Characterization of a 45‐kDa Flavoprotein and Evidence for a Rubredoxin, two Proteins that could Participate in Electron Transport from H2 to CO2 in Methanogenesis in Methanobacterium Thermoautotrophicum
Authors: Nölling Jörk , Ishii Masaharu , Koch Jürgen , Pihl Todd D. , Reeve John N. , Thauer Rudolf K. , Hedderich Reiner 
Published: March 2005

Methanobacterium thermoautotrophicum strains contain a flavoprotein (flavoprotein A) that copurifies with the H2:heterodisulfide oxidoreductase complex. In this study, we report the iron‐dependent synthesis and biochemical properties of flavoprotein A, cloning and sequencing of the flavoprotein‐A‐encoding gene (fpaA) and the co‐transcription of fpaA with two downstream open reading frames, one of which (rdxA) appears to encode a rubredoxin.

Native flavoprotein A has been shown to be a homodimer of a 45‐kDa polypeptide that contains 1.3 mol FMN/45‐kDa subunit but no iron or acid‐labile sulfur. Catalytic amounts of the H2:heterodisulfide oxidoreductase complex or of the F420‐reducing hydrogenase reduced flavoprotein A with H2, at specific rates of 0.3–0.4 U/mg enzyme, generating up to 70% flavin semiquinone before reduction to the flavin hydroquinone was observed. This intermediate accumulation of the semiquinone species had a kinetic rather than a thermodynamic basis, because the semiquinone form of flavoprotein A, generated by photo‐reduction, disproportionated quantitatively to the quinone and hydroquinone species. The midpoint potential of the quinone/hydroquinone couple was estimated to be 230±15 mV, at pH 7.6, versus the normal hydrogen electrode. Quantitation of Western blots demonstrated that flavoprotein A constituted approximately 1.5% of the soluble protein in cells grown in an iron‐sufficient medium but that this increased to about 6% of the cellular protein when the iron the medium was depleted. The increase in the flavoprotein A content of cells grown under iron‐limiting conditions was mirrored by a decrease in the content of the iron‐rich polyferredoxin that also copurified with the H2:heterodisulfide oxidoreductase complex.

The fpaA gene, cloned and sequenced from M. thermoautotrophicum strain ΔH, encodes 404 amino acids in a sequence that has a C‐terminal domain (approximately 130 amino acid residues) with features consistent with a flavodoxin structure. The remainder of flavoprotein A has sequences that are also predicted to be present in the N‐terminal region of the orf14 gene product, which also appears to be an enlarged flavodoxin, encoded in the nif region of Rhodobacter capsulatus. Immediately downstream from fpaA, two open reading frames designated orfX and rdxA, have been located and shown by Northern‐blot analyses to be co‐transcribed with fpaA, although approximately 50% of fpaA‐orfX‐rdxA transcripts terminated or were cleaved within rdxA. Primer extension studies revealed that transcription of this tran‐scriptional unit (the fpa operon) was initiated 32 nucleotides upstream of fpaA, at a site 25 nucleotides downstream from a sequence consistent with an archaeal TATA‐box promoter element. rdxA is predicted to encode a 19.6‐kDa polypeptide that is most closely related to rubredoxin I of Pseudomonas oleovorans, and that contains an N‐terminal motif with features found in all rubredoxins, including the four cysteine residues that coordinate the iron atom that provides the redox center of rubredoxins.