A new hydrolase specific for taurine-conjugates of bile acids.

Through the investigation of the bile acid-deconjugation activities of human intestinal anaerobes, a new enzyme was discovered in Peptostreptococcus intermedius which hydrolyzed specifically the taurine-conjugates, but not the glycine-conjugates of bile acids. However, the enzymes in Streptococcus faecalis and Lactobacillus brevis hydrolyzed chiefly the glycine-conjugates.     

A rice family 9 glycoside hydrolase isozyme with broad substrate specificity for hemicelluloses in type II cell walls

An auxin analog, 2,4-D, stimulates the activity of endo-1,4-beta-glucanase (EGase) in rice (Oryza sativa L.). The auxin-induced activity from three protein fractions was purified to homogeneity from primary root tissues (based on SDS-PAGE and isoelectric focusing after Coomassie brilliant blue staining). Amino acid sequencing indicated that the 20 N-terminal amino acid sequence of the three proteins was identical, suggesting that these proteins may be cognates of one EGase gene. An internal amino acid sequence of the the rice EGase (LVGGYYDAGDNVK) revealed that this enzyme belongs to glycosyl hydrolase family 9 (GHF9). The major isoform of this rice GHF9 [molecular weight based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS): 51,216, isoelectric point (pI): 5.5] specifically hydrolyzed 1,4-beta-glycosyl linkages of carboxymethyl (CM)-cellulose, phosphoric acid-swollen cellulose, 1,3-1,4-beta-glucan, arabinoxylan, xylan, glucomannan, cellooligosaccharides [with a degree of polymerization (DP) >3] and 1,4-beta-xylohexaose, indicating a broader substrate range compared with those of other characterized GHF9 enzymes or EGases from higher plants. Hydrolytic products of two major hemicellulosic polysaccharides in type II cell walls treated with the purified enzyme were profiled using high-performance anion exchange chromatography (HPAEC). The results suggested that endolytic attack by rice EGase is not restricted to either the cellulose-like domain of 1,3-1,4-beta-glucan or the unsubstituted 1,4-beta-xylosyl backbone of arabinoxylan, but results in the release of smaller oligosaccharides (DP <6) from graminaceous hemicelluloses. The comparatively broader substrate range of this EGase with respect to beta-1,4-glycan backbones (glucose and xylose) may partly reflect different roles of gramineous and non-gramineous GHF9 enzymes.     

A novel genetically engineered pathway for synthesis of poly(hydroxyalkanoic acids) in Escherichia coli

A new pathway to synthesize poly(hydroxyalkanoic acids) (PHA) was constructed by simultaneously expressing butyrate kinase (Buk) and phosphotransbutyrylase (Ptb) genes of Clostridium acetobutylicum and the two PHA synthase genes (phaE and phaC) of Thiocapsa pfennigii in Escherichia coli. The four genes were cloned into the BamHI and EcoRI sites of pBR322, and the resulting hybrid plasmid, pBPP1, conferred activities of all three enzymes to E. coli JM109. Cells of this recombinant strain accumulated PHAs when hydroxyfatty acids were provided as carbon sources. Homopolyesters of 3-hydroxybutyrate (3HB), 4-hydroxybutyrate (4HB), or 4-hydroxyvalerate (4HV) were obtained from each of the corresponding hydroxyfatty acids. Various copolyesters of those hydroxyfatty acids were also obtained when two of these hydroxyfatty acids were fed at equal amounts: cells fed with 3HB and 4HB accumulated a copolyester consisting of 88 mol% 3HB and 12 mol% 4HB and contributing to 68.7% of the cell dry weight. Cells fed with 3HB and 4HV accumulated a copolyester consisting of 94 mol% 3HB and 6 mol% 4HV and contributing to 64.0% of the cell dry weight. Cells fed with 3HB, 4HB, and 4HV accumulated a terpolyester consisting of 85 mol% 3HB, 13 mol% 4HB, and 2 mol% 4HV and contributing to 68.4% of the cell dry weight.     

Purification and characterization of a new hydrolase for conjugated bile acids, chenodeoxycholyltaurine hydrolase, from Bacteroides vulgatus

A new hydrolase for conjugated bile acids, tentatively named chenodeoxycholyltaurine hydrolase, was purified to homogeneity from Bacteroides vulgatus. This enzyme hydrolyzed taurine-conjugated bile acids but showed no activity toward glycine conjugates. Among the taurine conjugates, taurochenodeoxycholic acid was most effectively hydrolyzed, tauro-beta-muricholic and ursodeoxycholic acids were moderately well hydrolyzed, and cholic and 7 beta-cholic acids were hardly hydrolyzed, suggesting that this enzyme has a specificity for not only the amino acid moiety but also the steroidal moiety. The molecular weight of the enzyme was estimated to be approximately 140,000 by Sephacryl S-300 gel filtration and the subunit molecular weight of the enzyme was 36,000 by SDS-polyacrylamide gel electrophoresis. The optimum pH was in the range of 5.6 to 6.4. The NH2-terminal amino acid sequence of the enzyme was Met-Glu-Arg-Thr-Ile-Thr-Ile-Gln-Gln-Ile-Lys-Asp-Ala-Ala-Gln. The enzyme was activated by dithiothreitol, but inhibited by sulfhydryl inhibitors, p-hydroxymercuribenzoate, N-ethylmaleimide, and dithiodipyridine.     

Lysophosphatidic acids are new substrates for the phosphatase domain of soluble epoxide hydrolase

Soluble epoxide hydrolase (sEH) is a bifunctional enzyme that has a C-terminus epoxide hydrolase domain and an N-terminus phosphatase domain. The endogenous substrates of epoxide hydrolase are known to be epoxyeicosatrienoic acids, but the endogenous substrates of the phosphatase activity are not well understood. In this study, to explore the substrates of sEH, we investigated the inhibition of the phosphatase activity of sEH toward 4-methylumbelliferyl phosphate by using lecithin and its hydrolyzed products. Although lecithin itself did not inhibit the phosphatase activity, the hydrolyzed lecithin significantly inhibited it, suggesting that lysophospholipid or fatty acid can inhibit it. Next, we investigated the inhibition of phosphatase activity by lysophosphatidyl choline, palmitoyl lysophosphatidic acid, monopalmitoyl glycerol, and palmitic acid. Palmitoyl lysophosphatidic acid and fatty acid efficiently inhibited phosphatase activity, suggesting that lysophosphatidic acids (LPAs) are substrates for the phosphatase activity of sEH. As expected, palmitoyl, stearoyl, oleoyl, and arachidonoyl LPAs were efficiently dephosphorylated by sEH (Km, 3-7 μM; Vmax, 150-193 nmol/min/mg). These results suggest that LPAs are substrates of sEH, which may regulate physiological functions of cells via their metabolism.     

Metaviromics analysis of marine biofilm reveals a glycoside hydrolase endolysin with high specificity towards Acinetobacter baumannii

Multidrug-resistant (MDR) bacteria are a growing threat to the public health. Among them, the Gram-negative Acinetobacter baumannii is considered today as the most dangerous MDR pathogen. Phage-derived endolysins are peptidoglycan (PG) hydrolytic enzymes that can function as effective tools in the fight against MDR bacteria. In the present work, the viral diversity of a marine environmental sample (biofilm), formed near an industrial zone, was mined for the identification of a putative endolysin (AbLys2) that belongs to the glycoside hydrolase family 24 (GH24, EC 3.2.1.17). The coding sequence of AbLys2 was cloned and expressed in E. coli. The lytic activity and specificity of the recombinant enzyme were evaluated against suspensions of a range of Gram-positive and Gram-negative human pathogens using turbidity assays. AbLys2 displayed enhanced selectivity towards A. baumannii cells, compared to other bacteria. Kinetics analysis was carried out to characterize the dependence of its lytic activity on pH and showed that the enzyme exhibits its maximal activity at pH 5.5. Thermostability analysis showed that AbLys2 displays melting temperature T_m 47.1 °C. Florescence microscopy and cell viability assays established that AbLys2 is active towards live cultures of A. baumannii cells with an inhibitory concentration IC₅₀ 3.41 ± 0.09 μM. Molecular modeling allowed the prediction of important amino acid residues involved in catalysis. The results of the present study suggest that AbLys2 provides efficient lytic and antimicrobial activity towards A. baumannii cells and therefore is a promising new antimicrobial against this pathogen.     

A protocol for designing siRNAs with high functionality and specificity

Effective gene silencing by the RNA interference (RNAi) pathway requires a comprehensive understanding of the elements that influence small interfering RNA (siRNA) functionality and specificity. These include (i) sequence space restrictions that define the boundaries of siRNA targeting, (ii) structural and sequence features required for efficient siRNA performance, (iii) mechanisms that underlie nonspecific gene modulation and (iv) additional features specific to the intended use (i.e., inclusion of native sugar or base chemical modifications for increased stability or specificity, vector design, etc.). Attention to each of these factors enhances siRNA performance and heightens overall confidence in the output of RNAi-mediated functional genomic studies. Here, we provide a detailed protocol explaining the methodologies used for manual and web-based design of siRNAs.     

A DNA aptamer with high affinity and specificity for therapeutic anthracyclines

We describe the characterization of a DNA aptamer that displays high affinity and specificity for the anthracyclines daunomycin and doxorubicin, both of which are frequently used in chemotherapy. Aptamers were isolated from a pool of random sequences using a semiautomated procedure for magnetic beads. All selected aptamers displayed high affinity for the target molecule daunomycin. One aptamer was further characterized and exhibited a dissociation constant (KD) of 20 nM. To examine the aptamer's binding properties and clarify its applicability for diagnostic assays, its performance under various buffer conditions was evaluated. The aptamer proved to be very robust and not dependent on the presence of specific ions. It also tolerated a wide pH range and immobilization via 5'-biotinylation. Furthermore, a competition assay for sensitive daunomycin detection was established. This not only allows the determination of the aptamer's specificity but also allows the quantification of as little as 8.4 microg/L daunomycin and doxorubicin.     

Genetics of human S-adenosylhomocysteine hydrolase. A new polymorphism in man

Summary A specific staining procedure for the demonstration of S-adenosylhomocysteine hydrolase (SAAH, EC 3.3.1.1) is given. The enzyme has a broad tissue distribution and is also present in erythrocytes. The SAHH gene is polymorphic in the population of southwest Germany with two common alleles: SAHH ^*1=0.96 and SAHH ^*1=0.04. Family studies resulted in the expected segregation ratios. No evidence for close linkage with a total of 25 marker loci was found. But information from human mouse somatic-cell hybrids led to the localization of the SAHH gene to human chromosome 20, thereby confirming the findings of Hershfield and Francke (1982).Dedicated to Professor Dr. P. E. Becker on the occasion of his 75th birthday     

Expression and characterization of an epoxide hydrolase from Anopheles gambiae with high activity on epoxy fatty acids

In insects, epoxide hydrolases (EHs) play critical roles in the metabolism of xenobiotic epoxides from the food resources and in the regulation of endogenous chemical mediators, such as juvenile hormones. Using the baculovirus expression system, we expressed and characterized an epoxide hydrolase from Anopheles gambiae (AgEH) that is distinct in evolutionary history from insect juvenile hormone epoxide hydrolases (JHEHs). We partially purified the enzyme by ion exchange chromatography and isoelectric focusing. The experimentally determined molecular weight and pI were estimated to be 35 kD and 6.3 respectively, different than the theoretical ones. The AgEH had the greatest activity on long chain epoxy fatty acids such as 14,15-epoxyeicosatrienoic acids (14,15-EET) and 9,10-epoxy-12Z-octadecenoic acids (9,10-EpOME or leukotoxin) among the substrates evaluated. Juvenile hormone III, a terpenoid insect growth regulator, was the next best substrate tested. The AgEH showed kinetics comparable to the mammalian soluble epoxide hydrolases, and the activity could be inhibited by AUDA [12-(3-adamantan-1-yl-ureido) dodecanoic acid], a urea-based inhibitor designed to inhibit the mammalian soluble epoxide hydrolases. The rabbit serum generated against the soluble epoxide hydrolase of Mus musculus can both cross-react with natural and denatured forms of the AgEH, suggesting immunologically they are similar. The study suggests there are mammalian sEH homologs in insects, and epoxy fatty acids may be important chemical mediators in insects.     

Alteration of substrate chain-length specificity of type II synthase for polyhydroxyalkanoate biosynthesis by in vitro evolution: in vivo and in vitro enzyme assays

In our previous study, in vitro evolution of type II polyhydroxyalkanoate (PHA) synthase (PhaC1Ps) from Pseudomonas sp. 61-3 yielded eleven mutant enzymes capable of synthesizing homopolymer of (R)-3-hydroxybutyrate [P(3HB)] in recombinant Escherichia coli JM109. These recombinant strains were capable of accumulating up to approximately 400-fold more P(3HB) than strains expressing the wild-type enzyme. These mutations enhanced the ability of the enzyme to specifically incorporate the 3HB-coenzyme A (3HB-CoA) substrate or improved catalytic efficiency toward the various monomer substrates of C4 to C12 (R)-3-hydroxyacyl-CoAs which can intrinsically be channeled by PhaC1Ps into P(3HB-co-3HA) copolymerization. In this study, beneficial amino acid substitutions of PhaC1Ps were analyzed based on the accumulation level and the monomer composition of P(3HB-co-3HA) copolymers generated by E. coli LS5218 [fadR601 atoC(Con)] harboring the monomer supplying enzyme genes. Substitutions of Ser by Thr(Cys) at position 325 were found to lead to an increase in the total amount of P(3HB-co-3HA) accumulated, whereas 3HB fractions in the P(3HB-co-3HA) copolymer were enriched by substitutions of Gln by Lys(Arg, Met) at position 481. This strongly suggests that amino acid substitutions at positions 325 and 481 are responsible for synthase activity and/or substrate chain-length specificity of PhaC1Ps. These in vivo results were supported by the in vitro results obtained from synthase activity assays using representative single and double mutants and synthetic substrates, (R,S)-3HB-CoA and (R,S)-3-hydroxydecanoyl-CoA. Notably, the position 481 was found to be a determinant for substrate chain-length specificity of PhaC1Ps.     

Recombinant aprotinin homologue with new inhibitory specificity for cathepsin G.

The substitution of amino acids in the reactive site of aprotinin, a bovine serine proteinase inhibitor with potent activity against trypsin, plasmin and tissue kallikrein, led to a change in specificity of the inhibitor. Twelve new aprotinin variants prepared by recombinant DNA technology and expressed in Escherichia coli clearly demonstrated that the neighbouring groups of the P1 residue, in particular P'2, contribute to the specificity of the inhibitor, while earlier investigations on semisynthetically prepared variants revealed the importance of the P1 residue in dominating the inhibitory specificity. Recombinant aprotinin variants which act specifically against chymotrypsin-like proteinases, were obtained by substitution of the amino acids in position P1 and P'2 by hydrophobic amino acids like phenylalanine, tyrosine and leucine. Some of these variants, particularly those with phenylalanine or leucine substitutions, were also found to exhibit inhibitory activity against cathepsin G with an equilibrium constant of dissociation Ki of 10(-8) M. Inhibitory specificity against cathepsin G was not found in any semisynthetic variant prepared earlier.     

A quantum-theoretic approach to enzyme specificity: Proposals for a new type of biochemical control mechanism

A quantum-theoretic approach to the problem of enzymic specificity is presented. The concept of a “measuring system” analogized with the enzyme is utilized. Along these lines a quantum mechanical hypothesis for the mechanism of enzyme reactions was advanced (Enzymologia,35, 117–130, 1968). In the measuring process an ℐ-observable, linked to the proper values of the substrate'sA ₁...A _m observables will indicate the state of the measuring apparatus. On the corresponding Hilbert space of the enzymesubstrate complexH _ES , through the respective statistical operatorU _ES we get a “state” vector [s, a]. Theng:Γ _S xΓ _E →Γ _ES , that is, to an oriented pair 〈s, a〉 ∈Γ _S xΓ _E will correspond a “state” vector [s, a], and to a proper valuei _k of ℐ will correspond, throughg, the respective equivalence classes of Г-spaces. Introducing the concept of enzyme-substrate complex entropyL _ES , a theorem is demonstrated asserting thatL _S =L _ES -L _E + 1/2kn wheren is the number of the degrees of freedom which may fluctuate. The values ofL _ES are denoted “specific values,” and it is demonstrated that a microphysical systemS may be a substrate specific forE, if and only if it can realize one of theL _ES specific values. Along these lines a model of a stochastic process for the enzymic reaction is constructed, and the set of Kolmogorov equations for the respective probabilities is derived. When a “perturbation” is induced in our model, an interesting prediction concerning the fluctuations in the kinetics of the corresponding enzyme is obtained. A relevant experimental proof ensued from these theoretical considerations. When a “gentle perturbation” was induced in a substrate by mild X-ray or UV-irradiations, an interesting oscillatory behavior of enzymic activity was recorded. A biochemical control mechanism is constructed (a simple “flip-flop” type) utilizing nonoverlapping oscillations in the activity of two enzymes at a key metabolic intermediate level. Eventually, a relevant experimental proof for the respective control model is presented.     

A new method for the purification of DNA-binding proteins with sequence specificity

We describe a technique for a rapid and efficient isolation and purification of proteins binding to defined DNA sequences. Cloned double-stranded DNA was covalently coupled to m-aminobenzyloximethylcellulose in order to purify proteins which recognize and bind to specific sequences on the DNA. The purification of two DNA-binding proteins from Drosophila melanogaster is demonstrated using the respective cloned DNA sequences.     

A novel bovine spinal cord endoprotease with high specificity for dynorphin B

An endopeptidase that converts the opioid peptide dynorphin B (Tyr-Gly-Gly-Phe-Leu-Arg-aRg-Gln-Phe-Lys-Val-Val-Thr) to its bioactive fragment Leu-enkephalin-Arg6 was isolated from bovine spinal cord. The enzyme was purified about 230-fold from a concentrated spinal cord extract. Upon sodium dodecyl sulfate-polyacrylamide gel electrophoresis, it stained as a protein of Mr 55,000. The purified enzyme is optimally active at around pH7 and has essential thiol groups. It appears to be highly specific for dynorphin B (Km = 11 microM) but not for alpha-neoendorphin or dynorphin A, two other opioids included in the prodynorphin precursor. From its specificity, molecular size, and inhibitory spectrum, this enzyme is different from other known dynorphin-converting or -degrading enzymes and appears to be a unique and novel endoprotease.     

Thromboplastin. A short review of new findings]

Recent findings of thromboplastin (TRPL) investigations are presented in a brief survey. After enumerating the possibilities of separating this lipoprotein into two shares, the chemical characterization of protein and lipid fraction is represented, the possibilities and conditions of recombining both shares are mentioned and the effectiveness of TRPL in the exogenous coagulation system is illustrated. Furthermore, the liberation of TRPL by leukocytes is referred to and feasible mechanisms of this liberation are discussed. Finally the relations of TRPL to tumour cell materials promoting coagulation and from amnion liquid are discussed.