Figure Legends.
Figure 1 . Types of lysine acetylation in prokaryotes. (A) Enzymatic and chemical acetylation and their respective acetyl donor molecule. In bacteria, enzymatic acetylation is catalyzed by Gcn5-related N-acetyltransferase (GNAT). (B) The catalytic mechanism exerted by GNATs is a sequential mechanism where glutamate acts as a general base to deprotonate the amino group of the lysine, enabling nucleophilic attack of the Acetyl-CoA carbonyl, followed by the formation of a transient tetrahedral intermediate, that is resolved to yield the acetylated substrate amino group and coenzyme A. Overall structure of GNATs: (C) Cartoon representation of GNATS topology. The secondary structure elements are colored and represent the different motifs. Motifs C (β1–α1), D (β2–β3), A (β4–α3), and B (β5–α4) are colored orange, green, aquamarine, and blue, respectively. The least conserved secondary structure elements (strands β0 and β6 and helix α2) absent in some GNAT proteins are colored purple. (D) Crystal structure of the M. tuberculosis GNAT acetyltransferase Rv0819 in complex with Acetyl-CoA. The characteristic secondary structures of these enzymes are shown in different colors (PDB: 1OZP) (Vetting et al., 2003) [the figure was generated with PyMOL v.2.3.4 (DeLano, 2002). (E). Classification of GNATs in prokaryotes based on their domain organization and the arrangement of the GNAT domain [figure redrawn and modified from Blasl et al., 2021; Lammers, 2021].
Figure 2 . Lysine deacetylases (KDAC) can reverse enzymatic or non-enzymatic lysine acetylation. Sirtuins are NAD+-dependent lysine-deacetylases (A). Crystal structure of E. coli sirtuin deacetylase CobB in a complex with a lysine acetylated substrate (PDB: 1S5P). The characteristic secondary structures of these enzymes are shown in different colors (Zhao et al., 2004) [the figure was generated with PyMOL v.2.3.4 (DeLano, 2002)]. Catalytic mechanisms used by sirtuins: (B) Sirtuins are NAD+-dependent lysine deacetylases as a co-substrate for catalysis. In the reaction, the carbonyl-oxygen of the acetyl group of lysine performs a nucleophilic attack on the electrophilic C-1’ of the NAD+ ribose, resulting in the fast release of nicotinamide and the formation of a C-1´-O -alkylamidate intermediate. The intermediate is hydrolyzed, forming the deacetylated lysine and 2´-O -acetyl-ADP-ribose, which is in a non-enzymatic equilibrium with 3´-O -acetyl-ADP ribose. Zinc-dependent classical deacetylase (HDAC/KDAC). are metalloenzymes. (C) Crystal structure ofPseudomonas aeruginosa zinc-dependent deacetylase LpxC in a complex with the potent BB-78485 inhibitor (PDB: 2ves). LpxC domain consists of two homologous domains, I (colored in magenta) and II (colored in purple) (Mochalkin et al., 2008) [the figure was generated with PyMOL v.2.3.4 (DeLano, 2002). Catalytic mechanisms used by classical deacetylases (D). HDACs use a catalytic water molecule that is coordinated and polarized by the catalytic Zn2+ ion. The ion, together with a histidine residue, interacts with the carbonyl oxygen of the acetyl group. The histidine is polarized and oriented by an aspartic residue (Asp). It acts as a general base to deprotonate the water molecule, thereby increasing the nucleophilicity for attacking the carbonyl carbon of the acetyl group. A second histidine, again polarized and oriented by another Asp, acts as electrostatic catalysis. A tetrahedral oxyanion intermediate is formed, which is stabilized by a histidine and the Zn2+ ion, to release acetate and the deacetylated lysine finally [figure redrawn and modified from the decomposition of the oxyanionic tetrahedral intermediate [figure redrawn and modified from Ali et al., 2018; Blasl et al., 2021; Lammers, 2021].
Figure 3 . Regulation of the metabolic enzyme activity. Acetylation regulates: 1) The number of metabolic enzymes by promoting their degradation through the ubiquitin–proteasomal system; 2) The catalytic activity through a) neutralizing the positive charge of lysine residues in the active site or b) causing allosteric changes and; 3) The substrate accessibility to metabolic enzymes by modifying the conserved lysine residues to hinder the entry of substrate (Xiong & Guan, 2012; Liu et al., 2021). Created with BioRender.com
Figure 4. Factors contributing to non-enzymatic acetylation. Acetyl-CoA and acetyl-phosphate are very reactive molecules that, when increasing intracellular concentrations, can non-enzymatically acetylate lysine residues on many proteins. The pH value also plays an essential role in chemical acetylation since, at basic pH, deprotonation of the lysine side chain is favored, increasing its nucleophilicity. In addition to these factors, the efficiency of chemical acetylation also depends on the microenvironment of the protein.