Nuclear magnetic resonance studies of two-iron-two-sulfur ferredoxins. 2. Determination of the sequence of Anabaena variabilis ferredoxin II, assignment of aromatic resonances in proton spectra, and effects of chemical modifications

Investigation of the role of surface residues in the ferredoxin from Clostridium pasteurianum

Eleven mutant forms of the ferredoxin from Clostridium pasteurianum (CpFd; 2 Fe4S4; 6200 Da) have been isolated in which six surface carboxylates are changed systematically to their uncharged but stereochemically equivalent carboxamide analogues. Such changes provide molecules which vary in overall charge and its surface distribution but vary minimally in structure and reduction potential. Glu-17 and Asp-6, -27, -33, -35, and -39 were converted providing six single mutants, four double mutants and one triple mutant. The proteins were characterised by UV-visible spectroscopy, square-wave voltammetry and 1H NMR. Their ability to mediate electron transfer between spinach NADH:ferredoxin oxidoreductase and horse heart cytochrome c was assessed. Each mutant is 30-100% as active as the recombinant protein with the triple mutant D33,35,39N being least active. Second-order rate constants k2 for the oxidation of reduced mutant ferredoxins by [Co(NH3)6]3+ were measured at 25 degrees C and I = 0.1 M by stopped-flow techniques. Each mutant displayed saturation kinetics with k2 being 30-100% of that for the recombinant protein. The rates were moderately sensitive to ionic strength. Variation in association constant K could not be detected within the confidence limits of the data. Overall the effects of the mutations were minor. In contrast to human and Anabaena 7120 [Fe2S2]-ferredoxins, electron transfer does not appear to rely on the presence of one or two specific surface carboxylate residues. It may occur from multiple sites on the surface of CpFd with recognition processes for its many physiological redox partners being controlled by relative reduction potentials, in addition to unidentified criteria. The conclusions are consistent with previous results for another series of mutant CpFd proteins interacting with physiological redox partners pyruvate: Fd oxidoreductase and hydrogenase (J.M. Moulis, V. Davasse (1995) Biochemistry 34, 16781-16788).

Structure-function studies of [2Fe-2S] ferredoxins

The ability to overexpress [2Fe-2S] ferredoxins in Escherichia coli has opened up exciting research opportunities. High-resolution x-ray structures have been determined for the wild-type ferredoxins produced by the vegatative and heterocyst forms of Anabaena strain 7120 (in their oxidized states), and these have been compared to structural information derived from multidimensional, multinuclear NMR spectroscopy. The electron delocalization in in these proteins in their oxidized and reduced states has been studied by 1H, 2H, 13C, and 15N NMR spectroscopy. Site-directed mutagenesis has been used to prepare variants of these ferredoxins. Mutants (over 50) of the vegetative ferredoxin have been designed to explore questions about cluster assembly and stabilization and to determine which residues are important for recognition and electron transfer to the redox partner Anabaena ferredoxin reductase. The results have shown that serine can replace cysteine at each of the four cluster attachment sites and still support cluster assembly. Electron transfer has been demonstrated with three of the four mutants. Although these mutants are less stable than the wild-type ferredoxin, it has been possible to determine the x-ray structure of one (C49S) and to characterize all four by EPR and NMR. Mutagenesis has identified residues 65 and 94 of the vegetative ferredoxin as crucial to interaction with the reductase. Three-dimensional models have been obtained by x-ray diffraction analysis for several additional mutants: T48S, A50V, E94K (four orders of magnitude less active than wild type in functional assays), and A43S/A45S/T48S/A50N (quadruple mutant).

Pulse radiolysis and related studies on the Ru-modified His 16 derivative of Anabaena variabilis [2Fe-2S] ferredoxin

The preparation and characterisation of a Ru-modified derivative of the [2Fe-2S] ferredoxin FdI component of A. variabilis by attachment of Ru(NH3)5 to a surface histidine has been carried out. Metal analyses by ICP gave an Fe/Ru ratio of 1.97:1. From NMR the attachment is confirmed as a modification at His-16 and not His-92. No Ru-modification of the [2Fe-2S] FdI component of spinach, which has His-92 but no His-16, was observed. Histidine pKa values have been determined and anomalously low values for A. variabilis (5.3) and spinach (< 5.0) His-92 residues are noted, whereas His-16 gives a pKa of 6.95. Pulse radiolysis techniques with e-aq as reductant have been used to generate the metastable Fe(II)Fe(III)Ru(III) state from Fe(III)2Ru(III), k = 8.8 x 10(10) M-1 s-1. Intermolecular, k(inter) = 4.3 x 10(6) M-1 s-1 at approx. 19 degrees C, but no intramolecular electron-transfer (ET) Fe(II)Fe(III) to Ru(III) contribution was observed with Fe(III)2Ru(III) in the range 7-30 microM. The driving force for ET is approx. 500 mV, and the edge to edge distance from the C gamma of His-16 to the nearest cysteinyl S-atom attached to the Fe2S2 cluster is 16.1 A. Using the Beratan-Onuchic pathway approach, the most favourable ET intramolecular route consists of 20 covalent and 3 H-bonds, with a total distance from the S of Cys-49 to the C gamma of His-16 of 37.1 A. We note that the reduced Fe is on the remote side of the [2Fe-2S] cluster from the site of Ru-attachment.

Construction of metabolic operons catalyzing the de novo biosynthesis of indigo in Escherichia coli

The efficient production of the textile dye indigo by fermentation has been a goal since the early 1980's when the first bacterial strains capable of this synthesis were constructed. We report here the development of a recombinant microorganism that directly synthesizes indigo from glucose. This construction involved the cloning and genetic manipulation of at least 9 genes and modifications of the fermentation medium to help stabilize the biosynthetic activity. Directed genetic changes in two operons caused significant increases in reaction rates and in the stability of the catalytic enzymes. This example of whole cell catalysis by a recombinant Escherichia coli represents a novel and environmentally sound approach to the synthesis of a high value specialty chemical.

Proton nuclear magnetic resonance investigation of adrenodoxin. Assignment of aromatic resonances and evidence for a conformational similarity with ferredoxin from Spirulina platensis

Bovine, porcine and sheep adrenodoxin, and the trypsin-resistant form of bovine adrenodoxin have been studied by one- and two-dimensional 1H-NMR spectroscopy. Assignment of the resonances for all the aromatic amino acids with resolved aromatic resonances have been made by correlating NMR spectra with the amino acid sequences from various species. Slowly exchanging amide protons and downfield shifted alpha-protons of His10 and Phe11 suggest possible involvement in beta-sheet structure. The effects on the assigned resonances due to the specific spin-label with a nitroxide radical at Cys95 have been analyzed on a two-dimensional 1H-NMR spectrum. The present results provide evidence for a structural similarity with a model for the structure of adrenodoxin based on a sequence alignment with that of Spirulina platensis ferredoxin, for which X-ray crystallographic data is available. epsilon-Methyl groups of Met120 and Met122 have been assigned by comparing 1H-NMR spectra of adrenodoxin with those of the trypsin-resistant form of adrenodoxin which is specifically cleaved at Arg115. epsilon-Methyl groups of Met120 and Met122 have an exceptionally long longitudinal relaxation time compared with those of valyl and leucyl methyl groups, suggesting that the COOH-terminal peptide spanning over 13 amino acids rotates rather freely in the solvent.

Proton magnetic resonance spectra of adrenodoxin: features of the aromatic region

This paper presents the first 1H-NMR spectra of the aromatic region of adrenodoxin, a mammalian mitochondrial 2Fe-2S non-heme iron ferredoxin. One-dimensional proton NMR spectra of both reduced and oxidized adrenodoxin were recorded as a function of pH. Resonances due to two of the three histidines of adrenodoxin gave sharp signals in the one-dimensional proton NMR spectra. The pKa values of the resolved histidine resonances in the oxidized protein were 6.64 +/- 0.03 and 6.12 +/- 0.06. These values were unchanged when adrenodoxin was reduced by the addition of sodium dithionite. In addition, the oxidized protein showed a broadened histidine C-2H resonance with a pKa value of approx. 7. This resonance was not apparent in the spectra of the reduced protein. The resonances due to the single tyrosine in adrenodoxin were identified using convolution difference spectroscopy. In addition, a two-dimensional Fourier-transform double quantum filtered (proton, proton) chemical shift correlated (DQF-COSY) spectrum of oxidized adrenodoxin was obtained. The cross peaks of the resonances due to the tyrosine, the four phenylalanines, and two of the three histidines of adrenodoxin were resolved in the DQF-COSY spectrum. Reduction of the protein caused several changes in the aromatic region of the NMR spectra. The resonances assigned to the C2 proton of the histidine with a pKa of 6.6 shifted upfield approx. 0.15 ppm. In addition, when the protein was reduced one of the resonances assigned to a phenylalanine residue with a chemical shift of 7.50 ppm appeared to move downfield to 7.82 ppm.(ABSTRACT TRUNCATED AT 250 WORDS)

Genes encoding ferredoxins from Anabaena sp. PCC 7937 and Synechococcus sp. PCC 7942: structure and regulation

The gene encoding ferredoxin I (petF1) from the filamentous cyanobacterium Anabaena sp. PCC 7937 (Anabaena variabilis ATCC 29413) was cloned by low stringency hybridization with the ferredoxin cDNA from the higher plant Silene pratensis. The petF1 gene from the unicellular cyanobacterium Synechococcus sp. PCC 7942 (Anacystis nidulans R2) was cloned by low stringency hybridization with the petF1 gene from Anabaena sp. PCC 7937. One copy of the petF genes was detected in both organisms, and a single transcript of about 630 b was found for Synechococcus sp. PCC 7942. Both the Synechococcus sp. PCC 7942 and the Anabaena sp. PCC 7937 petF1 genes contain a 297 bp open reading frame coding for a small acidic protein, consisting of 98 amino-acid residues, with a molecular mass of about 10.5 kDa.The ferredoxin content of Synechococcus sp. PCC 7942 is strongly reduced under ironlimited growth conditions. The slight decrease in the amount of ferredoxin transcript found under iron limitation does not account for the more severe reduction in ferredoxin protein observed. The main regulation of the ferredoxin content probably is effected at the level of translation and/or degradation. Although ferredoxin expression can be strongly reduced by iron stress, the ferredoxin function seems to be indispensable, as Synechococcus sp. PCC 7942 appeared refractory to yield mutants lacking the petF1 gene.

Isolation and sequence of the gene for ferredoxin I from the cyanobacterium Anabaena sp. strain PCC 7120

The structural gene for ferredoxin I, petF, from the cyanobacterium Anabaena sp. strain PCC 7120 has been isolated from a recombinant lambda library. Mixtures of tetradecanucleotides and heptadecanucleotides, each containing all possible DNA sequences corresponding to two separate regions of the ferredoxin amino acid sequence, were synthesized and used as hybridization probes to identify a genomic clone containing the coding sequence for the petF gene. The sequence of the entire petF coding region and portions of the 3'- and 5'-flanking regions was determined. The DNA sequence of petF suggests that, in contrast to the nucleus-encoded plant protein, cyanobacterial apoferredoxin is not synthesized as a higher-molecular-weight precursor. The Anabaena petF gene is a single-copy gene. During growth on complete medium it was transcribed into a monocistronic mRNA species of approximately 500 bases that initiated 100 base pairs upstream from the petF coding region.