The Escherichia coli Protein YfeX Functions as a Porphyrinogen Oxidase, Not a Heme Dechelatase

Abstract

The protein YfeX from Escherichia coli has been proposed to be essential for the process of iron removal from heme by carrying out a dechelation of heme without cleavage of the porphyrin macrocycle. Since this proposed reaction is unique and would represent the first instance of the biological dechelation of heme, we undertook to characterize YfeX. Our data reveal that YfeX effectively decolorizes the dyes alizarin red and Cibacron blue F3GA and has peroxidase activity with pyrogallal but not guiacol. YfeX oxidizes protoporphyrinogen to protoporphyrin in vitro. However, we were unable to detect any dechelation of heme to free porphyrin with purified YfeX or in cellular extracts of E. coli overexpressing YfeX. Additionally, Vibrio fischeri, an organism that can utilize heme as an iron source when grown under iron limitation, is able to grow with heme as the sole source of iron when its YfeX homolog is absent. Plasmid-driven expression of YfeX in V. fischeri grown with heme did not result in accumulation of protoporphyrin. We propose that YfeX is a typical dye-decolorizing peroxidase (or DyP) and not a dechelatase. The protoporphyrin reported to accumulate when YfeX is overexpressed in E. coli likely arises from the intracellular oxidation of endogenously synthesized protoporphyrinogen and not from dechelation of exogenously supplied heme. Bioinformatic analysis of bacterial YfeX homologs does not identify any connection with iron acquisition but does suggest links to anaerobic-growth-related respiratory pathways. Additionally, some genes encoding homologs of YfeX have tight association with genes encoding a bacterial cytoplasmic encapsulating protein.

Characterization of a Mycobacterium tuberculosis Nanocompartment and Its Potential Cargo Proteins

“…This hypothesis was based on PPIX accumulation upon overexpression of Ec-YfeX in E. coli (11). However, another study reported that Ec-YfeX is a typical heme-dependent dye-decolorizing peroxidase and does not possess deferrocheletase activity (12). Recently, Rhodococcus jostii DypB (Rj-DypB) found in an operon with Enc (Rj-Enc), was shown to be a heme-dependent dye-decolorizing peroxidase with lignin-degrading capabilities (27).…”

“…DyP-type peroxidases are a novel family of fungal and bacterial heme-dependent peroxidases that can oxidize lignin and anthraquinone dyes in the presence of H 2 O 2 (9,10). However, the Escherichia coli DyP ortholog, Ec-YfeX, was proposed to possess deferrochelatase activity, where Ec-YfeX can catalyze the extraction of iron from heme without cleavage of the tetrapyrrole ring (11), although in a parallel study, Ec-YfeX was demonstrated to be a heme-dependent peroxidase with no detectable deferrochelatase activity (12). If Mt-DyP is a heme-dependent peroxidase, then Mt-DyP may protect M. tuberculosis against host oxidative assault by H 2 O 2 .…”

Distal Heme Pocket Residues of B-type Dye-decolorizing Peroxidase

“…It is possible that the different modulation of the peroxidative cycle in the DyPs reflects their different physiological roles. For example, C-and D-type DyPs may oxidize a variety of substrates such as dyes (5) and melanin (14), whereas Aand B-type DyPs may oxidize a specific substrate, such as porphyrinogen (11). Thus, although the lignin-and Mn 2ϩ -oxidizing activities of DypB from R. jostii RHA1 may be biotechnologically useful, it may not be physiologically relevant.…”

A structural and functional perspective of DyP-type peroxidase family

“…We have proposed a pathway for The amino acid sequences of Ajp II from auricula-judae and Irpex activity toward anthraquinone dyes (k cat /K m = 10 7 s À1 M À1 ) and a 135 low pH optimum [16]. Notably, two reports have classified AnaPX duce protoporphyrin IX from heme in vitro were not shown [27]. 186 Moreover, Mt-DyP also does not show this activity [24].…”