Fig. 1: The transcriptional regulator RutR is lysine acetylated.

a Promoter organization of RutR target genes (rutAG (upper panel), rutR (middle panel), and carAB (lower panel)). Open reading frames are depicted as blue boxes with labels/arrows indicating the gene/coding direction. Translational start codons are highlighted as black boxes. Small black boxes represent the promoter −35 and −10 elements. An arrow shows the transcription start site initiated by the indicated sigma factor. The red box shows the binding site of the repressor RutR in rutAB and rutR. Green boxes mark binding sites of NtrC. For carAB RutR acts as activator and is shown by a green box overlapping with PepA (aminopeptidase A) repressor binding site (red box). Further repressor binding sites (purine regulator (PurR), arginine regulator (ArgR)) are also shown by red boxes. The grey box represents the binding site of the integration host factor (IHF). b Alignment of the RutR-binding sequences in the promoter regions of rutR/rutAG and carAB in comparison to the defined RutR consensus sequence. The binding sequence of the RutR-related transcriptional regulator QacR from Staphylococcus aureus in the IR1 operator sequence downstream of the qacA and qacB promoters is shown. Numbering shows the position relative to the inversion site of the palindromic binding motifs. c Position of the lysines reported to be lysine-acetylated and studied here are highlighted in the structure of RutR•uracil (PDB: 4JYK). K21 is located in the N-terminal α1 helix, K52 is within α3 of the helix-turn-helix (HTH) motif of the DNA-binding domain (DBD), K62 is in the N-terminus of helix α4, K95 in the N-terminal side of α5 and K150 lies at the top of the ligand-binding domain (LBD) at the C-terminal end of α7. d Regulatory cycle of lysine acetylation in Escherichia coli. N-(ε)-lysine acetylation and/or N-(α)-acetylation is regulated enzymatically by the lysine acetyltransferases (KATs) PatZ /YfiQ, PhnO, YiaC, RimI, and YjaB using acetyl-CoA as acetyl group donor molecule or non-enzymatically by acetyl-phosphate. Acetyl-phosphate is generated by acetate-kinase (AckA) or by phosphotransacetylase (Pta). E. coli encodes one single NAD⁺-dependent sirtuin deacetylase, i.e. CobB, inhibited by nicotinamide (NA). The long isoform of CobB is inhibited by the second messenger cyclic-di-GMP (c-di-GMP)³⁸.