From Host Heme To Iron: The Expanding Spectrum of Heme Degrading Enzymes Used by Pathogenic Bacteria

Abstract

Iron is an essential nutrient for many bacteria. Since the metal is highly sequestered in host tissues, bound predominantly to heme, pathogenic bacteria often take advantage of heme uptake and degradation mechanisms to acquire iron during infection. The most common mechanism of releasing iron from heme is through oxidative degradation by heme oxygenases (HOs). In addition, an increasing number of proteins that belong to two distinct structural families have been implicated in aerobic heme catabolism. Finally, an enzyme that degrades heme anaerobically was recently uncovered, further expanding the mechanisms for bacterial heme degradation. In this analysis, we cover the spectrum and recent advances in heme degradation by infectious bacteria. We briefly explain heme oxidation by the two groups of recognized HOs to ground readers before focusing on two new types of proteins that are reported to be involved in utilization of heme iron. We discuss the structure and enzymatic function of proteins representing these groups, their biological context, and how they are regulated to provide a more complete look at their cellular role.

Keywords: heme binding; heme degradation; heme oxygenase; iron regulation; pathogenic bacteria.

Figure 1

The three oxidative steps of canonical heme oxidation and the chemical structure of staphylobilin and mycobilin. (A) The three oxidative steps of canonical heme oxidation. In the first step heme is oxidized to ferric-hydroperoxide, then it is self-hydroxylated to α-meso-hydroxyheme. Next it is oxidized to α-verdoheme, which is ultimately oxidized to α-biliverdin. (B) One of the two isomers of staphylobilin produced by IsdG/I. (C) One of the two isomers of mycobilin produced by MhuD.

Figure 2

Overall structure of canonical and IsdG-like heme oxygenases. (A) From left to right: HO-1, HmuO, and PigA. This family of enzymes are commonly referred to as the canonical HOs. They are α-only proteins and have been colored so that the proximal helix is in white and the distal helix is in blue. These helixes take an open conformation when the binding pocket is empty but tighten and close around the heme molecule. Note how the propionate groups in PigA are rotated compared to HO-1 and HmuO. (B) From left to right: IsdG, MhuD, Isd-LmHde. These enzymes represent the second group of HOs, the IsdG-like HOs. This group consists of α/β proteins that dimerize across their β-sheets. Both IsdG and MhuD have been colored so that one monomer is in white and the second monomer is in blue. The Isd-LmHde structure has been colored so that the N-terminal is in magenta and the C-terminal is in white.

Figure 3

Alternative heme ruffling in IsdG and MhuD. (A) Represents the heme ruffling in IsdG and (B) Represents the heme ruffling in MhuD. Notice in (A), how the IsdG bends the heme so that the β- and δ-meso carbons are pushed away from the histidine, causing the α-meso carbon to move toward the ligand. In (B), MhuD bends the heme so that the β- and δ-meso carbons are closer to the histidine ligand.

Figure 4

Overall structure of proteins with HemS motifs. (A) Represents ChuS, (B) Represents HemS, and (C) Represents PhuS. In all representations the N-terminal HemS domain is in white and the C-terminal HemS domain is in blue. Looking at the structure, ChuS consists of a mix of α-helices and β-strands arranged so that the β-sheets form the core of the enzyme and are flanked by three α-helices on one side and two on the other side. This configuration is conserved in the structure of HemS, although HemS is symmetrical, with three α-helices on each side.

Figure 5

Enzymes with FMN-binding domains. Proteins from the PNPOx-like subfamily contain a β-barrel with a Greek key topology (a protein structure consisting of four antiparallel strands connected by three hairpin loops that is named for a common pattern in Grecian decoration). The pictured enzymes also contain FMN-binding domains, although neither HutZ or HupZ can bind FMN. (A) (from left to right) a monomer of HugZ and a monomer of ChuZ. In both representations, the PNPOx domain is in white. In ChuZ, the canonical heme binding pocket is indicated by the orange arrow. (B) (from left to right) HutZ and HupZ. In both representations one monomer is colored blue and the other monomer is colored teal.