Simultaneous Biodegradation of Polyaromatic Hydrocarbons by a <Emphasis Type="Italic">Stenotrophomonas</Emphasis> sp: Characterization of <Emphasis Type="Italic">nid</Emphasis> Genes and Effect of Surfactants on Degradation

A polyaromatic hydrocarbon degrading bacterium was isolated from a petroleum contaminated site and designated as Stenotrophomonas sp. strain IITR87. It was found to utilize pyrene, phenanthrene and benzo(a)pyrene as sole carbon source, but not anthracene, chrysene and fluoranthene. Gas chromatography and mass spectroscopy analysis resulted in identification of pyrene metabolites namely monohydroxypyrene, 4-oxa-pyrene-5-one, dimethoxypyrene and monohydroxyphenanthrene. Southern hybridization using naphthalene dioxygenase gene (nidA) as probe against the DNA of strain IITR87 revealed the presence of nidA gene. PCR analysis suggests dispersed occurrence of nid genes in the genome instead of a cluster as reported in a PAH-degrading Mycobacterium vanbaalenii PYR-1. The nid genes in strain IITR87, dioxygenase large subunit (nidA), naphthalene dioxygenase small subunit (nidB) and aldehyde dehydrogenase gene (nidD) showed more than 97 % identity to the reported nid genes from Mycobacterium vanbaalenii PYR-1. Most significantly, the biodegradation of PAHs was enhanced 25–60 % in the presence of surfactants rhamnolipid and Triton X-100 due to increased solubilization and bioavailability. These results could be useful for the improved biodegradation of high-molecular-weight PAHs in contaminated habitats.     

A procedure for isolation of human protein C and protein S as by-products of the purification of factors VII, IX, X and prothrombin

A DEAE-Sephadex column chromatography step utilized to purify human Factor VII consistently yields a protein peak between the factor VII activity peak and prothrombin, factor X and factor IX activity peak (S.P. Bajaj, S.I. Rapaport, and S.F. Brown: J. Biol. Chem. 251, 253-259, 1981). We now report that this protein peak contains protein C and protein S. Preparative disc polyacrylamide gel electrophoresis of the proteins in this peak permitted a complete separation of protein C from protein S. Protein C at this step usually contained approximately 5-10% of Factor X, which could be removed by a goat anti-human Factor X antibody column. For a typical preparation, starting with 10L of plasma, the yield of Protein C was 5 mg and of protein S was 4 mg. Both proteins revealed apparent homogeneity in sodium dodecyl sulfate gel electrophoretic system. beta-Protein C and beta-protein S were not observed in our preparations starting with plasma collected directly into citrate anticoagulant containing benzamidine and soybean trypsin inhibitor, suggesting that these beta forms of protein C and protein S, isolated by other investigators, are slightly degraded forms of the native proteins. Antisera generated to these proteins were monospecific and could be used to monitor column fractions during purification. When examined by immunoelectrophoresis, the electrophoretic mobility of protein S in plasma was slower than that of isolated protein S. When exposed to plasmin, protein C was activated slightly and then rapidly degraded.     

Directed evolution of cellobiose utilization in Escherichia coli K12

The cellobiose catabolic system of Escherichia coli K12 is being used to study the role of cryptic genes in evolution of new functions. Escherichia coli does not use beta-glucoside sugars; however, mutations in several loci can activate the cryptic bgl operon and permit growth on the beta-glucoside sugars arbutin and salicin. Such Bgl+ mutants do not use cellobiose, which is the most common beta-glucoside in nature. We have isolated a Cel+ (cellobiose-utilizing) mutant from a Bgl+ mutant of E. coli K12. The Cel+ mutant grows well on cellobiose, arbutin, and salicin. Genes for utilization of these beta-glucosides are located at 37.8 min on the E. coli map. The genes of the bgl operon are not involved in cellobiose utilization. Introduction of a deletion covering bgl does not affect the ability to utilize cellobiose, arbutin, or salicin, indicating that the new Cel+ genes provide all three functions. Spontaneous cellobiose negative mutants also become arbutin and salicin negative. Analysis of beta-glucoside positive revertants of these mutants indicates that there are separate loci for utilization of each of the beta-glucoside sugars. The genes are closely linked and may be activated from a single locus. A fourth gene at an unknown location increases the growth rate on cellobiose. The cel genes constitute a second cryptic system for beta-glucoside utilization in E. coli K12.      

Experimental and theoretical evidence supporting the role of Gly363 in blood coagulation factor IXa (Gly193 in chymotrypsin) for proper activation of the proenzyme

Factor IX is the zymogen of the serine protease factor IXa involved in blood coagulation. In addition to a catalytic domain homologous to the chymotrypsin family, it has Ca2+, phospholipid, and factor VIIIa binding regions needed for full biologic activity. We isolated a nonfunctional factor IX protein designated factor IXEagle Rock (IXER) from a patient with hemophilia B. The variant protein is indistinguishable from normal factor IX (IXN) in its migration on sodium dodecyl sulfate-gel electrophoresis, isoelectric point in urea, carbohydrate content and distribution, number of gamma-carboxyglutamic acid residues, and beta-OH aspartic acid content, and in its binding to an anti-IXN monoclonal antibody which has been shown previously to inhibit the interaction of factor VIIIa with factor IXaN. Further, IXER is cleaved to yield a factor IXa-like molecule by factor XIa/Ca2+ at a rate similar to that observed for IXN. However, in contrast to IXaN, IXaER does not bind to antithrombin-III (specific inhibitor of IXaN) and does not catalyze the activation of factor X (substrate) to factor Xa. To identify the mutation in IXER, all eight exons of IXN and IXER gene were amplified by the polymerase chain reaction technique and cloned. A single point mutation (G----T) which results in the replacement of Val for Gly363 in the catalytic domain of IXER was identified. Gly363 in factor IXa corresponds to the universally conserved Gly193 in the active site sequence of the chymotrypsin serine protease family. X-ray crystallographic data in the literature demonstrate a critical role of this Gly in stabilizing the active conformation of chymotrypsin/trypsin in two major ways: 1) in the formation of the substrate binding site; and 2) in the development of the oxyanion hole. Our computer structural data support a concept that the Gly363----Val change prevents the development of the active site conformation in factor IXa such that the substrate binding site and the oxyanion hole are not formed in the mutated enzyme.     

EFFECT OF DIMETHYL SULFOXIDE ON ZINC65 UPTAKE,RESPIRATION, AND RNA AND PROTEIN METABOLISM IN BEAN (PHASEOLUS VULGARIS) TISSUES

The effect of dimethyl sulfoxide (DMSO) on zinc⁶⁵ uptake, respiration, RNA, and protein metabolism in various tissues of two bean (Phaseolus vulgaris L.) cultivars showing differential growth responses to zinc has been studied. At a concentration of 1%, DMSO stimulated zinc uptake in excised roots, stem-callus tissue, leaf disks, and enzymically isolated leaf cells, but did not significantly alter the uptake and incorporation of C¹⁴-uracil into RNA and C¹⁴-methionine into protein, although a slight inhibition was discernible in some tissues. At a higher concentration (10%) DMSO increased Zn⁶⁵ uptake in excise roots incubated for 2 hr; however, at the same concentration, C¹⁴-uracil and C¹⁴-methionine uptake and incorporation were considerably inhibited in all the tissues. Oxygen uptake as measured with Warburg manometers was impaired, and the inhibition showed a time and concentration dependency. The fact that DMSO inhibited respiration and RNA and protein metabolism, while at the same concentration zinc uptake was increased, suggests that zinc uptake in beans is primarily a non-metabolic process. The possible mechanisms of DMSO action are discussed in the light of its reported effects on membrane permeability and cell metabolism.     

Stoichiometry of binding of high molecular weight kininogen to factor XI/XIa

Factor XI is a dimeric protein and circulates in plasma complexed with high molecular weight kininogen (HMWK). We investigated the binding of HMWK to factor XIa utilizing two active site directed fluorescent probes: nitrobenzoxadiazole aminopentyl methylphosphonofluoridate for serine and dansyl-glu-gly-arg-chloromethyl ketone for histidine. In the presence of saturating amounts of HMWK, the fluorescence of factor XIa-fluorophore was quenched by approximately 28% for each probe. Titrations of the fluorescent factor XIa with HMWK revealed that each subunit of factor XIa binds one molecule of HMWK with a Kd approximately 3.4 X 10(-8)M.     

Differential inhibition of adenosine deaminase deficient peripheral blood lymphocytes and lymphoid line cells by deoxyadenosine and adenosine.

The response to mitogens of peripheral blood lymphocytes (PBL) from adenosine deaminase deficient (ADA^?) patients with Severe Combined Immunodeficiency (SCID), but not from normals, was more sensitive to inhibition by deoxyadenosine than by adenosine. In contrast, proliferation of long-term lymphoid line (B) cells from these patients was essentially equally inhibited by adenosine and deoxyadenosine. Deoxycytidine could “rescue” ADA^? PBLs from deoxyadenosine toxicity.     

Continuum diffusion reaction rate calculations of wild-type and mutant mouse acetylcholinesterase: adaptive finite element analysis

As described previously, continuum models, such as the Smoluchowski equation, offer a scalable framework for studying diffusion in biomolecular systems. This work presents new developments in the efficient solution of the continuum diffusion equation. Specifically, we present methods for adaptively refining finite element solutions of the Smoluchowski equation based on a posteriori error estimates. We also describe new, molecular-surface-based models, for diffusional reaction boundary criteria and compare results obtained from these models with the traditional spherical criteria. The new methods are validated by comparison of the calculated reaction rates with experimental values for wild-type and mutant forms of mouse acetylcholinesterase. The results show good agreement with experiment and help to define optimal reactive boundary conditions.     

Structure-function analysis of the reactive site in the first Kunitz-type domain of human tissue factor pathway inhibitor-2

Human tissue factor pathway inhibitor-2 (TFPI-2) is a Kunitz-type proteinase inhibitor that regulates a variety of serine proteinases involved in coagulation and fibrinolysis through their non-productive interaction with a P(1) residue (Arg-24) in its first Kunitz-type domain (KD1). Previous kinetic studies revealed that TFPI-2 was a more effective inhibitor of plasmin than several other serine proteinases, but the molecular basis for this specificity was unclear. In this study, we employed molecular modeling and mutagenesis strategies to produce several variants of human TFPI-2 KD1 in an effort to identify interactive site residues other than the P(1) Arg that contribute significantly to its inhibitory activity and specificity. Molecular modeling of KD1 based on the crystal structure of bovine pancreatic trypsin inhibitor revealed that KD1 formed a more energetically favorable complex with plasmin versus trypsin and/or the factor VIIa-tissue factor complex primarily due to strong ionic interactions between Asp-19 (P(6)) and Arg residues in plasmin (Arg-644, Arg-719, and Arg-767), Arg-24 (P(1)) with Asp-735 in plasmin, and Arg-29 (P(5)') with Glu-606 in plasmin. In addition, Leu-26 through Leu-28 (P(2)'-P(4)') in KD1 formed strong van der Waals contact with a hydrophobic cluster in plasmin (Phe-583, Met-585, and Phe-587). Mutagenesis of Asp-19, Tyr-20, Arg-24, Arg-29, and Leu-26 in KD1 resulted in substantial reductions in plasmin inhibitory activity relative to wild-type KD1, but the Asp-19 and Tyr-20 mutations revealed the importance of these residues in the specific inhibition of plasmin. In addition to the reactive site residues in the P(6)-P(5)' region of KD1, mutation of a highly conserved Phe at the P(18)' position revealed the importance of this residue in the inhibition of serine proteinases by KD1. Thus, together with the P(1) residue, the nature of other residues flanking the P(1) residue, particularly at P(6) and P(5)', strongly influences the inhibitory activity and specificity of human TFPI-2.