Size and charge isomer separation and estimation of molecular weights of proteins by disc gel electrophoresis

Purification and biochemical characterization of a novel cysteine protease of Entamoeba histolytica

Cysteine proteases are important virulence factors of Entamoeba histolytica, the causative agent of amoebiasis. A novel cysteine protease from parasite extracts was purified 15-fold by a procedure including concanavalin A-Sepharose, hydroxylapatite and DEAE-Sepharose chromatography. The purification resulted in the obtainment of an homogeneous protein with a molecular mass of 66 kDa on native PAGE. In 10% SDS/PAGE, three bands of 60, 54 and 50 kDa were evident. Each of the three specific mouse antisera raised against these proteins showed cross-reactivity with the three bands obtained from the purified eluate. The N-terminal sequencing of the first 10 amino acids from the three proteins showed 100% identity. These results support the hypothesis of a common precursor for the 60, 54 and 50-kDa proteins. Protease activity of the purified enzyme was demonstrated by electrophoresis in a gelatine-acrylamide copolymerized gel. Its activity was quantified by cleaving a synthetic fluorogenic peptide substrate such as N-carbobenzyloxy-arginyl-arginyl-7-amido-4-methylcoumarin. The optimum pH for the protease activity was 6.5; however, enzymatic activity was observed between pH 5 and pH 7.5. Typical of cysteine proteases, the enzyme was inhibited by 4-[(2S, 3S)-carboxyoxiran-2-ylcarbonyl-L-leucylamido]butylg uanidine and iodoacetamide, and activated by free sulfhydryl groups. The cellular location of the enzyme was examined on trophozoites before and after contact with red blood cells using indirect immunofluorescence and cellular fractionation. The 60-kDa cysteine protease translocated to the amoebic surface upon the interaction of trophozoites with red blood cells. This result provided evidence for participation of the 60-kDa protease in erythrophagocytosis.

The linker region between the helicase and primase domains of the bacteriophage T7 gene 4 protein is critical for hexamer formation

The gene 4 protein of bacteriophage T7, a functional hexamer, comprises DNA helicase and primase activities. Both activities depend on the unidirectional movement of the protein along single-stranded DNA in a reaction coupled to the hydrolysis of dTTP. We have characterized dTTPase activity and hexamer formation for the full-length gene 4 protein (gp4) as well as for three carboxyl-terminal fragments starting at residues 219 (gp4-C219), 241 (gp4-C241), and 272 (gp4-C272). The region between residues 242 and 271, residing between the primase and helicase domains, is critical for oligomerization of the gene 4 protein. A functional TPase active site is dependent on oligomerization. During native gel electrophoresis, gp4, gp4-C219, and gp4-C241 migrate as oligomers, whereas gp4-C272 is monomeric. The steady-state k(cat) for dTTPase activity of gp4-C272 increases sharply with protein concentration, indicating that it forms oligomers only at high concentrations. gp4-C219 and gp4-C241 both form a stable complex with gp4, whereas gp4-C272 interacts only weakly with gp4. Measurements of surface plasmon resonance indicate that a monomer of T7 DNA polymerase binds to a dimer of gp4, gp4-C219, or gp4-C241 but to a monomer of gp4-C272. Like the homologous RecA and F(1)-ATPase proteins, the oligomerization domain of the gene 4 protein is adjacent to the amino terminus of the NTP-binding domain.

Characterization of a tetrameric inositol monophosphatase from the hyperthermophilic bacterium Thermotoga maritima

Inositol monophosphatase (I-1-Pase) catalyzes the dephosphorylation step in the de novo biosynthetic pathway of inositol and is crucial for all inositol-dependent processes. An extremely heat-stable tetrameric form of I-1-Pase from the hyperthermophilic bacterium Thermotoga maritima was overexpressed in Escherichia coli. In addition to its different quaternary structure (all other known I-1-Pases are dimers), this enzyme displayed a 20-fold higher rate of hydrolysis of D-inositol 1-phosphate than of the L isomer. The homogeneous recombinant T. maritima I-1-Pase (containing 256 amino acids with a subunit molecular mass of 28 kDa) possessed an unusually high V(max) (442 micromol min(-1) mg(-1)) that was much higher than the V(max) of the same enzyme from another hyperthermophile, Methanococcus jannaschii. Although T. maritima is a eubacterium, its I-1-Pase is more similar to archaeal I-1-Pases than to the other known bacterial or mammalian I-1-Pases with respect to substrate specificity, Li(+) inhibition, inhibition by high Mg(2+) concentrations, metal ion activation, heat stability, and activation energy. Possible reasons for the observed kinetic differences are discussed based on an active site sequence alignment of the human and T. maritima I-1-Pases.

Chloroplast FtsY, chloroplast signal recognition particle, and GTP are required to reconstitute the soluble phase of light-harvesting chlorophyll protein transport into thylakoid membranes

The integration of light-harvesting chlorophyll proteins (LHCPs) into the thylakoid membrane proceeds in two steps. First, LHCP interacts with a chloroplast signal recognition particle (cpSRP) to form a soluble targeting intermediate called the transit complex. Second, LHCP integrates into the thylakoid membrane in the presence of GTP, at least one other soluble factor, and undefined membrane components. We previously determined that cpSRP is composed of 43- and 54-kDa polypeptides. We have examined the subunit stoichiometry of cpSRP and find that it is trimeric and composed of two subunits of cpSRP43/subunit of cpSRP54. A chloroplast homologue of FtsY, an Escherichia coli protein that is critical for the function of E. coli SRP, was found largely in the stroma unassociated with cpSRP. When chloroplast FtsY was combined with cpSRP and GTP, the three factors promoted efficient LHCP integration into thylakoid membranes in the absence of stroma, demonstrating that they are all required for reconstituting the soluble phase of LHCP transport.

Change in oligomerization specificity of the p53 tetramerization domain by hydrophobic amino acid substitutions

The tumor suppressor function of the wild-type p53 protein is transdominantly inhibited by tumor-derived mutant p53 proteins. Such transdominant inhibition limits the prospects for gene therapy approaches that aim to introduce wild-type p53 into cancer cells. The molecular mechanism for transdominant inhibition involves sequestration of wild-type p53 subunits into inactive wild-type/mutant hetero-tetramers. Thus, p53 proteins, whose oligomerization specificity is altered so they cannot interact with tumor-derived mutant p53, would escape transdominant inhibition. Aided by the known three-dimensional structure of the p53 tetramerization domain and by trial and error we designed a novel domain with seven amino acid substitutions in the hydrophobic core. A full-length p53 protein bearing this novel domain formed homo-tetramers and had tumor suppressor function, but did not hetero-oligomerize with tumor-derived mutant p53 and resisted transdominant inhibition. Thus, hydrophobic core residues influence the oligomerization specificity of the p53 tetramerization domain.

Mutant PTR1 proteins from Leishmania tarentolae: comparative kinetic properties and active-site labeling

PTR1, the gene promoting MTX resistance following gene amplification or DNA transfection in Leishmania tarentolae and selected mutants, has been cloned and heavily overexpressed (>100 mg/liter) in Escherichia coli strain BL21 (DE3). Protein has been purified, essentially to homogeneity, in two steps, via ammonium sulfate precipitation and chromatography on DEAE-Trisacryl. The active proteins are tetramers and display optimal pteridine reductase activity at pH 6.0 using biopterin as substrate and NADPH as the reduced dinucleotide cofactor. 2,4-Diaminopteridine substrate analogues are strong competitive inhibitors (K(i) approximately 38 --> 3 nM) against the pterin substrate and both NADP(+) and folate are inhibitors although somewhat weaker. Dihydropteridines are poor substrates compared to the fully oxidized pteridine. Kinetic analysis affords the usual Michaelis constants and in addition shows that inhibition by NADP(+) allows the formation of ternary nonproductive complexes with folate. The kinetic results are consistent with a sequential ordered bi-bi kinetic mechanism in which first NADPH and then pteridine bind to the free enzyme. Sequence comparisons suggest that PTR1 belongs to the short-chain dehydrogenase/reductase (SDR) family containing an amino-terminal glycine-rich dinucleotide binding site plus a catalytic Y(Xaa)(3)K motif. In accord with this observation, the mutants K16A, Y37D, and R39A and the double mutants K17A:R39A and Y37D:R39A all show a two- to threefold lower binding affinity for NADPH and exhibit low or zero activity. Two Y(Xaa)(3)K regions are present in wild-type PTR1 at 152 and 194. Only Y194F gives protein with zero activity. This observation coupled with affinity labeling of PTR1 by oNADP(+) (2', 3'-dialdehyde derivative of NADP(+)) followed by NaBH(4) reduction, V8 protease digestion, and mass spectral analysis suggests that the motif participating in catalysis is that at 194. The mutation K198Q eliminates inactivation by oNADP(+) supporting the hypothesis that K198 is associated with nucleotide orientation, as has been demonstrated for similar lysine residues in other members of the SDR family.

Molecular and biochemical characterization of the ADP-dependent phosphofructokinase from the hyperthermophilic archaeon Pyrococcus furiosus

Pyrococcus furiosus uses a modified Embden-Meyerhof pathway involving two ADP-dependent kinases. Using the N-terminal amino acid sequence of the previously purified ADP-dependent glucokinase, the corresponding gene as well as a related open reading frame were detected in the genome of P. furiosus. Both genes were successfully cloned and expressed in Escherichia coli, yielding highly thermoactive ADP-dependent glucokinase and phosphofructokinase. The deduced amino acid sequences of both kinases were 21.1% identical but did not reveal significant homology with those of other known sugar kinases. The ADP-dependent phosphofructokinase was purified and characterized. The oxygen-stable protein had a native molecular mass of approximately 180 kDa and was composed of four identical 52-kDa subunits. It had a specific activity of 88 units/mg at 50 degrees C and a pH optimum of 6.5. As phosphoryl group donor, ADP could be replaced by GDP, ATP, and GTP to a limited extent. The K(m) values for fructose 6-phosphate and ADP were 2.3 and 0.11 mM, respectively. The phosphofructokinase did not catalyze the reverse reaction, nor was it regulated by any of the known allosteric modulators of ATP-dependent phosphofructokinases. ATP and AMP were identified as competitive inhibitors of the phosphofructokinase, raising the K(m) for ADP to 0.34 and 0.41 mM, respectively.

Analytical titration curves of glycosyl hydrolase Cel45 by combined isoelectric focusing-electrophoresis

The electrical charge of endocellulase Cel45-core has been determined by combined isoelectric focusing-electrophoresis in the range of pH 3-9. In order to transform electrophoretic mobility to absolute electrical charge value, several corrections were applied: the frictional coefficient theoretically calculated from the molecular dimensions depends on porous gel structure and on the ionic strength of the solution. By comparing the curve calculated according to the Linderstrom-Lang equation, the number of charged electrical groups exposed to the solvent and their apparent ionization constants, pK(o)i, can be determined. Furthermore, the macromolecule structure can be assumed not to change in this pH range. This finding is necessary to understand the structure and the electrical properties of the entire Cel45 molecule.

Juvenile hormone biosynthesis, oocyte growth and vitellogenin accumulation in Choristoneura fumiferana and C. rosaceana: a comparative study

We assessed the effects of age and mating status on in vitro juvenile hormone (JH) biosynthesis, oocyte growth, egg production and vitellogenin (Vg) accumulation in the tortricid moths, Choristoneura fumiferana and C. rosaceana. To determine whether vitellogenesis is dependent on the presence of JH, we also examined the effects of decapitation and JH analog treatments on egg production. In both species, the corpora allata (CA) of adult females released fmol quantities of JH, with JH II being the major homolog produced. The CA began producing detectable quantities of JH around the time of emergence. Full activation of the CA was observed a few hours sooner in C. fumiferana than in C. rosaceana. In pharate adults and young virgin females of both species, growth of the basal oocyte reflected changes in CA activity. Decapitation of newly emerged females significantly reduced egg production, but treatment of decapitated females with the JH analog methoprene resulted in egg production that was similar to (C. fumiferana) or greater than (C. rosaceana) that of controls, indicating that JH is required for oocyte maturation. Vg was first observed in the hemolymph before the presumptive time of CA activation, suggesting that the synthesis of this protein is not dependent on JH. The presence of normal quantities of Vg in the hemolymph of pupae decapitated before CA activation confirmed this hypothesis. The Vg titer underwent a transient decline following CA activation and was significantly lower in mated than in virgin females of both species 3 and 5 days after copulation. Since CA activation at emergence and mating are both expected to cause a rise in the JH titer, we suggest that the declines in the levels of Vg result from JH-enhanced Vg uptake by the developing oocytes. Mating induced a significant increase in egg production but had no measurable impact on rates of JH biosynthesis in vitro.

Using native gel in two-dimensional PAGE for the detection of protein interactions in protein extract

A two-dimensional (2-D) gel electrophoresis system in which native and sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis (PAGE) are performed subsequently to analyze protein mixtures is described. Reasonably good resolution and excellent reproducibility was obtained when the proteins in the soluble protein extract from E. coli cells were separated using this procedure. Perhaps more importantly, the relevance of this native/SDS-2-D PAGE for the detection of protein interactions in a complicated protein mixture was examined using the interaction between interleukin-2 (IL-2) and its receptor alpha chain (IL-2Ralpha) in the E. coli protein extract as a model system. Native gel was used to preserve the interactions between the two molecules and SDS gel was used to maximize the separation of the denatured proteins. Mobility changes of these two proteins on 2-D maps resulted from the formation of IL-2/IL-2-2Ralpha complex were clearly observed despite of the presence of a large number of other protein spots. Thus, this approach is a useful complement to the standard 2-D gel electrophoresis system for analyzing complicated protein mixture, especially for the study of protein interactions.

Chloroplast Cpn20 forms a tetrameric structure in Arabidopsis thaliana

Chloroplast chaperonin 20 (Cpn20) in higher plants is a functional homologue of the Escherichia coli GroES, which is a critical regulator of chaperonin-mediated protein folding. The cDNA for a Cpn20 homologue of Arabidopsis thaliana was isolated. It was 958 bp long, encoding a protein of 253 amino acids. The protein was composed of an N-terminal chloroplast transit peptide, and the predicted mature region comprised two distinct GroES domains that showed 42% amino acid identity to each other. The isolated cDNA was constitutively expressed in transgenic tobacco. Immunogold labelling showed that Cpn20 is accumulated in chloroplasts of transgenic tobacco. A Northern blot analysis revealed that mRNA for the chloroplast Cpn20 is abundant in leaves and is increased by heat treatment. To examine the oligomeric structure of Cpn20, a histidine-tagged construct lacking the transit peptide was expressed in E. coli and purified by affinity chromatography. Gel-filtration and cross-linking analyses showed that the expressed products formed a tetramer. The expressed products could substitute for GroES to assist the refolding of citrate synthase under non-permissive conditions. The analysis on the subunit stoichiometry of the GroEL-Cpn20 complex also revealed that the functional complex is composed of a GroEL tetradecamer and a Cpn20 tetramer.

Oligomeric structure and regulation of Candida albicans glucosamine-6-phosphate synthase

Candida albicans glucosamine-6-phosphate (GlcN-6-P) synthase was purified to apparent homogeneity with 52% yield from recombinant yeast YRSC-65 cells efficiently overexpressing the GFA1 gene. The pure enzyme exhibited Km(Gln) = 1.56 mM and Km(Fru-6-P) = 1.41 mM and catalyzed GlcN-6-P formation with kcat = 1150 min-1. The isoelectric point of 4.6 +/- 0.05 was estimated from isoelectric chromatofocusing. Gel filtration, native polyacrylamide gel electrophoresis, subunit cross-linking, and SDS-polyacrylamide gel electrophoresis showed that the native enzyme was a homotetramer of 79.5-kDa subunits, with an apparent molecular mass of 330-340 kDa. Results of chemical modification of the enzyme by group-specific reagents established an essential role of a cysteinyl residue at the glutamine-binding site and histidyl, lysyl, arginyl, and tyrosyl moieties at the Fru-6-P-binding site. GlcN-6-P synthase in crude extract was effectively inhibited by UDP-GlcNAc (IC50 = 0.67 mM). Purification of the enzyme markedly decreased the sensitivity to the inhibitor, but this could be restored by addition of another effector, glucose 6-phosphate. Binding of UDP-GlcNAc to the pure enzyme in the presence of Glc-6-P showed strong negative cooperativity, with nH = 0.54, whereas in the absence of this sugar phosphate no cooperative effect was observed. Pure enzyme was a substrate for cAMP-dependent protein kinase, the action of which led to the substantial increase of GlcN-6-P synthase activity, correlated with an extent of protein phosphorylation. The maximal level of activity was observed for the enzyme molecules containing 1. 21 +/- 0.08 mol of phosphate/mol of GlcN-6-P synthase. Monitoring of GlcN-6-P synthase activity and its sensitivity to UDP-GlcNAc during yeast --> mycelia transformation of C. albicans cells, under in situ conditions, revealed a marked increase of the former and a substantial fall of the latter.

Quaternary structures of a catalytic subunit-regulatory subunit dimeric complex and the holoenzyme of the cAMP-dependent protein kinase by neutron contrast variation

Chimeric molecules of the cAMP-dependent protein kinase (PKA) holoenzyme (R2C2) and of a Delta1-91RC dimer were reconstituted using deuterated regulatory (R) and protiated catalytic (C) subunits. Small angle scattering with contrast variation has revealed the shapes and dispositions of R and C in the reconstituted complexes, leading to low resolution models for both forms. The crystal structures of C and a truncation mutant of R fit well within the molecular boundaries of the RC dimer model. The area of interaction between R and C is small, seemingly poised for dissociation upon a conformational transition within R induced by cAMP binding. Within the RC dimer, C has a "closed" conformation similar to that seen for C with a bound pseudosubstrate peptide. The model for the PKA holoenzyme has an extended dumbbell shape. The interconnecting bar is formed from the dimerization domains of the R subunits, arranged in an antiparallel configuration, while each lobe contains the cAMP-binding domains of one R interacting with one C. Our studies suggest that the PKA structure may be flexible via a hinge movement of each dumbbell lobe with respect to the dimerization domain. Sequence comparisons suggest that this hinge might be a property of the RII PKA isoforms.

Distribution of cathepsin E in the larval and adult organs of the bullfrog with special reference to the mature form in the larval fore-gut

The distibution of cathepsin E in several organs of the bullfrog, Rana catesbeiana, was analyzed at pre- and post-metamorphic stages by the acid proteinase assay, by visualization of enzyme activity on polyacrlamide fore-gut gels after electrophoresis and by immunoblotting with anti-cathepsin E serum. Cathepsin E was mainly distributed in the foregut at the larval stage and in the stomach, duodenum, large intestine and gall bladder at the post-metamorphic stage. In the larval fore-gut, a higher amount of the mature form of cathepsin E was observed in addition to the proform, but in other organs, including the stomach at the post-metamorphic stage, the mature form was barely detected. Developmental changes in the amount of cathepsin E were found in the digestive tract and the gall bladder by quantitative immunoblotting analysis. Finally, the larval fore-gut was stained immunohistochemically with anti-cathepsin E serum and the surface epithelium gave a strong immunoreactive signal.

Purification of Hsk1, a minichromosome maintenance protein kinase from fission yeast

Members of the Cdc7 family of protein kinases are essential for the initiation of DNA replication in all eukaryotes, but their precise biochemical function is unclear. We have purified the fission yeast Cdc7 homologue Hsk1 approximately 30,000-fold, to near homogeneity. Purified Hsk1 has protein kinase activity on several substrates and is capable of autophosphorylation. Point mutations in highly conserved regions of Hsk1 inactivate the kinase in vitro and in vivo. Overproduction of two of the mutant hsk1 alleles blocks initiation of DNA replication and deranges the mitotic checkpoint, a phenotype consistent with a role for Hsk1 in the early stages of initiation. The purified Hsk1 kinase can be separated into two active forms, a Hsk1 monomer and a heterodimer consisting of Hsk1 complexed with a co-purifying polypeptide, Dfp1. Association with Dfp1 stimulates phosphorylation of exogenous substrates but has little effect on autokinase activity. We have identified Dfp1 as the fission yeast homologue of budding yeast Dbf4. Purified Hsk1 phosphorylates the Cdc19 (Mcm2) subunit of the six-member minichromosome maintenance protein complex purified from fission yeast. Since minichromosome maintenance proteins have been implicated in the initiation of DNA replication, the essential function of Hsk1 at the G1/S transition may be mediated by phosphorylation of Cdc19. Furthermore, the phosphorylation of critical substrates by Hsk1 kinase is likely regulated by association with a Dbf4-like co-factor.

Characterization of spermidine binding to solubilized plasma membrane proteins from zucchini hypocotyls

In this work [14C]spermidine binding to total proteins solubilized from plasma membrane purified from zucchini (Cucurbita pepo L.) hypocotyls was investigated. Proteins were solubilized using octyl glucoside as a detergent. Specific polyamine binding was thermolabile, reversible, pH dependent with an optimum at pH 8.0, and had a Kd value of 5 &mgr;M, as determined by glass-fiber-filter assays. Sephadex G-25 M gel-filtration assays confirmed the presence of a spermidine-protein(s) complex with a specific binding activity. By sodium dodecyl sulfate-polyacrylamide gel electrophoresis and native polyacrylamide gel electrophoresis of collected fractions having the highest specific spermidine-binding activity, several protein bands (113, 75, 66, and 44 kD) were identified. The specificity of spermidine binding was examined by gel-filtration competition experiments performed using other polyamines and compounds structurally related to spermidine. Partial purification on Sephadex G-200 led to the identification of 66- and 44-kD protein bands, which may represent the putative spermidine-binding protein(s) on the plasmalemma.

Purification of a toxic factor from Arabian Gulf catfish epidermal secretions

The Arabian Gulf catfish, Arius bilineatus (Valenciennes) secretes a proteinaceous epidermal secretion when threatened or injured. A toxic factor has been isolated and purified from the crude extract (crude skin toxin) of these secretions by a combination of gel filtration on Sephacryl S-300 and preparative discontinuous polyacrylamide gel electrophoresis. The purified skin toxin has a molecular weight of 39,000 Da and an isoelectric point (pI) of 5.45. Injection of the purified skin toxin into rabbits i.v. and determination of the LD50 indicated that the protein had been purified approximately 30 fold by these procedures. Injection of the purified skin toxin into rabbits caused agitation, convulsions and death within 5 min. Analysis of plasma levels of lactate dehydrogenase, glutamate-oxaloacetate transaminase and glutamate pyruvate transaminase in injected rabbits indicated that the skin toxin caused cardiac and liver damage to the animals.

Chimeric structure of the NAD(P)+- and NADP+-dependent malic enzymes of Rhizobium (Sinorhizobium) meliloti

Malic enzymes catalyze the oxidative decarboxylation of malate to pyruvate in conjunction with the reduction of a nicotinamide cofactor. We determined the DNA sequence and transcriptional start sites of the genes encoding the diphosphopyridine nucleotide-dependent malic enzyme (DME, EC 1.1.1.39) and the triphosphopyridine nucleotide-dependent malic enzyme (TME, EC 1.1.1. 40) of Rhizobium (Sinorhizobium) meliloti. The predicted DME and TME proteins contain 770 and 764 amino acids, respectively, and are approximately 320 amino acids larger than previously characterized prokaryotic malic enzymes. The increased size of DME and TME resides in the C-terminal extensions which are similar in sequence to phosphotransacetylase enzymes (EC 2.3.1.8). Modified DME and TME proteins which lack this C-terminal region retain malic enzyme activity but are unable to oligomerize into the native state. Data base searches have revealed that similar chimeric malic enzymes were uniquely present in Gram-negative bacteria. Thus DME and TME appear to be members of a new class of malic enzyme characterized by the presence of a phosphotransacetylase-like domain at the C terminus of the protein.

Xanthine dehydrogenase from the phototrophic purple bacterium Rhodobacter capsulatus is more similar to its eukaryotic counterparts than to prokaryotic molybdenum enzymes

Fourteen Rhodobacter capsulatus mutants unable to grow with xanthine as sole nitrogen source were isolated by random Tn5 mutagenesis. Five of these Tn5 insertions were mapped within two adjacent chromosomal EcoRI fragments hybridizing to oligonucleotides synthesized according to conserved amino acid sequences of eukaryotic xanthine dehydrogenases. DNA sequence analysis of this region revealed two open reading frames, designated xdhA and xdhB, encoding xanthine dehydrogenase. The deduced amino acid sequence of XDHA contains binding sites for two [2Fe-2S] clusters and FAD, whereas XDHB is predicted to contain the molybdopterin cofactor. In contrast to R. capsulatus, these three cofactor binding sites reside within a single polypeptide chain in eukaryotic xanthine dehydrogenases. The amino acid sequence of xanthine dehydrogenase from R. capsulatus showed a higher degree of similarity to eukaryotic xanthine dehydrogenases than to the xanthine dehydrogenase-related aldehyde oxidoreductase from Desulphovibrio gigas. The expression of an xdhA-lacZ fusion was induced when hypoxanthine or xanthine was added as sole nitrogen source. Mutations in nifR1 (ntrC) and nifR4 (rpoN, encoding sigma54) had no influence on xdh gene expression. A putative activator sensing the availability of substrate seems to respond to xanthine but not to hypoxanthine. The transcriptional start site of xdhA was mapped by primer extension analysis. Comparison with known promoter elements revealed no significant homology. Xanthine dehydrogenase from R. capsulatus was purified to homogeneity. The enzyme consists of two subunits with molecular masses of 85 kDa and 50 kDa respectively. N-terminal amino acid sequencing of both subunits confirmed the predicted start codons. The molecular mass of the native enzyme was determined to be 275 kDa, indicating an alpha2beta2-subunit structure. Analysis of the molybdenum cofactor of xanthine dehydrogenase from R. capsulatus revealed that it contains the molybdopterin cofactor and not a molybdopterin dinucleotide derivative.

A dissimilatory sirohaem-sulfite-reductase-type protein from the hyperthermophilic archaeon Pyrobaculum islandicum

A sulfite-reductase-type protein was purified from the hyperthermophilic crenarchaeote Pyrobaculum islandicum grown chemoorganoheterotrophically with thiosulfate as terminal electron acceptor. In common with dissimilatory sulfite reductases the protein has an alpha 2 beta 2 structure and contains high-spin sirohaem, non-haem iron and acid-labile sulfide. The oxidized protein exhibits absorption maxima at 280, 392, 578 and 710 nm with shoulders at 430 and 610 nm. The isoelectric point of pH 8.4 sets the protein apart from all dissimilatory sulfite reductases characterized thus far. The genes for the alpha- and beta-subunits (dsrA and dsrB) are contiguous in the order dsrAdsrB and most probably comprise an operon with the directly following dsrG and dsrC genes. dsrG and dsrC encode products which are homologous to eukaryotic glutathione S-transferases and the proposed gamma-subunit of Desulfovibrio vulgaris sulfite reductase, respectively. dsrA and dsrB encode 44.2 kDa and 41.2 kDa peptides which show significant similarity to the two homologous subunits DsrA and DsrB of dissimilatory sulfite reductases. Phylogenetic analyses indicate a common protogenotic origin of the P. islandicum protein and the dissimilatory sulfite reductases from sulfate-reducing and sulfide-oxidizing prokaryotes. However, the protein from P. islandicum and the sulfite reductases from sulfate-reducers and from sulfur-oxidizers most probably evolved into three independent lineages prior to divergence of archaea and bacteria.

Ligand-induced conformational changes in cyclic nucleotide phosphodiesterases and cyclic nucleotide-dependent protein kinases

Three methods have been used to assess the conformational effects associated with ligand binding to two unrelated cyclic nucleotide receptor proteins: the cGMP-binding, cGMP-specific phosphodiesterase (cGB-PDE or PDE5A) and the cGMP-dependent protein kinase (PKG). The methods should be applicable to other proteins and to other types of modification such as phosphorylation. The procedures use either ion-exchange chromatography, size-exclusion chromatography, or native gel electrophoresis of these proteins in the absence and presence of regulatory ligands. Measurements from these respective approaches allow documentation of changes in the quaternary structure, surface electronegativity, and relative compactness (Stokes radius) of the protein molecule. The combined data allow the changes in protein conformation to be quantitated in terms of alterations in the axial ratio or length/width dimension of the molecule. The methods can be applied to partially purified proteins and to proteins that are available in limited quantities. Conformational changes due to stable modifications of proteins can be potentially examined in crude extracts of intact cells. Each of the methods can be tailored to optimize resolution of a particular protein under a variety of conditions. Activity measurements, Coomassie brilliant blue or silver staining of gels, radioautography, or Western blot analysis can be used for detection of the protein.

Purification and properties of methanol dehydrogenase from Methylocystis sp. GB 25

Methanol dehydrogenase (MDH) from Methylocystis sp. GB 25, which belongs to the group II of methanotrophic bacteria, is able to catalyse the oxidation of methanol to formate directly. The enzyme was purified 20-fold by a 5 step procedure to electrophoretic homogeneity. After cell disruption by French press, about 95% of MDH-activity was found in the soluble fraction. The relative molecular mass of the native enzyme has been estimated to be 122 kDa by gel filtration and 115 kDa by the method of Hedrick and Smith (1968). It seems to be composed of two identical subunits with a relative molecular mass of 62 kDa (estimated by SDS gel electrophoresis). The isoelectric point was found to be about 8.3. The amino terminal sequence shows a strong similarity to the alpha-chain of MDH from the facultative methylotrophic bacterium Methylobacterium extorquens AM1. PQQ, the probable prosthetic group of MDH, could be detected in the supernatant of the culture by using the apoenzyme of a membrane-bound glucose dehydrogenase from Pseudomonas aeruginosa but not absolutely in the absorption spectra of the enzyme after DEAE-chromatography. The purified MDH has an optimum activity at pH 9.0 and at 45 degrees C. MDH of Methylocystis sp. GB 25 oxidises only primary alcohols from methanol to heptanol and aldehydes from formaldehyde to propionaldehyde and the glutaraldehyde, respectively. The estimated Km-values show no dependence upon the chain length of substrates.

The biosynthesis and processing of vitellogenin in the fat bodies of females and males of the cockroach Leucophaea maderae

The juvenile hormone analog (JHA) methoprene was used to induce the synthesis of the yolk protein precursor vitellogenin (Vg) in adult females and males of the cockroach Leucophaea maderae. The female- and male-produced vitellogenin (VgF and VgM, respectively) contained polypeptides of 112, 95, 92, and 54 kDa. Also present in the secreted vitellogenins was a soffmall quantity of a short-lived transitional 155 kDa Vg polypeptide, and a variable amount of an 85 dDa species. Quantitatively, the VgF and VgM were significantly different in the Vg112 and Vg95 units (VgF > VgM), and in the Vg85 polypeptide (VgF < VgM). In the present study, the biosynthesis of Vg precursors in the fat bodies of females and males was examined using a short radiopulse with 35S-methionine/cysteine and 32P-orthophosphate. The glycosylation of the Vg precursors was examined by digestion with endoglycosidase H and by the inhibition of N-linked glycosylation with tunicamycin. The data showed that in both females and males, the synthesis of the vitellogenin precursor occurred in a stepwise fashion: (1) the co-translational glycosylation of Vg203; (2) the post-translational phosphorylation of Vg203 to form Vg220; (3) the proteolytic processing of Vg220 to form the constituent Vg polypeptides. The 203 and 220 kDa Vg precursors of females and males appeared to be similarly glycosylated and phosphorylated. The additional processing of Vg112 to Vg85 was more pronounced in the fat bodies of males than in females, and appears to account for the quantitative difference in the distribution of these polypeptides in VgF and VgM. Finally, the major oligosaccharides of VgF and VgM appear to be those of N-linked mannose residues. The treatment of females and males with tunicamycin indicated that the co-translational glycosylation of Vg precursors was required for the phosphorylation of the Vg precursor, as well as the secretion of Vg from the fat body.

Regulation of peanut glutamate dehydrogenase by methionine sulphoximine

Peanut glutamate dehydrogenase (GDH) was electrophoretically purified to homogeneity. Rotofor IEF fractionated the peanut GDH to 7 isoelectric (charge) isomers, which focused in the pH 5-8 range. Western blot analysis of the charge isomers using anti-GDH serum showed that methionine sulphoximine (MSX) treatment suppressed the b-subunit (69 KDa), but enhanced the a-subunit (45 KDa), and alpha-subunit (46 KDa) of the enzyme. The MSX-mediated suppression of the b-subunit increased the NH4+ Km value of the acidic charge isomers from 7.7 mM in the control to 50 mM in the MSX-treated peanut, and also increased the 2-ketoglutarate Km value of the basic charge isomers from 0.4 mM in the control to 7.0 mM in the MSX treatment. Therefore, the control peanut could salvage NH4+ with its GDH activity. But by increasing the NH4+ Km value, the MSX rendered the enzyme ineffective in NH4+ salvage. In the deamination direction, despite the enhancement of the a-, and alpha-subunits by MSX, the basic charge isomers of GDH had very high Km value for L-glu (50 mM), similar to that (25 mM) of the control. Thus, the GDHs of the control, and MSX treatment could not function in the deamination reaction in vivo. These results show that the treatment of peanut with MSX impaired the amination function of GDH.

Comparative analysis of storage proteins of fall webworm (Hyphantria cunea, Drury)

Two kinds of storage protein (SP-1 and SP-2) were purified from the hemolymph of last instar larvae of Hyphantria cunea by ultracentrifugation, chromatofocusing, and ion-exchange chromatography. SP-1 and SP-2 each consist of six subunits and have the molecular mass of 79 KDa and 82.5 KDa, respectively. These showed different patterns of appearance in fat body and hemolymph, and different SDS-PAGE patterns in non-reducing gels. Their stability in citrate-phosphate or Tris-HCl buffers differs and their immunological characteristics indicates that these are different storage proteins. Comparison with storage proteins of other species with respect to amino acid composition and N-terminal sequence, indicates that SP-1 can be classified as a methionine-rich storage protein but SP-2 cannot be regarded as a classical arylphorin.

Dimerization of the highly conserved light chain shared by dynein and myosin V

The Mr 8,000 light chain originally identified in Chlamydomonas flagellar dynein is also a component of both cytoplasmic dynein and myosin V. Furthermore, this small protein has been implicated as an inhibitor of neuronal nitric oxide synthase, suggesting that it may play multiple regulatory roles within the cell. Covalent cross-linking of both dynein and myosin V using 1,5-difluoro-2, 4-dinitrobenzene revealed that this light chain exists as a dimer in situ. This observation was confirmed using two additional amine-selective cross-linking reagents (dimethyl pimelimidate and disuccinimidyl suberate). When expressed as a C-terminal fusion with maltose-binding protein, the presence of the light chain caused the recombinant molecule to dimerize. Analysis of fusions containing truncated light chains identified the predicted amphiphilic helix (residues 14-32) as sufficient to cause dimerization; cross-linking required a second helical segment (residues 33-46). Together the data presented suggest that two light chains interact to form a parallel dimeric structure. This arrangement has significant implications for the potential functions of this highly conserved molecule and suggests a mechanism by which it might dissociate nitric oxide synthase.

The RNA molecule CsrB binds to the global regulatory protein CsrA and antagonizes its activity in Escherichia coli

The RNA-binding protein CsrA (carbon storage regulator) is a new kind of global regulator, which facilitates specific mRNA decay. A recombinant CsrA protein containing a metal-binding affinity tag (CsrA-H6) was purified to homogeneity and authenticated by N-terminal sequencing, matrix-assisted laser desorption/ionization time of flight mass spectrometry, and other studies. This protein was entirely contained within a globular complex of approximately 18 CsrA-H6 subunits and a single approximately 350-nucleotide RNA, CsrB. cDNA cloning and nucleotide sequencing revealed that the csrB gene is located downstream from syd in the 64-min region of the Escherichia coli K-12 genome and contains no open reading frames. The purified CsrA-CsrB ribonucleoprotein complex was active in regulating glg (glycogen biosynthesis) gene expression in vitro, as was the RNA-free form of the CsrA protein. Overexpression of csrB enhanced glycogen accumulation in E. coli, a stationary phase process that is repressed by CsrA. Thus, CsrB RNA is a second component of the Csr system, which binds to CsrA and antagonizes its effects on gene expression. A model for regulatory interactions in Csr is presented, which also explains previous observations on the homologous system in Erwinia carotovora. A highly repeated nucleotide sequence located within predicted stem-loops and other single-stranded regions of CsrB, CAGGA(U/A/C)G, is a plausible CsrA-binding element.

A stereo-inverting D-phenylglycine aminotransferase from Pseudomonas stutzeri ST-201: purification, characterization and application for D-phenylglycine synthesis

D-phenylglycine aminotransferase (D-PhgAT) from a newly isolated soil bacterium, Pseudomonas stutzeri ST-201, was purified to electrophoretic homogeneity and characterized. The molecular weight (M(r)) of the native enzyme was estimated to be 92,000. It is composed of two subunits identical in molecular weight (M(r)) = 47,500). The isoelectric point (pI) of the native enzyme was 5.0. The enzyme catalyzed reversible transamination specific for D-phenylglycine or D-4-hydroxyphenylglycine in which 2-oxoglutarate was an exclusive amino group acceptor and was converted into L-glutamic acid. Neither the D- nor L-isomer of phenylalanine, tyrosine, alanine, valine, leucine, isoleucine or serine could serve as a substrate. The enzyme was most active at alkaline pH with maximum activity at pH 9-10. The temperature for maximum activity was 35-45 degrees C. The apparent K(m) values for D-phenylglycine and for 2-oxoglutarate at 35 degrees C, pH 9.5 were 1.1 and 2.4 mM, respectively. The enzyme activity was strongly inhibited by typical inhibitors of pyridoxal phosphate-dependent enzymes. Possible application of this enzyme for synthesis of enantiomerically pure D-phenylglycine was demonstrated.

The catalytic domain of lambda site-specific recombinase

The Escherichia coli phage lambda integrase protein (Int) belongs to the large Int family of site-specific recombinases. It is a heterobivalent DNA binding protein that makes use of a high energy covalent phosphotyrosine intermediate to catalyze integrative and excisive recombination at specific chromosomal sites (att sites). A 293-amino acid carboxy-terminal fragment of Int (C65) has been cloned, characterized, and used to further dissect the protein. From this we have cloned and characterized a 188-amino acid, protease-resistant, carboxy-terminal fragment (C170) that we believe is the minimal catalytically competent domain of Int. C170 has topoisomerase activity and converts att suicide substrates to the covalent phosphotyrosine complexes characteristic of recombination intermediates. However, it does not show efficient binding to att site DNA in a native gel shift assay. We propose that lambda Int consists of three functional and structural domains: residues 1-64 specify recognition of "arm-type" DNA sequences distant from the region of strand exchange; residues 65-169 contribute to specific recognition of "core-type" sequences at the sites of strand exchange and possibly to protein-protein interactions; and residues 170-356 carry out the chemistry of DNA cleavage and ligation. The finding that the active site nucleophile Tyr-342 is in a uniquely protease-sensitive region complements and reinforces the recently solved C170 crystal structure, which places Tyr-342 at the center of a 17-amino acid flexible loop. It is proposed that C170 is likely to represent a generic Int family domain that thus affords a specific route to studying the chemistry of DNA cleavage and ligation in these recombinases.

Novel genes encoding 2-aminophenol 1,6-dioxygenase from Pseudomonas species AP-3 growing on 2-aminophenol and catalytic properties of the purified enzyme

2-Aminophenol 1,6-dioxygenase was purified from the cell extracts of Pseudomonas sp. AP-3 grown on 2-aminophenol. The product from 2-aminophenol by catalysis of the purified enzyme was identified as 2-aminomuconic 6-semialdehyde by gas chromatographic and mass spectrometric analyses. The molecular mass of the native enzyme was 140 kDa based on gel filtration. It was dissociated into molecular mass subunits of 32 (alpha-subunit) and 40 kDa (beta-subunit) by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, indicating that the dioxygenase was a heterotetramer of alpha2beta2. The genes coding for the alpha- and beta-subunits of the enzyme were cloned and sequenced. Open reading frames of the genes (amnA and amnB) were 816 and 918 base pairs in length, respectively. The amino acid sequences predicted from the open reading frames of amnA and amnB corresponded to the NH2-terminal amino acid sequences of the alpha-subunit (AmnA) and beta-subunit (AmnB), respectively. The deduced amino acid sequences of AmnB showed identities to some extent with HpaD (25.4%) and HpcB (24.4%) that are homoprotocatechuate 2,3-dioxygenases from Escherichia coli W and C, respectively, belonging to class III in the extradiol dioxygenases. On the other hand, AmnA had identity (23.3%) with only AmnB among the enzymes examined.

Transport of a large oligomeric protein by the cytoplasm to vacuole protein targeting pathway

Aminopeptidase I (API) is transported into the yeast vacuole by the cytoplasm to vacuole targeting (Cvt) pathway. Genetic evidence suggests that autophagy, a major degradative pathway in eukaryotes, and the Cvt pathway share largely the same cellular machinery. To understand the mechanism of the Cvt import process, we examined the native state of API. Dodecameric assembly of precursor API in the cytoplasm and membrane binding were rapid events, whereas subsequent vacuolar import appeared to be rate limiting. A unique temperature-sensitive API-targeting mutant allowed us to kinetically monitor its oligomeric state during translocation. Our findings indicate that API is maintained as a dodecamer throughout its import and will be useful to study the posttranslational movement of folded proteins across biological membranes.

Testis-specific expression of a functional retroposon encoding glucose-6-phosphate dehydrogenase in the mouse

The X-chromosomal gene glucose-6-phosphate dehydrogenase (G6pd) is known to be expressed in most cell types of mammalian species. In the mouse, we have detected a novel gene, designated G6pd-2, encoding a G6PD isoenzyme. G6pd-2 does not contain introns and appears to represent a retroposed gene. This gene is uniquely transcribed in postmeiotic spermatogenic cells in which the X-encoded G6pd gene is not transcribed. Expression of the G6pd-2 sequence in a bacterial system showed that the encoded product is an active enzyme. Zymogramic analysis demonstrated that recombinant G6PD-2, but not recombinant G6PD-1 (the X-chromosome-encoded G6PD), formed tetramers under reducing conditions. Under the same conditions, G6PD tetramers were also found in extracts of spermatids and spermatozoa, indicating the presence of G6pd-2-encoded isoenzyme in these cell types. G6pd-2 is one of the very few known expressed retroposons encoding a functional protein, and the presence of this gene is probably related to X chromosome inactivation during spermatogenesis.

Choline monooxygenase, an unusual iron-sulfur enzyme catalyzing the first step of glycine betaine synthesis in plants: prosthetic group characterization and cDNA cloning

Plants synthesize the osmoprotectant glycine betaine via the route choline --> betaine aldehyde --> glycine betaine. In spinach, the first step is catalyzed by choline monooxygenase (CMO), a ferredoxin-dependent stromal enzyme that has been hypothesized to be an oligomer of identical subunits and to be an Fe-S protein. Analysis by HPLC and matrix-assisted laser desorption ionization MS confirmed that native CMO contains only one type of subunit (Mr 42,864). Determination of acid-labile sulfur and nonheme iron demonstrated that there is one [2Fe-2S] cluster per subunit, and EPR spectral data indicated that this cluster is of the Rieske type--i.e., coordinated by two Cys and two His ligands. A full-length CMO cDNA (1,622 bp) was cloned from spinach using a probe generated by PCR amplification for which the primers were based on internal peptide sequences. The ORF encoded a 440-amino acid polypeptide that included a 60-residue transit peptide. The deduced amino acid sequence included two Cys-His pairs spaced 16 residues apart, a motif characteristic of Rieske-type Fe-S proteins. Larger regions that included this motif also showed some sequence similarity (approximately 40%) to Rieske-type proteins, particularly bacterial oxygenases. Otherwise there was very little similarity between CMO and proteins from plants or other organisms. RNA and immunoblot analyses showed that the expression of CMO in leaves increased several-fold during salinization. We conclude that CMO is a stress-inducible representative of a new class of plant oxygenases.

Comparative biochemistry of a cytosolic artiodactyl glycosidase

Artiodactyls possess abundant neutral glycosidase activity in liver, kidney and intestine. This enzyme is cytosolic and displays a more neutral pH optimum, more acidic isoelectric point and broader substrate range than the corresponding acidic beta-galactosidases. The neutral glycosidases were more thermolabile than the respective acidic beta-galactosidases and displayed a relative molecular mass approximating 60 kDa. This isozyme appeared to be a minor species in both rat and dog liver. The porcine enzyme was studied in more detail. Porcine neutral glycosidase activity was detected in 45-day gestational fetuses in both liver and kidney but not brain. Fetal kidney activities were about half those observed in adult kidney extracts. Porcine neutral glycosidase was immunologically distinct from acidic beta-galactosidase and was immunologically similar to the corresponding isozymes from deer, ovine and bovine liver. Porcine neutral glycosidase was moderately inhibited by D-galactonic acid gamma-lactone and strongly inhibited by D-gluconic acid delta-lactone; however, acidic beta-galactosidase was not inhibited by the delta-lactone. Inhibition by the gamma-lactone was competitive for both enzymes. 4-Methylumbelliferyl-beta-D-galactoside,-glucoside and -xyloside competed for the same active site. A polymorphism for fast- and slow-migrating isozymes of porcine neutral glycosidase was observed, which appeared to be under genetic control.

Multiplicity of antioxidant enzyme catalase in mouse liver cells

Multiplicity of catalase activity has been observed in crude homogenates from the tissue and cell lines of mouse liver by ethanol/Triton X-100/heat treatment. The five enzymatically active catalase bands were designated as CAT1, CAT2, CAT3, CAT4, and CAT5 with a nondenatured molecular mass of 270kDa, 258kDa, 229kDa, 210kDa, or 197kDa, respectively. Cultured mouse liver cell lines, mouse liver tissue homogenate, and pure mouse liver catalase showed only one catalase band (CAT1) after ethanol/Triton X-100 treatment at 4 degrees C for 72 hr. The same treatment but incubated at 37 degrees C for 72 hr yielded three bands (CAT2, CAT4, CAT5) in normal cell line, only one band (CAT5) in MNNG-transformed and SV40-transformed cells, two bands (CAT1, CAT4) in mouse liver tissue homogenates, and two bands (CAT1, CAT3) in pure mouse liver catalase. These five catalase bands were further biochemically characterized. The CAT1, CAT2, and CAT3 are sensitive to heat (68 degrees C, 1 min), while CAT4 and CAT5 are rather heat resistant. The sensitivity to catalase inhibitors, such as aminotriazole, azide, or cyanide varies among the isoforms. Protease inhibitors could prevent the formation of CAT3 and CAT4, but not CAT5. Treatment with protease, however, removed all forms of catalase except CAT5. We conclude from this study that the appearance of different catalase bands is likely due to epigenetic modification of the protein, particularly proteolysis. The lowered catalase activity in transformed cells might also be attributable to the loss of two catalase isoforms.

Characterization of the Aspergillus nidulans aspnd1 gene demonstrates that the ASPND1 antigen, which it encodes, and several Aspergillus fumigatus immunodominant antigens belong to the same family

For the first time, an immunodominant Aspergillus nidulans antigen (ASPND1) consistently reactive with serum samples from aspergilloma patients has been purified and characterized, and its coding gene (aspnd1) has been cloned and sequenced. ASPND1 is a glycoprotein with four N-glycosidically-bound sugar chains (around 2.1 kDa each) which are not necessary for reactivity with immune human sera. The polypeptide part is synthesized as a 277-amino-acid precursor of 30.6 kDa that after cleavage of a putative signal peptide of 16 amino acids, affords a mature protein of 261 amino acids with a molecular mass of 29 kDa and a pI of 4.24 (as deduced from the sequence). The ASPND1 protein is 53.1% identical to the AspfII allergen from Aspergillus fumigatus and 48% identical to an unpublished Candida albicans antigen. All of the cysteine residues and most of the glycosylation sites are perfectly conserved in the three proteins, suggesting a similar but yet unknown function. Analysis of the primary structure of the ASPND1 coding gene (aspnd1) has allowed the establishment of a clear relationship between several previously reported A. fumigatus and A. nidulans immunodominant antigens.

A broad-spectrum cytolytic toxin fromBacillus thuringiensisvar.kyushuensis

Bacillus thuringiensis (Bt) var. kyushuensis synthesizes a mosquitocidal crystalline inclusion containing several proteins ranging from 140 to 14 kDa. We have identified a 25 kDa protein protoxin in this inclusion which is not cytolytic, but when activated proteolytically to 23-22 kDa products is cytolytic to mosquito, lepidopteran and mammalian cells, can release entrapped glucose from liposomes and forms cation-selective channels in a planar lipid bilayer. This broad-spectrum cytolytic toxin is related antigenically to the 23 kDa toxin from Bt var. darmstadiensis strain 73-E10-2, but not to the 25 kDa CytA toxin of Bt var. israelensis. The cytolytic activity of these Bt var. kyushuensis toxins, like that of the latter two toxins, can be neutralized by incubation with liposomes containing phospholipids.

Cytochrome bd-type quinol oxidase in a mutant of Bacillus stearothermophilus deficient in caa3-type cytochrome c oxidase

Gram-positive thermophilic Bacillus species contain cytochrome caa3-type cytochrome c oxidase as a terminal oxidase in the respiratory chain. To identify alternative oxidases, we isolated B. stearothermophilus mutants defective in the caa3-type oxidase activity. One mutant contained little cytochrome a and had low cytochrome c oxidase activity. However, growth and the respiratory activity of membranes in the presence of NADH were close to normal, suggesting that the mutant contains an alternative electron transfer pathway. A novel oxidase was isolated from the membrane fraction of the mutant. The enzyme is a cytochrome bd-type quinol oxidase composed of two subunits of 52 and 40 kDa, whose N-terminal regions show sequence similarity to polypeptides of the bd-type oxidase from Escherichia coli and Azotobacter vinelandii. This is the first report of a bd-type terminal oxidase purified from a Gram-positive bacterium.

Identification of serum and urine proteins responsible for enhanced pigment production by group B streptococci as amylases

The serum and urine proteins responsible for enhanced pigment production in Streptococcus agalactiae in culture media were purified by chromatography and were identified as amylases by comparison of their amino acid composition with that calculated for proteins with known sequences. Similar pigment-enhancing activity was displayed by other amylases of nonanimal origin and by maltooligosaccharides.

Preparation and properties of pure, full-length IclR protein of Escherichia coli. Use of time-of-flight mass spectrometry to investigate the problems encountered

IclR protein, the repressor of the aceBAK operon of Escherichia coli, has been examined by time-of-flight mass spectrometry, with ionization by matrix assisted laser desorption or by electrospray. The purified protein was found to have a smaller mass than that predicted from the base sequence of the cloned iclR gene. Additional measurements were made on mixtures of peptides derived from IclR by treatment with trypsin and cyanogen bromide. They showed that the amino acid sequence is that predicted from the gene sequence, except that the protein has suffered truncation by removal of the N-terminal eight or, in some cases, nine amino acid residues. The peptide bond whose hydrolysis would remove eight residues is a typical target for the E. coli protease OmpT. We find that, by taking precautions to minimize Omp T proteolysis, or by eliminating it through mutation of the host strain, we can isolate full-length IclR protein (lacking only the N-terminal methionine residue). Full-length IclR is a much better DNA-binding protein than the truncated versions: it binds the aceBAK operator sequence 44-fold more tightly, presumably because of additional contacts that the N-terminal residues make with the DNA. Our experience thus demonstrates the advantages of using mass spectrometry to characterize newly purified proteins produced from cloned genes, especially where proteolysis or other covalent modification is a concern. This technique gives mass spectra from complex peptide mixtures that can be analyzed completely, without any fractionation of the mixtures, by reference to the amino acid sequence inferred from the base sequence of the cloned gene.