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Edited by Mark Estelle, University of California, San Diego, La Jolla, CA, and approved April 20, 2016 (received for review January 15, 2016)
Significance
Mediator complex relays the information from transcription factors to RNA polymerase II. Our results show that Mediator transmits auxin-dependent transcription through its compositional change in lateral root formation. The AUXIN/INDOLE 3-ACETIC ACID 14 (IAA14) transcriptional repressor inhibits the transcriptional activity of its binding partners AUXIN RESPONSE FACTOR 7 (ARF7) and ARF19 by interacting with the dissociable CDK8 kinase module (CKM) of Mediator, a putative blocker of RNA polymerase II recruitment. Auxin-induced degradation of IAA14 dissociates the CKM component but not other Mediator subunits from ARF7 binding to the upstream region of its target gene. We suggest that this compositional change in Mediator enables a quick switch of information transmission from ARFs to target gene expression in response to auxin.
Abstract
Mediator is a multiprotein complex that integrates the signals from transcription factors binding to the promoter and transmits them to achieve gene transcription. The subunits of Mediator complex reside in four modules: the head, middle, tail, and dissociable CDK8 kinase module (CKM). The head, middle, and tail modules form the core Mediator complex, and the association of CKM can modify the function of Mediator in transcription. Here, we show genetic and biochemical evidence that CKM-associated Mediator transmits auxin-dependent transcriptional repression in lateral root (LR) formation. The AUXIN/INDOLE 3-ACETIC ACID 14 (Aux/IAA14) transcriptional repressor inhibits the transcriptional activity of its binding partners AUXIN RESPONSE FACTOR 7 (ARF7) and ARF19 by making a complex with the CKM-associated Mediator. In addition, TOPLESS (TPL), a transcriptional corepressor, forms a bridge between IAA14 and the CKM component MED13 through the physical interaction. ChIP assays show that auxin induces the dissociation of MED13 but not the tail module component MED25 from the ARF7 binding region upstream of its target gene. These findings indicate that auxin-induced degradation of IAA14 changes the module composition of Mediator interacting with ARF7 and ARF19 in the upstream region of their target genes involved in LR formation. We suggest that this regulation leads to a quick switch of signal transmission from ARFs to target gene expression in response to auxin.
Mediator is a multiprotein complex that relays integrated information from transcriptional factors to RNA polymerase II (RNAPII) (1⇓–3). Mediator consists of ∼25–30 subunits, which are organized into three modules forming the core Mediator (head, middle, and tail) and the dissociable CDK8 kinase module (CKM) (3, 4). The Mediator structure, subunit organization, and RNAPII interaction are conserved across eukaryotes, whereas Mediator is not a fixed complex. Structural analyses show that Mediator conformation and module organization are altered in accordance with the interaction with RNAPII (5, 6). RNAPII interacts with the middle module of the core Mediator, leading to a conformation change that could facilitate holoenzyme formation. CKM binds to the middle module, which interferes with the interaction of RNAPII with the core Mediator in vitro. In addition, recent accumulating evidence has shown a wide range of Mediator functions involving in almost all stages of RNAPII transcription, such as epigenetic regulation, transcriptional elongation, termination, mRNA processing, noncoding RNA activation, and superenhancer formation (3, 7). In Arabidopsis, the core Mediator is composed of more than 21 subunits (8), and CKM consists of MED12/CRYPTIC PRECOCIOUS (CRP)/CENTER CITY (CCT), MED13/MACCHI-BOU2 (MAB2)/GRAND CENTRAL (GCT), CDK8/HUA ENHANCER3 (HEN3), and C-type cyclin (9⇓⇓–12). Analysis of Arabidopsis Mediator subunits has shown that the subunits are important in regulating various developmental processes, phytohormone signaling pathways, developmental phase transitions, and abiotic and biotic stress tolerance (13⇓–15). Mutants of MED12/CRP/CCT and MED13/MAB2/GCT display embryonic development defects similar to those in auxin-related mutants and the genetic links between auxin-insensitive mutants, suggesting the involvement of Arabidopsis CKM in the auxin signaling pathway (9⇓–11). The biological functions of the respective Mediator subunits are now emerging in plants; however, little is known about the molecular mechanism whereby Mediator integrates information from various transcription factors and transmits it to gene transcription.
Auxin plays a crucial role in various aspects of physiological and developmental processes (16). To control these processes, auxin coordinates the transcription of numerous auxin-induced genes through actions of the auxin signaling module, the AUXIN/INDOLE 3-ACETIC ACID (Aux/IAA) transcriptional repressors, and the AUXIN RESPONSE FACTOR (ARF) transcription factors (17, 18). The ARFs bind specific auxin response elements (AuxREs) in their target genes. The Aux/IAAs function as repressors of ARF-mediated transcription by forming multimers with ARFs (19, 20) and recruiting the Groucho/Tup family corepressor TOPLESS (TPL) and its family proteins (TPRs) (21, 22). Auxin induces the proteolysis of Aux/IAAs by the E3-ubiquitin ligase SCFTRANSPORT INHIBITOR RESPONSE 1 (TIR1)/AUXIN SIGNALING F-BOX PROTEINS complex to activate ARF-mediated transcription. However, the molecular mechanisms about how Mediator relays the information from the auxin signaling module ARF-Aux/IAA to general transcriptional machinery in response to auxin remain obscure. In this study, we describe the function of MAB2 and other Mediator subunits in lateral root (LR) initiation controlled by the auxin signaling module IAA14-ARF7-ARF19 and show the molecular mechanism of auxin-responsive compositional changes in Mediator and its importance in their target gene transcription.
Results and Discussion
MAB2 Is Required for IAA14-Dependent Repression of ARF7 and ARF19 Function.
To elucidate the molecular mechanism of the integration of signals from the Aux/IAA-ARF auxin signaling module and their transmission to target gene expression, we focus on the Mediator function in auxin-regulated LR formation. The LRs are initiated from the anticlinal cell division in the pericycle, a cell layer located deep within the primary root and attached to the outer side of the vascular bundle (23), and LRs grow through outer cell layers to appear on the surface of the root (Fig. S1A). Both ARF7 and ARF19 are required to activate the cell cycle in pericycle cells by inducing the expression of the target genes LATERAL ORGAN BOUNDARIES-DOMAIN16 (LBD16) and LBD29 (24⇓⇓–27). The solitary-root-1 (slr-1) mutation in IAA14, which stabilizes the IAA14 protein (28), converts the ARF7 and ARF19 function from transcriptional activation to repression, leading to complete loss of LR formation (Fig. 1 A and B). To define the function of CKM in auxin signaling in LR formation, we examined genetic interaction between MAB2/MED13 and the Aux/IAA-ARF module genes. The mab2-4 single mutant exhibited a phenotype with shorter roots than the WT and showed a disordered LR distribution, but there was no difference in LR development and density between them (Fig. 1 A–C and Fig. S1 A and B). The slr-1 mutant formed no LR initiation sites, whereas the mab2-4 slr-1 double mutant developed LRs showing a disorder distribution, such as the mab2 single mutant did (Fig. 1 A and B and Fig. S1B). In addition, auxin treatment increased LR density in mab2-4 slr-1 but did not in slr-1 (Fig. S1C), showing that the mab2 mutation restored the auxin responsiveness in the slr-1 background. The mab2-4 mutation also restored the expression of a direct target gene of ARF7 and ARF19 in LR formation, LBD16, in the slr-1 mutant backgrounds (Fig. 1 D–G). Similar restorations of LR formation with pericycle cell division and expression of ARF7 and ARF19 target genes in LR formation were found using transgenic plants expressing stabilized mIAA14-GFP protein under the control of the native IAA14 promoter and another mab2 allele, mab2-1 (Fig. 1 C and H and Fig. S2A). In addition, the restoration was dissolved by complementation with pMAB2::MAB2-c-Myc (Fig. S3). Next, we examined the genetic relationship between ARF7, ARF19, and MAB2 in LR formation. Like arf7 arf19 double mutants, the mab2-4 arf7-1 arf19-1 triple mutants had very few LRs (Fig. 1 A and B). The additional arf7-1 and arf19-1 mutations completely deleted LR formation in the mab2-4 slr-1 background (Fig. 1 A and B), indicating that the recovery of LR formation in slr-1 by mab2 depends on the ARF7 and ARF19 activity. In addition, to investigate whether mab2 affects the expression of IAA14, ARF7, and ARF19, we analyzed the expression of these genes in pIAA14::mIAA14-GFP–expressing Columbia and mab2-4. The expressions of mIAA14-GFP and ARFs were not affected by the mab2 mutations (Fig. S4). The mIAA14-GFP signal was also detected in the nuclei of the epidermal and stele cells in both genetic backgrounds (Fig. S2 B–G). These data indicate that MAB2 is involved in IAA14-dependent repression of ARF7 and ARF19 target genes.
Fig. 1.
The effect of mab2 on the SLR/IAA14-ARF7-ARF19 auxin signaling module in LR formation. (A) Fourteen-day-old seedlings of Columbia, mab2-4, slr-1, mab2-4 slr-1, arf7-1 arf19-1, mab2-4 arf7-1 arf19-1, and mab2-4 arf7-1 arf19-1 slr-1. (Scale bar: 1 mm.) (B) LR density (emerged LR number per primary root length) for Columbia (Col; n = 20), mab2-4 (n = 21), slr-1 (n = 20), mab2-4 slr-1 (n = 22), arf7-1 arf19-1 (n = 20), mab2-4 arf7-1 arf19-1 (n = 21), and mab2-4 arf7-1 arf19-1 slr-1 (n = 20). Seven-day-old seedlings were used in this analysis. Data are presented as means ± SD. A two-tailed Student’s t test was performed. NS, not significant. *Significant differences: P < 0.05. (C) Nomarski images of roots of WT, mab2-1, and pIAA14::mIAA14-GFP transgenic plants in WT and mab2-1 backgrounds at 8 d. The arrowheads indicate the cell wall. (Scale bar: 50 µm.) (D–G) Expression of pLBD16::β-glucuronidase (GUS) in the mature root region of Col (D), slr-1 (E), mab2-4 (F), and mab2-4 slr-1 (G) for 10-d-old seedlings. The arrowheads indicate the cell wall of LR primordia. (Scale bars: 50 µm.) (H) Expression of LBD16 in Col and mab2-4 expressing pIAA14::mIAA14-GFP. The roots at 7 d were harvested after auxin treatment (black) and without auxin treatment (white). The relative abundance of LBD16 mRNA to ACT8 mRNA was measured by quantitative RT-PCR. The value measured for Col without auxin treatment was set at one. Data represent means ± SD (n = 3 independent biological replicates). Different letters in each graph indicate the statistical differences (P < 0.05; Student’s t test).
Fig. S1.
LR formation in Arabidopsis. (A) Nomarski images of LR development in Arabidopsis Columbia (Col; Upper) and mab2-4 (Lower). LRs are initiated from the anticlinal cell division (white arrows) in the pericycle (black arrowheads) and grow through outer cell layers. (B) The frequency distribution of number of pericycle cell (PC) between neighboring LR primordia of WT (n = 16), mab2-4 (n = 16), and mab2-4 slr-1 (n = 16). (C) LR density for WT (n = 20), slr-1 (n = 20), mab2-4 (n = 21), and mab2-4 slr-1 (n = 22). Four-day-old seedlings were transferred to the media either with or without 1 \x{03bc}M NAA, a synthetic auxin, and incubated for an additional 72 h. Data are means ± SD. Student’s t test was performed, and asterisks represent significant differences. *P < 0.05; **P < 0.01.
Fig. S2.
The effects of mab2 on auxin responsibility in LR formation and stabilized IAA14 expression. (A) LR density for WT (n = 22), mab2-4 (n = 22), and pIAA14::mIAA14-GFP transgenic plants in WT (n = 22) and mab2-4 (n = 21) backgrounds. Four-day-old seedlings were transferred to the media either with or without 1 µM NAA, a synthetic auxin, and incubated for an additional 72 h. Data are means ± SD. Student’s t test was performed, and asterisks represent significant differences. *P < 0.05; **P < 0.01. (B–E) Expression of mIAA14-GFP driven by its own promoter in the stele (B and D) and epidermis (C and E) of WT (B and C) and mab2-4 (D and E) roots. (Scale bars: 50 µm.) (F and G) Immunolocalization of mIAA14-GFP (green) in nuclei (red) of WT (F) and mab2-4 (G). (Scale bars: 10 µm.)
Fig. S3.
Complementation test with pMAB2::MAB2-c-Myc. pMAB2::MAB2-c-Myc can fully complement LR phenotypes of the mab2-4 mutants expressing pIAA14::mIAA14-GFP. Pictures show 14-d-old seedlings of Columbia (Col), mab2-4, mab2-4 pMAB2::MAB2-c-Myc, pIAA14::mIAA14-GFP, mab2-4 pIAA14::mIAA14-GFP, and mab2-4 pMAB2::MAB2-c-Myc pIAA14::mIAA14-GFP. (Scale bars: 1 mm.) The graphs show LR density for each background (n = 20) using 7-d-old seedlings. Data are presented as means ± SD. Student’s t test was performed, and asterisks represent significant differences. *P < 0.05.
Fig. S4.
Expressions of ARF7 and ARF19 target genes and auxin signaling module genes in Columbia and mab2-4 expressing pIAA14::mIAA14-GFP. The roots at 7 d were harvested after auxin treatment (white) and without auxin treatment (black). The relative abundances of LBD16, LBD29, ARF7, ARF19, IAA14, and GFP mRNA to ACT8 mRNA were measured by quantitative RT-PCR. The value measured for Columbia expressing pIAA14::mIAA14-GFP without auxin treatment was set at one. Data represent means ± SD (n = 3 independent biological replicates). Different letters in each graph indicate the statistical differences (P < 0.05; Student’s t test).
CKM-Containing Mediator Is Involved in IAA14-Dependent Repression.
To examine the involvement of other CKM subunits in IAA14-dependent repression of the ARF function in LR formation, we constructed crp/med12 slr-1 and hen3/cdk8 slr-1 double mutants. Like mab2 slr-1, crp slr-1 and hen3 slr-1 developed LR and showed the auxin sensitivity in LR formation, showing that the crp and hen3 mutations restored the auxin responsiveness involved in LR formation in the slr-1 background (Fig. S5 A and B). These results indicate that CKM is involved in the IAA14-mediated block of LR formation. Furthermore, we investigated the function of the core Mediator in IAA14-mediated inhibition of LR formation. Mutations in MED17 and PHYTOCHROME AND FLOWERING TIME1 (PFT1)/MED25, which encode subunits of the head and tail Mediator module, respectively (8), also rescued the LR-less phenotype in pIAA14::mIAA14-GFP-expressing plants (Fig. S5C), indicating that not only CKM but also, other Mediator modules are involved in IAA14-dependent LR-less phenotype. Our genetic data suggest that CKM-containing Mediator transmits a signal from IAA14 to repress the expression of ARF7 and ARF19 target genes.
Fig. S5.
The genetic interaction between other CKM genes and SLR/IAA14. (A) LR density for Columbia (Col; n = 20), slr-1 (n = 20), crp-4 (n = 20), and crp-4 slr-1 (n = 20). (B) LR density for Landsberg erecta (Ler; n = 20), slr-1 (n = 20), hen3-1 (n = 20), and hen3-1 slr-1 (n = 22). Four-day-old seedlings were transferred to the media either with or without 1 µM NAA, a synthetic auxin, and incubated for an additional 72 h. (C) LR density for Col (n = 20), med17 (n = 20), pft1-2 (n = 20), and pIAA14::mIAA14-GFP transgenic plants in Col (n = 20), med17 (n = 20), or pft1-2 (n = 20) backgrounds. Data are means ± SD. Student’s t test was performed, and asterisks represent significant differences. *P < 0.05; **P < 0.01.
MAB2 Interacts with a Transcriptional Repressor Complex Including IAA14 and TPL.
To confirm the connection between IAA14 and CKM, we examined the physical interaction between IAA14 and MAB2. Although we observed no direct interaction between them in yeast (Fig. S6), we did observe interaction between stabilized mIAA14 and MAB2 by performing coimmunoprecipitation (Co-IP) assay using mab2-4 plants coexpressing MAB2-c-Myc and mIAA14-GFP (Fig. 2A). These results suggest that MAB2 indirectly interacts with IAA14. Recently, the corepressor TPL/TPR has been shown to mediate auxin-dependent transcriptional repression through direct interaction with Aux/IAA (22). In our study, we found that IAA14 interacted with TPL in yeast cells and plants (Fig. 2B and Fig. S6). We also found the tpl-1 mutation induced cell division in pericycle cells, resulting in LR formation in the presence of stabilized mIAA14-GFP, such as mab2 did (Fig. S7). In addition, the simultaneous mutation of TPL and MAB2 restored LR formation in plants expressing stabilized mIAA14 to the same extent as respective single mutations (Fig. S7 C and D). This result indicates that TPL functions in the same pathway with MAB2 in IAA14-dependent repression of ARF7 and ARF19 target genes. Furthermore, we found direct interaction between MAB2 and TPL/TPR and the TPL linking between IAA14 and MAB2 in yeast and protoplast cells (Fig. 2 C–F). These data are consistent with a previous report that HEN3, a component of CKM (11, 12), coexists with the transcription corepressor LEUNIG and the histone deacetylase HDA19 (29). However, we could not detect any interaction between MAB2 and TPL in plants coexpressing MAB2-c-Myc and TPL-HA under the normal growth condition (Fig. 2G). Only in the presence of the auxin antagonist auxinole, which stabilizes Aux/IAA by blocking TIR1–Aux/IAA interaction (30), did we find the stabilization of IAA14-GFP and the physical association with MAB2 and TPL in plants (Fig. 2G and Fig. S8), indicating that the interaction between MAB2 and TPL depends on Aux/IAA in plants. Our results suggest that the IAA14–TPL corepressor complex recruits CKM to change the module composition of Mediator.
Fig. 2.
Protein–protein interaction between MAB2 and the IAA14-TPL repressor complex. (A and B) Co-IP assays showing that mIAA14 interacts with MAB2 (A) and TPL (B). Protein extracts from 7-d-old-roots of mab2-4 expressing MAB2-c-Myc, tpl-1 expressing TPL-HA, Columbia (Col) expressing mIAA14-GFP, mab2-4 coexpressing mIAA14-GFP and MAB2-c-Myc, and tpl coexpressing TPL-HA and mIAA14-GFP were subjected to immunoprecipitation (IP) using an anti-GFP antibody. Input and IP fractions of MAB2-c-Myc (A), TPL-HA (B), and mIAA14-GFP were detected by immunoblots (IBs) using anti–c-Myc, anti-HA, and anti-GFP antibodies, respectively. The white arrowheads indicate the predicted positions of mIAA14-GFP, MAB2-c-Myc, and TPL-HA, respectively, identified by proper molecular weight bands (Fig. S15). (C) Yeast two-hybrid assay showing that MAB2 interacts with TPL and TPR2. The assay was performed with SD-Leu-Trp as well as SD-Leu-Trp-His. (D) Yeast three-hybrid assay showing that TPL forms a bridge between IAA14 and MAB2 and that the C terminus to the lissencephaly homology (CTLH) domain of TPL, essential for interaction with Aux/IAA, is required for the coexistence of three proteins. The assay was performed with SD-Leu-Trp (-LW) as well as SD-Leu-Trp-His (-LWH). AD, activation domain; BD, binding domain. (E and F) Bimolecular fluorescence complementation (BiFC) assay for TPL-dependent interaction between mIAA14 and MAB2 in Arabidopsis protoplast cells. Bright field (column 1), BiFC (column 2), and enhanced cyan fluorescent protein (ECFP) (column 3) fluorescence images of protoplast cells into which BiFC [Venus N (VN) –mIAA14/MAB2–Venus C (VC)] and additional constructs [TPL-ECFP or nuclear localization signal (NLS) –ECFP] were introduced. Merged image (column 4) shows BiFC and ECFP. (Scale bars: 10 µm.) (G) Co-IP assays showing that MAB2 associates with TPL only in the presence of the auxin antagonist auxinole. Protein extracts from 7-d-old-seedlings of mab2-4 expressing MAB2-c-Myc, tpl-1 expressing TPL-HA, and mab2 tpl coexpressing MAB2-c-Myc and TPL-HA pretreated with or without 10 µM auxinole for 18 h were subjected to IP using an anti–c-Myc antibody. Input and IP fractions of TPL-HA and MAB2-c-Myc were detected by IBs using anti-HA and anti–c-Myc antibodies, respectively. The white arrowheads indicate the predicted positions of TPL-HA and MAB2-c-Myc by proper molecular weight bands (Fig. S15).
Fig. S15.
Identification of the bands of interest. The bands of interest in Figs. 2 A, B, and G and 4B were identified by proper molecular weight bands of Precision Plus Protein Dual Color Standards (Bio-Rad) and are indicated by white arrowheads. Colored dots indicate the positions of the molecular weight bands. Col, Columbia; IB, immunoblot; IP, immunoprecipitation.
Fig. S6.
The yeast two-hybrid assay to examine the interaction between IAA14 and the subunits of the CKM module. IAA14 cannot interact with the subunits of the CKM module, but it can with TPL and TPR2 in yeasts. The assay was performed with SD-Leu-Trp (-LW) as well as SD-Leu-Trp-His (-LWH). AD, activation domain; BD, binding domain.
Fig. S7.
The genetic interaction between TPL and mIAA14 in LR development. (A) Fourteen-day-old seedlings of mIAA14-GFP expressing WT, mab2-1, tpl-1, and mab2-1 tpl-1. Ler, Landsberg erecta. (B and C) LR density for WT (n = 20), mab2-1 (n = 20), tpl-1 (n = 20), mab2-1 tpl-1 (n = 20), and transgenic plants in WT (n = 20), mab2-1 (n = 20), tpl-1 (n = 20), and mab2-1 tpl-1 (n = 20) backgrounds. Four-day-old seedlings were transferred to the media with either DMSO (white) or 1 µM NAA, a synthetic auxin, (black) and incubated for an additional 72 h. Data are means ± SD. Student’s t test was performed, and asterisks represent significant differences. NS, not significant. *P < 0.05; **P < 0.01. (D) Nomarski images of roots of WT, mab2-1, tpl-1, mab2-1 tpl-1, and pIAA14::mIAA14-GFP expressing plants in WT, mab2-1, tpl-1, and mab2-1 tpl-1 backgrounds at 8 d. The arrowheads indicate the cell wall. In mIAA14-GFP expressing mab2-1 tpl-1, LR primordia (yellow asterisks) were adjacently located. (Scale bars: 50 µm.)
Fig. S8.
The effect of auxinole on the stability of IAA14-GFP. Accumulation of IAA14-GFP protein in response to auxinole application. Protein extracts from 7-d-old-seedlings of pIAA14::IAA14-GFP expressing Columbia (Col) treated with 10 µM auxinole or DMSO for 18 h were subjected to an immunoblot (IB) assay with anti-GFP antibody.
IAA14 Recruits MAB2 to the Promoter Region of the Target Gene LBD16.
To confirm IAA14-dependent recruitment of CKM to the upstream region of the target gene LBD16, the ChIP assays for MAB2 were performed in the presence of auxin, auxinole, or mIAA14-GFP. We detected MAB2 binding weakly at regions I and II of LBD16 under the normal growth condition (Fig. 3 A and B and Fig. S9A). MAB2 dissociated from the 5′ upstream region of LBD16 in the presence of auxin (Fig. 3C and Fig. S9B). In contrast, in the presence of auxinole or mIAA14, MAB2 binding was strongly detected at regions I and II and weakly detected at regions III and IV close to TATA box upstream of the transcription start site of LBD16, where mIAA14 specifically bound at the region II-containing AuxRE (Fig. 3 D and E and Fig. S9 C and D). These results indicate IAA14-dependent MAB2 binding to the upstream region of LBD16. The region containing I–IV is shared by LBD16 and long noncoding RNA At2g42425, with expression that was up-regulated by auxin treatment and the mab2 mutation (Fig. 1H and Fig. S10). MAB2 binding at regions I and II under normal conditions suggests that these genes are ordinarily repressed by MAB2.
Fig. 3.
MAB2 binding in the upstream region of LBD16. (A) Schematic diagram of the LBD16 locus and amplified fragments for ChIP assays [I–V and negative control (NC)]. The locus that gives rise to auxin-induced long noncoding RNA (lncRNA) is located upstream of region I. (B–E) ChIP assays using 7-d-old seedlings of mab2-4 pMAB2::MAB2-c-Myc under the normal condition (B), treated with 1 µM 1-naphthaleneacetic acid (NAA), a synthetic auxin, for 2 h (C) and 10 µM auxinole for 18 h (D), and mab2-4 pMAB2::MAB2-c-Myc pIAA14::mIAA14-GFP (E). Control reaction was processed in parallel with mouse IgG. The y axis represents the ratio between the enriched DNA after immunoprecipitation and the input DNA before immunoprecipitation. Data represent means ± SD (n = 3 independent biological replicates). Asterisks indicate the statistical differences. A region ∼3,000 bp from the transcriptional start site of LBD16 was used as an NC. *P < 0.05 (Student’s t test); **P < 0.01 (Student’s t test).
Fig. S9.
ChIP analysis using Columbia (Col). ChIP assays using 7-d-old seedlings of Col under the normal condition with anti–c-Myc or anti-GFP antibodies (A), auxin-treated Col (1 µM NAA, a synthetic auxin, for 2 h) with an anti–c-Myc antibody (B), auxinole-treated Col (10 µM auxinole for 18 h) with an anti–c-Myc antibody (C), and auxin- or DMSO-treated Col with an anti-GFP antibody (D). Nuclear proteins were immunoprecipitated with respective antibodies, and the enriched DNA fragments were used for quantitative RT-PCR analysis. Control reaction was processed in parallel with mouse IgG. The y axis represents the ratio between the enriched DNA after immunoprecipitation and the input DNA before immunoprecipitation. Data represent means ± SD (n = 3 independent biological replicates). NC, negative control.
Fig. S10.
Auxin responsibility of long noncoding RNA expression. Expressions of At2g42425 long noncoding RNA transcribed from the locus upstream of LBD16 in Columbia (Col), mab2-4, and auxin-treated Col roots. WT roots at 7 d were harvested after treatment with 1 µM NAA, a synthetic auxin, for 2 h. The relative abundance of long noncoding RNA mRNA to UBC mRNA was measured by quantitative RT-PCR. The value measured for Col without auxin treatment was set at one. Data represent means ± SD (n = 3 independent biological replicates). Student’s t test was performed, and asterisks represent significant differences. **P < 0.01.
MED25 Stably Binds to the Upstream Region of LBD16 with ARF7.
We then investigated the connection of the core Mediator with the auxin signaling module ARF7-ARF19-IAA14 in LR formation. We found the physical interaction of ARF7 and ARF19 but not of IAA14 with PFT1/MED25, the subunit of the tail Mediator module (8), and MED8 of the head module but not of MED6 of the head module in yeast (Fig. 4A and Fig. S11) and genetic interaction between ARF7 and MED8 (Fig. S12), with mutation that reportedly affects auxin response in LR formation (31). In addition, we observed interaction between stabilized mIAA14 and MED25 by performing Co-IP assay using mIAA14-GFP–expressing plants (Fig. 4B). These results suggest that the core Mediator interacts with the auxin signaling module. Next, to examine the behavior of the core Mediator in the upstream region of LBD16, ChIP assays for MED25 were performed using MED25-GFP–expressing plants (32). MED25-GFP binding was detected at region II containing AuxRE, where ARF7 specifically bound under normal conditions and in the presence of auxin (Fig. 4C and Fig. S9D). These results indicate that ARF7 is stably associated with AuxRE in region II together with MED25 and that mIAA14, when bound to ARF7, recruits MAB2 to the upstream region of LBD16. Auxin-dependent degradation of IAA14 is suggested to cause the dissociation of MAB2 from the ARF7-containing transcriptional machinery. To confirm this suggestion, we performed Co-IP assay using arf7-1 arf19-1 mab2-4 coexpressing ARF7-GFP and MAB2-c-Myc. MAB2 and MED25 coexisted in the same protein complex as ARF7 in seedlings pretreated with auxinole (Fig. S13A). Subsequent exposure of these seedlings to auxin led to dissociation of MAB2 but not MED25 from the ARF7-containing protein complex, whereas subsequent exposure to auxinole caused no change in the interactions (Fig. S13A). We confirmed no change in the MAB2 and MED25 protein level with or without auxin (Fig. S13 B and C). These data indicate that auxin-dependent degradation of Aux/IAA dissociates MAB2 from ARF7-containing transcriptional machinery. Considering that all of these factors are expressed in the pericycle attached to the outer side of the vascular bundle (Fig. S14) (24, 28), this event could be coupled to auxin-regulated LR formation.
Fig. 4.
The interaction between ARF7 and Mediator subunits. (A) Yeast two-hybrid assay showing that MED25 interacts with IAA14, ARF7, and ARF19. The assay was performed with SD-Leu-Trp (-LW) as well as SD-Leu-Trp-His-Ade (-LWHA) supplemented with 10 mM 3-amino-1,2,4-triazole (3-AT), an inhibitor of His production. AD, activation domain; BD, binding domain. (B) Co-IP assays showing that mIAA14 interacts with MED25. Protein extracts from 7-d-old-roots of Columbia (Col) expressing mIAA14-GFP were subjected to immunoprecipitation (IP) using an anti-GFP antibody. Input and IP fractions of MED25 and mIAA14-GFP were detected by immunoblots (IBs) using anti-MED25 and anti-GFP antibodies, respectively. The white arrowheads indicate the predicted positions of MED25 and mIAA14-GFP. The asterisk shows a band of the putative degradation products of mIAA14-GFP identified by proper molecular weight bands (Fig. S15). (C) ChIP assays using 7-d-old seedlings of Col p35s::MED25-GFP (Upper) and arf7 arf19 pARF7::ARF7-GFP (Lower). Control reaction was processed in parallel with mouse IgG. The y axis represents the ratio between the enriched DNA after IP and the input DNA before IP. Data represent means ± SD (n = 3 independent biological replicates). A region ∼3,000 bp from the transcriptional start site of LBD16 was used as a negative control (NC). NS, not significant. **Statistical differences (P < 0.01; Student’s t test). (D) A model for auxin-responsive transcription through IAA14-ARF7-ARF19. (i) Under low-auxin condition, IAA14 forms a repressor complex with TPL and CKM to inactivate the ARF7 and ARF19 function. Mediator interacts with ARF7 and ARF19 as well as CKM, thus preventing Mediator from associating with RNAPII. (ii) When auxin concentrations are high, auxin promotes proteolysis of IAA14 and release of TPL and CKM, leading to derepression of both ARF7 and ARF19 and Mediator. (iii) Releasing ARF7 and ARF19 activates the transcription of target genes through the recruitment of RNAPII by CKM-dissociated Mediator.
Fig. S11.
The yeast two-hybrid assay to examine the interaction of the subunits of the core Mediator with IAA14, ARF7, and ARF19. The assay was performed with SD-Leu-Trp (-LW) as well as SD-Leu-Trp-His (-LWH) using MED8 and MED6, components of the head module, as the bait. AD, activation domain; BD, binding domain.
Fig. S12.
The genetic interaction of MED genes with ARF7 and ARF19. LR density for WT (n = 20), arf7-1 (n = 20), arf19-1 (n = 20), med8 (n = 21), pft1-2 (n = 20), arf7-1 arf19-1 (n = 22), arf7-1 med8 (n = 22), pft1-2 arf7-1 (n = 22), arf19-1 med8 (n =22), and pft1-2 arf19-1 (n = 22). The graphs show LR density for each background using 8-d-old seedlings. Data are means ± SD. Student’s t test was performed, and an asterisk represents a significant difference. Col, Columbia. *P < 0.05.
Fig. S13.
The effect of auxin on the interaction between ARF7 and Mediator subunits. (A) Co-IP results showing the association of Mediator subunits with ARF7 in response to auxin treatment. Protein extracts from 7-d-old seedlings of Columbia (Col) and arf7-1 arf19-1 mab2-4 coexpressing pARF7::ARF7-GFP and pMAB2::MAB2-c-Myc pretreated with 10 µM auxinole for 16 h (lane: pre) before incubating with 10 µM auxinole (lane: auxinole) or 1 µM NAA, a synthetic auxin, (lane: NAA) for 2 h were subjected to immunoprecipitation (IP) using an anti-GFP antibody. Input and IP fractions of MAB2–c-Myc (Top), MED25 (Middle), and mIAA14-GFP (Bottom) were detected by immunoblots (IBs) using anti–c-Myc, anti-MED25, and anti-GFP antibodies, respectively. The bands of interest were identified by proper molecular weight bands of Precision Plus Protein Dual Color Standards (Bio-Rad) and are indicated by arrowheads. Colored dots indicate the positions of the molecular weight bands. (B and C) Accumulation of MAB2 and MED25 proteins in response to auxin application. Protein extracts from 7 d-old-seedlings of mab2-4 pMAB2::MAB2-c-Myc and Col treated with 1 µM NAA or DMSO for 2 h were subjected to an IB assay with anti–c-Myc (B) or anti-MED25 (C) antibodies, respectively.
Fig. S14.
Expression of auxin signaling module MAB2 and MED25 in LR formation. (A) Relative expression of ARF7, ARF19, IAA14, TPL, MAB2, and MED25 in Arabidopsis root tips displayed by the Arabidopsis eFP browser (www.bar.utoronto.ca/efp/cgi-bin/efpWeb.cgi). (B–G) Immunolocalization of TPL-HA in roots of tpl-1 expressing TPL-HA (B) and Columbia (Col; C), MAB2-c-Myc in roots of mab2-4 expressing MAB2-c-Myc (D) and Col (E), MED25 in roots of Col (F), and a null allele pft1-2 (G). Nuclei were stained by SYTOX (blue). (Scale bars: 20 µm.)
In conclusion, we have shown that CKM-associated Mediator transmits repressive signals from the ARFs-IAA14-TPL complex to target gene expression, resulting in inhibited LR formation (Fig. 4D, i). Furthermore, auxin-induced proteolysis of IAA14 leads to the dissociation of CKM but not the core Mediator from ARF7 and ARF19 (Fig. 4D, ii). As a result, the active form of ARFs induces the expression of target genes through the core Mediator (Fig. 4D, iii). Considering that single mutations in the core Mediator subunits suppress the mIAA14-dependent LR-less phenotype (Fig. S5C), the mutations might affect the interaction between CKM and the core Mediator without much effect on the function of the core Mediator in auxin signaling (Fig. S12), leading to the dissociation of CKM from the core Mediator. If one considers that CKM structurally prevents RNAPII interaction with the core Mediator (5, 6), it follows that the IAA14-TPL repressor complex may inhibit the recruitment of RNAPII to target genes by associating CKM with the core Mediator, whereas CKM-dissociated Mediator may recruit RNAPII in the presence of auxin. This regulation can enable a quick transcriptional switch between activation and repression in response to auxin. Meanwhile, TPL controls the chromatin remodeling with histone deacetylases to repress transcription (21, 33, 34). Both repression mechanisms, CKM-dependent RNAPII exclusion and TPL-dependent chromatin remodeling, seem to be necessary to achieve auxin-dependent transcriptional repression, because both the mab2 and tpl-1 mutations partially rescued slr-1 phenotypes, respectively (Fig. 1 and Fig. S7). Thus, our findings provide insights into the role of TPL in repressing auxin signaling and propose a model for rapid auxin-dependent gene activation.
Materials and Methods
Plant Materials and Growth Conditions.
Arabidopsis thaliana accessions Columbia-0 and Landsberg erecta were used as the WTs. Descriptions of mab2-1, mab2-4, arf7-1, arf19-1, slr-1, crp-4, hen3-1, med17, pft1-2, med8, pIAA14::IAA14-GFP, pIAA14::mIAA14-GFP, pLBD16::β-glucuronidase (GUS), and p35S::MED25-GFP lines have been made previously (9, 11, 24, 25, 32, 35). The tpl-1 and pTPL::TPL-HA lines that we used were provided by Jeff Long (University of California, Los Angeles, CA), whereas hen3-1 mutant was obtained from the Arabidopsis Biological Resource Center (36). Seeds were surface-sterilized, plated on Murashige and Skoog medium plates, and germinated as described previously (37). Plants were transferred to soil and grown at 23 °C under constant light as described previously (37).
Transgenic Plants.
To construct pARF7::ARF7-GFP, ARF7 cDNA was subcloned into the pDONR201 vector (Invitrogen) and transferred to the pGWB-GFP(C) vector under a 2.5-kb ARF7 promoter. [The pGWB-GFP(C) vector was constructed by inserting the GFP coding region into the XbaI/SacI sites of the pGWB1 vector (38).] We transformed pARF7::ARF7-GFP into LR-less arf7-1 arf19-1 plants by floral dipping using Agrobacterium tumefaciens (strain MP90) (39). Four kanamycin-resistant transformants developed LR but less than the WT, indicating that pARF7::ARF7-GFP partially complemented the double-mutant phenotype (24). To generate pMAB2::MAB2-c-Myc, MAB2 cDNA was subcloned into the pDONR221 vector (Invitrogen) and transferred to the pGWB16 vector (38) under a 2.0-kb MAB2 promoter. We transformed pMAB2::MAB2-c-Myc into heterozygous mab2-4 plants by floral dipping using A. tumefaciens (strain MP90) (39). Thirteen kanamycin-resistant transformants homozygous for the mab2-4 mutation displayed normal cotyledon development and fertility, indicating that pMAB2::MAB2-c-Myc complemented the mab2 phenotype (11). The transgene was introduced into mab2-4 pIAA14::mIAA14-GFP, tpl-1 pTPL::TPL-HA, and arf7 arf19 pARF7::ARF7-GFP plants by crossing to construct the mab2-4 pMAB2::MAB2-c-Myc pIAA14::mIAA14-GFP, tpl-1 mab2-4 pTPL::TPL-HA pMAB2::MAB2-c-Myc, and arf7-1 arf19-1 mab2-4 pARF7::ARF7-GFP pMAB2::MAB2-c-Myc plants, respectively.
Yeast Two- and Three-Hybrid Assays.
The yeast two-hybrid assay was performed as described previously (11). Empty vectors were used as negative controls, and pBD-p53 and pAD-T7 were used as positive controls. In the yeast three-hybrid assay, full-length TPL and TPL without the C terminus to the lissencephaly homology domain (TPLΔ C terminus to the lissencephaly homology) cDNAs were subcloned into p427-TEF. The plasmids were introduced into the AH109 strain together with pAD-GAL4-MAB2 and pBD-GAL4-IAA14. We selected p427-TEF–introduced yeasts on the basis of their resistance to G418 (200 µg/L; Wako). The empty vector p427-TEF was used as negative controls. Interaction was detected by the expression of the HIS3 reporter gene.
Co-IP and Immunoblot.
For Co-IP assays, root parts of 7-d-old seedlings were homogenized in a protein extraction buffer (50 mM Tris⋅HCl, pH 7.5, 150 mM NaCl, 1% Nonidet P-40, 0.6 mM phenylmethyl sulphonyl fluoride, Roche protease inhibitor mixture). We conducted immunoprecipitation from protein extracts using the µMACS GFP-Tagged Protein Isolation Kit (Miltenyi Biotec) and the µMACS c-myc–Tagged Protein Isolation Kit (Miltenyi Biotec) according to the manufacturer's instructions. Immunoblot assays were performed using anti-GFP (JL-8; Clontech), anti-HA (12CA5; Roche), anti–c-Myc (9E10 Santa Cruz Biotechnology), and anti-MED25 antibodies (32). The bands of interest were identified by proper molecular weight bands of Precision Plus Protein Dual Color Standards (Bio-Rad).
ChIP Assay.
The ChIP assays were performed according to the previously reported protocol (40) with slight modification; 2 or 4 g 7-d-old seedlings were used as samples. In nuclei isolation buffer, Roche protease inhibitor mixture was used in place of pepstatin A and aprotinin. After preclearing with Salmon Sperm DNA-Protein G Agarose Beads (Millipore), cross-linked chromatin from seedlings was immunoprecipitated with anti-GFP antibody (GFP-20; Sigma-Aldrich), anti-Myc antibody (9E10; Abcam), or normal mouse IgG (Santa Cruz Biotechnology). The ratio between the bound DNA after immunoprecipitation and the input DNA before immunoprecipitation was calculated for all of the representative primer sets spanning the LBD16 genomic region shown in Table S1.
View this table:
Table S1.
List of primers used in this study
SI Materials and Methods
Immunolocalization Analysis.
Five-day-old seedlings were fixed for 1 h with 4% (wt/vol) paraformaldehyde in 1× microtubules stabilizing buffer, and cut root tips of 7-d-old seedlings were fixed overnight at −20 °C in a methanol:acetic acid solution (3:1). After dehydration in ethanol series and infiltration with butanol, samples were embedded in paraffin. Subsequent processes were performed as previously described (41). Antibodies and nuclear fluorescent dye were diluted as followed: 1:150 for rabbit anti-GFP (Thermo Fisher Scientific), 1:200 for mouse anti-HA (12CA5; Roche), 1:100 for anti–c-Myc (9E10; Santa Cruz Biotechnology), 1:300 for anti-MED25 antibodies, 1:500 for Alexa 488-conjugated anti-rabbit secondary antibody (Invitrogen), and 1:1,000 for SYTOX Orange (Life Technology).
Microscopy.
The GUS staining, fixation, and whole-mount clearing preparation of roots were performed in essentially the same manner as described previously (42), and samples were observed with an Olympus BX-52 Microscope equipped with Nomarski Optics (Olympus). For confocal microscopy, roots were analyzed with an Olympus FV1000 Confocal Microscope (Olympus).
RNA Extraction and Quantitative RT-PCR.
Total RNA was extracted from roots of 7-d-old seedlings treated with DMSO or 1 µM 1-naphthaleneacetic acid (NAA) for 2 h using the RNeasy Plant Mini Kit (Qiagen). Each treatment was done in three replicates. First-strand cDNA was synthesized from DNase-treated total RNA (2 µg) using SuperScript II Reverse Transcriptase (Invitrogen) with an oligo (dT)24 primer (Invitrogen) for UBC and LBD16 or an At2g42425-r2 primer (5′-GTACACGAGCACTAAGTGAAGA-3′) for long noncoding RNA. Quantitative RT-PCR was performed on the LightCycler 96 (Roche) with the KAPA SYBR FAST qPCR Kit (KAPA BIOSYSTEMS) and the gene-specific primer sets according to the manufacturer’s instructions. ACT8 (Fig. S4) and UBC (Fig. 1H) were measured for an internal control and used to normalize the data. Relative amounts of LBD16 and long noncoding RNA (At2g42425) transcripts were calculated as fold change relative to values measured for WT plants (Columbia) without auxin treatment, which was arbitrarily set to one. All primer sequences are listed in Table S1.
Bimolecular Fluorescence Complementation.
MAB2 and mIAA14 ORFs were cloned into bimolecular fluorescence complementation (BiFC) vectors (43). TPL ORF and AtWRKY6 nuclear localization signal sequence (44), corresponding to the region spanning amino acids 1–543 were cloned into enhanced cyan fluorescent protein (ECFP)-tagged fluorescent protein expression vector. For the BiFC experiments, 3 µg each Venus N terminus- and Venus C terminus-tagged protein expression vector (Venus N terminus-mIAA14 and MAB2-Venus C terminus, respectively) and 3 µg ECFP-tagged protein expression plasmid (TPL-ECFP or nuclear localization signal–ECFP) were cotransformed into Arabidopsis protoplasts as previously described (45). After incubation at 23 °C for 12 h in the dark, the Venus (BiFC) and ECFP fluorescence was analyzed by the confocal microscopy.
Acknowledgments
We thank Jeff Long for providing tpl-1 and pTPL::TPL-HA lines, Takashi Araki for providing crp-4, Taku Demura for providing pAD-GWRFC and pBD-GWRFC vectors, and Kenichiro Hayashi for providing auxinole. This work was partly supported by Ministry of Education, Culture, Sports, Science and Technology (MEXT) Grants-in-Aid for Scientific Research on Priority Areas 14036222 (to M.T.) and 19060007 (to M.T.), MEXT Grant-in-Aid for Young Scientists (B) 20770034, MEXT Grant-in-Aid for Scientific Research on Innovative Areas 26113513, and the Global Center of Excellence Program in the Nara Institute of Science and Technology (Frontier Biosciences: Strategies for Survival and Adaptation in a Changing Global Environment), MEXT (M.F.).
Footnotes
- ↵1To whom correspondence should be addressed. Email: ma-furut{at}agr.nagoya-u.ac.jp.
↵2Present address: Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan.
Author contributions: M.F. designed research; J.I., H.F., M.O., C.L., and M.F. performed research; J.I., H.F., M.O., L.L., C.L., M.T., and M.F. contributed new reagents/analytic tools; J.I. and M.F. analyzed data; and J.I., M.T., and M.F. wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission.
This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1600739113/-/DCSupplemental.
Freely available online through the PNAS open access option.
References
Auxin-dependent composition change in Mediator
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