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Metabolic pathway meeting utilizing docking domains from sort I cis-AT polyketide synthases

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  • Tang, T.-C. et al. Supplies design by artificial biology. Nat. Rev. Mater. 6, 332–350 (2021).

    ADS 
    CAS 
    Article 

    Google Scholar 

  • Liu, Z., Wang, J. & Nielsen, J. Yeast artificial biology advances biofuel manufacturing. Curr. Opin. Microbiol. 65, 33–39 (2022).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Courdavault, V., O’Connor, S. E., Oudin, A., Besseau, S. & Papon, N. In the direction of the microbial manufacturing of plant-derived anticancer medicine. Developments Most cancers 6, 444–448 (2020).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Dutta, S. et al. Construction of a modular polyketide synthase. Nature 510, 512 (2014).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Kerfeld, C. A., Aussignargues, C., Zarzycki, J., Ci, F. & Sutter, M. Bacterial microcompartments. Nat. Rev. Microbiol. 16, 277–290 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Artzi, L., Bayer, E. A. & Moraïs, S. Cellulosomes: bacterial nanomachines for dismantling plant polysaccharides. Nat. Rev. Microbiol. 15, 83 (2016).

    PubMed 
    Article 
    CAS 

    Google Scholar 

  • Castellana, M. et al. Enzyme clustering accelerates processing of intermediates by way of metabolic channeling. Nat. Biotechnol. 32, 1011–1018 (2014).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Dueber, J. E., Wu, G. C., Malmirchegini, G. R., Moon, T. S. & Keasling, J. D. Artificial protein scaffolds present modular management over metabolic flux. Nat. Biotechnol. 27, 753–759 (2009).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Fu, J. et al. Multi-enzyme complexes on DNA scaffolds able to substrate channelling with a synthetic swinging arm. Nat. Nanotechnol. 9, 531–536 (2014).

    ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Delebecque, C. J., Silver, P. A. & Lindner, A. B. Designing and utilizing RNA scaffolds to assemble proteins. Nat. Protoc. 7, 1797–1807 (2012).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Value, J. V., Chen, L., Whitaker, W. B., Papoutsakis, E. & Chen, W. Scaffoldless engineered enzyme meeting for enhanced methanol utilization. Proc. Natl Acad. Sci. USA 113, 12691–12696 (2016).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Lim, S., Kim, J., Kim, Y., Xu, D. & Clark, D. S. CRISPR/Cas-directed programmable meeting of multi-enzyme complexes. Chem. Commun. 56, 4950–4953 (2020).

    CAS 
    Article 

    Google Scholar 

  • Berckman, E. A. & Chen, W. Exploiting dCas9 fusion proteins for dynamic meeting of artificial metabolons. Chem. Commun. 55, 8219–8222 (2019).

    CAS 
    Article 

    Google Scholar 

  • Wheeldon, I. et al. Substrate channelling as an method to cascade reactions. Nat. Chem. 8, 299–309 (2016).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Sweetlove, L. J. & Fernie, A. R. The function of dynamic enzyme assemblies and substrate channelling in metabolic regulation. Nat. Commun. 9, 2136 (2018).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Vanderstraeten, J. & Briers, Y. Artificial protein scaffolds for the colocalisation of co-acting enzymes. Biotechnol. Adv. 44, 107627 (2020).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Ji, D., Li, J., Xu, F., Ren, Y. & Wang, Y. Enhance the biosynthesis of baicalein and scutellarein through manufacturing self-assembly enzyme reactor in vivo. ACS Synth. Biol. 10, 1087–1094 (2021).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Berckman, E. A. & Chen, W. A modular method for dCas9-mediated enzyme cascading through orthogonal bioconjugation. Chem. Commun. 56, 11426–11428 (2020).

    CAS 
    Article 

    Google Scholar 

  • Lee, S. H., Park, S. J. & Hong, S. H. Manufacturing of gamma-aminobutyric acid from glucose by introduction of artificial scaffolds between isocitrate dehydrogenase, glutamate synthase and glutamate decarboxylase in recombinant Escherichia coli. J. Biotechnol. 207, 52–57 (2015).

    PubMed 
    Article 
    CAS 

    Google Scholar 

  • Li, T., Chen, X., Cai, Y. & Dai, J. Synthetic Protein Scaffold System (AProSS): an environment friendly methodology to optimize exogenous metabolic pathways in Saccharomyces cerevisiae. Metab. Eng. 49, 13–20 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Kang, W. et al. Modular enzyme meeting for enhanced cascade biocatalysis and metabolic flux. Nat. Commun. 10, 4248 (2019).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Qu, J. et al. Artificial multienzyme complexes, catalytic nanomachineries for cascade biosynthesis in vivo. ACS Nano 13, 9895–9906 (2019).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Lim, S., Jung, G. A., Glover, D. J. & Clark, D. S. Enhanced enzyme exercise by way of scaffolding on customizable self-assembling protein filaments. Small 15, 1805558 (2019).

    Article 
    CAS 

    Google Scholar 

  • Tippmann, S. et al. Affibody scaffolds enhance sesquiterpene manufacturing in Saccharomyces cerevisiae. ACS Synth. Biol. 6, 19–28 (2017).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Lee, M. J. et al. Engineered artificial scaffolds for organizing proteins throughout the bacterial cytoplasm. Nat. Chem. Biol. 14, 142 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Zhang, Y. et al. Auxiliary module promotes the synthesis of carboxysomes in E. coli to attain high-efficiency CO2 assimilation. ACS Synth. Biol. 10, 707–715 (2021).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Nivina, A., Yuet, Okay. P., Hsu, J. & Khosla, C. Evolution and variety of assembly-line polyketide synthases. Chem. Rev. 119, 12524–12547 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Ibrahim, N. Okay. Ixabepilone: overview of effectiveness, security, and tolerability in metastatic breast most cancers. Entrance. Oncol. 11, 2549 (2021).

    Google Scholar 

  • Fischbach, M. A. & Walsh, C. T. Meeting-line enzymology for polyketide and nonribosomal peptide antibiotics: logic, equipment, and mechanisms. Chem. Rev. 106, 3468–3496 (2006).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Robbins, T., Liu, Y.-C., Cane, D. E. & Khosla, C. Construction and mechanism of meeting line polyketide synthases. Curr. Opin. Struct. Biol. 41, 10–18 (2016).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Herbst, D. A., Townsend, C. A. & Maier, T. The architectures of iterative sort I PKS and FAS. Nat. Prod. Rep. 35, 1046–1069 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Cogan, D. P. et al. Mapping the catalytic conformations of an assembly-line polyketide synthase module. Science 374, 729–734 (2021).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Helfrich, E. J. & Piel, J. Biosynthesis of polyketides by trans-AT polyketide synthases. Nat. Prod. Rep. 33, 231–316 (2016).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Weissman, Okay. J. Genetic engineering of modular PKSs: from combinatorial biosynthesis to artificial biology. Nat. Prod. Rep. 33, 203–230 (2016).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Broadhurst, R. W., Nietlispach, D., Wheatcroft, M. P., Leadlay, P. F. & Weissman, Okay. J. The construction of docking domains in modular polyketide synthases. Chem. Biol. 10, 723–731 (2003).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Khosla, C., Tang, Y., Chen, A. Y., Schnarr, N. A. & Cane, D. E. Construction and mechanism of the 6-deoxyerythronolide B synthase. Annu. Rev. Biochem. 76, 195–221 (2007).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Gokhale, R. S., Tsuji, S. Y., Cane, D. E. & Khosla, C. Dissecting and exploiting intermodular communication in polyketide synthases. Science 284, 482–485 (1999).

    ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Aparicio, J. F. et al. Group of the biosynthetic gene cluster for rapamycin in Streptomyces hygroscopicus: evaluation of the enzymatic domains within the modular polyketide synthase. Gene 169, 9–16 (1996).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Waldron, C. et al. Cloning and evaluation of the spinosad biosynthetic gene cluster of Saccharopolyspora spinosa. Chem. Biol. 8, 487–499 (2001).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Izumikawa, M., Murata, M., Tachibana, Okay., Ebizuka, Y. & Fujii, I. Cloning of modular sort I polyketide synthase genes from salinomycin producing pressure of Streptomyces albus. Bioorg. Medicinal Chem. 11, 3401–3405 (2003).

    CAS 
    Article 

    Google Scholar 

  • Thattai, M., Burak, Y. & Shraiman, B. I. The origins of specificity in polyketide synthase protein interactions. PLoS Comput. Biol. 3, e186 (2007).

    ADS 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Buchholz, T. J. et al. Structural foundation for binding specificity between subclasses of modular polyketide synthase docking domains. ACS Chem. Biol. 4, 41–52 (2009).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Dodge, G. J., Maloney, F. P. & Smith, J. L. Protein–protein interactions in “cis-AT” polyketide synthases. Nat. Prod. Rep. 35, 1082–1096 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Miyazawa, T., Hirsch, M., Zhang, Z. & Keatinge-Clay, A. T. An in vitro platform for engineering and harnessing modular polyketide synthases. Nat. Commun. 11, 1–7 (2020).

    Article 
    CAS 

    Google Scholar 

  • Yan, J., Gupta, S., Sherman, D. H. & Reynolds, Okay. A. Useful dissection of a multimodular polypeptide of the pikromycin polyketide synthase into monomodules through the use of a matched pair of heterologous docking domains. ChemBioChem 10, 1537–1543 (2009).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Peng, H., Ishida, Okay., Sugimoto, Y., Jenke-Kodama, H. & Hertweck, C. Emulating evolutionary processes to morph aureothin-type modular polyketide synthases and related oxygenases. Nat. Commun. 10, 1–14 (2019).

    Article 
    CAS 

    Google Scholar 

  • Su, L. et al. Engineering the stambomycin modular polyketide synthase yields 37-membered mini-stambomycins. Nat. Commun. 13, 1–16 (2022).

    ADS 
    CAS 

    Google Scholar 

  • Eng, C. H. et al. ClusterCAD: a computational platform for sort I modular polyketide synthase design. Nucleic Acids Res. 46, D509–D515 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Meinke, J. L. et al. Using 25-residue docking motifs from modular polyketide synthases as orthogonal protein connectors. ACS Synth. Biol. 8, 2017–2024 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Zhang, C., Chen, X. & Too, H.-P. Microbial astaxanthin biosynthesis: latest achievements, challenges, and commercialization outlook. Appl. Microbiol. Biotechnol. 104, 5725–5737 (2020).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Ram, S., Mitra, M., Shah, F., Tirkey, S. R. & Mishra, S. Micro organism as an alternate biofactory for carotenoid manufacturing: A evaluate of its purposes, alternatives and challenges. J. Funct. Meals 67, 103867 (2020).

    CAS 
    Article 

    Google Scholar 

  • Saini, R. Okay. & Keum, Y. S. Microbial platforms to provide commercially important carotenoids at industrial scale: an up to date evaluate of vital points. J. Ind. Microbiol. Biotechnol. 46, 657–674 (2019).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Zhang, C. Biosynthesis of carotenoids and apocarotenoids by microorganisms and their industrial potential. Prog. Carotenoid Res. 85 (2018).

  • Ma, T. et al. Genome mining of astaxanthin biosynthetic genes from Sphingomonas sp. ATCC 55669 for heterologous overproduction in Escherichia coli. Biotechnol. J. 11, 228–237 (2016).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Paniagua-Michel, J., Olmos-Soto, J. & Ruiz, M.A. Pathways of carotenoid biosynthesis in micro organism and microalgae. Strategies Mol. Biol. 892, 1-12 (2012).

  • Foong, L. C., Loh, C. W. L., Ng, H. S. & Lan, J. C. W. Latest growth within the manufacturing methods of microbial carotenoids. World J. Microbiol. Biotechnol. 37, 1–11 (2021).

    Article 
    CAS 

    Google Scholar 

  • Gokhale, R. S., Hunziker, D., Cane, D. E. & Khosla, C. Mechanism and specificity of the terminal thioesterase area from the erythromycin polyketide synthase. Chem. Biol. 6, 117–125 (1999).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Tsuji, S. Y., Cane, D. E. & Khosla, C. Selective protein-protein interactions direct channeling of intermediates between polyketide synthase modules. Biochemistry 40, 2326–2331 (2001).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Motamedi, H. & Shafiee, A. The biosynthetic gene cluster for the macrolactone ring of the immunosuppressant FK506. Eur. J. Biochem. 256, 528–534 (1998).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • He, J. & Hertweck, C. Iteration as programmed occasion throughout polyketide meeting; molecular evaluation of the aureothin biosynthesis gene cluster. Chem. Biol. 10, 1225–1232 (2003).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Novy, R. Overcoming the codon bias of E. coli for enhanced protein expression. Improvements 12, 1–3 (2001).

    Google Scholar 

  • Schägger, H. Tricine–sds-page. Nat. Protoc. 1, 16–22 (2006).

    PubMed 
    Article 
    CAS 

    Google Scholar 

  • Müller-Esparza, H., Osorio-Valeriano, M., Steube, N., Thanbichler, M. & Randau, L. Bio-Layer Interferometry evaluation of the goal binding exercise of CRISPR-Cas effector complexes. Entrance. Mol. Biosci. 7, 98 (2020).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Kumar, P., Li, Q., Cane, D. E. & Khosla, C. Intermodular communication in modular polyketide synthases: structural and mutational evaluation of linker mediated protein−protein recognition. J. Am. Chem. Soc. 125, 4097–4102 (2003).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Yoon, S.-H. et al. Combinatorial expression of bacterial complete mevalonate pathway for the manufacturing of β-carotene in E. coli. J. Biotechnol. 140, 218–226 (2009).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • George, Okay. W. et al. Built-in evaluation of isopentenyl pyrophosphate (IPP) toxicity in isoprenoid-producing Escherichia coli. Metab. Eng. 47, 60–72 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Stange, C. Carotenoids in Nature: Biosynthesis, Regulation and Perform Vol. 79 (Springer, 2016).

  • Bozhüyük, Okay. A., Micklefield, J. & Wilkinson, B. Engineering enzymatic meeting traces to provide new antibiotics. Curr. Opin. Microbiol. 51, 88–96 (2019).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Miyazawa, T., Fitzgerald, B. J. & Keatinge-Clay, A. T. Preparative manufacturing of an enantiomeric pair by engineered polyketide synthases. Chem. Commun. 57, 8762–8765 (2021).

    CAS 
    Article 

    Google Scholar 

  • Wang, Y., Correa Marrero, M., Medema, M. H. & van Dijk, A. D. Coevolution-based prediction of protein–protein interactions in polyketide biosynthetic meeting traces. Bioinformatics 36, 4846–4853 (2020).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Gaitatzis, N. et al. The biosynthesis of the fragrant myxobacterial electron transport inhibitor stigmatellin is directed by a novel sort of modular polyketide synthase. J. Biol. Chem. 277, 13082–13090 (2002).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Li, T., Tripathi, A., Yu, F., Sherman, D. H. & Rao, A. DDAP: docking area affinity and biosynthetic pathway prediction device for sort I polyketide synthases. Bioinformatics 36, 942–944 (2020).

    CAS 
    PubMed 
    Article 

    Google Scholar 

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