1
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Kwon J, Bae M, Szamosvári D, Cassilly CD, Bolze AS, Jackson DR, Xavier RJ, Clardy J. Collinsella aerofaciens Produces a pH-Responsive Lipid Immunogen. J Am Chem Soc 2023; 145:7071-7074. [PMID: 36952265 PMCID: PMC10080676 DOI: 10.1021/jacs.3c00250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Some members of the human gut microbiota profoundly influence their host's physiology, health, and therapeutic responses, but the responsible molecules and mechanisms are largely unknown. As part of a project to identify immunomodulators produced by gut microbes, we analyzed the metabolome of Collinsella aerofaciens, an actinomycete that figures prominently in numerous association studies. The associations are typically positive correlations of C. aerofaciens with pro-inflammatory responses and undesirable outcomes, but an association with favorable responses to PD-1/PD-L1 cancer immunotherapy is a notable exception. A phenotypic assay-guided screen using dendritic cells (mBMDCs) and cytokine readouts identified the active compound, which was structurally characterized as a lysoglycoglycerolipid with an acetal-bearing β-galactofuranose head group (CaLGL-1, 1). The structural assignment was confirmed through total synthesis. Assays with tlr2-/-, tlr4-/-, and wt mBMDCs revealed TLR2-dependent signaling. CaLGL-1 is produced by a conversion of a bacterially biosynthesized plasmalogen (CaPlsM, 3) to CaLGL-1 (1) in a low-pH environment.
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Affiliation(s)
- Jaeyoung Kwon
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Blavatnik Institute, Boston, Massachusetts 02115, United States
- Natural Product Informatics Research Center, Korea Institute of Science and Technology (KIST), Gangneung 25451, Republic of Korea
| | - Munhyung Bae
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Blavatnik Institute, Boston, Massachusetts 02115, United States
- College of Pharmacy, Gachon University, Incheon 21936, Republic of Korea
| | - Dávid Szamosvári
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Blavatnik Institute, Boston, Massachusetts 02115, United States
| | - Chelsi D Cassilly
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Blavatnik Institute, Boston, Massachusetts 02115, United States
| | - Andrew S Bolze
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - David R Jackson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Blavatnik Institute, Boston, Massachusetts 02115, United States
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Blavatnik Institute, Boston, Massachusetts 02115, United States
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2
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Ancajas CF, Alam S, Alves DS, Zhou Y, Wadsworth NM, Cassilly CD, Ricks TJ, Carr AJ, Reynolds TB, Barrera FN, Best MD. Cellular Labeling of Phosphatidylserine Using Clickable Serine Probes. ACS Chem Biol 2023; 18:377-384. [PMID: 36745020 DOI: 10.1021/acschembio.2c00813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Phosphatidylserine (PS) is a key lipid that plays important roles in disease-related biological processes, and therefore, the means to track PS in live cells are invaluable. Herein, we describe the metabolic labeling of PS in Saccharomyces cerevisiae cells using analogues of serine, a PS precursor, derivatized with azide moieties at either the amino (N-l-SerN3) or carbonyl (C-l-SerN3) groups. The conservative click tag modification enabled these compounds to infiltrate normal lipid biosynthetic pathways, thereby producing tagged PS molecules as supported by mass spectrometry studies, thin-layer chromatography (TLC) analysis, and further derivatization with fluorescent reporters via click chemistry to enable imaging in yeast cells. This approach shows strong prospects for elucidating the complex biosynthetic and trafficking pathways involving PS.
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Affiliation(s)
- Christelle F Ancajas
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Shahrina Alam
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Daiane S Alves
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Yue Zhou
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Nicholas M Wadsworth
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Chelsi D Cassilly
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Tanei J Ricks
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Adam J Carr
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Todd B Reynolds
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Michael D Best
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
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3
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Vélez Justiniano YA, Goeres DM, Sandvik EL, Kjellerup BV, Sysoeva TA, Harris JS, Warnat S, McGlennen M, Foreman CM, Yang J, Li W, Cassilly CD, Lott K, HerrNeckar LE. Mitigation and use of biofilms in space for the benefit of human space exploration. Biofilm 2023; 5:100102. [PMID: 36660363 PMCID: PMC9843197 DOI: 10.1016/j.bioflm.2022.100102] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 10/31/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 01/08/2023] Open
Abstract
Biofilms are self-organized communities of microorganisms that are encased in an extracellular polymeric matrix and often found attached to surfaces. Biofilms are widely present on Earth, often found in diverse and sometimes extreme environments. These microbial communities have been described as recalcitrant or protective when facing adversity and environmental exposures. On the International Space Station, biofilms were found in human-inhabited environments on a multitude of hardware surfaces. Moreover, studies have identified phenotypic and genetic changes in the microorganisms under microgravity conditions including changes in microbe surface colonization and pathogenicity traits. Lack of consistent research in microgravity-grown biofilms can lead to deficient understanding of altered microbial behavior in space. This could subsequently create problems in engineered systems or negatively impact human health on crewed spaceflights. It is especially relevant to long-term and remote space missions that will lack resupply and service. Conversely, biofilms are also known to benefit plant growth and are essential for human health (i.e., gut microbiome). Eventually, biofilms may be used to supply metabolic pathways that produce organic and inorganic components useful to sustaining life on celestial bodies beyond Earth. This article will explore what is currently known about biofilms in space and will identify gaps in the aerospace industry's knowledge that should be filled in order to mitigate or to leverage biofilms to the advantage of spaceflight.
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Affiliation(s)
- Yo-Ann Vélez Justiniano
- ECLSS Development Branch, NASA Marshall Space Flight Center, Huntsville, AL, USA,Corresponding author.
| | - Darla M. Goeres
- The Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA,Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA
| | | | - Birthe Veno Kjellerup
- Department of Civil and Environmental Engineering, University of Maryland, College Park, MD, USA
| | - Tatyana A. Sysoeva
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, USA
| | - Jacob S. Harris
- Biomedical and Environmental Science Division, NASA Johnson Space Center, Houston, TX, USA
| | - Stephan Warnat
- The Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA,Mechanical Engineering, Montana State University, Bozeman, MT, USA
| | - Matthew McGlennen
- The Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA,Mechanical Engineering, Montana State University, Bozeman, MT, USA
| | - Christine M. Foreman
- The Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA,Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA
| | - Jiseon Yang
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA
| | - Wenyan Li
- Laboratory Support Services and Operations (LASSO), NASA Kennedy Space Center, Cape Canaveral, FL, USA
| | | | - Katelynn Lott
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, USA
| | - Lauren E. HerrNeckar
- ECLSS Development Branch, NASA Marshall Space Flight Center, Huntsville, AL, USA
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4
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Bae M, Cassilly CD, Liu X, Park SM, Tusi BK, Chen X, Kwon J, Filipčík P, Bolze AS, Liu Z, Vlamakis H, Graham DB, Buhrlage SJ, Xavier RJ, Clardy J. Akkermansia muciniphila phospholipid induces homeostatic immune responses. Nature 2022; 608:168-173. [PMID: 35896748 PMCID: PMC9328018 DOI: 10.1038/s41586-022-04985-7] [Citation(s) in RCA: 107] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 06/16/2022] [Indexed: 12/12/2022]
Abstract
Multiple studies have established associations between human gut bacteria and host physiology, but determining the molecular mechanisms underlying these associations has been challenging1-3. Akkermansia muciniphila has been robustly associated with positive systemic effects on host metabolism, favourable outcomes to checkpoint blockade in cancer immunotherapy and homeostatic immunity4-7. Here we report the identification of a lipid from A. muciniphila's cell membrane that recapitulates the immunomodulatory activity of A. muciniphila in cell-based assays8. The isolated immunogen, a diacyl phosphatidylethanolamine with two branched chains (a15:0-i15:0 PE), was characterized through both spectroscopic analysis and chemical synthesis. The immunogenic activity of a15:0-i15:0 PE has a highly restricted structure-activity relationship, and its immune signalling requires an unexpected toll-like receptor TLR2-TLR1 heterodimer9,10. Certain features of the phospholipid's activity are worth noting: it is significantly less potent than known natural and synthetic TLR2 agonists; it preferentially induces some inflammatory cytokines but not others; and, at low doses (1% of EC50) it resets activation thresholds and responses for immune signalling. Identifying both the molecule and an equipotent synthetic analogue, its non-canonical TLR2-TLR1 signalling pathway, its immunomodulatory selectivity and its low-dose immunoregulatory effects provide a molecular mechanism for a model of A. muciniphila's ability to set immunological tone and its varied roles in health and disease.
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Affiliation(s)
- Munhyung Bae
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute, Boston, MA, USA
- College of Pharmacy, Gachon University, Incheon, South Korea
| | - Chelsi D Cassilly
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute, Boston, MA, USA
| | - Xiaoxi Liu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute, Boston, MA, USA
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sung-Moo Park
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Betsabeh Khoramian Tusi
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Xiangjun Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jaeyoung Kwon
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute, Boston, MA, USA
- Natural Product Informatics Research Center, Korea Institute of Science and Technology (KIST), Ganeung, South Korea
| | - Pavel Filipčík
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
- SBGrid Consortium, Harvard Medical School, Blavatnik Institute, Boston, MA, USA
| | | | - Zehua Liu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel B Graham
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sara J Buhrlage
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute, Boston, MA, USA
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute, Boston, MA, USA.
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5
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Szamosvári D, Bae M, Bang S, Tusi BK, Cassilly CD, Park SM, Graham DB, Xavier RJ, Clardy J. Lyme Disease, Borrelia burgdorferi, and Lipid Immunogens. J Am Chem Soc 2022; 144:2474-2478. [PMID: 35129341 DOI: 10.1021/jacs.1c12202] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The human immune system detects potentially pathogenic microbes with receptors that respond to microbial metabolites. While the overall immune signaling pathway is known in considerable detail, the initial molecular signals, the microbially produced immunogens, for important diseases like Lyme disease (LD) are often not well-defined. The immunogens for LD are produced by the spirochete Borrelia burgdorferi, and a galactoglycerolipid (1) has been identified as a key trigger for the inflammatory immune response that characterizes LD. This report corrects the original structural assignment of 1 to 3, a change of an α-galactopyranose to an α-galactofuranose headgroup. The seemingly small change has important implications for the diagnosis, prevention, and treatment of LD.
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Affiliation(s)
- Dávid Szamosvári
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Blavatnik Institute, Boston, Massachusetts 02115, United States
| | - Munhyung Bae
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Blavatnik Institute, Boston, Massachusetts 02115, United States
| | - Sunghee Bang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Blavatnik Institute, Boston, Massachusetts 02115, United States
| | - Betsabeh Khoramian Tusi
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States.,Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Chelsi D Cassilly
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Blavatnik Institute, Boston, Massachusetts 02115, United States
| | - Sung-Moo Park
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States.,Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Daniel B Graham
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States.,Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States.,Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Blavatnik Institute, Boston, Massachusetts 02115, United States
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6
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Zhou Y, Cassilly CD, Reynolds TB. Mapping the Substrate-Binding Sites in the Phosphatidylserine Synthase in Candida albicans. Front Cell Infect Microbiol 2022; 11:765266. [PMID: 35004345 PMCID: PMC8727905 DOI: 10.3389/fcimb.2021.765266] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/29/2021] [Indexed: 12/02/2022] Open
Abstract
The fungal phosphatidylserine (PS) synthase, a membrane protein encoded by the CHO1 gene, is a potential drug target for pathogenic fungi, such as Candida albicans. However, both substrate-binding sites of C. albicans Cho1 have not been characterized. Cho1 has two substrates: cytidyldiphosphate-diacylglycerol (CDP-DAG) and serine. Previous studies identified a conserved CDP-alcohol phosphotransferase (CAPT) binding motif, which is present within Cho1. We tested the CAPT motif for its role in PS synthesis by mutating conserved residues using alanine substitution mutagenesis. PS synthase assays revealed that mutations in all but one conserved amino acid within the CAPT motif resulted in decreased Cho1 function. In contrast, there were no clear motifs in Cho1 for binding serine. Therefore, to identify the serine binding site, PS synthase sequences from three fungi were aligned with sequences of a similar enzyme, phosphatidylinositol (PI) synthase, from the same fungi. This revealed a motif that was unique to PS synthases. Using alanine substitution mutagenesis, we found that some of the residues in this motif are required for Cho1 function. Two alanine substitution mutants, L184A and R189A, exhibited contrasting impacts on PS synthase activity, and were characterized for their Michaelis-Menten kinetics. The L184A mutant displayed enhanced PS synthase activity and showed an increased Vmax. In contrast, R189A showed decreased PS synthase activity and increased Km for serine, suggesting that residue R189 is involved in serine binding. These results help to characterize PS synthase substrate binding, and should direct rational approaches for finding Cho1 inhibitors that may lead to better antifungals.
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Affiliation(s)
- Yue Zhou
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, TN, United States
| | - Chelsi D Cassilly
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, TN, United States
| | - Todd B Reynolds
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, TN, United States
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7
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Henke MT, Brown EM, Cassilly CD, Vlamakis H, Xavier RJ, Clardy J. Capsular polysaccharide correlates with immune response to the human gut microbe Ruminococcus gnavus. Proc Natl Acad Sci U S A 2021; 118:e2007595118. [PMID: 33972416 PMCID: PMC8157926 DOI: 10.1073/pnas.2007595118] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Active inflammatory bowel disease (IBD) often coincides with increases of Ruminococcus gnavus, a gut microbe found in nearly everyone. It was not known how, or if, this correlation contributed to disease. We investigated clinical isolates of R. gnavus to identify molecular mechanisms that would link R. gnavus to inflammation. Here, we show that only some isolates of R. gnavus produce a capsular polysaccharide that promotes a tolerogenic immune response, whereas isolates lacking functional capsule biosynthetic genes elicit robust proinflammatory responses in vitro. Germ-free mice colonized with an isolate of R. gnavus lacking a capsule show increased measures of gut inflammation compared to those colonized with an encapsulated isolate in vivo. These observations in the context of our earlier identification of an inflammatory cell-wall polysaccharide reveal how some strains of R. gnavus could drive the inflammatory responses that characterize IBD.
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Affiliation(s)
- Matthew T Henke
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Eric M Brown
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Chelsi D Cassilly
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Hera Vlamakis
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Ramnik J Xavier
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA 02114
| | - Jon Clardy
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115;
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8
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Jackson DR, Cassilly CD, Plichta DR, Vlamakis H, Liu H, Melville SB, Xavier RJ, Clardy J. Plasmalogen Biosynthesis by Anaerobic Bacteria: Identification of a Two-Gene Operon Responsible for Plasmalogen Production in Clostridium perfringens. ACS Chem Biol 2021; 16:6-13. [PMID: 33350306 PMCID: PMC7812594 DOI: 10.1021/acschembio.0c00673] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [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] [Indexed: 01/06/2023]
Abstract
![]()
Plasmalogens are vinyl ether-containing
lipids produced by mammals
and bacteria. The aerobic biosynthetic pathway in eukaryotes and bacteria
is known, but the anaerobic pathway has remained a mystery. Here,
we describe a two-gene operon (plasmalogen synthase, pls) responsible for plasmalogen production in the anaerobic bacterium Clostridium perfringens. While aerobic plasmalogen biosynthesis
involves an oxidative conversion of an ether to a vinyl ether, anaerobic
plasmalogen biosynthesis uses the reductive conversion of an ester
to an aldehyde equivalent. Heterologous expression of the C. perfringens pls operon in E. coli conferred
the ability to produce plasmalogens. The pls operon
is predicted to encode a multidomain complex similar to benzoyl-CoA
reductase/hydroxylacyl-CoA dehydratase (BCR/HAD) enzymes. Versions
of this operon can be found in a wide range of obligate and facultative
anaerobic bacteria, including many human gut microbes.
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Affiliation(s)
- David R. Jackson
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston Massachusetts 02115, United States
| | - Chelsi D. Cassilly
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston Massachusetts 02115, United States
| | - Damian R. Plichta
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Hualan Liu
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Stephen B. Melville
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Ramnik J. Xavier
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston Massachusetts 02115, United States
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Ye L, Bae M, Cassilly CD, Jabba SV, Thorpe DW, Martin AM, Lu HY, Wang J, Thompson JD, Lickwar CR, Poss KD, Keating DJ, Jordt SE, Clardy J, Liddle RA, Rawls JF. Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways. Cell Host Microbe 2020; 29:179-196.e9. [PMID: 33352109 DOI: 10.1016/j.chom.2020.11.011] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 09/08/2020] [Accepted: 11/19/2020] [Indexed: 12/12/2022]
Abstract
The intestinal epithelium senses nutritional and microbial stimuli using epithelial sensory enteroendocrine cells (EEC). EECs communicate nutritional information to the nervous system, but whether they also relay signals from intestinal microbes remains unknown. Using in vivo real-time measurements of EEC and nervous system activity in zebrafish, we discovered that the bacteria Edwardsiella tarda activate EECs through the receptor transient receptor potential ankyrin A1 (Trpa1) and increase intestinal motility. Microbial, pharmacological, or optogenetic activation of Trpa1+EECs directly stimulates vagal sensory ganglia and activates cholinergic enteric neurons by secreting the neurotransmitter 5-hydroxytryptamine (5-HT). A subset of indole derivatives of tryptophan catabolism produced by E. tarda and other gut microbes activates zebrafish EEC Trpa1 signaling. These catabolites also directly stimulate human and mouse Trpa1 and intestinal 5-HT secretion. These results establish a molecular pathway by which EECs regulate enteric and vagal neuronal pathways in response to microbial signals.
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Affiliation(s)
- Lihua Ye
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC 27710, USA; Division of Gastroenterology, Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Munhyung Bae
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Chelsi D Cassilly
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Sairam V Jabba
- Department of Anesthesiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Daniel W Thorpe
- Flinders Medical Research Institute, College of Medicine and Public Health, Flinders University, Adelaide, Australia
| | - Alyce M Martin
- Flinders Medical Research Institute, College of Medicine and Public Health, Flinders University, Adelaide, Australia
| | - Hsiu-Yi Lu
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jinhu Wang
- Division of Cardiology, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - John D Thompson
- Department of Cell Biology, Regeneration Next, Duke University School of Medicine, Durham, NC 27710, USA
| | - Colin R Lickwar
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC 27710, USA; Division of Gastroenterology, Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kenneth D Poss
- Department of Cell Biology, Regeneration Next, Duke University School of Medicine, Durham, NC 27710, USA
| | - Damien J Keating
- Flinders Medical Research Institute, College of Medicine and Public Health, Flinders University, Adelaide, Australia
| | - Sven-Eric Jordt
- Department of Anesthesiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Rodger A Liddle
- Division of Gastroenterology, Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Department of Veterans Affairs, Durham, NC 27705, USA
| | - John F Rawls
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC 27710, USA; Division of Gastroenterology, Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA.
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Fukuda TTH, Cassilly CD, Gerdt JP, Henke MT, Helfrich EJN, Mevers E. Research Tales from the Clardy Laboratory: Function-Driven Natural Product Discovery. J Nat Prod 2020; 83:744-755. [PMID: 32105475 DOI: 10.1021/acs.jnatprod.9b01086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Over the past 70 years, the search for small molecules from nature has transformed biomedical research: natural products are the basis for half of all pharmaceuticals; the quest for total synthesis of natural products fueled development of methodologies for organic synthesis; and their biosynthesis presented unprecedented biochemical transformations, expanding our chemo-enzymatic toolkit. Initially, the discovery of small molecules was driven by bioactivity-guided fractionation. However, this approach yielded the frequent rediscovery of already known metabolites. As a result, focus shifted to identifying novel scaffolds through either structure-first methods or genome mining, relegating function as a secondary concern. Over the past two decades, the laboratory of Jon Clardy has taken an alternative route and focused on an ecology-driven, function-first approach in pursuit of uncovering bacterial small molecules with biological activity. In this review, we highlight several examples that showcase this ecology-first approach. Though the highlighted systems are diverse, unifying themes are (1) to understand how microbes interact with their host or environment, (2) to gain insights into the environmental roles of microbial metabolites, and (3) to explore pharmaceutical potential from these ecologically relevant metabolites.
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Affiliation(s)
- Taise T H Fukuda
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Departamento de Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Avenida do Café, s/n, 14040-903, Ribeirão Preto, SP, Brazil
| | - Chelsi D Cassilly
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Joseph P Gerdt
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Matthew T Henke
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Eric J N Helfrich
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Emily Mevers
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
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Tams RN, Cassilly CD, Anaokar S, Brewer WT, Dinsmore JT, Chen YL, Patton-Vogt J, Reynolds TB. Overproduction of Phospholipids by the Kennedy Pathway Leads to Hypervirulence in Candida albicans. Front Microbiol 2019; 10:86. [PMID: 30792701 PMCID: PMC6374345 DOI: 10.3389/fmicb.2019.00086] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [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: 11/15/2018] [Accepted: 01/16/2019] [Indexed: 12/18/2022] Open
Abstract
Candida albicans is an opportunistic human fungal pathogen that causes life-threatening systemic infections, as well as oral mucosal infections. Phospholipids are crucial for pathogenesis in C. albicans, as disruption of phosphatidylserine (PS) and phosphatidylethanolamine (PE) biosynthesis within the cytidine diphosphate diacylglycerol (CDP-DAG) pathway causes avirulence in a mouse model of systemic infection. The synthesis of PE by this pathway plays a crucial role in virulence, but it was unknown if downstream conversion of PE to phosphatidylcholine (PC) is required for pathogenicity. Therefore, the enzymes responsible for methylating PE to PC, Pem1 and Pem2, were disrupted. The resulting pem1Δ/Δ pem2Δ/Δ mutant was not less virulent in mice, but rather hypervirulent. Since the pem1Δ/Δ pem2Δ/Δ mutant accumulated PE, this led to the hypothesis that increased PE synthesis increases virulence. To test this, the alternative Kennedy pathway for PE/PC synthesis was exploited. This pathway makes PE and PC from exogenous ethanolamine and choline, respectively, using three enzymatic steps. In contrast to Saccharomyces cerevisiae, C. albicans was found to use one enzyme, Ept1, for the final enzymatic step (ethanolamine/cholinephosphotransferase) that generates both PE and PC. EPT1 was overexpressed, which resulted in increases in both PE and PC synthesis. Moreover, the EPT1 overexpression strain is hypervirulent in mice and causes them to succumb to system infection more rapidly than wild-type. In contrast, disruption of EPT1 causes loss of PE and PC synthesis by the Kennedy pathway, and decreased kidney fungal burden during the mouse systemic infection model, indicating a mild loss of virulence. In addition, the ept1Δ/Δ mutant exhibits decreased cytotoxicity against oral epithelial cells in vitro, whereas the EPT1 overexpression strain exhibits increased cytotoxicity. Taken altogether, our data indicate that mutations that result in increased PE synthesis cause greater virulence and mutations that decrease PE synthesis attenuate virulence.
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Affiliation(s)
- Robert N Tams
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Chelsi D Cassilly
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Sanket Anaokar
- Department of Biological Sciences, Duquesne University, Pittsburgh, PA, United States
| | - William T Brewer
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Justin T Dinsmore
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Ying-Lien Chen
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
| | - Jana Patton-Vogt
- Department of Biological Sciences, Duquesne University, Pittsburgh, PA, United States
| | - Todd B Reynolds
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
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Ricks TJ, Cassilly CD, Carr AJ, Alves DS, Alam S, Tscherch K, Yokley TW, Workman CE, Morrell-Falvey JL, Barrera FN, Reynolds TB, Best MD. Labeling of Phosphatidylinositol Lipid Products in Cells through Metabolic Engineering by Using a Clickable myo-Inositol Probe. Chembiochem 2018; 20:172-180. [PMID: 30098105 DOI: 10.1002/cbic.201800248] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [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: 05/08/2018] [Revised: 07/30/2018] [Indexed: 12/28/2022]
Abstract
Phosphatidylinositol (PI) lipids control critical biological processes, so aberrant biosynthesis often leads to disease. As a result, the capability to track the production and localization of these compounds in cells is vital for elucidating their complex roles. Herein, we report the design, synthesis, and application of clickable myo-inositol probe 1 a for bioorthogonal labeling of PI products. To validate this platform, we initially conducted PI synthase assays to show that 1 a inhibits PI production in vitro. Fluorescence microscopy experiments next showed probe-dependent imaging in T-24 human bladder cancer and Candida albicans cells. Growth studies in the latter showed that replacement of myo-inositol with probe 1 a led to an enhancement in cell growth. Finally, fluorescence-based TLC analysis and mass spectrometry experiments support the labeling of PI lipids. This approach provides a promising means for tracking the complex biosynthesis and trafficking of these lipids in cells.
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Affiliation(s)
- Tanei J Ricks
- Department of Chemistry, University of Tennessee, 1420 Circle Park Drive, Knoxville, TN, 37996, USA
| | - Chelsi D Cassilly
- Department of Microbiology, University of Tennessee, 1414 Cumberland Avenue, Knoxville, TN, 37996-0840, USA
| | - Adam J Carr
- Department of Chemistry, University of Tennessee, 1420 Circle Park Drive, Knoxville, TN, 37996, USA
| | - Daiane S Alves
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, 1414 Cumberland Avenue, Knoxville, TN, 37996-0840, USA
| | - Shahrina Alam
- Department of Chemistry, University of Tennessee, 1420 Circle Park Drive, Knoxville, TN, 37996, USA
| | - Kathrin Tscherch
- Department of Chemistry, University of Tennessee, 1420 Circle Park Drive, Knoxville, TN, 37996, USA
| | - Timothy W Yokley
- Department of Chemistry, University of Tennessee, 1420 Circle Park Drive, Knoxville, TN, 37996, USA
| | - Cameron E Workman
- Department of Chemistry, University of Tennessee, 1420 Circle Park Drive, Knoxville, TN, 37996, USA
| | | | - Francisco N Barrera
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, 1414 Cumberland Avenue, Knoxville, TN, 37996-0840, USA
| | - Todd B Reynolds
- Department of Microbiology, University of Tennessee, 1414 Cumberland Avenue, Knoxville, TN, 37996-0840, USA
| | - Michael D Best
- Department of Chemistry, University of Tennessee, 1420 Circle Park Drive, Knoxville, TN, 37996, USA
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Cassilly CD, Reynolds TB. PS, It's Complicated: The Roles of Phosphatidylserine and Phosphatidylethanolamine in the Pathogenesis of Candida albicans and Other Microbial Pathogens. J Fungi (Basel) 2018; 4:jof4010028. [PMID: 29461490 PMCID: PMC5872331 DOI: 10.3390/jof4010028] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 02/09/2018] [Accepted: 02/13/2018] [Indexed: 12/24/2022] Open
Abstract
The phospholipids phosphatidylserine (PS) and phosphatidylethanolamine (PE) play important roles in the virulence of Candida albicans and loss of PS synthesis or synthesis of PE from PS (PS decarboxylase) severely compromises virulence in C. albicans in a mouse model of systemic candidiasis. This review discusses synthesis of PE and PS in C. albicans and mechanisms by which these lipids impact virulence in this fungus. This is further compared to how PS and PE synthesis impact virulence in other fungi, parasites and bacteria. Furthermore, the impact of PS asymmetry on virulence and extracellular vesicle formation in several microbes is reviewed. Finally, the potential for PS and PE synthases as drug targets in these various kingdoms is also examined.
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Affiliation(s)
- Chelsi D Cassilly
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA.
| | - Todd B Reynolds
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA.
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Cassilly CD, Farmer AT, Montedonico AE, Smith TK, Campagna SR, Reynolds TB. Role of phosphatidylserine synthase in shaping the phospholipidome of Candida albicans. FEMS Yeast Res 2017; 17:2966860. [PMID: 28158422 DOI: 10.1093/femsyr/fox007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [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: 07/09/2016] [Accepted: 01/31/2017] [Indexed: 01/06/2023] Open
Abstract
Phosphatidylserine (PS) synthase (Cho1p) and the PS decarboxylase enzymes (Psd1p and Psd2p), which synthesize PS and phosphatidylethanolamine (PE), respectively, are crucial for Candida albicans virulence. Mutations that disrupt these enzymes compromise virulence. These enzymes are part of the cytidine diphosphate-diacylglycerol pathway (i.e. de novo pathway) for phospholipid synthesis. Understanding how losses of PS and/or PE synthesis pathways affect the phospholipidome of Candida is important for fully understanding how these enzymes impact virulence. The cho1Δ/Δ and psd1Δ/Δ psd2Δ/Δ mutations cause similar changes in levels of phosphatidic acid, phosphatidylglycerol, phosphatidylinositol and PS. However, only slight changes were seen in PE and phosphatidylcholine (PC). This finding suggests that the alternative mechanism for making PE and PC, the Kennedy pathway, can compensate for loss of the de novo synthesis pathway. Candida albicans Cho1p, the lipid biosynthetic enzyme with the most potential as a drug target, has been biochemically characterized, and analysis of its substrate specificity and kinetics reveal that these are similar to those previously published for Saccharomyces cerevisiae Cho1p.
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Affiliation(s)
- Chelsi D Cassilly
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
| | - Abigail T Farmer
- Department of Chemistry, University of Tennessee, Knoxville, TN 37996, USA
| | | | - Terry K Smith
- Biomedical Sciences Research Complex, Schools of Biology and Chemistry, The North Haugh, The University St. Andrews, Fife KY16 9ST, UK
| | - Shawn R Campagna
- Department of Chemistry, University of Tennessee, Knoxville, TN 37996, USA
| | - Todd B Reynolds
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
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Cassilly CD, Maddox MM, Cherian PT, Bowling JJ, Hamann MT, Lee RE, Reynolds TB. SB-224289 Antagonizes the Antifungal Mechanism of the Marine Depsipeptide Papuamide A. PLoS One 2016; 11:e0154932. [PMID: 27183222 PMCID: PMC4868317 DOI: 10.1371/journal.pone.0154932] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 04/21/2016] [Indexed: 12/20/2022] Open
Abstract
In order to expand the repertoire of antifungal compounds a novel, high-throughput phenotypic drug screen targeting fungal phosphatidylserine (PS) synthase (Cho1p) was developed based on antagonism of the toxin papuamide A (Pap-A). Pap-A is a cyclic depsipeptide that binds to PS in the membrane of wild-type Candida albicans, and permeabilizes its plasma membrane, ultimately causing cell death. Organisms with a homozygous deletion of the CHO1 gene (cho1ΔΔ) do not produce PS and are able to survive in the presence of Pap-A. Using this phenotype (i.e. resistance to Pap-A) as an indicator of Cho1p inhibition, we screened over 5,600 small molecules for Pap-A resistance and identified SB-224289 as a positive hit. SB-224289, previously reported as a selective human 5-HT1B receptor antagonist, also confers resistance to the similar toxin theopapuamide (TPap-A), but not to other cytotoxic depsipeptides tested. Structurally similar molecules and truncated variants of SB-224289 do not confer resistance to Pap-A, suggesting that the toxin-blocking ability of SB-224289 is very specific. Further biochemical characterization revealed that SB-224289 does not inhibit Cho1p, indicating that Pap-A resistance is conferred by another undetermined mechanism. Although the mode of resistance is unclear, interaction between SB-224289 and Pap-A or TPap-A suggests this screening assay could be adapted for discovering other compounds which could antagonize the effects of other environmentally- or medically-relevant depsipeptide toxins.
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Affiliation(s)
- Chelsi D. Cassilly
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Marcus M. Maddox
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee, 38105, United States of America
| | - Philip T. Cherian
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee, 38105, United States of America
| | - John J. Bowling
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee, 38105, United States of America
| | - Mark T. Hamann
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, Medical University of South Carolina, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Richard E. Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee, 38105, United States of America
| | - Todd B. Reynolds
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
- * E-mail:
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