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Rational engineering strategies for achieving high-yield, high-quality and high-stability of natural product production in actinomycetes. Metab Eng 2021; 67:198-215. [PMID: 34166765 DOI: 10.1016/j.ymben.2021.06.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/30/2021] [Accepted: 06/19/2021] [Indexed: 12/11/2022]
Abstract
Actinomycetes are recognized as excellent producers of microbial natural products, which have a wide range of applications, especially in medicine, agriculture and stockbreeding. The three main indexes of industrialization (titer, purity and stability) must be taken into overall consideration in the manufacturing process of natural products. Over the past decades, synthetic biology techniques have expedited the development of industrially competitive strains with excellent performances. Here, we summarize various rational engineering strategies for upgrading the performance of industrial actinomycetes, which include enhancing the yield of natural products, eliminating the by-products and improving the genetic stability of engineered strains. Furthermore, the current challenges and future perspectives for optimizing the industrial strains more systematically through combinatorial engineering strategies are also discussed.
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Kalkreuter E, Bingham KS, Keeler AM, Lowell AN, Schmidt JJ, Sherman DH, Williams GJ. Computationally-guided exchange of substrate selectivity motifs in a modular polyketide synthase acyltransferase. Nat Commun 2021; 12:2193. [PMID: 33850151 PMCID: PMC8044089 DOI: 10.1038/s41467-021-22497-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 02/26/2021] [Indexed: 11/28/2022] Open
Abstract
Polyketides, one of the largest classes of natural products, are often clinically relevant. The ability to engineer polyketide biosynthesis to produce analogs is critically important. Acyltransferases (ATs) of modular polyketide synthases (PKSs) catalyze the installation of malonyl-CoA extenders into polyketide scaffolds. ATs have been targeted extensively to site-selectively introduce various extenders into polyketides. Yet, a complete inventory of AT residues responsible for substrate selection has not been established, limiting the scope of AT engineering. Here, molecular dynamics simulations are used to prioritize ~50 mutations within the active site of EryAT6 from erythromycin biosynthesis, leading to identification of two previously unexplored structural motifs. Exchanging both motifs with those from ATs with alternative extender specificities provides chimeric PKS modules with expanded and inverted substrate specificity. Our enhanced understanding of AT substrate selectivity and application of this motif-swapping strategy are expected to advance our ability to engineer PKSs towards designer polyketides.
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Affiliation(s)
- Edward Kalkreuter
- Department of Chemistry, NC State University, Raleigh, NC, USA
- Comparative Medicine Institute, NC State University, Raleigh, NC, USA
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Kyle S Bingham
- Department of Chemistry, NC State University, Raleigh, NC, USA
- UNC Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Aaron M Keeler
- Department of Chemistry, NC State University, Raleigh, NC, USA
| | - Andrew N Lowell
- Life Sciences Institute, Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
- Department of Chemistry, Virginia Tech, Blacksburg, VA, USA
| | - Jennifer J Schmidt
- Life Sciences Institute, Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - David H Sherman
- Life Sciences Institute, Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
- Department of Chemistry, Department of Microbiology & Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Gavin J Williams
- Department of Chemistry, NC State University, Raleigh, NC, USA.
- Comparative Medicine Institute, NC State University, Raleigh, NC, USA.
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Heng E, Tan LL, Zhang MM, Wong FT. CRISPR-Cas strategies for natural product discovery and engineering in actinomycetes. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.01.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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