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Lowry B, Walsh CT, Khosla C. In Vitro Reconstitution of Metabolic Pathways: Insights into Nature's Chemical Logic. Synlett 2015; 26:1008-1025. [PMID: 26207083 PMCID: PMC4507746 DOI: 10.1055/s-0034-1380264] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In vitro analysis of metabolic pathways is becoming a powerful method to gain a deeper understanding of Nature's core biochemical transformations. With astounding advancements in biotechnology, purification of a metabolic pathway's constitutive enzymatic components is becoming a tractable problem, and such in vitro studies allow scientists to capture the finer details of enzymatic reaction mechanisms, kinetics, and the identity of organic product molecules. In this review, we present eleven metabolic pathways that have been the subject of in vitro reconstitution studies in the literature in recent years. In addition, we have selected and analyzed subset of four case studies within these eleven examples that exemplify remarkable organic chemistry occurring within biology. These examples serves as tangible reminders that Nature's biochemical routes obey the fundamental principles of organic chemistry, and the chemical mechanisms are reminiscent of those featured in traditional synthetic organic routes. The illustrations of biosynthetic chemistry depicted in this review may inspire the development of biomimetic chemistries via abiotic chemical techniques.
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Affiliation(s)
- Brian Lowry
- Department of Chemical Engineering, Stanford University, 443 Via Ortega, Stanford, CA 94305, USA;
| | - Christopher T Walsh
- Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, 443 Via Ortega, Stanford, CA 94305
| | - Chaitan Khosla
- Department of Chemical Engineering, Stanford University, 443 Via Ortega, Stanford, CA 94305, USA; ; Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, 443 Via Ortega, Stanford, CA 94305 ; Department of Chemistry, 333 Campus Drive Mudd Building, Stanford University, Stanford, CA 94305, USA;
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Teufel R, Stull F, Meehan MJ, Michaudel Q, Dorrestein PC, Palfey B, Moore BS. Biochemical Establishment and Characterization of EncM's Flavin-N5-oxide Cofactor. J Am Chem Soc 2015; 137:8078-85. [PMID: 26067765 DOI: 10.1021/jacs.5b03983] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The ubiquitous flavin-dependent monooxygenases commonly catalyze oxygenation reactions by means of a transient C4a-peroxyflavin. A recent study, however, suggested an unprecedented flavin-oxygenating species, proposed as the flavin-N5-oxide (Fl(N5[O])), as key to an oxidative Favorskii-type rearrangement in the biosynthesis of the bacterial polyketide antibiotic enterocin. This stable superoxidized flavin is covalently tethered to the enzyme EncM and converted into FADH2 (Fl(red)) during substrate turnover. Subsequent reaction of Fl(red) with molecular oxygen restores the postulated Fl(N5[O]) via an unknown pathway. Here, we provide direct evidence for the Fl(N5[O]) species via isotope labeling, proteolytic digestion, and high-resolution tandem mass spectrometry of EncM. We propose that formation of this species occurs by hydrogen-transfer from Fl(red) to molecular oxygen, allowing radical coupling of the formed protonated superoxide and anionic flavin semiquinone at N5, before elimination of water affords the Fl(N5[O]) cofactor. Further biochemical and spectroscopic investigations reveal important features of the Fl(N5[O]) species and the EncM catalytic mechanism. We speculate that flavin-N5-oxides may be intermediates or catalytically active species in other flavoproteins that form the anionic semiquinone and promote access of oxygen to N5.
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Affiliation(s)
- Robin Teufel
- †Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, California 92093, United States
| | - Frederick Stull
- ‡Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Michael J Meehan
- §Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, California 92093, United States
| | - Quentin Michaudel
- ⊥Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Pieter C Dorrestein
- †Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, California 92093, United States.,§Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, California 92093, United States
| | - Bruce Palfey
- ‡Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States.,∥Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Bradley S Moore
- †Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, California 92093, United States.,§Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, California 92093, United States
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Bonet B, Teufel R, Crüsemann M, Ziemert N, Moore BS. Direct capture and heterologous expression of Salinispora natural product genes for the biosynthesis of enterocin. JOURNAL OF NATURAL PRODUCTS 2015; 78:539-42. [PMID: 25382643 PMCID: PMC4380194 DOI: 10.1021/np500664q] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Heterologous expression of secondary metabolic pathways is a promising approach for the discovery and characterization of bioactive natural products. Herein we report the first heterologous expression of a natural product from the model marine actinomycete genus Salinispora. Using the recently developed method of yeast-mediated transformation-associated recombination for natural product gene clusters, we captured a type II polyketide synthase pathway from Salinispora pacifica with high homology to the enterocin pathway from Streptomyces maritimus and successfully produced enterocin in two different Streptomyces host strains. This result paves the way for the systematic interrogation of Salinispora's promising secondary metabolome.
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Affiliation(s)
- Bailey Bonet
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, California 92037, United States
| | - Robin Teufel
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, California 92037, United States
| | - Max Crüsemann
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, California 92037, United States
| | - Nadine Ziemert
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, California 92037, United States
- E-mail:
| | - Bradley S. Moore
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, California 92037, United States
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
- E-mail:
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Cochrane RVK, Vederas JC. Highly selective but multifunctional oxygenases in secondary metabolism. Acc Chem Res 2014; 47:3148-61. [PMID: 25250512 DOI: 10.1021/ar500242c] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Biosynthesis of bioactive natural products frequently features oxidation at multiple sites. Starting from a relatively reduced chemical scaffold that is assembled by controlled polymerization of small precursors, for example, acetate or amino acids, a diverse range of redox reactions can generate very complex and highly oxygenated structures. Their formation often involves C-H activation reactions catalyzed by oxygenase enzymes, either monooxygenases or dioxygenases. The former category includes the cytochrome P450s and flavin-dependent oxygenases, whereas examples of the latter are the non-heme iron α-ketoglutarate-dependent oxygenases. Oxygenases can catalyze a plethora of reactions ranging from hydroxylations and epoxidations to dehydrogenations, cyclizations, and rearrangements. The specific transformations are usually possible only with the use of these enzymatic catalysts. Aside from the ability of oxygenases to specifically oxidize unactivated carbon skeletons, some have recently been demonstrated to possess a fascinating ability to catalyze multiple reactions in a highly ordered fashion at different sites starting with a single substrate molecule. In the past, oxygenases associated with secondary metabolite pathways were considered to be highly regio-, stereo-, and substrate specific, with one oxidizing enzyme encoded in the gene cluster corresponding to one oxidation location in the natural product itself. However, it is becoming progressively clear that this "one oxygenase, one oxidation site" relationship is not necessarily a valid assumption. Multifunctional oxidases are known to occur in higher plants, fungi, and bacteria. Natural product gene clusters that contain multifunctional oxidase enzymes are responsible for production of lovastatin (a cholesterol-lowering agent and precursor to simvastatin), scopolamine (an anticholinergic drug), and cytochalasin E (an angiogenesis inhibitor), among many others. As opposed to simply being substrate promiscuous, these enzymes show very high substrate specificity and catalyze several oxidative reactions in a single pathway, with each oxidation being a prerequisite for the next. The basis for their specificity and highly ordered sequence is not yet well understood. In the lovastatin pathway, LovA is a cytochrome P450 that introduces a double bond and a hydroxyl group. H6H is an α-ketoglutarate-dependent oxygenase that hydroxylates (-)-atropine and then closes the newly introduced oxygen onto a neighboring methylene to generate the epoxide of scopolamine. CcsB is a flavin-dependent Baeyer-Villigerase that converts a ketone to a carbonate by double oxidation, a reaction not possible without enzymes. Recent crystallographic studies of other multifunctional oxygenases, such as AurH, a cytochrome P450 from Streptomyces thioluteus involved in aureothin biosynthesis, have indicated a steric switch mechanism. After the initial hydroxylation reaction catalyzed by AurH, the enzyme is thought to undergo a substrate-induced conformational change. In this Account, advances in our knowledge of these fascinating multifunctional enzymes and their potential will be explored.
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Affiliation(s)
| | - John C. Vederas
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2 Canada
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Abstract
Natural products are important sources of pharmaceuticals, in part owing to their diverse biological activities. Enzymes from natural product biosynthetic pathways have become attractive candidates as biocatalysts for modifying the structures and bioactivities of these complex compounds. Numerous enzymes have been harvested to generate innovative scaffolds, large-scale synthesis of chiral building blocks, and semisynthesis of medicinally relevant natural product derivatives. This review discusses recent examples from three areas: (a) polyketide catalytic domain engineering geared toward synthesis of new polyketides, (b) engineering of tailoring enzymes (other than oxidative enzymes) as biocatalysts, and (c) in vitro total synthesis of natural products using purified enzyme components. With the availability of exponentially increasing genomic information and new genome mining tools, many new and powerful biocatalysts tailored for pharmaceutical synthesis will likely emerge from secondary metabolism.
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An enzymatic platform for the synthesis of isoprenoid precursors. PLoS One 2014; 9:e105594. [PMID: 25153179 PMCID: PMC4143292 DOI: 10.1371/journal.pone.0105594] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 07/23/2014] [Indexed: 12/13/2022] Open
Abstract
The isoprenoid family of compounds is estimated to contain ∼65,000 unique structures including medicines, fragrances, and biofuels. Due to their structural complexity, many isoprenoids can only be obtained by extraction from natural sources, an inherently risky and costly process. Consequently, the biotechnology industry is attempting to genetically engineer microorganisms that can produce isoprenoid-based drugs and fuels on a commercial scale. Isoprenoid backbones are constructed from two, five-carbon building blocks, isopentenyl 5-pyrophosphate and dimethylallyl 5-pyrophosphate, which are end-products of either the mevalonate or non-mevalonate pathways. By linking the HMG-CoA reductase pathway (which produces mevalonate) to the mevalonate pathway, these building block can be synthesized enzymatically from acetate, ATP, NAD(P)H and CoA. Here, the enzymes in these pathways are used to produce pathway intermediates and end-products in single-pot reactions and in remarkably high yield, ∼85%. A strategy for the regio-specific incorporation of isotopes into isoprenoid backbones is developed and used to synthesize a series of isotopomers of diphosphomevalonate, the immediate end-product of the mevalonate pathway. The enzymatic system is shown to be robust and capable of producing quantities of product in aqueous solutions that meet or exceed the highest levels achieved using genetically engineered organisms in high-density fermentation.
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58
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Teufel R, Kaysser L, Villaume MT, Diethelm S, Carbullido MK, Baran PS, Moore BS. One-Pot Enzymatic Synthesis of Merochlorin A and B. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405694] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Teufel R, Kaysser L, Villaume MT, Diethelm S, Carbullido MK, Baran PS, Moore BS. One-pot enzymatic synthesis of merochlorin A and B. Angew Chem Int Ed Engl 2014; 53:11019-22. [PMID: 25115835 DOI: 10.1002/anie.201405694] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Indexed: 11/06/2022]
Abstract
The polycycles merochlorin A and B are complex halogenated meroterpenoid natural products with significant antibacterial activities and are produced by the marine bacterium Streptomyces sp. strain CNH-189. Heterologously produced enzymes and chemical synthesis are employed herein to fully reconstitute the merochlorin biosynthesis in vitro. The interplay of a dedicated type III polyketide synthase, a prenyl diphosphate synthase, and an aromatic prenyltransferase allow formation of a highly unusual aromatic polyketide-terpene hybrid intermediate which features an unprecedented branched sesquiterpene moiety from isosesquilavandulyl diphosphate. As supported by in vivo experiments, this precursor is furthermore chlorinated and cyclized to merochlorin A and isomeric merochlorin B by a single vanadium-dependent haloperoxidase, thus completing the remarkably efficient pathway.
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Affiliation(s)
- Robin Teufel
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037 (USA) http://scrippsscholars.ucsd.edu/bsmoore
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60
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Agudo R, Reetz MT. Designer cells for stereocomplementary de novo enzymatic cascade reactions based on laboratory evolution. Chem Commun (Camb) 2014; 49:10914-6. [PMID: 24135920 DOI: 10.1039/c3cc46229c] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Designer cells for a synthetic cascade reaction harnessing selective redox reactions were devised, featuring two successive regioselective P450-catalyzed CH-activating oxidations of 1-cyclohexene carboxylic acid methyl ester followed by stereoselective olefin-reduction catalysed by (R)- or (S)-selective mutants of an enoate reductase.
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Affiliation(s)
- Rubén Agudo
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein Str., 35032 Marburg, Germany
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61
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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.
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Affiliation(s)
- Irina Koryakina
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA
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62
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Ma HM, Zhou Q, Tang YM, Zhang Z, Chen YS, He HY, Pan HX, Tang MC, Gao JF, Zhao SY, Igarashi Y, Tang GL. Unconventional origin and hybrid system for construction of pyrrolopyrrole moiety in kosinostatin biosynthesis. ACTA ACUST UNITED AC 2014; 20:796-805. [PMID: 23790490 DOI: 10.1016/j.chembiol.2013.04.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 04/22/2013] [Accepted: 04/24/2013] [Indexed: 12/14/2022]
Abstract
Kosinostatin (KST), an antitumor antibiotic, features a pyrrolopyrrole moiety spirally jointed to a five-membered ring of an anthraquinone framework glycosylated with a γ-branched octose. By a combination of in silico analysis, genetic characterization, biochemical assay, and precursor feeding experiments, a biosynthetic pathway for KST was proposed, which revealed (1) the pyrrolopyrrole moiety originates from nicotinic acid and ribose, (2) the bicyclic amidine is constructed by a process similar to the tryptophan biosynthetic pathway, and (3) a discrete adenylation enzyme and a peptidyl carrier protein (PCP) are responsible for producing a PCP-tethered building block parallel to type II polyketide synthase (PKS) rather than for the PKS priming step by providing the starter unit. These findings provide an opportunity to further explore the inexplicable enzymatic logic that governs the formation of pyrrolopyrrole moiety and the spirocyclic skeleton.
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Affiliation(s)
- Hong-Min Ma
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
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63
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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]
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64
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Statistical experimental design guided optimization of a one-pot biphasic multienzyme total synthesis of amorpha-4,11-diene. PLoS One 2013; 8:e79650. [PMID: 24278153 PMCID: PMC3835790 DOI: 10.1371/journal.pone.0079650] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 10/04/2013] [Indexed: 01/20/2023] Open
Abstract
In vitro synthesis of chemicals and pharmaceuticals using enzymes is of considerable interest as these biocatalysts facilitate a wide variety of reactions under mild conditions with excellent regio-, chemo- and stereoselectivities. A significant challenge in a multi-enzymatic reaction is the need to optimize the various steps involved simultaneously so as to obtain high-yield of a product. In this study, statistical experimental design was used to guide the optimization of a total synthesis of amorpha-4,11-diene (AD) using multienzymes in the mevalonate pathway. A combinatorial approach guided by Taguchi orthogonal array design identified the local optimum enzymatic activity ratio for Erg12:Erg8:Erg19:Idi:IspA to be 100∶100∶1∶25∶5, with a constant concentration of amorpha-4,11-diene synthase (Ads, 100 mg/L). The model also identified an unexpected inhibitory effect of farnesyl pyrophosphate synthase (IspA), where the activity was negatively correlated with AD yield. This was due to the precipitation of farnesyl pyrophosphate (FPP), the product of IspA. Response surface methodology was then used to optimize IspA and Ads activities simultaneously so as to minimize the accumulation of FPP and the result showed that Ads to be a critical factor. By increasing the concentration of Ads, a complete conversion (∼100%) of mevalonic acid (MVA) to AD was achieved. Monovalent ions and pH were effective means of enhancing the specific Ads activity and specific AD yield significantly. The results from this study represent the first in vitro reconstitution of the mevalonate pathway for the production of an isoprenoid and the approaches developed herein may be used to produce other isopentenyl pyrophosphate (IPP)/dimethylallyl pyrophosphate (DMAPP) based products.
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Teufel R, Miyanaga A, Michaudel Q, Stull F, Louie G, Noel JP, Baran PS, Palfey B, Moore BS. Flavin-mediated dual oxidation controls an enzymatic Favorskii-type rearrangement. Nature 2013; 503:552-556. [PMID: 24162851 PMCID: PMC3844076 DOI: 10.1038/nature12643] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 09/09/2013] [Indexed: 12/25/2022]
Abstract
Flavoproteins catalyze a diversity of fundamental redox reactions and are one of the most studied enzyme families1,2. As monooxygenases, they are universally thought to control oxygenation by means of a peroxyflavin species that transfers a single atom of molecular oxygen to an organic substrate1,3,4. Here we report that the bacterial flavoenzyme EncM5,6 catalyzes the peroxyflavin-independent oxygenation-dehydrogenation dual oxidation of a highly reactive poly(β-carbonyl). The crystal structure of EncM with bound substrate mimics coupled with isotope labeling studies reveal previously unknown flavin redox biochemistry. We show that EncM maintains an unanticipated stable flavin oxygenating species, proposed to be a flavin-N5-oxide, to promote substrate oxidation and trigger a rare Favorskii-type rearrangement that is central to the biosynthesis of the antibiotic enterocin. This work provides new insight into the fine-tuning of the flavin cofactor in offsetting the innate reactivity of a polyketide substrate to direct its efficient electrocyclization.
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Affiliation(s)
- Robin Teufel
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, 92093, USA
| | - Akimasa Miyanaga
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, 92093, USA
| | - Quentin Michaudel
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Frederick Stull
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Gordon Louie
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics, La Jolla, California 92037, USA
| | - Joseph P Noel
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics, La Jolla, California 92037, USA
| | - Phil S Baran
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Bruce Palfey
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, USA.,Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, 92093, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, USA
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66
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Reetz MT. Biocatalysis in organic chemistry and biotechnology: past, present, and future. J Am Chem Soc 2013; 135:12480-96. [PMID: 23930719 DOI: 10.1021/ja405051f] [Citation(s) in RCA: 522] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Enzymes as catalysts in synthetic organic chemistry gained importance in the latter half of the 20th century, but nevertheless suffered from two major limitations. First, many enzymes were not accessible in large enough quantities for practical applications. The advent of recombinant DNA technology changed this dramatically in the late 1970s. Second, many enzymes showed a narrow substrate scope, often poor stereo- and/or regioselectivity and/or insufficient stability under operating conditions. With the development of directed evolution beginning in the 1990s and continuing to the present day, all of these problems can be addressed and generally solved. The present Perspective focuses on these and other developments which have popularized enzymes as part of the toolkit of synthetic organic chemists and biotechnologists. Included is a discussion of the scope and limitation of cascade reactions using enzyme mixtures in vitro and of metabolic engineering of pathways in cells as factories for the production of simple compounds such as biofuels and complex natural products. Future trends and problems are also highlighted, as is the discussion concerning biocatalysis versus nonbiological catalysis in synthetic organic chemistry. This Perspective does not constitute a comprehensive review, and therefore the author apologizes to those researchers whose work is not specifically treated here.
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Affiliation(s)
- Manfred T Reetz
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein Strasse, 35032 Marburg, Germany.
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67
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Lipson JM, Thomsen M, Moore BS, Clausen RP, La Clair JJ, Burkart MD. A tandem chemoenzymatic methylation by S-adenosyl-L-methionine. Chembiochem 2013; 14:950-3. [PMID: 23650044 DOI: 10.1002/cbic.201300221] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Indexed: 12/14/2022]
Abstract
Keep 'em methylated: The in situ preparation of the cofactor AdoMet was achieved by allowing the biosynthetic enzyme SalL to operate in the reverse direction by presentation of 5'-chloro-5'-deoxyadenosine at low salt concentrations. This reaction was readily coupled with DNA and small molecule methyltransferases to afford a regioselective method for chemo-enzymatic methylation and isotope incorporation.
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Affiliation(s)
- Joseph M Lipson
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
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68
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Kalaitzis JA. Discovery, biosynthesis, and rational engineering of novel enterocin and wailupemycin polyketide analogues. Methods Mol Biol 2013; 1055:171-89. [PMID: 23963911 DOI: 10.1007/978-1-62703-577-4_13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The marine actinomycete Streptomyces maritimus produces a structurally diverse set of unusual polyketide natural products including the major metabolite enterocin. Investigations of enterocin biosynthesis revealed that the unique carbon skeleton is derived from an aromatic polyketide pathway which is genetically coded by the 21.3 kb enc gene cluster in S. maritimus. Characterization of the enc biosynthesis gene cluster and subsequent manipulation of it via heterologous expression and/or mutagenesis enabled the discovery of other enc-based metabolites that were produced in only very minor amounts in the wild type. Also described are techniques used to harness the enterocin biosynthetic machinery in order to generate unnatural enc-derived polyketide analogues. This review focuses upon the molecular methods used in combination with classical natural products detection and isolation techniques to access minor metabolites of the S. maritimus secondary metabolome.
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Affiliation(s)
- John A Kalaitzis
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia
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69
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Abstract
Riboflavin-based coenzymes, tightly bound to enzymes catalyzing substrate oxidations and reductions, enable an enormous range of chemical transformations in biosynthetic pathways. Flavoenzymes catalyze substrate oxidations involving amine and alcohol oxidations and desaturations to olefins, the latter setting up Diels-Alder cyclizations in lovastatin and solanapyrone biosyntheses. Both C(4a) and N(5) of the flavin coenzymes are sites for covalent adduct formation. For example, the reactivity of dihydroflavins with molecular oxygen leads to flavin-4a-OOH adducts which then carry out a diverse range of oxygen transfers, including Baeyer-Villiger type ring expansions, olefin epoxidations, halogenations via transient HOCl generation, and an oxidative Favorskii rerrangement during enterocin assembly.
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Affiliation(s)
- Christopher T Walsh
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave., Boston, MA 02115, USA.
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Richter M, Busch B, Ishida K, Moore BS, Hertweck C. Pyran formation by an atypical CYP-mediated four-electron oxygenation-cyclization cascade in an engineered aureothin pathway. Chembiochem 2012; 13:2196-9. [PMID: 22961965 DOI: 10.1002/cbic.201200406] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Indexed: 01/17/2023]
Abstract
Small changes, big effect: A new aureothin derivative, aureopyran, which features an unusual pyran backbone, was generated by simply altering the enzymatic methylation topology. The α-pyrone ring hampers the correct placement of the polyketide backbone in the multifunctional cytochrome P450 monooxygenase AurH. Instead of a tetrahydrofuran ring, an oxo intermediate is formed that readily undergoes a rare electrocyclization reaction.
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Affiliation(s)
- Martin Richter
- Dept. Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena, Germany
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71
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Li S, Anand K, Tran H, Yu F, Finefield JM, Sunderhaus JD, McAfoos TJ, Tsukamoto S, Williams RM, Sherman DH. Comparative analysis of the biosynthetic systems for fungal bicyclo[2.2.2]diazaoctane indole alkaloids: the (+)/(-)-notoamide, paraherquamide and malbrancheamide pathways. MEDCHEMCOMM 2012; 3:987-996. [PMID: 23213353 PMCID: PMC3511817 DOI: 10.1039/c2md20029e] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The biosynthesis of fungal bicyclo[2.2.2]diazaoctane indole alkaloids with a wide spectrum of biological activities have attracted increasing interest. Their intriguing mode of assembly has long been proposed to feature a non-ribosomal peptide synthetase, a presumed intramolecular Diels-Alderase, a variant number of prenyltransferases, and a series of oxidases responsible for the diverse tailoring modifications of their cyclodipeptide-based structural core. Until recently, the details of these biosynthetic pathways have remained largely unknown due to lack of information on the fungal derived biosynthetic gene clusters. Herein, we report a comparative analysis of four natural product metabolic systems of a select group of bicyclo[2.2.2]diazaoctane indole alkaloids including (+)/(-)-notoamide, paraherquamide and malbrancheamide, in which we propose an enzyme for each step in the biosynthetic pathway based on deep annotation and on-going biochemical studies.
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Affiliation(s)
- Shengying Li
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Krithika Anand
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Hong Tran
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Fengan Yu
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | - James D. Sunderhaus
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Timothy J. McAfoos
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Sachiko Tsukamoto
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Kumamoto 862-0973, Japan
| | - Robert M. Williams
- University of Colorado Cancer Center, Aurora, Colorado 80045, USA
- Departments of Medicinal Chemistry, Microbiology & Immunology, and Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - David H. Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA
- Departments of Medicinal Chemistry, Microbiology & Immunology, and Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
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72
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Structure-guided expansion of the substrate range of methylmalonyl coenzyme A synthetase (MatB) of Rhodopseudomonas palustris. Appl Environ Microbiol 2012; 78:6619-29. [PMID: 22773649 DOI: 10.1128/aem.01733-12] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Malonyl coenzyme A (malonyl-CoA) and methylmalonyl-CoA are two of the most commonly used extender units for polyketide biosynthesis and are utilized to synthesize a vast array of pharmaceutically relevant products with antibacterial, antiparasitic, anticholesterol, anticancer, antifungal, and immunosuppressive properties. Heterologous hosts used for polyketide production such as Escherichia coli often do not produce significant amounts of methylmalonyl-CoA, however, requiring the introduction of other pathways for the generation of this important building block. Recently, the bacterial malonyl-CoA synthetase class of enzymes has been utilized to generate malonyl-CoA and methylmalonyl-CoA directly from malonate and methylmalonate. We demonstrate that in the purple photosynthetic bacterium Rhodopseudomonas palustris, MatB (RpMatB) acts as a methylmalonyl-CoA synthetase and is required for growth on methylmalonate. We report the apo (1.7-Å resolution) and ATP-bound (2.0-Å resolution) structure and kinetic analysis of RpMatB, which shows similar activities for both malonate and methylmalonate, making it an ideal enzyme for heterologous polyketide biosynthesis. Additionally, rational, structure-based mutagenesis of the active site of RpMatB led to substantially higher activity with ethylmalonate and butylmalonate, demonstrating that this enzyme is a prime target for expanded substrate specificity.
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73
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Kwon SJ, Mora-Pale M, Lee MY, Dordick JS. Expanding nature's small molecule diversity via in vitro biosynthetic pathway engineering. Curr Opin Chem Biol 2012; 16:186-95. [DOI: 10.1016/j.cbpa.2012.02.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Revised: 02/01/2012] [Accepted: 02/01/2012] [Indexed: 12/15/2022]
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74
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Kharel MK, Rohr J. Delineation of gilvocarcin, jadomycin, and landomycin pathways through combinatorial biosynthetic enzymology. Curr Opin Chem Biol 2012; 16:150-61. [PMID: 22465094 DOI: 10.1016/j.cbpa.2012.03.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Revised: 03/08/2012] [Accepted: 03/09/2012] [Indexed: 11/30/2022]
Abstract
The exact sequence of events in biosyntheses of natural products is essential not only to understand and learn from nature's strategies and tricks to assemble complex natural products, but also for yield optimization of desired natural products, and for pathway engineering and muta-synthetic preparation of analogues of bioactive natural products. Biosyntheses of natural products were classically studied applying in vivo experiments, usually by combining incorporation experiments with stable-isotope labeled precursors with cross-feeding experiments of putative intermediates. Later genetic studies were dominant, which consist of gene cluster determination and analysis of gene inactivation experiments. From such studies various biosynthetic pathways were proposed, to a large extent just through in silico analyses of the biosynthetic gene clusters after DNA sequencing. Investigations of the complex biosyntheses of the angucycline group anticancer drugs landomycin, jadomycin and gilvocarcin revealed that in vivo and in silico studies were insufficient to delineate the true biosynthetic sequence of events. Neither was it possible to unambiguously assign enzyme activities, especially where multiple functional enzymes were involved. However, many of the intriguing ambiguities could be solved after in vitro reconstitution of major segments of these pathways, and subsequent systematic variations of the used enzyme mixtures. This method has been recently termed 'combinatorial biosynthetic enzymology'.
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Affiliation(s)
- Madan K Kharel
- Midway College School of Pharmacy, 120 Scott Perry Drive, Paintsville, KY 42240, USA
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75
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Krauser S, Kiefer P, Heinzle E. Multienzyme Whole-Cell In Situ Biocatalysis for the Production of Flaviolin in Permeabilized Cells of Escherichia coli. ChemCatChem 2012. [DOI: 10.1002/cctc.201100351] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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76
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Pahari P, Kharel MK, Shepherd MD, van Lanen SG, Rohr J. Enzymatic Total Synthesis of Defucogilvocarcin M and Its Implications for Gilvocarcin Biosynthesis. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201105882] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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77
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Pahari P, Kharel MK, Shepherd MD, van Lanen SG, Rohr J. Enzymatic total synthesis of defucogilvocarcin M and its implications for gilvocarcin biosynthesis. Angew Chem Int Ed Engl 2011; 51:1216-20. [PMID: 22223167 DOI: 10.1002/anie.201105882] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Revised: 11/03/2011] [Indexed: 11/08/2022]
Affiliation(s)
- Pallab Pahari
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536-0596, USA
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78
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Abstract
The largely unexplored marine world that presumably harbors the most biodiversity may be the vastest resource to discover novel 'validated' structures with novel modes of action that cover biologically relevant chemical space. Several challenges, including the supply problem and target identification, need to be met for successful drug development of these often complex molecules; however, approaches are available to overcome the hurdles. Advances in technologies such as sampling strategies, nanoscale NMR for structure determination, total chemical synthesis, fermentation and biotechnology are all crucial to the success of marine natural products as drug leads. We illustrate the high degree of innovation in the field of marine natural products, which in our view will lead to a new wave of drugs that flow into the market and pharmacies in the future.
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79
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Pistorius D, Li Y, Mann S, Müller R. Unprecedented Anthranilate Priming Involving Two Enzymes of the Acyl Adenylating Superfamily in Aurachin Biosynthesis. J Am Chem Soc 2011; 133:12362-5. [DOI: 10.1021/ja203653w] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dominik Pistorius
- Helmholtz-Institut für Pharmazeutische Forschung Saarland, Helmholtz Zentrum für Infektionsforschung Braunschweig and Pharmazeutische Biotechnologie, Universität des Saarlandes, Postfach 151150, 66041 Saarbrücken, Germany
| | - Yanyan Li
- Helmholtz-Institut für Pharmazeutische Forschung Saarland, Helmholtz Zentrum für Infektionsforschung Braunschweig and Pharmazeutische Biotechnologie, Universität des Saarlandes, Postfach 151150, 66041 Saarbrücken, Germany
| | - Stéphane Mann
- Chimie ParisTech, ENSCP, Laboratoire Charles Friedel, UMR 7223-CNRS, 75005 Paris, France
| | - Rolf Müller
- Helmholtz-Institut für Pharmazeutische Forschung Saarland, Helmholtz Zentrum für Infektionsforschung Braunschweig and Pharmazeutische Biotechnologie, Universität des Saarlandes, Postfach 151150, 66041 Saarbrücken, Germany
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80
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Kalaitzis JA, Cheng Q, Meluzzi D, Xiang L, Izumikawa M, Dorrestein PC, Moore BS. Policing starter unit selection of the enterocin type II polyketide synthase by the type II thioesterase EncL. Bioorg Med Chem 2011; 19:6633-8. [PMID: 21531566 DOI: 10.1016/j.bmc.2011.04.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 04/05/2011] [Accepted: 04/11/2011] [Indexed: 11/18/2022]
Abstract
Enterocin is an atypical type II polyketide synthase (PKS) product from the marine actinomycete 'Streptomyces maritimus'. The enterocin biosynthesis gene cluster (enc) codes for proteins involved in the assembly and attachment of the rare benzoate primer that initiates polyketide assembly with the addition of seven malonate molecules and culminates in a Favorskii-like rearrangement of the linear poly-β-ketone to give its distinctive non-aromatic, caged core structure. Fundamental to enterocin biosynthesis, which utilizes a single acyl carrier protein (ACP), EncC, for both priming with benzoate and elongating with malonate, involves maintaining the correct balance of acyl-EncC substrates for efficient polyketide assembly. Here, we report the characterization of EncL as a type II thioesterase that functions to edit starter unit (mis)priming of EncC. We performed a series of in vivo mutational studies, heterologous expression experiments, in vitro reconstitution studies, and Fourier-transform mass spectrometry-monitored competitive enzyme assays that together support the proposed selective hydrolase activity of EncL toward misprimed acetyl-ACP over benzoyl-ACP to facilitate benzoyl priming of the enterocin PKS complex. While this system resembles the R1128 PKS that also utilizes an editing thioesterase (ZhuC) to purge acetate molecules from its initiation module ACP in favor of alkylacyl groups, the enterocin system is distinct in its usage of a single ACP for both priming and elongating reactions with different substrates.
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Affiliation(s)
- John A Kalaitzis
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
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81
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Abstract
The years 2000 through mid-2010 marked a transformational period in understanding of the biosynthesis of marine natural products. During this decade the field emerged from one largely dominated by chemical approaches to understanding biosynthetic pathways to one incorporating the full force of modern molecular biology and bioinformatics. Fusion of chemical and biological approaches yielded great advances in understanding the genetic and enzymatic basis for marine natural product biosynthesis. Progress was particularly pronounced for marine microbes, especially actinomycetes and cyanobacteria. During this single decade, both the first complete marine microbial natural product biosynthetic gene cluster sequence was released as well as the first entire genome sequence for a secondary metabolite-rich marine microbe. The decade also saw tremendous progress in recognizing the key role of marine microbial symbionts of invertebrates in natural product biosynthesis. Application of genetic and enzymatic knowledge led to genetic engineering of novel “unnatural” natural products during this time, as well as opportunities for discovery of novel natural products through genome mining. The current review highlights selected seminal studies from 2000 through to June 2010 that illustrate breakthroughs in understanding of marine natural product biosynthesis at the genetic, enzymatic, and small-molecule natural product levels. A total of 154 references are cited.
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Affiliation(s)
- Amy L. Lane
- Department of Chemistry, University of North Florida, Jacksonville, FL, 32224, USA.
| | - Bradley S. Moore
- Scripps Institution of Oceanography and the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA, 92093, USA
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82
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Grand challenge commentary: Transforming biosynthesis into an information science. Nat Chem Biol 2010; 6:859-61. [PMID: 21079588 DOI: 10.1038/nchembio.487] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Engineering biosynthetic pathways to natural products is a challenging endeavor that promises to provide new therapeutics and tools to manipulate biology. Information-guided design strategies and tools could unlock the creativity of a wide spectrum of scientists and engineers by decoupling expertise from implementation.
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83
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Kharel MK, Pahari P, Lian H, Rohr J. Enzymatic total synthesis of rabelomycin, an angucycline group antibiotic. Org Lett 2010; 12:2814-7. [PMID: 20486694 DOI: 10.1021/ol1009009] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A one-pot enzymatic total synthesis of angucycline antibiotic rabelomycin was accomplished, starting from acetyl-CoA and malonyl-CoA, using a mixture of polyketide synthase (PKS) enzymes of the gilvocarcin, ravidomycin, and jadomycin biosynthetic pathways. The in vitro results were compared to in vivo catalysis using analogous sets of enzymes.
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Affiliation(s)
- Madan Kumar Kharel
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, USA
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84
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Werneburg M, Busch B, He J, Richter ME, Xiang L, Moore BS, Roth M, Dahse HM, Hertweck C. Exploiting enzymatic promiscuity to engineer a focused library of highly selective antifungal and antiproliferative aureothin analogues. J Am Chem Soc 2010; 132:10407-13. [PMID: 20662518 PMCID: PMC2925430 DOI: 10.1021/ja102751h] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Aureothin is a shikimate-polyketide hybrid metabolite from Streptomyces thioluteus with a rare nitroaryl moiety, a chiral tetrahydrofuran ring, and an O-methylated pyrone ring. The antimicrobial and antitumor activities of aureothin have caught our interest in modulating its structure as well as its bioactivity profile. In an integrated approach using mutasynthesis, biotransformation, and combinatorial biosynthesis, a defined library of aureothin analogues was generated. The promiscuity of the polyketide synthase assembly line toward different starter units and the plasticity of the pyrone and tetrahydrofuran ring formation were exploited. A selection of 15 new aureothin analogues with modifications at the aryl residue, the pyrone ring, and the oxygenated backbone was produced on a preparative scale and fully characterized. Remarkably, various new aureothin derivatives are less cytotoxic than aureothin but have improved antiproliferative activities. Furthermore, we found that the THF ring is crucial for the remarkably selective activity of aureothin analogues against certain pathogenic fungi.
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Affiliation(s)
- Martina Werneburg
- Leibniz Institute for Natural Product Research and Infection Biology,
HKI, Dept. of Biomolecular Chemistry, Beutenbergstr. 11a, 07745 Jena, Germany,
and the Friedrich Schiller University, Jena, Germany, and the Scripps
Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical
Sciences, University of California at San Diego, La Jolla, California,
92093-0204 U.S.A
| | - Benjamin Busch
- Leibniz Institute for Natural Product Research and Infection Biology,
HKI, Dept. of Biomolecular Chemistry, Beutenbergstr. 11a, 07745 Jena, Germany,
and the Friedrich Schiller University, Jena, Germany, and the Scripps
Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical
Sciences, University of California at San Diego, La Jolla, California,
92093-0204 U.S.A
| | - Jing He
- Leibniz Institute for Natural Product Research and Infection Biology,
HKI, Dept. of Biomolecular Chemistry, Beutenbergstr. 11a, 07745 Jena, Germany,
and the Friedrich Schiller University, Jena, Germany, and the Scripps
Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical
Sciences, University of California at San Diego, La Jolla, California,
92093-0204 U.S.A
| | - Martin E.A. Richter
- Leibniz Institute for Natural Product Research and Infection Biology,
HKI, Dept. of Biomolecular Chemistry, Beutenbergstr. 11a, 07745 Jena, Germany,
and the Friedrich Schiller University, Jena, Germany, and the Scripps
Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical
Sciences, University of California at San Diego, La Jolla, California,
92093-0204 U.S.A
| | - Longkuan Xiang
- Leibniz Institute for Natural Product Research and Infection Biology,
HKI, Dept. of Biomolecular Chemistry, Beutenbergstr. 11a, 07745 Jena, Germany,
and the Friedrich Schiller University, Jena, Germany, and the Scripps
Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical
Sciences, University of California at San Diego, La Jolla, California,
92093-0204 U.S.A
| | - Bradley S. Moore
- Leibniz Institute for Natural Product Research and Infection Biology,
HKI, Dept. of Biomolecular Chemistry, Beutenbergstr. 11a, 07745 Jena, Germany,
and the Friedrich Schiller University, Jena, Germany, and the Scripps
Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical
Sciences, University of California at San Diego, La Jolla, California,
92093-0204 U.S.A
| | - Martin Roth
- Leibniz Institute for Natural Product Research and Infection Biology,
HKI, Dept. of Biomolecular Chemistry, Beutenbergstr. 11a, 07745 Jena, Germany,
and the Friedrich Schiller University, Jena, Germany, and the Scripps
Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical
Sciences, University of California at San Diego, La Jolla, California,
92093-0204 U.S.A
| | - Hans-Martin Dahse
- Leibniz Institute for Natural Product Research and Infection Biology,
HKI, Dept. of Biomolecular Chemistry, Beutenbergstr. 11a, 07745 Jena, Germany,
and the Friedrich Schiller University, Jena, Germany, and the Scripps
Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical
Sciences, University of California at San Diego, La Jolla, California,
92093-0204 U.S.A
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology,
HKI, Dept. of Biomolecular Chemistry, Beutenbergstr. 11a, 07745 Jena, Germany,
and the Friedrich Schiller University, Jena, Germany, and the Scripps
Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical
Sciences, University of California at San Diego, La Jolla, California,
92093-0204 U.S.A
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85
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Walsh CT, Fischbach MA. Natural products version 2.0: connecting genes to molecules. J Am Chem Soc 2010; 132:2469-93. [PMID: 20121095 DOI: 10.1021/ja909118a] [Citation(s) in RCA: 323] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Natural products have played a prominent role in the history of organic chemistry, and they continue to be important as drugs, biological probes, and targets of study for synthetic and analytical chemists. In this Perspective, we explore how connecting Nature's small molecules to the genes that encode them has sparked a renaissance in natural product research, focusing primarily on the biosynthesis of polyketides and non-ribosomal peptides. We survey monomer biogenesis, coupling chemistries from templated and non-templated pathways, and the broad set of tailoring reactions and hybrid pathways that give rise to the diverse scaffolds and functionalization patterns of natural products. We conclude by considering two questions: What would it take to find all natural product scaffolds? What kind of scientists will be studying natural products in the future?
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Affiliation(s)
- Christopher T Walsh
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA.
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86
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Zhou H, Qiao K, Gao Z, Meehan MJ, Li JWH, Zhao X, Dorrestein PC, Vederas JC, Tang Y. Enzymatic synthesis of resorcylic acid lactones by cooperation of fungal iterative polyketide synthases involved in hypothemycin biosynthesis. J Am Chem Soc 2010; 132:4530-1. [PMID: 20222707 PMCID: PMC2861853 DOI: 10.1021/ja100060k] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hypothemycin is a macrolide protein kinase inhibitor from the fungus Hypomyces subiculosus. During biosynthesis, its carbon framework is assembled by two iterative polyketide synthases (PKSs), Hpm8 (highly reducing) and Hpm3 (nonreducing). These were heterologously expressed in Saccharomyces cerevisiae BJ5464-NpgA, purified to near homogeneity, and reconstituted in vitro to produce (6'S,10'S)-trans-7',8'-dehydrozearalenol (1) from malonyl-CoA and NADPH. The structure of 1 was determined by X-ray crystallographic analysis. In the absence of functional Hpm3, the reducing PKS Hpm8 produces and offloads truncated pyrone products instead of the expected hexaketide. The nonreducing Hpm3 is able to accept an N-acetylcysteamine thioester of a correctly functionalized hexaketide to form 1, but it is unable to initiate polyketide formation from malonyl-CoA. We show that the starter-unit:ACP transacylase (SAT) of Hpm3 is critical for crosstalk between the two enzymes and that the rate of biosynthesis of 1 is determined by the rate of hexaketide formation by Hpm8.
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Affiliation(s)
- Hui Zhou
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095
| | - Kangjian Qiao
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095
| | - Zhizeng Gao
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Michael J. Meehan
- Skaggs School of Pharmacy and Pharmaceutical Sciences and Departments of Pharmacology, Chemistry and Biochemistry, University of California, San Diego, CA 92093
| | - Jesse W.-H. Li
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Xiling Zhao
- Skaggs School of Pharmacy and Pharmaceutical Sciences and Departments of Pharmacology, Chemistry and Biochemistry, University of California, San Diego, CA 92093
| | - Pieter C. Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences and Departments of Pharmacology, Chemistry and Biochemistry, University of California, San Diego, CA 92093
| | - John C. Vederas
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095
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87
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Roberts AA, Ryan KS, Moore BS, Gulder TA. Total (bio)synthesis: strategies of nature and of chemists. Top Curr Chem (Cham) 2010; 297:149-203. [PMID: 21495259 PMCID: PMC3109256 DOI: 10.1007/128_2010_79] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The biosynthetic pathways to a number of natural products have been reconstituted in vitro using purified enzymes. Many of these molecules have also been synthesized by organic chemists. Here we compare the strategies used by nature and by chemists to reveal the underlying logic and success of each total synthetic approach for some exemplary molecules with diverse biosynthetic origins.
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88
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Kim MI, Kwon SJ, Dordick JS. In vitro precursor-directed synthesis of polyketide analogues with coenzyme a regeneration for the development of antiangiogenic agents. Org Lett 2009; 11:3806-9. [PMID: 19653678 DOI: 10.1021/ol901243e] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Polyketide analogues are produced via in vitro reconstruction of a precursor-directed polyketide biosynthetic pathway. Malonyl-CoA synthetase (MCS) was used in conjunction with chalcone synthase (CHS), thereby allowing efficient use of synthetic starter molecules and malonate as extender. Coenzyme-A was recycled up to 50 times. The use of a simple immobilization procedure resulted in up to a 30-fold higher yield of pyrone CHS products than that obtained with the free enzyme solutions.
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Affiliation(s)
- Moon Il Kim
- Department of Chemical and Biological Engineering, Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
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89
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90
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91
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92
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Gulder TAM, Moore BS. Chasing the treasures of the sea - bacterial marine natural products. Curr Opin Microbiol 2009; 12:252-60. [PMID: 19481972 DOI: 10.1016/j.mib.2009.05.002] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2009] [Revised: 05/06/2009] [Accepted: 05/06/2009] [Indexed: 10/20/2022]
Abstract
Bacterial marine natural products are an important source of novel lead structures for drug discovery. The cytotoxic properties of many of these secondary metabolites are of particular interest for the development of new anticancer agents. Tremendous advances in marine molecular biology, genome sequencing, and bioinformatics have paved the way to fully exploit the biomedical potential of marine bacterial products. In addition, unique biosynthetic enzymes discovered from bacteria from the sea have begun to emerge as powerful biocatalysts in medicinal chemistry and total synthesis. The increasingly interdisciplinary field of marine natural product chemistry thus strongly impacts future developments in medicine, chemistry, and biology.
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Affiliation(s)
- Tobias A M Gulder
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, and the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093, USA
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93
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Kalaitzis JA, Cheng Q, Thomas PM, Kelleher NL, Moore BS. In vitro biosynthesis of unnatural enterocin and wailupemycin polyketides. JOURNAL OF NATURAL PRODUCTS 2009; 72:469-72. [PMID: 19215142 PMCID: PMC2765504 DOI: 10.1021/np800598t] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Nature has evolved finely tuned strategies to synthesize rare and complex natural products such as the enterocin family of polyketides from the marine bacterium Streptomyces maritimus. Herein we report the directed ex vivo multienzyme syntheses of 24 unnatural 5-deoxyenterocin and wailupemycin F and G analogues, 18 of which are new. We have generated molecular diversity by priming the enterocin biosynthesis enzymes with unnatural substrates and have illustrated further the uniqueness of this type II polyketide synthase by way of exploiting its unusual starter unit biosynthesis pathways.
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Affiliation(s)
- John A. Kalaitzis
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California, 92093-0204
| | - Qian Cheng
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California, 92093-0204
| | - Paul M. Thomas
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Neil L. Kelleher
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Bradley S. Moore
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California, 92093-0204
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California, 92093-0204
- Corresponding author. Tel: (858) 822-6650. Fax: (858) 558-3702. E-mail:
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94
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Worthington AS, Hur GH, Meier JL, Cheng Q, Moore BS, Burkart MD. Probing the compatibility of type II ketosynthase-carrier protein partners. Chembiochem 2009; 9:2096-103. [PMID: 18666307 DOI: 10.1002/cbic.200800198] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Drug discovery often begins with the screening of large compound libraries to identify lead compounds. Recently, the enzymes that are involved in the biosynthesis of natural products have been investigated for their potential to generate new, diverse compound libraries. There have been several approaches toward this end, including altering the substrate specificities of the enzymes involved in natural product biosynthesis and engineering functional communication between enzymes from different biosynthetic pathways. While there exist assays to assess the substrate specificity of enzymes involved in these pathways, there is no simple method for determining whether enzymes from different synthases will function cooperatively to generate the desired product(s). Herein we report a method that provides insight into both substrate specificity and compatibility of protein-protein interactions between the acyl carrier protein (ACP) and ketosynthase (KS) domains involved in fatty acid and polyketide biosynthesis. Our technique uses a one-pot chemoenzymatic method to generate post-translationally modified ACPs that are capable of covalently interacting with KS domains from different biosynthetic systems. The extent of interaction between ACPs and KSs from different systems is easily detected and quantified by a gel-based method. Our results are consistent with previous studies of substrate specificity and ACP-KS binding interactions and provide new insight into unnatural substrate and protein interactions.
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Affiliation(s)
- Andrew S Worthington
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, USA
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95
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Watanabe K, Oguri H, Oikawa H. Enzymatic Synthesis of Molecular Skeletons of Complex Antitumor Antibiotics with Non-ribosomal Peptide Synthetases. J SYN ORG CHEM JPN 2009. [DOI: 10.5059/yukigoseikyokaishi.67.1152] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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96
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97
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98
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Schultheisz HL, Szymczyna BR, Scott LG, Williamson JR. Pathway engineered enzymatic de novo purine nucleotide synthesis. ACS Chem Biol 2008; 3:499-511. [PMID: 18707057 PMCID: PMC2746247 DOI: 10.1021/cb800066p] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A general method for isotopic labeling of the purine base moiety of nucleotides and RNA has been developed through biochemical pathway engineering in vitro. A synthetic scheme was designed and implemented utilizing recombinant enzymes from the pentose phosphate and de novo purine synthesis pathways, with regeneration of folate, aspartate, glutamine, ATP, and NADPH cofactors, in a single-pot reaction. Syntheses proceeded quickly and efficiently in comparison to chemical methods with isolated yields up to 66% for 13C-, 15N-enriched ATP and GTP. The scheme is robust and flexible, requiring only serine, NH4+, glucose, and CO2 as stoichiometric precursors in labeled form. Using this approach, U-13C- GTP, U-13C, 15N- GTP, 13C 2,8- ATP, and U-15N- GTP were synthesized on a millimole scale, and the utility of the isotope labeling is illustrated in NMR spectra of HIV-2 transactivation region RNA containing 13C 2,8-adenosine and 15N 1,3,7,9,2-guanosine. Pathway engineering in vitro permits complex synthetic cascades to be effected, expanding the applicability of enzymatic synthesis.
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Affiliation(s)
- Heather L. Schultheisz
- Departments of Molecular Biology and Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, MB33, La Jolla, CA 92037 USA
| | - Blair R. Szymczyna
- Departments of Molecular Biology and Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, MB33, La Jolla, CA 92037 USA
| | - Lincoln G. Scott
- Cassia, LLC, 4045 Sorrento Valley Boulevard, San Diego, CA 92121 USA
| | - James R. Williamson
- Departments of Molecular Biology and Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, MB33, La Jolla, CA 92037 USA
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Simmons TL, Coates RC, Clark BR, Engene N, Gonzalez D, Esquenazi E, Dorrestein PC, Gerwick WH. Biosynthetic origin of natural products isolated from marine microorganism-invertebrate assemblages. Proc Natl Acad Sci U S A 2008; 105:4587-94. [PMID: 18250337 PMCID: PMC2290810 DOI: 10.1073/pnas.0709851105] [Citation(s) in RCA: 138] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2007] [Indexed: 11/18/2022] Open
Abstract
In all probability, natural selection began as ancient marine microorganisms were required to compete for limited resources. These pressures resulted in the evolution of diverse genetically encoded small molecules with a variety of ecological and metabolic roles. Remarkably, many of these same biologically active molecules have potential utility in modern medicine and biomedical research. The most promising of these natural products often derive from organisms richly populated by associated microorganisms (e.g., marine sponges and ascidians), and often there is great uncertainty about which organism in these assemblages is making these intriguing metabolites. To use the molecular machinery responsible for the biosynthesis of potential drug-lead natural products, new tools must be applied to delineate their genetic and enzymatic origins. The aim of this perspective is to highlight both traditional and emerging techniques for the localization of metabolic pathways within complex marine environments. Examples are given from the literature as well as recent proof-of-concept experiments from the authors' laboratories.
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Affiliation(s)
| | | | | | | | | | | | - Pieter C. Dorrestein
- Departments of Chemistry and Biochemistry
- Pharmacology, and
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093
| | - William H. Gerwick
- *Scripps Institution of Oceanography
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093
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Du L, Zhu X, Gerber R, Huffman J, Lou L, Jorgenson J, Yu F, Zaleta-Rivera K, Wang Q. Biosynthesis of sphinganine-analog mycotoxins. J Ind Microbiol Biotechnol 2008; 35:455-64. [PMID: 18214562 DOI: 10.1007/s10295-008-0316-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2007] [Accepted: 01/10/2008] [Indexed: 10/22/2022]
Abstract
Sphinganine-analog mycotoxins (SAMT) are polyketide-derived natural products produced by a number of plant pathogenic fungi and are among the most economically important mycotoxins. The toxins are structurally similar to sphinganine, a key intermediate in the biosynthesis of ceramides and sphingolipids, and competitive inhibitors for ceramide synthase. The inhibition of ceramide and sphingolipid biosynthesis is associated with several fatal diseases in domestic animals and esophageal cancer and neural tube defects in humans. SAMT contains a highly reduced, acyclic polyketide carbon backbone, which is assembled by a single module polyketide synthase. The biosynthesis of SAMT involves a unique polyketide chain-releasing mechanism, in which a pyridoxal 5'-phosphate-dependent enzyme catalyzes the termination, offloading and elongation of the polyketide chain. This leads to the introduction of a new carbon-carbon bond and an amino group to the polyketide chain. The mechanism is fundamentally different from the thioesterase/cyclase-catalyzed polyketide chain releasing found in bacterial and other fungal polyketide biosynthesis. Genetic data suggest that the ketosynthase domain of the polyketide synthase and the chain-releasing enzyme are important for controlling the final product structure. In addition, several post-polyketide modifications have to take place before SAMT become mature toxins.
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Affiliation(s)
- L Du
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA.
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