Different Modes of Action of Genetic and Chemical Downregulation of Histone Deacetylases with Respect to Plant Development and Histone Modifications

Abstract

A high degree of developmental plasticity enables plants to adapt to continuous, often unfavorable and unpredictable changes in their environment. At the molecular level, adaptive advantages for plants are primarily provided by epigenetic machinery including DNA methylation, histone modifications, and the activity of noncoding RNA molecules. Using a mass spectrometry-based proteomic approach, we examined the levels of acetylated histone peptide forms in Arabidopsis plants with a loss of function of histone deacetylase 6 (HDA6), and in plants germinated in the presence of HDA inhibitors trichostatin A (TSA) and sodium butyrate (NaB). Our analyses revealed particular lysine sites at histone sequences targeted by the HDA6 enzyme, and by TSA- and NaB-sensitive HDAs. Compared with plants exposed to drugs, more dramatic changes in the overall profiles of histone post-translational modifications were identified in hda6 mutants. However, loss of HDA6 was not sufficient by itself to induce hyperacetylation to the maximum degree, implying complementary activities of other HDAs. In contrast to hda6 mutants that did not exhibit any obvious phenotypic defects, the phenotypes of seedlings exposed to HDA inhibitors were markedly affected, showing that the effect of these drugs on early plant development is not limited to the modulation of histone acetylation levels.

The Effect of Sodium Butyrate on Adventitious Shoot Formation Varies among the Plant Species and the Explant Types

“…The reported positive effects of HDIs include increasing salinity stress tolerance in Arabidopsis [ 51 , 52 , 53 ] and cassava [ 54 ], improving embryogenic cell proliferation, and doubled haploid production in Brassica napus, and improving totipotency and embryogenic growth in Arabidopsis [ 25 ]. In contrast, several studies have reported negative effects of HDIs, such as arresting embryo maturation in the two conifer species [ 31 ] and impairing seed germination and seedling development in several plant species [ 30 , 32 , 34 , 36 ].…”

“…TSA has been reported to induce various plant physiological responses, including inhibition of embryo maturation, inhibition of seed germination and seedling development, promotion of embryogenic cell proliferation, and inhibition of somatic embryogenesis, depending on the treatment concentration [ 25 , 30 , 31 , 32 , 33 , 34 ]. Similarly, NaB has been reported to induce a wide variety of plant physiological responses, such as repression of seed germination and seedling development, cell division in explants, and inhibition of early seedling development and root elongation, which also depend on the treatment concentration [ 34 , 35 , 36 ]. In addition, Furuta et al (2011) reported that TSA induces similar effects as cytokinin on callus formation in Arabidopsis [ 37 ].…”

Trimethylacetic Anhydride–Based Derivatization Facilitates Quantification of Histone Marks at the MS1 Level

“…The relative abundances of specific histone H4–modified peptide forms were calculated following a published approach ( 21 ). Briefly, areas of peaks assigned to all the forms were treated as composition.…”

10-hydroxy-2E-decenoic Acid (10HDA) is not a Caste-differentiation Factor in Melipona Scutellaris Stingless Bees

“…Histone acetylation is controlled by the balance of activities of two enzyme families: histone acetyltransferases (HATs) -which acetylate lysine residues of histones, promoting gene expression -and histone deacetylases (HDACs)which remove these Ɛ-acetyl-lysine residues, promoting condensation of chromatin and reduction in gene expression [50][51][52] . In the current study, we investigate the importance of histone acetylation and nutritional factors to caste differentiation in Melipona.…”