The electronic and magnetic properties of rubredoxin: a low-temperature magnetic circular dichroism study.

Oxidized rubredoxin from Clostridium pasteurianum has been investigated by magnetic circular dichroism (MCD) spectroscopy over the temperature range 1.5 to 150 K and at magnetic fields between 0 and 4.5 tesla. The results show that studies of the temperature and field dependence of MCD transitions afford insight into the polarization of electronic transitions for ground states with large g-value anisotropy, in addition to estimates of ground-state g values and zero-field splitting parameters. In agreement with the assignment made by Eaton and Lovenberg (Eaton, W.A. and Lovenberg, W. (1973) in Iron-Sulfur Proteins, Vol. II (Lovenberg, W., ed.), pp. 131-162, Academic Press, New York), the ultraviolet-visible spectrum of oxidized rubredoxin is assigned to two S----Fe(III) charge transfer transitions (both 6A1----6T2 under tetrahedral symmetry), each spanning a range of 650-430 nm and 430-330 nm, respectively. The observed splitting in each of these transitions is attributed to a predominant axial distortion in the excited state resulting in effective D2d symmetry.

Isoelectric focusing of ferredoxins, flavordoxins and a rubredoxin.

Isoelectric points of ferredoxins, flavodoxins and a rubredoxin from a range of sources were measured by electrofocusing over the pH range between 2.5 and 5.0 on thin layers of polyacrylamide gel. The pH gradient along the gel was measured directly by a surface electrode. The isoelectric points of the plant-type ferredoxins were between approx. 3.15 and 3.35, and those of the flavodoxins close to 3.5. Ferredoxin, rubredoxin and flavodoxin from Clostridium pasteurianum had isolectric points of the of 2.75, 2.9, and 3.1, respectively. The values for the isoelectric points ferredoxins are significantly lower than previous results in the literature suggest.

Isolation and characterization of a novel four-chain ether lipid from Clostridium butyricum: the phosphatidylglycerol acetal of plasmenylethanolamine.

We describe the isolation and characterization of a novel four-chain ether phospholipid in Clostridium butyricum grown on petroselinic acid in the absence of biotin. The results of quantitative analyses of hydrolytic products, selective hydrolysis by mild acid or phospholipase C, 1H-, 13C-, and 31P-NMR, and fast atom bombardment-mass spectroscopy (FABMS) have resulted in the determination of the structure of this lipid as a phosphatidylglycerol acetal of plasmenylethanolamine. Smaller amounts of this lipid have been found in cells grown under similar conditions in the presence of oleic, cis-vaccenic, elaidic or dihydrosterculic acids. It also appears to be present in small amounts in cells grown with biotin. This lipid is structurally related to the more plentiful glycerol acetal of plasmenylethanolamine found in these cells.

Lipid shape as a determinant of lipid composition in Clostridium butyricum. The effects of incorporation of various fatty acids on the ratios of the major ether lipids.

The lipid composition of Clostridium butyricum is strongly influenced by the aliphatic chain compositions of the membrane lipids. Growth on cis-monounsaturated fatty acids in the absence of biotin was shown to affect the relative proportions of phosphatidylethanolamine, plasmenylethanolamine, and the glycerol acetal of plasmenylethanolamine most strongly, with smaller effects on the acidic lipids, phosphatidylglycerol and cardiolipin. The ratio of the glycerol acetal of plasmenylethanolamine to total phosphatidylethanolamine in cells grown on a series of fatty acids is shown to decrease in the following order; cis-vaccenic acid greater than or equal to oleic acid = C19-cyclopropane fatty acid greater than linoleic acid greater than petroselinic acid greater than elaidic acid greater than 14-methylhexadecanoic acid (anteiso-C17) greater than 12-methyltridecanoic acid (iso-C14). All fatty acids were extensively incorporated into the lipid acyl, alkenyl, and alkyl chains. There was considerable chain-elongation of the iso-C14 to iso-C16. The results are consistent with the hypothesis that the membrane lipid composition is strongly influenced by lipid shape and that the observed changes in lipid composition serve to stabilize the bilayer arrangement of the cell membrane.

Purification and properties of paramagnetic protein from Clostridium pasteurianum W5.

The purification to homogeneity of the non-heme iron protein, sometimes referred to as either "red protein" or "paramagnetic protein", from Clostridium pasteurianum W5 extracts is described and its physicochemical properties studied. This paramagnetic protein (g= 1.94) has a molecular weight of about 25000 and contains two iron and two acid-labile sulfur atoms per mol of protein. Its midpoint potential at pH 7.5, as determined by electron paramagnetic resonance titration, is -300 mV. Optical circular dichroism and electron paramagnetic resonance spectra of the paramagnetic protein are similar to those of two iron-two acid-labile sulfur ferredoxins. The biochemical reduction of the purified protein was also studied.

Isolation and characterization of two rubredoxins from Clostridium thermoaceticum.

Two rubredoxins with similar molecular weights (about 6000) have been purified from Clostridium thermoaceticum, a thermophile and strict anaerobe. They exhibit minor differences in several properties like elution pattern from DEAE-cellulose column, isoelectric point, amino acid composition, absorption and EPR spectra and redox potential. Their chemical and physical properties are similar to those of other rubredoxins from anaerobic microorganisms.

Phospholipid aliphatic chain composition modulates lipid class composition, but not lipid asymmetry in Clostridium butyricum.

The phospholipid composition of the butyric acid-producing clostridia is responsive to the degree of enrichment of the lipids with cis-unsaturated fatty acids. When Clostridium butyricum and Clostridium beijerinckii are grown on oleic acid in media devoid of biotin, the acyl and alk-1-enyl chains of the phospholipids become highly enriched with 18:1 and C19-cyclopropane. Under these conditions there is a marked increase in the glycerol acetals of the major plasmalogens of these organisms. We have grown both species on mixtures of palmitate and oleate in the absence of biotin. The alk-1-enyl chains were highly enriched with C18-unsaturated and C19-cyclopropane residues at all but the highest ratios of palmitate to oleate (80:20, w/w) added to the medium. At ratios of palmitate to oleate greater than or equal to 40:60, the saturated acid was incorporated predominantly into the phospholipid acyl chains in both organisms. The effects of increasing unsaturation of the acyl chains as the ratio of oleate to palmitate was increased was examined in C. butyricum. In cells grown on mixtures of palmitate and oleate equal to or exceeding 40% palmitate, the ratio of glycerol acetal lipid to total phosphatidylethanolamine (PE) was relatively constant. As the proportion of oleic acid added to the medium was increased, the ratio of glycerol acetal lipid to PE increased from 0.7 to 2.0. Thus the ratio of the polar lipids appears to respond to the content of phospholipids that contain two unsaturated chains. The fraction of PE present as plasmalogen remained relatively stable (0.82 +/- 0.05) at varying ratios of medium oleic and palmitic acids. Both the glycerol acetal of ethanolamine plasmalogen, and ethanolamine plasmalogen, are shown to be 80% or more in the outer monolayer of the cell membrane. These two polar lipids represent approx. 50% of the phospholipids in cells grown on exogenous fatty acid. The bulk of the remainder is polyglycerol phosphatides. We suggest that the ability of both species to grow with highly unsaturated membranes is related to their ability to modulate their polar lipid composition.

2H-NMR studies on ether lipid-rich bacterial membranes: deuterium order profile of Clostridium butyricum.

Palmitic acid specifically deuterated at different carbon atoms, has been incorporated biosynthetically into the membrane lipids of Clostridium butyricum. The lipids of this organism are rich in plasmalogens and their glycerol acetals and exhibit an unusual fatty acyl and alkenyl chain distribution with saturated chains mainly at the sn-2 position and unsaturated chains at the sn-1 position. The ordering of the deuterated hydrocarbon chains in whole cells was measured with deuterium nuclear magnetic resonance and was compared to the order profiles of isolated cell membranes and membranes formed from the total phospholipid extract. The shape of the order profiles was similar for all three membranes, but the absolute values of the order profiles in whole cells and isolated membranes were lower than those of the liposomal lipids. The order profiles have the same characteristic shape as those found for the lamellar liquid-crystalline phases of synthetic diacylphospholipids.

The iron electron-nuclear double resonance (ENDOR) of 4-Fe clusters in iron-sulfur proteins from Chromatium and Clostridium pasteurianum.

Iron electron-nuclear double resonance (ENDOR) measurements were made of the 4-Fe clusters in oxidized Chromatium high-potential iron-sulfur protein, dithionite-reduced high-potential iron-sulfur protein in 80% dimethylsulphoxide, fully reduced Clostridium pasteurianum ferredoxin in aqueous solution and in 80% dimethylsulfoxide. The hyperfine couplings determined show that: i) the electron distribution in each case is nearly symmetric; ii) there are two types of iron in oxidized high potential iron-sulfur protein; iii) only one type of iron is observed in each fully reduced 4-Fe cluster; iv) the data also suggest a greater electron delocalization onto the ligands as compared to the 2-Fe ferredoxins.

Production, purification and characterization of Clostridium difficile toxic proteins different from toxin A and from toxin B.

The purification and characterization of three new proteins called C1, C2, and C3 from Clostridium difficile are described. Their estimated molecular mass were about 350 (C1), 270 (C2) and 140 (C3) kDa, consisting of subunits of 39 (C1), 43 (C2) and 41 (C3) kDa, respectively. Immunodiffusion revealed that the three proteins contained similar but not identical antigenic determinants to toxin A. Each protein induced a cytotonic effect on hamster ovaric cells; the combined proteins, had a specific activity on cells 5-times higher than that of toxin A. In rat intestinal loops, they induced a clear fluid secretion, while toxin A elicited a haemorrhagic fluid response. The cytotonic activities of all three proteins were abolished by antiserum against toxin A, while antiserum against toxin B inhibited only the activity of the 270 kDa protein. In contrast to toxin A, the cytotoxicity of the three proteins was inactivated by trypsin. Thus, the chemical, antigenic and biological properties of these proteins differed from those of toxin A and toxin B.

Comparison of beef liver and Penicillium vitale catalases.

The structures of Penicillium vitale and beef liver catalase have been determined to atomic resolution. Both catalases are tetrameric proteins with deeply buried heme groups. The amino acid sequence of beef liver catalase is known and contains (at least) 506 amino acid residues. Although the sequence of P. vitale catalase has not yet been determined chemically, 670 residues have been built into the 2 A resolution electron density map and have been given tentative assignments. A large portion of each catalase molecule (91% of residues in beef liver catalase and 68% of residues in P. vitale catalase) shows structural homology. The root-mean-square deviation between 458 equivalenced C alpha atoms is 1.17 A. The dissimilar parts include a small fragment of the N-terminal arm and an additional "flavodoxin-like" domain at the carboxy end of the polypeptide chain of P. vitale catalase. In contrast, beef liver catalase contains one bound NADP molecule per subunit in a position equivalent to the chain region, leading to the flavodoxin-like domain, of P. vitale catalase. The position and orientation of the buried heme group in the two catalases, relative to the mutually perpendicular molecular dyad axes, are identical within experimental error. A mostly hydrophobic channel leads to the buried heme group. The surface opening to the channel differs due to the different disposition of the amino-terminal arm and the presence of the additional flavodoxin-like domain in P. vitale catalase. Possible functional implications of these comparisons are discussed.

Structure of oxidized flavodoxin from Anacystis nidulans.

The structure of oxidized flavodoxin from the cyanobacterium Anacystis nidulans has been determined at 2.5 A resolution with phases calculated from ethylmercury phosphate and dimercuriacetate derivatives. The determination of partial sequences, including a total of 85 residues, has assisted in the interpretation of the electron density. Preliminary refinement of a partial model (1072 atoms) has reduced R to 0.349 for the 10.997 reflections between 2.0 and 5.0 A with 1 greater than 2 sigma. The polypeptide backbone, which comprises 167 residues in the current model, adopts the familiar beta-alpha-beta conformation found in other flavodoxins and in the nucleotide-binding domains of the pyridine-nucleotide dehydrogenases, with five parallel strands in the central sheet. Comparison with flavodoxin from Clostridium MP (138 residues) shows that extra residues of A. nidulans flavodoxin are accommodated in a major insertion about 20 residues in length, which forms a lobe adjacent to the fifth strand of parallel sheet, and in additions to several external segments. Residues added between the fourth sheet strand and the start of the third helix alter the environment of the pyrimidine end of the flavin mononucleotide ring. The flavin mononucleotide phosphate binds to the start of helix 1, interacting with hydroxyamino acids and with main-chain amide groups. Two hydrophobic residues, both tentatively identified as Trp, enclose the isoalloxazine ring; the solvent-exposed Trp is nearly parallel to the flavin ring. The hydrophobic environment provided by these residues must be partly responsible for the pronounced vibrational resolution of the flavin spectrum near 450 nm. The flavin ring is tilted relative to its orientation in Clostridium MP flavodoxin. In addition, atoms N-3 and O-2 alpha of the isoalloxazine appear to form hydrogen bonds to the backbone at CO97 and NH99 in a conformation entirely different from that found in Clostridium MP flavodoxin but structurally analogous to Desulfovibrio vulgaris flavodoxin.

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.

A high-molecular-mass cell wall protein released from Clostridium tyrobutyricum by heat treatment.

Analysis of the cell wall of 4 strains of Clostridium tyrobutyricum reveals an unusually high protein content (35-40% dry weight). Brief heat treatment of whole cells of these stains causes release of two proteins, flagellin and a cell wall component of high molecular mass (110-125 kDa in the different strains). This component represents approx. 5% of the dry cell weight.

Purification and characterisation of two forms of toxin B produced by Clostridium difficile.

Toxin B from Clostridium difficile was purified to homogeneity by gel filtration and high resolution ion exchange chromatography. Two forms of toxin B were found. Form 1 which seemed to consist of two identical subunits of 220-300 kDa; femtogram amounts of this toxin induced rounding of fibroblast cells. Form 2 contained subunits of 43 kDa and 105 kDa; the stoichiometric ratio probably being 4:1; picogram amounts were needed to induce rounding of fibroblast cells. Immunological studies suggested that both subunit types were antigenic and had epitopes which were identical with those of form 1.

Differential levels of ferredoxin and rubredoxin in Clostridium acetobutylicum.

Ferredoxin and rubredoxin levels have been determined in DEAE-cellulose treated extracts of Clostridium acetobutylicum using specific enzymatic assays. In contrast to ferredoxin, the content of rubredoxin is affected by various culture conditions; it fluctuates in the proportions of 1 to 3 according to the growth phase, 1 to 8 according to the medium composition, and 1 to 40 according to the pH. Highest rubredoxin level is obtained at the end of the acid phase when the cells grow in chemically defined medium, the pH of which is not controlled. Such variations suggest that rubredoxin as well as rubredoxin-reductase take part in an electron transport chain system inducible by the culture conditions.

Purification and characterization of a heat stable ferredoxin isolated from Clostridium thermocellum.

A thermostable ferredoxin was purified from Clostridium thermocellum. The final preparation was homogeneous as judged by electrophoresis in sodium dodecyl sulfate polyacrylamide gel and sedimentation equilibrium. It contains eight atoms of iron and eight acid-labile sulfur groups per molecule, the molecular weight is estimated to be 6 400 and the isoelectric point 3.35. Its amino-acid composition is characterized by the absence of histidine residues and the presence of eight cysteine residues. The absorption spectrum has a maximum at 390 nm with a molar absorption coefficient of 39 x 10(3) M1 cm-1, similar to that of other bacterial eight iron ferredoxins. The purified ferredoxin has high thermal stability, since the spectrophotometric absorption of the protein at 390 nm did not change after one hour at 70 degrees C and only thirty five per cent of absorbance were lost after one hour at 80 degrees C. With regard to the electron carrier activity, the stability is slightly higher, only twenty five per cent of the activity were lost after one hour at 80 degrees C. During pyruvate oxidation, ferredoxin functions in the transfer of electrons to hydrogenase and also in the back reaction during pyridine nucleotide reduction by a ferredoxin -NAD oxidoreductase using hydrogen as electron donor.

Structure of the extracellular ferredoxin from Rhodospirillum rubrum: close similarity to clostridial ferredoxins.

The amino acid sequence of an [8Fe-8S] ferredoxin isolated from the culture medium of Rhodospirillum rubrum, a photosynthetic purple non-sulfur bacterium, was determined by a combination of various conventional procedures. The sequence was A-Y-K-I-E-E-T-C-I-S-C-G-A-C-A-A-E-C-P-V-N-A-I-E-Q-G-D-T-I-F-V-V-N-A-D-T-C-I-D-C - G-N-C-A-N-V-C-P-V-G-A-P-V-A-E (55 amino acid residues). It lacked methionine, leucine, histidine, arginine, and tryptophan. The molecular weight was calculated to be 5,568 excluding iron and sulfur atoms. The distribution of 8 cysteine residues was exactly the same as that of clostridial-type ferredoxin, suggesting retention of the duplication of the bacterial ancestral ferredoxin gene. The extracellular ferredoxin of R. rubrum was compared with other ferredoxins observed in closely related photosynthetic bacteria and the evolutionary significance of this ferredoxin is discussed.

Latex particle agglutination for detecting and identifying Clostridium difficile.

A total of 329 selective enrichment broth cultures were tested for detection of Clostridium difficile by latex particle agglutination (LPA), gas-liquid chromatography, and bacterial culture. Of 53 broths positive by LPA, 36 were positive by gas-liquid chromatography, and 42 were positive by bacterial culture. The sensitivity and specificity of LPA relative to bacterial culture was 95.6% and 96.3%, respectively, while the sensitivity and specificity of gas-liquid chromatography relative to bacterial culture was 84.6% and 100%, respectively. The high predictive value of a negative test (99%) should make LPA on broth cultures a good screening test for detecting C difficile. Of several other Clostridium spp tested in pure culture, strains of C sordellii and C bifermentans also gave a positive result by LPA. These results, together with the low cost and simple facilities required, suggest that the LPA test will be a useful procedure for the presumptive identification of C difficile in selective enrichment broths and for the identification of pure cultures.

Purification and amino acid sequence of two small, acid-soluble proteins from Clostridium bifermentans spores.

Clostridium bifermentans spores contain two major small, acid-soluble, proteins (SASP) termed SASP-alpha and beta. The amino acid sequences of SASP-alpha and beta are almost identical, and are very similar to those of alpha/beta-type SASP from spores of C. perfringens and various Bacillus species. However, the C. bifermentans proteins contain an extra five amino acids in the middle of their sequence. Surprisingly, no gamma-type SASP were found in C. bifermentans or C. perfringens spores, although these are the most prominent SASP in spores of Bacillus species.