Plant Immune Kinase MPK6 Targets Chromatin Protein DEK2 to Control Defense Genes

When a plant senses an attacking pathogen, one of its earliest moves inside the cell is to switch on a cascade of mitogen-activated protein kinases, or MAPKs, that phosphorylate downstream targets and rewire the cell’s program. A new study in Arabidopsis thaliana has now identified an unexpected target of this signaling machinery: a nuclear chromatin protein called DEK2. The work shows that the immune kinase MPK6 directly phosphorylates DEK2, and that this chromatin remodeler helps govern how defense-related genes are transcribed, with measurable consequences for how plants cope with both bacterial and fungal pathogens.

The researchers began with a large-scale quantitative phosphoproteomic screen of chromatin-associated proteins after treating plants with flg22, a well-characterized peptide derived from bacterial flagellin that is recognized by the FLS2 receptor and triggers pattern-triggered immunity. Among the proteins whose phosphorylation changed, one peptide from DEK2, modified on the serine at position 238, stood out. The modification was induced by flg22 in wild-type plants and in mpk3 and, to a lesser extent, mpk4 mutants, but it was absent in the mpk6 mutant background. That pattern pointed squarely at MPK6 as the kinase responsible for this phosphorylation event in vivo.

To confirm the connection, the team ran a series of biochemical tests. In vitro kinase assays with recombinant proteins, analyzed by mass spectrometry, showed that constitutively active MPK6 phosphorylates DEK2 at the same serine site identified in living plants. GST pull-down experiments demonstrated a physical interaction between the two proteins, and bimolecular fluorescence complementation in Nicotiana benthamiana leaf epidermal cells placed the DEK2-MPK6 interaction in the nucleoplasm. Together, these assays establish DEK2 as a genuine substrate of MPK6 rather than a coincidental hit from the phosphoproteomic screen.

To probe DEK2’s function, the researchers characterized two independent T-DNA insertion mutants, dek2-1 and dek2-2, both of which showed reduced full-length transcript levels and no obvious developmental defects at four weeks of age. When four-week-old plants were spray-inoculated with the hemibiotrophic bacterium Pseudomonas syringae pv. tomato DC3000, bacterial counts were similar across genotypes at three hours after infection, but by 48 hours both dek2 mutants carried significantly more bacteria in their leaves and displayed more severe disease symptoms than wild type. The loss of DEK2 therefore leaves plants more vulnerable to this bacterial pathogen once infection is established.

Paradoxically, several early immune readouts were enhanced rather than weakened in the mutant. The dek2-1 plants produced more flg22-triggered reactive oxygen species than wild type, and both mutants deposited more flg22-induced callose, another hallmark of pattern-triggered immunity. Yet MAPK activation in response to flg22 was compromised in both mutants. The picture that emerges is not a simple on-off switch: DEK2 appears to fine-tune multiple layers of the immune response, some of which are amplified in its absence while overall resistance to Pst DC3000 deteriorates.

Transcriptomics helped explain this complexity. RNA sequencing of 14-day-old seedlings, comparing dek2-1 with wild type under untreated conditions and 24 hours after treatment with a Pst DC3000 hrcC- strain defective in type III secretion, revealed 298 differentially expressed genes in unstressed plants, with 61.7 percent upregulated and 38.3 percent downregulated. The upregulated genes were enriched for defense, hormone and immune-response functions, while downregulated genes clustered around photosynthesis and energy metabolism. Under pathogen-associated stress, 254 genes were downregulated in the mutant and 131 upregulated, with clusters linked to defense responses, glucosinolate metabolism and hormone signaling. Many defense-related transcription factors, including MYBs, ERFs and bHLHs, appeared among the affected groups.

Hormone measurements reinforced the transcriptional story. Untreated dek2-1 plants contained higher levels of jasmonic acid and its active form JA-Ile than wild type, along with lower abscisic acid, and after hrcC- treatment salicylic acid levels were markedly reduced compared with wild type. Genes in the jasmonate biosynthesis pathway, such as LOX, AOC and AOS, were upregulated in the mutant. Because jasmonic acid is central to resistance against necrotrophic fungi, the team tested Botrytis cinerea: two days after drop-inoculation with spores, dek2 mutants developed smaller necrotic lesions than wild type, indicating enhanced resistance to this fungus even as bacterial susceptibility increased. The study is careful to note that at three hours after bacterial infection no differences in bacterial titers or stomatal entry were detected, and roles at other time points or redundancy with other DEK family members cannot be ruled out.

To find where DEK2 acts on the genome, the researchers generated complementation lines expressing a DEK2-YFP fusion under the native promoter and performed ChIP-seq on two-week-old seedlings. The analysis identified 4,269 high-confidence DEK2 binding sites associated with 4,253 genes. Binding was concentrated around transcription start sites and transcription end sites, overlapped with nucleosome-free regions mapped by ATAC-seq, and was anti-correlated with nucleosome occupancy measured by MNase-seq. DEK2 enrichment correlated positively with transcript levels, with highly expressed genes showing stronger binding. De novo motif discovery with HOMER uncovered a GC-rich consensus, TGGGCC, the binding site of class I TCP transcription factors, along with motifs for ZNF, bZIP and WRKY families. Yeast two-hybrid tests against six class I TCPs found a strong interaction with TCP20, confirmed by BiFC, and DEK2 showed clear enrichment at TCP20 target genes involved in defense, including MKK9, ERF1, ERF6, WEI2 and PBL39. Notably, an electrophoretic mobility shift assay showed that DEK2 alone did not bind the TCP DNA motif, supporting the idea that transcription factors recruit DEK2 to specific loci rather than DEK2 recognizing the sequence by itself.

The most striking biochemical finding concerns histone marks. The dek2-1 transcriptome profile most closely resembled that of the atxr5/6 mom1 triple mutant, hinting at a link to histone methylation. Recombinant DEK2 bound histone H3 strongly and H4 partially in pull-down assays, but quantitative peptide pull-downs and microscale thermophoresis showed it failed to recognize singly methylated H3 peptides, with only weak binding to H3K9me1 at a dissociation constant around 304 micromolar. An in silico chromatin-state analysis, however, revealed strong enrichment of DEK2-bound sequences in chromatin states 1 and 2, the latter characterized by the coexistence of the opposing marks H3K4me3 and H3K27me3. When the binding assays were repeated with bivalently modified peptides, DEK2 specifically recognized H3K4me3K27me3 with a dissociation constant of roughly 65 micromolar. Separate ChIP experiments confirmed that both marks co-occur at the same loci on tested DEK2 target genes, and only DEK2 target genes that were upregulated in the mutant showed enrichment in the bivalent state 2.

The authors propose a working model in which DEK2, recruited by transcription factors and bound to bivalent H3K4me3K27me3 marks, modulates the expression of defense genes under unstressed conditions, and upon pathogen attack or PAMP treatment may be phosphorylated by MPK6 and dissociate from the transcription factor complex, driving target gene expression. They are explicit about the limits of the current evidence: direct proof linking DEK2 phosphorylation to chromatin dissociation is lacking, the fate of the bivalent marks after DEK2 leaves remains unknown, and the model is offered as a framework for interpreting the data rather than a settled mechanism. Even so, the study opens an intriguing window onto how plant immune signaling reaches into the nucleus to reshape chromatin-level gene control, and it adds DEK2 to the short list of validated MPK6 substrates in plant immunity.

Subject of Research: Identification of the Arabidopsis chromatin protein DEK2 as an MPK6 substrate that regulates immune-related gene transcription and plant defense.

Article Title: The MPK6 target AtDEK2, a chromatin remodeler, modulates transcription of immune-related genes and governs plant immunity

Article References: Alhoraibi, H., Alejandro-Martinez, S., Latrasse, D., Mandal, P., Faivre, L., He, X., Manza, D., Abulfaraj, A. A., Alharbi, S., Mariappan, K., Artyukh, O., Abdulhakim, F., Aljedaani, F., David, S., Almeida-Trapp, M., Bigeard, J., Pflieger, D., Fischle, W., Arold, S. T., … Rayapuram, N. (2026). The MPK6 target AtDEK2, a chromatin remodeler, modulates transcription of immune-related genes and governs plant immunity. Discover Immunity, 3(1), Article 6. https://doi.org/10.1007/s44368-026-00022-1

Image Credits: AI Generated

DOI: 10.1007/s44368-026-00022-1

Keywords: MPK6, DEK2, Arabidopsis thaliana, plant immunity, chromatin remodeling, MAPK signaling, histone marks, H3K4me3K27me3, pattern-triggered immunity, jasmonic acid, Botrytis cinerea, Pseudomonas syringae