The transcriptional regulator BZR1 mediates trade-off between plant innate immunity and growth.

The molecular mechanisms underlying the trade-off between plant innate immunity and steroid-mediated growth are controversial. Here, we report that activation of the transcription factor BZR1 is required and sufficient for suppression of immune signaling by brassinosteroids (BR). BZR1 induces the expression of several WRKY transcription factors that negatively control early immune responses. In addition, BZR1 associates with WRKY40 to mediate the antagonism between BR and immune signaling. We reveal that BZR1-mediated inhibition of immunity is particularly relevant when plant fast growth is required, such as during etiolation. Thus, BZR1 acts as an important regulator mediating the trade-off between growth and immunity upon integration of environmental cues. DOI: http://dx.doi.org/10.7554/eLife.00983.001.

Introduction

The trade-off between plant growth and immunity needs to be finely regulated to ensure proper allocation of resources in an efficient and timely manner upon effective integration of environmental cues (Pieterse et al., 2012). A key aspect of plant immunity is the perception of pathogen-associated molecular patterns (PAMPs) by surface-localized pattern-recognition receptors (PRRs), leading to PAMP-triggered immunity (PTI) (Dodds and Rathjen, 2010). PRRs of the leucine-rich repeat receptor kinases (LRR-RKs) class rely on the regulatory LRR-RK BAK1 (BRASSINOSTEROID INSENSITIVE 1-ASSOCIATED KINASE 1) for signaling (Monaghan and Zipfel, 2012); that is the case of FLS2 (FLAGELLIN SENSITIVE 2) and EFR (EF-TU RECEPTOR), which perceive bacterial flagellin (or the active peptide flg22) and EF-Tu (or the active peptide elf18) respectively. BAK1 also interacts with the LRR-RK BRI1 (BRASSINOSTEROID INSENSITIVE 1), the main receptor for the growth-promoting steroid hormones brassinosteroids (BR), and is a positive regulator of BR-mediated growth (Kim and Wang, 2010). Hence, a crosstalk between the BR- and PAMP-triggered signaling pathways resulting from competition for BAK1 was hypothesized. While a unidirectional antagonism between BR and PTI signaling has been recently described in Arabidopsis (Albrecht et al., 2012; Belkhadir et al., 2012), the exact underlying mechanisms are still controversial. Activation of the BR signaling pathway via either transgenic overexpression of BRI1 or the BR biosynthetic gene DWF4 or expression of the activated BRI1 allele BRI1 suppresses PTI outputs (Belkhadir et al., 2012). One such output, the PAMP-triggered callose deposition, could be restored by over-expression of BAK1-HA, suggesting that BAK1 is a limiting factor (Belkhadir et al., 2012). However, exogenous BR treatment of wild-type plants does not affect the FLS2-BAK1 complex formation upon FLS2 activation, while it results in decreased PTI responses (Albrecht et al., 2012).

Results and discussion

In order to clarify the role of BAK1 in the BR-PTI crosstalk, we investigated FLS2-BAK1 complex formation in the transgenic Arabidopsis lines overexpressing BRI1 or DWF4 or expressing BRI1 (Belkhadir et al., 2012). Upon treatment with flg22, FLS2 associated normally with BAK1 in these transgenic plants, and neither FLS2 nor BAK1 accumulation was altered (Figure 1—figure supplement 1A). Moreover, these plants displayed a weaker reactive oxygen species (ROS) burst in response to chitin (Figure 1—figure supplement 1B), whose signaling pathway is BAK1-independent (Shan et al., 2008; Ranf et al., 2011). This result is consistent with the previous finding that exogenous BR treatment can also inhibit the chitin-induced ROS burst (Albrecht et al., 2012). BAK1-HA is not fully functional in BR signaling and exerts a dominant-negative effect on the endogenous BAK1 (Figure 1—figure supplement 1C), which may explain that introduction of the BAK1-HA transgene can override the suppression of immunity triggered by overexpression of BRI1 (Belkhadir et al., 2012); BAK1-HA does not exert such a dominant negative effect, however, on PTI signaling (Figure 1—figure supplement 1D). Taken together, these results indicate that the BR-mediated suppression of PTI is triggered independently of a competition between BRI1 and PRRs for BAK1.

Figure 1—figure supplement 1.

The BR-mediated suppression of PTI can be triggered independently of a competition for BAK1.

(A) Co-IP of BAK1 and FLS2 in Col-0, 35S:BRI1-cit, 35S:BRI1-cit and 35S:DWF4 seedlings treated with 1 μM flg22 for 10 min. Coimmunoprecipitated proteins were analyzed by using anti-FLS2 or anti-BAK1 antibodies. (B) Chitin-triggered ROS burst in Col-0, 35S:BRI1-cit and 35S:DWF4 plants. Chitin was used at a concentration of 1 mg/ml. Total photon counts were integrated between minutes two and 40 after PAMP treatment. Bars represent SE of n = 28 rosette leaf discs. (C) Root length of seven-day-old Col-0, BAK1p:BAK1-HA (in Col-0 WT background) or bak1-3 seedlings grown on medium supplemented or not with 10 nM BL. Bars represent SE of 12 ≤ n ≤ 17. Asterisks indicate a statistically significant difference between treatments according to a Student's t-test (p<0.05). (D) Flg22-triggered ROS burst in Col-0, BAK1p:BAK1-HA (in Col-0 WT background) or bak1-3 plants. Leaf discs of four- to five-week-old Arabidopsis plants were used in these assays. Flg22 was used at a concentration of 50 nM. Total photon counts were integrated between minutes two and 40 after PAMP treatment. Bars represent SE of n = 28 rosette leaf discs. All experiments were repeated at least twice with similar results.

DOI: http://dx.doi.org/10.7554/eLife.00983.004

We sought to determine at which level of the BR signaling pathway the antagonism initiates. After BR perception by BRI1 and activation of the BRI1-BAK1 complex, the BR signal transduction cascade includes inactivation of BIN2 (BR INSENSITIVE 2) and BIN2-like kinases, a family of GSK3-like kinases acting as negative regulators of the pathway (Vert and Chory, 2006). This leads to dephosphorylation of BZR1 (BRASSINAZOLE RESISTANT 1) and BES1/BZR2 (BRI1-EMS-SUPPRESSOR 1/BRASSINAZOLE RESISTANT 2), two bHLH transcription factors acting as major regulators of BR-induced transcriptional changes, which then become active (Wang et al., 2002; Yin et al., 2002). Treatment with the chemicals LiCl and bikinin, which inhibit GSK3-like kinases (De Rybel et al., 2009; Yan et al., 2009), resulted in impaired flg22-triggered ROS burst (Figure 1A,B), as observed upon genetic or ligand-induced activation of the BR pathway. Furthermore, a triple mutant in BIN2 and the two closest related GSK3-like kinases, BIL1 (BIN2-LIKE 1) and BIL2 (triple GSK3 mutant; Vert and Chory, 2006), shows a similar impairment in response to either flg22 or chitin (Figure 1C). Interestingly, in spite of regulating MAPKs involved in stomata development (Kim et al., 2012; Khan et al., 2013), neither BR treatment nor loss of function of BIN2 affect flg22-triggered MAPK activation (Figure 1—figure supplement 2), contrary to what has been recently suggested (Choudhary et al., 2012; Zhu et al., 2013). These results indicate that the BR-PTI crosstalk occurs downstream of BIN2.

Figure 1.

Activation of BZR1 is sufficient to inhibit the PAMP-triggered ROS burst.

(A) and (B) Flg22-triggered ROS burst after LiCl (A) or bikinin (B) treatment. Leaf discs were pre-treated with a 10 mM LiCl solution for 5 hr or with a 50 μM bikinin solution for 16 hr. (C) Flg22- or chitin-triggered ROS burst in Col-0 and the triple GSK3 mutant plants. (D) Flg22- or chitin-induced ROS burst in Col-0 and BZR1Δ plants. (E) Elf18-triggered ROS burst in bri1-5 and bri1-5/BZR1Δ plants. In all cases, bars represent SE of n = 28 rosette leaf discs. Asterisks indicate a statistically significant difference compared to the corresponding control (mock treatment [A and B], Col-0 [C and D] or bri1-5 [E]), according to a Student’s t-test (p<0.05). Leaf discs of four- to five-week-old Arabidopsis plants were used in these assays. Flg22 and elf18 were used at a concentration of 50 nM; chitin was used at a concentration of 1 mg/ml. Total photon counts were integrated between minutes two and 40 after PAMP treatment. All experiments were repeated at least three times with similar results.

DOI: http://dx.doi.org/10.7554/eLife.00983.003

(A) Co-IP of BAK1 and FLS2 in Col-0, 35S:BRI1-cit, 35S:BRI1-cit and 35S:DWF4 seedlings treated with 1 μM flg22 for 10 min. Coimmunoprecipitated proteins were analyzed by using anti-FLS2 or anti-BAK1 antibodies. (B) Chitin-triggered ROS burst in Col-0, 35S:BRI1-cit and 35S:DWF4 plants. Chitin was used at a concentration of 1 mg/ml. Total photon counts were integrated between minutes two and 40 after PAMP treatment. Bars represent SE of n = 28 rosette leaf discs. (C) Root length of seven-day-old Col-0, BAK1p:BAK1-HA (in Col-0 WT background) or bak1-3 seedlings grown on medium supplemented or not with 10 nM BL. Bars represent SE of 12 ≤ n ≤ 17. Asterisks indicate a statistically significant difference between treatments according to a Student's t-test (p<0.05). (D) Flg22-triggered ROS burst in Col-0, BAK1p:BAK1-HA (in Col-0 WT background) or bak1-3 plants. Leaf discs of four- to five-week-old Arabidopsis plants were used in these assays. Flg22 was used at a concentration of 50 nM. Total photon counts were integrated between minutes two and 40 after PAMP treatment. Bars represent SE of n = 28 rosette leaf discs. All experiments were repeated at least twice with similar results.

DOI: http://dx.doi.org/10.7554/eLife.00983.004

(A) MAPK activation in Col-0 seedlings upon treatment with 1 μM flg22 (F) and/or epiBL (B) for 10 min (with or without a 90-min or 5-hr BL pre-treatment). (B) Quantification of total MAPK activation in the experiment shown in (A), measured as pixel intensity using ImageJ. Results are the average of two independent blots, corresponding to two independent biological replicated. (C) MAPK activation in Col-0 and Triple GSK3 mutant seedlings upon treatment with 1 μM flg22. (D) Quantification of total MAPK activation in the experiment shown in (C), measured as pixel intensity using ImageJ. Results are the average of two independent blots, corresponding to two independent biological replicated. Proteins were separated in a 10% acrylamide gel and transferred to PVDF membranes. Membranes were blotted with phospho-p44/42 MAPK (Erk1/2; Thr202/Tyr204) rabbit monoclonal antibodies. Bars represent SD.

DOI: http://dx.doi.org/10.7554/eLife.00983.005

(A) Flg22- or chitin-triggered ROS burst in BZR1 plants. (B) Flg22-triggered ROS burst in BES1 plants. (C) Flg22-triggered ROS burst in mock- or bikinin-treated Col-0 or bri1-5 plants. Leaf discs were pre-treated with a 50 μM bikinin solution for 16 hr. (D) Flg22-triggered ROS burst in mock- or BRZ-treated Col-0 or BZR1Δ plants. Leaf discs were pre-treated with a 2.5 μM BRZ solution for 16 hr. In all cases, bars represent SE of 21 ≤ n ≤ 28. Asterisks indicate a statistically significant difference compared to Col-0 (A and B) or mock-treatment (C and D) according to a Student's t-test (p<0.05). Flg22 was used at a concentration of 50 nM; chitin was used at a concentration of 1 mg/ml. Total photon counts were integrated between minutes two and 40 after PAMP treatment.

DOI: http://dx.doi.org/10.7554/eLife.00983.006

Figure 1—figure supplement 2.

PAMP-triggered MAPK activation is not impaired upon activation of BR signaling.

(A) MAPK activation in Col-0 seedlings upon treatment with 1 μM flg22 (F) and/or epiBL (B) for 10 min (with or without a 90-min or 5-hr BL pre-treatment). (B) Quantification of total MAPK activation in the experiment shown in (A), measured as pixel intensity using ImageJ. Results are the average of two independent blots, corresponding to two independent biological replicated. (C) MAPK activation in Col-0 and Triple GSK3 mutant seedlings upon treatment with 1 μM flg22. (D) Quantification of total MAPK activation in the experiment shown in (C), measured as pixel intensity using ImageJ. Results are the average of two independent blots, corresponding to two independent biological replicated. Proteins were separated in a 10% acrylamide gel and transferred to PVDF membranes. Membranes were blotted with phospho-p44/42 MAPK (Erk1/2; Thr202/Tyr204) rabbit monoclonal antibodies. Bars represent SD.

DOI: http://dx.doi.org/10.7554/eLife.00983.005

Transgenic expression of two different constitutively active versions of BZR1, BZR1Δ (Gampala et al., 2007) and BZR1S173A (Ryu et al., 2007), results in impaired flg22- or chitin-triggered ROS burst (Figure 1D, Figure 1—figure supplement 3A). Consistent with previous results (Albrecht et al., 2012; Figure 1—figure supplements 1A and 2), plants expressing BZR1Δ or BZR1 display normal FLS2-BAK1 complex formation and MAPK activation upon flg22 treatment (Figure 2A,B, Figure 2—figure supplement 1A,B), but are impaired in PAMP-triggered marker gene expression, seedling growth inhibition (SGI) (Figure 2C–E) and induced resistance to P. syringae pv. tomato (Pto) DC3000 (Figure 2F, Figure 2—figure supplement 1C), and are more susceptible to the non-host strain Pseudomonas syringae pv. cilantro (Pci) 0788-9 (Lewis et al., 2010) (Figure 2G). Notably, transgenic expression of a constitutively active form of BES1, BES1S171A (Gampala et al., 2007), does not impact the flg22-triggered ROS burst (Figure 1—figure supplement 3B). We then tested if activation of BZR1 is sufficient to inhibit PTI signaling. Induction of BR signaling by bikinin treatment still represses elf18-induced ROS burst in the BRI1 mutant bri1-5 (we used elf18 in this experiment because bri1-5 is in the Ws-2 background, which is a natural fls2 mutant) (Figure 1—figure supplement 3C). bri1-5/BZR1Δ plants (Gampala et al., 2007) still exhibited reduced PAMP-triggered ROS burst (Figure 1E), and treatment with the BR biosynthetic inhibitor brassinazole (BRZ) did not affect the BZR1Δ effect (Figure 1—figure supplement 3D). Interestingly, BRZ treatment of wild-type Col-0 plants results in increased ROS production (Figure 1—figure supplement 3D), which is consistent with the fact that BR inhibits PTI responses and suggests that endogenous concentrations of the hormone exert this effect. These results demonstrate that activation of BZR1 affects PTI signaling independently of BR perception or synthesis.

Figure 1—figure supplement 3.

Activation of BZR1, but not BES1, is sufficient to inhibit the PAMP-triggered ROS burst.

(A) Flg22- or chitin-triggered ROS burst in BZR1 plants. (B) Flg22-triggered ROS burst in BES1 plants. (C) Flg22-triggered ROS burst in mock- or bikinin-treated Col-0 or bri1-5 plants. Leaf discs were pre-treated with a 50 μM bikinin solution for 16 hr. (D) Flg22-triggered ROS burst in mock- or BRZ-treated Col-0 or BZR1Δ plants. Leaf discs were pre-treated with a 2.5 μM BRZ solution for 16 hr. In all cases, bars represent SE of 21 ≤ n ≤ 28. Asterisks indicate a statistically significant difference compared to Col-0 (A and B) or mock-treatment (C and D) according to a Student's t-test (p<0.05). Flg22 was used at a concentration of 50 nM; chitin was used at a concentration of 1 mg/ml. Total photon counts were integrated between minutes two and 40 after PAMP treatment.

DOI: http://dx.doi.org/10.7554/eLife.00983.006

Figure 2.

Activation of BZR1 results in the suppression of specific PTI outputs.

(A) Co-immunoprecipitation (Co-IP) of BAK1 and FLS2 in Col-0 and BZR1Δ seedlings after 10 min mock (−) or 1 μM flg22 (+) treatment. Proteins were separated in a 10% acrylamide gel and transferred to PVDF membranes. Membranes were blotted with anti-FLS2 or anti-BAK1 antibodies. (B) MAPK activation in Col-0 and BZR1Δ seedlings upon 1 μM flg22 treatment. Proteins were separated in a 10% acrylamide gel and transferred to PVDF membranes. Membranes were blotted with phospho-p44/42 MAPK (Erk1/2; Thr202/Tyr204) rabbit monoclonal antibodies. CBB: Coomassie brilliant blue. (C) Marker gene (At2g17700 and NHL10) expression in Col-0 and BZR1Δ seedlings after 1 hr mock (−) or 1 μM flg22 (+) treatment, as determined by qPCR. Bars represent SE of n = 3. (D) and (E) Seedling growth inhibition of 10-day-old Col-0 or BZR1Δ seedlings induced by increasing concentrations of flg22, as indicated. Scale bar (D), 1 cm. Bars (E) represent SE of 8 ≤ n ≤ 16. (F) Flg22-induced resistance to P. syringae pv. tomato DC3000 in Col-0 and BZR1Δ plants. Plants were pre-treated with 1 μM flg22 or water 24 hr prior to bacterial infiltration. Bars represent SE of n = 4. This experiment was repeated seven times with similar results. (G) Susceptibility of Col-0 and BZR1Δ plants to P. syringae pv. cilantro 0788-9. Bars represent SE of n = 4. Asterisks indicate a statistically significant difference compared to Col-0 according to a Student’s t-test (p<0.05); ns = not significant. All experiments were repeated at least twice with similar results unless otherwise stated.

DOI: http://dx.doi.org/10.7554/eLife.00983.007

(A) Co-IP of BAK1 and FLS2 in Col-0 and BZR1 seedlings treated with 1 μM flg22 for 10 min. Co-immunoprecipitated proteins were analyzed by using anti-FLS2 or anti-BAK1 antibodies. (B) MAPK activation in Col-0 and BZR1 seedlings upon treatment with 1 μM flg22. Membranes were blotted with phospho-p44/42 MAPK (Erk1/2; Thr202/Tyr204) rabbit monoclonal antibodies. (C) Flg22-induced resistance to Pto DC3000 in BZR1 plants. Plants were pre-treated with 1 μM flg22 or water 24 hr prior to bacterial inoculation. Bars represent SE of n = 4. Asterisks indicate a statistically significant difference compared to mock-treated plants according to a Student's t-test (p<0.05); ns = not significant. All experiments were repeated at least twice with similar results.

DOI: http://dx.doi.org/10.7554/eLife.00983.008

Figure 2—figure supplement 1.

Expression of the constitutively active BZR1S173A results in the suppression of specific PTI outputs.

(A) Co-IP of BAK1 and FLS2 in Col-0 and BZR1 seedlings treated with 1 μM flg22 for 10 min. Co-immunoprecipitated proteins were analyzed by using anti-FLS2 or anti-BAK1 antibodies. (B) MAPK activation in Col-0 and BZR1 seedlings upon treatment with 1 μM flg22. Membranes were blotted with phospho-p44/42 MAPK (Erk1/2; Thr202/Tyr204) rabbit monoclonal antibodies. (C) Flg22-induced resistance to Pto DC3000 in BZR1 plants. Plants were pre-treated with 1 μM flg22 or water 24 hr prior to bacterial inoculation. Bars represent SE of n = 4. Asterisks indicate a statistically significant difference compared to mock-treated plants according to a Student's t-test (p<0.05); ns = not significant. All experiments were repeated at least twice with similar results.

DOI: http://dx.doi.org/10.7554/eLife.00983.008

To understand how BZR1 mediates the BR-PTI crosstalk, we performed meta-analysis of microarray and ChIP-chip data containing BR-regulated and BZR1 or BES1 target genes (Sun et al., 2010; Yu et al., 2011). Functional enrichment of BR-regulated genes unveiled a statistically significant over-representation of defense-related GO terms of the Biological Process ontology (Table 1), indicating that BR signaling regulates the expression of defense-related genes. Independent analysis of BR-regulated BZR1 or BES1 targets confirmed BZR1 as the main transcription factor involved in the regulation of defense gene expression (Table 1). Two out of four over-represented GO terms of the Molecular Function ontology among the BR-regulated BZR1 targets are transcription factor and transcription repressor activity (Table 2). Interestingly, several defense-related GO terms are also over-represented in the subset of BR-regulated BZR1-targeted transcription factors (Table 3), pointing at a BZR1-mediated secondary transcriptional wave of defense-related genes.

Table 1.

Defense-related Gene Ontology terms (Biological Process ontology) over-represented among all BR-regulated genes, BR-regulated BZR1 targets and BR-regulated BES1 targets

DOI: http://dx.doi.org/10.7554/eLife.00983.009

Defense-related GO term	Observed frequency (%)	Expected frequency (%)	p-value
BR-Regulated genes
response to bacterium	2.2	1	3.31 × 10−08
defense response to bacterium	1.9	0.8	3.31 × 10−08
response to chitin	1.4	0.5	1.78 × 10−07
defense response	4.7	3	3.32 × 10−07
response to fungus	1.5	0.7	3.4 × 10−06
response to nematode	0.7	0.2	0.000532
defense response to fungus	1	0.5	0.0035
BR-regulated BZR1 targets
response to chitin	2.6	0.5	9.13 × 10−13
response to bacterium	2.3	1	0.00112
defense response to bacterium	1.9	0.8	0.00154
response to fungus	1.6	0.7	0.00495
BR-regulated BES1 targets
response to chitin	2.4	0.5	0.00439

Table 2.

Gene Ontology terms (Molecular Function ontology) over-represented among all BR-regulated BZR1 targets

DOI: http://dx.doi.org/10.7554/eLife.00983.010

Over-represented GO term	Observed frequency (%)	Expected frequency (%)	p value
BR-regulated BZR1 targets
nucleic acid binding transcription factor activity	14.8	10.2	0.000223
transferase activity	21.6	16.8	0.00333
kinase activity	11.6	8.1	0.00702
transcription repressor activity	1.1	0.3	0.01

Table 3.

Defense-related Gene Ontology terms (Biological Process ontology) over-represented among the BZR1-target BR-regulated transcription factors

DOI: http://dx.doi.org/10.7554/eLife.00983.011

Defense-related GO Term	Observed frequency (%)	Expected frequency (%)	p value
BZR1-target BR-regulated TFs
response to chitin	16.6	0.5	1.36 × 10−26
defense response to bacterium	7.6	0.8	4.71 × 10−07
response to bacterium	7.6	1	4.51 × 10−06
regulation of defense response to virus by host	1.4	0	0.000964
regulation of immune effector process	1.4	0	0.00151
regulation of defense response to virus	1.4	0	0.00151
regulation of defense response	2.8	0.3	0.00484
defense response	8.3	3	0.00603
response to fungus	3.4	0.7	0.01
defense response to fungus	2.8	0.5	0.02

To identify BZR1-regulated transcription factors with a prominent role in defense, we performed promoter enrichment analysis on the subset of defense-related BR-regulated genes, and found the W-box motif as the only significantly over-represented motif (Table 4). The W-box motif is the binding site for the WRKY family of transcription factors (Rushton et al., 2010), and several members of this family are BR-regulated BZR1-targets (Table 5). We hypothesized that WRKYs that are BR-induced and BZR1 targets may be involved in PTI signaling. Notably, wrky11, wrky15, wrky18 and wrky70 mutants displayed enhanced PAMP-triggered ROS (Figure 3A), suggesting that these transcription factors act as negative regulators of early PTI signaling. This is in accordance with their role as negative regulators of immunity (Figure 3—figure supplement 1A; Journot-Catalino et al., 2006). Therefore, the BZR1-mediated inhibition of PTI might be partially explained by the up-regulation of genes encoding WRKY transcription factors that negatively control the expression of genes involved in early PTI signaling.

Table 4.

Over-represented cis-acting promoter elements among the defense-related BR-regulated genes according to Athena (http://www.bioinformatics2.wsu.edu/cgi-bin/Athena/cgi/home.pl)

DOI: http://dx.doi.org/10.7554/eLife.00983.012

Enriched TF site	% promoters	p value
Defense-related BR-regulated genes
W-box	72.4	<10−6

Table 5.

BR-regulated BZR1-target WRKY genes

DOI: http://dx.doi.org/10.7554/eLife.00983.013

AGI number	WRKY TF
BR-Induced BZR1 targets
AT4G31800	WRKY18
AT4G31550	WRKY11
AT4G23810	WRKY53
AT3G56400	WRKY70
AT5G49520	WRKY48
AT5G52830	WRKY27
AT1G69310	WRKY57
AT2G23320	WRKY15 (Yu et al., 2011)
BR-repressed BZR1 targets
AT4G01250	WRKY22
AT1G80840	WRKY40
AT2G24570	WRKY17
AT2G23320	WRKY15 (Sun et al., 2010)
AT2G30590	WRKY21

Figure 3.

WRKY transcription factors play a dual role on the BR-mediated regulation of PTI signaling.

(A) Flg22-triggered ROS burst in mutants in each BR-induced BZR1-targeted WRKY. Leaf discs of four- to five-week-old Arabidopsis plants were used in these assays. Flg22 was used at a concentration of 50 nM. Total photon counts were integrated between minutes two and 40 after PAMP treatment. Bars represent SE of n = 28. Asterisks indicate a statistically significant difference compared to Col-0 according to a Student’s t-test (p<0.05). (B) Flg22-triggered ROS burst in epiBL (BL)- or mock- pre-treated wrky40 mutant or wild-type plants. Leaf discs of four- to five-week-old plants were pre-treated with a 1 μM BL solution or mock solution for 8 hr. Flg22 was used at a concentration of 50 nM. Total photon counts were integrated between minutes two and 40 after PAMP treatment. Bars represent SE of n = 21. Asterisks indicate a statistically significant difference compared to Col-0 according to a Student’s t-test (p<0.05). (C) Co-IP of BZR1-GFP transiently expressed in N. benthamiana, alone or together with WRKY40-HA or WRKY6-HA. BZR1-GFP was immunoprecipitated with an anti-GFP antibody. Immuniprecipitated or total proteins were separated in a 10% acrylamide gel and transferred to PVDF membranes. Membranes were blotted with anti-HA or anti-GFP antibodies. CBB: Coomassie brilliant blue. (D) Co-IP of BZR1-GFP transiently expressed in Arabidopsis protoplasts, alone or together with WRKY40-HA. BZR1-GFP was immunoprecipitated with an anti-GFP antibody. Immuniprecipitated or total proteins were separated in a 10% acrylamide gel and transferred to PVDF membranes. Membranes were blotted with anti-HA or anti-GFP antibodies. CBB: Coomassie brilliant blue. All experiments were repeated at least twice with similar results.

DOI: http://dx.doi.org/10.7554/eLife.00983.014

(A) and (B) Pto DC3000 infections in Col-0, wrky11, wrky15, and wrky18 (A) and in Col-0 and wrky40 (B) plants. Bars represent SE of n = 4. Asterisks indicate a statistically significant difference compared to Col-0 plants according to a Student's t-test (p<0.05); ns = not significant. All experiments were repeated at least three times with similar results.

DOI: http://dx.doi.org/10.7554/eLife.00983.015

Figure 3—figure supplement 1.

Mutants in WRKY11, WRKY15, WRKY18 and WRKY40 are more resistant to Pto DC3000.

(A) and (B) Pto DC3000 infections in Col-0, wrky11, wrky15, and wrky18 (A) and in Col-0 and wrky40 (B) plants. Bars represent SE of n = 4. Asterisks indicate a statistically significant difference compared to Col-0 plants according to a Student's t-test (p<0.05); ns = not significant. All experiments were repeated at least three times with similar results.

DOI: http://dx.doi.org/10.7554/eLife.00983.015

One of the WRKY genes targeted by BZR1 is WRKY40 (Sun et al., 2010). Interestingly, all described targets of WRKY40 (Pandey et al., 2010) are also targets of BZR1 (Sun et al., 2010) (Table 6). The over-representation of the W-box motif among BZR1 targets (Table 7) suggests that BZR1 may interact with WRKY transcription factors (such as WRKY40) to cooperatively regulate transcription. WRKY40 has been described as a negative regulator of defense against biotrophic pathogens and insects (Xu et al., 2006; Pandey et al., 2010; Brotman et al., 2013; Schon et al., 2013; Schweizer et al., 2013). In agreement with this, we found that a null wrky40 mutant is more resistant to Pto DC3000 (Figure 3—figure supplement 1B). Strikingly, wrky40 plants are partially impaired in the BR-mediated suppression of PAMP-triggered ROS (Figure 3B), suggesting that WRKY40 may act coordinately with BZR1 to suppress immunity. Indeed, we found that BZR1 associates with WRKY40, but not WRKY6, in co-immunoprecipitation experiments when transiently co-expressed in Nicotiana benthamiana leaves (Figure 3C) or Arabidopsis protoplasts (Figure 3D). Collectively, these results indicate that BZR1 and WRKY40 form a protein complex that may participate in the transcriptional inhibition of PTI signaling.

Table 6.

Overlap between the targets of WRKY40 and BZR1

DOI: http://dx.doi.org/10.7554/eLife.00983.016

Known targets of WRKY40 (Pandey et al., 2010)	Targets of BZR1 (Sun et al., 2010)
Confirmed by ChIP
EDS1	Yes
RRTF1	Yes
JAZ8	Yes
Putative (according to expression analyses)
LOX2	Yes
AOS	Yes
JAZ7	Yes
JAZ10	Yes

Table 7.

Representation of the W-box motif among the BR-regulated BZR1 targets according to Athena (http://www.bioinformatics2.wsu.edu/cgi-bin/Athena/cgi/home.pl)

DOI: http://dx.doi.org/10.7554/eLife.00983.017

BZR1 targets	% of promoters with W-box motif(s)	p value
BR-induced	66	<10−10
BR-repressed	72	<10−4

BZR1, together with DELLAs and PIF4, is part of a core transcription module that integrates hormonal (gibberellin [GA] and BR) and environmental (light) signals (Gallego-Bartolome et al., 2012; Li et al., 2012; Oh et al., 2012; Bai et al., 2012b). In the dark, BZR1 is activated by endogenous BR and GA to promote growth, partially through the synergistic interaction with PIF4 (Jaillais and Vert, 2012). Because etiolation requires rapid growth, we hypothesized that plants may prioritize growth over immunity in dark conditions. In fact, we found that PAMP-triggered SGI was partially impaired in dark-grown seedlings (Figure 4A–D). This impairment was abolished in the BR-insensitive mutants bri1-301 and bin2-1 (Figure 4A, Figure 4—figure supplement 2A), indicating that BR signaling is responsible for the dark-induced suppression of this PTI response. Activation of BZR1 in the BZR1Δ line mimicked the dark-induced suppression of SGI in both light and dark (Figure 4B). However, activation of BES1 in the BES1 line did not impact SGI (Figure 4—figure supplement 3A). Consistent with the previous results, exogenous BR treatment suppressed SGI in both light and dark (Figure 4C, Figure 4—figure supplement 2B,C). While treatment with GA alone did not have a dramatic effect on SGI, co-treatment with BL and GA resulted in an enhancement of the BR-mediated suppression of SGI (Figure 4C, Figure 4—figure supplement 2B), indicating an additive effect of these two hormones when applied together. Moreover, treatment with the GA synthesis inhibitors paclobutrazol (PAC) or uniconazole (Uni) abolished the effect of BL on SGI (Figure 4—figure supplement 1A,B and Figure 4—figure supplement 2B,C), and this effect was reduced in the GA biosynthetic mutant ga1-3 (Figure 4—figure supplement 1C). Taken together, these results demonstrate that BR suppress at least one PTI output, SGI, in the dark in a GA-dependent manner, most likely through activation of BZR1. Notably, although the wrky40 mutant undergoes etiolation normally (Figure 4—figure supplement 2D), it shows a diminished suppression of SGI in the dark (Figure 4D, Figure 4—figure supplement 2D), supporting the idea that WRKY40 is required for the BZR1-mediated inhibition of PTI.

Figure 4.

Activation of BR signaling and BZR1 prioritizes growth over immunity in the dark.

(A) and (B) Relative seedling growth inhibition of 10-day-old (A) Col-0, bri1-301 and bin2-1 or (B) Col-0 and BZR1Δ seedlings induced by increasing concentrations of flg22 in either light or dark. (C) Relative seedling growth inhibition of 10-day-old Col-0 seedlings grown on medium supplemented or not with BL (1 μM), GA (1 μM), BL+GA (1 μM + 1 μM) or mock solution in light or dark. (D) Relative seedling growth inhibition of Col-0 or wrky40 seedlings induced by increasing concentrations of flg22 in either light or dark. Bars represent SE of n = 16 (A, B and D) or n = 8 (C) Asterisks indicate a statistically significant difference compared to Col-0 in the same condition (light or dark and same concentration of flg22), according to a Student’s t-test (p<0.05); ‘a’ indicates a statistically significant difference compared to the same genotype/treatment and concentration of flg22 in light, according to a Student’s t-test (p<0.05). All experiments were repeated at least three times with similar results. Values are relative to Col-0 (A, B and D) or mock-treated seedlings (C) (set to 100). Absolute values of these experiments are shown in Figure 4—figure supplement 3. (E) Schematic model depicting the BZR1-mediated inhibition of PTI. Upon BR- and DELLA-dependent activation, BZR1 induces the expression of negative regulators of PTI, such as WRKY11, WRKY15, WRKY18, or HBI1. In addition, BZR1 also inhibits the expression of immune genes, acting cooperatively with WRKY40 and possibly other WRKYs. Ultimately, the BZR1-mediated changes in transcription would lead to the suppression of PTI signaling. The PTI signaling pathway is shadowed in violet; the BR signaling pathway is shadowed in green.

DOI: http://dx.doi.org/10.7554/eLife.00983.018

Seedling growth inhibition of 10-day-old Col-0 seedlings grown on medium supplemented or not with (A) BL (1 μM), paclobutrazol (PAC; 1 μM), BL+PAC (1 μM + 1 μM) and PAC+GA (1 μM + 1 μM), or (B) uniconazole (Uni; 100 μM), BL (1 μM) and Uni+BL (100 μM + 1 μM) induced by increasing concentrations of flg22 in light or dark. (C) Seedling growth inhibition of 10-day-old Ler and ga1-3 seedlings grown on medium supplemented or not with BL (1 μM). Bars represent SE of n = 8. Asterisks indicate a statistically significant difference compared to Col-0 in the same condition (light or dark and same concentration of flg22), according to a Student's t-test (p<0.05); ‘a’ indicates a statistically significant difference compared to the same genotype/treatment and concentration of flg22 in light, according to a Student's t-test (p<0.05). Values are relative to mock-treated seedlings (set to 100). All experiments were repeated at least twice with similar results.

DOI: http://dx.doi.org/10.7554/eLife.00983.019

Representative seedlings of the seedling growth inhibition experiments depicted in: (A) Figure 4A; (B) Figure 4—figure supplement 1A; (C) Figure 4–figure supplement 1B; (D) Figure 4D. Scale bar, 1 cm.

DOI: http://dx.doi.org/10.7554/eLife.00983.020

(A) Seedling growth inhibition of 10-day-old Col-0 or BES1 seedlings induced by increasing concentrations of flg22. (B) Absolute fresh weight values of the seedling growth inhibition assay depicted in Figure 4B, dark. (C) Absolute fresh weight values of the seedling growth inhibition assay depicted in Figure 4A. (D) Absolute fresh weight values of the seedling growth inhibition assay depicted in Figure 4C. (E) Absolute fresh weight values of the seedling growth inhibition assay depicted in Figure 4—figure supplement 1A. (F) Absolute fresh weight values of the seedling growth inhibition assay depicted in Figure 4—figure supplement 1B. (G) Absolute fresh weight values of the seedling growth inhibition assay depicted in Figure 4D. Error bars represent SE as indicated in Figure 4, Figure 4—figure supplement 1.

DOI: http://dx.doi.org/10.7554/eLife.00983.021

Figure 4—figure supplement 2.

Phenotype of the light- or dark-grown seedlings used in the seedling growth inhibition assays (Figure 4 and Figure 4—figure supplement 1).

Representative seedlings of the seedling growth inhibition experiments depicted in: (A) Figure 4A; (B) Figure 4—figure supplement 1A; (C) Figure 4–figure supplement 1B; (D) Figure 4D. Scale bar, 1 cm.

DOI: http://dx.doi.org/10.7554/eLife.00983.020

Figure 4—figure supplement 3.

Absolute fresh weight values of seedling growth inhibition assays.

(A) Seedling growth inhibition of 10-day-old Col-0 or BES1 seedlings induced by increasing concentrations of flg22. (B) Absolute fresh weight values of the seedling growth inhibition assay depicted in Figure 4B, dark. (C) Absolute fresh weight values of the seedling growth inhibition assay depicted in Figure 4A. (D) Absolute fresh weight values of the seedling growth inhibition assay depicted in Figure 4C. (E) Absolute fresh weight values of the seedling growth inhibition assay depicted in Figure 4—figure supplement 1A. (F) Absolute fresh weight values of the seedling growth inhibition assay depicted in Figure 4—figure supplement 1B. (G) Absolute fresh weight values of the seedling growth inhibition assay depicted in Figure 4D. Error bars represent SE as indicated in Figure 4, Figure 4—figure supplement 1.

DOI: http://dx.doi.org/10.7554/eLife.00983.021

Figure 4—figure supplement 1.

The BR-mediated suppression of seedling growth inhibition in the dark requires GA synthesis.

Seedling growth inhibition of 10-day-old Col-0 seedlings grown on medium supplemented or not with (A) BL (1 μM), paclobutrazol (PAC; 1 μM), BL+PAC (1 μM + 1 μM) and PAC+GA (1 μM + 1 μM), or (B) uniconazole (Uni; 100 μM), BL (1 μM) and Uni+BL (100 μM + 1 μM) induced by increasing concentrations of flg22 in light or dark. (C) Seedling growth inhibition of 10-day-old Ler and ga1-3 seedlings grown on medium supplemented or not with BL (1 μM). Bars represent SE of n = 8. Asterisks indicate a statistically significant difference compared to Col-0 in the same condition (light or dark and same concentration of flg22), according to a Student's t-test (p<0.05); ‘a’ indicates a statistically significant difference compared to the same genotype/treatment and concentration of flg22 in light, according to a Student's t-test (p<0.05). Values are relative to mock-treated seedlings (set to 100). All experiments were repeated at least twice with similar results.

DOI: http://dx.doi.org/10.7554/eLife.00983.019

Previously, a unidirectional negative crosstalk between the growth-promoting hormone BR and PTI had been described (Albrecht et al., 2012; Belkhadir et al., 2012). In this work, we show that activation of one of two major BR-activated transcription factors, BZR1, is sufficient to suppress PTI, measured as PAMP-triggered ROS production, PAMP-triggered gene expression, SGI or induced resistance (Figures 1 and 2, Figure 1—figure supplement 3, Figure 2—figure supplement 1). Of note, another PTI output, MAPK activation, is not affected by activation of the BR pathway (Figure 2B, Figure 1—figure supplement 2, Figure 2—figure supplement 1B). BR treatment results in BZR1-dependent changes in the expression of defense-related genes, among which several members of the WRKY family of transcription factors can be found. Because the promoters of BR-regulated defense-related genes are enriched in the W-box motif (Table 4), BZR1-targeted WRKY transcription factors could be responsible for a secondary wave of transcription, ultimately leading to the suppression of PTI. In agreement with this idea, a subset of WRKYs induced by BR (WRKY11, WRKY15 and WRKY18) (Figure 3A) act as negative regulators of PAMP-triggered ROS, potentially by controlling the steady-state expression of genes encoding components required for this response. The over-representation of the W-box motif among the BZR1 targets (Table 7) raises the possibility that, additionally, WRKY transcription factors could also act together with BZR1 to cooperatively regulate gene expression. We found that WRKY40 associates with BZR1 directly or indirectly in planta (Figure 3C,D); in the absence of WRKY40, the BR-mediated suppression of PAMP-triggered ROS burst is partially impaired (Figure 3B). Therefore, WRKYs may play a dual role in the BZR1-mediated suppression of defense, as both co- and secondary regulators of defense gene expression. Given that the loss of BR-mediated suppression of PAMP-triggered ROS burst in the wrky40 mutant is only partial, BZR1 may interact with other members of the WRKY family, such as WRKY18 or WRKY60, to repress immunity.

Furthermore, we recently described that the bHLH transcription factor HBI1, which is a BRZ1 target (Sun et al., 2010; Bai et al., 2012a), negatively regulates PTI (Malinovsky et al., under revision). All together, these results illustrate that BZR1 controls the expression of transcription factors (e.g. WRKY11, WRKY15, WRKY18 and HBI1), which themselves might control the expression of PTI components (see model in Figure 4E) whose identities remain to be identified.

Plants need to finely regulate allocation of resources upon integration of environmental cues, both biotic and abiotic, in order to rapidly and readily adapt to changing conditions and ensure survival in a cost-efficient manner. Dark conditions impose an energetic limitation due to lack of photo-assimilates; in this situation, the restoration of normal photosynthesis by reaching light is an essential requirement to guarantee perpetuation, and as such must be given priority (Casal, 2013). We hypothesize that when plants face conditions that require rapid growth, such as when germinating in soil or when under a canopy, limited resources are invested in this developmental process at the expense of immunity in what must be a quantitative choice. Indeed, we show that etiolated seedlings do not arrest their growth in response to PAMPs as light-grown seedlings do, as measured by total fresh weight (Figure 4A–D). In addition, BR signaling, acting cooperatively with GA signaling, is required for the dark-induced suppression of this PTI response (Figure 4C, Figure 4—figure supplement 1), and activation of BZR1 is sufficient to exert this effect regardless of light conditions (Figure 4B). Although seedlings were used in these experiments due to technical reasons, BR also regulate growth at later developmental stages, so this phenomenon may be more general. Based on these findings, we propose a model in which BZR1 regulates the expression of defense genes, assisted by WRKY40 (and potentially other WRKYs), ultimately resulting in a quantitative suppression of immunity (Figure 4E). Because the activation status of BZR1 depends on BR, GA and light signaling, BZR1 would act as a molecular integrator of these inputs to effectively regulate the trade-off between growth and immunity.

Materials and methods

Plant materials and growth conditions

Col-0 plants were used as control. The transgenic lines BZR1Δ, bri1-5/BZR1Δ and BES1 (Gampala et al., 2007), BZR1 and BZR1-CFP (Ryu et al., 2007), 35S:BRI1-cit, BRI1p:BRI1-cit, 35S:DWF4 and BAK1-HA (Belkhadir et al., 2012) are published. The mutant lines Triple GSK3 mutant (Vert and Chory, 2006), bri1-5 (Noguchi et al., 1999), bri1-301 (Xu et al., 2008), bin2-1 (Peng et al., 2008), wrky11 (Journot-Catalino et al., 2006), wrky18, wrky53 and wrky70 (Wang et al., 2006) wrky27 (Mukhtar et al., 2008), wrky40 (Pandey et al., 2010) and ga1-3 (Navarro et al., 2008) are published. wrky15 mutant was identified in the ZIGIA population (Wisman et al., 1998a, 1998b); wrky48 and wrky57 are from the SALK collection (Alonso et al., 2003).

Arabidopsis plants and seedlings were grown as described in Albrecht et al. (2012).

Chemicals

Flg22 and elf18 peptides were purchased from Peptron, and chitin oligosaccharide from Yaizu Suisankagaku. epiBL was purchased from Xiamen Topusing Chemical. LiCl, bikinin, brassinazole and GA were purchased from Sigma (St Louis, MO, USA). Paclobutrazol was purchased from Duchefa (Haarlem, NL). Uniconazole was purchased from Sigma.

ROS assays

The measurement of ROS generation was performed as described in Albrecht et al. (2012). Leaf discs from five-week-old Arabidopsis plants were used in each experiment, as indicated in the figure legends. Total photon counts were measured over 40 min by using a high-resolution photon counting system (HRPCS218) (Photek, St Leonards on Sea, UK) coupled to an aspherical wide lens (Sigma Imaging, Welwyn Garden City, UK).

Protein extraction and IP experiments

Protein extraction and immunoprecipitation of Arabidopsis was performed as described in Schwessinger et al. (2011). Arabidopsis mesophyll protoplasts were prepared from 4 to 5-week-old plants, transfected with the indicated constructs and incubated for 16 hr prior to BL treatment. Protein extraction of N. benthamiana was performed as described in Schwessinger et al. (2011); immunoprecipitations were performed using the μMACS GFP Isolation Kit (Miltenyi Biotec, Church Lane Bisley, UK), following the manufacturer’s instructions. In N. benthamiana, BZR1-GFP was expressed from the pUb-cYFP-Dest vector (Grefen et al., 2010); WRKY40-HA and WRKY6-HA were expressed from the pAM-PAT vector (AY436765; GeneBank). In protoplasts, WRKY40-HA was expressed from the pGWB414 vector (Nakagawa et al., 2007); the construct to express BZR1-GFP has been described elsewhere (Ryu et al., 2007). In both cases, samples were treated with 1 μM epiBL solution for 1 hr prior to protein extraction.

MAP kinase activation assays

MAP kinase activation assays were performed as described in Schwessinger et al. (2011). Phospho-p44/42 MAPK (Erk1/2; Thr202/Tyr204) rabbit monoclonal antibodies (Cell Signaling Technologies, Hitchin, UK) were used according to the manufacturer’s protocol.

RNA isolation and qPCR assays

RNA isolation was performed from ten-day-old seedling following the protocol described in Onate-Sanchez and Vicente-Carbajosa (2008). First-strand cDNA synthesis was performed with the SuperScript III RNA transcriptase (Invitrogen, Paisley, UK) and oligo(dT) primer, according to the manufacturer’s instructions. For qPCR reactions, the reaction mixture consisted of cDNA first-strand template, primers (5 nmol each) and SYBR Green JumpStart Taq ReadyMix (Sigma). qPCR was performed in a BioRad CFX96 real-time system. UBQ10 was used as the internal control; expression in mock-treated Col-0 seedlings was used as the calibrator, with the expression level set to one. Relative expression was determined using the comparative Ct method (2-ΔΔCt). Each data point is the mean value of three experimental replicate determinations. Primers for At2g17740 are described in Albrecht et al. (2012); for NHL10 are described in Boudsocq et al. (2010); for LOX2 are described in Pandey et al. (2010); for UBQ10 (U-box) are described in Albrecht et al. (2012).

Seedling growth inhibition assay

Seedling growth inhibition assays were performed as described in Nekrasov et al. (2009). In brief, four-day-old Arabidopsis seedlings were grown in liquid Murashige–Skoog medium containing 1% sucrose supplemented with flg22 and the appropriate chemicals. Seedlings were weighed between 6 and 10 days after treatment.

Bacterial infections

Induced resistance assays were performed as described previously (Zipfel et al., 2004). In brief, water or a 1 μM flg22 solution were infiltrated with a needleless syringe into leaves of four-week-old Arabidopsis plants 24 hr prior to bacterial inoculation (Pto DC3000, 105 cfu/ml). Bacterial growth was determined 2 days after inoculation by plating serial dilutions of leaf extracts.

Spray inoculation of P. syringae pv. cilantro (Pci) 0788-9 was performed as described in Schwessinger et al. (2011). In brief, bacteria were grown in an overnight culture in LB medium, cells were harvested by centrifugation, and pellets were re-suspended to OD600 = 0.02 in 10 mM MgCl2 with 0.04% Silwet L-77. Bacterial suspensions were sprayed onto leaf surfaces and plants were kept uncovered. Bacterial growth was determined 3 days after inoculation by plating serial dilutions of leaf extracts.

Meta-analysis

Functional enrichment analyses of the Biological Process ontology were performed using VirtualPlant (Katari et al., 2010). Functional enrichment analysis of the Molecular Function ontology was performed using the Classification SuperViewer tool of the Bio-Array Resource for Arabidopsis Functional Genomics, BAR (Toufighi et al., 2005). Promoter analyses were performed using Athena (O’Connor et al., 2005).

eLife posts the editorial decision letter and author response on a selection of the published articles (subject to the approval of the authors). An edited version of the letter sent to the authors after peer review is shown, indicating the substantive concerns or comments; minor concerns are not usually shown. Reviewers have the opportunity to discuss the decision before the letter is sent (see review process). Similarly, the author response typically shows only responses to the major concerns raised by the reviewers.

Thank you for sending your work entitled “The transcriptional regulator BZR1 mediates trade-off between plant innate immunity and growth” for consideration at eLife. Your article has been favorably evaluated by a Senior editor, Detlef Weigel, and 3 reviewers, one of whom, Thorsten Nürnberger, is a member of our Board of Reviewing Editors.

The Reviewing editor and the other reviewers discussed their comments before we reached this decision, and the Reviewing editor has assembled the following comments to help you prepare a revised submission.

The manuscript reports on a molecular mechanism underlying opposing plant physiological programs, such as growth and immunity. This is an important yet incompletely understood problem in plant biology. The authors have convincingly demonstrated that two factors, BZR1 and WRKY40, play a crucial role in brassinolide-mediated suppression of immunity. The authors should, however, respond to the referees’ issues listed below prior to final acceptance of their work:

1) BL treatment reverts PAMP-triggered SGI only partially, but never fully (see Figure 4). Likewise, constitutively active BZR also results in partial SGI complementation only, suggesting that other factors than BZR (and brassinolide) are implicated in regulation of this trade-off. Thus, calling BZR a master regulator is not fully justified. Similarly, there is the caveat that seedling growth might not always be regulated in the same way as overall vegetative growth. The authors may therefore provide more adequate statements throughout the text.

2) The synergistic effect of GA and BL (shown in Figure 4 and its figure supplements) is not fully convincing. In fact, in a few cases restoration of SGI by combined hormone treatment seems to be even smaller than that observed with BL alone. As PAC inhibitor specificity is not really clear, it is suggested that the authors either analyze appropriate BL/GA-deficient mutants for a synergistic effect or, alternatively, opt to omit the GA part, which would weaken an otherwise very strong paper.

3) The long time of pre-incubation with BL (8 hrs) before flg22 treatment raises some concern as it is expected that the system has already shifted to a new steady state equilibrium. Here, the authors have to show that the brassinosteroid signaling is still active at this point and has not been reset through feedbacks. For instance, the authors could check the BZR phosphorylation status in a time course until flg22 challenge, or nuclear target gene transcription.

4) The authors state that PTI suppression might be particularly important during rapid growth phases, such as de-etiolation. Somewhat surprising here is that they then use fresh weight to measure growth. Given that brassinosteroids mainly regulate cell elongation and considering that during seedling establishment, cell expansion is the by far dominant growth mechanism, it is surprising that the authors have not considered determining hypocotyl elongation. This is an even more rapid growth phase, as compared to the authors’ fresh weight measurements at 10 days after germination. As such experiments can be rapidly conducted it should be tested experimentally whether such data match with those obtained by fresh weight measurements.

5) The manuscript would substantially benefit if the authors could provide more direct evidence that BZR1 and WRKY40 indeed cooperate in gene regulation. For instance, the authors could conduct relatively straightforward protoplast transfection experiments with BZR1 and WRKY40 alone or together as effectors, and a LOX2 promoter construct as a reporter. Such an experiment would strongly support the finding of a biologically relevant BZR1-WRKY40 interaction. Alternatively, chromatin-IP assays would be suited to prove that both WRKY40 and BZR1 are associated with the LOX2 promoter.

6) The finding that WRKY40 participates in the PTI inhibition is important. While BZR1 activation leads to reduced PTI responses and disease resistance to bacteria, it is not clear if WRKY40 also negatively impact disease resistance. An flg22-protection assay should be performed here.

1) BL treatment reverts PAMP-triggered SGI only partially, but never fully (see ). Likewise, constitutively active BZR also results in partial SGI complementation only, suggesting that other factors than BZR (and brassinolide) are implicated in regulation of this trade-off. Thus, calling BZR a master regulator is not fully justified. Similarly, there is the caveat that seedling growth might not always be regulated in the same way as overall vegetative growth. The authors may therefore provide more adequate statements throughout the text.

We have now amended the text to take into account these remarks.

2) The synergistic effect of GA and BL (shown in and its figure supplements) is not fully convincing. In fact, in a few cases restoration of SGI by combined hormone treatment seems to be even smaller than that observed with BL alone. As PAC inhibitor specificity is not really clear, it is suggested that the authors either analyze appropriate BL/GA-deficient mutants for a synergistic effect or, alternatively, opt to omit the GA part, which would weaken an otherwise very strong paper.

Figure 4C shows that combined treatment of BL+GA in the light has a more potent effect than BL or GA alone. In the dark, SGI is already partially suppressed, and this effect remains after exogenous application of the hormones. Thus, we do not fully understand the comment about the additive effect between the hormones being unclear. We have now added statistical analysis of Figure 4C to make this point clearer.

Regarding the specificity of PAC, we have now added results (new Figure 4–figure supplement 1B) obtained after treatment with another GA biosynthesis inhibitor, uniconazole, which nicely corroborate those previously obtained with PAC. Furthermore, we report that the BL-induced inhibition of flg22-triggered SGI is hindered in the GA biosynthetic mutant ga1-3 (new Figure 4–figure supplement 1C), further confirming that the effect imposed by BL requires GA.

3) The long time of pre-incubation with BL (8 hrs) before flg22 treatment raises some concern as it is expected that the system has already shifted to a new steady state equilibrium. Here, the authors have to show that the brassinosteroid signaling is still active at this point and has not been reset through feedbacks. For instance, the authors could check the BZR phosphorylation status in a time course until flg22 challenge, or nuclear target gene transcription.

Most results presented in this manuscript were obtained using transgenic or mutant lines with constitutive or increased BR responses, or during constant incubation with BL, in the case of seedling growth inhibition assays (e.g., Figure 4). In Albrecht et al. (2012), we also showed that co-treatment with BL inhibited flg22-induced gene expression. In the current manuscript, we only used pre-treatment in Figure 3B (8h) and Figure 1–figure supplement 2A (90 min or 5h). Nevertheless, to address the reviewers’ concern, we have tested whether BR signaling was still active after long treatments by looking at the phosphorylation status of BZR1, and found that BR signaling is still active even after an 8-hour BL treatment (this experiment has been repeated three times with similar results) (see Author response image 1 below).

Author response image 1.

BL-induced dephosphorylation of BZR1 is maintained after an 8-hour BL treatment. Ten-day-old transgenic Arabidopsis seedlings expressing BZR1-YFP were treated with 1μM BL or mock solution for the indicated time. Proteins were detected using an anti-GFP antibody conjugated to HRP.

4) The authors state that PTI suppression might be particularly important during rapid growth phases, such as de-etiolation. Somewhat surprising here is that they then use fresh weight to measure growth. Given that brassinosteroids mainly regulate cell elongation and considering that during seedling establishment, cell expansion is the by far dominant growth mechanism, it is surprising that the authors have not considered determining hypocotyl elongation. This is an even more rapid growth phase, as compared to the authors’ fresh weight measurements at 10 days after germination. As such experiments can be rapidly conducted it should be tested experimentally whether such data match with those obtained by fresh weight measurements.

We measured hypocotyl length upon flg22 treatment in light-grown seedlings and did not find any impact) (see Author response image 2 below). This is different to what we observed when measuring total fresh weight, and most likely reflects the fact that hypocotyls are already extremely short in Arabidopsis seedlings grown in light. In contrast, hypocotyls elongate greatly during etiolation; yet, no impact of flg22 treatment could be observed (see Author response image 2 below), which is entirely consistent with the lack of flg22 responsiveness in dark-grown seedlings reported already in this study. Therefore, hypocotyl length measurement does not appear as a suitable assay to compare the impact of BR regulation on PTI between light and dark conditions, which is one of the major aims of our study.

Author response image 2.

Hypocotyl length of light- or dark-grown Arabidopsis seedlings in increasing concentrations of flg22. Seedlings were grown in MS plates for four days, then transferred to liquid MS supplemented with flg22 at the indicated concentrations. Hypocotyl length was measured four days later. Bars represent SE with n=8.

5) The manuscript would substantially benefit if the authors could provide more direct evidence that BZR1 and WRKY40 indeed cooperate in gene regulation. For instance, the authors could conduct relatively straightforward protoplast transfection experiments with BZR1 and WRKY40 alone or together as effectors, and a LOX2 promoter construct as a reporter. Such an experiment would strongly support the finding of a biologically relevant BZR1-WRKY40 interaction. Alternatively, chromatin-IP assays would be suited to prove that both WRKY40 and BZR1 are associated with the LOX2 promoter.

We now provide additional results to support the reported BZR1-WRKY40 protein interaction (Figure 3C–E). However, while we could previously show that LOX2 transcript levels were reduced by BL treatment in a WRKY40-dependent manner in seedlings (Figure 3D in the previous version) (a result that is reproducible), we then encountered difficulties studing LOX2 gene regulation in other systems (e.g., protoplasts or N. benthamiana), systems that would be required to perform the suggested experiments in the allocated time. Furthermore, we requested previously published materials, such as LOX2::GUS and LOX2::LUC constructs or transgenic lines; but, unfortunately, these tools either are not available anymore or can no longer be used due to severe silencing of both reporter constructs. While the Kombrink lab is currently generating these tools again, we also considered making a LOX2::LUC construct ourselves. However, the expression of this reporter transgene has been previously reported to be quasi undetectable in the absence of exogenous MeJA treatment (Jensen et al., Plant J 2002), which would make the suggested experiment (i.e., testing whether BZR1+WRKY40 inhibit LOX2 expression more potently than BZR1 or WRKY40 alone) extremely technically challenging. For these different reasons, we have decided to omit the results on LOX2 expression from the revised manuscript. Nevertheless, the results provided still convincingly show that BZR1 acts together with WRKY40 both genetically (Figure 3B) and biochemically (Figure 3C–E) to regulate the BR-mediated inhibition of PTI. The exact mechanisms underlying the latter regulation will be within the scope of future studies.

6) The finding that WRKY40 participates in the PTI inhibition is important. While BZR1 activation leads to reduced PTI responses and disease resistance to bacteria, it is not clear if WRKY40 also negatively impact disease resistance. An flg22-protection assay should be performed here.

Our previous data showed that wrky40 plants were more resistant to Pto DC3000 (Figure 4–figure supplement 1B), indicating that WRKY40 is a negative regulator of immunity. This is consistent with other reports (Xu et al., Plant Cell 2006; Pandey et al., Plant J 2010; Schon et al., MPMI 2013; Brotman et al., PLOS Pathog 2013; Schweizer et al., Front Plant Sci 2013). When we measured flg22-induced resistance, we observed that the flg22 treatment could not further decrease Pto DC3000 titers in wrky40 plants (Author response image 3 below).

Author response image 3.

Flg22-induced resistance to P. syringae pv. tomato DC3000 in Col-0 and wrky40 plants. Plants were pre-treated with 1 μM flg22 or water 24 hours prior to bacterial infiltration. Results are the average of three independent biological replicates; bars represent SE.