101
|
Chu L, Lipshultz JM, MacMillan DWC. Merging Photoredox and Nickel Catalysis: The Direct Synthesis of Ketones by the Decarboxylative Arylation of α-Oxo Acids. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201501908] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
102
|
Chu L, Lipshultz JM, MacMillan DWC. Merging Photoredox and Nickel Catalysis: The Direct Synthesis of Ketones by the Decarboxylative Arylation of α-Oxo Acids. Angew Chem Int Ed Engl 2015; 54:7929-33. [PMID: 26014029 DOI: 10.1002/anie.201501908] [Citation(s) in RCA: 248] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Indexed: 11/06/2022]
Abstract
The direct decarboxylative arylation of α-oxo acids has been achieved by synergistic visible-light-mediated photoredox and nickel catalysis. This method offers rapid entry to aryl and alkyl ketone architectures from simple α-oxo acid precursors via an acyl radical intermediate. Significant substrate scope is observed with respect to both the oxo acid and arene coupling partners. This mild decarboxylative arylation can also be utilized to efficiently access medicinal agents, as demonstrated by the rapid synthesis of fenofibrate.
Collapse
Affiliation(s)
- Lingling Chu
- Merck Center for Catalysis at Princeton University, Washington Road, Princeton, NJ 08544 (USA) http://www.princeton.edu/chemistry/macmillan/
| | - Jeffrey M Lipshultz
- Merck Center for Catalysis at Princeton University, Washington Road, Princeton, NJ 08544 (USA) http://www.princeton.edu/chemistry/macmillan/
| | - David W C MacMillan
- Merck Center for Catalysis at Princeton University, Washington Road, Princeton, NJ 08544 (USA) http://www.princeton.edu/chemistry/macmillan/.
| |
Collapse
|
103
|
Jiang H, Wang YY, Guo YY, Shen JJ, Zhang XS, Luo HD, Ren NN, Jiang XH, Li YQ. An acyltransferase domain of FK506 polyketide synthase recognizing both an acyl carrier protein and coenzyme A as acyl donors to transfer allylmalonyl and ethylmalonyl units. FEBS J 2015; 282:2527-39. [PMID: 25865045 DOI: 10.1111/febs.13296] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 04/07/2015] [Accepted: 04/08/2015] [Indexed: 11/30/2022]
Abstract
UNLABELLED Acyltransferase (AT) domains of polyketide synthases (PKSs) usually use coenzyme A (CoA) as an acyl donor to transfer common acyl units to acyl carrier protein (ACP) domains, initiating incorporation of acyl units into polyketides. Two clinical immunosuppressive agents, FK506 and FK520, are biosynthesized by the same PKSs in several Streptomyces strains. In this study, characterization of AT4FkbB (the AT domain of the fourth module of FK506 PKS) in transacylation reactions showed that AT4FkbB recognizes both an ACP domain (ACPT csA) and CoA as acyl donors for transfer of a unique allylmalonyl (AM) unit to an acyl acceptor ACP domain (ACP4FkbB), resulting in FK506 production. In addition, AT4FkbB uses CoA as an acyl donor to transfer an unusual ethylmalonyl (EM) unit to ACP4FkbB, resulting in FK520 production, and transfers AM units to non-native ACP acceptors. Characterization of AT4FkbB in self-acylation reactions suggests that AT4FkbB controls acyl unit specificity in transacylation reactions but not in self-acylation reactions. Generally, AT domains of PKSs only recognize one acyl donor; however, we report here that AT4FkbB recognizes two acyl donors for the transfer of different acyl units. DATABASE Nucleotide sequence data have been submitted to the GenBank database under accession numbers KJ000382 and KJ000383.
Collapse
Affiliation(s)
- Hui Jiang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory of Microbial Biochemistry and Metabolism Engineering of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Yue-Yue Wang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuan-Yang Guo
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jie-Jie Shen
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiao-Sheng Zhang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hong-Dou Luo
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ni-Ni Ren
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xin-Hang Jiang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yong-Quan Li
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory of Microbial Biochemistry and Metabolism Engineering of Zhejiang Province, Hangzhou, Zhejiang, China
| |
Collapse
|
104
|
Sun H, Liu Z, Zhao H, Ang EL. Recent advances in combinatorial biosynthesis for drug discovery. DRUG DESIGN DEVELOPMENT AND THERAPY 2015; 9:823-33. [PMID: 25709407 PMCID: PMC4334309 DOI: 10.2147/dddt.s63023] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Because of extraordinary structural diversity and broad biological activities, natural products have played a significant role in drug discovery. These therapeutically important secondary metabolites are assembled and modified by dedicated biosynthetic pathways in their host living organisms. Traditionally, chemists have attempted to synthesize natural product analogs that are important sources of new drugs. However, the extraordinary structural complexity of natural products sometimes makes it challenging for traditional chemical synthesis, which usually involves multiple steps, harsh conditions, toxic organic solvents, and byproduct wastes. In contrast, combinatorial biosynthesis exploits substrate promiscuity and employs engineered enzymes and pathways to produce novel “unnatural” natural products, substantially expanding the structural diversity of natural products with potential pharmaceutical value. Thus, combinatorial biosynthesis provides an environmentally friendly way to produce natural product analogs. Efficient expression of the combinatorial biosynthetic pathway in genetically tractable heterologous hosts can increase the titer of the compound, eventually resulting in less expensive drugs. In this review, we will discuss three major strategies for combinatorial biosynthesis: 1) precursor-directed biosynthesis; 2) enzyme-level modification, which includes swapping of the entire domains, modules and subunits, site-specific mutagenesis, and directed evolution; 3) pathway-level recombination. Recent examples of combinatorial biosynthesis employing these strategies will also be highlighted in this review.
Collapse
Affiliation(s)
- Huihua Sun
- Metabolic Engineering Research Laboratory, Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research, Singapore
| | - Zihe Liu
- Metabolic Engineering Research Laboratory, Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research, Singapore
| | - Huimin Zhao
- Metabolic Engineering Research Laboratory, Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research, Singapore ; Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ee Lui Ang
- Metabolic Engineering Research Laboratory, Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research, Singapore
| |
Collapse
|
105
|
Sugimoto Y, Ishida K, Traitcheva N, Busch B, Dahse HM, Hertweck C. Freedom and Constraint in Engineered Noncolinear Polyketide Assembly Lines. ACTA ACUST UNITED AC 2015; 22:229-40. [DOI: 10.1016/j.chembiol.2014.12.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 11/26/2014] [Accepted: 12/06/2014] [Indexed: 10/24/2022]
|
106
|
Multigene editing in the Escherichia coli genome via the CRISPR-Cas9 system. Appl Environ Microbiol 2015; 81:2506-14. [PMID: 25636838 DOI: 10.1128/aem.04023-14] [Citation(s) in RCA: 807] [Impact Index Per Article: 89.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An efficient genome-scale editing tool is required for construction of industrially useful microbes. We describe a targeted, continual multigene editing strategy that was applied to the Escherichia coli genome by using the Streptococcus pyogenes type II CRISPR-Cas9 system to realize a variety of precise genome modifications, including gene deletion and insertion, with a highest efficiency of 100%, which was able to achieve simultaneous multigene editing of up to three targets. The system also demonstrated successful targeted chromosomal deletions in Tatumella citrea, another species of the Enterobacteriaceae, with highest efficiency of 100%.
Collapse
|
107
|
Li Y, Fiers WD, Bernard S, Smith JL, Aldrich CC, Fecik RA. Polyketide intermediate mimics as probes for revealing cryptic stereochemistry of ketoreductase domains. ACS Chem Biol 2014; 9:2914-22. [PMID: 25299319 PMCID: PMC4273979 DOI: 10.1021/cb5006883] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 10/09/2014] [Indexed: 12/27/2022]
Abstract
Among natural product families, polyketides have shown the most promise for combinatorial biosynthesis of natural product-like libraries. Though recent research in the area has provided many mechanistic revelations, a basic-level understanding of kinetic and substrate tolerability is still needed before the full potential of combinatorial biosynthesis can be realized. We have developed a novel set of chemical probes for the study of ketoreductase domains of polyketide synthases. This chemical tool-based approach was validated using the ketoreductase of pikromycin module 2 (PikKR2) as a model system. Triketide substrate mimics 12 and 13 were designed to increase stability (incorporating a nonhydrolyzable thioether linkage) and minimize nonessential functionality (truncating the phosphopantetheinyl arm). PikKR2 reduction product identities as well as steady-state kinetic parameters were determined by a combination of LC-MS/MS analysis of synthetic standards and a NADPH consumption assay. The d-hydroxyl product is consistent with bioinformatic analysis and results from a complementary biochemical and molecular biological approach. When compared to widely employed substrates in previous studies, diketide 63 and trans-decalone 64, substrates 12 and 13 showed 2-10 fold lower K(M) values (2.4 ± 0.8 and 7.8 ± 2.7 mM, respectively), indicating molecular recognition of intermediate-like substrates. Due to an abundance of the nonreducable enol-tautomer, the k(cat) values were attenuated by as much as 15-336 fold relative to known substrates. This study reveals the high stereoselectivity of PikKR2 in the face of gross substrate permutation, highlighting the utility of a chemical probe-based approach in the study of polyketide ketoreductases.
Collapse
Affiliation(s)
- Yang Li
- Department
of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - William D. Fiers
- Department
of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Steffen
M. Bernard
- Chemical Biology Program, Department of Biological
Chemistry,
and Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Janet L. Smith
- Chemical Biology Program, Department of Biological
Chemistry,
and Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Courtney C. Aldrich
- Department
of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Robert A. Fecik
- Department
of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
108
|
Weber T, Charusanti P, Musiol-Kroll EM, Jiang X, Tong Y, Kim HU, Lee SY. Metabolic engineering of antibiotic factories: new tools for antibiotic production in actinomycetes. Trends Biotechnol 2014; 33:15-26. [PMID: 25497361 DOI: 10.1016/j.tibtech.2014.10.009] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 10/21/2014] [Accepted: 10/31/2014] [Indexed: 12/15/2022]
Abstract
Actinomycetes are excellent sources for novel bioactive compounds, which serve as potential drug candidates for antibiotics development. While industrial efforts to find and develop novel antimicrobials have been severely reduced during the past two decades, the increasing threat of multidrug-resistant pathogens and the development of new technologies to find and produce such compounds have again attracted interest in this field. Based on improvements in whole-genome sequencing, novel methods have been developed to identify the secondary metabolite biosynthetic gene clusters by genome mining, to clone them, and to express them in heterologous hosts in much higher throughput than before. These technologies now enable metabolic engineering approaches to optimize production yields and to directly manipulate the pathways to generate modified products.
Collapse
Affiliation(s)
- Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, Hørsholm, Denmark
| | - Pep Charusanti
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, Hørsholm, Denmark; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Ewa Maria Musiol-Kroll
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, Hørsholm, Denmark
| | - Xinglin Jiang
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, Hørsholm, Denmark
| | - Yaojun Tong
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, Hørsholm, Denmark
| | - Hyun Uk Kim
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, Hørsholm, Denmark; Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, BioInformatics Research Center, and BioProcess Engineering Research Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
| | - Sang Yup Lee
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, Hørsholm, Denmark; Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, BioInformatics Research Center, and BioProcess Engineering Research Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea.
| |
Collapse
|
109
|
Hari TPA, Labana P, Boileau M, Boddy CN. An evolutionary model encompassing substrate specificity and reactivity of type I polyketide synthase thioesterases. Chembiochem 2014; 15:2656-61. [PMID: 25354333 DOI: 10.1002/cbic.201402475] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Indexed: 11/10/2022]
Abstract
Bacterial polyketides are a rich source of chemical diversity and pharmaceutical agents. Understanding the biochemical basis for their biosynthesis and the evolutionary driving force leading to this diversity is essential to take advantage of the enzymes as biocatalysts and to access new chemical diversity for drug discovery. Biochemical characterization of the thioesterase (TE) responsible for 6-deoxyerythronolide macrocyclization shows that a small, evolutionarily accessible change to the substrate can increase the chemical diversity of products, including macrodiolide formation. We propose an evolutionary model in which TEs are by nature non-selective for the type of chemistry they catalyze, producing a range of metabolites. As one metabolite becomes essential for improving fitness in a particular environment, the TE evolves to enrich for that corresponding reactivity. This hypothesis is supported by our phylogenetic analysis, showing convergent evolution of macrodiolide-forming TEs.
Collapse
Affiliation(s)
- Taylor P A Hari
- Departments of Chemistry and Biology, Centre for Catalysis Research and Innovation, University of Ottawa, Ottawa, ON K1N 6N5 (Canada)
| | | | | | | |
Collapse
|
110
|
Affiliation(s)
- Mohammad R. Seyedsayamdost
- Department of Biological
Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Jon Clardy
- Department of Biological
Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| |
Collapse
|
111
|
|
112
|
Kotowska M, Pawlik K. Roles of type II thioesterases and their application for secondary metabolite yield improvement. Appl Microbiol Biotechnol 2014; 98:7735-46. [PMID: 25081554 PMCID: PMC4147253 DOI: 10.1007/s00253-014-5952-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 07/09/2014] [Accepted: 07/10/2014] [Indexed: 12/31/2022]
Abstract
A large number of antibiotics and other industrially important microbial secondary metabolites are synthesized by polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs). These multienzymatic complexes provide an enormous flexibility in formation of diverse chemical structures from simple substrates, such as carboxylic acids and amino acids. Modular PKSs and NRPSs, often referred to as megasynthases, have brought about a special interest due to the colinearity between enzymatic domains in the proteins working as an “assembly line” and the chain elongation and modification steps. Extensive efforts toward modified compound biosynthesis by changing organization of PKS and NRPS domains in a combinatorial manner laid good grounds for rational design of new structures and their controllable biosynthesis as proposed by the synthetic biology approach. Despite undeniable progress made in this field, the yield of such “unnatural” natural products is often not satisfactory. Here, we focus on type II thioesterases (TEIIs)—discrete hydrolytic enzymes often encoded within PKS and NRPS gene clusters which can be used to enhance product yield. We review diverse roles of TEIIs (removal of aberrant residues blocking the megasynthase, participation in substrate selection, intermediate, and product release) and discuss their application in new biosynthetic systems utilizing PKS and NRPS parts.
Collapse
Affiliation(s)
- Magdalena Kotowska
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, ul. Rudolfa Weigla 12, 53-114, Wroclaw, Poland,
| | | |
Collapse
|
113
|
Diversity-oriented combinatorial biosynthesis of benzenediol lactone scaffolds by subunit shuffling of fungal polyketide synthases. Proc Natl Acad Sci U S A 2014; 111:12354-9. [PMID: 25049383 DOI: 10.1073/pnas.1406999111] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Combinatorial biosynthesis aspires to exploit the promiscuity of microbial anabolic pathways to engineer the synthesis of new chemical entities. Fungal benzenediol lactone (BDL) polyketides are important pharmacophores with wide-ranging bioactivities, including heat shock response and immune system modulatory effects. Their biosynthesis on a pair of sequentially acting iterative polyketide synthases (iPKSs) offers a test case for the modularization of secondary metabolic pathways into "build-couple-pair" combinatorial synthetic schemes. Expression of random pairs of iPKS subunits from four BDL model systems in a yeast heterologous host created a diverse library of BDL congeners, including a polyketide with an unnatural skeleton and heat shock response-inducing activity. Pairwise heterocombinations of the iPKS subunits also helped to illuminate the innate, idiosyncratic programming of these enzymes. Even in combinatorial contexts, these biosynthetic programs remained largely unchanged, so that the iPKSs built their cognate biosynthons, coupled these building blocks into chimeric polyketide intermediates, and catalyzed intramolecular pairing to release macrocycles or α-pyrones. However, some heterocombinations also provoked stuttering, i.e., the relaxation of iPKSs chain length control to assemble larger homologous products. The success of such a plug and play approach to biosynthesize novel chemical diversity bodes well for bioprospecting unnatural polyketides for drug discovery.
Collapse
|
114
|
Wright GD. Something old, something new: revisiting natural products in antibiotic drug discovery. Can J Microbiol 2014; 60:147-54. [DOI: 10.1139/cjm-2014-0063] [Citation(s) in RCA: 160] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Antibiotic discovery is in crisis. Despite a growing need for new drugs resulting from the increasing number of multi-antibiotic-resistant pathogens, there have been only a handful of new antibiotics approved for clinical use in the past 2 decades. Faced with scientific, economic, and regulatory challenges, the pharmaceutical sector seems unable to respond to what has been called an “apocalyptic” threat. Natural products produced by bacteria and fungi are genetically encoded products of natural selection that have been the mainstay sources of the antibiotics in current clinical use. The pharmaceutical industry has largely abandoned these compounds in favor of large libraries of synthetic molecules because of difficulties in identifying new natural product antibiotics scaffolds. Advances in next-generation genome sequencing, bioinformatics, and analytical chemistry are combining to overcome barriers to natural products. Coupled with new strategies in antibiotic discovery, including inhibition of resistance, novel drug combinations, and new targets, natural products are poised for a renaissance to address what is a pressing health care crisis.
Collapse
Affiliation(s)
- Gerard D. Wright
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| |
Collapse
|
115
|
Pandey RP, Parajuli P, Koirala N, Lee JH, Park YI, Sohng JK. Glucosylation of isoflavonoids in engineered Escherichia coli. Mol Cells 2014; 37:172-7. [PMID: 24599002 PMCID: PMC3935630 DOI: 10.14348/molcells.2014.2348] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 12/03/2013] [Accepted: 12/04/2013] [Indexed: 11/27/2022] Open
Abstract
A glycosyltransferase, YjiC, from Bacillus licheniformis has been used for the modification of the commercially available isoflavonoids genistein, daidzein, biochanin A and formononetin. The in vitro glycosylation reaction, using UDP-α-D-glucose as a donor for the glucose moiety and aforementioned four acceptor molecules, showed the prominent glycosylation at 4' and 7 hydroxyl groups, but not at the 5(th) hydroxyl group of the A-ring, resulting in the production of genistein 4'-O-β-D-glucoside, genistein 7-O-β-D-glucoside (genistin), genistein 4',7-O-β-D-diglucoside, biochanin A-7-O-β-D-glucoside (sissotrin), daidzein 4'-O-β-D-glucoside, daidzein 7-O-β-D-glucoside (daidzin), daidzein 4', 7-O-β-D-diglucoside, and formononetin 7-O-β-D-glucoside (ononin). The structures of all the products were elucidated using high performance liquid chromatography-photo diode array and high resolution quadrupole time-of-flight electrospray ionization mass spectrometry (HR QTOFESI/MS) analysis, and were compared with commercially available standard compounds. Significantly higher bioconversion rates of all four isoflavonoids was observed in both in vitro as well as in vivo bioconversion reactions. The in vivo fermentation of the isoflavonoids by applying engineered E. coli BL21(DE3)/ΔpgiΔzwfΔushA overexpressing phosphoglucomutase (pgm) and glucose 1-phosphate uridyltransferase (galU), along with YjiC, found more than 60% average conversion of 200 μM of supplemented isoflavonoids, without any additional UDP-α-D-glucose added in fermentation medium, which could be very beneficial to large scale industrial production of isoflavonoid glucosides.
Collapse
Affiliation(s)
- Ramesh Prasad Pandey
- Department of Pharmaceutical Engineering, Institute of Biomolecule Reconstruction, Sun Moon University, Asan 336-708,
Korea
| | - Prakash Parajuli
- Department of Pharmaceutical Engineering, Institute of Biomolecule Reconstruction, Sun Moon University, Asan 336-708,
Korea
| | - Niranjan Koirala
- Department of Pharmaceutical Engineering, Institute of Biomolecule Reconstruction, Sun Moon University, Asan 336-708,
Korea
| | - Joo Ho Lee
- Department of Pharmaceutical Engineering, Institute of Biomolecule Reconstruction, Sun Moon University, Asan 336-708,
Korea
| | - Yong Il Park
- Department of Biotechnology, The Catholic University of Korea, Bucheon 420-743,
Korea
| | - Jae Kyung Sohng
- Department of Pharmaceutical Engineering, Institute of Biomolecule Reconstruction, Sun Moon University, Asan 336-708,
Korea
| |
Collapse
|
116
|
Cummings M, Breitling R, Takano E. Steps towards the synthetic biology of polyketide biosynthesis. FEMS Microbiol Lett 2014; 351:116-25. [PMID: 24372666 PMCID: PMC4237116 DOI: 10.1111/1574-6968.12365] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 12/16/2013] [Accepted: 12/17/2013] [Indexed: 11/29/2022] Open
Abstract
Nature is providing a bountiful pool of valuable secondary metabolites, many of which possess therapeutic properties. However, the discovery of new bioactive secondary metabolites is slowing down, at a time when the rise of multidrug-resistant pathogens and the realization of acute and long-term side effects of widely used drugs lead to an urgent need for new therapeutic agents. Approaches such as synthetic biology are promising to deliver a much-needed boost to secondary metabolite drug development through plug-and-play optimized hosts and refactoring novel or cryptic bacterial gene clusters. Here, we discuss this prospect focusing on one comprehensively studied class of clinically relevant bioactive molecules, the polyketides. Extensive efforts towards optimization and derivatization of compounds via combinatorial biosynthesis and classical engineering have elucidated the modularity, flexibility and promiscuity of polyketide biosynthetic enzymes. Hence, a synthetic biology approach can build upon a solid basis of guidelines and principles, while providing a new perspective towards the discovery and generation of novel and new-to-nature compounds. We discuss the lessons learned from the classical engineering of polyketide synthases and indicate their importance when attempting to engineer biosynthetic pathways using synthetic biology approaches for the introduction of novelty and overexpression of products in a controllable manner.
Collapse
Affiliation(s)
- Matthew Cummings
- Faculty of Life Sciences, Manchester Institute of Biotechnology, The University of ManchesterManchester, UK
| | - Rainer Breitling
- Faculty of Life Sciences, Manchester Institute of Biotechnology, The University of ManchesterManchester, UK
| | - Eriko Takano
- Faculty of Life Sciences, Manchester Institute of Biotechnology, The University of ManchesterManchester, UK
| |
Collapse
|
117
|
Koryakina I, McArthur JB, Draelos MM, Williams GJ. Promiscuity of a modular polyketide synthase towards natural and non-natural extender units. Org Biomol Chem 2014; 11:4449-58. [PMID: 23681002 DOI: 10.1039/c3ob40633d] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Combinatorial biosynthesis approaches that involve modular type I polyketide synthases (PKSs) are proven strategies for the synthesis of polyketides. In general however, such strategies are usually limited in scope and utility due to the restricted substrate specificity of polyketide biosynthetic machinery. Herein, a panel of chemo-enzymatically synthesized acyl-CoA's was used to probe the promiscuity of a polyketide synthase. Promiscuity determinants were dissected, revealing that the KS is remarkably tolerant to a diverse array of extender units, while the AT likely discriminates between extender units that are native to the producing organism. Our data provides a clear blueprint for future enzyme engineering efforts, and sets the stage for harnessing extender unit promiscuity by employing various in vivo polyketide diversification strategies.
Collapse
Affiliation(s)
- Irina Koryakina
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA
| | | | | | | |
Collapse
|
118
|
Minami A, Oikawa H. Synthesis of Natural Products with Biosynthetic Machinery. J SYN ORG CHEM JPN 2014. [DOI: 10.5059/yukigoseikyokaishi.72.548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
119
|
Lin TY, Borketey LS, Prasad G, Waters SA, Schnarr NA. Sequence, cloning, and analysis of the fluvirucin B1 polyketide synthase from Actinomadura vulgaris. ACS Synth Biol 2013; 2:635-42. [PMID: 23654262 DOI: 10.1021/sb4000355] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fluvirucin B1 , produced by Actinomadura vulgaris, is a 14-membered macrolactam active against a variety of infectious fungi as well as influenza A. Despite considerable interest from the synthetic community, very little information is available regarding the biosynthetic origins of the fluvirucins. Herein, we report the identification and initial characterization of the fluvirucin B1 polyketide synthase and related enzymes. The cluster consists of five extender modules flanked by an N-terminal acyl carrier protein and C-terminal thioesterase domain. All but one of the synthase modules contain the full complement of tailoring domains (ketoreductase, dehydratase, and enoyl reductase) as determined by sequence homology with known polyketide synthases. Acitve site analyses of several key components of the cluster are performed to further verify that this gene cluster is associated with production of fluvirucin B1 . This work will both open doors toward a better understanding of macrolactam formation and provide an avenue to genetics-based diversification of fluvirucin structure.
Collapse
Affiliation(s)
- Tsung-Yi Lin
- Department of Chemistry, University of Massachusetts, 710 N. Pleasant Street,
Amherst, Massachusetts 01003, United States
| | - Lawrence S. Borketey
- Department of Chemistry, University of Massachusetts, 710 N. Pleasant Street,
Amherst, Massachusetts 01003, United States
| | - Gitanjeli Prasad
- Department of Chemistry, University of Massachusetts, 710 N. Pleasant Street,
Amherst, Massachusetts 01003, United States
| | - Stephanie A. Waters
- Department of Chemistry, University of Massachusetts, 710 N. Pleasant Street,
Amherst, Massachusetts 01003, United States
| | - Nathan A. Schnarr
- Department of Chemistry, University of Massachusetts, 710 N. Pleasant Street,
Amherst, Massachusetts 01003, United States
| |
Collapse
|
120
|
Lowry B, Robbins T, Weng CH, O'Brien RV, Cane DE, Khosla C. In vitro reconstitution and analysis of the 6-deoxyerythronolide B synthase. J Am Chem Soc 2013; 135:16809-12. [PMID: 24161212 DOI: 10.1021/ja409048k] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Notwithstanding an extensive literature on assembly line polyketide synthases such as the 6-deoxyerythronolide B synthase (DEBS), a complete naturally occurring synthase has never been reconstituted in vitro from purified protein components. Here, we describe the fully reconstituted DEBS and quantitatively characterize some of the properties of the assembled system that have never been explored previously. The maximum turnover rate of the complete hexamodular system is 1.1 min(-1), comparable to the turnover rate of a truncated trimodular derivative (2.5 min(-1)) but slower than that of a bimodular derivative (21 min(-1)). In the presence of similar concentrations of methylmalonyl- and ethylmalonyl-CoA substrates, DEBS synthesizes multiple regiospecifically modified analogues, one of which we have analyzed in detail. Our studies lay the foundation for biochemically interrogating and rationally engineering polyketide assembly lines in an unprecedented manner.
Collapse
Affiliation(s)
- Brian Lowry
- Department of Chemical Engineering, ‡Department of Chemistry, §School of Medicine, and ⊥Medical Science Training Program, Stanford University , Stanford, California 94305, United States
| | | | | | | | | | | |
Collapse
|
121
|
Peirú S, Gramajo HC, Menzella HG. Recombinant approaches to large polyketide molecules as potential drugs. DRUG DISCOVERY TODAY. TECHNOLOGIES 2013; 7:e95-e146. [PMID: 24103720 DOI: 10.1016/j.ddtec.2010.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
122
|
Cobb RE, Ning JC, Zhao H. DNA assembly techniques for next-generation combinatorial biosynthesis of natural products. J Ind Microbiol Biotechnol 2013; 41:469-77. [PMID: 24127070 DOI: 10.1007/s10295-013-1358-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 09/25/2013] [Indexed: 12/30/2022]
Abstract
Natural product scaffolds remain important leads for pharmaceutical development. However, transforming a natural product into a drug entity often requires derivatization to enhance the compound's therapeutic properties. A powerful method by which to perform this derivatization is combinatorial biosynthesis, the manipulation of the genes in the corresponding pathway to divert synthesis towards novel derivatives. While these manipulations have traditionally been carried out via restriction digestion/ligation-based cloning, the shortcomings of such techniques limit their throughput and thus the scope of corresponding combinatorial biosynthesis experiments. In the burgeoning field of synthetic biology, the demand for facile DNA assembly techniques has promoted the development of a host of novel DNA assembly strategies. Here we describe the advantages of these recently developed tools for rapid, efficient synthesis of large DNA constructs. We also discuss their potential to facilitate the simultaneous assembly of complete libraries of natural product biosynthetic pathways, ushering in the next generation of combinatorial biosynthesis.
Collapse
Affiliation(s)
- Ryan E Cobb
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | | | | |
Collapse
|
123
|
Deoxysugar pathway interchange for erythromycin analogues heterologously produced through Escherichia coli. Metab Eng 2013; 20:92-100. [PMID: 24060454 DOI: 10.1016/j.ymben.2013.09.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 08/30/2013] [Accepted: 09/11/2013] [Indexed: 01/16/2023]
Abstract
The overall erythromycin biosynthetic pathway can be sub-divided into macrocyclic polyketide formation and polyketide tailoring to produce the final bioactive molecule. In this study, the native deoxysugar tailoring reactions were exchanged for the purpose of demonstrating the production of alternative final erythromycin compounds. Both the d-desosamine and l-mycarose deoxysugar pathways were replaced with the alternative d-mycaminose and d-olivose pathways to produce new erythromycin analogues through the Escherichia coli heterologous system. Both analogues exhibited bioactivity against multiple antibiotic-resistant Bacillus subtilis strains. Besides demonstrating an intrinsic flexibility for the biosynthetic system to accommodate alternative tailoring pathways, the results offer an initial attempt to leverage the E. coli platform for erythromycin analogue production.
Collapse
|
124
|
Genome-scale engineering for systems and synthetic biology. Mol Syst Biol 2013; 9:641. [PMID: 23340847 PMCID: PMC3564264 DOI: 10.1038/msb.2012.66] [Citation(s) in RCA: 209] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 12/16/2012] [Indexed: 12/15/2022] Open
Abstract
This review provides an overview of methodologies and technologies enabling genome-scale engineering, focusing on the design, construction, and testing of modified genomes in a variety of organisms. Future applications for systems and synthetic biology are discussed. Genome-modification technologies enable the rational engineering and perturbation of biological systems. Historically, these methods have been limited to gene insertions or mutations at random or at a few pre-defined locations across the genome. The handful of methods capable of targetedgene editing suffered from low efficiencies, significant labor costs, or both. Recent advances have dramatically expanded our ability to engineer cells in a directed and combinatorial manner. Here, we review current technologies and methodologies for genome-scale engineering, discuss the prospects for extending efficient genome modification to new hosts, and explore the implications of continued advances toward the development of flexibly programmable chasses, novel biochemistries, and safer organismal and ecological engineering.
Collapse
|
125
|
Walker MC, Thuronyi BW, Charkoudian LK, Lowry B, Khosla C, Chang MCY. Expanding the fluorine chemistry of living systems using engineered polyketide synthase pathways. Science 2013; 341:1089-94. [PMID: 24009388 PMCID: PMC4057101 DOI: 10.1126/science.1242345] [Citation(s) in RCA: 139] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Organofluorines represent a rapidly expanding proportion of molecules that are used in pharmaceuticals, diagnostics, agrochemicals, and materials. Despite the prevalence of fluorine in synthetic compounds, the known biological scope is limited to a single pathway that produces fluoroacetate. Here, we demonstrate that this pathway can be exploited as a source of fluorinated building blocks for introduction of fluorine into natural-product scaffolds. Specifically, we have constructed pathways involving two polyketide synthase systems, and we show that fluoroacetate can be used to incorporate fluorine into the polyketide backbone in vitro. We further show that fluorine can be inserted site-selectively and introduced into polyketide products in vivo. These results highlight the prospects for the production of complex fluorinated natural products using synthetic biology.
Collapse
Affiliation(s)
- Mark C. Walker
- Departments of Chemistry and Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA 94720-1460
| | - Benjamin W. Thuronyi
- Departments of Chemistry and Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA 94720-1460
| | - Louise K. Charkoudian
- Departments of Chemistry, Chemical Engineering, and Biochemistry, Stanford University, Stanford, CA 94305
| | - Brian Lowry
- Departments of Chemistry, Chemical Engineering, and Biochemistry, Stanford University, Stanford, CA 94305
| | - Chaitan Khosla
- Departments of Chemistry, Chemical Engineering, and Biochemistry, Stanford University, Stanford, CA 94305
| | - Michelle C. Y. Chang
- Departments of Chemistry and Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA 94720-1460
| |
Collapse
|
126
|
Li YY, Chang X, Yu WB, Li H, Ye ZQ, Yu H, Liu BH, Zhang Y, Zhang SL, Ye BC, Li YX. Systems perspectives on erythromycin biosynthesis by comparative genomic and transcriptomic analyses of S. erythraea E3 and NRRL23338 strains. BMC Genomics 2013; 14:523. [PMID: 23902230 PMCID: PMC3733707 DOI: 10.1186/1471-2164-14-523] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 07/26/2013] [Indexed: 11/20/2022] Open
Abstract
Background S. erythraea is a Gram-positive filamentous bacterium used for the industrial-scale production of erythromycin A which is of high clinical importance. In this work, we sequenced the whole genome of a high-producing strain (E3) obtained by random mutagenesis and screening from the wild-type strain NRRL23338, and examined time-series expression profiles of both E3 and NRRL23338. Based on the genomic data and transcriptpmic data of these two strains, we carried out comparative analysis of high-producing strain and wild-type strain at both the genomic level and the transcriptomic level. Results We observed a large number of genetic variants including 60 insertions, 46 deletions and 584 single nucleotide variations (SNV) in E3 in comparison with NRRL23338, and the analysis of time series transcriptomic data indicated that the genes involved in erythromycin biosynthesis and feeder pathways were significantly up-regulated during the 60 hours time-course. According to our data, BldD, a previously identified ery cluster regulator, did not show any positive correlations with the expression of ery cluster, suggesting the existence of alternative regulation mechanisms of erythromycin synthesis in S. erythraea. Several potential regulators were then proposed by integration analysis of genomic and transcriptomic data. Conclusion This is a demonstration of the functional comparative genomics between an industrial S. erythraea strain and the wild-type strain. These findings help to understand the global regulation mechanisms of erythromycin biosynthesis in S. erythraea, providing useful clues for genetic and metabolic engineering in the future.
Collapse
|
127
|
Zhang K, Nelson KM, Bhuripanyo K, Grimes KD, Zhao B, Aldrich CC, Yin J. Engineering the substrate specificity of the DhbE adenylation domain by yeast cell surface display. ACTA ACUST UNITED AC 2013; 20:92-101. [PMID: 23352143 DOI: 10.1016/j.chembiol.2012.10.020] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 10/19/2012] [Accepted: 10/25/2012] [Indexed: 01/30/2023]
Abstract
The adenylation (A) domains of nonribosomal peptide synthetases (NRPSs) activate aryl acids or amino acids to launch their transfer through the NRPS assembly line for the biosynthesis of many medicinally important natural products. In order to expand the substrate pool of NRPSs, we developed a method based on yeast cell surface display to engineer the substrate specificities of the A-domains. We acquired A-domain mutants of DhbE that have 11- and 6-fold increases in k(cat)/K(m) with nonnative substrates 3-hydroxybenzoic acid and 2-aminobenzoic acid, respectively and corresponding 3- and 33-fold decreases in k(cat)/K(m) values with the native substrate 2,3-dihydroxybenzoic acid, resulting in a dramatic switch in substrate specificity of up to 200-fold. Our study demonstrates that yeast display can be used as a high throughput selection platform to reprogram the "nonribosomal code" of A-domains.
Collapse
Affiliation(s)
- Keya Zhang
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | | | | | | | | | | | | |
Collapse
|
128
|
Jiang M, Pfeifer BA. Metabolic and pathway engineering to influence native and altered erythromycin production through E. coli. Metab Eng 2013; 19:42-9. [PMID: 23747605 DOI: 10.1016/j.ymben.2013.05.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 05/24/2013] [Accepted: 05/30/2013] [Indexed: 11/16/2022]
Abstract
The heterologous production of the complex antibiotic erythromycin through Escherichia coli provides a unique challenge in metabolic engineering. In addition to introducing the 19 foreign genes needed for heterologous biosynthesis, E. coli metabolism must be engineered to provide the propionyl-CoA and (2S)-methylmalonyl-CoA substrates required to allow erythromycin formation. In this work, three different pathways to propionyl-CoA were compared in the context of supporting E. coli erythromycin biosynthesis. The comparison revealed that alternative citramalate and threonine metabolic pathways (both starting from exogenous glycerol) were capable of supporting final compound formation equal to a proven pathway reliant upon exogenous propionate. Furthermore, two pathways to (2S)-methylmalonyl-CoA were compared in the production of a novel benzyl-erythromycin analog. A pathway dependent upon exogenous methylmalonate improved selectivity and facilitated antibiotic assessment of this new analog.
Collapse
Affiliation(s)
- Ming Jiang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Department of Chemical and Biological Engineering, The State University of New York at Buffalo, Buffalo, NY 14260, USA
| | | |
Collapse
|
129
|
Dunn BJ, Khosla C. Engineering the acyltransferase substrate specificity of assembly line polyketide synthases. J R Soc Interface 2013; 10:20130297. [PMID: 23720536 DOI: 10.1098/rsif.2013.0297] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Polyketide natural products act as a broad range of therapeutics, including antibiotics, immunosuppressants and anti-cancer agents. This therapeutic diversity stems from the structural diversity of these small molecules, many of which are produced in an assembly line manner by modular polyketide synthases. The acyltransferase (AT) domains of these megasynthases are responsible for selection and incorporation of simple monomeric building blocks, and are thus responsible for a large amount of the resulting polyketide structural diversity. The substrate specificity of these domains is often targeted for engineering in the generation of novel, therapeutically active natural products. This review outlines recent developments that can be used in the successful engineering of these domains, including AT sequence and structural data, mechanistic insights and the production of a diverse pool of extender units. It also provides an overview of previous AT domain engineering attempts, and concludes with proposed engineering approaches that take advantage of current knowledge. These approaches may lead to successful production of biologically active 'unnatural' natural products.
Collapse
Affiliation(s)
- Briana J Dunn
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
| | | |
Collapse
|
130
|
Fukushima EO, Seki H, Sawai S, Suzuki M, Ohyama K, Saito K, Muranaka T. Combinatorial Biosynthesis of Legume Natural and Rare Triterpenoids in Engineered Yeast. ACTA ACUST UNITED AC 2013; 54:740-9. [DOI: 10.1093/pcp/pct015] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
|
131
|
Lussier FX, Colatriano D, Wiltshire Z, Page JE, Martin VJJ. Engineering microbes for plant polyketide biosynthesis. Comput Struct Biotechnol J 2013; 3:e201210020. [PMID: 24688680 PMCID: PMC3962132 DOI: 10.5936/csbj.201210020] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 01/28/2013] [Accepted: 01/31/2013] [Indexed: 01/01/2023] Open
Abstract
Polyketides are an important group of secondary metabolites, many of which have important industrial applications in the food and pharmaceutical industries. Polyketides are synthesized from one of three classes of enzymes differentiated by their biochemical features and product structure: type I, type II or type III polyketide synthases (PKSs). Plant type III PKS enzymes, which will be the main focus of this review, are relatively small homodimeric proteins that catalyze iterative decarboxylative condensations of malonyl units with a CoA-linked starter molecule. This review will describe the plant type III polyketide synthetic pathway, including the synthesis of chalcones, stilbenes and curcuminoids, as well as recent work on the synthesis of these polyketides in heterologous organisms. The limitations and bottlenecks of heterologous expression as well as attempts at creating diversity through the synthesis of novel “unnatural” polyketides using type III PKSs will also be discussed. Although synthetic production of plant polyketides is still in its infancy, their potential as useful bioactive compounds makes them an extremely interesting area of study.
Collapse
Affiliation(s)
- François-Xavier Lussier
- Department of Biology, Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec, Canada, H4B 1R6
| | - David Colatriano
- Department of Biology, Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec, Canada, H4B 1R6
| | - Zach Wiltshire
- Department of Biology, Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec, Canada, H4B 1R6
| | - Jonathan E Page
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, Saskatchewan, Canada, S7N 0W9
| | - Vincent J J Martin
- Department of Biology, Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec, Canada, H4B 1R6
| |
Collapse
|
132
|
Koryakina I, Williams GJ. Mutant malonyl-CoA synthetases with altered specificity for polyketide synthase extender unit generation. Chembiochem 2013; 12:2289-93. [PMID: 23106079 DOI: 10.1002/cbic.201100383] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Tailoring guide: We have used structure-guided saturation mutagenesis followed by colorimetric screening to identify mutant malonyl-CoA synthetases with altered substrate specificity. One particular mutant displayed a 240-fold shift in specificity (see graphic). These mutant enzymes will be useful tools for providing extender units to probe the activity of polyketide synthases.
Collapse
Affiliation(s)
- Irina Koryakina
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA
| | | |
Collapse
|
133
|
Lucas X, Senger C, Erxleben A, Grüning BA, Döring K, Mosch J, Flemming S, Günther S. StreptomeDB: a resource for natural compounds isolated from Streptomyces species. Nucleic Acids Res 2013; 41:D1130-6. [PMID: 23193280 PMCID: PMC3531085 DOI: 10.1093/nar/gks1253] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Revised: 10/10/2012] [Accepted: 11/04/2012] [Indexed: 11/12/2022] Open
Abstract
Bacteria from the genus Streptomyces are very important for the production of natural bioactive compounds such as antibiotic, antitumour or immunosuppressant drugs. Around two-thirds of all known natural antibiotics are produced by these bacteria. An enormous quantity of crucial data related to this genus has been generated and published, but so far no freely available and comprehensive database exists. Here, we present StreptomeDB (http://www.pharmaceutical-bioinformatics.de/streptomedb/). To the best of our knowledge, this is the largest database of natural products isolated from Streptomyces. It contains >2400 unique and diverse compounds from >1900 different Streptomyces strains and substrains. In addition to names and molecular structures of the compounds, information about source organisms, references, biological role, activities and synthesis routes (e.g. polyketide synthase derived and non-ribosomal peptides derived) is included. Data can be accessed through queries on compound names, chemical structures or organisms. Extraction from the literature was performed through automatic text mining of thousands of articles from PubMed, followed by manual curation. All annotated compound structures can be downloaded from the website and applied for in silico screenings for identifying new active molecules with undiscovered properties.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Stefan Günther
- Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, D-79104 Freiburg, Germany
| |
Collapse
|
134
|
Cobb RE, Luo Y, Freestone T, Zhao H. Drug Discovery and Development via Synthetic Biology. Synth Biol (Oxf) 2013. [DOI: 10.1016/b978-0-12-394430-6.00010-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
|
135
|
Xu W, Qiao K, Tang Y. Structural analysis of protein-protein interactions in type I polyketide synthases. Crit Rev Biochem Mol Biol 2012; 48:98-122. [PMID: 23249187 DOI: 10.3109/10409238.2012.745476] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Polyketide synthases (PKSs) are responsible for synthesizing a myriad of natural products with agricultural, medicinal relevance. The PKSs consist of multiple functional domains of which each can catalyze a specified chemical reaction leading to the synthesis of polyketides. Biochemical studies showed that protein-substrate and protein-protein interactions play crucial roles in these complex regio-/stereo-selective biochemical processes. Recent developments on X-ray crystallography and protein NMR techniques have allowed us to understand the biosynthetic mechanism of these enzymes from their structures. These structural studies have facilitated the elucidation of the sequence-function relationship of PKSs and will ultimately contribute to the prediction of product structure. This review will focus on the current knowledge of type I PKS structures and the protein-protein interactions in this system.
Collapse
Affiliation(s)
- Wei Xu
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
| | | | | |
Collapse
|
136
|
Ichikawa N, Sasagawa M, Yamamoto M, Komaki H, Yoshida Y, Yamazaki S, Fujita N. DoBISCUIT: a database of secondary metabolite biosynthetic gene clusters. Nucleic Acids Res 2012. [PMID: 23185043 PMCID: PMC3531092 DOI: 10.1093/nar/gks1177] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
This article introduces DoBISCUIT (Database of BIoSynthesis clusters CUrated and InTegrated, http://www.bio.nite.go.jp/pks/), a literature-based, manually curated database of gene clusters for secondary metabolite biosynthesis. Bacterial secondary metabolites often show pharmacologically important activities and can serve as lead compounds and/or candidates for drug development. Biosynthesis of each secondary metabolite is catalyzed by a number of enzymes, usually encoded by a gene cluster. Although many scientific papers describe such gene clusters, the gene information is not always described in a comprehensive manner and the related information is rarely integrated. DoBISCUIT integrates the latest literature information and provides standardized gene/module/domain descriptions related to the gene clusters.
Collapse
Affiliation(s)
- Natsuko Ichikawa
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-49-10 Nishihara, Shibuya-ku, Tokyo 151-0006, Japan
| | | | | | | | | | | | | |
Collapse
|
137
|
Caffrey P. Dissecting complex polyketide biosynthesis. Comput Struct Biotechnol J 2012; 3:e201210010. [PMID: 24688670 PMCID: PMC3962154 DOI: 10.5936/csbj.201210010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 11/06/2012] [Accepted: 11/07/2012] [Indexed: 12/17/2022] Open
Abstract
Numerous bioactive natural products are synthesised by modular polyketide synthases. These compounds can be made in high yield by native multienzyme assembly lines. However, formation of analogues by genetically engineered systems is often considerably less efficient. Biochemical studies on intact polyketide synthase proteins have amassed a body of knowledge that is substantial but still incomplete. Recently, the constituent enzymes have been structurally characterised as discrete domains or didomains. These recombinant proteins have been used to reconstitute single extension cycles in vitro. This has given further insights into how the final stereochemistry of chiral centres in polyketides is determined. In addition, this approach has revealed how domains co-operate to ensure efficient transfer of growing intermediates along the assembly line. This work is leading towards more effective re-programming of these enzymes for use in synthesis of new medicinal compounds.
Collapse
Affiliation(s)
- Patrick Caffrey
- School of Biomolecular and Biomedical Science, Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
| |
Collapse
|
138
|
Yuzawa S, Kim W, Katz L, Keasling JD. Heterologous production of polyketides by modular type I polyketide synthases in Escherichia coli. Curr Opin Biotechnol 2012; 23:727-35. [DOI: 10.1016/j.copbio.2011.12.029] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 12/19/2011] [Accepted: 12/21/2011] [Indexed: 11/15/2022]
|
139
|
Kushnir S, Sundermann U, Yahiaoui S, Brockmeyer A, Janning P, Schulz F. Minimally Invasive Mutagenesis Gives Rise to a Biosynthetic Polyketide Library. Angew Chem Int Ed Engl 2012; 51:10664-9. [DOI: 10.1002/anie.201202438] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 06/29/2012] [Indexed: 11/08/2022]
|
140
|
Kushnir S, Sundermann U, Yahiaoui S, Brockmeyer A, Janning P, Schulz F. Aufbau einer biosynthetischen Polyketid-Bibliothek durch minimalinvasive Mutagenese. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201202438] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
141
|
Mechanistic insights into validoxylamine A 7'-phosphate synthesis by VldE using the structure of the entire product complex. PLoS One 2012; 7:e44934. [PMID: 23028689 PMCID: PMC3441724 DOI: 10.1371/journal.pone.0044934] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 08/10/2012] [Indexed: 11/29/2022] Open
Abstract
The pseudo-glycosyltransferase VldE catalyzes non-glycosidic C-N coupling between an unsaturated cyclitol and a saturated aminocyclitol with the conservation of the stereochemical configuration of the substrates to form validoxylamine A 7′-phosphate, the biosynthetic precursor of the antibiotic validamycin A. To study the molecular basis of its mechanism, the three-dimensional structures of VldE from Streptomyces hygroscopicus subsp. limoneus was determined in apo form, in complex with GDP, in complex with GDP and validoxylamine A 7′-phosphate, and in complex with GDP and trehalose. The structure of VldE with the catalytic site in both an “open” and “closed” conformation is also described. With these structures, the preferred binding of the guanine moiety by VldE, rather than the uracil moiety as seen in OtsA could be explained. The elucidation of the VldE structure in complex with the entirety of its products provides insight into the internal return mechanism by which catalysis occurs with a net retention of the stereochemical configuration of the donated cyclitol.
Collapse
|
142
|
Prasad G, Borketey LS, Lin TY, Schnarr NA. A mechanism-based fluorescence transfer assay for examining ketosynthase selectivity. Org Biomol Chem 2012; 10:6717-23. [PMID: 22806124 PMCID: PMC4232300 DOI: 10.1039/c2ob26008e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Since their discovery, polyketide synthases have received massive attention from researchers hoping to harness their potential as a platform for generating new and improved therapeutics. Despite significant strides toward this end, inherent specificities within the enzymes responsible for polyketide production have severely limited these efforts. We have developed a mechanism-based, fluorescence transfer assay for a key enzyme component of all polyketide synthases, the ketosynthase domain. As demonstrated, this method can be used with both ketosynthase-containing didomains and full modules. As proof of principle, the ketosynthase domain from module 6 of the 6-deoxyerythronolide synthase is examined for its ability to accept a variety of simple thioester substrates. Consistent with its natural hexaketide substrate, we find that this ketosynthase prefers longer, α-branched thioesters and its ability to distinguish these structural features is quite remarkable. Substrate electronics are also tested via a variety of p-substituted aromatic groups. In all, we expect this technique to find considerable use in the field of polyketide biosynthesis and engineering due to its extraordinary simplicity and very distinct visible readout.
Collapse
Affiliation(s)
- Gitanjeli Prasad
- Department of Chemistry, University of Massachusetts, Amherst, 01003, USA
| | | | | | | |
Collapse
|
143
|
Abstract
Metabolism is a highly interconnected web of chemical reactions that power life. Though the stoichiometry of metabolism is well understood, the multidimensional aspects of metabolic regulation in time and space remain difficult to define, model and engineer. Complex metabolic conversions can be performed by multiple species working cooperatively and exchanging metabolites via structured networks of organisms and resources. Within cells, metabolism is spatially regulated via sequestration in subcellular compartments and through the assembly of multienzyme complexes. Metabolic engineering and synthetic biology have had success in engineering metabolism in the first and second dimensions, designing linear metabolic pathways and channeling metabolic flux. More recently, engineering of the third dimension has improved output of engineered pathways through isolation and organization of multicell and multienzyme complexes. This review highlights natural and synthetic examples of three-dimensional metabolism both inter- and intracellularly, offering tools and perspectives for biological design.
Collapse
|
144
|
Abstract
Recursive pathways are broadly defined as those that catalyze a series of reactions such that the key, bond-forming functional group of the substrate is always regenerated in each cycle, allowing for a new cycle of reactions to begin. Recursive carbon-chain elongation pathways in nature produce fatty acids, polyketides, isoprenoids and α-keto acids (αKAs), which all use modular or iterative approaches for chain elongation. Recently, an artificial pathway for αKA elongation has been built that uses an engineered isopropylmalate synthase to recursively condense acetyl-CoA with αKAs. This synthetic approach expands the possibilities for recursive pathways beyond the modular or iterative synthesis of natural products and serves as a case study for understanding the challenges of building recursive pathways from nonrecursive enzymes. There exists the potential to design synthetic recursive pathways far beyond what nature has evolved.
Collapse
|
145
|
Curran KA, Alper HS. Expanding the chemical palate of cells by combining systems biology and metabolic engineering. Metab Eng 2012; 14:289-97. [PMID: 22595280 DOI: 10.1016/j.ymben.2012.04.006] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 04/15/2012] [Accepted: 04/24/2012] [Indexed: 10/28/2022]
Abstract
The field of Metabolic Engineering has recently undergone a transformation that has led to a rapid expansion of the chemical palate of cells. Now, it is conceivable to produce nearly any organic molecule of interest using a cellular host. Significant advances have been made in the production of biofuels, biopolymers and precursors, pharmaceuticals and nutraceuticals, and commodity and specialty chemicals. Much of this rapid expansion in the field has been, in part, due to synergies and advances in the area of systems biology. Specifically, the availability of functional genomics, metabolomics and transcriptomics data has resulted in the potential to produce a wealth of new products, both natural and non-natural, in cellular factories. The sheer amount and diversity of this data however, means that uncovering and unlocking novel chemistries and insights is a non-obvious exercise. To address this issue, a number of computational tools and experimental approaches have been developed to help expedite the design process to create new cellular factories. This review will highlight many of the systems biology enabling technologies that have reduced the design cycle for engineered hosts, highlight major advances in the expanded diversity of products that can be synthesized, and conclude with future prospects in the field of metabolic engineering.
Collapse
Affiliation(s)
- Kathleen A Curran
- Department of Chemical Engineering, The University of Texas at Austin, 1 University Station, C0400, Austin, TX 78712, USA
| | | |
Collapse
|
146
|
Abstract
Natural products and their derivatives play an important role in modern healthcare as frontline treatments for many diseases and as inspiration for chemically synthesized therapeutics. With advances in sequencing and recombinant DNA technology, many of the biosynthetic pathways responsible for the production of these chemically complex yet valuable compounds have been elucidated. With an ever-expanding toolkit of biosynthetic components, metabolic engineering is an increasingly powerful method to improve natural product titers and generate novel compounds. Heterologous production platforms have enabled access to pathways from difficult to culture strains, systems biology and metabolic modeling tools have resulted in increasing predictive and analytic capabilities, advances in expression systems and regulation have enabled the fine-tuning of pathways for increased efficiency, and characterization of individual pathway components has facilitated the construction of hybrid pathways for the production of new compounds. These advances in the many aspects of metabolic engineering not only have yielded fascinating scientific discoveries but also make it an increasingly viable approach for the optimization of natural product biosynthesis.
Collapse
Affiliation(s)
- Lauren B Pickens
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
| | | | | |
Collapse
|
147
|
|
148
|
Wong FT, Khosla C. Combinatorial biosynthesis of polyketides--a perspective. Curr Opin Chem Biol 2012; 16:117-23. [PMID: 22342766 DOI: 10.1016/j.cbpa.2012.01.018] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 12/19/2011] [Accepted: 01/27/2012] [Indexed: 12/29/2022]
Abstract
Since their discovery, polyketide synthases have been attractive targets of biosynthetic engineering to make 'unnatural' natural products. Although combinatorial biosynthesis has made encouraging advances over the past two decades, the field remains in its infancy. In this enzyme-centric perspective, we discuss the scientific and technological challenges that could accelerate the adoption of combinatorial biosynthesis as a method of choice for the preparation of encoded libraries of bioactive small molecules. Borrowing a page from the protein structure prediction community, we propose a periodic challenge program to vet the most promising methods in the field, and to foster the collective development of useful tools and algorithms.
Collapse
Affiliation(s)
- Fong T Wong
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, United States
| | | |
Collapse
|
149
|
|
150
|
Wright G. Antibiotics: A New Hope. ACTA ACUST UNITED AC 2012; 19:3-10. [DOI: 10.1016/j.chembiol.2011.10.019] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Revised: 10/12/2011] [Accepted: 10/14/2011] [Indexed: 12/21/2022]
|