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Nucleotide sequence of a rice root ferredoxin-NADP+ reductase cDNA and its induction by nitrate.

A ferredoxin-NADP+ reductase (FNR) cDNA was isolated from a lambda gt 11 cDNA library constructed from the roots of nitrate-induced rice (Oryza sativa L. cv. Kinmaze) seedlings. The nucleotide sequence of this clone contains a 1134 nucleotide open reading frame. The N-terminal 62 amino acid stretch was assigned to the transit sequence, followed by 316 residues for the mature protein. The rice root FNR shows only 49% sequence identity to that of the leaf enzyme, but the regions of the binding sites to ferredoxin, NADP-PPi and NADP+ are highly conserved between the two enzymes. The root FNR mRNA was induced transiently by the addition of nitrate, but not by ammonia. The results support the view that the root FNR is involved in the nitrate assimilation in nonchlorophyllous tissues.

Amino Acid Sequence↗

Cloning and sequencing of the gene encoding spinach ferredoxin-dependent glutamate synthase.

The nucleotide sequences of two cDNA clones, totalling 4948 bp in length, encoding 98% of the 1483 amino acids of the mature form of the ferredoxin-dependent glutamate synthase of spinach chloroplasts have been determined. The amino-terminal sequence of the enzyme has been determined by direct sequencing of the protein. The deduced amino-acid sequence of the spinach enzyme is 83% identical to that of the ferredoxin-dependent maize enzyme and shows significant sequence homology to two prokaryotic NAD(P)H-dependent glutamate synthases. Analysis of spinach genomic DNA indicates the presence of a single-copy gene for the spinach enzyme. Northern analysis reveals the presence of a single 5.5 kb transcript, which is present in higher levels in young spinach leaves than in older leaves.

Amino Acid Sequence↗

Characterization of an fdxN mutant of Rhodobacter capsulatus indicates that ferredoxin I serves as electron donor to nitrogenase.

A mutant of Rhodobacter capsulatus, carrying an insertion into the fdxN gene encoding ferredoxin I (FdI), has been studied by biochemical analysis and genetic complementation experiments. When compared to the wild-type strain, the fdxN mutant exhibited altered nitrogen fixing ability and 20-fold lower levels of nitrogenase activity as assayed in vivo. When assayed in vitro with an artificial reductant, nitrogenase activity was only 3- to 4-fold lower than in the wild type. These results suggested that the FdI-deleted mutant had impaired electron transport to nitrogenase. Immunochemical assay of both nitrogenase components showed that the fdxN mutant contained about 4-fold less enzyme than wild-type cells. Results of pulse-chase labeling experiments using [35S]methionine indicated that nitrogenase was significantly less stable in the FdI-deleted mutant. When a copy of fdxN was introduced in the mutant in trans, the resulting strain appeared to be fully complemented with respect to both diazotrophic growth and nitrogenase activity. Depending on whether fdxN expression was driven by a nif promoter or a fructose-inducible promoter, FdI was synthesized either at wild-type level or in 10-fold lower amounts. The strain producing 10-fold less FdI did, however, display normal N2-fixing ability. Analysis of cytosolic proteins by bidimensional electrophoresis revealed that the fdxN mutant produced a 14 kDa polypeptide in amounts about 3-fold greater than wild-type cells. This protein was identified by N-terminal microsequencing as a recently purified [2Fe-2S] ferredoxin, called FdV, which cannot reduce nitrogenase. It is concluded that FdI serves as the main electron donor to nitrogenase in R. capsulatus and that an ancillary electron carrier, distinct of FdV, is responsible for the residual nitrogenase activity observed in the FdI-deleted mutant.

Base Sequence↗

The three-iron cluster in a ferredoxin from Desulphovibrio gigas. A low-temperature magnetic circular dichroism study.

Ferredoxin II from Desulphovibrio gigas is a tetrameric protein containing a novel iron-sulphur cluster consisting of three iron atoms. The low-temperature magnetic circular dichroism (MCD) spectra of the oxidized and dithionite-reduced forms of ferredoxin II have been measured over the wavelength range approx. 300-800 nm. Both oxidation levels of the cluster are shown to be paramagnetic, although only the oxidized form gives an EPR signal. MCD magnetization curves have been constructed over the temperature range approx. 1.5-150 K and at fields between 0 and 5.1 Tesla. The curve for the oxidized protein can be fitted to a ground state of spin S = 1/2 with an isotropic g factor of 2.01. There is evidence for the thermal population of a low-lying electronic state above 50 K. The reduced protein gives a distinctive set of magnetization curves that are tentatively assigned to a ground state of S = 2, with a predominantly axial zero-field distortion that leaves the doublet Ms = +/-2 lowest in energy. The zero-field components have a maximum energy spread of approx. 15 cm-1. which places an upper limit of 4 cm-1 on the axial zero-field parameter D. The MCD spectra of the oxidized and reduced forms of the cluster are quite distinctive from one another. The spectra of the oxidized state are also different from those of oxidized high-potential iron protein from Chromatium and should provide a useful criterion for distinguishing between four- and three-iron clusters in their highest oxidation levels.

Circular Dichroism↗

Molecular heterogeneity of ferredoxin-NADP+ reductase from spinach leaves.

Highly purified ferredoxin-NADP+ reductase from spinach leaves showed at least eight different protein bands in the electrofocused gel. All of them were catalytically active and were adsorbed on a ferredoxin-Sepharose 4B affinity column. The N-terminal amino acid sequence of the main component species was analyzed by the automatic Edman degradation method. It was found that when the reductase was stored at 4 degrees C, new protein bands appeared in isoelectric focusing and sodium dodecyl sulfate polyacrylamide gel electrophoreses, but the appearance of the bands was suppressed by the addition of a protease inhibitor, diisopropyl fluorophosphate. This indicates that the molecular heterogeneity of the reductase may result from the digestion with a protease present in spinach leaves.

Amino Acid Sequence↗

Structural differences between [2Fe-2S] clusters in spinach ferredoxin and in the "red paramagnetic protein" from Clostridium pasteurianum. A resonance Raman study.

The [2Fe-2S] ferredoxin ("Red paramagnetic protein", RPP) from C. pasteurianum has been found to be composed of two identical subunits of 10,000 +/- 2 000 daltons, each containing a [2Fe-2S] cluster. Resonance Raman (RR) spectra of RPP have been obtained at 23 degrees K, and compared to those of spinach ferredoxin (Sp Fd). Ten modes of the [2Fe-2S] chromophore were observed in the 100-450 cm-1 range. Assignments of non fundamental modes in the 500-900 cm-1 range allowed correlations between fundamental stretching modes of RPP and Sp Fd. Although assuming a [2Fe-2S] structure, the chromophore of RPP differs from that of Sp Fd by its conformation and by a slight weakening of Fe-S bonds, involving both the inorganic core and the cysteine ligands.

Clostridium↗

Evolution of Alu repeats surrounding the human ferredoxin gene.

Ferredoxin is an iron-sulfur protein that serves as an electron carrier for the mitochondrial oxidation/reduction system. During the characterization of the human ferredoxin gene, we have identified three Alu sequences surrounding it. When these Alu sequences were compared with others, all three of them are more related to the consensus Alu than the 7SL gene, the progenitor of the Alu family. It suggests that they are members of the modern Alu family. Their sequences differ from the Alu consensus sequence by about 5%, indicating that they were inserted into the chromosome about 35 million years ago.

Base Sequence↗

Resonance Raman spectroscopy of Azotobacter vinelandii ferredoxin I. Vibrational features of the [3Fe-3S] cluster.

Low temperature resonance Raman spectra have been obtained for Clostridium pasteurianum and Bacillus stearothermophilus ferredoxins. Several heretofore undetected fundamental bands have been observed and these data have been used to discriminate the vibrational contribution of the [3Fe-3S] cluster to the spectrum of Azotobacter vinelandii ferredoxin I. The vibrational features of the [3Fe-3S] core distinguish it from other 3-iron clusters and imply structural differences among this class of iron-sulfur clusters.

Azotobacter↗

Purification and biochemical characterization of hepatic ferredoxin (hepatoredoxin) from bovine liver mitochondria.

Hepatic ferredoxin (hepatoredoxin) was purified from bovine liver mitochondria. The monomeric molecular mass of the hepatoredoxin was larger than that of adrenocortical ferredoxin (adrenodoxin) from bovine adrenocortical mitochondria at 14 kDa. We studied the amino acid residues and NH2-terminal sequence of this protein. The hepatoredoxin was organ-specific protein. The optical absorption spectrum of oxidized hepatoredoxin had two peaks, at 414 and 455 nm in the visible region. Hepatoredoxin formed an immunoprecipitin line against anti-adrenodoxin immunoglobulin in Ouchterlony double diffusion, and an immunochemical staining band in Western blotting.

Adrenodoxin↗

The crystal structure of the three-iron ferredoxin II from Desulfovibrio gigas.

The crystal structure of oxidized ferredoxin II from the sulfate-reducing bacterium Desulfovibrio gigas has been determined and refined at 1.7 A resolution. The folding of the polypeptide chain is similar to that of the 2[4Fe-4S] ferredoxin in Peptococcus aerogenes, except for an extended helical segment near the C-terminus. The single [3Fe-4S] cluster in D. gigas is similar to a [4Fe-4S] cluster, but lacks one Fe atom and is coordinated to Cys-8, -14 and -50. The side chain of Cys-11 is not bound to the cluster, but is rotated toward the solvent and modified by some, as yet undetermined, chemical group. Cys-18 and Cys-42 form a disulfide bridge. A previously undetected extra amino acid is found after residue 55.

Desulfovibrio↗

The petFI gene encoding ferredoxin I is located close to the str operon on the cyanelle genome of Cyanophora paradoxa.

The petFI gene encoding ferredoxin I was localized in the large single copy region of cyanelle DNA by heterologous hybridization. Sequence analysis revealed an ORF of 99 amino acids (including the N-terminal processed methionine) at a position 477 bp from the 3' end of tufA but on the opposite strand. The 25 amino-terminal residues well corresponded to partial sequences obtained with purified cyanelle ferredoxin. The assignment of yet another gene that is not found on the genomes of chlorophyll b-type plastids to cyanelle DNA again corroborates the special position of cyanelles serving as a model for plastid evolution from endocytobiotic cyanobacteria.

Amino Acid Sequence↗

Isolation of a cDNA fragment coding for Chlamydomonas reinhardtii ferredoxin and expression of the recombinant protein in Escherichia coli.

A cDNA clone coding for mature C. reinhardtii ferredoxin has been isolated from a cDNA library using PCR and two oligonucleotide primers based on the N- and C-termini of the protein's amino acid sequence. The nucleotidic sequence of the PCR fragment (299 bp) agreed well with the amino acid sequence since a single conservative substitution (Thr-7 to Ser) could be deduced. The PCR fragment was inserted into the expression vector pTrc 99A, using the incorporated NcoI and BamHI restriction sites and the construction used to transform E. coli (DH5 alpha F'). After subsequent large scale expression and purification of the recombinant protein, biochemical and biophysical analysis have indicated that the product isolated from E. coli is homologous to native ferredoxin isolated from green algae.

Amino Acid Sequence↗

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.

Electrochemistry↗

Selective chemical modification of amino acid residues in the flavin adenine dinucleotide binding site of NADPH-ferredoxin reductase.

1. An apo-NADPH-ferredoxin reductase was prepared from holo-NADPH-ferredoxin reductase (EC 1.18.1.2) from bovine adrenocortical mitochondria. 2. Amino acid residues of the apo-reductase were modified selectively, to identify the FAD-binding site of the reductase, with chemical reagents such as diethylpyrocarbonate, 5,5'-dithiobis(2-nitrobenzoate), tetranitromethane, pyridoxal 5'-phosphate, p-nitrophenylglyoxal, diisopropylfluorophosphate and N-bromosuccinimide. The binding of FAD to the apo-reductase was measured as quenching of the fluorescence of FAD caused by the binding between apo-reductase and FAD. The quenching was blocked when the apo-reductase was modified with diethylpyrocarbonate and restored on the addition of hydroxylamine. 3. The blocking of the quenching occurred in a competitive manner as to FAD in the presence of diethylpyrocarbonate. However, when the apo-reductase was modified with 5,5'-dithiobis(2-nitrobenzoate), the blocking of the quenching occurred in a non-competitive manner. 4. These results suggested that a histidyl residue of the apo-reductase is essential for the binding of FAD to the reductase. This was confirmed by amino acid sequencing of the modified apo-reductase.

Amino Acid Sequence↗

Determination of the amino acid sequence of adreno-ferredoxin from sheep adrenocortical mitochondria.

1. An adreno-ferredoxin was purified from sheep adrenocortical mitochondria. 2. Its amino acid composition and amino acid sequence were determined chemically. 3. It was found to be composed of 127 amino acid residues, including two tyrosyl residues. 4. The amino acid sequences of various ferredoxins of the two iron and two sulfur type were compared with respect to amino acid homology.

Adrenal Cortex↗

Preliminary X-ray diffraction studies on a ferredoxin from the thermophilic archaebacterium, Thermoplasma acidophilum.

A ferredoxin from the thermophilic archaebacterium, Thermoplasma acidophilum, is supposed to contain two (4Fe-4S) active centers; one center could be linked by four cysteine residues to the protein and the other bonded with three cysteines and an unknown group. This ferredoxin has been crystallized by salting-out against 2.3 M-ammonium sulfate solution. The space group is P21212 with cell dimensions of a = 59.20 A, b = 52.77 A and c = 41.28 A. Four molecules pack in the unit cell with Vm = 2.03 A3/dalton.

Amino Acid Sequence↗

Protein chemotaxonomy of genus Datura: identical amino acid sequence of ferredoxin from two varieties of Datura stramonium.

The complete amino acid sequence of the respective [2Fe-2S] ferredoxins from two varieties of Datura stramonium, D. stramonium var. stramonium and D. stramonium var. tatula, have been determined by automated Edman degradation of the entire Cm-protein and of the peptides obtained by tryptic digestion and CNBr treatment. The ferredoxins from the two plants exhibited identical amino acid sequences, suggesting a very close taxonomic relationship between the two. This result supports the proposal by Blakeslee and others that these plants, at first named by Linnaeus as two distinct species, i.e. D. stramonium L. and D. tatula L., should be considered two varieties of a single species.

Amino Acid Sequence↗

Proton n.m.r. of ferredoxin from Clostridium pasteurianum.

Proton magnetic resonance spectra at 500 MHz are reported for the oxidized and reduced forms of the 2[4Fe-4S]-ferredoxin from Clostridium pasteurianum. The reduced protein showed additional peaks in the 10-60 ppm region, which were previously unobserved, and there were significant differences between oxidized and reduced states in the whole region. The electron exchange rate in partially reduced ferredoxin is slow on the n.m.r. time scale when reduced with sodium dithionite, but fast when zinc reduced methyl viologen is used as reducing agent. We explain the difference between fast and slow exchange as being due to the different chemical properties of the two reducing agents.

Clostridium↗