微生物代谢组学的研究方法与进展

代谢组学、基因组学、转录组学和蛋白质组学是系统生物学研究的重要组成部分。近年来,在代谢组学领域,微生物代谢组学的研究受到人们的重视,成为研究的热点。本文综述了微生物代谢组学的研究方法,包括样品处理、分析平台、数据处理和生物学解释等,并讨论了微生物代谢组学在代谢工程方面的应用潜力,以及微生物代谢组学的研究前景和所面临的挑战。     

放线菌来源生物碱的生物合成机制

生物碱类天然产物通常具有复杂多样的化学结构和广泛的生物活性,因此备受生物学、化学、药学领域研究者的关注。微生物是仅次于植物的生物碱类天然产物重要来源,微生物尤其是放线菌产生的众多次生代谢产物中,也包括很多生物碱。对放线菌来源生物碱的骨架结构和药效基团生物合成研究,不仅能够丰富人们对天然产物结构形成原理的理解,还可以为运用合成生物学技术人工合成此类化合物提供重要的遗传元件。本文从模块化生物合成和非模块化生物合成两种方式,综述放线菌来源生物碱的生物合成基因簇、途径及其酶催化反应过程。     

微生物代谢物组学的研究方法与进展*

代谢物组学、基因组学、转录组学和蛋白质组学是系统生物学研究的重要组成部分。近年来,在代谢物组学领域,微生物代谢物组学的研究受到人们的重视,成为研究的热点。本文综述了微生物代谢物组学的研究方法,包括样品处理、分析平台、数据处理和生物学解释等,并讨论了微生物代谢物组学在代谢工程方面的应用潜力,以及微生物代谢物组学的研究前景和所面临的挑战。     

代谢组学及其研究进展

1　代谢组学的定义和特点　　近年来,随着人类基因组测序工作的完成,人们对生命过程的理解有了很大的提高,研究的热点转移到基因的功能和几个“组学”研究,包括研究核糖核酸(RNA)转录过程的转录组学、研究某个过程中所有蛋白及其功能的蛋白组学、研究代谢产物的变化及代谢途径的代谢组学。　　代谢组学作为一门新发展的技术,它是通过考察生物体系受刺激或扰动后(如将某个特定的基因变异或环境变化后)其代谢产物的变化或其随时间的变化,来研究生物体系的代谢途径的一种技术[1];它所关注的是相对分子质量为1000以下的小分子。代谢组学的代表…     

近期工业微生物关键技术和应用

近年来,随着宏基因组学、蛋白质组学和代谢组学等技术的发展,工业微生物技术在资源、医药和手性合成等领域已经成为热点技术,并开拓了电子和纳米技术等新的应用领域。本文综述了几项最新的工业微生物技术,主要包括:微生物环氧化水解酶催化合成手性二醇、微生物甲酸脱氢酶用于再生氧化还原反应的辅因子、通过噬菌体展示技术得到纳米级金属丝、代谢网络改造和重建用于传统发酵生产以及有机溶剂耐受菌和宏基因组技术的应用。     

近期工业微生物关键技术和应用

近年来,随着宏基因组学、蛋白质组学和代谢组学等技术的发展,工业微生物技术在资源、医药和手性合成等领域已经成为热点技术,并开拓了电子和纳米技术等新的应用领域.本文综述了几项最新的工业微生物技术,主要包括:微生物环氧化水解酶催化合成手性二醇、微生物甲酸脱氢酶用于再生氧化还原反应的辅因子、通过噬菌体展示技术得到纳米级金属丝、代谢网络改造和重建用于传统发酵生产以及有机溶剂耐受菌和宏基因组技术的应用.     

代谢组学及其在微生物领域的研究进展

代谢组学、基因组学和蛋白质组学是系统生物学研究的重要组成部分。本文在文献和作者本人研究的基础上,对代谢组学的产生和技术平台及其在环境微生物领域的研究进展进行了评述。     

基于质谱分析的新精神活性物质代谢研究进展

近年来,新精神活性物质愈发泛滥,滋生了违法犯罪等社会问题,严重危害公众健康和社会安定。新精神活性物质在人体内代谢迅速,通过质谱方法检测其特征代谢物能够有效确定摄入情况。该文通过检索、整理和讨论相关文献,综述了近5年新精神活性物质体外、体内的代谢研究,总结了不同方法的适用性和优缺点,并与真实人体样本数据进行了比较。最后展望了代谢研究方法的发展趋势,以期为鉴定代谢产物,推断代谢途径与生物标志物等新精神活性物质代谢研究提供参考。     

基于非靶向代谢组学的茄梨和红茄梨成熟期果皮代谢产物的差异分析

为了探究西洋梨品种茄梨及其红色芽变红茄梨成熟期果皮代谢产物差异,采用超高效液相色谱-质谱联用技术,对茄梨和红茄梨成熟期果皮进行非靶向代谢组学研究。通过主成分分析和正交偏最小二乘判别分析,构建了多变量统计分析模型,结合模型和变量重要性投影与最大差异倍数值,基于精确质量数、二级碎片以及同位素分布,使用PMDB(Plant Metabolome Database)数据库进行定性,筛选并鉴定出茄梨和红茄梨果皮中显著性变化(P<0.05, VIP(variable importance in project)≥1)的差异代谢物有83种,主要包括酚酸类、黄酮类和氨基酸类物质,涉及类黄酮代谢、氨基酸代谢、苯丙烷类代谢等代谢途径,其中53种物质含量上调,30种物质表达下调。通过KEGG(Kyoto Encyclopedia of Genes and Genomes)数据库进一步对差异代谢物质进行通路富集分析,差异代谢物主要分布在20条代谢途径中,P<0.05的代谢途径有6条,分别是类黄酮生物合成、黄酮和黄酮醇生物合成、苯丙烷生物合成、丁酸酯代谢、苯丙氨酸代谢、酪氨酸代谢。这些差异代谢物的变化可能是导致茄梨和红茄梨果皮色泽不同的原因。该研究从植物代谢组学角度初步揭示了茄梨和红茄梨成熟期果皮的代谢产物差异性。     

~(13)C核磁共振谱与生物合成研究

植物、动物和微生物代谢产生了许多次生物质,这些物质密切联系着人类的生活,例如抗生素、中草药活性成分、香料、色素、性引诱剂等等。研究这些次生代谢产物的生物合成已成为天然有机化学中十分活跃的一个分支。生物合成是研究这些次生物质的生源途径,即搞清楚     

近期工业微生物关键技术和应用

近年来,随着宏基因组学、蛋白质组学和代谢组学等技术的发展,工业微生物技术在资源、医药和手性合成等领域已经成为热点技术,并开拓了电子和纳米技术等新的应用领域.本文综述了几项最新的工业微生物技术,主要包括:微生物环氧化水解酶催化合成手性二醇、微生物甲酸脱氢酶用于再生氧化还原反应的辅因子、通过噬菌体展示技术得到纳米级金属丝、代谢网络改造和重建用于传统发酵生产以及有机溶剂耐受菌和宏基因组技术的应用.     

Reshaping the 2-Pyrone Synthase Active Site for Chemoselective Biosynthesis of Polyketides

Engineering enzymes with novel reactivity and applying them in metabolic pathways to produce valuable products are quite challenging due to the intrinsic complexity of metabolic networks and the need for high in vivo catalytic efficiency. Triacetic acid lactone (TAL), naturally generated by 2-pyrone synthase (2PS), is a platform molecule that can be produced via microbial fermentation and further converted into value-added products. However, these conversions require extra synthetic steps under harsh conditions. We herein report a biocatalytic system for direct generation of TAL derivatives under mild conditions with controlled chemoselectivity by rationally engineering the 2PS active site and then rewiring the biocatalytic pathway in the metabolic network of E. coli to produce high-value products, such as kavalactone precursors, with yields up to 17 mg/L culture. Computer modeling indicates sterics and hydrogen-bond interactions play key roles in tuning the selectivity, efficiency and yield.     

Total synthesis approaches to natural product derivatives based on the combination of chemical synthesis and metabolic engineering

Secondary metabolites are an extremely diverse and important group of natural products with industrial and biomedical implications. Advances in metabolic engineering of both native and heterologous secondary metabolite producing organisms have allowed the directed synthesis of desired novel products by exploiting their biosynthetic potentials. Metabolic engineering utilises knowledge of cellular metabolism to alter biosynthetic pathways. An important technique that combines chemical synthesis with metabolic engineering is mutasynthesis (mutational biosynthesis; MBS), which advanced from precursor-directed biosynthesis (PDB). Both techniques are based on the cellular uptake of modified biosynthetic intermediates and their incorporation into complex secondary metabolites. Mutasynthesis utilises genetically engineered organisms in conjunction with feeding of chemically modified intermediates. From a synthetic chemist's point of view the concept of mutasynthesis is highly attractive, as the method combines chemical expertise with Nature's synthetic machinery and thus can be exploited to rapidly create small libraries of secondary metabolites. However, in each case, the method has to be critically compared with semi- and total synthesis in terms of practicability and efficiency. Recent developments in metabolic engineering promise to further broaden the scope of outsourcing chemically demanding steps to biological systems.     

Metabolic Engineering of Microbial Cell Factories for Biosynthesis of Flavonoids: A Review

Flavonoids belong to a class of plant secondary metabolites that have a polyphenol structure. Flavonoids show extensive biological activity, such as antioxidative, anti-inflammatory, anti-mutagenic, anti-cancer, and antibacterial properties, so they are widely used in the food, pharmaceutical, and nutraceutical industries. However, traditional sources of flavonoids are no longer sufficient to meet current demands. In recent years, with the clarification of the biosynthetic pathway of flavonoids and the development of synthetic biology, it has become possible to use synthetic metabolic engineering methods with microorganisms as hosts to produce flavonoids. This article mainly reviews the biosynthetic pathways of flavonoids and the development of microbial expression systems for the production of flavonoids in order to provide a useful reference for further research on synthetic metabolic engineering of flavonoids. Meanwhile, the application of co-culture systems in the biosynthesis of flavonoids is emphasized in this review.     

Metabolomics approach based on utra-performance liquid chromatography coupled to mass spectrometry with chemometrics methods for high-throughput analysis of metabolite biomarkers to explore the abnormal metabolic pathways associated with myocardial dysfunction

Ultra-performance liquid chromatography/mass spectrometry-based metabolomics can been used for discovery of metabolite biomarkers to explore the metabolic pathway of diseases. Identification of metabolic pathways is key to understanding the pathogenesis and mechanism of disease. Myocardial dysfunction induced by sepsis (SMD) is a severe complication of septic shock and represents major causes of death in intensive care units; however its pathological mechanism is still not clear. In this study, ultrahigh-pressure liquid chromatography with mass spectrometry-based metabolomics with chemometrics anaylsis and multivariate pattern recognition analysis were used to detect urinary metabolic profile changes in a lipopolysaccharide-induced SMD mouse model. Multivariate statistical analysis including principal component analysis and orthogonapartial least squares discriminant analysis for the discrimination of SMD was conducted to identify potential biomarkers. A total of 19 differential metabolites were discovered by high-resolution mass spectrometry-based urinary metabolomics strategy. The altered biochemical pathways based on these metabolites showed that tyrosine metabolism, phenylalanine metabolism, ubiquinone biosynthesis and vitamin B6 metabolism were closely connected to the pathological processes of SMD. Consequently, integrated chemometric analyses of these metabolic pathways are necessary to extract information for the discovery of novel insights into the pathogenesis of disease.     

Measuring the metabolome: current analytical technologies

The post-genomics era has brought with it ever increasing demands to observe and characterise variation within biological systems. This variation has been studied at the genomic (gene function), proteomic (protein regulation) and the metabolomic (small molecular weight metabolite) levels. Whilst genomics and proteomics are generally studied using microarrays (genomics) and 2D-gels or mass spectrometry (proteomics), the technique of choice is less obvious in the area of metabolomics. Much work has been published employing mass spectrometry, NMR spectroscopy and vibrational spectroscopic techniques, amongst others, for the study of variations within the metabolome in many animal, plant and microbial systems. This review discusses the advantages and disadvantages of each technique, putting the current status of the field of metabolomics in context, and providing examples of applications for each technique employed.     

细胞蛋白质组学和代谢组学整合策略表征散斑型BTB/POZ蛋白质突变调控的关键代谢通路

散斑型BTB/POZ蛋白（SPOP）是前列腺癌中突变率最高的蛋白质之一。该研究通过整合细胞蛋白质组学和代谢组学的方法，揭示SPOP突变引起的代谢紊乱及其调控的代谢通路。首先，系统地研究了LNCaP SPOP野生型及突变型高表达细胞中的代谢变化。代谢组学结果显示，SPOP野生型和突变型（SPOP_Y87N和SPOP_F133L）导入的LNCaP细胞在偏最小二乘法判别分析（PLS-DA）得分图上得到了很好的区分。进一步通过单因素方差分析发现，SPOP突变引起富马酸、苹果酸、柠檬酸、天冬氨酸和天冬酰胺等代谢物含量的增加。蛋白质组学共发现909种蛋白质在两种LNCaP SPOP突变体细胞中发生变化。分别对差异代谢物和差异蛋白质进行通路富集分析，发现三羧酸循环、氨酰基-转运核糖核酸生物合成在代谢组学和蛋白质组学分析中都发生了明显改变。最后，在SPOP敲除的Du145细胞中验证了上述研究结果。该研究证明SPOP突变可促进三羧酸循环。     

Untargeted metabolomic study on the insomnia effect of Suan‐Zao‐Ren decoction in the rat serum and brain using ultra‐high‐performance liquid chromatography quadrupole time‐of‐flight mass spectrometry combined with data processing analysis

Insomnia is a common clinical disease that can seriously damage the normal lives of sufferers. Suan‐Zao‐Ren decoction has been used to treat insomnia for a long time. However, the underlying molecular mechanism of Suan‐Zao‐Ren decoction is still not clear. In this study, the nontargeted metabolomics based on high‐resolution mass spectrometry and multiple statistical approaches were initially used to investigate the changes of potential serum and brain biomarkers and metabolic pathways in the insomnia model rat. Principal component analysis‐discriminate analysis indicated that the Suan‐Zao‐Ren decoction treatment improved the metabolic phenotype insomnia. Moreover, the heatmap analysis identified the most important biomarkers involved in insomnia. According to the pathway analysis, phenylalanine metabolism, tryptophan metabolism, and so on were recognized as the most affected metabolic pathways associated with insomnia disease. These findings provided a comprehensive understanding of the regulative effects of Suan‐Zao‐Ren decoction on the host metabolic phenotype of the insomnia rats. Our work demonstrated that the metabolomics approach is a promising tool that could help us to conduct the exploration of the therapeutic effects and mechanism of traditional Chinese medicines.