Synthetic Chromatin Acylation by an Artificial Catalyst System

Ishiguro, Tadashi; Amamoto, Yoshifumi; Tanabe, Kazuhisa; Liu, Jiaan; Kajino, Hidetoshi; Fujimura, Akiko; Aoi, Yuki; Osakabe, Akihisa; Horikoshi, Naoki; Kurumizaka, Hitoshi; Yamatsugu, Kenzo; Kawashima, Shinichi; Kanai, Motomu

doi:10.1016/j.chempr.2017.04.002

Cited by 33 publications

(52 citation statements)

References 55 publications

(73 reference statements)

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“…In a recent study, this was effectively overcome by DMAP incorporation in surface-cross-linked micelles (SCMs) 29, creating a hydrophobic microenvironment that facilitates efficient catalysis for (phosphate)ester hydrolysis even under acidic conditions (Table 1 reaction 11b). 117 Other recent literature examples of 6 catalysis include the application of DMAP for affinity protein-labeling 118 , the activation of thioesters via a DMAP-SH analogue for acyl transfer reactions 119 , a DMAP artificial catalyst system for histone-selective acylation using nucleosomebinding catalysts and acyl donors (in analogy to histone acetyltransferases) 120 (Table 1 -reaction 15). 122,123 An analogue of DABCO, 3-quinuclidinol 31 was found as an optimal catalyst for the MBH reaction, demonstrating the largest effect on reaction rate acceleration compared to 4 and 6.…”

Section: Nucleophilic and General/specific Base Catalysismentioning

confidence: 99%

Organocatalysis in aqueous media

2019

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Section: Nucleophilic and General/specific Base Catalysismentioning

confidence: 99%

Organocatalysis in aqueous media

2019

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“…We have previously developed artificial catalyst systems composed of a nucleosome-binding catalyst (8DMAP) and acyl donors, including an acetyl donor (3NMD8R, 1 ) and a malonyl donor (3Mal8R, 3 ) 20 (Fig. 1A ).…”

Section: Resultsmentioning

confidence: 99%

“…Nucleosomes were reconstituted and purified as described previously 20 . To a solution of recombinant nucleosomes (0.346 µM for DNA concentration) in 20 mM Tris-HCl (pH 7.5) buffer, 8DMAP and an acyl donor ( 1 , 2 , or 3 ) were sequentially added.…”

Section: Methodsmentioning

confidence: 99%

“…For example, malonylation introduces an acyl group with a similar molecular size to butyrylation, but the malonyl group has an anionic carboxylate group. Our biochemical analyses using recombinant nucleosomes that are acetylated or malonylated by artificial catalyst systems suggest that histone malonylation has a greater effect on inter-nucleosome interactions than acetylation does 20 , 21 , while the functions of acidic acyl groups on histones in living cells remain to be elucidated. Enzymes that catalyze the removal of acyl groups other than the acetyl group have been only partly identified thus far.…”

Section: Introductionmentioning

confidence: 95%

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LC–MS/MS-based quantitative study of the acyl group- and site-selectivity of human sirtuins to acylated nucleosomes

Tanabe

Liu

Kato

et al. 2018

Sci Rep

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Chromatin structure and gene expression are dynamically regulated by posttranslational modifications of histones. Recent advance in mass spectrometry has identified novel types of lysine acylations, such as butyrylation and malonylation, whose functions and regulations are likely different from those of acetylation. Sirtuins, nicotinamide adenine dinucleotide (NAD+)-dependent histone deacetylases, catalyze various deacylations. However, it is poorly understood how distinct sirtuins regulate the histone acylation states of nucleosomes that have many lysine residues. Here, we provide mass spectrometry-based quantitative information about the acyl group- and site-selectivity of all human sirtuins on acylated nucleosomes. The acyl group- and site-selectivity of each sirtuin is unique to its subtype. Sirt5 exclusively removes negatively-charged acyl groups, while Sirt1/2/3/6/7 preferentially remove hydrophobic acyl groups; Sirt1 and Sirt3 selectively remove acetyl group more than butyryl group, whereas Sirt2 and Sirt6 showed the opposite selectivity. Investigating site-selectivity for active sirtuins revealed acylated lysines on H4 tails to be poor substrates and acylated H3K18 to be a good substrate. Furthermore, we found Sirt7 to be a robust deacylase of H3K36/37, and its activity reliant on nucleosome-binding at its C-terminal basic region. All together, our quantitative dataset provides a useful resource in understanding chromatin regulations by histone acylations.

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“…17c). 213,214 Using the DMAP-SH/thioester system, they successfully achieved site selective histone acylation on native chromatin in a recognition driven manner. Hamachi and coworkers explored a newly designed affinity-guided system by employing pyridinium oxime as an acyl transfer catalyst and NASA as an acyl donor [affinity-guided oxime (AGOX) chemistry] (Fig.…”

Section: •3 Chemical Labeling Using Affinity-guided Catalystsmentioning

confidence: 99%

Recent Progress in Chemical Modification of Proteins

Sakamoto

Hamachi

2018

ANAL. SCI.

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Chemical modification of proteins is important for creating a myriad of engineered proteins and for elucidating the function and dynamics of proteins in live cells. A wide variety of chemical protein modification methods have been developed and can be categorized into three classes: (i) modification of proteins using the reactivity of naturally occurring amino acids; (ii) modification by bioorthogonal reactions using unnatural amino acids, most of which can be siteselectively incorporated into proteins-of-interest using genetic codon expansion techniques; and (iii) recognition driven chemical modification, which is the only approach that allows modification of endogenous proteins without any genetic manipulation even under heavily crowded and multi-molecular conditions, as in live cells and organisms. All of these approaches have merits and limitations. In this review, we summarize these approaches and discuss their characteristics with respect to specificity, reaction rate and versatility.

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Synthetic Chromatin Acylation by an Artificial Catalyst System

Cited by 33 publications

References 55 publications

Organocatalysis in aqueous media

Organocatalysis in aqueous media

LC–MS/MS-based quantitative study of the acyl group- and site-selectivity of human sirtuins to acylated nucleosomes

Recent Progress in Chemical Modification of Proteins

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