A Ferredoxin- and F ₄₂₀ H ₂ -Dependent, Electron-Bifurcating, Heterodisulfide Reductase with Homologs in the Domains Bacteria and Archaea

Abstract

Heterodisulfide reductases (Hdr) of the HdrABC class are ancient enzymes and a component of the anaerobic core belonging to the prokaryotic common ancestor. The ancient origin is consistent with the widespread occurrence of genes encoding putative HdrABC homologs in metabolically diverse prokaryotes predicting diverse physiological functions; however, only one HdrABC has been characterized and that was from a narrow metabolic group of obligate CO2-reducing methanogenic anaerobes (methanogens) from the domain Archaea. Here we report the biochemical characterization of an HdrABC homolog (HdrA2B2C2) from the acetate-utilizing methanogen Methanosarcina acetivorans with unusual properties structurally and functionally distinct from the only other HdrABC characterized. Homologs of the HdrA2B2C2 archetype are present in phylogenetically and metabolically diverse species from the domains Bacteria and Archaea. The expression of the individual HdrA2, HdrB2, and HdrB2C2 enzymes in Escherichia coli, and reconstitution of an active HdrA2B2C2 complex, revealed an intersubunit electron transport pathway dependent on ferredoxin or coenzyme F420 (F420H2) as an electron donor. Remarkably, HdrA2B2C2 couples the previously unknown endergonic oxidation of F420H2 and reduction of ferredoxin with the exergonic oxidation of F420H2 and reduction of the heterodisulfide of coenzyme M and coenzyme B (CoMS-SCoB). The unique electron bifurcation predicts a role for HdrA2B2C2 in Fe(III)-dependent anaerobic methane oxidation (ANME) by M. acetivorans and uncultured species from ANME environments. HdrA2B2C2, ubiquitous in acetotrophic methanogens, was shown to participate in electron transfer during acetotrophic growth of M. acetivorans and proposed to be essential for growth in the environment when acetate is limiting.

High-Quality Draft Genome Sequence of “ Candidatus Methanoperedens sp.” Strain BLZ2, a Nitrate-Reducing Anaerobic Methane-Oxidizing Archaeon Enriched in an Anoxic Bioreactor

“…It has been suggested that HdrABC/FrhB catalyzes the confurcation of electrons from CoM-SH, CoB-SH, and Fd red to F 420 ( 7 ). Interestingly, in the present data set, four copies of hdrA were identified, two of which were fused with mvhD (see also reference 8 ). Furthermore, a gene cluster was identified that contains hdrABC as well as frhB and two copies of mvhD , with mvhD possibly being involved in electron transfer.…”

Genetic, Biochemical, and Molecular Characterization of Methanosarcina barkeri Mutants Lacking Three Distinct Classes of Hydrogenase

“…2). Two alternative sources can be envisioned: first, Fpo could produce F 420/red (standard reduction potential [E 0 =] ϭ Ϫ360 mV) using reduced methanophenazine (E 0 = ϭ Ϫ165 mV) as the electron donor via reverse electron transport driven by the proton motive force; second, a soluble heterodisulfide reductase could produce F 420/red via electron bifurcation using CoM-S-S-CoB and Fd red as the substrates (as suggested previously [22,23]). In the former mechanism, reduced methanophenazine would be derived from H 2 using Vht; in the latter, Fd red would be derived from H 2 via Ech.…”

Flavin-Based Electron Bifurcation, Ferredoxin, Flavodoxin, and Anaerobic Respiration With Protons (Ech) or NAD+ (Rnf) as Electron Acceptors: A Historical Review

“…The gene encoding the flavin-harboring HdrA subunit is not only found in methanogenic and methanotrophic archaea (Costa et al, 2013 ; Costa and Leigh, 2014 ; Lang et al, 2015 ; Browne et al, 2017 ; Yan et al, 2017 ) but also in sulfate reducing anaerobic bacteria and archaea (Grein et al, 2013 ; Meyer et al, 2013 , 2014 ; Price et al, 2014 ; Ramos et al, 2015 ; Otwell et al, 2016 ), sulfur-oxidizing bacteria (Mangold et al, 2011 ; Grein et al, 2013 ; Liu et al, 2013 ), strict anaerobes having the capacity to degrade aromatic compounds (Boll et al, 2014 , 2016 ), Syntrophorhabdus aromaticivorans (Nobu et al, 2015 ) and some acetogenic bacteria (Mock et al, 2014 ).…”