How the microbiome liberates iron from heme

Abstract

The microbiome is a hidden organ system with diverse metabolic roles. Using Bacteroides thetaiotaomicron (B theta) as a model, we asked how microbiome species process iron, the quintessential biometal supporting respiration and life as we know it, when iron is provided in complex with protoporphyrin IX (PPIX) as heme. An intestinal transporter for heme has not been unequivocally identified. Canonical pathways for reclaiming heme iron from host cells or the diet require O2, which is unavailable in the GI tract and many pathological microenvironments. HmuS, a homolog of cobalamine-(vitamin B12) and chlorophyll-building chelatases, is widespread in anaerobic microbial ecosystems. In this work, we provide direct physiological, biochemical, and structural evidence for the anaerobic removal of iron from heme by HmuS, a de-chelatase that deconstructs heme to PPIX and Fe(II). We show that heme can be used as a sole iron source by B theta, yielding PPIX, and that hmuS inactivation under these conditions is lethal. Iron removal from heme depends on the B theta membrane fraction, NADH, and O2 exclusion. Absorbance spectra indicate that heterologously expressed HmuS is isolated with a non-substrate heme bound and can accommodate multiple heme equivalents under saturating conditions. Solution of the cryoEM structure reveals heme and two cations at sites that are conserved across the HmuS family and the chelatase superfamily, respectively. The proposed structure-based mechanism for iron removal further links biosynthetic and biodegradative pathways for heme, chlorophyll, and vitamin B12, three ancient and biologically crucial metallocofactors. Significance StatementIron in its heme and non-heme forms is essential for nearly all life. This work defines a microbial mechanism for metabolizing heme that is widespread in gastrointestinal and other anaerobic ecosystems. To date, an intestinal cellular transporter for heme has not been unequivocally identified. However, heme, abundant in both red meat diets and animal cells, is converted by the bacterial HmuS enzyme into a non-heme form from which the iron can be repurposed. HmuS enzymes form a distinct de-chelatase subset of a superfamily of chelatases that catalyze metal insertion into chlorophyll and vitamin B12, indicating convergence of metabolic pathways for biosynthesis and degradation of three of lifes essential metallocofactors. Understanding HmuS function supports engineered approaches to directing microbiome-host metabolism and offsetting heme-associated pathologies including anemia, inflammation, and cancer.