Recent advances in modular co-culture engineering for synthesis of natural products

https://doi.org/10.1016/j.copbio.2019.09.004Get rights and content

Highlights

  • Modular co-culture engineering for the production of natural products.

  • Advantages of modular co-culture engineering in the field of biosynthesis.

  • Designs and strategies for engineering microbial co-cultures.

  • Novel approaches are helping to improve properties of modular co-culture system.

The microbial production of natural products has been traditionally accomplished in a single organism engineered to accommodate target biosynthetic pathways. Often times, such approaches result in large metabolic burdens as key cofactors, precursor metabolites and energy are channeled to pathways of structurally complex chemicals. Recently, modular co-culture engineering has emerged as a new approach to efficiently conduct heterologous biosynthesis and greatly enhance the production of natural products. This review highlights recent advances that leverage Escherichia coli-based modular co-culture engineering for making natural products. Potential future perspectives for studies in this promising field are addressed as well.

Introduction

Natural products discovered in plants, animals and microbes have been applied in many important aspects of human life since ancient times for different purposes. Because of their enormous molecular diversity and broad bioactivities, their roles include functional foods, fragrances, and pharmaceuticals. Many of these natural products have found applications as drugs such as artemisinin and paclitaxel for effective treatment of diseases [1,2]. However, the supply of natural products has been dramatically limited by the lack of effective methods for their production. Many natural products have complex chemical structures that make the associated chemical syntheses rather inefficient, complicated, and costly [3]. Even though common commercial sources that rely on extraction from native producers exist, such production methods are problematic because of their long-term sustainability and low overall abundance in their hosts [4]. The emerging fields of synthetic biology and metabolic engineering have substantially enhanced our abilities to program microbial organisms to provide alternative means for overproducing bioactive and high-value chemicals to chemical synthesis and traditional extraction [5,6].

Over the past few decades, researchers have produced a variety of natural compounds through constructing, regulating and optimizing the metabolic pathways of model host microorganisms including Escherichia coli and Saccharomyces cerevisiae. The majority of synthetic biology and metabolic engineering efforts on the heterologous production of chemicals was accomplished using a consolidated approach that relied on a single host cell in monoculture fermentation [7]. However, it has been challenging to provide an optimal environment for functionally expressing all enzymes involved in the complete biosynthetic pathways of complex compounds [5]. Recently, modular co-culture engineering approaches have been employed to make up for deficiencies of monoculture fermentation and improve biosynthesis efficiency of natural products [7].

Owing to features such as rapid growth, simple cultured conditions, easy genetic manipulation, and well characterized biochemistry, E. coli has become one of the most preferred production hosts and has been used extensively for the production of natural products both in monocultures and co-cultures [8]. Therefore, in this review, we will focus on current advances in modular co-culture engineering together with accompanying applications involving E. coli-based hosts for production of natural products. Using their biosynthetic origins, natural compounds were mainly grouped in four categories in this review for convenience: polyphenols, alkaloids, terpenoids, and other chemicals. Finally, we also discuss how the design and construction strategies of modular co-culture engineering have played important roles in producing natural products.

Section snippets

Advantages of modular co-culture engineering

Microbial consortia are ubiquitous in nature and are responsible for a variety of complex activities. In industry, they have been utilized in many fields for decades, especially in the food and pharmaceutical industries [9]. Microbial cocultures can also be engineered in order to produce complex chemicals at high yields [10]. Modular co-culture metabolic engineering involves the modularization of a complete biosynthetic pathway, with individual modules accommodated in different hosts for

Modular co-culture engineering for synthesis of natural products

Recently, an increasing number of researchers have devoted themselves to the biosynthesis of natural products using modular co-culture engineering because of its benefits. Recent advances involving the synthesis of natural products by co-culture fermentation with E. coli-E. coli and E. coli-other species are summarized in Table 1.

Biosynthesis of polyphenols in co-culture system

As a diverse family of plant secondary metabolites, polyphenols are synthesized from the aromatic amino acids, phenylalanine and tyrosine [34]. They have been commonly used as health-promoting natural products owing to their bioactivates, such as antioxidant, anti-inflammatory, and antiviral effects. [35]. As shown in Table 1, polyphenols are currently the most studied natural products biosynthesized by modular co-culture engineering, including resveratrol, naringenin and afzelechin. For the

Consortia process for bioproduction of alkaloids

Alkaloids are a class of natural products that contain nitrogen moieties. Most of alkaloids derive from amines that are produced by the decarboxylation of amino acids [39]. Although the production of some alkaloids, like noscapine, strictosidine and opioids, has been tried in mono-culture, to our knowledge, there has been only one study that reported on the biosynthesis of alkaloids using an E. coli co-culture [30,40, 41, 42]. Considering some plants enzymes are not functionally expressed in

Co-culture fermentation for synthesis of terpenoids

Terpenoids represent a numerous group of structurally diverse chemicals that are formed by five-carbon building blocks (isoprene) [4]. The biosynthesis of terpenoids has been explored mostly in a single microbe because of their complex structures [43]. In one study, the production of α-pinene was improved by 1.9-fold (166.5 mg/L) using a combined strategy of tolerance, evolution and E. coli-E. coli modular co-culture engineering [24••]. In this study, pinene tolerance was improved by using

Production of other chemicals by cocultivation system

Recently, synthetic E. coli-Corynebacterium glutamicum consortia were constructed to biosynthesize lysine and value-added products derived from l-lysine, such as pipecolic acid and cadaverine from starch or sucrose [33••]. The commensalism-based synthetic consortia employed an l-lysine autotrophic, naturally sucrose-negative E. coli and a fructose importer deleted (ptsF) C. glutamicum mutant for the production of lysine from sucrose. The mutualistic synthetic consortia composed of a lysine

Conclusions and future perspectives

To date, more and more applications of modularization co-culture strategies to achieve division of labor have been demonstrated, indicating that modular co-culture engineering provides an effective and robust toolkit for biosynthesis of various biochemicals, especially of the more structurally complex natural products with long biosynthetic pathways. This new approach not only significantly expedites the achievement of higher product yields but also facilitates biosynthetic pathway refactoring

Conflicts of interest statement

Nothing declared.

References and recommended reading

Papers of particular interest, published within the period of review, have been highlighted as:

  • • of special interest

  • •• of outstanding interest

Acknowledgements

This work was supported by the China Scholarship Council. The authors also would like to acknowledge funding from the RPI Biocatalysis and Metabolic Engineering Constellation Fund.

References (48)

  • N.H. Thuan et al.

    Engineering co-culture system for production of apigetrin in Escherichia coli

    J Ind Microbiol Biotechnol

    (2018)
  • Z. Chen et al.

    Metabolic engineering of Escherichia coli for microbial synthesis of monolignols

    Metab Eng

    (2017)
  • W. Zhang et al.

    Production of naringenin from D-xylose with co-culture of E. coli and S. cerevisiae

    Eng Life Sci

    (2017)
  • E. Sgobba et al.

    Synthetic Escherichia coli-Corynebacterium glutamicum consortia for L-lysine production from starch and sucrose

    Bioresour Technol

    (2018)
  • T. Bhanja Dey et al.

    Antioxidant phenolics and their microbial production by submerged and solid state fermentation process: a review

    Trends Food Sci Technol

    (2016)
  • S. Brown et al.

    De novo production of the plant-derived alkaloid strictosidine in yeast

    Proc Natl Acad Sci U S A

    (2015)
  • B.F. Pfleger et al.

    Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes

    Nat Biotechnol

    (2006)
  • H. Lu et al.

    Modular metabolic engineering for biobased chemical production

    Trends Biotechnol

    (2019)
  • N.I. Johns et al.

    Principles for designing synthetic microbial communities

    Curr Opin Microbiol

    (2016)
  • Y. Tu

    The discovery of artemisinin (qinghaosu) and gifts from Chinese medicine

    Nat Med

    (2011)
  • A.L. Demain et al.

    Natural products for cancer chemotherapy

    Microb Biotechnol

    (2011)
  • S.Y. Park et al.

    Metabolic engineering of microorganisms for the production of natural compounds

    Adv Biosyst

    (2017)
  • H. Zhang et al.

    Engineering Escherichia coli coculture systems for the production of biochemical products

    Proc Natl Acad Sci U S A

    (2015)
  • J. Kamran et al.

    Advances in the development and application of microbial consortia for metabolic engineering

    Metab Eng Commun

    (2019)
  • Cited by (0)

    4

    Present address: Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.

    View full text