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Mitochondrial ferredoxin is required for heme A synthesis in Saccharomyces cerevisiae.

Heme A is a prosthetic group of all eukaryotic and some prokaryotic cytochrome oxidases. This heme differs from heme B (protoheme) at two carbon positions of the porphyrin ring. The synthesis of heme A begins with farnesylation of the vinyl group at carbon C-2 of heme B. The heme O product of this reaction is then converted to heme A by a further oxidation of a methyl to a formyl group on C-8. In a previous study (Barros, M. H., Carlson, C. G., Glerum, D. M., and Tzagoloff, A. (2001) FEBS Lett. 492, 133-138) we proposed that the formyl group is formed by an initial hydroxylation of the C-8 methyl by a three-component monooxygenase consisting of Cox15p, ferredoxin, and ferredoxin reductase. In the present study three lines of evidence confirm a requirement of ferredoxin in heme A synthesis. 1) Temperature-conditional yah1 mutants grown under restrictive conditions display a decrease in heme A relative to heme B. 2) The incorporation of radioactive delta-aminolevulinic acid into heme A is reduced in yah1 ts but not in the wild type after the shift to the restrictive temperature; and 3) the overexpression of Cox15p in cytochrome oxidase mutants that accumulate heme O leads to an increased mitochondrial concentration of heme A. The increase in heme A is greater in mutants that overexpress Cox15p and ferredoxin. These results are consistent with a requirement of ferredoxin and indirectly of ferredoxin reductase in hydroxylation of heme O.

Adrenodoxin↗

Purification and characterization of a [3Fe-4S][4Fe-4S] type ferredoxin from hyperthermophilic archaeon, Pyrobaculum islandicum.

A ferredoxin was purified from the hyperthermophilic archaeon, Pyrobaculum islandicum. EPR spectra and metal content analyses suggested that the ferredoxin molecule contained one [3Fe-4S] and one [4Fe-4S] cluster. The ferredoxin was rapidly reduced by 2-oxoglutarate: ferredoxin oxidoreductase purified from P. islandicum, indicating that it functions physiologically as an electron sink for the redox enzymes participating in glycolytic metabolism. Furthermore, the amino acid sequence of the P. islandicum ferredoxin was compared with those of several other bacterial ferredoxins.

Amino Acid Sequence↗

Separation and identification of two native forms of spinach ferredoxin by hydrophobic chromatography.

Hydrophobic chromatography on a TSK-gel Phenyl-5PW column separated highly purified spinach ferredoxin into two distinct molecular species in their native forms. The two ferredoxins showed almost the same absorption spectra in spite of a difference in amino acid composition. Both ferredoxins were active in the NADPH-cytochrome c reducing system, and no significant difference was observed between their activities. The new separation method was also applied to ferredoxins highly purified from wheat plants and barley. Interestingly, all ferredoxin preparations so far examined contained two molecular species of ferredoxin.

Amino Acids↗

Complete amino acid sequence of Halobacterium halobium ferredoxin containing an Nepsilon-acetyllysine residue.

1. The complete amino acid sequence of the 2Fe-2S ferredoxin from Halobacterium halobium was determined to be: (formula see text):2. The apoferredoxin chain consists of 128 amino acid residues and has a molecular weight of 14,330. 3. There are only four cysteines in this ferredoxin molecule; they should be involved in the binding of the two iron atoms at the active center. Ther relative positions of these cysteines are similar to those of the cysteines in chloroplast ferredoxins. 4. There is a high degree of homology between H. halobium ferredoxin and chloroplast ferredoxins, though the latter molecules contain only about 98 amino acid residues. 5. H. halobium ferredoxin contains a single residue of Nepsilon-acetyllysine.

Amino Acid Sequence↗

Amino acid sequence of Chlorogloeopsis fritschii ferredoxin: taxonomic and evolutionary aspects.

The amino acid sequence of Chlorogloeopsis fritschii ferredoxin was determined for its carboxymethylated derivative by using solid-phase sequencing, fragmentation with various enzymes, and manual Edman degradation procedures. The ferredoxin was composed of 98 amino acid residues and lacked methionine and tryptophan. The sequence was as follows: Ala-Thr-Tyr-Lys-Val-Thr-Leu-Ile-Asn-Asp-Ala-Glu- Gly-Leu-Asn-Gln-Thr-Ile-Glu-Val-Asp-Asp-Asp-Thr-Tyr-Ile-Leu-Asp-Ala-Ala-Glu- Glu-Ala-Gly-Leu-Asp-Leu-Pro-Tyr-Ser-Cys-Arg-Ala-Gly-Ala-Cys-Ser-Thr-Cys-Ala-Gly-Lys-Ile-Lys-Ser-Gly-Thr-Val-Asp-Gln-Ser-Asp-Gln-Ser-Phe-Leu-Asp-Asp-Asp- Gln-Ile-Glu-Ala-Gly-Tyr-Val-Leu-Thr-Cys-Val-Ala-Tyr-Pro-Thr-Ser-Asp-Cys-Thr-Ile-Glu-Thr-His-Lys-Glu-Glu-Glu-Leu-Tyr. A phylogenetic tree was constructed on the basis of a comparison of various algal ferredoxins and it was found that C. fritschii ferredoxin was closely related to Mastigocladus laminosus ferredoxin, though they are in different genera of the blue-green algae. Aspects of the taxonomy and molecular evolution of blue-green algal ferredoxins are discussed.

Amino Acid Sequence↗

Amino acid sequence of a ferredoxin from thermoacidophilic archaebacterium, Sulfolobus acidocaldarius. Presence of an N6-monomethyllysine and phyletic consideration of archaebacteria.

The amino acid sequence of a ferredoxin from a thermoacidophilic archaebacterium, Sulfolobus acidocaldarius, was determined by a combination of various conventional methods to be as follows: Gly-Ile-Asp-Pro-Tyr-Arg-Thr-His-Lys-Pro-Val-Val-Gly-Asp-Ser-Ser-Gly-His- Lys-Ile -Tyr-Gly-Pro-Val-Glu-Ser-Pro-Lys(Me)-Val-Leu-Gly-Val-His-Gly-Thr-Ile-Val -Gly-Va l-Asp-Phe-Asp-Leu-Cys-Ile-Ala-Asp-Gly-Ser-Cys-Ile-Thr-Ala-Cys-Pro-Val-As n-Val-P he-Gln-Trp-Tyr-Glu-Thr-Pro-Gly-His-Pro-Ala-Ser-Glu-Lys-Lys-Ala-Asp-Pro-V al-Asn- Glu-Gln-Ala-Cys-Ile-Phe-Cys-Met-Ala-Cys-Val-Asn-Val-Cys-Pro-Val-Ala-Ala- Ile-Asp -Val-Lys-Pro-Pro. It was composed of 103 amino acid residues giving a molecular weight of 10,908 excluding Fe and S atoms. This ferredoxin contained an N6-monomethyllysine residue at position 29 which was determined by a comparison of the elution profile of the acid hydrolysates of the protein and peptides on an amino acid analyzer with three methyl derivatives of lysine and also by field desorption mass spectrometry of a purified peptide. The ferredoxin has only 7 cysteine residues, which probably participate in constructing the Fe-S clusters of this ferredoxin, indicating the presence of a unique chelate structure. Comparison of this ferredoxin with other archaebacterial ferredoxins indicated that the archaebacteria might have multiple origins in an evolutionary tree.

Amino Acid Sequence↗

Purification, crystallization and preliminary X-ray analysis of ferredoxin isolated from thermophilic cyanobacterium Mastigocladus laminosus.

Ferredoxins are soluble iron-sulfur proteins that are involved in numerous electron-transfer reactions. Plant-type ferredoxins, which carry a single [2Fe-2S] cluster, serve as the electron acceptors of Photosystem I. The ferredoxin from the thermophilic cyanobacterium Mastigocladus laminosus has unique thermostable properties. The isolated protein is active at temperatures of higher than 338 K. The gene encoding the ferredoxin from M. laminosus was subcloned into an expression vector and overproduced in Escherichia coli. The recombinant protein was purified to near-homogeneity and crystallized using the hanging-drop method. Thin needle-like crystals were grown in several crystallization conditions but were unsuitable for X-ray analysis owing to poor scattering. In order to obtain better diffracting crystals, ferredoxin was purified directly from M. laminosus cells. Single crystals were obtained using 30% PEG 4000, 0.32 M Mg(NO(3))(2), 20 mM Tris-HCl pH 8.2. These crystals diffracted to 1.25 A resolution using synchrotron radiation and were found to belong to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 28.45, b = 50.93, c = 110.91 A. The asymmetric unit was found to contain two ferredoxin molecules, with a corresponding V(M) of 1.9 A(3) Da(-1) and a solvent content of 34%. The present study indicates that overcoming the poor diffraction of crystals obtained from recombinant protein can be achieved by producing crystals from protein purified from the native host.

Cloning, Molecular↗

A new plant-type ferredoxin from halobacteria.

A stable, 2Fe-type ferredoxin has been prepared from Halobacterium halobium and purified by chromatography. A similar ferredoxin was also found in three other Halobacteria. The ferredoxin is present in large amounts-about 1 percent of the total soluble protein. From amino acid composition a molecular weight of 14800 +/- 200 was calculated. The ferredoxin was found to contain two atoms each of iron and sulphide. The midpoint redox potential of the protein is about -345 mV. The electron paramagnetic resonance spectrum of the reduced form shows much similarity to plant and algal ferredoxins with gx = 1.90, gy = 1.97 and gz = 2.07. The same similarity is observed in the optical absorption, optical rotatory dispersion and circular dichroism spectra. However it does not seem to mediate electron transport in the NADP-photoreduction system of chloroplasts. Extracts of the bacterial cells catalyze the reduction of the ferredoxin by NADH.

Amino Acids↗

Purification, properties and complete amino acid sequence of the ferredoxin from a green alga, Chlamydomonas reinhardtii.

The ferredoxin was purified from the green alga, Chlamydomonas reinhardtii. The protein showed typical absorption and circular dichroism spectra of a [2Fe-2S] ferredoxin. When compared with spinach ferredoxin, the C. reinhardtii protein was less effective in the catalysis of NADP+ photoreduction, but its activity was higher in the light activation of C. reinhardtii malate dehydrogenase (NADP). The complete amino acid sequence was determined by automated Edman degradation of the whole protein and of peptides obtained by trypsin and chymotrypsin digestions and by CNBr cleavage. The protein consists of 94 residues, with Tyr at both NH2 and COOH termini. The positions of the four cysteines binding the two iron atoms are similar to those found in other [2Fe-2S] ferredoxins. The primary structure of C. reinhardtii ferredoxin showed a great homology (about 80%) with ferredoxins from two other green algae.

Amino Acid Sequence↗

A four-iron, four-sulfide ferredoxin with high thermostability from Clostridium thermoaceticum.

A ferredoxin containing only one [Fe4S4] cluster was purified from Clostridium thermoaceticum. It has a molecular weight of about 7,300, a partial specific volume of 0.67, and an isoelectric point of 3.25. Its absorption spectrum has two maxima at 390 nm (epsilon = 16.8 X 10(3)M-1cm-1) and at 280 nm (epsilon = 24.2 X 10(3)M-1cm-1). The absorption at 390 nm is almost half that of other clostridial ferredoxins, which have two [Fe4S4] clusters, and is similar to other ferredoxins with only one [Fe4S4] cluster. The ferredoxin had high thermal stability and retained over 50% of its activity after treatment at 80 degrees C. It functions in the transfer of electrons from pyruvate to nicotinamide adenine dinucleotide phosphate (NADP), which indicates the presence of pyruvate:ferredoxin oxidoreductase and reduced ferredoxin-NADP reductase in C, thermoaceticum. NADPH is used in the synthesis of acetate from CO2 in this organism.

Amino Acids↗

Isolation and nucleotide sequence analysis of the ferredoxin I gene from the cyanobacterium Anacystis nidulans R2.

Two mixed oligonucleotide probes derived from conserved regions of the Synechocystis sp. strain PCC 6714 ferredoxin amino acid sequence were utilized to isolate an Anacystis nidulans R2 clone containing the ferredoxin I gene. Nucleotide sequence analysis revealed a 297-base-pair (bp) open reading frame with a deduced amino acid sequence having high homology to other cyanobacterial ferredoxins. Assuming proteolytic cleavage of the initial methionine residue, the molecular weight of the mature A. nidulans R2 ferredoxin was 10,370. The initial methionine residue was preceded by a probable ribosome-binding site sequence, AGGA. Northern hybridization analysis with the cloned ferredoxin gene indicated an RNA transcript of approximately 450 bp. S1 nuclease mapping localized the transcription start site to a position 64 bases upstream from the initial methionine residue. The nucleotide sequence 14 to 8 bp preceding the transcription start site resembled a typical Escherichia coli promoter, but the sequence in the -35 region did not. Southern hybridization detected only a single copy of the ferredoxin sequence in the A. nidulans R2 genome.

Amino Acid Sequence↗

Reduced ferredoxin: CO2 oxidoreductase from Clostridium pasteurianum. Effect of ligands to transition metals on the activity and the stability of the enzyme.

Reduced ferredoxin: CO2 oxidoreductase (CO2-reductase) from Clostridium pasteurianum catalyzes the reduction of CO2 to formate at the expense of reduced ferredoxin, an isotopic exchange between CO2 and formate in the absence of ferredoxin, and the oxidation of formate to CO2 with oxidized ferredoxin. The three activities were found to be equally affected by monovalent anions known to be ligands to transition metals: The enzyme was reversibly inhibited by azide (Ki = 0.004mM), cyanate (Ki = 0.3 mM), thiocyanate (Ki = 1mM), nitrite (Ki = 0.4mM), nitrate (Ki = 6mM), chlorate (Ki = 3mM), fluoride (Ki = 5mM), and by chloride, bromide, iodide (Ki greater than 5mM). There was no observable effect of pH on the inhibition constants. The enzyme was not inhibited by carbon monoxide. The enzyme was irreversibly inactivated by low concentrations (10muM) of cyanide. The rate of inactivation increased with increasing pH with an inflection point near pH 9.5. Reduced ferredoxin and formate rather than oxidized ferredoxin or CO2 protected the enzyme from inactivation by cyanide. The enzyme was protected by azide and cyanate from inactivation. In the presence of high concentrations of the monovalent anions the rate of inactivation by heat (55 degrees C), by molecular oxygen, and by cyanide was decreased by a factor of more than 100. Half maximal protection was observed at the Ki concentrations of the two reversible inhibitors. The data are interpreted to indicate that a transition metal of weak "a class" character and a disulfide are catalytically significant groups of CO2-reductase from C. pasteurianum.

Anions↗

On the reduction of aliphatic and aromatic nitro compounds by Clostridia, the role of ferredoxin and its stabilization.

Crude extracts of a variety of Clostridium species reduce aromatic and aliphatic nitro compounds in the presence of hydrogen gas. Using different Clostridia, the uptake of hydrogen by p-nitrobenzoate is about 5--10 times faster than by 2-nitroethanol. Structurally rather different aliphatic nitro compounds show rates which differ by less than a factor of 3. Hydrogenase from Clostridium kluyveri and ferredoxins from Clostridium spec. La 1 and spinach have been purified. The combinations of the hydrogenase and each one of the ferredoxins catalyse the hydrogen uptake by nitro compounds. Clostridial flavodoxin also transfer electrons onto nitro compounds. Nitroaryl and nitroalkyl compounds behave differently with ferredoxin. The first reduction step (1-electron transfer) of p-nitrobenzoate leads to the nitro radical anion which can be detected by EPR measurements. Nitro alkanes seem to form a rather unstable radical which decomposes partially to form nitrite. Furthermore, 2-(N-hydroxyimino)- and 2-(N-hydroxyamino)ethanol, a nitrogen radical of 2-(N-hydroxyamino)ethanol as well as glycol and 1,4-butanediol were detected as intermediates and side products during the reduction of 2-nitro-ethanol to 2-aminoethanol. While the hydrogenase from Clostridium kluyveri seems not to be affected by any reduction intermediate, the ferredoxin from Clostridium spec. La 1 is inactivated by nitrite in a few minutes. Ferrous and sulfide ions in concentrations substoichiometric to that of nitrite stabilize and even reactivate the ferredoxin in the presence of 2-mercaptoethanol. A mechanism for the reduction of aliphatic nitro compounds catalysed by hydrogenase and ferredoxin is proposed.

Clostridium↗

[Cloning and sequence analysis of Trichomonas vaginalis ferredoxin gene].

OBJECTIVE: To construct a recombinant plasmid containing ferredoxin gene of Trichomonas vaginalis. METHODS: Total DNA was extracted from Trichomonas vaginalis with Chelex-100 method and used as templates for PCR. Primers were designed based on the published sequence of the ferredoxin gene and used to amplify the Trichomonas vaginalis gene using PCR method. The ferredoxin gene obtained by PCR technique was directionally cloned into plasmid pMD-18T simple vector. The constructed recombinant plasmid was transferred into E. coli JM109. The transformants were screened and identified by PCR and restriction analysis. The DNA sequence of the gene was determined by Sanger's method. RESULTS: The size of amplified ferredoxin gene was 306bp. The correct recombinant plasmid was isolated and confirmed by PCR and restriction analysis. The DNA sequence of cloned gene was the same as the published sequence. CONCLUSION: The ferredoxin gene was successfully amplified and cloned into plasmid pMD-18T simple vector. The cloned ferredoxin gene could be used to produce recombinant protein and for study of its function.

Amino Acid Sequence↗

[Fluorescent properties of b-type ferredoxins].

Fluroescent spectra of six b-type ferredoxins of plant and animal origins were obtained. All investigated proteins do not contain tryptophan. The emission maxima of the native proteins, apoproteins prepared by various methods, and denaturated proteins are compared. The effects of pH, ionic strength and ferricyanide on the ferredoxins fluorescence were studied. "Unusual" emission at 340nm noted previously for adrenal ferredoxin was observed for spinach and Chenopodium album ferredoxins too. The localization of tyrosine fluorescent maximum at 340nm in the ferredoxins is not due to interaction of tyrosine with the iron-sulfur center. The data obtained allow to suggest that the tyrosine residues in ferredoxins have different environments.

Adrenal Glands↗

Biosynthesis of phycobilins. Ferredoxin-mediated reduction of biliverdin catalyzed by extracts of Cyanidium caldarium.

Cell-free extract of the unicellular rhodophyte, Cyanidium caldarium catalyzes enzymatic reduction of biliverdin IX alpha to phycocyanobilin, the chromophore of the light-harvesting phycobiliprotein, phycocyanin. The enzyme activity is soluble, and the required reductant is NADPH. The extract has been separated into three protein fractions, all of which are required to reconstitute biliverdin reduction. One fraction contains ferredoxin, which was identified by its absorption spectrum. This fraction could be replaced with commercial ferredoxin derived from spinach or the red alga, Porphyra umbilicalis. The second protein fraction contains ferredoxin-NADP+ reductase, which was identified by the ability to catalyze ferredoxin-dependent reduction of cytochrome c in the presence of NADPH. This fraction could be replaced with commercial spinach ferredoxin-NADP+ reductase. These two components appear to be identical to previously described components of the algal heme oxygenase system that catalyzes biliverdin IX alpha formation from protoheme in C. caldarium extracts. The third protein fraction, in the presence of the first two (or their commercial counterparts) plus NADPH, catalyzes the reduction of biliverdin IX alpha to phycocyanobilin. The results indicate that the transformation of biliverdin to phycocyanobilin catalyzed by C. caldarium extracts is a ferredoxin-linked reduction process. The results also suggest the possibility that heme oxygenation and biliverdin reduction may occur in C. caldarium on associated enzyme systems.

Biliverdine↗

Genetic analysis of functional differences among distinct ferredoxins in Rhodobacter capsulatus.

Rhodobacter capsulatus has been known to possess two ferredoxins (I and II) with distinct physicochemical and structural properties: ferredoxin I is a 2[4Fe-4S] type and the other is a [3Fe-4S] [4Fe-4S] type. To analyze their possible functional differences, their genes (fdxN and fdxA) were cloned, sequenced, and subjected to interposon mutagenesis experiments. The former gene was adjacent to a gene encoding a chloroplast-type [2Fe-2S] ferredoxin (fdxC). Mutants with inactivated fdxN and/or fdxC were obtained, and they showed virtually no growth under nitrogen-fixing conditions. Complementation experiments confirmed that both fdxN and fdxC were required for nitrogen fixation. On the other hand, we have not been able to disrupt fdxA under the screening conditions surveyed, including conditions that do not require nitrogenase activity for growth, suggesting that ferredoxin II could have an unknown essential role(s). These indicate functional differences among multiple ferredoxins in one bacterium other than in cyanobacterial heterocysts and indispensability of certain ferredoxins in nitrogen fixation other than Rhizobium meliloti FdxN.

Amino Acid Sequence↗

Magnetization of the oxidized and reduced three-iron cluster of Desulfovibrio gigas ferredoxin II.

The saturation magnetizations of the three iron cluster of ferredoxin II of Desulfovibrio gigas in both the oxidized and reduced states have been studied at fixed magnetic fields up to 4.5 tesla over the temperature range from 1.8 to 200 K. The low field (0.3 tesla) susceptibility of oxidized ferredoxin II obeys the Curie law over this entire temperature range. This establishes -2Jox greater than 200 cm-1 as the lower limit for the antiferromagnetic exchange coupling of oxidized ferredoxin II. The saturation magnetizations of reduced ferredoxin II at several fixed fields yield a nested family of curves which can be fit with spin S = 2 and D = -2.7(4) cm-1 (with E/D assigned the value 0.23 as determined by Mössbauer and EPR spectra). The low field susceptibility of reduced ferredoxin II also obeys the Curie law from approximately 4 up to 200 K. This establishes -2Jred greater than 40 cm-1 as the lower limit for the antiferromagnetic coupling of reduced ferredoxin II.

Desulfovibrio↗