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.