Identification and isolation of the polyferredoxin from Methanobacterium thermoautotrophicum strain delta H

Characterization of a novel ferredoxin with N-terminal extension from Clostridium acetobutylicum ATCC 824

A gene (CAC2657) encoding a ferredoxin (EFR1) from the strictly anaerobic soil bacterium Clostridium acetobutylicum was cloned and expressed in Escherichia coli. The ferredoxin gene encodes a polypeptide of 27 kDa that incorporates 2[4Fe-4S] clusters. An extended N-terminal region of 187 amino acid (aa) residues precedes ferredoxin domain. The EFR1 expressed in E. coli is a trimeric protein. The iron and sulfur content of the reconstituted protein agrees with that expected of a trimeric form of the protein. The ferredoxin domain of EFR1 is closely related to ferredoxin of C. pasteurianum; and can be fitted to the X-ray crystal structure with a root mean square deviation of 0.62 As for the Calpha atoms of the generated 3D simulation model. In cultures of C. acetobutylicum the efr1 gene shows higher relative expression on induction with Trinitrotoluene (TNT) compared to that from uninduced control cultures.

Spectroscopic and functional properties of novel 2[4Fe-4S] cluster-containing ferredoxins from the green sulfur bacterium Chlorobium tepidum

Two distinct ferredoxins, Fd I and Fd II, were isolated and purified to homogeneity from photoautotrophically grown Chlorobium tepidum, a moderately thermophilic green sulfur bacterium that assimilates carbon dioxide by the reductive tricarboxylic acid cycle. Both ferredoxins serve a crucial role as electron donors for reductive carboxylation, catalyzed by a key enzyme of this pathway, pyruvate synthase/pyruvate ferredoxin oxidoreductase. The reduction potentials of Fd I and Fd II were determined by cyclic voltammetry to be -514 and -584 mV, respectively, which are more electronegative than any previously studied Fds in which two [4Fe-4S] clusters display a single transition. Further spectroscopic studies indicated that the CD spectrum of oxidized Fd I closely resembled that of Fd II; however, both spectra appeared to be unique relative to ferredoxins studied previously. Double integration of the EPR signal of the two Fds yielded approximately approximately 2.0 spins per molecule, compatible with the idea that C. tepidum Fd I and Fd II accept 2 electrons upon reduction. These results suggest that the C. tepidum Fd I and Fd II polypeptides each contain two bound [4Fe-4S] clusters. C. tepidum Fd I and Fd II are novel 2[4Fe-4S] Fds, which were shown previously to function as biological electron donors or acceptors for C. tepidum pyruvate synthase/pyruvate ferredoxin oxidoreductase (Yoon, K.-S., Hille, R., Hemann, C. F., and Tabita, F. R. (1999) J. Biol. Chem. 274, 29772-29778). Kinetic measurements indicated that Fd I had approximately 2.3-fold higher affinity than Fd II. The results of amino acid sequence alignments, molecular modeling, oxidation-reduction potentials, and spectral properties strongly indicate that the C. tepidum Fds are chimeras of both clostridial-type and chromatium-type Fds, suggesting that the two Fds are likely intermediates in the evolutional development of 2[4Fe-4S] clusters compared with the well described clostridial and chromatium types.

Characterization of the Self-Condensation Equilibrium of [Fe(4)S(4)(SH)(4)](2-): Spectroscopic Identification of a Unique Sulfido-Bridged Acyclic Tricubane Cluster

Our interest in higher nuclearity sulfido-bridged Fe-S clusters, because of their occurrence in several proteins including nitrogenase, prompted us to investigate the solution chemistry of the functionalized cluster [Fe(4)S(4)(SH)(4)](2)(-) (1). (n-Pr(4)N)(2)[1] crystallizes in space group P2(1)/n of the monoclinic system with a = 26.201(1) Å, b = 11.4999(5) Å, c = 28.090(1) Å, and beta = 110.735(1) degrees. The X-ray structure reveals the conventional cubane-type geometry with an [Fe(4)S(4)](2+) core symmetry more closely approaching T(d)() than the tetragonally distorted D(2)(d)() symmetry reported for the (PPh(4))(2)[1] (Müller, A.; Schladerbeck, N. H.; Bögge, H. J. Chem. Soc., Chem. Commun. 1987, 35). In solution, 1 exists in dynamic equilibrium with self-condensation products formed through elimination of H(2)S and formation of sulfido-bridged cluster oligomers, one of which (4) is prevalent. The self-condensation equilibrium is shifted toward cluster 1. When acetonitrile solutions of 1 were treated with thiols more acidic than H(2)S, it was possible to detect hydrosulfido terminal ligand substitution products of 1 as well as those of the major self-condensation product 4. Detailed analysis of the products in acetonitrile solutions of 1, as well as those generated in solutions of 1 treated with acidic thiol, by electrospray mass spectrometry, and both (19)F and (1)H NMR spectroscopy indicates the presence of a sulfido-bridged acyclic trimer of [Fe(4)S(4)](2+) clusters, i.e. {[Fe(4)S(4)(SH)(3)](2)[Fe(4)S(4)(SH)(2)](&mgr;-S)(2)}(6)(-) (4), a hitherto unprecedented Fe-S structural pattern, as the principal Fe-S cluster self-condensation product.

Novel zinc-containing ferredoxin family in thermoacidophilic archaea

The dicluster-type ferredoxins from the thermoacidophilic archaea such as Thermoplasma acidophilum and Sulfolobus sp. are known to contain an unusually long extension of unknown function in the N-terminal region. Recent x-ray structural analysis of the Sulfolobus ferredoxin has revealed the presence of a novel zinc center, which is coordinated by three histidine ligand residues in the N-terminal region and one aspartate in the ferredoxin core domain. We report here the quantitative metal analyses together with electron paramagnetic resonance and resonance Raman spectra of T. acidophilum ferredoxin, demonstrating the presence of a novel zinc center in addition to one [3Fe-4S] and one [4Fe-4S] cluster (Fe/Zn = 6.8 mol/mol). A phylogenetic tree constructed for several archaeal monocluster and dicluster type ferredoxins suggests that the zinc-containing ferredoxins of T. acidophilum and Sulfolobus sp. form an independent subgroup, which is more distantly related to the ferredoxins from the hyperthermophiles than those from the methanogenic archaea, indicating the existence of a novel group of ferredoxins, namely, a "zinc-containing ferredoxin family" in the thermoacidophilic archaea. Inspection of the N-terminal extension regions of the archaeal zinc-containing ferredoxins suggested strict conservation of three histidine and one aspartate residues as possible ligands to the novel zinc center.

A polyferredoxin with eight [4Fe-4S] clusters as a subunit of molybdenum formylmethanofuran dehydrogenase from Methanosarcina barkeri

Formylmethanofuran dehydrogenase (Fmd) from Methanosarcina barkeri is a molybdenum iron-sulfur protein involved in methanogenesis. The enzyme contains approximately 30 mol non-heme iron/mol and 30 mol acid-labile sulfur/mol. We report here the cloning and sequencing of the encoding genes, and that these genes form a transcription unit fmdEFACDB. Evidence is provided that the subunit FmdB harbours the molybdenum-containing active site and may bind one [4Fe-4S] cluster. fmdF encodes a protein with four tandemly repeated bacterial-ferredoxin-like domains and is predicted to be a polyferredoxin that could contain as many as 32 iron atoms in eight [4Fe-4S] clusters. The other genes code for proteins without sequence motifs characteristic for iron-sulfur proteins. These findings suggest that most of the iron-sulfur clusters present in the purified formylmethanofuran dehydrogenase are associated with the subunit FmdF. The finding that FmdF forms a tight complex with the other subunits of formylmethanofuran dehydrogenase indicates a function of the polyferredoxin in the reaction catalyzed by the enzyme. fmdE encodes a protein not present in the purified enzyme. All six genes of the fmd operon were expressed in Escherichia coli and yielded proteins of expected molecular masses. A malE-fmdF gene fusion was constructed and expressed in E. coli, making the apoprotein of the polyferredoxin available in preparative amounts.

The tungsten formylmethanofuran dehydrogenase from Methanobacterium thermoautotrophicum contains sequence motifs characteristic for enzymes containing molybdopterin dinucleotide

Formylmethanofuran dehydrogenases are molybdenum or tungsten iron-sulfur proteins containing a pterin dinucleotide cofactor. We report here on the primary structures of the four subunits FwdABCD of the tungsten enzyme from Methanobacterium thermoautotrophicum which were determined by cloning and sequencing the encoding genes fwdABCD. FwdB was found to contain sequence motifs characteristic for molybdopterin-dinucleotide-containing enzymes indicating that this subunit harbors the active site. FwdA, FwdC and FwdD showed no significant sequence similarity to proteins in the data bases. Northern blot analysis revealed that the four fwd genes form a transcription unit together with three additional genes designated fwdE, fwdF and fwdG. A 17.8-kDa protein and an 8.6-kDa protein, both containing two [4Fe-4S] cluster binding motifs, were deduced from fwdE and fwdG. The open reading frame fwdF encodes a 38.6-kDa protein containing eight binding motifs for [4Fe-4S] clusters suggesting the gene product to be a novel polyferredoxin. All seven fwd genes were expressed in Escherichia coli yielding proteins of the expected size. The fwd operon was found to be located in a region of the M. thermoautotrophicum genome encoding molybdenum enzymes and proteins involved in molybdopterin biosynthesis.

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

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 photoreduction, 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 delta H, 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 transcriptional 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.(ABSTRACT TRUNCATED AT 400 WORDS)

Purification and structural characterization of a flavoprotein induced by iron limitation in Methanobacterium thermoautotrophicum Marburg

Cells of Methanobacterium thermoautotrophicum (strain Marburg) grown under iron-limiting conditions were found to synthesize a soluble polypeptide as one of the major cell proteins. This polypeptide purified as a homotetramer (170 kDa [subunit molecular mass, 43 kDa]) had a UV-visible spectrum typical of flavoproteins and contained 0.7 mol of flavin mononucleotide per mol of monomer. Quantitative analysis by immunoblotting with polyclonal antibodies indicated that the flavoprotein, which amounts to about 0.6% of soluble cell protein under iron-sufficient conditions (> or = 50 microM Fe2+), was induced fivefold by iron limitation (< 12 microM Fe2+). The flavoprotein-encoding gene, fprA, was cloned and sequenced. Sequence analysis revealed a well-conserved archaebacterial consensus promoter upstream of fprA, a flavodoxin signature within fprA, and 28% amino acid identity with a putative flavin mononucleotide-containing protein of Rhodobacter capsulatus which is found within an operon involved in nitrogen fixation. A possible physiological function for the flavoprotein is discussed.

Structural aspects and immunolocalization of the F420-reducing and non-F420-reducing hydrogenases from Methanobacterium thermoautotrophicum Marburg

The F420-reducing hydrogenase and the non-F420-reducing hydrogenase (EC 1.12.99.1.) were isolated from a crude extract of Methanobacterium thermoautotrophicum Marburg. Electron microscopy of the negatively stained F420-reducing hydrogenase revealed that the enzyme is a complex with a diameter of 15.6 nm. It consists of two ring-like, stacked, parallel layers each composed of three major protein masses arranged in rotational symmetry. Each of these masses appeared to be subdivided into smaller protein masses. Electron microscopy of negatively stained samples taken from intermediate steps of the purification process revealed the presence of enzyme particles bound to inside-out membrane vesicles. Linker particles of 10 to 20 kDa which mediate the attachment of the hydrogenase to the cytoplasmic membrane were seen. Immunogold labelling confirmed that the F420-reducing hydrogenase is a membrane-bound enzyme. Electron microscopy of the negatively stained purified non-F420-reducing hydrogenase revealed that the enzyme is composed of three subunits exhibiting different diameters (5, 4, and 2 to 3 nm). According to immunogold labelling experiments, approximately 70% of the non-F420-reducing hydrogenase protein molecules were located at the cell periphery; the remaining 30% were cytoplasmic. No linker particles were observed for this enzyme.

H2: heterodisulfide oxidoreductase complex from Methanobacterium thermoautotrophicum. Composition and properties

The reduction of the heterodisulfide (CoM-S-S-HTP) of coenzyme M (H-S-CoM) and N-7-mercaptoheptanoylthreonine phosphate (H-S-HTP) with H2 is an energy-conserving step in most methanogenic Archaea. In this study, we show that in Methanobacterium thermoautotrophicum (strain Marburg) this reaction is catalyzed by a stable H2-heterodisulfide oxidoreductase complex of F420-non-reducing hydrogenase and heterodisulfide reductase. This complex, which was loosely associated with the cytoplasmic membrane, was purified 17-fold with 80% yield to apparent homogeneity. The purified complex was composed of six different subunits of apparent molecular masses 80, 51, 41, 36, 21 and 17 kDa, and 1 mol complex, with apparent molecular mass 250 kDa, contained approximately 0.6 mol nickel, 0.9 mol FAD, 26 mol non-heme iron and 22 mol acid-labile sulfur. In 25 mM Chaps, the complex partially dissociated into two subcomplexes. The first subcomplex was was composed of the 51-, 41- and 17-kDa subunits; 1 mol trimer contained 0.7 mol nickel, 10 mol non-heme iron and 9 mol acid-labile sulfur and exhibited F420-non-reducing hydrogenase activity. The other subcomplex was composed of the 80-, 36- and 21-kDa subunits; 1 mol trimer contained 0.8 mol FAD, 22 mol non-heme iron and 15 mol acid-labile sulfur and exhibited heterodi-sulfide-reductase activity. The stimulatory effects of potassium phosphate, a membrane component, uracil derivatives and coenzyme F430 on the H2:heterodisulfide-oxidoreductase activity of the purified complex are described.