Noncanonical coproporphyrin-dependent bacterial heme biosynthesis pathway that does not use protoporphyrin

Abstract

It has been generally accepted that biosynthesis of protoheme (heme) uses a common set of core metabolic intermediates that includes protoporphyrin. Herein, we show that the Actinobacteria and Firmicutes (high-GC and low-GC Gram-positive bacteria) are unable to synthesize protoporphyrin. Instead, they oxidize coproporphyrinogen to coproporphyrin, insert ferrous iron to make Fe-coproporphyrin (coproheme), and then decarboxylate coproheme to generate protoheme. This pathway is specified by three genes named hemY, hemH, and hemQ. The analysis of 982 representative prokaryotic genomes is consistent with this pathway being the most ancient heme synthesis pathway in the Eubacteria. Our results identifying a previously unknown branch of tetrapyrrole synthesis support a significant shift from current models for the evolution of bacterial heme and chlorophyll synthesis. Because some organisms that possess this coproporphyrin-dependent branch are major causes of human disease, HemQ is a novel pharmacological target of significant therapeutic relevance, particularly given high rates of antimicrobial resistance among these pathogens.

From chlorite dismutase towards HemQ–the role of the proximal H-bonding network in haeme binding

“…Recently, Dailey and co-workers proposed a novel haeme biosynthesis pathway for Gram-positive bacteria in which HemQ acts as a coprohaeme decarboxylase to yield protohaeme; in this reaction, coprohaeme has to bind to HemQ, react with presumably H 2 O 2 to release two CO 2 molecules to yield and release haeme b. This finding is also supported by other studies [7][8][9][10]. Nevertheless, the mechanism of this reaction is unknown.…”

“…For LmHemQ, it was shown that the protein is able to bind and release haeme reversibly, indicating a regulatory haeme sensing role during haeme biosynthesis in Gram-positive bacteria [5], as was also suggested by physiological studies of SaHemQ and BsHemQ [3,4]. Reversible haeme binding of the cofactor (substrate) is also a prerequisite for HemQs to act as coprohaeme decarboxylase (thereby binding coprohaeme and releasing protohaeme) [7].…”

Antibacterial photosensitization through activation of coproporphyrinogen oxidase

“…To determine whether '882 retains activity against CgoX from other Gram-positive organisms, recombinant Bacillus subtilis and P. acnes CgoX were purified (7). K m and V max values were determined to characterize baseline activity of the enzymes, and each was tested for '882-induced activation (Fig.…”

“…Until recently, it was thought that the heme biosynthesis pathway was conserved across all species, limiting its utility as a potential therapeutic target to treat infectious diseases. However, Dailey et al (7,8) discovered that Gram-positive bacteria use a distinct pathway to synthesize the critical cellular cofactor heme (Fig. 1A).…”

“…1A). Specifically, Gram-positive heme biosynthesis diverges at the conversion of coproporphyrinogen III (CPGIII) to coproporphyrin III (CPIII) through a six-electron oxidation by coproporphyrinogen oxidase (CgoX, formally known as HemY), as opposed to being converted to protoporphyrin IX (PPIX) in the classical pathway by a distinct series of enzymes (7,9,10). The divergence of the heme biosynthesis machinery between humans and Gram-positive bacteria provides a unique opportunity for the development of antibiotics targeting this pathway as a strategy to treat infections.…”