied cytokinin concentrations in the presence of the auxin 2,4-dichlorophenoxyacetic acid (Fig. 7C). After 3 weeks, segments of wild-type roots responded by forming green calli at the two highest cytokinin concentrations tested, whereas the arr1 arr12 double mutant did not, as has been described previously (Mason et al., 2005 Taken together, these data show that the GeBP, GPL1, and GPL2 genes play redundant roles in cytokinin responses.
Cytokinin receptors are predicted to signal through His-phosphotransfer proteins to alter the phosphorylation of ARRs (Hutchison and Kieber, 2002
We next asked whether the triple mutant was still responsive to exogenous cytokinin relative to wild types by measuring transcript levels of three ARRs in the absence and presence of the cytokinin trans-zeatin (Fig. 8, C and D). In the absence of cytokinin, all ARR transcript levels were higher in the triple mutant than in wild types. Upon exogenous cytokinin treatment, levels of the three ARR transcripts increased in the wild types within 1 h (Fig. 8, C and D) with ARR7 being induced the most. In the triple mutant, ARR transcript levels also increased but cytokinin induction was weaker than in wild type for all three ARR genes. Thus ARR induction in the triple mutant was partially insensitive to exogenous cytokinin treatment, indicating that the triple mutant has a reduced responsiveness to exogenous cytokinins. Overall we conclude that transcript levels of type-A ARR response genes are regulated redundantly by the GeBP, GPL1, and GPL2 genes.
To distinguish between a direct or indirect repression of ARR gene expression by GeBP/GPLs, we generated a version of GPL2 with a constitutive transcriptional-activation activity. In this version, GPL2 is fused to the strong AD from the viral TF VP16 (Parcy et al., 1998
To determine the cytokinin sensitivity of the 35S:VP16:GPL2 transgenic lines, plants were grown in the presence of exogenous cytokinins (Fig. 9C). Rosettes of 35S:VP16:GPL2 plants exhibited a reduced growth relative to 35S:VP16, 35S::GPL2, or wild-type rosettes and were therefore more sensitive to exogenous cytokinin (Fig. 9C). This result is consistent with an increased cytokinin signaling due to the reduction in ARR transcript levels. Similarly, in root inhibition assays, 35S:VP16:GPL2 plants exhibited shorter roots relative to 35S:VP16, 35S::GPL2, or wild-type roots and were therefore more sensitive to exogenous cytokinin (data not shown). These results strongly support the role of GeBP/GPL genes in the regulation of cytokinin response genes.
Here we have characterized GeBP family members in Arabidopsis whose functions were unknown. A set of molecular and genetic tools were used to dissect the role of the GeBP and GPL genes in Arabidopsis development.
Proteins cannot be assigned to functional categories solely on the basis of sequence similarity to proteins or domains of known function. The GeBP/GPL proteins have not been classified as Leu-zipper TFs in databases. Leu-zipper motifs can be defined as coiled coils consisting of four to seven repeats of seven amino acids denoted a to g (Mason et al., 2006 This work allows the classification of GeBP/GPL as Leu-zipper proteins. Because homeodomain Leu-zipper proteins represent a subset of the large homeodomain family in plants, we suggest that GeBP/GPL proteins represent a novel form of DNA-binding Leu-zipper proteins within this family of 21 members.
According to their GUS expression patterns, the three most similar genes, GeBP, GPL1, and GPL2, are specifically expressed in aerial parts of the plant. There is a good correlation between the expression and function of these genes because cytokinin-related phenotypes were only visible in assays of aerial development, whereas none of the single, double, or triple mutants were affected in their root development or their cytokinin-sensitivity in root growth assays. Furthermore, the effects of gebp1, gpl1, and gpl2 mutations were generally additive in our experiments providing evidence for functional overlap within the family. One exception is the dark-induced leaf senescence assay where the triple mutant was not as distinguishable from the single and double mutants as in the other physiological or molecular assays. In this assay, however, leaves were separated from the main plant, and the SAM, where GeBP/GPL genes are mainly expressed, was not present. Therefore the functional redundancy of these genes in isolated leaves might be less striking. The expression of GeBP/GPL genes in leaf/cotyledon vascular tissues, hydathodes, and pedicel distal bulges suggests a role in vascular development. Cytokinins play an important role in the regulation of protoxylem formation in roots (Ye, 2002
Type-A ARRs are considered to be primary cytokinin response genes that act as redundant negative regulators of cytokinin signaling and their transcription is rapidly elevated in response to exogenous cytokinin (D'Agostino et al., 2000
This function of GeBP/GPL genes in triggering the cytokinin response is in agreement with the role of cytokinin in SAM function. In Arabidopsis, cytokinin biosynthesis is necessary for SAM function and is positively regulated by KNOX genes (Jasinski et al., 2005 Our analysis of the GeBP/GPL genes has led us to uncover their role in the regulation of the cytokinin response, namely the down-regulation of the negative feedback loop in cytokinin signaling. Future work is needed to determine whether GeBP family members that lack the Leu-zipper motif also participate in hormonal regulation in Arabidopsis and other plant species such as rice (Oryza sativa) and potato that have orthologous genes.
Plant Material and Growth Conditions
Seeds were sown on soil or surface-sterilized and grown in petri dishes on MS Basal Salt Mixture medium (Sigma). Plants were grown at 22°C in long days (16 h of 100 µE light). The Arabidopsis (Arabidopsis thaliana) Landsberg erecta (Ler) and Columbia (Col-0) ecotypes were the wild types used. The gebp-1 line having a Ds transposon insertion in the GeBP locus (Ler background) has been described previously (Curaba et al., 2003
The MatchMaker III system (CLONTECH) was used for yeast two-hybrid experiments. GeBP and GLP cDNAs were cloned from Gateway entry vectors into both pGADT7 and pGBKT7 vectors between EcoRI and XhoI sites and between EcoRI and SalI sites, respectively. Because yeast growth on permissive medium was impaired by strong expression of GeBP and GPL proteins, the long constitutive promoter PADH in the pGBKT7 and pGADT7 vectors was replaced by the short version from pGAD10 (CLONTECH). Yeast strain AH109 was cotransformed according to the manufacturer's instructions and selected on synthetic drop-out medium without Leu and Trp permissive medium. Individual colonies were grown in liquid culture and tested on synthetic drop-out medium supplement without Leu, Trp, adenine, and His selective medium supplemented with 5 to 10 mM 3-amino-1,2,4-triazole for 4 d at 30°C. The coiled-coil region in GeBP (Ala-176–Lys-209) was predicted with the program at http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_lupas.html (Lupas et al., 1991
The megaprimer extension technique (Sambrook and Russell, 2001
BiFC vectors were kindly provided by Dr. François Parcy (University Joseph Fourier). The GeBP cDNA was cloned upstream or downstream of both N-terminal and C-terminal fragments of the YFP gene using the Gateway cloning system (Invitrogen). Fusions were under the control of the 35S promoter. The four expression vectors were introduced separately into Agrobacterium and the four combinations of N-YFP and C-YFP fusions were independently coinfiltrated into tobacco leaves as previously described (Lavy et al., 2002
Oligonucleotides used for PCR amplification are given in Supplemental Table S1 online. GeBP/GPL cDNAs were produced from total RNA from 3-week-old rosettes. Genomic DNAs were cloned into pENTR/D-TOPO vector (Invitrogen), whereas cDNAs and promoters were cloned into pDONR221 (Invitrogen) using BP clonase (Invitrogen). A GeBP cDNA with no stop codon was also generated in pDONR221 for BiFC constructs where either the C-terminal or the N-terminal part of YFP was downstream of GeBP. GFP fusion lines for intracellular localization were made by cloning cDNAs into the pH7WGF2.0 vector (Plant Systems Biology, VIB-Ghent University) using LR clonase (Invitrogen) and stable transformation of the constructs into Arabidopsis. Transcriptional fusion lines with the GUS reporter gene were made by cloning GeBP/GPL promoters into the pKGWFS7 vector (Plant Systems Biology, VIB-Ghent University) and stable transformation of Arabidopsis with the constructs. For each construct, at least seven GUS-staining lines were studied. For GUS staining, plants were incubated 8 to 12 h with GUS substrate and destained as described (Gallagher, 1992
Arabidopsis T-DNA insertion lines were screened by DNA sequence comparison as T-DNA or Ds transposon insertion site information was made available by Salk Institute Genomic Analysis (http://signal.salk.edu/index.html) and Cold Spring Harbor Laboratory (http://genetrap.cshl.org/). Gene-specific primers were used in combination with T-DNA or Ds transposon-specific primers to identify and confirm insertions by PCR (see Supplemental Table S1). These primer combinations and gene-specific primer combinations flanking the sites of insertions were used to distinguish heterozygous from homozygous plants. Only lines homozygous for T-DNA insertions were used in subsequent assays. Regarding the GPL2 gene, it should be noted that The Arabidopsis Information Resource (TAIR) annotation for At5g14280 is composed of four exons with the first three exons encoding a peptide homologous to GeBP and the fourth exon corresponding to a putative C-terminal extension. However, no ESTs or cDNAs have been described that cover the putative exon3-exon4 junction, and we could not detect transcripts overlapping this junction by reverse transcription (RT)-PCR. In addition, two nonoverlapping TAIR ESTs (137F3XP and RAFL17-19-N04) and data from the Massively Parallel Signature Sequencing technique (http://mpss.udel.edu/at/) indicate that exon4 is transcribed independently of the GPL-like ORF. Therefore, the GPL2 gene is likely to be restricted to the first three exons of the At5g14280 annotation, and T-DNA insertions in the putative exon4 were not considered as GPL2 mutant lines. Double-insertion mutants were generated by crossing two single-insertion mutants. The gebp-1 allele was used to construct double mutants in which the GeBP function is impaired. To obtain the gebp-1 gpl1-1 gpl2-1 triple mutant, gebp-1 gpl2-1 double homozygous plants were crossed to plants homozygous for gebp-1 and heterozygous for gpl1-1. Plants homozygous for gebp-1 and gpl1-1 alleles and heterozygous for the gpl2-1 allele were identified in the F2 generation and selfed to produce F3 plants among which gebp-1 gpl1-1 gpl2-1 triple homozygous mutants were identified. F4 to F6 generations were used for the experiments described here.
For growth in the presence of cytokinin, surface-sterilized seeds were sown in petri dishes containing MS medium supplemented with kinetin (10 µg mL–1; Sigma) and plants were grown for 20 d at 22°C in a long day (16 h of 100 µmol s–1 cm–2 light). Chlorophyll content was measured after methanol extraction at 665 and 652 nm as described previously (Porra et al., 1989
For the callus induction assay, root segments were excised from 10-d-old seedlings grown on MS medium and were incubated in the presence of 2,4-dichlorophenoxyac etic acid (30 ng mL–1) and various concentrations of kinetin for 24 d as previously described (Higuchi et al., 2004
For the ARR transcript level assay, surface-sterilized seeds were sown in petri dishes containing MS medium and plants were grown for 14 d. Some petri dishes were sprayed with trans-zeatin (Sigma) as previously described (Kim et al., 2006 Significant changes were assessed using the ANOVA (P < 0.05) test with the StatEL software (ad Science). Single mutants gpl1, gpl2, and gpl3 together with the double mutants gpl1 gpl2 and arr1 arr12 were tested with Col as the control group. Double mutants gebp gpl1 and gebp gpl2 together with the triple mutant gebp gpl1gpl2 were tested with Col and Ler as the control group and were considered significantly different if their mean value was above or under both control groups. The single mutant gebp was tested with Ler using the Mann and Whitney test. Arabidopsis Genome Initiative locus identifiers for the GeBP/GPL genes are as follows: GeBP (At4g00270), GPL1 (At2g25650), GPL2 (At5g14280), and GPL3 (At2g36340).
The following materials are available in the online version of this article.
We thank Dr. G. Eric Schaller (Dartmouth College) for the gift of the arr1 arr12 double mutant. We thank François Parcy (Université Joseph Fourier) for providing the BiFc and Alligator vectors, Jean-Pierre Alcaraz (Université Joseph Fourier) for his help in sequencing, and Cécile Cottet (Université Joseph Fourier) for her help in confocal analysis. Received October 4, 2007; accepted December 23, 2007; published December 27, 2007.
1 These authors contributed equally to the article.
2 Present address: Laboratoire Vignes, Biotechnologies et Environnement, Université de Haute-Alsace, 33, rue de Herrlisheim, 68008 Colmar, France.
3 Present address: Center for Integrative Genomics, University of Lausanne, Genopode Building, 1015 Lausanne, Switzerland. The authors responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) are: Daniel Perazza (daniel.perazza{at}ujf-grenoble.fr) and Gilles Vachon (gilles.vachon{at}ujf-grenoble.fr).
[C] Some figures in this article are displayed in color online but in black and white in the print edition.
[W] The online version of this article contains Web-only data. www.plantphysiol.org/cgi/doi/10.1104/pp.107.110270 * Corresponding author; e-mail gilles.vachon{at}ujf-grenoble.fr.
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