Modulation of the bacterial CobB sirtuin deacylase activity by N-terminal acetylation

Abstract

<jats:p>In eukaryotic cells, the N-terminal amino moiety of many proteins is modified by N-acetyltransferases (NATs). This protein modification can alter the folding of the target protein; can affect binding interactions of the target protein with substrates, allosteric effectors, or other proteins; or can trigger protein degradation. In prokaryotes, only ribosomal proteins are known to be N-terminally acetylated, and the acetyltransferases responsible for this modification belong to the Rim family of proteins. Here, we report that, in<jats:italic>Salmonella enterica</jats:italic>, the sirtuin deacylase CobB long isoform (CobB<jats:sub>L</jats:sub>) is N-terminally acetylated by the YiaC protein of this bacterium. Results of in vitro acetylation assays showed that CobB<jats:sub>L</jats:sub>was acetylated by YiaC; liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to confirm these results. Results of in vitro and in vivo experiments showed that CobB<jats:sub>L</jats:sub>deacetylase activity was negatively affected when YiaC acetylated its N terminus. We report 1) modulation of a bacterial sirtuin deacylase activity by acetylation, 2) that the Gcn5-related YiaC protein is the acetyltransferase that modifies CobB<jats:sub>L</jats:sub>, and 3) that YiaC is an NAT. Based on our data, we propose the name of NatA (<jats:italic>N</jats:italic>-acyltransferase A) in lieu of YiaC to reflect the function of the enzyme.</jats:p>

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

“…Along that line, also for the reported lysine acetyltransferase YiaC an activity as N-terminal acetyltransferase was recently shown suggesting a role of N-terminal acetylation in bacteria (Christensen et al, 2018;Parks and Escalante-Semerena, 2020). YiaC was shown to act as N-terminal acetyltransferase for the long isoform of CobB in Salmonella enterica impairing CobB deacetylase activity (Parks and Escalante-Semerena, 2020). Notably, also in plastids of plants a novel family of GNAT protein acetyltransferases was discovered with a dual N-terminal and lysine acetyltransferase activity suggesting that these enzymes developed during evolution prior to development of photosynthetic plants (Bienvenut et al, 2020).…”

“…As stated above, RimI is active in acetylation of N-(ε)-amino groups of lysine side chains and also in acetylation of N-terminal amino groups in proteins acting additionally as N-(α)-acetyltransferase. Along that line, also for the reported lysine acetyltransferase YiaC an activity as N-terminal acetyltransferase was recently shown suggesting a role of N-terminal acetylation in bacteria (Christensen et al, 2018;Parks and Escalante-Semerena, 2020). YiaC was shown to act as N-terminal acetyltransferase for the long isoform of CobB in Salmonella enterica impairing CobB deacetylase activity (Parks and Escalante-Semerena, 2020).…”

“…However, CobB was shown to exist in two isoforms, a long (CobB L ) and an N-terminally by 37 residues shorter short isoform (CobB S ) (Tucker and Escalante-Semerena, 2010;Umehara et al, 2018). CobB L was shown to be N-terminally acetylated by the acetyltransferase YiaC/NatA impairing CobB L 's catalytic activity, shown to have a dual activity acetylating N-α-and N-ε-amino groups in proteins (Parks and Escalante-Semerena, 2020). The N-terminal region was shown to be important for binding to the intracellular signaling molecule c-di-GMP (Figure 5A and Supplementary Figure 2).…”

Bacterial Sirtuins Overview: An Open Niche to Explore

“…More recently, regulation of the long isoform of CobB by N-terminal acetylation has been reported and negatively affects its deacetylase activity. Moreover, YiaC, a putative S. enterica acetyltransferase has been identified as the responsible for CobB N-terminal acetylation (Parks and Escalante-Semerena, 2020).…”

Investigation of the Importance of Protein 3D Structure for Assessing Conservation of Lysine Acetylation Sites in Protein Homologs

“…The most well-studied bacterial Nε-acetyltransferase is YfiQ (or PatZ), which has been shown to acetylate a variety of bacterial proteins and is important for many cellular processes, including bacterial pathogenesis, virulence and stress resistance (Starai and Escalante-Semerena, 2004;Ma and Wood, 2011;Castano-Cerezo et al, 2014;Liu et al, 2018;Luu and Carabetta, 2021). Four additional KATs in E. coli have also been identified (YiaC, YjaB, PhnO, and RimI) (Christensen et al, 2018), but RimI and YiaC are also able to acetylate Nα-amines of proteins (Vetting et al, 2008;Parks and Escalante-Semerena, 2020). Recent studies have highlighted the diversity of proteins that are acetylated in prokaryotes, but deep knowledge of how acetylation affects their physiology remains relatively limited.…”