Critical review of non‐histone human substrates of metal‐dependent lysine deacetylases

Abstract

Lysine acetylation is a posttranslational modification that occurs on thousands of human proteins, most of which are cytoplasmic. Acetylated proteins are involved in numerous cellular processes and human diseases. Therefore, how the acetylation/deacetylation cycle is regulated is an important question. Eleven metal‐dependent lysine deacetylases (KDACs) have been identified in human cells. These enzymes, along with the sirtuins, are collectively responsible for reversing lysine acetylation. Despite several large‐scale studies which have characterized the acetylome, relatively few of the specific acetylated residues have been matched to a proposed KDAC for deacetylation. To understand the function of lysine acetylation, and its association with diseases, specific KDAC‐substrate pairs must be identified. Identifying specific substrates of a KDAC is complicated both by the complexity of assaying relevant activity and by the non‐catalytic interactions of KDACs with cellular proteins. Here, we discuss in vitro and cell‐based experimental strategies used to identify KDAC‐substrate pairs and evaluate each for the purpose of directly identifying non‐histone substrates of metal‐dependent KDACs. We propose criteria for a combination of reproducible experimental approaches that are necessary to establish a direct enzymatic relationship. This critical analysis of the literature identifies 108 proposed non‐histone substrate‐KDAC pairs for which direct experimental evidence has been reported. Of these, five pairs can be considered well‐established, while another thirteen pairs have both cell‐based and in vitro evidence but lack independent replication and/or sufficient cell‐based evidence. We present a path forward for evaluating the remaining substrate leads and reliably identifying novel KDAC substrates.

Role of Fluorination in the Histone Deacetylase 6 (HDAC6) Selectivity of Benzohydroxamate-Based Inhibitors

“…1 The acetylation status of histones is involved in the regulation of chromatin accessibility to transcription factor complexes and therefore gene expression, 2 whereas acetylation of nonhistone proteins affects their function and stability and may strongly impact cell physiology. 3 HDAC inhibitors (HDACis) are considered promising therapeutic alternatives to the available cancer chemotherapies, and several inhibitors of Zn-dependent HDACs have been approved for the treatment of human malignancies. 4 The first generation of compounds inhibit all or most of the HDAC isoforms and cause side effects including hematological and gastrointestinal tract toxicity and fatigue, that limit their use in many indications.…”

“…HDACs are found in different cellular compartments and have been found to deacetylate, or more in general deacylate, different histone or nonhistone protein or nonprotein substrates . The acetylation status of histones is involved in the regulation of chromatin accessibility to transcription factor complexes and therefore gene expression, whereas acetylation of nonhistone proteins affects their function and stability and may strongly impact cell physiology . HDAC inhibitors (HDACis) are considered promising therapeutic alternatives to the available cancer chemotherapies, and several inhibitors of Zn-dependent HDACs have been approved for the treatment of human malignancies .…”

Genetic screen for suppressors of increased silencing in rpd3 mutants in Saccharomyces cerevisiae identifies a potential role for H3K4 methylation

“…While therapeutic results have been seen using drugs that inhibit chromatin enzymes, the global effects of removing one chromatin-modifying activity on the myriad of others and all possible interactions and potential side-effects are not fully characterized. Other possibilities to consider are that chromatin-modifying enzymes have been shown to act on nonhistone targets ( Toro and Watt 2020 ; Di Blasi et al 2021 ), and some chromatin-modifying complexes have additional nonenzymatic functions ( Morgan and Shilatifard 2020 ) which could also be relevant in our system. Therefore, an understanding of the downstream effects of changes in the activity of protein complexes containing chromatin writers, erasers, readers, and the individual modified target residues (on both nucleosomes and nonhistone proteins) continues to warrant further study at both the global level and at individual genomic loci.…”

Roles of Histone Deacetylases in Acute Myeloid Leukemia With Fusion Proteins

“…Besides, an increasing number of non-histone proteins have been identified as substrates of HDACs, such as p53, Stat3, Hsp90, GATA1, Tubulin, and b-catenin, which display vital roles during the progress of carcinogenesis (83)(84)(85). Via deacetylation, HDAC1 can affect the stability of tumor suppressor gene p53, arresting the interaction with DNA, inverting the function of p53.…”