KDAC8 substrate specificity quantified by a biologically relevant,label‐free deacetylation assay

Analysis of the human proteome has identified thousands of unique protein sequences that contain acetylated lysine residues in vivo. These modifications regulate a variety of biological processes and are reversed by the lysine deacetylase (KDAC) family of enzymes. Despite the known prevalence and importance of acetylation, the details of KDAC substrate recognition are not well understood. While several methods have been developed to monitor protein deacetylation, none are particularly suited for identifying enzyme‐substrate pairs of label‐free substrates across the entire family of lysine deacetylases. Here, we present a fluorescamine‐based assay which is more biologically relevant than existing methods and amenable to probing substrate specificity. Using this assay, we evaluated the activity of KDAC8 and other lysine deacetylases, including a sirtuin, for several peptides derived from known acetylated proteins. KDAC8 showed clear preferences for some peptides over others, indicating that the residues immediately surrounding the acetylated lysine play an important role in substrate specificity. Steady‐state kinetics suggest that the sequence surrounding the acetylated lysine affects binding affinity and catalytic rate independently. Our results provide direct evidence that potential KDAC8 substrates previously identified through cell based experiments can be directly deacetylated by KDAC8. Conversely, the data from this assay did not correlate well with predictions from previous screens for KDAC8 substrates using less biologically relevant substrates and assay conditions. Combining results from our assay with mass spectrometry‐based experiments and cell‐based experiments will allow the identification of specific KDAC‐substrate pairs and lead to a better understanding of the biological consequences of these interactions.     

Suppression of centrosome duplication and amplification by deacetylases

Centrosome duplication is controlled both negatively and positively by a number of proteins. The activities and stabilities of those regulatory proteins are in many cases controlled by posttranslational modifications. Although acetylation and deacetylation are highly common posttranslational modifications, their roles in the regulation of centrosome duplication had not been closely examined. Here, through focusing on the deacetylases, we investigated the role of acetylation/deacetylation in the regulation of centrosome duplication and induction of abnormal amplification of centrosomes. We found that the deacetylation event negatively controls centrosome duplication and amplification. Of the 18 total known deacetylases (HDAC1–11, SIRT1–7), ten deacetylases possess the activity to suppress centrosome amplification, and their centrosome amplification suppressing activities are strongly associated with their abilities to localize to centrosomes. Among them, HDAC1, HDAC5 and SIRT1 show the highest suppressing activities, but each of them suppresses centrosome duplication and/or amplification with its unique mechanism.     

First Synthesis And Antimicrobial Activity Of N- and S-α-L-Arabinopyranosyl-1,2,4-Triazoles

Arabinosylation of some 4-amino- and 4-arylideneamino-5-(pyridin-3-yl)-2,4-dihydro-[1,2,4]-triazole-3-thiones with 2,3,4-tri-O-acetyl-β-L-arabinopyranosyl bromide led to an efficient synthetic approach to the corresponding N-and S-α-L-arabinopyranosides. Structure assignment of these two regiosiomers was based on chemical and spectroscopic evidences. Antimicrobial activities of two selected regioisomeric N-and S-α-L-arabinopyranosides were compared. The N-α-L-arabinopyranoside showed higher inhibitory effect than its regioisomeric S-α-L-arabinopyranoside against Aspergillus fumigatus, Penicillium italicum, Staphylococcus aureus, and Pseudomonas aeruginosa.     

Regioselective Glycosylation: Synthesis of α-Indoline Nucleosides

Novel indoline ribonucleosides with the α-N-glycoside configuration are synthesized with very high regioselectivity in 90–96% yield, using TMS protected indolines and 2,3-O-(1-methylethylidene)-5-O-(triphenylmethyl)-α/β-d-ribofuranose. The structures of these ribonucleosides were elucidated with X-ray crystallography as well as 2D (NOESY, COSY, and HMQC) NMR spectroscopy.     

Influence of substituent groups in regioselective acylation of nucleosides by Novozym 435 lipase

A comparative study on the substrate recognition was conducted successfully in Novozym 435-mediated acylation of various 2′- or 5-substituted nucleosides with acyl donors carrying different aliphatic chain lengths (C6, C10, and C14). The unexpected results revealed that the physicochemical property of the substituents (such as the size, hydrophobicity, and substitutional position) in nucleosides profoundly influenced the behavior of the enzyme. The different substrate-binding patterns derived from the existence of the substituents in 2′- or 5-position of the nucleosides could account for this. Moreover, another possible factor governing the regioselectivity might be ascribed to the interaction between the substituent and acyl donor in addition to the geometrical configuration of the lipase's active site.     

Deacetylation and methylation at histone H3 lysine 9 (H3K9) coordinate chromosome condensation during cell cycle progression

Interphasic chromatin condenses into the chromosomes in order to facilitate the correct segregation of genetic information. It has been previously reported that the phosphorylation and methylation of the N-terminal tail of histone H3 are responsible for chromosome condensation. In this study, we demonstrate that the deacetylation and methylation of histone H3 lysine 9 (H3K9) are required for proper chromosome condensation. We confirmed that H3K9ac levels were reduced, whereas H3K9me3 levels were increased in mitotic cells, via immunofluorescence and Western blot analysis. Nocodazole treatment induced G2/M arrest but co-treatment with TSA, an HDAC inhibitor, delayed cell cycle progression. However, the HMTase inhibitor, AdoX, had no effect on nocodazole-induced G2/M arrest, thereby indicating that sequential modifications of H3K9 are required for proper chromosome condensation. The expression of SUV39H1 and SETDB1, H3K9me3-responsible HMTases, are specifically increased along with H3K9me3 in nocodazole-arrested buoyant cells, which suggests that the increased expression of those proteins is an important step in chromosome condensation. H3K9me3 was highly concentrated in the vertical chromosomal axis during prophase and prometaphase. Collectively, the results of this study indicate that sequential modifications at H3K9 are associated with correct chromosome condensation, and that H3K9me3 may be relevant to the condensation of chromosome length.     

Acetylation of pregnane X receptor protein determines selective function independent of ligand activation

Pregnane X receptor (PXR), like other members of its class of nuclear receptors, undergoes post-translational modification [PTM] (e.g., phosphorylation). However, it is unknown if acetylation (a major and common form of protein PTM) is observed on PXR and, if it is, whether it is of functional consequence. PXR has recently emerged as an important regulatory protein with multiple ligand-dependent functions. In the present work we show that PXR is indeed acetylated in vivo. SIRT1 (Sirtuin 1), a NAD-dependent class III histone deacetylase and a member of the sirtuin family of proteins, partially mediates deacetylation of PXR. Most importantly, the acetylation status of PXR regulates its selective function independent of ligand activation.     

Regioselective ring opening of exo- and endo-3,4-benzylidene acetals of arabinopyranoside derivatives with Lewis acids and reducing agents

Dioxolane type 3,4-benzylidene acetals of benzyl β-l-arabinose either as a mixture or pure exo- and endo-isomers cleavaged with BF₃·OEt₂/Et₃SiH in dichloromethane or acetonitrile regioselectively, provided the 4-O-benzyl-3-hydroxy derivative. The reaction with TiCl₄/Et₃SiH or Cu(OTf)₂/Et₃SiH provided a mixture of 3- and 4-O-benzyl derivatives whereas with Cu(OTf)₂/BH₃·THF gave only hydrolyzed product. The regioselectivity of the reaction was proved to be directed by the acetyl substitution at C-2. Benzyl substitution provided a mixture of 3- and 4-O-benzyl derivatives in 1:1 ratio whereas non-substitution yielded the same mixture in 2:1 ratio.     

Class IIb HDAC6 regulates endothelial cell migration and angiogenesis by deacetylation of cortactin

Histone deacetylases (HDACs) deacetylate histones and non-histone proteins, thereby affecting protein activity and gene expression. The regulation and function of the cytoplasmic class IIb HDAC6 in endothelial cells (ECs) is largely unexplored. Here, we demonstrate that HDAC6 is upregulated by hypoxia and is essential for angiogenesis. Silencing of HDAC6 in ECs decreases sprouting and migration in vitro and formation of functional vascular networks in matrigel plugs in vivo. HDAC6 regulates zebrafish vessel formation, and HDAC6-deficient mice showed a reduced formation of perfused vessels in matrigel plugs. Consistently, overexpression of wild-type HDAC6 increases sprouting from spheroids. HDAC6 function requires the catalytic activity but is independent of ubiquitin binding and deacetylation of α-tubulin. Instead, we found that HDAC6 interacts with and deacetylates the actin-remodelling protein cortactin in ECs, which is essential for zebrafish vessel formation and which mediates the angiogenic effect of HDAC6. In summary, we show that HDAC6 is necessary for angiogenesis in vivo and in vitro, involving the interaction and deacetylation of cortactin that regulates EC migration and sprouting.