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Nava A, Roberts J, Haushalter RW, Wang Z, Keasling JD. Module-Based Polyketide Synthase Engineering for de Novo Polyketide Biosynthesis. ACS Synth Biol 2023; 12:3148-3155. [PMID: 37871264 PMCID: PMC10661043 DOI: 10.1021/acssynbio.3c00282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Indexed: 10/25/2023]
Abstract
Polyketide retrobiosynthesis, where the biosynthetic pathway of a given polyketide can be reversibly engineered due to the colinearity of the polyketide synthase (PKS) structure and function, has the potential to produce millions of organic molecules. Mixing and matching modules from natural PKSs is one of the routes to produce many of these molecules. Evolutionary analysis of PKSs suggests that traditionally used module boundaries may not lead to the most productive hybrid PKSs and that new boundaries around and within the ketosynthase domain may be more active when constructing hybrid PKSs. As this is still a nascent area of research, the generality of these design principles based on existing engineering efforts remains inconclusive. Recent advances in structural modeling and synthetic biology present an opportunity to accelerate PKS engineering by re-evaluating insights gained from previous engineering efforts with cutting edge tools.
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Affiliation(s)
- Alberto
A. Nava
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Jacob Roberts
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Bioengineering, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Robert W. Haushalter
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Zilong Wang
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jay D. Keasling
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
- Department
of Bioengineering, University of California,
Berkeley, Berkeley, California 94720, United States
- Center
for Synthetic Biochemistry, Shenzhen Institutes
for Advanced Technologies, Shenzhen 518055, P.R. China
- The
Novo
Nordisk Foundation Center for Biosustainability, Technical University Denmark, Kemitorvet, Building 220, Kongens Lyngby 2800, Denmark
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2
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Charov K, Burkart MD. In silico identification and in vitro evaluation of a protein-protein interaction inhibitor of Escherichia coli fatty acid biosynthesis. Chem Biol Drug Des 2021; 98:94-101. [PMID: 33905605 DOI: 10.1111/cbdd.13851] [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: 08/29/2020] [Revised: 01/27/2021] [Accepted: 02/14/2021] [Indexed: 11/29/2022]
Abstract
To combat the rise in antibiotic resistance, new targets must be identified and probes against them developed. Protein-protein interactions (PPI) of bacterial type II fatty acid biosynthesis (FAS-II) represent an untapped, yet rich area for new antibiotic discovery. Here, we present a computational and in vitro workflow for the discovery of new inhibitors of PPI in Escherichia coli FAS-II. As part of this study, we identified suramin, an existing treatment for African sleeping sickness, to effectively block the interaction of E. coli dehydratase FabA and the acyl carrier protein EcACP, with an IC50 = 85 μΜ. This finding validates a workflow that combines in silico screening with in vitro PPI assays to identify probes appropriate for further optimization.
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Affiliation(s)
- Katherine Charov
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
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3
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Chen N, Wang C. Chemical Labeling of Protein 4'-Phosphopantetheinylation. Chembiochem 2021; 22:1357-1367. [PMID: 33289264 DOI: 10.1002/cbic.202000747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/01/2020] [Indexed: 11/11/2022]
Abstract
Nature uses a diverse array of protein post-translational modifications (PTMs) to regulate protein structure, activity, localization, and function. Among them, protein 4'-phosphopantetheinylation derived from coenzyme A (CoA) is an essential PTM for the biosynthesis of fatty acids, polyketides, and nonribosomal peptides in prokaryotes and eukaryotes. To explore its functions, various chemical probes mimicking the natural structure of 4'-phosphopantetheinylation have been developed. In this minireview, we summarize these chemical probes and describe their applications in direct and metabolic labeling of proteins in bacterial and mammalian cells.
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Affiliation(s)
- Nan Chen
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering, Ministry of Education, Peking University, Beijing, 100871, P. R. China
| | - Chu Wang
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering, Ministry of Education, Peking University, Beijing, 100871, P. R. China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, P. R. China
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4
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Cho CA, Liang C, Perera J, Brimble MA, Swift S, Jin J. Guanidinylated Amphiphilic Polycarbonates with Enhanced Antimicrobial Activity by Extending the Length of the Spacer Arm and Micelle Self-Assembly. Macromol Biosci 2020; 20:e2000065. [PMID: 32459065 DOI: 10.1002/mabi.202000065] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/01/2020] [Indexed: 01/23/2023]
Abstract
Nine guanidinylated amphiphilic polycarbonates are rationally designed and synthesized. Each polymer has the same biodegradable backbone but different side groups. The influence of the hydrophobic/hydrophilic effect on antimicrobial activities and cytotoxicity is systematically investigated. The results verify that tuning the length of the spacer arm between the cationic guanidine group and the polycarbonate backbone is an efficient design strategy to alter the hydrophobic/hydrophilic balance without changing the cationic charge density. A spacer arm of six methylene units (CH2 )6 shows the best antimicrobial activity (minimum inhibitory concentration, MIC = 40 µg mL-1 against Escherichia coli, MIC = 20 µg mL-1 against Staphylococcus aureus, MIC = 40 µg mL-1 against Candida albicans) with low hemolytic activity (HC50 > 2560 µg mL-1 ). Furthermore, the guanidinylated polycarbonates exhibit the ability to self-assemble and present micelle-like nanostructure due to their intrinsic amphiphilic macromolecular structure. Transmission electron microscopy and dynamic light scattering measurements confirm polymer micelle formation in aqueous solution with sizes ranging from 82 to 288 nm.
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Affiliation(s)
- Chloe A Cho
- School of Chemical Sciences, University of Auckland, Auckland, 1142, New Zealand
| | - Chao Liang
- School of Chemical Sciences, University of Auckland, Auckland, 1142, New Zealand
| | - Janesha Perera
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, 1142, New Zealand
| | - Margaret A Brimble
- School of Chemical Sciences, University of Auckland, Auckland, 1142, New Zealand
| | - Simon Swift
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, 1142, New Zealand
| | - Jianyong Jin
- School of Chemical Sciences, University of Auckland, Auckland, 1142, New Zealand
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5
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Konno S, La Clair JJ, Burkart MD. Trapping the Complex Molecular Machinery of Polyketide and Fatty Acid Synthases with Tunable Silylcyanohydrin Crosslinkers. Angew Chem Int Ed Engl 2018; 57:17009-17013. [PMID: 30379389 PMCID: PMC6407627 DOI: 10.1002/anie.201806865] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/19/2018] [Indexed: 12/14/2022]
Abstract
Many families of natural products are synthesized by large multidomain biological machines commonly referred to as megasynthases. While the advance of mechanism-based tools has opened new windows into the structural features within the protein-protein interfaces guiding carrier protein dependent enzymes, there is an immediate need for tools that can be engaged to link co-translated domains in a site-selective manner. Now, the use of silylcyanohydrins is demonstrated in a two-step, two-site selective crosslinking for the trapping of carrier-protein interactions within megasynthases. This advance provides a new tool to trap intermediate states within multimodular systems, a key step toward understanding the specificities within fatty acid (FAS) and polyketide (PKS) synthases.
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Affiliation(s)
- Sho Konno
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - James J La Clair
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
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6
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Konno S, La Clair JJ, Burkart MD. Trapping the Complex Molecular Machinery of Polyketide and Fatty Acid Synthases with Tunable Silylcyanohydrin Crosslinkers. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806865] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Sho Konno
- Department of Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - James J. La Clair
- Department of Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
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7
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Ungati H, Govindaraj V, Mugesh G. The Remarkable Effect of Halogen Substitution on the Membrane Transport of Fluorescent Molecules in Living Cells. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/anie.201804128 erratum in: angew chem int ed engl.2019; 58] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Affiliation(s)
- Harinarayana Ungati
- Department of Inorganic and Physical Chemistry; Indian Institute of Science; Bangalore 560012 India
| | - Vijayakumar Govindaraj
- Department of Inorganic and Physical Chemistry; Indian Institute of Science; Bangalore 560012 India
| | - Govindasamy Mugesh
- Department of Inorganic and Physical Chemistry; Indian Institute of Science; Bangalore 560012 India
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8
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Ungati H, Govindaraj V, Mugesh G. The Remarkable Effect of Halogen Substitution on the Membrane Transport of Fluorescent Molecules in Living Cells. Angew Chem Int Ed Engl 2018; 57:8989-8993. [DOI: 10.1002/anie.201804128] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 05/10/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Harinarayana Ungati
- Department of Inorganic and Physical Chemistry; Indian Institute of Science; Bangalore 560012 India
| | - Vijayakumar Govindaraj
- Department of Inorganic and Physical Chemistry; Indian Institute of Science; Bangalore 560012 India
| | - Govindasamy Mugesh
- Department of Inorganic and Physical Chemistry; Indian Institute of Science; Bangalore 560012 India
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9
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Ungati H, Govindaraj V, Mugesh G. The Remarkable Effect of Halogen Substitution on the Membrane Transport of Fluorescent Molecules in Living Cells. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804128] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Harinarayana Ungati
- Department of Inorganic and Physical Chemistry; Indian Institute of Science; Bangalore 560012 India
| | - Vijayakumar Govindaraj
- Department of Inorganic and Physical Chemistry; Indian Institute of Science; Bangalore 560012 India
| | - Govindasamy Mugesh
- Department of Inorganic and Physical Chemistry; Indian Institute of Science; Bangalore 560012 India
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10
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Ungati H, Govindaraj V, Mugesh G. The Remarkable Effect of Halogen Substitution on the Membrane Transport of Fluorescent Molecules in Living Cells. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/anie.201804128 erratum in: angew chem int ed engl.2019; 58(8): 2177.pmid: 29846997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Harinarayana Ungati
- Department of Inorganic and Physical Chemistry; Indian Institute of Science; Bangalore 560012 India
| | - Vijayakumar Govindaraj
- Department of Inorganic and Physical Chemistry; Indian Institute of Science; Bangalore 560012 India
| | - Govindasamy Mugesh
- Department of Inorganic and Physical Chemistry; Indian Institute of Science; Bangalore 560012 India
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11
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Kittilä T, Mollo A, Charkoudian LK, Cryle MJ. New Structural Data Reveal the Motion of Carrier Proteins in Nonribosomal Peptide Synthesis. Angew Chem Int Ed Engl 2016; 55:9834-40. [PMID: 27435901 PMCID: PMC5113783 DOI: 10.1002/anie.201602614] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Indexed: 12/28/2022]
Abstract
The nonribosomal peptide synthetases (NRPSs) are one of the most promising resources for the production of new bioactive molecules. The mechanism of NRPS catalysis is based around sequential catalytic domains: these are organized into modules, where each module selects, modifies, and incorporates an amino acid into the growing peptide. The intermediates formed during NRPS catalysis are delivered between enzyme centers by peptidyl carrier protein (PCP) domains, which makes PCP interactions and movements crucial to NRPS mechanism. PCP movement has been linked to the domain alternation cycle of adenylation (A) domains, and recent complete NRPS module structures provide support for this hypothesis. However, it appears as though the A domain alternation alone is insufficient to account for the complete NRPS catalytic cycle and that the loaded state of the PCP must also play a role in choreographing catalysis in these complex and fascinating molecular machines.
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Affiliation(s)
- Tiia Kittilä
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Aurelio Mollo
- Department of Chemistry, Haverford College, Haverford, PA, 19041, USA
| | | | - Max J Cryle
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany. .,EMBL Australia, Monash University, Clayton, Victoria, 3800, Australia. .,The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology and ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, 3800, Australia.
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12
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Kittilä T, Mollo A, Charkoudian LK, Cryle MJ. Neue Strukturdaten geben Einblick in die Bewegungen von Transportproteinen in der nicht-ribosomalen Peptidsynthese. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602614] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Tiia Kittilä
- Abteilung Biomolekulare Mechanismen; Max-Planck-Institut für Medizinische Forschung; Jahnstraße 29 69120 Heidelberg Deutschland
| | - Aurelio Mollo
- Department of Chemistry; Haverford College; Haverford PA 19041 USA
| | | | - Max J. Cryle
- Abteilung Biomolekulare Mechanismen; Max-Planck-Institut für Medizinische Forschung; Jahnstraße 29 69120 Heidelberg Deutschland
- EMBL Australia; Monash University; Clayton Victoria 3800 Australien
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology and ARC Centre of Excellence in Advanced Molecular Imaging; Monash University; Clayton VIC 3800 Australien
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13
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Finzel K, Lee DJ, Burkart MD. Using modern tools to probe the structure-function relationship of fatty acid synthases. Chembiochem 2015; 16:528-547. [PMID: 25676190 PMCID: PMC4545599 DOI: 10.1002/cbic.201402578] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Indexed: 12/25/2022]
Abstract
Fatty acid biosynthesis is essential to life and represents one of the most conserved pathways in nature, preserving the same handful of chemical reactions across all species. Recent interest in the molecular details of the de novo fatty acid synthase (FAS) has been heightened by demand for renewable fuels and the emergence of multidrug-resistant bacterial strains. Central to FAS is the acyl carrier protein (ACP), a protein chaperone that shuttles the growing acyl chain between catalytic enzymes within the FAS. Human efforts to alter fatty acid biosynthesis for oil production, chemical feedstock, or antimicrobial purposes has been met with limited success, due in part to a lack of detailed molecular information behind the ACP-partner protein interactions inherent to the pathway. This review will focus on recently developed tools for the modification of ACP and analysis of protein-protein interactions, such as mechanism-based crosslinking, and the studies exploiting them. Discussion specific to each enzymatic domain will focus first on mechanism and known inhibitors, followed by available structures and known interactions with ACP. Although significant unknowns remain, new understandings of the intricacies of FAS point to future advances in manipulating this complex molecular factory.
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Affiliation(s)
- Kara Finzel
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0358 (USA)
| | - D. John Lee
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0358 (USA)
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0358 (USA)
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