1
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Zhao Z, Fan J, Yang P, Wang Z, Opiyo SO, Mackey D, Xia Y. Involvement of Arabidopsis Acyl Carrier Protein 1 in PAMP-Triggered Immunity. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:681-693. [PMID: 35343247 DOI: 10.1094/mpmi-02-22-0049-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Plant fatty acids (FAs) and lipids are essential in storing energy and act as structural components for cell membranes and signaling molecules for plant growth and stress responses. Acyl carrier proteins (ACPs) are small acidic proteins that covalently bind the fatty acyl intermediates during the elongation of FAs. The Arabidopsis thaliana ACP family has eight members. Through reverse genetic, molecular, and biochemical approaches, we have discovered that ACP1 localizes to the chloroplast and limits the magnitude of pattern-triggered immunity (PTI) against the bacterial pathogen Pseudomonas syringae pv. tomato. Mutant acp1 plants have reduced levels of linolenic acid (18:3), which is the primary precursor for biosynthesis of the phytohormone jasmonic acid (JA), and a corresponding decrease in the abundance of JA. Consistent with the known antagonistic relationship between JA and salicylic acid (SA), acp1 mutant plants also accumulate a higher level of SA and display corresponding shifts in JA- and SA-regulated transcriptional outputs. Moreover, methyl JA and linolenic acid treatments cause an apparently enhanced decrease of resistance against P. syringae pv. tomato in acp1 mutants than that in WT plants. The ability of ACP1 to prevent this hormone imbalance likely underlies its negative impact on PTI in plant defense. Thus, ACP1 links FA metabolism to stress hormone homeostasis to be negatively involved in PTI in Arabidopsis plant defense. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Zhenzhen Zhao
- Department of Plant Pathology, The Ohio State University, 2021 Coffey Road, Columbus, OH 43210, U.S.A
| | - Jiangbo Fan
- Department of Plant Pathology, The Ohio State University, 2021 Coffey Road, Columbus, OH 43210, U.S.A
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., Shanghai, 200240, China
| | - Piao Yang
- Department of Plant Pathology, The Ohio State University, 2021 Coffey Road, Columbus, OH 43210, U.S.A
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Stephen Obol Opiyo
- Department of Plant Pathology, The Ohio State University, 2021 Coffey Road, Columbus, OH 43210, U.S.A
| | - David Mackey
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH 43210, U.S.A
| | - Ye Xia
- Department of Plant Pathology, The Ohio State University, 2021 Coffey Road, Columbus, OH 43210, U.S.A
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2
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Dibble CC, Barritt SA, Perry GE, Lien EC, Geck RC, DuBois-Coyne SE, Bartee D, Zengeya TT, Cohen EB, Yuan M, Hopkins BD, Meier JL, Clohessy JG, Asara JM, Cantley LC, Toker A. PI3K drives the de novo synthesis of coenzyme A from vitamin B5. Nature 2022; 608:192-198. [PMID: 35896750 PMCID: PMC9352595 DOI: 10.1038/s41586-022-04984-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 06/16/2022] [Indexed: 12/18/2022]
Abstract
In response to hormones and growth factors, the class I phosphoinositide-3-kinase (PI3K) signalling network functions as a major regulator of metabolism and growth, governing cellular nutrient uptake, energy generation, reducing cofactor production and macromolecule biosynthesis1. Many of the driver mutations in cancer with the highest recurrence, including in receptor tyrosine kinases, Ras, PTEN and PI3K, pathologically activate PI3K signalling2,3. However, our understanding of the core metabolic program controlled by PI3K is almost certainly incomplete. Here, using mass-spectrometry-based metabolomics and isotope tracing, we show that PI3K signalling stimulates the de novo synthesis of one of the most pivotal metabolic cofactors: coenzyme A (CoA). CoA is the major carrier of activated acyl groups in cells4,5 and is synthesized from cysteine, ATP and the essential nutrient vitamin B5 (also known as pantothenate)6,7. We identify pantothenate kinase 2 (PANK2) and PANK4 as substrates of the PI3K effector kinase AKT8. Although PANK2 is known to catalyse the rate-determining first step of CoA synthesis, we find that the minimally characterized but highly conserved PANK49 is a rate-limiting suppressor of CoA synthesis through its metabolite phosphatase activity. Phosphorylation of PANK4 by AKT relieves this suppression. Ultimately, the PI3K–PANK4 axis regulates the abundance of acetyl-CoA and other acyl-CoAs, CoA-dependent processes such as lipid metabolism and proliferation. We propose that these regulatory mechanisms coordinate cellular CoA supplies with the demands of hormone/growth-factor-driven or oncogene-driven metabolism and growth. The PI3K–PANK4 axis regulates coenzyme A synthesis, the abundance of acetyl-CoA, and CoA-dependent processes such as lipid metabolism, and these regulatory mechanisms coordinate cellular CoA supplies with the demands of hormone and growth-factor-driven or oncogene-driven metabolism and growth.
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Affiliation(s)
- Christian C Dibble
- Department of Pathology, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
| | - Samuel A Barritt
- Department of Pathology, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Grace E Perry
- Department of Pathology, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Evan C Lien
- Department of Pathology, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Renee C Geck
- Department of Pathology, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Sarah E DuBois-Coyne
- Department of Pathology, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - David Bartee
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Thomas T Zengeya
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Emily B Cohen
- Department of Pathology, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Min Yuan
- Mass Spectrometry Core, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Benjamin D Hopkins
- Department of Genetics and Genomic Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jordan L Meier
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | - John G Clohessy
- Preclinical Murine Pharmacogenetics Facility and Mouse Hospital, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - John M Asara
- Mass Spectrometry Core, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Lewis C Cantley
- The Sandra and Edward Meyer Cancer Center, Weill Medical College of Cornell University, New York, NY, USA
| | - Alex Toker
- Department of Pathology, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA. .,Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.
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3
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Gulick AM, Aldrich CC. Trapping interactions between catalytic domains and carrier proteins of modular biosynthetic enzymes with chemical probes. Nat Prod Rep 2019; 35:1156-1184. [PMID: 30046790 DOI: 10.1039/c8np00044a] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: up to early 2018 The Nonribosomal Peptide Synthetases (NRPSs) and Polyketide Synthases (PKSs) are families of modular enzymes that produce a tremendous diversity of natural products, with antibacterial, antifungal, immunosuppressive, and anticancer activities. Both enzymes utilize a fascinating modular architecture in which the synthetic intermediates are covalently attached to a peptidyl- or acyl-carrier protein that is delivered to catalytic domains for natural product elongation, modification, and termination. An investigation of the structural mechanism therefore requires trapping the often transient interactions between the carrier and catalytic domains. Many novel chemical probes have been produced to enable the structural and functional investigation of multidomain NRPS and PKS structures. This review will describe the design and implementation of the chemical tools that have proven to be useful in biochemical and biophysical studies of these natural product biosynthetic enzymes.
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Affiliation(s)
- Andrew M Gulick
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 955 Main St, Buffalo, NY 14203, USA.
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4
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Barajas JF, Finzel K, Valentic TR, Shakya G, Gamarra N, Martinez D, Meier JL, Vagstad AL, Newman AG, Townsend CA, Burkart MD, Tsai SC. Structural and Biochemical Analysis of Protein-Protein Interactions Between the Acyl-Carrier Protein and Product Template Domain. Angew Chem Int Ed Engl 2018; 55:13005-13009. [PMID: 27653519 DOI: 10.1002/anie.201605401] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 08/18/2016] [Indexed: 11/08/2022]
Abstract
In fungal non-reducing polyketide synthases (NR-PKS) the acyl-carrier protein (ACP) carries the growing polyketide intermediate through iterative rounds of elongation, cyclization and product release. This process occurs through a controlled, yet enigmatic coordination of the ACP with its partner enzymes. The transient nature of ACP interactions with these catalytic domains imposes a major obstacle for investigation of the influence of protein-protein interactions on polyketide product outcome. To further our understanding about how the ACP interacts with the product template (PT) domain that catalyzes polyketide cyclization, we developed the first mechanism-based crosslinkers for NR-PKSs. Through in vitro assays, in silico docking and bioinformatics, ACP residues involved in ACP-PT recognition were identified. We used this information to improve ACP compatibility with non-cognate PT domains, which resulted in the first gain-of-function ACP with improved interactions with its partner enzymes. This advance will aid in future combinatorial biosynthesis of new polyketides.
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Affiliation(s)
- Jesus F Barajas
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Kara Finzel
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Timothy R Valentic
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Gaurav Shakya
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Nathan Gamarra
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Delsy Martinez
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Jordan L Meier
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Anna L Vagstad
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218, USA
| | - Adam G Newman
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218, USA
| | - Craig A Townsend
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218, USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Shiou-Chuan Tsai
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA.
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5
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Miyanaga A, Ouchi R, Ishikawa F, Goto E, Tanabe G, Kudo F, Eguchi T. Structural Basis of Protein–Protein Interactions between a trans-Acting Acyltransferase and Acyl Carrier Protein in Polyketide Disorazole Biosynthesis. J Am Chem Soc 2018; 140:7970-7978. [DOI: 10.1021/jacs.8b04162] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Akimasa Miyanaga
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Risako Ouchi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Fumihiro Ishikawa
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Ena Goto
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Genzoh Tanabe
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Tadashi Eguchi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8551, Japan
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6
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Barajas JF, Finzel K, Valentic TR, Shakya G, Gamarra N, Martinez D, Meier JL, Vagstad AL, Newman AG, Townsend CA, Burkart MD, Tsai SC. Structural and Biochemical Analysis of Protein-Protein Interactions Between the Acyl-Carrier Protein and Product Template Domain. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605401] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jesus F. Barajas
- Department of Molecular Biology and Biochemistry; Chemistry, and Pharmaceutical Sciences; University of California, Irvine; Irvine CA 92697 USA
| | - Kara Finzel
- Department of Chemistry and Biochemistry; University of California, San Diego; La Jolla CA 92093 USA
| | - Timothy R. Valentic
- Department of Molecular Biology and Biochemistry; Chemistry, and Pharmaceutical Sciences; University of California, Irvine; Irvine CA 92697 USA
| | - Gaurav Shakya
- Department of Molecular Biology and Biochemistry; Chemistry, and Pharmaceutical Sciences; University of California, Irvine; Irvine CA 92697 USA
| | - Nathan Gamarra
- Department of Molecular Biology and Biochemistry; Chemistry, and Pharmaceutical Sciences; University of California, Irvine; Irvine CA 92697 USA
| | - Delsy Martinez
- Department of Molecular Biology and Biochemistry; Chemistry, and Pharmaceutical Sciences; University of California, Irvine; Irvine CA 92697 USA
| | - Jordan L. Meier
- Department of Chemistry and Biochemistry; University of California, San Diego; La Jolla CA 92093 USA
| | - Anna L. Vagstad
- Department of Chemistry; The Johns Hopkins University; 3400 North Charles Street Baltimore MD 21218 USA
| | - Adam G. Newman
- Department of Chemistry; The Johns Hopkins University; 3400 North Charles Street Baltimore MD 21218 USA
| | - Craig A. Townsend
- Department of Chemistry; The Johns Hopkins University; 3400 North Charles Street Baltimore MD 21218 USA
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry; University of California, San Diego; La Jolla CA 92093 USA
| | - Shiou-Chuan Tsai
- Department of Molecular Biology and Biochemistry; Chemistry, and Pharmaceutical Sciences; University of California, Irvine; Irvine CA 92697 USA
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7
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Beld J, Lee DJ, Burkart MD. Fatty acid biosynthesis revisited: structure elucidation and metabolic engineering. MOLECULAR BIOSYSTEMS 2015; 11:38-59. [PMID: 25360565 PMCID: PMC4276719 DOI: 10.1039/c4mb00443d] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Fatty acids are primary metabolites synthesized by complex, elegant, and essential biosynthetic machinery. Fatty acid synthases resemble an iterative assembly line, with an acyl carrier protein conveying the growing fatty acid to necessary enzymatic domains for modification. Each catalytic domain is a unique enzyme spanning a wide range of folds and structures. Although they harbor the same enzymatic activities, two different types of fatty acid synthase architectures are observed in nature. During recent years, strained petroleum supplies have driven interest in engineering organisms to either produce more fatty acids or specific high value products. Such efforts require a fundamental understanding of the enzymatic activities and regulation of fatty acid synthases. Despite more than one hundred years of research, we continue to learn new lessons about fatty acid synthases' many intricate structural and regulatory elements. In this review, we summarize each enzymatic domain and discuss efforts to engineer fatty acid synthases, providing some clues to important challenges and opportunities in the field.
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Affiliation(s)
- Joris Beld
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA.
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8
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The chain-flipping mechanism of ACP (acyl carrier protein)-dependent enzymes appears universal. Biochem J 2014; 460:157-63. [PMID: 24825445 DOI: 10.1042/bj20140239] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
ACPs (acyl carrier proteins) play essential roles in the synthesis of fatty acids, polyketides and non-ribosomal polypeptides. ACP function requires the modification of the protein by attachment of 4'-phosphopantetheine to a conserved serine residue. The phosphopantetheine thiol acts to tether the starting materials and intermediates as their thioesters. ACPs are small highly soluble proteins composed of four α-helices. The helices form a bundle that acts as a hydrophobic sleeve that sequesters the acyl chains and activated thioesters from solvent. However, in the synthesis of fatty acids and complex lipids the enzymes of the pathway must access the thioester and the proximal carbon atoms in order to perform the needed chemistry. How such access is provided without exposure of the acyl chains to solvent has been a longstanding question due to the lack of acyl-ACP-enzyme complexes, a situation generally attributed to the brevity of the interactions of acyl-ACPs with their cognate enzymes. As discussed in the present review the access question has now been answered by four recent crystal structures, each of which shows that the entire acyl chain plus the 4'-phosphopantetheine prosthetic group partitions from the ACP hydrophobic sleeve into a hydrophobic pocket or groove of the enzyme protein, a process termed chain flipping.
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9
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Kosa NM, Pham KM, Burkart MD. Chemoenzymatic exchange of phosphopantetheine on protein and peptide. Chem Sci 2014; 5:1179-1186. [PMID: 26998215 PMCID: PMC4795179 DOI: 10.1039/c3sc53154f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Evaluation of new acyl carrier protein hydrolase (AcpH, EC 3.1.4.14) homologs from proteobacteria and cyanobacteria reveals significant variation in substrate selectivity and kinetic parameters for phosphopantetheine hydrolysis from carrier proteins. Evaluation with carrier proteins from both primary and secondary metabolic pathways reveals an overall preference for acyl carrier protein (ACP) substrates from type II fatty acid synthases, as well as variable activity for polyketide synthase ACPs and peptidyl carrier proteins (PCP) from non-ribosomal peptide synthases. We also demonstrate the kinetic parameters of these homologs for AcpP and the 11-mer peptide substrate YbbR. These findings enable the fully reversible labeling of all three classes of natural product synthase carrier proteins as well as full and minimal fusion protein constructs.
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Affiliation(s)
- Nicolas M. Kosa
- Department of Chemistry and Biochemistry, University of California, San Diego (UCSD), La Jolla, California, USA
| | - Kevin M. Pham
- Department of Chemistry and Biochemistry, University of California, San Diego (UCSD), La Jolla, California, USA
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego (UCSD), La Jolla, California, USA
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10
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Beld J, Sonnenschein EC, Vickery CR, Noel JP, Burkart MD. The phosphopantetheinyl transferases: catalysis of a post-translational modification crucial for life. Nat Prod Rep 2014; 31:61-108. [PMID: 24292120 PMCID: PMC3918677 DOI: 10.1039/c3np70054b] [Citation(s) in RCA: 240] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Covering: up to 2013. Although holo-acyl carrier protein synthase, AcpS, a phosphopantetheinyl transferase (PPTase), was characterized in the 1960s, it was not until the publication of the landmark paper by Lambalot et al. in 1996 that PPTases garnered wide-spread attention being classified as a distinct enzyme superfamily. In the past two decades an increasing number of papers have been published on PPTases ranging from identification, characterization, structure determination, mutagenesis, inhibition, and engineering in synthetic biology. In this review, we comprehensively discuss all current knowledge on this class of enzymes that post-translationally install a 4'-phosphopantetheine arm on various carrier proteins.
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Affiliation(s)
- Joris Beld
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA.
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11
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Probing the selectivity and protein·protein interactions of a nonreducing fungal polyketide synthase using mechanism-based crosslinkers. ACTA ACUST UNITED AC 2013; 20:1135-46. [PMID: 23993461 DOI: 10.1016/j.chembiol.2013.07.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Revised: 06/28/2013] [Accepted: 07/07/2013] [Indexed: 01/05/2023]
Abstract
Protein·protein interactions, which often involve interactions among an acyl carrier protein (ACP) and ACP partner enzymes, are important for coordinating polyketide biosynthesis. However, the nature of such interactions is not well understood, especially in the fungal nonreducing polyketide synthases (NR-PKSs) that biosynthesize toxic and pharmaceutically important polyketides. Here, we employ mechanism-based crosslinkers to successfully probe ACP and ketosynthase (KS) domain interactions in NR-PKSs. We found that crosslinking efficiency is closely correlated with the strength of ACP·KS interactions and that KS demonstrates strong starter unit selectivity. We further identified positively charged surface residues by KS mutagenesis, which mediates key interactions with the negatively charged ACP surface. Such complementary/matching contact pairs can serve as "adapter surfaces" for future efforts to generate new polyketides using NR-PKSs.
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12
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Ishikawa F, Haushalter RW, Lee DJ, Finzel K, Burkart MD. Sulfonyl 3-alkynyl pantetheinamides as mechanism-based cross-linkers of acyl carrier protein dehydratase. J Am Chem Soc 2013; 135:8846-9. [PMID: 23718183 DOI: 10.1021/ja4042059] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Acyl carrier proteins (ACPs) play a central role in acetate biosynthetic pathways, serving as tethers for substrates and growing intermediates. Activity and structural studies have highlighted the complexities of this role, and the protein-protein interactions of ACPs have recently come under scrutiny as a regulator of catalysis. As existing methods to interrogate these interactions have fallen short, we have sought to develop new tools to aid their study. Here we describe the design, synthesis, and application of pantetheinamides that can cross-link ACPs with catalytic β-hydroxy-ACP dehydratase (DH) domains by means of a 3-alkynyl sulfone warhead. We demonstrate this process by application to the Escherichia coli fatty acid synthase and apply it to probe protein-protein interactions with noncognate carrier proteins. Finally, we use solution-phase protein NMR spectroscopy to demonstrate that sulfonyl 3-alkynyl pantetheinamide is fully sequestered by the ACP, indicating that the crypto-ACP closely mimics the natural DH substrate. This cross-linking technology offers immediate potential to lock these biosynthetic enzymes in their native binding states by providing access to mechanistically cross-linked enzyme complexes, presenting a solution to ongoing structural challenges.
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Affiliation(s)
- Fumihiro Ishikawa
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, USA
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13
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Xu W, Qiao K, Tang Y. Structural analysis of protein-protein interactions in type I polyketide synthases. Crit Rev Biochem Mol Biol 2012; 48:98-122. [PMID: 23249187 DOI: 10.3109/10409238.2012.745476] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Polyketide synthases (PKSs) are responsible for synthesizing a myriad of natural products with agricultural, medicinal relevance. The PKSs consist of multiple functional domains of which each can catalyze a specified chemical reaction leading to the synthesis of polyketides. Biochemical studies showed that protein-substrate and protein-protein interactions play crucial roles in these complex regio-/stereo-selective biochemical processes. Recent developments on X-ray crystallography and protein NMR techniques have allowed us to understand the biosynthetic mechanism of these enzymes from their structures. These structural studies have facilitated the elucidation of the sequence-function relationship of PKSs and will ultimately contribute to the prediction of product structure. This review will focus on the current knowledge of type I PKS structures and the protein-protein interactions in this system.
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Affiliation(s)
- Wei Xu
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
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14
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Kosa NM, Haushalter RW, Smith AR, Burkart MD. Reversible labeling of native and fusion-protein motifs. Nat Methods 2012; 9:981-4. [PMID: 22983458 PMCID: PMC4128096 DOI: 10.1038/nmeth.2175] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 08/23/2012] [Indexed: 11/09/2022]
Abstract
The reversible covalent attachment of chemical probes to proteins has long been sought as a means to visualize and manipulate proteins. Here we demonstrate the full reversibility of post-translational custom pantetheine modification of Escherichia coli acyl carrier protein for visualization and functional studies. We use this iterative enzymatic methodology in vitro to reversibly label acyl carrier protein variants and apply these tools to NMR structural studies of protein-substrate interactions.
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Affiliation(s)
- Nicolas M. Kosa
- University of California San Diego, La Jolla, California, USA
| | | | - Andrew R. Smith
- University of California San Diego, La Jolla, California, USA
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15
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Crosby J, Crump MP. The structural role of the carrier protein--active controller or passive carrier. Nat Prod Rep 2012; 29:1111-37. [PMID: 22930263 DOI: 10.1039/c2np20062g] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Common to all FASs, PKSs and NRPSs is a remarkable component, the acyl or peptidyl carrier protein (A/PCP). These take the form of small individual proteins in type II systems or discrete folded domains in the multi-domain type I systems and are characterized by a fold consisting of three major α-helices and between 60-100 amino acids. This protein is central to these biosynthetic systems and it must bind and transport a wide variety of functionalized ligands as well as mediate numerous protein-protein interactions, all of which contribute to efficient enzyme turnover. This review covers the structural and biochemical characterization of carrier proteins, as well as assessing their interactions with different ligands, and other synthase components. Finally, their role as an emerging tool in biotechnology is discussed.
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Affiliation(s)
- John Crosby
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
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Ishikawa F, Haushalter RW, Burkart MD. Dehydratase-specific probes for fatty acid and polyketide synthases. J Am Chem Soc 2011; 134:769-72. [PMID: 22188524 DOI: 10.1021/ja2082334] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We targeted the development of a dehydratase (DH)-specific reactive probe that can facilitate detection, enrichment, and identification of DH enzymes in fatty acid synthases (FASs) and polyketide synthases (PKSs). The first reported mechanism-based inactivator, 3-decynoyl-N-acetylcysteamine (3-decynoyl-NAC), while active against the Escherichia coli β-hydroxydecanoyl thiol ester DH FabA, translates poorly to an activity-based probe because of nonspecific reactivity of the thioester moiety. Here we describe the design, synthesis, and utility of a DH-specific probe that contains a sulfonyl 3-alkyne reactive warhead engineered to avoid hydrolysis or nonenzymatic inactivation. When coupled with a fluorescent tag, this probe targets DH enzymes from recombinant type I and type II FAS and PKS enzyme systems and in whole proteomes. Activity studies, including FabA inactivation and antibiotic susceptibility, suggest that this sulfonyl 3-alkyne scaffold selectively targets a common DH mechanism. These studies indicate that the DH-specific mechanism-based probe can greatly accelerate both the functional characterization and molecular identification of virtually any type of FAS and PKS in complex proteomes.
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Affiliation(s)
- Fumihiro Ishikawa
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, USA
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Liu Y, Zheng T, Bruner SD. Structural basis for phosphopantetheinyl carrier domain interactions in the terminal module of nonribosomal peptide synthetases. CHEMISTRY & BIOLOGY 2011; 18:1482-8. [PMID: 22118682 PMCID: PMC3238681 DOI: 10.1016/j.chembiol.2011.09.018] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 09/14/2011] [Accepted: 09/26/2011] [Indexed: 01/07/2023]
Abstract
Phosphopantetheine-modified carrier domains play a central role in the template-directed, biosynthesis of several classes of primary and secondary metabolites. Fatty acids, polyketides, and nonribosomal peptides are constructed on multidomain enzyme assemblies using phosphopantetheinyl thioester-linked carrier domains to traffic and activate building blocks. The carrier domain is a dynamic component of the process, shuttling pathway intermediates to sequential enzyme active sites. Here, we report an approach to structurally fix carrier domain/enzyme constructs suitable for X-ray crystallographic analysis. The structure of a two-domain construct of Escherichia coli EntF was determined with a conjugated phosphopantetheinyl-based inhibitor. The didomain structure is locked in an active orientation relevant to the chemistry of nonribosomal peptide biosynthesis. This structure provides details into the interaction of phosphopantetheine arm with the carrier domain and the active site of the thioesterase domain.
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Affiliation(s)
- Ye Liu
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts USA 02167
| | - Tengfei Zheng
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts USA 02167
| | - Steven D. Bruner
- Department of Chemistry, University of Florida, Gainesville, Florida, USA 32611,Correspondence: Steven Bruner, , (352) 392-0525
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Proteomic analysis of polyketide and nonribosomal peptide biosynthesis. Curr Opin Chem Biol 2010; 15:48-56. [PMID: 21087894 DOI: 10.1016/j.cbpa.2010.10.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Accepted: 10/15/2010] [Indexed: 01/18/2023]
Abstract
Polyketides and non-ribosomal peptides are in a class of natural products important both as drug sources and as dangerous toxins and virulence factors. While studies over the last two decades have provided substantial characterization of the modular synthases that produce these compounds at the genetic level, their understanding at the protein level is much less understood. New proteomic platforms called an orthogonal active site identification system (OASIS) and proteomic interrogation of secondary metabolism (PrISM) have been developed to identify and quantify natural product synthase enzymes. Reviewed here, these tools offer the means to discover and analyze modular synthetic pathways that are limited by genetic techniques, opening the tools of contemporary proteomics to natural product sciences.
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