PIF4 Coordinates Thermosensory Growth and Immunity in Arabidopsis

Abstract

Temperature is a key seasonal signal that shapes plant growth. Elevated ambient temperature accelerates growth and developmental transitions [1] while compromising plant defenses, leading to increased susceptibility [2, 3]. Suppression of immunity at elevated temperature is at the interface of trade-off between growth and defense [2, 4]. Climate change and the increase in average growth-season temperatures threaten biodiversity and food security [5, 6]. Despite its significance, the molecular mechanisms that link thermosensory growth and defense responses are not known. Here we show that PHYTOCHROME INTERACTING FACTOR 4 (PIF4)-mediated thermosensory growth and architecture adaptations are directly linked to suppression of immunity at elevated temperature. PIF4 positively regulates growth and development and negatively regulates immunity. We also show that natural variation of PIF4-mediated temperature response underlies variation in the balance between growth and defense among Arabidopsis natural strains. Importantly, we find that modulation of PIF4 function alters temperature sensitivity of defense. Perturbation of PIF4-mediated growth has resulted in temperature-resilient disease resistance. This study reveals a molecular link between thermosensory growth and immunity in plants. Elucidation of the molecular mechanisms that define environmental signal integration is key to the development of novel strategies for breeding temperature-resilient disease resistance in crops.

Keywords: PHYB; PIF4; adaptation; environmental signal integration; growth-defense trade-off; immunity; natural variation; temperature resilience; thermosensory growth.

Graphical abstract

Figure 1

PIF4 Is Essential for the Suppression of Immunity by Elevated Temperature Analysis of snc1-1 pif4-101 double mutants shows that temperature-induced suppression of snc1-1 phenotypes is PIF4 dependent. (A) Morphological phenotypes of 4-week-old plants grown at 22°C and 27°C under a short-day photoperiod. (B) Temperature-induced suppression of disease resistance of snc1-1 is PIF4 dependent. Resistance phenotype of the indicated genotypes to P. syringae pv. tomato (Pto) DC3000 (A₆₀₀ 0.02) at 22°C and 27°C (mean ± SD; n ≥ 8). ^∗∗p ≤ 0.01, ^∗∗∗p ≤ 0.001 (two-way ANOVA with Tukey’s multiple comparison test) compared to the corresponding Col-0 or as indicated; cfu, colony forming unit. (C and D) Gene expression analysis of defense marker genes PR1 (C) and PR5 (D) by qRT-PCR (mean ± SD of three biological replicates) from 3-week-old plants. ^∗∗p ≤ 0.01, ^∗∗∗p ≤ 0.001 (two-way ANOVA with Tukey’s multiple comparison test) significantly different from either Col-0 or between the indicated pairs. See also Figure S1.

Figure 2

PIF4 Is a Negative Regulator of Immunity (A and B) Downregulation of growth-related genes (A) and upregulation of defense genes (B) in pif4-101 as shown by qRT-PCR (mean ± SD of three biological replicates) from 1-week-old seedlings grown at 22°C under a short-day photoperiod. (C) Enrichment of defense GO terms in genes upregulated in 1-week-old pif4-101 (Dataset S1) seedlings grown at 22°C under a short-day photoperiod. (D) Increased disease resistance of pif4-101 and pifQ mutants to Pto DC3000 (A₆₀₀ 0.002; mean ± SD; n = 8). (E) Schematic representation of PIF4Δb, which lacks the basic domain. (F) Reduced hypocotyl elongation growth and rosette phenotype in two independent lines overexpressing PIF4Δb. (G) Overexpression of PIF4Δb leads to downregulation of growth (blue) and upregulation of defense (red) genes (data are the average of three biological replicates; see also Figure S1) in 22°C short-day-grown seedlings for 1 week. (H) Disease-resistance phenotype of 35S:PIF4Δb to Pto DC3000 (A₆₀₀ 0.02; mean ± SD; n ≥ 12). (I) PIF4-FLAG OE showing enhanced elongation growth. (J and K) Disease-resistance phenotype of PIF4-FLAG OE (J) and 35S:PHYB-FLAG (K) lines to Pto DC3000 (A₆₀₀ 0.02; mean ± SD; n ≥ 12). ^∗p ≤ 0.05, ^∗∗p ≤ 0.01, ^∗∗∗p ≤ 0.001 (Student’s t test) significantly different from Col-0. In (D), (H), (J), and (K), plants grown at 22°C under a short-day photoperiod for 4 weeks were used for the resistance assays. See also Figure S1.

Figure 3

Natural Variation of PIF4-Mediated Thermosensory Growth and Immunity (A–C) No-0 shows robust growth (A) and enhanced thermosensory flowering (B) and hypocotyl growth (C). (D and E) Gene expression of growth (D) and defense markers (E) in No-0 as shown by qRT-PCR (mean ± SD of three biological replicates). (F) GO analysis showing that genes downregulated in No-0 (see also Data S2) are enriched for defense GO terms. (G) No-0 shows increased susceptibility to Pto DC3000 (A₆₀₀ 0.02; mean ± SD; n ≥ 10). (H) Diagrammatic representation of PHYB^No-0 showing polymorphisms at the nucleotide and amino acid level. (I) Resistance to Pto DC3000 (A₆₀₀ 0.02) of F₂ segregants of a Col-0 × No-0 cross showing co-segregation of growth and defense phenotypes. Three-week-old plants grown in 22°C under a short-day photoperiod were used for the experiment. (J) Transgenic expression of PHYB:PHYB^Col-0 fully complements gene expression phenotypes of No-0 (mean of three biological replicates; see also Figure S2). (K) Disease-resistance phenotypes of two independent transgenic lines of No-0 complemented with PHYB:PHYB^Col-0. (L) Overexpression of PIF4Δb in No-0 leads to increased resistance to Pto DC3000 (A₆₀₀ 0.02) (two independent transgenic lines are shown). In (C)–(E) and (J), 1-week-old seedlings grown at 22°C under a short-day photoperiod were used for the experiments. In (G), (K), and (L), 4-week-old plants grown at 22°C under a short-day photoperiod were used for the resistance assays. ^∗p ≤ 0.05, ^∗∗p ≤ 0.01, ^∗∗∗p ≤ 0.001 (Student’s t test) significantly different from either Col-0 (in B–E and G) or No-0 (in I, K, and L). See also Figures S2 and S3.

Figure 4

PIF4-Mediated Thermosensory Signaling Modulates Temperature Sensitivity of Immunity (A) Increased PIF4 function (in PIF4-OE, phyb-9, and No-0) leads to increased susceptibility to Pto DC3000 (A₆₀₀ 0.002) at lower temperatures, phenocopying wild-type plants grown at higher temperature. (B) Two-way ANOVA analysis with Tukey’s multiple comparison test of data from (A); ^∗p ≤ 0.05, ^∗∗p ≤ 0.01, ^∗∗∗p ≤ 0.001; ns, not significant. (C) PHYB overexpression leads to temperature-resilient disease resistance to Pto DC3000 (A₆₀₀ 0.002) (mean ± SD; n = 8). ^∗p ≤ 0.05, ^∗∗p ≤ 0.01, ^∗∗∗p ≤ 0.001 (two-way ANOVA with Tukey’s multiple comparison test) significantly different from either Col-0 at respective temperatures or between the indicated pairs. See also Figure S4. (D) Model showing PIF4 function at the interface of growth and defense responses. While promoting thermosensory growth, PIF4 negatively regulates immunity. See also Figure S4.