PAH utilization by Pseudomonas rhodesiae KK1 isolated from a former manufactured-gas plant site

Pseudomonas rhodesiae KK1 was isolated from a former manufactured-gas plant site, due to its ability to grow rapidly in a mixture of polycyclic aromatic hydrocarbons (PAHs). Radiorespirometric analysis revealed that strain KK1 was found to be able to mineralize anthracene, naphthalene and phenanthrene. Notably, phenanthrene-grown cells were able to mineralize anthracene much more rapidly than naphthalene-grown cells. Comparative analysis of amino acid sequences from 17 randomly selected dioxygenases capable of hydroxylating unactivated aromatic nuclei indicated that the enzymes for catabolism of PAHs, such as naphthalene and phenanthrene, might exist redundantly in strain KK1. Northern hybridization for cells grown on naphthalene or phenanthrene, using the putative naphthalene or phenanthrene dioxygenase gene fragment as a probe, suggested that the enzyme for naphthalene catabolism might share some homology in deduced amino acid sequences with phenanthrene dioxygenases. Also, it was found that three lipids (17:0 cyclo, 18:1 omega7c, 19:0 cyclo) increased in response to both naphthalene and phenanthrene, while the shift of other lipids varied from substrate to substrate.     

Lysosomal prenylcysteine lyase is a FAD-dependent thioether oxidase

Prenylated proteins contain either a 15-carbon farnesyl or a 20-carbon geranylgeranyl isoprenoid covalently attached via a thioether bond to a cysteine residue at or near their C terminus. As prenylated proteins comprise up to 2% of the total protein in eukaryotic cells, and the thioether bond is a stable modification, their degradation raises a metabolic challenge to cells. A lysosomal enzyme termed prenylcysteine lyase has been identified that cleaves prenylcysteines to cysteine and an unidentified isoprenoid product. Here we show that the isoprenoid product of prenylcysteine lyase is the C-1 aldehyde of the isoprenoid moiety (farnesal in the case of C-15). The enzyme requires molecular oxygen as a cosubstrate and utilizes a noncovalently bound flavin cofactor in an NAD(P)H-independent manner. Additionally, a stoichiometric amount of hydrogen peroxide is produced during the reaction. These surprising findings indicate that prenylcysteine lyase utilizes a novel oxidative mechanism to cleave thioether bonds and provide insight into the unique role this enzyme plays in the cellular metabolism of prenylcysteines.     

Molecular recognition of the substrate diphosphate group governs product diversity in trichodiene synthase mutants

The X-ray crystal structures of Y305F trichodiene synthase and its complex with coproduct inorganic pyrophosphate (PP(i)) and of Y305F and D100E trichodiene synthases in ternary complexes with PP(i) and aza analogues of the bisabolyl carbocation intermediate are reported. The Y305F substitution in the basic D(302)RRYR motif does not cause large changes in the overall structure in comparison with the wild-type enzyme in either the uncomplexed enzyme or its complex with PP(i). However, the loss of the Y305F-PP(i) hydrogen bond appears to be compensated by a very slight shift in the position of the side chain of R304. The putative bisabolyl carbocation mimic, R-azabisabolene, binds in a conformation and orientation that does not appear to mimic that of the actual carbocation intermediate, suggesting that the avid inhibition by R- and S-azabisabolenes arises more from favorable electrostatic interactions with PP(i) rather than any special resemblance to a reaction intermediate. Greater enclosed active-site volumes result from the Y305F and D100E mutations that appear to confer greater variability in ligand-binding conformations and orientations, which results in the formation of aberrant cyclization products. Because the binding conformations and orientations of R-azabisabolene to Y305F and D100E trichodiene synthases do not correspond to binding conformations required for product formation and because the binding conformations and orientations of diverse substrate and carbocation analogues to other cyclases such as 5-epi-aristolochene synthase and bornyl diphosphate synthase generally do not correspond to catalytically productive complexes, we conclude that the formation of transient carbocation intermediates in terpene cyclization reactions is generally under kinetic rather than thermodynamic control.     

Characterization of a thermostable L-arabinose (D-galactose) isomerase from the hyperthermophilic eubacterium Thermotoga maritima

The araA gene encoding L-arabinose isomerase (AI) from the hyperthermophilic bacterium Thermotoga maritima was cloned and overexpressed in Escherichia coli as a fusion protein containing a C-terminal hexahistidine sequence. This gene encodes a 497-amino-acid protein with a calculated molecular weight of 56,658. The recombinant enzyme was purified to homogeneity by heat precipitation followed by Ni(2+) affinity chromatography. The native enzyme was estimated by gel filtration chromatography to be a homotetramer with a molecular mass of 232 kDa. The purified recombinant enzyme had an isoelectric point of 5.7 and exhibited maximal activity at 90 degrees C and pH 7.5 under the assay conditions used. Its apparent K(m) values for L-arabinose and D-galactose were 31 and 60 mM, respectively; the apparent V(max) values (at 90 degrees C) were 41.3 U/mg (L-arabinose) and 8.9 U/mg (D-galactose), and the catalytic efficiencies (k(cat)/K(m)) of the enzyme were 74.8 mM(-1).min(-1) (L-arabinose) and 8.5 mM(-1).min(-1) (D-galactose). Although the T. maritima AI exhibited high levels of amino acid sequence similarity (>70%) to other heat-labile mesophilic AIs, it had greater thermostability and higher catalytic efficiency than its mesophilic counterparts at elevated temperatures. In addition, it was more thermostable in the presence of Mn(2+) and/or Co(2+) than in the absence of these ions. The enzyme carried out the isomerization of D-galactose to D-tagatose with a conversion yield of 56% for 6 h at 80 degrees C.     

Mutagenesis of the glucoamylase signal peptide of Saccharomyces diastaticus and functional analysis in Saccharomyces cerevisiae

To improve the efficiency of the glucoamylase signal peptide (GSP) of Saccharomyces diastaticus for the secretion of foreign proteins, hybrid plasmids containing one of four types of GSP mutant (m1, Pro(-18)-->Leu(-18); m2, Tyr(-13)-->Leu(-13); m3, Ser(-9)-->Leu(-9); m4, Asn(-5)-->Pro(-5)) were constructed and evaluated in Saccharomyces cerevisiae using Bacillus endo-1,4-beta-D-glucanase (CMCase) as a reporter gene. CMCase secretion by m1, m2 and m3 GSP mutants was increased, likely resulting from a higher probability of the modified GSP to assume an alpha-helical structure. Especially in the case of m3, the substitution of Leu for a polar residue, Ser(-9), in the hydrophobic region resulted in approximately a twofold increase in extracellular CMCase activity. In mutant 4, which disrupts the alpha-helix of GSP, CMCase was less efficiently secreted.     

Adaptive optimization of a continuous culture with the use of a bilevel forgetting factor

An adaptive optimization algorithm using a dynamic identification scheme with a bilevel forgetting factor (BFF) has been developed. The simulation results show superiority of this method to other methods when applied to maximize the cellular productivity of a continuous culture of baker's yeast, Saccharomyces cerievisiae. Within the limited ranges of tuning parameters tested the BFF algorithm is found to be superior in terms of initial optimization speed and accuracy and reoptimization speed and accuracy when there is an external change and long term stability (removal of "blowing up" phenomena). Algorithms tested include those based on a constant forgetting factor, an adaptive variable forgetting factor (VFF) and moving window (MW) identification.     

Effects of acanthoic acid on TNF-alpha gene expression and haptoglobin synthesis.

Tumour necrosis factor-alpha (TNF-alpha) is a major pro-inflammatory cytokine inducing the synthesis and release of many inflammatory mediators. It is involved in immune regulation, autoimmune diseases, and inflammation. Our previous study demonstrated that acanthoic acid, (-)-pimara-9(11), 15-dien-19-oic acid, a pimaradiene diterpene isolated from Acanthopanax koreanum, inhibited TNF-alpha production. To extend our understanding of inhibitory effects of acanthoic acid on TNF-alpha production, its effects on TNF-alpha gene expression was tested. Based on the results from RT-PCR and promoter analysis of TNF-alpha, it was found that acanthoic acid suppressed TNF-alpha gene expression. But the same concentration of acanthoic acid had no effect on IL-6 gene expression. Haptoglobin is an acute phase protein which is induced by TNF-alpha. When liver cells were treated with acanthoic acid, haptoglobin synthesis was blocked by acanthoic acid. These data confirmed that acanthoic acid inhibited gene expression and biological function of TNF-alpha.     

IL-6 Undergoes Transition from in vitro Autocrine Growth Factor toin vivo Growth Inhibitor of B Lymphoma Cells

IL-6 is a multifunctional cytokine involved in differentiation and proliferation of immune cells. Moreover, it has diverse effects on the proliferation of tumor cells in vivo and in vitro. Although stimulating cell growth of multiple myeloma cells, it inhibits the proliferation of B16 melanoma cells and lung cancer cells. B9.55 cells, B-cell lymphoma, are IL-6-dependent cells, definitely requiring exogenous IL-6 for growth. When the cDNA for IL-6 was transfected into B9.55 cells, they began growing in an autocrine pattern without exogenous IL-6. To investigate the effects of IL-6 on B9.55 lymphoma in vivo, IL-6-transfected B9.55 cells (B9.G7) or neotransfected B9.55 cells (B9.vec) were injected subcutaneously into syngeneic mice. Initially, B9.G7 outgrew B9.vec, but after 3 weeks, B9.G7 grew slower than B9.vec. In addition, 5 µg of recombinant human IL-6 was injected daily into the tumor site. Reduced tumor sizes of IL-6-treated rats, similar to those observed in mice which received B9.G7, indicated that IL-6 itself is the mediator of tumor regression. When B9.G7 cells were injected into the irradiated normal mice, tumor regression was released compared with the untreated normal control, suggesting that radiosensitive host components were involved in the regression of B9.G7 cell growth. However, the tumor regression of B9.G7 cells was not released in SCID mice. Histologically, B9.G7 tumor demonstrated severe necrosis and apoptotic cells with infiltration of host inflammatory cells. Above data indicate that IL-6 functions as an autocrine growth factor for B9.G7 cells in vitro, but behaves as an autocrine inhibiting factor in vivo. These contrasting effects of IL-6 on tumor cells in vitro and in vivo will be facilitative in understanding the interaction of cytokines and host immune systems.They have contributed equally to this work.     

Antitumor effects of IL-6 on murine liver tumor cells in vivo

IL-6 is a pleiotropic cytokine that is capable of modulating the diverse functions of hepatocytes such as acute phase responses and inflammation in the liver. To learn its antitumor effects in vivo, the cDNA of IL-6 was transfected into murine liver cells, TIB cells. IL-6-transfected TIB cells (TIB73-IL-6 or TIB75-IL-6) produced much higher levels of IL-6 compared with vector-transfected TIB cells (TIB73-vec or TIB75-vec). To investigate the effects of IL-6 on TIB tumor growth in vivo, IL-6-transfected TIB cells or vector-transfected TIB cells were injected subcutaneously into syngeneic mice. Vector-transfected TIB cells grew rapidly 3 weeks after injection, but IL-6-transfected TIB cells did not grow at all for up to 6 weeks. Pathologically, IL-6-transfected TIB cells demonstrated a severe necrosis and apoptotic pattern. Taken together, these results indicate that IL-6 functions as a growth inhibiting factor in vivo, and another biological role of IL-6 in the liver is suggested.     

Serotonergic genes and amygdala activity in response to negative affective facial stimuli in Korean women

Serotonergic genes have been implicated in mood disorders, alcoholism and certain personality traits. We investigated the possible relationship between several polymorphisms in the serotonin (5-HT) system and amygdala responses to negative facial stimuli in Korean women using functional magnetic resonance imaging. All participants were genotyped with regard to the following polymorphisms: the serotonin transporter-gene-linked polymorphic region (5-HTTLPR), tryptophan hydroxylase 2 (TPH2) G(-703)T, 5-HT(1A) C(-1019)G and 5-HT(2A) single nucleotide polymorphism (SNP) rs6311. We found increased activations in response to angry facial stimuli in the bilateral amygdala of subjects with the long allele of 5-HTTLPR compared with those with two copies of the short allele. Higher activations in response to sad facial stimuli were found in the bilateral amygdala of subjects with the T/T genotype of 5-HT(2A) SNP rs6311, compared with C allele carriers, and in subjects with the G/G genotype of TPH2 G(-703)T, compared with those with T/T and G/T genotypes. Our results for individuals from an Asian population countered a previous finding for a Caucasian population and identified the moderating role of genetic background in the relationships between these serotonergic gene polymorphisms and amygdala function elicited by negative emotional stimuli.