INDETERMINATE-DOMAIN 4 (IDD4) coordinates immune responses with plant-growth in Arabidopsis thaliana

Abstract

INDETERMINATE DOMAIN (IDD)/ BIRD proteins are a highly conserved plant-specific family of transcription factors which play multiple roles in plant development and physiology. Here, we show that mutation in IDD4/IMPERIAL EAGLE increases resistance to the hemi-biotrophic pathogen Pseudomonas syringae, indicating that IDD4 may act as a repressor of basal immune response and PAMP-triggered immunity. Furthermore, the idd4 mutant exhibits enhanced plant-growth indicating IDD4 as suppressor of growth and development. Transcriptome comparison of idd4 mutants and IDD4ox lines aligned to genome-wide IDD4 DNA-binding studies revealed major target genes related to defense and developmental-biological processes. IDD4 is a phospho-protein that interacts and becomes phosphorylated on two conserved sites by the MAP kinase MPK6. DNA-binding studies of IDD4 after flg22 treatment and with IDD4 phosphosite mutants show enhanced binding affinity to ID1 motif-containing promoters and its function as a transcriptional regulator. In contrast to the IDD4-phospho-dead mutant, the IDD4 phospho-mimicking mutant shows altered susceptibility to PstDC3000, salicylic acid levels and transcriptome reprogramming. In summary, we found that IDD4 regulates various hormonal pathways thereby coordinating growth and development with basal immunity.

Phosphorylation regulates the activity of INDETERMINATE-DOMAIN (IDD/BIRD) proteins in response to diverse environmental conditions

“…45 IDD4 is an integral part of the immune MAP kinase signaling pathway, and the MAP kinase MPK6 phosphorylates IDD4 as shown in in vitro kinase assays followed by LC-MS/MS analysis. 43 The MS/MS spectra for IDD4 revealed that MPK6 modifies the amino acid residue S-73 that has also been identified in several phosphoproteomic studies (Table 1). This phosphosite is conserved in all members of the IDD/BIRD family (Figure 1c).…”

“…6 To unravel the biological function of these phosphosites, phospho-modified IDD4 versions were generated by substituting S-73 and T-130 by either alanine to obtain a phospho-dead version (IDD4-AA) or aspartic acid to obtain a phospho-mimicking (IDD4-DD) variant thereby purporting the unphosphorylated and the phosphorylated IDD4 conformation, respectively. 43 Phosphosite-mutated IDD4 plants show an opposite response to pathogen attack and transcriptome reprogramming and underscore the function of IDD4 in regulating genes related to immunity and plant growth. Chromatinimmunoprecipitation studies revealed the predominate binding of IDD4 to the ID1 motif 46 in close proximity to the transcriptional start sequence of putative target genes.…”

“…Chromatinimmunoprecipitation studies revealed the predominate binding of IDD4 to the ID1 motif 46 in close proximity to the transcriptional start sequence of putative target genes. 43 Furthermore, the ID1 sequence was identified as main binding site of IDD1, 2, 3, 4, 5, 6, 7, 8, 10, 11 and 15 after DNA affinity purification sequencing 47 and in DNA-shift experiments. 4,13,48 In this context, the IDD4phospho-mimicking version shows a stronger affinity to the ID1 element and acts as a transcriptional activator of particular major downstream targets.…”

“…42 Chloroplast maturation and import, as well as chlorophyll biogenesis, seem to be targeted by IDD4, as shown by the binding to the promoter regions of genes involved in these processes. 43 Underpinned by their reduced area, width, height and circularity, the idd5 mutant is also compromised in chloroplast biogenesis and morphology. 44 The size and number of chloroplast starch granules are affected in the idd5 mutant confirming a function of IDD5 in starch accumulation and chloroplast biogenesis.…”

“…Recently, we reported that IDD4 acts as a plant growth suppressor and concomitantly as a repressor of basal immunity in response to the hemibiotrophic pathogen PstDC3000. 43 We showed that the knockout of IDD4 increases salicylic acid (SA) levels under untreated conditions and following pathogen perception. Interestingly, the expression of an IDD4 chimeric repressor construct in Arabidopsis wild-type plants (iddSRDX) confers improved basal resistance after hemibiotrophic infection and notably following infection by the necrotrophic fungus Botrytis cinerea.…”