HutW from Vibrio cholerae Is an Anaerobic Heme-Degrading Enzyme with Unique Functional Properties

A Novel Heme-Degrading Enzyme that Regulates Heme and Iron Homeostasis and Promotes Virulence in Enterococcus faecalis

Enterococcus faecalis, a gut commensal, is a leading cause of opportunistic infections. Its virulence is linked to its ability to thrive in hostile environments, which includes host-imposed metal starvation. We recently showed that E. faecalis evades iron starvation using five dedicated transporters that collectively scavenge iron from host tissues and other iron-deprived conditions. Interestingly, heme, the most abundant source of iron in the human body, supported growth of a strain lacking all five iron transporters (Δ5Fe). To release iron from heme, many bacterial pathogens utilize heme oxygenase enzymes to degrade the porphyrin that coordinates the iron ion of heme. Although E. faecalis lacks these enzymes, bioinformatics revealed a potential ortholog of the anaerobic heme-degrading enzyme anaerobilin synthase, found in Escherichia coli and a few other Gram-negative bacteria. Here, we demonstrated that deletion of OG1RF_RS05575 in E. faecalis (ΔRS05575) or in the Δ5Fe background (Δ5FeΔRS05575) led to intracellular heme accumulation and hypersensitivity under anaerobic conditions, suggesting RS05575 encodes an anaerobilin synthase, the first of its kind described in Gram-positive bacteria. Additionally, deletion of RS05575, either alone or in the Δ5Fe background, impaired E. faecalis colonization in the mouse gastrointestinal tract and virulence in mouse peritonitis and rabbit infective endocarditis models. These results reveal that RS05575 is responsible for anaerobic degradation of heme and identify this relatively new enzyme class as a novel factor in bacterial pathogenesis. Findings from this study are likely to have broad implications, as homologues of RS05575 are found in other Gram-positive facultative anaerobes.

A dye-decolorizing peroxidase from Vibrio cholerae can demetallate heme

Iron is an essential element for bacterial survival. Bacterial pathogens have therefore developed methods to obtain iron. Vibrio cholerae, the intestinal pathogen that causes cholera, utilizes heme as an iron source. DyP from V. cholerae (VcDyP) is a dye-decolorizing peroxidase. When VcDyP was expressed in Escherichia coli and purified, it was found to contain protoporphyrin IX (PPIX) but not heme, indicating that the protein possesses deferrochelatase activity. Here, we examined the demetallation reaction of VcDyP using fluorescence spectroscopy. Treatment of heme-reconstituted VcDyP with sodium dithionite under anaerobic conditions led to an increase in the fluorescence intensity at 624 nm, suggesting the formation of PPIX. Although the same reaction was conducted using myoglobin, horseradish peroxidase and hemin, no increase in the fluorescence was observed. Therefore, demetallation of heme is specific to VcDyP. This reaction was faster at lower pH, but the amplitudes of the fluorescence increase were larger at pH 6.5-7.5, in clear contrast to the dye-decolorizing activity with the optimal pH of 4.5. In contrast to HutZ from V. cholerae, which is a heme-degrading enzyme that cleaves the heme macrocycle to release iron, VcDyP can remove iron from heme without degradation. To our knowledge, VcDyP is the first enzyme whose demetallation activity has been confirmed at neutral pH. Our results show that VcDyP is a bifunctional protein that degrades anthraquinone dyes and demetallates heme.

HutZ from Aliivibrio fischeri Inhibits HutW-Mediated Anaerobilin Formation by Sequestering Heme

Anaerobilin synthase catalyzes the decyclization of the heme protoporphyrin ring, an O2-independent reaction that liberates iron and produces the linear tetrapyrrole, anaerobilin. The marine bacterium Aliivibrio fischeri, the enteric pathogen Escherichia coli O157:H7, and the opportunistic oral pathogen Fusobacterium nucleatum encode anaerobilin synthase as part of their heme uptake/utilization operons, designated chu (E. coli O157:H7), hmu (F. nucleatum), and hut (A. fischeri). F. nucleatum and E. coli O157:H7 contain accessory proteins (ChuS, ChuY, and HmuF) encoded in their respective operons that mitigate against the cytotoxicity of labile heme and anaerobilin by functioning in heme trafficking and anaerobilin reduction. However, the hut operon of A. fischeri and other members of the Vibrionaceae family including the enteric pathogen Vibrio cholerae do not contain homologues to these accessory proteins, raising questions as to how members of this family mitigate against anaerobilin and heme toxicity. Herein, we show that HutW (anaerobilin synthase) from A. fischeri produces anaerobilin, but that HutX and HutZ, encoded downstream of HutW, do not catalyze anaerobilin reduction in the presence of excess NAD(P)H, FAD, and FMN. However, we show that HutZ prevents labile heme and anaerobilin cytotoxicity by binding tightly to heme, sequestering it from HutW, and preventing anaerobilin formation. Thus, A. fischeri is seemingly unable to extract iron from heme using the hutWXZ gene products. Our results further suggest that the structurally distinct chu, hmu, and hut operons have functionally converged to protect the cell from anaerobilin accumulation and heme cytotoxicity.

Heme utilization by the enterococci

Heme consists of a tetrapyrrole ring ligating an iron ion and has important roles in biological systems. While well-known as the oxygen-binding molecule within hemoglobin of mammals, heme is also cofactor for several enzymes and a major iron source for bacteria within the host. The enterococci are a diverse group of Gram-positive bacteria that exist primarily within the gastrointestinal tract of animals. However, some species within this genus can transform into formidable opportunistic pathogens, largely owing to their extraordinary adaptability to hostile environments. Although enterococci cannot synthesize heme nor depend on heme to grow, several species within the genus encode proteins that utilize heme as a cofactor, which appears to increase their fitness and ability to thrive in challenging environments. This includes more efficient energy generation via aerobic respiration and protection from reactive oxygen species. Here, we review the significance of heme to enterococci, primarily the major human pathogen Enterococcus faecalis, use bioinformatics to assess the prevalence of hemoproteins throughout the genus, and highlight recent studies that underscore the central role of the heme-E. faecalis relationship in host-pathogen dynamics and interspecies bacterial interactions.

Comparative phenotype and transcriptome analysis revealed the role of ferric uptake regulator (Fur) in the virulence of Vibrio harveyi isolated from diseased American eel (Anguilla rostrata)

Vibrio harveyi is commonly found in salt and brackish water and is recognized as a serious bacterial pathogen in aquaculture worldwide. In this study, we cloned the ferric uptake regulator (fur) gene from V. harveyi wild-type strain HA_1, which was isolated from diseased American eels (Anguilla rostrata) and has a length of 450 bp, encoding 149 amino acids. Then, a mutant strain, HA_1-Δfur, was constructed through homologous recombination of a suicide plasmid (pCVD442). The HA_1-Δfur mutant exhibited weaker biofilm formation and swarming motility, and 18-fold decrease (5.5%) in virulence to the American eels; compared to the wild-type strain, the mutant strain showed time and diameter differences in growth and haemolysis, respectively. Additionally, the adhesion ability of the mutant strain was significantly decreased. Moreover, there were 15 different biochemical indicators observed between the two strains. Transcriptome analysis revealed that 875 genes were differentially expressed in the Δfur mutant, with 385 up-regulated and 490 down-regulated DEGs. GO and KEGG enrichment analysis revealed that, compared to the wild-type strain, the type II and type VI secretion systems (T2SS and T6SS), amino acid synthesis and transport and energy metabolism pathways were significantly down-regulated, but the ABC transporters and biosynthesis of siderophore group non-ribosomal peptides pathways were up-regulated in the Δfur strain. The qRT-PCR results further confirmed that DEGs responsible for amino acid transport and energy metabolism were positively regulated, but DEGs involved in iron acquisition were negatively regulated in the Δfur strain. These findings suggest that the virulence of the Δfur strain was significantly decreased, which is closely related to phenotype changing and gene transcript regulation.

Evidence for Porphyrin-Mediated Electron Transfer in the Radical SAM Enzyme HutW

Bacteria that infect the human gut must compete for essential nutrients, including iron, under a variety of different metabolic conditions. Several enteric pathogens, including Vibrio cholerae and Escherichia coli O157:H7, have evolved mechanisms to obtain iron from heme in an anaerobic environment. Our laboratory has demonstrated that a radical S-adenosylmethionine (SAM) methyltransferase is responsible for the opening of the heme porphyrin ring and release of iron under anaerobic conditions. Furthermore, the enzyme in V. cholerae, HutW, has recently been shown to accept electrons from NADPH directly when SAM is utilized to initiate the reaction. However, how NADPH, a hydride donor, catalyzes the single electron reduction of a [4Fe-4S] cluster, and/or subsequent electron/proton transfer reactions, was not addressed. In this work, we provide evidence that the substrate, in this case, heme, facilitates electron transfer from NADPH to the [4Fe-4S] cluster. This study uncovers a new electron transfer pathway adopted by radical SAM enzymes and further expands our understanding of these enzymes in bacterial pathogens.

Nutritional immunity: the battle for nutrient metals at the host-pathogen interface

Trace metals are essential micronutrients required for survival across all kingdoms of life. From bacteria to animals, metals have critical roles as both structural and catalytic cofactors for an estimated third of the proteome, representing a major contributor to the maintenance of cellular homeostasis. The reactivity of metal ions engenders them with the ability to promote enzyme catalysis and stabilize reaction intermediates. However, these properties render metals toxic at high concentrations and, therefore, metal levels must be tightly regulated. Having evolved in close association with bacteria, vertebrate hosts have developed numerous strategies of metal limitation and intoxication that prevent bacterial proliferation, a process termed nutritional immunity. In turn, bacterial pathogens have evolved adaptive mechanisms to survive in conditions of metal depletion or excess. In this Review, we discuss mechanisms by which nutrient metals shape the interactions between bacterial pathogens and animal hosts. We explore the cell-specific and tissue-specific roles of distinct trace metals in shaping bacterial infections, as well as implications for future research and new therapeutic development.

Class C Radical SAM Methyltransferases Involved in Anaerobic Heme Degradation

Class C radical SAM methyltransferases catalyze a diverse array of difficult chemical transformations in the biosynthesis of a range of compounds of biomedical importance. Phylogenetic analysis suggests that all of these enzymes are related to "CpdH" (formerly "HemN") and "HemW", proteins with essential roles in anaerobic heme biosynthesis and heme transport, respectively. These functions are essential to anaerobic metabolism in Escherichia coli. Interestingly, evolution has come full circle, and the divergence of this protein sequence/fold has resulted in the class C radical SAM methyltransferases. Several pathogenic organisms have further adapted this fold to catalyze the anaerobic degradation of heme. In this review, we summarize what is known about the mechanism of anaerobic heme degradation and the evolutionary implications.

Functional Diversity of HemN-like Proteins

HemN is a radical S-adenosylmethionine (SAM) enzyme that catalyzes the anaerobic oxidative decarboxylation of coproporphyrinogen III to produce protoporphyrinogen IX, a key intermediate in heme biosynthesis. Proteins homologous to HemN (HemN-like proteins) are widespread in both prokaryotes and eukaryotes. Although these proteins are in most cases annotated as anaerobic coproporphyrinogen III oxidases (CPOs) in the public database, many of them are actually not CPOs but have diverse functions such as methyltransferases, cyclopropanases, heme chaperones, to name a few. This Perspective discusses the recent advances in the understanding of HemN-like proteins, and particular focus is placed on the diverse chemistries and functions of this growing protein family.

Making and breaking carbon-carbon bonds in class C radical SAM methyltransferases

Radical S-adenosylmethionine (SAM) enzymes utilize a [4Fe-4S]¹⁺ cluster and S-(5'-adenosyl)-L-methionine, (SAM), to generate a highly reactive radical and catalyze what is arguably the most diverse set of chemical reactions for any known enzyme family. At the heart of radical SAM catalysis is a highly reactive 5'-deoxyadenosyl radical intermediate (5'-dAdo●) generated through reductive cleavage of SAM or nucleophilic attack of the unique iron of the [4Fe-4S]⁺ cluster on the 5' C atom of SAM. Spectroscopic studies reveal the 5'-dAdo● is transiently captured in an FeC bond (Ω species). In the presence of substrate, homolytic scission of this metal‑carbon bond regenerates the 5'-dAdo● for catalytic hydrogen atom abstraction. While reminiscent of the adenosylcobalamin mechanism, radical SAM enzymes appear to encompass greater catalytic diversity. In this review we discuss recent developments for radical SAM enzymes involved in unique chemical rearrangements, specifically regarding class C radical SAM methyltransferases. Illuminating this class of radical SAM enzymes is especially significant as many enzymes have been shown to play critical roles in pathogenesis and the synthesis of novel antimicrobial compounds.