1
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Ghosh S, Sanchez AM, Schwer B, Prucker I, Jork N, Jessen HJ, Shuman S. Activities and genetic interactions of fission yeast Aps1, a Nudix-type inositol pyrophosphatase and inorganic polyphosphatase. mBio 2024:e0108424. [PMID: 38940614 DOI: 10.1128/mbio.01084-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 05/28/2024] [Indexed: 06/29/2024] Open
Abstract
Inositol pyrophosphate 1,5-IP8 regulates expression of a fission yeast phosphate homeostasis regulon, comprising phosphate acquisition genes pho1, pho84, and tgp1, via its action as an agonist of precocious termination of transcription of the upstream lncRNAs that repress PHO mRNA synthesis. 1,5-IP8 levels are dictated by a balance between the Asp1 N-terminal kinase domain that converts 5-IP7 to 1,5-IP8 and three inositol pyrophosphatases-the Asp1 C-terminal domain (a histidine acid phosphatase), Siw14 (a cysteinyl-phosphatase), and Aps1 (a Nudix enzyme). In this study, we report the biochemical and genetic characterization of Aps1 and an analysis of the effects of Asp1, Siw14, and Aps1 mutations on cellular inositol pyrophosphate levels. We find that Aps1's substrate repertoire embraces inorganic polyphosphates, 5-IP7, 1-IP7, and 1,5-IP8. Aps1 displays a ~twofold preference for hydrolysis of 1-IP7 versus 5-IP7 and aps1∆ cells have twofold higher levels of 1-IP7 vis-à-vis wild-type cells. While neither Aps1 nor Siw14 is essential for growth, an aps1∆ siw14∆ double mutation is lethal on YES medium. This lethality is a manifestation of IP8 toxicosis, whereby excessive 1,5-IP8 drives derepression of tgp1, leading to Tgp1-mediated uptake of glycerophosphocholine. We were able to recover an aps1∆ siw14∆ mutant on ePMGT medium lacking glycerophosphocholine and to suppress the severe growth defect of aps1∆ siw14∆ on YES by deleting tgp1. However, the severe growth defect of an aps1∆ asp1-H397A strain could not be alleviated by deleting tgp1, suggesting that 1,5-IP8 levels in this double-pyrophosphatase mutant exceed a threshold beyond which overzealous termination affects other genes, which results in cytotoxicity. IMPORTANCE Repression of the fission yeast PHO genes tgp1, pho1, and pho84 by lncRNA-mediated interference is sensitive to changes in the metabolism of 1,5-IP8, a signaling molecule that acts as an agonist of precocious lncRNA termination. 1,5-IP8 is formed by phosphorylation of 5-IP7 and catabolized by inositol pyrophosphatases from three distinct enzyme families: Asp1 (a histidine acid phosphatase), Siw14 (a cysteinyl phosphatase), and Aps1 (a Nudix hydrolase). This study entails a biochemical characterization of Aps1 and an analysis of how Asp1, Siw14, and Aps1 mutations impact growth and inositol pyrophosphate pools in vivo. Aps1 catalyzes hydrolysis of inorganic polyphosphates, 5-IP7, 1-IP7, and 1,5-IP8 in vitro, with a ~twofold preference for 1-IP7 over 5-IP7. aps1∆ cells have twofold higher levels of 1-IP7 than wild-type cells. An aps1∆ siw14∆ double mutation is lethal because excessive 1,5-IP8 triggers derepression of tgp1, leading to toxic uptake of glycerophosphocholine.
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Affiliation(s)
- Shreya Ghosh
- Molecular Biology Program, Sloan Kettering Institute, New York, New York, USA
| | - Ana M Sanchez
- Molecular Biology Program, Sloan Kettering Institute, New York, New York, USA
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, New York, USA
| | - Beate Schwer
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Isabel Prucker
- Institute of Organic Chemistry, University of Freiburg, Freiburg, Germany
| | - Nikolaus Jork
- Institute of Organic Chemistry, University of Freiburg, Freiburg, Germany
| | - Henning J Jessen
- Institute of Organic Chemistry, University of Freiburg, Freiburg, Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Stewart Shuman
- Molecular Biology Program, Sloan Kettering Institute, New York, New York, USA
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2
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Mihiret YE, Schaaf G, Kamleitner M. Protein pyrophosphorylation by inositol phosphates: a novel post-translational modification in plants? FRONTIERS IN PLANT SCIENCE 2024; 15:1347922. [PMID: 38455731 PMCID: PMC10917965 DOI: 10.3389/fpls.2024.1347922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/01/2024] [Indexed: 03/09/2024]
Abstract
Inositol pyrophosphates (PP-InsPs) are energy-rich molecules harboring one or more diphosphate moieties. PP-InsPs are found in all eukaryotes evaluated and their functional versatility is reflected in the various cellular events in which they take part. These include, among others, insulin signaling and intracellular trafficking in mammals, as well as innate immunity and hormone and phosphate signaling in plants. The molecular mechanisms by which PP-InsPs exert such functions are proposed to rely on the allosteric regulation via direct binding to proteins, by competing with other ligands, or by protein pyrophosphorylation. The latter is the focus of this review, where we outline a historical perspective surrounding the first findings, almost 20 years ago, that certain proteins can be phosphorylated by PP-InsPs in vitro. Strikingly, in vitro phosphorylation occurs by an apparent enzyme-independent but Mg2+-dependent transfer of the β-phosphoryl group of an inositol pyrophosphate to an already phosphorylated serine residue at Glu/Asp-rich protein regions. Ribosome biogenesis, vesicle trafficking and transcription are among the cellular events suggested to be modulated by protein pyrophosphorylation in yeast and mammals. Here we discuss the latest efforts in identifying targets of protein pyrophosphorylation, pointing out the methodological challenges that have hindered the full understanding of this unique post-translational modification, and focusing on the latest advances in mass spectrometry that finally provided convincing evidence that PP-InsP-mediated pyrophosphorylation also occurs in vivo. We also speculate about the relevance of this post-translational modification in plants in a discussion centered around the protein kinase CK2, whose activity is critical for pyrophosphorylation of animal and yeast proteins. This enzyme is widely present in plant species and several of its functions overlap with those of PP-InsPs. Until now, there is virtually no data on pyrophosphorylation of plant proteins, which is an exciting field that remains to be explored.
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Affiliation(s)
| | | | - Marília Kamleitner
- Department of Plant Nutrition, Institute of Crop Science and Resource Conservation, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
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3
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Gu C, Li X, Zong G, Wang H, Shears SB. IP8: A quantitatively minor inositol pyrophosphate signaling molecule that punches above its weight. Adv Biol Regul 2024; 91:101002. [PMID: 38064879 DOI: 10.1016/j.jbior.2023.101002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 11/27/2023] [Indexed: 02/25/2024]
Abstract
The inositol pyrophosphates (PP-IPs) are specialized members of the wider inositol phosphate signaling family that possess functionally significant diphosphate groups. The PP-IPs exhibit remarkable functionally versatility throughout the eukaryotic kingdoms. However, a quantitatively minor PP-IP - 1,5 bisdiphosphoinositol tetrakisphosphate (1,5-IP8) - has received considerably less attention from the cell signalling community. The main purpose of this review is to summarize recently-published data which have now brought 1,5-IP8 into the spotlight, by expanding insight into the molecular mechanisms by which this polyphosphate regulates many fundamental biological processes.
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Affiliation(s)
- Chunfang Gu
- Inositol signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709 USA
| | - Xingyao Li
- Inositol signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709 USA
| | - Guangning Zong
- Inositol signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709 USA
| | - Huanchen Wang
- Inositol signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709 USA.
| | - Stephen B Shears
- Inositol signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709 USA.
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4
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Li Q, Feng P, Tang H, Lu F, Mou B, Zhao L, Li N, Yang Y, Fu C, Long W, Xiao X, Li C, Wu W, Wang G, Liu B, Tang T, Ma M, Wang H. Genome-wide identification of resistance genes and cellular analysis of key gene knockout strain under 5-hydroxymethylfurfural stress in Saccharomyces cerevisiae. BMC Microbiol 2023; 23:382. [PMID: 38049732 PMCID: PMC10694885 DOI: 10.1186/s12866-023-03095-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/29/2023] [Indexed: 12/06/2023] Open
Abstract
In bioethanol production, the main by-product, 5-hydroxymethylfurfural (HMF), significantly hinders microbial fermentation. Therefore, it is crucial to explore genes related to HMF tolerance in Saccharomyces cerevisiae for enhancing the tolerance of ethanol fermentation strains. A comprehensive analysis was conducted using genome-wide deletion library scanning and SGAtools, resulting in the identification of 294 genes associated with HMF tolerance in S. cerevisiae. Further KEGG and GO enrichment analysis revealed the involvement of genes OCA1 and SIW14 in the protein phosphorylation pathway, underscoring their role in HMF tolerance. Spot test validation and subcellular structure observation demonstrated that, following a 3-h treatment with 60 mM HMF, the SIW14 gene knockout strain exhibited a 12.68% increase in cells with abnormal endoplasmic reticulum (ER) and a 22.41% increase in the accumulation of reactive oxygen species compared to the BY4741 strain. These findings indicate that the SIW14 gene contributes to the protection of the ER structure within the cell and facilitates the clearance of reactive oxygen species, thereby confirming its significance as a key gene for HMF tolerance in S. cerevisiae.
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Affiliation(s)
- Qian Li
- College of Life Science, Leshan Normal University, No. 778 Binhe Road, Leshan, 614000, Sichuan, China
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Peng Feng
- College of Life Science, Leshan Normal University, No. 778 Binhe Road, Leshan, 614000, Sichuan, China
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, 614000, Sichuan, China
| | - Hao Tang
- Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Ministry of Education, Sichuan Normal University, Chengdu, 610068, China
| | - Fujia Lu
- College of Life Science, Leshan Normal University, No. 778 Binhe Road, Leshan, 614000, Sichuan, China
| | - Borui Mou
- College of Life Science, Leshan Normal University, No. 778 Binhe Road, Leshan, 614000, Sichuan, China
| | - Lan Zhao
- Jiangxi Forestry Science and Technology Promotion and Publicity Education Center, Nanchang, 330000, Jiangxi, China
| | - Nan Li
- College of Life Science, Leshan Normal University, No. 778 Binhe Road, Leshan, 614000, Sichuan, China
| | - Yaojun Yang
- College of Life Science, Leshan Normal University, No. 778 Binhe Road, Leshan, 614000, Sichuan, China
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, 614000, Sichuan, China
| | - Chun Fu
- College of Life Science, Leshan Normal University, No. 778 Binhe Road, Leshan, 614000, Sichuan, China
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, 614000, Sichuan, China
| | - Wencong Long
- College of Life Science, Leshan Normal University, No. 778 Binhe Road, Leshan, 614000, Sichuan, China
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, 614000, Sichuan, China
| | - Ximeng Xiao
- College of Life Science, Leshan Normal University, No. 778 Binhe Road, Leshan, 614000, Sichuan, China
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, 614000, Sichuan, China
| | - Chaohao Li
- Leshan Institute of Product Quality Supervision and Testing, Leshan, 614000, Sichuan, China
| | - Wei Wu
- Leshan Institute of Product Quality Supervision and Testing, Leshan, 614000, Sichuan, China
| | - Gang Wang
- College of Life Science, Leshan Normal University, No. 778 Binhe Road, Leshan, 614000, Sichuan, China
- Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialization in Southern Sichuan, College of Life Science, Leshan Normal University, Leshan, 614000, Sichuan, China
| | - Beidong Liu
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9C, 413 90, Göteburg, Sweden
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Tianle Tang
- Key Laboratory of Tropical Transitional Medicine of Ministry of Education, Hainan Medical University, No.3 Xueyuan Road, Haikou, 571199, Hainan, China
| | - Menggen Ma
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China.
| | - Hanyu Wang
- College of Life Science, Leshan Normal University, No. 778 Binhe Road, Leshan, 614000, Sichuan, China.
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, 614000, Sichuan, China.
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5
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Sanchez AM, Schwer B, Jork N, Jessen HJ, Shuman S. Activities, substrate specificity, and genetic interactions of fission yeast Siw14, a cysteinyl-phosphatase-type inositol pyrophosphatase. mBio 2023; 14:e0205623. [PMID: 37772819 PMCID: PMC10653929 DOI: 10.1128/mbio.02056-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 08/09/2023] [Indexed: 09/30/2023] Open
Abstract
IMPORTANCE The inositol pyrophosphate signaling molecule 1,5-IP8 modulates fission yeast phosphate homeostasis via its action as an agonist of RNA 3'-processing and transcription termination. Cellular 1,5-IP8 levels are determined by a balance between the activities of the inositol polyphosphate kinase Asp1 and several inositol pyrophosphatase enzymes. Here, we characterize Schizosaccharomyces pombe Siw14 (SpSiw14) as a cysteinyl-phosphatase-family pyrophosphatase enzyme capable of hydrolyzing the phosphoanhydride substrates inorganic pyrophosphate, inorganic polyphosphate, and inositol pyrophosphates 5-IP7, 1-IP7, and 1,5-IP8. Genetic analyses implicate SpSiw14 in 1,5-IP8 catabolism in vivo, insofar as: loss of SpSiw14 activity is lethal in the absence of the Nudix-type inositol pyrophosphatase enzyme Aps1; and siw14∆ aps1∆ lethality depends on synthesis of 1,5-IP8 by the Asp1 kinase. Suppression of siw14∆ aps1∆ lethality by loss-of-function mutations of 3'-processing/termination factors points to precocious transcription termination as the cause of 1,5-IP8 toxicosis.
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Affiliation(s)
- Ana M. Sanchez
- Molecular Biology Program, Sloan Kettering Institute, New York, New York, USA
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, New York, USA
| | - Beate Schwer
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Nikolaus Jork
- Institute of Organic Chemistry and Centre for Integrative Biological Signaling Studies, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Henning J. Jessen
- Institute of Organic Chemistry and Centre for Integrative Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Stewart Shuman
- Molecular Biology Program, Sloan Kettering Institute, New York, New York, USA
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6
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Chabert V, Kim GD, Qiu D, Liu G, Michaillat Mayer L, Jamsheer K M, Jessen HJ, Mayer A. Inositol pyrophosphate dynamics reveals control of the yeast phosphate starvation program through 1,5-IP 8 and the SPX domain of Pho81. eLife 2023; 12:RP87956. [PMID: 37728314 PMCID: PMC10511240 DOI: 10.7554/elife.87956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023] Open
Abstract
Eukaryotic cells control inorganic phosphate to balance its role as essential macronutrient with its negative bioenergetic impact on reactions liberating phosphate. Phosphate homeostasis depends on the conserved INPHORS signaling pathway that utilizes inositol pyrophosphates and SPX receptor domains. Since cells synthesize various inositol pyrophosphates and SPX domains bind them promiscuously, it is unclear whether a specific inositol pyrophosphate regulates SPX domains in vivo, or whether multiple inositol pyrophosphates act as a pool. In contrast to previous models, which postulated that phosphate starvation is signaled by increased production of the inositol pyrophosphate 1-IP7, we now show that the levels of all detectable inositol pyrophosphates of yeast, 1-IP7, 5-IP7, and 1,5-IP8, strongly decline upon phosphate starvation. Among these, specifically the decline of 1,5-IP8 triggers the transcriptional phosphate starvation response, the PHO pathway. 1,5-IP8 inactivates the cyclin-dependent kinase inhibitor Pho81 through its SPX domain. This stimulates the cyclin-dependent kinase Pho85-Pho80 to phosphorylate the transcription factor Pho4 and repress the PHO pathway. Combining our results with observations from other systems, we propose a unified model where 1,5-IP8 signals cytosolic phosphate abundance to SPX proteins in fungi, plants, and mammals. Its absence triggers starvation responses.
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Affiliation(s)
- Valentin Chabert
- Département d'immunobiologie, Université de LausanneEpalingesSwitzerland
| | - Geun-Don Kim
- Département d'immunobiologie, Université de LausanneEpalingesSwitzerland
| | - Danye Qiu
- Institute of Organic Chemistry, Centre for Integrative Biological Signalling Studies, University of FreiburgFreiburgGermany
| | - Guizhen Liu
- Institute of Organic Chemistry, Centre for Integrative Biological Signalling Studies, University of FreiburgFreiburgGermany
| | | | | | - Henning J Jessen
- Institute of Organic Chemistry, Centre for Integrative Biological Signalling Studies, University of FreiburgFreiburgGermany
| | - Andreas Mayer
- Département d'immunobiologie, Université de LausanneEpalingesSwitzerland
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7
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Sanchez AM, Garg A, Schwer B, Shuman S. Duf89 abets lncRNA control of fission yeast phosphate homeostasis via its antagonism of precocious lncRNA transcription termination. RNA (NEW YORK, N.Y.) 2023; 29:808-825. [PMID: 36882296 PMCID: PMC10187668 DOI: 10.1261/rna.079595.123] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 02/13/2023] [Indexed: 05/18/2023]
Abstract
Fission yeast phosphate homeostasis gene pho1 is actively repressed during growth in phosphate-rich medium by transcription in cis of a long noncoding (lnc) RNA from the 5' flanking prt(nc-pho1) gene. Pho1 expression is: (i) derepressed by genetic maneuvers that favor precocious lncRNA 3'-processing and termination, in response to DSR and PAS signals in prt; and (ii) hyperrepressed in genetic backgrounds that dampen 3'-processing/termination efficiency. Governors of 3'-processing/termination include the RNA polymerase CTD code, the CPF (cleavage and polyadenylation factor) complex, termination factors Seb1 and Rhn1, and the inositol pyrophosphate signaling molecule 1,5-IP8 Here, we present genetic and biochemical evidence that fission yeast Duf89, a metal-dependent phosphatase/pyrophosphatase, is an antagonist of precocious 3'-processing/termination. We show that derepression of pho1 in duf89Δ cells correlates with squelching the production of full-length prt lncRNA and is erased or attenuated by: (i) DSR/PAS mutations in prt; (ii) loss-of-function mutations in components of the 3'-processing and termination machinery; (iii) elimination of the CTD Thr4-PO4 mark; (iv) interdicting CTD prolyl isomerization by Pin1; (v) inactivating the Asp1 kinase that synthesizes IP8; and (vi) loss of the putative IP8 sensor Spx1. The findings that duf89Δ is synthetically lethal with pho1-derepressive mutations CTD-S7A and aps1Δ-and that this lethality is rescued by CTD-T4A, CPF/Rhn1/Pin1 mutations, and spx1Δ-implicate Duf89 more broadly as a collaborator in cotranscriptional regulation of essential fission yeast genes. The duf89-D252A mutation, which abolishes Duf89 phosphohydrolase activity, phenocopied duf89 +, signifying that duf89Δ phenotypes are a consequence of Duf89 protein absence, not absence of Duf89 catalysis.
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Affiliation(s)
- Ana M Sanchez
- Molecular Biology Program, Sloan Kettering Institute, New York, New York 10065, USA
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, New York 10065, USA
| | - Angad Garg
- Molecular Biology Program, Sloan Kettering Institute, New York, New York 10065, USA
| | - Beate Schwer
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan Kettering Institute, New York, New York 10065, USA
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8
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Gaugler P, Schneider R, Liu G, Qiu D, Weber J, Schmid J, Jork N, Häner M, Ritter K, Fernández-Rebollo N, Giehl RFH, Trung MN, Yadav R, Fiedler D, Gaugler V, Jessen HJ, Schaaf G, Laha D. Arabidopsis PFA-DSP-Type Phosphohydrolases Target Specific Inositol Pyrophosphate Messengers. Biochemistry 2022; 61:1213-1227. [PMID: 35640071 DOI: 10.1021/acs.biochem.2c00145] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Inositol pyrophosphates are signaling molecules containing at least one phosphoanhydride bond that regulate a wide range of cellular processes in eukaryotes. With a cyclic array of phosphate esters and diphosphate groups around myo-inositol, these molecular messengers possess the highest charge density found in nature. Recent work deciphering inositol pyrophosphate biosynthesis in Arabidopsis revealed important functions of these messengers in nutrient sensing, hormone signaling, and plant immunity. However, despite the rapid hydrolysis of these molecules in plant extracts, very little is known about the molecular identity of the phosphohydrolases that convert these messengers back to their inositol polyphosphate precursors. Here, we investigate whether Arabidopsis Plant and Fungi Atypical Dual Specificity Phosphatases (PFA-DSP1-5) catalyze inositol pyrophosphate phosphohydrolase activity. We find that recombinant proteins of all five Arabidopsis PFA-DSP homologues display phosphohydrolase activity with a high specificity for the 5-β-phosphate of inositol pyrophosphates and only minor activity against the β-phosphates of 4-InsP7 and 6-InsP7. We further show that heterologous expression of Arabidopsis PFA-DSP1-5 rescues wortmannin sensitivity and deranged inositol pyrophosphate homeostasis caused by the deficiency of the PFA-DSP-type inositol pyrophosphate phosphohydrolase Siw14 in yeast. Heterologous expression in Nicotiana benthamiana leaves provided evidence that Arabidopsis PFA-DSP1 also displays 5-β-phosphate-specific inositol pyrophosphate phosphohydrolase activity in planta. Our findings lay the biochemical basis and provide the genetic tools to uncover the roles of inositol pyrophosphates in plant physiology and plant development.
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Affiliation(s)
- Philipp Gaugler
- Department of Plant Nutrition, Institute of Crop Science and Resource Conservation, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany
| | - Robin Schneider
- Department of Plant Nutrition, Institute of Crop Science and Resource Conservation, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany
| | - Guizhen Liu
- Department of Chemistry and Pharmacy and CIBSS-Centre for Integrative Biological Signalling Studies, Albert-Ludwigs University Freiburg, 79104 Freiburg, Germany
| | - Danye Qiu
- Department of Chemistry and Pharmacy and CIBSS-Centre for Integrative Biological Signalling Studies, Albert-Ludwigs University Freiburg, 79104 Freiburg, Germany
| | - Jonathan Weber
- Department of Plant Nutrition, Institute of Crop Science and Resource Conservation, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany
| | - Jochen Schmid
- Center for Plant Molecular Biology, Department of Plant Physiology, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Nikolaus Jork
- Department of Chemistry and Pharmacy and CIBSS-Centre for Integrative Biological Signalling Studies, Albert-Ludwigs University Freiburg, 79104 Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104 Freiburg, Germany
| | - Markus Häner
- Department of Chemistry and Pharmacy and CIBSS-Centre for Integrative Biological Signalling Studies, Albert-Ludwigs University Freiburg, 79104 Freiburg, Germany
| | - Kevin Ritter
- Department of Chemistry and Pharmacy and CIBSS-Centre for Integrative Biological Signalling Studies, Albert-Ludwigs University Freiburg, 79104 Freiburg, Germany
| | - Nicolás Fernández-Rebollo
- Center for Plant Molecular Biology, Department of Plant Physiology, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Ricardo F H Giehl
- Department of Physiology & Cell Biology, Leibniz-Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
| | - Minh Nguyen Trung
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany.,Department of Chemistry, Humboldt Universität zu Berlin, 12489 Berlin, Germany
| | - Ranjana Yadav
- Department of Biochemistry, Indian Institute of Science (IISc), Bengaluru 560012, India
| | - Dorothea Fiedler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany.,Department of Chemistry, Humboldt Universität zu Berlin, 12489 Berlin, Germany
| | - Verena Gaugler
- Department of Plant Nutrition, Institute of Crop Science and Resource Conservation, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany
| | - Henning J Jessen
- Department of Chemistry and Pharmacy and CIBSS-Centre for Integrative Biological Signalling Studies, Albert-Ludwigs University Freiburg, 79104 Freiburg, Germany
| | - Gabriel Schaaf
- Department of Plant Nutrition, Institute of Crop Science and Resource Conservation, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany
| | - Debabrata Laha
- Department of Biochemistry, Indian Institute of Science (IISc), Bengaluru 560012, India
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9
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Wang H, Perera L, Jork N, Zong G, Riley AM, Potter BVL, Jessen HJ, Shears SB. A structural exposé of noncanonical molecular reactivity within the protein tyrosine phosphatase WPD loop. Nat Commun 2022; 13:2231. [PMID: 35468885 PMCID: PMC9038691 DOI: 10.1038/s41467-022-29673-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 03/25/2022] [Indexed: 01/06/2023] Open
Abstract
Structural snapshots of protein/ligand complexes are a prerequisite for gaining atomic level insight into enzymatic reaction mechanisms. An important group of enzymes has been deprived of this analytical privilege: members of the protein tyrosine phosphatase (PTP) superfamily with catalytic WPD-loops lacking the indispensable general-acid/base within a tryptophan-proline-aspartate/glutamate context. Here, we provide the ligand/enzyme crystal complexes for one such PTP outlier: Arabidopsis thaliana Plant and Fungi Atypical Dual Specificity Phosphatase 1 (AtPFA-DSP1), herein unveiled as a regioselective and efficient phosphatase towards inositol pyrophosphate (PP-InsP) signaling molecules. Although the WPD loop is missing its canonical tripeptide motif, this structural element contributes to catalysis by assisting PP-InsP delivery into the catalytic pocket, for a choreographed exchange with phosphate reaction product. Subsequently, an intramolecular proton donation by PP-InsP substrate is posited to substitute functionally for the absent aspartate/glutamate general-acid. Overall, we expand mechanistic insight into adaptability of the conserved PTP structural elements.
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Affiliation(s)
- Huanchen Wang
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA.
| | - Lalith Perera
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Nikolaus Jork
- Institute of Organic Chemistry, and CIBSS - the Center for Integrative Biological Signaling Studies, University of Freiburg, 79104, Freiburg, Germany
| | - Guangning Zong
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Andrew M Riley
- Drug Discovery and Medicinal Chemistry, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - Barry V L Potter
- Drug Discovery and Medicinal Chemistry, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - Henning J Jessen
- Institute of Organic Chemistry, and CIBSS - the Center for Integrative Biological Signaling Studies, University of Freiburg, 79104, Freiburg, Germany
| | - Stephen B Shears
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA.
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10
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Riemer E, Pullagurla NJ, Yadav R, Rana P, Jessen HJ, Kamleitner M, Schaaf G, Laha D. Regulation of plant biotic interactions and abiotic stress responses by inositol polyphosphates. FRONTIERS IN PLANT SCIENCE 2022; 13:944515. [PMID: 36035672 PMCID: PMC9403785 DOI: 10.3389/fpls.2022.944515] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 07/20/2022] [Indexed: 05/14/2023]
Abstract
Inositol pyrophosphates (PP-InsPs), derivatives of inositol hexakisphosphate (phytic acid, InsP6) or lower inositol polyphosphates, are energy-rich signaling molecules that have critical regulatory functions in eukaryotes. In plants, the biosynthesis and the cellular targets of these messengers are not fully understood. This is because, in part, plants do not possess canonical InsP6 kinases and are able to synthesize PP-InsP isomers that appear to be absent in yeast or mammalian cells. This review will shed light on recent discoveries in the biosynthesis of these enigmatic messengers and on how they regulate important physiological processes in response to abiotic and biotic stresses in plants.
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Affiliation(s)
- Esther Riemer
- Departmentof Plant Nutrition, Institute of Crop Science and Resource Conservation, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
- *Correspondence: Esther Riemer,
| | | | - Ranjana Yadav
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Priyanshi Rana
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Henning J. Jessen
- Department of Chemistry and Pharmacy & CIBSS – The Center of Biological Signaling Studies, Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Marília Kamleitner
- Departmentof Plant Nutrition, Institute of Crop Science and Resource Conservation, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Gabriel Schaaf
- Departmentof Plant Nutrition, Institute of Crop Science and Resource Conservation, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Debabrata Laha
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
- Debabrata Laha,
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11
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Mohanrao R, Manorama R, Ganguli S, Madhusudhanan MC, Bhandari R, Sureshan KM. Novel Substrates for Kinases Involved in the Biosynthesis of Inositol Pyrophosphates and Their Enhancement of ATPase Activity of a Kinase. Molecules 2021; 26:molecules26123601. [PMID: 34208421 PMCID: PMC8231259 DOI: 10.3390/molecules26123601] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/07/2021] [Accepted: 06/07/2021] [Indexed: 11/16/2022] Open
Abstract
IP6K and PPIP5K are two kinases involved in the synthesis of inositol pyrophosphates. Synthetic analogs or mimics are necessary to understand the substrate specificity of these enzymes and to find molecules that can alter inositol pyrophosphate synthesis. In this context, we synthesized four scyllo-inositol polyphosphates-scyllo-IP5, scyllo-IP6, scyllo-IP7 and Bz-scyllo-IP5-from myo-inositol and studied their activity as substrates for mouse IP6K1 and the catalytic domain of VIP1, the budding yeast variant of PPIP5K. We incubated these scyllo-inositol polyphosphates with these kinases and ATP as the phosphate donor. We tracked enzyme activity by measuring the amount of radiolabeled scyllo-inositol pyrophosphate product formed and the amount of ATP consumed. All scyllo-inositol polyphosphates are substrates for both the kinases but they are weaker than the corresponding myo-inositol phosphate. Our study reveals the importance of axial-hydroxyl/phosphate for IP6K1 substrate recognition. We found that all these derivatives enhance the ATPase activity of VIP1. We found very weak ligand-induced ATPase activity for IP6K1. Benzoyl-scyllo-IP5 was the most potent ligand to induce IP6K1 ATPase activity despite being a weak substrate. This compound could have potential as a competitive inhibitor.
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Affiliation(s)
- Raja Mohanrao
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Kerala 695551, India; (R.M.); (M.C.M.)
| | - Ruth Manorama
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India; (R.M.); (S.G.)
| | - Shubhra Ganguli
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India; (R.M.); (S.G.)
- Manipal Academy of Higher Education, Manipal 576104, India
| | - Mithun C. Madhusudhanan
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Kerala 695551, India; (R.M.); (M.C.M.)
| | - Rashna Bhandari
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India; (R.M.); (S.G.)
- Correspondence: (R.B.); (K.M.S.)
| | - Kana M. Sureshan
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Kerala 695551, India; (R.M.); (M.C.M.)
- Correspondence: (R.B.); (K.M.S.)
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12
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Zong G, Jork N, Hostachy S, Fiedler D, Jessen HJ, Shears SB, Wang H. New structural insights reveal an expanded reaction cycle for inositol pyrophosphate hydrolysis by human DIPP1. FASEB J 2021; 35:e21275. [PMID: 33475202 DOI: 10.1096/fj.202001489r] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/30/2020] [Accepted: 11/30/2020] [Indexed: 11/11/2022]
Abstract
Nudix hydrolases attract considerable attention for their wide range of specialized activities in all domains of life. One particular group of Nudix phosphohydrolases (DIPPs), through their metabolism of diphosphoinositol polyphosphates (PP-InsPs), regulates the actions of these polyphosphates upon bioenergetic homeostasis. In the current study, we describe, at an atomic level, hitherto unknown properties of human DIPP1.We provide X-ray analysis of the catalytic core of DIPP1 in crystals complexed with either natural PP-InsPs, alternative PP-InsP stereoisomers, or non-hydrolysable methylene bisphosphonate analogs ("PCP-InsPs"). The conclusions that we draw from these data are interrogated by studying the impact upon catalytic activity upon mutagenesis of certain key residues. We present a picture of a V-shaped catalytic furrow with overhanging ridges constructed from flexible positively charged side chains; within this cavity, the labile phosphoanhydride bond is appropriately positioned at the catalytic site by an extensive series of interlocking polar contacts which we analogize as "suspension cables." We demonstrate functionality for a triglycine peptide within a β-strand which represents a non-canonical addition to the standard Nudix catalytic core structure. We describe pre-reaction enzyme/substrate states which we posit to reflect a role for electrostatic steering in substrate capture. Finally, through time-resolved analysis, we uncover a chronological sequence of DIPP1/product post-reaction states, one of which may rationalize a role for InsP6 as an inhibitor of catalytic activity.
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Affiliation(s)
- Guangning Zong
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Nikolaus Jork
- Institute of Organic Chemistry, CIBSS - Center for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Sarah Hostachy
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Dorothea Fiedler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Henning J Jessen
- Institute of Organic Chemistry, CIBSS - Center for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Stephen B Shears
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Huanchen Wang
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
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13
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Shears SB, Wang H. Metabolism and Functions of Inositol Pyrophosphates: Insights Gained from the Application of Synthetic Analogues. Molecules 2020; 25:E4515. [PMID: 33023101 PMCID: PMC7583957 DOI: 10.3390/molecules25194515] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 09/25/2020] [Accepted: 09/27/2020] [Indexed: 12/17/2022] Open
Abstract
Inositol pyrophosphates (PP-InsPs) comprise an important group of intracellular, diffusible cellular signals that a wide range of biological processes throughout the yeast, plant, and animal kingdoms. It has been difficult to gain a molecular-level mechanistic understanding of the actions of these molecules, due to their highly phosphorylated nature, their low levels, and their rapid metabolic turnover. More recently, these obstacles to success are being surmounted by the chemical synthesis of a number of insightful PP-InsP analogs. This review will describe these analogs and will indicate the important chemical and biological information gained by using them.
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Affiliation(s)
- Stephen B. Shears
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA;
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14
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Genome-wide functional analysis of phosphatases in the pathogenic fungus Cryptococcus neoformans. Nat Commun 2020; 11:4212. [PMID: 32839469 PMCID: PMC7445287 DOI: 10.1038/s41467-020-18028-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 07/30/2020] [Indexed: 12/13/2022] Open
Abstract
Phosphatases, together with kinases and transcription factors, are key components in cellular signalling networks. Here, we present a systematic functional analysis of the phosphatases in Cryptococcus neoformans, a fungal pathogen that causes life-threatening fungal meningoencephalitis. We analyse 230 signature-tagged mutant strains for 114 putative phosphatases under 30 distinct in vitro growth conditions, revealing at least one function for 60 of these proteins. Large-scale virulence and infectivity assays using insect and mouse models indicate roles in pathogenicity for 31 phosphatases involved in various processes such as thermotolerance, melanin and capsule production, stress responses, O-mannosylation, or retromer function. Notably, phosphatases Xpp1, Ssu72, Siw14, and Sit4 promote blood-brain barrier adhesion and crossing by C. neoformans. Together with our previous systematic studies of transcription factors and kinases, our results provide comprehensive insight into the pathobiological signalling circuitry of C. neoformans. Phosphatases are key components in cellular signalling networks. Here, the authors present a systematic functional analysis of phosphatases of the fungal pathogen Cryptococcus neoformans, revealing roles in virulence, stress responses, O-mannosylation, retromer function and other processes.
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15
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Abstract
The specific non-invasive control of intracellular signaling events requires advanced tools that enter cells by diffusion and are controllable by light. Here, we detail the synthesis and application of membrane-permeant caged inositol pyrophosphates with respect to cell entry and cell distribution. We recently published the synthesis of these tools as well as their effect on PH-domain localization in HeLa cells and oscillations of the intracellular calcium concentration in β-cells, which are known to drive insulin secretion. In this chapter, we discuss the possibilities and limitations when using cell-penetrating inositol pyrophosphates. We provide a detailed protocol for the application in live mouse β-cells and we discuss the image analysis needed for following effects on calcium signaling.
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16
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Austin S, Mayer A. Phosphate Homeostasis - A Vital Metabolic Equilibrium Maintained Through the INPHORS Signaling Pathway. Front Microbiol 2020; 11:1367. [PMID: 32765429 PMCID: PMC7381174 DOI: 10.3389/fmicb.2020.01367] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/27/2020] [Indexed: 12/12/2022] Open
Abstract
Cells face major changes in demand for and supply of inorganic phosphate (Pi). Pi is often a limiting nutrient in the environment, particularly for plants and microorganisms. At the same time, the need for phosphate varies, establishing conflicts of goals. Cells experience strong peaks of Pi demand, e.g., during the S-phase, when DNA, a highly abundant and phosphate-rich compound, is duplicated. While cells must satisfy these Pi demands, they must safeguard themselves against an excess of Pi in the cytosol. This is necessary because Pi is a product of all nucleotide-hydrolyzing reactions. An accumulation of Pi shifts the equilibria of these reactions and reduces the free energy that they can provide to drive endergonic metabolic reactions. Thus, while Pi starvation may simply retard growth and division, an elevated cytosolic Pi concentration is potentially dangerous for cells because it might stall metabolism. Accordingly, the consequences of perturbed cellular Pi homeostasis are severe. In eukaryotes, they range from lethality in microorganisms such as yeast (Sethuraman et al., 2001; Hürlimann, 2009), severe growth retardation and dwarfism in plants (Puga et al., 2014; Liu et al., 2015; Wild et al., 2016) to neurodegeneration or renal Fanconi syndrome in humans (Legati et al., 2015; Ansermet et al., 2017). Intracellular Pi homeostasis is thus not only a fundamental topic of cell biology but also of growing interest for medicine and agriculture.
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Affiliation(s)
- Sisley Austin
- Département de Biochimie, Université de Lausanne, Lausanne, Switzerland
| | - Andreas Mayer
- Département de Biochimie, Université de Lausanne, Lausanne, Switzerland
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17
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Steidle EA, Morrissette VA, Fujimaki K, Chong L, Resnick AC, Capaldi AP, Rolfes RJ. The InsP 7 phosphatase Siw14 regulates inositol pyrophosphate levels to control localization of the general stress response transcription factor Msn2. J Biol Chem 2019; 295:2043-2056. [PMID: 31848224 DOI: 10.1074/jbc.ra119.012148] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Indexed: 12/28/2022] Open
Abstract
The environmental stress response (ESR) is critical for cell survival. Yeast cells unable to synthesize inositol pyrophosphates (PP-InsPs) are unable to induce the ESR. We recently discovered a diphosphoinositol pentakisphosphate (PP-InsP5) phosphatase in Saccharomyces cerevisiae encoded by SIW14 Yeast strains deleted for SIW14 have increased levels of PP-InsPs. We hypothesized that strains with high inositol pyrophosphate levels will have an increased stress response. We examined the response of the siw14Δ mutant to heat shock, nutrient limitation, osmotic stress, and oxidative treatment using cell growth assays and found increased resistance to each. Transcriptional responses to oxidative and osmotic stresses were assessed using microarray and reverse transcriptase quantitative PCR. The ESR was partially induced in the siw14Δ mutant strain, consistent with the increased stress resistance, and the mutant strain further induced the ESR in response to oxidative and osmotic stresses. The levels of PP-InsPs increased in WT cells under oxidative stress but not under hyperosmotic stress, and they were high and unchanging in the mutant. Phosphatase activity of Siw14 was inhibited by oxidation that was reversible. To determine how altered PP-InsP levels affect the ESR, we performed epistasis experiments with mutations in rpd3 and msn2/4 combined with siw14Δ. We show that mutations in msn2Δ and msn4Δ, but not rpd3, are epistatic to siw14Δ by assessing growth under oxidative stress conditions and expression of CTT1 Msn2-GFP nuclear localization was increased in the siw14Δ. These data support a model in which the modulation of PP-InsPs influence the ESR through general stress response transcription factors Msn2/4.
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Affiliation(s)
| | | | - Kotaro Fujimaki
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - Lucy Chong
- Division of Neurosurgery, Colket Translational Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104
| | - Adam C Resnick
- Division of Neurosurgery, Colket Translational Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104
| | - Andrew P Capaldi
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - Ronda J Rolfes
- Department of Biology, Georgetown University, Washington, D. C. 20057.
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18
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Randall TA, Gu C, Li X, Wang H, Shears SB. A two-way switch for inositol pyrophosphate signaling: Evolutionary history and biological significance of a unique, bifunctional kinase/phosphatase. Adv Biol Regul 2019; 75:100674. [PMID: 31776069 DOI: 10.1016/j.jbior.2019.100674] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 10/30/2019] [Accepted: 11/06/2019] [Indexed: 11/25/2022]
Abstract
The inositol pyrophosphates (PP-InsPs) are a unique subgroup of intracellular signals with diverse functions, many of which can be viewed as reflecting an overarching role in metabolic homeostasis. Thus, considerable attention is paid to the enzymes that synthesize and metabolize the PP-InsPs. One of these enzyme families - the diphosphoinositol pentakisphosphate kinases (PPIP5Ks) - provides an extremely rare example of separate kinase and phosphatase activities being present within the same protein. Herein, we review the current state of structure/function insight into the PPIP5Ks, the separate specialized activities of the two metazoan PPIP5K genes, and we describe a phylogenetic analysis that places PPIP5K evolutionary origin within the Excavata, the very earliest of eukaryotes. These different aspects of PPIP5K biology are placed in the context of a single, overriding question. Why are they bifunctional: i.e., what is the particular significance of the ability to turn PP-InsP signaling on or off from two separate 'switches' in a single protein?
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Affiliation(s)
- Thomas A Randall
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Chunfang Gu
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Xingyao Li
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Huanchen Wang
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Stephen B Shears
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA.
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19
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Florio TJ, Lokareddy RK, Gillilan RE, Cingolani G. Molecular Architecture of the Inositol Phosphatase Siw14. Biochemistry 2019; 58:534-545. [PMID: 30548067 DOI: 10.1021/acs.biochem.8b01044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Siw14 is a recently discovered inositol phosphatase implicated in suppressing prion propagation in Saccharomyces cerevisiae. In this paper, we used hybrid structural methods to decipher Siw14 molecular architecture. We found the protein exists in solution as an elongated monomer that is ∼140 Å in length, containing an acidic N-terminal domain and a basic C-terminal dual-specificity phosphatase (DSP) domain, structurally similar to the glycogen phosphatase laforin. The two domains are connected by a protease susceptible linker and do not interact in vitro. The crystal structure of Siw14-DSP reveals a highly basic phosphate-binding loop and an ∼10 Å deep substrate-binding crevice that evolved to dephosphorylate pyro-phosphate moieties. A pseudoatomic model of the full-length phosphatase generated from solution, crystallographic, biochemical, and modeling data sheds light on the interesting zwitterionic nature of Siw14, which we hypothesized may play a role in discriminating negatively charged inositol phosphates.
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Affiliation(s)
- Tyler J Florio
- Department of Biochemistry and Molecular Biology , Thomas Jefferson University , 233 South 10th Street , Philadelphia , Pennsylvania 19107 , United States
| | - Ravi K Lokareddy
- Department of Biochemistry and Molecular Biology , Thomas Jefferson University , 233 South 10th Street , Philadelphia , Pennsylvania 19107 , United States
| | - Richard E Gillilan
- Macromolecular Diffraction Facility, Cornell High Energy Synchrotron Source (MacCHESS) , Cornell University , 161 Synchrotron Drive , Ithaca , New York 14853 , United States
| | - Gino Cingolani
- Department of Biochemistry and Molecular Biology , Thomas Jefferson University , 233 South 10th Street , Philadelphia , Pennsylvania 19107 , United States.,Institute of Biomembranes and Bioenergetics , National Research Council , Via Amendola 165/A , 70126 Bari , Italy
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