Class I histone deacetylases (HDAC1–3) are histone lysine delactylases

Abstract

Lysine L-lactylation [K(L-la)] is a newly discovered histone mark stimulated under conditions of high glycolysis, such as the Warburg effect. K(L-la) is associated with functions that are different from the widely studied histone acetylation. While K(L-la) can be introduced by the acetyltransferase p300, histone delactylases enzymes remained unknown. Here, we report the systematic evaluation of zinc- and nicotinamide adenine dinucleotide–dependent histone deacetylases (HDACs) for their ability to cleave ε- N -L-lactyllysine marks. Our screens identified HDAC1–3 and SIRT1–3 as delactylases in vitro. HDAC1–3 show robust activity toward not only K(L-la) but also K(D-la) and diverse short-chain acyl modifications. We further confirmed the de-L-lactylase activity of HDACs 1 and 3 in cells. Together, these data suggest that histone lactylation is installed and removed by regulatory enzymes as opposed to spontaneous chemical reactivity. Our results therefore represent an important step toward full characterization of this pathway’s regulatory elements.

Investigation of Carboxylic Acid Isosteres and Prodrugs for Inhibition of the Human SIRT5 Lysine Deacylase Enzyme**

“…The sulfonates (5,6), sulfonamide (7), phosphonate (8), boronates (9)(10)(11), and fluorophenols (12,13) all exhibited poor inhibition of SIRT5. Among the series of heterocycles in our array of compounds (14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26), on the other hand, the 1,2,4-oxadiazol-5(4H)-one ( 16) and the tetrazole (24) exhibited similar IC 50 values to the parent compound (1), while the 2-hydroxy-isoxazole ( 22) also had a sub-micromolar IC 50 value (Figure 1). Finally, substituting the carboxylic acid for a hydroxamic acid (27) resulted in substantial loss of potency.…”

“…[3][4][5][6] Sirtuins 1-3 and 6 have exhibited preference for aliphatic acyl chains of different length ranging from ɛ-N-acetyllysine (Kac) to ɛ-N-myristoyllysine (Kmyr), [7][8][9] which is also reflected by hydrophobic binding pockets. [10][11][12][13] Moreover, SIRT1-3 has recently been reported to cleave both the D and L stereoisomers of ɛ-N-lactyllysine (Klac); [14,15] albeit, with lower efficiency than the zinc-dependent histone deacetylases (HDACs) 1-3. [15] Sirtuin 4 has been reported to cleave negatively charged modifications, such as ɛ-N-methylglutaconyllysine (Kmgc) and ɛ-N-(3-hydroxy-3-methylglutaryl)lysine (Khmg), [16,17] as well as ɛ-N-lipoyllysine (Klip) and ɛ-N-biotinyllysine (Kbio).…”

“…[10][11][12][13] Moreover, SIRT1-3 has recently been reported to cleave both the D and L stereoisomers of ɛ-N-lactyllysine (Klac); [14,15] albeit, with lower efficiency than the zinc-dependent histone deacetylases (HDACs) 1-3. [15] Sirtuin 4 has been reported to cleave negatively charged modifications, such as ɛ-N-methylglutaconyllysine (Kmgc) and ɛ-N-(3-hydroxy-3-methylglutaryl)lysine (Khmg), [16,17] as well as ɛ-N-lipoyllysine (Klip) and ɛ-N-biotinyllysine (Kbio). [18] Sirtuin 7 has been reported to cleave long chain acyl groups [19,20] and ɛ-Nglutaryllysine (Kglut), [21] and has been reported to be activated by oligonucleotides.…”

A bioorthogonal chemical reporter for the detection and identification of protein lactylation

“…These results therefore suggest that protein lactylation is reversible and likely regulated by the HDAC family, consistent with a very recent report. 8 Furthermore, we examined the applicability and generality of YnLac for the metabolic labelling of proteins in various cell lines. Robust protein labelling by YnLac was observed for all cell types tested (Fig.…”

Chemical Biology Tools for Protein Lysine Acylation

“…Further pull-down experiments with cell lysates allowed the successful identification of 475 and 472 putative substrates of p300 and GCN5, respectively. Among them, two novel substrates of GCN5, Kcr p300 [28] CBP, PCAF hMOF [29] WB; IP/WB Sirt1 [44] Sirt1-3 [46] HDAC1 & 3 [29] HDAC1-3 & 8 [44] IF/WB AfBP IP/WB IF/WB AF9 [89] YEATS2 [91] MOZ/DPF2 [92] Taf14 [90] ITC/Microarray/X-ray/IP X-ray/NMR/Pull-Down Ksucc GCN5 [30] p300 [34] IP-MS WB Sirt5 [20] Sirt7 [21] LC-MS/MS/X-ray IP/LC-MS/MS GAS41 [93] Pull-Down/X-ray Kmal NA NR Sirt5 [20] LC-MS/MS/X-ray NA NR Kglu GCN5 [35] IP/WB Sirt5 [47] Sirt7 [35] FL probe/LC-MS/WB MCR/WB/LC-MS/MS NA NR Khib p300 [31] Tip60 [32] WB/IF WB/MS HDAC2 [32] HDAC3 [32] WB/MS NA NR Kbhb p300 [33] WB HDAC1 & 2 [33] Sirt3 [53] WB/LC X-ray/WB NA NR Klip LIPT1-2 [22][23] WB Sirt4 [8] Sirt2 [48] IP/LC-MS/MS AfBP NA NR Kmyr NMT1-2 [24] LC-MS/X-ray /MCR HDAC8 [50] , Sirt2 [25] Sirt6 [26] , Sirt7 [52] MCR NA NR Kbz NA NR Sirt2 [4] LC-MS/WB DPF, YEATS [27] ITC/Microarray/X-ray/IF Kla p300 [2] LC-MS/WB HDAC1 & 3 [126] FL Probe/WB NA NR Kinic CBP, p300 [5] WB HDAC3 [5] IF namely the structural...…”