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PubMed1978

Sorghum proteinase inhibitors: purification and some biochemical properties.

An investigation has been carried out on the proteinase inhibitors of grain sorghum (Sorghum bicolor (L.) Moench). One of the inhibitors has been isolated in a pure form and characterized. The proteinase inhibitor was extracted from the acetone-defatted sorghum meal and purified by selective thermal denaturation, ammonium sulfate fractionation, Sephadex gel filtration and DEAE-cellulose chromatography (DEAE-preparation II). This preparation was demonstrated to be a mixture of three inhibitor components by polyacrylamide disc gel electrophoresis. Further resolution of this mixture into Inhibitors I to III was achieved by QAE-Sephadex chromatography. Sorghum Inhibitor III was homogeneous by the criteria of disc gel electrophoresis and has been more fully characterized. A molecular weight of 25,000 was obtained for Inhibitor III by gel filtration and was in agreement with the value calculated from the amino acid composition of the inhibitor. The N-terminal amino acid residue of Inhibitor III, a single chain protein, was isoleucine. Sorghum proteinase inhibitors inhibit specifically the serine proteinases and are inactive towards the other classes of proteinases. Inhibitor III is primarily a chymotrypsin inhibitor, whereas Inhibitors I and II inhibit both trypsin and chymotrypsin.

Amino Acids↗

PubMed1975

Ribonucleoside diphosphate reductase induced by bacteriophage T4. III. Isolation and characterization of proteins B1 and B2.

Ribonucleoside diphosphate reductase determined by bacteriophage T4 consists of a tight complex (alpha2beta2) of the polypeptide chains alpha (Mr = 80,000 to 85,000) and beta (Mr = 35,000). The alpha2 dimer (= protein B1) was purified from Escherichia coli B infected with T4 mutant nrdB55 (Yeh, Y.C., and Tessman, I. (1972) Virology 47, 767-772) which carries an amber mutation in the gene coding for the beta polypeptide chain. Protein B1 contained binding sites for dATP, an allosteric effector of the reductase. The beta2 dimer (= protein B2) was purified by selective desorption with 1 M guanidine HCl from a dATP-Sepharose affinity column containing adsorbed native T4 ribonucleotide reductase. Protein B2, isolated this way, was enzymatically inactive due to partial loss of its iron but it could be reactivated by treatment with ferrous iron. Active protein B2 contained two atoms of non-heme iron per molecule and exhibited the optical and electron spin resonance spectra previously demonstrated in the native enzyme. The T4-induced proteins B1 and B2 were unable to reduce ribonucleotides when assayed separately but were active in combination. The proteins did not form catalytically functional hybrids with proteins B1 and B2 of Escherichia coli ribonucleotide reductase, neither did they cross-react immunologically with the latter. 5-Hydroxymethyl-dCTP, at concentrations above 10 muM, was a positive allosteric effector of T4 ribonucleotide reductase promoting the reduction of the pyrimidine ribonucleotides CDP and UDP. The nucleotide had little effect on E. coli ribonucleotide reductase.

Coliphages↗

PubMed1993

Characterization of the Streptococcus pneumoniae maltosaccharide regulator MalR, a member of the LacI-GalR family of repressors displaying distinctive genetic features.

The gene encoding a transcriptional repressor of the maltosaccharide utilization operons of the Gram-positive bacterium Streptococcus pneumoniae (malR) has been cloned and sequenced. The genetic structure of the locus reveals the presence of an upstream gene necessary for growth on maltotetraose medium (malA). The phenotype of malR- and malA- mutants obtained by interruption of the coding regions suggests that both genes could belong to the same transcription unit. Two copies of a DNA motif consisting of three conserved regions of 59, 42, and 49 nucleotides were found located upstream and downstream of the malA-malR putative operon. These DNA structures are almost identical to the reported Box sequences associated with several genes of S. pneumoniae. The protein encoded by malR was visualized and partially purified after selective expression in Escherichia coli, whereas the product of malA was identified in vitro. The amino acid sequence of MalR displays similarities with the Lac and Gal family of repressors. The highest similarities were found when comparing MalR with the E. coli MalI repressor, which is related with an indirect induction pathway of the maltose regulon. The significance of these similarities is discussed in terms of the possible evolutionary pathways followed by structural and regulatory genes of sugar utilization systems in bacteria.

Amino Acid Sequence↗

PubMed1995

The isolation of U1 RNA-binding antibody fragments from autoimmune human-derived bacteriophage display libraries.

Almost seventy percent of systemic lupus erythematosus (SLE) patients produce autoantibodies specific for U1 RNA, the RNA component of the U1snRNP complex involved in pre-mRNA splicing. Human anti-U1 RNA antibodies from SLE patients provide an ideal model for studying protein-RNA interactions. In addition, a more in depth look at the mechanism by which an antibody interacts with U1 RNA will lend insight into immune disregulation and may have therapeutic potential in the treatment of autoimmune disease. The possibility of cloning an anti-U1 RNA antibody has been investigated using "phage Fab display," a method involving the display of Fab fragments on the outer surface of filamentous phage. Human Fab cDNA libraries were constructed using total RNA collected from leukophoresed anti-U1 RNA antibody-positive SLE patient sera. The resulting Fab genes were subcloned into a phagemid expression vector which produced phage displaying Fab fragments in E.coli1. Libraries were enriched for U1 RNA-binding clones after several rounds of affinity selection against purified, in vitro transcribed U1 RNA. Putative U1 RNA-binding clones were identified by colony lift and the corresponding Fab genes were expressed and purified from E.coli for binding studies. Results demonstrate that RNA-binding Fab can be isolated from combinatorial phage display libraries.

Amino Acid Sequence↗

PubMed1996

Cleavage of structural components of mammalian vitreous by endogenous matrix metalloproteinase-2

Our goal was to determine if the major endogenous vitreous matrix metalloproteinase (MMP-2) could digest known collagenous components of the vitreous body. Matrix metalloproteinase-2 and its associated inhibitors were isolated from porcine vitreous by affinity column chromatography. The inhibitors were inactivated by chemical modification with dithiothreitol and iodoacetamide. The latent MMP-2 was then activated with the organo-mercurial, p-aminophenyl mercuric acetate (APMA). Bovine vitreous fibrillar collagens (types II, V/XI and IX) were isolated by pepsin extraction and differential salt precipitation. Intact type IX collagen was purified by selective salt precipitation followed by ion exchange and size exclusion chromatography. These isolated collagens were incubated for 6 to 24 h with different concentrations of activated MMP-2, and the extent of collagen degradation was analyzed. Activated MMP-2 was also introduced into freshly isolated vitreous gels and the degree of liquefaction was determined. Our results showed that the activated MMP-2 has no apparent effect upon type II collagen but can degrade type V/XI collagen and type IX collagen fragments (COL2 and COL2 + COL3). In addition, when the type IX collagen was in the intact helical form, MMP-2 appeared to selectively digest alpha3 (IX) chains. This suggested that vitreous MMP-2 preferentially cleaved certain vitreous collagen chains into large fragments than small peptides. MMP-2 also disrupted the vitreous gel in vitro, releasing proteins but not hexuronic acid or sulfated glycosaminoglycans into the liquefied supernatant. We conclude that MMP-2 activity should be considered as a potential mechanism of vitreous liquefaction that is seen in aging and various pathological states. Keywords: matrix metalloproteinase; type II collagen; type IX collagen; type V/XI collagen; vitreous; pig

Journal Article↗

PubMed1996

Expression and polarization of intercellular adhesion molecule-1 on human intestinal epithelia: consequences for CD11b/CD18-mediated interactions with neutrophils.

BACKGROUND: Epithelial dysfunction and patient symptoms in inflammatory intestinal diseases such as ulcerative colitis and Crohn's disease correlate with migration of neutrophils (PMN) across the intestinal epithelium. In vitro modeling of PMN transepithelial migration has revealed distinct differences from transendothelial migration. By using polarized monolayers of human intestinal epithelia (T84), PMN transepithelial migration has been shown to be dependent on the leukocyte integrin CD11b/CD18 (Mac-1), but not on CD11a/CD18 (LFA-1). Since intercellular adhesion molecule-I (ICAM-1) is an important endothelial counterreceptor for these integrins, its expression in intestinal epithelia and role in PMN-intestinal epithelial interactions was investigated. MATERIALS AND METHODS: A panel of antibodies against different domains of ICAM-1, polarized monolayers of human intestinal epithelia (T84), and natural human colonic epithelia were used to examine the polarity of epithelial ICAM-1 surface expression and the functional role of ICAM-1 in neutrophil-intestinal epithelial adhesive interactions. RESULTS: While no surface expression of ICAM-1 was detected on unstimulated T84 cells, interferon-gamma (IFN gamma) elicited a marked expression of ICAM-1 that selectively polarized to the apical epithelial membrane. Similarly, apically restricted surface expression of ICAM-1 was detected in natural human colonic epithelium only in association with active inflammation. With or without IFN gamma pre-exposure, physiologically directed (basolateral-to-apical) transepithelial migration of PMN was unaffected by blocking monoclonal antibodies (mAbs) to ICAM-1. In contrast, PMN migration across IFN gamma-stimulated monolayers in the reverse (apical-to-basolateral) direction was inhibited by anti-ICAM-1 antibodies. Adhesion studies revealed that T84 cells adhered selectively to purified CD11b/CD18 and such adherence, with or without IFN gamma pre-exposure, was unaffected by ICAM-1 mAb. Similarly, freshly isolated epithelial cells from inflamed human intestine bound to CD11b/CD18 in an ICAM-1-independent fashion. CONCLUSIONS: These data indicate that ICAM-1 is strictly polarized in intestinal epithelia and does not represent a counterreceptor for neutrophil CD11b/CD18 during physiologically directed transmigration, but may facilitate apical membrane-PMN interactions after the arrival of PMN in the intestinal lumen.

Antibodies, Monoclonal↗

PubMedDate not supplied

Polymerase chain reaction amplification of Guthrie card deoxyribonucleic acid: extraction of nucleic acid from filter matrices.

This study evaluated two deoxyribonucleic acid (DNA) extraction methods for Guthrie card bloodspots. Our water-based extraction technique was compared with a commercial kit (GFX extraction system). In contrast to our nondenaturing method, the GFX system utilizes chaotropes to extract DNA. Extracted DNA is subsequently purified by selective elution from a glass fiber matrix. To evaluate DNA extraction, polymerase chain reaction (PCR) for a 491 bp region encoding the cystic fibrosis delta F508 mutation was performed and PCR products electrophoresed on polyacrylamide gels and stained with ethidium bromide. Amplification of GFX-extracted DNA required low sample volume (1 to 5 microL) indicating the presence of residual PCR inhibitors. The GFX volumes (1/20 to 1/4 punch) were comparable to our standard conditions and represented 0.16-0.80 microL whole blood (20 to 40 ng DNA). The GFX-extracted DNA was found to be stable (6 mo, -15 degrees C). Performance time for the GFX method was less than our standard water-based extraction (about 30 min), but more costly. The GFX extraction kit was adaptable for limited sample (i.e., extraction of a 3 mm punch yields 20 amplifications). The GFX extraction kit provides a useful means to standardize Guthrie card DNA extraction.

Blood Chemical Analysis↗

PubMed1997

Characterization of hydroperoxides and carbonyl compounds obtained by lipoxygenase extracts of selected microorganisms.

Partially purified lipoxygenase (LOX) extracts were obtained from Fusarium proliferatum, Fusarium oxysporum, Chlorella pyrenoidosa, and Saccharomyces cerevisiae; the enzymatic extract of F. proliferatum showed the highest LOX activity while those of F. oxysporum and S. cerevisiae demonstrated only 27.8 and 16.5% of the activity at pH 8.0, and 61.2 and 9.7% of the enzyme activity at pH 10.0, respectively. The lowest LOX activity was that in the C. pyrenoidosa extract. The microbial enzymatic preparations were assayed with linoleic acid as substrate, which was bioconverted into 9- and 13-hydroperoxides (HPODEs) by all four extracts; in addition, the LOX activity in the F. oxysporum extract produced the 10- and 12-HPODEs from linoleic acid while that of the C. pyrenoidosa extract produced only the 10-HPODE. When assayed with the 9- and 13-HPODEs as substrates, the selected microbial extracts had secondary enzyme activities, one of which produced hexanal. The highest hexanal-producing activity was 1.51 and 1.39 nmol hexanol/mg protein/min in the F. proliferatum and C. pyrenoidosa extracts, respectively, while those of F. oxysporum and S. cerevisiae had approximately 15% of the HPODE-cleaving enzyme activity. The C. pyrenoidosa extract had the highest proportion of pentanone, which was produced at only one-fourth the concentration by the HPODE-cleaving enzyme activity in the three other microbial enzymatic extracts.

Chlorella↗

PubMed2002

Quantitative trait locus mapping in chickens by selective DNA pooling with dinucleotide microsatellite markers by using purified DNA and fresh or frozen red blood cells as applied to marker-assisted selection.

Many large, half-sib sire families are an integral component of chicken genetic improvement programs. These family structures include a sufficient number of individuals for mapping quantitative trait loci (QTL) at high statistical power. However, realizing this statistical power through individual or selective genotyping is yet too costly to be feasible under current genotyping methodologies. Genotyping costs can be greatly reduced through selective DNA pooling, involving densitometric estimates of marker allele frequencies in pooled DNA samples. When using dinucleotide microsatellite markers, however, such estimates are often confounded by overlapping "shadow" bands and can be confounded further by differential amplification of alleles. In the present study a shadow correction procedure provided accurate densitometric estimates of allele frequency for dinucleotide microsatellite markers in pools made from chicken purified DNA samples, fresh blood samples, and frozen-thawed blood samples. In a retrospective study, selective DNA pooling with thawed blood samples successfully identified two QTL previously shown by selective genotyping to affect resistance in chickens to Marek's disease. It is proposed that use of selective DNA pooling can provide relatively low-cost mapping and use in marker-assisted selection of QTL that affect production traits in chickens.

Alleles↗

PubMed1991

Modulation of protease specificity by a change in the enzyme microenvironment. Selectivity modification on a model substrate, purified soluble proteins and gluten.

Subtilisin BPN' activity on a synthetic substrate is found to decrease with the concentration of soluble additives such as sugars and polyols, the catalytic efficiency of the enzyme being related to the water activity in the reaction medium. Limited hydrolysis of B chain of insulin is followed and the cleavage priority determined. When carried out in glycerol-containing medium, both enzyme catalytic behaviour and specificity are perturbed; a different cleavage order and a selectivity restriction are observed. The experiments were generalised to purified proteins and to an insoluble protein complex. The hydrolysis kinetics of purified gliadins by pepsin and of gluten by a Bacillus neutral protease are modulated in presence of water activity depressors. Glycerol is able to increase both pepsin efficiency and gluten protein solubility. The hydrolysis order is affected by water-structuring molecules in the enzyme microenvironment and new peptides appear whatever the size and initial solubility of the substrate.

Amino Acid Sequence↗

PubMed2026

The large mitochondrial genome of Syndiclis anlungensis (Lauraceae): Genome structure, comparative analysis, and phylogenetic relationships among Syndiclis species.

The complete mitochondrial genome (mitogenome) of Syndiclis anlungensis, a critically endangered tropical tree, was determined in this study. The mitogenome spans 2,368,454 bp across four contigs and harbors 41 protein-coding genes, 22 tRNA genes, and three rRNA genes. Potential mutation regions, including 1317 repeat sequences and 698 simple sequence repeats (SSRs), were accurately located in the S. anlungensis mitogenome. Sixty-five transferred fragments of the repeats were found between its mitochondrial and chloroplast genomes. When compared to three other Laurales mitogenomes, extensive gene order shuffling is evident, leaving only five conserved gene clusters intact. Codon usage analysis reveals a pronounced A/T bias in both mitochondrial and chloroplast genes, and three mitochondrial genes (atp9, rps19, and sdh3) stand out for their high divergence across eleven Syndiclis taxa. Selection analyses indicate strong purifying pressure on rpl2, rpl16, and sdh3 (Ka/Ks < 1), with no positive selection detected. Using 41 mitochondrial protein-coding gene sequences from sixteen and three individuals of Syndiclis and Beilschmiedia species, respectively, our phylogenetic tree recovers Syndiclis as monophyletic, with two well-supported clades: one includes S. anlungensis, S. chinensis, S. lotungensis, S. marlipoensis, and a putative new Syndiclis species from Yunnan; the other contains S. furfuracea, S. hongkongensis, S. kwangsiensis, and three putative new Syndiclis species from Guangdong and Vietnam.

Genome, Mitochondrial↗

PubMed1999

Genetic selection of phage engineered for receptor-mediated gene transfer to mammalian cells.

Although phage display is a powerful way of selecting ligands against purified target proteins, it is less effective for selecting functional ligands for complex targets like living cells. Accordingly, phage display has had limited utility in the development of targeting agents for gene therapy vectors. By adapting a filamentous bacteriophage for gene delivery to mammalian cells, however, we show here that it is possible to screen phage libraries for functional ligands capable of delivering DNA to cells. For example, when targeted with epidermal growth factor (EGF), M13 bacteriophage were capable of delivering a green fluorescent protein (GFP) gene to EGF receptor bearing cells in a ligand-, time-, and phage concentration-dependent manner. The EGF-targeted phage transduced COS-1 cells in a highly specific manner as demonstrated by competition with excess free EGF or alternatively with anti-EGF receptor antibodies. We further demonstrate that EGF-phage can be selected, by their ability to transduce EGF receptor bearing cells from libraries of peptide display phage. When phage were incubated with COS-1 cells, EGF ligand-encoding sequences were recovered by PCR from FACsorted, GFP-positive cells and the EGF-displaying phage were enriched 1 million-fold by four rounds of selection. These data suggest the feasibility of applying molecular evolution to phage gene delivery to select novel cell-specific DNA-targeting ligands. The same approach could be used to select genetically altered phage that are specifically designed and evolved as gene therapy vectors.

Animals↗

PubMed1990

Evolution of the segregation ratio: modification of gene conversion and meiotic drive.

We compare the evolutionary pressures that direct the modification of gene conversion and meiotic drive at loci subject to purifying and overdominant viability selection. Gene conversion differs from meiotic drive in that modifers do not affect their own segregation ratios, even when linked to the viability locus. Segregation distortion generates gametic level disequilibria between alleles at the viability locus and modifiers of gene conversion and meiotic drive: enhancers of segregation distortion become positively associated with driven alleles. Suppression of gene conversion evolves if the driven allele is marginally disadvantageous (overdominant viability selection), and higher rates evolve if the driven alleles are relatively advantageous (purifying viability selection). Gametic disequilibria permit enhancers of meiotic drive that are linked to the driven locus to promote their own segregation. We attribute the failure of genetic modifiers of gene conversion and meiotic drive to maximinize mean fitness to the generation of such associations.

Biological Evolution↗

PubMed2006

Efficient protein selection based on ribosome display system with purified components.

Using the PURE (Protein synthesis Using Recombinant Elements) system, we developed an efficient and highly controllable ribosome display method for selection of functional protein. The PURE system is composed of purified factors and enzymes that are responsible for gene expression in Escherichia coli. We performed the detailed analyses and optimization of the ribosome display system and demonstrated the formation of stable mRNA/ribosome/polypeptide ternary complexes. As complex formation is fundamental to successful ribosome display, these improvements resulted in a dramatic increase in the mRNA recovery rate. As a result, a approximately 12,000-fold enrichment of single-chain antibody (scFv) cDNA was achieved in a single round of selection. Specific selection of scFv mRNA from a 1:10(10) dilution in competitor mRNA was achieved with only three rounds of affinity selection. These findings, together with the results in the accompanying paper [T. Matsuura, H. Yanagida, J. Ushioda, I. Urabe, T. Yomo, Nascent chain, RNA, and ribosome complexes generated by pure translation system (see the accompanying paper).], demonstrate that the PURE system can provide a basis for reliable and reproducible ribosome display.

Cell-Free System↗

PubMed1984

Purification of a specific inhibitor of reverse transcriptase from human placenta.

Human placental extracts contain a factor which specifically and reversibly inhibits the reverse transcriptase of mammalian retroviruses. This placental inhibitor has been partially purified and characterized. It elutes at 0.1-0.2 M phosphate on hydroxyapatite chromatography and can be further purified by phosphocellulose chromatography where it elutes at 0.4 M KCl. By these purification procedures, specific activities of 40-70,000 units of inhibitor per mg of protein were obtained. The size of the inhibitor is about 60-65,000 daltons as estimated by velocity sedimentation. The inhibitor purified by these techniques selectively inhibits the activity of purified reverse transcriptase from Rauscher murine leukemia virus and baboon endogenous virus. It is substantially less active against the reverse transcriptase of avian myeloblastosis virus. The specificity of this inhibitor for mammalian enzymes and particularly for the human placental reverse transcriptase suggests that it plays a role in the regulation of DNA synthesis in human placental development.

Animals↗

PubMed1991

The yeast mitochondrial RNA polymerase specificity factor, MTF1, is similar to bacterial sigma factors.

We have purified the protein that confers selective promoter recognition on the core subunit of the yeast mitochondrial RNA polymerase. The N-terminal sequence of the 43-kDa specificity factor identified it as the product of the MTF1 gene described by Lisowsky and Michaelis (1988). We confirmed that MTF1 encoded the specificity factor by analyzing extracts from a yeast strain bearing a disruption of the gene. The extracts contained normal levels of core RNA polymerase but lacked selective transcription activity; adding the purified 43-kDa protein restored selective transcription. Comparison of the MTF1 protein sequence to the family of bacterial sigma factors has revealed striking similarity to domains identified with--10 promoter recognition, promoter melting, and holoenzyme stability.

Amino Acid Sequence↗

PubMed1977

A rapid procedure for selectively isolating the major glycoprotein from purified rat brain myelin.

Treatment of the chloroform/methanol-insoluble residue of rat brain myelin with lithium 3,5-di-iodosalicylate solubilized the major myelin-associated glycoprotein along with most other proteins and glycoproteins. Equilibration of the extract with phenol resulted in the selective partitioning of the major glycoprotein into the aqueous phase, whereas nearly all of the other proteins and glycoproteins went into the phenol phase.

Animals↗

PubMed1984

Inability of purified Pseudomonas aeruginosa exopolysaccharide to bind selected antibiotics.

It has been proposed that the exopolysaccharide (alginate) of mucoid Pseudomonas aeruginosa strains which infect cystic fibrosis patients might bind and hence protect this pathogen from antibiotics. To test this hypothesis, we employed equilibrium dialysis to measure the binding between several antibiotics and purified Pseudomonas alginate. Binding was calculated from the residual concentrations of antibiotics in free solution by a biological assay. The detectable binding of antibiotics to alginate was consistent with expectations; the positively charged antibiotics steptomycin and tobramycin, bound to the polyanion (0.047 and 0.024 mumol/mg of alginate, respectively), whereas the neutral species, clindamycin and penicillin, bound negligibly or not at all (0.0011 and 0 mumol/mg of alginate, respectively). When these experiments were performed in the presence of physiological concentrations of saline, none of the antibiotics bound to the polysaccharide. Since the binding observed was abrogated by salt concentrations typical of the tracheobronchial secretions of cystic fibrosis patients, the data suggest that tight binding of antibiotics to the exopolysaccharide of a mucoid P. aeruginosa strain does not provide increased antibiotic resistance.

Anti-Bacterial Agents↗