Corynebacterium diphtheriae HmuT: dissecting the roles of conserved residues in heme pocket stabilization

Deciphering the role of the distal pocket in Staphylococcus aureus coproheme decarboxylase

Coproheme decarboxylase (ChdC) catalyzes the sequential oxidative decarboxylation of coproheme III propionate side chains at positions 2 and 4 to form heme b by activation of two molecules of H2O2 at its substrate's iron center. The coproheme III binding pocket lacks the distal His-Arg pair that polarizes and acts as a catalytic base toward activation of coordinated H2O2 in canonical heme-dependent peroxidases. Instead ChdC from Staphylococcus aureus has a Gln (Q185). This report presents thermodynamic, kinetic, and spectroscopic results that provide comparative insight into how wild type (WT) and Q185A and Q185R variant ChdCs activate H2O2. Reactivities with H2O2 and cyanide affinities at pH 7.5 follow the trend: WT > Q185R > Q185A. Both variants exhibited greater catalase efficiency than WT ChdC. Vibrational resonance Raman signatures of ferric coproheme-CN- and ferrous coproheme-CO complexes of WT, Q185A, and Q185R SaChdCs revealed that the Arg mutation does not significantly alter the distal environment while Q185A has a more open active site. Together these data are consistent with a modest role for Q185 in promoting the decarboxylation reaction. A model for the proton transfer required for H2O2 activation that involves the Gln185 iminol tautomer is presented. The three ChdCs reacted with chlorite to generate harderoheme III and heme b to varying extents. In reaction with chlorite, coproheme III:SaChdC was cleanly converted to harderoheme III:SaChdC, which exhibited vinyl bending and stretching modes at 423 and 1622 cm-1, respectively. Differences in SaChdC reactivity with ClO2- and H2O2 relative to those of chlorite dismutase and peroxidases, respectively, are discussed.

The Exoproteome and Surfaceome of Toxigenic Corynebacterium diphtheriae 1737 and Its Response to Iron Restriction and Growth on Human Hemoglobin

Toxin-producing Corynebacterium diphtheriae strains are the etiological agents of the severe upper respiratory disease, diphtheria. A global phylogenetic analysis revealed that biotype gravis is particularly lethal as it produces diphtheria toxin and a range of other virulence factors, particularly when it encounters low levels of iron at sites of infection. To gain insight into how it colonizes its host, we have identified iron-dependent changes in the exoproteome and surfaceome of C. diphtheriae strain 1737 using a combination of whole-cell fractionation, intact cell surface proteolysis, and quantitative proteomics. In total, we identified 1414 of the predicted 2265 proteins (62%) encoded by its reference genome. For each protein, we quantified its degree of secretion and surface exposure, revealing that exoproteases and hydrolases predominate in the exoproteome, while the surfaceome is enriched with adhesins, particularly DIP2093. Our analysis provides insight into how components in the heme-acquisition system are positioned, showing pronounced surface exposure of the strain-specific ChtA/ChtC paralogues and high secretion of the species-conserved heme-binding HtaA protein, suggesting it functions as a hemophore. Profiling the response of the exoproteome and surfaceome after microbial exposure to human hemoglobin and iron limitation reveals potential virulence factors that may be expressed at sites of infection. Data are available via ProteomeXchange with identifier PXD051674.

Development and atomic structure of a new fluorescence-based sensor to probe heme transfer in bacterial pathogens

Heme is the most abundant source of iron in the human body and is actively scavenged by bacterial pathogens during infections. Corynebacterium diphtheriae and other species of actinobacteria scavenge heme using cell wall associated and secreted proteins that contain Conserved Region (CR) domains. Here we report the development of a fluorescent sensor to measure heme transfer from the C-terminal CR domain within the HtaA protein (CR2) to other hemoproteins within the heme-uptake system. The sensor contains the CR2 domain inserted into the β2 to β3 turn of the Enhanced Green Fluorescent Protein (EGFP). A 2.45 Å crystal structure reveals the basis of heme binding to the CR2 domain via iron-tyrosyl coordination and shares conserved structural features with CR domains present in Corynebacterium glutamicum. The structure and small angle X-ray scattering experiments are consistent with the sensor adopting a V-shaped structure that exhibits only small fluctuations in inter-domain positioning. We demonstrate heme transfer from the sensor to the CR domains located within the HtaA or HtaB proteins in the heme-uptake system as measured by a ∼ 60% increase in sensor fluorescence and native mass spectrometry.

Structure-Based Mechanism for Oxidative Decarboxylation Reactions Mediated by Amino Acids and Heme Propionates in Coproheme Decarboxylase (HemQ)

Coproheme decarboxylase catalyzes two sequential oxidative decarboxylations with H2O2 as the oxidant, coproheme III as substrate and cofactor, and heme b as the product. Each reaction breaks a C-C bond and results in net loss of hydride, via steps that are not clear. Solution and solid-state structural characterization of the protein in complex with a substrate analog revealed a highly unconventional H2O2-activating distal environment with the reactive propionic acids (2 and 4) on the opposite side of the porphyrin plane. This suggested that, in contrast to direct C-H bond cleavage catalyzed by a high-valent iron intermediate, the coproheme oxidations must occur through mediating amino acid residues. A tyrosine that hydrogen bonds to propionate 2 in a position analogous to the substrate in ascorbate peroxidase is essential for both decarboxylations, while a lysine that salt bridges to propionate 4 is required solely for the second. A mechanism is proposed in which propionate 2 relays an oxidizing equivalent from a coproheme compound I intermediate to the reactive deprotonated tyrosine, forming Tyr•. This residue then abstracts a net hydrogen atom (H•) from propionate 2, followed by migration of the unpaired propionyl electron to the coproheme iron to yield the ferric harderoheme and CO2 products. A similar pathway is proposed for decarboxylation of propionate 4, but with a lysine residue as an essential proton shuttle. The proposed reaction suggests an extended relay of heme-mediated e-/H+ transfers and a novel route for the conversion of carboxylic acids to alkenes.