Electron transport components from methanogenic bacteria: the ferredoxin from Methanosarcina barkeri (strain Fusaro)

Comment on "Applicability of perturbed matrix method for charge transfer studies at bio/metallic interfaces: a case of azurin" by O. Kontkanen, D. Biriukov and Z. Futera, Phys. Chem. Chem. Phys., 2023, , 12479

Polarizability is a fundamental property of all molecular systems describing the deformation of the molecular electronic density in response to an applied electric field. The question of whether polarizability of the active site needs to be included in theories of enzymatic activity remains open. Hybrid quantum mechanical/molecular mechanical calculations are hampered by difficulties faced by many quantum-chemistry algorithms to provide sufficiently accurate estimates of the anisotropic second-rank tensor of molecular polarizability. In this Comment, we provide general theoretical arguments for the values of polarizability of the quantum region or a molecule which have to be reproduced by electronic structure calculations.

Comparison of gut microflora of donkeys in high and low altitude areas

Donkeys’ gut microbe is critical for their health and adaptation to the environment. Little research has been conducted on the donkey gut microbiome compared with other domestic animals. The Tibetan Plateau is an extreme environment. In this study, 6 Qinghai donkeys (QH) from the Tibetan Plateau and 6 Dezhou donkeys (DZ) were investigated, and the contents of 4 parts—stomach, small intestine, cecum, and rectum—were collected. 16S rRNA sequencing and metagenomic sequencing were used to analyze the composition and diversity of gut microbial communities in donkeys. The results showed that the flora diversity and richness of the hindgut were significantly higher than those of the foregut (p < 0.01), with no sex differences, and the community structure and composition of the same or adjacent regions (stomach, small intestine, cecum, and rectum) were similar. Besides, the flora diversity and richness of QH on the Tibetan Plateau were significantly higher than those of DZ (p < 0.05). The major pathways associated with QH were signal transduction mechanisms and carbohydrate transport and metabolism, and Bacteroidales were the major contributors to these functions. Our study provides novel insights into the contribution of microbiomes to the adaptive evolution of donkeys.

Extremely thermophilic fermentative archaebacteria of the genus desulfurococcus from deep-sea hydrothermal vents

Two strains of extremely thermophilic, anaerobic bacteria are described that are representative of isolates obtained from a variety of oceanic hydrothermal vent sites at depths from 2,000 to 3,700 m. The isolates were similar in their requirements for complex organic media, elemental sulfur, and seawater-range salinities (optimum, 2.1 to 2.4%); their high tolerance for sulfide (100 mM) and oxic conditions below growth-range temperatures (50 to 95 degrees C); and their archaebacterial characteristics: absence of murein, presence of certain diand tetraethers, and response to specific antibiotics. The two strains (S and SY, respectively) differed slightly in their optimum growth temperatures (85 and 90 degrees C, optimum pHs for growth (7.5 and 7.0), and DNA base compositions (52.01 and 52.42 G+C mol%). At their in situ pressure of about 250 atm (25,313 kPa), growth rates at 80 and 90 degrees C were about 40% lower than those at 1 atm (101.29 kPa), and no growth occurred at 100 and 110 degrees C, respectively, at either pressure. In yeast extract medium, only 2% of the organic carbon was used and appeared to stem largely from the proteinaceous constituents. According to physiological criteria, the isolates belong to the genus Desulfurococcus.

Structural and biochemical characterization of flavoredoxin from the archaeon Methanosarcina acetivorans

Flavoredoxin is a FMN-containing electron transfer protein that functions in the energy-yielding metabolism of Desulfovibrio gigas of the Bacteria domain. Although characterization of this flavoredoxin is the only one reported, a database search revealed homologues widely distributed in both the Bacteria and Archaea domains that define a novel family. To improve our understanding of this family, a flavoredoxin from Methanosarcina acetivorans of the Archaea domain was produced in Escherichia coli and biochemically characterized, and a high-resolution crystal structure was determined. The protein was shown to be a homodimer with a subunit molecular mass of 21 kDa containing one noncovalently bound FMN per monomer. Redox titration showed an E(m) of -271 mV with two electrons, consistent with no semiquinone observed in the potential range studied, a result suggesting the flavoredoxin functions as a two-electron carrier. However, neither of the obligate two-electron carriers, NAD(P)H and coenzyme F420H2, was a competent electron donor, whereas 2[4Fe-4S] ferredoxin reduced the flavoredoxin. The X-ray crystal structure determined at 2.05 A resolution revealed a homodimer containing one FMN per monomer, consistent with the biochemical characterization. The isoalloxazine ring of FMN was shown buried within a narrow groove approximately 10 A from the positively charged protein surface that possibly facilitates interaction with the negatively charged ferredoxin. The structure provides a basis for predicting the mechanism by which electrons are transferred between ferredoxin and FMN. The FMN is bound with hydrogen bonds to the isoalloxazine ring and electrostatic interactions with the phosphate moiety that, together with sequence analyses of homologues, indicate a novel FMN binding motif for the flavoredoxin family.

Ferredoxin-dependent methane formation from acetate in cell extracts ofMethanosarcina barkeri(strain MS)

Cell extracts of Methanosarcina barkeri grown on acetate catalyzed the conversion of acetyl-CoA to CO2 and CH4 at a specific rate of 50 nmol min-1 mg-1. When ferredoxin was removed from the extracts by DEAE-Sephacel anion exchange chromatography, the extracts were inactive but full activity was restored upon addition of purified ferredoxin from M. barkeri or from Clostridium pasteurianum. The apparent Km for ferredoxin from M. barkeri was determined to be 2.5 M. A ferredoxin dependence was also found for the formation of CO2, H2 and methylcoenzyme M from acetyl-CoA, when methane formation was inhibited by bromoethanesulfonate. Reduction of methyl-coenzyme M with H2 did not require ferredoxin. These and other data indicate that ferredoxin is involved as electron carrier in methanogenesis from acetate. Methanogenesis from acetyl-CoA in cell extracts was not dependent on the membrane fraction, which contains the cytochromes.

Catalytic properties, molecular composition and sequence alignments of pyruvate: ferredoxin oxidoreductase from the methanogenic archaeon Methanosarcina barkeri (strain Fusaro)

Methanosarcina barkeri (strain Fusaro) was grown on pyruvate as methanogenic substrate [Bock, A. K., Prieger-Kraft, A. & Schönheit, P. (1994) Arch. Microbiol. 161, 33-46]. The first enzyme of pyruvate catabolism, pyruvate oxidoreductase, which catalyzes oxidation of pyruvate to acetyl-CoA was purified about 90-fold to apparent electrophoretic homogeneity. The purified enzyme catalyzed the CoA-dependent oxidation of pyruvate with ferredoxin as an electron acceptor which defines the enzyme as a pyruvate: ferredoxin oxidoreductase. The deazaflavin, coenzyme F420, which has been proposed to be the physiological electron acceptor of pyruvate oxidoreductase in methanogens, was not reduced by the purified enzyme. In addition to ferredoxin and viologen dyes, flavin nucleotides served as electron acceptors. Pyruvate: ferredoxin oxidoreductase also catalyzed the oxidation of 2-oxobutyrate but not the oxidation of 2-oxoglutarate, indolepyruvate, phenylpyruvate, glyoxylate, 3-hydroxypyruvate and oxaloacetate. The apparent Km values of pyruvate:ferredoxin oxidoreductase were 70 microM for pyruvate, 6 microM for CoA and 30 microM for clostridial ferredoxin. The apparent Vmax with ferredoxin was about 30 U/mg (at 37 degrees C) with a pH optimum of approximately 7. The temperature optimum was approximately 60 degrees C and the Arrhenius activation energy was 40 kJ/mol (between 30 degrees C and 60 degrees C). The enzyme was extremely oxygen sensitive, losing 90% of its activity upon exposure to air for 1 h at 0 degrees C. Sodium nitrite inhibited the enzyme with a Ki of about 10 mM. The native enzyme had an apparent molecular mass of approximately 130 kDa and was composed of four different subunits with apparent molecular masses of 48, 30, 25, and 15 kDa which indicates that the enzyme has an alpha beta gamma delta structure. The enzyme contained 1 mol/mol thiamine diphosphate, and about 12 mol/mol each of non-heme iron and acid-labile sulfur. FAD, FMN and lipoic acid were not found. The N-terminal amino acid sequences of the four subunits were determined. The sequence of the alpha-subunit was similar to the N-terminal amino acid sequence of the alpha-subunit of the heterotetrameric pyruvate:ferredoxin oxidoreductases of the hyperthermophiles Archaeoglobus fulgidus, Pyrococcus furiosus and Thermotoga maritima and of the mesophile Helicobacter pylori, and to the N-terminal amino acid sequence of the homodimeric pyruvate:ferredoxin oxidoreductase from proteobacteria and from cyanobacteria. No sequence similarities were found, however, between the alpha-subunit of the M. barkeri enzyme and the heterodimeric pyruvate:ferredoxin oxidoreductase of the archaeon Halobacterium halobium.

Characterization and determination of the redox properties of the 2[4Fe-4S] ferredoxin from Methanosarcina barkeri strain MS

Ferredoxin was purified from methanol-grown Methanosarcina barkeri strain MS. It was isolated as a dimer with a subunit molecular weight of 6,200. The protein contained 7.4 mol iron and 7.2 mol acid-labile sulfur per monomer. In the reduced state the ferredoxin exhibited an EPR spectrum characteristic of two spin-coupled [4Fe-4S]1+ clusters. The EM of the [4Fe-4S]2+:1+ couple was -322 mV +/- 3 mV vs. NHE at 21 degrees C and pH 7.0. The midpoint potential was temperature but not pH dependent. At the physiological temperature of 37 degrees C the Em was -340 mV.

Characterization of the iron-sulfur clusters in ferredoxin from acetate-grown Methanosarcina thermophila

Ferredoxin from Methanosarcina thermophila is an electron acceptor for the CO dehydrogenase complex which decarbonylates acetyl-coenzyme A and oxidizes the carbonyl group to carbon dioxide in the pathway for conversion of the methyl group of acetate to methane (K. C. Terlesky and J. G. Ferry, J. Biol. Chem. 263:4080-4082, 1988). Resonance Raman spectroscopy and electron paramagnetic resonance spectroelectrochemistry indicated that the ferredoxin contained two [4Fe-4S] clusters per monomer of 6,790 Da, each with a midpoint potential of -407 mV. A [3Fe-4S] species, with a midpoint potential of +103 mV, was also detected in the protein at high redox potentials. Quantitation of the [3Fe-4S] and [4Fe-4S] centers revealed 0.4 and 2.1 spins per monomer, respectively. The iron-sulfur clusters were unstable in the presence of air, and the rate of cluster loss increased with increasing temperature. A ferredoxin preparation, with a low spin quantitation of [4Fe-4S] centers, was treated with Fe2+ and S2-, which resulted in an increase in [4Fe-4S] and a decrease in [3Fe-4S] clusters. The results of these studies suggest the [3Fe-4S] species may be an artifact formed from degradation of [4Fe-4S] clusters.

A purified ferredoxin from Giardia duodenalis

A ferredoxin has been purified to homogeneity from the ancient protozoan parasite Giardia duodenalis. As far as we know, this is the first electron transport protein to be characterised from the organism. The ferredoxin exhibits absorption maxima at 296 and 406 nm with molar absorption coefficients of epsilon 296 = 16,650 +/- 240 M-1 cm-1 and epsilon 406 = 13,100 +/- 370 M-1 cm-1 respectively. The A406/A296 ratio ranged over 0.78-0.82. The molecular mass of the apoprotein calculated by mass spectrometry was 5730 +/- 100Da and the minimum molecular mass by amino acid analysis was 5926Da. There were four cysteine residues/molecule protein but no methionine, arginine, histidine or tyrosine. The absence of these latter residues is consistent with the amino acid content of most ferredoxins. The N-terminal amino acid sequence exhibited greatest similarity to Desulfovibrio gigas ferredoxin II and indicated the potential to coordinate an iron-sulfur cluster. There were 3.21 +/- 0.41 mol sulfide and 2.65 +/- 0.06 mol iron/mol protein. Electron paramagnetic resonance studies of this protein have indicated the presence of an iron-sulfur centre consistent with those of known ferredoxins. Ferredoxin serves as a biological electron acceptor from giardial pyruvate dehydrogenase with metronidazole as a terminal electron acceptor. Such a pathway may serve as a possible mechanism for the reductive activation of metronidazole in this parasite. A second ferredoxin has been purified to homogeneity, but at this stage there is insufficient material to fully characterise this protein. No other low-molecular-mass electron transport proteins have been identified in Giardia under the growth conditions described.

Cloning, nucleotide sequence, and transcriptional analyses of the gene encoding a ferredoxin from Methanosarcina thermophila

A mixed 17-mer oligonucleotide deduced from the N terminus of a ferredoxin isolated from Methanosarcina thermophila was used to probe a lambda gt11 library prepared from M. thermophila genomic DNA; positive clones contained either a 5.7- or 2.1-kbp EcoRI insert. An open reading frame (fdxA) located within the 5.7-kbp insert had a deduced amino acid sequence that was identical to the first 26 N-terminal residues reported for the ferredoxin isolated from M. thermophila, with the exception of the initiator methionine. fdxA had the coding capacity for a 6,230-Da protein which contained eight cysteines with spacings typical of 2[4Fe-4S] ferredoxins. An open reading frame (ORF1) located within the 2.1-kbp EcoRI fragment also had the potential to encode a 2[4Fe-4S] bacterial-type ferredoxin (5,850 Da). fdxA and ORF1 were present as single copies in the genome, and each was transcribed on a monocistronic mRNA. While the fdxA- and ORF1-specific mRNAs were detected in cells grown on methanol and trimethylamine, only the fdxA-specific transcript was present in acetate-grown cells. The apparent transcriptional start sites of fdxA and ORF1, as determined by primer extension analyses, lay 21 to 28 bases downstream of sequences with high identity to the consensus methanogen promoter.

Amino acid sequence and molecular modelling of a thermostable two (4Fe-4S) ferredoxin from the archaebacterium Methanococcus thermolithotrophicus

The amino acid sequence of a two (4Fe-4S) ferredoxin from the methanogenic bacterium Methanococcus thermolithotrophicus (FdMt) has been determined. This thermostable protein comprises 60 amino acid residues (Mr 6541) and two (4Fe-4S) clusters chelated to the protein through the eight cysteines. FdMt contains a relatively high number of lysines [5], threonines [4] and valines [10]. The three-dimensional molecular model generated from the Peptococcus aerogenes X-ray structure keeps the characteristic overall ferredoxin folding thanks to complementary substitutions of residues of the hydrophobic core. The major structural features of the model are the different environments of both clusters, and the patch of three lysines at one end of the molecule. The possible role of several structural factors in the thermostability of the protein is discussed.

Sodium, protons, and energy coupling in the methanogenic bacteria

In this review, I focus on the bioenergetics of the methanogenic bacteria, with particular attention directed to the roles of transmembrane electrochemical gradients of sodium and proton. In addition, the mechanism of coupling ATP synthesis to methanogenic electron transfer is addressed. Evidence is reviewed which suggests that the methanogens possess great diversity in their bioenergetic machinery. In particular, in some methanogens the primary ion which is translocated coupled to metabolic energy is the proton, while others appear to utilize sodium. In addition, ATP synthesis driven by methanogenic electron transfer is accomplished in some organisms by a chemiosmotic mechanism and is coupled by a more direct mechanism in others. A possible explanation for this diversity (which is consistent with the relatedness of these organisms to each other and to other members of the Archaebacteria as determined by molecular biological techniques) is discussed.

Isolation, characterization, and biological activity of the Methanococcus thermolithotrophicus ferredoxin

A ferredoxin has been isolated from the thermophilic methanogen Methanococcus thermolithotrophicus. The native protein was a monomer exhibiting a molecular weight of 7,262, calculated from the amino acid composition. Its absorption spectrum had two maxima at 390 and 283 nm, with an absorbance ratio A390/A283 of 0.79. The absorption at 390 nm (E = 29 mM-1 cm-1) and the content of iron of the protein are in agreement with the presence of two 4Fe-4S clusters in M. thermolithotrophicus ferredoxin. Its amino acid composition showed the presence of eight cysteine residues, which is the required number of cysteines for the binding of two 4Fe-4S clusters. The protein was characterized by the lack of histidine, arginine, and leucine and a high content of valine. It was unusually stable to high temperatures but not to oxygen. The ESR spectrum of the protein in the oxidized state showed a minor signal at g = 2.01, corresponding to an oxidized 3Fe-4S cluster. The protein, which was difficult to reduce with dithionite or reduced mediators, exhibited in its reduced state a spectrum typical of two interacting reduced 4Fe-4S clusters. M. thermolithotrophicus ferredoxin functioned as an electron acceptor for the CO dehydrogenase complex with an extract free of ferredoxin. No reaction was detected with F420 or hydrogenase.

Iron-sulfur centers involved in methanogenic electron transfer in Methanobacterium thermoautotrophicum (delta-H)

Utilizing a subcellular particulate preparation from Methanobacterium thermoautotrophicum (delta-H) which contains all detectable methanogenic electron transfer activity, we present the results of the effects of the anaerobic addition of oxidized factor F420 and of methyl coenzyme M plus ATP on the EPR signals from reduced iron-sulfur centers and a rapidly-relaxing radical species. Based on these results, we report the existence of a minimum of three iron-sulfur centers which are capable of donating electrons to these cofactors.

The bioenergetics of methanogenesis

The reduction of CO2 or any other methanogenic substrate to methane serves the same function as the reduction of oxygen, nitrate or sulfate to more reduced products. These exergonic reactions are coupled to the production of usable energy generated through a charge separation and a protonmotive-force-driven ATPase. For the understanding of how methanogens derive energy from C-1 unit reduction one must study the biochemistry of the chemical reactions involved and how these are coupled to the production of a charge separation and subsequent electron transport phosphorylation. Data on methanogenesis by a variety of organisms indicates ubiquitous use of CH3-S-CoM as the final electron acceptor in the production of methane through the methyl CoM reductase and of 5-deazaflavin as a primary source of reducing equivalents. Three known enzymes serve as catalysts in the production of reduced 5-deazaflavin: hydrogenase, formate dehydrogenase and CO dehydrogenase. All three are potential candidates for proton pumps. In the organisms that must oxidize some of their substrate to obtain electrons for the reduction of another portion of the substrate to methane (e.g., those using formate, methanol or acetate), the latter two enzymes may operate in the oxidizing direction. CO2 is the most frequent substrate for methanogenesis but is the only substrate that obligately requires the presence of H2 and hydrogenase. Growth on methanol requires a B12-containing methanol-CoM methyl transferase and does not necessarily need any other methanogenic enzymes besides the methyl-CoM reductase system when hydrogenase is present. When bacteria grow on methanol alone it is not yet clear if they get their reducing equivalents from a reversal of methanogenic enzymes, thus oxidizing methyl groups to CO2. An alternative (since these and acetate-catabolizing methanogens possess cytochrome b) is electron transport and possible proton pumping via a cytochrome-containing electron transport chain. Several of the actual components of the methanogenic pathway from CO2 have been characterized. Methanofuran is apparently the first carbon-carrying cofactor in the pathway, forming carboxy-methanofuran. Formyl-FAF or formyl-methanopterin (YFC, a very rapidly labelled compound during 14C pulse labeling) has been implicated as an obligate intermediate in methanogenesis, since methanopterin or FAF is an essential component of the carbon dioxide reducing factor in dialyzed extract methanogenesis. FAF also carries the carbon at the methylene and methyl oxidation levels.(ABSTRACT TRUNCATED AT 400 WORDS)

Reductive activation of methanol: 5-hydroxybenzimidazolylcobamide methyltransferase of Methanosarcina barkeri

Methanol: 5-hydroxybenzimidazolylcobamide methyltransferase (MT1) from Methanosarcina barkeri, which is one of the enzymes responsible for the transmethylation from methanol to coenzyme M, was found to be activated in the presence of hydrogenase and ferredoxin. This activation was shown to involve a reduction of the bound corrinoid to the Co (I) level, and was demonstrated by spectrophotometry and chemical conversion of reduced MT1 to its methylated form. The reducing system of hydrogenase and ferredoxin was able to reduce dithiols, like dithiodiethanesulfonate and cystine to their monomers, in the presence of a corrinoid, which acts as an electron carrier. The ferredoxin was purified 133-fold and was tentatively identified on the basis of spectral properties and iron content of 3.8-4.0 atoms iron per molecule ferredoxin (12,000 daltons).