1
|
Ray KA, Lutgens JD, Bista R, Zhang J, Desai RR, Hirsch M, Miyazawa T, Cordova A, Keatinge-Clay AT. Assessing and harnessing updated polyketide synthase modules through combinatorial engineering. Nat Commun 2024; 15:6485. [PMID: 39090122 PMCID: PMC11294587 DOI: 10.1038/s41467-024-50844-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 07/23/2024] [Indexed: 08/04/2024] Open
Abstract
The modular nature of polyketide assembly lines and the significance of their products make them prime targets for combinatorial engineering. The recently updated module boundary has been successful for engineering short synthases, yet larger synthases constructed using the updated boundary have not been investigated. Here we describe our design and implementation of a BioBricks-like platform to rapidly construct 5 triketide, 25 tetraketide, and 125 pentaketide synthases to test every module combination of the pikromycin synthase. Anticipated products are detected from 60% of the triketide synthases, 32% of the tetraketide synthases, and 6.4% of the pentaketide synthases. We determine ketosynthase gatekeeping and module-skipping are the principal impediments to obtaining functional synthases. The platform is also employed to construct active hybrid synthases by incorporating modules from the erythromycin, spinosyn, and rapamycin assembly lines. The relaxed gatekeeping of a ketosynthase in the rapamycin synthase is especially encouraging in the quest to produce designer polyketides.
Collapse
Affiliation(s)
- Katherine A Ray
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Joshua D Lutgens
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ramesh Bista
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Jie Zhang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ronak R Desai
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Melissa Hirsch
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Takeshi Miyazawa
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Antonio Cordova
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Adrian T Keatinge-Clay
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
| |
Collapse
|
2
|
Scat S, Weissman KJ, Chagot B. Insights into docking in megasynthases from the investigation of the toblerol trans-AT polyketide synthase: many α-helical means to an end. RSC Chem Biol 2024; 5:669-683. [PMID: 38966669 PMCID: PMC11221535 DOI: 10.1039/d4cb00075g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/16/2024] [Indexed: 07/06/2024] Open
Abstract
The fidelity of biosynthesis by modular polyketide synthases (PKSs) depends on specific moderate affinity interactions between successive polypeptide subunits mediated by docking domains (DDs). These sequence elements are notably portable, allowing their transplantation into alternative biosynthetic and metabolic contexts. Herein, we use integrative structural biology to characterize a pair of DDs from the toblerol trans-AT PKS. Both are intrinsically disordered regions (IDRs) that fold into a 3 α-helix docking complex of unprecedented topology. The C-terminal docking domain (CDD) resembles the 4 α-helix type (4HB) CDDs, which shows that the same type of DD can be redeployed to form complexes of distinct geometry. By carefully re-examining known DD structures, we further extend this observation to type 2 docking domains, establishing previously unsuspected structural relations between DD types. Taken together, these data illustrate the plasticity of α-helical DDs, which allow the formation of a diverse topological spectrum of docked complexes. The newly identified DDs should also find utility in modular PKS genetic engineering.
Collapse
Affiliation(s)
- Serge Scat
- Université de Lorraine, CNRS, IMoPA F-54000 Nancy France
| | | | | |
Collapse
|
3
|
Enzymology of assembly line synthesis by modular polyketide synthases. Nat Chem Biol 2023; 19:401-415. [PMID: 36914860 DOI: 10.1038/s41589-023-01277-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 01/31/2023] [Indexed: 03/16/2023]
Abstract
Modular polyketide synthases (PKSs) run catalytic reactions over dozens of steps in a highly orchestrated manner. To accomplish this synthetic feat, they form megadalton multienzyme complexes that are among the most intricate proteins on earth. Polyketide products are of elaborate chemistry with molecular weights of usually several hundred daltons and include clinically important drugs such as erythromycin (antibiotic), rapamycin (immunosuppressant) and epothilone (anticancer drug). The term 'modular' refers to a hierarchical structuring of modules and domains within an overall assembly line arrangement, in which PKS organization is colinearly translated into the polyketide structure. New structural information obtained during the past few years provides substantial direct insight into the orchestration of catalytic events within a PKS module and leads to plausible models for synthetic progress along assembly lines. In light of these structural insights, the PKS engineering field is poised to enter a new era of engineering.
Collapse
|
4
|
Keatinge-Clay AT, Miyazawa T, Zhang J, Ray KA, Lutgens JD, Bista R, Lin SN. Crystal structures reveal the framework of cis -acyltransferase modular polyketide synthases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.11.528132. [PMID: 36798387 PMCID: PMC9934609 DOI: 10.1101/2023.02.11.528132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
Although the domains of cis -acyltransferase ( cis -AT) modular polyketide synthases (PKS's) have been understood at atomic resolution for over a decade, the domain-domain interactions responsible for the architectures and activities of these giant molecular assembly lines remain largely uncharacterized. The multimeric structure of the α 6 β 6 fungal fatty acid synthase (FAS) provides 6 equivalent reaction chambers for its acyl carrier protein (ACP) domains to shuttle carbon building blocks and the growing acyl chain between surrounding, oriented enzymatic domains. The presumed homodimeric oligomerization of cis -AT assembly lines is insufficient to provide similar reaction chambers; however, the crystal structure of a ketosynthase (KS)+AT didomain presented here and three already reported show an interaction between the AT domains appropriate for lateral multimerization. This interaction was used to construct a framework for the pikromycin PKS from its KS, AT, and docking domains that contains highly-ordered reaction chambers. Its AT domains also mediate vertical interactions, both with upstream KS domains and downstream docking domains.
Collapse
|
5
|
Engineering the stambomycin modular polyketide synthase yields 37-membered mini-stambomycins. Nat Commun 2022; 13:515. [PMID: 35082289 PMCID: PMC8792006 DOI: 10.1038/s41467-022-27955-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 12/21/2021] [Indexed: 12/14/2022] Open
Abstract
The modular organization of the type I polyketide synthases (PKSs) would seem propitious for rational engineering of desirable analogous. However, despite decades of efforts, such experiments remain largely inefficient. Here, we combine multiple, state-of-the-art approaches to reprogram the stambomycin PKS by deleting seven internal modules. One system produces the target 37-membered mini-stambomycin metabolites − a reduction in chain length of 14 carbons relative to the 51-membered parental compounds − but also substantial quantities of shunt metabolites. Our data also support an unprecedented off-loading mechanism of such stalled intermediates involving the C-terminal thioesterase domain of the PKS. The mini-stambomycin yields are reduced relative to wild type, likely reflecting the poor tolerance of the modules downstream of the modified interfaces to the non-native substrates. Overall, we identify factors contributing to the productivity of engineered whole assembly lines, but our findings also highlight the need for further research to increase production titers. Genetic engineering of the type I polyketide synthases (PKSs) to produce desirable analogous remains largely inefficient. Here, the authors leverage multiple approaches to delete seven internal modules from the stambomycin PKS and generate 37-membered mini-stambomycin macrolactones.
Collapse
|
6
|
Klaus M, Rossini E, Linden A, Paithankar KS, Zeug M, Ignatova Z, Urlaub H, Khosla C, Köfinger J, Hummer G, Grininger M. Solution Structure and Conformational Flexibility of a Polyketide Synthase Module. JACS AU 2021; 1:2162-2171. [PMID: 34977887 PMCID: PMC8717363 DOI: 10.1021/jacsau.1c00043] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Indexed: 05/28/2023]
Abstract
Polyketide synthases (PKSs) are versatile C-C bond-forming enzymes that are broadly distributed in bacteria and fungi. The polyketide compound family includes many clinically useful drugs such as the antibiotic erythromycin, the antineoplastic epothilone, and the cholesterol-lowering lovastatin. Harnessing PKSs for custom compound synthesis remains an open challenge, largely because of the lack of knowledge about key structural properties. Particularly, the domains-well characterized on their own-are poorly understood in their arrangement, conformational dynamics, and interplay in the intricate quaternary structure of modular PKSs. Here, we characterize module 2 from the 6-deoxyerythronolide B synthase by small-angle X-ray scattering and cross-linking mass spectrometry with coarse-grained structural modeling. The results of this hybrid approach shed light on the solution structure of a cis-AT type PKS module as well as its inherent conformational dynamics. Supported by a directed evolution approach, we also find that acyl carrier protein (ACP)-mediated substrate shuttling appears to be steered by a nonspecific electrostatic interaction network.
Collapse
Affiliation(s)
- Maja Klaus
- Institute
of Organic Chemistry and Chemical Biology, Buchmann Institute for
Molecular Life Sciences, Goethe University
Frankfurt, Max-von-Laue Strasse 15, Frankfurt am Main 60438, Germany
| | - Emanuele Rossini
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue
Strasse 3, Frankfurt am Main 60438, Germany
| | - Andreas Linden
- Max
Planck Institute for Biophysical Chemistry, Am Fassberg 11, Goettingen 37077, Germany
- Institute
for Clinical Chemistry, University Medical
Center Göttingen, Robert Koch Strasse 40, Goettingen 37075, Germany
| | - Karthik S. Paithankar
- Institute
of Organic Chemistry and Chemical Biology, Buchmann Institute for
Molecular Life Sciences, Goethe University
Frankfurt, Max-von-Laue Strasse 15, Frankfurt am Main 60438, Germany
| | - Matthias Zeug
- Institute
of Organic Chemistry and Chemical Biology, Buchmann Institute for
Molecular Life Sciences, Goethe University
Frankfurt, Max-von-Laue Strasse 15, Frankfurt am Main 60438, Germany
| | - Zoya Ignatova
- Institute
for Biochemistry and Molecular Biology, University of Hamburg, Notkestrasse 85, Hamburg 22607, Germany
| | - Henning Urlaub
- Max
Planck Institute for Biophysical Chemistry, Am Fassberg 11, Goettingen 37077, Germany
- Institute
for Clinical Chemistry, University Medical
Center Göttingen, Robert Koch Strasse 40, Goettingen 37075, Germany
| | - Chaitan Khosla
- Department
of Chemistry, Stanford ChEM-H, Department of Chemical Engineering Stanford University, Stanford, California 94305, United States
| | - Jürgen Köfinger
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue
Strasse 3, Frankfurt am Main 60438, Germany
| | - Gerhard Hummer
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue
Strasse 3, Frankfurt am Main 60438, Germany
- Institute
of Biophysics, Goethe University Frankfurt, Max-von-Laue Strasse 1, Frankfurt am Main 60438, Germany
| | - Martin Grininger
- Institute
of Organic Chemistry and Chemical Biology, Buchmann Institute for
Molecular Life Sciences, Goethe University
Frankfurt, Max-von-Laue Strasse 15, Frankfurt am Main 60438, Germany
| |
Collapse
|
7
|
Fage CD, Kosol S, Jenner M, Öster C, Gallo A, Kaniusaite M, Steinbach R, Staniforth M, Stavros VG, Marahiel MA, Cryle MJ, Lewandowski JR. Communication Breakdown: Dissecting the COM Interfaces between the Subunits of Nonribosomal Peptide Synthetases. ACS Catal 2021. [DOI: 10.1021/acscatal.1c02113] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Christopher D. Fage
- Department of Chemistry/Biochemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry CV4 7AL, U.K
| | - Simone Kosol
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry CV4 7AL, U.K
| | - Matthew Jenner
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry CV4 7AL, U.K
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, U.K
| | - Carl Öster
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry CV4 7AL, U.K
| | - Angelo Gallo
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry CV4 7AL, U.K
| | - Milda Kaniusaite
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
| | - Roman Steinbach
- Department of Chemistry/Biochemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
| | - Michael Staniforth
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry CV4 7AL, U.K
| | - Vasilios G. Stavros
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry CV4 7AL, U.K
| | - Mohamed A. Marahiel
- Department of Chemistry/Biochemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
| | - Max J. Cryle
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
| | - Józef R. Lewandowski
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry CV4 7AL, U.K
| |
Collapse
|
8
|
Watzel J, Duchardt-Ferner E, Sarawi S, Bode HB, Wöhnert J. Cooperation between a T Domain and a Minimal C-Terminal Docking Domain to Enable Specific Assembly in a Multiprotein NRPS. Angew Chem Int Ed Engl 2021; 60:14171-14178. [PMID: 33876501 PMCID: PMC8251938 DOI: 10.1002/anie.202103498] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Indexed: 01/27/2023]
Abstract
Non-ribosomal peptide synthetases (NRPS) produce natural products from amino acid building blocks. They often consist of multiple polypeptide chains which assemble in a specific linear order via specialized N- and C-terminal docking domains (N/C DDs). Typically, docking domains function independently from other domains in NRPS assembly. Thus, docking domain replacements enable the assembly of "designer" NRPS from proteins that normally do not interact. The multiprotein "peptide-antimicrobial-Xenorhabdus" (PAX) peptide-producing PaxS NRPS is assembled from the three proteins PaxA, PaxB and PaxC. Herein, we show that the small C DD of PaxA cooperates with its preceding thiolation (T1 ) domain to bind the N DD of PaxB with very high affinity, establishing a structural and thermodynamical basis for this unprecedented docking interaction, and we test its functional importance in vivo in a truncated PaxS assembly line. Similar docking interactions are apparently present in other NRPS systems.
Collapse
Affiliation(s)
- Jonas Watzel
- Molecular Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Elke Duchardt-Ferner
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Sepas Sarawi
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.,Molecular Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Helge B Bode
- Department of Natural Products in Organismic Interactions, Max-Planck-Institute for Terrestrial Microbiology, 35043, Marburg, Germany.,Senckenberg Gesellschaft für Naturforschung, 60325, Frankfurt am Main, Germany.,Molecular Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Jens Wöhnert
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| |
Collapse
|
9
|
Watzel J, Duchardt‐Ferner E, Sarawi S, Bode HB, Wöhnert J. Kooperation zwischen T‐Domäne und minimaler C‐terminaler Docking‐Domäne für funktionelle Proteininteraktionen in Multiprotein‐NRPS. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Jonas Watzel
- Molekulare Biotechnologie Institut für Molekulare Biowissenschaften Goethe-Universität Frankfurt 60438 Frankfurt am Main Deutschland
| | - Elke Duchardt‐Ferner
- Institut für Molekulare Biowissenschaften und Biomolekulares Magnetresonanz Zentrum (BMRZ) Goethe-Universität Frankfurt 60438 Frankfurt am Main Deutschland
| | - Sepas Sarawi
- Institut für Molekulare Biowissenschaften und Biomolekulares Magnetresonanz Zentrum (BMRZ) Goethe-Universität Frankfurt 60438 Frankfurt am Main Deutschland
- Molekulare Biotechnologie Institut für Molekulare Biowissenschaften Goethe-Universität Frankfurt 60438 Frankfurt am Main Deutschland
| | - Helge B. Bode
- Abteilung Naturstoffe in organismischen Interaktionen Max-Planck-Institut für terrestrische Mikrobiologie 35043 Marburg Deutschland
- Senckenberg Gesellschaft für Naturforschung 60325 Frankfurt am Main Deutschland
- Molekulare Biotechnologie Institut für Molekulare Biowissenschaften Goethe-Universität Frankfurt 60438 Frankfurt am Main Deutschland
| | - Jens Wöhnert
- Institut für Molekulare Biowissenschaften und Biomolekulares Magnetresonanz Zentrum (BMRZ) Goethe-Universität Frankfurt 60438 Frankfurt am Main Deutschland
| |
Collapse
|
10
|
Smith HG, Beech MJ, Lewandowski JR, Challis GL, Jenner M. Docking domain-mediated subunit interactions in natural product megasynth(et)ases. J Ind Microbiol Biotechnol 2021; 48:6152290. [PMID: 33640957 PMCID: PMC9113145 DOI: 10.1093/jimb/kuab018] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 02/24/2021] [Indexed: 12/19/2022]
Abstract
Polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) multienzymes produce numerous high value metabolites. The protein subunits which constitute these megasynth(et)ases must undergo ordered self-assembly to ensure correct organisation of catalytic domains for the biosynthesis of a given natural product. Short amino acid regions at the N- and C-termini of each subunit, termed docking domains (DDs), often occur in complementary pairs, which interact to facilitate substrate transfer and maintain pathway fidelity. This review details all structurally characterised examples of NRPS and PKS DDs to date and summarises efforts to utilise DDs for the engineering of biosynthetic pathways.
Collapse
Affiliation(s)
- Helen G Smith
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Matthew J Beech
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | | | - Gregory L Challis
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, VIC 3800, Australia
| | - Matthew Jenner
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
| |
Collapse
|
11
|
|