20S proteasomes and protein degradation "by default"

The degradation of the majority of cellular proteins is mediated by the proteasomes. Ubiquitin-dependent proteasomal protein degradation is executed by a number of enzymes that interact to modify the substrates prior to their engagement with the 26S proteasomes. Alternatively, certain proteins are inherently unstable and undergo "default" degradation by the 20S proteasomes. Puzzlingly, proteins are by large subjected to both degradation pathways. Proteins with unstructured regions have been found to be substrates of the 20S proteasomes in vitro and, therefore, unstructured regions may serve as signals for protein degradation "by default" in the cell. The literature is loaded with examples where engagement of a protein into larger complexes increases protein stability, possibly by escaping degradation "by default". Our model suggests that formation of protein complexes masks the unstructured regions, making them inaccessible to the 20S proteasomes. This model not only provides molecular explanations for a recent theoretical "cooperative stability" principle, but also provokes new predictions and explanations in the field of protein regulation and functionality.     

Emulsification and degradation of "Bunker C" fuel oil by microorganisms

An enrichment culture procedure has been used to isolate mixed culture systems which grow upon “Bunker C” fuel oil. When inoculated into a mineral salts aqueous medium containing Bunker C oil, the mixed cultures initiate oil emulsification. Emulsification usually is observed in 24–48 hr. The role of microbes in this emulsification will be discussed. It appears that certain metabolic products produced by the microbe possess properties of surfactants. Bacteria and fungi have been isolated which possess the ability to cause emulsification. Freeze-dried biomass is also capable of emulsifying oil. Chromatographic analyses of biodegraded Bunker C fuel oil show that microorganisms selectively metabolize the n-paraffin fraction.     

Controlling degradation of low-molecular-weight natural polymer "dextrin" using gamma irradiation

Dextrin, which is widely used throughout many industries for their functional properties, was selected for studying the influences of gamma irradiation on its viscosity, physicochemical properties and dextrin granule structure. The formation of radicals during irradiation process of dextrin in air condition was investigated by electron spin resonance (ESR) showing the influence of irradiation and storage parameters on the nature and concentration of the free radicals. Two major radicals or groups of radicals are observed. The radicals show g-values varying among g=2.0102+/-0.0002 and g=2.0126+/-0.0006. Irradiation was observed to induce increases in the intensity of single. The material left behind after irradiation treatment was characterized using thermal analysis, TGA and DSC. A structural analysis was made using SEM and X-ray diffraction to investigate whether the partial hydrolysis had any influence on the granular structure and the crystallinity of the dextrin. The results show that dextrin undergoes oxidative degradation under the influence of gamma radiation.     

Estimating global "blue carbon" emissions from conversion and degradation of vegetated coastal ecosystems

Recent attention has focused on the high rates of annual carbon sequestration in vegetated coastal ecosystems-marshes, mangroves, and seagrasses-that may be lost with habitat destruction ('conversion'). Relatively unappreciated, however, is that conversion of these coastal ecosystems also impacts very large pools of previously-sequestered carbon. Residing mostly in sediments, this 'blue carbon' can be released to the atmosphere when these ecosystems are converted or degraded. Here we provide the first global estimates of this impact and evaluate its economic implications. Combining the best available data on global area, land-use conversion rates, and near-surface carbon stocks in each of the three ecosystems, using an uncertainty-propagation approach, we estimate that 0.15-1.02 Pg (billion tons) of carbon dioxide are being released annually, several times higher than previous estimates that account only for lost sequestration. These emissions are equivalent to 3-19% of those from deforestation globally, and result in economic damages of $US 6-42 billion annually. The largest sources of uncertainty in these estimates stems from limited certitude in global area and rates of land-use conversion, but research is also needed on the fates of ecosystem carbon upon conversion. Currently, carbon emissions from the conversion of vegetated coastal ecosystems are not included in emissions accounting or carbon market protocols, but this analysis suggests they may be disproportionally important to both. Although the relevant science supporting these initial estimates will need to be refined in coming years, it is clear that policies encouraging the sustainable management of coastal ecosystems could significantly reduce carbon emissions from the land-use sector, in addition to sustaining the well-recognized ecosystem services of coastal habitats.     

"Immunoreactive dynorphin" in Escherichia coli: tracer degradation by a heat-stable endopeptidase

Escherichia coli cells contain and secrete into the growth medium a heat-stable tryptic enzyme, which degrades the radiolabeled dynorphin tracer peptide during radioimmunoassay, simulating the presence of "immunoreactive dynorphin". The validity of an immunoassay procedure, in each new application, must remain in doubt until tracer integrity has been proved.     

Anaerobic degradation of p-ethylphenol by "Aromatoleum aromaticum" strain EbN1: pathway, regulation, and involved proteins

The denitrifying “Aromatoleum aromaticum” strain EbN1 was demonstrated to utilize p-ethylphenol under anoxic conditions and was suggested to employ a degradation pathway which is reminiscent of known anaerobic ethylbenzene degradation in the same bacterium: initial hydroxylation of p-ethylphenol to 1-(4-hydroxyphenyl)-ethanol followed by dehydrogenation to p-hydroxyacetophenone. Possibly, subsequent carboxylation and thiolytic cleavage yield p-hydroxybenzoyl-coenzyme A (CoA), which is channeled into the central benzoyl-CoA pathway. Substrate-specific formation of three of the four proposed intermediates was confirmed by gas chromatographic-mass spectrometric analysis and also by applying deuterated p-ethylphenol. Proteins suggested to be involved in this degradation pathway are encoded in a single large operon-like structure (~15 kb). Among them are a p-cresol methylhydroxylase-like protein (PchCF), two predicted alcohol dehydrogenases (ChnA and EbA309), a biotin-dependent carboxylase (XccABC), and a thiolase (TioL). Proteomic analysis (two-dimensional difference gel electrophoresis) revealed their specific and coordinated upregulation in cells adapted to anaerobic growth with p-ethylphenol and p-hydroxyacetophenone (e.g., PchF up to 29-fold). Coregulated proteins of currently unknown function (e.g., EbA329) are possibly involved in p-ethylphenol- and p-hydroxyacetophenone-specific solvent stress responses and related to other aromatic solvent-induced proteins of strain EbN1.     

Fbxw7-dependent degradation of Notch is required for control of "stemness" and neuronal-glial differentiation in neural stem cells

Control of the growth and differentiation of neural stem cells is fundamental to brain development and is largely dependent on the Notch signaling pathway. The mechanism by which the activity of Notch is regulated during brain development has remained unclear, however. Fbxw7 (also known as Fbw7, SEL-10, hCdc4, or hAgo) is the F-box protein subunit of an Skp1-Cul1-F-box protein (SCF)-type ubiquitin ligase complex that plays a central role in the degradation of Notch family members. We now show that mice with brain-specific deletion of Fbxw7 (Nestin-Cre/Fbxw7(F/F) mice) die shortly after birth with morphological abnormalities of the brain and the absence of suckling behavior. The maintenance of neural stem cells was sustained in association with the accumulation of Notch1 and Notch3, as well as up-regulation of Notch target genes in the mutant mice. Astrogenesis was also enhanced in the mutant mice in vivo, and the differentiation of neural progenitor cells was skewed toward astrocytes rather than neurons in vitro, with the latter effect being reversed by treatment of the cells with a pharmacological inhibitor of the Notch signaling pathway. Our results thus implicate Fbxw7 as a key regulator of the maintenance and differentiation of neural stem cells in the brain.     

基于PSR框架,针对土壤侵蚀小流域的土地质量评价

土壤侵蚀与水土流失是我国土地退化的重要形式.建立基于"压力-状态-响应(PSR)"模式的土地质量指标体系能够比较明确反映出土地质量变化的因果关系,从而有助于决策者采取合适的土地政策和管理措施,进行退化土地的恢复重建.在我国水土流失较为严重的黄土高原丘陵沟壑区,选取安塞县大南沟小流域进行案例分析,分别以栅格(10m×10m)和小流域整体为评价对象建立起基于PSR框架,针对土壤侵蚀的土地质量指标体系.前者(以栅格为评价对象)的压力指标主要为坡度,状态指标包括土壤侵蚀强度、土壤肥力和植被盖度,响应指标为土地利用类型;后者(以小流域整体为评价对象)指标包括3个方面,即基于栅格计算的指标、统计指标和格局指标.具体的的压力指标包括地形压力、耕地压力、农作物收入压力以及格局压力等指标,状态指标包括土壤侵蚀强度、土壤肥力、植物盖度、流域出口水土流失和格局状态指标,响应指标包括非农地面积比重和梯田占农地面积比重等指标.以小流域1998年土地利用图为基础,运用模型模拟和统计分析对小流域整体和小流域内土地质量的相对差异进行了评价.结果表明,小流域平均坡度27.85°,最大坡度高达59.39°,耕地平均坡度24.56°,耕地面积比重42.8%,农作物收入比重63%,小流域整体压力评价等级为5等;小流域平均土壤侵蚀强度为36.39t/hm2,流域出口的侵蚀总量为6.03t/hm2,土壤肥力低,植被盖度平均为2.83%;整体状态评价等级为4等;小流域非耕地面积比重为57.2%,梯田占耕地面积比重只有4.01%,小流域整体响应评价等级为4等.小流域内部土地质量的空间异质性较低,流域面积一半的土地质量等级均为4等.不同土地利用类型的土地质量差别较大,质量由高到低依次为林地/灌木林、荒草地、果园/经济林、休闲地、耕地.该研究可为流域土地规划和不同流域土地质量的比较提供一定的科学依据.     

Cytoplasmically "sequestered" wild type p53 protein is resistant to Mdm2-mediated degradation.

The Mdm2 oncoprotein mediates p53 degradation at cytoplasmic proteasomes and is the principal regulator for maintaining low, often undetectable levels of p53 in unstressed cells. However, a subset of human tumors including neuroblastoma constitutively harbor high levels of wild type p53 protein localized to the cytoplasm. Here we show that the abnormal p53 accumulation in such cells is due to a profound resistance to Mdm2-mediated degradation. Overexpression of Mdm2 in neuroblastoma (NB)(1) cell lines failed to decrease the high steady state levels of endogenous p53. Moreover, exogenous p53, when introduced into these cells, was also resistant to Mdm2-directed degradation. This resistance is not due to a lack of Mdm2 expression in NB cells or a lack of p53-Mdm2 interaction, nor is it due to a deficiency in the ubiquitination state of p53 or proteasome dysfunction. Instead, Mdm2-resistant p53 from NB cells is associated with covalent modification of p53 and masking of the modification-sensitive PAb 421 epitope. This system provides evidence for an important level of regulation of Mdm2-directed p53 destruction in vivo that is linked to p53 modification.     

Chemical synthesis of 6"'-alpha-maltotriosyl-maltohexaose as substrate for enzymes in starch biosynthesis and degradation.

A branched nonasaccharide 6"'-alpha-maltotriosyl-maltohexaose was synthesised in 40 steps from D-glucose and maltose. Phenyl O-(2,3,4,6-tetra-O-benzyl-alpha-D-glucopyranosyl)-(1-->4)-O- (2,3,6-tri-O-benzyl-alpha-D-glucopyranosyl)-(1-->4)-2,3-di-O-benzyl-1-th io- beta-D-glucopyranoside and O-(2,3,4,6-tetra-O-benzyl-alpha-D-glucopyranosyl)-(1-->4)-O-(2,3,6-tri- O-benzyl-alpha-D-glucopyranosyl)-(1-->4)-2,3,6-tri-O-benzyl-alpha, beta-D-glucopyranosyl trichloroacetimidate were coupled by a general condensation reaction to form the per-O-benzylated branched hexasaccharide phenyl thioglycoside. The phenylthio group of this compound was converted into a trichloroacetimidate, which was coupled with phenyl O-(2,3,6-tri-O-benzyl-alpha-D-glucopyranosyl)-(1-->4)-O-(2,3,6-tri-O- benzyl-alpha-D-glucopyranosyl)-(1-->4)-2,3,6-tri-O-benzyl-1-thio-beta-D- glucopyranoside to afford the per-O-benzylated branched nonasaccharide phenyl thioglycoside. Replacement of the phenylthio group with a free OH-group followed by hydrogenolysis gave the desired product. The synthons reported for this synthesis constitute a versatile tool for the chemical synthesis of other complex carbohydrates.     

海洋石油降解微生物及其降解机理

微生物修复作为一种新型环保的生物修复技术,已成为海洋石油污染生物修复的核心技术。对海洋石油降解微生物的种类即细菌、蓝藻、真菌以及藻类进行了总结,对微生物对石油烃的降解途径与降解机理进行了综述。微生物降解烷烃的过程包括末端氧化、烷基氢过氧化物以及环己烷降解3种形式。微生物对芳香烃的降解是通过芳香烃被氧化酶氧化导致苯环开环来实现的。微生物对多环芳烃的降解是在单加氧酶或双加氧酶的催化作用下被最终降解为二氧化碳和水而被分解。并对影响石油烃降解微生物的因素包括温度、营养物质等因素进行了分析。     

Kinetics of base-catalyzed degradation of phenyl d-gluco-pyranosides

The kinetics of base-catalyzed cleavage of the glycosidic linkage in phenyl α- and β-d-glucopyranoside have been studied at various concentrations of base, and are interpreted in terms of formation of anionic species as reactive intermediates, accompanied by a minor mechanism of bimolecular, nucleophilic substitution.The data indicate that, in <M sodium hydroxide solution, more than 80% of the cleavage reaction proceeds through an intramolecular-displacement process facilitated by the anchimeric assistance of the hydroxyl group at C-6, and C-2, for the α- and β-d-glycoside, respectively. However, the bimolecular substitution reaction becomes increasingly apparent as the alkalinity is raised above 1.5M concentration of base.     

Enzymatic degradation of dibutyl phthalate and toxicity of its degradation products

Dibutyl phthalate (DBP) was more efficiently degraded by cutinase compared to yeast esterase; i.e. almost 80% of initial DBP (500 mg l⁻¹) was decomposed within 7.5 h, and nearly 50% of the degraded DBP disappeared within the initial 30 min. The toxicity of the final DBP degradation products were investigated using various recombinant bioluminescent bacteria. Butyl methyl phthalate, the major product of degradation by the esterase, was an oxidative toxic hazard that damaged protein synthesis.     

Aerobic degradation of dinitrotoluenes and pathway for bacterial degradation of 2,6-dinitrotoluene

An oxidative pathway for the mineralization of 2,4-dinitrotoluene (2, 4-DNT) by Burkholderia sp. strain DNT has been reported previously. We report here the isolation of additional strains with the ability to mineralize 2,4-DNT by the same pathway and the isolation and characterization of bacterial strains that mineralize 2, 6-dinitrotoluene (2,6-DNT) by a different pathway. Burkholderia cepacia strain JS850 and Hydrogenophaga palleronii strain JS863 grew on 2,6-DNT as the sole source of carbon and nitrogen. The initial steps in the pathway for degradation of 2,6-DNT were determined by simultaneous induction, enzyme assays, and identification of metabolites through mass spectroscopy and nuclear magnetic resonance. 2,6-DNT was converted to 3-methyl-4-nitrocatechol by a dioxygenation reaction accompanied by the release of nitrite. 3-Methyl-4-nitrocatechol was the substrate for extradiol ring cleavage yielding 2-hydroxy-5-nitro-6-oxohepta-2,4-dienoic acid, which was converted to 2-hydroxy-5-nitropenta-2,4-dienoic acid. 2, 4-DNT-degrading strains also converted 2,6-DNT to 3-methyl-4-nitrocatechol but did not metabolize the 3-methyl-4-nitrocatechol. Although 2,6-DNT prevented the degradation of 2,4-DNT by 2,4-DNT-degrading strains, the effect was not the result of inhibition of 2,4-DNT dioxygenase by 2,6-DNT or of 4-methyl-5-nitrocatechol monooxygenase by 3-methyl-4-nitrocatechol.     

Stability and degradation of mRNA

Differential mRNA stability plays an important role in the regulation of gene expression. Several recent advances have helped to define the general pathways by which mRNA is degraded in prokaryotic cells, although many details remain to be elucidated. Much less is known about the pathways of degradation in eukaryotic cells, but recent studies on specific systems have highlighted both differences from and similarities to prokaryotic pathways.     

Uncoupling retro-translocation and degradation in the ER-associated degradation of a soluble protein

Aberrant polypeptides in the endoplasmic reticulum (ER) are retro-translocated to the cytoplasm and degraded by the 26S proteasome via ER-associated degradation (ERAD). To begin to resolve the requirements for the retro-translocation and degradation steps during ERAD, a cell-free assay was used to investigate the contributions of specific factors in the yeast cytosol and in ER-derived microsomes during the ERAD of a model, soluble polypeptide. As ERAD was unaffected when cytoplasmic chaperone activity was compromised, we asked whether proteasomes on their own supported both export and degradation in this system. Proficient ERAD was observed if wild-type cytosol was substituted with either purified yeast or mammalian proteasomes. Moreover, addition of only the 19S cap of the proteasome catalyzed ATP-dependent export of the polypeptide substrate, which was degraded upon subsequent addition of the 20S particle.     

高效降解机油微生物的筛选及除油效果初探

从多处受石油及其制品污染的土壤中筛选到六株对高浓度机油等相关石油制品具有降解能力的微生物菌种。对该六株菌种的单独和混合降解机油的效果进行了研究,并考察了营养成分对机油降解的影响。实验表明:Px01菌种具有最强的除油能力,在合适条件下,Px01培养液的机油降解速率可达0.502g/L.d。混合菌的除油效果明显好于单菌,最高降解速率可到0.64g/L.d。混合菌的营养要求较低,添加有机营养元素对混合微生物的生长和机油降解没有显著的促进作用。由于所筛选驯化得到的微生物菌种针对高浓度含机油废水的降油效果显著,因此具有良好的应用前景。