51
|
Allen G, Bromley M, Kaye SJ, Keszenman-Pereyra D, Zucchi TD, Price J, Birch M, Oliver JD, Turner G. Functional analysis of a mitochondrial phosphopantetheinyl transferase (PPTase) gene pptB in Aspergillus fumigatus. Fungal Genet Biol 2011; 48:456-64. [DOI: 10.1016/j.fgb.2010.12.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Revised: 12/13/2010] [Accepted: 12/13/2010] [Indexed: 11/28/2022]
|
52
|
Hollenhorst MA, Bumpus SB, Matthews ML, Bollinger JM, Kelleher NL, Walsh CT. The nonribosomal peptide synthetase enzyme DdaD tethers N(β)-fumaramoyl-l-2,3-diaminopropionate for Fe(II)/α-ketoglutarate-dependent epoxidation by DdaC during dapdiamide antibiotic biosynthesis. J Am Chem Soc 2011; 132:15773-81. [PMID: 20945916 DOI: 10.1021/ja1072367] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The gene cluster from Pantoea agglomerans responsible for biosynthesis of the dapdiamide antibiotics encodes an adenylation-thiolation didomain protein, DdaD, and an Fe(II)/α-ketoglutarate-dependent dioxygenase homologue, DdaC. Here we show that DdaD, a nonribosomal peptide synthetase module, activates and sequesters N(β)-fumaramoyl-l-2,3-diaminopropionate as a covalently tethered thioester for subsequent oxidative modification of the fumaramoyl group. DdaC catalyzes Fe(II)- and α-ketoglutarate-dependent epoxidation of the covalently bound N(β)-fumaramoyl-l-2,3-diaminopropionyl-S-DdaD species to generate N(β)-epoxysuccinamoyl-DAP (DAP = 2,3-diaminopropionate) in thioester linkage to DdaD. After hydrolytic release, N(β)-epoxysuccinamoyl-DAP can be ligated to l-valine by the ATP-dependent ligase DdaF to form the natural antibiotic N(β)-epoxysuccinamoyl-DAP-Val.
Collapse
Affiliation(s)
- Marie A Hollenhorst
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | | | | | | | | | | |
Collapse
|
53
|
Enzymatic properties of ALDH1L2, a mitochondrial 10-formyltetrahydrofolate dehydrogenase. Chem Biol Interact 2011; 191:129-36. [PMID: 21238436 DOI: 10.1016/j.cbi.2011.01.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 01/06/2011] [Accepted: 01/08/2011] [Indexed: 12/13/2022]
Abstract
10-Formyltetrahydrofolate dehydrogenase (FDH, ALDH1L1), an abundant cytosolic enzyme of folate metabolism, shares significant sequence similarity with enzymes of the aldehyde dehydrogenase (ALDH) family. The enzyme converts 10-formyltetrahydrofolate (10-fTHF) to tetrahydrofolate and CO(2) in an NADP(+)-dependent manner. The mechanism of this reaction includes three consecutive steps with the final occurring in an ALDH-homologous domain. We have recently identified a mitochondrial isoform of FDH (mtFDH), which is the product of a separate gene, ALDH1L2. Its overall identity to cytosolic FDH is about 74%, and the identity between the ALDH domains rises up to 79%. In the present study, human mtFDH was expressed in Escherichia coli, purified to homogeneity, and characterized. While the recombinant enzyme was capable of catalyzing the 10-fTHF hydrolase reaction, it did not produce detectable levels of ALDH activity. Despite the lack of typical ALDH catalysis, mtFDH was able to perform the characteristic 10-fTHF dehydrogenase reaction after reactivation by recombinant 4'-phosphopantetheinyl transferase (PPT) in the presence of coenzyme A. Using site-directed mutagenesis, it was determined that PPT modifies mtFDH specifically at Ser375. The C-terminal domain of mtFDH (residues 413-923) was also expressed in E. coli and characterized. This domain was found to exist as a tetramer and to catalyze an esterase reaction that is typical of other ALDH enzymes. Taken together, our studies suggest that ALDH1L2 has enzymatic properties similar to its cytosolic counterpart, although the inability to catalyze the ALDH reaction with short-chain aldehyde substrates remains an unresolved issue at present.
Collapse
|
54
|
Lee JJ, Son J, Ha HH, Chang YT. Fluorescent labeling of membrane proteins on the surface of living cells by a self-catalytic glutathione S-transferase omega 1 tag. MOLECULAR BIOSYSTEMS 2011; 7:1270-6. [DOI: 10.1039/c0mb00327a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
55
|
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.
Collapse
|
56
|
Foley TL, Yasgar A, Garcia CJ, Jadhav A, Simeonov A, Burkart MD. Preparation of FRET reporters to support chemical probe development. Org Biomol Chem 2010; 8:4601-6. [PMID: 20725690 DOI: 10.1039/c0ob00322k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In high throughput screening (HTS) campaigns, the quality and cost of commercial reagents suitable for pilot studies often create obstacles upon scale-up to a full screen. We faced such challenges in our efforts to implement an HTS for inhibitors of the phosphopantetheinyl transferase Sfp using an assay that had been validated using commercially available reagents. Here we demonstrate a facile route to the synthetic preparation of reactive tetraethylrhodamine and quencher probes, and their application to economically produce fluorescent and quencher-modified substrates. These probes were prepared on a scale that would allow a full, quantitative HTS of more than 350,000 compounds.
Collapse
Affiliation(s)
- Timothy L Foley
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
| | | | | | | | | | | |
Collapse
|
57
|
Surveys of non-ribosomal peptide and polyketide assembly lines in fungi and prospects for their analysis in vitro and in vivo. Fungal Genet Biol 2010; 48:49-61. [PMID: 20601041 DOI: 10.1016/j.fgb.2010.06.012] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Revised: 06/02/2010] [Accepted: 06/21/2010] [Indexed: 12/16/2022]
Abstract
With many bioactive non-ribosomal peptides and polyketides produced in fungi, studies of their biosyntheses are an active area of research. Practical limitations of working with mega-dalton synthetases including cell lysis and protein extraction to recombinant gene and pathway expression has slowed understanding of many secondary metabolic processes relative to bacterial counterparts. Recent advances in accessing fungal biosynthetic machinery are beginning to change this. Here we describe the successes of some studies of thiotemplate biosynthesis in fungal systems, along with very recent advances in chemical tagging and mass spectrometric strategies to selectively study biosynthetic conveyer belts in isolation, and within a few years, in endogenous fungal proteomes.
Collapse
|
58
|
Leggans EK, Akey DL, Smith JL, Fecik RA. A general scheme for synthesis of substrate-based polyketide labels for acyl carrier proteins. Bioorg Med Chem Lett 2010; 20:5939-42. [PMID: 20801036 DOI: 10.1016/j.bmcl.2010.05.089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Revised: 05/19/2010] [Accepted: 05/21/2010] [Indexed: 10/19/2022]
Abstract
A general strategy to enzymatically label acyl carrier proteins (ACPs) of polyketide synthases has been developed. Incorporation of a chloromethyl ketone or vinyl ketone moiety into polyketide chain elongation intermediate mimics allows for the synthesis of CoA adducts. These CoA adducts undergo enzymatic reaction with Sfp, a phosphopantetheinyl transferase, to afford labeled CurB carrier proteins.
Collapse
Affiliation(s)
- Erick K Leggans
- Department of Medicinal Chemistry, University of Minnesota, 717 Delaware Street SE, Room 456, Minneapolis, MN 55414-2959, USA
| | | | | | | |
Collapse
|
59
|
Zettler J, Mootz HD. Biochemical evidence for conformational changes in the cross-talk between adenylation and peptidyl-carrier protein domains of nonribosomal peptide synthetases. FEBS J 2010; 277:1159-71. [PMID: 20121951 DOI: 10.1111/j.1742-4658.2009.07551.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Nonribosomal peptide synthetases serve as multidomain protein templates for producing a wealth of pharmaceutically important natural products. For the correct assembly of the desired natural product the interactions between the different catalytic centres and the reaction intermediates bound to the peptidyl carrier protein must be precisely controlled at spatial and temporal levels. We have investigated the interplay between the adenylation (A) domain and the peptidyl carrier protein in the gramicidin S synthetase I (EC 5.1.1.11) via partial tryptic digests, native PAGE and gel-filtration analysis, as well as by chemical labeling experiments. Our data imply that the 4'-phosphopantetheine moiety of the peptidyl carrier protein changes its position as a result of a conformational change in the A domain, which is induced by the binding of an amino acyl adenylate mimic. The productive interaction between the two domains at the stage of the amino acyl transfer onto the 4'-phosphopantetheine moiety is accompanied by a highly compact protein conformation of the holo-protein. These results provide the first biochemical evidence for the occurrence of conformational changes in the cross-talk between A and peptidyl carrier protein domains of a multidomain nonribosomal peptide synthetase.
Collapse
|
60
|
Meier JL, Niessen S, Hoover HS, Foley TL, Cravatt BF, Burkart MD. An orthogonal active site identification system (OASIS) for proteomic profiling of natural product biosynthesis. ACS Chem Biol 2009; 4:948-57. [PMID: 19785476 DOI: 10.1021/cb9002128] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
A significant gap exists between genetics-based investigations of polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) biosynthetic pathways and our understanding of their regulation, interaction, and activity in living systems. To help bridge this gap, here we present an orthogonal active site identification system (OASIS) for the proteomic identification and analysis of PKS/NRPS biosynthetic enzymes. OASIS probes target conserved features of PKS/NRPS active sites to provide activity-based enrichment of modular synthases, followed by analysis through multidimensional protein identification technology (MudPIT) LC-MS/MS analysis. When applied to the model bacterium Bacillus subtilis, this functional proteomics method detects and quantifies all four modular synthases in the organism. Furthermore, tandem application of multiple OASIS probes enhances identification of specific PKS/NRPS modules from complex proteomic mixtures. By expanding the dynamic range of proteomic analysis for PKS/NRPS enzymes, OASIS offers a valuable tool for strain comparison, culture condition optimization, and enzyme discovery.
Collapse
Affiliation(s)
- Jordan L. Meier
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92037-0358
| | - Sherry Niessen
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Center for Physiological Proteomics, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Heather S. Hoover
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Center for Physiological Proteomics, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Timothy L. Foley
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92037-0358
| | - Benjamin F. Cravatt
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Center for Physiological Proteomics, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92037-0358
| |
Collapse
|
61
|
Strickland KC, Hoeferlin LA, Oleinik NV, Krupenko NI, Krupenko SA. Acyl carrier protein-specific 4'-phosphopantetheinyl transferase activates 10-formyltetrahydrofolate dehydrogenase. J Biol Chem 2009; 285:1627-33. [PMID: 19933275 DOI: 10.1074/jbc.m109.080556] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
4'-Phosphopantetheinyl transferases (PPTs) catalyze the transfer of 4'-phosphopantetheine (4-PP) from coenzyme A to a conserved serine residue of their protein substrates. In humans, the number of pathways utilizing the 4-PP post-translational modification is limited and may only require a single broad specificity PPT for all phosphopantetheinylation reactions. Recently, we have shown that one of the enzymes of folate metabolism, 10-formyltetrahydrofolate dehydrogenase (FDH), requires a 4-PP prosthetic group for catalysis. This moiety acts as a swinging arm to couple the activities of the two catalytic domains of FDH and allows the conversion of 10-formyltetrahydrofolate to tetrahydrofolate and CO2. In the current study, we demonstrate that the broad specificity human PPT converts apo-FDH to holoenzyme and thus activates FDH catalysis. Silencing PPT by small interfering RNA in A549 cells prevents FDH modification, indicating the lack of alternative enzymes capable of accomplishing this transferase reaction. Interestingly, PPT-silenced cells demonstrate significantly reduced proliferation and undergo strong G(1) arrest, suggesting that the enzymatic function of PPT is essential and nonredundant. Our study identifies human PPT as the FDH-modifying enzyme and supports the hypothesis that mammals utilize a single enzyme for all phosphopantetheinylation reactions.
Collapse
Affiliation(s)
- Kyle C Strickland
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425, USA
| | | | | | | | | |
Collapse
|
62
|
Foley TL, Young BS, Burkart MD. Phosphopantetheinyl transferase inhibition and secondary metabolism. FEBS J 2009; 276:7134-45. [PMID: 19895578 DOI: 10.1111/j.1742-4658.2009.07425.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Efforts to isolate carrier protein-mediated synthases from natural product-producing organisms using reporter-linked post-translational modification have been complicated by the efficiency of the endogenous process. To address this issue, we chose to target endogenous phosphopantetheinyl transferases (PPTases) for inhibitor design to facilitate natural product synthase isolation through a chemical genetics approach. Herein we validate secondary metabolism-associated PPTase for chemical probe development. We synthesized and evaluated a panel of compounds based on the anthranilate 4H-oxazol-5-one pharmacophore previously described to attenuate PPTase activity within bacterial cultures. Through the use of a new high-throughput Förster resonance energy transfer assay, we demonstrated that these compounds exclusively inhibit fatty acid synthase-specific PPTases. In vivo, a lead compound within this panel demonstrated selective antibiotic activity in a Bacillus subtilis model. Further evaluation demonstrated that the compound enhances actinorhodin production in Streptomyces coelicolor, revealing the ability of this class of molecules to stimulate precocious secondary metabolite production.
Collapse
Affiliation(s)
- Timothy L Foley
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA 92093-0358, USA
| | | | | |
Collapse
|
63
|
Lee KKM, Silva NAD, Kealey JT. Determination of the extent of phosphopantetheinylation of polyketide synthases expressed in Escherichia coli and Saccharomyces cerevisiae. Anal Biochem 2009; 394:75-80. [DOI: 10.1016/j.ab.2009.07.010] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Revised: 07/07/2009] [Accepted: 07/07/2009] [Indexed: 12/01/2022]
|
64
|
Yasgar A, Foley TL, Jadhav A, Inglese J, Burkart MD, Simeonov A. A strategy to discover inhibitors of Bacillus subtilis surfactin-type phosphopantetheinyl transferase. MOLECULAR BIOSYSTEMS 2009; 6:365-75. [PMID: 20094656 DOI: 10.1039/b913291k] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Surfactin-type phosphopantetheinyl transferases (Sfp-PPTases) are responsible for modifying type I polyketide and non-ribosomal peptide synthases of prokaryotes and have been implicated in the activation of a variety of pathogen-associated virulence factors. As such, inhibitors of this enzyme class represent enticing leads for antibiotic development and can serve as tools in studies of bacterial metabolism. Currently, no small molecule inhibitors of Sfp-PPTase are known, highlighting the need for efficient methods for PPTase inhibitor identification and development. Herein, we present the design and implementation of a robust and miniaturized high-throughput kinetic assay for inhibitors of Sfp-PPTase using the substrate combination of rhodamine-labeled coenzyme A and Black Hole Quencher-2 labeled consensus acceptor peptide YbbR. Upon PPTase-catalyzed transfer of the rhodamine-labeled phosphopantetheinyl arm onto the acceptor peptide, the fluorescent donor and quencher are covalently joined and the fluorescence signal is reduced. This assay was miniaturized to a low 4 microL volume in 1536-well format and was used to screen the library of pharmacologically active compounds (LOPAC(1280)). Top inhibitors identified by the screen were further characterized in secondary assays, including protein phosphopantetheinylation detected by gel electrophoresis. The present assay enables the screening of large compound libraries against Sfp-PPTase in a robust and automated fashion and is applicable to designing assays for related transferase enzymes.
Collapse
Affiliation(s)
- Adam Yasgar
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-3370, USA.
| | | | | | | | | | | |
Collapse
|
65
|
Phelan VV, Du Y, McLean JA, Bachmann BO. Adenylation enzyme characterization using gamma -(18)O(4)-ATP pyrophosphate exchange. ACTA ACUST UNITED AC 2009; 16:473-8. [PMID: 19477411 DOI: 10.1016/j.chembiol.2009.04.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2008] [Revised: 03/27/2009] [Accepted: 04/17/2009] [Indexed: 11/15/2022]
Abstract
We present here a rapid, highly sensitive nonradioactive assay for adenylation enzyme selectivity determination and characterization. This method measures the isotopic back exchange of unlabeled pyrophosphate into gamma-(18)O(4)-labeled ATP via matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MS), electrospray ionization liquid chromatography MS, or electrospray ionization liquid chromatography-tandem MS and is demonstrated for both nonribosomal (TycA, ValA) and ribosomal synthetases (TrpRS, LysRS) of known specificity. This low-volume (6 microl) method detects as little as 0.01% (600 fmol) exchange, comparable in sensitivity to previously reported radioactive assays and readily adaptable to kinetics measurements and high throughput analysis of a wide spectrum of synthetases. Finally, a previously uncharacterized A-T didomain from anthramycin biosynthesis in the thermophile S. refuinius was demonstrated to selectively activate 4-methyl-3-hydroxyanthranilic acid at 47 degrees C, providing biochemical evidence for a new aromatic beta-amino acid activating adenylation domain and the first functional analysis of the anthramycin biosynthetic gene cluster.
Collapse
Affiliation(s)
- Vanessa V Phelan
- Department of Chemistry, Vanderbilt University, Nashville, TN 37204, USA
| | | | | | | |
Collapse
|
66
|
Stack D, Frizzell A, Tomkins K, Doyle S. Solid phase 4'-phosphopantetheinylation: fungal thiolation domains are targets for chemoenzymatic modification. Bioconjug Chem 2009; 20:1514-22. [PMID: 19627078 DOI: 10.1021/bc900071j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
No data exist on the ability of thiolation domains from fungal non-ribosomal peptide synthetases to undergo 4'-phosphopantetheinylation, using either biotinylated or fluorescently labeled coenzyme A analogues, mediated by 4'-phosphopantetheinyl transferases (PPTase). Yet, this is a key requirement to confirm the amino acid recognition function, and coding potential, of either non-ribosomal peptide synthetases or recombinantly expressed regions of these enzymes (e.g., didomains or modules). Moreover, determination of 4'-phosphopantetheinylation activity remains cumbersome. Here, we demonstrate that a recombinant fungal PPTase catalyzes the solution-phase transfer of either biotin- or fluorescein-labeled 4'-phosphopantetheine region of coenzyme A to a fungal thiolation domain, which is either part of a non-ribosomal peptide synthetase didomain (72 kDa), derived from Aspergillus fumigatus, or fused to a non-native protein (glutathione s-transferase). Significantly, we demonstrate that this reaction can unexpectedly occur when the target protein (4.4 pmol) is immobilized on a solid surface. These findings (i) confirm that thiolation domains of fungal origin, in native or non-native configuration, can accept modified 4'-phosphopantetheine residues via PPTase-mediated labeling and (ii) illustrate a novel, high-throughput method to determine PPTase activity.
Collapse
Affiliation(s)
- Deirdre Stack
- National Institute for Cellular Biotechnology, Department of Biology, National University of Ireland Maynooth, Co. Kildare, Ireland
| | | | | | | |
Collapse
|
67
|
Zou Y, Yin J. Phosphopantetheinyl transferase catalyzed site-specific protein labeling with ADP conjugated chemical probes. J Am Chem Soc 2009; 131:7548-9. [PMID: 19441828 DOI: 10.1021/ja902464v] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Phosphopantetheinyl transferase (PPTase) catalyzed protein modification has been demonstrated as an efficient method for site specific protein labeling with small molecules of diverse structures. Previously coenzyme A conjugated small molecule probes have been used as the substrates of PPTase for the covalent attachment of the probes to a specific Ser residue in the carrier proteins or short peptide tags through a phosphopantetheinyl linkage. Here we discovered that small molecules directly conjugated to the 5'-diphosphate moiety of ADP can serve as the substrates of a mutant Sfp PPTase, R4-4. Based on this, we used R4-4 to transfer small molecule labels to the carrier protein or peptide tags fused to the target protein through structurally simplified synthetic linkers. The synthesis of ADP conjugated small molecule probes can be easily accomplished by one-step coupling between phosphate derivatized probes and morpholidate-activated AMP. The use of ADP-small molecule conjugates for PPTase catalyzed protein labeling would further expand the structural and functional diversity of the chemical probes attached to the target protein to elucidate or engineer their biological activities.
Collapse
Affiliation(s)
- Yekui Zou
- Department of Chemistry, University of Chicago, 929 East 57th Street, GCIS E505A, Chicago, Illinois 60637, USA
| | | |
Collapse
|
68
|
Wong LS, Khan F, Micklefield J. Selective Covalent Protein Immobilization: Strategies and Applications. Chem Rev 2009; 109:4025-53. [DOI: 10.1021/cr8004668] [Citation(s) in RCA: 387] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Lu Shin Wong
- School of Chemistry and Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Farid Khan
- School of Chemistry and Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Jason Micklefield
- School of Chemistry and Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| |
Collapse
|
69
|
Foley TL, Burkart MD. A homogeneous resonance energy transfer assay for phosphopantetheinyl transferase. Anal Biochem 2009; 394:39-47. [PMID: 19573516 DOI: 10.1016/j.ab.2009.06.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2009] [Revised: 06/24/2009] [Accepted: 06/25/2009] [Indexed: 11/25/2022]
Abstract
Phosphopantetheinyl transferase plays an essential role in activating fatty acid, polyketide, and nonribosomal peptide biosynthetic pathways, catalyzing covalent attachment of a 4'-phosphopantetheinyl group to a conserved residue within carrier protein domains. This enzyme has been validated as an essential gene to primary metabolism and presents a target for the identification of antibiotics with a new mode of action. Here we report the development of a homogeneous resonance energy transfer assay using fluorescent coenzyme A derivatives and a surrogate peptide substrate that can serve to identify inhibitors of this enzyme class. This assay lays a blueprint for translation of these techniques to other transferase enzymes that accept fluorescent substrate analogues.
Collapse
Affiliation(s)
- Timothy L Foley
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | | |
Collapse
|
70
|
Mercer AC, Meier JL, Torpey JW, Burkart MD. In vivo modification of native carrier protein domains. Chembiochem 2009; 10:1091-100. [PMID: 19308927 DOI: 10.1002/cbic.200800838] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Carrier proteins are central to the biosynthesis of primary and secondary metabolites in all organisms. Here we describe metabolic labeling and manipulation of native acyl carrier proteins in both type I and II fatty acid synthases. By utilizing natural promiscuity in the CoA biosynthetic pathway in combination with synthetic pantetheine analogues, we demonstrate metabolic labeling of endogenous carrier proteins with reporter tags in Gram-positive and Gram-negative bacteria and in a human carcinoma cell line. The highly specific nature of the post-translational modification that was utilized for tagging allows for simple visualization of labeled carrier proteins, either by direct fluorescence imaging or after chemical conjugation to a fluorescent reporter. In addition, we demonstrate the utility of this approach for the isolation and enrichment of carrier proteins by affinity purification. Finally, we use these techniques to identify a carrier protein from an unsequenced organism, a finding that validates this proteomic approach to natural product biosynthetic enzyme discovery.
Collapse
Affiliation(s)
- Andrew C Mercer
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, USA
| | | | | | | |
Collapse
|
71
|
Hur GH, Meier JL, Baskin J, Codelli JA, Bertozzi CR, Marahiel MA, Burkart MD. Crosslinking studies of protein-protein interactions in nonribosomal peptide biosynthesis. CHEMISTRY & BIOLOGY 2009; 16:372-81. [PMID: 19345117 PMCID: PMC2743379 DOI: 10.1016/j.chembiol.2009.02.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2008] [Revised: 02/09/2009] [Accepted: 02/11/2009] [Indexed: 11/25/2022]
Abstract
Selective protein-protein interactions between nonribosomal peptide synthetase (NRPS) proteins, governed by communication-mediating (COM) domains, are responsible for proper translocation of biosynthetic intermediates to produce the natural product. In this study, we developed a crosslinking assay, utilizing bioorthogonal probes compatible with carrier protein modification, for probing the protein interactions between COM domains of NRPS enzymes. Employing the Huisgen 1,3-dipolar cycloaddition of azides and alkynes, we examined crosslinking of cognate NRPS modules within the tyrocidine pathway and demonstrated the sensitivity of our panel of crosslinking probes toward the selective protein interactions of compatible COM domains. These studies indicate that copper-free crosslinking substrates uniquely offer a diagnostic probe for protein-protein interactions. Likewise, these crosslinking probes serve as ideal chemical tools for structural studies between NRPS modules where functional assays are lacking.
Collapse
Affiliation(s)
- Gene H. Hur
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093
| | - Jordan L. Meier
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093
| | - Jeremy Baskin
- Department of Chemistry, University of California, Berkeley, B-84 Hildebrand Hall, Berkeley, California 94720
| | - Julian A. Codelli
- Department of Chemistry, University of California, Berkeley, B-84 Hildebrand Hall, Berkeley, California 94720
| | - Carolyn R. Bertozzi
- Department of Chemistry, University of California, Berkeley, B-84 Hildebrand Hall, Berkeley, California 94720
| | - Mohamed A. Marahiel
- Fachbereich Chemie/Biochemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse, 35043 Marburg, Germany
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093
| |
Collapse
|
72
|
Green KD, Pflum MKH. Exploring kinase cosubstrate promiscuity: monitoring kinase activity through dansylation. Chembiochem 2009; 10:234-7. [PMID: 19107758 DOI: 10.1002/cbic.200800393] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Keith D Green
- University of Michigan, Life Science Institute, 210 Washtenaw Avenue, Room 4191, Ann Arbor, MI 48109, USA
| | | |
Collapse
|
73
|
Worthington AS, Hur GH, Meier JL, Cheng Q, Moore BS, Burkart MD. Probing the compatibility of type II ketosynthase-carrier protein partners. Chembiochem 2009; 9:2096-103. [PMID: 18666307 DOI: 10.1002/cbic.200800198] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Drug discovery often begins with the screening of large compound libraries to identify lead compounds. Recently, the enzymes that are involved in the biosynthesis of natural products have been investigated for their potential to generate new, diverse compound libraries. There have been several approaches toward this end, including altering the substrate specificities of the enzymes involved in natural product biosynthesis and engineering functional communication between enzymes from different biosynthetic pathways. While there exist assays to assess the substrate specificity of enzymes involved in these pathways, there is no simple method for determining whether enzymes from different synthases will function cooperatively to generate the desired product(s). Herein we report a method that provides insight into both substrate specificity and compatibility of protein-protein interactions between the acyl carrier protein (ACP) and ketosynthase (KS) domains involved in fatty acid and polyketide biosynthesis. Our technique uses a one-pot chemoenzymatic method to generate post-translationally modified ACPs that are capable of covalently interacting with KS domains from different biosynthetic systems. The extent of interaction between ACPs and KSs from different systems is easily detected and quantified by a gel-based method. Our results are consistent with previous studies of substrate specificity and ACP-KS binding interactions and provide new insight into unnatural substrate and protein interactions.
Collapse
Affiliation(s)
- Andrew S Worthington
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, USA
| | | | | | | | | | | |
Collapse
|
74
|
Zou Y, Yin J. Alkyne-functionalized chemical probes for assaying the substrate specificities of the adenylation domains in nonribosomal peptide synthetases. Chembiochem 2009; 9:2804-10. [PMID: 18988209 DOI: 10.1002/cbic.200800480] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Yekui Zou
- Department of Chemistry, The University of Chicago, 929 E. 57th Street, GCIS E505A, Chicago, IL 60637, USA
| | | |
Collapse
|
75
|
|
76
|
Sunbul M, Yin J. Site specific protein labeling by enzymatic posttranslational modification. Org Biomol Chem 2009; 7:3361-71. [DOI: 10.1039/b908687k] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
77
|
Meier JL, Burkart MD. The chemical biology of modular biosynthetic enzymes. Chem Soc Rev 2009; 38:2012-45. [DOI: 10.1039/b805115c] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
78
|
Chapter 9. Synthetic probes for polyketide and nonribosomal peptide biosynthetic enzymes. Methods Enzymol 2009; 458:219-54. [PMID: 19374985 DOI: 10.1016/s0076-6879(09)04809-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Polyketides and nonribosomal peptides constitute two classes of small molecule natural products that are well-known for their ability to impact important biological processes in a multitude of ways. The modular biosynthetic enzymes responsible for production of these compounds (PKS and NRPS enzymes) have been the subject of extensive genetic, biochemical, and structural characterization, in part due to the potential utility their successful reengineering may have for the production of new therapeutics. In this chapter, we provide background as well as specific techniques in which synthetically produced small molecule probes have been applied to help better understand the mechanism and structure of PKS and NRPS biosynthetic pathways, as well as to help streamline their discovery process. The continued development and application of these methods has the potential to greatly complement our current approaches to the study of natural product biosynthesis.
Collapse
|
79
|
Sunbul M, Zhang K, Yin J. Chapter 10 using phosphopantetheinyl transferases for enzyme posttranslational activation, site specific protein labeling and identification of natural product biosynthetic gene clusters from bacterial genomes. Methods Enzymol 2009; 458:255-75. [PMID: 19374986 DOI: 10.1016/s0076-6879(09)04810-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Phosphopantetheinyl transferases (PPTases) covalently attach the phosphopantetheinyl group derived from coenzyme A (CoA) to acyl carrier proteins or peptidyl carrier proteins as part of the enzymatic assembly lines of fatty acid synthases (FAS), polyketide synthases (PKS), and nonribosomal peptide synthetases (NRPS). PPTases have demonstrated broad substrate specificities for cross-species modification of carrier proteins embedded in PKS or NRPS modules. PPTase Sfp from Bacillus subtilis and AcpS from Escherichia coli also transfer small molecules of diverse structures from their CoA conjugates to the carrier proteins. Short peptide tags have thus been developed as efficient substrates of Sfp and AcpS for site-specific labeling of the peptide-tagged fusion proteins with biotin or organic fluorophores. This chapter discusses the use of PPTases for in vivo and in vitro modification of PKS and NRPS enzymes and for site-specific protein labeling. We also describe a phage selection method based on PPTase-catalyzed carrier protein modification for the identification of PKS or NRPS genes from bacterial genomes.
Collapse
Affiliation(s)
- Murat Sunbul
- Department of Chemistry, The University of Chicago, Chicago, Illinois, USA
| | | | | |
Collapse
|
80
|
Mercer AC, Meier JL, Hur GH, Smith AR, Burkart MD. Antibiotic evaluation and in vivo analysis of alkynyl Coenzyme A antimetabolites in Escherichia coli. Bioorg Med Chem Lett 2008; 18:5991-4. [PMID: 18701278 PMCID: PMC3269959 DOI: 10.1016/j.bmcl.2008.07.078] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2008] [Accepted: 07/18/2008] [Indexed: 01/18/2023]
Abstract
Pantothenamides have been the subject of much study as potential inhibitors of CoA and carrier protein dependent biosynthetic pathways. Based on an initial observation of growth inhibition in Escherichia coli by 3, we have synthesized a small panel of pantetheine analogues and re-examined the inhibitory properties of this class of antibiotics with an emphasis on understanding the ability of these compounds to act as substrates of native CoA and carrier protein utilizing biosynthetic pathways. Our findings suggest that a secondary structure-activity relationship is an important factor in the antibiotic activity of these compounds.
Collapse
Affiliation(s)
- Andrew C Mercer
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
| | | | | | | | | |
Collapse
|
81
|
Sunbul M, Yen M, Zou Y, Yin J. Enzyme catalyzed site-specific protein labeling and cell imaging with quantum dots. Chem Commun (Camb) 2008:5927-9. [PMID: 19030541 DOI: 10.1039/b812162a] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have developed an efficient method for one-step covalent labeling of cell surface proteins with quantum dots based on enzyme catalyzed site-specific modification of short peptide tags.
Collapse
Affiliation(s)
- Murat Sunbul
- Department of Chemistry, The University of Chicago, 929 East 57th Street, GCIS E505A, Chicago, IL 60637, USA
| | | | | | | |
Collapse
|
82
|
Zou Y, Yin J. Cu-free cycloaddition for identifying catalytic active adenylation domains of nonribosomal peptide synthetases by phage display. Bioorg Med Chem Lett 2008; 18:5664-7. [DOI: 10.1016/j.bmcl.2008.08.085] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Revised: 08/22/2008] [Accepted: 08/22/2008] [Indexed: 11/29/2022]
|
83
|
Wittmann M, Linne U, Pohlmann V, Marahiel MA. Role of DptE and DptF in the lipidation reaction of daptomycin. FEBS J 2008; 275:5343-54. [DOI: 10.1111/j.1742-4658.2008.06664.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
84
|
Kruh NA, Borgaro JG, Ruzsicska BP, Xu H, Tonge PJ. A novel interaction linking the FAS-II and phthiocerol dimycocerosate (PDIM) biosynthetic pathways. J Biol Chem 2008; 283:31719-25. [PMID: 18703500 DOI: 10.1074/jbc.m802169200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The fatty acid biosynthesis (FAS-II) pathway in Mycobacterium tuberculosis generates long chain fatty acids that serve as the precursors to mycolic acids, essential components of the mycobacterial cell wall. Enzymes in the FAS-II pathway are thought to form one or more noncovalent multi-enzyme complexes within the cell, and a bacterial two-hybrid screen was used to search for missing components of the pathway and to furnish additional data on interactions involving these enzymes in vivo. Using the FAS-II beta-ketoacyl synthase, KasA, as bait, an extensive bacterial two-hybrid screen of a M. tuberculosis genome fragment library unexpectedly revealed a novel interaction between KasA and PpsB as well as PpsD, two polyketide modules involved in the biosynthesis of the virulence lipid phthiocerol dimycocerosate (PDIM). Sequence analysis revealed that KasA interacts with PpsB and PpsD in the region of the acyl carrier domain of each protein, raising the possibility that lipids could be transferred between the FAS-II and PDIM biosynthetic pathways. Subsequent studies utilizing purified proteins and radiolabeled lipids revealed that fatty acids loaded onto PpsB were transferred to KasA and also incorporated into long chain fatty acids synthesized using a Mycobacterium smegmatis lysate. These data suggest that in addition to producing PDIMs, the growing phthiocerol product can also be shuttled into the FAS-II pathway via KasA as an entry point for further elongation. Interactions between these biosynthetic pathways may exist as a simple means to increase mycobacterial lipid diversity, enhancing functionality and the overall complexity of the cell wall.
Collapse
Affiliation(s)
- Nicole A Kruh
- Graduate Program in Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York 11794-3400, USA
| | | | | | | | | |
Collapse
|
85
|
Crawford JM, Vagstad AL, Ehrlich KC, Udwary DW, Townsend CA. Acyl-carrier protein-phosphopantetheinyltransferase partnerships in fungal fatty acid synthases. Chembiochem 2008; 9:1559-63. [PMID: 18551496 DOI: 10.1002/cbic.200700659] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jason M Crawford
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | | | | | | | | |
Collapse
|
86
|
Sims JW, Schmidt EW. Thioesterase-Like Role for Fungal PKS-NRPS Hybrid Reductive Domains. J Am Chem Soc 2008; 130:11149-55. [DOI: 10.1021/ja803078z] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- James W. Sims
- Department of Medicinal Chemistry, University of Utah, 30 South 2000 East Rm 201, Salt Lake City, Utah, 84112
| | - Eric W. Schmidt
- Department of Medicinal Chemistry, University of Utah, 30 South 2000 East Rm 201, Salt Lake City, Utah, 84112
| |
Collapse
|
87
|
Zhou Z, Koglin A, Wang Y, McMahon AP, Walsh CT. An eight residue fragment of an acyl carrier protein suffices for post-translational introduction of fluorescent pantetheinyl arms in protein modification in vitro and in vivo. J Am Chem Soc 2008; 130:9925-30. [PMID: 18593165 DOI: 10.1021/ja802657n] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Genetically encoded tags for tracking a given protein continue to be of great interest in a multitude of in vitro and in vivo contexts. Acyl carrier proteins, both free-standing and as embedded 80-100 residue domains, contain a specific serine side chain that undergoes post-translational pantetheinylation from CoASH as donor substrate. We have previously used phage display methods to select a 12 residue fragment that retains recognition for modification by the Escherichia coli phosphopantetheinyltransferase (PPTase) AcpS. In this work, we have used (15)N-HSQC based NMR titration experiments of a 12-residue peptide substrate with AcpS to identify six specifically interacting residues (S3, L4, D5, M6, W9, and L11) without the formation of any notable secondary structure. Synthesis of a corresponding octapeptide containing 5 of the 6 interacting residues generated a minimal fragment capable of efficient post-translational phosphopantetheinylation. Genetic insertion of this eight residue coding sequence into the proteins sonic hedgehog and transferrin receptor enabled good in vitro and in vivo PPTase-mediated modification by a series of fluorescent CoAs, leading to a set of fluorescent proteins with a peptide tag minimally perturbant to protein folds.
Collapse
Affiliation(s)
- Zhe Zhou
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School,Boston, Massachusetts 02115, USA
| | | | | | | | | |
Collapse
|
88
|
Meluzzi D, Zheng WH, Hensler M, Nizet V, Dorrestein PC. Top-down mass spectrometry on low-resolution instruments: characterization of phosphopantetheinylated carrier domains in polyketide and non-ribosomal biosynthetic pathways. Bioorg Med Chem Lett 2008; 18:3107-11. [PMID: 18006314 PMCID: PMC2519147 DOI: 10.1016/j.bmcl.2007.10.104] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2007] [Accepted: 10/29/2007] [Indexed: 11/23/2022]
Abstract
Mass spectrometry (MS) is an important tool for studying non-ribosomal peptide, polyketide, and fatty acid biosynthesis. Here we describe a new approach using multi-stage tandem MS on a common ion trap instrument to obtain high-resolution measurements of the masses of substrates and intermediates bound to phosphopantetheinylated (holo) carrier proteins. In particular, we report the chemical formulas of 12 diagnostic MS(3) fragments of the phosphopantetheine moiety ejected from holo carrier proteins during MS(2). We demonstrate our method by observing the formation of holo-AcpC, a putative acyl carrier protein from Streptococcus agalactiae.
Collapse
Affiliation(s)
- Dario Meluzzi
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093-0636, USA
| | - Wei Hao Zheng
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093-0636, USA
| | - Mary Hensler
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093-0636, USA
| | - Victor Nizet
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093-0636, USA
- Department of Pediatrics, University of California at San Diego, La Jolla, CA 92093-0636, USA
| | - Pieter C. Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093-0636, USA
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093-0636, USA
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093-0636, USA
| |
Collapse
|
89
|
Meier JL, Barrows-Yano T, Foley TL, Wike CL, Burkart MD. The unusual macrocycle forming thioesterase of mycolactone. MOLECULAR BIOSYSTEMS 2008; 4:663-71. [PMID: 18493665 DOI: 10.1039/b801397g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mycolactone is a polyketide natural product secreted by Mycobacterium ulcerans, the organism responsible for the tropical skin disease Buruli ulcer. The finding that this small molecule virulence factor is sufficient to reconstitute the necrotic pathology associated with Buruli ulcer suggests that a better understanding of mycolactone biosynthesis, particularly the processes which are distinct from those in human metabolism, may provide a unique avenue for the development of selective therapeutics. In the present study we have cloned, expressed, and biochemically characterized the putative macrocycle forming thioesterase for mycolactone, MLSA2 TE. We have evaluated the enzyme both as the truncated thioesterase domain and as a carrier protein-linked didomain construct. The results of these analyses distinguish MLSA2 TE from traditional fatty acid and polyketide synthase TE-domains in terms of its sequence, kinetic parameters, and susceptibility to traditional active-site directed inhibitors. These findings suggest that MLSA2 TE utilizes a unique biochemical mechanism for macrocycle formation.
Collapse
Affiliation(s)
- Jordan L Meier
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, USA
| | | | | | | | | |
Collapse
|
90
|
Kopp F, Linne U, Oberthür M, Marahiel MA. Harnessing the chemical activation inherent to carrier protein-bound thioesters for the characterization of lipopeptide fatty acid tailoring enzymes. J Am Chem Soc 2008; 130:2656-66. [PMID: 18237171 DOI: 10.1021/ja078081n] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Here, we report a new experimental approach utilizing an amide ligation reaction for the characterization of acyl carrier protein (ACP)-bound reaction intermediates, which are otherwise difficult to analyze by traditional biochemical methods. To explore fatty acid tailoring enzymes of the calcium-dependent antibiotic (CDA) biosynthetic pathway, this strategy enabled the transformation of modified fatty acids, covalently bound as thioesters to an ACP, into amide ligation products that can be directly analyzed and compared to synthetic standards by HPLC-MS. The driving force of the amide formation is the thermodynamic activation inherent to thioester-bound compounds. Using this novel method, we were able to characterize the ACP-mediated biosynthesis of the unique 2,3-epoxyhexanoyl moiety of CDA, revealing a new type of FAD-dependent oxidase HxcO with intrinsic enoyl-ACP epoxidase activity, as well as a second enoyl-ACP epoxidase, HcmO. In general, our approach should be widely applicable for the in vitro characterization of other biosynthetic systems acting on carrier proteins, such as integrated enzymes from NRPS and PKS assembly lines or tailoring enzymes of fatty and amino acid precursor synthesis.
Collapse
Affiliation(s)
- Florian Kopp
- Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Strasse, D-35032 Marburg, Germany
| | | | | | | |
Collapse
|
91
|
Stack D, Neville C, Doyle S. Nonribosomal peptide synthesis in Aspergillus fumigatus and other fungi. MICROBIOLOGY-SGM 2007; 153:1297-1306. [PMID: 17464044 DOI: 10.1099/mic.0.2006/006908-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In fungi, nonribosomal peptide synthetases (NRP synthetases) are large multi-functional enzymes containing adenylation, thiolation (or peptidyl carrier protein, PCP) and condensation domains. These enzymes are often encoded within gene clusters. Multiple NRP synthetase ORFs have also been identified in fungi (14 in Aspergillus fumigatus). LeaA, a methyltransferase, is involved in secondary metabolite gene cluster regulation in Aspergillus spp. The NRP synthetases GliP and FtmA respectively direct the biosynthesis of the toxic metabolites gliotoxin and brevianamide F, a precursor of bioactive prenylated alkaloids. The NRP synthetase Pes1 has been shown to mediate resistance to oxidative stress, and in plant-pathogenic ascomycetes (e.g. Cochliobolus heterostrophus) an NRP synthetase, encoded by the NPS6 gene, significantly contributes to virulence and resistance to oxidative stress. Adenylation (A) domains within NRP synthetases govern the specificity of amino acid incorporation into nonribosomally synthesized peptides. To date there have only been limited demonstrations of A domain specificity (e.g. A. fumigatus GliP and in Beauveria bassiana) in fungi. Indeed, only in silico prediction data are available on A domain specificity of NRP synthetases from most fungi. NRP synthetases are activated by 4'-phosphopantetheinylation of serine residues within PCP domains by 4'-phosphopantetheinyl transferases (4'-PPTases). Coenzyme A acts as the 4'-phosphopantetheine donor, and labelled coenzyme A can be used to affinity-label apo-NRP synthetases. Emerging fungal gene disruption and gene cluster expression strategies, allied to proteomic strategies, are poised to facilitate a greater understanding of the coding potential of NRP synthetases in fungi.
Collapse
Affiliation(s)
- Deirdre Stack
- Department of Biology and National Institute for Cellular Biotechnology, National University of Ireland, Maynooth, Co. Kildare, Ireland
| | - Claire Neville
- Department of Biology and National Institute for Cellular Biotechnology, National University of Ireland, Maynooth, Co. Kildare, Ireland
| | - Sean Doyle
- Department of Biology and National Institute for Cellular Biotechnology, National University of Ireland, Maynooth, Co. Kildare, Ireland
| |
Collapse
|
92
|
Thurley S, Röglin L, Seitz O. Hairpin peptide beacon: dual-labeled PNA-peptide-hybrids for protein detection. J Am Chem Soc 2007; 129:12693-5. [PMID: 17927187 DOI: 10.1021/ja075487r] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stefanie Thurley
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, D-12489, Berlin, Germany
| | | | | |
Collapse
|
93
|
Donato H, Krupenko NI, Tsybovsky Y, Krupenko SA. 10-formyltetrahydrofolate dehydrogenase requires a 4'-phosphopantetheine prosthetic group for catalysis. J Biol Chem 2007; 282:34159-66. [PMID: 17884809 DOI: 10.1074/jbc.m707627200] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
10-Formyltetrahydrofolate dehydrogenase (FDH) consists of two independent catalytic domains, N- and C-terminal, connected by a 100-amino acid residue linker (intermediate domain). Our previous studies on structural organization and enzymatic properties of rat FDH suggest that the overall enzyme reaction, i.e. NADP(+)-dependent conversion of 10-formyltetrahydrofolate to tetrahydrofolate and CO(2), consists of two steps: (i) hydrolytic cleavage of the formyl group in the N-terminal catalytic domain, followed by (ii) NADP(+)-dependent oxidation of the formyl group to CO(2) in the C-terminal aldehyde dehydrogenase domain. In this mechanism, it was not clear how the formyl group is transferred between the two catalytic domains after the first step. This study demonstrates that the intermediate domain functions similarly to an acyl carrier protein. A 4'-phosphopantetheine swinging arm bound through a phosphoester bond to Ser(354) of the intermediate domain transfers the formyl group between the catalytic domains of FDH. Thus, our study defines the intermediate domain of FDH as a novel carrier protein and provides the previously lacking component of the FDH catalytic mechanism.
Collapse
Affiliation(s)
- Henry Donato
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 173 Ashley Avenue, Charleston, SC 29425, USA
| | | | | | | |
Collapse
|
94
|
Yen M, Yin J. High-throughput profiling of posttranslational modification enzymes by phage display. Biotechniques 2007; 43:31, 33, 35 passim. [PMID: 17695643 DOI: 10.2144/000112502] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Phage display has been used as a high-throughput platform for identifying proteins or peptides with desired binding or catalytic activities from a complex proteome. Recently, phage display has been applied to profile the catalytic activities of posttranslational modification (PTM) enzymes. Here, we highlight recent work elucidating the downstream targets of PTM enzymes by phage display, including the genome-wide profiling of biosynthetic enzymes subject to phosphopantetheinyl transferase (PPTase) modification.
Collapse
Affiliation(s)
- Michelle Yen
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | | |
Collapse
|
95
|
Meier JL, Mercer AC, Rivera H, Burkart MD. Synthesis and evaluation of bioorthogonal pantetheine analogues for in vivo protein modification. J Am Chem Soc 2007; 128:12174-84. [PMID: 16967968 DOI: 10.1021/ja063217n] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In vivo carrier protein tagging has recently become an attractive target for the site-specific modification of fusion systems and new approaches to natural product proteomics. A detailed study of pantetheine analogues was performed in order to identify suitable partners for covalent protein labeling inside living cells. A rapid synthesis of pantothenamide analogues was developed and used to produce a panel which was evaluated for in vitro and in vivo protein labeling. Kinetic comparisons allowed the construction of a structure-activity relationship to pinpoint the linker, dye, and bioorthogonal reporter of choice for carrier protein labeling. Finally bioorthogonal pantetheine analogues were shown to target carrier proteins with high specificity in vivo and undergo chemoselective ligation to reporters in crude cell lysate. The methods demonstrated here allow carrier proteins to be visualized and isolated for the first time without the need for antibody techniques and set the stage for the future use of carrier protein fusions in chemical biology.
Collapse
Affiliation(s)
- Jordan L Meier
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0358, USA
| | | | | | | |
Collapse
|
96
|
Liu Y, Bruner SD. Rational manipulation of carrier-domain geometry in nonribosomal peptide synthetases. Chembiochem 2007; 8:617-21. [PMID: 17335097 DOI: 10.1002/cbic.200700010] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ye Liu
- Department of Chemistry, Boston College, Eugene F. Merkert Chemistry Center, Chestnut Hill, MA 02467, USA
| | | |
Collapse
|
97
|
Zhou Z, Cironi P, Lin AJ, Xu Y, Hrvatin S, Golan DE, Silver PA, Walsh CT, Yin J. Genetically encoded short peptide tags for orthogonal protein labeling by Sfp and AcpS phosphopantetheinyl transferases. ACS Chem Biol 2007; 2:337-46. [PMID: 17465518 DOI: 10.1021/cb700054k] [Citation(s) in RCA: 169] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Short peptide tags S6 and A1, each 12 residues in length, were identified from a phage-displayed peptide library as efficient substrates for site-specific protein labeling catalyzed by Sfp and AcpS phosphopantetheinyl transferases (PPTases), respectively. S6 and A1 tags were selected for useful levels of orthogonality in reactivities with the PPTases: the catalytic efficiency, kcat/Km of Sfp-catalyzed S6 serine phosphopantetheinylation was 442-fold greater than that for AcpS. Conversely, the kcat/Km of AcpS-catalyzed A1 labeling was 30-fold higher than that for Sfp-catalyzed A1 labeling. S6 and A1 peptide tags can be fused to N- or C-termini of proteins for orthogonal labeling of target proteins in cell lysates or on live cell surfaces. The development of the orthogonal S6 and A1 tags represents a significant enhancement of PPTase-catalyzed protein labeling, allowing tandem or iterative covalent attachment of small molecules of diverse structures to the target proteins with high efficiency and specificity.
Collapse
Affiliation(s)
- Zhe Zhou
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
98
|
Qiao C, Wilson DJ, Bennett EM, Aldrich CC. A mechanism-based aryl carrier protein/thiolation domain affinity probe. J Am Chem Soc 2007; 129:6350-1. [PMID: 17469819 PMCID: PMC2538614 DOI: 10.1021/ja069201e] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
99
|
Mercer AC, Burkart MD. The ubiquitous carrier protein--a window to metabolite biosynthesis. Nat Prod Rep 2007; 24:750-73. [PMID: 17653358 DOI: 10.1039/b603921a] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nature has developed a remarkable strategy to isolate metabolites from the milieu of the cell for chemical modification through the use of carrier proteins. Common to both primary and secondary metabolic pathways, acyl-carrier proteins constitute a conserved protein architecture which mediate the biosynthesis of a variety of metabolic products. Analogies have been made between the carrier protein and solid phase resin for chemical synthesis, as both entities provide a mechanism to separate compounds of interest from complex mixtures for selective chemical modification. However, there is significantly more to the carrier protein than an attachment point. In this review, we aim to systematically characterize the role of carrier proteins in various metabolic pathways and outline their utility in biosynthesis and biotechnology; 185 references are cited.
Collapse
Affiliation(s)
- Andrew C Mercer
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, USA
| | | |
Collapse
|
100
|
Yin J, Straight PD, Hrvatin S, Dorrestein PC, Bumpus SB, Jao C, Kelleher NL, Kolter R, Walsh CT. Genome-Wide High-Throughput Mining of Natural-Product Biosynthetic Gene Clusters by Phage Display. ACTA ACUST UNITED AC 2007; 14:303-12. [PMID: 17379145 DOI: 10.1016/j.chembiol.2007.01.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2006] [Revised: 12/26/2006] [Accepted: 01/09/2007] [Indexed: 10/23/2022]
Abstract
We have developed a phage-display method for high-throughput mining of bacterial gene clusters encoding the natural-product biosynthetic enzymes, polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs). This method uses the phosphopantetheinyl transferase activity of Sfp to specifically biotinylate NRPS and PKS carrier-protein domains expressed from a library of random genome fragments fused to a gene encoding a phage coat protein. Subsequently, the biotinylated phages are enriched through selection on streptavidin-coated plates. Using this method, we isolated phage clones from the multiple NRPS and PKS gene clusters encoded in the genomes of Bacillus subtilis and Myxococcus xanthus. Due to the rapid and unambiguous identification of carrier domains, this method will provide an efficient tool for high-throughput cloning of NRPS and PKS gene clusters from many individual bacterial genomes and multigenome environmental DNA.
Collapse
Affiliation(s)
- Jun Yin
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | | | | | | | | | | | | | | | | |
Collapse
|