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Degradation Pathway (degradation + pathway)
Kinds of Degradation Pathway Selected AbstractssiRNA-mediated Knockdown of the Heme Synthesis and Degradation Pathways: Modulation of Treatment Effect of 5-Aminolevulinic Acid-based Photodynamic Therapy in Urothelial Cancer Cell LinesPHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 4 2009Makito Miyake Photodynamic therapy mediated by 5-aminolevulinic acid (ALA-PDT) has been developed as a therapeutic modality for refractory superficial bladder cancers. Here, in experiments using urothelial cancer cell lines, we investigated the effects of siRNA modulating heme-synthetic and degradation pathways for ALA-PDT. Targeted knockdown of ferrochelatase (FECH) suppressed heme synthesis and significantly increased intracellular protoporphyrin IX (PpIX) accumulation, leading to enhanced phototoxicity in four of five cell lines. Heme oxygenase-1 (HO-1) is recognized as important for cytoprotection against oxidative stress such as PDT. Targeted knockdown of HO-1 leads to decreased intracellular PpIX accumulation, resulting in a failure to enhance ALA-PDT effect in four cell lines. Knockdown of HO-1 caused marked growth inhibition in UM-UC-2 overexpressing HO-1, whereas no inhibitory effect was observed in UM-UC-3 lacking HO-1 expression. Moreover, HO-1 protein levels and (GT)n repeat polymorphism of the HO-1 gene promoter region were examined with the implication that the constitutive expressions of HO-1 protein were associated with a shorter (GT)n repeat. Our results suggested that (1) FECH siRNA improved the phototoxicity of ALA-PDT, (2) overexpression of HO-1 was associated with shorter (GT)n repeat of the promoter region, and (3) siRNA-mediated knockdown of HO-1 could suppress the growth of bladder cancer cells overexpressing HO-1. [source] Transcription dynamics of the functional tfdA gene during MCPA herbicide degradation by Cupriavidus necator AEO106 (pRO101) in agricultural soilENVIRONMENTAL MICROBIOLOGY, Issue 3 2008Mette Haubjerg Nicolaisen Summary A modified protocol for simultaneous extraction of RNA and DNA, followed by real-time polymerase chain reaction quantification, was used to investigate tfdA gene expression during in situ degradation of the herbicide MCPA (4-chloro-2-methylphenoxy-acetic acid) in soil. tfdA encodes an ,-ketoglutarate-dependent dioxygenase catalysing the first step in the degradation pathway of MCPA and 2,4-D (2,4-dichlorophenoxy-acetic acid). A linear recovery of tfdA mRNA over three orders of magnitude was shown, and the tfdA mRNA level was normalized using the tfdA mRNA/DNA ratio. The density of active cells required for tfdA mRNA detection was 105 cells g,1 soil. Natural soil microcosms inoculated with Cupriavidus necator (formerly Ralstonia eutropha) AEO106 (pRO101) cells were amended with four different MCPA concentrations (2, 20, 50 and 150 mg kg,1). Mineralization rates were estimated by quantification of 14CO2 emission from degradation of 14C-MCPA. tfdA mRNA was detected 1 h after amendment at all four concentrations. In soils amended with 2 and 20 mg kg,1, the mRNA/DNA ratio for tfdA demonstrated a sharp transient maximum of tfdA expression from no to full expression within 3 and 6 h respectively, followed by a decline and complete loss of expression after 19 and 43 h. A more complex pattern of tfdA expression was observed for the higher 50 and 150 mg kg,1 amendments; this coincided with growth of C. necator AEO106 (pRO101) in the system. Repeated amendment with MCPA after 2 weeks in the 20 mg kg,1 scenario revealed a sharp increase of tfdA mRNA, and absence of a mineralization lag phase. For all amendments, tfdA mRNA was detectable only during active mineralization, and thus revealed a direct correlation between tfdA mRNA presence and microbial degrader activity. The present study demonstrates that direct analysis of functional gene expression dynamics by quantification of mRNA can indeed be made in natural soil. [source] Development and application of polymerase chain reaction primers based on fhcD for environmental detection of methanopterin-linked C1 -metabolism in bacteriaENVIRONMENTAL MICROBIOLOGY, Issue 8 2005Marina G. Kalyuzhnaya Summary In this work we describe development and testing of a novel pair of environmental primers targeting fhcD, a conserved gene in the H4MTP-linked C1 -transfer pathway, and demonstrate that these primers enable confident detection of a broad variety of fhcD genes originating from phylogenetically diverse bacteria. The new primer pair was employed to analyse fhcD diversity in Lake Washington sediment, uncovering the presence of 40 fhcD phylotypes. Based on phylogenetic analyses, the phylotypes identified were affiliated with ,-, ,- and ,-proteobacteria, and Planctomycetes, while a number of sequences formed deep branches suggesting the presence of unknown groups of microorganisms. To assess the physiological potential and the possible substrate repertoire of the fhcD- containing species in Lake Washington, we conducted enrichments of natural populations on a variety of C1 substrates, and observed specific shifts in community structure in response to different C1 substrates. A specific shift in community structure was also observed in the presence of humic acids suggesting that C1 transfer metabolism linked to H4MPT may be part of the degradation pathway for this natural polymer, possibly involving formaldehyde production. Overall, our data suggest that C1 oxidation reactions linked to H4MPT are much more widespread in natural environments than previously thought. [source] Aqueous photolysis of 8:2 fluorotelomer alcoholENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 8 2005Suzanne A. Gauthier Abstract The 8:2 fluorotelomer alcohol (8:2 FTOH) was photodegraded in aqueous hydrogen peroxide solutions, synthetic field water (SFW) systems, and Lake Ontario (Canada) water samples. It was found to undergo indirect photolysis, with the data suggesting that the hydroxyl radical was the main degradation agent and that nitrate promoted photolysis whereas dissolved organic carbon inhibited it. The half-lives of 8:2 FTOH were 0.83 ± 0.20 h (10 mM H2O2), 38.0 ± 6.0 h (100 ,M H2O2), 30.5 ± 8.0 to 163.1 ± 3.0 h (SFW systems), and 93.2 ± 10.0 h (Lake Ontario). No significant loss of the parent compound by direct photolysis could be observed. The major monitored products were the 8:2 fluorotelomer aldehyde, the 8:2 fluorotelomer acid (8:2 FTCA), and perfluorooctanoate (PFOA); the minor monitored products were the 8:2 fluorotelomer unsaturated acid (8:2 FTUCA) and perfluorononanoate (PFNA). The intermediates, 8:2 FTCA and 8:2 FTUCA, were photodegraded to verify the degradation pathway, and a mechanism for the photolysis was proposed whereby the end products of the photolysis pathway were PFOA (major) and PFNA (minor). [source] Differential alteration of lipid antigen presentation to NKT cells due to imbalances in lipid metabolismEUROPEAN JOURNAL OF IMMUNOLOGY, Issue 6 2007Jens Schümann Abstract Deficiencies in enzymes of the lysosomal glycosphingolipid degradation pathway or in lysosomal lipid transfer proteins cause an imbalance in lipid metabolism and induce accumulation of certain lipids. A possible impact of such an imbalance on the presentation of lipid antigens to lipid-reactive T cells has only been hypothesized but not extensively studied so far. Here we demonstrate that presentation of lipid antigens to, and development of, lipid-reactive CD1d-restricted NKT cells, are impaired in mice deficient in the lysosomal enzyme ,-galactosidase (,Gal) or the lysosomal lipid transfer protein Niemann-Pick C (NPC) 2. Importantly, the residual populations of NKT cells selected in ,Gal,/, and NPC2,/, mice showed differential TCR and CD4 repertoire characteristics, suggesting that differential selecting CD1d:lipid antigen complexes are formed. Furthermore, we provide direct evidence that accumulation of lipids impairs lipid antigen presentation in both cases. However, the mechanisms by which imbalanced lipid metabolism affected lipid antigen presentation were different. Based on these results, the impact of lipid accumulation should be generally considered in the interpretation of immunological deficiencies found in mice suffering from lipid metabolic disorders. [source] ,-MSH and cAMP signalling in normal human melanocytesEXPERIMENTAL DERMATOLOGY, Issue 9 2004R. Buscà Melanocytes are neural crest-derived skin cells specialized in the synthesis of melanin pigments responsible, in human, for skin and hair colour. The pro-opiomelanocortin peptide, ,-MSH is a strong melanogenic agent secreted by keratinocytes following UV radiation. ,-MSH through the binding to the MC1R and activation of the cyclic AMP pathway plays a pivotal role in melanocyte differentiation and in the regulation of skin pigmentation. During the last few years, we have elucidated the molecular events linking the cAMP pathway to melanogenesis upregulation. This cascade involves the activation of protein kinase A and CREB transcription factor, leading to the upregulation of the expression of microphthalmia-associated transcription factor (MITF). MITF binds and activates the melanogenic gene promoters thereby increasing their expression, which results in an increased melanin synthesis. Beyond this simplified scheme, other intracellular signalling pathways are regulated by cAMP and participate to the regulation of melanocyte differentiation. Indeed, cAMP inhibits the phosphatidyl inositol 3-kinase pathway, leading to the inhibition of AKT and to the activation of GSK3,. This kinase phosphorylates MITF and allows its binding to the target sequence. Such pathways are involved in the upregulation of melanogenesis. ,-MSH and cAMP signalling also regulate melanocyte dendricity, and melanosome transport through the inhibition of the Rho GTPase cascade that function downstream the PI3 kinase. It should be also mentioned that cAMP activates the ERK pathway through a melanocyte-specific pathway involving Ras and B-Raf. The activation of ERK and RSK1 leads to the phosphorylation of MITF and target MITF to the proteasome degradation pathway. Interestingly, several proteins involved in melanocyte differentiation by ,-MSH (MC1R, PI3K, B-Raf and MITF) have also been implicated in the development of melanoma, suggesting that the cAMP pathway could influence melanocyte transformation. [source] CHIP participates in protein triage decisions by preferentially ubiquitinating Hsp70-bound substratesFEBS JOURNAL, Issue 16 2010Marta Stankiewicz The E3 ubiquitin ligase CHIP (C-terminus of Hsc70-interacting protein) is believed to be a central player in the cellular triage decision, as it links the molecular chaperones Hsp70/Hsc70 and Hsp90 to the ubiquitin proteasomal degradation pathway. To better understand the decision process, we determined the affinity of CHIP for Hsp70 and Hsp90 using isothermal titration calorimetry. We analyzed the influence of CHIP on the ATPase cycles of both chaperones in the presence of co-chaperones and a substrate, and determined the ubiquitination efficacy of CHIP in the presence of the chaperones. We found that CHIP has a sixfold higher affinity for Hsp90 compared with Hsc70. CHIP had no influence on ADP dissociation or ATP association, but reduced the Hsp70 cochaperone Hdj1-stimulated single-turnover ATPase rates of Hsc70 and Hsp70. CHIP did not influence the ATPase cycle of Hsp90 in the absence of co-chaperones or in the presence of the Hsp90 cochaperones Aha1 or p23. Polyubiquitination of heat-denatured luciferase and the native substrate p53 was much more efficient in the presence of Hsc70 and Hdj1 than in the presence of Hsp90, indicating that CHIP preferentially ubiquitinates Hsp70-bound substrates. Structured digital abstract ,,MINT-7904367: CHIP (uniprotkb:Q9UNE7) and HSP 90-beta (uniprotkb:P08238) physically interact (MI:0915) by molecular sieving (MI:0071) ,,MINT-7904785: HSP 90-beta (uniprotkb:P08238) and p23 (uniprotkb:Q15185) bind (MI:0407) by molecular sieving (MI:0071) ,,MINT-7904047: CHIP (uniprotkb:Q9UNE7), HSP 90-beta (uniprotkb:P08238) and p23 (uniprotkb:Q15185) physically interact (MI:0915) by molecular sieving (MI:0071) ,,MINT-7903424: Alpha-lactalbumin (uniprotkb:P00711), HSP70 (uniprotkb:P08107) and CHIP (uniprotkb:Q9UNE7) physically interact (MI:0915) by molecular sieving (MI:0071) ,,MINT-7903354: CHIP (uniprotkb:Q9UNE7) and HSC70 (uniprotkb:P11142) bind (MI:0407) by isothermal titration calorimetry (MI:0065) ,,MINT-7903373: CHIP (uniprotkb:Q9UNE7) and HSP90-beta (uniprotkb:P08238) bind (MI:0407) by isothermal titration calorimetry (MI:0065) [source] Intracellular degradation of somatostatin-14 following somatostatin-receptor 3-mediated endocytosis in rat insulinoma cellsFEBS JOURNAL, Issue 19 2008Dirk Roosterman Somatostatin receptor (SSTR) endocytosis influences cellular responsiveness to agonist stimulation and somatostatin receptor scintigraphy, a common diagnostic imaging technique. Recently, we have shown that SSTR1 is differentially regulated in the endocytic and recycling pathway of pancreatic cells after agonist stimulation. Additionally, SSTR1 accumulates and releases internalized somatostatin-14 (SST-14) as an intact and biologically active ligand. We also demonstrated that SSTR2A was sequestered into early endosomes, whereas internalized SST-14 was degraded by endosomal peptidases and not routed into lysosomal degradation. Here, we examined the fate of peptide agonists in rat insulinoma cells expressing SSTR3 by biochemical methods and confocal laser scanning microscopy. We found that [125I]Tyr11-SST-14 rapidly accumulated in intracellular vesicles, where it was degraded in an ammonium chloride-sensitive manner. In contrast, [125I]Tyr1-octreotide accumulated and was released as an intact peptide. Rhodamine-B-labeled SST-14, however, was rapidly internalized into endosome-like vesicles, and fluorescence signals colocalized with the lysosomal marker protein cathepsin D. Our data show that SST-14 was cointernalized with SSTR3, was uncoupled from the receptor, and was sorted into an endocytic degradation pathway, whereas octreotide was recycled as an intact peptide. Chronic stimulation of SSTR3 also induced time-dependent downregulation of the receptor. Thus, the intracellular processing of internalized SST-14 and the regulation of SSTR3 markedly differ from the events mediated by the other SSTR subtypes. [source] Determination of the metal ion dependence and substrate specificity of a hydratase involved in the degradation pathway of biphenyl/chlorobiphenylFEBS JOURNAL, Issue 4 2005Pan Wang BphH is a divalent metal ion-dependent hydratase that catalyzes the formation of 2-keto-4-hydroxypentanoate from 2-hydroxypent-2,4-dienoate (HPDA). This reaction lies on the catabolic pathway of numerous aromatics, including the significant environmental pollutant, polychlorinated biphenyls (PCBs). BphH from the PCB degrading bacterium, Burkholderia xenoverans LB400, was overexpressed and purified to homogeneity. Atomic absorption spectroscopy and Scatchard analysis reveal that only one divalent metal ion is bound to each enzyme subunit. The enzyme exhibits the highest activity when Mg2+ was used as cofactor. Other divalent cations activate the enzyme in the following order of effectiveness: Mg2+ > Mn2+ > Co2+ > Zn2+ > Ca2+. This differs from the metal activation profile of the homologous hydratase, MhpD. UV-visible spectroscopy of the Co2+,BphH complex indicates that the divalent metal ion is hexa-coordinated in the enzyme. The nature of the metal ion affected only the kcat and not the Km values in the BphH hydration of HPDA, suggesting that cation has a catalytic rather than just a substrate binding role. BphH is able to transform alternative substrates substituted with methyl- and chlorine groups at the 5-position of HPDA. The specificity constants (kcat/Km) for 5-methyl and 5-chloro substrates are, however, lowered by eight- and 67-fold compared with the unsubstituted substrate. Significantly, kcat for the chloro-substituted substrate is eightfold lower compared with the methyl-substituted substrate, showing that electron withdrawing substituent at the 5-position of the substrate has a negative influence on enzyme catalysis. [source] Complementary pathways of dissolved organic carbon removal pathways in clear-water Amazonian ecosystems: photochemical degradation and bacterial uptakeFEMS MICROBIOLOGY ECOLOGY, Issue 1 2006André M. Amado Abstract Dissolved organic carbon (DOC) photochemical reactions establish important links between DOC and planktonic bacteria. We hypothesize that seasonal changes in DOC quality, related to the flood pulse, drive the effects of light,DOC interactions on uptake by planktonic bacteria uptake in clear-water Amazonian ecosystems. Water samples from two ecosystems (one lake and one stream) were incubated in sunlight during different hydrological periods and were then exposed to bacterial degradation. Photochemical and bacterial degradation were driven by seasonal DOC inputs. Bacterial mineralization was the main degradation pathway of autochthonous DOC in the lake, while allochthonous DOC was more available for photochemical oxidation. We suggest that sunlight enhances the bacterial uptake of refractory DOC but does not alter uptake of labile forms. We also observed a positive relationship between sunlight and bacterial degradation of DOC, instead of competition. We conclude that photochemical reactions and bacteria complementarily degrade the different sources of DOC during the flood pulse in Amazonian clear-water aquatic ecosystems. [source] Expression of caveolin-1 in hepatic cells increases oxidized LDL uptake and preserves the expression of lipoprotein receptors,JOURNAL OF CELLULAR BIOCHEMISTRY, Issue 4 2009To Quyen Truong Abstract Oxidized LDL (OxLDL) that are positively associated with the risk of developing cardiovascular diseases are ligands of scavenger receptor-class B type I (SR-BI) and cluster of differentiation-36 (CD36) which can be found in caveolae. The contribution of these receptors in human hepatic cell is however unknown. The HepG2 cell, a human hepatic parenchymal cell model, expresses these receptors and is characterized by a very low level of caveolin-1. Our aim was to define the contribution of human CD36, SR-BI, and caveolin-1 in the metabolism of OxLDL in HepG2 cells and conversely the effects of OxLDL on the levels/localization of these receptors. By comparing mildly (M)- and heavily (H)-OxLDL metabolism between control HepG2 cells and HepG2 cells overexpressing CD36, SR-BI, or caveolin-1, we found that (1) CD36 increases M- and H-OxLDL-protein uptake; (2) SR-BI drives M-OxLDL through a degradation pathway at the expense of the cholesterol ester (CE) selective uptake pathway; (3) caveolin-1 increases M- and H-OxLDL-protein uptake and decreases CE selective uptake from M-OxLDL. Also, incubation with M- or H-OxLDL decreases the levels of SR-BI and LDL-receptor in control HepG2 cells which can be overcome by caveolin-1 expression. In addition, OxLDL move CD36 from low to high buoyant density membrane fractions, as well as caveolin-1 in cells overexpressing this protein. Thus, hepatic caveolin-1 expression has significant effects on OxLDL metabolism and on lipoprotein receptor levels. J. Cell. Biochem. 108: 906,915, 2009. © 2009 Wiley-Liss, Inc. [source] HSPA1A is an important regulator of the stability and function of ZNF198 and its oncogenic derivative, ZNF198,FGFR1JOURNAL OF CELLULAR BIOCHEMISTRY, Issue 5 2007Chitta S. Kasyapa Abstract Mass spectroscopy analysis demonstrated that the HSPA1A protein is found in complex with the ZNF198 protein which is involved in a chromosome rearrangement with the FGFR1 gene in an atypical myeloproliferative disease. HSPA1A is a member of the HSP70 family of genes which has been shown to be inducible in a variety of circumstances. Exogenous expression of the ZNF198,FGFR1 fusion kinase gene as well as ZNF198 in a model cell system results in a large (>650-fold) increase in HSP70 mRNA levels. Using KNK437, a specific inhibitor of HSP70 transcription, we have demonstrated that an important function of HSPA1A is to stabilize the ZNF198 and ZNF198,FGFR1 proteins. In the absence of HSPA1A, specific functions of ZNF198,FGFR1 such as STAT3 phosphorylation is also lost. Treatment of cells with KNK437 in the presence of MG132, an inhibitor of proteasomal degradation of proteins, suggested that only the ZNF198,FGFR1 protein is subject to the proteasomal degradation pathway, while ZNF198 is not. These observations suggest an important role for HSPA1A in ZNF198 and ZNF198,FGFR1 mediated cellular function. J. Cell. Biochem. 102: 1308,1317, 2007. © 2007 Wiley-Liss, Inc. [source] Evidence that both 1,,25-dihydroxyvitamin D3 and 24-hydroxylated D3 enhance human osteoblast differentiation and mineralizationJOURNAL OF CELLULAR BIOCHEMISTRY, Issue 3 2006M. van Driel Abstract Vitamin D plays a major role in the regulation of mineral homeostasis and affects bone metabolism. So far, detailed knowledge on the vitamin D endocrine system in human bone cells is limited. Here we investigated the direct effects of 1,,25-(OH)2D3 on osteoblast differentiation and mineralization. Also, we studied the impact of 24-hydroxylation, generally considered as the first step in the degradation pathway of vitamin D, as well as the role of the nuclear and presumed membrane vitamin D receptor (VDR). For this we used a human osteoblast cell line (SV-HFO) that has the potency to differentiate during culture forming a mineralized extracellular matrix in a 3-week period. Transcriptional analyses demonstrated that both 1,,25-(OH)2D3 and the 24-hydroxylated metabolites 24R,25-(OH)2D3 and 1,,24R,25-(OH)3D3 induced gene transcription. All metabolites dose-dependently increased alkaline phosphatase (ALP) activity and osteocalcin (OC) production (protein and RNA), and directly enhanced mineralization. 1,,24R,25-(OH)3D3 stimulated ALP activity and OC production most potently, while for mineralization it was equipotent to 1,,25-(OH)2D3. The nuclear VDR antagonist ZK159222 almost completely blocked the effects of all metabolites. Interestingly, 1,,25-(OH)2D3, an inhibitor of membrane effects of 1,,25-(OH)2D3 in the intestine, induced gene transcription and increased ALP activity, OC expression and mineralization. In conclusion, not only 1,,25-(OH)2D3, but also the presumed 24-hydroxylated "degradation" products stimulate differentiation of human osteoblasts. 1,,25-(OH)2D3 as well as the 24-hydroxylated metabolites directly enhance mineralization, with the nuclear VDR playing a central role. The intestinal antagonist 1,,25-(OH)2D3 acts in bone as an agonist and directly stimulates mineralization in a nuclear VDR-dependent way. J. Cell. Biochem. 99: 922,935, 2006. © 2006 Wiley-Liss, Inc. [source] Zn2+ mediates ischemia-induced impairment of the ubiquitin-proteasome system in the rat hippocampusJOURNAL OF NEUROCHEMISTRY, Issue 5 2009Min Chen Abstract Deposition of ubiquitinated protein aggregates is a hallmark of neurodegeneration in both acute neural injuries, such as stroke, and chronic conditions, such as Parkinson's disease, but the underlying mechanisms are poorly understood. In the present study, we examined the role of Zn2+ in ischemia-induced impairment of the ubiquitin-proteasome system in the CA1 region of rat hippocampus after transient global ischemia. We found that scavenging endogenous Zn2+ reduced ischemia-induced ubiquitin conjugation and free ubiquitin depletion. Furthermore, exposure to zinc chloride increased ubiquitination and inhibited proteasomal enzyme activity in cultured hippocampal neurons in a concentration- and time-dependent manner. Further studies of the underlying mechanisms showed that Zn2+ -induced ubiquitination required p38 activation. These findings indicate that alterations in Zn2+ homeostasis impair the protein degradation pathway. [source] Synphilin-1 degradation by the ubiquitin-proteasome pathway and effects on cell survivalJOURNAL OF NEUROCHEMISTRY, Issue 2 2002Gwang Lee Abstract Parkinson's disease is characterized by loss of nigral dopaminergic neurons and the presence of cytoplasmic inclusions known as Lewy bodies. ,-Synuclein and its interacting partner synphilin-1 are among constituent proteins in these aggregates. The presence of ubiquitin and proteasome subunits in these inclusions supports a role for this protein degradation pathway in the processing of proteins involved in this disease. To begin elucidating the kinetics of synphilin-1 in cells, we studied its degradation pathway in HEK293 cells that had been engineered to stably express FLAG-tagged synphilin-1. Pulse-chase experiments revealed that this protein is relatively stable with a half-life of about 16 h. Treatment with proteasome inhibitors resulted in attenuation of degradation and the accumulation of high molecular weight ubiquitinated synphilin-1 in immunoprecipitation/immunoblot experiments. Additionally, proteasome inhibitors stimulated the formation of peri-nuclear inclusions which were immunoreactive for synphilin-1, ubiquitin and ,-synuclein. Cell viability studies revealed increased susceptibility of synphilin-1 over-expressing cells to proteasomal dysfunction. These observations indicate that synphilin-1 is ubiquitinated and degraded by the proteasome. Accumulation of ubiquitinated synphilin-1 due to impaired clearance results in its aggregation as peri-nuclear inclusions and in poor cell survival. [source] Analysis of the Stability and Degradation Products of TriptolideJOURNAL OF PHARMACY AND PHARMACOLOGY: AN INTERNATI ONAL JOURNAL OF PHARMACEUTICAL SCIENCE, Issue 1 2000YAN PING MAO Triptolide is the major active ingredient of the Chinese herbal remedy Tripterygium wilfordii Hook F. (TwHF). As triptolide content is used to estimate the potency of preparations of TwHF, assessment of its stability is warranted. The accelerated stability of triptolide was investigated in 5% ethanol solution in a light-protected environment at pH 6.9, within a temperature range of 60,90°C. The observed degradation rate followed first-order kinetics. The degradation rate constant (K25°C) obtained by trending line analysis of Arrhenius plots of triptolide was 1.4125 times 10,4 h,1. The times to degrade 10% (t1/10) and 50% (t1/2) at 25°C were 31 and 204 days, respectively. Stability tests of triptolide in different solvents and different pH conditions (pH 4,10) in a light-protected environment at room temperature demonstrated that basic medium and a hydrophilic solvent were the major factors that accelerated the degradation of triptolide. Triptolide exhibited the fastest degradation rate at pH 10 and the slowest rate at pH 6. In a solvent comparison, triptolide was found to be very stable in chloroform. The stability of triptolide in organic polar solvents tested at both 100% and 90% concentration was greater in ethanol than in methanol than in dimethylsulphoxide. Stability was also greater in a mixture of solvent: pH 6 buffer (9:1) than in 100% solvent alone. An exception was ethyl acetate, which is less polar than the other solvents tested, but permitted more rapid degradation of triptolide. Two of the degradation products of triptolide were isolated and identified by HPLC and mass spectroscopy as triptriolide and triptonide. This suggested that the decomposition of triptolide occurred at the C12 and C13 epoxy group and the C14 hydroxyl. The opening of the C12 and C13 epoxy is an irreversible reaction, but the reaction occurring on the C14 hydroxyl is reversible. These results show that the major degradation pathway of triptolide involves decomposition of the C12 and C13 epoxy group. Since this reaction is very slow at 4°C at pH 6, stability is enhanced under these conditions. [source] Degradation of nitroaromatic compounds: a model to study evolution of metabolic pathwaysMOLECULAR MICROBIOLOGY, Issue 4 2009Maia Kivisaar Summary Although many nitroaromatic compounds have been in nature for only a few decades, bacteria have already evolved the ability to metabolize them. Both horizontal transfer of genes and mutagenesis induced under stressful conditions might facilitate evolution of new catabolic pathways. Nitrotoluene degradation pathways are supposedly derived from an ancestral naphthalene degradation pathway. The 2-nitrotoluene degradation genes in Acidovorax sp. strain JS42 are controlled by the transcriptional activator NtdR, which differs from NagR, the activator of the naphthalene degradation operon in Ralstonia sp. strain U2, by only five amino acids. Both regulators respond to salicylate, an intermediate of naphthalene degradation, but NtdR also recognizes a wide range of nitroaromatic compounds. In this issue of Molecular Microbiology, Ju et al. present results of site-directed mutagenesis of NtdR and NagR and show how the nitrotoluene-responsive regulator NtdR can be generated from a NagR-like ancestor by only a few mutations. The reconstructed hypothetical pathway for the evolution of NtdR from NagR demonstrates stepwise broadening of the effector range of the evolving protein without loss of the original activity. These results provide strong evidence for the idea that promiscuity of proteins is an important step in the evolution of new functions. [source] Isolated sulfite oxidase deficiency: mutation analysis and DNA-based prenatal diagnosisPRENATAL DIAGNOSIS, Issue 5 2002J. L. Johnson Abstract Isolated sulfite oxidase deficiency is an autosomal recessive, neurological disorder resulting from a defect in SUOX, the gene encoding the enzyme that catalyzes the terminal reaction in the sulfur amino acid degradation pathway. In its classical, severe form, sulfite oxidase deficiency leads to intractable seizures, severe and progressive brain pathology and death at an early age. We report here on clinical features and mutational analysis of the genetic defect in a newborn with sulfite oxidase deficiency. Cultured fibroblasts from this patient exhibited no detectable sulfite oxidase activity, and a unique four base pair deletion was present in the cDNA isolated from the same source. Identification of the same genetic defect in a heterozygous state in each of the parents and the monitoring of subsequent pregnancies in this family by DNA-based prenatal diagnosis are also described. The deletion mutation was identified in a homozygous state in uncultured chorionic villus tissue from the second pregnancy that was subsequently terminated. In the third pregnancy, the presence of sulfite oxidase activity and identification of the mutation in a heterozygous state suggested that the fetus was not affected. This pregnancy resulted in the birth of a normal child. Copyright © 2002 John Wiley & Sons, Ltd. [source] Plant stress granules and mRNA processing bodies are distinct from heat stress granulesTHE PLANT JOURNAL, Issue 4 2008Christian Weber Summary Similar to the situation in mammalian cells and yeast, messenger ribonucleo protein (mRNP) homeostasis in plant cells depends on rapid transitions between three functional states, i.e. translated mRNPs in polysomes, stored mRNPs and mRNPs under degradation. Studies in mammalian cells showed that whenever the dynamic exchange of the components between these states is disrupted, stalled mRNPs accumulate in cytoplasmic aggregates, such as stress granules (SGs) or processing bodies (PBs). We identified PBs and SGs in plant cells by detection of DCP1, DCP2 and XRN4, as marker proteins for the 5,,3, mRNA degradation pathway, and eIF4E, as well as the RNA binding proteins RBP47 and UBP1, as marker proteins for stored mRNPs in SGs. Cycloheximide-inhibited translation, stress treatments and mutants defective in mRNP homeostasis were used to study the dynamic transitions of mRNPs between SGs and PBs. SGs and PBs can be clearly discriminated from the previously described heat stress granules (HSGs), which evidently do not contain mRNPs. Thus, the role of HSGs as putative mRNP storage sites must be revised. [source] Expression, purification, crystallization and preliminary X-ray analysis of maleylacetate reductase from Burkholderia sp. strain SJ98ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 12 2009Archana Chauhan Maleylacetate reductase (EC 1.3.1.32) is an important enzyme that is involved in the degradation pathway of aromatic compounds and catalyzes the reduction of maleylacetate to 3-oxoadipate. The gene pnpD encoding maleylacetate reductase in Burkholderia sp. strain SJ98 was cloned, expressed in Escherichia coli and purified by affinity chromatography. The enzyme was crystallized in both native and SeMet-derivative forms by the sitting-drop vapour-diffusion method using PEG 3350 as a precipitant at 293,K. The crystals belonged to space group P21212, with unit-cell parameters a = 72.91, b = 85.94, c = 53.07,Å. X-ray diffraction data for the native and SeMet-derivative crystal were collected to 2.7 and 2.9,Å resolution, respectively. [source] Purification, crystallization and preliminary X-ray diffraction analysis of disease-related mutants of p97ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 11 2009Wai-Kwan Tang The human type II AAA+ protein p97 participates in various cellular activities, presumably through its involvement in the ubiquitin,proteasome degradation pathway. Mutations in p97 have been implicated in patients with inclusion-body myopathy associated with Paget's disease of the bone and frontotemporal dementia (IBMPFD). In this work, three mutant p97 N-D1 fragments, R86A, R95G and R155H, were crystallized in the presence of ATP,S with PEG 3350 as a main precipitant, yielding two different crystal forms. The R155H mutant crystal belonged to space group R3, with unit-cell parameters in the hexagonal setting of a = b = 134.2, c = 182.9,Å, and was merohedrally twinned, with an estimated twin fraction of 0.34. The crystals of the R86A and R95G mutants belonged to space group P1, with similar unit-cell parameters of a = 90.89, b = 102.6, c = 107.2,Å, , = 97.5, , = 90.6, , = 91.5° and a = 92.76, b = 103.7, c = 107.7,Å, , = 97.7, , = 91.9, , = 89.7°, respectively. [source] Crystallization and preliminary X-ray analysis of AAMS amidohydrolase, the final enzyme in degradation pathway I of pyridoxineACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 8 2009Jun Kobayashi ,-(N -Acetylaminomethylene)succinic acid (AAMS) amidohydrolase from Mesorhizobium loti MAFF303099, which is involved in a degradation pathway of vitamin B6 and catalyzes the degradation of AAMS to acetic acid, ammonia, carbon dioxide and succinic semialdehyde, has been overexpressed in Escherichia coli. To elucidate the reaction mechanism based on the tertiary structure, the recombinant enzyme was purified and crystallized by the sitting-drop vapour-diffusion method using PEG 8000 as precipitant. A crystal of the enzyme belonged to the monoclinic space group C2, with unit-cell parameters a = 393.2, b = 58.3, c = 98.9,Å, , = 103.4°, and diffraction data were collected to 2.7,Å resolution. The VM value and calculation of the self-rotation function suggested that three dimers with a threefold symmetry were possibly present in the asymmetric unit. [source] Cloning the bacterial bphC gene into Nicotiana tabacum to improve the efficiency of PCB phytoremediationBIOTECHNOLOGY & BIOENGINEERING, Issue 1 2009M. Novakova Abstract The aim of this work is to increase the efficiency of the biodegradation of polychlorinated biphenyls (PCBs) by the introduction of bacterial genes into the plant genome. For this purpose, we selected the bphC gene encoding 2,3-dihydroxybiphenyl-1,2-dioxygenase from Pseudomonas testosteroni B-356 to be cloned into tobacco plants. The dihydroxybiphenyldioxygenase enzyme is the third enzyme in the biphenyl degradation pathway, and its unique function is the cleavage of biphenyl. Three different constructs were designed and prepared in E. coli: the bphC gene being fused with the ,-glucuronidase (GUS) gene, with the luciferase (LUC) gene, and with histidine tail in three separate plant cloning vectors. The GUS and LUC genes were chosen because they can be used as markers for the easy detection of transgenic plants, while histidine tail better enables the isolation of protein expressed in plant tissue. The prepared vectors were then introduced into cells of Agrobacterium tumefaciens. The transient expression of the prepared genes was first studied in cells of Nicotiana tabacum. Once this ability had been established, model tobacco plants were transformed by agrobacterial infection with the bphC/GUS, bphC/LUC, and bphC/His genes. The transformed regenerants were selected on media using a selective antibiotic, and the presence of transgenes and mRNA was determined by PCR and RT-PCR. The expression of the fused proteins BphC/GUS and BphC/LUC was confirmed histochemically by analysis of the expression of their detection markers. Western blot analysis was performed to detect the presence of the BphC/His protein immunochemically using a mouse anti-His antibody. Growth and viability of transgenic plants in the presence of PCBs was compared with control plants. Biotechnol. Bioeng. 2009;102: 29,37. © 2008 Wiley Periodicals, Inc. [source] Rationally engineered biotransformation of p -nitrophenolBIOTECHNOLOGY PROGRESS, Issue 3 2010Matthew de la Peña Mattozzi Abstract An operon encoding enzymes responsible for degradation of the EPA priority contaminant para -nitrophenol (PNP) from Pseudomonas sp. ENV2030 contains more genes than would appear to be necessary to mineralize PNP. To determine some necessary genes for PNP degradation, the genes encoding the proposed enzymes in the degradation pathway (pnpADEC) were assembled into a broad-host-range, BioBricks-compatible vector under the control of a constitutive promoter. These were introduced into Escherichia coli DH10b and two Pseudomonas putida strains, one with a knockout of the aromatic transport TtgB and the parent with the native transporter. The engineered strains were assayed for PNP removal. E. coli DH10b harboring several versions of the refactored pathway was able to remove PNP from the medium up to a concentration of 0.2 mM; above which PNP was toxic to E. coli. A strain of P. putida harboring the PNP pathway genes was capable of removing PNP from the medium up to 0.5 mM. When P. putida harboring the native PNP degradation cluster was exposed to PNP, pnpADEC were induced, and the resulting production of ,-ketoadipate from PNP induced expression of its chromosomal degradation pathway (pcaIJF). In contrast, pnpADEC were expressed constitutively from the refactored constructs because none of the regulatory genes found in the native PNP degradation cluster were included. Although P. putida harboring the refactored construct was incapable of growing exclusively on PNP as a carbon source, evidence that the engineered pathway was functional was demonstrated by the induced expression of chromosomal pcaIJF. © 2010 American Institute of Chemical Engineers Biotechnol. Prog., 2010 [source] Crystallization and preliminary X-ray data analysis of ,-alanine synthase from Drosophila melanogasterACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 10 2007Stina Lundgren ,-Alanine synthase catalyzes the last step in the reductive degradation pathway for uracil and thymine, which represents the main clearance route for the widely used anticancer drug 5-fluorouracil. Crystals of the recombinant enzyme from Drosophila melanogaster, which is closely related to the human enzyme, were obtained by the hanging-drop vapour-diffusion method. They diffracted to 3.3,Å at a synchrotron-radiation source, belong to space group C2 (unit-cell parameters a = 278.9, b = 95.0, c = 199.3,Å, , = 125.8°) and contain 8,10 molecules per asymmetric unit. [source] Reciprocal 13C-Labeling: A Method for Investigating the Catabolism of CosubstratesBIOTECHNOLOGY PROGRESS, Issue 2 2002Bjarke Christensen The principle of reciprocal labeling is to use a uniformly 13C-labeled substrate as the primary carbon source and a naturally labeled cosubstrate. Metabolites derived from a naturally labeled cosubstrate, in this case amino acids, can then be identified by their relatively lower content of 13C, and information on the degradation pathway can be deduced. The technique is based on GC,MS measurements of amino acid labeling patterns, making the technique well suited for investigating the relative importance of amino acid biosynthesis and amino acid uptake from the medium, as the 13C content of the amino acids incorporated into biomass is a direct measure of the amino acid biosyntheses. The technique is illustrated by the investigation of the degradation of phenoxyacetic acid, a medium component that is essential for production of penicillin V by Penicillium chrysogenum. Glucose was used as the uniformly labeled primary carbon source. [source] Oxaliplatin induces mitotic catastrophe and apoptosis in esophageal cancer cellsCANCER SCIENCE, Issue 1 2008Chew Yee Ngan The platinum-based chemotherapeutic agent oxaliplatin displays a wide range of antitumor activities. However, the underlying molecular responses to oxaliplatin in esophageal cancer remain largely unknown. In the present study, we investigated the effect of oxaliplatin on two esophageal cancer cell lines, squamous cell carcinoma (TE3) and adenocarcinoma (TE7). Following cell-cycle arrest at G2 phase after oxaliplatin treatment, TE3 cells died via apoptosis and TE7 cells died via mitotic catastrophe. Survivin was inhibited more in TE7 cells compared with TE3 cells, but inhibition of survivin using small interfering RNA induced mitotic catastrophe in both cell lines. Further investigations indicated that survivin promoter activity was also inhibited by oxaliplatin. Among mitotic catastrophe-associated proteins, 14,3-3, was decreased in TE7 cells; no evident changes were observed for aurora kinases. Oxaliplatin-induced apoptosis in the TE3 cells was caspase dependent. However, downregulation of Bad, Bid, Puma, and Noxa, lack of cytochrome c release, and limited loss of mitochondrial membrane potential in early phase indicated possible initiation by pathways other than the mitochondrial pathway. Mechanistic studies showed that downregulation of survivin by oxaliplatin in TE7 cells was partially due to the proteasome-mediated protein degradation pathway and partially due to the downregulation of Sp1 transcription factor. Similar results were obtained for another gastric adenocarcinoma cell line, MKN45, in which survivin was previously shown to be inhibited by oxaliplatin. These data indicate that survivin may be a key target for oxaliplatin. The ability of oxaliplatin to induce different modes of cell death may contribute to its efficacy in esophageal cancer. (Cancer Sci 2008; 99: 129,139) [source] Hydrogen ,leakage' during methanogenesis from methanol and methylamine: implications for anaerobic carbon degradation pathways in aquatic sedimentsENVIRONMENTAL MICROBIOLOGY, Issue 4 2007Niko Finke Summary The effect of variations in H2 concentrations on methanogenesis from the non-competitive substrates methanol and methylamine (used by methanogens but not by sulfate reducers) was investigated in methanogenic marine sediments. Imposed variations in sulfate concentration and temperature were used to drive systematic variations in pore water H2 concentrations. Specifically, increasing sulfate concentrations and decreasing temperatures both resulted in decreasing H2 concentrations. The ratio of CO2 and CH4 produced from 14C-labelled methylamine and methanol showed a direct correlation with the H2 concentration, independent of the treatment, with lower H2 concentrations resulting in a shift towards CO2. We conclude that this correlation is driven by production of H2 by methylotrophic methanogens, followed by loss to the environment with a magnitude dependent on the extracellular H2 concentrations maintained by hydrogenotrophic methanogens (in the case of the temperature experiment) or sulfate reducers (in the case of the sulfate experiment). Under sulfate-free conditions, the loss of reducing power as H2 flux out of the cell represents a loss of energy for the methylotrophic methanogens while, in the presence of sulfate, it results in a favourable free energy yield. Thus, hydrogen leakage might conceivably be beneficial for methanogens in marine sediments dominated by sulfate reduction. In low-sulfate systems such as methanogenic marine or freshwater sediments it is clearly detrimental , an adverse consequence of possessing a hydrogenase that is subject to externally imposed control by pore water H2 concentrations. H2 leakage in methanogens may explain the apparent exclusion of acetoclastic methanogenesis in sediments dominated by sulfate reduction. [source] A tripartite motif protein TRIM11 binds and destabilizes Humanin, a neuroprotective peptide against Alzheimer's disease-relevant insultsEUROPEAN JOURNAL OF NEUROSCIENCE, Issue 6 2003Takako Niikura Abstract Humanin (HN) is a newly identified neuroprotective peptide that specifically suppresses Alzheimer's disease (AD)-related neurotoxicity. HN peptide has been detected in the human AD brain as well as in mouse testis and colon by immunoblot and immunohistochemical analyses. By means of yeast two-hybrid screening, we identified TRIM11 as a novel HN-interacting protein. TRIM11, which is a member of protein family containing a tripartite motif (TRIM), is composed of a RING finger domain, which is a putative E3 ubiquitin ligase, a B-box domain, a coiled-coil domain and a B30.2 domain. Deletion of the B30.2 domain in TRIM11 abolished the interaction with HN, whereas the B30.2 domain alone did not interact with HN. For their interaction, at least the coiled-coil domain was indispensable together with the B30.2 domain. The intracellular level of glutathione S -transferase-fused or EGFP-fused HN peptides or plain HN was drastically reduced by the coexpression of TRIM11. Disruption of the RING finger domain by deleting the first consensus cysteine or proteasome inhibitor treatment significantly diminished the effect of TRIM11 on the intracellular level of HN. These results suggest that TRIM11 plays a role in the regulation of intracellular HN level through ubiquitin-mediated protein degradation pathways. [source] Microbial biodegradation of polyaromatic hydrocarbonsFEMS MICROBIOLOGY REVIEWS, Issue 6 2008Ri-He Peng Abstract Polycyclic aromatic hydrocarbons (PAHs) are widespread in various ecosystems and are pollutants of great concern due to their potential toxicity, mutagenicity and carcinogenicity. Because of their hydrophobic nature, most PAHs bind to particulates in soil and sediments, rendering them less available for biological uptake. Microbial degradation represents the major mechanism responsible for the ecological recovery of PAH-contaminated sites. The goal of this review is to provide an outline of the current knowledge of microbial PAH catabolism. In the past decade, the genetic regulation of the pathway involved in naphthalene degradation by different gram-negative and gram-positive bacteria was studied in great detail. Based on both genomic and proteomic data, a deeper understanding of some high-molecular-weight PAH degradation pathways in bacteria was provided. The ability of nonligninolytic and ligninolytic fungi to transform or metabolize PAH pollutants has received considerable attention, and the biochemical principles underlying the degradation of PAHs were examined. In addition, this review summarizes the information known about the biochemical processes that determine the fate of the individual components of PAH mixtures in polluted ecosystems. A deeper understanding of the microorganism-mediated mechanisms of catalysis of PAHs will facilitate the development of new methods to enhance the bioremediation of PAH-contaminated sites. [source] | ||||||||||||||||||||||||||||