Discrimination and Integration of Stress Signals by Pathogenic Bacteria

Abstract

For pathogenic bacteria, the ability to sense and respond to environmental stresses encountered within the host is critically important, allowing them to adapt to changing conditions and express virulence genes appropriately. This review considers the diverse molecular mechanisms by which stress conditions are sensed by bacteria, how related signals are discriminated, and how stress responses are integrated, highlighting recent studies in selected bacterial pathogens of clinical relevance.

Figure 1. Sensing of H₂O₂ by OxyR

The Pseudomonas aeruginosa OxyR structure suggests a role for H₂O molecules in H₂O₂ sensing. (A) Peroxidatic Cys¹⁹⁹ is in a hydrophobic pocket of OxyR. Hydrophobic and hydrophilic residues are shown in red and white, respectively. Panel B shows the structure of PaOxyR with the conserved residues forming the pocket where the three H₂O molecules reside. Conserved amino acids (purple) were identified using the ConSurf server with input of 75 OxyR orthologs identified by PSI-BLAST in the SWISS-PROT protein sequence database (Celniker et al., 2013; Ashkenazy et al., 2010). (C) Three H₂O molecules (green spheres) establish a network of hydrogen bonding with amino acid residues in the vicinity of Cys¹⁹⁹. Red dashes show putative hydrogen-bonding of H₂O with the backbone, and side-chains of conserved residues. The H₂O molecule most proximal to Cys¹⁹⁹ is replaced by H₂O₂. The two H₂O molecules remaining in the pocket aid in the protonation of a leaving OH⁻ group arising from peroxidatic cleavage of H₂O₂ by the Cys¹⁹⁹-reduced thiol. Residues interacting with the three H₂O molecules are highly conserved (purple) in OxyR, suggesting a common mechanism of H₂O₂ sensing among OxyR orthologs. PDB code 4Y0M was used for PyMol analysis.

Figure 2. Mechanisms of signal transduction in response to NO· and H₂O₂

(A) Reduced H-NOX from Shewanella oneidensis with the penta-coordinated heme (yellow) bound to His¹⁰³. (B) Binding of NO· (blue and red spheres) to the H-NOX heme severs the bond between His¹⁰³ and Fe²⁺. Free His¹⁰³ rotates the αF helix (green), activating signal transduction. Recent structures of the H₂O₂ sensor OxyR from Pseudomonas aeruginosa have revealed the molecular mechanism of sensing and signal transduction in response to H₂O₂. (C) Peroxidatic Cys¹⁹⁹ and Cys²⁰⁸ are 15–17Å apart in opposite ends of an α-helix (green). (D) Oxidation of Cys¹⁹⁹ by H₂O₂ produces a sulfenic acid (-SOH) intermediate that is mimicked by a C199D mutation. Oxidation of Cys¹⁹⁹ triggers new hydrogen-bonding interactions between the sulfenylated group and Arg²⁰¹ and Phe²⁰⁰ (not shown). (E) The new hydrogen-bonding disorganizes the intervening α-helix, increasing the reactivity of Cys²⁰⁸ and facilitating formation of a disulfide. (C) and (D) show structures of reduced and OxyR C199D proteins from P. aeruginosa, whereas (E) shows oxidized OxyR from Escherichia coli. PDB codes 4U99, 4U9B, 4Y0M, 4XWS, and 1IBA were used to generate the images in panels (A–E), respectively.

Figure 3. Discrimination of O₂ and NO· by H-NOX proteins

Dedicated sensors of reactive species discriminate closely related diatomic gases. H-NOX proteins from Caldoanaerobacter subterraneus (A) and Shewanella oneidensis (B) can discriminate between O₂ and NO·, respectively. The heme (yellow) of C. subterraneus H-NOX is hexa-coordinated with O₂, the porphyrin ring, and the imidazole group of His¹⁰². O₂ maintains hydrogen-bonding interactions (red dashes) with the hydroxyl group of Tyr¹⁴⁰. In contrast, the heme of NO·-dedicated sensors such as S. oneidensis H-NOX is penta-coordinated. Panel (B) shows the NO· molecule (red and blue spheres) in the proximal face of the porphyrin ring. The short side-chain of Cys¹⁴¹ does not allow hydrogen-bonding after NO· binding at the distal face of the porphyrin ring (not shown). PDB codes 1U55 and 4U9B were used for the analysis of C. subterraneus H-NOX and S. oneidensis H-NOX, respectively.