Structure of Arabidopsis HISTONE DEACETYLASE15

Chen, Chia-Yang; Tu, Yi-Tsung; Hsu, Jhe-Cheng; Hung, Heng-Chen; Liu, Ting-Chun; Lee, Yu-Hsuan; Chou, Chun; Cheng, Ya-Jung; Wu, Keqiang

doi:10.1104/pp.20.00604

Cited by 14 publications

(15 citation statements)

References 70 publications

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“…It is possible that strong interaction of AtWHY1 with itself in chloroplasts represses the nuclear localization of WHY1 in tobacco cells, which could explain why interaction of WHY1 and HDA15 was not detected in this assay (Figure S2). HDA15‐GFPn and HDA15‐GFPc were transformed to Arabidopsis protoplast and used as positive controls (Chen et al, 2020), and WHY2 instead of WHY1 was used as a negative control. The transformed proteins isolated from protoplasts were detected by immunodetection using a GFP antibody (Figure 1C).…”

Section: Resultsmentioning

confidence: 99%

WHIRLY1 recruits the histone deacetylase HDA15 repressing leaf senescence and flowering in Arabidopsis

Huang

Lan

et al. 2022

JIPB

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Leaf senescence is controlled by a complex regulatory network in which robustness is ensured by the activity of transcription factors and epigenetic regulators. However, how these coordinate the process of leaf senescence remains poorly understood. We found that WHIRLY1 interacts with Histone Deacetylase (HDA)15, a Reduced Potassium Dependence3 (RPD3)/ HDA1-type HDA, by using green fluorescent protein-nanotrap-mass spectrum assays. The development-dependent interaction between WHIRLY1 and HDA15 was further confirmed by bimolecular fluorescence complementation assays and co-immunoprecipitation assays in Arabidopsis. Multi-omics genome-wide transcriptome and H3K9 acetylome enrichment analysis showed that HDA15 delays leaf senescence and flowering by repressing the expression of the positive regulators of leaf senescence and flowering, such as LOX2 and LARP1C, and reducing H3K9ac levels at these loci; WHIRLY1 and HDA15 co-target to the region near the transcription start site of a subset of nutrient recycling-related genes (e.g., Glutathione S-transferases 10, non-coding RNA, and photosystem II protein D1 synthesizer attenuator PDIL1-2), as well as WRKY53 and ELF4, and co-repress their expression by removing H3K9 acetylation. Our study revealed a key transcription regulatory node of nutrient recycling and senescence-associated genes involved in leaf senescence and flowering via the recruitment of HDA15 by the single-stranded DNA/RNA-binding protein WHIRLY1.

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Section: Resultsmentioning

confidence: 99%

WHIRLY1 recruits the histone deacetylase HDA15 repressing leaf senescence and flowering in Arabidopsis

Huang

Lan

et al. 2022

JIPB

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“…Furthermore, MYB96 forms a complex with HDA15 to repress the expression of RHO GTPASE OF PLANTS in ABA and drought stress responses ( Lee and Seo, 2019 ). In addition, HDA15 can be phosphorylated in vivo and HDA15 phosphorylation results in the loss of enzymatic activity and functions ( Chen et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

HISTONE DEACETYLASE 15 and MOS4-associated complex subunits 3A/3B coregulate intron retention of ABA-responsive genes

Chen

Huang

et al. 2022

Plant Physiology

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Histone deacetylases (HDAs) play an important role in transcriptional regulation of multiple biological processes. In this study, we investigated the function of HDA15 in abscisic acid (ABA) responses. We used immunopurification coupled with mass spectrometry-based proteomics to identify proteins interacting with HDA15 in Arabidopsis (Arabidopsis thaliana). HDA15 interacted with the core subunits of the MOS4-Associated Complex (MAC), MAC3A and MAC3B, with interaction between HDA15 and MAC3B enhanced by ABA. hda15 and mac3a/mac3b mutants were ABA-insensitive during seed germination and hyposensitive to salinity. RNA sequencing (RNA-seq) analysis demonstrated that HDA15 and MAC3A/MAC3B co-regulate ABA-responsive intron retention (IR). Furthermore, HDA15 reduced the histone acetylation level of genomic regions near ABA-responsive IR sites, and the association of MAC3B with ABA-responsive pre-mRNA was dependent on HDA15. Our results indicate that HDA15 is involved in ABA responses by interacting with MAC3A/MAC3B to mediate splicing of introns.

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“…Arabidopsis HDACs can be categorized into three families: Reduced Potassium Dependence3/Histone Deacetylase 1 (RPD3/HDA1), Silent Information Regulator2 (SIR2), and Histone Deacetylase 2 (HD2) (Alinsug et al., 2009). There are 12 HDACs in the RPD3/HDA1 superfamily, which can be subdivided into three classes: class I (RPD3‐like) (HDA6, 7, 9, 10, 17, and 19), class II (HDA5, 8, 14, 15, and 18), and class IV (HDA2) (Alinsug et al., 2009; Chen et al., 2020).…”

Section: Introductionmentioning

confidence: 99%

“…In Arabidopsis, phosphomimetics of HDA6 on Ser427 and Ser429 results in increased deacetylase activity, whereas mutation of Ser427 to alanine disrupts the interaction of HDA6 with SUVH5 and SUVH6 (Yu et al., 2017). Phosphorylation of HDA15 negatively regulates its enzymatic activity and results in its relocation from the nucleolus into the nucleoplasm (Chen et al., 2020). Ser448 and Ser452 of HDA15 are also conserved in other Arabidopsis class II HDACs and the human class IIb HDACs HDAC6 and HDAC10 (Chen et al., 2020).…”

Section: Introductionmentioning

confidence: 99%

Arabidopsis cyclin‐dependent kinase C2 interacts with HDA15 and is involved in far‐red light‐mediated hypocotyl cell elongation

Chen

Chang

et al. 2022

The Plant Journal

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SUMMARY Histone deacetylases (HDAs) regulate many aspects of plant development and responses to environmental changes. Previous studies have demonstrated that the Arabidopsis histone deacetylase HDA15 is a positive regulator in far‐red (FR) light‐mediated inhibition of hypocotyl elongation. Furthermore, HDA15 can be phosphorylated and its enzymatic activity is negatively regulated by phosphorylation. However, the kinases that can phosphorylate HDA15 are still unknown. Cyclin‐dependent kinases (CDKs) are a large family of serine/threonine protein kinases and have been identified as major regulators of the cell cycle and transcription. In this study, we show that the cyclin‐dependent kinase CDKC2 interacts with HDA15 both in vitro and in vivo. In vitro kinase assays show that CDKC2 phosphorylates HDA15. Genetic evidence suggests that HDA15 acts downstream of CDKC2 in hypocotyl elongation under FR light. Furthermore, HDA15 and CDKC2 function synergistically in the regulation of FR‐mediated cell elongation. The expression of cell wall organization‐ and auxin signaling‐related genes under FR light is increased in hda15 and cdkc2/hda15 mutants. Taken together, our study indicates that CDKC2 can phosphorylate HDA15 and plays an important role in FR light‐regulated hypocotyl elongation.

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Structure of Arabidopsis HISTONE DEACETYLASE15

Cited by 14 publications

References 70 publications

WHIRLY1 recruits the histone deacetylase HDA15 repressing leaf senescence and flowering in Arabidopsis

WHIRLY1 recruits the histone deacetylase HDA15 repressing leaf senescence and flowering in Arabidopsis

HISTONE DEACETYLASE 15 and MOS4-associated complex subunits 3A/3B coregulate intron retention of ABA-responsive genes

Arabidopsis cyclin‐dependent kinase C2 interacts with HDA15 and is involved in far‐red light‐mediated hypocotyl cell elongation

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