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Patel KD, Oliver RA, Lichstrahl MS, Li R, Townsend CA, Gulick AM. The structure of the monobactam-producing thioesterase domain of SulM forms a unique complex with the upstream carrier protein domain. J Biol Chem 2024:107489. [PMID: 38908753 DOI: 10.1016/j.jbc.2024.107489] [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: 03/05/2024] [Revised: 06/01/2024] [Accepted: 06/12/2024] [Indexed: 06/24/2024] Open
Abstract
Nonribosomal peptide synthetases (NRPSs) are responsible for the production of important biologically active peptides. The large, multidomain NRPSs operate through an assembly line strategy in which the growing peptide is tethered to carrier domains that deliver the intermediates to neighboring catalytic domains. While most NRPS domains catalyze standard chemistry of amino acid activation, peptide bond formation and product release, some canonical NRPS catalytic domains promote unexpected chemistry. The paradigm monobactam antibiotic sulfazecin is produced through the activity of a terminal thioesterase domain of SulM, which catalyzes an unusual β-lactam forming reaction in which the nitrogen of the C-terminal N-sulfo-2,3-diaminopropionate residue attacks its thioester tether to release the monobactam product. We have determined the structure of the thioesterase domain as both a free-standing domain and a didomain complex with the upstream holo peptidyl-carrier domain. The position of variant lid helices results in an active site pocket that is quite constrained, a feature that is likely necessary to orient the substrate properly for β-lactam formation. Modeling of a sulfazecin tripeptide into the active site identifies a plausible binding mode identifying potential interactions for the sulfamate and the peptide backbone with Arg2849 and Asn2819, respectively. The overall structure is similar to the β-lactone forming thioesterase domain that is responsible for similar ring closure in the production of obafluorin. We further use these insights to enable bioinformatic analysis to identify additional, uncharacterized β-lactam-forming biosynthetic gene clusters by genome mining.
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Affiliation(s)
- Ketan D Patel
- Department of Structural Biology, University at Buffalo, SUNY, Buffalo, NY, 14203, USA
| | - Ryan A Oliver
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218 USA
| | - Michael S Lichstrahl
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218 USA
| | - Rongfeng Li
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218 USA
| | - Craig A Townsend
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218 USA
| | - Andrew M Gulick
- Department of Structural Biology, University at Buffalo, SUNY, Buffalo, NY, 14203, USA.
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2
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Patel KD, Oliver RA, Lichstrahl MS, Li R, Townsend CA, Gulick AM. The structure of the monobactam-producing thioesterase domain of SulM forms a unique complex with the upstream carrier protein domain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.06.588331. [PMID: 38617275 PMCID: PMC11014566 DOI: 10.1101/2024.04.06.588331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Nonribosomal peptide synthetases (NRPSs) are responsible for the production of important biologically active peptides. The large, multidomain NRPSs operate through an assembly line strategy in which the growing peptide is tethered to carrier domains that deliver the intermediates to neighboring catalytic domains. While most NRPS domains catalyze standard chemistry of amino acid activation, peptide bond formation and product release, some canonical NRPS catalytic domains promote unexpected chemistry. The paradigm monobactam antibiotic sulfazecin is produced through the activity of a terminal thioesterase domain that catalyzes an unusual β-lactam forming reaction in which the nitrogen of the C-terminal N-sulfo-2,3-diaminopropionate residue attacks its thioester tether to release the β-lactam product. We have determined the structure of the thioesterase domain as both a free-standing domain and a didomain complex with the upstream holo peptidyl-carrier domain. The structure illustrates a constrained active site that orients the substrate properly for β-lactam formation. In this regard, the structure is similar to the β-lactone forming thioesterase domain responsible for the production of obafluorin. Analysis of the structure identifies features that are responsible for this four-membered ring closure and enable bioinformatic analysis to identify additional, uncharacterized β-lactam-forming biosynthetic gene clusters by genome mining.
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Affiliation(s)
- Ketan D. Patel
- Department of Structural Biology, University at Buffalo, SUNY, Buffalo, NY, 14203, USA
| | - Ryan A. Oliver
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218 USA
| | - Michael S. Lichstrahl
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218 USA
| | - Rongfeng Li
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218 USA
| | - Craig A. Townsend
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218 USA
| | - Andrew M. Gulick
- Department of Structural Biology, University at Buffalo, SUNY, Buffalo, NY, 14203, USA
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3
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Peng YJ, Chen Y, Zhou CZ, Miao W, Jiang YL, Zeng X, Zhang CC. Modular catalytic activity of nonribosomal peptide synthetases depends on the dynamic interaction between adenylation and condensation domains. Structure 2024; 32:440-452.e4. [PMID: 38340732 DOI: 10.1016/j.str.2024.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/22/2023] [Accepted: 01/16/2024] [Indexed: 02/12/2024]
Abstract
Nonribosomal peptide synthetases (NRPSs) are large multidomain enzymes for the synthesis of a variety of bioactive peptides in a modular and pipelined fashion. Here, we investigated how the condensation (C) domain and the adenylation (A) domain cooperate with each other for the efficient catalytic activity in microcystin NRPS modules. We solved two crystal structures of the microcystin NRPS modules, representing two different conformations in the NRPS catalytic cycle. Our data reveal that the dynamic interaction between the C and the A domains in these modules is mediated by the conserved "RXGR" motif, and this interaction is important for the adenylation activity. Furthermore, the "RXGR" motif-mediated dynamic interaction and its functional regulation are prevalent in different NRPSs modules possessing both the A and the C domains. This study provides new insights into the catalytic mechanism of NRPSs and their engineering strategy for synthetic peptides with different structures and properties.
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Affiliation(s)
- Ye-Jun Peng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, People's Republic of China; University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yuxing Chen
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, People's Republic of China
| | - Cong-Zhao Zhou
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, People's Republic of China
| | - Wei Miao
- Key Laboratory of Lake and Watershed Science for Water Security, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China; Hubei Hongshan Laboratory, Wuhan 430070, People's Republic of China
| | - Yong-Liang Jiang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, People's Republic of China.
| | - Xiaoli Zeng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, People's Republic of China; Key Laboratory of Lake and Watershed Science for Water Security, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China.
| | - Cheng-Cai Zhang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, People's Republic of China; Key Laboratory of Lake and Watershed Science for Water Security, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China; Hubei Hongshan Laboratory, Wuhan 430070, People's Republic of China.
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4
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Kihika JK, Pearman JK, Wood SA, Rhodes LL, Smith KF, Miller MR, Butler J, Ryan KG. Fatty acid production and associated gene pathways are altered by increased salinity and dimethyl sulfoxide treatments during cryopreservation of Symbiodinium pilosum (Symbiodiniaceae). Cryobiology 2024; 114:104855. [PMID: 38301952 DOI: 10.1016/j.cryobiol.2024.104855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 01/29/2024] [Indexed: 02/03/2024]
Abstract
The Symbiodinium genus is ancestral among other Symbiodiniaceae lineages with species that are both symbiotic and free living. Changes in marine ecosystems threaten their existence and crucial ecological roles. Cryopreservation offers an avenue for their long-term storage for future habitat restoration after coral bleaching. In our previous study we demonstrated that high salinity treatments of Symbiodiniaceae isolates led to changes in their fatty acid (FA) profiles and higher cell viabilities after cryopreservation. In this study, we investigated the role of increased salinity on FA production and the genes involved in FA biosynthesis and degradation pathways during the cryopreservation of Symbiodinium pilosum. Overall, there was a twofold increase in mass of FAs produced by S. pilosum after being cultured in medium with increased salinity (54 parts per thousand; ppt). Dimethyl sulfoxide (Me2SO) led to a ninefold increase of FAs in standard salinity (SS) treatment, compared to a fivefold increase in increased salinity (IS) treatments. The mass of the FA classes returned to baseline during recovery. Transcriptomic analyses showed an acyl carrier protein gene was significantly upregulated after Me2SO treatment in the SS cultures. Cytochrome P450 reductase genes were significantly down regulated after Me2SO addition in SS treatment preventing FA degradation. These changes in the expression of FA biosynthesis and degradation genes contributed to more FAs in SS treated isolates. Understanding how increased salinity changes FA production and the roles of specific genes in regulating FA pathways will help improve current freezing protocols for Symbiodiniaceae and other marine microalgae.
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Affiliation(s)
- Joseph K Kihika
- Cawthron Institute, Private Bag 2, Nelson, 7042, New Zealand; School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand.
| | - John K Pearman
- Cawthron Institute, Private Bag 2, Nelson, 7042, New Zealand
| | - Susanna A Wood
- Cawthron Institute, Private Bag 2, Nelson, 7042, New Zealand
| | - Lesley L Rhodes
- Cawthron Institute, Private Bag 2, Nelson, 7042, New Zealand
| | - Kirsty F Smith
- Cawthron Institute, Private Bag 2, Nelson, 7042, New Zealand; School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | | | - Juliette Butler
- Cawthron Institute, Private Bag 2, Nelson, 7042, New Zealand
| | - Ken G Ryan
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand
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5
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Buyachuihan L, Stegemann F, Grininger M. How Acyl Carrier Proteins (ACPs) Direct Fatty Acid and Polyketide Biosynthesis. Angew Chem Int Ed Engl 2024; 63:e202312476. [PMID: 37856285 DOI: 10.1002/anie.202312476] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 10/21/2023]
Abstract
Megasynthases, such as type I fatty acid and polyketide synthases (FASs and PKSs), are multienzyme complexes responsible for producing primary metabolites and complex natural products. Fatty acids (FAs) and polyketides (PKs) are built by assembling and modifying small acyl moieties in a stepwise manner. A central aspect of FA and PK biosynthesis involves the shuttling of substrates between the domains of the multienzyme complex. This essential process is mediated by small acyl carrier proteins (ACPs). The ACPs must navigate to the different catalytic domains within the multienzyme complex in a particular order to guarantee the fidelity of the biosynthesis pathway. However, the precise mechanisms underlying ACP-mediated substrate shuttling, particularly the factors contributing to the programming of the ACP movement, still need to be fully understood. This Review illustrates the current understanding of substrate shuttling, including concepts of conformational and specificity control, and proposes a confined ACP movement within type I megasynthases.
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Affiliation(s)
- Lynn Buyachuihan
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Franziska Stegemann
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Martin Grininger
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
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6
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Qu Y, Niu Z, Ding Q, Zhao T, Kong T, Bai B, Ma J, Zhao Y, Zheng J. Ensemble Learning with Supervised Methods Based on Large-Scale Protein Language Models for Protein Mutation Effects Prediction. Int J Mol Sci 2023; 24:16496. [PMID: 38003686 PMCID: PMC10671426 DOI: 10.3390/ijms242216496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/11/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023] Open
Abstract
Machine learning has been increasingly utilized in the field of protein engineering, and research directed at predicting the effects of protein mutations has attracted increasing attention. Among them, so far, the best results have been achieved by related methods based on protein language models, which are trained on a large number of unlabeled protein sequences to capture the generally hidden evolutionary rules in protein sequences, and are therefore able to predict their fitness from protein sequences. Although numerous similar models and methods have been successfully employed in practical protein engineering processes, the majority of the studies have been limited to how to construct more complex language models to capture richer protein sequence feature information and utilize this feature information for unsupervised protein fitness prediction. There remains considerable untapped potential in these developed models, such as whether the prediction performance can be further improved by integrating different models to further improve the accuracy of prediction. Furthermore, how to utilize large-scale models for prediction methods of mutational effects on quantifiable properties of proteins due to the nonlinear relationship between protein fitness and the quantification of specific functionalities has yet to be explored thoroughly. In this study, we propose an ensemble learning approach for predicting mutational effects of proteins integrating protein sequence features extracted from multiple large protein language models, as well as evolutionarily coupled features extracted in homologous sequences, while comparing the differences between linear regression and deep learning models in mapping these features to quantifiable functional changes. We tested our approach on a dataset of 17 protein deep mutation scans and indicated that the integrated approach together with linear regression enables the models to have higher prediction accuracy and generalization. Moreover, we further illustrated the reliability of the integrated approach by exploring the differences in the predictive performance of the models across species and protein sequence lengths, as well as by visualizing clustering of ensemble and non-ensemble features.
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Affiliation(s)
- Yang Qu
- Cixi Biomedical Research Institute, Wenzhou Medical University, Ningbo 315300, China; (Y.Q.); (Z.N.); (Q.D.); (T.Z.)
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315300, China; (T.K.); (B.B.); (J.M.)
| | - Zitong Niu
- Cixi Biomedical Research Institute, Wenzhou Medical University, Ningbo 315300, China; (Y.Q.); (Z.N.); (Q.D.); (T.Z.)
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315300, China; (T.K.); (B.B.); (J.M.)
| | - Qiaojiao Ding
- Cixi Biomedical Research Institute, Wenzhou Medical University, Ningbo 315300, China; (Y.Q.); (Z.N.); (Q.D.); (T.Z.)
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315300, China; (T.K.); (B.B.); (J.M.)
| | - Taowa Zhao
- Cixi Biomedical Research Institute, Wenzhou Medical University, Ningbo 315300, China; (Y.Q.); (Z.N.); (Q.D.); (T.Z.)
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315300, China; (T.K.); (B.B.); (J.M.)
| | - Tong Kong
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315300, China; (T.K.); (B.B.); (J.M.)
| | - Bing Bai
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315300, China; (T.K.); (B.B.); (J.M.)
| | - Jianwei Ma
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315300, China; (T.K.); (B.B.); (J.M.)
| | - Yitian Zhao
- Cixi Biomedical Research Institute, Wenzhou Medical University, Ningbo 315300, China; (Y.Q.); (Z.N.); (Q.D.); (T.Z.)
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315300, China; (T.K.); (B.B.); (J.M.)
| | - Jianping Zheng
- Cixi Biomedical Research Institute, Wenzhou Medical University, Ningbo 315300, China; (Y.Q.); (Z.N.); (Q.D.); (T.Z.)
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315300, China; (T.K.); (B.B.); (J.M.)
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7
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Patel KD, MacDonald MR, Ahmed SF, Singh J, Gulick AM. Structural advances toward understanding the catalytic activity and conformational dynamics of modular nonribosomal peptide synthetases. Nat Prod Rep 2023; 40:1550-1582. [PMID: 37114973 PMCID: PMC10510592 DOI: 10.1039/d3np00003f] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Indexed: 04/29/2023]
Abstract
Covering: up to fall 2022.Nonribosomal peptide synthetases (NRPSs) are a family of modular, multidomain enzymes that catalyze the biosynthesis of important peptide natural products, including antibiotics, siderophores, and molecules with other biological activity. The NRPS architecture involves an assembly line strategy that tethers amino acid building blocks and the growing peptides to integrated carrier protein domains that migrate between different catalytic domains for peptide bond formation and other chemical modifications. Examination of the structures of individual domains and larger multidomain proteins has identified conserved conformational states within a single module that are adopted by NRPS modules to carry out a coordinated biosynthetic strategy that is shared by diverse systems. In contrast, interactions between modules are much more dynamic and do not yet suggest conserved conformational states between modules. Here we describe the structures of NRPS protein domains and modules and discuss the implications for future natural product discovery.
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Affiliation(s)
- Ketan D Patel
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| | - Monica R MacDonald
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| | - Syed Fardin Ahmed
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| | - Jitendra Singh
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| | - Andrew M Gulick
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
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8
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Trottmann F, Fiedler J, Ishida K, Ishida-Ito M, Little RF, Hertweck C. Bacterial Pathogen Channels Medium-Sized Fatty Acids into Malleicyprol Biosynthesis. ACS Chem Biol 2023; 18:1557-1563. [PMID: 37319349 DOI: 10.1021/acschembio.3c00188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Bacterial pathogens of the Burkholderia pseudomallei (BP) group cause life-threatening infections in both humans and animals. Critical for the virulence of these often antibiotic-resistant pathogens is the polyketide hybrid metabolite malleicyprol, which features two chains, a short cyclopropanol-substituted chain and a long hydrophobic alkyl chain. The biosynthetic origin of the latter has remained unknown. Here, we report the discovery of novel overlooked malleicyprol congeners with varied chain lengths and identify medium-sized fatty acids as polyketide synthase (PKS) starter units that constitute the hydrophobic carbon tails. Mutational and biochemical analyses show that a designated coenzyme A-independent fatty acyl-adenylate ligase (FAAL, BurM) is essential for recruiting and activating fatty acids in malleicyprol biosynthesis. In vitro reconstitution of the BurM-catalyzed PKS priming reaction and analysis of ACP-bound building blocks reveal a key role of BurM in the toxin assembly. Insights into the function and role of BurM hold promise for the development of enzyme inhibitors as novel antivirulence therapeutics to combat infections with BP pathogens.
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Affiliation(s)
- Felix Trottmann
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
| | - Jonas Fiedler
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
| | - Keishi Ishida
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
| | - Mie Ishida-Ito
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
| | - Rory F Little
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
- Natural Product Chemistry, Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany
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9
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Enhanced Rishirilide Biosynthesis by a Rare In-Cluster Phosphopantetheinyl Transferase in Streptomyces xanthophaeus. Microbiol Spectr 2022; 10:e0324722. [PMID: 36326495 PMCID: PMC9769936 DOI: 10.1128/spectrum.03247-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Phosphopantetheinyl transferases (PPTases) play important roles in activating apo-acyl carrier proteins (apo-ACPs) and apo-peptidyl carrier proteins (apo-PCPs) in both primary and secondary metabolism. PPTases catalyze the posttranslational modifications of those carrier proteins by covalent attachment of the 4'-phosphopantetheine group to a conserved serine residue. The protein-protein interactions between a PPTase and a cognate acyl or peptidyl carrier protein have important regulatory functions in microbial biosynthesis, but the molecular mechanism underlying their specific recognition remains elusive. In this study, we identified a new rishirilide biosynthetic gene cluster with a rare in-cluster PPTase from Streptomyces xanthophaeus no2. The function of this Sfp-type PPTase, SxrX, in rishirilide production was confirmed using genetic mutagenesis and biochemical characterization. We applied molecular modeling and site-directed mutagenesis to identify key residues mediating the protein-protein interaction between SxrX and its cognate ACP. In addition, six natural products were isolated from wild-type S. xanthophaeus no2 and the ΔsxrX mutant, including rishirilide A and lupinacidin A, that exhibited antimicrobial and anticancer activities, respectively. SxrX is the first Sfp-type PPTase identified from an aromatic polyketide biosynthetic gene cluster and shown to be responsible for high-level production of rishirilide derivatives. IMPORTANCE Genome mining has been a vital means for natural product drug discovery in the postgenomic era. The rishirilide-type polyketides have attracted attention due to their potent bioactivity, but the poor robustness of production hosts has limited further research and development. This study not only identifies a hyperproducer of rishirilides but also reveals a rare, in-cluster PPTase SxrX that plays an important role in boosting rishirilide biosynthesis. Experimental and computational investigations revealed new insights on the protein-protein interaction between SxrX and its cognate ACP with wide implications for understanding polyketide biosynthesis.
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10
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Winter AJ, Rowe MT, Weir ANM, Akter N, Mbatha SZ, Walker PD, Williams C, Song Z, Race PR, Willis CL, Crump MP. Programmed Iteration Controls the Assembly of the Nonanoic Acid Side Chain of the Antibiotic Mupirocin. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 134:e202212393. [PMID: 38505625 PMCID: PMC10947060 DOI: 10.1002/ange.202212393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Indexed: 11/11/2022]
Abstract
Mupirocin is a clinically important antibiotic produced by Pseudomonas fluorescens NCIMB 10586 that is assembled by a complex trans-AT polyketide synthase. The polyketide fragment, monic acid, is esterified by a 9-hydroxynonanoic acid (9HN) side chain which is essential for biological activity. The ester side chain assembly is initialised from a 3-hydroxypropionate (3HP) starter unit attached to the acyl carrier protein (ACP) MacpD, but the fate of this species is unknown. Herein we report the application of NMR spectroscopy, mass spectrometry, chemical probes and in vitro assays to establish the remaining steps of 9HN biosynthesis. These investigations reveal a complex interplay between a novel iterative or "stuttering" KS-AT didomain (MmpF), the multidomain module MmpB and multiple ACPs. This work has important implications for understanding the late-stage biosynthetic steps of mupirocin and will be important for future engineering of related trans-AT biosynthetic pathways (e.g. thiomarinol).
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Affiliation(s)
| | | | | | - Nahida Akter
- School of ChemistryUniversity of BristolBristolBS8 1TSUK
| | | | - Paul D. Walker
- School of ChemistryUniversity of BristolBristolBS8 1TSUK
| | | | - Zhongshu Song
- School of ChemistryUniversity of BristolBristolBS8 1TSUK
| | - Paul R. Race
- School of BiochemistryUniversity of BristolBristolBS8 1TDUK
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11
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Winter AJ, Rowe MT, Weir ANM, Akter N, Mbatha SZ, Walker PD, Williams C, Song Z, Race PR, Willis CL, Crump MP. Programmed Iteration Controls the Assembly of the Nonanoic Acid Side Chain of the Antibiotic Mupirocin. Angew Chem Int Ed Engl 2022; 61:e202212393. [PMID: 36227272 PMCID: PMC10098928 DOI: 10.1002/anie.202212393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Indexed: 11/12/2022]
Abstract
Mupirocin is a clinically important antibiotic produced by Pseudomonas fluorescens NCIMB 10586 that is assembled by a complex trans-AT polyketide synthase. The polyketide fragment, monic acid, is esterified by a 9-hydroxynonanoic acid (9HN) side chain which is essential for biological activity. The ester side chain assembly is initialised from a 3-hydroxypropionate (3HP) starter unit attached to the acyl carrier protein (ACP) MacpD, but the fate of this species is unknown. Herein we report the application of NMR spectroscopy, mass spectrometry, chemical probes and in vitro assays to establish the remaining steps of 9HN biosynthesis. These investigations reveal a complex interplay between a novel iterative or "stuttering" KS-AT didomain (MmpF), the multidomain module MmpB and multiple ACPs. This work has important implications for understanding the late-stage biosynthetic steps of mupirocin and will be important for future engineering of related trans-AT biosynthetic pathways (e.g. thiomarinol).
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Affiliation(s)
| | - Matthew T. Rowe
- School of Chemistry University of Bristol Bristol BS8 1TS UK
| | | | - Nahida Akter
- School of Chemistry University of Bristol Bristol BS8 1TS UK
| | | | - Paul D. Walker
- School of Chemistry University of Bristol Bristol BS8 1TS UK
| | | | - Zhongshu Song
- School of Chemistry University of Bristol Bristol BS8 1TS UK
| | - Paul R. Race
- School of Biochemistry University of Bristol Bristol BS8 1TD UK
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12
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King S, Quick A, King K, Walker AR, Shields RC. Activation of TnSmu1, an integrative and conjugative element, by an ImmR-like transcriptional regulator in Streptococcus mutans. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36201342 DOI: 10.1099/mic.0.001254] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Integrative and conjugative elements (ICEs) are chromosomally encoded mobile genetic elements that can transfer DNA between bacterial strains. Recently, as part of efforts to determine hypothetical gene functions, we have discovered an important regulatory module encoded on an ICE known as TnSmu1 on the Streptococcus mutans chromosome. The regulatory module consists of a cI-like repressor with a helix-turn-helix DNA binding domain immR Smu (immunity repressor) and a metalloprotease immA Smu (anti-repressor). It is not possible to create an in-frame deletion mutant of immR Smu and repression of immR Smu with CRISPRi (CRISPR interference) causes substantial cell defects. We used a bypass of essentiality (BoE) screen to discover genes that allow deletion of the regulatory module. This revealed that conjugation genes, located within TnSmu1, can restore the viability of an immR Smu mutant. Deletion of immR Smu also leads to production of a circular intermediate form of TnSmu1, which is also inducible by the genotoxic agent mitomycin C. To gain further insights into potential regulation of TnSmu1 by ImmRSmu and broader effects on S. mutans UA159 physiology, we used CRISPRi and RNA-seq. Strongly induced genes included all the TnSmu1 mobile element, genes involved in amino acid metabolism, transport systems and a type I-C CRISPR-Cas system. Lastly, bioinformatic analysis shows that the TnSmu1 mobile element and its associated genes are well distributed across S. mutans isolates. Taken together, our results show that activation of TnSmu1 is controlled by the immRA Smu module, and that activation is deleterious to S. mutans, highlighting the complex interplay between mobile elements and their host.
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Affiliation(s)
- Shawn King
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR, USA
| | - Allison Quick
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR, USA
| | - Kalee King
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR, USA
| | | | - Robert C Shields
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR, USA
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13
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Singh BK, Biswas R, Bhattacharyya S, Basak A, Das AK. The C‐terminal end of mycobacterial HadBC regulates AcpM interaction during the FAS‐II pathway: a structural perspective. FEBS J 2022; 289:4963-4980. [DOI: 10.1111/febs.16405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 01/22/2022] [Accepted: 02/15/2022] [Indexed: 11/26/2022]
Affiliation(s)
- Bina Kumari Singh
- School of Biosciences Indian Institute of Technology Kharagpur India
| | - Rupam Biswas
- Department of Biotechnology Indian Institute of Technology Kharagpur India
| | - Sudipta Bhattacharyya
- Department of Bioscience & Bioengineering Indian Institute of Technology Jodhpur India
| | - Amit Basak
- Department of Chemistry Indian Institute of Technology Kharagpur India
| | - Amit K. Das
- Department of Biotechnology Indian Institute of Technology Kharagpur India
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14
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Chen A, Jiang Z, Burkart MD. Enzymology of standalone elongating ketosynthases. Chem Sci 2022; 13:4225-4238. [PMID: 35509474 PMCID: PMC9006962 DOI: 10.1039/d1sc07256k] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/09/2022] [Indexed: 12/16/2022] Open
Abstract
The β-ketoacyl-acyl carrier protein synthase, or ketosynthase (KS), catalyses carbon-carbon bond formation in fatty acid and polyketide biosynthesis via a decarboxylative Claisen-like condensation. In prokaryotes, standalone elongating KSs interact with the acyl carrier protein (ACP) which shuttles substrates to each partner enzyme in the elongation cycle for catalysis. Despite ongoing research for more than 50 years since KS was first identified in E. coli, the complex mechanism of KSs continues to be unravelled, including recent understanding of gating motifs, KS-ACP interactions, substrate recognition and delivery, and roles in unsaturated fatty acid biosynthesis. In this review, we summarize the latest studies, primarily conducted through structural biology and molecular probe design, that shed light on the emerging enzymology of standalone elongating KSs.
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Affiliation(s)
- Aochiu Chen
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Ziran Jiang
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
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15
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Bartholow TG, Sztain T, Young MA, Lee DJ, Davis TD, Abagyan R, Burkart MD. Control of Unsaturation in De Novo Fatty Acid Biosynthesis by FabA. Biochemistry 2022; 61:608-615. [PMID: 35255690 PMCID: PMC9769579 DOI: 10.1021/acs.biochem.2c00094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Carrier protein-dependent biosynthesis provides a thiotemplated format for the production of natural products. Within these pathways, many reactions display exquisite substrate selectivity, a regulatory framework proposed to be controlled by protein-protein interactions (PPIs). In Escherichia coli, unsaturated fatty acids are generated within the de novo fatty acid synthase by a chain length-specific interaction between the acyl carrier protein AcpP and the isomerizing dehydratase FabA. To evaluate PPI-based control of reactivity, interactions of FabA with AcpP bearing multiple sequestered substrates were analyzed through NMR titration and guided high-resolution docking. Through a combination of quantitative binding constants, residue-specific perturbation analysis, and high-resolution docking, a model for substrate control via PPIs has been developed. The in silico results illuminate the mechanism of FabA substrate selectivity and provide a structural rationale with atomic detail. Helix III positioning in AcpP communicates sequestered chain length identity recognized by FabA, demonstrating a powerful strategy to regulate activity by allosteric control. These studies broadly illuminate carrier protein-dependent pathways and offer an important consideration for future inhibitor design and pathway engineering.
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Affiliation(s)
- Thomas G Bartholow
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Terra Sztain
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Megan A Young
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - D John Lee
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Tony D Davis
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Ruben Abagyan
- School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
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16
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Cho YI, Armstrong CL, Sulpizio A, Acheampong KK, Banks KN, Bardhan O, Churchill SJ, Connolly-Sporing AE, Crawford CE, Cruz Parrilla PL, Curtis SM, De La Ossa LM, Epstein SC, Farrehi CJ, Hamrick GS, Hillegas WJ, Kang A, Laxton OC, Ling J, Matsumura SM, Merino VM, Mukhtar SH, Shah NJ, Londergan CH, Daly CA, Kokona B, Charkoudian LK. Engineered Chimeras Unveil Swappable Modular Features of Fatty Acid and Polyketide Synthase Acyl Carrier Proteins. Biochemistry 2022; 61:217-227. [PMID: 35073057 PMCID: PMC9357449 DOI: 10.1021/acs.biochem.1c00798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The strategic redesign of microbial biosynthetic pathways is a compelling route to access molecules of diverse structure and function in a potentially environmentally sustainable fashion. The promise of this approach hinges on an improved understanding of acyl carrier proteins (ACPs), which serve as central hubs in biosynthetic pathways. These small, flexible proteins mediate the transport of molecular building blocks and intermediates to enzymatic partners that extend and tailor the growing natural products. Past combinatorial biosynthesis efforts have failed due to incompatible ACP-enzyme pairings. Herein, we report the design of chimeric ACPs with features of the actinorhodin polyketide synthase ACP (ACT) and of the Escherichia coli fatty acid synthase (FAS) ACP (AcpP). We evaluate the ability of the chimeric ACPs to interact with the E. coli FAS ketosynthase FabF, which represents an interaction essential to building the carbon backbone of the synthase molecular output. Given that AcpP interacts with FabF but ACT does not, we sought to exchange modular features of ACT with AcpP to confer functionality with FabF. The interactions of chimeric ACPs with FabF were interrogated using sedimentation velocity experiments, surface plasmon resonance analyses, mechanism-based cross-linking assays, and molecular dynamics simulations. Results suggest that the residues guiding AcpP-FabF compatibility and ACT-FabF incompatibility may reside in the loop I, α-helix II region. These findings can inform the development of strategic secondary element swaps that expand the enzyme compatibility of ACPs across systems and therefore represent a critical step toward the strategic engineering of "un-natural" natural products.
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Affiliation(s)
- Yae In Cho
- Department of Chemistry, Haverford College, Haverford, PA 19041
| | | | - Ariana Sulpizio
- Department of Chemistry, Haverford College, Haverford, PA 19041
| | | | | | - Oishi Bardhan
- Department of Chemistry, Haverford College, Haverford, PA 19041
| | | | | | | | | | - Sarah M. Curtis
- Department of Chemistry, Haverford College, Haverford, PA 19041
| | | | | | | | | | | | - Austin Kang
- Department of Chemistry, Haverford College, Haverford, PA 19041
| | | | - Joie Ling
- Department of Chemistry, Haverford College, Haverford, PA 19041
| | | | | | | | - Neel J. Shah
- Department of Chemistry, Haverford College, Haverford, PA 19041
| | | | - Clyde A. Daly
- Department of Chemistry, Haverford College, Haverford, PA 19041
| | - Bashkim Kokona
- Department of Chemistry, Haverford College, Haverford, PA 19041
- Spark Therapeutics, Philadelphia PA 19041
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17
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Tsybovsky Y, Sereda V, Golczak M, Krupenko NI, Krupenko SA. Structure of putative tumor suppressor ALDH1L1. Commun Biol 2022; 5:3. [PMID: 35013550 PMCID: PMC8748788 DOI: 10.1038/s42003-021-02963-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 12/10/2021] [Indexed: 11/08/2022] Open
Abstract
Putative tumor suppressor ALDH1L1, the product of natural fusion of three unrelated genes, regulates folate metabolism by catalyzing NADP+-dependent conversion of 10-formyltetrahydrofolate to tetrahydrofolate and CO2. Cryo-EM structures of tetrameric rat ALDH1L1 revealed the architecture and functional domain interactions of this complex enzyme. Highly mobile N-terminal domains, which remove formyl from 10-formyltetrahydrofolate, undergo multiple transient inter-domain interactions. The C-terminal aldehyde dehydrogenase domains, which convert formyl to CO2, form unusually large interfaces with the intermediate domains, homologs of acyl/peptidyl carrier proteins (A/PCPs), which transfer the formyl group between the catalytic domains. The 4'-phosphopantetheine arm of the intermediate domain is fully extended and reaches deep into the catalytic pocket of the C-terminal domain. Remarkably, the tetrameric state of ALDH1L1 is indispensable for catalysis because the intermediate domain transfers formyl between the catalytic domains of different protomers. These findings emphasize the versatility of A/PCPs in complex, highly dynamic enzymatic systems.
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Affiliation(s)
- Yaroslav Tsybovsky
- Cancer Research Technology Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, 8560 Progress Drive, Frederick, MD, 21701, USA.
| | - Valentin Sereda
- Nutrition Research Institute, University of North Carolina at Chapel Hill, 500 Laureate Way, Kannapolis, NC, 28081, USA
| | - Marcin Golczak
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH, 44106, USA
| | - Natalia I Krupenko
- Nutrition Research Institute, University of North Carolina at Chapel Hill, 500 Laureate Way, Kannapolis, NC, 28081, USA
- Department of Nutrition, University of North Carolina at Chapel Hill, 135 Dauer Drive, Chapel Hill, NC, 27599, USA
| | - Sergey A Krupenko
- Nutrition Research Institute, University of North Carolina at Chapel Hill, 500 Laureate Way, Kannapolis, NC, 28081, USA.
- Department of Nutrition, University of North Carolina at Chapel Hill, 135 Dauer Drive, Chapel Hill, NC, 27599, USA.
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18
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Abstract
Fatty acid (FA) biosynthesis plays a central role in the metabolism of living cells as building blocks of biological membranes, energy reserves of the cell, and precursors to second messenger molecules. In keeping with its central metabolic role, FA biosynthesis impacts several cellular functions and its misfunction is linked to disease, such as cancer, obesity, and non-alcoholic fatty liver disease. Cellular FA biosynthesis is conducted by fatty acid synthases (FAS). All FAS enzymes catalyze similar biosynthetic reactions, but the functional architectures adopted by these cellular catalysts can differ substantially. This variability in FAS structure amongst various organisms and the essential role played by FA biosynthetic pathways makes this metabolic route a valuable target for the development of antibiotics. Beyond cellular FA biosynthesis, the quest for renewable energy sources has piqued interest in FA biosynthetic pathway engineering to generate biofuels and fatty acid derived chemicals. For these applications, based on FA biosynthetic pathways, to succeed, detailed metabolic, functional and structural insights into FAS are required, along with an intimate knowledge into the regulation of FAS. In this review, we summarize our present knowledge about the functional, structural, and regulatory aspects of FAS.
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Affiliation(s)
- Aybeg N Günenc
- Research Group for Structural Biochemistry and Mechanisms, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Benjamin Graf
- Research Group for Structural Biochemistry and Mechanisms, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Holger Stark
- Department of Structural Dynamics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Ashwin Chari
- Research Group for Structural Biochemistry and Mechanisms, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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19
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Bartholow TG, Sztain T, Young MA, Davis TD, Abagyan R, Burkart MD. Protein-protein interaction based substrate control in the E. coli octanoic acid transferase, LipB. RSC Chem Biol 2021; 2:1466-1473. [PMID: 34704050 PMCID: PMC8495967 DOI: 10.1039/d1cb00125f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/27/2021] [Indexed: 12/16/2022] Open
Abstract
Lipoic acid is an essential cofactor produced in all organisms by diverting octanoic acid derived as an intermediate of type II fatty acid biosynthesis. In bacteria, octanoic acid is transferred from the acyl carrier protein (ACP) to the lipoylated target protein by the octanoyltransferase LipB. LipB has a well-documented substrate selectivity, indicating a mechanism of octanoic acid recognition. The present study reveals the precise protein-protein interactions (PPIs) responsible for this selectivity in Escherichia coli through a combination of solution-state protein NMR titration with high-resolution docking of the experimentally examined substrates. We examine the structural changes of substrate-bound ACP and determine the precise geometry of the LipB interface. Thermodynamic effects from varying substrates were observed by NMR, and steric occlusion of docked models indicates how LipB interprets proper substrate identity via allosteric binding. This study provides a model for elucidating how substrate identity is transferred through the ACP structure to regulate activity in octanoyl transferases.
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Affiliation(s)
- Thomas G Bartholow
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093-0358 USA
| | - Terra Sztain
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093-0358 USA
| | - Megan A Young
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093-0358 USA
| | - Tony D Davis
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093-0358 USA
| | - Ruben Abagyan
- School of Pharmacy and Pharmaceutical Sciences, University of California San Diego La Jolla CA 92093 USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093-0358 USA
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20
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Dietl A, Barends TRM. Dynamics in an unusual acyl carrier protein from a ladderane lipid-synthesizing organism. Proteins 2021; 90:73-82. [PMID: 34310758 DOI: 10.1002/prot.26187] [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: 11/18/2020] [Accepted: 07/16/2021] [Indexed: 11/09/2022]
Abstract
Anaerobic ammonium-oxidizing (anammox) bacteria express a distinct acyl carrier protein implicated in the biosynthesis of the highly unusual "ladderane" lipids these organisms produce. This "anammox-specific" ACP, or amxACP, shows several unique features such as a conserved FF motif and an unusual sequence in the functionally important helix III. Investigation of the protein's structure and dynamics, both in the crystal by ensemble refinement and by MD simulations, reveals that helix III adopts a rare six-residue-long 310 -helical conformation that confers a large degree of conformational and positional variability on this part of the protein. This way of introducing structural flexibility by using the inherent properties of 310 -helices appears unique among ACPs. Moreover, the structure suggests a role for the FF motif in shielding the thioester linkage between the protein's prosthetic group and its acyl cargo from hydrolysis.
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Affiliation(s)
- Andreas Dietl
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Thomas R M Barends
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
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21
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Booysen E, Dicks LMT. Does the Future of Antibiotics Lie in Secondary Metabolites Produced by Xenorhabdus spp.? A Review. Probiotics Antimicrob Proteins 2021; 12:1310-1320. [PMID: 32844362 DOI: 10.1007/s12602-020-09688-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The over-prescription of antibiotics for treatment of infections is primarily to blame for the increase in bacterial resistance. Added to the problem is the slow rate at which novel antibiotics are discovered and the many processes that need to be followed to classify antimicrobials safe for medical use. Xenorhabdus spp. of the family Enterobacteriaceae, mutualistically associated with entomopathogenic nematodes of the genus Steinernema, produce a variety of antibacterial peptides, including bacteriocins, depsipeptides, xenocoumacins and PAX (peptide antimicrobial-Xenorhabdus) peptides, plus additional secondary metabolites with antibacterial and antifungal activity. The secondary metabolites of some strains are active against protozoa and a few have anti-carcinogenic properties. It is thus not surprising that nematodes invaded by a single strain of a Xenorhabdus species are not infected by other microorganisms. In this review, the antimicrobial compounds produced by Xenorhabdus spp. are listed and the gene clusters involved in synthesis of these secondary metabolites are discussed. We also review growth conditions required for increased production of antimicrobial compounds.
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Affiliation(s)
- E Booysen
- Department of Microbiology, Stellenbosch University, Stellenbosch, 7600, South Africa
| | - L M T Dicks
- Department of Microbiology, Stellenbosch University, Stellenbosch, 7600, South Africa.
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22
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Mindrebo JT, Chen A, Kim WE, Re RN, Davis TD, Noel JP, Burkart MD. Structure and Mechanistic Analyses of the Gating Mechanism of Elongating Ketosynthases. ACS Catal 2021; 11:6787-6799. [DOI: 10.1021/acscatal.1c00745] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Jeffrey T. Mindrebo
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
- Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Aochiu Chen
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Woojoo E. Kim
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Rebecca N. Re
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Tony D. Davis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Joseph P. Noel
- Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, California 92037, United States
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
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23
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Bonhomme S, Dessen A, Macheboeuf P. The inherent flexibility of type I non-ribosomal peptide synthetase multienzymes drives their catalytic activities. Open Biol 2021; 11:200386. [PMID: 34034506 PMCID: PMC8150014 DOI: 10.1098/rsob.200386] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Non-ribosomal peptide synthetases (NRPSs) are multienzymes that produce complex natural metabolites with many applications in medicine and agriculture. They are composed of numerous catalytic domains that elongate and chemically modify amino acid substrates or derivatives and of non-catalytic carrier protein domains that can tether and shuttle the growing products to the different catalytic domains. The intrinsic flexibility of NRPSs permits conformational rearrangements that are required to allow interactions between catalytic and carrier protein domains. Their large size coupled to this flexibility renders these multi-domain proteins very challenging for structural characterization. Here, we summarize recent studies that offer structural views of multi-domain NRPSs in various catalytically relevant conformations, thus providing an increased comprehension of their catalytic cycle. A better structural understanding of these multienzymes provides novel perspectives for their re-engineering to synthesize new bioactive metabolites.
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Affiliation(s)
- Sarah Bonhomme
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France
| | - Andréa Dessen
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France.,Brazilian Biosciences National Laboratory (LNBio), CNPEM, Campinas 13084-971, São Paulo, Brazil
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24
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Snowden JS, Alzahrani J, Sherry L, Stacey M, Rowlands DJ, Ranson NA, Stonehouse NJ. Structural insight into Pichia pastoris fatty acid synthase. Sci Rep 2021; 11:9773. [PMID: 33963233 PMCID: PMC8105331 DOI: 10.1038/s41598-021-89196-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 04/19/2021] [Indexed: 11/24/2022] Open
Abstract
Type I fatty acid synthases (FASs) are critical metabolic enzymes which are common targets for bioengineering in the production of biofuels and other products. Serendipitously, we identified FAS as a contaminant in a cryoEM dataset of virus-like particles (VLPs) purified from P. pastoris, an important model organism and common expression system used in protein production. From these data, we determined the structure of P. pastoris FAS to 3.1 Å resolution. While the overall organisation of the complex was typical of type I FASs, we identified several differences in both structural and enzymatic domains through comparison with the prototypical yeast FAS from S. cerevisiae. Using focussed classification, we were also able to resolve and model the mobile acyl-carrier protein (ACP) domain, which is key for function. Ultimately, the structure reported here will be a useful resource for further efforts to engineer yeast FAS for synthesis of alternate products.
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Affiliation(s)
- Joseph S Snowden
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Jehad Alzahrani
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Lee Sherry
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Martin Stacey
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - David J Rowlands
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
| | - Nicola J Stonehouse
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
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25
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Bharmoria P, Bisht M, Gomes MC, Martins M, Neves MC, Mano JF, Bdikin I, Coutinho JAP, Ventura SPM. Protein-olive oil-in-water nanoemulsions as encapsulation materials for curcumin acting as anticancer agent towards MDA-MB-231 cells. Sci Rep 2021; 11:9099. [PMID: 33907277 PMCID: PMC8079396 DOI: 10.1038/s41598-021-88482-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 03/18/2021] [Indexed: 02/02/2023] Open
Abstract
The sustainable cellular delivery of the pleiotropic drug curcumin encounters drawbacks related to its fast autoxidation at the physiological pH, cytotoxicity of delivery vehicles and poor cellular uptake. A biomaterial compatible with curcumin and with the appropriate structure to allow the correct curcumin encapsulation considering its poor solubility in water, while maintaining its stability for a safe release was developed. In this work, the biomaterial developed started by the preparation of an oil-in-water nanoemulsion using with a cytocompatible copolymer (Pluronic F 127) coated with a positively charged protein (gelatin), designed as G-Cur-NE, to mitigate the cytotoxicity issue of curcumin. These G-Cur-NE showed excellent capacity to stabilize curcumin, to increase its bio-accessibility, while allowing to arrest its autoxidation during its successful application as an anticancer agent proved by the disintegration of MDA-MB-231 breast cancer cells as a proof of concept.
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Affiliation(s)
- Pankaj Bharmoria
- Department of Chemistry, CICECO-Aveiro Institute of Materials, University of Aveiro, 3810-193, Aveiro, Portugal.
- Department of Applied Chemistry, Chalmers University of Technology, Kemivägen 4, 412 96, Gothenburg, Sweden.
| | - Meena Bisht
- Department of Chemistry, CICECO-Aveiro Institute of Materials, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Maria C Gomes
- Department of Chemistry, CICECO-Aveiro Institute of Materials, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Margarida Martins
- Department of Chemistry, CICECO-Aveiro Institute of Materials, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Márcia C Neves
- Department of Chemistry, CICECO-Aveiro Institute of Materials, University of Aveiro, 3810-193, Aveiro, Portugal
| | - João F Mano
- Department of Chemistry, CICECO-Aveiro Institute of Materials, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Igor Bdikin
- TEMA, Department of Mechanical Engineering, University of Aveiro, 3810-193, Aveiro, Portugal
| | - João A P Coutinho
- Department of Chemistry, CICECO-Aveiro Institute of Materials, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Sónia P M Ventura
- Department of Chemistry, CICECO-Aveiro Institute of Materials, University of Aveiro, 3810-193, Aveiro, Portugal.
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26
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Abstract
Enzymes in multistep metabolic pathways utilize an array of regulatory mechanisms to maintain a delicate homeostasis [K. Magnuson, S. Jackowski, C. O. Rock, J. E. Cronan, Jr, Microbiol. Rev. 57, 522-542 (1993)]. Carrier proteins in particular play an essential role in shuttling substrates between appropriate enzymes in metabolic pathways. Although hypothesized [E. Płoskoń et al., Chem. Biol. 17, 776-785 (2010)], allosteric regulation of substrate delivery has never before been demonstrated for any acyl carrier protein (ACP)-dependent pathway. Studying these mechanisms has remained challenging due to the transient and dynamic nature of protein-protein interactions, the vast diversity of substrates, and substrate instability [K. Finzel, D. J. Lee, M. D. Burkart, ChemBioChem 16, 528-547 (2015)]. Here we demonstrate a unique communication mechanism between the ACP and partner enzymes using solution NMR spectroscopy and molecular dynamics to elucidate allostery that is dependent on fatty acid chain length. We demonstrate that partner enzymes can allosterically distinguish between chain lengths via protein-protein interactions as structural features of substrate sequestration are translated from within the ACP four-helical bundle to the protein surface, without the need for stochastic chain flipping. These results illuminate details of cargo communication by the ACP that can serve as a foundation for engineering carrier protein-dependent pathways for specific, desired products.
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27
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Bartholow TG, Sztain T, Patel A, Lee DJ, Young MA, Abagyan R, Burkart MD. Elucidation of transient protein-protein interactions within carrier protein-dependent biosynthesis. Commun Biol 2021; 4:340. [PMID: 33727677 PMCID: PMC7966745 DOI: 10.1038/s42003-021-01838-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 02/11/2021] [Indexed: 01/31/2023] Open
Abstract
Fatty acid biosynthesis (FAB) is an essential and highly conserved metabolic pathway. In bacteria, this process is mediated by an elaborate network of protein•protein interactions (PPIs) involving a small, dynamic acyl carrier protein that interacts with dozens of other partner proteins (PPs). These PPIs have remained poorly characterized due to their dynamic and transient nature. Using a combination of solution-phase NMR spectroscopy and protein-protein docking simulations, we report a comprehensive residue-by-residue comparison of the PPIs formed during FAB in Escherichia coli. This technique describes and compares the molecular basis of six discrete binding events responsible for E. coli FAB and offers insights into a method to characterize these events and those in related carrier protein-dependent pathways.
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Affiliation(s)
- Thomas G Bartholow
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Terra Sztain
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Ashay Patel
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - D John Lee
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
- Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Megan A Young
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Ruben Abagyan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA.
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28
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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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29
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Baer MD, Shanklin J, Raugei S. Atomistic insight on structure and dynamics of spinach acyl carrier protein with substrate length. Biophys J 2021; 120:3841-3853. [PMID: 33631202 PMCID: PMC8456182 DOI: 10.1016/j.bpj.2020.12.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 12/08/2020] [Accepted: 12/10/2020] [Indexed: 01/02/2023] Open
Abstract
The plant acyl-acyl carrier protein (ACP) desaturases are a family of soluble enzymes that convert saturated fatty acyl-ACPs into their cis-monounsaturated equivalents in an oxygen-dependent reaction. These enzymes play a key role in biosynthesis of monounsaturated fatty acids in plants. ACPs are central proteins in fatty acid biosynthesis that deliver acyl chains to desaturases. They have been reported to show a varying degree of local dynamics and structural variability depending on the acyl chain size. It has been suggested that substrate-specific changes in ACP structure and dynamics have a crucial impact on the desaturase enzymatic activity. Using molecular dynamics simulations, we investigated the intrinsic solution structure and dynamics of ACP from spinach with four different acyl chains: capric (C10), myristic (C14), palmitic (C16), and stearic (C18) acids. We found that the fatty acids can adopt two distinct structural binding motifs, which feature different binding free energies and influence the ACP dynamics in a different manner. Docking simulations of ACP to castor Δ9-desaturase and ivy Δ4-desaturase suggest that ACP desaturase interactions could lead to a preferential selection between the motifs.
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Affiliation(s)
- Marcel D Baer
- Pacific Northwest National Laboratory, Physical and Computational Sciences Directorate, Richland, Washington.
| | - John Shanklin
- Biology Department, Brookhaven National Laboratory, Upton, New York
| | - Simone Raugei
- Pacific Northwest National Laboratory, Physical and Computational Sciences Directorate, Richland, Washington
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30
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Sulpizio A, Crawford CEW, Koweek RS, Charkoudian LK. Probing the structure and function of acyl carrier proteins to unlock the strategic redesign of type II polyketide biosynthetic pathways. J Biol Chem 2021; 296:100328. [PMID: 33493513 PMCID: PMC7949117 DOI: 10.1016/j.jbc.2021.100328] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 02/04/2023] Open
Abstract
Type II polyketide synthases (PKSs) are protein assemblies, encoded by biosynthetic gene clusters in microorganisms, that manufacture structurally complex and pharmacologically relevant molecules. Acyl carrier proteins (ACPs) play a central role in biosynthesis by shuttling malonyl-based building blocks and polyketide intermediates to catalytic partners for chemical transformations. Because ACPs serve as central hubs in type II PKSs, they can also represent roadblocks to successfully engineering synthases capable of manufacturing 'unnatural natural products.' Therefore, understanding ACP conformational dynamics and protein interactions is essential to enable the strategic redesign of type II PKSs. However, the inherent flexibility and transience of ACP interactions pose challenges to gaining insight into ACP structure and function. In this review, we summarize how the application of chemical probes and molecular dynamic simulations has increased our understanding of the structure and function of type II PKS ACPs. We also share how integrating these advances in type II PKS ACP research with newfound access to key enzyme partners, such as the ketosynthase-chain length factor, sets the stage to unlock new biosynthetic potential.
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Affiliation(s)
- Ariana Sulpizio
- Department of Chemistry, Haverford College, Haverford, Pennsylvania, USA
| | | | - Rebecca S Koweek
- Department of Chemistry, Haverford College, Haverford, Pennsylvania, USA
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31
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Thongkawphueak T, Winter AJ, Williams C, Maple HJ, Soontaranon S, Kaewhan C, Campopiano DJ, Crump MP, Wattana-Amorn P. Solution Structure and Conformational Dynamics of a Doublet Acyl Carrier Protein from Prodigiosin Biosynthesis. Biochemistry 2021; 60:219-230. [PMID: 33416314 DOI: 10.1021/acs.biochem.0c00830] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The acyl carrier protein (ACP) is an indispensable component of both fatty acid and polyketide synthases and is primarily responsible for delivering acyl intermediates to enzymatic partners. At present, increasing numbers of multidomain ACPs have been discovered with roles in molecular recognition of trans-acting enzymatic partners as well as increasing metabolic flux. Further structural information is required to provide insight into their function, yet to date, the only high-resolution structure of this class to be determined is that of the doublet ACP (two continuous ACP domains) from mupirocin synthase. Here we report the solution nuclear magnetic resonance (NMR) structure of the doublet ACP domains from PigH (PigH ACP1-ACP2), which is an enzyme that catalyzes the formation of the bipyrrolic intermediate of prodigiosin, a potent anticancer compound with a variety of biological activities. The PigH ACP1-ACP2 structure shows each ACP domain consists of three conserved helices connected by a linker that is partially restricted by interactions with the ACP1 domain. Analysis of the holo (4'-phosphopantetheine, 4'-PP) form of PigH ACP1-ACP2 by NMR revealed conformational exchange found predominantly in the ACP2 domain reflecting the inherent plasticity of this ACP. Furthermore, ensemble models obtained from SAXS data reveal two distinct conformers, bent and extended, of both apo (unmodified) and holo PigH ACP1-ACP2 mediated by the central linker. The bent conformer appears to be a result of linker-ACP1 interactions detected by NMR and might be important for intradomain communication during the biosynthesis. These results provide new insights into the behavior of the interdomain linker of multiple ACP domains that may modulate protein-protein interactions. This is likely to become an increasingly important consideration for metabolic engineering in prodigiosin and other related biosynthetic pathways.
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Affiliation(s)
- Thitapa Thongkawphueak
- Department of Chemistry, Special Research Unit for Advanced Magnetic Resonance and Center of Excellence for Innovation in Chemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Ashley J Winter
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K
| | - Christopher Williams
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K.,BrisSynBio, Centre for Synthetic Biology Research, Life Sciences Building, Tyndall Avenue, University of Bristol, Bristol BS8 1TQ, U.K
| | - Hannah J Maple
- School of Social and Community Medicine, University of Bristol, Oakfield House, Bristol BS8 2BN, U.K
| | - Siriwat Soontaranon
- Synchrotron Light Research Institute (Public Organization), Nakhon Ratchasima 30000, Thailand
| | - Chonthicha Kaewhan
- Synchrotron Light Research Institute (Public Organization), Nakhon Ratchasima 30000, Thailand
| | - Dominic J Campopiano
- School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, U.K
| | - Matthew P Crump
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K.,BrisSynBio, Centre for Synthetic Biology Research, Life Sciences Building, Tyndall Avenue, University of Bristol, Bristol BS8 1TQ, U.K
| | - Pakorn Wattana-Amorn
- Department of Chemistry, Special Research Unit for Advanced Magnetic Resonance and Center of Excellence for Innovation in Chemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
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32
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Walker PD, Weir ANM, Willis CL, Crump MP. Polyketide β-branching: diversity, mechanism and selectivity. Nat Prod Rep 2021; 38:723-756. [PMID: 33057534 DOI: 10.1039/d0np00045k] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: 2008 to August 2020 Polyketides are a family of natural products constructed from simple building blocks to generate a diverse range of often complex chemical structures with biological activities of both pharmaceutical and agrochemical importance. Their biosynthesis is controlled by polyketide synthases (PKSs) which catalyse the condensation of thioesters to assemble a functionalised linear carbon chain. Alkyl-branches may be installed at the nucleophilic α- or electrophilic β-carbon of the growing chain. Polyketide β-branching is a fascinating biosynthetic modification that allows for the conversion of a β-ketone into a β-alkyl group or functionalised side-chain. The overall transformation is catalysed by a multi-protein 3-hydroxy-3-methylglutaryl synthase (HMGS) cassette and is reminiscent of the mevalonate pathway in terpene biosynthesis. The first step most commonly involves the aldol addition of acetate to the electrophilic carbon of the β-ketothioester catalysed by a 3-hydroxy-3-methylglutaryl synthase (HMGS). Subsequent dehydration and decarboxylation selectively generates either α,β- or β,γ-unsaturated β-alkyl branches which may be further modified. This review covers 2008 to August 2020 and summarises the diversity of β-branch incorporation and the mechanistic details of each catalytic step. This is extended to discussion of polyketides containing multiple β-branches and the selectivity exerted by the PKS to ensure β-branching fidelity. Finally, the application of HMGS in data mining, additional β-branching mechanisms and current knowledge of the role of β-branches in this important class of biologically active natural products is discussed.
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Affiliation(s)
- P D Walker
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - A N M Weir
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - C L Willis
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - M P Crump
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
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33
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Beaupre BA, Moran GR. N5 Is the New C4a: Biochemical Functionalization of Reduced Flavins at the N5 Position. Front Mol Biosci 2020; 7:598912. [PMID: 33195440 PMCID: PMC7662398 DOI: 10.3389/fmolb.2020.598912] [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: 08/25/2020] [Accepted: 10/05/2020] [Indexed: 12/31/2022] Open
Abstract
For three decades the C4a-position of reduced flavins was the known site for covalency within flavoenzymes. The reactivity of this position of the reduced isoalloxazine ring with the dioxygen ground-state triplet established the C4a as a site capable of one-electron chemistry. Within the last two decades new types of reduced flavin reactivity have been documented. These studies reveal that the N5 position is also a protean site of reactivity, that is capable of nucleophilic attack to form covalent bonds with substrates. In addition, though the precise mechanism of dioxygen reactivity is yet to be definitively demonstrated, it is clear that the N5 position is directly involved in substrate oxygenation in some enzymes. In this review we document the lineage of discoveries that identified five unique modes of N5 reactivity that collectively illustrate the versatility of this position of the reduced isoalloxazine ring.
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Affiliation(s)
- Brett A Beaupre
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Graham R Moran
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
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34
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Molecular Basis for Polyketide Ketoreductase-Substrate Interactions. Int J Mol Sci 2020; 21:ijms21207562. [PMID: 33066287 PMCID: PMC7588967 DOI: 10.3390/ijms21207562] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/11/2020] [Accepted: 10/12/2020] [Indexed: 11/16/2022] Open
Abstract
Polyketides are a large class of structurally and functionally diverse natural products with important bioactivities. Many polyketides are synthesized by reducing type II polyketide synthases (PKSs), containing transiently interacting standalone enzymes. During synthesis, ketoreductase (KR) catalyzes regiospecific carbonyl to hydroxyl reduction, determining the product outcome, yet little is known about what drives specific KR-substrate interactions. In this study, computational approaches were used to explore KR-substrate interactions based on previously solved apo and mimic cocrystal structures. We found five key factors guiding KR-substrate binding. First, two major substrate binding motifs were identified. Second, substrate length is the key determinant of substrate binding position. Third, two key residues in chain length specificity were confirmed. Fourth, phosphorylation of substrates is critical for binding. Finally, packing/hydrophobic effects primarily determine the binding stability. The molecular bases revealed here will help further engineering of type II PKSs and directed biosynthesis of new polyketides.
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35
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Hai Y, Jenner M, Tang Y. Fungal siderophore biosynthesis catalysed by an iterative nonribosomal peptide synthetase. Chem Sci 2020; 11:11525-11530. [PMID: 34094397 PMCID: PMC8162485 DOI: 10.1039/d0sc03627g] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Siderophores play a vital role in the viability of fungi and are essential for the virulence of many pathogenic fungal species. Despite their importance in fungal physiology and pathogenesis, the programming rule of siderophore assembly by fungal nonribosomal peptide synthetases (NRPSs) remains unresolved. Here, we report the characterization of the bimodular fungal NRPS, SidD, responsible for construction of the extracellular siderophore fusarinine C. The use of intact protein mass spectrometry, together with in vitro biochemical assays of native and dissected enzymes, provided snapshots of individual biosynthetic steps during NPRS catalysis. The adenylation and condensation domain of SidD can iteratively load and condense the amino acid building block cis-AMHO, respectively, to synthesize fusarinine C. Our study showcases the iterative programming features of fungal siderophore-producing NRPSs.
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Affiliation(s)
- Yang Hai
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles California 90095 USA
| | - Matthew Jenner
- Department of Chemistry, Warwick Integrative Synthetic Biology Center, University of Warwick Coventry UK
- Warwick Integrative Synthetic Biology (WISB) Centre, University of Warwick Coventry UK
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles California 90095 USA
- Department of Chemistry and Biochemistry, University of California Los Angeles California 90095 USA
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36
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Mindrebo JT, Misson LE, Johnson C, Noel JP, Burkart MD. Activity Mapping the Acyl Carrier Protein: Elongating Ketosynthase Interaction in Fatty Acid Biosynthesis. Biochemistry 2020; 59:3626-3638. [PMID: 32857494 DOI: 10.1021/acs.biochem.0c00605] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Elongating ketosynthases (KSs) catalyze carbon-carbon bond-forming reactions during the committed step for each round of chain extension in both fatty acid synthases (FASs) and polyketide synthases (PKSs). A small α-helical acyl carrier protein (ACP) shuttles fatty acyl intermediates between enzyme active sites. To accomplish this task, the ACP relies on a series of dynamic interactions with multiple partner enzymes of FAS and associated FAS-dependent pathways. Recent structures of the Escherichia coli FAS ACP, AcpP, in covalent complexes with its two cognate elongating KSs, FabF and FabB, provide high-resolution details of these interfaces, but a systematic analysis of specific interfacial interactions responsible for stabilizing these complexes has not yet been undertaken. Here, we use site-directed mutagenesis with both in vitro and in vivo activity analyses to quantitatively evaluate these contacting surfaces between AcpP and FabF. We delineate the FabF interface into three interacting regions and demonstrate the effects of point mutants, double mutants, and region deletion variants. Results from these analyses reveal a robust and modular FabF interface capable of tolerating seemingly critical interface mutations with only the deletion of an entire region significantly compromising activity. Structure and sequence analyses of FabF orthologs from related type II FAS pathways indicate significant conservation of type II FAS KS interface residues and, overall, support its delineation into interaction regions. These findings strengthen our mechanistic understanding of molecular recognition events between ACPs and FAS enzymes and provide a blueprint for engineering ACP-dependent biosynthetic pathways.
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Affiliation(s)
- Jeffrey T Mindrebo
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States.,Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Laetitia E Misson
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Caitlin Johnson
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Joseph P Noel
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
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37
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Selection and validation of suitable reference genes for quantitative real time PCR analysis of gene expression studies in patchouli under Meloidogyne incognita attack and PGPR treatment. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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38
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Structural basis for selectivity in a highly reducing type II polyketide synthase. Nat Chem Biol 2020; 16:776-782. [PMID: 32367018 DOI: 10.1038/s41589-020-0530-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 03/27/2020] [Indexed: 01/18/2023]
Abstract
In type II polyketide synthases (PKSs), the ketosynthase-chain length factor (KS-CLF) complex catalyzes polyketide chain elongation with the acyl carrier protein (ACP). Highly reducing type II PKSs, represented by IgaPKS, produce polyene structures instead of the well-known aromatic skeletons. Here, we report the crystal structures of the Iga11-Iga12 (KS-CLF) heterodimer and the covalently cross-linked Iga10=Iga11-Iga12 (ACP=KS-CLF) tripartite complex. The latter structure revealed the molecular basis of the interaction between Iga10 and Iga11-Iga12, which differs from that between the ACP and KS of Escherichia coli fatty acid synthase. Furthermore, the reaction pocket structure and site-directed mutagenesis revealed that the negative charge of Asp 113 of Iga11 prevents further condensation using a β-ketoacyl product as a substrate, which distinguishes IgaPKS from typical type II PKSs. This work will facilitate the future rational design of PKSs.
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39
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Structural Characterization of an ACP from Thermotoga maritima: Insights into Hyperthermal Adaptation. Int J Mol Sci 2020; 21:ijms21072600. [PMID: 32283632 PMCID: PMC7178038 DOI: 10.3390/ijms21072600] [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: 03/12/2020] [Revised: 04/06/2020] [Accepted: 04/07/2020] [Indexed: 12/30/2022] Open
Abstract
Thermotoga maritima, a deep-branching hyperthermophilic bacterium, expresses an extraordinarily stable Thermotoga maritima acyl carrier protein (Tm-ACP) that functions as a carrier in the fatty acid synthesis system at near-boiling aqueous environments. Here, to understand the hyperthermal adaptation of Tm-ACP, we investigated the structure and dynamics of Tm-ACP by nuclear magnetic resonance (NMR) spectroscopy. The melting temperature of Tm-ACP (101.4 °C) far exceeds that of other ACPs, owing to extensive ionic interactions and tight hydrophobic packing. The D59 residue, which replaces Pro/Ser of other ACPs, mediates ionic clustering between helices III and IV. This creates a wide pocket entrance to facilitate the accommodation of long acyl chains required for hyperthermal adaptation of the T. maritima cell membrane. Tm-ACP is revealed to be the first ACP that harbor an amide proton hyperprotected against hydrogen/deuterium exchange for I15. The hydrophobic interactions mediated by I15 appear to be the key driving forces of the global folding process of Tm-ACP. Our findings provide insights into the structural basis of the hyperthermal adaptation of ACP, which might have allowed T. maritima to survive in hot ancient oceans.
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40
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Mindrebo JT, Patel A, Kim WE, Davis TD, Chen A, Bartholow TG, La Clair JJ, McCammon JA, Noel JP, Burkart MD. Gating mechanism of elongating β-ketoacyl-ACP synthases. Nat Commun 2020; 11:1727. [PMID: 32265440 PMCID: PMC7138838 DOI: 10.1038/s41467-020-15455-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 03/06/2020] [Indexed: 12/20/2022] Open
Abstract
Carbon-carbon bond forming reactions are essential transformations in natural product biosynthesis. During de novo fatty acid and polyketide biosynthesis, β-ketoacyl-acyl carrier protein (ACP) synthases (KS), catalyze this process via a decarboxylative Claisen-like condensation reaction. KSs must recognize multiple chemically distinct ACPs and choreograph a ping-pong mechanism, often in an iterative fashion. Here, we report crystal structures of substrate mimetic bearing ACPs in complex with the elongating KSs from Escherichia coli, FabF and FabB, in order to better understand the stereochemical features governing substrate discrimination by KSs. Complemented by molecular dynamics (MD) simulations and mutagenesis studies, these structures reveal conformational states accessed during KS catalysis. These data taken together support a gating mechanism that regulates acyl-ACP binding and substrate delivery to the KS active site. Two active site loops undergo large conformational excursions during this dynamic gating mechanism and are likely evolutionarily conserved features in elongating KSs.
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Affiliation(s)
- Jeffrey T Mindrebo
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA.,Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Ashay Patel
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Woojoo E Kim
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Tony D Davis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Aochiu Chen
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Thomas G Bartholow
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - James J La Clair
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA.,Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA.,Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Joseph P Noel
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA. .,Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA. .,Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA.
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41
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Corpuz JC, Podust LM, Davis TD, Jaremko MJ, Burkart MD. Dynamic visualization of type II peptidyl carrier protein recognition in pyoluteorin biosynthesis. RSC Chem Biol 2020; 1:8-12. [PMID: 33305272 PMCID: PMC7723355 DOI: 10.1039/c9cb00015a] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Using a covalent chemical probe and X-ray crystallography coupled to nuclear magnetic resonance data, we elucidated the dynamic molecular basis of protein recognition between the carrier protein and adenylation domain in pyoluteorin biosynthesis. These findings reveal a unique binding mode, which contrasts previously solved carrier protein and partner protein interfaces. The interface interactions of a type II peptidyl carrier protein and partner enzyme are observed to be unique and dynamic.![]()
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Affiliation(s)
- Joshua C Corpuz
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
| | - Larissa M Podust
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California-San Diego, 9500 Gilman Dr., La Jolla, CA 92093-0755, USA
| | - Tony D Davis
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
| | - Matt J Jaremko
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
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42
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Kilgour SL, Kilgour DPA, Prasongpholchai P, O'Connor PB, Tosin M. A Light-Activated Acyl Carrier Protein "Trap" for Intermediate Capture in Type II Iterative Polyketide Biocatalysis. Chemistry 2019; 25:16515-16518. [PMID: 31596972 PMCID: PMC6972679 DOI: 10.1002/chem.201903662] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 10/03/2019] [Indexed: 01/24/2023]
Abstract
A discrete acyl carrier protein (ACP) bearing a photolabile nonhydrolysable carba(dethia) malonyl pantetheine cofactor was chemoenzymatically prepared and utilised for the trapping of biosynthetic polyketide intermediates following light activation. From the in vitro assembly of the polyketides SEK4 and SEK4b, by the type II actinorhodin "minimal" polyketide synthase (PKS), a range of putative ACP-bound diketides, tetraketides, pentaketides and hexaketides were identified and characterised by FT-ICR-MS, providing direct insights on active site accessibility and substrate processing for this enzyme class.
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Affiliation(s)
| | - David P. A. Kilgour
- Department of Chemistry and ForensicsNottingham Trent UniversityNottinghamNG11 8NSUK
| | | | - Peter B. O'Connor
- Department of ChemistryUniversity of WarwickLibrary RoadCoventryCV4 7ALUK
| | - Manuela Tosin
- Department of ChemistryUniversity of WarwickLibrary RoadCoventryCV4 7ALUK
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43
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Pass-back chain extension expands multimodular assembly line biosynthesis. Nat Chem Biol 2019; 16:42-49. [PMID: 31636431 PMCID: PMC6917876 DOI: 10.1038/s41589-019-0385-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 09/06/2019] [Indexed: 11/26/2022]
Abstract
Modular nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) enzymatic assembly lines are large and dynamic protein machines that generally effect a linear sequence of catalytic cycles. Here we report the heterologous reconstitution and comprehensive characterization of two hybrid NRPS-PKS assembly lines that defy many standard rules of assembly line biosynthesis to generate a large combinatorial library of cyclic lipodepsipeptide protease inhibitors called thalassospiramides. We generate a series of precise domain-inactivating mutations in thalassospiramide assembly lines and present evidence for an unprecedented biosynthetic model that invokes inter-module substrate activation and tailoring, module skipping, and pass-back chain extension, whereby the ability to pass the growing chain back to a preceding module is flexible and substrate-driven. Expanding bidirectional inter-module domain interactions could represent a viable mechanism for generating chemical diversity without increasing the size of biosynthetic assembly lines and challenges our understanding of the potential elasticity of multi-modular megaenzymes.
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44
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Canestrari MJ, Serrano B, Bartoli J, Prima V, Bornet O, Puppo R, Bouveret E, Guerlesquin F, Viala JP. Deciphering the specific interaction between the acyl carrier protein IacP and the T3SS‐major hydrophobic translocator SipB from
Salmonella. FEBS Lett 2019; 594:251-265. [DOI: 10.1002/1873-3468.13593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/13/2019] [Accepted: 08/28/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Mickaël J. Canestrari
- LISM Institut de Microbiologie de la Méditerranée CNRS and Aix‐Marseille University France
| | - Bastien Serrano
- LISM Institut de Microbiologie de la Méditerranée CNRS and Aix‐Marseille University France
| | - Julia Bartoli
- LISM Institut de Microbiologie de la Méditerranée CNRS and Aix‐Marseille University France
| | - Valérie Prima
- LISM Institut de Microbiologie de la Méditerranée CNRS and Aix‐Marseille University France
| | - Olivier Bornet
- NMR Platform Institut de Microbiologie de la Méditerranée CNRS and Aix‐Marseille University France
| | - Rémy Puppo
- Proteomics Platform‐ IBISA2 Institut de Microbiologie de la Méditerranée CNRS and Aix‐Marseille University France
| | - Emmanuelle Bouveret
- LISM Institut de Microbiologie de la Méditerranée CNRS and Aix‐Marseille University France
| | - Françoise Guerlesquin
- LISM Institut de Microbiologie de la Méditerranée CNRS and Aix‐Marseille University France
| | - Julie P. Viala
- LISM Institut de Microbiologie de la Méditerranée CNRS and Aix‐Marseille University France
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45
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Liao J, Pang K, Sun G, Pai T, Hsu P, Lin J, Sun K, Hsieh C, Tang S. Chimeric 6-methylsalicylic acid synthase with domains of acyl carrier protein and methyltransferase from Pseudallescheria boydii shows novel biosynthetic activity. Microb Biotechnol 2019; 12:920-931. [PMID: 31199579 PMCID: PMC6681407 DOI: 10.1111/1751-7915.13445] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 05/06/2019] [Accepted: 05/17/2019] [Indexed: 01/09/2023] Open
Abstract
Polyketides are important secondary metabolites, many of which exhibit potent pharmacological applications. Biosynthesis of polyketides is carried out by a single polyketide synthase (PKS) or multiple PKSs in successive elongations of enzyme-bound intermediates related to fatty acid biosynthesis. The polyketide gene PKS306 from Pseudallescheria boydii NTOU2362 containing domains of ketosynthase (KS), acyltransferase (AT), dehydratase (DH), acyl carrier protein (ACP) and methyltransferase (MT) was cloned in an attempt to produce novel chemical compounds, and this PKS harbouring green fluorescent protein (GFP) was expressed in Saccharomyces cerevisiae. Although fluorescence of GFP and fusion protein analysed by anti-GFP antibody were observed, no novel compound was detected. 6-methylsalicylic acid synthase (6MSAS) was then used as a template and engineered with PKS306 by combinatorial fusion. The chimeric PKS containing domains of KS, AT, DH and ketoreductase (KR) from 6MSAS with ACP and MT from PKS306 demonstrated biosynthesis of a novel compound. The compound was identified with a deduced chemical formula of C7 H10 O3 , and the chemical structure was named as 2-hydroxy-2-(propan-2-yl) cyclobutane-1,3-dione. The novel compound synthesized by the chimeric PKS in this study demonstrates the feasibility of combinatorial fusion of PKS genes to produce novel polyketides.
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Affiliation(s)
- Ji‐Long Liao
- Department of Bioscience and BiotechnologyCenter of Excellence for the OceansNational Taiwan Ocean UniversityNo. 2 Pei‐Ning RoadKeelung20224Taiwan
| | - Ka‐Lai Pang
- Department of Marine BiologyCenter of Excellence for the OceansNational Taiwan Ocean UniversityNo. 2 Pei‐Ning RoadKeelung20224Taiwan
| | - Guang‐Huan Sun
- Division of UrologyDepartment of SurgeryNational Defense Medical CenterTri‐Service General HospitalNo. 325, Sec. 2, Cheng‐gong Rd.TaipeiTaiwan
| | - Tun‐Wen Pai
- Department of Computer Science and EngineeringNational Taiwan Ocean UniversityNo. 2 Pei‐Ning RoadKeelung20224Taiwan
| | - Pang‐Hung Hsu
- Department of Bioscience and BiotechnologyCenter of Excellence for the OceansNational Taiwan Ocean UniversityNo. 2 Pei‐Ning RoadKeelung20224Taiwan
| | - Jyuan‐Siou Lin
- Department of Bioscience and BiotechnologyCenter of Excellence for the OceansNational Taiwan Ocean UniversityNo. 2 Pei‐Ning RoadKeelung20224Taiwan
| | - Kuang‐Hui Sun
- Department of Biotechnology and Laboratory Science in MedicineNational Yang‐Ming UniversityNo. 155, Sec. 2, Linong StreetTaipeiTaiwan
- Department of Education and ResearchTaipei City HospitalTaipeiTaiwan
| | | | - Shye‐Jye Tang
- Department of Bioscience and BiotechnologyCenter of Excellence for the OceansNational Taiwan Ocean UniversityNo. 2 Pei‐Ning RoadKeelung20224Taiwan
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46
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Masud AJ, Kastaniotis AJ, Rahman MT, Autio KJ, Hiltunen JK. Mitochondrial acyl carrier protein (ACP) at the interface of metabolic state sensing and mitochondrial function. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:118540. [PMID: 31473256 DOI: 10.1016/j.bbamcr.2019.118540] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/23/2019] [Accepted: 08/27/2019] [Indexed: 12/20/2022]
Abstract
Acyl carrier protein (ACP) is a principal partner in the cytosolic and mitochondrial fatty acid synthesis (FAS) pathways. The active form holo-ACP serves as FAS platform, using its 4'-phosphopantetheine group to present covalently attached FAS intermediates to the enzymes responsible for the acyl chain elongation process. Mitochondrial unacylated holo-ACP is a component of mammalian mitoribosomes, and acylated ACP species participate as interaction partners in several ACP-LYRM (leucine-tyrosine-arginine motif)-protein heterodimers that act either as assembly factors or subunits of the electron transport chain and Fe-S cluster assembly complexes. Moreover, octanoyl-ACP provides the C8 backbone for endogenous lipoic acid synthesis. Accumulating evidence suggests that mtFAS-generated acyl-ACPs act as signaling molecules in an intramitochondrial metabolic state sensing circuit, coordinating mitochondrial acetyl-CoA levels with mitochondrial respiration, Fe-S cluster biogenesis and protein lipoylation.
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Affiliation(s)
- Ali J Masud
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | | | - M Tanvir Rahman
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Kaija J Autio
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - J Kalervo Hiltunen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.
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47
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Sztain T, Bartholow TG, McCammon JA, Burkart MD. Shifting the Hydrolysis Equilibrium of Substrate Loaded Acyl Carrier Proteins. Biochemistry 2019; 58:3557-3560. [PMID: 31397556 DOI: 10.1021/acs.biochem.9b00612] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Acyl carrier proteins (ACP)s transport intermediates through many primary and secondary metabolic pathways. Studying the effect of substrate identity on ACP structure has been hindered by the lability of the thioester bond that attaches acyl substrates to the 4'-phosphopantetheine cofactor of ACP. Here we show that an acyl acyl-carrier protein synthetase (AasS) can be used in real time to shift the hydrolysis equilibrium toward favoring acyl-ACP during solution NMR spectroscopy. Only 0.005 molar equivalents of AasS enables 1 week of stability to palmitoyl-AcpP from Escherichia coli. 2D NMR spectra enabled with this method revealed that the tethered palmitic acid perturbs nearly every secondary structural region of AcpP. This technique will allow previously unachievable structural studies of unstable acyl-ACP species, contributing to the understanding of these complex biosynthetic pathways.
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Affiliation(s)
- Terra Sztain
- Department of Chemistry and Biochemistry , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093-0358 , United States
| | - Thomas G Bartholow
- Department of Chemistry and Biochemistry , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093-0358 , United States
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093-0358 , United States.,Department of Pharmacology , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093-0340 , United States
| | - Michael D Burkart
- Department of Chemistry and Biochemistry , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093-0358 , United States
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48
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Kosol S, Jenner M, Lewandowski JR, Challis GL. Protein-protein interactions in trans-AT polyketide synthases. Nat Prod Rep 2019; 35:1097-1109. [PMID: 30280735 DOI: 10.1039/c8np00066b] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: up to 2018 The construction of polyketide natural products by type I modular polyketide synthases (PKSs) requires the coordinated action of several protein subunits to ensure biosynthetic fidelity. This is particularly the case for trans-AT PKSs, which in contrast to most cis-AT PKSs, contain split modules and employ several trans-acting catalytic domains. This article summarises recent advances in understanding the protein-protein interactions underpinning subunit assembly and intra-subunit communication in such systems and highlights potential avenues and approaches for future research.
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Affiliation(s)
- Simone Kosol
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
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49
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Izoré T, Cryle MJ. The many faces and important roles of protein-protein interactions during non-ribosomal peptide synthesis. Nat Prod Rep 2019; 35:1120-1139. [PMID: 30207358 DOI: 10.1039/c8np00038g] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Covering: up to July 2018 Non-ribosomal peptide synthetase (NRPS) machineries are complex, multi-domain proteins that are responsible for the biosynthesis of many important, peptide-derived compounds. By decoupling peptide synthesis from the ribosome, NRPS assembly lines are able to access a significant pool of amino acid monomers for peptide synthesis. This is combined with a modular protein architecture that allows for great variation in stereochemistry, peptide length, cyclisation state and further modifications. The architecture of NRPS assembly lines relies upon a repetitive set of catalytic domains, which are organised into modules responsible for amino acid incorporation. Central to NRPS-mediated biosynthesis is the carrier protein (CP) domain, to which all intermediates following initial monomer activation are bound during peptide synthesis up until the final handover to the thioesterase domain that cleaves the mature peptide from the NRPS. This mechanism makes understanding the protein-protein interactions that occur between different NRPS domains during peptide biosynthesis of crucial importance to understanding overall NRPS function. This endeavour is also highly challenging due to the inherent flexibility and dynamics of NRPS systems. In this review, we present the current state of understanding of the protein-protein interactions that govern NRPS-mediated biosynthesis, with a focus on insights gained from structural studies relating to CP domain interactions within these impressive peptide assembly lines.
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Affiliation(s)
- Thierry Izoré
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology and ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia.
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50
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Park J, Lee Y, Cheon D, Kim Y. Structure and dynamics of human and bacterial acyl carrier proteins and their interactions with fatty acid synthesis proteins. Biochem Biophys Res Commun 2019; 516:1183-1189. [PMID: 31296387 DOI: 10.1016/j.bbrc.2019.07.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 07/05/2019] [Indexed: 11/17/2022]
Abstract
Acyl carrier protein (ACP) is highly conserved across taxa and plays key roles in the fatty acid synthesis system by mediating acyl group delivery and shuttling. Here, we compared the structural and dynamic features of human type Ι ACP (hACP) and Escherichia coli type II ACP (EcACP). Analysis of chemical shift perturbations upon octanoyl group attachment showed perturbations in hACP only near acyl-group attachment sites, whereas EcACP showed the perturbation at residues in the hydrophobic cavity. This difference confirmed that hACP does not sequester the acyl chain in the hydrophobic cavity, which is blocked by hydrophobic triad residues (L34, L39, and V64). Moreover, hACP showed more flexible backbone dynamics than EcACP, especially in the front of α1α2 loop. We further investigated the interactions of hACP with Streptomyces coelicolor ACP synthase (ScAcpS), which is used to convert apo mammalian ACP to the holo form. Similar to protein-protein interface (PPI) found in hACP-hAcpS crystal structure, docking simulation and binding affinity measurements showed that the hydrophobic residues in universal recognition helix II of hACP contribute mainly to ScAcpS binding with binding affinity of 9.2 ± 9.1 × 104 M. In contrast, interaction found in EcACP-EcAcpS crystal structure is dominated by electrostatic interactions. These results suggest that ScAcpS has relatively relaxed substrate specificity and a similar charge distribution to hAcpS. These fundamental differences of the charge distribution in hAcpS, ScAcpS and EcAcpS largely affect the interaction with hACP. These findings can provide a useful resource for development of novel antibiotics inhibiting PPI in bacterial FAS proteins with specificity.
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Affiliation(s)
- Jungwoo Park
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, South Korea
| | - Yeongjoon Lee
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, South Korea
| | - Dasom Cheon
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, South Korea
| | - Yangmee Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, South Korea.
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