土壤中高环多环芳烃微生物降解的研究进展

微生物修复是去除土壤中多环芳烃(PAHs)的主要措施。本文以微生物修复PAHs污染土壤的理论基础及其难点为主线,全面综述了土壤中高环PAHs的微生物降解机理。近年来,富集分离得到的以高环PAHs为唯一碳源和能源的优势降解菌逐渐增多,其中,主要是代谢降解四环PAHs的单株降解菌,一些降解菌还能以共代谢方式利用五环PAHs。高环PAHs污染土壤修复的一个难点是其低生物可利用性,微生物通过释放生物表面活性剂、形成生物膜以及分泌胞外多糖提高高环PAHs的生物可利用性,从而加速其降解。真菌和细菌联合作用能增强污染土壤实地修复的效果。因此,通过微生物修复技术来去除土壤中PAHs具有环境友好性、经济适用性以及可持续应用性。     

微藻-细菌共生体系在废水处理中的应用

在微藻-细菌协同共生的过程中,藻类光合作用释放的氧气被异养微生物利用来矿化水体中的污染物,细菌呼吸为藻类提供二氧化碳作为碳源。近年来,藻类-细菌协同共生体系在污水处理中的应用得到了广泛的研究。本文重点综述了菌藻协同共生体系中微藻与细菌之间的三种相互作用,以及菌藻协同共生体系在废水处理中的应用。菌藻协同共生体系中的微藻与细菌通过营养交换、信号转导及基因转移等相互作用实现共赢。该体系广泛用于处理富营养化、重金属、药物、多环芳烃(polycyclicaromatic hydrocarbons,PAHs)、石油烃化合物等难降解的有机污染的水体。对于氮、磷等营养物质的去除,其主要机理涉及同化作用、厌氧氨氧化作用、硝化与反硝化作用、磷酸化作用等。对重金属、药物、石油烃化合物及其他有机化合物的去除机制主要是生物吸附、生物富集及细胞内外的生物降解。     

污染土壤中苯并(a)芘的微生物降解途径研究进展

苯并(a)芘(BaP)是一种具有强致癌、致畸和致突变的多环芳烃(PAHs)。为了修复BaP污染的土壤,探索其降解途径是很重要的。为此,综述了国内外有关污染土壤中苯并(a)芘的微生物降解情况,对不同真菌、细菌降解苯并(a)芘的能力、代谢途径、共代谢底物以及环境影响因素进行了介绍和比较,提出了苯并(a)芘中间代谢产物的累积及其环境毒性方面的研究是修复苯并(a)芘污染土壤的重要方向。     

接种功能内生细菌Diaphorobacter sp.Phe15减少蔬菜亚细胞菲积累的体外试验研究

[目的]土壤中的多环芳烃(polycyclic aromatic hydrocarbons, PAHs)可被蔬菜根系吸收并在可食部分积累进而通过食物链威胁人群健康。接种功能内生细菌能有效减低蔬菜中PAHs的积累,而关于其对蔬菜亚细胞组分中PAHs积累的影响却鲜有报道。[方法]采用体外实验,研究了接种具有菲降解功能的菌株Diaphorobacter sp. Phe15对空心菜茎叶亚细胞组分中菲积累的影响及PAHs代谢相关酶活性的响应。[结果]接种Phe15可以可加速空心菜茎叶亚细胞中菲的降解,显著削减空心菜亚细胞组分中菲的含量,接菌后空心菜亚细胞组分中菲降解率达90%以上。此外,接种功能菌Phe15可以影响空心菜亚细胞组分中PAHs代谢相关酶系的活性,空心菜亚细胞水平POD、PPO、C230活性整体得到提高,且酶系活性与空心菜体内菲积累呈负相关关系。[结论]接种具有菲降解功能的菌株Phe15增加了空心菜亚细胞水平PAHs代谢相关酶系活性,进而降低空心菜体内菲的积累,研究结果为利用功能内生细菌削减蔬菜中多环芳烃污染提供了一定的参考和理论依据。     

工业真菌中的交替氧化酶

真菌是现代微生物发酵产业的主力军之一。交替呼吸途径(Alternative respiration pathway,ARP),以其非磷酸化电子传递途径,起到了能量溢流(Energy overflow)的作用,调节细胞能量代谢,平衡碳代谢和电子传递,有利于代谢产物的积累。此外,交替呼吸对真菌的抗逆反应和条件致病菌的生理作用也都具有非常重要的影响。交替氧化酶(Alternative oxidase,AOX)是线粒体中交替呼吸途径的末端氧化酶,广泛存在于高等植物及部分真菌和藻类中。由于交替氧化酶对水杨氧肟酸(Salicylhydroxamic acid,SHAM)敏感而对细胞色素呼吸抑制剂氰化物不敏感,交替氧化酶AOX介导的交替呼吸途径又被称为抗氰呼吸途径(Cyanide-resistant respiration,CRR)。近年来,研究交替呼吸途径和交替氧化酶已成为细胞呼吸代谢领域的热门课题。本文主要对真菌交替呼吸途径和交替氧化酶的结构与其在工业真菌体内功能的最新研究进展作一简要的综述。     

多环芳烃(PAHs)微生物降解的原位表征方法

多环芳烃(polycyclic aromatic hydrocarbons,PAHs)是一类在环境中广泛存在的持久性有机污染物,微生物降解是去除环境中多环芳烃污染的主要途径。传统的有关PAHs微生物降解的研究主要依靠分离培养技术,难以准确认识PAHs微生物降解的原位过程及机制。近年来发展起来的原位表征方法可以在基因及单细胞水平研究PAHs在复杂环境中的微生物降解过程,能够原位表征具有PAHs降解功能的微生物及其功能基因和代谢活性,是阐明PAHs原位降解过程及分子机制的强有力的手段。该文综述了宏基因组技术(meta-genomics)、稳定同位素探针技术(stable isotope probe,SIP)、荧光原位杂交技术(fluorescence in situ hybridization,FISH)、拉曼光谱技术(Raman spectra)以及二次离子质谱技术(secondary ion mass spectrometry,SIMS)等原位表征技术在PAHs微生物降解研究领域的应用及其存在的问题和发展趋势等。PAHs微生物降解过程及机制的原位表征将为缓解与修复PAHs污染提供科学基础。     

海藻糖的生物合成与分解途经及其生物学功能

海藻糖是一类在干旱、低温、热击或脱水等逆境环境下具有独特抗逆保护作用的二糖,广泛分布于藻类、细菌、真菌和动植物体内。近年来,随着对海藻糖研究的深入,海藻糖已经被广泛应用到食品、医药、化妆品和分子生物学研究等领域。该文简述了海藻糖在生物体内的代谢途径、生物学功能和研究进展,并对灭蚊真菌Pythiumsp.GY1938菌株海藻糖代谢酶基因的研究前景加以展望。     

细菌降解多环芳烃上游途径的遗传学研究进展*

多环芳烃是一类毒性较大的环境污染物。微生物降解和转化是消除此类污染物的理想方法,已发现多种细菌具有这种功能。主要针对细菌在多环芳烃降解中上游途径的代谢酶及基因簇的组成进行综述,阐述了酶的遗传学特点,并探讨了PAHs代谢基因的进化。这有助于了解PAHs的细菌降解机制,并为有效实施生物修复提供理论依据。     

细菌降解多环芳烃上游途径的遗传学研究进展

多环芳烃是一类毒性较大的环境污染物。微生物降解和转化是消除此类污染物的理想方法,已发现多种细菌具有这种功能。主要针对细菌在多环芳烃降解中上游途径的代谢酶及基因簇的组成进行综述,阐述了酶的遗传学特点,并探讨了PAHs代谢基因的进化。这有助于了解PAHs的细菌降解机制,并为有效实施生物修复提供理论依据。     

水相Cd2+在南美白对虾体内的富集及氧化应激特征

为阐明水相环境中重金属镉元素(Cadmium, Cd)在甲壳类海产品中的富集与代谢过程、亚细胞微区分布特征和生物体氧化应激效应, 文章以南美白对虾(Litopenaeus vannamei)为研究对象, 应用双箱动力学模型设置了水环境下不同Cd暴露水平的富集吸收与清水净化释放试验, 实时监测南美白对虾内脏团和肌肉组织的Cd含量及谷胱甘肽巯基转移酶(Glutathione S-transferase, GST)、谷胱甘肽过氧化物酶(Glutathione peroxidase, GPx)和过氧化氢酶(Catalase, CAT)酶活力随时间变化情况, 同时结合差速离心技术分析了Cd富集后在机体内脏组织团中的亚细胞微区分布特征。实验得出南美白对虾对水环境中Cd的富集能力与水体暴露浓度呈明显的正相关关系, 内脏团组织是南美白对虾最主要的Cd元素吸收与代谢组织, 其对Cd的吸收速率、净化速率、生物富集因子及平衡状态时Cd含量均显著高于肌肉组织, 在相同暴露剂量下前者的生物富集因子平均为后者的75.5倍, 肌肉组织的Cd生物学半衰期明显长于内脏组织; Cd主要储存于类金属硫蛋白(Metallothionein-like protein, MTLP)和细胞碎片(Cell debris, CD)组分中, 少部分存在于细胞器(Organelle, ORG)、富含金属颗粒(Metal-rich granules, MRG)和热敏感蛋白(Heat sensitive protein, HSP), 且随着富集过程的持续, Cd的亚细胞微区分布发生动态变化, MTLP、ORG和HSP中Cd含量百分比逐渐升高, CD和MRG中的Cd含量百分比呈逐渐下降; 在肝脏和肌肉组织中GST、GPx和CAT酶活力在Cd富集阶段均持续显著升高, 在净化释放阶段处于下降趋势, 同一试验组下肝脏组织中抗氧化酶酶活力明显高于对应的肌肉组织。研究旨在阐述甲壳类海洋生物对环境中Cd元素的富集与分布特征, 了解Cd富集可能性机理, 为海洋甲壳类Cd污染风险评价与环境控制提供科学依据。     

Systems biology based metabolic engineering for non-natural chemicals

Production of chemicals in microorganisms is no longer restricted to products arising from native metabolic potential. In this review, we highlight the evolution of metabolic engineering studies, from the production of natural chemicals fermented from biomass hydrolysates, to the engineering of microorganisms for the production of non-natural chemicals. Advances in synthetic biology are accelerating the successful development of microbial cell factories to directly produce value-added chemicals. Here we outline the emergence of novel computational tools for the creation of synthetic pathways, for designing artificial enzymes for non-natural reactions and for re-wiring host metabolism to increase the metabolic flux to products. We also highlight exciting opportunities for applying directed evolution of enzymes, dynamic control of growth and production, growth-coupling strategies as well as decoupled strategies based on orthogonal pathways in the context of non-natural chemicals.     

Environmental contaminants in pathogenesis of breast cancer

This review is an attempt to comprehend the diverse groups of environmental chemical contaminants with a potential for pathogenesis of breast cancer, their probable sources and the possible mechanisms by which these environmental contaminants act and interplay with other risk factors. Estrogens are closely related to the pathogenesis of breast cancer. Oxidative catabolism of estrogen, mediated by various cytochrome P450 enzymes, generates reactive free radicals that can cause oxidative damage. The same enzymes of estrogenic metabolic pathways catalyze biological activation of several environmental (xenobiotic) chemicals. Xenobiotic chemicals may exert their pathological effects through generation of reactive free radicals. Breast tissue can be a target of several xenobiotic agents. DNA-reactive metabolites of different xenobiotic compounds have been detected in breast tissue. Many phase I and II xenobiotic metabolizing enzymes are expressed in both normal and cancerous breast tissues. These enzymes play a significant role in the activation/detoxification of xenobiotic and endogenous compounds including estrogens. More than 30 carcinogenic chemicals are present in tobacco smoke; many of them are fat-soluble, resistant to metabolism and can be stored in breast adipose tissue. Similarly, pesticides are also known to cause oxidative stress; while some act as endocrine disruptor, some are shown to suppress apoptosis in estrogen sensitive cell lines. Reports have shown an association of smoking (both active and passive) and pesticides with breast cancer risk. However, the issues have remained controversial. Different mutagenic substances that are generated in the cooking process e.g., heterocyclic amines and polycyclic aromatic hydrocarbons (PAHs) can be a threat to breast tissue. PAHs and dioxins exert their adverse effects through the aryl hydrocarbon receptor (AhR), which activates several genes involved in the metabolisms of xenobiotic compounds and endogenous estrogens. These chemicals also induce AhR-dependent mitochondrial dysfunction. Many of the environmental pollutants suppress the immune system, which are implicated to risk. A better understanding about the biological effects of different environmental carcinogenic compounds and determination of their impact on rising incidence of breast cancer will be beneficial in improving preventive policy against breast cancer.     

Comparative genomics of two closely related unicellular thermo-acidophilic red algae, Galdieria sulphuraria and Cyanidioschyzon merolae, reveals the molecular basis of the metabolic flexibility of Galdieria sulphuraria and significant differences in carbohydrate metabolism of both algae

Unicellular algae serve as models for the study and discovery of metabolic pathways, for the functional dissection of cell biological processes such as organellar division and cell motility, and for the identification of novel genes and gene functions. The recent completion of several algal genome sequences and expressed sequence tag collections and the establishment of nuclear and organellar transformation methods has opened the way for functional genomics approaches using algal model systems. The thermo-acidophilic unicellular red alga Galdieria sulphuraria represents a particularly interesting species for a genomics approach owing to its extraordinary metabolic versatility such as heterotrophic and mixotrophic growth on more than 50 different carbon sources and its adaptation to hot acidic environments. However, the ab initio prediction of genes required for unknown metabolic pathways from genome sequences is not trivial. A compelling strategy for gene identification is the comparison of similarly sized genomes of related organisms with different physiologies. Using this approach, candidate genes were identified that are critical to the metabolic versatility of Galdieria. Expressed sequence tags and high-throughput genomic sequence reads covering >70% of the G. sulphuraria genome were compared to the genome of the unicellular, obligate photoautotrophic red alga Cyanidioschyzon merolae. More than 30% of the Galdieria sequences did not relate to any of the Cyanidioschyzon genes. A closer inspection of these sequences revealed a large number of membrane transporters and enzymes of carbohydrate metabolism that are unique to Galdieria. Based on these data, it is proposed that genes involved in the uptake of reduced carbon compounds and enzymes involved in their metabolism are crucial to the metabolic flexibility of G. sulphuraria.     

Bridging epigenetics and metabolism

Recent research suggests that chromatin-modifying enzymes are metabolic sensors regulating gene expression. Epigenetics is linked to metabolomics in response to the cellular microenvironment. Specific metabolites involved in this sensing mechanism include S-adenosylmethionine, acetyl-CoA, alphaketoglutarate and NAD⁺. Although the core metabolic pathways involving glucose have been emphasized as the source of these metabolites, the reprogramming of pathways involving non-essential amino acids may also play an important role, especially in cancer. Examples include metabolic pathways for glutamine, serine and glycine. The coupling of these pathways to the intermediates affecting epigenetic regulation occurs by “parametabolic” mechanisms. The metabolism of proline may play a special role in this parametabolic linkage between metabolism and epigenetics. Both proline degradation and biosynthesis are robustly affected by oncogenes or suppressor genes, and they can modulate intermediates involved in epigenetic regulation. A number of mechanisms in a variety of animal species have been described by our laboratory and by others. The challenge we now face is to identify the specific chromatin-modifying enzymes involved in coupling of proline metabolism to altered reprogramming of gene expression.     

Production of bulk chemicals via novel metabolic pathways in microorganisms

Metabolic engineering has been playing important roles in developing high performance microorganisms capable of producing various chemicals and materials from renewable biomass in a sustainable manner. Synthetic and systems biology are also contributing significantly to the creation of novel pathways and the whole cell-wide optimization of metabolic performance, respectively. In order to expand the spectrum of chemicals that can be produced biotechnologically, it is necessary to broaden the metabolic capacities of microorganisms. Expanding the metabolic pathways for biosynthesizing the target chemicals requires not only the enumeration of a series of known enzymes, but also the identification of biochemical gaps whose corresponding enzymes might not actually exist in nature; this issue is the focus of this paper. First, pathway prediction tools, effectively combining reactions that lead to the production of a target chemical, are analyzed in terms of logics representing chemical information, and designing and ranking the proposed metabolic pathways. Then, several approaches for potentially filling in the gaps of the novel metabolic pathway are suggested along with relevant examples, including the use of promiscuous enzymes that flexibly utilize different substrates, design of novel enzymes for non-natural reactions, and exploration of hypothetical proteins. Finally, strain optimization by systems metabolic engineering in the context of novel metabolic pathways constructed is briefly described. It is hoped that this review paper will provide logical ways of efficiently utilizing ‘big’ biological data to design and develop novel metabolic pathways for the production of various bulk chemicals that are currently produced from fossil resources.     

Proteomic determination of metabolic enzymes of the amnion cell: Basis for a possible diagnostic tool?

Amniocentesis is a valuable and standard procedure for prenatal diagnosis of genetic or inborn errors of metabolism. Amnion cells are cultivated and chromosomes or proteins can be examined to provide molecular diagnosis. Mainly individual proteins are searched for based upon pedigrees and/or anamnesis. As inborn errors of metabolism involve a vast diversity of metabolic enzymes, we aimed to find a screening method for a large series of metabolic enzymes. Amnion cells were obtained from amniocentesis and subjected to proteomic analysis. We used two-dimensional gel electrophoresis with in-gel digestion followed by matrix-assisted laser desorption/ionization-time of flight analysis, to identify metabolic enzymes. Furthermore, we compared metabolic proteins in amnion cells from controls with those from Down Syndrome (DS). Enzymes involved in carbohydrate handling, amino acid handling, -purine metabolism and intermediary metabolism as well as miscellaneous metabolic pathways were detected. Protein levels of several enzymes were significantly deranged in samples obtained from patients with DS. This approach, with the advantage of the concomitant determination of many enzyme proteins, may form the basis for future metabolic screens when amniocentesis is carried out.     

Nucleus-encoded genes for plastid-targeted proteins in Helicosporidium: functional diversity of a cryptic plastid in a parasitic alga

Plastids are the organelles of plants and algae that house photosynthesis and many other biochemical pathways. Plastids contain a small genome, but most of their proteins are encoded in the nucleus and posttranslationally targeted to the organelle. When plants and algae lose photosynthesis, they virtually always retain a highly reduced "cryptic" plastid. Cryptic plastids are known to exist in many organisms, although their metabolic functions are seldom understood. The best-studied example of a cryptic plastid is from the intracellular malaria parasite, Plasmodium, which has retained a plastid for the biosynthesis of fatty acids, isoprenoids, and heme by the use of plastid-targeted enzymes. To study a completely independent transformation of a photosynthetic plastid to a cryptic plastid in another alga-turned-parasite, we conducted an expressed sequence tag (EST) survey of Helicosporidium. This parasite has recently been recognized as a highly derived green alga. Based on phylogenetic relationships to other plastid homologues and the presence of N-terminal transit peptides, we have identified 20 putatively plastid-targeted enzymes that are involved in a wide variety of metabolic pathways. Overall, the metabolic diversity of the Helicosporidium cryptic plastid exceeds that of the Plasmodium plastid, as it includes representatives of most of the pathways known to operate in the Plasmodium plastid as well as many others. In particular, several amino acid biosynthetic pathways have been retained, including the leucine biosynthesis pathway, which was only recently recognized in plant plastids. These two parasites represent different evolutionary trajectories in plastid metabolic adaptation.