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

Tu, Yi-Tsung; Chen, Chia-Yang; Huang, Yi-Sui; Chang, Chung-Han; Yen, Ming‐Ren; Hsieh, Jo-Wei Allison; Chen, Pao‐Yang; Wu, Keqiang

doi:10.1093/plphys/kiac271

Cited by 14 publications

(13 citation statements)

References 63 publications

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“…Another study showed the interaction between HDA15 and the core subunits of the MOS4‐associated complex (MAC), MAC3A and MAC3B. Both hda15 and mac3a / mac3b mutants were ABA‐hyposensitive during germination and 3‐week‐old plants showed an increased survival rate when exposed to 300 m m NaCl for 2 weeks (Tu et al., 2022). It is unknown so far whether the single loss of other class II HDACs results in altered stress phenotypes.…”

Section: Introductionmentioning

confidence: 99%

Proteome‐wide lysine acetylation profiling to investigate the involvement of histone deacetylase HDA5 in the salt stress response of Arabidopsis leaves

et al. 2023

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Post-translational modifications (PTMs) of proteins play important roles in the acclimation of plants to environmental stress. Lysine acetylation is a dynamic and reversible PTM, which can be removed by histone deacetylases. Here we investigated the role of lysine acetylation in the response of Arabidopsis leaves to 1 week of salt stress. A quantitative mass spectrometry analysis revealed an increase in lysine acetylation of several proteins from cytosol and plastids, which was accompanied by altered histone deacetylase activities in the salt-treated leaves. While activities of HDA14 and HDA15 were decreased upon salt stress, HDA5 showed a mild and HDA19 a strong increase in activity. Since HDA5 is a cytosolic-nuclear enzyme from the class II histone deacetylase family with yet unknown protein substrates, we performed a lysine acetylome analysis on hda5 mutants and characterized its substrate proteins. Next to histone H2B, the salt stressresponsive transcription factor GT2L and the dehydration-related protein ERD7 were identified as HDA5 substrates. In addition, in protein-protein interaction studies, HDA18 was discovered, among other interacting proteins, to work in a complex together with HDA5. Altogether, this study revealed the substrate proteins of HDA5 and identified new lysine acetylation sites which are hyperacetylated upon salt stress. The identification of specific histone deacetylase substrate proteins, apart from histones, will be important to unravel the acclimation response of Arabidopsis to salt stress and their role in plant physiology.

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Section: Introductionmentioning

confidence: 99%

Proteome‐wide lysine acetylation profiling to investigate the involvement of histone deacetylase HDA5 in the salt stress response of Arabidopsis leaves

et al. 2023

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“…In yeast and mammals, HDACs are identified to be components of multi-protein co-repressor complexes, such as SIN3, NuRD, CoREST and NCoR/SMRT [ 30 ]. A recent work co-purified HDA15 with the SIN3 homologue SNL2 (SIN3-LIKE2) [ 31 ], a scaffold protein playing a role in control of seed germination [ 32 ], which suggested that HDA15 may associate with SNL2-containing protein complex in repressing GA20ox1/2 expression. In summary, HDA15 may associate with GA signal-related transcription factors and co-repressor complexes in repressing GA20ox1/2 expression in the regulation of PHYB-dependent seed germination.…”

Section: Discussionmentioning

confidence: 99%

Histone Deacetylase HDA15 Restrains PHYB-Dependent Seed Germination via Directly Repressing GA20ox1/2 Gene Expression

Feng

Wang

et al. 2022

Cells

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Seed germination is essential for the colonization of the land plants. Light is a major environmental factor affecting seed germination, which is predominantly regulated by photoreceptor phytochrome B (PHYB). PHYB is activated by red light (designated as PHYB-on) whereas it is inactivated by far-red light (referred as PHYB-off). We previously reported that Arabidopsis histone deacetylase HDA15 interacts with phytochrome-interacting factor1 (PIF1) to repress seed germination under PHYB-off conditions. Here, we show that HDA15 plays a negative role in regulating seed germination under PHYB-on conditions. Overexpression of HDA15 in Arabidopsis restrains PHYB-dependent seed germination, while gibberellin (GA) relieves the repressive role of HDA15 under PHYB-off conditions. We further show that HDA15 directly binds to GA20ox1 and GA20ox2, two key GA biosynthesis genes and represses their expression by removal of histone H3 and H4 acetylation. Moreover, the levels of HDA15 transcript and HDA15 protein are up-regulated in the phyB mutant. Collectively, our work proposes that HDA15 acts as a negative regulator of PHYB-dependent seed germination by directly repressing GA20ox1/2 gene expression.

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“…The HDA15 protein extracted from 2‐day‐old etiolated seedlings of Col‐0 wild type was immunoprecipitated by an HDA15 antibody (Liu et al., 2013) and isolated by sodium dodecyl sulfate‐polyacrylamide gel electrophoresis (SDS‐PAGE) in four biological replicates (Tu et al., 2022). After trypsin digestion and desalting, peptides were used to perform LC–MS/MS by a Thermo Orbitrap Elite Mass Spectrometer and for Mascot analysis.…”

Section: Methodsmentioning

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

Cited by 14 publications

References 63 publications

Proteome‐wide lysine acetylation profiling to investigate the involvement of histone deacetylase HDA5 in the salt stress response of Arabidopsis leaves

Proteome‐wide lysine acetylation profiling to investigate the involvement of histone deacetylase HDA5 in the salt stress response of Arabidopsis leaves

Histone Deacetylase HDA15 Restrains PHYB-Dependent Seed Germination via Directly Repressing GA20ox1/2 Gene Expression

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

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