Structure and DNA-binding traits of the transition state regulator AbrB

Abstract

The AbrB protein from Bacillus subtilis is a DNA-binding global regulator controlling the onset of a vast array of protective functions under stressful conditions. Such functions include biofilm formation, antibiotic production, competence development, extracellular enzyme production, motility, and sporulation. AbrB orthologs are known in a variety of prokaryotic organisms, most notably in all infectious strains of Clostridia, Listeria, and Bacilli. Despite its central role in bacterial response and defense, its structure has been elusive because of its highly dynamic character. Orienting its N- and C-terminal domains with respect to one another has been especially problematic. Here, we have generated a structure of full-length, tetrameric AbrB using nuclear magnetic resonance, chemical crosslinking, and mass spectrometry. We note that AbrB possesses a strip of positive electrostatic potential encompassing its DNA-binding region and that its C-terminal domain aids in DNA binding.

Figure 1

The NMR structure of AbrBC. (A) The 10 lowest energy structures from water refinement. Individual monomers are green and blue. (B) Alternate view of AbrBC with relevant structural features labeled. (C) Electrostatic surface potential of AbrBC (same view as Figure 1A, rotated 180°); blue is positive charge and red is negative.

Figure 2

The fully assembled structure of AbrB. (A) Schematic of the AbrB-BS tetramer with alternating colors corresponding to individual AbrB monomers. (B) Ribbon structure with crosslinks formed from AbrBC lysines to AbrBN lysines (in Å); yellow and red lines represent crosslinks to the neighboring AbrBN domains; orange lines represent the crosslink from K9-K76. N- and C- domains were visually docked according to the cross linking/MS data and then energy minimized via AMBER resulting in distances shown. (C) Electrostatic surface potential of AbrB (blue = positive, red = negative). (D) The conformational space sampling of AbrBN (red to cyan) with fixed positional restraints on AbrBC (grey).

Figure 3

AbrB upon binding DNA. (A) Model of the docked complex of AbrB and target promoter abrB8 using HADDOCK. (B) Overlay of Figure 2A and a docked complex (blue) with all residues allowed to be fully flexible (grey). (C) and (D) alternate views of electrostatic surface potential of AbrB bound to abrB8 DNA.