Molecular cloning of the gene encoding a 2Fe-2S ferredoxin from extremely halophilic archaeon Haloarcula japonica strain TR-1

A ferredoxin was purified from extremely halophilic archaeon Haloarcula japonica strain TR-1, and then characterized. The Ha. japonica ferredoxin proved to contain a 2Fe-2S cluster. A part of the gene encoding the ferredoxin was amplified by PCR. Subsequently, the entire ferredoxin gene was cloned from chromosomal DNA of Ha. japonica using the PCR product as a probe. The structural gene consisted of an open reading frame of 387 nucleotides. The deduced amino acid sequence showed 89-98% identities with those of the ferredoxins from other extremely halophilic archaea.     

Horsetail (Equisetum telmateia) ferredoxins I and II. Amino acid sequences

Two ferredoxins were isolated from horsetail (Equisetum telmateia) and their amino acid sequences were determined by use of a sequence analyzer in combination with carboxypeptidase digestion and manual Edman degradation of tryptic peptides of carboxymethyl-ferredoxins. Ferredoxins I and II each had only four cysteine residues in a total of 95 and 93 residues, respectively. The amino-terminal residues of both ferredoxins were heterogeneous, but alanine was concluded to be their genuine terminal residue. The comparison of these isozymelike molecules showed 29 differences in amino acid residues with three inverted replacements. One gap was inserted in ferredoxin II at position 32 to align the ferredoxins with greatest homology. Despite the many differences in amino acid residues there was no difference in net charges of the two ferredoxins.     

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.     

Overexpression in Escherichia coli and affinity purification of chick kidney ferredoxin

Vertebrate ferredoxins are 12-14-kDa iron-sulfur proteins, some of which transfer electrons to mitochondrial cytochrome P450s. The function of many of these cytochrome P450s is to catalyze stereospecific hydroxylation of endogenous steroids. As part of our interest in the kidney mitochondrial 1 alpha-hydroxylation of 25-hydroxyvitamin D3, we have constructed an expression plasmid coding for a fusion protein containing the chick kidney ferredoxin. We subcloned chick kidney ferredoxin cDNA, obtained from our vitamin D-deficient chick kidney library by polymerase chain reaction (Brandt, M. E., Gabrik, A. H., and Vickery, L. E. (1991) Gene (Amst.) 97, 113-117) into Qiagen's pQE9, which contains an N-terminal 6xHis tag (peptide sequence for 6 adjacent histidines present in the recombinant proteins). The coding sequence was preceded by a factor Xa cleavage site. The resulting plasmid, pQTcFdx, was overexpressed in Escherichia coli, and the soluble fusion protein was purified from the cell lysate in one step by Ni(II)-nitrilotriacetic acid-agarose chromatography. We obtained 7-10 mg of greater than 99% homogeneous fusion protein from a 1-liter culture and 4-6 mg of mature ferredoxin cleaved by factor Xa. The fusion protein possessed an absorption spectrum and an electron paramagnetic resonance spectrum quantitatively indistinguishable from those published for ferredoxin purified from adrenal glands and placenta or expressed in E. coli with another vector. The fusion protein was active in supporting the 1 alpha-hydroxylation of 25-hydroxyvitamin D3 in a reconstitution assay of a solubilized, partially purified preparation of cytochrome P450 from vitamin D-deficient chick kidney. We conclude that the procedure described here is an efficient way to produce and purify vertebrate ferredoxin; the [2Fe-2S] cofactor is assembled in vivo and effectively incorporated into the fusion protein in E. coli; slight alterations at the N terminus do not alter incorporation of the [2Fe-2S] cofactor or the biological activity of ferredoxin, and post-translational modifications, such as phosphorylation, are not an absolute requirement for ferredoxin electron transporting activity. The recombinant ferredoxin can be used for physical studies and other structure-function studies.     

Site-directed mutations of the 4Fe-ferredoxin from the hyperthermophilic archaeon Pyrococcus furiosus: role of the cluster-coordinating aspartate in physiological electron transfer reactions

Ferredoxin from the hyperthermophilic archaeon Pyrococcus furiosus is a monomeric protein (7.5 kDa) that contains a single [4Fe-4S]1+, 2+ cluster. The protein is unusual in that its cluster is coordinated by three Cys and one Asp residue, rather than by the typical four Cys residues. Site-directed mutagenesis has been used to obtain mutant forms in which the cluster-coordinating Asp was replaced by Cys (D14C) and also by Ser (D14S), together with a third mutant (A1K) which contained N-Met-Lys at the N-terminus instead of N-Ala. Analyses using UV-visible absorption, far-UV circular dichroism, and EPR spectroscopy showed that there were no gross structural differences between the native and the three mutant forms and that they each contained a [4Fe-4S] cluster. The reduction potentials, determined by direct electrochemistry (at 23 degrees C, pH 8.0), of the D14S, D14C, and A1K mutants were -490, -422, and -382 mV, respectively, which compare with values of -375 mV for native [4Fe-4S]-containing ferredoxin and -160 mV for the [3Fe-4S]-containing form. The native, D14C, and A1K proteins functioned as electron acceptors in vitroat 80 degrees C for pyruvate ferredoxin oxidoreductase (POR) and aldehyde ferredoxin oxidoreductase (AOR) from P. furiosus using pyruvate and crotonaldehyde as substrates, respectively. The calculated kcat/Km values were similar for the three proteins when ferredoxin reduction was measured either directly by visible absorption or indirectly by coupling ferredoxin reoxidation to the reduction of metronidazole. In contrast, using the D14S mutant and the 3Fe-form of the native ferredoxin as electron acceptors, the activity with AOR was virtually undetectable, and with POR the calculated kcat/Km values were at least 3-fold lower than those obtained with the native (4Fe-), D14C, and A1K proteins. The ability of this 4Fe-ferredoxin to accept electrons from two oxidoreductases of the same organism is therefore not absolutely dependent upon Asp14, as this residue can be effectively replaced by Cys. However, the efficiency of electron transfer is compromised if Asp14 is replaced by Ser, or if the 4Fe-cluster is converted to the 3Fe-form, but Asp14 does not appear to offer any kinetic advantage over the expected Cys.     

Actinic brachial plexus lesion

OBJECTIVES: To prove or disprove this assumption that in neuropathy patients with abundant spontaneous activity, peak-ratio interference pattern analysis may lead to false negative results. METHODS: Spontaneous activity >100 microV, automatically analysed by turn/amplitude analysis and expressed as (turns/second)/2 ((T/S)/2), and interference patterns, analysed by the peak-ratio technique, were recorded, one after the other, from the right anterior tibial muscle of 21 patients with neuropathy, aged 36-87 years. RESULTS: The mean number of spontaneous discharges ((T/S)/2) was 12.3 (range 5.5-26) and its mean amplitude 261 microV (range 146-478 microV). Despite this abundant spontaneous activity, peak-ratio analysis was neurogenic in 81% of the patients. All peak-ratio parameters were independent on the amount and amplitude of spontaneous discharges. CONCLUSIONS: Spontaneous discharges >100 microV could be adequately assessed by means of the turn/amplitude analysis and did not influence peak-ratio analysis in neuropathies.     

Mass-spectrometric identification and sequence location of the ten residues of the new amino acid (gamma-Carboxyglutamic acid) in the N-terminal region of prothrombin

The detailed mass-spectrometric evidence for our original findings [Magnusson et al. (1974) FEBS Lett. 44, 189-193] of ten gamma-carboxyglutamic acid residues in the N-terminal calcium-binding polypeptide of prothrombin is presented. The identification and sequence location of gamma-carboxyglutamic acid was made by electron-impact and field-desorption studies on acetyl permethyl peptide derivatives, and on the free amino acid. Details of the derivatives formed, and how this new amino acid may be easily recognized and sequenced from the mass spectrum, are given as a basis for future work.     

Purification and molecular characterization of the tungsten-containing formaldehyde ferredoxin oxidoreductase from the hyperthermophilic archaeon Pyrococcus furiosus: the third of a putative five-member tungstoenzyme family

Pyrococcus furiosus is a hyperthermophilic archaeon which grows optimally near 100 degreesC by fermenting peptides and sugars to produce organic acids, CO2, and H2. Its growth requires tungsten, and two different tungsten-containing enzymes, aldehyde ferredoxin oxidoreductase (AOR) and glyceraldehyde-3-phosphate ferredoxin oxidoreductase (GAPOR), have been previously purified from P. furiosus. These two enzymes are thought to function in the metabolism of peptides and carbohydrates, respectively. A third type of tungsten-containing enzyme, formaldehyde ferredoxin oxidoreductase (FOR), has now been characterized. FOR is a homotetramer with a mass of 280 kDa and contains approximately 1 W atom, 4 Fe atoms, and 1 Ca atom per subunit, together with a pterin cofactor. The low recovery of FOR activity during purification was attributed to loss of sulfide, since the purified enzyme was activated up to fivefold by treatment with sulfide (HS-) under reducing conditions. FOR uses P. furiosus ferredoxin as an electron acceptor (Km = 100 microM) and oxidizes a range of aldehydes. Formaldehyde (Km = 15 mM for the sulfide-activated enzyme) was used in routine assays, but the physiological substrate is thought to be an aliphatic C5 semi- or dialdehyde, e.g., glutaric dialdehyde (Km = 1 mM). Based on its amino-terminal sequence, the gene encoding FOR (for) was identified in the genomic database, together with those encoding AOR and GAPOR. The amino acid sequence of FOR corresponded to a mass of 68.7 kDa and is highly similar to those of the subunits of AOR (61% similarity and 40% identity) and GAPOR (50% similarity and 23% identity). The three genes are not linked on the P. furiosus chromosome. Two additional (and nonlinked) genes (termed wor4 and wor5) that encode putative tungstoenzymes with 57% (WOR4) and 56% (WOR5) sequence similarity to FOR were also identified. Based on sequence motif similarities with FOR, both WOR4 and WOR5 are also proposed to contain a tungstobispterin site and one [4Fe-4S] cluster per subunit.     

Studies on monotreme proteins. VII. Amino acid sequence of myoglobin from the platypus, Ornithoryhynchus anatinus

Myoglobin isolated from skeletal muscle of the platypus contains 153 amino acid residues. The complete amino acid sequence has been determined following cleavage with cyanogen bromide and further digestion of the four fragments with trypsin, chymotrypsin, pepsin and thermolysin. Sequences of the purified peptides were determined by the dansyl-Edman procedure. The amino acid sequence showed 25 differences from human myoglobin and 24 from kangaroo myoglobin. Amino acid sequences in myoglobins are more conserved than sequences in the alpha- and beta-globin chains, and platypus myoglobin shows a similar number of variations in sequence to kangaroo myoglobin when compared with myoglobin of other species. The date of divergence of the platypus from other mammals was estimated at 102 +/- 31 million years, based on the number of amino acid differences between species and allowing for mutations during the evolutionary period. This estimate differs widely from the estimate given by similar treatment of the alpha- and beta-chain sequences and a constant rate of mutation of globin chains is not supported.     

Fibular shortening in poliomyelitis

We have determined the nucleotide and encoded amino acid sequences of the capsid, membrane precursor, membrane, envelope, and nonstructural NS1 protein genes of a dengue-2 virus (D2-04) isolated from a patient in Hainan, China. The sequenced region contains a gene organization similar to that of other flaviviruses. The overall amino acid sequence similarity between D2-04 and other dengue-2 viruses is greater than 92%, whereas that between D2-04 and members of the other dengue serotypes is about 65%.     

Characterization and primary structure of a base non-specific and acid ribonuclease from Dictyostelium discoideum

A base non-specific and acid RNase was isolated from cellular slime mold (Dictyostelium discoideum) cells in a homogeneous state (about 2.4 kDa) by SDS-polyacrylamide gel electrophoresis. The RNase (RNase DdI) has a pH optimum of 5.0. The amino acid sequence of RNase DdI was determined by a combination of protein chemistry, a search of Data base, Dicty cDB and further sequence analysis of cDNA from the same bank. RNase DdI consists of 198 amino acid residues, and about 13.3, 0.9, 1.2, 3.3, and 1.0 residues of mannose, xylose, glucose, GlcNAc, and GalNAc, respectively. RNase DdI has two characteristic conserved segments of the RNase T2 family, and thus belongs to the RNase T2 family. Considering the fact that most of the RNase activity of D. discoideum is present in the lysosomal fraction [Wiener and Ashworth (1970) Biochem. J. 118, 505-512], it was concluded that the lysosomal RNase in D. discoideum is a member of the RNase T2 family. The amino acid sequence of RNase DdI is highly homologous with that of Physarum polycephalum RNase (RNase Phyb), and its amino acid sequence seems to be similar to those of plant/animal type RNases, rather than fungal RNases. The location of RNase DdI in the phylogenetic tree of the RNase T2 family was estimated.     

Hepatocyte attachment on biodegradable modified chitosan membranes: in vitro evaluation for the development of liver organoids

Electron transfer reactions involving protein-protein interactions require the formation of a transient complex which brings together the two redox centres exchanging electrons. This is the case for the flavoprotein ferredoxin:NADP+ reductase (FNR) from the cyanobacterium Anabaena, an enzyme which interacts with ferredoxin in the photosynthetic pathway to receive the electrons required for NADP+ reduction. The reductase shows a concave cavity in its structure into which small proteins such as ferredoxin can fit. Flavodoxin, an FMN-containing protein that is synthesised in cyanobacteria under iron-deficient conditions, plays the same role as ferredoxin in its interaction with FNR in spite of its different structure, size and redox cofactor. There are a number of negatively charged amino acid residues on the surface of ferredoxin and flavodoxin that play a role in the electron transfer reaction with the reductase. Thus far, in only one case has charge replacement of one of the acidic residues produced an increase in the rate of electron transfer, whereas in several other cases a decrease in the rate is observed. In the most dramatic example, replacement of Glu at position 94 of Anabaena ferredoxin results in virtually the complete loss of ability to transfer electrons. Charge-reversal of positively charged amino acid residues in the reductase also produces strong effects on the rate of electron transfer. Several degrees of impairment have been observed, the most significant involving a positively charged Lys at position 75 which appears to be essential for the stability of the complex between the reductase and ferredoxin. The results presented in this paper provide a clear demonstration of the importance of electrostatic interactions on the stability of the transient complex formed during electron transfer by the proteins presently under study.     

The crystal structure of zinc-containing ferredoxin from the thermoacidophilic archaeon Sulfolobus sp. strain 7

The crystal structure of ferredoxin from the thermoacidophilic archaeon Sulfolobus sp. strain 7 was determined by multiple isomorphous replacement supplemented with anomalous scattering effects of iron atoms in the Fe-S clusters, and refined at 2.0 A resolution to a crystallographic R value of 0.173. The structural model contains a polypeptide chain of 103 amino acid residues, 2 [3Fe-4S] clusters, and 31 water molecules; in this model, the cluster corresponding to cluster II in bacterial dicluster ferredoxins loses the fourth iron atom although it may originally be a [4Fe-4S] cluster. The structure of the archaeal ferredoxin consists of two parts: the core fold part (residues 37-103) and the N-terminal extension part (residues 1-36). The "core fold" part has an overall main-chain folding common to bacterial dicluster ferredoxins, containing two clusters as the active center, two alpha-helices near the clusters, and two sheets of two-stranded antiparallel beta-sheet (the terminal and central beta-sheets). The "N-terminal extension" part is mainly formed by a one-turn alpha-helix and a three-stranded antiparallel beta-sheet. The beta-sheet in the N-terminal extension is hydrogen-bonded with the terminal beta-sheet in the core fold to form a larger beta-sheet. The distinct structural feature of this archaeal ferredoxin lies in the zinc-binding center where the zinc ion is tetrahedrally ligated by four amino acid residues (His 16, His 19, and His 34 from the N-terminal extension, and Asp 76 from the core fold). The zinc ion in the zinc-binding center is located at the interface between the core fold and the N-terminal extension, and connects the beta-sheet in the N-terminal extension and the central beta-sheet in the core fold through the zinc ligation. Thus, the zinc ion plays an important role in stabilizing the structure of the present archaeal ferredoxin by connecting the N-terminal extension and the core fold, which may be common to thermoacidophilic archaeal ferredoxins.     

Cloning, cDNA sequence analysis and patch clamp studies of a toxin from the venom of the armed spider (Phoneutria nigriventer)

The cDNAs (Tx3-2 and Pn3A) encoding precursor of toxin Tx3-2 and an isoform called Pn3A have been isolated from a library constructed from stimulated venom glands of the spider Phoneutria nigriventer. The cDNA of Tx3-2 reveals the presence of a signal peptide of 21 amino acids and of an intervening propeptide (with 16 amino acids) preceding the toxin sequence, which was followed by additional amino acid residues at the C-terminus (C-terminal peptide), implying post-translational modifications of the synthesised peptide. The deduced amino acid sequence for the mature toxin confirms the previous sequence published. In addition, by using the whole-cell patch clamp technique, we have determined that purified Tx3-2 decreases L-type currents present in GH3 cells. Finally, the presence of the cDNA Pn3A, with high sequence identity with Tx3-2, reveals the existence of a putative new toxin showing, at the cDNA level, 85.4% identity in its whole segment.     

Clinico-statistical analysis of the approach to retained foreign bodies in the extremities

Secondary structures, functionally important residues, antigenic sites, membrane spanning segments and hydropathicity of light harvesting chlorophyll a/b binding polypeptides (LHC) are predicted by theoretical methods from the amino acid sequence of the polypeptides. The reported structural features of the Pea LHC (Lhcb 1 gene product) from electron crystallographic studies have been compared by alignment with other types of chlorophyll a/b binding polypeptides for structural prediction. Fifteen conserved residues D85, D89, E113, H116, E/Q133, E/Q181, E189, D/N233, E252, N/H255, Q/E269, E/D/Q280, N281, H285, D288 (number indicates position in the aligned sequence), are identified which are potential ligands to Mg2+ of chlorophylls. Three amino acid residues D89, E/Q131 and D/N 233 are proposed as ligands to chlorophylls b2, a7 and b2 respectively, for which ligands are not identified in electron crystallographic study.     

Cloning and mapping of murine Nfe2l1

The murine homologue of the human NFE2L1 basic leucine-zipper gene was isolated from an early embryo library. The deduced amino acid sequence shows 97% identity between the two proteins. Significant sequence similarity is also seen with the p45 subunit of NF-E2 and with the Drosophila CNC protein. Murine Nfe2l1 maps to chromosome 11DE with similar sequence at 7D1-7F1 and 2E4-2G.     

Charge pair interactions stabilizing ferredoxin-ferredoxin reductase complexes. Identification by complementary site-specific mutations

Ferredoxin reductase (Fd-reductase) supplies electrons to mitochondrial steroid hydroxylase cytochrome P450 enzymes via a [2Fe-2S] ferredoxin. Chemical labeling studies with bovine Fd-reductase have implicated Lys-243 as important in binding to bovine ferredoxin (Hamamoto, I., Kazutaka, K., Tanaka, S., and Ichikawa, Y. (1988) Biochim. Biophys. Acta 953, 207-213). We have used site-directed mutagenesis to examine the role of charged residues in this region of human Fd-reductase in ferredoxin binding. Mutant proteins were expressed in Escherichia coli and were assayed for activity by ferredoxin-mediated electron transfer to cytochrome c. Replacement of Lys-242 (homologous to Lys-243 in bovine Fd-reductase) with Gln and replacement of Arg-241 with Ser had little effect (2.7- and 3.6-fold increased Km, respectively). In contrast, mutants at positions 239 and 243 (R239S and R243Q) exhibited markedly lower affinity for ferredoxin (17.5- and 1,600-fold increased Km, respectively). Studies were also carried out with two ferredoxin charge mutants shown previously to have lowered affinity for Fd-reductase (Coghlan, V. M., and Vickery, L. E. (1991) J. Biol. Chem. 266, 18606-18612). Comparisons of the binding of ferredoxin mutants D76N and D79N to Fd-reductase mutants R239S and R243Q suggest that Arg-239 and Arg-243 of Fd-reductase each interact directly with both Asp-76 and Asp-79 of ferredoxin during formation of the complex between the two proteins. These results support the hypothesis that specific electrostatic interactions involving this region are important in stabilizing the ferredoxin-Fd-reductase complex.     

Sequence and functional analysis of cloned guinea pig and rat serotonin 5-HT1D receptors: common pharmacological features within the 5-HT1D receptor subfamily

This study was undertaken to investigate the pharmacology of cloned guinea pig and rat 5-hydroxytryptamine (serotonin; 5-HT)1D receptor sites. Guinea pig, rat, and mouse 5-HT1D receptor genes were cloned, and their amino acid sequences were compared with those of the human, dog, and rabbit. The overall amino acid sequence identity between these 5-HT1D receptors is high and varies between 86 and 99%. The sequence homology is slightly more divergent (13-27%) in the N-terminal extracellular region of these 5-HT1D receptors. Guinea pig and rat 5-HT1D receptors, stably and separately expressed in rat C6 glial cells, are negatively coupled to cyclic AMP formation upon stimulation with agonists, as previously found for cloned human 5-HT1D receptor sites. The cyclic AMP data show some common pharmacological features for the 5-HT1D receptors of guinea pig, rat, and human: an almost similar rank order of potency for the investigated 5-HT1D receptor agonists, stereoselectivity for the binding affinity and agonist potency of R(+)-8-hydroxy-2-(di-n-propylamino)tetralin, and equal 5-HT1D receptor-mediated antagonist potency for methiothepin and the 5-HT2 receptor antagonists ritanserin and ketanserin. In conclusion, the pharmacology of the cloned 5-HT1D receptor subtype seems, unlike the 5-HT1B receptor subtype, conserved among various mammal species such as the human, guinea pig, and rat.