Degradation of I-Naphthol by a Soil Pseudomonad

A soil Pseudomonas sp. grew with 1-naphthol as sole organic carbon source and produced a 3,4-dihydro-dihydroxy-1(2H)-naphthalenone as the main early intermediary metabolite. Washed 1-naphthol-grown organisms oxidized naphthalene, 1- or 2-naphthol, salicylic acid and, to some extent, 2,3-dihydroxybenzoic acid.     

Degradation of Triphenyltin by a Fluorescent Pseudomonad

Triphenyltin (TPT)-degrading bacteria were screened by a simple technique using a post-column high-performance liquid chromatography using 3,3′,4′,7-tetrahydroxyflavone as a post-column reagent for determination of TPT and its metabolite, diphenyltin (DPT). An isolated strain, strain CNR15, was identified as Pseudomonas chlororaphis on the basis of its morphological and biochemical features. The incubation of strain CNR15 in a medium containing glycerol, succinate, and 130 μM TPT resulted in the rapid degradation of TPT and the accumulation of approximately 40 μM DPT as the only metabolite after 48 h. The culture supernatants of strain CNR15, grown with or without TPT, exhibited a TPT degradation activity, whereas the resting cells were not capable of degrading TPT. TPT was stoichiometrically degraded to DPT by the solid-phase extract of the culture supernatant, and benzene was detected as another degradation product. We found that the TPT degradation was catalyzed by low-molecular-mass substances (approximately 1,000 Da) in the extract, termed the TPT-degrading factor. The other fluorescent pseudomonads, P. chlororaphis ATCC 9446, Pseudomonas fluorescens ATCC 13525, and Pseudomonas aeruginosa ATCC 15692, also showed TPT degradation activity similar to strain CNR15 in the solid-phase extracts of their culture supernatants. These results suggest that the extracellular low-molecular-mass substance that is universally produced by the fluorescent pseudomonad could function as a potent catalyst to cometabolite TPT in the environment.     

Modulation of Affinity of a Marine Pseudomonad for Toluene and Benzene by Hydrocarbon Exposure

Trace (microgram liter⁻¹) quantities of either toluene or benzene injected into an amino-acid-limited continuous culture of Pseudomonas sp. strain T2 were utilized immediately with affinities of 2.6 and 6.8 liters g of cells⁻¹ h⁻¹, respectively, and yielded large amounts of organic products, carbon dioxide, and cells. The immediate utilization of hydrocarbons by hydrocarbon-deprived organisms helps to establish the nutritional value of nonpolar substrates in the environment. The observation of small Michaelis constants for toluene transport led to tests of metabolic competition between hydrocarbons; however, competitive inhibition of toluene metabolism was not found for benzene, naphthalene, xylene, dodecane, or amino acids. Benzene and terpenes were inhibitory at milligram liter⁻¹ concentrations. Toluene was metabolized by a strongly inducible system when compared with benzene. The capacity of toluene to effect larger affinity values increased with exposure time and concentration. The kinetics of induction suggested saturation phenomena, resulting in an induction constant, K_ind, of 96 μg of toluene liter⁻¹. Maximal induction of amino-acid-grown cells required about 80 h, with the affinity reaching 317 liters g of cells⁻¹ h⁻¹.     

Degradation of Mitochondrial Phospholipids During Experimental Cerebral Ischemia in Rats

Changes in content of brain mitochondrial phospholipids were examined in rats after 30 and 60 min of decapitation ischemia compared with controls, to explore the degradation of the mitochondrial membrane and its relation to dysfunction of mitochondria. Activities of respiratory functions and respiratory enzymes (cytochrome c oxidase; F0F1-ATPase) decreased significantly during ischemia. Considerable decreases in cardiolipin and phosphatidylinositol content were observed after 60 min, and other phospholipids showed similar but nonsignificant decreases in content. The amount of polyunsaturated fatty acids chains, such as arachidonic and docosahexaenoic acids, was reduced in each phospholipid, in some cases significantly, after 30 and 60 min of ischemia in time-dependent manners. Degradation of mitochondrial phospholipids during ischemia associated with the deterioration of mitochondrial respiratory functions suggested the significance of such changes in phospholipid content in disintegration of cellular energy metabolism during cerebral ischemia.     

Mitoptosis: Different Pathways for Mitochondrial Execution

Mitoptosis was described as a sort of mitochondrial death program. It could be associated with both necrosis and apoptosis, although degenerating mitochondria are also found in autophagic vacuoles. It was demonstrated that several molecules might contribute to the remodeling and rearrangement of mitochondrial membranes, leading to mitochondria rupture and disruption. Here, we hypothesize that, at least in T cells, two main pathways of mitoptosis can occur: an inner membrane mitoptosis (IMM), in which only the internal matrix and cristae are lost while the external mitochondrial envelope remains unaltered, and an outer membrane mitoptosis (OMM) where only swollen internal cristae are detected as remnants. We suggest that the study of these processes could provide useful insights not only to the field of cell death but also to the study of the pathogenic mechanisms of mitochondria-associated human diseases.

Addendum to:

Death Receptor Ligation Triggers Membrane Scrambling Between Golgi and Mitochondria

S. Ouasti, P. Matarrese, R. Paddon, R. Khosravi-Far, M. Sorice, A. Tinari, W. Malorni, M. Degli Esposti

Cell Death Differ 2006; Epub ahead of print     

Degradation of Membrane Phospholipids in Plant Cells Cultured in Sucrose-free Medium

It has been generally accepted that autophagy contributes to the degradation of cellular components under nutrient starvation conditions. In a previous study, however, we showed that the degradation of membrane phospholipids occurs mainly by mechanisms distinct from autophagy in suspension-cultured tobacco (Nicotiana tabacum) BY-2 cells. In response to deprivation of sucrose, the amounts of total phospholipids and a major phospholipid, phosphatidylcholine (PC), decreased. 3-Methyladenine, which inhibits autophagy, did not affect the degradation of total phospholipids or PC. On the other hand, glycerol inhibited PC degradation although it did not block autophagy. In the present study, we labeled intracellular phospholipidsby loading cells with a fluorochrome-labeled fatty acid and observed cellular morphology by fluorescence microscopy. Most cellular membrane structures were stained at the start of starvation; but 12 h after starvation treatment, concomitant with PC degradation, fluorescence on membranes disappeared and instead the centralvacuole became fluorescent. 3-Methyladenine did not inhibit this process, whereas glycerol did. These results suggest that the degradation of membrane phospholipids can be traced by light microscopy and support the notion that autophagy is not a main contributor to the degradation of membrane phospholipids in tobacco cells cultured in sucrose-free medium.     

Pathways of Propionate Degradation by Enriched Methanogenic Cultures

A mixed methanogenic culture was highly enriched in a growth medium containing propionate as the sole organic carbon and energy source. With this culture, the pathways of propionate degradation were studied by use of ¹⁴C-radiotracers. Propionate was first metabolized to acetate, carbon dioxide, and hydrogen by nonmethanogenic organisms. Formate was not excreted. The carbon dioxide originated exclusively from the carboxyl group of propionate, whereas both [2-¹⁴C]- and [3-¹⁴C]propionate lead to the production of radioactive acetate. The methyl and carboxyl groups of the acetate produced were equally labeled, regardless of whether [2-¹⁴C]- or [3-¹⁴C]propionate was used. These observations suggest that in the culture, propionate was degraded through a randomizing pathway.     

Reversed-Phase High-Performance Liquid Chromatography of Products of Microbiological Degradation of Toluene

Conditions have been selected for reversed-phase high-performance liquid chromatographic assay of intermediate products formed in the course of utilization of toluene by Pseudomonas putida. The composition of products indicates that degradation of toluene by strain BS590-P proceeds primarily through the formation of benzoate and catechol. This is followed by degradation of catechol via ortho-cleavage. In strain BS3701-P, toluene oxidation involves both the side chain and the aromatic ring.     

Directed Evolution of Toluene ortho-Monooxygenase for Enhanced 1-Naphthol Synthesis and Chlorinated Ethene Degradation

Trichloroethylene (TCE) is the most frequently detected groundwater contaminant, and 1-naphthol is an important chemical manufacturing intermediate. Directed evolution was used to increase the activity of toluene ortho-monooxygenase (TOM) of Burkholderia cepacia G4 for both chlorinated ethenes and naphthalene oxidation. When expressed in Escherichia coli, the variant TOM-Green degraded TCE (2.5 +/- 0.3 versus 1.39 +/- 0.05 nmol/min/mg of protein), 1,1-dichloroethylene, and trans-dichloroethylene more rapidly. Whole cells expressing TOM-Green synthesized 1-naphthol at a rate that was six times faster than that mediated by the wild-type enzyme at a concentration of 0.1 mM (0.19 +/- 0.03 versus 0.029 +/- 0.004 nmol/min/mg of protein), whereas at 5 mM, the mutant enzyme was active (0.07 +/- 0.03 nmol/min/mg of protein) in contrast to the wild-type enzyme, which had no detectable activity. The regiospecificity of TOM-Green was unchanged, with greater than 97% 1-naphthol formed. The beneficial mutation of TOM-Green is the substitution of valine to alanine in position 106 of the alpha-subunit of the hydroxylase, which appears to act as a smaller "gate" to the diiron active center. This hypothesis was supported by the ability of E. coli expressing TOM-Green to oxidize the three-ring compounds, phenanthrene, fluorene, and anthracene faster than the wild-type enzyme. These results show clearly that random, in vitro protein engineering can be used to improve a large multisubunit protein for multiple functions, including environmental restoration and green chemistry.     

Engineering of Quasi-Natural Pseudomonas putida Strains for Toluene Metabolism through an ortho-Cleavage Degradation Pathway

To construct a bacterial catalyst for bioconversion of toluene and several alkyl and chloro- and nitro-substituted derivatives into the corresponding benzoates, the upper TOL operon of plasmid pWW0 of Pseudomonas putida was fully reassembled as a single gene cassette along with its cognate regulatory gene, xylR. The corresponding DNA segment was then targeted to the chromosome of a P. putida strain by using a genetic technique that allows deletion of all recombinant tags inherited from previous cloning steps and leaves the otherwise natural strain bearing exclusively the DNA segment encoding the phenotype of interest. The resulting strains grew on toluene as the only carbon source through a two-step process: conversion of toluene into benzoate, mediated by the upper TOL enzymes, and further metabolism of benzoate through the housekeeping ortho-ring cleavage pathway of the catechol intermediate.     

Energetics of Anaerobic Degradation Pathways of Chlorinated Aliphatic Compounds

Abstract This minireview explores the energetics of the (anaerobic) oxidative and fermentative degradation of halogenated ethenes and ethanes. It is shown that these pathways are viable alternatives to the traditional routes that start with one or more reductive dechlorination steps. In contrast to reductive dehalogenation, oxidative and fermentative degradation pathways do not require an external source of reducing equivalents. This suggests that organisms that use these pathways are most likely to be found at high redox potentials, i.e, under conditions where competition for reducing equivalents is great. Received: 10 February 2000; Accepted: 6 April 2000; Online Publication: 13 June 2000     

Therapeutic Targeting of MLL Degradation Pathways in MLL-Rearranged Leukemia

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硫代葡萄糖苷的降解途径及其产物的研究进展

硫代葡萄糖苷(GS)是一类广泛存在于植物界的次生代谢产物,其降解产物具有多种活跃的化学和生物活性.GS种类繁多,根据其侧链R基团来源不同可以分为脂肪族、芳香族和吲哚族3大类.GS降解过程受多种因素影响而难以控制:不同种类的GS在硫苷酶作用下产生异硫氰酸酯类、腈类、硫氰酸酯类、环腈类、恶唑烷酮类化合物等,在较高温度下能发生自降解,在强酸、强碱以及某些化学物质的作用下也不稳定,也能在微生物作用下有效降解.该文从影响GS降解的内源和外源因素入手,系统阐述了GS的酶降解、热降解、化学降解、微生物降解等途径及其产物,为理论研究和生产实践中GS降解的控制提供信息.     

Degradation of Toluene Hydrocarbon by Isolated Yeast Strains: Molecular Genetic Approaches for Identification and Characterization

Removal of petroleum benzene, toluene, and xylene compounds from the environment is necessary to ensure quality life. In this research, 41 yeasts were isolated from oily soils. Among them, nine yeasts named KKUs (A5, A6, A12, A20, A23, A24, A26, A29, and A38) were selected based on their use of benzene, toluene, and xylene as a sole carbon and energy source. Based on their growth rates, all selected yeasts displayed a high efficiency for toluene degradation, but had no ability to degrade benzene and a low ability to degrade xylene, except A29 and A38, which could not degrade xylene. HPLC analysis for toluene removal indicated that A6, A12, A20, A23, A24, and A26 almost completely removed the toluene compound after 3 days of incubation (92.74, 94.61, 95.05, 91.74, 91.85, and 97.29%, respectively). In addition, strains A29 and A38 showed moderate degradation (88.29 and 85.30%, respectively), while the ability of A5 was low (39.00%). The isolates were identified based on amplifying and sequencing the D1/D2 domain of the 26S rRNA gene. Alignments and comparisons of the 26S rRNA gene sequences of the isolates with those available in GenBank, plus phylogenetic analysis, proved isolates as Rhodotorula lactose KKU-A5, Rhodotorula nymphaeae KKU-A6, Rhodotorula graminis KKU-A12, Rhodotorula minuta KKU-A20, Exophiala dermatitidis KKU-A23, Candida davisiana KKU-A24, Rhodotorula slooffiae KKU-A26, Rhodotorula mucilaginosa KKU-A29, and Rhodosporidium diobovatum KKU-A38. Random amplified polymorphic DNA-PCR fingerprinting was accomplished within seven toluene-degrading red yeasts (A5, A6, A12, A20, A26, A29, and A38). The results indicated no correlation between the random amplified polymorphic DNA profile and the geographic origin of the isolates.     

Comparative Genomic Analysis and Benzene,Toluene, Ethylbenzene,and o-, m-, and p-Xylene (BTEX) Degradation Pathways of Pseudoxanthomonas spadix BD-a59

Pseudoxanthomonas spadix BD-a59, isolated from gasoline-contaminated soil, has the ability to degrade all six BTEX (benzene, toluene, ethylbenzene, and o-, m-, and p-xylene) compounds. The genomic features of strain BD-a59 were analyzed bioinformatically and compared with those of another fully sequenced Pseudoxanthomonas strain, P. suwonensis 11-1, which was isolated from cotton waste compost. The genome of strain BD-a59 differed from that of strain 11-1 in many characteristics, including the number of rRNA operons, dioxygenases, monooxygenases, genomic islands (GIs), and heavy metal resistance genes. A high abundance of phage integrases and GIs and the patterns in several other genetic measures (e.g., GC content, GC skew, Karlin signature, and clustered regularly interspaced short palindromic repeat [CRISPR] gene homology) indicated that strain BD-a59''s genomic architecture may have been altered through horizontal gene transfers (HGT), phage attack, and genetic reshuffling during its evolutionary history. The genes for benzene/toluene, ethylbenzene, and xylene degradations were encoded on GI-9, -13, and -21, respectively, which suggests that they may have been acquired by HGT. We used bioinformatics to predict the biodegradation pathways of the six BTEX compounds, and these pathways were proved experimentally through the analysis of the intermediates of each BTEX compound using a gas chromatograph and mass spectrometry (GC-MS). The elevated abundances of dioxygenases, monooxygenases, and rRNA operons in strain BD-a59 (relative to strain 11-1), as well as other genomic characteristics, likely confer traits that enhance ecological fitness by enabling strain BD-a59 to degrade hydrocarbons in the soil environment.     

Methane Fermentation of Ferulate and Benzoate: Anaerobic Degradation Pathways

The anaerobic biodegradation of ferulate and benzoate in stabilized methanogenic consortia was examined in detail. Up to 99% of the ferulate and 98% of the benzoate were converted to carbon dioxide and methane. Methanogenesis was inhibited with 2-bromoethanesulfonic acid, which reduced the gas production and enhanced the buildup of intermediates. Use of high-performance liquid chromatography and two gas chromatographic procedures yielded identification of the following compounds: caffeate, p-hydroxycinnamate, cinnamate, phenylpropionate, phenylacetate, benzoate, and toluene during ferulate degradation; and benzene, cyclohexane, methylcyclohexane, cyclohexanecarboxylate, cyclohexanone, 1-methylcyclohexanone, pimelate, adipate, succinate, lactate, heptanoate, caproate, isocaproate, valerate, butyrate, isobutyrate, propionate, and acetate during the degradation of either benzoate or ferulate. Based on the identification of the above compounds, more complete reductive pathways for ferulate and benzoate are proposed.     

Initial Studies on the Regulation of Toluene Degradation by Pseudomonas Putida F1

Pseudomonas putida Fl oxidizes toluene through cis-toluene dihydrodiol to 3-methylcatechol. The latter compound is the substrate for “meta” fission of the aromatic nucleus. Kinetic and induction experiments indicate that the genes encoding enzymes for these reactions are part of an operon, designated the tod operon, that is coordinately induced and regulated. Strains unable to utilize toluene as a growth substrate were isolated at high frequencies by using screening procedures that utilize the redox dye, 2,3,5-triphenyl-2H-tetrazolium chloride. Biochemical characterization of strains with mutations in the structural genes of the tod operon showed that toluene induces the first four enzymes in toluene degradation by P. putida Fl. The isolation and characterization of pleiotropicnegative mutants together with mutants altered in terms of their expression of tod genes suggests that the tod operon may be under the control of a positive regulatory element.     

Linking Land and Sea: Different Pathways for Marine Subsidies

Nutrients and energy derived from marine autotrophs subsidize shore ecosystems, increasing productivity and affecting food web dynamics and structure. In this study we examined how the inland reach of such inflow effects depends on vectors carrying the marine inflow inland and on landscape structure. We used stable isotopes of carbon and nitrogen to examine the roles of arthropod vectors in carrying marine-derived nutrients inland in two very different shore ecosystems: shore meadows in Sweden with marine inflows of algae and emerging chironomid midges; and sandy beaches and shore dunes in south-western Australia with marine inflows of algae and seagrass. In a colonization experiment, we found that deposited wrack on the beach is quickly colonized by both grazers and predators. However, in both systems we found a larger inland reach of the marine subsidy than could be accounted for by deposited macrophytes on shores alone, and that dipterans and spiders potentially functioned as vectors for the inflow. Our results indicate that marine inflows are important for near-shore terrestrial ecosystems well above the water’s edge, and that this effect is largely due to arthropod vectors (mainly dipterans and spiders) in both low-productivity sandy beach ecosystems at the Indian Ocean coast of Australia, and more productive shore meadows on the Baltic Sea coast of Sweden. Our findings also suggest that the type of vector transporting marine material inland may be as important as the productivity contrast between ecosystems for explaining the degree of marine influence on the terrestrial system.     

Role of Vac8 in Cellular Degradation Pathways in Pichia pastoris

We have identified the Pichia pastoris Vac8 homolog, a 60-64 kDa armadillo repeat protein, and have examined the role of PpVac8 in the degradative pathways involving the yeast vacuole. We report here that PpVac8 is required for glucose-induced pexophagy and mitophagy, but not ethanol-induced pexophagy or starvation-induced autophagy. This has been demonstrated by the persistence of peroxisomal alcohol oxidase activity and GFP-labeled mitochondria in mutants lacking PpVac8 during glucose adaptation. During glucose-induced micropexophagy, in the absence of PpVac8, the vacuole was invaginated with arm-like “segmented” extensions that almost completely surrounded the adjacent peroxisomes. PpVac8-GFP was found at the vacuolar membrane and concentrated at the base of the sequestering membranes that extend from the vacuole to engulf the peroxisomes. The localization of PpVac8-GFP to the vacuolar membrane occurred independent of PpAtg1, PpAtg9 or PpAtg11. Mutagenesis of the palmitoylated cysteines to alanines or deletion of the myristoylation and palmitoylation sites of PpVac8, resulted in an impaired vacuolar association and decreased degradation of alcohol oxidase. Deletion of the central armadillo repeat domains of the PpVac8 did not alter its association with the vacuolar membrane, but resulted in a nonfunctional protein that suppressed the formation of the arm-like extensions from the vacuole to engulf the peroxisomes. PpVac8 is essential for the trafficking of PpAtg11, but not PpAtg1 or PpAtg18, to the vacuole membrane. Together, our results support a role for PpVac8 in early (formation of sequestering membranes) and late (post-MIPA membrane fusion) molecular events of glucose-induced pexophagy.