石油烃降解酶及其基因的结构、功能和表达调控

研究烃降解酶及其基因是进行石油微生物分子检测和工程菌构建的重要基础.本文对目前烃降解酶及其基因的结构、功能和调控机制的最新研究进展进行了总结.催化烷烃好氧降解的起始酶有几类加氧酶,膜整合甲烷单加氧酶、萘-1,2-双加氧酶和异丙苯双加氧酶的晶体结构已经被解析.烷基或芳基琥珀酸合酶催化烃厌氧代谢的主要起始反应,而Azoarcus sp.乙苯厌氧代谢起始反应由乙苯脱氢酶催化.在细菌中,烃代谢相关基因主要通过形成操纵子进行表达调控,基因转录受烃或类似物诱导,并受细胞全局调控.一些微生物由于存在多种烃代谢途径而可能具有复杂的基因调控机制.此外,生态学研究表明,环境中烃降解基因的诱导动态与实验室内纯培养分析不同.在分析石油降解工程菌构建有待解决问题的基础上,提出了烃代谢综合调控和环境中相关酶及基因诱导研究的重要性,并对未来烃降解酶及其基因在有毒物降解理论研究和生物修复上的应用进行了展望.     

深海细菌Celeribacter indicus P73~T对菲的降解机制

来自深海环境的多环芳烃降解菌Celeribacter indicus P73~T能够高效降解菲,为揭示菲生物降解的分子机制,对其降解途径进行分析.通过GC-MS联用技术鉴定出菌株P73~T降解菲的2个重要的中间代谢产物,1-羟基-2-萘甲酸和1-萘酚.通过分析菌株P73~T全基因组,发现了菲降解基因簇(P73_0346-P73_0354),编码包括环羟基化双加氧酶、二氢二醇脱氢酶、环裂解双加氧酶、异构酶、水合醛缩酶等.通过验证环羟基化双加氧酶大亚基基因突变株ΔP73_0346::kan的菲降解能力,证实基因P73_0346编码了菲双加氧酶.依据代谢物检测、基因组分析和突变株功能验证结果,推测菌株P73~T降解菲经由菲C3,4-双加氧途径,更进一步地确定了参与此途径的菲双加氧酶等降解相关基因.本研究不仅揭示了菲降解的分子机制,也为菲污染的生物修复技术提供了理论依据.     

LHG1菌株的分离和降解环己烷的研究

通过选择性培养从石油废水污染的土壤中分离出一株以环己烷为唯一碳源和能源的降解菌株 Ｌ Ｈ Ｇ１ ,对 Ｌ Ｈ Ｇ１ 菌株的降解特性进行了研究．确定 Ｌ Ｈ Ｇ１ 菌株最适培养条件为：培养时间６０ ～１００ ｈ 、环己烷浓度４６０ ～７７０ ｍｇ／ Ｌ、ｐ Ｈ６ ～８ 、ρ（ Ｎａ Ｃｌ） ＝ １０ ｇ Ｌ－ １ 、θ＝ ２５ ～４０ ℃． Ｌ Ｈ Ｇ１ 菌株能够利用环烷烃代谢的中间产物环己酮和环戊酮．此外, Ｌ Ｈ Ｇ１ 菌株还能降解液体石蜡、固体石蜡、萘和苯酚等链烃、芳香烃和酚类     

假单胞菌反式氯双烯内酯异构酶基因克隆和序列分析

从土壤中分离得到一株降解2,4-二氯酚能力较强的假单胞菌菌株GT241-1,从该菌株中克隆出参与降解2,4-二氯酚的反式氯双烯内酯异构酶基因(dcpE).克隆策略是采用Southern杂交对其邻近基因进行定位后构建基因组文库,再用斑点杂交从基因文库中筛选目的转化子.经序列测定得知,dcpE基因编码区1062bp.核苷酸和推测的编码氨基酸序列分析表明,dcpE与已在GenBank登记的相关基因有一定的差异.图5表1参12     

青枯雷尔氏菌GMI1000菌株龙胆酸1,2-双加氧酶活性中心关键氨基酸残基的鉴定

生物信息学分析表明,位于青枯雷尔氏菌GMI1000菌株的染色体上的读码框RSc1087可能编码一个龙胆酸1,2-双加氧酶.本研究克隆、表达了该基因,并通过亲和层析对该基因表达产物进行了纯化.酶学测试结果证实,该基因编码的正是龙胆酸1,2-双加氧酶.SDS-PAGE结果表明,该酶亚基分子量约为38×103.基因的定点突变揭示105位、107位和146位组氨酸残基是该酶活性中心的关键氨基酸残基.     

青枯雷尔氏菌GMll000菌株龙胆酸1，2-双加氧酶活性中心关键氨基酸残基的鉴定

生物信息学分析表明,位于青枯雷尔氏菌GMI1000菌株的染色体上的读码框RSc1087可能编码一个龙胆酸1,2-双加氧酶.本研究克隆、表达了该基因,并通过亲和层析对该基因表达产物进行了纯化.酶学测试结果证实,该基因编码的正是龙胆酸1,2-双加氧酶.SDS-PAGE结果表明,该酶亚基分子量约为38×103.基因的定点突变揭示105位、107位和146位组氨酸残基是该酶活性中心的关键氨基酸残基.     

固定化毛霉对工业和农田污染土壤中多环芳烃的降解和生物有效性评价

为了探讨微生物修复不同类型多环芳烃污染土壤的可行性,应用固定化毛霉对多环芳烃污染工业土壤及农田土壤进行微生物修复,用羟丙基-β-环糊精(HPCD)提取模拟评价多环芳烃的微生物可利用性,并分析多环芳烃微生物降解和生物可利用性的相关关系.焦化厂污染土壤中多环芳烃的30 d降解率为77.6%,沈抚灌区污染土壤中多环芳烃的30 d降解率为54.2%,焦化厂土壤和污灌区农田土壤中多环芳烃降解差异明显.焦化厂土壤和污灌区土壤中多环芳烃的30 d降解量和多环芳烃的环糊精可提取量具有相关性,各环数多环芳烃的环糊精可提取量变化解释了焦化厂和污灌区土壤中多环芳烃降解的差异机制,说明可用环糊精提取量预测微生物降解土壤多环芳烃的情况.     

烷基化多环芳烃的细菌降解研究进展

烷基化多环芳烃（alkylated polycyclic aromatic hydrocarbons, A-PAHs）是以多环芳烃（PAHs）为母环,具有烷基侧链的稠环芳香烃,是一类在环境中广泛存在的持久性有机污染物.微生物降解是其在环境中降解去除的主要途径,与真菌、藻类等相比,细菌降解A-PAHs得到更多的关注.本文对APAHs的污染现状及生态毒性,细菌降解甲基萘、甲基菲的研究进展进行了概述,以PAHs的降解酶和降解基因作为参考,总结了A-PAHs可能涉及的降解酶及降解基因.本文有助于了解环境中A-PAHs的生物降解研究现状,为寻找高效的A-PAHs降解方法及减轻其生态风险提供理论依据.     

萘降解菌NAP_A的分离、降解性能和分子系统学研究

该文研究降解多环芳烃类环境污染物的微生物资源、降解活性和分子系统特征.利用萘-无机盐选择性培养基分离萘降解菌,用培养技术和气相色谱法检测菌株对底物的利用和降解情况,用分子克隆技术获得菌株的16S rRNA基因并测序,用DNAMAN软件对菌株的16S rRNA基因序列进行比对和系统发育分析.从淄博张店污水处理厂的活性污泥中分离到一株能降解萘的菌株NAP_A.此菌株在30 ～35 ℃和pH 7条件下较快的降解底物萘,其中30 ℃下,10 d内可以将初始质量浓度为320 mg·L-1的萘降解90％± 4.5％.对菌株NAP_A的16S rRNA基因进行了克隆和测序(EU142847),基于菌株NAP_A和相关菌株的16S rRNA基因进行系统发育分析,结果表明菌株NAP_A位于苍白杆菌属的分枝中,其中与假中间苍白杆菌种的同源性最高,可达99％,因此推断NAP_A菌是一株假中间苍白杆菌.此前并无苍白杆菌属成员降解多环芳烃的报道.这是首例苍白杆菌属成员降解多环芳烃的报道,对今后在环境污染防治中开发利用此类细菌具有指导意义.     

高浓度含油废水中不同组分烃的生物强化去除特性

为探究石油烃降解菌群对高浓度含油废水中不同组分烃的生物降解特性,向含油水相中接种石油烃降解菌群LW-10(Accession number:SRR15082184)进行降解实验.利用GC-MS研究了LW-10对原油中不同组分烃的降解性能,采用流式细胞术检测降解体系中的菌量变化.利用qPCR技术对控制不同组分烃降解的关键基因进行检测.结果表明,原油浓度为5000 mg·L^-1的含油废水中接种LW-10降解17 d,对原油中烷烃和多环芳烃组分的降解率分别为96.7%和28.4%.体系中的降解菌总浓度与高活性菌浓度由接种时的1.0×10⁸ cfu·mL^-1增加至2.1×10⁹ cfu·mL^-1和8.3×10⁸ cfu·mL^-1.检测的3种石油烃降解功能基因中,烷烃单加氧酶基因alkB2拷贝数由1.06×10⁸ copy·mL^-1变为2.84×10⁸copy·mL^-1...     

五氯酚(PCP)高效降解菌Psendomonas sp.CS5的研究

从曾受五氯酚(pentachlorophenol,简称PCP,下同)污染废水的活性污泥中,经驯化富集和分离筛选获得一株PCP降解菌,菌号为CS-W-98-5.在24h内该菌降解w(PCP)=400×10     

Microbial community and functional genes in the rhizosphere of alfalfa in crude oil-contaminated soil

A rhizobox system constructed with crude oil-contaminated soil was vegetated with alfalfa (Medicago sativa L.) to evaluate the rhizosphere effects on the soil microbial population and functional structure, and to explore the potential mechanisms by which plants enhance the removal of crude oil in soil. During the 80-day experiment, 31.6% of oil was removed from the adjacent rhizosphere (AR); this value was 27% and 53%higher than the percentage of oil removed from the far rhizosphere (FR) and from the non-rhizosphere (NR), respectively. The populations of heterotrophic bacteria and hydrocarbon-degrading bacteria were higher in the AR and FR than in the NR. However, the removal rate of crude oil was positively correlated with the proportion of hydrocarbon-degrading bacteria in the rhizosphere. In total, 796, 731, and 379 functional genes were detected by microarray in the AR, FR, and NR, respectively. Higher proportions of functional genes related to carbon degradation and organic remediation, were found in rhizosphere soil compared with NR soil, suggesting that the rhizosphere selectively increased the abundance of these specific functional genes. The increase in water-holding capacity and decrease in pH as well as salinity of the soil all followed the order of AR>FR>NR. Canonical component analysis showed that salinity was the most important environmental factor influencing the microbial functional structure in the rhizosphere and that salinity was negatively correlated with the abundance of carbon and organic degradation genes.     

海洋环境中多环芳烃的微生物降解研究进展

多环芳烃 (PAHs)是一类广泛分布于海洋环境中的含有两个苯环以上的有毒有害污染物 ,主要来源于人类活动和能源利用过程 ,如石油、煤、木材等的燃烧过程 ,石油及石油化工产品的生产过程 ,海上通过地面径流、污水排放及机动车辆等燃料不完全燃烧后的废气随大气颗粒的沉降进入海洋环境中 .由于多环芳烃的潜在毒性、致癌性及致畸诱变作用[1,2 ] ,通过生物累积及食物链的传递作用 ,给海洋生物、生态环境和人体健康带来极大危害 ,已引起各国环境科学家的极大重视 .美国环保局在上世纪 80年代把 16种未带分支的多环芳烃确定为环境中的优先污染物[…     

2-氯苯甲酸好氧降解菌的降解特性

分离出 2株以 2 -氯苯甲酸为唯一碳源的细菌W1和W2 ,这 2株菌对 2 -氯苯甲酸的降解均表现为一级动力学反应。W1降解酶系为诱导酶 ,对 2 -氯苯甲酸的降解动力学常数为 -0 .1 34h- 1;W2降解酶系为非诱导酶 ,对 2 -氯苯甲酸的降解动力学常数为 -0 .0 388h- 1。W1还能够降解 4 -氯苯甲酸、苯、甲苯和邻苯二酚 ,但不能降解 3-氯苯甲酸、2 ,4 -二氯苯甲酸、乙苯、丙苯和萘。W1菌体质粒和染色体提取实验表明 ,其降解基因位于染色体上。     

苏云金芽胞杆菌YBT-1520中SigL及其增强子结合蛋白的结构与功能分析

为揭示SigL及其增强子结合蛋白(EBPs)在苏云金芽胞杆菌(Bt)中的调控功能,在全基因组测序的基础上,采用生物信息学方法,对YBT-1520菌株的SigL及其EBPs的结构和功能进行深入分析.结果表明,YBT-1520基因组中存在1个SigL和6个EBPs,而且EBPs在结构上具有丰富的多样性,包含了EBPs的所有可能的结构域组织类型.SigL所调控的基因涉及11个假定的COG代谢途径,其中包括能量代谢、氨基酸代谢、翻译与细胞周期等.根据EBPs在基因组的位置推测,YBT-1520的EBPs参与γ-氨基丁酸代谢途径、精氨酸代谢途径、支链脂肪酸降解途径、多糖分解代谢等代谢途径的调控.本研究将为揭示Bt杀虫晶体蛋白大量表达的调控机制提供新的思路.     

Identification of two alkane hydroxylases involved in long-chain n-alkane degradation by Dietzia sp. DQ12-45-1b北大核心CSCD

The aim of this study was to identify genes involved in long-chain alkane degradation in Dietzia sp. DQ12-45-1b. Functional genes were annotated by genome analysis. Induction of alkane hydroxylase genes by C28 n-alkane was analyzed by using quantitative real-time PCR in wild-type Dietzia sp. DQ12-45-1b and its alkW1 gene knockout mutant strain M 5-5. From the genome of Dietzia sp. DQ12-45-1b, two homologues, G1 and G2 genes were annotated, which showed 50% amino acid sequence similarity with AlmA from Acinetobacter sp. DSM17874, and 48% amino acid sequence similarity with LadA from Geobacillus thermodenitrificans NG80-2, respectively. In addition, G1 showed 71% amino acid sequence similarity with G1a, and G2 showed 34% and 87% amino acid sequence similarities with G2a and G2ß, respectively, which were annotated from Dietzia sp. E1 genome. In addition, the alkW1 gene knockout strain M 5-5 could grow with C28 n-alkane as the sole carbon source, indicating the presence of potential long-chain alkane hydroxylase gene(s) other than alkW1 in Diezia sp. DQ12-45-1b. Accordingly, induction of G1 and G2 genes was observed when Dietzia ap. DQ12-45-1b and alkW1 knockout mutant strain M 5-5 grew with C28 n-alkane as sole carbon source. The results indicated that G1 and G2 genes are mostly responsible for the degradation of long-chain alkanes in Dietzia sp. DQ12-45-1b, which has unique multiple alkane hydroxylase systems.     

Acid Orange 7 degradation using methane as the sole carbon source and electron donor

• AO7 degradation was coupled with anaerobic methane oxidation. • Higher concentration of AO7 inhibited the degradation. • The maximum removal rate of AO7 reached 280 mg/(L·d) in HfMBR. • ANME-2d dominated the microbial community in both batch reactor and HfMBR. • ANME-2d alone or synergistic with the partner bacteria played a significant role. Azo dyes are widely applied in the textile industry but are not entirely consumed during the dyeing process and can thus be discharged to the environment in wastewater. However, azo dyes can be degraded using various electron donors, and in this paper, Acid Orange 7 (AO7) degradation performance is investigated using methane (CH₄) as the sole electron donor. Methane has multiple sources and is readily available and inexpensive. Experiments using ¹³C-labeled isotopes showed that AO7 degradation was coupled with anaerobic oxidation of methane (AOM) and, subsequently, affected by the initial concentrations of AO7. Higher concentrations of AO7 could inhibit the activity of microorganisms, which was confirmed by the long-term performance of AO7 degradation, with maximum removal rates of 8.94 mg/(L·d) in a batch reactor and 280 mg/(L·d) in a hollow fiber membrane bioreactor (HfMBR). High-throughput sequencing using 16S rRNA genes showed that Candidatus Methanoperedens, affiliated to ANME-2d, dominated the microbial community in the batch reactor and HfMBR. Additionally, the relative abundance of Proteobacteria bacteria (Phenylobacterium, Pseudomonas, and Geothermobacter) improved after AO7 degradation. This outcome suggested that ANME-2d alone, or acting synergistically with partner bacteria, played a key role in the process of AO7 degradation coupled with AOM.     

基于RNA干扰的家蝇几丁质酶2的幼虫转录组测序

几丁质酶是昆虫几丁质降解过程中的重要酶类,在昆虫整个生长发育过程中发挥着重要作用.为筛选及挖掘与防治有害医学昆虫相关的分子靶标,根据家蝇几丁质酶2(Musca domestica chitinase 2,MdCht2)基因序列设计并合成双链RNA(double-stranded RNA,dsRNA),采用微量注射法向家蝇2龄幼虫导入dsRNA,对对照组及干扰组的样本进行转录组测序,筛选差异表达基因,进行GO(gene ontology)功能注释和KEGG(kyoto encyclopedia of genes and genomes)通路富集分析.结果显示,注射dsRNA 24 h后,幼虫MdCht2 mRNA的表达显著下降,提示导入的dsRNA干扰了MdCht2的表达.经转录组测序,与对照组相比,显著差异基因共213条,其中78条基因为上调表达,135条基因为下调表达.随机选取8条显著差异基因通过实时荧光定量PCR(qRT-PCR)进行验证,该结果与转录组结果趋势一致.根据功能注释发现这些差异基因与生长发育、脂类代谢、免疫调控等途径相关.本研究通过RNA干扰和转录组测序技术处理家蝇获得大量差异基因,结果可为后续几丁质酶相关基因的挖掘和鉴定及功能研究提供一定的数据基础.(图7表4参46)     

Isolation of a strain that degrades 1,2,4-trichlorobenzene and characterization of its degradative plasmid

The genetic information encoding metabolic pathways for xenobiotic compounds in bacteria often resides on catabolic plasmids. The aim of the present work was to know the location of the genes for degrading 1,2,4-trichlorobenzen. In this paper a 1,2,4-trichlorobenzene-degrading strain THSL-1 was isolated from the soil of Tianjin Chemical Plant using 1,2,4-trichlorobenzene as the sole carbon source. The strain was identified as Pseudomonas stutzeri through morphologic survey and 16S rDNA sequence determination. A plasmid was discovered from strain THSL-1 by using the alkali lysis method. When the plasmid was transformed into E. coli. JM109 by the CaCl2 method, the transformant could grow using 1,2,4-trichlorobenzene as the sole carbon source and had the degradation function of 1,2,4-trichlorobenzene. Therefore, it could be deemed that the plasmid carried the degradative genes of 1,2,4-trichlorobenzene. The average size of the plasmid was finally determined to be 40.2 Kb using selectively three kinds of restricted inscribed enzymes (HindIII, BamHI, and XholI) for single cutting and double cutting the plasmid pTHSL-1, respectively.     

Toxic effect of sodium perfluorononyloxy-benzenesulfonate on Pseudomonas stutzeri in aerobic denitrification,cell structure and gene expression

• OBS inhibited the growth of P. stutzeri and destroyed its structure. • OBS was toxic to the aerobic denitrification process of P. stutzeri. • OBS induced the production of ROS in P. stutzeri. • OBS affected the expression of key genes involved in denitrification and SOD. The toxicities of sodium perfluorononyloxy-benzenesulfonate (OBS) to animals and plants are similar to those of perfluorooctane sulfonate. However, the mechanism of its toxicity to aerobic denitrifying bacteria is still unclear. In the present study, the ecotoxicity of OBS on an aerobic denitrifying strain, Pseudomonas stutzeri, was evaluated. The results showed that a dosage of OBS clearly affected the growth and aerobic denitrification of P. stutzeri. When compared with an unamended control, the degradation efficiency of the total nitrogen decreased by 30.13% during exposure to 200 mg/L of OBS, and the complete degradation time of nitrate-nitrogen was delayed by 4 h. The lactate dehydrogenase and superoxide dismutase produced by the bacteria increased with the concentration of OBS, and reactive oxygen species were also detected by confocal laser scanning microscope imaging. Transmission electron microscope imaging revealed chromosome deformation of the cells and damage to cell content; moreover, outer membrane vesicles were secreted from the bacteria, which was the important detoxification mechanism of P. stutzeri to OBS. Expression of the genes involved in aerobic nitrification and oxidative stress were also changed under OBS stress, which further confirmed the toxicity of OBS to P. stutzeri. This study reveals the environmental exposure risk of OBS from the perspective of microorganisms.