Kegg Pathway: Carbazole degradation

Mol Nutr Food Res. 2008 Jul; 52(7): 840-8
Knaup B, Kempf M, Fuchs J, Valotis A, Kahle K, Oehme A, Richling E, Schreier P

In order to study the human intestinal transit and metabolism of D-galacturonic acid and amidated pectin a number of model experiments were carried out. Both substrates were incubated under aerobic conditions at 37 degrees C using saliva (2 min) and simulated gastric juice (4 h). Under anaerobic conditions the substrates were incubated at 37 degrees C using human ileostomy and colostomy fluids, each obtained from three different donors, for 10 and for 24 h, respectively. D-Galacturonic acid, SCFA (acetic acid, propionic acid, and butyric acid), as well as methanol were analyzed photometrically after Carbazole reaction, GC-flame ionization detection (GC-FID), and headspace solid-phase microextraction GC/MS (HS-SPME-GC/MS), respectively. D-Galacturonic acid and amidated pectin were found to be stable during incubations with saliva and simulated gastric juice, whereas both substrates underwent degradation in the course of human ileostomy and colostomy fluid incubations. D-Galacturonic acid was practically completely decomposed within 10 h and SCFA, with acetic acid as the major representative, were formed up to 98% of the incubated substrate in colostomy effluent. The amidated pectin was only degraded in part, revealing stable amounts of 22-35% and 3-17% in ileostomy (after 10 h) and colostomy fluid (after 24 h), respectively. SCFA were generated up to 59% of the applied amidated pectin. In parallel, 19-60% and 52-67% of the available methyl ester groups were cleaved in the course of incubations with ileostomy and colostomy fluids, respectively. The results demonstrate for the first time that D-galacturonic acid and amidated pectin are stable in human saliva and simulated gastric juice. The degradation of both compounds during incubation with ileostomy effluent is highlighted, providing evidence for a considerable metabolic potential of the small intestine.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008 Jul 1; 64(Pt 7): 632-5
Umeda T, Katsuki J, Usami Y, Inoue K, Noguchi H, Fujimoto Z, Ashikawa Y, Yamane H, Nojiri H

Novosphingobium sp. KA1 uses Carbazole 1,9a-dioxygenase (CARDO) as the first dioxygenase in its Carbazole-degradation pathway. The CARDO of KA1 contains a terminal oxygenase component and two electron-transfer components: ferredoxin and ferredoxin reductase. In contrast to the CARDO systems of other species, the ferredoxin component of KA1 is a putidaredoxin-type protein. This novel ferredoxin was crystallized at 293 K by the hanging-drop vapour-diffusion method using PEG MME 550 as the precipitant under anaerobic conditions. The crystals belong to space group C222(1) and diffraction data were collected to a resolution of 1.9 A (the diffraction limit was 1.6 A).

Appl Microbiol Biotechnol. 2008 Sep; 80(3): 485-97
Shintani M, Matsui K, Takemura T, Yamane H, Nojiri H

In artificial environmental samples, the behavior of the IncP-7 conjugative plasmid pCAR1, which is involved in the catabolism of Carbazole, was monitored. Sterile soil and water samples supplemented with Carbazole were prepared. After inoculation with Pseudomonas putida harboring pCAR1, seven species of the genus Pseudomonas, and three other bacterial species, were monitored for Carbazole degradation, bacterial survival, and conjugative transfer of pCAR1. In artificial soils, more than 90% of the Carbazole was degraded in samples with high water content, suggesting that the water content is a key factor in Carbazole degradation in artificial soils. In three of the artificial environmental water samples, more than 95% of the Carbazole was degraded. Transconjugants were detected in some artificial water samples, but not in the artificial soil samples, suggesting that pCAR1 is preferably transferred in aqueous environments. Composition analysis of the artificial water samples and examination of conjugative transfer indicated that the presence of the divalent cations Ca(2+) and Mg(2+) promoted the plasmid transfer. The presence of Carbazole also increases in incidence of transconjugants, probably by enhancing their growth. In contrast, humic acids in the liquid layer of artificial soil samples appeared to prevent conjugative transfer.

Curr Microbiol. 2008 Sep; 57(3): 251-7
Guo W, Li D, Tao Y, Gao P, Hu J

A stable microbial consortium, separated from a refinery wastewater sample, was able to utilize Carbazole as the sole source of carbon, nitrogen, and energy, and liberated ammonia from excess nitrogen. Two bacterial strains (NCY and NCW) were isolated from the microbial consortium using a nutrient agar plate. Based on the 16S rDNA sequence analysis, the two bacteria were identified as Chryseobacterium sp. NCY and Achromobacter sp. NCW, respectively. No intermediates of Carbazole degradation were detected by high-performance liquid chromatography. The substrate specificity assay showed that the consortium could utilize compounds similar to Carbazole, such as phenanthrene, naphthalene, and imidazole. Neither the pure strain NCY nor NCW could degrade Carbazole after domestication for several times. It was suggested that the two bacteria formed a microbial consortium capable of metabolizing Carbazole.

Appl Biochem Biotechnol. 2008 Jun 24;
Patel H, Gupte A, Gupte S

The biodegradation of fluoranthene, a high molecular weight polycyclic aromatic hydrocarbon (PAH), was investigated in submerged culture using the wood decaying fungus isolated from forest locality in Gujarat, India. The basidiomycete fungal isolate was found to have an ability to grow on sabaroud dextrose agar containing 50 mgl(-1) of each naphthalene, anthracene, acenaphthene, benzo (a) anthracene, pyrene, flouranthene, Carbazole, and biphenyl. The involvement of extracellular fungal peroxidases such as manganese peroxidase (MnP) and laccase (Phenol oxidase) in the degradation of fluoranthene was studied. On the eighth day of incubation 54.09% of 70 mg l(-1) fluoranthene was removed. There after no PAHs removal was observed till the 20th day of the incubation period. The isolate was identified as Pleurotus ostreatus by 18S rRNA, 5.8S rRNA, and partial 28S rRNA gene sequencing. To the best of our knowledge this is the first time Pleurotus ostreatus have been reported to degrade such a high concentration of fluoranthene within much lower time period of incubation. Depletion in the residual fluoranthene in the culture medium was determined by HPLC. Attempts were made to identify the degradation product in the culture medium with the help of FT-IR, NMR, and HPTLC analysis. In the present study positive correlation between fluoranthene degradation and the ligninolytic enzyme (MnP and laccase) production is observed, thus this isolate can play an effective role for bioremediation of PAHs contaminated sites.

J Phys Chem A. 2008 May 29; 112(21): 4742-8
Fitilis I, Fakis M, Polyzos I, Giannetas V, Persephonis P, Mikroyannidis J

Two photon absorption (TPA) and photophysical properties of three new symmetrical chromophores with electron accepting phthalimide edge substituents have been studied. The three chromophores contain fluorene, alcoxy-substituted divinyl benzene, and Carbazole moieties as central cores, respectively. The femtosecond time-resolved fluorescence upconversion spectroscopy and two photon excited fluorescence technique have been carried out. The effect of solvent polarity on TPA and on photophysics has also been determined. Ultrafast fluorescence dynamics, with decay times ranging from 1 to 13 ps, are revealed in polar solvents. This is attributed to the relaxation of the chromophores to the intramolecular charge transfer state. The chromophore bearing fluorene central core, being of the type A-pi-A, is the most efficient concerning TPA. Strong TPA, with a cross section value as high as 2100 GM at an excitation wavelength of 770 nm is found in acetophenone which is a solvent of intermediate polarity. The TPA spectra were also reproduced using a sum over states three-state model. A study of the TPA induced photobleaching of the fluorene molecule, doped in a solid poly(methyl-methacrylate) film, has shown that this material is very promising for efficient TPA optical data storage.

Nature. 2008 May 1; 453(7191): 46-7
Stevens EA, Bradfield CA

Biosci Biotechnol Biochem. 2008 Apr; 72(4): 1111-4
Hisada N, Satsu H, Mori A, Totsuka M, Kamei J, Nozawa T, Shimizu M

The intestinal permeability of low-molecular-weight hyaluronan (LMW-HA) was investigated by using cultured monolayers of Caco-2 cells. The amount of LMW-HA that permeated the Caco-2 monolayers was measured by a Carbazole assay. The permeability of LMW-HA increased inversely with the molecular size and was dose-dependent. The transport was observed to be energy-independent, and was correlated with the tight junction (TJ) permeability. These results suggest that LMW-HA permeated the Caco-2 cell monolayers via the paracellular pathway.

Nature. 2008 May 1; 453(7191): 65-71
Quintana FJ, Basso AS, Iglesias AH, Korn T, Farez MF, Bettelli E, Caccamo M, Oukka M, Weiner HL

Regulatory T cells (T(reg)) expressing the transcription factor Foxp3 control the autoreactive components of the immune system. The development of T(reg) cells is reciprocally related to that of pro-inflammatory T cells producing interleukin-17 (T(H)17). Although T(reg) cell dysfunction and/or T(H)17 cell dysregulation are thought to contribute to the development of autoimmune disorders, little is known about the physiological pathways that control the generation of these cell lineages. Here we report the identification of the ligand-activated transcription factor aryl hydrocarbon receptor (AHR) as a regulator of T(reg) and T(H)17 cell differentiation in mice. AHR activation by its ligand 2,3,7,8-tetrachlorodibenzo-p-dioxin induced functional T(reg) cells that suppressed experimental autoimmune encephalomyelitis. On the other hand, AHR activation by 6-formylindolo[3,2-b]Carbazole interfered with T(reg) cell development, boosted T(H)17 cell differentiation and increased the severity of experimental autoimmune encephalomyelitis in mice. Thus, AHR regulates both T(reg) and T(H)17 cell differentiation in a ligand-specific fashion, constituting a unique target for therapeutic immunomodulation.

Bioorg Med Chem Lett. 2008 Apr 1; 18(7): 2368-72
Underiner TL, Ruggeri B, Aimone L, Albom M, Angeles T, Chang H, Hudkins RL, Hunter K, Josef K, Robinson C, Weinberg L, Yang S, Zulli A

Orally bioavailable, dual inhibitors of TIE-2/VEGF-R2 were identified by elaborating the C3/N13 SAR around a fused pyrrolodihydroindazoloCarbazole scaffold. Analogs bearing a C3-thiophencarbonyl group were evaluated in enzymatic and cellular biochemical assays; two orally bioavailable analogs were further profiled in functional assays and found to inhibit microvessel growth in rat aortic explant cultures and inhibit Ang-1-stimulated chemotaxis of HUVECs.

Bioorg Med Chem Lett. 2008 Mar 15; 18(6): 1916-21
Dandu R, Zulli AL, Bacon ER, Underiner T, Robinson C, Chang H, Miknyoczki S, Grobelny J, Ruggeri BA, Yang S, Albom MS, Angeles TS, Aimone LD, Hudkins RL

Fused dihydroindazolopyrroloCarbazole oximes have been identified as low nanomolar, potent dual TIE-2 and VEGF-R2 receptor tyrosine kinase inhibitors with excellent cellular potency. Development of the structure-activity relationships (SAR) led to identification of compounds 35 and 40 as potent, selective dual TIE-2/VEGF-R2 inhibitors with favorable pharmacokinetic properties. Compound 35 was orally active in tumor models with no observed toxicity.

J Am Chem Soc. 2008 Apr 16; 130(15): 5368-77
Dounay AB, Humphreys PG, Overman LE, Wrobleski AD

A 1,2,3,4-tetrahydro-9a,4a-(iminoethano)-9H-Carbazole (4) is a central structural feature of the Strychnos alkaloid minfiensine (1) and akuammiline alkaloids such as vincorine (5) and echitamine (6). A cascade catalytic asymmetric Heck-iminium cyclization was developed that rapidly provides 3,4-dihydro-9a,4a-(iminoethano)-9H-Carbazoles in high enantiomeric purity. Two sequences were developed for advancing 3,4-dihydro-9a,4a-(iminoethano)-9H-Carbazole 27 to (+)-minfiensine. In our first-generation approach, a reductive Heck cyclization was employed to form the fifth ring of (+)-minfiensine. In a second more concise total synthesis, an intramolecular palladium-catalyzed ketone enolate vinyl iodide coupling was employed to construct the final ring of (+)-minfiensine. This second-generation total synthesis of enantiopure (+)-minfiensine was accomplished in 6.5% overall yield and 15 steps from 1,2-cyclohexanedione and anisidine 13. A distinctive feature of this sequence is the use of palladium-catalyzed reactions to form all carbon-carbon bonds in the transformation of these simple precursors to (+)-minfiensine.

J Med Chem. 2008 Feb 28; 51(4): 1048-52
Fousteris MA, Papakyriakou A, Koutsourea A, Manioudaki M, Lampropoulou E, Papadimitriou E, Spyroulias GA, Nikolaropoulos SS

Pyrrolo[2,3- a]Carbazole derivatives were synthesized, and their effects on CDK1/cyclinB activity were evaluated. The most potent and efficacious inhibitor was found to be ethyl 9-chloro-1H-pyrrolo[2,3-alpha]Carbazole-2-carboxylate (1e), exhibiting an IC50 in the low micromolar range and leading to 90% at higher concentrations. Using a computational model for CDK1-1e, binding we have observed that 1e exhibited two likely binding modes in the ATP-binding cleft that involve interactions with Lys130, Thr14, and Asp146 of the enzyme.

Mol Pharmacol. 2008 May; 73(5): 1454-64
Lee CW, Lin CC, Luo SF, Lee HC, Lee IT, Aird WC, Hwang TL, Yang CM

Up-regulation of vascular cell adhesion molecule-1 (VCAM-1) involves adhesions between both circulating and resident leukocytes and the human tracheal smooth muscle cells (HTSMCs) during airway inflammatory reaction. We have demonstrated previously that tumor necrosis factor (TNF)-alpha-induced VCAM-1 expression is regulated by mitogen-activated protein kinases, nuclear factor-kappaB, and p300 activation in HTSMCs. In addition to this pathway, phosphorylation of Akt and CaM kinase II has been implicated in histone acetyltransferase and histone deacetylase 4 (HDAC4) activation. Here, we investigated whether these different mechanisms participated in TNF-alpha-induced VCAM-1 expression and enhanced neutrophil adhesion. TNF-alpha significantly increased HTSMC-neutrophil adhesions, and this effect was associated with increased expression of VCAM-1 on the HTSMCs and was blocked by the selective inhibitors of Src [4-amino-5-(4-methylphenyl)-7-(t-butyl)pyrazolo[3,4-d]-pyrimidine (PP1)], epidermal growth factor receptor [EGFR; 4-(3'-chloroanilino)-6,7-dimethoxy-quinazoline, (AG1478)], phosphatidylinositol 3-kinase (PI3K) [2-(4-morpholinyl)-8-phenyl-1(4H)-benzopyran-4-one hydrochloride(LY294002) and wortmannin],calcium[1,2-bis(2-aminophenoxy) ethane-N,N,N',N'-tetraacetic acid-acetoxymethyl ester; BAPTA-AM], phosphatidylinositol-phospholipase C (PLC) [1-[6-[[17beta-methoxyestra-1,3,5(10)-trien-17-yl]amino]hexyl]-1H-pyrrole-2,5-dione (U73122)], protein kinase C (PKC) [12-(2-cyanoethyl)-6,7,12, 13-tetrahydro-13-methyl-5-oxo-5H-indolo(2,3-a)pyrrolo(3,4-c)-Carbazole (Gö6976), rottlerin, and 3-1-[3-(amidinothio)propyl-1H-indol-3-yl]-3-(1-methyl-1H-indol-3-yl) maleimide (bisindolylmaleimide IX) (Ro 31-8220)], CaM (calmidazolium chloride), CaM kinase II [(8R(*),9S(*),11S(*))-(-)-9-hydroxy-9-methoxycarbonyl-8-methyl-14-n-propoxy-2,3,9, 10-tetrahydro-8,11-epoxy, 1H,8H, 11H-2,7b,11a-triazadibenzo[a,g]cycloocta[cde]trinden-1-one (KT5926) and 1-[N,O-bis(5-isoquinolinesulfonyl)-N-methyl-l-tyrosyl]-4-phenylpiperazine (KN62)], p300 (curcumin), and HDAC (trichostatin A) or transfection with short interfering RNAs for Src, Akt, PKCalpha, PKCmu, and HDAC4. At gene regulation level, reverse-transcriptase polymerase chain reaction and promoter assays revealed that expression of VCAM-1 was also attenuated by these signaling molecule inhibitors. Moreover, TNF-alpha induced Akt and CaM kinase II phosphorylation via cascades through Src/EGFR/PI3K and PLC/calcium/CaM, respectively. Finally, activation of Akt and CaM kinase II may eventually lead to the acetylation of histone residues and phosphorylation of histone deacetylase. These findings revealed that TNF-alpha induced VCAM-1 expression via multiple signaling pathways. Blockade of these pathways may be selectively targeted to reduce neutrophil adhesion via VCAM-1 suppression and attenuation of the inflammatory responses in airway diseases.

J Invest Dermatol. 2008 Jul; 128(7): 1620-5
Gaitanis G, Magiatis P, Stathopoulou K, Bassukas ID, Alexopoulos EC, Velegraki A, Skaltsounis AL

Malassezia yeasts are connected with seborrheic dermatitis (SD) whereas M. furfur pathogenicity is associated with the production of bioactive indoles. In this study, the production of indoles by M. furfur isolates from healthy and diseased skin was compared, the respective HPLC patterns were analyzed, and substances that are preferentially synthesized by strains isolated from SD lesions were isolated and characterized. Malassezin, pityriacitrin, indole-3-carbaldehyde, and indolo[3,2-b]Carbazole (ICZ) were isolated by HPLC from extracts of M. furfur grown in L-tryptophan agar, and identified by nuclear magnetic resonance and mass spectroscopy. Of these, ICZ, a potent ligand of the aryl hydrocarbon receptor (AhR), is described for the first time to our knowledge as a M. furfur metabolite. HPLC-photodiode array detection analysis of strain extracts from 7 healthy subjects and 10 SD patients showed that M. furfur isolates from only SD patients consistently produce malassezin and ICZ. This discriminatory production of AhR agonists provides initial evidence for a previously unreported mechanism triggering development of SD and indicates that the variable pathogenicity patterns recorded for M. furfur-associated SD conditions may be attributed to selective production (P<0.001) of measurable bioactive indoles.

J Phys Chem A. 2008 Feb 14; 112(6): 1245-50
Görner H

The photochemistry of diphenylamine (DPA), N-methyldiphenylamine (MeDPA), and triphenylamine (TPA) was studied in solution at room temperature. The major photoprocess was cyclization, and the quantum yields were Phicyc = 0.02-0.6. The photoinduced oxygen uptake/consumption, studied in air-saturated acetonitrile-water or methanol-water, was efficient. Three subsequent transients, the polyphenylamine triplet state, the 4a,4b-dihydroCarbazole triplet state, and its labile ground state, were accessible by laser flash photolysis prior to Carbazole formation. Their yields were determined and compared with the Phicyc values. Oxygen can reduce or enhance Phicyc since one step, quenching of the polyphenylamine triplet state, blocks cyclization and one step, scavenging of dihydroCarbazole, favors cyclization since it competes successfully with the back-reaction to the substrate. The former is dominant for DPA in solvents with low and high polarity and the latter is dominant for MeDPA preferentially in nonpolar solvents as well as for TPA in all solvents.

Bioorg Med Chem Lett. 2008 Feb 1; 18(3): 929-33
Smaill JB, Lee HH, Palmer BD, Thompson AM, Squire CJ, Baker EN, Booth RJ, Kraker A, Hook K, Denny WA

Pyrrolo[3,4-c]Carbazoles bearing solubilising basic side chains at the 8-position retain potent Wee1 and Chk1 inhibitory properties in isolated enzyme assays, and evidence of G2/M checkpoint abrogation in several cellular assays. Co-crystal structure studies confirm that the primary binding to the Wee1 enzyme is as described previously, with the C-8 side chains residing in an area of bulk tolerance.

Mutagenesis. 2008 Jan; 23(1): 67-73
de Waard PW, de Kok TM, Maas LM, Peijnenburg AA, Hoogenboom RL, Aarts JM, van Schooten FJ

Several compounds originating from cruciferous vegetables and citrus fruits bind to and activate the aryl hydrocarbon receptor (AhR). This receptor plays an important role in the toxicity of the known tumour promoter and potent AhR-agonist 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). However, vegetables and fruits are generally considered as healthy. Therefore, besides the AhR activation, the natural AhR agonists (NAhRAs) are assumed to show other health-concerning effects. AhR activation induces several cytochrome P450 phase I enzymes involved, e.g. in the bioactivation of carcinogenic polycyclic aromatic hydrocarbons, like benzo[a]pyrene (BaP), and may as such stimulate DNA adduct formation of those compounds. Therefore, the influence of TCDD, indolo[3,2-b]Carbazole (ICZ, an NAhRA originating from cruciferous vegetables) and an NAhRA-containing extract of grapefruit juice (GJE) on BaP-DNA adduct formation in the human Caco-2 cell line was studied. Also, we investigated if different effects of TCDD, ICZ and GJE on adduct formation could be related to the modulation of transcription of biotransformation- and DNA-repair enzymes. Co-exposure to high AhR-activating concentrations of both TCDD and ICZ significantly reduced the amount of BaP-DNA adducts at 0.1 microM BaP, while at higher concentrations of BaP no influence was observed. In contrast, exposure to 0.1 microM BaP combined with GJE showed a significant increase in BaP-DNA adducts, and a significant decrease at 0.3 and 1 microM BaP. These differences could not be related to transcription of the phase I and II enzymes CYP1A1, CYP1B1, NQO1, GSTP1 and UGT1A6 or to transcription of the nucleotide excision repair enzymes ERCC1, XPA, XPC, XPF and XPG. We conclude that ICZ showed a similar effect on BaP-DNA adduct formation than TCDD, while GJE influenced the adduct formation in a different way. The difference in the influence on adduct formation may be due to effects at the level of enzyme activity, rather than gene expression.

Toxicol In Vitro. 2008 Mar; 22(2): 396-410
de Waard WJ, Aarts JM, Peijnenburg AA, Baykus H, Talsma E, Punt A, de Kok TM, van Schooten FJ, Hoogenboom LA

Cruciferous vegetables and citrus fruits are reported to possess health-beneficial properties, but also have been shown to contain natural aryl hydrocarbon receptor (AhR) agonists (NAhRAs). Binding to the AhR is widely assumed to activate the main pathway by which dioxins, like 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) exert their toxicity. To establish whether or not activation of the AhR pathway by NAhRAs and dioxin-like substances results in similar cellular responses, gene expression profiles induced in Caco-2 cells were studied using microarray analysis. Cells were exposed to indolo[3,2-b]Carbazole (ICZ), an acid reaction product from cruciferous vegetables, and to extracts of citrus pulp and grapefruit juice. Gene expression profiles induced by these NAhRAs were compared to those of the xenobiotic AhR agonists TCDD and benzo[a]pyrene (B[a]P). Over 20 genes were found more than 1.5 times up- or down-regulated by TCDD, and the expression of most of these genes was modulated in the same direction and to a similar extent by B[a]P and the NAhRAs. Results were confirmed by RT-PCR, and many of these genes may be involved in dioxin-related toxic effects. In conclusion, this in vitro study showed similar effects induced by NAhRAs, TCDD and B[a]P at the transcriptome level in a human intestinal cell line.

Methods Mol Med. 2007; 135: 201-9
Mort JS, Roughley PJ

Quantitation of glycosaminoglycans (GAGs) in the form of aggrecan fragments released from cartilage in culture is a simple way to determine the efficacy of different cytokines alone or in combination in simulating cartilage catabolism. Two approaches for GAG assay are described, with special attention being paid to the advantages and limitations of each method.