1
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Yang L, Zhou H, Chen G, Li H, Yang D, Pan L. Expression and Purification of Glycosyltransferase DnmS from Streptomyces peucetius ATCC 27952 and Study on Catalytic Characterization of Its Reverse Glycosyltransferase Reaction. Microorganisms 2023; 11:microorganisms11030762. [PMID: 36985335 PMCID: PMC10058486 DOI: 10.3390/microorganisms11030762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023] Open
Abstract
Anthracyclines are an important class of natural antitumor drugs. They have a conservative aromatic tetracycline backbone that is substituted with different deoxyglucoses. The deoxyglucoses are crucial for the biological activity of many bacterial natural products after the proper modification from glycosyltransferases (GTs). The difficulty in obtaining highly purified active GTs has prevented biochemical studies on natural product GTs. In this paper, a new Escherichia coli fusion plasmid pGro7′, which introduces the Streptomyces coelicolor chaperone genes groEL1, groES and groEL2, was constructed. The glycosyltransferase DnmS from Streptomyces peucetius ATCC 27952 was co-expressed with the plasmid pGro7′, and unprecedented high-efficiency and soluble expression of DnmS in the E. coli expression system was realized. Subsequently, the reverse glycosylation reaction characteristics of DnmS and DnmQ were verified. We found that DnmS and DnmQ had the highest enzyme activity when they participated in the reaction at the same time. These studies provide a strategy for the soluble expression of GTs in Streptomyces and confirm the reversibility of the catalytic reaction of GTs. This provides a powerful method for the production of active anthracyclines and to enhance the diversity of natural products.
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Affiliation(s)
- Liyan Yang
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning 530007, China
| | - Huimin Zhou
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning 530007, China
| | - Guiguang Chen
- College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Hongliang Li
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning 530007, China
| | - Dengfeng Yang
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning 530007, China
- Institute of Biology, Guangxi Academy of Sciences, Nanning 530007, China
- Correspondence: (D.Y.); (L.P.)
| | - Lixia Pan
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning 530007, China
- College of Food and Quality Engineering, Nanning University, Nanning 530200, China
- Correspondence: (D.Y.); (L.P.)
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2
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Zhang L, Toplak M, Saleem-Batcha R, Höing L, Jakob R, Jehmlich N, von Bergen M, Maier T, Teufel R. Bacterial Dehydrogenases Facilitate Oxidative Inactivation and Bioremediation of Chloramphenicol. Chembiochem 2023; 24:e202200632. [PMID: 36353978 DOI: 10.1002/cbic.202200632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/09/2022] [Indexed: 11/11/2022]
Abstract
Antimicrobial resistance represents a major threat to human health and knowledge of the underlying mechanisms is therefore vital. Here, we report the discovery and characterization of oxidoreductases that inactivate the broad-spectrum antibiotic chloramphenicol via dual oxidation of the C3-hydroxyl group. Accordingly, chloramphenicol oxidation either depends on standalone glucose-methanol-choline (GMC)-type flavoenzymes, or on additional aldehyde dehydrogenases that boost overall turnover. These enzymes also enable the inactivation of the chloramphenicol analogues thiamphenicol and azidamfenicol, but not of the C3-fluorinated florfenicol. Notably, distinct isofunctional enzymes can be found in Gram-positive (e. g., Streptomyces sp.) and Gram-negative (e. g., Sphingobium sp.) bacteria, which presumably evolved their selectivity for chloramphenicol independently based on phylogenetic analyses. Mechanistic and structural studies provide further insights into the catalytic mechanisms of these biotechnologically interesting enzymes, which, in sum, are both a curse and a blessing by contributing to the spread of antibiotic resistance as well as to the bioremediation of chloramphenicol.
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Affiliation(s)
- Lei Zhang
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
| | - Marina Toplak
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
| | - Raspudin Saleem-Batcha
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Lars Höing
- Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Roman Jakob
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research UFZ GmbH, Leipzig, Germany.,German Centre for Integrative Biodiversity Research, (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany.,University of Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Brüderstraße 34, 04103, Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research UFZ GmbH, Leipzig, Germany.,German Centre for Integrative Biodiversity Research, (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany.,University of Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Brüderstraße 34, 04103, Leipzig, Germany
| | - Timm Maier
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Robin Teufel
- Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
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3
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Stout CN, Renata H. Reinvigorating the Chiral Pool: Chemoenzymatic Approaches to Complex Peptides and Terpenoids. Acc Chem Res 2021; 54:1143-1156. [PMID: 33543931 DOI: 10.1021/acs.accounts.0c00823] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Biocatalytic transformations that leverage the selectivity and efficiency of enzymes represent powerful tools for the construction of complex natural products. Enabled by innovations in genome mining, bioinformatics, and enzyme engineering, synthetic chemists are now more than ever able to develop and employ enzymes to solve outstanding chemical problems, one of which is the reliable and facile generation of stereochemistry within natural product scaffolds. In recognition of this unmet need, our group has sought to advance novel chemoenzymatic strategies to both expand and reinvigorate the chiral pool. Broadly defined, the chiral pool comprises cheap, enantiopure feedstock chemicals that serve as popular foundations for asymmetric total synthesis. Among these building blocks, amino acids and enantiopure terpenes, whose core structures can be mapped onto several classes of structurally and pharmaceutically intriguing natural products, are of particular interest to the synthetic community.In this Account, we summarize recent efforts from our group in leveraging biocatalytic transformations to expand the chiral pool, as well as efforts toward the efficient application of these transformations in natural products total synthesis, the ultimate testing ground for any novel methodology. First, we describe several examples of enzymatic generation of noncanonical amino acids as means to simplify the synthesis of peptide natural products. By extracting amino acid hydroxylases from native biosynthetic pathways, we obtain efficient access to hydroxylated variants of proline, lysine, arginine, and their derivatives. The newly installed hydroxyl moiety then becomes a chemical handle that can facilitate additional complexity generation, thereby expanding the pool of amino acid-derived building blocks available for peptide synthesis. Next, we present our efforts in enzymatic C-H oxidations of diverse terpene scaffolds, in which traditional chemistry can be combined with strategic applications of biocatalysis to selectively and efficiently derivatize several commercial terpenoid skeletons. The synergistic logic of this approach enables a small handful of synthetic intermediates to provide access to a plethora of terpenoid natural product families. Taken together, these findings demonstrate the advantages of applying enzymes in total synthesis in conjunction with established methodologies, as well as toward the expansion of the chiral pool to enable facile incorporation of stereochemistry during synthetic campaigns.
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Affiliation(s)
- Carter N. Stout
- Department of Chemistry, Scripps Research, 110 Scripps Way, Jupiter, Florida 33458, United States
| | - Hans Renata
- Department of Chemistry, Scripps Research, 110 Scripps Way, Jupiter, Florida 33458, United States
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4
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Park D, Swayambhu G, Lyga T, Pfeifer BA. Complex natural product production methods and options. Synth Syst Biotechnol 2021; 6:1-11. [PMID: 33474503 PMCID: PMC7803631 DOI: 10.1016/j.synbio.2020.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/19/2020] [Accepted: 12/21/2020] [Indexed: 12/29/2022] Open
Abstract
Natural products have had a major impact upon quality of life, with antibiotics as a classic example of having a transformative impact upon human health. In this contribution, we will highlight both historic and emerging methods of natural product bio-manufacturing. Traditional methods of natural product production relied upon native cellular host systems. In this context, pragmatic and effective methodologies were established to enable widespread access to natural products. In reviewing such strategies, we will also highlight the development of heterologous natural product biosynthesis, which relies instead on a surrogate host system theoretically capable of advanced production potential. In comparing native and heterologous systems, we will comment on the base organisms used for natural product biosynthesis and how the properties of such cellular hosts dictate scaled engineering practices to facilitate compound distribution. In concluding the article, we will examine novel efforts in production practices that entirely eliminate the constraints of cellular production hosts. That is, cell free production efforts will be introduced and reviewed for the purpose of complex natural product biosynthesis. Included in this final analysis will be research efforts made on our part to test the cell free biosynthesis of the complex polyketide antibiotic natural product erythromycin.
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Affiliation(s)
- Dongwon Park
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - Girish Swayambhu
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - Thomas Lyga
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - Blaine A Pfeifer
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, NY, USA
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5
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Kallscheuer N, Kage H, Milke L, Nett M, Marienhagen J. Microbial synthesis of the type I polyketide 6-methylsalicylate with Corynebacterium glutamicum. Appl Microbiol Biotechnol 2019; 103:9619-9631. [DOI: 10.1007/s00253-019-10121-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/26/2019] [Accepted: 09/04/2019] [Indexed: 12/28/2022]
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6
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Grüninger MJ, Buchholz PCF, Mordhorst S, Strack P, Müller M, Hubrich F, Pleiss J, Andexer JN. Chorismatases – the family is growing. Org Biomol Chem 2019; 17:2092-2098. [DOI: 10.1039/c8ob03038c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A newly discovered subfamily of chorismatases catalyses the same reaction as chorismate lyases (cleavage of chorismate to 4-hydroxybenzoate), but does not suffer from product inhibition.
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Affiliation(s)
- Mads J. Grüninger
- Institute of Pharmaceutical Sciences
- University of Freiburg
- 79104 Freiburg
- Germany
| | - Patrick C. F. Buchholz
- Institute of Biochemistry and Technical Biochemistry
- University of Stuttgart
- 70569 Stuttgart
- Germany
| | - Silja Mordhorst
- Institute of Pharmaceutical Sciences
- University of Freiburg
- 79104 Freiburg
- Germany
| | - Patrick Strack
- Institute of Pharmaceutical Sciences
- University of Freiburg
- 79104 Freiburg
- Germany
| | - Michael Müller
- Institute of Pharmaceutical Sciences
- University of Freiburg
- 79104 Freiburg
- Germany
| | - Florian Hubrich
- Institute of Pharmaceutical Sciences
- University of Freiburg
- 79104 Freiburg
- Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry
- University of Stuttgart
- 70569 Stuttgart
- Germany
| | - Jennifer N. Andexer
- Institute of Pharmaceutical Sciences
- University of Freiburg
- 79104 Freiburg
- Germany
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7
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Roth S, Kilgore MB, Kutchan TM, Müller M. Exploiting the Catalytic Diversity of Short-Chain Dehydrogenases/Reductases: Versatile Enzymes from Plants with Extended Imine Substrate Scope. Chembiochem 2018; 19:1849-1852. [PMID: 29931726 DOI: 10.1002/cbic.201800291] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Indexed: 01/20/2023]
Abstract
Numerous short-chain dehydrogenases/reductases (SDRs) have found biocatalytic applications in C=O and C=C (enone) reduction. For NADPH-dependent C=N reduction, imine reductases (IREDs) have primarily been investigated for extension of the substrate range. Here, we show that SDRs are also suitable for a broad range of imine reductions. The SDR noroxomaritidine reductase (NR) is involved in Amaryllidaceae alkaloid biosynthesis, serving as an enone reductase. We have characterized NR by using a set of typical imine substrates and established that the enzyme is active with all four tested imine compounds (up to 99 % conversion, up to 92 % ee). Remarkably, NR reduced two keto compounds as well, thus highlighting this enzyme family's versatility. Using NR as a template, we have identified an as yet unexplored SDR from the Amaryllidacea Zephyranthes treatiae with imine-reducing activity (≤95 % ee). Our results encourage the future characterization of SDR family members as a means of discovering new imine-reducing enzymes.
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Affiliation(s)
- Sebastian Roth
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Matthew B Kilgore
- Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, MO, 63132, USA
| | - Toni M Kutchan
- Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, MO, 63132, USA
| | - Michael Müller
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
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8
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Herbst DA, Huitt-Roehl CR, Jakob RP, Kravetz JM, Storm PA, Alley JR, Townsend CA, Maier T. The structural organization of substrate loading in iterative polyketide synthases. Nat Chem Biol 2018; 14:474-479. [PMID: 29610486 DOI: 10.1038/s41589-018-0026-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 02/07/2018] [Indexed: 11/09/2022]
Abstract
Polyketide synthases (PKSs) are microbial multienzymes for the biosynthesis of biologically potent secondary metabolites. Polyketide production is initiated by the loading of a starter unit onto an integral acyl carrier protein (ACP) and its subsequent transfer to the ketosynthase (KS). Initial substrate loading is achieved either by multidomain loading modules or by the integration of designated loading domains, such as starter unit acyltransferases (SAT), whose structural integration into PKS remains unresolved. A crystal structure of the loading/condensing region of the nonreducing PKS CTB1 demonstrates the ordered insertion of a pseudodimeric SAT into the condensing region, which is aided by the SAT-KS linker. Cryo-electron microscopy of the post-loading state trapped by mechanism-based crosslinking of ACP to KS reveals asymmetry across the CTB1 loading/-condensing region, in accord with preferential 1:2 binding stoichiometry. These results are critical for re-engineering the loading step in polyketide biosynthesis and support functional relevance of asymmetric conformations of PKSs.
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Affiliation(s)
- Dominik A Herbst
- Department of Biozentrum, University of Basel, Basel, Switzerland
| | | | - Roman P Jakob
- Department of Biozentrum, University of Basel, Basel, Switzerland
| | - Jacob M Kravetz
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Philip A Storm
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Jamie R Alley
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Craig A Townsend
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Timm Maier
- Department of Biozentrum, University of Basel, Basel, Switzerland.
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9
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Skiba MA, Maloney FP, Dan Q, Fraley AE, Aldrich CC, Smith JL, Brown WC. PKS-NRPS Enzymology and Structural Biology: Considerations in Protein Production. Methods Enzymol 2018; 604:45-88. [PMID: 29779664 PMCID: PMC5992914 DOI: 10.1016/bs.mie.2018.01.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The structural diversity and complexity of marine natural products have made them a rich and productive source of new bioactive molecules for drug development. The identification of these new compounds has led to extensive study of the protein constituents of the biosynthetic pathways from the producing microbes. Essential processes in the dissection of biosynthesis have been the elucidation of catalytic functions and the determination of 3D structures for enzymes of the polyketide synthases and nonribosomal peptide synthetases that carry out individual reactions. The size and complexity of these proteins present numerous difficulties in the process of going from gene to structure. Here, we review the problems that may be encountered at the various steps of this process and discuss some of the solutions devised in our and other labs for the cloning, production, purification, and structure solution of complex proteins using Escherichia coli as a heterologous host.
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Affiliation(s)
| | | | - Qingyun Dan
- University of Michigan, Ann Arbor, MI, United States
| | - Amy E Fraley
- University of Michigan, Ann Arbor, MI, United States
| | | | - Janet L Smith
- University of Michigan, Ann Arbor, MI, United States.
| | - W Clay Brown
- University of Michigan, Ann Arbor, MI, United States.
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10
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Mattay J, Hüttel W. Pipecolic Acid Hydroxylases: A Monophyletic Clade amongcis-Selective Bacterial Proline Hydroxylases that Discriminatesl-Proline. Chembiochem 2017; 18:1523-1528. [DOI: 10.1002/cbic.201700187] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Johanna Mattay
- Institute of Pharmaceutical Sciences; University of Freiburg; Albertstrasse 25 79104 Freiburg Germany
| | - Wolfgang Hüttel
- Institute of Pharmaceutical Sciences; University of Freiburg; Albertstrasse 25 79104 Freiburg Germany
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11
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Zore OV, Pande P, Okifo O, Basu AK, Kasi RM, Kumar CV. Nanoarmoring: strategies for preparation of multi-catalytic enzyme polymer conjugates and enhancement of high temperature biocatalysis. RSC Adv 2017; 7:29563-29574. [PMID: 29403641 PMCID: PMC5796544 DOI: 10.1039/c7ra05666d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
We report a general and modular approach for the synthesis of multi enzyme-polymer conjugates (MECs) consisting of five different enzymes of diverse isoelectric points and distinct catalytic properties conjugated within a single universal polymer scaffold. The five model enzymes chosen include glucose oxidase (GOx), acid phosphatase (AP), lactate dehydrogenase (LDH), horseradish peroxidase (HRP) and lipase (Lip). Poly(acrylic acid) (PAA) is used as the model synthetic polymer scaffold that will covalently conjugate and stabilize multiple enzymes concurrently. Parallel and sequential synthetic protocols are used to synthesise MECs, 5-P and 5-S, respectively. Also, five different single enzyme-PAA conjugates (SECs) including GOx-PAA, AP-PAA, LDH-PAA, HRP-PAA and Lip-PAA are synthesized. The composition, structure and morphology of MECs and SECs are confirmed by agarose gel electrophoresis, dynamic light scattering, circular dichroism spectroscopy and transmission electron microscopy. The bioreactor comprising MEC functions as a single biocatalyst can carry out at least five different or orthogonal catalytic reactions by virtue of the five stabilized enzymes, which has never been achieved to-date. Using activity assays relevant for each of the enzymes, for example AP, the specific activity of AP at room temperature and 7.4 pH in PB is determined and set at 100%. Interestingly, MECs 5-P and 5-S show specific activities of 1800% and 600%, respectively, compared to 100% specific activity of AP at room temperature (RT). The catalytic efficiencies of 5-P and 5-S are 1.55 × 10-3 and 1.68 × 10-3, respectively, compared to 9.11 × 10-5 for AP under similar RT conditions. Similarly, AP relevant catalytic activities of 5-P and 5-S at 65 °C show 100 and 300%, respectively, relative to native AP activity at RT as the native AP is catalytically inactive at 65 °C The catalytic activity trends suggest: (1) MECs show enhanced catalytic activities compared to native enzymes under similar assay conditions and (2) 5-S is better suited for high temperature biocatalysis, while both 5-S and 5-P are suitable for room temperature biocatalysis. Initial cytotoxicity results show that these MECs are non-lethal to human cells including human embryonic kidney [HEK] cells when treated with doses of 0.01 mg mL-1 for 72 h. This cytotoxicity data is relevant for future biological applications.
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Affiliation(s)
- Omkar V. Zore
- Department of Chemistry, University of Connecticut Storrs, CT 06269-3060, USA
- Institute of Materials Science, U-3136, University of Connecticut Storrs, CT 06269-3069, USA
| | - Paritosh Pande
- Department of Chemistry, University of Connecticut Storrs, CT 06269-3060, USA
| | | | - Ashis K. Basu
- Department of Chemistry, University of Connecticut Storrs, CT 06269-3060, USA
| | - Rajeswari M. Kasi
- Department of Chemistry, University of Connecticut Storrs, CT 06269-3060, USA
- Institute of Materials Science, U-3136, University of Connecticut Storrs, CT 06269-3069, USA
| | - Challa V. Kumar
- Department of Chemistry, University of Connecticut Storrs, CT 06269-3060, USA
- Institute of Materials Science, U-3136, University of Connecticut Storrs, CT 06269-3069, USA
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT 06269-3125, USA
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12
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Herbst DA, Jakob RP, Zähringer F, Maier T. Mycocerosic acid synthase exemplifies the architecture of reducing polyketide synthases. Nature 2016; 531:533-7. [DOI: 10.1038/nature16993] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 01/12/2016] [Indexed: 11/09/2022]
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13
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14
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Poust S, Hagen A, Katz L, Keasling JD. Narrowing the gap between the promise and reality of polyketide synthases as a synthetic biology platform. Curr Opin Biotechnol 2014; 30:32-9. [DOI: 10.1016/j.copbio.2014.04.011] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 04/09/2014] [Accepted: 04/11/2014] [Indexed: 11/27/2022]
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15
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Bukhari HST, Jakob RP, Maier T. Evolutionary origins of the multienzyme architecture of giant fungal fatty acid synthase. Structure 2014; 22:1775-1785. [PMID: 25456814 DOI: 10.1016/j.str.2014.09.016] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 09/08/2014] [Accepted: 09/13/2014] [Indexed: 12/23/2022]
Abstract
Fungal fatty acid synthase (fFAS) is a key paradigm for the evolution of complex multienzymes. Its 48 functional domains are embedded in a matrix of scaffolding elements, which comprises almost 50% of the total sequence and determines the emergent multienzymes properties of fFAS. Catalytic domains of fFAS are derived from monofunctional bacterial enzymes, but the evolutionary origin of the scaffolding elements remains enigmatic. Here, we identify two bacterial protein families of noncanonical fatty acid biosynthesis starter enzymes and trans-acting polyketide enoyl reductases (ERs) as potential ancestors of scaffolding regions in fFAS. The architectures of both protein families are revealed by representative crystal structures of the starter enzyme FabY and DfnA-ER. In both families, a striking structural conservation of insertions to scaffolding elements in fFAS is observed, despite marginal sequence identity. The combined phylogenetic and structural data provide insights into the evolutionary origins of the complex multienzyme architecture of fFAS.
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Affiliation(s)
- Habib S T Bukhari
- Biozentrum, Universität Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Roman P Jakob
- Biozentrum, Universität Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Timm Maier
- Biozentrum, Universität Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland.
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16
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Asymmetric Stetter reactions catalyzed by thiamine diphosphate-dependent enzymes. Appl Microbiol Biotechnol 2014; 98:9681-90. [DOI: 10.1007/s00253-014-5850-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Revised: 05/21/2014] [Accepted: 05/22/2014] [Indexed: 10/25/2022]
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17
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The structural basis of autotransporter translocation by TamA. Nat Struct Mol Biol 2013; 20:1318-20. [DOI: 10.1038/nsmb.2689] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 09/11/2013] [Indexed: 01/08/2023]
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18
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Jiang M, Fang L, Pfeifer BA. Improved heterologous erythromycin A production through expression plasmid re-design. Biotechnol Prog 2013; 29:862-9. [PMID: 23804312 DOI: 10.1002/btpr.1759] [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: 04/12/2013] [Revised: 05/14/2013] [Indexed: 01/15/2023]
Abstract
The production of complex compounds from technically convenient microorganisms is an emerging route to the chemical diversity found in the surrounding environment. In this study, the antibiotic compound erythromycin A is produced from Escherichia coli as an alternative to native production through the soil bacterium Saccharopolyspora erythraea. By doing so, there is an opportunity to apply and refine engineering strategies for the manipulation of the erythromycin biosynthetic pathway and for the overproduction of this and other complex natural compounds. Previously, E. coli-derived production was enabled by the introduction of the entire erythromycin pathway (20 genes total) using separately selectable expression plasmids which demonstrated negative effects on final biosynthesis through metabolic burden and plasmid instability. In this study, improvements to final production were made by altering the design of the expression plasmids needed for biosynthetic pathway introduction. Specifically, the total number of genes and plasmids was pruned to reduce both metabolic burden and plasmid instability. Further, a comparison was conducted between species-specific (E. coli vs. S. coelicolor) protein chaperonins. Results indicate improvements in growth and plasmid retention metrics. The newly designed expression platform also increased erythromycin A production levels 5-fold. In conclusion, the steps outlined in this report were designed to upgrade the E. coli erythromycin A production system, led to improved final compound titers, and suggest additional forms of pathway engineering to further improve results from heterologous production attempts.
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Affiliation(s)
- Ming Jiang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
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19
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Tracking down biotransformation to the genetic level: identification of a highly flexible glycosyltransferase from Saccharothrix espanaensis. Appl Environ Microbiol 2013; 79:5224-32. [PMID: 23793643 DOI: 10.1128/aem.01652-13] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Saccharothrix espanaensis is a member of the order Actinomycetales. The genome of the strain has been sequenced recently, revealing 106 glycosyltransferase genes. In this paper, we report the detection of a glycosyltransferase from Saccharothrix espanaensis which is able to rhamnosylate different phenolic compounds targeting different positions of the molecules. The gene encoding the flexible glycosyltransferase is not located close to a natural product biosynthetic gene cluster. Therefore, the native function of this enzyme might be not the biosynthesis of a secondary metabolite but the glycosylation of internal and external natural products as part of a defense mechanism.
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20
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Hüttel W. Biocatalytic Production of Chemical Building Blocks in Technical Scale with α-Ketoglutarate-Dependent Dioxygenases. CHEM-ING-TECH 2013. [DOI: 10.1002/cite.201300008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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21
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Zotchev SB, Sekurova ON, Katz L. Genome-based bioprospecting of microbes for new therapeutics. Curr Opin Biotechnol 2012; 23:941-7. [DOI: 10.1016/j.copbio.2012.04.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 04/03/2012] [Accepted: 04/05/2012] [Indexed: 01/16/2023]
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22
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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]
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23
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Abstract
Advanced biofuels produced by microorganisms have similar properties to petroleum-based fuels, and can 'drop in' to the existing transportation infrastructure. However, producing these biofuels in yields high enough to be useful requires the engineering of the microorganism's metabolism. Such engineering is not based on just one specific feedstock or host organism. Data-driven and synthetic-biology approaches can be used to optimize both the host and pathways to maximize fuel production. Despite some success, challenges still need to be met to move advanced biofuels towards commercialization, and to compete with more conventional fuels.
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24
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Hoertz AJ, Hamburger JB, Gooden DM, Bednar MM, McCafferty DG. Studies on the biosynthesis of the lipodepsipeptide antibiotic Ramoplanin A2. Bioorg Med Chem 2012; 20:859-65. [DOI: 10.1016/j.bmc.2011.11.062] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Revised: 11/22/2011] [Accepted: 11/28/2011] [Indexed: 11/16/2022]
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25
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Moncrieffe MC, Fernandez MJ, Spiteller D, Matsumura H, Gay NJ, Luisi BF, Leadlay PF. Structure of the glycosyltransferase EryCIII in complex with its activating P450 homologue EryCII. J Mol Biol 2011; 415:92-101. [PMID: 22056329 PMCID: PMC3391682 DOI: 10.1016/j.jmb.2011.10.036] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 10/18/2011] [Accepted: 10/20/2011] [Indexed: 11/20/2022]
Abstract
In the biosynthesis of the clinically important antibiotic erythromycin D, the glycosyltransferase (GT) EryCIII, in concert with its partner EryCII, attaches a nucleotide-activated sugar to the macrolide scaffold with high specificity. To understand the role of EryCII, we have determined the crystal structure of the EryCIII·EryCII complex at 3.1 Å resolution. The structure reveals a heterotetramer with a distinctive, elongated quaternary organization. The EryCIII subunits form an extensive self-complementary dimer interface at the center of the complex, and the EryCII subunits lie on the periphery. EryCII binds in the vicinity of the putative macrolide binding site of EryCIII but does not make direct interactions with this site. Our biophysical and enzymatic data support a model in which EryCII stabilizes EryCIII and also functions as an allosteric activator of the GT.
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Klein C, Hüttel W. A Simple Procedure for Selective Hydroxylation of L-Proline and L-Pipecolic Acid with Recombinantly Expressed Proline Hydroxylases. Adv Synth Catal 2011. [DOI: 10.1002/adsc.201000863] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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27
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Abstract
The development of coimmobilized multi-enzymatic systems is increasingly driven by economic and environmental constraints that provide an impetus to develop alternatives to conventional multistep synthetic methods. As in nature, enzyme-based systems work cooperatively to direct the formation of desired products within the defined compartmentalization of a cell. In an attempt to mimic biology, coimmobilization is intended to immobilize a number of sequential or cooperating biocatalysts on the same support to impart stability and enhance reaction kinetics by optimizing catalytic turnover. There are three primary reasons for the utilization of coimmobilized enzymes: to enhance the efficiency of one of the enzymes by the in-situ generation of its substrate, to simplify a process that is conventionally carried out in several steps and/or to eliminate undesired by-products of an enzymatic reaction. As such, coimmobilization provides benefits that span numerous biotechnological applications, from biosensing of molecules to cofactor recycling and to combination of multiple biocatalysts for the synthesis of valuable products.
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Affiliation(s)
- Lorena Betancor
- Madrid Institute for Advanced Studies, Campus Universitario de Cantoblanco, Madrid, Spain.
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Zhang H, Wang Y, Wu J, Skalina K, Pfeifer BA. Complete Biosynthesis of Erythromycin A and Designed Analogs Using E. coli as a Heterologous Host. ACTA ACUST UNITED AC 2010; 17:1232-40. [DOI: 10.1016/j.chembiol.2010.09.013] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Revised: 09/05/2010] [Accepted: 09/14/2010] [Indexed: 10/18/2022]
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Tosin M, Betancor L, Stephens E, Ariel Li WM, Spencer JB, Leadlay PF. Synthetic Chain Terminators Off-Load Intermediates from a Type I Polyketide Synthase. Chembiochem 2010; 11:539-46. [DOI: 10.1002/cbic.200900772] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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30
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Porter JL, Tobias NJ, Hong H, Tuck KL, Jenkin GA, Stinear TP. Transfer, stable maintenance and expression of the mycolactone polyketide megasynthase mls genes in a recombination-impaired Mycobacterium marinum. Microbiology (Reading) 2009; 155:1923-1933. [DOI: 10.1099/mic.0.027029-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The human pathogenMycobacterium ulceransproduces a polyketide metabolite called mycolactone with potent immunomodulatory activity.M. ulceransstrain Agy99 has a 174 kb plasmid called pMUM001 with three large genes (mlsA1, 51 kb;mlsA2, 7.2 kb;mlsB, 43 kb) that encode type I polyketide synthases (PKS) required for the biosynthesis of mycolactone, as demonstrated by transposon mutagenesis. However, there have been no reports of transfer of themlslocus to another mycobacterium to demonstrate that these genes are sufficient for mycolactone production because in addition to their large size, themlsgenes contain a high level of internal sequence repetition, such that the entire 102 kb locus is composed of only 9.5 kb of unique DNA. The combination of their large size and lack of stability during laboratory passage makes them a challenging prospect for transfer to a more rapidly growing and genetically tractable host. Here we describe the construction of two bacterial artificial chromosomeEscherichia coli/Mycobacteriumshuttle vectors, one based on the pMUM001 origin of replication bearingmlsB, and the other based on the mycobacteriophage L5 integrase, bearingmlsA1andmlsA2. The combination of these two constructs permitted the two-step transfer of the entire 174 kb pMUM001 plasmid toMycobacterium marinum, a rapidly growing non-mycolactone-producing mycobacterium that is a close genetic relative ofM. ulcerans. To improve the stability of themlslocus inM. marinum,recAwas inactivated by insertion of a hygromycin-resistance gene using double-crossover allelic exchange. As expected, the ΔrecAmutant displayed increased susceptibility to UV killing and a decreased frequency of homologous recombination. Southern hybridization and RT-PCR confirmed the stable transfer and expression of themlsgenes in both wild-typeM. marinumand therecAmutant. However, neither mycolactone nor its predicted precursor metabolites were detected in either strain. These experiments show that it is possible to successfully manipulate and stably transfer the largemlsgenes, but that other bacterial host factors appear to be required to facilitate mycolactone production.
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Affiliation(s)
- Jessica L. Porter
- Department of Microbiology, Monash University, Clayton 3800, Victoria, Australia
| | - Nicholas J. Tobias
- Department of Microbiology, Monash University, Clayton 3800, Victoria, Australia
| | - Hui Hong
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, UK
| | - Kellie L. Tuck
- School of Chemistry, Monash University, Clayton 3800, Victoria, Australia
| | - Grant A. Jenkin
- Department of Microbiology, Monash University, Clayton 3800, Victoria, Australia
| | - Timothy P. Stinear
- Department of Microbiology, Monash University, Clayton 3800, Victoria, Australia
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