Post-translational Lysine Ac(et)ylation in Bacteria: A Biochemical, Structural, and Synthetic Biological Perspective

Abstract

Ac(et)ylation is a post-translational modification present in all domains of life. First identified in mammals in histones to regulate RNA synthesis, today it is known that is regulates fundamental cellular processes also in bacteria: transcription, translation, metabolism, cell motility. Ac(et)ylation can occur at the ε-amino group of lysine side chains or at the α-amino group of a protein. Furthermore small molecules such as polyamines and antibiotics can be acetylated and deacetylated enzymatically at amino groups. While much research focused on N-(ε)-ac(et)ylation of lysine side chains, much less is known about the occurrence, the regulation and the physiological roles on N-(α)-ac(et)ylation of protein amino termini in bacteria. Lysine ac(et)ylation was shown to affect protein function by various mechanisms ranging from quenching of the positive charge, increasing the lysine side chains’ size affecting the protein surface complementarity, increasing the hydrophobicity and by interfering with other post-translational modifications. While N-(ε)-lysine ac(et)ylation was shown to be reversible, dynamically regulated by lysine acetyltransferases and lysine deacetylases, for N-(α)-ac(et)ylation only N-terminal acetyltransferases were identified and so far no deacetylases were discovered neither in bacteria nor in mammals. To this end, N-terminal ac(et)ylation is regarded as being irreversible. Besides enzymatic ac(et)ylation, recent data showed that ac(et)ylation of lysine side chains and of the proteins N-termini can also occur non-enzymatically by the high-energy molecules acetyl-coenzyme A and acetyl-phosphate. Acetyl-phosphate is supposed to be the key molecule that drives non-enzymatic ac(et)ylation in bacteria. Non-enzymatic ac(et)ylation can occur site-specifically with both, the protein primary sequence and the three dimensional structure affecting its efficiency. Ac(et)ylation is tightly controlled by the cellular metabolic state as acetyltransferases use ac(et)yl-CoA as donor molecule for the ac(et)ylation and sirtuin deacetylases use NAD+ as co-substrate for the deac(et)ylation. Moreover, the accumulation of ac(et)yl-CoA and acetyl-phosphate is dependent on the cellular metabolic state. This constitutes a feedback control mechanism as activities of many metabolic enzymes were shown to be regulated by lysine ac(et)ylation. Our knowledge on lysine ac(et)ylation significantly increased in the last decade predominantly due to the huge methodological advances that were made in fields such as mass-spectrometry, structural biology and synthetic biology. This also includes the identification of additional acylations occurring on lysine side chains with supposedly different regulatory potential. This review highlights recent advances in the research field. Our knowledge on enzymatic regulation of lysine ac(et)ylation will be summarized with a special focus on structural and mechanistic characterization of the enzymes, the mechanisms underlying non-enzymatic/chemical ac(et)ylation are explained, recent technological progress in the field are presented and selected examples highlighting the important physiological roles of lysine ac(et)ylation are summarized.

Biochemical, structural, and functional studies reveal that MAB_4324c from Mycobacterium abscessus is an active tandem repeat N‐acetyltransferase

“…Lysine acetylation is a ubiquitous posttranslational modification in bacteria [44], and this is particularly true in mycobacteria. In M. tuberculosis , about 140 proteins involved in numerous metabolic processes were shown to be acetylated [52].…”

Protein acetylation effects on enzyme activity and metabolic pathway fluxes

“…It has to be recalled that the enzymes with the lowest catalytic efficiencies (lowest Vmax/Km ratios) may exert significant control on the metabolite concentrations 16–19 . This scenario may be more complicated because, in contrast to eukaryotes where enzymatic and nonenzymatic protein acetylation depends on acetyl‐CoA, in bacteria, acetyl‐phosphate seems to mediate most nonenzymatic acetylation 15 …”

“…It has been proposed that acetyltransferases and deacetylases are sensors of the cellular metabolic state and of the NAD + level. 15 However, the Km and Vmax values of Sirts have not been determined and hence this proposal lacks kinetic and metabolic basis. In addition, whether the sirtuin Km values are relatively high (in the millimolar range) or low (in the low micromolar range), hence these enzymes will not be able to sense the physiological variations of acetyl-CoA and NAD + .…”

“…[16][17][18][19] This scenario may be more complicated because, in contrast to eukaryotes where enzymatic and nonenzymatic protein acetylation depends on acetyl-CoA, in bacteria, acetyl-phosphate seems to mediate most nonenzymatic acetylation. 15 Acetylation of proteins in Archaea and its effect on metabolism is still poorly understood. In the hyperthermophilic Archaeon Sulfolobus islandicus a proteomic analysis showed that 26% of its total proteins were N-ε-acetylated on K residues and 44% of the identified proteins were N-terminal-acetylated.…”

“…It has been proposed that acetyltransferases and deacetylases are sensors of the cellular metabolic state and of the NAD + level 15 . However, the Km and Vmax values of Sirts have not been determined and hence this proposal lacks kinetic and metabolic basis.…”