Fig. 6: RutR contains an unstructured histone-like N-terminal tail contributing to dsDNA-binding. | Nature Communications

Fig. 6: RutR contains an unstructured histone-like N-terminal tail contributing to dsDNA-binding.

From: Bacteria employ lysine acetylation of transcriptional regulators to adapt gene expression to cellular metabolism

Fig. 6

a. Localization of K7 and K11 in the histone-like N-terminal tail of RutR in the AlphaFold2 model85,86. The AlphaFold2 model was superimposed with chain B of the structure of K52-acetylated RutR. The structures are highly similar with an overall r.m.s.d. of 1.15 Å. The N-terminal tail is highly flexible supported by the finding that no electron density was obtained for the N-terminal 12 (chain A) or 11 (chain B) residues in the RutR AcK52 structure solved here (PDB: 6Z1B). The AlphaFold2 model supports that these N-terminal residues are unstructured represented by the low model confidence score (pLDDT < 50). b Deletion of the unstructured histone-like N-terminal tail in RutR Δ1-12 impairs dsDNA-binding. Left panel: RutR Δ1-12 binds to boxrutA and boxcarA dsDNA as shown by EMSAs. boxrutA, boxcarA, and control dsDNA fragments are incubated with increasing concentrations of RutR proteins as indicated. Experiments were performed in duplicates. Right panels: RutR Δ1-12 impairs binding towards both, boxrutA and boxcarA, dsDNA as shown by ITC (DP: differential power); boxrutA: left diagram; boxcarA: right diagram. All interactions were conducted in three biologically independent experiments (n = 3) and the values in the table are given as means ± standard deviations (Supplementary Table 3). Source data are provided as Source Data files. c Electrostatic surface representation of the AlphaFold2 model of RutR. The positions of acetylated lysines in RutR are indicated. The unstructured N-terminal tails encompassing the α-N-terminus, K7, and K11 are positively charged as visible by the blue color. Acetylation of the α-amino groups and of the ε-amino groups of K7 and K11 would neutralize this positive charge affecting electrostatic steering of RutR to boxrutA and boxcarA dsDNA. The basic patch consisting of 19-KKK-21 in α1 is shown and K52 in the HTH of the DNA-binding domain and K62 in the N-terminus of α4 are also contributing to the positive surface potential in this region of RutR. K150 is located at the top of the LBD. The electrostatic potential was calculated by the APBS plugin in PyMOL (with k: Boltzmann constant, T: temperature, e: unit charge). The figure was prepared by PyMOL144.

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