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Zhu J, Lau K, Puschmann R, Harmel RK, Zhang Y, Pries V, Gaugler P, Broger L, Dutta AK, Jessen HJ, Schaaf G, Fernie AR, Hothorn LA, Fiedler D, Hothorn M. Two bifunctional inositol pyrophosphate kinases/phosphatases control plant phosphate homeostasis. eLife 2019; 8:43582. [PMID: 31436531 PMCID: PMC6731061 DOI: 10.7554/elife.43582] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 08/21/2019] [Indexed: 12/15/2022] Open
Abstract
Many eukaryotic proteins regulating phosphate (Pi) homeostasis contain SPX domains that are receptors for inositol pyrophosphates (PP-InsP), suggesting that PP-InsPs may regulate Pi homeostasis. Here we report that deletion of two diphosphoinositol pentakisphosphate kinases VIH1/2 impairs plant growth and leads to constitutive Pi starvation responses. Deletion of phosphate starvation response transcription factors partially rescues vih1 vih2 mutant phenotypes, placing diphosphoinositol pentakisphosphate kinases in plant Pi signal transduction cascades. VIH1/2 are bifunctional enzymes able to generate and break-down PP-InsPs. Mutations in the kinase active site lead to increased Pi levels and constitutive Pi starvation responses. ATP levels change significantly in different Pi growth conditions. ATP-Mg2+ concentrations shift the relative kinase and phosphatase activities of diphosphoinositol pentakisphosphate kinases in vitro. Pi inhibits the phosphatase activity of the enzyme. Thus, VIH1 and VIH2 relay changes in cellular ATP and Pi concentrations to changes in PP-InsP levels, allowing plants to maintain sufficient Pi levels.
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Affiliation(s)
- Jinsheng Zhu
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Kelvin Lau
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Robert Puschmann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany.,Department of Chemistry, Humboldt Universität zu Berlin, Berlin, Germany
| | - Robert K Harmel
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany.,Department of Chemistry, Humboldt Universität zu Berlin, Berlin, Germany
| | - Youjun Zhang
- Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.,Center of Plant System Biology and Biotechnology, Plovdiv, Bulgaria
| | - Verena Pries
- Institute of Crop Science and Resource Conservation, Department of Plant Nutrition, University of Bonn, Bonn, Germany
| | - Philipp Gaugler
- Institute of Crop Science and Resource Conservation, Department of Plant Nutrition, University of Bonn, Bonn, Germany
| | - Larissa Broger
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Amit K Dutta
- Institute of Organic Chemistry, Freiburg im Breisgau, Germany
| | | | - Gabriel Schaaf
- Institute of Crop Science and Resource Conservation, Department of Plant Nutrition, University of Bonn, Bonn, Germany
| | - Alisdair R Fernie
- Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Ludwig A Hothorn
- Institute of Biostatistics, Leibniz University, Hannover, Germany
| | - Dorothea Fiedler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany.,Department of Chemistry, Humboldt Universität zu Berlin, Berlin, Germany
| | - Michael Hothorn
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
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Filipuzzi I, Thomas JR, Pries V, Estoppey D, Salcius M, Studer C, Schirle M, Hoepfner D. Direct Interaction of Chivosazole F with Actin Elicits Cell Responses Similar to Latrunculin A but Distinct from Chondramide. ACS Chem Biol 2017; 12:2264-2269. [PMID: 28796488 DOI: 10.1021/acschembio.7b00385] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [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
The microbial metabolite Chivosazole F has been described to affect the cytoskeleton and to inhibit actin polymerization in vitro. Applying orthogonal genomic and proteomics approaches, we now show for the first time that Chivosazole F exerts its effect by directly interacting with actin and demonstrate the cellular impact of Chivosazole F in an unbiased, genome-wide context in yeast and in mammalian cells. Furthermore, mutation-based resistance mapping identifies two SNPs located in the putative Chivosazole F binding site of actin. Comparing chemogenomic profiles and responses to the Chivosazole F-resistant SNPs shows a partially conserved mechanism of action for Chivosazole F and Latrunculin A, but clear divergence from Chondramide. In addition, C14orf80 is an evolutionarily highly conserved ORF, lacking any functional annotation. As editing of C14orf80 leads to Chivosazole F hyper-resistance, we propose a function for this gene product in counteracting perturbation of actin filaments.
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Affiliation(s)
- Ireos Filipuzzi
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum
1 Novartis Campus, CH-4056 Basel, Switzerland
| | - Jason Ray Thomas
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Verena Pries
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum
1 Novartis Campus, CH-4056 Basel, Switzerland
| | - David Estoppey
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum
1 Novartis Campus, CH-4056 Basel, Switzerland
| | - Michael Salcius
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Christian Studer
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum
1 Novartis Campus, CH-4056 Basel, Switzerland
| | - Markus Schirle
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Dominic Hoepfner
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum
1 Novartis Campus, CH-4056 Basel, Switzerland
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Filipuzzi I, Cotesta S, Perruccio F, Knapp B, Fu Y, Studer C, Pries V, Riedl R, Helliwell SB, Petrovic KT, Movva NR, Sanglard D, Tao J, Hoepfner D. High-Resolution Genetics Identifies the Lipid Transfer Protein Sec14p as Target for Antifungal Ergolines. PLoS Genet 2016; 12:e1006374. [PMID: 27855158 PMCID: PMC5147771 DOI: 10.1371/journal.pgen.1006374] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 09/20/2016] [Indexed: 12/25/2022] Open
Abstract
Invasive infections by fungal pathogens cause more deaths than malaria worldwide. We found the ergoline compound NGx04 in an antifungal screen, with selectivity over mammalian cells. High-resolution chemogenomics identified the lipid transfer protein Sec14p as the target of NGx04 and compound-resistant mutations in Sec14p define compound-target interactions in the substrate binding pocket of the protein. Beyond its essential lipid transfer function in a variety of pathogenic fungi, Sec14p is also involved in secretion of virulence determinants essential for the pathogenicity of fungi such as Cryptococcus neoformans, making Sec14p an attractive antifungal target. Consistent with this dual function, we demonstrate that NGx04 inhibits the growth of two clinical isolates of C. neoformans and that NGx04-related compounds have equal and even higher potency against C. neoformans. Furthermore NGx04 analogues showed fungicidal activity against a fluconazole resistant C. neoformans strain. In summary, we present genetic evidence that NGx04 inhibits fungal Sec14p and initial data supporting NGx04 as a novel antifungal starting point. Emerging resistance to antibiotics led to an inglorious revival of infectious diseases. Furthermore, in the past 30 years, only one novel anti-fungal target has been discovered which was used to develop therapies against. Therefore pathogen-selective targets and knowledge about possible resistance determinants are of utmost importance to successfully develop new medicines. Here we describe the identification of anti-fungal ergolines, targeting the lipid transfer protein Sec14p, and inhibiting the growth of two clinical isolates of the pathogenic fungus Cryptococcus neoformans. Both, compound and target represent attractive points for further investigations: Sec14p as it differs significantly from the human homolog and as it has been implicated in fungal viability and pathogenicity, and, ergolines as they are used in the clinic against a variety of diseases demonstrating both efficacy and safety.
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Affiliation(s)
- Ireos Filipuzzi
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, Switzerland
- * E-mail:
| | - Simona Cotesta
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, Switzerland
| | - Francesca Perruccio
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, Switzerland
| | - Britta Knapp
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, Switzerland
| | - Yue Fu
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Christian Studer
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, Switzerland
| | - Verena Pries
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, Switzerland
| | - Ralph Riedl
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, Switzerland
| | - Stephen B. Helliwell
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, Switzerland
| | - Katarina T. Petrovic
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, Switzerland
| | - N. Rao Movva
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, Switzerland
| | - Dominique Sanglard
- Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland
| | - Jianshi Tao
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Dominic Hoepfner
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, Switzerland
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Pries V, Cotesta S, Riedl R, Aust T, Schuierer S, Tao J, Filipuzzi I, Hoepfner D. Advantages and Challenges of Phenotypic Screens. ACTA ACUST UNITED AC 2015; 21:306-15. [DOI: 10.1177/1087057115610488] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 09/16/2015] [Indexed: 11/15/2022]
Abstract
Phenotypic screens are effective starting points to identify compounds with desirable activities. To find novel antifungals, we conducted a phenotypic screen in Saccharomyces cerevisiae and identified two discrete scaffolds with good growth inhibitory characteristics. Lack of broad-spectrum activity against pathogenic fungi called for directed chemical compound optimization requiring knowledge of the molecular target. Chemogenomic profiling identified effects on geranylgeranyltransferase I (GGTase I), an essential enzyme that prenylates proteins involved in cell signaling, such as Cdc42p and Rho1p. Selection of resistant mutants against both compounds confirmed the target hypothesis and enabled mapping of the compound binding site to the substrate binding pocket. Differential resistance-conferring mutations and selective substrate competition demonstrate distinct binding modes for the two chemotypes. Exchange of the S. cerevisiae GGTase I subunits with those of Candida albicans resulted in an absence of growth inhibition for both compounds, thus confirming the identified target as well as the narrow antifungal spectrum of activity. This prenylation pathway is reported to be nonessential in pathogenic species and challenges the therapeutic value of these leads while demonstrating the importance of an integrated target identification platform following a phenotypic screen.
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Affiliation(s)
- Verena Pries
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Simona Cotesta
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Ralph Riedl
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Thomas Aust
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Sven Schuierer
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Jianshi Tao
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Ireos Filipuzzi
- Novartis Institutes for BioMedical Research, Basel, Switzerland
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Ziegler S, Pries V, Hedberg C, Waldmann H. Identifizierung der Zielproteine bioaktiver Verbindungen: Die Suche nach der Nadel im Heuhaufen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208749] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Ziegler S, Pries V, Hedberg C, Waldmann H. Target identification for small bioactive molecules: finding the needle in the haystack. Angew Chem Int Ed Engl 2013; 52:2744-92. [PMID: 23418026 DOI: 10.1002/anie.201208749] [Citation(s) in RCA: 353] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Indexed: 01/10/2023]
Abstract
Identification and confirmation of bioactive small-molecule targets is a crucial, often decisive step both in academic and pharmaceutical research. Through the development and availability of several new experimental techniques, target identification is, in principle, feasible, and the number of successful examples steadily grows. However, a generic methodology that can successfully be applied in the majority of the cases has not yet been established. Herein we summarize current methods for target identification of small molecules, primarily for a chemistry audience but also the biological community, for example, the chemist or biologist attempting to identify the target of a given bioactive compound. We describe the most frequently employed experimental approaches for target identification and provide several representative examples illustrating the state-of-the-art. Among the techniques currently available, protein affinity isolation using suitable small-molecule probes (pulldown) and subsequent mass spectrometric analysis of the isolated proteins appears to be most powerful and most frequently applied. To provide guidance for rapid entry into the field and based on our own experience we propose a typical workflow for target identification, which centers on the application of chemical proteomics as the key step to generate hypotheses for potential target proteins.
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Affiliation(s)
- Slava Ziegler
- Max-Planck-Institut für molekulare Physiologie, Abt. Chemische Biologie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.
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Dückert H, Pries V, Khedkar V, Menninger S, Bruss H, Bird AW, Maliga Z, Brockmeyer A, Janning P, Hyman A, Grimme S, Schürmann M, Preut H, Hübel K, Ziegler S, Kumar K, Waldmann H. Natural product-inspired cascade synthesis yields modulators of centrosome integrity. Nat Chem Biol 2011; 8:179-84. [PMID: 22198731 DOI: 10.1038/nchembio.758] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Accepted: 10/07/2011] [Indexed: 12/23/2022]
Abstract
In biology-oriented synthesis, the scaffolds of biologically relevant compound classes inspire the synthesis of focused compound collections enriched in bioactivity. This criterion is, in particular, met by the scaffolds of natural products selected in evolution. The synthesis of natural product-inspired compound collections calls for efficient reaction sequences that preferably combine multiple individual transformations in one operation. Here we report the development of a one-pot, twelve-step cascade reaction sequence that includes nine different reactions and two opposing kinds of organocatalysis. The cascade sequence proceeds within 10-30 min and transforms readily available substrates into complex indoloquinolizines that resemble the core tetracyclic scaffold of numerous polycyclic indole alkaloids. Biological investigation of a corresponding focused compound collection revealed modulators of centrosome integrity, termed centrocountins, which caused fragmented and supernumerary centrosomes, chromosome congression defects, multipolar mitotic spindles, acentrosomal spindle poles and multipolar cell division by targeting the centrosome-associated proteins nucleophosmin and Crm1.
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Affiliation(s)
- Heiko Dückert
- Max-Planck-Institut für Molekulare Physiologie, Abteilung Chemische Biologie, Dortmund, Germany
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