聚酮类抗生素组合生物合成

组合生物合成是公认的产生大量"非天然"的天然产物的一种有效方法,也是近年来药物创新与应用的研究热点和重要手段之一。目前,组合生物合成在聚酮类抗生素等生物活性物质的开发应用研究中已经取得了显著的成果。结合文献中的例子,回顾了运用组合生物合成在天然产物的基础上产生更多结构及功能多样性的聚酮类抗生素的方法和思路,并对某些方法所存在的问题与不足进行了讨论。     

真菌聚酮化合物生物合成研究进展

具有广泛生物活性的真菌聚酮化合物因具有复杂的化学结构,其生物合成途径一般包含多样且新颖的酶催化反应。文中主要综述了2013-2016年来源于还原性聚酮合成酶(HR-PKSs)、非还原性聚酮合成酶(NR-PKSs)、聚酮-非核糖体多肽合成酶(PKS-NRPSs)和还原性-非还原性聚酮合成酶(HR-NR PKSs)杂合型等四大类型的真菌聚酮类化合物的生物合成研究进展。众多真菌聚酮类化合物生物机理的阐明,为未来新型真菌聚酮类天然产物生物合成基因簇的挖掘、新结构化合物的发现及其类似物的研究提供了方向和理论基础。     

潮霉素A的生物合成研究进展

潮霉素A是一种从吸水链霉菌中发现的具有广谱生物学活性的抗生素。它在吸水链霉菌Streptomy-ces hygroscopicus NRRL 2388中的生物合成基因簇已被克隆并测序,其生物合成机制、遗传操作等方面的研究也取得了一定的进展。就潮霉素A的化学结构、生物合成基因簇的组织结构、生物合成和抗性机制等方面的研究进展进行综述。     

花色素苷生物合成的遗传和发育调控

概述了高等植物花色素苷生物合成过程的遗传和发育调控的研究进展。重点介绍花色素苷生物合成的结构基因和调控基困的分子克隆,调控基因对结构基因的调控功能。     

肽类抗生素生物合成基因簇在Escherichia coli中的异源表达

微生物能够产生众多结构和生物活性多样的次生代谢产物,而其生物合成基因簇的挖掘和异源表达是药物创新和产量提高的必要前提. 在过去20年里,大量重要天然产物的生物合成基因簇在微生物中被不断的发现. 在这些被挖掘的基因簇中,肽类抗生素的生物合成基因簇占了很大比重.肽类抗生素因具有抗菌、抗肿瘤、抗病毒等多种生物学活性而备受化学家和药物学家的重视. 如能了解它们的生物合成机制,实现其基因簇的异源表达,将使合理化遗传修饰生物合成通路获取结构类似物（药物开发）和提高产量成为可能. 大肠杆菌作为最广泛、最成功的表达体系,常用来表达外源基因,但一般只能表达一个或几个基因,却很少有用它来表达整个生物合成基因簇. 2001年,Khosla和Cane在E.coli中成功异源表达了一个复杂聚酮天然产物（红霉素苷原6dEB）基因簇. 这是首个有关在E.coli中异源表达天然产物生物合成基因簇的研究. 至此之后,大肠杆菌开始作为生物合成基因簇的异源表达宿主,越来越受到相关领域的重视. 紧接着核糖体肽和非核糖体肽生物合成基因簇也相继在大肠杆菌中成功异源表达. 本文对肽类抗生素生物合成基因簇在E.coli中的异源表达进行了综述.     

多氧霉素及其生物合成的研究进展

多氧霉素(Polyoxins)是高效广谱抗真菌核苷类抗生素,在农业上广泛用于防治植物真菌病害。本文综述了多氧霉素化学结构和理化性质,尤其是武汉大学组合生物合成与新药发现(教育部)重点实验室近年来在该抗生素生物合成基因簇的克隆、生物合成途径的阐明以及多氧霉素组合生物合成等多个方面的研究进展与成果,并对今后以多氧霉素为代表的核苷类抗生素的生物合成研究进行了展望。     

以生物合成为基础的红霉素A的产量提高和结构改造

红霉素A是一种广谱大环内酯类抗生素,在临床上应用广泛。其生物合成包括由聚酮合酶催化的十四元环骨架形成,以及羟基化、糖基化、甲基化后修饰。基于对红霉素A生物合成机制的认识,可以对产生菌种进行定向的遗传操作,达到产量提高和结构改造等目的。本文综述了近年来在红霉素A高产菌株改造和化学结构衍生方面所取得的研究进展,为相关研究人员提供参考。     

ε-聚赖氨酸生物合成及其产生菌遗传转化研究进展

ε-聚赖氨酸(ε-poly-L-lysine,ε-PL)是由25-35个L-赖氨酸(L-lysine)通过α-ε酰胺键连接的具有很强抗菌活性的聚合物,是自然界中迄今为止仅发现的2种均聚氨基酸(ε-聚赖氨酸和γ-聚谷氨酸)之一。目前,研究发现ε-聚赖氨酸的合成酶是一种非核糖体肽合成酶,它催化前体物质L-lysine经多轮缩合反应合成链长不均一的ε-聚赖氨酸,与I型聚酮合成酶的合成过程相似。ε-聚赖氨酸的合成不受降解酶控制。同时,针对产生菌遗传转化的穿梭质粒载体pLAE001和pLAE003已构建成功,为进一步探索ε-聚赖氨酸生物合成提供了条件。本文主要就ε-聚赖氨酸生物合成及产生菌遗传转化体系进行综述。另外,扼要介绍了作者所在课题组的相关研究工作、取得的进展并提出了相应的见解,论文最后部分对组合生物合成在ε-PL产生菌菌种改造中的应用前景进行了探讨。     

蛋白质生物合成支路

蛋白质生物合成支路金由辛（中国科学院上海生物化学研究所,上海２０００３１）关键词蛋白质生物合成,支路６０年代中期遗传密码破译后,蛋白质生物合成的轮廓已经清楚。ｍＲＮＡ作为蛋白质生物合成的直接模板,分子内含有遗传信息。它就是以连续不重叠方式排列的三联体...     

基于生物合成机制的天然产物结构多样性研究

天然产物尤其是次级代谢产物在药物化学和化学生物学中扮演重要角色.基于天然产物获得结构多样性的类似物对于新药的筛选和医学研究具有重要意义.天然产物均由生物体代谢产生,在了解其生物合成机制的基础上,对生物合成过程进行合理化改造,可以极大地丰富天然产物的结构多样性,获得许多具有重要生理活性和有机化学不易合成的天然产物类似物.本文以硫肽类抗生素中的硫链丝菌素和聚酮聚肽类化合物为例,对生物合成方法在天然产物结构多样性中的应用进行总结和展望.     

Genome-scale metabolic models as platforms for strain design and biological discovery

Genome-scale metabolic models (GEMs) have been developed and used in guiding systems’ metabolic engineering strategies for strain design and development. This strategy has been used in fermentative production of bio-based industrial chemicals and fuels from alternative carbon sources. However, computer-aided hypotheses building using established algorithms and software platforms for biological discovery can be integrated into the pipeline for strain design strategy to create superior strains of microorganisms for targeted biosynthetic goals. Here, I described an integrated workflow strategy using GEMs for strain design and biological discovery. Specific case studies of strain design and biological discovery using Escherichia coli genome-scale model are presented and discussed. The integrated workflow presented herein, when applied carefully would help guide future design strategies for high-performance microbial strains that have existing and forthcoming genome-scale metabolic models.     

Max Bergmann award lecture:Macromolecular medicinal chemistry as applied to metabolic diseases

This review presents the scope of research presented in an October 2016 lecture pertaining to the award of the 2015 Max Bergmann Medal. The advancement in synthetic and biosynthetic chemistry as applied to the discovery of novel macromolecular drug candidates is reviewed. The evolution of the technology from the design, synthesis, and development of the first biosynthetic peptides through the emergence of peptide‐based incretin agonists that function by multiple biological mechanisms is exemplified by the progression of such peptides from preclinical to clinical study. A closing section highlights recent progress made in total chemical synthesis of insulin and related peptides.     

Recent developments towards the heterologous expression of complex bacterial natural product biosynthetic pathways

The heterologous expression of natural product biosynthetic pathways is of increasing interest in biotechnology and drug discovery. It enables the (over)production of structurally complex substances through transfer of the biosynthetic genes from the original producer to more amenable heterologous hosts, and provides the basis to generate novel analogs through biosynthetic engineering. Furthermore, the lateral transfer of 'silent' (not expressed under standard laboratory conditions) secondary metabolite pathways or metagenomic DNA into surrogate host strains is expected to yield new, potentially bioactive compounds. This review discusses recent reports on the heterologous production of natural products with emphasis on polyketide and nonribosomally biosynthesized peptide compounds.     

New strategies and approaches for engineering biosynthetic gene clusters of microbial natural products

With the rapidly growing number of sequenced microbial (meta)genomes, enormous cryptic natural product (NP) biosynthetic gene clusters (BGCs) have been identified, which are regarded as a rich reservoir for novel drug discovery. A series of powerful tools for engineering BGCs has accelerated the discovery and development of pharmaceutically active NPs. Here, we describe recent advances in the strategies for BGCs manipulation, which are driven by emerging technologies, including efficient DNA recombination systems, versatile CRISPR/Cas9 genome editing tools and diverse DNA assembly methods. We further discuss how these approaches could be used for genome mining studies and industrial strain improvement.     

植物多胺代谢途径研究进展

多胺是一类小分子生物活性物质,广泛存在于生物体内,与植物的生长发育、衰老及抗逆性都有着密切的联系。目前,在植物中的多胺合成途径已经基本揭示,其生理作用在分子水平上逐步得到阐明。对多胺合成突变体和各种转基因植物的研究也使得人们更深入地了解了多胺以及其合成代谢相关酶在植物生长发育等生理过程中的重要作用。以下概述了植物多胺代谢途径,重点综述了代谢途径中各基因的功能及遗传操作的最新进展,并对将来的研究方向尤其是相关基因在植物抗逆境 (包括生物和非生物逆境) 基因工程方面的应用作了讨论。     

Construction of a microbial natural product library for chemical biology studies

The RIKEN Natural Products Depository (NPDepo) is a public depository of small molecules. Currently, the NPDepo chemical library contains 39,200 pure compounds, half of which are natural products and their derivatives. In order to reinforce the uniqueness of our chemical library, we have improved our strategies for the collection of microbial natural products. Firstly, a microbial metabolite fraction library coupled with an MP (microbial products) plot database provides a powerful resource for the efficient isolation of microbial metabolites. Secondly, biosynthetic studies of microbial metabolites have enabled us to not only access ingenious biosynthetic machineries, but also obtain a variety of biosynthetic intermediates. Our chemical library contributes to the discovery of molecular probes for increasing our understanding of complex biological processes and for eventually developing new drug leads.     

Synthetic biology and metabolic engineering of actinomycetes for natural product discovery

Actinomycetes are one of the most valuable sources of natural products with industrial and medicinal importance. After more than half a century of exploitation, it has become increasingly challenging to find novel natural products with useful properties as the same known compounds are often repeatedly re-discovered when using traditional approaches. Modern genome mining approaches have led to the discovery of new biosynthetic gene clusters, thus indicating that actinomycetes still harbor a huge unexploited potential to produce novel natural products. In recent years, innovative synthetic biology and metabolic engineering tools have greatly accelerated the discovery of new natural products and the engineering of actinomycetes. In the first part of this review, we outline the successful application of metabolic engineering to optimize natural product production, focusing on the use of multi-omics data, genome-scale metabolic models, rational approaches to balance precursor pools, and the engineering of regulatory genes and regulatory elements. In the second part, we summarize the recent advances of synthetic biology for actinomycetal metabolic engineering including cluster assembly, cloning and expression, CRISPR/Cas9 technologies, and chassis strain development for natural product overproduction and discovery. Finally, we describe new advances in reprogramming biosynthetic pathways through polyketide synthase and non-ribosomal peptide synthetase engineering. These new developments are expected to revitalize discovery and development of new natural products with medicinal and other industrial applications.     

Cover Image,Volume 116, Number 9, September 2019

The new and rapid advancement in the complexity of biologics drug discovery has been driven by a deeper understanding of biological systems combined with innovative new therapeutic modalities, paving the way to breakthrough therapies for previously intractable diseases. These exciting times in biomedical innovation require the development of novel technologies to facilitate the sophisticated, multifaceted, high-paced workflows necessary to support modern large molecule drug discovery. A high-level aspiration is a true integration of “lab-on-a-chip” methods that vastly miniaturize cellulmical experiments could transform the speed, cost, and success of multiple workstreams in biologics development. Several microscale bioprocess technologies have been established that incrementally address these needs, yet each is inflexibly designed for a very specific process thus limiting an integrated holistic application. A more fully integrated nanoscale approach that incorporates manipulation, culture, analytics, and traceable digital record keeping of thousands of single cells in a relevant nanoenvironment would be a transformative technology capable of keeping pace with today's rapid and complex drug discovery demands. The recent advent of optical manipulation of cells using light-induced electrokinetics with micro- and nanoscale cell culture is poised to revolutionize both fundamental and applied biological research. In this review, we summarize the current state of the art for optical manipulation techniques and discuss emerging biological applications of this technology. In particular, we focus on promising prospects for drug discovery workflows, including antibody discovery, bioassay development, antibody engineering, and cell line development, which are enabled by the automation and industrialization of an integrated optoelectronic single-cell manipulation and culture platform. Continued development of such platforms will be well positioned to overcome many of the challenges currently associated with fragmented, low-throughput bioprocess workflows in biopharma and life science research.     

Mining novel biosynthetic machineries of secondary metabolites from actinobacteria

ABSTRACT

Secondary metabolites produced by actinobacteria have diverse structures and important biological activities, making them a useful source of drug development. Diversity of the secondary metabolites indicates that the actinobacteria exploit various chemical reactions to construct a structural diversity. Thus, studying the biosynthetic machinery of these metabolites should result in discovery of various enzymes catalyzing interesting and useful reactions. This review summarizes our recent studies on the biosynthesis of secondary metabolites from actinobacteria, including the biosynthesis of nonproteinogenic amino acids used as building blocks of nonribosomal peptides, the type II polyketide synthase catalyzing polyene scaffold, the nitrous acid biosynthetic pathway involved in secondary metabolite biosynthesis and unique cytochrome P450 catalyzing nitrene transfer. These findings expand the knowledge of secondary metabolite biosynthesis machinery and provide useful tools for future bioengineering.