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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.
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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.
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2
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Wang TT, Hu YL, Li YF, Kong XL, Li YM, Sun PY, Wang DX, Li YY, Zhang YZ, Han QL, Zhu XH, An QQ, Liu LL, Liu Y, Li HC. Polyketide synthases mutation in tuberculosis transmission revealed by whole genomic sequence, China, 2011-2019. Front Genet 2024; 14:1217255. [PMID: 38259610 PMCID: PMC10800454 DOI: 10.3389/fgene.2023.1217255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 11/30/2023] [Indexed: 01/24/2024] Open
Abstract
Introduction: Tuberculosis (TB) is an infectious disease caused by a bacterium called Mycobacterium tuberculosis (Mtb). Previous studies have primarily focused on the transmissibility of multidrug-resistant (MDR) or extensively drug-resistant (XDR) Mtb. However, variations in virulence across Mtb lineages may also account for differences in transmissibility. In Mtb, polyketide synthase (PKS) genes encode large multifunctional proteins which have been shown to be major mycobacterial virulence factors. Therefore, this study aimed to identify the role of PKS mutations in TB transmission and assess its risk and characteristics. Methods: Whole genome sequences (WGSs) data from 3,204 Mtb isolates was collected from 2011 to 2019 in China. Whole genome single nucleotide polymorphism (SNP) profiles were used for phylogenetic tree analysis. Putative transmission clusters (≤10 SNPs) were identified. To identify the role of PKS mutations in TB transmission, we compared SNPs in the PKS gene region between "clustered isolates" and "non-clustered isolates" in different lineages. Results: Cluster-associated mutations in ppsA, pks12, and pks13 were identified among different lineage isolates. They were statistically significant among clustered strains, indicating that they may enhance the transmissibility of Mtb. Conclusion: Overall, this study provides new insights into the function of PKS and its localization in M. tuberculosis. The study found that ppsA, pks12, and pks13 may contribute to disease progression and higher transmission of certain strains. We also discussed the prospective use of mutant ppsA, pks12, and pks13 genes as drug targets.
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Affiliation(s)
- Ting-Ting Wang
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yuan-Long Hu
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yi-Fan Li
- Department of Pulmonary and Critical Care Medicine, The Third Affiliated Hospital of Shandong First Medical University (Affiliated Hospital of Shandong Academy of Medical Sciences), Jinan, China
| | - Xiang-Long Kong
- Shandong Artificial Intelligence Institute Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Ya-Meng Li
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | | | - Da-Xing Wang
- People’s Hospital of Huaiyin Jinan, Jinan, China
| | - Ying-Ying Li
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yu-Zhen Zhang
- Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Qi-Lin Han
- Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Xue-Han Zhu
- Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Qi-Qi An
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to 11 Shandong University, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Li-Li Liu
- People’s Hospital of Huaiyin Jinan, Jinan, China
| | - Yao Liu
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to 11 Shandong University, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Huai-Chen Li
- Shandong University of Traditional Chinese Medicine, Jinan, China
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to 11 Shandong University, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
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3
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Patil RS, Sharma S, Bhaskarwar AV, Nambiar S, Bhat NA, Koppolu MK, Bhukya H. TetR and OmpR family regulators in natural product biosynthesis and resistance. Proteins 2023. [PMID: 37874037 DOI: 10.1002/prot.26621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 08/30/2023] [Accepted: 10/06/2023] [Indexed: 10/25/2023]
Abstract
This article provides a comprehensive review and sequence-structure analysis of transcription regulator (TR) families, TetR and OmpR/PhoB, involved in specialized secondary metabolite (SSM) biosynthesis and resistance. Transcription regulation is a fundamental process, playing a crucial role in orchestrating gene expression to confer a survival advantage in response to frequent environmental stress conditions. This process, coupled with signal sensing, enables bacteria to respond to a diverse range of intra and extracellular signals. Thus, major bacterial signaling systems use a receptor domain to sense chemical stimuli along with an output domain responsible for transcription regulation through DNA-binding. Sensory and output domains on a single polypeptide chain (one component system, OCS) allow response to stimuli by allostery, that is, DNA-binding affinity modulation upon signal presence/absence. On the other hand, two component systems (TCSs) allow cross-talk between the sensory and output domains as they are disjoint and transmit information by phosphorelay to mount a response. In both cases, however, TRs play a central role. Biosynthesis of SSMs, which includes antibiotics, is heavily regulated by TRs as it diverts the cell's resources towards the production of these expendable compounds, which also have clinical applications. These TRs have evolved to relay information across specific signals and target genes, thus providing a rich source of unique mechanisms to explore towards addressing the rapid escalation in antimicrobial resistance (AMR). Here, we focus on the TetR and OmpR family TRs, which belong to OCS and TCS, respectively. These TR families are well-known examples of regulators in secondary metabolism and are ubiquitous across different bacteria, as they also participate in a myriad of cellular processes apart from SSM biosynthesis and resistance. As a result, these families exhibit higher sequence divergence, which is also evident from our bioinformatic analysis of 158 389 and 77 437 sequences from TetR and OmpR family TRs, respectively. The analysis of both sequence and structure allowed us to identify novel motifs in addition to the known motifs responsible for TR function and its structural integrity. Understanding the diverse mechanisms employed by these TRs is essential for unraveling the biosynthesis of SSMs. This can also help exploit their regulatory role in biosynthesis for significant pharmaceutical, agricultural, and industrial applications.
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Affiliation(s)
- Rachit S Patil
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Siddhant Sharma
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Aditya V Bhaskarwar
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Souparnika Nambiar
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Niharika A Bhat
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Mani Kanta Koppolu
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Hussain Bhukya
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
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4
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Zhang J, Bista R, Miyazawa T, Keatinge-Clay AT. Boosting titers of engineered triketide and tetraketide synthases to record levels through T7 promoter tuning. Metab Eng 2023; 78:93-98. [PMID: 37257684 PMCID: PMC11059570 DOI: 10.1016/j.ymben.2023.05.008] [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: 11/22/2022] [Revised: 05/24/2023] [Accepted: 05/28/2023] [Indexed: 06/02/2023]
Abstract
Modular polyketide synthases (PKS's) are promising platforms for the rational engineering of designer polyketides and commodity chemicals, yet their low productivities are a barrier to the practical biosynthesis of these compounds. Previously, we engineered triketide lactone synthases such as Pik167 using the recently updated module definition and showed they generate hundreds of milligrams of product per liter of Escherichia coli K207-3 shake flask culture. As the molar ratio between the 2 polypeptides of Pik167 is highly skewed, we sought to attenuate the strength of the T7 promoter controlling the production of the smaller, better-expressing polypeptide and thereby increase production of the first polypeptide under the control of an unoptimized T7 promoter. Through this strategy, a 1.8-fold boost in titer was obtained. After a further 1.5-fold boost obtained by increasing the propionate concentration in the media from 20 to 80 mM, a record titer of 791 mg L-1 (627 mg L-1 isolated) was achieved, a 2.6-fold increase overall. Spurred on by this result, the tetraketide synthase Pik1567 was engineered and the T7 promoter attenuation strategy was applied to its second and third genes. A 5-fold boost, from 20 mg L-1 to 100 mg L-1, in the titer of its tetraketide product was achieved.
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Affiliation(s)
- Jie Zhang
- Department of Molecular Biosciences, The University of Texas at Austin, 100 E. 24th St., Austin, TX, 78712, USA
| | - Ramesh Bista
- Department of Molecular Biosciences, The University of Texas at Austin, 100 E. 24th St., Austin, TX, 78712, USA
| | - Takeshi Miyazawa
- Department of Molecular Biosciences, The University of Texas at Austin, 100 E. 24th St., Austin, TX, 78712, USA
| | - Adrian T Keatinge-Clay
- Department of Molecular Biosciences, The University of Texas at Austin, 100 E. 24th St., Austin, TX, 78712, USA.
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5
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Guzman KM, Cogan DP, Brodsky KL, Soohoo AM, Li X, Sevillano N, Mathews II, Nguyen KP, Craik CS, Khosla C. Discovery and Characterization of Antibody Probes of Module 2 of the 6-Deoxyerythronolide B Synthase. Biochemistry 2023. [PMID: 37184546 DOI: 10.1021/acs.biochem.3c00156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Fragment antigen-binding domains of antibodies (Fabs) are powerful probes of structure-function relationships of assembly line polyketide synthases (PKSs). We report the discovery and characterization of Fabs interrogating the structure and function of the ketosynthase-acyltransferase (KS-AT) core of Module 2 of the 6-deoxyerythronolide B synthase (DEBS). Two Fabs (AC2 and BB1) were identified to potently inhibit the catalytic activity of Module 2. Both AC2 and BB1 were found to modulate ACP-mediated reactions catalyzed by this module, albeit by distinct mechanisms. AC2 primarily affects the rate (kcat), whereas BB1 increases the KM of an ACP-mediated reaction. A third Fab, AA5, binds to the KS-AT fragment of DEBS Module 2 without altering either parameter; it is phenotypically reminiscent of a previously characterized Fab, 1B2, shown to principally recognize the N-terminal helical docking domain of DEBS Module 3. Crystal structures of AA5 and 1B2 bound to the KS-AT fragment of Module 2 were solved to 2.70 and 2.65 Å resolution, respectively, and revealed entirely distinct recognition features of the two antibodies. The new tools and insights reported here pave the way toward advancing our understanding of the structure-function relationships of DEBS Module 2, arguably the most well-studied module of an assembly line PKS.
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Affiliation(s)
- Katarina M Guzman
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Dillon P Cogan
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Krystal L Brodsky
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Alexander M Soohoo
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Xiuyuan Li
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Natalia Sevillano
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94158, United States
| | - Irimpan I Mathews
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Khanh P Nguyen
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94158, United States
| | - Chaitan Khosla
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Sarafan ChEM-H, Stanford University, Stanford, California 94305, United States
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6
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Wang J, Wang X, Li X, Kong L, Du Z, Li D, Gou L, Wu H, Cao W, Wang X, Lin S, Shi T, Deng Z, Wang Z, Liang J. C-N bond formation by a polyketide synthase. Nat Commun 2023; 14:1319. [PMID: 36899013 PMCID: PMC10006239 DOI: 10.1038/s41467-023-36989-w] [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: 06/15/2022] [Accepted: 02/28/2023] [Indexed: 03/12/2023] Open
Abstract
Assembly-line polyketide synthases (PKSs) are molecular factories that produce diverse metabolites with wide-ranging biological activities. PKSs usually work by constructing and modifying the polyketide backbone successively. Here, we present the cryo-EM structure of CalA3, a chain release PKS module without an ACP domain, and its structures with amidation or hydrolysis products. The domain organization reveals a unique "∞"-shaped dimeric architecture with five connected domains. The catalytic region tightly contacts the structural region, resulting in two stabilized chambers with nearly perfect symmetry while the N-terminal docking domain is flexible. The structures of the ketosynthase (KS) domain illustrate how the conserved key residues that canonically catalyze C-C bond formation can be tweaked to mediate C-N bond formation, revealing the engineering adaptability of assembly-line polyketide synthases for the production of novel pharmaceutical agents.
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Affiliation(s)
- Jialiang Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaojie Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,Department of Molecular Biology, Shanghai Jikaixing Biotech Inc., Shanghai, 200131, China
| | - Xixi Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - LiangLiang Kong
- National Facility for Protein Science in Shanghai, Chinese Academy of Sciences, Shanghai, 201204, China
| | - Zeqian Du
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Dandan Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Lixia Gou
- School of Life Science, North China University of Science and Technology, Tangshan, Hebei, China
| | - Hao Wu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Cao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaozheng Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Ting Shi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Zhijun Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Jingdan Liang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
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7
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Metabolic pathway assembly using docking domains from type I cis-AT polyketide synthases. Nat Commun 2022; 13:5541. [PMID: 36130947 PMCID: PMC9492657 DOI: 10.1038/s41467-022-33272-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 09/09/2022] [Indexed: 11/21/2022] Open
Abstract
Engineered metabolic pathways in microbial cell factories often have no natural organization and have challenging flux imbalances, leading to low biocatalytic efficiency. Modular polyketide synthases (PKSs) are multienzyme complexes that synthesize polyketide products via an assembly line thiotemplate mechanism. Here, we develop a strategy named mimic PKS enzyme assembly line (mPKSeal) that assembles key cascade enzymes to enhance biocatalytic efficiency and increase target production by recruiting cascade enzymes tagged with docking domains from type I cis-AT PKS. We apply this strategy to the astaxanthin biosynthetic pathway in engineered Escherichia coli for multienzyme assembly to increase astaxanthin production by 2.4-fold. The docking pairs, from the same PKSs or those from different cis-AT PKSs evidently belonging to distinct classes, are effective enzyme assembly tools for increasing astaxanthin production. This study addresses the challenge of cascade catalytic efficiency and highlights the potential for engineering enzyme assembly. Assembly artificial pathway in design connecting media can increase biosynthetic efficiency, but the choice of connecting media is limited. Here, the authors develop a new protein assembly strategy using a pool of docking peptides from polyketide synthase and show its application in astaxanthin biosynthesis in E. coli.
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8
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Sirirungruang S, Ad O, Privalsky TM, Ramesh S, Sax JL, Dong H, Baidoo EEK, Amer B, Khosla C, Chang MCY. Engineering site-selective incorporation of fluorine into polyketides. Nat Chem Biol 2022; 18:886-893. [PMID: 35817967 PMCID: PMC10030150 DOI: 10.1038/s41589-022-01070-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 05/23/2022] [Indexed: 02/01/2023]
Abstract
Although natural products and synthetic small molecules both serve important medicinal functions, their structures and chemical properties are relatively distinct. To expand the molecular diversity available for drug discovery, one strategy is to blend the effective attributes of synthetic and natural molecules. A key feature found in synthetic compounds that is rare in nature is the use of fluorine to tune drug behavior. We now report a method to site-selectively incorporate fluorine into complex structures to produce regioselectively fluorinated full-length polyketides. We engineered a fluorine-selective trans-acyltransferase to produce site-selectively fluorinated erythromycin precursors in vitro. We further demonstrated that these analogs could be produced in vivo in Escherichia coli on engineering of the fluorinated extender unit pool. By using engineered microbes, elaborate fluorinated compounds can be produced by fermentation, offering the potential for expanding the identification and development of bioactive fluorinated small molecules.
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Affiliation(s)
| | - Omer Ad
- Department of Chemistry, University of California, Berkeley, CA, USA
| | | | - Swetha Ramesh
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Joel L Sax
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Hongjun Dong
- Department of Chemistry, University of California, Berkeley, CA, USA
| | - Edward E K Baidoo
- Joint Bioenergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Energy, Agile BioFoundry, Emeryville, CA, USA
| | - Bashar Amer
- Joint Bioenergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chaitan Khosla
- Department of Chemistry, Stanford University, Stanford, CA, USA
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
| | - Michelle C Y Chang
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- Department of Chemistry, University of California, Berkeley, CA, USA.
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA.
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9
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Chisuga T, Miyanaga A, Eguchi T. Protein-protein Recognition Involved in the Intermodular Transacylation Reaction in Modular Polyketide Synthase in the Biosynthesis of Vicenistatin. Chembiochem 2022; 23:e202200200. [PMID: 35501288 PMCID: PMC9401018 DOI: 10.1002/cbic.202200200] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 04/29/2022] [Indexed: 11/25/2022]
Abstract
The ketosynthase (KS) domain is a core domain found in modular polyketide synthases (PKSs). To maintain the polyketide biosynthetic fidelity, the KS domain must only accept an acyl group from the acyl carrier protein (ACP) domain of the immediate upstream module even when they are separated into different polypeptides. Although it was reported that both the docking domain‐based interactions and KS‐ACP compatibility are important for the interpolypeptide transacylation reaction in 6‐deoxyerythronolide B synthase, it is not clear whether these findings are broadly applied to other modular PKSs. Herein, we describe the importance of protein‐protein recognition in the intermodular transacylation between VinP1 module 3 and VinP2 module 4 in vicenistatin biosynthesis. We compared the transacylation activity and crosslinking efficiency of VinP2 KS4 against the cognate VinP1 ACP3 with the noncognate one. As a result, it appeared that VinP2 KS4 distinguishes the cognate ACP3 from other ACPs.
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Affiliation(s)
- Taichi Chisuga
- Tokyo Institute of Technology - Ookayama Campus: Tokyo Kogyo Daigaku, Chemistry, JAPAN
| | - Akimasa Miyanaga
- Tokyo Institute of Technology - Ookayama Campus: Tokyo Kogyo Daigaku, Chemistry, JAPAN
| | - Tadashi Eguchi
- Tokyo Institute of Technology, Chemistry, O-okayama, Meguro-ku, 1528551, Tokyo, JAPAN
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10
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Clayton J, Ellis-Guardiola K, Mahoney BJ, Soule J, Clubb RT, Wereszczynski J. Directed inter-domain motions enable the IsdH Staphylococcus aureus receptor to rapidly extract heme from human hemoglobin. J Mol Biol 2022; 434:167623. [DOI: 10.1016/j.jmb.2022.167623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/07/2022] [Accepted: 05/01/2022] [Indexed: 11/29/2022]
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11
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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.
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12
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Gu D, Zhang W. Engineered biosynthesis of alkyne-tagged polyketides. Methods Enzymol 2022; 665:347-373. [PMID: 35379442 PMCID: PMC9829517 DOI: 10.1016/bs.mie.2021.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Polyketides have demonstrated their significance as therapeutics, industrial products, pesticides, and biological probes following intense study over the past decades. Tagging polyketides with a bioorthogonal functionality enables various applications such as diversification, quantification, visualization and mode-of-action elucidation. The terminal alkyne moiety, as a small, stable and highly selective clickable functionality, is widely adopted in tagging natural products. De novo biosynthesis of alkyne-tagged polyketides offers the unique advantage of reducing the background from feeding the biorthogonal moiety itself, leading to the accomplishment of in situ generation of a clickable functionality for bioorthogonal reactions. Here, we introduce several engineering strategies to apply terminal alkyne biosynthetic machinery, represented by JamABC, which produces a short terminal alkyne-bearing fatty acyl chain on a carrier protein, to functions with different downstream polyketide synthases (PKSs). Successful results in engineering type III and type I PKSs provide engineering guidelines and strategies that are applicable to additional PKSs to produce targeted alkyne-tagged metabolites for chemical and biological applications.
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Affiliation(s)
- Di Gu
- Department of Chemistry, University of California, Berkeley, CA, United States
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, United States,Chan Zuckerberg Biohub, San Francisco, CA, United States,Corresponding author:
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13
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Cogan DP, Zhang K, Li X, Li S, Pintilie GD, Roh SH, Craik CS, Chiu W, Khosla C. Mapping the catalytic conformations of an assembly-line polyketide synthase module. Science 2021; 374:729-734. [PMID: 34735239 DOI: 10.1126/science.abi8358] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Dillon P Cogan
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Kaiming Zhang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.,MOE Key Laboratory for Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Xiuyuan Li
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Shanshan Li
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.,MOE Key Laboratory for Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Grigore D Pintilie
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Soung-Hun Roh
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.,Department of Biological Sciences, Institute of Molecular Biology & Genetics, Seoul National University, Seoul 151-742, Korea
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA 94158, USA
| | - Wah Chiu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.,Division of CryoEM and Bioimaging, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Chaitan Khosla
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.,Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA.,Stanford ChEM-H, Stanford, CA 94305, USA
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14
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15
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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.
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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
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16
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Park D, Swayambhu G, Lyga T, Pfeifer BA. Complex natural product production methods and options. Synth Syst Biotechnol 2021; 6:1-11. [PMID: 33474503 PMCID: PMC7803631 DOI: 10.1016/j.synbio.2020.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/19/2020] [Accepted: 12/21/2020] [Indexed: 12/29/2022] Open
Abstract
Natural products have had a major impact upon quality of life, with antibiotics as a classic example of having a transformative impact upon human health. In this contribution, we will highlight both historic and emerging methods of natural product bio-manufacturing. Traditional methods of natural product production relied upon native cellular host systems. In this context, pragmatic and effective methodologies were established to enable widespread access to natural products. In reviewing such strategies, we will also highlight the development of heterologous natural product biosynthesis, which relies instead on a surrogate host system theoretically capable of advanced production potential. In comparing native and heterologous systems, we will comment on the base organisms used for natural product biosynthesis and how the properties of such cellular hosts dictate scaled engineering practices to facilitate compound distribution. In concluding the article, we will examine novel efforts in production practices that entirely eliminate the constraints of cellular production hosts. That is, cell free production efforts will be introduced and reviewed for the purpose of complex natural product biosynthesis. Included in this final analysis will be research efforts made on our part to test the cell free biosynthesis of the complex polyketide antibiotic natural product erythromycin.
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Affiliation(s)
- Dongwon Park
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - Girish Swayambhu
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - Thomas Lyga
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - Blaine A Pfeifer
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, NY, USA
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17
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Vasilenko EA, Gorshkova EN, Astrakhantseva IV, Drutskaya MS, Tillib SV, Nedospasov SA, Mokhonov VV. The structure of myeloid cell-specific TNF inhibitors affects their biological properties. FEBS Lett 2020; 594:3542-3550. [PMID: 32865225 DOI: 10.1002/1873-3468.13913] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/25/2020] [Accepted: 07/06/2020] [Indexed: 11/05/2022]
Abstract
Spatial organization and conformational changes of antibodies may significantly affect their biological functions. We assessed the effect of mutual organization of the two VH H domains within bispecific antibodies recognizing human TNF and the surface molecules of murine myeloid cells (F4/80 or CD11b) on TNF retention and inhibition. TNF-neutralizing properties in vitro and in vivo of MYSTI-2 and MYSTI-3 antibodies were compared with new variants with interchanged VH H domains and different linker sequences. The most effective structure of MYSTI-2 and MYSTI-3 proteins required the Ser/Gly-containing 'superflexible' linker. The orientation of the modules was crucial for the activity of the proteins, but not for MYSTI-3 with the Pro/Gln-containing 'semi-rigid' linker. Our results may contribute toward the development of more effective drug prototypes.
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Affiliation(s)
| | | | - Irina V Astrakhantseva
- Lobachevsky State University, Nizhny Novgorod, Russia.,Sirius University of Science and Technology, Sochi, Russia
| | - Marina S Drutskaya
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Sergei V Tillib
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Sergei A Nedospasov
- Sirius University of Science and Technology, Sochi, Russia.,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Lomonosov Moscow State University, Moscow, Russia
| | - Vladislav V Mokhonov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Blokhina Scientific Research Institute of Epidemiology and Microbiology of Nizhny Novgorod, Nizhny Novgorod, Russia
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18
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Hwang S, Lee N, Cho S, Palsson B, Cho BK. Repurposing Modular Polyketide Synthases and Non-ribosomal Peptide Synthetases for Novel Chemical Biosynthesis. Front Mol Biosci 2020; 7:87. [PMID: 32500080 PMCID: PMC7242659 DOI: 10.3389/fmolb.2020.00087] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 04/16/2020] [Indexed: 12/16/2022] Open
Abstract
In nature, various enzymes govern diverse biochemical reactions through their specific three-dimensional structures, which have been harnessed to produce many useful bioactive compounds including clinical agents and commodity chemicals. Polyketide synthases (PKSs) and non-ribosomal peptide synthetases (NRPSs) are particularly unique multifunctional enzymes that display modular organization. Individual modules incorporate their own specific substrates and collaborate to assemble complex polyketides or non-ribosomal polypeptides in a linear fashion. Due to the modular properties of PKSs and NRPSs, they have been attractive rational engineering targets for novel chemical production through the predictable modification of each moiety of the complex chemical through engineering of the cognate module. Thus, individual reactions of each module could be separated as a retro-biosynthetic biopart and repurposed to new biosynthetic pathways for the production of biofuels or commodity chemicals. Despite these potentials, repurposing attempts have often failed owing to impaired catalytic activity or the production of unintended products due to incompatible protein–protein interactions between the modules and structural perturbation of the enzyme. Recent advances in the structural, computational, and synthetic tools provide more opportunities for successful repurposing. In this review, we focused on the representative strategies and examples for the repurposing of modular PKSs and NRPSs, along with their advantages and current limitations. Thereafter, synthetic biology tools and perspectives were suggested for potential further advancement, including the rational and large-scale high-throughput approaches. Ultimately, the potential diverse reactions from modular PKSs and NRPSs would be leveraged to expand the reservoir of useful chemicals.
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Affiliation(s)
- Soonkyu Hwang
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Namil Lee
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Suhyung Cho
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Bernhard Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States.,Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States.,The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Byung-Kwan Cho
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,Intelligent Synthetic Biology Center, Daejeon, South Korea
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19
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Porterfield WB, Poenateetai N, Zhang W. Engineered Biosynthesis of Alkyne-Tagged Polyketides by Type I PKSs. iScience 2020; 23:100938. [PMID: 32146323 PMCID: PMC7063234 DOI: 10.1016/j.isci.2020.100938] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/21/2020] [Accepted: 02/20/2020] [Indexed: 01/20/2023] Open
Abstract
Polyketides produced by modular polyketide synthases (PKSs) are important small molecules widely used as drugs, pesticides, and biological probes. Tagging these polyketides with a clickable functionality enables the visualization, diversification, and mode of action study through bio-orthogonal chemistry. We report the de novo biosynthesis of alkyne-tagged polyketides by modular type I PKSs through starter unit engineering. Specifically, we use JamABC, a terminal alkyne biosynthetic machinery from the jamaicamide B biosynthetic pathway, in combination with representative modular PKSs. We demonstrate that JamABC works as a trans loading system for engineered type I PKSs to produce alkyne-tagged polyketides. In addition, the production efficiency can be improved by enhancing the interactions between the carrier protein (JamC) and PKSs using docking domains and site-directed mutagenesis of JamC. This work thus provides engineering guidelines and strategies that are applicable to additional modular type I PKSs to produce targeted alkyne-tagged metabolites for chemical and biological applications. Alkyne-tagged polyketides are de novo biosynthesized using type I PKSs Docking domains and ACP mutagenesis improve alkyne starter unit translocation Docking domains, but not ACP mutagenesis, perturb alkyne biosynthetic machinery
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Affiliation(s)
- William B Porterfield
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94709, USA
| | - Nannalin Poenateetai
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94709, USA
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94709, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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20
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An in vitro platform for engineering and harnessing modular polyketide synthases. Nat Commun 2020; 11:80. [PMID: 31900404 PMCID: PMC6941969 DOI: 10.1038/s41467-019-13811-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 11/21/2019] [Indexed: 11/15/2022] Open
Abstract
To harness the synthetic power of modular polyketide synthases (PKSs), many aspects of their biochemistry must be elucidated. A robust platform to study these megadalton assembly lines has not yet been described. Here, we in vitro reconstitute the venemycin PKS, a short assembly line that generates an aromatic product. Incubating its polypeptides, VemG and VemH, with 3,5-dihydroxybenzoic acid, ATP, malonate, coenzyme A, and the malonyl-CoA ligase MatB, venemycin production can be monitored by HPLC and NMR. Multi-milligram quantities of venemycin are isolable from dialysis-based reactors without chromatography, and the enzymes can be recycled. Assembly line engineering is performed using pikromycin modules, with synthases designed using the updated module boundaries outperforming those using the traditional module boundaries by over an order of magnitude. Using combinations of VemG, VemH, and their engineered derivatives, as well as the alternate starter unit 3-hydroxybenzoic acid, a combinatorial library of six polyketide products is readily accessed. A robust platform to study modular polyketide synthases (PKSs) in vitro is still unavailable. Here, the authors report the reconstitution of the venemycin PKS, engineer hybrid venemycin/pikromycin PKSs, and obtain much improved yields through employing the updated module boundaries.
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21
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Massicard JM, Soligot C, Weissman KJ, Jacob C. Manipulating polyketide stereochemistry by exchange of polyketide synthase modules. Chem Commun (Camb) 2020; 56:12749-12752. [DOI: 10.1039/d0cc05068g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Exchange of polyketide synthase (PKS) modules by genetic engineering leads to efficient modification of polyketide stereochemistry.
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Affiliation(s)
| | - Claire Soligot
- Université de Lorraine
- UR AFPA
- USC 340 INRAE
- F-54000 Nancy
- France
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22
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Nivina A, Yuet KP, Hsu J, Khosla C. Evolution and Diversity of Assembly-Line Polyketide Synthases. Chem Rev 2019; 119:12524-12547. [PMID: 31838842 PMCID: PMC6935866 DOI: 10.1021/acs.chemrev.9b00525] [Citation(s) in RCA: 151] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Indexed: 12/11/2022]
Abstract
Assembly-line polyketide synthases (PKSs) are among the most complex protein machineries known in nature, responsible for the biosynthesis of numerous compounds used in the clinic. Their present-day diversity is the result of an evolutionary path that has involved the emergence of a multimodular architecture and further diversification of assembly-line PKSs. In this review, we provide an overview of previous studies that investigated PKS evolution and propose a model that challenges the currently prevailing view that gene duplication has played a major role in the emergence of multimodularity. We also analyze the ensemble of orphan PKS clusters sequenced so far to evaluate how large the entire diversity of assembly-line PKS clusters and their chemical products could be. Finally, we examine the existing techniques to access the natural PKS diversity in natural and heterologous hosts and describe approaches to further expand this diversity through engineering.
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Affiliation(s)
- Aleksandra Nivina
- Department
of Chemistry, Stanford ChEM-H, Department of Chemical Engineering Stanford
University, Stanford, California 94305, United States
| | - Kai P. Yuet
- Department
of Chemistry, Stanford ChEM-H, Department of Chemical Engineering Stanford
University, Stanford, California 94305, United States
| | - Jake Hsu
- Department
of Chemistry, Stanford ChEM-H, Department of Chemical Engineering Stanford
University, Stanford, California 94305, United States
| | - Chaitan Khosla
- Department
of Chemistry, Stanford ChEM-H, Department of Chemical Engineering Stanford
University, Stanford, California 94305, United States
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23
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Chevrette MG, Gutiérrez-García K, Selem-Mojica N, Aguilar-Martínez C, Yañez-Olvera A, Ramos-Aboites HE, Hoskisson PA, Barona-Gómez F. Evolutionary dynamics of natural product biosynthesis in bacteria. Nat Prod Rep 2019; 37:566-599. [PMID: 31822877 DOI: 10.1039/c9np00048h] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Covering: 2008 up to 2019The forces of biochemical adaptive evolution operate at the level of genes, manifesting in complex phenotypes and the global biodiversity of proteins and metabolites. While evolutionary histories have been deciphered for some other complex traits, the origins of natural product biosynthesis largely remain a mystery. This fundamental knowledge gap is surprising given the many decades of research probing the genetic, chemical, and biophysical mechanisms of bacterial natural product biosynthesis. Recently, evolutionary thinking has begun to permeate this otherwise mechanistically dominated field. Natural products are now sometimes referred to as 'specialized' rather than 'secondary' metabolites, reinforcing the importance of their biological and ecological functions. Here, we review known evolutionary mechanisms underlying the overwhelming chemical diversity of bacterial secondary metabolism, focusing on enzyme promiscuity and the evolution of enzymatic domains that enable metabolic traits. We discuss the mechanisms that drive the assembly of natural product biosynthetic gene clusters and propose formal definitions for 'specialized' and 'secondary' metabolism. We further explore how biosynthetic gene clusters evolve to synthesize related molecular species, and in turn how the biological and ecological roles that emerge from metabolic diversity are acted on by selection. Finally, we reconcile chemical, functional, and genetic data into an evolutionary model, the dynamic chemical matrix evolutionary hypothesis, in which the relationships between chemical distance, biomolecular activity, and relative fitness shape adaptive landscapes.
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Affiliation(s)
- Marc G Chevrette
- Wisconsin Institute for Discovery, Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA.
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24
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Meinke JL, Simon AJ, Wagner DT, Morrow BR, You S, Ellington AD, Keatinge-Clay AT. Employing 25-Residue Docking Motifs from Modular Polyketide Synthases as Orthogonal Protein Connectors. ACS Synth Biol 2019; 8:2017-2024. [PMID: 31469555 DOI: 10.1021/acssynbio.9b00047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The proteins of trans-acyltransferase modular polyketide synthases (PKSs) self-organize into assembly lines, enabling the multienzyme biosynthesis of complex organic molecules. Docking domains comprised of ∼25 residues at the C- and N-termini of these polypeptides (CDDs and NDDs) help drive this association through the formation of four-helix bundles. Molecular connectors like these are desired in synthetic contexts, such as artificial biocatalytic systems and biomaterials, to orthogonally join proteins. Here, the ability of six CDD/NDD pairs to link non-PKS proteins is examined using green fluorescent protein (GFP) variants. As observed through size-exclusion chromatography and Förster resonance energy transfer (FRET), matched but not mismatched pairs of Venus+CDD and NDD+mTurquoise2 fusion proteins associate with low micromolar affinities.
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25
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Li T, Tripathi A, Yu F, Sherman DH, Rao A. DDAP: docking domain affinity and biosynthetic pathway prediction tool for type I polyketide synthases. Bioinformatics 2019; 36:942-944. [PMID: 31504190 PMCID: PMC8215927 DOI: 10.1093/bioinformatics/btz677] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/25/2019] [Accepted: 08/30/2019] [Indexed: 01/31/2023] Open
Abstract
SUMMARY DDAP is a tool for predicting the biosynthetic pathways of the products of type I modular polyketide synthase (PKS) with the focus on providing a more accurate prediction of the ordering of proteins and substrates in the pathway. In this study, the module docking domain (DD) affinity prediction performance on a hold-out testing dataset reached 0.88 as measured by the area under the receiver operating characteristic (ROC) curve (AUC); the Mean Reciprocal Ranking (MRR) of pathway prediction reached 0.67. DDAP has advantages compared to previous informatics tools in several aspects: (i) it does not rely on large databases, making it a high efficiency tool, (ii) the predicted DD affinity is represented by a probability (0-1), which is more intuitive than raw scores, (iii) its performance is competitive compared to the current popular rule-based algorithm. DDAP is so far the first machine learning based algorithm for type I PKS DD affinity and pathway prediction. We also established the first database of type I modular PKSs, featuring a comprehensive annotation of available docking domains information in bacterial biosynthetic pathways. AVAILABILITY AND IMPLEMENTATION The DDAP database is available at https://tylii.github.io/ddap. The prediction algorithm DDAP is freely available on GitHub (https://github.com/tylii/ddap) and released under the MIT license. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Tingyang Li
- Department of Computational Medicine and Bioinformatics, MI, USA
| | - Ashootosh Tripathi
- Natural Products Discovery Core, Life Sciences Institute, MI, USA,Department of Medicinal Chemistry, MI, USA
| | - Fengan Yu
- Natural Products Discovery Core, Life Sciences Institute, MI, USA
| | - David H Sherman
- Natural Products Discovery Core, Life Sciences Institute, MI, USA,Department of Medicinal Chemistry, MI, USA,Department of Chemistry, Department of Microbiology and Immunology, MI, USA
| | - Arvind Rao
- To whom correspondence should be addressed.
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26
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Feng Y, Yu Z, Zhang S, Xue Z, Huang J, Zhang H, Wan X, Chen A, Wang J. Isolation and Characterization of New 16-Membered Macrolides from the aveA3 Gene Replacement Mutant Strain Streptomyces avermitilis TM24 with Acaricidal and Nematicidal Activities. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:4782-4792. [PMID: 30973721 DOI: 10.1021/acs.jafc.9b00079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Polyketides represent an important class of biologically active and structurally diverse compounds found in nature. They are biosynthesized from acyl CoA precursors by polyketide synthases (PKSs). The use of combinatorial biosynthesis to form hybrid PKSs is considered to be an excellent approach for the development of novel polyketides. Here, 10 new 16-membered macrolide compounds were isolated from the broth of the genetically engineered strain Streptomyces avermitilis TM24, in which the PKS gene aveA3 was seamlessly replaced by the milbemycin PKS gene milA3. Their structures were elucidated on the basis of NMR and MS spectroscopic analyses. The acaricidal and nematicidal activities of them against Tetranychus cinnabarinus and Bursaphelenchus xylophilus were tested. The results indicated that compound 1 had potent acaricidal activity against adult mites with an LC50 value of 0.0022 mg L-1, while compounds 5 and 7 possessed potent nematicidal activity with LC50 values of 4.56 and 4.30 mg L-1, respectively.
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Affiliation(s)
- Youling Feng
- Provincial Joint Engineering Laboratory of Biopesticide Preparation, School of Forestry & Biotechnology , Zhejiang Agricultural and Forestry University , Lin'An 311300 , People's Republic of China
| | - Zhen Yu
- Zhejiang Key Laboratory of Antifungal Drugs , Zhejiang Hisun Pharmaceutical Co., Ltd. , Taizhou 318000 , People's Republic of China
| | - Shaoyong Zhang
- Zhejiang Key Laboratory of Antifungal Drugs , Zhejiang Hisun Pharmaceutical Co., Ltd. , Taizhou 318000 , People's Republic of China
| | - Zhenglian Xue
- College of Biochemical Engineering , Anhui Polytechnic University , Wuhu 241000 , People's Republic of China
| | - Jun Huang
- Zhejiang Key Laboratory of Antifungal Drugs , Zhejiang Hisun Pharmaceutical Co., Ltd. , Taizhou 318000 , People's Republic of China
- Zhejiang Makohs Biotech Co., Ltd. , Taizhou 318000 , People's Republic of China
| | - Hui Zhang
- Zhejiang Key Laboratory of Antifungal Drugs , Zhejiang Hisun Pharmaceutical Co., Ltd. , Taizhou 318000 , People's Republic of China
| | - Xu Wan
- Provincial Joint Engineering Laboratory of Biopesticide Preparation, School of Forestry & Biotechnology , Zhejiang Agricultural and Forestry University , Lin'An 311300 , People's Republic of China
| | - Anliang Chen
- Provincial Joint Engineering Laboratory of Biopesticide Preparation, School of Forestry & Biotechnology , Zhejiang Agricultural and Forestry University , Lin'An 311300 , People's Republic of China
| | - Jidong Wang
- Zhejiang Key Laboratory of Antifungal Drugs , Zhejiang Hisun Pharmaceutical Co., Ltd. , Taizhou 318000 , People's Republic of China
- College of Biochemical Engineering , Anhui Polytechnic University , Wuhu 241000 , People's Republic of China
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27
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Dodge GJ, Maloney FP, Smith JL. Protein-protein interactions in "cis-AT" polyketide synthases. Nat Prod Rep 2018; 35:1082-1096. [PMID: 30188553 PMCID: PMC6207950 DOI: 10.1039/c8np00058a] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: up to the end of 2018 Polyketides are a valuable source of bioactive and clinically important molecules. The biosynthesis of these chemically complex molecules has led to the discovery of equally complex polyketide synthase (PKS) pathways. Crystallography has yielded snapshots of individual catalytic domains, di-domains, and multi-domains from a variety of PKS megasynthases, and cryo-EM studies have provided initial views of a PKS module in a series of defined biochemical states. Here, we review the structural and biochemical results that shed light on the protein-protein interactions critical to catalysis by PKS systems with an embedded acyltransferase. Interactions include those that occur both within and between PKS modules, as well as with accessory enzymes.
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Affiliation(s)
- Greg J Dodge
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA 48109.
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28
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Musiol-Kroll EM, Wohlleben W. Acyltransferases as Tools for Polyketide Synthase Engineering. Antibiotics (Basel) 2018; 7:antibiotics7030062. [PMID: 30022008 PMCID: PMC6164871 DOI: 10.3390/antibiotics7030062] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 07/14/2018] [Accepted: 07/16/2018] [Indexed: 12/16/2022] Open
Abstract
Polyketides belong to the most valuable natural products, including diverse bioactive compounds, such as antibiotics, anticancer drugs, antifungal agents, immunosuppressants and others. Their structures are assembled by polyketide synthases (PKSs). Modular PKSs are composed of modules, which involve sets of domains catalysing the stepwise polyketide biosynthesis. The acyltransferase (AT) domains and their “partners”, the acyl carrier proteins (ACPs), thereby play an essential role. The AT loads the building blocks onto the “substrate acceptor”, the ACP. Thus, the AT dictates which building blocks are incorporated into the polyketide structure. The precursor- and occasionally the ACP-specificity of the ATs differ across the polyketide pathways and therefore, the ATs contribute to the structural diversity within this group of complex natural products. Those features make the AT enzymes one of the most promising tools for manipulation of polyketide assembly lines and generation of new polyketide compounds. However, the AT-based PKS engineering is still not straightforward and thus, rational design of functional PKSs requires detailed understanding of the complex machineries. This review summarizes the attempts of PKS engineering by exploiting the AT attributes for the modification of polyketide structures. The article includes 253 references and covers the most relevant literature published until May 2018.
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Affiliation(s)
- Ewa Maria Musiol-Kroll
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.
| | - Wolfgang Wohlleben
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.
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Synthetic biology of polyketide synthases. ACTA ACUST UNITED AC 2018; 45:621-633. [DOI: 10.1007/s10295-018-2021-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 02/03/2018] [Indexed: 12/31/2022]
Abstract
Abstract
Complex reduced polyketides represent the largest class of natural products that have applications in medicine, agriculture, and animal health. This structurally diverse class of compounds shares a common methodology of biosynthesis employing modular enzyme systems called polyketide synthases (PKSs). The modules are composed of enzymatic domains that share sequence and functional similarity across all known PKSs. We have used the nomenclature of synthetic biology to classify the enzymatic domains and modules as parts and devices, respectively, and have generated detailed lists of both. In addition, we describe the chassis (hosts) that are used to assemble, express, and engineer the parts and devices to produce polyketides. We describe a recently developed software tool to design PKS system and provide an example of its use. Finally, we provide perspectives of what needs to be accomplished to fully realize the potential that synthetic biology approaches bring to this class of molecules.
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Liu T, Mazmouz R, Neilan BA. An In Vitro and In Vivo Study of Broad-Range Phosphopantetheinyl Transferases for Heterologous Expression of Cyanobacterial Natural Products. ACS Synth Biol 2018; 7:1143-1151. [PMID: 29562128 DOI: 10.1021/acssynbio.8b00091] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phosphopantetheinyl transferases catalyze the post-translational modification of carrier proteins involved in both primary and secondary metabolism. The functional expression of polyketide synthases and nonribosomal peptide synthetases requires the activation of all carrier protein domains by phosphopantetheinyl transferases. Here we describe the characterization of five bacterial phosphopantetheinyl transferases by their substrate specificity and catalytic efficiency of four cyanobacterial carrier proteins. Comparative in vitro phosphopantetheinylation analysis showed Sfp possesses the highest catalytic efficiency over various carrier proteins. In vivo coexpression of phosphopantetheinyl transferases with carrier proteins revealed a broad range substrate specificity of phosphopantetheinyl transferases; all studied phosphopantetheinyl transferases were capable of converting apo- carrier proteins, sourced from diverse biosynthetic enzymes, to their active holo form. Phosphopantetheinyl transferase coexpression with the hybrid nonribosomal peptide synthetases/polyketide synthases responsible for microcystin biosynthesis confirmed that the higher in vitro activity of Sfp translated in vivo to a higher yield of production.
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Affiliation(s)
- Tianzhe Liu
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Rabia Mazmouz
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW 2308, Australia
| | - Brett A. Neilan
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW 2308, Australia
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31
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Wang F, Zhou H, Olademehin OP, Kim SJ, Tao P. Insights into Key Interactions between Vancomycin and Bacterial Cell Wall Structures. ACS OMEGA 2018; 3:37-45. [PMID: 29399648 PMCID: PMC5793038 DOI: 10.1021/acsomega.7b01483] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 12/19/2017] [Indexed: 05/18/2023]
Abstract
Vancomycin is a glycopeptide antibiotic used for the treatment of serious infections by Gram-positive pathogens. Vancomycin inhibits cell wall biosynthesis by targeting the d-Ala-d-Ala terminus of peptidoglycan (PG). The highly cross-linked heptapeptide aglycon structure of vancomycin is the d-Ala-d-Ala binding site. The first residue of vancomycin is N-methyl-leucine, which is crucial for the dipeptide binding. The removal of N-methyl-leucine by Edman degradation results in desleucyl-vancomycin devoid of antimicrobial activities. To investigate the function of N-methyl-leucine for the dipeptide binding in vancomycin, molecular dynamics simulations of vancomycin and three N-terminus-modified vancomycin derivatives: desleucyl-vancomycin, vancomycinNtoC, and vancomycinSar, binding to a PG unit of the sequence l-Ala-d-iso-Gln-l-Lys-d-Ala-d-Ala with an intact pentaglycine bridge structure attached to the bridge link of l-Lys were carried out. Glycopeptide-PG binding interactions were characterized by root-mean-square-deviation contour analysis of atomic positions in vancomycin and its three analogues bound to a PG unit. The overall sampling space for four glycopeptide-PG complexes shows four distinct distributions with a continuous change between the conformational spaces. The hydrogen bond analyses show that multiple hydrogen bonds between the d-Ala-d-Ala and the vancomycin aglycon structure strengthened the dipeptide binding. The simulations revealed that the removal or chemical modification of N-methyl-leucine significantly weakens the dipeptide binding to the aglycon structure and provides interesting structural insights into glycopeptide-PG binding interactions.
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Affiliation(s)
- Feng Wang
- Department
of Chemistry, Center for Drug Discovery, Design, and Delivery (CD4),
Center for Scientific Computation, Southern
Methodist University, Dallas, Texas 75275, United States
| | - Hongyu Zhou
- Department
of Chemistry, Center for Drug Discovery, Design, and Delivery (CD4),
Center for Scientific Computation, Southern
Methodist University, Dallas, Texas 75275, United States
| | - Olatunde P. Olademehin
- Department
of Chemistry and Biochemistry, Baylor University, Waco, Texas 76706, United States
| | - Sung Joon Kim
- Department
of Chemistry and Biochemistry, Baylor University, Waco, Texas 76706, United States
| | - Peng Tao
- Department
of Chemistry, Center for Drug Discovery, Design, and Delivery (CD4),
Center for Scientific Computation, Southern
Methodist University, Dallas, Texas 75275, United States
- E-mail: . Phone: 1-214-768-8802. Fax: 1-214-768-4089 (P.T.)
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Miyanaga A, Kudo F, Eguchi T. Protein–protein interactions in polyketide synthase–nonribosomal peptide synthetase hybrid assembly lines. Nat Prod Rep 2018; 35:1185-1209. [DOI: 10.1039/c8np00022k] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The protein–protein interactions in polyketide synthase–nonribosomal peptide synthetase hybrids are summarized and discussed.
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Affiliation(s)
- Akimasa Miyanaga
- Department of Chemistry
- Tokyo Institute of Technology
- Tokyo 152-8551
- Japan
| | - Fumitaka Kudo
- Department of Chemistry
- Tokyo Institute of Technology
- Tokyo 152-8551
- Japan
| | - Tadashi Eguchi
- Department of Chemistry
- Tokyo Institute of Technology
- Tokyo 152-8551
- Japan
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33
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Klaus M, Grininger M. Engineering strategies for rational polyketide synthase design. Nat Prod Rep 2018; 35:1070-1081. [DOI: 10.1039/c8np00030a] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
In this review, we highlight strategies in engineering polyketide synthases (PKSs). We focus on important protein–protein interactions that constitute an intact PKS assembly line.
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Affiliation(s)
- Maja Klaus
- Institute of Organic Chemistry and Chemical Biology
- Buchmann Institute for Molecular Life Sciences
- Cluster of Excellence for Macromolecular Complexes
- Goethe University Frankfurt
- 60438 Frankfurt am Main
| | - Martin Grininger
- Institute of Organic Chemistry and Chemical Biology
- Buchmann Institute for Molecular Life Sciences
- Cluster of Excellence for Macromolecular Complexes
- Goethe University Frankfurt
- 60438 Frankfurt am Main
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Barajas JF, Blake-Hedges JM, Bailey CB, Curran S, Keasling JD. Engineered polyketides: Synergy between protein and host level engineering. Synth Syst Biotechnol 2017; 2:147-166. [PMID: 29318196 PMCID: PMC5655351 DOI: 10.1016/j.synbio.2017.08.005] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 08/26/2017] [Accepted: 08/26/2017] [Indexed: 01/01/2023] Open
Abstract
Metabolic engineering efforts toward rewiring metabolism of cells to produce new compounds often require the utilization of non-native enzymatic machinery that is capable of producing a broad range of chemical functionalities. Polyketides encompass one of the largest classes of chemically diverse natural products. With thousands of known polyketides, modular polyketide synthases (PKSs) share a particularly attractive biosynthetic logic for generating chemical diversity. The engineering of modular PKSs could open access to the deliberate production of both existing and novel compounds. In this review, we discuss PKS engineering efforts applied at both the protein and cellular level for the generation of a diverse range of chemical structures, and we examine future applications of PKSs in the production of medicines, fuels and other industrially relevant chemicals.
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Key Words
- ACP, Acyl carrier protein
- AT, Acyltransferase
- CoL, CoA-Ligase
- Commodity chemical
- DE, Dimerization element
- DEBS, 6-deoxyerythronolide B synthase
- DH, Dehydratase
- ER, Enoylreductase
- FAS, Fatty acid synthases
- KR, Ketoreductase
- KS, Ketosynthase
- LM, Loading module
- LTTR, LysR-type transcriptional regulator
- Metabolic engineering
- Natural products
- PCC, Propionyl-CoA carboxylase
- PDB, Precursor directed biosynthesis
- PK, Polyketide
- PKS, Polyketide synthase
- Polyketide
- Polyketide synthase
- R, Reductase domain
- SARP, Streptomyces antibiotic regulatory protein
- SNAC, N-acetylcysteamine
- Synthetic biology
- TE, Thioesterase
- TKL, Triketide lactone
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Affiliation(s)
| | | | - Constance B. Bailey
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Samuel Curran
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Comparative Biochemistry Graduate Group, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jay. D. Keasling
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- QB3 Institute, University of California, Berkeley, Emeryville, CA 94608, USA
- Department of Chemical & Biomolecular Engineering, Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, DK2970 Horsholm, Denmark
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35
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Abstract
X-ray scattering is uniquely suited to the study of disordered systems and thus has the potential to provide insight into dynamic processes where diffraction methods fail. In particular, while X-ray crystallography has been a staple of structural biology for more than half a century and will continue to remain so, a major limitation of this technique has been the lack of dynamic information. Solution X-ray scattering has become an invaluable tool in structural and mechanistic studies of biological macromolecules where large conformational changes are involved. Such systems include allosteric enzymes that play key roles in directing metabolic fluxes of biochemical pathways, as well as large, assembly-line type enzymes that synthesize secondary metabolites with pharmaceutical applications. Furthermore, crystallography has the potential to provide information on protein dynamics via the diffuse scattering patterns that are overlaid with Bragg diffraction. Historically, these patterns have been very difficult to interpret, but recent advances in X-ray detection have led to a renewed interest in diffuse scattering analysis as a way to probe correlated motions. Here, we will review X-ray scattering theory and highlight recent advances in scattering-based investigations of protein solutions and crystals, with a particular focus on complex enzymes.
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Affiliation(s)
- Steve P Meisburger
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - William C Thomas
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - Maxwell B Watkins
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - Nozomi Ando
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
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36
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Engineered biosynthesis of milbemycins in the avermectin high-producing strain Streptomyces avermitilis. Microb Cell Fact 2017; 16:9. [PMID: 28095865 PMCID: PMC5240415 DOI: 10.1186/s12934-017-0626-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 01/04/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Milbemycins, produced from Streptomyces hygroscopicus subsp. aureolacrimosus and Streptomyces bingchenggensis, are 16-membered macrolides that share structural similarity with avermectin produced from Streptomyces avermitilis. Milbemycins possess strong acaricidal, insecticidal, and anthelmintic activities but low toxicity. Due to the high commercial value of the milbemycins and increasing resistance to the avermectins and their derivatives, it is imperative to develop an efficient combinatorial biosynthesis system exploiting an overproduction host strain to produce the milbemycins and novel analogs in large quantities. RESULTS The respective replacement of AveA1 and AveA3 (or module 7 in AveA3) of the avermectin polyketide synthase (PKS) in the avermectin high-producing strain S. avermitilis SA-01 with MilA1 and MilA3 (or module 7 in MilA3) of the milbemycin PKS resulted in the production of milbemycins A3, A4, and D in small amounts and their respective C5-O-methylated congener milbemycins B2, B3, and G as major products with total titers of approximately 292 mg/l. Subsequent inactivation of the C5-O-methyltransferase AveD led to a production of milbemycins A3/A4 (the main components of the commercial product milbemectin) in approximately 225 and 377 mg/l in the flask and 5 l fermenter culture, respectively, along with trace amounts of milbemycin D. CONCLUSIONS We demonstrated that milbemycin biosynthesis can be engineered in the avermectin-producing S. avermitilis by combinatorial biosynthesis with only a slight decrease in its production level. Application of a similar strategy utilizing higher producing industrial strains will provide a more efficient combinatorial biosynthesis system based on S. avermitilis for further enhanced production of the milbemycins and their novel analogs with improved insecticidal potential.
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37
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Robbins T, Liu YC, Cane DE, Khosla C. Structure and mechanism of assembly line polyketide synthases. Curr Opin Struct Biol 2016; 41:10-18. [PMID: 27266330 PMCID: PMC5136517 DOI: 10.1016/j.sbi.2016.05.009] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 05/19/2016] [Accepted: 05/20/2016] [Indexed: 11/16/2022]
Abstract
Assembly line polyketide synthases (PKSs) are remarkable biosynthetic machines with considerable potential for structure-based engineering. Several types of protein-protein interactions, both within and between PKS modules, play important roles in the catalytic cycle of a multimodular PKS. Additionally, vectorial biosynthesis is enabled by the energetic coupling of polyketide chain elongation to the channeling of intermediates between successive modules. A combination of high-resolution analysis of smaller PKS components and lower resolution characterization of intact modules and bimodules has yielded insights into the structure and organization of a prototypical assembly line PKS. This review discusses our understanding of key structure-function relationships in this family of megasynthases, along with a recap of key unanswered questions in the field.
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Affiliation(s)
- Thomas Robbins
- Department of Chemistry, Stanford University, Stanford, CA 94305, United States
| | - Yu-Chen Liu
- Department of Chemistry, Stanford University, Stanford, CA 94305, United States
| | - David E Cane
- Department of Chemistry, Brown University, Providence, RI 02912-9108, United States
| | - Chaitan Khosla
- Department of Chemistry, Stanford University, Stanford, CA 94305, United States; Department of Chemical Engineering, Stanford University, Stanford, CA 94305, United States.
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38
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Huang Y, Tang GL, Pan G, Chang CY, Shen B. Characterization of the Ketosynthase and Acyl Carrier Protein Domains at the LnmI Nonribosomal Peptide Synthetase-Polyketide Synthase Interface for Leinamycin Biosynthesis. Org Lett 2016; 18:4288-91. [PMID: 27541042 PMCID: PMC5013926 DOI: 10.1021/acs.orglett.6b02033] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Leinamycin (LNM) is biosynthesized by a hybrid nonribosomal peptide synthetase (NRPS)-acyltransferase (AT)-less type I polyketide synthase (PKS). Characterization of LnmI revealed ketosynthase (KS)-acyl carrier protein (ACP)-KS domains at the NRPS-PKS interface. Inactivation of the KS domain or ACP domain in vivo abolished LNM production, and the ACP domain can be phosphopantetheinylated in vitro. The LnmI KS-ACP-KS architecture represents a new mechanism for functional crosstalk between NRPS and AT-less type I PKS in the biosynthesis of hybrid peptide-polyketide natural products.
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Affiliation(s)
- Yong Huang
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin , Madison, Wisconsin 53705, United States
| | - Gong-Li Tang
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin , Madison, Wisconsin 53705, United States
| | | | | | - Ben Shen
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin , Madison, Wisconsin 53705, United States
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39
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Lin Z, Chen D, Liu W. Biosynthesis-based artificial evolution of microbial natural products. Sci China Chem 2016. [DOI: 10.1007/s11426-016-0062-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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40
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41
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Biosynthetic Genes for the Tetrodecamycin Antibiotics. J Bacteriol 2016; 198:1965-1973. [PMID: 27137499 DOI: 10.1128/jb.00140-16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 04/26/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED We recently described 13-deoxytetrodecamycin, a new member of the tetrodecamycin family of antibiotics. A defining feature of these molecules is the presence of a five-membered lactone called a tetronate ring. By sequencing the genome of a producer strain, Streptomyces sp. strain WAC04657, and searching for a gene previously implicated in tetronate ring formation, we identified the biosynthetic genes responsible for producing 13-deoxytetrodecamycin (the ted genes). Using the ted cluster in WAC04657 as a reference, we found related clusters in three other organisms: Streptomyces atroolivaceus ATCC 19725, Streptomyces globisporus NRRL B-2293, and Streptomyces sp. strain LaPpAH-202. Comparing the four clusters allowed us to identify the cluster boundaries. Genetic manipulation of the cluster confirmed the involvement of the ted genes in 13-deoxytetrodecamycin biosynthesis and revealed several additional molecules produced through the ted biosynthetic pathway, including tetrodecamycin, dihydrotetrodecamycin, and another, W5.9, a novel molecule. Comparison of the bioactivities of these four molecules suggests that they may act through the covalent modification of their target(s). IMPORTANCE The tetrodecamycins are a distinct subgroup of the tetronate family of secondary metabolites. Little is known about their biosynthesis or mechanisms of action, making them an attractive subject for investigation. In this paper we present the biosynthetic gene cluster for 13-deoxytetrodecamycin in Streptomyces sp. strain WAC04657. We identify related clusters in several other organisms and show that they produce related molecules.
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42
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Klaus M, Ostrowski MP, Austerjost J, Robbins T, Lowry B, Cane DE, Khosla C. Protein-Protein Interactions, Not Substrate Recognition, Dominate the Turnover of Chimeric Assembly Line Polyketide Synthases. J Biol Chem 2016; 291:16404-15. [PMID: 27246853 DOI: 10.1074/jbc.m116.730531] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Indexed: 01/08/2023] Open
Abstract
The potential for recombining intact polyketide synthase (PKS) modules has been extensively explored. Both enzyme-substrate and protein-protein interactions influence chimeric PKS activity, but their relative contributions are unclear. We now address this issue by studying a library of 11 bimodular and 8 trimodular chimeric PKSs harboring modules from the erythromycin, rifamycin, and rapamycin synthases. Although many chimeras yielded detectable products, nearly all had specific activities below 10% of the reference natural PKSs. Analysis of selected bimodular chimeras, each with the same upstream module, revealed that turnover correlated with the efficiency of intermodular chain translocation. Mutation of the acyl carrier protein (ACP) domain of the upstream module in one chimera at a residue predicted to influence ketosynthase-ACP recognition led to improved turnover. In contrast, replacement of the ketoreductase domain of the upstream module by a paralog that produced the enantiomeric ACP-bound diketide caused no changes in processing rates for each of six heterologous downstream modules compared with those of the native diketide. Taken together, these results demonstrate that protein-protein interactions play a larger role than enzyme-substrate recognition in the evolution or design of catalytically efficient chimeric PKSs.
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Affiliation(s)
- Maja Klaus
- From the Departments of Chemistry and Chemical Engineering and Stanford ChEM-H, Stanford University, Stanford, California 94305 and
| | - Matthew P Ostrowski
- From the Departments of Chemistry and Chemical Engineering and Stanford ChEM-H, Stanford University, Stanford, California 94305 and
| | - Jonas Austerjost
- From the Departments of Chemistry and Chemical Engineering and Stanford ChEM-H, Stanford University, Stanford, California 94305 and
| | - Thomas Robbins
- From the Departments of Chemistry and Chemical Engineering and Stanford ChEM-H, Stanford University, Stanford, California 94305 and
| | - Brian Lowry
- From the Departments of Chemistry and Chemical Engineering and Stanford ChEM-H, Stanford University, Stanford, California 94305 and
| | - David E Cane
- the Department of Chemistry, Brown University, Providence, Rhode Island 02192-9108
| | - Chaitan Khosla
- From the Departments of Chemistry and Chemical Engineering and Stanford ChEM-H, Stanford University, Stanford, California 94305 and
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43
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Structural insights into the regulation of NADPH binding to reductase domains of nonribosomal peptide synthetases: A concerted loop movement model. J Struct Biol 2016; 194:368-74. [PMID: 26993465 DOI: 10.1016/j.jsb.2016.03.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 03/15/2016] [Accepted: 03/15/2016] [Indexed: 11/22/2022]
Abstract
The termination module of nonribosomal peptide synthetases (NRPS) and polyketide synthases (PKS) offloads the final product as an acid (occasionally also accompanied by cyclization) upon hydrolysis by employing thioesterase domains (TE-domains). Reductase domains (R-domains) of short-chain dehydrogenase/reductase (SDR) family offer an alternative offloading mechanism by reducing 4'-phosphopantetheine (4'-PPant) arm-tethered peptidyl chain, a thioester, to an aldehyde or an alcohol. Recent studies have highlighted their functional importance, for instance in the glycopeptidolipid (GPL) biosynthesis of Mycobacterium smegmatis, where the resulting alcoholic group is the site for subsequent modifications such as glycosylations. The mechanistic understanding of how these R-domains function in the context of multi-modular NRPS and PKS is poorly understood. In this study, conformational differences in functionally important loops, not reported previously, were identified in a new crystal form of R-domain which may be relevant to functioning in the context of assembly-line NRPS and PKS enzymology. Here, we propose a concerted loop movement model that allows gating of cofactor binding to these enzymes, enabling the release of the final product only after the substrate has reached the active site during biosynthesis, and therefore distinct from a canonical single domain SDR family of enzymes.
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44
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Dorival J, Annaval T, Risser F, Collin S, Roblin P, Jacob C, Gruez A, Chagot B, Weissman KJ. Characterization of Intersubunit Communication in the Virginiamycin trans-Acyl Transferase Polyketide Synthase. J Am Chem Soc 2016; 138:4155-67. [DOI: 10.1021/jacs.5b13372] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Jonathan Dorival
- UMR
7365, Ingénierie Moléculaire et Physiopathologie Articulaire
(IMoPA), CNRS-Université de Lorraine, Biopôle de l’Université de Lorraine, Campus Biologie Santé, 9
Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy CEDEX, France
| | - Thibault Annaval
- UMR
7365, Ingénierie Moléculaire et Physiopathologie Articulaire
(IMoPA), CNRS-Université de Lorraine, Biopôle de l’Université de Lorraine, Campus Biologie Santé, 9
Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy CEDEX, France
| | - Fanny Risser
- UMR
7365, Ingénierie Moléculaire et Physiopathologie Articulaire
(IMoPA), CNRS-Université de Lorraine, Biopôle de l’Université de Lorraine, Campus Biologie Santé, 9
Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy CEDEX, France
| | - Sabrina Collin
- UMR
7365, Ingénierie Moléculaire et Physiopathologie Articulaire
(IMoPA), CNRS-Université de Lorraine, Biopôle de l’Université de Lorraine, Campus Biologie Santé, 9
Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy CEDEX, France
| | - Pierre Roblin
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin BP 48, 91192 Gif-sur-Yvette CEDEX, France
- UR1268 Biopolymères, Interactions Assemblages (BIA), INRA, Rue de la Géraudière
BP 71627, 44316 Nantes CEDEX 3, France
| | - Christophe Jacob
- UMR
7365, Ingénierie Moléculaire et Physiopathologie Articulaire
(IMoPA), CNRS-Université de Lorraine, Biopôle de l’Université de Lorraine, Campus Biologie Santé, 9
Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy CEDEX, France
| | - Arnaud Gruez
- UMR
7365, Ingénierie Moléculaire et Physiopathologie Articulaire
(IMoPA), CNRS-Université de Lorraine, Biopôle de l’Université de Lorraine, Campus Biologie Santé, 9
Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy CEDEX, France
| | - Benjamin Chagot
- UMR
7365, Ingénierie Moléculaire et Physiopathologie Articulaire
(IMoPA), CNRS-Université de Lorraine, Biopôle de l’Université de Lorraine, Campus Biologie Santé, 9
Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy CEDEX, France
| | - Kira J. Weissman
- UMR
7365, Ingénierie Moléculaire et Physiopathologie Articulaire
(IMoPA), CNRS-Université de Lorraine, Biopôle de l’Université de Lorraine, Campus Biologie Santé, 9
Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy CEDEX, France
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45
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Lowry B, Li X, Robbins T, Cane DE, Khosla C. A Turnstile Mechanism for the Controlled Growth of Biosynthetic Intermediates on Assembly Line Polyketide Synthases. ACS CENTRAL SCIENCE 2016; 2:14-20. [PMID: 26878060 PMCID: PMC4731828 DOI: 10.1021/acscentsci.5b00321] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Indexed: 05/09/2023]
Abstract
Vectorial polyketide biosynthesis on an assembly line polyketide synthase is the most distinctive property of this family of biological machines, while providing the key conceptual tool for the bioinformatic decoding of new antibiotic pathways. We now show that the action of the entire assembly line is synchronized by a previously unrecognized turnstile mechanism that prevents the ketosynthase domain of each module from being acylated by a new polyketide chain until the product of the prior catalytic cycle has been passed to the downstream module from the corresponding acyl carrier protein domain. The turnstile is closed by virtue of tight coupling to the signature decarboxylative condensation reaction catalyzed by the ketosynthase domain of each polyketide synthase module. Reopening of the turnstile is coupled to the eventual chain translocation step that vacates the module. At the maximal rate of substrate turnover, one would expect the chain release step to initiate a cascade of chain translocation events that sequentially migrate back upstream, thereby repriming each module and setting up the assembly line for the next round of polyketide chain elongation.
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Affiliation(s)
- Brian Lowry
- Departments
of Chemistry and Chemical Engineering, Stanford
University, Stanford, California 94305, United States
| | - Xiuyuan Li
- Departments
of Chemistry and Chemical Engineering, Stanford
University, Stanford, California 94305, United States
| | - Thomas Robbins
- Departments
of Chemistry and Chemical Engineering, Stanford
University, Stanford, California 94305, United States
| | - David E. Cane
- Department
of Chemistry, Brown University, Providence, Rhode Island 02912-9108, United States
| | - Chaitan Khosla
- Departments
of Chemistry and Chemical Engineering, Stanford
University, Stanford, California 94305, United States
- E-mail: . Tel: (650) 723-6538
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The substrate promiscuity of a phosphopantetheinyl transferase SchPPT for coenzyme A derivatives and acyl carrier proteins. Arch Microbiol 2016; 198:193-7. [PMID: 26748983 DOI: 10.1007/s00203-015-1179-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/24/2015] [Accepted: 12/09/2015] [Indexed: 10/22/2022]
Abstract
Phosphopantetheinyl transferases (PPTases) catalyze the posttranslational modification of acyl carrier proteins (ACPs) in fatty acid synthases (FASs), ACPs in polyketide synthases, and peptidyl carrier proteins (PCPs) in nonribosomal peptide synthetases (NRPSs) in all organisms. Some bacterial PPTases have broad substrate specificities for ACPs/PCPs and/or coenzyme A (CoA)/CoA analogs, facilitating their application in metabolite production in hosts and/or labeling of ACPs/PCPs, respectively. Here, a group II PPTase SchPPT from Streptomyces chattanoogensis L10 was characterized to accept a heterologous ACP and acetyl-CoA. Thus, SchPPT is a promiscuous PPTase and may be used on polyketide production in heterologous bacterial host and labeling of ACPs.
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47
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Weissman KJ. Genetic engineering of modular PKSs: from combinatorial biosynthesis to synthetic biology. Nat Prod Rep 2016; 33:203-30. [DOI: 10.1039/c5np00109a] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This reviews covers on-going efforts at engineering the gigantic modular polyketide synthases (PKSs), highlighting both notable successes and failures.
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Affiliation(s)
- Kira J. Weissman
- UMR 7365
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA)
- CNRS-Université de Lorraine
- Biopôle de l'Université de Lorraine
- 54505 Vandœuvre-lès-Nancy Cedex
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48
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Sanyal S, Coker DF, MacKernan D. How flexible is a protein: simple estimates using FRET microscopy. MOLECULAR BIOSYSTEMS 2016; 12:2988-91. [DOI: 10.1039/c6mb00410e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A simple numerical procedure to measure the flexibility of linker proteins used in unimolecular FRET probes.
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49
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Affiliation(s)
- Sarah E. O'Connor
- The John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom;
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50
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Integrating mass spectrometry and genomics for cyanobacterial metabolite discovery. J Ind Microbiol Biotechnol 2015; 43:313-24. [PMID: 26578313 DOI: 10.1007/s10295-015-1705-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 10/03/2015] [Indexed: 01/01/2023]
Abstract
Filamentous marine cyanobacteria produce bioactive natural products with both potential therapeutic value and capacity to be harmful to human health. Genome sequencing has revealed that cyanobacteria have the capacity to produce many more secondary metabolites than have been characterized. The biosynthetic pathways that encode cyanobacterial natural products are mostly uncharacterized, and lack of cyanobacterial genetic tools has largely prevented their heterologous expression. Hence, a combination of cutting edge and traditional techniques has been required to elucidate their secondary metabolite biosynthetic pathways. Here, we review the discovery and refined biochemical understanding of the olefin synthase and fatty acid ACP reductase/aldehyde deformylating oxygenase pathways to hydrocarbons, and the curacin A, jamaicamide A, lyngbyabellin, columbamide, and a trans-acyltransferase macrolactone pathway encoding phormidolide. We integrate into this discussion the use of genomics, mass spectrometric networking, biochemical characterization, and isolation and structure elucidation techniques.
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