1
|
Rapp PB, Baccile JA, Galimidi RP, Vielmetter J. Engineering Antigen-Specific Tolerance to an Artificial Protein Hydrogel. ACS Biomater Sci Eng 2024; 10:2188-2199. [PMID: 38479351 DOI: 10.1021/acsbiomaterials.3c01430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Artificial protein hydrogels are an emerging class of biomaterials with numerous prospective applications in tissue engineering and regenerative medicine. These materials are likely to be immunogenic due to their frequent incorporation of novel amino acid sequence domains, which often serve a functional role within the material itself. We engineered injectable "self" and "nonself" artificial protein hydrogels, which were predicted to have divergent immune outcomes in vivo on the basis of their primary amino acid sequence. Following implantation in mouse, the nonself gels raised significantly higher antigel antibody titers than the corresponding self gels. Prophylactic administration of a fusion antibody targeting the nonself hydrogel epitopes to DEC-205, an endocytic receptor involved in Treg induction, fully suppressed the elevated antibody titer against the nonself gels. These results suggest that the clinical immune response to artificial protein biomaterials, including those that contain highly antigenic sequence domains, can be tuned through the induction of antigen-specific tolerance.
Collapse
Affiliation(s)
- Peter B Rapp
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, California 91125, United States
| | - Joshua A Baccile
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, California 91125, United States
| | - Rachel P Galimidi
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, California 91125, United States
| | - Jost Vielmetter
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, California 91125, United States
| |
Collapse
|
2
|
McBee DP, Hulsey ZN, Hedges MR, Baccile JA. Biological Demands and Toxicity of Isoprenoid Precursors in Bacillus Subtilis Through Cell-Permeant Analogs of Isopentenyl Pyrophosphate and Dimethylallyl Pyrophosphate. Chembiochem 2024:e202400064. [PMID: 38568158 DOI: 10.1002/cbic.202400064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/28/2024] [Indexed: 04/25/2024]
Abstract
Bacterial isoprenoids are necessary for many biological processes, including maintaining membrane integrity, facilitating intercellular communication, and preventing oxidative damage. All bacterial isoprenoids are biosynthesized from two five carbon structural isomers, isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP), which are cell impermeant. Herein, we demonstrate exogenous delivery of IPP and DMAPP into Bacillus subtilis by utilizing a self-immolative ester (SIE)-caging approach. We initially evaluated native B. subtilis esterase activity, which revealed a preference for short straight chain esters. We then examined the viability of the SIE-caging approach in B. subtilis and demonstrate that the released caging groups are well tolerated and the released IPP and DMAPP are bioavailable, such that isoprenoid biosynthesis can be rescued in the presence of pathway inhibitors. We further show that IPP and DMAPP are both toxic and inhibit growth of B. subtilis at the same concentration. Lastly, we establish the optimal ratio of IPP to DMAPP (5 : 1) for B. subtilis growth and find that, surprisingly, DMAPP alone is insufficient to rescue isoprenoid biosynthesis under high concentrations of fosmidomycin. These findings showcase the potential of the SIE-caging approach in B. subtilis and promise to both aid in novel isoprenoid discovery and to inform metabolic engineering efforts in bacteria.
Collapse
Affiliation(s)
- Dillon P McBee
- Department of Chemistry, University of Tennessee, Knoxville, TN, United States
| | - Zackary N Hulsey
- Department of Chemistry, University of Tennessee, Knoxville, TN, United States
| | - Makayla R Hedges
- Department of Chemistry, University of Tennessee, Knoxville, TN, United States
| | - Joshua A Baccile
- Department of Chemistry, University of Tennessee, Knoxville, TN, United States
| |
Collapse
|
3
|
Rossi FM, McBee DP, Trybala TN, Hulsey ZN, Gonzalez Curbelo C, Mazur W, Baccile JA. Membrane Permeant Analogs for Independent Cellular Introduction of the Terpene Precursors Isopentenyl- and Dimethylallyl-Pyrophosphate. Chembiochem 2023; 24:e202200512. [PMID: 36354788 DOI: 10.1002/cbic.202200512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 11/09/2022] [Indexed: 11/12/2022]
Abstract
Isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP) are the central five-carbon precursors to all terpenes. Despite their significance, exogenous, independent delivery of IPP and DMAPP to cells is impossible as the negatively charged pyrophosphate makes these molecules membrane impermeant. Herein, we demonstrate a facile method to circumvent this challenge through esterification of the β-phosphate with two self-immolative esters (SIEs) that neutralize the negatively charged pyrophosphate to yield membrane-permeant analogs of IPP and DMAPP. Following cellular incorporation, general esterase activity initiates cleavage of the SIEs, resulting in traceless release of IPP and DMAPP for metabolic utilization. Addition of the synthesized IPP and DMAPP precursor analogs rescued cell growth of glioblastoma (U-87MG) cancer cells concurrently treated with the HMG-CoA reductase inhibitor pitavastatin, which otherwise abrogates cell growth via blocking production of IPP and DMAPP. This work demonstrates a new application of a prodrug strategy to incorporate a metabolic intermediate and promises to enable future interrogation of the distinct biological roles of IPP and DMAPP.
Collapse
Affiliation(s)
- Francis M Rossi
- Department of Chemistry, University of Tennessee, Knoxville, TN, USA.,Department of Chemistry SUNY Cortland, Cortland, NY, USA
| | - Dillon P McBee
- Department of Chemistry, University of Tennessee, Knoxville, TN, USA
| | - Thomas N Trybala
- Department of Chemistry, University of Tennessee, Knoxville, TN, USA
| | - Zackary N Hulsey
- Department of Chemistry, University of Tennessee, Knoxville, TN, USA
| | | | - William Mazur
- Department of Chemistry, University of Tennessee, Knoxville, TN, USA
| | - Joshua A Baccile
- Department of Chemistry, University of Tennessee, Knoxville, TN, USA
| |
Collapse
|
4
|
Lou J, Qualls ML, Hudson MM, McBee DP, Baccile JA, Best MD. Reactive Oxygen Species (ROS) Activated Liposomal Cell Delivery using a Boronate-Caged Guanidine Lipid. Chemistry 2022; 28:e202201057. [PMID: 35639353 PMCID: PMC9388614 DOI: 10.1002/chem.202201057] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Indexed: 08/18/2023]
Abstract
We report boronate-caged guanidine-lipid 1 that activates liposomes for cellular delivery only upon uncaging of this compound by reactive oxygen species (ROS) to produce cationic lipid products. These liposomes are designed to mimic the exceptional cell delivery properties of cell-penetrating peptides (CPPs), while the inclusion of the boronate cage is designed to enhance selectivity such that cell entry will only be activated in the presence of ROS. Boronate uncaging by hydrogen peroxide was verified by mass spectrometry and zeta potential (ZP) measurements. A microplate-based fluorescence assay was developed to study the ROS-mediated vesicle interactions between 1-liposomes and anionic membranes, which were further elucidated via dynamic light scattering (DLS) analysis. Cellular delivery studies utilizing fluorescence microscopy demonstrated significant enhancements in cellular delivery only when 1-liposomes were incubated with hydrogen peroxide. Our results showcase that lipid 1 exhibits strong potential as an ROS-responsive liposomal platform for targeted drug delivery applications.
Collapse
Affiliation(s)
- Jinchao Lou
- Department of Chemistry, University of Tennessee, 1420 Circle Drive, Knoxville, TN, 37996, USA
| | - Megan L Qualls
- Department of Chemistry, University of Tennessee, 1420 Circle Drive, Knoxville, TN, 37996, USA
| | - Macy M Hudson
- Department of Chemistry, University of Tennessee, 1420 Circle Drive, Knoxville, TN, 37996, USA
| | - Dillon P McBee
- Department of Chemistry, University of Tennessee, 1420 Circle Drive, Knoxville, TN, 37996, USA
| | - Joshua A Baccile
- Department of Chemistry, University of Tennessee, 1420 Circle Drive, Knoxville, TN, 37996, USA
| | - Michael D Best
- Department of Chemistry, University of Tennessee, 1420 Circle Drive, Knoxville, TN, 37996, USA
| |
Collapse
|
5
|
Qualls ML, Lou J, McBee DP, Baccile JA, Best MD. Cyclic Disulfide Liposomes for Membrane Functionalization and Cellular Delivery. Chemistry 2022; 28:e202201164. [DOI: 10.1002/chem.202201164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Megan L. Qualls
- Department of Chemistry University of Tennessee 1420 Circle Drive Knoxville TN, 37996 USA
| | - Jinchao Lou
- Department of Chemistry University of Tennessee 1420 Circle Drive Knoxville TN, 37996 USA
| | - Dillon P. McBee
- Department of Chemistry University of Tennessee 1420 Circle Drive Knoxville TN, 37996 USA
| | - Joshua A. Baccile
- Department of Chemistry University of Tennessee 1420 Circle Drive Knoxville TN, 37996 USA
| | - Michael D. Best
- Department of Chemistry University of Tennessee 1420 Circle Drive Knoxville TN, 37996 USA
| |
Collapse
|
6
|
Qualls ML, Lou J, McBee DP, Baccile JA, Best MD. Cover Feature: Cyclic Disulfide Liposomes for Membrane Functionalization and Cellular Delivery (Chem. Eur. J. 45/2022). Chemistry 2022. [DOI: 10.1002/chem.202202129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Megan L. Qualls
- Department of Chemistry University of Tennessee 1420 Circle Drive Knoxville TN, 37996 USA
| | - Jinchao Lou
- Department of Chemistry University of Tennessee 1420 Circle Drive Knoxville TN, 37996 USA
| | - Dillon P. McBee
- Department of Chemistry University of Tennessee 1420 Circle Drive Knoxville TN, 37996 USA
| | - Joshua A. Baccile
- Department of Chemistry University of Tennessee 1420 Circle Drive Knoxville TN, 37996 USA
| | - Michael D. Best
- Department of Chemistry University of Tennessee 1420 Circle Drive Knoxville TN, 37996 USA
| |
Collapse
|
7
|
Baccile JA, Voorhees PJ, Chillo AJ, Berry M, Morgenstern R, Schwertfeger TJ, Rossi FM, Nelson CDS. Front Cover: Site‐Specific Small Molecule Labeling of an Internal Loop in JC Polyomavirus Pentamers Using the π‐Clamp‐Mediated Cysteine Conjugation (ChemBioChem 21/2021). Chembiochem 2021. [DOI: 10.1002/cbic.202100317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Joshua A. Baccile
- Division of Chemistry and Chemical Engineering California Institute of Technology Pasadena CA, 91106 USA
| | - Peter J. Voorhees
- Department of Biological Sciences SUNY Cortland Cortland NY, 13045 USA
| | - Anthony J. Chillo
- Department of Biological Sciences SUNY Cortland Cortland NY, 13045 USA
| | - Madeline Berry
- Department of Chemistry SUNY Cortland Cortland NY, 13045 USA
| | | | | | | | | |
Collapse
|
8
|
Baccile JA, Voorhees PJ, Chillo AJ, Berry M, Morgenstern R, Schwertfeger TJ, Rossi FM, Nelson CDS. Site-Specific Small Molecule Labeling of an Internal Loop in JC Polyomavirus Pentamers Using the π-Clamp-Mediated Cysteine Conjugation. Chembiochem 2021; 22:3037-3041. [PMID: 34018291 DOI: 10.1002/cbic.202100188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/19/2021] [Indexed: 12/21/2022]
Abstract
The major capsid protein VP1 of JC Polyomavirus assembles into pentamers that serve as a model for studying viral entry of this potentially severe human pathogen. Previously, labeling of viral proteins utilized large fusion proteins or non-specific amine- or cysteine-functionalization with fluorescent dyes. Imaging of these sterically hindered fusion proteins or heterogeneously labeled virions limits reproducibility and could prevent the detection of subtle trafficking phenomena. Here we advance the π-clamp-mediated cysteine conjugation for site-selective fluorescent labeling of VP1-pentamers. We demonstrate a one-step synthesis of a probe consisting of a bio-orthogonal click chemistry handle bridged to a perfluoro-biphenyl π-clamp reactive electrophile by a polyethylene glycol linker. We expand the scope of the π-clamp conjugation by demonstrating selective labeling of an internal, surface exposed loop in VP1. Thus, the π-clamp conjugation offers a general method to selectively bioconjugate tags-of-interest to viral proteins without impeding their ability to bind and enter cells.
Collapse
Affiliation(s)
- Joshua A Baccile
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91106, USA
| | - Peter J Voorhees
- Department of Biological Sciences, SUNY Cortland, Cortland, NY, 13045, USA
| | - Anthony J Chillo
- Department of Biological Sciences, SUNY Cortland, Cortland, NY, 13045, USA
| | - Madeline Berry
- Department of Chemistry, SUNY Cortland, Cortland, NY, 13045, USA
| | | | | | - Francis M Rossi
- Department of Chemistry, SUNY Cortland, Cortland, NY, 13045, USA
| | | |
Collapse
|
9
|
Hoki JS, Le HH, Mellott KE, Zhang YK, Fox BW, Rodrigues PR, Yu Y, Helf MJ, Baccile JA, Schroeder FC. Deep Interrogation of Metabolism Using a Pathway-Targeted Click-Chemistry Approach. J Am Chem Soc 2020; 142:18449-18459. [PMID: 33053303 DOI: 10.1021/jacs.0c06877] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Untargeted metabolomics indicates that the number of unidentified small-molecule metabolites may exceed the number of protein-coding genes for many organisms, including humans, by orders of magnitude. Uncovering the underlying metabolic networks is essential for elucidating the physiological and ecological significance of these biogenic small molecules. Here we develop a click-chemistry-based enrichment strategy, DIMEN (deep interrogation of metabolism via enrichment), that we apply to investigate metabolism of the ascarosides, a family of signaling molecules in the model organism C. elegans. Using a single alkyne-modified metabolite and a solid-phase azide resin that installs a diagnostic moiety for MS/MS-based identification, DIMEN uncovered several hundred novel compounds originating from diverse biosynthetic transformations that reveal unexpected intersection with amino acid, carbohydrate, and energy metabolism. Many of the newly discovered transformations could not be identified or detected by conventional LC-MS analyses without enrichment, demonstrating the utility of DIMEN for deeply probing biochemical networks that generate extensive yet uncharacterized structure space.
Collapse
Affiliation(s)
- Jason S Hoki
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Henry H Le
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Karlie E Mellott
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Ying K Zhang
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Bennett W Fox
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Pedro R Rodrigues
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Yan Yu
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Maximilian J Helf
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Joshua A Baccile
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| |
Collapse
|
10
|
Baccile JA, Le HH, Pfannenstiel BT, Bok JW, Gomez C, Brandenburger E, Hoffmeister D, Keller NP, Schroeder FC. Diketopiperazine Formation in Fungi Requires Dedicated Cyclization and Thiolation Domains. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201909052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Joshua A. Baccile
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology Cornell University Ithaca NY USA
- Present Address: Division of Chemistry and Chemical Engineering California Institute of Technology Pasadena CA USA
| | - Henry H. Le
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology Cornell University Ithaca NY USA
| | - Brandon T. Pfannenstiel
- Departments of Bacteriology Medical Microbiology and Immunology University of Wisconsin-Madison Madison WI USA
| | - Jin Woo Bok
- Departments of Bacteriology Medical Microbiology and Immunology University of Wisconsin-Madison Madison WI USA
| | - Christian Gomez
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology Cornell University Ithaca NY USA
| | - Eileen Brandenburger
- Department of Pharmaceutical Microbiology Hans-Knöll-Institute Friedrich Schiller University Jena Germany
| | - Dirk Hoffmeister
- Department of Pharmaceutical Microbiology Hans-Knöll-Institute Friedrich Schiller University Jena Germany
| | - Nancy P. Keller
- Departments of Bacteriology Medical Microbiology and Immunology University of Wisconsin-Madison Madison WI USA
| | - Frank C. Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology Cornell University Ithaca NY USA
| |
Collapse
|
11
|
Baccile JA, Le HH, Pfannenstiel BT, Bok JW, Gomez C, Brandenburger E, Hoffmeister D, Keller NP, Schroeder FC. Diketopiperazine Formation in Fungi Requires Dedicated Cyclization and Thiolation Domains. Angew Chem Int Ed Engl 2019; 58:14589-14593. [PMID: 31342608 DOI: 10.1002/anie.201909052] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Indexed: 01/08/2023]
Abstract
Cyclization of linear dipeptidyl precursors derived from nonribosomal peptide synthetases (NRPSs) into 2,5-diketopiperazines (DKPs) is a crucial step in the biosynthesis of a large number of bioactive natural products. However, the mechanism of DKP formation in fungi has remained unclear, despite extensive studies of their biosyntheses. Here we show that DKP formation en route to the fungal virulence factor gliotoxin requires a seemingly extraneous couplet of condensation (C) and thiolation (T) domains in the NRPS GliP. In vivo truncation of GliP to remove the CT couplet or just the T domain abrogated production of gliotoxin and all other gli pathway metabolites. Point mutation of conserved active sites in the C and T domains diminished cyclization activity of GliP in vitro and abolished gliotoxin biosynthesis in vivo. Verified NRPSs of other fungal DKPs terminate with similar CT domain couplets, suggesting a conserved strategy for DKP biosynthesis by fungal NRPSs.
Collapse
Affiliation(s)
- Joshua A Baccile
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA.,Present Address: Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Henry H Le
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Brandon T Pfannenstiel
- Departments of Bacteriology, Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Jin Woo Bok
- Departments of Bacteriology, Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Christian Gomez
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Eileen Brandenburger
- Department of Pharmaceutical Microbiology, Hans-Knöll-Institute, Friedrich Schiller University, Jena, Germany
| | - Dirk Hoffmeister
- Department of Pharmaceutical Microbiology, Hans-Knöll-Institute, Friedrich Schiller University, Jena, Germany
| | - Nancy P Keller
- Departments of Bacteriology, Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| |
Collapse
|
12
|
Falcke JM, Bose N, Artyukhin AB, Rödelsperger C, Markov GV, Yim JJ, Grimm D, Claassen MH, Panda O, Baccile JA, Zhang YK, Le HH, Jolic D, Schroeder FC, Sommer RJ. Linking Genomic and Metabolomic Natural Variation Uncovers Nematode Pheromone Biosynthesis. Cell Chem Biol 2018; 25:787-796.e12. [PMID: 29779955 DOI: 10.1016/j.chembiol.2018.04.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 02/28/2018] [Accepted: 04/04/2018] [Indexed: 11/17/2022]
Abstract
In the nematodes Caenorhabditis elegans and Pristionchus pacificus, a modular library of small molecules control behavior, lifespan, and development. However, little is known about the final steps of their biosynthesis, in which diverse building blocks from primary metabolism are attached to glycosides of the dideoxysugar ascarylose, the ascarosides. We combine metabolomic analysis of natural isolates of P. pacificus with genome-wide association mapping to identify a putative carboxylesterase, Ppa-uar-1, that is required for attachment of a pyrimidine-derived moiety in the biosynthesis of ubas#1, a major dauer pheromone component. Comparative metabolomic analysis of wild-type and Ppa-uar-1 mutants showed that Ppa-uar-1 is required specifically for the biosynthesis of ubas#1 and related metabolites. Heterologous expression of Ppa-UAR-1 in C. elegans yielded a non-endogenous ascaroside, whose structure confirmed that Ppa-uar-1 is involved in modification of a specific position in ascarosides. Our study demonstrates the utility of natural variation-based approaches for uncovering biosynthetic pathways.
Collapse
Affiliation(s)
- Jan M Falcke
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Neelanjan Bose
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Alexander B Artyukhin
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Christian Rödelsperger
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Gabriel V Markov
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany; Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 8227 Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Joshua J Yim
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany; Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Dominik Grimm
- Machine Learning and Computational Biology Research Group, Max Planck Institute for Intelligent Systems, 72076 Tübingen, Germany
| | - Marc H Claassen
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Oishika Panda
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Joshua A Baccile
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Ying K Zhang
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Henry H Le
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Dino Jolic
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
| | - Ralf J Sommer
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
| |
Collapse
|
13
|
Khalid S, Baccile JA, Spraker JE, Tannous J, Imran M, Schroeder FC, Keller NP. NRPS-Derived Isoquinolines and Lipopetides Mediate Antagonism between Plant Pathogenic Fungi and Bacteria. ACS Chem Biol 2018; 13:171-179. [PMID: 29182847 DOI: 10.1021/acschembio.7b00731] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Bacterial-fungal interactions are presumed to be mediated chiefly by small-molecule signals; however, little is known about the signaling networks that regulate antagonistic relationships between pathogens. Here, we show that the ralstonins, lipopeptides produced by the plant pathogenic bacteria Ralstonia solanacearum, interfere with germination of the plant-pathogenic fungus Aspergillus flavus by down-regulating expression of a cryptic biosynthetic gene cluster (BGC), named imq. Comparative metabolomic analysis of overexpression strains of the transcription factor ImqK revealed imq-dependent production of a family of tripeptide-derived alkaloids, the imizoquins. These alkaloids are produced via a nonribosomal peptide synthetase- (NRPS-)derived tripeptide and contain an unprecedented tricyclic imidazo[2,1-a]isoquinoline ring system. We show that the imizoquins serve a protective role against oxidative stress that is essential for normal A. flavus germination. Supplementation of purified imizoquins restored wildtype germination to a ΔimqK A. flavus strain and protected the fungus from ROS damage. Whereas the bacterial ralstonins retarded A. flavus germination and suppressed expression of the imq cluster, the fungal imizoquins in turn suppressed growth of R. solanacearum. We suggest such reciprocal small-molecule-mediated antagonism is a common feature in microbial encounters affecting pathogenicity and survival of the involved species.
Collapse
Affiliation(s)
- Saima Khalid
- Departments
of Bacteriology, Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, Wisconsin, United States
- Department
of Microbiology, Qauid-i-Azam University, Islamabad, Pakistan
| | - Joshua A. Baccile
- Boyce
Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, United States
| | - Joseph E. Spraker
- Department
of Plant Pathology, University of Wisconsin—Madison, Madison, Wisconsin, United States
| | - Joanna Tannous
- Departments
of Bacteriology, Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, Wisconsin, United States
| | - Muhammad Imran
- Department
of Microbiology, Qauid-i-Azam University, Islamabad, Pakistan
| | - Frank C. Schroeder
- Boyce
Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, United States
| | - Nancy P. Keller
- Departments
of Bacteriology, Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, Wisconsin, United States
| |
Collapse
|
14
|
Hind SR, Hoki JS, Baccile JA, Boyle PC, Schroeder FC, Martin GB. Detecting the interaction of peptide ligands with plant membrane receptors. ACTA ACUST UNITED AC 2017; 2:240-269. [PMID: 29098191 DOI: 10.1002/cppb.20053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The field of plant receptor biology has rapidly expanded in recent years, however the demonstration of direct interaction between receptor-ligand pairs remains a challenge. Click chemistry has revolutionized small molecule research but lacks popularity in plant research. Here we describe a method that tests for the direct physical interaction of a candidate receptor protein and a peptide ligand. This protocol describes the generation of the ligand probe, transient expression of a receptor protein, enrichment of membrane-bound receptors, photo-crosslinking and click chemistry-mediated reporter addition, and detection of the receptor-ligand complex. Copper-based click chemistry confers several advantages, including the versatility to use almost any azide-containing reporter molecule for detection or visualization of the complex and addition of the reporter molecule after receptor-ligand binding which reduces the need for bulky ligand modifications that could interfere with the interaction.
Collapse
Affiliation(s)
| | - Jason S Hoki
- Boyce Thompson Institute, Ithaca, New York.,Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York
| | - Joshua A Baccile
- Boyce Thompson Institute, Ithaca, New York.,Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York
| | | | - Frank C Schroeder
- Boyce Thompson Institute, Ithaca, New York.,Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York
| | - Gregory B Martin
- Boyce Thompson Institute, Ithaca, New York.,School of Integrative Plant Science, Cornell University, Ithaca, New York
| |
Collapse
|
15
|
Liberti MV, Dai Z, Wardell SE, Baccile JA, Liu X, Gao X, Baldi R, Mehrmohamadi M, Johnson MO, Madhukar NS, Shestov AA, Chio IIC, Elemento O, Rathmell JC, Schroeder FC, McDonnell DP, Locasale JW. A Predictive Model for Selective Targeting of the Warburg Effect through GAPDH Inhibition with a Natural Product. Cell Metab 2017; 26:648-659.e8. [PMID: 28918937 PMCID: PMC5629112 DOI: 10.1016/j.cmet.2017.08.017] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 04/25/2017] [Accepted: 08/18/2017] [Indexed: 01/09/2023]
Abstract
Targeted cancer therapies that use genetics are successful, but principles for selectively targeting tumor metabolism that is also dependent on the environment remain unknown. We now show that differences in rate-controlling enzymes during the Warburg effect (WE), the most prominent hallmark of cancer cell metabolism, can be used to predict a response to targeting glucose metabolism. We establish a natural product, koningic acid (KA), to be a selective inhibitor of GAPDH, an enzyme we characterize to have differential control properties over metabolism during the WE. With machine learning and integrated pharmacogenomics and metabolomics, we demonstrate that KA efficacy is not determined by the status of individual genes, but by the quantitative extent of the WE, leading to a therapeutic window in vivo. Thus, the basis of targeting the WE can be encoded by molecular principles that extend beyond the status of individual genes.
Collapse
Affiliation(s)
- Maria V Liberti
- Department of Pharmacology and Cancer Biology, Duke Cancer Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Ziwei Dai
- Department of Pharmacology and Cancer Biology, Duke Cancer Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Suzanne E Wardell
- Department of Pharmacology and Cancer Biology, Duke Cancer Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Joshua A Baccile
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Xiaojing Liu
- Department of Pharmacology and Cancer Biology, Duke Cancer Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xia Gao
- Department of Pharmacology and Cancer Biology, Duke Cancer Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Robert Baldi
- Department of Pharmacology and Cancer Biology, Duke Cancer Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mahya Mehrmohamadi
- Department of Pharmacology and Cancer Biology, Duke Cancer Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Marc O Johnson
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Neel S Madhukar
- Department of Physiology and Biophysics, Meyer Cancer Center, Institute for Precision Medicine and Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Alexander A Shestov
- Molecular Imaging and Metabolomics Lab, Radiology Department, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Iok I Christine Chio
- Cold Spring Harbor Laboratory, Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Olivier Elemento
- Department of Physiology and Biophysics, Meyer Cancer Center, Institute for Precision Medicine and Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Jeffrey C Rathmell
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Donald P McDonnell
- Department of Pharmacology and Cancer Biology, Duke Cancer Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke Cancer Institute, Duke University School of Medicine, Durham, NC 27710, USA.
| |
Collapse
|
16
|
McClure RA, Goering AW, Ju KS, Baccile JA, Schroeder FC, Metcalf WW, Thomson RJ, Kelleher NL. Elucidating the Rimosamide-Detoxin Natural Product Families and Their Biosynthesis Using Metabolite/Gene Cluster Correlations. ACS Chem Biol 2016; 11:3452-3460. [PMID: 27809474 DOI: 10.1021/acschembio.6b00779] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
As microbial genome sequencing becomes more widespread, the capacity of microorganisms to produce an immense number of metabolites has come into better view. Utilizing a metabolite/gene cluster correlation platform, the biosynthetic origins of a new family of natural products, the rimosamides, were discovered. The rimosamides were identified in Streptomyces rimosus and associated with their NRPS/PKS-type gene cluster based upon their high frequency of co-occurrence across 179 strains of actinobacteria. This also led to the discovery of the related detoxin gene cluster. The core of each of these families of natural products contains a depsipeptide bond at the point of bifurcation in their unusual branched structures, the origins of which are definitively assigned to nonlinear biosynthetic pathways via heterologous expression in Streptomyces lividans. The rimosamides were found to antagonize the antibiotic activity of blasticidin S against Bacillus cereus.
Collapse
Affiliation(s)
- Ryan A. McClure
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Anthony W. Goering
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Kou-San Ju
- Carl R.
Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Joshua A. Baccile
- Boyce Thompson
Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Frank C. Schroeder
- Boyce Thompson
Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - William W. Metcalf
- Carl R.
Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department of Microbiology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Regan J. Thomson
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil. L Kelleher
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| |
Collapse
|
17
|
Hind SR, Strickler SR, Boyle PC, Dunham DM, Bao Z, O'Doherty IM, Baccile JA, Hoki JS, Viox EG, Clarke CR, Vinatzer BA, Schroeder FC, Martin GB. Tomato receptor FLAGELLIN-SENSING 3 binds flgII-28 and activates the plant immune system. Nat Plants 2016; 2:16128. [PMID: 27548463 DOI: 10.1038/nplants.2016.128] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 07/22/2016] [Indexed: 05/13/2023]
Abstract
Plants and animals detect the presence of potential pathogens through the perception of conserved microbial patterns by cell surface receptors. Certain solanaceous plants, including tomato, potato and pepper, detect flgII-28, a region of bacterial flagellin that is distinct from that perceived by the well-characterized FLAGELLIN-SENSING 2 receptor. Here we identify and characterize the receptor responsible for this recognition in tomato, called FLAGELLIN-SENSING 3. This receptor binds flgII-28 and enhances immune responses leading to a reduction in bacterial colonization of leaf tissues. Further characterization of FLS3 and its signalling pathway could provide new insights into the plant immune system and transfer of the receptor to other crop plants offers the potential of enhancing resistance to bacterial pathogens that have evolved to evade FLS2-mediated immunity.
Collapse
Affiliation(s)
- Sarah R Hind
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853, USA
| | - Susan R Strickler
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853, USA
| | - Patrick C Boyle
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853, USA
| | - Diane M Dunham
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853, USA
| | - Zhilong Bao
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853, USA
| | - Inish M O'Doherty
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Joshua A Baccile
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Jason S Hoki
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Elise G Viox
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853, USA
| | - Christopher R Clarke
- Department of Plant Pathology, Physiology and Weed Sciences, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Boris A Vinatzer
- Department of Plant Pathology, Physiology and Weed Sciences, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Frank C Schroeder
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Gregory B Martin
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853, USA
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| |
Collapse
|
18
|
Baccile JA, Spraker JE, Le HH, Brandenburger E, Gomez C, Bok JW, Macheleidt J, Brakhage AA, Hoffmeister D, Keller NP, Schroeder FC. Plant-like biosynthesis of isoquinoline alkaloids in Aspergillus fumigatus. Nat Chem Biol 2016; 12:419-24. [PMID: 27065235 PMCID: PMC5049701 DOI: 10.1038/nchembio.2061] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 02/22/2016] [Indexed: 01/09/2023]
Abstract
Natural product discovery efforts have focused primarily on microbial biosynthetic gene clusters (BGCs) containing large multi-modular PKSs and NRPSs; however, sequencing of fungal genomes has revealed a vast number of BGCs containing smaller NRPS-like genes of unknown biosynthetic function. Using comparative metabolomics, we show that a BGC in the human pathogen Aspergillus fumigatus named fsq, which contains an NRPS-like gene lacking a condensation domain, produces several novel isoquinoline alkaloids, the fumisoquins. These compounds derive from carbon-carbon bond formation between two amino acid-derived moieties followed by a sequence that is directly analogous to isoquinoline alkaloid biosynthesis in plants. Fumisoquin biosynthesis requires the N-methyltransferase FsqC and the FAD-dependent oxidase FsqB, which represent functional analogs of coclaurine N-methyltransferase and berberine bridge enzyme in plants. Our results show that BGCs containing incomplete NRPS modules may reveal new biosynthetic paradigms and suggest that plant-like isoquinoline biosynthesis occurs in diverse fungi.
Collapse
Affiliation(s)
- Joshua A Baccile
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Joseph E Spraker
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Henry H Le
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Eileen Brandenburger
- Department of Pharmaceutical Microbiology at the Hans-Knöll-Institute, Friedrich Schiller University, Jena, Germany
| | - Christian Gomez
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Jin Woo Bok
- Institute for Microbiology, Friedrich Schiller University, Jena, Germany
| | - Juliane Macheleidt
- Institute for Microbiology, Friedrich Schiller University, Jena, Germany.,Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Axel A Brakhage
- Institute for Microbiology, Friedrich Schiller University, Jena, Germany.,Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Dirk Hoffmeister
- Department of Pharmaceutical Microbiology at the Hans-Knöll-Institute, Friedrich Schiller University, Jena, Germany
| | - Nancy P Keller
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| |
Collapse
|
19
|
Macheleidt J, Scherlach K, Neuwirth T, Schmidt-Heck W, Straßburger M, Spraker J, Baccile JA, Schroeder FC, Keller NP, Hertweck C, Heinekamp T, Brakhage AA. Transcriptome analysis of cyclic AMP-dependent protein kinase A-regulated genes reveals the production of the novel natural compound fumipyrrole by Aspergillus fumigatus. Mol Microbiol 2015; 96:148-62. [PMID: 25582336 DOI: 10.1111/mmi.12926] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2015] [Indexed: 01/31/2023]
Abstract
Aspergillus fumigatus is an opportunistic human pathogenic fungus causing life-threatening infections in immunocompromised patients. Adaptation to different habitats and also virulence of the fungus depends on signal perception and transduction by modules such as the cyclic AMP-dependent protein kinase A (PKA) pathway. Here, by transcriptome analysis, 632 differentially regulated genes of this important signaling cascade were identified, including 23 putative transcriptional regulators. The highest upregulated transcription factor gene was located in a previously unknown secondary metabolite gene cluster, which we named fmp, encoding an incomplete non-ribosomal peptide synthetase, FmpE. Overexpression of the regulatory gene fmpR using the Tet(On) system led to the specific expression of the other six genes of the fmp cluster. Metabolic profiling of wild type and fmpR overexpressing strain by HPLC-DAD and HPLC-HRESI-MS and structure elucidation by NMR led to identification of 5-benzyl-1H-pyrrole-2-carboxylic acid, which we named fumipyrrole. Fumipyrrole was not described as natural product yet. Chemical synthesis of fumipyrrole confirmed its structure. Interestingly, deletion of fmpR or fmpE led to reduced growth and sporulation of the mutant strains. Although fmp cluster genes were transcribed in infected mouse lungs, deletion of fmpR resulted in wild-type virulence in a murine infection model.
Collapse
Affiliation(s)
- Juliane Macheleidt
- Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), 07745, Jena, Germany; Institute for Microbiology, Friedrich Schiller University, 07745, Jena, Germany
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Wever WJ, Bogart JW, Baccile JA, Chan AN, Schroeder FC, Bowers AA. Chemoenzymatic synthesis of thiazolyl peptide natural products featuring an enzyme-catalyzed formal [4 + 2] cycloaddition. J Am Chem Soc 2015; 137:3494-7. [PMID: 25742119 DOI: 10.1021/jacs.5b00940] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thiocillins from Bacillus cereus ATCC 14579 are members of the well-known thiazolyl peptide class of natural product antibiotics, the biosynthesis of which has recently been shown to proceed via post-translational modification of ribosomally encoded precursor peptides. It has long been hypothesized that the final step of thiazolyl peptide biosynthesis involves a formal [4 + 2] cycloaddition between two dehydroalanines, a unique transformation that had eluded enzymatic characterization. Here we demonstrate that TclM, a single enzyme from the thiocillin biosynthetic pathway, catalyzes this transformation. To facilitate characterization of this new class of enzyme, we have developed a combined chemical and biological route to the complex peptide substrate, relying on chemical synthesis of a modified C-terminal fragment and coupling to a 38-residue leader peptide by means of native chemical ligation (NCL). This strategy, combined with active enzyme, provides a new chemoenzymatic route to this promising class of antibiotics.
Collapse
Affiliation(s)
- Walter J Wever
- †Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jonathan W Bogart
- †Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Joshua A Baccile
- ‡Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Andrew N Chan
- §Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Frank C Schroeder
- ‡Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Albert A Bowers
- †Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| |
Collapse
|
21
|
Wiemann P, Lechner BE, Baccile JA, Velk TA, Yin WB, Bok JW, Pakala S, Losada L, Nierman WC, Schroeder FC, Haas H, Keller NP. Perturbations in small molecule synthesis uncovers an iron-responsive secondary metabolite network in Aspergillus fumigatus. Front Microbiol 2014; 5:530. [PMID: 25386169 PMCID: PMC4208449 DOI: 10.3389/fmicb.2014.00530] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 09/23/2014] [Indexed: 11/13/2022] Open
Abstract
Iron plays a critical role in survival and virulence of the opportunistic pathogen Aspergillus fumigatus. Two transcription factors, the GATA-factor SreA and the bZip-factor HapX oppositely monitor iron homeostasis with HapX activating iron acquisition pathways (e.g., siderophores) and shutting down iron consumptive pathways (and SreA) during iron starvation conditions whereas SreA negatively regulates HapX and corresponding pathways during iron sufficiency. Recently the non-ribosomal peptide, hexadehydroastechrome (HAS; a tryptophan-derived iron (III)-complex), has been found important in A. fumigatus virulence. We found that HAS overproduction caused an iron starvation phenotype, from alteration of siderophore pools to regulation of iron homeostasis gene expression including sreA. Moreover, we uncovered an iron dependent secondary metabolism network where both SreA and HapX oppositely regulate multiple other secondary metabolites including HAS. This circuitry links iron-acquisition and consumption pathways with secondary metabolism-thus placing HAS as part of a metabolic feedback circuitry designed to balance iron pools in the fungus and presenting iron availability as one environmental trigger of secondary metabolism.
Collapse
Affiliation(s)
- Philipp Wiemann
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison Madison, WI, USA
| | - Beatrix E Lechner
- Division of Molecular Biology/Biocenter, Innsbruck Medical University Innsbruck, Austria
| | - Joshua A Baccile
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University Ithaca, NY, USA
| | - Thomas A Velk
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison Madison, WI, USA
| | - Wen-Bing Yin
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison Madison, WI, USA
| | - Jin Woo Bok
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison Madison, WI, USA
| | - Suman Pakala
- The J. Craig Venter Institute Rockville, MD, USA
| | | | | | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University Ithaca, NY, USA
| | - Hubertus Haas
- Division of Molecular Biology/Biocenter, Innsbruck Medical University Innsbruck, Austria
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison Madison, WI, USA ; Department of Bacteriology, University of Wisconsin-Madison Madison, WI, USA
| |
Collapse
|
22
|
Yin WB, Baccile JA, Bok JW, Chen Y, Keller NP, Schroeder FC. A nonribosomal peptide synthetase-derived iron(III) complex from the pathogenic fungus Aspergillus fumigatus. J Am Chem Soc 2013; 135:2064-7. [PMID: 23360537 DOI: 10.1021/ja311145n] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Small molecules (SMs) play central roles as virulence factors of pathogenic fungi and bacteria; however, genomic analyses suggest that the majority of microbial SMs have remained uncharacterized. Based on microarray analysis followed by comparative metabolomics of overexpression/knockout mutants, we identified a tryptophan-derived iron(III)-complex, hexadehydro-astechrome (HAS), as the major product of the cryptic has nonribosomal peptide synthetase (NRPS) gene cluster in the human pathogen Aspergillus fumigatus. Activation of the has cluster created a highly virulent A. fumigatus strain that increased mortality of infected mice. Comparative metabolomics of different mutant strains allowed to propose a pathway for HAS biosynthesis and further revealed cross-talk with another NRPS pathway producing the anticancer fumitremorgins.
Collapse
Affiliation(s)
- Wen-Bing Yin
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Wisconsin 53706, USA
| | | | | | | | | | | |
Collapse
|
23
|
Baccile JA, Morrell MA, Falotico RM, Milliken BT, Drew DL, Rossi FM. Modular synthesis of photocleavable peptides using click chemistry. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2012.02.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|