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Title: ClusterCAD: a computational platform for type I modular polyketide synthase design

Abstract

Here, we present ClusterCAD, a web-based toolkit designed to leverage the collinear structure and deterministic logic of type I modular polyketide synthases (PKSs) for synthetic biology applications. The unique organization of these megasynthases, combined with the diversity of their catalytic domain building blocks, has fueled an interest in harnessing the biosynthetic potential of PKSs for the microbial production of both novel natural product analogs and industrially relevant small molecules. However, a limited theoretical understanding of the determinants of PKS fold and function poses a substantial barrier to the design of active variants, and identifying strategies to reliably construct functional PKS chimeras remains an active area of research. In this work, we formalize a paradigm for the design of PKS chimeras and introduce ClusterCAD as a computational platform to streamline and simplify the process of designing experiments to test strategies for engineering PKS variants. ClusterCAD provides chemical structures with stereochemistry for the intermediates generated by each PKS module, as well as sequence- and structure-based search tools that allow users to identify modules based either on amino acid sequence or on the chemical structure of the cognate polyketide intermediate. ClusterCAD can be accessed at https://clustercad.jbei.org and at http://clustercad.igb.uci.edu.

Authors:
 [1];  [2];  [3];  [4];  [2];  [5];  [4];  [6]
  1. Univ. of California, Berkeley, CA (United States). Dept. of Chemical and Biomolecular Engineering
  2. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Agile BioFoundry, Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Systems and Engineering Division
  3. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Systems and Engineering Division
  4. Univ. of California, Irvine, CA (United States). Dept. of Computer Science and Inst. for Genomics and Bioinformatics
  5. Univ. of California, Berkeley, CA (United States). QB3 Inst.
  6. Univ. of California, Berkeley, CA (United States). Dept. of Chemical and Biomolecular Engineering and QB3 Inst. and Dept. of Bioengineering; Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Agile BioFoundry, Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Systems and Engineering Division; Technical Univ. of Denmark, Horsholm (Denmark). Novo Nordisk Foundation Center for Biosustainability
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Energy Efficiency and Renewable Energy (EERE), Bioenergy Technologies Office (EE-3B); OpenEye Scientific Software, Santa Fe, NM (United States); ChemAxon, Budapest (Hungary); Defense Advanced Research Projects Agency (DARPA); National Science Foundation (NSF)
OSTI Identifier:
1433111
Grant/Contract Number:  
AC02-05CH11231; BM0101020-05450-1004171; 28712; AC02-05C11231; HR0011-15-2-0045; CBET-1437775; EEC-0540879; MCB-1341894; IIS-1321053; DGE 1106400
Resource Type:
Accepted Manuscript
Journal Name:
Nucleic Acids Research
Additional Journal Information:
Journal Volume: 46; Journal Issue: D1; Related Information: © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.; Journal ID: ISSN 0305-1048
Publisher:
Oxford University Press
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICS AND COMPUTING; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Eng, Clara H., Backman, Tyler W H, Bailey, Constance B., Magnan, Christophe, Garcia Martin, Hector, Katz, Leonard, Baldi, Pierre, and Keasling, Jay D. ClusterCAD: a computational platform for type I modular polyketide synthase design. United States: N. p., 2017. Web. doi:10.1093/nar/gkx893.
Eng, Clara H., Backman, Tyler W H, Bailey, Constance B., Magnan, Christophe, Garcia Martin, Hector, Katz, Leonard, Baldi, Pierre, & Keasling, Jay D. ClusterCAD: a computational platform for type I modular polyketide synthase design. United States. doi:10.1093/nar/gkx893.
Eng, Clara H., Backman, Tyler W H, Bailey, Constance B., Magnan, Christophe, Garcia Martin, Hector, Katz, Leonard, Baldi, Pierre, and Keasling, Jay D. Wed . "ClusterCAD: a computational platform for type I modular polyketide synthase design". United States. doi:10.1093/nar/gkx893. https://www.osti.gov/servlets/purl/1433111.
@article{osti_1433111,
title = {ClusterCAD: a computational platform for type I modular polyketide synthase design},
author = {Eng, Clara H. and Backman, Tyler W H and Bailey, Constance B. and Magnan, Christophe and Garcia Martin, Hector and Katz, Leonard and Baldi, Pierre and Keasling, Jay D.},
abstractNote = {Here, we present ClusterCAD, a web-based toolkit designed to leverage the collinear structure and deterministic logic of type I modular polyketide synthases (PKSs) for synthetic biology applications. The unique organization of these megasynthases, combined with the diversity of their catalytic domain building blocks, has fueled an interest in harnessing the biosynthetic potential of PKSs for the microbial production of both novel natural product analogs and industrially relevant small molecules. However, a limited theoretical understanding of the determinants of PKS fold and function poses a substantial barrier to the design of active variants, and identifying strategies to reliably construct functional PKS chimeras remains an active area of research. In this work, we formalize a paradigm for the design of PKS chimeras and introduce ClusterCAD as a computational platform to streamline and simplify the process of designing experiments to test strategies for engineering PKS variants. ClusterCAD provides chemical structures with stereochemistry for the intermediates generated by each PKS module, as well as sequence- and structure-based search tools that allow users to identify modules based either on amino acid sequence or on the chemical structure of the cognate polyketide intermediate. ClusterCAD can be accessed at https://clustercad.jbei.org and at http://clustercad.igb.uci.edu.},
doi = {10.1093/nar/gkx893},
journal = {Nucleic Acids Research},
number = D1,
volume = 46,
place = {United States},
year = {2017},
month = {10}
}

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Works referenced in this record:

Macrolide biosynthesis. 3. Stereochemistry of the chain-elongation steps of erythromycin biosynthesis
journal, August 1986

  • Cane, David E.; Liang, Tzyy Chyau.; Taylor, Paul B.
  • Journal of the American Chemical Society, Vol. 108, Issue 16
  • DOI: 10.1021/ja00276a042

Minimum Information about a Biosynthetic Gene cluster
journal, August 2015

  • Medema, Marnix H.; Kottmann, Renzo; Yilmaz, Pelin
  • Nature Chemical Biology, Vol. 11, Issue 9
  • DOI: 10.1038/nchembio.1890

A Polylinker Approach to Reductive Loop Swaps in Modular Polyketide Synthases
journal, November 2008

  • Kellenberger, Laurenz; Galloway, Ian S.; Sauter, Guido
  • ChemBioChem, Vol. 9, Issue 16
  • DOI: 10.1002/cbic.200800332

Structural rearrangements of a polyketide synthase module during its catalytic cycle
journal, June 2014

  • Whicher, Jonathan R.; Dutta, Somnath; Hansen, Douglas A.
  • Nature, Vol. 510, Issue 7506
  • DOI: 10.1038/nature13409

Divergence of multimodular polyketide synthases revealed by a didomain structure
journal, May 2012

  • Zheng, Jianting; Gay, Darren C.; Demeler, Borries
  • Nature Chemical Biology, Vol. 8, Issue 7
  • DOI: 10.1038/nchembio.964

Direct production of ivermectin-like drugs after domain exchange in the avermectin polyketide synthase of Streptomyces avermitilis ATCC31272
journal, January 2003

  • Gaisser, Sabine; Kellenberger, Laurenz; Kaja, Andrew L.
  • Organic & Biomolecular Chemistry, Vol. 1, Issue 16
  • DOI: 10.1039/b304022d

SeMPI: a genome-based secondary metabolite prediction and identification web server
journal, April 2017

  • Zierep, Paul F.; Padilla, Natàlia; Yonchev, Dimitar G.
  • Nucleic Acids Research, Vol. 45, Issue W1
  • DOI: 10.1093/nar/gkx289

Exploiting the mosaic structure of trans-acyltransferase polyketide synthases for natural product discovery and pathway dissection
journal, January 2008

  • Nguyen, TuAnh; Ishida, Keishi; Jenke-Kodama, Holger
  • Nature Biotechnology, Vol. 26, Issue 2
  • DOI: 10.1038/nbt1379

SBSPKSv2: structure-based sequence analysis of polyketide synthases and non-ribosomal peptide synthetases
journal, April 2017

  • Khater, Shradha; Gupta, Money; Agrawal, Priyesh
  • Nucleic Acids Research, Vol. 45, Issue W1
  • DOI: 10.1093/nar/gkx344

Multiple genetic modifications of the erythromycin polyketide synthase to produce a library of novel "unnatural" natural products
journal, March 1999

  • McDaniel, R.; Thamchaipenet, A.; Gustafsson, C.
  • Proceedings of the National Academy of Sciences, Vol. 96, Issue 5
  • DOI: 10.1073/pnas.96.5.1846

The status of type I polyketide synthase ketoreductases
journal, January 2013

  • Zheng, Jianting; Keatinge-Clay, Adrian T.
  • Med. Chem. Commun., Vol. 4, Issue 1
  • DOI: 10.1039/C2MD20191G

Combinatorial biosynthesis of reduced polyketides
journal, December 2005

  • Weissman, Kira J.; Leadlay, Peter F.
  • Nature Reviews Microbiology, Vol. 3, Issue 12
  • DOI: 10.1038/nrmicro1287

Heuristics for Similarity Searching of Chemical Graphs Using a Maximum Common Edge Subgraph Algorithm
journal, March 2002

  • Raymond, John W.; Gardiner, Eleanor J.; Willett, Peter
  • Journal of Chemical Information and Computer Sciences, Vol. 42, Issue 2
  • DOI: 10.1021/ci010381f

Structure of a modular polyketide synthase
journal, June 2014

  • Dutta, Somnath; Whicher, Jonathan R.; Hansen, Douglas A.
  • Nature, Vol. 510, Issue 7506
  • DOI: 10.1038/nature13423

In Vitro Analysis of Carboxyacyl Substrate Tolerance in the Loading and First Extension Modules of Borrelidin Polyketide Synthase
journal, September 2014

  • Hagen, Andrew; Poust, Sean; de Rond, Tristan
  • Biochemistry, Vol. 53, Issue 38
  • DOI: 10.1021/bi500951c

Stereospecific acyl transfers on the erythromycin-producing polyketide synthase
journal, January 1994


Bio-based production of fuels and industrial chemicals by repurposing antibiotic-producing type I modular polyketide synthases: opportunities and challenges
journal, November 2016

  • Yuzawa, Satoshi; Keasling, Jay D.; Katz, Leonard
  • The Journal of Antibiotics, Vol. 70, Issue 4
  • DOI: 10.1038/ja.2016.136

Gain of Function Mutagenesis of the Erythromycin Polyketide Synthase. 2. Engineered Biosynthesis of an Eight-Membered Ring Tetraketide Lactone
journal, November 1997

  • Kao, Camilla M.; McPherson, Michael; McDaniel, Robert N.
  • Journal of the American Chemical Society, Vol. 119, Issue 46
  • DOI: 10.1021/ja972609e

Atom pairs as molecular features in structure-activity studies: definition and applications
journal, May 1985

  • Carhart, Raymond E.; Smith, Dennis H.; Venkataraghavan, R.
  • Journal of Chemical Information and Modeling, Vol. 25, Issue 2
  • DOI: 10.1021/ci00046a002

BLAST+: architecture and applications
journal, January 2009

  • Camacho, Christiam; Coulouris, George; Avagyan, Vahram
  • BMC Bioinformatics, Vol. 10, Issue 1
  • DOI: 10.1186/1471-2105-10-421

A Model of Structure and Catalysis for Ketoreductase Domains in Modular Polyketide Synthases
journal, January 2003

  • Reid, Ralph; Piagentini, Misty; Rodriguez, Eduardo
  • Biochemistry, Vol. 42, Issue 1
  • DOI: 10.1021/bi0268706

Engineering the acyltransferase substrate specificity of assembly line polyketide synthases
journal, August 2013

  • Dunn, Briana J.; Khosla, Chaitan
  • Journal of The Royal Society Interface, Vol. 10, Issue 85
  • DOI: 10.1098/rsif.2013.0297

Mechanistic Analysis of Acyl Transferase Domain Exchange in Polyketide Synthase Modules
journal, May 2003

  • Hans, Marcus; Hornung, Andreas; Dziarnowski, Agnieszka
  • Journal of the American Chemical Society, Vol. 125, Issue 18
  • DOI: 10.1021/ja029539i

Insights into Substrate Modification by Dehydratases from Type I Polyketide Synthases
journal, May 2017

  • Faille, Alexandre; Gavalda, Sabine; Slama, Nawel
  • Journal of Molecular Biology, Vol. 429, Issue 10
  • DOI: 10.1016/j.jmb.2017.03.026

Structure and Mechanism of the 6-Deoxyerythronolide B Synthase
journal, June 2007


Beyond ethylmalonyl-CoA: The functional role of crotonyl-CoAcarboxylase/reductase homologs in expanding polyketide diversity
journal, January 2012

  • Wilson, Micheal C.; Moore, Bradley S.
  • Nat. Prod. Rep., Vol. 29, Issue 1
  • DOI: 10.1039/C1NP00082A

Alcohol Stereochemistry in Polyketide Backbones Is Controlled by the β-Ketoreductase Domains of Modular Polyketide Synthases
journal, March 1998

  • Kao, Camilla M.; McPherson, Michael; McDaniel, Robert N.
  • Journal of the American Chemical Society, Vol. 120, Issue 10
  • DOI: 10.1021/ja973913a

Engineered intermodular and intramodular polyketide synthase fusions
journal, September 1997


The structures of type I polyketide synthases
journal, January 2012

  • Keatinge-Clay, Adrian T.
  • Natural Product Reports, Vol. 29, Issue 10
  • DOI: 10.1039/c2np20019h

Stereocontrol within polyketide assembly lines
journal, January 2016

  • Keatinge-Clay, Adrian T.
  • Natural Product Reports, Vol. 33, Issue 2
  • DOI: 10.1039/C5NP00092K

SCRATCH: a protein structure and structural feature prediction server
journal, July 2005

  • Cheng, J.; Randall, A. Z.; Sweredoski, M. J.
  • Nucleic Acids Research, Vol. 33, Issue Web Server
  • DOI: 10.1093/nar/gki396

antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters
journal, May 2015

  • Weber, Tilmann; Blin, Kai; Duddela, Srikanth
  • Nucleic Acids Research, Vol. 43, Issue W1
  • DOI: 10.1093/nar/gkv437

On-line enzymatic tailoring of polyketides and peptides in thiotemplate systems
journal, April 2016


Broadening substrate specificity of a chain-extending ketosynthase through a single active-site mutation
journal, January 2016

  • Murphy, Annabel C.; Hong, Hui; Vance, Steve
  • Chemical Communications, Vol. 52, Issue 54
  • DOI: 10.1039/C6CC03501A

Coupled Methyl Group Epimerization and Reduction by Polyketide Synthase Ketoreductase Domains. Ketoreductase-Catalyzed Equilibrium Isotope Exchange
journal, October 2013

  • Garg, Ashish; Khosla, Chaitan; Cane, David E.
  • Journal of the American Chemical Society, Vol. 135, Issue 44
  • DOI: 10.1021/ja408944s

Elucidation of the Cryptic Epimerase Activity of Redox-Inactive Ketoreductase Domains from Modular Polyketide Synthases by Tandem Equilibrium Isotope Exchange
journal, July 2014

  • Garg, Ashish; Xie, Xinqiang; Keatinge-Clay, Adrian
  • Journal of the American Chemical Society, Vol. 136, Issue 29
  • DOI: 10.1021/ja5056998

A Tylosin Ketoreductase Reveals How Chirality Is Determined in Polyketides
journal, August 2007


Evaluating Ketoreductase Exchanges as a Means of Rationally Altering Polyketide Stereochemistry
journal, May 2015

  • Annaval, Thibault; Paris, Cédric; Leadlay, Peter F.
  • ChemBioChem, Vol. 16, Issue 9
  • DOI: 10.1002/cbic.201500113

    Works referencing / citing this record:

    Technical Advances to Accelerate Modular Type I Polyketide Synthase Engineering towards a Retro-biosynthetic Platform
    journal, June 2019

    • Pang, Bo; Valencia, Luis E.; Wang, Jessica
    • Biotechnology and Bioprocess Engineering, Vol. 24, Issue 3
    • DOI: 10.1007/s12257-019-0083-9

    Computer-aided re-engineering of nonribosomal peptide and polyketide biosynthetic assembly lines
    journal, January 2019

    • Alanjary, Mohammad; Cano-Prieto, Carolina; Gross, Harald
    • Natural Product Reports, Vol. 36, Issue 9
    • DOI: 10.1039/c9np00021f

    RetSynth: determining all optimal and sub-optimal synthetic pathways that facilitate synthesis of target compounds in chassis organisms
    journal, September 2019