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Engineered Biosynthesis of Natural Products in Heterologous Hosts

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Engineered Biosynthesis of Natural Products in Heterologous Hosts Chem Soc Rev View Article Online REVIEW ARTICLE View Journal Engineered biosynthesis of natural products in heterologous hosts Cite this: DOI: 10.1039/c5cs00025d Yunzi Luo,†‡ab Bing-Zhi Li,‡ac Duo Liu,‡ac Lu Zhang,ac Yan Chen,ac Bin Jia,ac Bo-Xuan Zeng,ac Huimin Zhaob and Ying-Jin Yuan*ac Natural products produced by microorganisms and plants are a major resource of antibacterial and anticancer drugs as well as industrially useful compounds. However, the native producers often suffer from Received 12th January 2015 low productivity and titers. Here we summarize the recent applications of heterologous biosynthesis for the DOI: 10.1039/c5cs00025d production of several important classes of natural products such as terpenoids, flavonoids, alkaloids, and polyketides. In addition, we will discuss the new tools and strategies at multi-scale levels including gene, www.rsc.org/csr pathway, genome and community levels for highly efficient heterologous biosynthesis of natural products. 1. Introduction market share in pharmaceuticalindustryinthepast30years, comprising 61% of anticancer compounds and 49% of anti- Molecules from natural sources, especially bacteria, fungi and infectives.2 For example, erythromycin from Saccharopolyspora ery- plants, have proven to be a large reservoir for new pharmaceuticals, thraea is an antibiotic, which has an antimicrobial spectrum similar therapeutic agents and industrially useful compounds.1 To date, to that of penicillin and can be used to treat various diseases.3 natural products and their derivatives command a substantial Lovastatin (Merck’s Mevacor) isolated from Aspergillus terreus is often used to reduce risk of cardiovascular disease, while paclitaxel a Key Laboratory of Systems Bioengineering (Ministry of Education), extracted from the bark of the Pacific yew, Taxus brevifolia,isa Tianjin University, Tianjin, 300072, P. R. China. E-mail: [email protected]; mitotic inhibitor used in cancer chemotherapy. There are also Fax: +86-22-27403888 important natural products discovered from other diverse sources, b Department of Chemical and Biomolecular Engineering and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 600 South Mathews Ave, such as insects and marine sources. In the old days before 1940s, Urbana, IL 61801, USA natural products of interest are isolated directly from plant sources c SynBio Research Platform, Collaborative Innovation Center of Chemical Science (Fig. 1A). However, bioactive compounds from natural sources are Published on 11 May 2015. Downloaded by University of Illinois - Urbana 26/05/2015 23:14:08. and Engineering (Tianjin), School of Chemical Engineering and Technology, usually secondary metabolites of their native producers, thus in Tianjin University, Tianjin, 300072, P. R. China some cases, they exist at a relatively low level comparing with the † Current address: State Key Laboratory of Biotherapy/Collaborative Innovation production of primary metabolites. Therefore, in most cases, direct Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, P. R. China. Renmin South Road 3, No. 17, Chengdu, Sichuan, 610041, P. R. China. isolation and extraction is not an environmental friendly, sustainable ‡ Equal contribution. and economical solution. Combinatorial chemistry was also Dr Yunzi Luo received her PhD in Dr Bing-Zhi Li is an associate Chemical and Biomolecular Engi- professor of Pharmaceutical Engi- neering from the University of neering in Tianjin University. He Illinois at Urbana and Champaign received his BS degree from in 2014. Her research has focused Nankai University in 2005 and his on natural products discovery and PhD from Tianjin University in synthetic biology. Dr Luo was a 2010. His research expertise is in postdoctoral research fellow at the synthetic biology and lignocellulose Institute for Genomic Biology of bioconversion. He has published University of Illinois at Urbana and more than 20 peer-reviewed inter- Champaign. She has published national papers. 11 papers in peer-reviewed inter- Yunzi Luo national journals and 2 book Bing-Zhi Li chapters. This journal is © The Royal Society of Chemistry 2015 Chem. Soc. Rev. View Article Online Review Article Chem Soc Rev introduced to synthesize and screen small molecules of medicinal engineering of microbial biosynthetic pathways towards the design importance (Fig. 1B). Still, due to the structure complexity of and creation of novel metabolic circuits and biological systems. With natural products, chemical synthesis of these compounds is the newly developed biosystems, the yield of target natural products often impractical. could be increased noticeably in a heterologous host. For example, To solve these problems, researchers have engineered and opti- Keasling and his colleagues successfully redesigned the biosynthesis mized natural products biosynthetic pathways for decades. As process of the artemisinin precursor, artemisinic acid, in hetero- genetic manipulation is either difficult or yet-to-be established for logous hosts Escherichia coli and Saccharomyces cerevisiae,5–7 which the majority of organisms, heterologous expression of a single gene, produced the artemisinic acid with a much higher productivity, titer acassetteofgenes,oranentirebiosyntheticgeneclusterina and yield and now the process has been transferred to a pharma- genetically tractable host is a practical alternative route for identify- ceutical company for commercialization. In addition, with the ing and engineering the corresponding natural product. In recent versatility of synthetic biology approaches, new compounds could years, with the third revolution in biotechnology, which requires the be discovered or generated by pathway refactoring or advanced convergence of life science, physical science and engineering dis- combinatorial biosynthesis (Fig. 1C).8,9 ciplines, new solutions have beenproposedfordrugdiscovery, Microbes, especially E. coli and yeast, have proven to be energy and food crisis.4 The first revolution of biology was evidenced useful organisms for heterologous biosynthesis of secondary by the discovery of the double helix structure of DNA by James metabolites for decades. They have been engineered to balance Watson and Francis Crick, while the second revolution began with and optimize natural product biosynthetic pathways for cost- the human genome project. Now, with the dawn of the post- effective production of high value compounds, as well as to genomics era came the third revolutionary change, which shifts discover novel compounds.10 Recent advances in synthetic the paradigm of the biology field from the understanding and biology and genome engineering facilitate the development of new tools for construction, controlling and optimization of metabolic pathways in microbes for heterologous biosynthesis. Herein, we review the recent progresses made in heterologous Duo Liu is currently a PhD biosynthesis of several different classes of important natural candidate in the Department of products, as well as how the newly developed synthetic biology Biochemical Engineering in Tianjin tools could help future heterologous biosynthesis of valuable University. He has worked on the natural products. In addition, we will highlight some of the most modular strategies of synthetic recent advances in heterologous biosynthesis of natural product biology for combinatorial construc- in the past five years. tion of yeast metabolic system for natural product biosynthesis. 2. Heterologous biosynthesis of major classes of high value natural products Natural products are a very important source for the develop- Published on 11 May 2015. Downloaded by University of Illinois - Urbana 26/05/2015 23:14:08. Duo Liu ment of medicines. Many natural products and the derivatives Dr Huimin Zhao is the Centennial Dr Ying-Jin Yuan is currently a Endowed Chair Professor of professor of Biochemical Engi- chemical and biomolecular engi- neering in Tianjin University. He neering, and professor of chemistry, received his PhD degree from biochemistry, biophysics, and Tianjin University in 1991. He is bioengineering at the University of now the director of Key Laboratory Illinois at Urbana-Champaign of Systems Bioengineering, Ministry (UIUC). He received his BS degree of Education, China. His research in Biology from the University of interests include synthetic biology, Science and Technology of China systems biotechnology, bioenergy, in 1992 and his PhD degree in biopharmaceutical engineering Chemistry from the California and plant cell culture. Dr Yuan is Huimin Zhao Institute of Technology in 1998. Ying-Jin Yuan the Fellow of IChemE. Dr Yuan has His primary research interests are published more than 180 inter- in the development and applications of synthetic biology tools to national peer-reviewed papers and address society’s most daunting challenges in human health and 30 patents. energy, and in the fundamental aspects of enzyme catalysis and gene regulation. Chem. Soc. Rev. This journal is © The Royal Society of Chemistry 2015 View Article Online Chem Soc Rev Review Article Fig. 1 Routes for heterologous biosynthesis of natural products. (A) Synthesis of natural products by traditional isolation from plants. (B) Synthesis and screening of small molecules by combinatorial chemistry. (C) Production of natural products by heterologous biosynthesis in microbes. have been developed as antibacterial, anticancer, antifungal, the MVA pathway in yeast-like fungi. In yeast, some highly antiviral and antiparasitic drugs.2 Butler
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