Chromatin phosphoproteomics unravels a function for AT-hook motif nuclear localized protein AHL13 in PAMP-triggered immunity
Edited by Cyril Zipfel, University of Zurich, Zurich, Switzerland, and accepted by Editorial Board Member Sheng Yang He November 30, 2020 (received for review March 16, 2020)
Significance
Mitogen-activated protein kinases (MAPKs) function in all eukaryotes in signaling extracellular stimuli to intracellular responses and ultimately link them to chromatin events by targeting transcription factors and chromatin remodeling complexes. In plants, MAPKs play crucial roles in immunity, development, and stress responses, but so far no attempts have been made to identify phosphorylation of chromatin-associated proteins. By using a phosphoproteomic approach on MAPK mutants, we identified a number of chromatin-associated MAPK substrates and characterize an AT-hook motif containing nuclear localized (AHL) DNA-binding protein 13 in plant immunity and demonstrate that phosphorylation regulates AHL13 protein stability and, in turn, its function in response to pathogens.
Abstract
In many eukaryotic systems during immune responses, mitogen-activated protein kinases (MAPKs) link cytoplasmic signaling to chromatin events by targeting transcription factors, chromatin remodeling complexes, and the RNA polymerase machinery. So far, knowledge on these events is scarce in plants and no attempts have been made to focus on phosphorylation events of chromatin-associated proteins. Here we carried out chromatin phosphoproteomics upon elicitor-induced activation of Arabidopsis. The events in WT were compared with those in mpk3, mpk4, and mpk6 mutant plants to decipher specific MAPK targets. Our study highlights distinct signaling networks involving MPK3, MPK4, and MPK6 in chromatin organization and modification, as well as in RNA transcription and processing. Among the chromatin targets, we characterized the AT-hook motif containing nuclear localized (AHL) DNA-binding protein AHL13 as a substrate of immune MAPKs. AHL13 knockout mutant plants are compromised in pathogen-associated molecular pattern (PAMP)-induced reactive oxygen species production, expression of defense genes, and PAMP-triggered immunity. Transcriptome analysis revealed that AHL13 regulates key factors of jasmonic acid biosynthesis and signaling and affects immunity toward Pseudomonas syringae and Botrytis cinerea pathogens. Mutational analysis of the phosphorylation sites of AHL13 demonstrated that phosphorylation regulates AHL13 protein stability and thereby its immune functions.
Data Availability
The MS proteomics data have been deposited to the ProteomeXchange Consortium via PRIDE (91) partner repository (dataset identifier PXD009823 and DOI: https://doi.org/10.6019/PXD009823). The RNA-seq data have been deposited in the National Center for Biotechnology Information’s Gene Expression Omnibus database, https://www.ncbi.nlm.nih.gov/geo (accession no. GSE119465).
Acknowledgments
We thank Véronique Legros, Huma Khurram, and Huoming Zhang for technical assistance in mass spectometry; Stéphanie Pateyron and Alexandra Avon for technical support in molecular biology; and Jean Colcombet for kindly providing the constitutively active MAPK vectors. This work was supported by Agence Nationale de la Recherche ANR-2010-JCJC-1608 and ANR-14-CE19-0014 (to D.P.); Investissement d’Avenir Infrastructures Nationales en Biologie et Santé program (ProFI project, ANR-10-INBS-08); and by King Abdullah University of Science and Technology BAS/1/1062-01-01 (to H.H.). The Institute of Plant Sciences Paris-Saclay benefits from the support of the LabEx Saclay Plant Sciences (ANR-10-LABX-0040-SPS). M.A.-T. was supported by a Humboldt-Capes fellowship.
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© 2021. Published under the PNAS license.
Data Availability
The MS proteomics data have been deposited to the ProteomeXchange Consortium via PRIDE (91) partner repository (dataset identifier PXD009823 and DOI: https://doi.org/10.6019/PXD009823). The RNA-seq data have been deposited in the National Center for Biotechnology Information’s Gene Expression Omnibus database, https://www.ncbi.nlm.nih.gov/geo (accession no. GSE119465).
Submission history
Published online: January 8, 2021
Published in issue: January 19, 2021
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Acknowledgments
We thank Véronique Legros, Huma Khurram, and Huoming Zhang for technical assistance in mass spectometry; Stéphanie Pateyron and Alexandra Avon for technical support in molecular biology; and Jean Colcombet for kindly providing the constitutively active MAPK vectors. This work was supported by Agence Nationale de la Recherche ANR-2010-JCJC-1608 and ANR-14-CE19-0014 (to D.P.); Investissement d’Avenir Infrastructures Nationales en Biologie et Santé program (ProFI project, ANR-10-INBS-08); and by King Abdullah University of Science and Technology BAS/1/1062-01-01 (to H.H.). The Institute of Plant Sciences Paris-Saclay benefits from the support of the LabEx Saclay Plant Sciences (ANR-10-LABX-0040-SPS). M.A.-T. was supported by a Humboldt-Capes fellowship.
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This article is a PNAS Direct Submission. C.Z. is a guest editor invited by the Editorial Board.
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The authors declare no competing interest.
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Chromatin phosphoproteomics unravels a function for AT-hook motif nuclear localized protein AHL13 in PAMP-triggered immunity, Proc. Natl. Acad. Sci. U.S.A.
118 (3) e2004670118,
https://doi.org/10.1073/pnas.2004670118
(2021).
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