柠檬烯和红没药烯的微生物代谢工程

柠檬烯和红没药烯均为植物天然产物,分别属于单萜类和倍半萜类化合物,能够预防和治疗癌症等多种疾病。以其作为前体物,还可以转化合成多种具有高附加值的工业产品,例如药品、保健品、化妆品及生物燃料等。目前柠檬烯和红没药烯的工业生产主要是通过植物提取法实现的,但从植物组织中提取柠檬烯和红没药烯存在着产物含量低和分离纯化困难等缺点。微生物代谢工程的快速发展为这些植物天然产物的生产提供了一条更具潜力的生物合成路线。利用微生物代谢工程技术构建生产这些有价值的植物天然产物的微生物细胞工厂具有绿色清洁、可持续发展和经济效益好等独特优势。文中系统综述了近年来代谢工程技术在微生物合成柠檬烯和红没药烯过程中的应用进展,包括所涉及的宿主菌株、关键酶、代谢途径及其改造等,并探讨了其未来发展方向。     

Characteristics of the development and biosynthetic activity of a mixed culture of microorganisms

The growth of microbial populations and their biosynthesis of proteinases with the fibrinolytic activity were studied in an artificial ecosystem composed of a strain producing the enzymes (Nocardia minima 1) and a zero strain (Arthrobacter citreus VKM 654). The microorganisms in the association were shown to interact in terms of amensalism via metabolites if the enzyme-producing strain dominated.     

后基因组时代微生物天然产物高效发掘体系设计与展望

微生物天然产物具有丰富的化学结构多样性和诱人的生物活性,持续启迪着创新医药和农药的发现。近年来,随着高通量测序技术的快速发展,巨大的微生物基因组数据揭示了多样生物合成和新颖天然产物的潜能远高于以前的认知。然而,如何高效地激活隐性的生物合成基因簇 (BGCs) 并识别相应的化合物,以及避免已知代谢产物的重复发现等挑战依然严峻。本文描述了面对这些问题时基因组学、生物信息学、机器学习、代谢组学、基因编辑和合成生物学等新技术在发现药用先导化合物过程中提供的机遇;总结并论述了在潜力菌株优选、BGCs的生物信息学预测、沉默 BGCs的高效激活以及目标产物的识别和跟踪方面的新见解;提出了基于潜力菌株选择和多组学挖掘技术从微生物天然产物中高效发现先导结构的系统线路 (SPLSD),并讨论了未来天然产物药用先导发现的机遇和挑战。     

Introduction of New Tools for Chemical Biology Research on Microbial Metabolites

Recently, high-throughput screening (HTS) has become the mainstream technique for drug discovery. Compounds that are synthesized by combinatorial chemistry might be more suitable than natural products to apply to HTS, because the purification procedure is a drawback of using natural products. Nevertheless, natural products remain an extremely important source of drugs. To overcome the demerits of natural products, we are constructing the RIKEN Natural Products Depository (NPDepo) that is focused primarily on microbial metabolites. In this review, I describe (i) engineering pathways for biosynthetic gene clusters of microbial metabolites, (ii) construction of fraction libraries of microbial metabolites, and (iii) the development of a new screening system using a chemical array and a protein library produced by GLORIA.     

Analysis of intracellular metabolites of Corynebacterium glutamicum at high cell density with automated sampling and filtration and assessment of engineered enzymes for effective l‐lysine production

Engineering of enzymes and pathways is generally required for the development of efficient strains for bioproduction processes. To this end, quantitative and reliable data of intracellular metabolites are highly desired, but often not available, especially for conditions more close to industrial applications, i.e. at high cell density and product concentration. Here, we investigated the intracellular metabolite profiles of an engineered l ‐lysine‐producing Corynebacterium glutamicum strain and the corresponding wild‐type strain to assess the impacts of deregulation of product inhibition of the key enzymes aspartate kinase and phosphoenolpyruvate carboxylase and to identify potentials for their further improvement. A bioreactor system with automated fast‐sampling, filtration and on‐filter quenching of the metabolism was used for a more reliable determination of intracellular metabolites in batch cultures with optical cell density (OD₆₆₀) up to 40. The l ‐lysine‐producing strain showed substantially different metabolite profiles in the amino acid metabolism, including increased intracellular pool sizes in the l ‐lysine‐, l ‐homoserine‐ and l ‐threonine pathways and decreased intracellular pool sizes for all other determined amino acids. By comparing data of in vitro inhibition of the engineered enzymes and determined intracellular concentrations of the inhibitors it was found that the inferred in vivo activities of these enzymes are still significantly below their in vitro maximums. This work demonstrates the usefulness of metabolic analysis for assessing the impact of engineered enzymes and identifying targets for further strain development.     

洛伐他汀工业菌株土曲霉HZ01的次级代谢产物合成分析

【目的】分析洛伐他汀工业生产菌株土曲霉HZ01的次级代谢产物合成能力,为后期的遗传改造、次级代谢产物及其基因簇挖掘提供指导。【方法】对洛伐他汀发酵条件下的样品进行了转录组分析,同时运用色谱分离技术及波谱学方法对主要次级代谢产物进行了分离和结构鉴定。【结果】洛伐他汀合成相关基因转录水平非常高,还有4个聚酮合酶(PKS)、6个非核糖体多肽合成酶(NRPS)和1个PKS-NRPS杂合酶基因进行了转录,其他PKS和NRPS基因都处于沉默状态。此外,从该菌的发酵产物中分离鉴定了10个主要副产物并确定了其结构。【结论】土曲霉HZ01是一株优良的洛伐他汀生产菌株,在构建次级代谢产物异源合成细胞工厂和鉴定次级代谢产物生物合成途径方面具有很好的应用潜力。     

Microbial decolouration of azo dyes: A review

The textile industry is a substantial consumer of water and produces enormous volumes of contaminated water; the most important contaminants are azo dyes. Microbial processes for the treatment of textile wastewater have the advantage of being cost-effective and environmentally friendly and producing less sludge. The most promising microorganisms for wastewater treatment are those isolated from sites contaminated with dyes or from the sludge of treatment plants because they have adapted to survive in adverse conditions. The mechanism of microbial decolouration occurs from adsorption, enzymatic degradation or a combination of both. Both reductases and oxidases are involved in the microbial degradation process. The goal of microbial treatment is to decolourise and detoxify the dye-contaminated effluents. In this review, we summarise the methodologies used to evaluate the toxicity of azo dyes and their degradation products. Recent studies on the decolouration or degradation of azo dyes using algae, yeast, filamentous fungi and bacteria, genetically modified microorganisms, microbial consortia and microbiological systems combined with Advanced Oxidation Processes (AOPs) and Microbial Fuel Cells (MFCs) are discussed in this review.     

铜绿假单胞菌生防菌株抑菌代谢产物及其生防应用研究进展

微生物次生代谢产物的研究对开发微生物源农药具有重要意义。近年来一系列根际来源的铜绿假单胞菌被分离和鉴定,因其产生抑菌次生代谢产物,具有很好的生物防治效果。本文将系统综述铜绿假单胞菌生防菌株的种类及其抑菌代谢产物的多样性,并进一步介绍铜绿假单胞菌生防菌株的抑菌代谢产物合成机制及其遗传改造,简要讨论铜绿假单胞菌生防菌株抑菌代谢产物在生物防治上的应用和前景。     

Pipecolic acid in microbes: biosynthetic routes and enzymes

Pipecolic acid is an important precursor of many useful microbial secondary metabolites. Pipecolic acid-derived moieties are often crucial for the biological activities of some microbial natural products with pharmaceutical applications. Understanding the biogenesis of pipecolic acid in microorganisms would be a significant step toward the mutasynthesis of novel analogs of choice. This review focuses on various microbial pathways and enzymes for pipecolic acid synthesis, especially those related to the origination of pipecolic acid moieties in secondary metabolites.     

Microbial sucrose isomerases: producing organisms, genes and enzymes

Sucrose isomerase (SI) activity is used industrially for the conversion of sucrose into isomers, particularly isomaltulose or trehalulose, which have properties advantageous over sucrose for some food uses. All of the known microbial SIs are TIM barrel proteins that convert sucrose without need for any cofactors, with varying kinetics and product specificities. The current analysis was undertaken to bridge key gaps between the information in patents and scientific publications about the microbes and enzymes useful for sucrose isomer production.This analysis shows that microbial SIs can be considered in 5 structural classes with corresponding functional distinctions that broadly align with the taxonomic differences between producing organisms. The most widely used bacterial strain for industrial production of isomaltulose, widely referred to as “Protaminobacter rubrum” CBS 574.77, is identified as Serratia plymuthica. The strain producing the most structurally divergent SI, with a high product specificity for trehalulose, widely referred to as “Pseudomonas mesoacidophila” MX-45, is identified as Rhizobium sp.Each tested SI-producer is shown to have a single SI gene and enzyme, so the properties reported previously for the isolated proteins can reasonably be associated with the products of the genes subsequently cloned from the same isolates and SI classes. Some natural isolates with potent SI activity do not catabolize the isomer under usual production conditions. The results indicate that their industrial potential may be further enhanced by selection for variants that do not catabolize the sucrose substrate.     

CRISPR/Cas9编辑大肠杆菌工程菌生产氨基葡萄糖

【背景】氨基葡萄糖(glucosamine, GlcN)及其衍生物N-乙酰氨基葡萄糖(N-acetylglucosamine,GlcNAc)是合成糖胺聚糖的重要前体物质,在医药、化妆品和保健品领域具有广泛的应用价值。传统的生产方式存在诸多弊端,如环境污染、原料限制、不适于海鲜易过敏人群等问题,因此利用微生物发酵法生产GlcN和GlcNAc越来越受到青睐。【目的】利用微生物发酵生产并提高N-乙酰氨基葡萄糖的产量,探索分子改造及发酵条件优化策略。【方法】以大肠杆菌MG1655为出发菌株,首先利用表达载体共表达大肠杆菌来源的glmS和酿酒酵母来源的gna1,构建GlcNAc的生物合成路径,然后利用CRISPR/Cas9技术敲除GlcNAc的分解代谢与转运途径,以提高GlcNAc的产量,最后结合发酵条件优化使GlcNAc的产量得到进一步提升。【结果】通过分子改造得到一株产GlcNAc菌株RY-5,发酵20 h后GlcNAc的产量达到了2.36 g/L,相较于初始构建的菌株RY-1提高了29倍,进一步对装液量和诱导剂IPTG的添加时间等条件进行发酵优化,GlcNAc产量达到了7.74g/L,与优...     

后基因组时代基因组重排在微生物菌种选育中的应用及展望

基因组重排作为一种实用高效的育种技术,在缺乏遗传背景认知和可操作遗传体系等条件下,可以突破微生物种属间的限制,经过多轮递推的原生质体融合来加速其人工定向进化,在微生物菌种改良及代谢产物开发和产业化等研究领域得到了广泛应用。步入后基因组时代,快速发展的组学和生物信息学使基因组重排成为连接各种微生物育种方法的重要纽带,为我们深入探索微生物复杂的代谢网络和全局调控机制,更为精准地实施对微生物的人工调控和定向进化提供了契机。本文系统性地回顾了近年来基因组重排在微生物菌种选育中的应用研究,尤其针对围绕其开展的组学研究进行了详细阐述,并对基因组重排与组学、生物信息学和合成生物学等新兴技术的联合应用进行了展望。     

成像质谱在微生物代谢产物研究中的应用

微生物代谢产物的结构和功能多样,对相邻微生物和环境会产生重要影响。传统的天然产物分离方法不能系统全面地监测单一或混合微生物样品中代谢物的合成和释放模式。成像质谱能够同时可视化观察从单一微生物菌落到复杂微生物群落的多个代谢产物的时空分布,可以用于发现重要的生物活性分子,观察微生物菌落的代谢交流,以及跟踪微生物之间相互竞争过程中代谢物的修饰等方面的研究。本文综述了成像质谱在微生物代谢产物研究中的最新进展,展望了该技术的应用前景。     

Microbial production of small medicinal molecules and biologics: From nature to synthetic pathways

Natural products are promising chemicals due to their structural diversity and bioactivities. Over the decades, a vast variety of gene clusters encoding natural products have been identified and overexpressed in microbes. Recently, the development of metabolic engineering, synthetic biology and bioinformatics strategies have facilitated target discovery and design. Microbial cells have been therefore constantly engineered for product accumulation. This review summarizes approaches of domesticating microbial hosts in producing major classes of natural products, with an emphasis on recent advances.     

Character of interactions of saprophytic soil microflora via gaseous metabolites

The character of interaction between saprophytic soil bacteria via gaseous metabolites was studied. It was established that, at the metabolic level, a diverse character of interspecies interrelationships between bacteria exist, directly influencing their reproduction and preservation in soil. Volatile compounds produced by bacteria are able to act as both intra-and interspecies regulators of microbial communities. The soil microbiocenosis composition may be therefore regulated by volatile products of metabolism of saprophytic soil bacteria. Methanol released by bacteria into the environment plays an important role in this process.     

产β-内酰胺酶金黄色葡萄球菌的耐药分析

目的对产β-内酰胺酶金黄色葡萄球菌的标本分布和药物敏感试验进行分析,为临床使用抗生素提供依据。方法按照《全国临床检验操作规程》的要求接种．对分离出的220株金黄色葡萄球菌（Sta phylococcs aureus,Sau）,用头孢菌素显色法测定其β-内酰胺酶。结果220株金黄色葡萄球菌中产β-内酰胺酶171株,产酶率为77．7％,产酶株除对万古霉素、替考拉宁、利福平及复方新诺明敏感外,对其它的抗生素均呈现不同程度耐药,其中青霉素G、氨苄西林耐药率均为99．4％,红霉素为86．1％。结论产β-内酰胺酶株对青霉素类、大环内酯类抗生素呈现高度耐药,临床治疗不宜使用此类抗生素,提示临床选择药物时,应在药敏试验的指导下合理选择抗生素。     

红树林样品不经分离的微生物群体培养物生物活性研究

从海南、广西与广东三省的红树林区采集了181个样品,不进行微生物分离而直接作发酵剂接种到发酵培养基进行发酵,取发酵上清液进行抗细菌、抗真菌与肿瘤细胞毒活性的测定。同时对样品进行可培养微生物的分离与生物活性测定。结果显示:不同样品类型的生物活性差异较大。在15个具有强抗活性的样品中,有5个样品分离到的单株菌均无任何生物活性,说明这5个样品的生物活性可能是由微生物的群体作用产生的,也可能是某种没有培养出的微生物产生的。初步表明了探索微生物混合培养获得生物活性代谢产物的可能性。     

Old and new glycopeptide antibiotics: From product to gene and back in the post-genomic era

Glycopeptide antibiotics are drugs of last resort for treating severe infections caused by multi-drug resistant Gram-positive pathogens. First-generation glycopeptides (vancomycin and teicoplanin) are produced by soil-dwelling actinomycetes. Second-generation glycopeptides (dalbavancin, oritavancin, and telavancin) are semi-synthetic derivatives of the progenitor natural products. Herein, we cover past and present biotechnological approaches for searching for and producing old and new glycopeptide antibiotics. We review the strategies adopted to increase microbial production (from classical strain improvement to rational genetic engineering), and the recent progress in genome mining, chemoenzymatic derivatization, and combinatorial biosynthesis for expanding glycopeptide chemical diversity and tackling the never-ceasing evolution of antibiotic resistance.     

粘细菌基因组学研究进展

粘细菌(Myxobacteria)隶属于δ变形菌纲(Deltaproteobacteria)的粘球菌目(Myxococcales),是一类革兰氏阴性杆状细菌。它是继放线菌和真菌之后又一重要的活性次级代谢产物产生菌,尽管如此,由于分离纯化困难,粘细菌的研究进展一直较为缓慢。随着测序技术的进步和生物信息学的应用,大量粘细菌基因组被完成测序和报道。本文对粘细菌研究意义及该类资源开发价值、分离培养存在的困难进行了阐述,对粘细菌基因组注释及目前已测菌株的全基因组进行了归纳总结,同时介绍了基因组学在粘细菌生态、捕食机制、子实体形成以及次级代谢产物合成方面的研究进展。本文有助于了解基因组学在粘细菌研究中的重要价值,为联合应用多组学技术深入研究粘细菌代谢机制和社会性行为提供了参考,对粘细菌基础研究、资源发掘和开发利用具有重要意义。