Posttranslational Modifications of the Master Transcriptional Regulator NPR1 Enable Dynamic but Tight Control of Plant Immune Responses

Abstract

NPR1, a master regulator of basal and systemic acquired resistance in plants, confers immunity through a transcriptional cascade, which includes transcription activators (e.g., TGA3) and repressors (e.g., WRKY70), leading to the massive induction of antimicrobial genes. How this single protein orchestrates genome-wide transcriptional reprogramming in response to immune stimulus remains a major question. Paradoxically, while NPR1 is essential for defense gene induction, its turnover appears to be required for this function, suggesting that NPR1 activity and degradation are dynamically regulated. Here we show that sumoylation of NPR1 by SUMO3 activates defense gene expression by switching NPR1's association with the WRKY transcription repressors to TGA transcription activators. Sumoylation also triggers NPR1 degradation, rendering the immune induction transient. SUMO modification of NPR1 is inhibited by phosphorylation at Ser55/Ser59, which keeps NPR1 stable and quiescent. Thus, posttranslational modifications enable dynamic but tight and precise control of plant immune responses.

Figure 1. NPR1 sumoylation is induced by SA treatment

(A) Equal numbers of yeast cells carrying BD, or BD-NPR1, and AD or AD-SUMO proteins (SUMO1, SUMO2, SUMO3 and SUMO5) were spotted on SD-LW and SD-LWHA selective medium. AD, Gal4 activation domain; BD, Gal4 DNA-binding domain. (B) Alignment of SIMs from NPR1, USP25 (human ubiquitin specific peptidase 25) and BLM (Bloom syndrome, RecQ helicase-like). The SIM consensus [VIL]-[VIL]-x-[VIL] is underlined and the amino acids shaded in black match the consensus motif. (C) Yeast cells carrying BD, or BD-NPR1 (NPR1), npr1^sim1 (sim1), npr1^sim2 (sim2), or npr1^sim3 (sim3) mutants and AD or AD-SUMO3 were grown and tested as in (A). (D) Split luciferase assays. The NPR1, npr1^sim3 (sim3) and SUMO3 proteins were fused to either the C- or N-terminal half of luciferase (cLUC or nLUC), and transiently expressed in N. benthamiana. The luciferase activities were monitored by a CCD camera two days after infiltration. (E) E. coli sumoylation assay. Proteins were extracted from E. coli BL21 (C41) cells coexpressing E1 heterodimer (SAE1b and SAE2), E2 (SCE1a), the mature SUMO3(SUMO3ΔC) and either NPR1-GST (NPR1) or npr1^sim3-GST (sim3), purified using GST-magnetic beads and analyzed by western blot using α-GST and α-SUMO3 antibodies. GG, wild-type SUMO3ΔC; AA, mutant SUMO3ΔC with the di-glycine (GG) required for conjugation replaced by alanines. CBB, Coomassie Brilliant Blue protein stain. (F) Co-IP from yeast cells expressing BD-cMyc and AD-HA-SUMO3, BD-cMyc-NPR1 and AD-HA, or BD-cMyc-NPR1 and AD-HA-SUMO3. Equal amounts of cell culture were untreated (-) or treated (+) with 100 μM MG115 and incubated for 3 hr. Proteins were purified with cMyc-magnetic beads and analyzed by western blot using α-SUMO3 and α-NPR1 antibodies. (G) In planta sumoylation of NPR1. IP of NPR1-GFP and npr1^sim3-GFP (sim3-GFP) was conducted using total protein extract (Input) from leaves treated with water (-) or (+) 0.5 mM SA for 6 hr. Samples were adjusted for equal amounts of total protein and IP samples were analyzed by western blotting (WB) using α-GFP and α-SUMO3 antibodies. See also Figure S1.

Figure 2. Sumoylation Facilitates Proteasome-Mediated Degradation of NPR1

(A) Protein degradation assay in yeast. Cells were expressing BD-cMyc-NPR1 (NPR1) or BD-cMyc-npr1^sim mutants (sim1, sim2, and sim3) and AD-HA-SUMO3 (SUMO3). Cells were treated with Cycloheximide (100μg/ml) for 1.5 hr. Proteins were extracted and analyzed by western blotting using an α-cMyc antibody. Star indicates a loading control. (B) Interaction of BD-cMyc-NPR1 (NPR1) and AD-HA-SUMO3 (SUMO3) or AD-HA-sumo3-AA (sumo3-AA) mutant in yeast. (C) Degradation of NPR1 in yeast. Yeast cells were expressing BD-cMyc-NPR1 (NPR1) and AD-HA-SUMO3 (SUMO3) or the AD-HA-sumo3-AA (sumo3-AA) mutant. Total protein was analyzed as in (A). (D) In vitro degradation of NPR1-GFP and npr1^sim3-GFP (sim3-GFP). Protein extracts from 35S:NPR1-GFP (in npr1-2) (NPR1-GFP), and two different lines of 35S:npr1^sim3-GFP (sim3-GFP #3 and sim3-GFP #12; in npr1-2) plants were incubated at room temperature for the time points indicated. The proteasome inhibitor MG115 (50 μM) was used. Proteins were analyzed by western blotting using an α-GFP antibody. CBB, Coomassie Brilliant Blue protein stain. (E) Confocal micrographs of transgenic Arabidopsis expressing 35S:NPR1-GFP (NPR1-GFP) or 35S:npr1^sim3-GFP (sim3-GFP). Arrow indicates nucleus. Bars = 10 μm. (F) Confocal micrographs of N. benthamiana co-expressing free mCherry and 35S:NPR1-GFP (NPR1-GFP) or 35S:npr1^sim3-GFP (sim3-GFP) 24 hr after Agrobacterium infiltration. Close-up images show nuclear bodies. Bars = 25 μm. See also Figure S2.

Figure 3. Phosphorylation of IκB-like Sequences Ser11/Ser15 and Ser55/Ser59 Differentially Influences NPR1 Sumoylation and Protein Stability

(A) Sequence alignments of IκB-like sequences. The identical amino acids in the IκB-like sites are shaded black, conserved amino acids are shaded in grey and phosphorylatable serines are marked by *. (B) Interactions among BD-cMyc-NPR1 (NPR1) or BD-cMyc-npr1^S11/15A (S11/15A), BD-cMyc-npr1^S11/15D (S11/15D), BD-cMyc-npr1^S55/59A (S55/59A), BD-cMyc-npr1^S55/59D (S55/59D) mutants and AD-HA-SUMO3 in yeast. Equal numbers of cells were spotted on SD-LW and SD-LWHA plates. (C) Split luciferase assays. The NPR1 or npr1-phosphomimic mutants and SUMO3 proteins were fused to the N- or C-terminal half of luciferase (nLUC or cLUC), and transiently expressed in N. benthamiana. The luciferase activities were monitored by a CCD camera two days after infiltration. (D) E. coli sumoylation assay. Proteins were extracted from E. coli BL21 (C41) cells coexpressing E1 heterodimer (SAE1b and SAE2), E2 (SCE1a), the mature SUMO3 (SUMO3ΔC) and either NPR1-GST (NPR1), npr1^S11/15D-GST (S11/15D) or npr1^S55/59D-GST (S55/59D). Proteins were purified using GST-magnetic beads and analyzed by western blot using α-GST and α-SUMO3 antibodies. GG, wild-type SUMO3ΔC; AA, mutant SUMO3ΔC with the di-glycine (GG) required for conjugation replaced by alanines. CBB, Coomassie Brilliant Blue protein stain. (E) Degradation of NPR1 and npr1 mutants in yeast. Total protein was extracted from equal amounts of cell culture and analyzed by western blotting using an α-cMyc antibody. CBB, Coomassie Brilliant Blue protein stain. (F) In vitro degradation assay. Protein extracts from 35S:NPR1-GFP (NPR1), 35S:npr1^S11/15A-GFP (S11/15A), 35S:npr1^S11/15D-GFP (S11/15D), 35S:npr1^S55/59A-GFP (S55/59A), 35S:npr1^S55/59D-GFP (S55/59D) were incubated at room temperature for the time points indicated. The proteasome inhibitor MG115 (50 μM) was used. Proteins were analyzed by western blotting using an α-GFP antibody. (G) Degradation assay. Yeast cells carrying BD-cMyc-NPR1 (NPR1) or BD-cMyc-npr1^S11/15A (S11/15A), BD-cMyc-npr1^S11/15D (S11/15D), BD-cMyc-npr1^S55/59A (S55/59A), BD-cMyc-npr1^S55/59D (S55/59D) mutants and AD-HA-SUMO3 (SUMO3) or AD-HA-sumo3-AA (sumo3-AA) were grown and total protein was analyzed as in (E). (H) Confocal micrographs of transgenic Arabidopsis 35S:npr1^S11/15A-GFP (S11/15A-GFP), 35S:npr1^S11/15D-GFP (S11/15D-GFP), 35S:npr1^S55/59A-GFP (S55/59A-GFP), 35S:npr1^S55/59D-GFP (S55/59D-GFP). Arrow indicates nucleus. Bars = 10 μm. (I) Confocal micrographs of N. benthamiana co-expressing free mCherry and 35S:NPR1-GFP (NPR1-GFP) or 35S:npr1^S55/59D-GFP (S55/59D-GFP) 24 hr after Agrobacterium infiltration. Close-up images show nuclear bodies. Bars = 25 μm. See also Figure S3.

Figure 4. NPR1 Interaction with SUMO3 Is Required for and Dominant over Phosphorylation at Ser11/Ser15

(A) In planta phosphorylation of Ser11/Ser15. Total protein was extracted from seedlings expressing 35S:NPR1-GFP (NPR1), 35S:npr1^S11/15A-GFP (S11/15A), 35S:npr1^S55/59A-GFP (S55/59A), 35S:npr1^S55/59D-GFP (S55/59D), 35S:npr1^sim3-GFP (sim3) treated with water (-) or (+) 0.3 mM SA for 8 hr. Proteins were analyzed by western blotting using α-GFP and α-pS11/15 phospho-specific antibodies. CBB, Coomassie Brilliant Blue protein stain. (B) Interaction of BD-cMyc-NPR1 (NPR1), BD-cMyc-npr1^sim3 (sim3), BD-cMyc-npr1^S11/15D (S11/15D) or BD-cMyc-npr1^S11/15D_sim3 (S11/15D_sim3) and AD-HA-SUMO3 in yeast. Equal numbers of cells were spotted on SD-LW and SD-LWHA plates. (C) Split luciferase assay. The NPR1, npr1^sim3 (sim3), npr1^S11/15D (S11/15D), or npr1^S11/15D_sim3 (S11/15D_sim3) and SUMO3 proteins were fused to the N- or C-terminal half of luciferase (nLUC or cLUC) and transiently expressed in N. benthamiana. The luciferase activities were monitored by a CCD camera two days after infiltration. (D) Degradation assay. Yeast total protein was extracted from equal amounts of cell culture as described in (B), after growth overnight in SD-LW liquid media, analyzed by SDS-PAGE and western blotting using an α-cMyc antibody. Star indicates a nonspecific protein used as a loading control. (E) In vitro degradation assay. Protein extracts from 35S:npr1^S11/15D-GFP (S11/15D-GFP) and 35S:npr1^S11/15D_sim3-GFP (S11/15D_sim3-GFP) were incubated at room temperature for the time points indicated. The proteasome inhibitor MG115 (50 μM) was used. Proteins were analyzed by western blotting using an α-GFP antibody. (F) Confocal micrographs of transgenic Arabidopsis expressing 35S:npr1^S11/15D-GFP (S11/15D-GFP) and 35S:npr1^S11/15D_sim3-GFP (S11/15D_sim3-GFP). Arrow indicates nucleus. Bars = 10 μm.

Figure 5. Sumoylation of NPR1 Determines Its Interactions with Partner Proteins

(A) Interaction of BD-NPR3 (NPR3) or BD-NPR4 (NPR4), and AD-NPR1 (NPR1), AD-npr1^sim3 (sim3), AD-npr1^S11/15D (S11/15D) or AD-npr1^S11/15D_sim3 (S11/15D_sim3) in yeast. Equal numbers of cells were spotted on SD-LW and SD-LWH plates containing 3 mM 3-AT with or without 100 μM SA. (B) Interaction of BD-NPR3 (NPR3) or BD-NPR4 (NPR4), and AD-NPR1 (NPR1) or AD-npr1^S11/15A (S11/15A), AD-npr1^S11/15D (S11/15D), AD-npr1^S55/59A (S55/59A), AD-npr1^S55/59D (S55/59D) in yeast. Cultures were grown and analyzed as in (A). (C) Interaction of BD-NPR1 (NPR1) or BD-npr1^sim3 (sim3) and AD-TGA3 (TGA3) or AD-WRKY70 (WRKY70) in yeast. Equal numbers of cells were spotted on SD-LW and SD-LWHA plates. (D) Interaction of BD-NPR1 (NPR1), BD-npr1^S11/15A (S11/15A), BD-npr1^S11/15D (S11/15D), BD-npr1^S55/59A (S55/59A), BD-npr1^S55/59D (S55/59D), and AD-TGA3 (TGA3) or AD-WRKY70 (WRKY70) in yeast. Cultures were analyzed as in (C). (E) In vitro pull down assay. Equal amounts of GST-tagged NPR1 and npr1^sim3 proteins produced using the E. coli sumoylation system were mixed with in vitro synthesized HA-tagged TGA3 or WRKY70. The Co-IP was performed using HA-magnetic beads and the proteins were analyzed western blotting using an α-GST antibody (upper panel), or the Co-IP was performed using GST-magnetic beads and the proteins were analyzed by western blotting using an α-HA antibody (lower panel). CBB, Coomassie Brilliant Blue protein stain. (F) ChIP assay was performed using 35S:NPR1-GFP (NPR1) and 35S:npr1^sim3-GFP (sim3). Plants were untreated (-) or treated (+) with 1 mM SA for 16 hr. Upper panel: diagram of the PR1 gene with the analyzed cis analyzed cis elements (as-1 elements and W-boxes) and the coding region (cds) highlighted by short horizontal lines 1, 2, and 3, respectively. The fold enrichments of untreated and SA-treated samples after ChIP were determined through qPCR and calculated against input. The error bars represent ± SEM (n = 3). The experiment was performed twice with similar results. See also Figures S4 and S5.

Figure 6. Phosphorylation at Ser55/Ser59 and Sumoylation of NPR1 Are Required for Safe Storage and Transient Activation of NPR1-Mediated Defense

(A) Three-week-old 35S:NPR1-GFP (in npr1-2) (NPR1), 35S:npr1^sim3-GFP (in npr1-2) (sim3), and npr1-2 plants were inoculated with Psm ES4326 (OD_600nm = 0.0001). Growth of Psm was determined at 0 and 3 days after infection. Error bars represent 95% confidence intervals, n = 8. cfu, colony-forming units. dpi, days post inoculation. This experiment was repeated three times with similar results. (B) Infection of 35S:NPR1-GFP (in npr1-2) (NPR1), 35S:npr1^S55/59D-GFP (in npr1-2) (S55/59D), and npr1-2 mutant plants was carried out as in (A). (C) In planta phosphorylation of Ser55/Ser59. Seedlings expressing 35S:NPR1-GFP, 35S:npr1^S11/15A-GFP (S11/15A), 35S:npr1^S55/59A-GFP (S55/59A), and the npr1-2 mutant were treated with water (-) or (+) 0.3 mM SA and 50 μM MG115 for 4 or 6 hr. Protein extracts were analyzed by western blotting using α-GFP and α-pS55/59 phospho-specific antibodies. Signal intensities were measured using ImageJ software and the ratios of phos-S55/59 to NPR1-GFP are indicated. Extracts from seedlings expressing GFP-tagged npr1^S11/15A, npr1^S55/59A, and npr1-2 treated with water for 4 hr were included as control samples for antibody specificity. CBB, Coomassie Brilliant Blue protein stain. (D) Gene expression analysis. RNA was extracted from 35S:NPR1-GFP (NPR1), 35S:npr1^S55/59A-GFP (S55/59A) and npr1-2 plants. The expression of PR1 and PR2 was analyzed using qPCR and normalized against ubiquitin 5 (UBQ5). Error bars represent SD (n = 3). (E) Photograph of three-week-old npr1-2, 35S:NPR1-GFP (NPR1), 35S:npr1^S55/59A-GFP (S55/59A), 35S:npr1^S55/59D-GFP (S55/59D), 35S:npr1^sim3 (sim3), 35S:npr1^S11/15A (S11/15A), 35S:npr1^S11/15D (S11/15D) and 35S:npr1^S11/15D_sim3 (S11/15D_sim3) plants. (F) Gene expression analysis. RNA was extracted from three-week-old 35S:NPR1-GFP (NPR1), 35S:npr1^sim3-GFP (sim3) and npr1-2 plants treated with 1 mM SA. Tissue samples were collected during a time course after SA treatment. The expression of PR1 and PR2 was analyzed as in (D). (G) Three-week-old 35S:NPR1-GFP (NPR1), 35S:npr1^sim3-GFP (sim3) and npr1-2 plants were treated without (-) or with (+) 1 mM SA and inoculated 24 hr later with Psm ES4326 (OD_600nm =0.001). Growth of Psm was determined three days after infection. Error bars represent 95%confidence intervals, n = 8. cfu, colony-forming units. dpi, days post inoculation. Statistical analysis was performed using two-way ANOVA, ** p-value < 0.005, *** p -value < 0.0005.This experiment was carried out three times with similar results. (H) Three-week-old 35S:NPR1-GFP (NPR1), 35S:npr1^S55/59D-GFP (S55/59D) and npr1-2 plants were treated without (-) or with (+) 1 mM SA and inoculated 24 hr later with Psm ES4326 (OD_600nm= 0.001). Growth of Psm and statistical analysis were conducted as in (G). * p-value < 0.05, ** p-value < 0.005. (I) Gene expression analysis. RNA was extracted from three-week-old 35S:NPR1-GFP (in npr1-2) (NPR1), 35S:npr1^S55/59D-GFP (in npr1-2) (S55/59D) and npr1-2 plants treated with 1 mM SA for 24 hr. The expression of PR1 and PR2 was analyzed as in (F). See also Figure S6.

Figure 7. The Interplay between Sumoylation and Phosphorylation of NPR1 Controls Its Differential Transcription Cofactor Activity as a Master Immune Switch

SA accumulation promotes dephosphorylation of Ser55/Ser59 through an unknown mechanism and induces sumoylation of NPR1, resulting in dissociation from WRKY70 and inactivation of this repressor. Modification of NPR1 by SUMO3 is required for its phosphorylation at Ser11/Ser15 to form a signal amplification loop to generate more activated NPR1. This activated form of NPR1 interacts with the TGA3 transcription activator to induce PR1 gene expression. Subsequently, the modified NPR1 is ubiquitinated and targeted for degradation by the 26S proteasome mediated by interaction with NPR3 to ensure the transient nature of the immune induction. P: phosphorylation, S: sumoylation, as1: as-1 element, W: W-box