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Song Y, Zhang C, Omenn GS, O’Meara MJ, Welch JD. Predicting the Structural Impact of Human Alternative Splicing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.21.572928. [PMID: 38187531 PMCID: PMC10769328 DOI: 10.1101/2023.12.21.572928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Protein structure prediction with neural networks is a powerful new method for linking protein sequence, structure, and function, but structures have generally been predicted for only a single isoform of each gene, neglecting splice variants. To investigate the structural implications of alternative splicing, we used AlphaFold2 to predict the structures of more than 11,000 human isoforms. We employed multiple metrics to identify splicing-induced structural alterations, including template matching score, secondary structure composition, surface charge distribution, radius of gyration, accessibility of post-translational modification sites, and structure-based function prediction. We identified examples of how alternative splicing induced clear changes in each of these properties. Structural similarity between isoforms largely correlated with degree of sequence identity, but we identified a subset of isoforms with low structural similarity despite high sequence similarity. Exon skipping and alternative last exons tended to increase the surface charge and radius of gyration. Splicing also buried or exposed numerous post-translational modification sites, most notably among the isoforms of BAX. Functional prediction nominated numerous functional differences among isoforms of the same gene, with loss of function compared to the reference predominating. Finally, we used single-cell RNA-seq data from the Tabula Sapiens to determine the cell types in which each structure is expressed. Our work represents an important resource for studying the structure and function of splice isoforms across the cell types of the human body.
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Affiliation(s)
- Yuxuan Song
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Chengxin Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Gilbert S. Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Matthew J. O’Meara
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Joshua D. Welch
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Computer Science and Engineering, University of Michigan, Ann Arbor, MI, USA
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2
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Paixao IC, Mizutani N, Matsuda M, Andriani RT, Kawai T, Nakagawa A, Okochi Y, Okamura Y. Role of K364 next to the active site cysteine in voltage-dependent phosphatase activity of Ci-VSP. Biophys J 2023:S0006-3495(23)00038-3. [PMID: 36680342 DOI: 10.1016/j.bpj.2023.01.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 10/16/2022] [Accepted: 01/18/2023] [Indexed: 01/22/2023] Open
Abstract
Voltage-sensing phosphatase (VSP) consists of the voltage sensor domain (VSD) similar to that of voltage-gated ion channels and the cytoplasmic phosphatase region with remarkable similarity to the phosphatase and tensin homolog deleted on chromosome 10 (PTEN). Membrane depolarization activates VSD, leading to dephosphorylation of three species of phosphoinositides (phosphatidylinositol phosphates (PIPs)), PI(3,4,5)P3, PI(4,5)P2, and PI(3,4)P2. VSP dephosphorylates 3- and 5-phosphate of PIPs, unlike PTEN, which shows rigid 3-phosphate specificity. In this study, a bioinformatics search showed that some mammals have VSP orthologs with amino acid diversity in the active center motif, Cx5R, which is highly conserved among protein tyrosine phosphatases and PTEN-related phosphatases; lysine next to the active site cysteine in the Cx5R motif was substituted for methionine in VSP orthologs of Tasmanian devil, koala, and prairie deer mouse, and leucine in opossum. Since lysine at the corresponding site in PTEN is known to be critical for enzyme activities, we attempted to address the significance of amino acid diversity among VSP orthologs at this site. K364 was changed to different amino acids in sea squirt VSP (Ci-VSP), and voltage-dependent phosphatase activity in Xenopus oocyte was studied using fluorescent probes for PI(4,5)P2 and PI(3,4)P2. All mutants retained both 5-phosphatase and 3-phosphatase activity, indicating that lysine at this site is dispensable for 3-phosphatase activity, unlike PTEN. Notably, K364M mutant showed increased activity both of 5-phosphatase and 3-phosphatase compared with the wild type (WT). It also showed slower kinetics of voltage sensor motion. Malachite green assay of K364M mutant did not show significant difference of phosphatase activity from WT, suggesting tighter interaction between substrate binding and voltage sensing. Mutation corresponding to K364M in the zebrafish VSP led to enhanced voltage-dependent dephosphorylation of PI(4,5)P2. Further studies will provide clues to understanding of substrate preference in PIPs phosphatases as well as to customization of a molecular tool.
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Affiliation(s)
- Ian Costa Paixao
- Department of Physiology, Graduate School of Medicine, Osaka University, Suita, Japan; Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Natsuki Mizutani
- Department of Physiology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Makoto Matsuda
- Department Oncogene Research, Research Institute for Microbial Diseases, Osaka University, Suita, Japan; Laboratory for Supramolecular Crystallography, Institute for Protein Research, Osaka University, Suita, Japan
| | - Rizki Tsari Andriani
- Department of Physiology, Graduate School of Medicine, Osaka University, Suita, Japan; Graduate School of Medicine, Osaka University JSPS International Research Fellow, Suita, Japan
| | - Takafumi Kawai
- Department of Physiology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Atsushi Nakagawa
- Laboratory for Supramolecular Crystallography, Institute for Protein Research, Osaka University, Suita, Japan
| | - Yoshifumi Okochi
- Department of Physiology, Graduate School of Medicine, Osaka University, Suita, Japan.
| | - Yasushi Okamura
- Department of Physiology, Graduate School of Medicine, Osaka University, Suita, Japan; Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.
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3
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Voltage-sensing phosphatase (Vsp) regulates endocytosis-dependent nutrient absorption in chordate enterocytes. Commun Biol 2022; 5:948. [PMID: 36088390 PMCID: PMC9464190 DOI: 10.1038/s42003-022-03916-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 08/30/2022] [Indexed: 11/11/2022] Open
Abstract
Voltage-sensing phosphatase (Vsp) is a unique membrane protein that translates membrane electrical activities into the changes of phosphoinositide profiles. Vsp orthologs from various species have been intensively investigated toward their biophysical properties, primarily using a heterologous expression system. In contrast, the physiological role of Vsp in native tissues remains largely unknown. Here we report that zebrafish Vsp (Dr-Vsp), encoded by tpte gene, is functionally expressed on the endomembranes of lysosome-rich enterocytes (LREs) that mediate dietary protein absorption via endocytosis in the zebrafish mid-intestine. Dr-Vsp-deficient LREs were remarkably defective in forming endosomal vacuoles after initial uptake of dextran and mCherry. Dr-Vsp-deficient zebrafish exhibited growth restriction and higher mortality during the critical period when zebrafish larvae rely primarily on exogenous feeding via intestinal absorption. Furthermore, our comparative study on marine invertebrate Ciona intestinalis Vsp (Ci-Vsp) revealed co-expression with endocytosis-associated genes in absorptive epithelial cells of the Ciona digestive tract, corresponding to zebrafish LREs. These findings signify a crucial role of Vsp in regulating endocytosis-dependent nutrient absorption in specialized enterocytes across animal species. The physiological role of Vsp in zebrafish is assessed, revealing Vsp expression in the mid-intestine for dietary protein absorption. A comparative study on marine invertebrate Ciona intestinalis suggests conservation of Vsp function in the GI tract.
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4
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Mizutani N, Kawanabe A, Jinno Y, Narita H, Yonezawa T, Nakagawa A, Okamura Y. Interaction between S4 and the phosphatase domain mediates electrochemical coupling in voltage-sensing phosphatase (VSP). Proc Natl Acad Sci U S A 2022; 119:e2200364119. [PMID: 35733115 PMCID: PMC9245683 DOI: 10.1073/pnas.2200364119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 05/13/2022] [Indexed: 11/18/2022] Open
Abstract
Voltage-sensing phosphatase (VSP) consists of a voltage sensor domain (VSD) and a cytoplasmic catalytic region (CCR), which is similar to phosphatase and tensin homolog (PTEN). How the VSD regulates the innate enzyme component of VSP remains unclear. Here, we took a combined approach that entailed the use of electrophysiology, fluorometry, and structural modeling to study the electrochemical coupling in Ciona intestinalis VSP. We found that two hydrophobic residues at the lowest part of S4 play an essential role in the later transition of VSD-CCR coupling. Voltage clamp fluorometry and disulfide bond locking indicated that S4 and its neighboring linker move as one helix (S4-linker helix) and approach the hydrophobic spine in the CCR, a structure located near the cell membrane and also conserved in PTEN. We propose that the hydrophobic spine operates as a hub for translating an electrical signal into a chemical one in VSP.
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Affiliation(s)
- Natsuki Mizutani
- Laboratory of Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Akira Kawanabe
- Laboratory of Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yuka Jinno
- Laboratory of Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hirotaka Narita
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Tomoko Yonezawa
- Laboratory of Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Atsushi Nakagawa
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yasushi Okamura
- Laboratory of Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
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5
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The structural basis of PTEN regulation by multi-site phosphorylation. Nat Struct Mol Biol 2021; 28:858-868. [PMID: 34625746 PMCID: PMC8549118 DOI: 10.1038/s41594-021-00668-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 08/26/2021] [Indexed: 12/12/2022]
Abstract
Phosphatase and tensin homolog (PTEN) is a phosphatidylinositol-3,4,5-triphosphate (PIP3) phospholipid phosphatase that is commonly mutated or silenced in cancer. PTEN's catalytic activity, cellular membrane localization and stability are orchestrated by a cluster of C-terminal phosphorylation (phospho-C-tail) events on Ser380, Thr382, Thr383 and Ser385, but the molecular details of this multi-faceted regulation have remained uncertain. Here we use a combination of protein semisynthesis, biochemical analysis, NMR, X-ray crystallography and computational simulations on human PTEN and its sea squirt homolog, VSP, to obtain a detailed picture of how the phospho-C-tail forms a belt around the C2 and phosphatase domains of PTEN. We also visualize a previously proposed dynamic N-terminal α-helix and show that it is key for PTEN catalysis but disordered upon phospho-C-tail interaction. This structural model provides a comprehensive framework for how C-tail phosphorylation can impact PTEN's cellular functions.
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6
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Tsutsui H, Mizutani N, Okamura Y. Engineering voltage sensing phosphatase (VSP). Methods Enzymol 2021; 654:85-114. [PMID: 34120726 DOI: 10.1016/bs.mie.2021.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Voltage sensing phosphatase (VSP), consists of a voltage sensor domain (VSD) like that found in voltage-gated ion channels and a phosphoinositide (PIP) phosphatase region exhibiting remarkable structural similarity to a tumor suppressor enzyme, PTEN. Membrane depolarization activates the enzyme activity through tight coupling between the VSD and enzyme region. The VSD of VSP has a unique nature; it is a self-contained module that can be transferred to other proteins, conferring voltage sensitivity. Thanks to this nature, numerous versions of gene-encoded voltage indicators (GEVIs) have been developed through combination of a fluorescent protein with the VSD of VSP. In addition, VSP itself can also serve as a tool to alter PIP levels in cells. Cellular levels of PIPs, PI(4,5)P2 in particular, can be acutely and transiently reduced using a simple voltage protocol after heterologous expression of VSP. Recent progress in our understanding of the molecular structure and mechanisms underlying VSP facilitates optimization of its molecular properties for its use as a molecular tool.
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Affiliation(s)
- Hidekazu Tsutsui
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), Nomi, Ishikawa, Japan.
| | - Natsuki Mizutani
- Graduate School of Medicine, Japan Advanced Institute of Science and Technology (JAIST), Osaka University, Suita, Osaka, Japan
| | - Yasushi Okamura
- Graduate School of Medicine, Japan Advanced Institute of Science and Technology (JAIST), Osaka University, Suita, Osaka, Japan.
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7
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Abstract
The tumor suppressor phosphatase and tensin homolog on chromosome 10 (PTEN) is a tightly regulated enzyme responsible for dephosphorylating the progrowth lipid messenger molecule phosphatidylinositol 3,4,5-trisphosphate (PIP3) on the plasma membrane. The carboxy-terminal tail (CTT) of PTEN is key for regulation of the enzyme. When phosphorylated, the unstructured CTT interacts with the phosphatase-C2 superdomain to inactivate the enzyme by preventing membrane association. PTEN mutations associated with cancer also inactivate the enzyme. Alternate translation-initiation sites generate extended isoforms of PTEN, such as PTEN-L that has multiple roles in cells. The extended amino-terminal region bears a signal sequence and a polyarginine sequence to facilitate exit from and entry into cells, respectively, and a membrane-binding helix that activates the enzyme. This amino-terminal region also facilitates mitochondrial and nucleolar localization. This review explores PTEN structure and its impact on localization and regulation.
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8
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Tu T, Chen J, Chen L, Stiles BL. Dual-Specific Protein and Lipid Phosphatase PTEN and Its Biological Functions. Cold Spring Harb Perspect Med 2020; 10:cshperspect.a036301. [PMID: 31548229 DOI: 10.1101/cshperspect.a036301] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Phosphatase and tensin homolog deleted on chromosome 10 (PTEN) encodes a 403-amino acid protein with an amino-terminal domain that shares sequence homology with the actin-binding protein tensin and the putative tyrosine-protein phosphatase auxilin. Crystal structure analysis of PTEN has revealed a C2 domain that binds to phospholipids in membranes and a phosphatase domain that displays dual-specific activity toward both tyrosine (Y), serine (S)/threonine (T), as well as lipid substrates in vitro. Characterized primarily as a lipid phosphatase, PTEN plays important roles in multiple cellular processes including cell growth/survival as well as metabolism.
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Affiliation(s)
- Taojian Tu
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90033, USA
| | - Jingyu Chen
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90033, USA
| | - Lulu Chen
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90033, USA
| | - Bangyan L Stiles
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90033, USA.,Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
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9
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Okamura Y, Kawanabe A, Kawai T. Voltage-Sensing Phosphatases: Biophysics, Physiology, and Molecular Engineering. Physiol Rev 2019; 98:2097-2131. [PMID: 30067160 DOI: 10.1152/physrev.00056.2017] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Voltage-sensing phosphatase (VSP) contains a voltage sensor domain (VSD) similar to that in voltage-gated ion channels, and a phosphoinositide phosphatase region similar to phosphatase and tensin homolog deleted on chromosome 10 (PTEN). The VSP gene is conserved from unicellular organisms to higher vertebrates. Membrane depolarization induces electrical driven conformational rearrangement in the VSD, which is translated into catalytic enzyme activity. Biophysical and structural characterization has revealed details of the mechanisms underlying the molecular functions of VSP. Coupling between the VSD and the enzyme is tight, such that enzyme activity is tuned in a graded fashion to the membrane voltage. Upon VSP activation, multiple species of phosphoinositides are simultaneously altered, and the profile of enzyme activity depends on the history of the membrane potential. VSPs have been the obvious candidate link between membrane potential and phosphoinositide regulation. However, patterns of voltage change regulating VSP in native cells remain largely unknown. This review addresses the current understanding of the biophysical biochemical properties of VSP and provides new insight into the proposed functions of VSP.
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Affiliation(s)
- Yasushi Okamura
- Department of Physiology, Laboratory of Integrative Physiology, Graduate School of Medicine, Osaka University , Osaka , Japan ; and Graduate School of Frontier Biosciences, Osaka University , Osaka , Japan
| | - Akira Kawanabe
- Department of Physiology, Laboratory of Integrative Physiology, Graduate School of Medicine, Osaka University , Osaka , Japan ; and Graduate School of Frontier Biosciences, Osaka University , Osaka , Japan
| | - Takafumi Kawai
- Department of Physiology, Laboratory of Integrative Physiology, Graduate School of Medicine, Osaka University , Osaka , Japan ; and Graduate School of Frontier Biosciences, Osaka University , Osaka , Japan
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10
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Kawanabe A, Hashimoto M, Nishizawa M, Nishizawa K, Narita H, Yonezawa T, Jinno Y, Sakata S, Nakagawa A, Okamura Y. The hydrophobic nature of a novel membrane interface regulates the enzyme activity of a voltage-sensing phosphatase. eLife 2018; 7:41653. [PMID: 30484774 PMCID: PMC6298786 DOI: 10.7554/elife.41653] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 11/28/2018] [Indexed: 01/24/2023] Open
Abstract
Voltage-sensing phosphatases (VSP) contain a voltage sensor domain (VSD) similar to that of voltage-gated ion channels but lack a pore-gate domain. A VSD in a VSP regulates the cytoplasmic catalytic region (CCR). However, the mechanisms by which the VSD couples to the CCR remain elusive. Here we report a membrane interface (named ‘the hydrophobic spine’), which is essential for the coupling of the VSD and CCR. Our molecular dynamics simulations suggest that the hydrophobic spine of Ciona intestinalis VSP (Ci-VSP) provides a hinge-like motion for the CCR through the loose membrane association of the phosphatase domain. Electrophysiological experiments indicate that the voltage-dependent phosphatase activity of Ci-VSP depends on the hydrophobicity and presence of an aromatic ring in the hydrophobic spine. Analysis of conformational changes in the VSD and CCR suggests that the VSP has two states with distinct enzyme activities and that the second transition depends on the hydrophobic spine.
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Affiliation(s)
- Akira Kawanabe
- Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Masaki Hashimoto
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | | | | | - Hirotaka Narita
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Tomoko Yonezawa
- Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yuka Jinno
- Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Souhei Sakata
- Department of Physiology, Division of Life Sciences, Faculty of Medicine, Osaka Medical College, Osaka, Japan
| | | | - Yasushi Okamura
- Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Osaka, Japan.,Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
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11
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Sakata S, Okamura Y. Dynamic structural rearrangements and functional regulation of voltage-sensing phosphatase. J Physiol 2018; 597:29-40. [PMID: 30311949 DOI: 10.1113/jp274113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/02/2018] [Indexed: 11/08/2022] Open
Abstract
The voltage-sensing phosphatase (VSP) consists of a voltage sensor domain (VSD) and a cytoplasmic catalytic region. The latter contains a phosphatase domain and a C2 domain, showing remarkable similarity to the tumour suppressor enzyme PTEN. In VSP, membrane depolarization induces a conformational change in the VSD, which activates the phosphoinositide phosphatase. The final outcome in VSP is enzymatic activity in the cytoplasmic region, unlike in voltage-gated ion channels where conformational change of the transmembrane pore is induced by the VSD. Therefore, it is crucial to detect structural change in the cytoplasmic catalytic region to gain insights into the operating mechanisms of VSP. This review summarizes a recent study in which a method of genetic incorporation of a non-canonical amino acid, Anap, was used to detect dynamic membrane voltage-controlled rearrangements of the structure of the catalytic region of sea squirt VSP (Ci-VSP). Upon membrane depolarization, both the phosphatase domain and the C2 domain move in a similar time frame, suggesting that the two regions are coupled to each other. Measurement of Förster resonance energy transfer (FRET) between Anap introduced into the C2 domain of Ci-VSP and dipicrylamine in the cell membrane suggested no large movement of the enzyme towards the membrane. Fluorescence changes in Anap induced by different membrane potentials indicate the presence of multiple conformations of the active enzyme.
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Affiliation(s)
- Souhei Sakata
- Department of Physiology, Division of Life Sciences, Faculty of Medicine, Osaka Medical College, Takatsuki, Osaka, Japan
| | - Yasushi Okamura
- Laboratory of Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
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12
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Leitner MG, Hobiger K, Mavrantoni A, Feuer A, Oberwinkler J, Oliver D, Halaszovich CR. A126 in the active site and TI167/168 in the TI loop are essential determinants of the substrate specificity of PTEN. Cell Mol Life Sci 2018; 75:4235-4250. [PMID: 29987362 PMCID: PMC6182344 DOI: 10.1007/s00018-018-2867-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 06/19/2018] [Accepted: 07/03/2018] [Indexed: 01/16/2023]
Abstract
PTEN prevents tumor genesis by antagonizing the PI3 kinase/Akt pathway through D3 site phosphatase activity toward PI(3,4)P2 and PI(3,4,5)P3. The structural determinants of this important specificity remain unknown. Interestingly, PTEN shares remarkable homology to voltage-sensitive phosphatases (VSPs) that dephosphorylate D5 and D3 sites of PI(4,5)P2, PI(3,4)P2, and PI(3,4,5)P3. Since the catalytic center of PTEN and VSPs differ markedly only in TI/gating loop and active site motif, we wondered whether these differences explained the variation of their substrate specificity. Therefore, we introduced mutations into PTEN to mimic corresponding sequences of VSPs and studied phosphatase activity in living cells utilizing engineered, voltage switchable PTENCiV, a Ci-VSP/PTEN chimera that retains D3 site activity of the native enzyme. Substrate specificity of this enzyme was analyzed with whole-cell patch clamp in combination with total internal reflection fluorescence microscopy and genetically encoded phosphoinositide sensors. In PTENCiV, mutating TI167/168 in the TI loop into the corresponding ET pair of VSPs induced VSP-like D5 phosphatase activity toward PI(3,4,5)P3, but not toward PI(4,5)P2. Combining TI/ET mutations with an A126G exchange in the active site removed major sequence variations between PTEN and VSPs and resulted in D5 activity toward PI(4,5)P2 and PI(3,4,5)P3 of PTENCiV. This PTEN mutant thus fully reproduced the substrate specificity of native VSPs. Importantly, the same combination of mutations also induced D5 activity toward PI(3,4,5)P3 in native PTEN demonstrating that the same residues determine the substrate specificity of the tumor suppressor in living cells. Reciprocal mutations in VSPs did not alter their substrate specificity, but reduced phosphatase activity. In summary, A126 in the active site and TI167/168 in the TI loop are essential determinants of PTEN's substrate specificity, whereas additional features might contribute to the enzymatic activity of VSPs.
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Affiliation(s)
- Michael G Leitner
- Institute of Physiology and Pathophysiology, Philipps-University Marburg, Deutschhausstr. 1-2, 35037, Marburg, Germany
- Division of Physiology, Department of Physiology and Medical Physics, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Kirstin Hobiger
- Institute of Physiology and Pathophysiology, Philipps-University Marburg, Deutschhausstr. 1-2, 35037, Marburg, Germany
| | - Angeliki Mavrantoni
- Institute of Physiology and Pathophysiology, Philipps-University Marburg, Deutschhausstr. 1-2, 35037, Marburg, Germany
| | - Anja Feuer
- Institute of Physiology and Pathophysiology, Philipps-University Marburg, Deutschhausstr. 1-2, 35037, Marburg, Germany
| | - Johannes Oberwinkler
- Institute of Physiology and Pathophysiology, Philipps-University Marburg, Deutschhausstr. 1-2, 35037, Marburg, Germany
| | - Dominik Oliver
- Institute of Physiology and Pathophysiology, Philipps-University Marburg, Deutschhausstr. 1-2, 35037, Marburg, Germany
- DFG Research Training Group GRK 2213, Membrane Plasticity in Tissue Development and Remodeling, Philipps-University Marburg, 35043, Marburg, Germany
- Center for Mind, Brain and Behavior (CMBB), Universities of Marburg and Giessen, Marburg/Giessen, Germany
| | - Christian R Halaszovich
- Institute of Physiology and Pathophysiology, Philipps-University Marburg, Deutschhausstr. 1-2, 35037, Marburg, Germany.
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13
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Zhang J, Chen X, Xue Y, Gamper N, Zhang X. Beyond voltage-gated ion channels: Voltage-operated membrane proteins and cellular processes. J Cell Physiol 2018; 233:6377-6385. [PMID: 29667735 DOI: 10.1002/jcp.26555] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 02/20/2018] [Indexed: 12/26/2022]
Abstract
Voltage-gated ion channels were believed to be the only voltage-sensitive proteins in excitable (and some non-excitable) cells for a long time. Emerging evidence indicates that the voltage-operated model is shared by some other transmembrane proteins expressed in both excitable and non-excitable cells. In this review, we summarize current knowledge about voltage-operated proteins, which are not classic voltage-gated ion channels as well as the voltage-dependent processes in cells for which single voltage-sensitive proteins have yet to be identified. Particularly, we will focus on the following. (1) Voltage-sensitive phosphoinositide phosphatases (VSP) with four transmembrane segments homologous to the voltage sensor domain (VSD) of voltage-gated ion channels; VSPs are the first family of proteins, other than the voltage-gated ion channels, for which there is sufficient evidence for the existence of the VSD domain; (2) Voltage-gated proton channels comprising of a single voltage-sensing domain and lacking an identified pore domain; (3) G protein coupled receptors (GPCRs) that mediate the depolarization-evoked potentiation of Ca2+ mobilization; (4) Plasma membrane (PM) depolarization-induced but Ca2+ -independent exocytosis in neurons. (5) Voltage-dependent metabolism of phosphatidylinositol 4,5-bisphosphate (PtdIns[4,5]P2 , PIP2 ) in the PM. These recent discoveries expand our understanding of voltage-operated processes within cellular membranes.
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Affiliation(s)
- Jianping Zhang
- Department of Pharmacology, Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Xingjuan Chen
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, Indiana.,Beijing Key Laboratory of Diabetes Prevention and Research, Lu He Hospital, Capital Medical University, Beijing, China
| | - Yucong Xue
- Department of Pharmacology, Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Nikita Gamper
- Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Xuan Zhang
- Department of Pharmacology, Hebei University of Chinese Medicine, Shijiazhuang, China
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14
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Membrane properties that shape the evolution of membrane enzymes. Curr Opin Struct Biol 2018; 51:80-91. [PMID: 29597094 DOI: 10.1016/j.sbi.2018.03.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 03/14/2018] [Accepted: 03/15/2018] [Indexed: 02/07/2023]
Abstract
Spectacular recent progress in structural biology has led to determination of the structures of many integral membrane enzymes that catalyze reactions in which at least one substrate also is membrane bound. A pattern of results seems to be emerging in which the active site chemistry of these enzymes is usually found to be analogous to what is observed for water soluble enzymes catalyzing the same reaction types. However, in light of the chemical, structural, and physical complexity of cellular membranes plus the presence of transmembrane gradients and potentials, these enzymes may be subject to membrane-specific regulatory mechanisms that are only now beginning to be uncovered. We review the membrane-specific environmental traits that shape the evolution of membrane-embedded biocatalysts.
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15
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Sakata S, Matsuda M, Kawanabe A, Okamura Y. Domain-to-domain coupling in voltage-sensing phosphatase. Biophys Physicobiol 2017; 14:85-97. [PMID: 28744425 PMCID: PMC5515349 DOI: 10.2142/biophysico.14.0_85] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 05/10/2017] [Indexed: 01/12/2023] Open
Abstract
Voltage-sensing phosphatase (VSP) consists of a transmembrane voltage sensor and a cytoplasmic enzyme region. The enzyme region contains the phosphatase and C2 domains, is structurally similar to the tumor suppressor phosphatase PTEN, and catalyzes the dephosphorylation of phosphoinositides. The transmembrane voltage sensor is connected to the phosphatase through a short linker region, and phosphatase activity is induced upon membrane depolarization. Although the detailed molecular characteristics of the voltage sensor domain and the enzyme region have been revealed, little is known how these two regions are coupled. In addition, it is important to know whether mechanism for coupling between the voltage sensor domain and downstream effector function is shared among other voltage sensor domain-containing proteins. Recent studies in which specific amino acid sites were genetically labeled using a fluorescent unnatural amino acid have enabled detection of the local structural changes in the cytoplasmic region of Ciona intestinalis VSP that occur with a change in membrane potential. The results of those studies provide novel insight into how the enzyme activity of the cytoplasmic region of VSP is regulated by the voltage sensor domain.
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Affiliation(s)
- Souhei Sakata
- Department of Physiology, Division of Life Sciences, Faculty of Medicine, Osaka Medical College, Takatsuki, Osaka 569-8686, Japan
| | - Makoto Matsuda
- Laboratory of Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Akira Kawanabe
- Laboratory of Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yasushi Okamura
- Laboratory of Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan.,Graduate School of Frontier Bioscience, Osaka University
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16
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Rosasco MG, Gordon SE, Bajjalieh SM. Characterization of the Functional Domains of a Mammalian Voltage-Sensitive Phosphatase. Biophys J 2016; 109:2480-2491. [PMID: 26682807 DOI: 10.1016/j.bpj.2015.11.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 10/27/2015] [Accepted: 11/03/2015] [Indexed: 12/12/2022] Open
Abstract
Voltage-sensitive phosphatases (VSPs) are proteins that directly couple changes in membrane electrical potential to inositol lipid phosphatase activity. VSPs thus couple two signaling pathways that are critical for cellular functioning. Although a number of nonmammalian VSPs have been characterized biophysically, mammalian VSPs are less well understood at both the physiological and biophysical levels. In this study, we aimed to address this gap in knowledge by determining whether the VSP from mouse, Mm-VSP, is expressed in the brain and contains a functional voltage-sensing domain (VSD) and a phosphatase domain. We report that Mm-VSP is expressed in neurons and is developmentally regulated. To address whether the functions of the VSD and phosphatase domain are retained in Mm-VSP, we took advantage of the modular nature of these domains and expressed each independently as a chimeric protein in a heterologous expression system. We found that the Mm-VSP VSD, fused to a viral potassium channel, was able to drive voltage-dependent gating of the channel pore. The Mm-VSP phosphatase domain, fused to the VSD of a nonmammalian VSP, was also functional: activation resulted in PI(4,5)P2 depletion that was sufficient to inhibit the PI(4,5)P2-regulated KCNQ2/3 channels. While testing the functionality of the VSD and phosphatase domain, we observed slight differences between the activities of Mm-VSP-based chimeras and those of nonmammalian VSPs. Although the properties of VSP chimeras may not completely reflect the properties of native VSPs, the differences we observed in voltage-sensing and phosphatase activity provide a starting point for future experiments to investigate the function of Mm-VSP and other mammalian VSPs. In conclusion, our data reveal that both the VSD and the lipid phosphatase domain of Mm-VSP are functional, indicating that Mm-VSP likely plays an important role in mouse neurophysiology.
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Affiliation(s)
- Mario G Rosasco
- Department of Pharmacology, University of Washington, Seattle, Washington; Department of Physiology and Biophysics, University of Washington, Seattle, Washington
| | - Sharona E Gordon
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington
| | - Sandra M Bajjalieh
- Department of Pharmacology, University of Washington, Seattle, Washington.
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17
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Voltage-dependent motion of the catalytic region of voltage-sensing phosphatase monitored by a fluorescent amino acid. Proc Natl Acad Sci U S A 2016; 113:7521-6. [PMID: 27330112 DOI: 10.1073/pnas.1604218113] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The cytoplasmic region of voltage-sensing phosphatase (VSP) derives the voltage dependence of its catalytic activity from coupling to a voltage sensor homologous to that of voltage-gated ion channels. To assess the conformational changes in the cytoplasmic region upon activation of the voltage sensor, we genetically incorporated a fluorescent unnatural amino acid, 3-(6-acetylnaphthalen-2-ylamino)-2-aminopropanoic acid (Anap), into the catalytic region of Ciona intestinalis VSP (Ci-VSP). Measurements of Anap fluorescence under voltage clamp in Xenopus oocytes revealed that the catalytic region assumes distinct conformations dependent on the degree of voltage-sensor activation. FRET analysis showed that the catalytic region remains situated beneath the plasma membrane, irrespective of the voltage level. Moreover, Anap fluorescence from a membrane-facing loop in the C2 domain showed a pattern reflecting substrate turnover. These results indicate that the voltage sensor regulates Ci-VSP catalytic activity by causing conformational changes in the entire catalytic region, without changing their distance from the plasma membrane.
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18
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Phosphoinositide 5- and 3-phosphatase activities of a voltage-sensing phosphatase in living cells show identical voltage dependence. Proc Natl Acad Sci U S A 2016; 113:E3686-95. [PMID: 27222577 DOI: 10.1073/pnas.1606472113] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Voltage-sensing phosphatases (VSPs) are homologs of phosphatase and tensin homolog (PTEN), a phosphatidylinositol 3,4-bisphosphate [PI(3,4)P2] and phosphatidylinositol 3,4,5-trisphosphate [PI(3,4,5)P3] 3-phosphatase. However, VSPs have a wider range of substrates, cleaving 3-phosphate from PI(3,4)P2 and probably PI(3,4,5)P3 as well as 5-phosphate from phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] and PI(3,4,5)P3 in response to membrane depolarization. Recent proposals say these reactions have differing voltage dependence. Using Förster resonance energy transfer probes specific for different PIs in living cells with zebrafish VSP, we quantitate both voltage-dependent 5- and 3-phosphatase subreactions against endogenous substrates. These activities become apparent with different voltage thresholds, voltage sensitivities, and catalytic rates. As an analytical tool, we refine a kinetic model that includes the endogenous pools of phosphoinositides, endogenous phosphatase and kinase reactions connecting them, and four exogenous voltage-dependent 5- and 3-phosphatase subreactions of VSP. We show that apparent voltage threshold differences for seeing effects of the 5- and 3-phosphatase activities in cells are not due to different intrinsic voltage dependence of these reactions. Rather, the reactions have a common voltage dependence, and apparent differences arise only because each VSP subreaction has a different absolute catalytic rate that begins to surpass the respective endogenous enzyme activities at different voltages. For zebrafish VSP, our modeling revealed that 3-phosphatase activity against PI(3,4,5)P3 is 55-fold slower than 5-phosphatase activity against PI(4,5)P2; thus, PI(4,5)P2 generated more slowly from dephosphorylating PI(3,4,5)P3 might never accumulate. When 5-phosphatase activity was counteracted by coexpression of a phosphatidylinositol 4-phosphate 5-kinase, there was accumulation of PI(4,5)P2 in parallel to PI(3,4,5)P3 dephosphorylation, emphasizing that VSPs can cleave the 3-phosphate of PI(3,4,5)P3.
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19
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Kim DM, Nimigean CM. Voltage-Gated Potassium Channels: A Structural Examination of Selectivity and Gating. Cold Spring Harb Perspect Biol 2016; 8:a029231. [PMID: 27141052 PMCID: PMC4852806 DOI: 10.1101/cshperspect.a029231] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Voltage-gated potassium channels play a fundamental role in the generation and propagation of the action potential. The discovery of these channels began with predictions made by early pioneers, and has culminated in their extensive functional and structural characterization by electrophysiological, spectroscopic, and crystallographic studies. With the aid of a variety of crystal structures of these channels, a highly detailed picture emerges of how the voltage-sensing domain reports changes in the membrane electric field and couples this to conformational changes in the activation gate. In addition, high-resolution structural and functional studies of K(+) channel pores, such as KcsA and MthK, offer a comprehensive picture on how selectivity is achieved in K(+) channels. Here, we illustrate the remarkable features of voltage-gated potassium channels and explain the mechanisms used by these machines with experimental data.
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Affiliation(s)
- Dorothy M Kim
- Department of Anesthesiology, Weill Cornell Medical College, New York, New York 10065
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medical College, New York, New York 10065
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20
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Meekins DA, Vander Kooi CW, Gentry MS. Structural mechanisms of plant glucan phosphatases in starch metabolism. FEBS J 2016; 283:2427-47. [PMID: 26934589 DOI: 10.1111/febs.13703] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Revised: 01/31/2016] [Accepted: 02/29/2016] [Indexed: 01/12/2023]
Abstract
Glucan phosphatases are a recently discovered class of enzymes that dephosphorylate starch and glycogen, thereby regulating energy metabolism. Plant genomes encode two glucan phosphatases, called Starch EXcess4 (SEX4) and Like Sex Four2 (LSF2), that regulate starch metabolism by selectively dephosphorylating glucose moieties within starch glucan chains. Recently, the structures of both SEX4 and LSF2 were determined, with and without phosphoglucan products bound, revealing the mechanism for their unique activities. This review explores the structural and enzymatic features of the plant glucan phosphatases, and outlines how they are uniquely adapted to perform their cellular functions. We outline the physical mechanisms used by SEX4 and LSF2 to interact with starch glucans: SEX4 binds glucan chains via a continuous glucan-binding platform comprising its dual-specificity phosphatase domain and carbohydrate-binding module, while LSF2 utilizes surface binding sites. SEX4 and LSF2 both contain a unique network of aromatic residues in their catalytic dual-specificity phosphatase domains that serve as glucan engagement platforms and are unique to the glucan phosphatases. We also discuss the phosphoglucan substrate specificities inherent to SEX4 and LSF2, and outline structural features within the active site that govern glucan orientation. This review defines the structural mechanism of the plant glucan phosphatases with respect to phosphatases, starch metabolism and protein-glucan interaction, thereby providing a framework for their application in both agricultural and industrial settings.
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Affiliation(s)
- David A Meekins
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, KY, USA.,Division of Biology, Kansas State University, Manhattan, KS, USA
| | - Craig W Vander Kooi
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, KY, USA
| | - Matthew S Gentry
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, KY, USA
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21
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Allosteric substrate switching in a voltage-sensing lipid phosphatase. Nat Chem Biol 2016; 12:261-7. [PMID: 26878552 PMCID: PMC4798927 DOI: 10.1038/nchembio.2022] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 12/31/2015] [Indexed: 11/29/2022]
Abstract
Allostery provides a critical control over enzyme activity, biasing the catalytic site between inactive and active states. We find the Ciona intestinalis voltage-sensing phosphatase (Ci-VSP), which modifies phosphoinositide signaling lipids (PIPs), to have not one but two sequential active states with distinct substrate specificities, whose occupancy is allosterically controlled by sequential conformations of the voltage sensing domain (VSD). Using fast FRET reporters of PIPs to monitor enzyme activity and voltage clamp fluorometry to monitor conformational changes in the VSD, we find that Ci-VSP switches from inactive to a PIP3-preferring active state when the VSD undergoes an initial voltage sensing motion and then into a second PIP2-preferring active state when the VSD activates fully. This novel 2-step allosteric control over a dual specificity enzyme enables voltage to shape PIP concentrations in time, and provides a mechanism for the complex modulation of PIP-regulated ion channels, transporters, cell motility and endo/exocytosis.
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22
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Castle PM, Zolman KD, Kohout SC. Voltage-sensing phosphatase modulation by a C2 domain. Front Pharmacol 2015; 6:63. [PMID: 25904865 PMCID: PMC4389355 DOI: 10.3389/fphar.2015.00063] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 03/10/2015] [Indexed: 11/13/2022] Open
Abstract
The voltage-sensing phosphatase (VSP) is the first example of an enzyme controlled by changes in membrane potential. VSP has four distinct regions: the transmembrane voltage-sensing domain (VSD), the inter-domain linker, the cytosolic catalytic domain, and the C2 domain. The VSD transmits the changes in membrane potential through the inter-domain linker activating the catalytic domain which then dephosphorylates phosphatidylinositol phosphate (PIP) lipids. The role of the C2, however, has not been established. In this study, we explore two possible roles for the C2: catalysis and membrane-binding. The Ci-VSP crystal structures show that the C2 residue Y522 lines the active site suggesting a contribution to catalysis. When we mutated Y522 to phenylalanine, we found a shift in the voltage dependence of activity. This suggests hydrogen bonding as a mechanism of action. Going one step further, when we deleted the entire C2 domain, we found voltage-dependent enzyme activity was no longer detectable. This result clearly indicates the entire C2 is necessary for catalysis as well as for modulating activity. As C2s are known membrane-binding domains, we tested whether the VSP C2 interacts with the membrane. We probed a cluster of four positively charged residues lining the top of the C2 and suggested by previous studies to interact with phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] (Kalli et al., 2014). Neutralizing those positive charges significantly shifted the voltage dependence of activity to higher voltages. We tested membrane binding by depleting PI(4,5)P2 from the membrane using the 5HT2C receptor and found that the VSD motions as measured by voltage clamp fluorometry (VCF) were not changed. These results suggest that if the C2 domain interacts with the membrane to influence VSP function it may not occur exclusively through PI(4,5)P2. Together, this data advances our understanding of the VSP C2 by demonstrating a necessary and critical role for the C2 domain in VSP function.
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Affiliation(s)
- Paul M Castle
- Department of Cell Biology and Neuroscience, Montana State University Bozeman, MT, USA
| | - Kevin D Zolman
- Department of Cell Biology and Neuroscience, Montana State University Bozeman, MT, USA
| | - Susy C Kohout
- Department of Cell Biology and Neuroscience, Montana State University Bozeman, MT, USA
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23
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Hobiger K, Friedrich T. Voltage sensitive phosphatases: emerging kinship to protein tyrosine phosphatases from structure-function research. Front Pharmacol 2015; 6:20. [PMID: 25713537 PMCID: PMC4322731 DOI: 10.3389/fphar.2015.00020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 01/21/2015] [Indexed: 02/03/2023] Open
Abstract
The transmembrane protein Ci-VSP from the ascidian Ciona intestinalis was described as first member of a fascinating family of enzymes, the voltage sensitive phosphatases (VSPs). Ci-VSP and its voltage-activated homologs from other species are stimulated by positive membrane potentials and dephosphorylate the head groups of negatively charged phosphoinositide phosphates (PIPs). In doing so, VSPs act as control centers at the cytosolic membrane surface, because they intervene in signaling cascades that are mediated by PIP lipids. The characteristic motif CX5RT/S in the active site classifies VSPs as members of the huge family of cysteine-based protein tyrosine phosphatases (PTPs). Although PTPs have already been well-characterized regarding both, structure and function, their relationship to VSPs has drawn only limited attention so far. Therefore, the intention of this review is to give a short overview about the extensive knowledge about PTPs in relation to the facts known about VSPs. Here, we concentrate on the structural features of the catalytic domain which are similar between both classes of phosphatases and their consequences for the enzymatic function. By discussing results obtained from crystal structures, molecular dynamics simulations, and mutagenesis studies, a possible mechanism for the catalytic cycle of VSPs is presented based on that one proposed for PTPs. In this way, we want to link the knowledge about the catalytic activity of VSPs and PTPs.
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Affiliation(s)
- Kirstin Hobiger
- Department of Neurophysiology, Institute of Physiology and Pathophysiology, Philipps-Universität Marburg Marburg, Germany
| | - Thomas Friedrich
- Max-Volmer-Laboratory of Biophysical Chemistry, Institute of Chemistry, Technische Universität Berlin Berlin, Germany
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24
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Hsu F, Mao Y. The structure of phosphoinositide phosphatases: Insights into substrate specificity and catalysis. Biochim Biophys Acta Mol Cell Biol Lipids 2014; 1851:698-710. [PMID: 25264170 DOI: 10.1016/j.bbalip.2014.09.015] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 09/10/2014] [Accepted: 09/17/2014] [Indexed: 12/17/2022]
Abstract
Phosphoinositides (PIs) are a group of key signaling and structural lipid molecules involved in a myriad of cellular processes. PI phosphatases, together with PI kinases, are responsible for the conversion of PIs between distinctive phosphorylation states. PI phosphatases are a large collection of enzymes that are evolved from at least two disparate ancestors. One group is distantly related to endonucleases, which apply divalent metal ions for phosphoryl transfer. The other group is related to protein tyrosine phosphatases, which contain a highly conserved active site motif Cys-X5-Arg (CX5R). In this review, we focus on structural insights to illustrate current understandings of the molecular mechanisms of each PI phosphatase family, with emphasis on their structural basis for substrate specificity determinants and catalytic mechanisms. This article is part of a Special Issue entitled Phosphoinositides.
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Affiliation(s)
- FoSheng Hsu
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Yuxin Mao
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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25
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Mutua J, Jinno Y, Sakata S, Okochi Y, Ueno S, Tsutsui H, Kawai T, Iwao Y, Okamura Y. Functional diversity of voltage-sensing phosphatases in two urodele amphibians. Physiol Rep 2014; 2:e12061. [PMID: 25347851 PMCID: PMC4187576 DOI: 10.14814/phy2.12061] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Voltage-sensing phosphatases (VSPs) share the molecular architecture of the voltage sensor domain (VSD) with voltage-gated ion channels and the phosphoinositide phosphatase region with the phosphatase and tensin homolog (PTEN), respectively. VSPs enzymatic activities are regulated by the motions of VSD upon depolarization. The physiological role of these proteins has remained elusive, and insights may be gained by investigating biological variations in different animal species. Urodele amphibians are vertebrates with potent activities of regeneration and also show diverse mechanisms of polyspermy prevention. We cloned cDNAs of VSPs from the testes of two urodeles; Hynobius nebulosus and Cynops pyrrhogaster, and compared their expression and voltage-dependent activation. Their molecular architecture is highly conserved in both Hynobius VSP (Hn-VSP) and Cynops VSP (Cp-VSP), including the positively-charged arginine residues in the S4 segment of the VSD and the enzymatic active site for substrate binding, yet the C-terminal C2 domain of Hn-VSP is significantly shorter than that of Cp-VSP and other VSP orthologs. RT-PCR analysis showed that gene expression pattern was distinct between two VSPs. The voltage sensor motions and voltage-dependent phosphatase activities were investigated electrophysiologically by expression in Xenopus oocytes. Both VSPs showed "sensing" currents, indicating that their voltage sensor domains are functional. The phosphatase activity of Cp-VSP was found to be voltage dependent, as shown by its ability to regulate the conductance of coexpressed GIRK2 channels, but Hn-VSP lacked such phosphatase activity due to the truncation of its C2 domain.
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Affiliation(s)
- Joshua Mutua
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Yuka Jinno
- Laboratory of Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Souhei Sakata
- Laboratory of Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Yoshifumi Okochi
- Laboratory of Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Shuichi Ueno
- Laboratory of Molecular Developmental Biology, Department of Applied Molecular Biosciences, Graduate School of Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Hidekazu Tsutsui
- Laboratory of Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Takafumi Kawai
- Laboratory of Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Yasuhiro Iwao
- Laboratory of Molecular Developmental Biology, Department of Applied Molecular Biosciences, Graduate School of Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Yasushi Okamura
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan Laboratory of Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
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26
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Nakanishi A, Wada Y, Kitagishi Y, Matsuda S. Link between PI3K/AKT/PTEN Pathway and NOX Proteinin Diseases. Aging Dis 2014; 5:203-11. [PMID: 24900943 DOI: 10.14336/ad.2014.0500203] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 10/27/2013] [Accepted: 10/30/2013] [Indexed: 12/17/2022] Open
Abstract
Accumulating evidence has revealed that thePI3K/AKT/PTENpathway acts as a pivotal determinant of cell fate regarding senescence and apoptosis, which is mediated by intracellular reactive oxygen species (ROS) generation. NADPH oxidase (NOX) family of enzymes generates the ROS. The regulation of NOX enzymes is complex, with many members of this family exhibiting complexity in terms of subunit composition, cellular location, and tissue-specific expression. Cells are continuously exposed to the ROS, which represent mutagens and are thought to be a major contributor to several diseases including cancer and aging process. Therefore, cellular ROS sensing and metabolism are firmly regulated by a variety of proteins involved in the redox mechanism. In this review, the roles of oxidative stress in PI3K/AKT/PTEN signaling are summarized with a focus on the links between the pathways and NOX protein in several diseases including cancer and aging.
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Affiliation(s)
| | - Yoko Wada
- Department of Food Science and Nutrition, Nara Women's University, Kita-Uoya Nishimachi, Nara 630-8506, Japan
| | - Yasuko Kitagishi
- Department of Food Science and Nutrition, Nara Women's University, Kita-Uoya Nishimachi, Nara 630-8506, Japan
| | - Satoru Matsuda
- Department of Food Science and Nutrition, Nara Women's University, Kita-Uoya Nishimachi, Nara 630-8506, Japan
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27
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Kalli AC, Devaney I, Sansom MSP. Interactions of phosphatase and tensin homologue (PTEN) proteins with phosphatidylinositol phosphates: insights from molecular dynamics simulations of PTEN and voltage sensitive phosphatase. Biochemistry 2014; 53:1724-32. [PMID: 24588644 PMCID: PMC4167384 DOI: 10.1021/bi5000299] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
![]()
The
phosphatase and tensin homologue (PTEN) and the Ciona
intestinalis voltage sensitive phosphatase (Ci-VSP) are both
phosphatidylinositol phosphate (PIP) phosphatases that contain a C2
domain. PTEN is a tumor suppressor protein that acts as a phosphatase
on PIP3 in mammalian cell membranes. It contains two principal
domains:
a phosphatase domain (PD) and a C2 domain. Despite detailed structural
and functional characterization, less is known about its mechanism
of interaction with PIP-containing lipid bilayers. Ci-VSP consists
of an N-terminal transmembrane voltage sensor domain and a C-terminal
PTEN domain, which in turn contains a PD and a C2 domain. The nature
of the interaction of the PTEN domain of Ci-VSP with membranes has
not been well established. We have used multiscale molecular dynamics
simulations to define the interaction mechanisms
of PTEN and of the Ci-VSP PTEN domains with PIP-containing lipid bilayers.
Our results suggest a novel mechanism of association of the PTEN with
such bilayers, in which an initial electrostatics-driven encounter
of the protein and bilayer is followed by reorientation of the protein
to optimize its interactions with PIP molecules in the membrane. Although
a PIP3 molecule binds close to the active site of PTEN,
our simulations suggest a further conformational change of the protein
may be required for catalytically productive binding to occur. Ci-VSP
interacted with membranes in an orientation comparable to that of
PTEN but bound directly to PIP-containing membranes without a subsequent
reorientation step. Again, PIP3 bound close to the active
site of the Ci-VSP PD, but not in a catalytically productive manner.
Interactions of Ci-VSP with the bilayer induced clustering of PIP
molecules around the protein.
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Affiliation(s)
- Antreas C Kalli
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, U.K
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28
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Li Q, Wanderling S, Paduch M, Medovoy D, Singharoy A, McGreevy R, Villalba-Galea C, Hulse RE, Roux B, Schulten K, Kossiakoff A, Perozo E. Structural mechanism of voltage-dependent gating in an isolated voltage-sensing domain. Nat Struct Mol Biol 2014; 21:244-52. [PMID: 24487958 PMCID: PMC4116111 DOI: 10.1038/nsmb.2768] [Citation(s) in RCA: 191] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 01/10/2014] [Indexed: 01/26/2023]
Abstract
The transduction of transmembrane electric fields into protein motion has an essential role in the generation and propagation of cellular signals. Voltage-sensing domains (VSDs) carry out these functions through reorientations of positive charges in the S4 helix. Here, we determined crystal structures of the Ciona intestinalis VSD (Ci-VSD) in putatively active and resting conformations. S4 undergoes an ~5-Å displacement along its main axis, accompanied by an ~60° rotation. This movement is stabilized by an exchange in countercharge partners in helices S1 and S3 that generates an estimated net charge transfer of ~1 eo. Gating charges move relative to a ''hydrophobic gasket' that electrically divides intra- and extracellular compartments. EPR spectroscopy confirms the limited nature of S4 movement in a membrane environment. These results provide an explicit mechanism for voltage sensing and set the basis for electromechanical coupling in voltage-dependent enzymes and ion channels.
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Affiliation(s)
- Qufei Li
- Department of Biochemistry and Molecular Biology, The University
of Chicago, Chicago, IL 60637, USA
| | - Sherry Wanderling
- Department of Biochemistry and Molecular Biology, The University
of Chicago, Chicago, IL 60637, USA
| | - Marcin Paduch
- Department of Biochemistry and Molecular Biology, The University
of Chicago, Chicago, IL 60637, USA
| | - David Medovoy
- Department of Biochemistry and Molecular Biology, The University
of Chicago, Chicago, IL 60637, USA
| | - Abhishek Singharoy
- Department of Physics and Beckman Institute, University of
Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ryan McGreevy
- Department of Physics and Beckman Institute, University of
Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Carlos Villalba-Galea
- Department of Physiology and Biophysics, Virginia Commonwealth
University School of Medicine, Richmond, VA 23298, USA
| | - Raymond E. Hulse
- Department of Biochemistry and Molecular Biology, The University
of Chicago, Chicago, IL 60637, USA
| | - Benoit Roux
- Department of Biochemistry and Molecular Biology, The University
of Chicago, Chicago, IL 60637, USA
| | - Klaus Schulten
- Department of Physics and Beckman Institute, University of
Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Anthony Kossiakoff
- Department of Biochemistry and Molecular Biology, The University
of Chicago, Chicago, IL 60637, USA
| | - Eduardo Perozo
- Department of Biochemistry and Molecular Biology, The University
of Chicago, Chicago, IL 60637, USA
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29
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Yamaguchi S, Kurokawa T, Taira I, Aoki N, Sakata S, Okamura Y, Homma KJ. Potential role of voltage-sensing phosphatases in regulation of cell structure through the production of PI(3,4)P2. J Cell Physiol 2014; 229:422-33. [PMID: 24038012 DOI: 10.1002/jcp.24463] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 08/21/2013] [Indexed: 11/06/2022]
Abstract
Voltage-sensing phosphatase, VSP, consists of the transmembrane domain, operating as the voltage sensor, and the cytoplasmic domain with phosphoinositide-phosphatase activities. The voltage sensor tightly couples with the cytoplasmic phosphatase and membrane depolarization induces dephosphorylation of several species of phosphoinositides. VSP gene is conserved from urochordate to human. There are some diversities among VSP ortholog proteins; range of voltage of voltage sensor motions as well as substrate selectivity. In contrast with recent understandings of biophysical mechanisms of VSPs, little is known about its physiological roles. Here we report that chick ortholog of VSP (designated as Gg-VSP) induces morphological feature of cell process outgrowths with round cell body in DF-1 fibroblasts upon its forced expression. Expression of the voltage sensor mutant, Gg-VSPR153Q with shifted voltage dependence to a lower voltage led to more frequent changes of cell morphology than the wild-type protein. Coexpression of PTEN that dephosphorylates PI(3,4)P2 suppressed this effect by Gg-VSP, indicating that the increase of PI(3,4)P2 leads to changes of cell shape. In addition, visualization of PI(3,4)P2 with the fluorescent protein fused with the TAPP1-derived pleckstrin homology (PH) domain suggested that Gg-VSP influenced the distribution of PI(3,4)P2 . These findings raise a possibility that one of the VSP's functions could be to regulate cell morphology through voltage-sensitive tuning of phosphoinositide profile.
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Affiliation(s)
- Shinji Yamaguchi
- Faculty of Pharmaceutical Sciences, Department of Life and Health Sciences, Teikyo University, Tokyo, Japan
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30
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Sakata S, Okamura Y. Phosphatase activity of the voltage-sensing phosphatase, VSP, shows graded dependence on the extent of activation of the voltage sensor. J Physiol 2013; 592:899-914. [PMID: 24277865 DOI: 10.1113/jphysiol.2013.263640] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The voltage-sensing phosphatase (VSP) consists of a voltage sensor and a cytoplasmic phosphatase region, and the movement of the voltage sensor is coupled to the phosphatase activity. However, its coupling mechanisms still remain unclear. One possible scenario is that the phosphatase is activated only when the voltage sensor is in a fully activated state. Alternatively, the enzymatic activity of single VSP proteins could be graded in distinct activated states of the voltage sensor, and partial activation of the voltage sensor could lead to partial activation of the phosphatase. To distinguish between these two possibilities, we studied a voltage sensor mutant of zebrafish VSP, where the voltage sensor moves in two steps as evidenced by analyses of charge movements of the voltage sensor and voltage clamp fluorometry. Measurements of the phosphatase activity toward phosphatidylinositol 4,5-bisphosphate revealed that both steps of voltage sensor activation are coupled to the tuning of phosphatase activities, consistent with the idea that the phosphatase activity is graded by the magnitude of the movement of the voltage sensor.
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Affiliation(s)
- Souhei Sakata
- Laboratory of Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, 2-2 Yamada-Oka, Suita, Osaka 565-0871, Japan.
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31
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Lumb CN, Sansom MSP. Defining the membrane-associated state of the PTEN tumor suppressor protein. Biophys J 2013; 104:613-21. [PMID: 23442912 DOI: 10.1016/j.bpj.2012.12.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 11/28/2012] [Accepted: 12/04/2012] [Indexed: 11/19/2022] Open
Abstract
Phosphatase and tensin-homolog deleted on chromosome 10 (PTEN) is a tumor-suppressor protein that regulates phosphatidylinositol 3-kinase (PI3-K) signaling by binding to the plasma membrane and hydrolyzing the 3' phosphate from phosphatidylinositol (3,4,5)-trisphosphate (PI(3,4,5)P3) to form phosphatidylinositol (4,5)-bisphosphate (PI(4,5)P2). Several loss-of-function mutations in PTEN that impair lipid phosphatase activity and membrane binding are oncogenic, leading to the development of a variety of cancers, but information about the membrane-associated state of PTEN remains sparse. We have modeled a membrane-associated state of the truncated PTEN structure bound to PI(3,4,5)P3 via multiscale molecular dynamics simulations. We show that the location of the membrane-binding surface agrees with experimental observations and is robust to changes in lipid composition. The level of membrane interaction is substantially reduced in the phosphatase domain for the triple mutant R161E/K163E/K164E, in line with experimental results. We observe clustering of anionic lipids around the C2 domain in preference to the phosphatase domain, suggesting that the C2 domain is involved in nonspecific interactions with negatively charged lipid headgroups. Finally, our simulations suggest that the oncogenicity of the R335L mutation may be due to a reduction in the interaction of the mutant PTEN with anionic lipids.
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Affiliation(s)
- Craig N Lumb
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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32
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Hobiger K, Utesch T, Mroginski MA, Seebohm G, Friedrich T. The linker pivot in Ci-VSP: the key to unlock catalysis. PLoS One 2013; 8:e70272. [PMID: 23922964 PMCID: PMC3726396 DOI: 10.1371/journal.pone.0070272] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 06/17/2013] [Indexed: 11/18/2022] Open
Abstract
In the voltage-sensitive phosphatase Ci-VSP, conformational changes in the transmembrane voltage sensor domain (VSD) are transduced to the intracellular catalytic domain (CD) leading to its dephosphorylation activity against membrane-embedded phosphoinositides. The linker between both domains is proposed to be crucial for the VSD-CD coupling. With a combined approach of electrophysiological measurements on Xenopus oocytes and molecular dynamics simulations of a Ci-VSP model embedded in a lipid bilayer, we analyzed how conformational changes in the linker mediate the interaction between the CD and the activated VSD. In this way, we identified specific residues in the linker that interact with well-defined amino acids in one of the three loops forming the active site of the protein, named TI loop. With our results, we shed light into the early steps of the coupling process between the VSD and the CD, which are based on fine-tuned electrostatic and hydrophobic interactions between the linker, the membrane and the CD.
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Affiliation(s)
- Kirstin Hobiger
- Institute of Chemistry, Max-Volmer-Laboratory of Biophysical Chemistry, Technische Universität Berlin, Berlin, Germany.
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33
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Yu KR, Kim YJ, Jung SK, Ku B, Park H, Cho SY, Jung H, Chung SJ, Bae KH, Lee SC, Kim BY, Erikson RL, Ryu SE, Kim SJ. Structural basis for the dephosphorylating activity of PTPRQ towards phosphatidylinositide substrates. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1522-9. [DOI: 10.1107/s0907444913010457] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Accepted: 04/17/2013] [Indexed: 12/24/2022]
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34
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Abstract
Phosphoinositides (PIs) make up only a small fraction of cellular phospholipids, yet they control almost all aspects of a cell's life and death. These lipids gained tremendous research interest as plasma membrane signaling molecules when discovered in the 1970s and 1980s. Research in the last 15 years has added a wide range of biological processes regulated by PIs, turning these lipids into one of the most universal signaling entities in eukaryotic cells. PIs control organelle biology by regulating vesicular trafficking, but they also modulate lipid distribution and metabolism via their close relationship with lipid transfer proteins. PIs regulate ion channels, pumps, and transporters and control both endocytic and exocytic processes. The nuclear phosphoinositides have grown from being an epiphenomenon to a research area of its own. As expected from such pleiotropic regulators, derangements of phosphoinositide metabolism are responsible for a number of human diseases ranging from rare genetic disorders to the most common ones such as cancer, obesity, and diabetes. Moreover, it is increasingly evident that a number of infectious agents hijack the PI regulatory systems of host cells for their intracellular movements, replication, and assembly. As a result, PI converting enzymes began to be noticed by pharmaceutical companies as potential therapeutic targets. This review is an attempt to give an overview of this enormous research field focusing on major developments in diverse areas of basic science linked to cellular physiology and disease.
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Affiliation(s)
- Tamas Balla
- Section on Molecular Signal Transduction, Program for Developmental Neuroscience, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA.
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35
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Kitagishi Y, Matsuda S. Redox regulation of tumor suppressor PTEN in cancer and aging (Review). Int J Mol Med 2013; 31:511-5. [PMID: 23313933 DOI: 10.3892/ijmm.2013.1235] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 12/18/2012] [Indexed: 11/05/2022] Open
Abstract
Phosphatase and tensin homologue deleted on chromosome 10 (PTEN) has been shown to act as a tumor suppressor whose function includes important roles in regulating oxidative stress, indicating a potential role in oxidative damage-associated cancer. Accumulating evidence has revealed that PTEN also acts as a pivotal determinant of cell fate, regarding senescence and apoptosis, which is mediated by intracellular reactive oxygen species (ROS) generation. Cells are continuously exposed to ROS, which represent mutagens and are thought to be a major contributor to cancer and the aging process. Therefore, cellular ROS sensing and metabolism are firmly regulated by a variety of proteins involved in the redox mechanism. In this review, PTEN and the roles of oxidative stress in phosphoinositide-3 kinase/AKT signaling are summarized with a focus on the links between the pathways and ROS in cancer and aging.
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Affiliation(s)
- Yasuko Kitagishi
- Department of Environmental Health Science, Nara Women's University, Nara 630-8506, Japan
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36
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Gericke A, Leslie NR, Lösche M, Ross AH. PtdIns(4,5)P2-mediated cell signaling: emerging principles and PTEN as a paradigm for regulatory mechanism. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 991:85-104. [PMID: 23775692 DOI: 10.1007/978-94-007-6331-9_6] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
PtdIns(4,5)P2 (phosphatidylinositol 4,5-bisphosphate) is a relatively common anionic lipid that regulates cellular functions by multiple mechanisms. Hydrolysis of PtdIns(4,5)P2 by phospholipase C yields inositol trisphosphate and diacylglycerol. Phosphorylation by phosphoinositide 3-kinase yields PtdIns(3,4,5)P3, which is a potent signal for survival and proliferation. Also, PtdIns(4,5)P2 can bind directly to integral and peripheral membrane proteins. As an example of regulation by PtdIns(4,5)P2, we discuss phosphatase and tensin homologue deleted on chromosome 10 (PTEN) in detail. PTEN is an important tumor suppressor and hydrolyzes PtdIns(3,4,5)P3. PtdIns(4,5)P2 enhances PTEN association with the plasma membrane and activates its phosphatase activity. This is a critical regulatory mechanism, but a detailed description of this process from a structural point of view is lacking. The disordered lipid bilayer environment hinders structural determinations of membrane-bound PTEN. A new method to analyze membrane-bound protein measures neutron reflectivity for proteins bound to tethered phospholipid membranes. These methods allow determination of the orientation and shape of membrane-bound proteins. In combination with molecular dynamics simulations, these studies will provide crucial structural information that can serve as a foundation for our understanding of PTEN regulation in normal and pathological processes.
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Affiliation(s)
- Arne Gericke
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, MA 01609, USA
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37
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Villalba-Galea CA. Voltage-Controlled Enzymes: The New JanusBifrons. Front Pharmacol 2012; 3:161. [PMID: 22993507 PMCID: PMC3440755 DOI: 10.3389/fphar.2012.00161] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2012] [Accepted: 08/19/2012] [Indexed: 12/25/2022] Open
Abstract
The Ciona intestinalis voltage-sensitive phosphatase, Ci-VSP, was the first Voltage-controlled Enzyme (VEnz) proven to be under direct command of the membrane potential. The discovery of Ci-VSP conjugated voltage sensitivity and enzymatic activity in a single protein. These two facets of Ci-VSP activity have provided a unique model for studying how membrane potential is sensed by proteins and a novel mechanism for control of enzymatic activity. These facets make Ci-VSP a fascinating and versatile enzyme. Ci-VSP has a voltage sensing domain (VSD) that resembles those found in voltage-gated channels (VGC). The VSD resides in the N-terminus and is formed by four putative transmembrane segments. The fourth segment contains charged residues which are likely involved in voltage sensing. Ci-VSP produces sensing currents in response to changes in potential, within a defined range of voltages. Sensing currents are analogous to “gating” currents in VGC. As known, these latter proteins contain four VSDs which are entangled in a complex interaction with the pore domain – the effector domain in VGC. This complexity makes studying the basis of voltage sensing in VGC a difficult enterprise. In contrast, Ci-VSP is thought to be monomeric and its catalytic domain – the VSP’s effector domain – can be cleaved off without disrupting the basic electrical functioning of the VSD. For these reasons, VSPs are considered a great model for studying the activity of a VSD in isolation. Finally, VSPs are also phosphoinositide phosphatases. Phosphoinositides are signaling lipids found in eukaryotes and are involved in many processes, including modulation of VGC activity and regulation of cell proliferation. Understanding VSPs as enzymes has been the center of attention in recent years and several reviews has been dedicated to this area. Thus, this review will be focused instead on the other face of this true JanusBifrons and recapitulate what is known about VSPs as electrically active proteins.
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Affiliation(s)
- Carlos A Villalba-Galea
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine Richmond, VA, USA
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38
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Halaszovich CR, Leitner MG, Mavrantoni A, Le A, Frezza L, Feuer A, Schreiber DN, Villalba-Galea CA, Oliver D. A human phospholipid phosphatase activated by a transmembrane control module. J Lipid Res 2012; 53:2266-74. [PMID: 22896666 DOI: 10.1194/jlr.m026021] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
In voltage-sensitive phosphatases (VSPs), a transmembrane voltage sensor domain (VSD) controls an intracellular phosphoinositide phosphatase domain, thereby enabling immediate initiation of intracellular signals by membrane depolarization. The existence of such a mechanism in mammals has remained elusive, despite the presence of VSP-homologous proteins in mammalian cells, in particular in sperm precursor cells. Here we demonstrate activation of a human VSP (hVSP1/TPIP) by an intramolecular switch. By engineering a chimeric hVSP1 with enhanced plasma membrane targeting containing the VSD of a prototypic invertebrate VSP, we show that hVSP1 is a phosphoinositide-5-phosphatase whose predominant substrate is PI(4,5)P(2). In the chimera, enzymatic activity is controlled by membrane potential via hVSP1's endogenous phosphoinositide binding motif. These findings suggest that the endogenous VSD of hVSP1 is a control module that initiates signaling through the phosphatase domain and indicate a role for VSP-mediated phosphoinositide signaling in mammals.
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Affiliation(s)
- Christian R Halaszovich
- Institute of Physiology and Pathophysiology, Philipps-Universität Marburg, 35037 Marburg, Germany
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3' Phosphatase activity toward phosphatidylinositol 3,4-bisphosphate [PI(3,4)P2] by voltage-sensing phosphatase (VSP). Proc Natl Acad Sci U S A 2012; 109:10089-94. [PMID: 22645351 DOI: 10.1073/pnas.1203799109] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Voltage-sensing phosphatases (VSPs) consist of a voltage-sensor domain and a cytoplasmic region with remarkable sequence similarity to phosphatase and tensin homolog deleted on chromosome 10 (PTEN), a tumor suppressor phosphatase. VSPs dephosphorylate the 5' position of the inositol ring of both phosphatidylinositol 3,4,5-trisphosphate [PI(3,4,5)P(3)] and phosphatidylinositol 4,5-bisphosphate [PI(4,5)P(2)] upon voltage depolarization. However, it is unclear whether VSPs also have 3' phosphatase activity. To gain insights into this question, we performed in vitro assays of phosphatase activities of Ciona intestinalis VSP (Ci-VSP) and transmembrane phosphatase with tensin homology (TPTE) and PTEN homologous inositol lipid phosphatase (TPIP; one human ortholog of VSP) with radiolabeled PI(3,4,5)P(3). TLC assay showed that the 3' phosphate of PI(3,4,5)P(3) was not dephosphorylated, whereas that of phosphatidylinositol 3,4-bisphosphate [PI(3,4)P(2)] was removed by VSPs. Monitoring of PI(3,4)P(2) levels with the pleckstrin homology (PH) domain from tandem PH domain-containing protein (TAPP1) fused with GFP (PH(TAPP1)-GFP) by confocal microscopy in amphibian oocytes showed an increase of fluorescence intensity during depolarization to 0 mV, consistent with 5' phosphatase activity of VSP toward PI(3,4,5)P(3). However, depolarization to 60 mV showed a transient increase of GFP fluorescence followed by a decrease, indicating that, after PI(3,4,5)P(3) is dephosphorylated at the 5' position, PI(3,4)P(2) is then dephosphorylated at the 3' position. These results suggest that substrate specificity of the VSP changes with membrane potential.
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40
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Liu L, Kohout SC, Xu Q, Müller S, Kimberlin CR, Isacoff EY, Minor DL. A glutamate switch controls voltage-sensitive phosphatase function. Nat Struct Mol Biol 2012; 19:633-41. [PMID: 22562138 PMCID: PMC3529583 DOI: 10.1038/nsmb.2289] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Accepted: 04/03/2012] [Indexed: 12/29/2022]
Abstract
Ciona intestinalis voltage sensing phosphatase Ci-VSP couples a voltage-sensing domain (VSD) to a lipid phosphatase similar to the tumor suppressor PTEN. How the VSD controls enzyme function has been unclear. Here, we present high-resolution crystal structures of the Ci-VSP enzymatic domain that reveal conformational changes in a key loop, termed the “gating loop”, that controls access to the active site by a mechanism in which residue Glu411 directly competes with substrate. Structure-based mutations that restrict gating loop conformation impair catalytic function and demonstrate that Glu411 also contributes to substrate selectivity. Structure-guided mutations further define an interaction between the gating loop and linker that connects the phosphatase to the VSD for voltage control of enzyme activity. Together, the data suggest that functional coupling between the gating loop and the linker forms the heart of the regulatory mechanism that controls voltage-dependent enzyme activation.
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Affiliation(s)
- Lijun Liu
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California, USA
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41
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42
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New insights in the activity of voltage sensitive phosphatases. Cell Signal 2012; 24:1541-7. [PMID: 22481094 DOI: 10.1016/j.cellsig.2012.03.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 03/13/2012] [Accepted: 03/20/2012] [Indexed: 11/23/2022]
Abstract
The Ciona intestinalis voltage sensitive phosphatase (Ci-VSP) was the first proven enzyme to be under direct control of the membrane potential. Ci-VSP belongs to a family of proteins known as Protein Tyrosine Phosphatases (PTP), which are a group of enzymes that catalyze the removal of phosphate groups from phosphatidylinositides and phosphorylated tyrosine residues on proteins. What makes Ci-VSP and similar phosphatases unique is the presence of a Voltage Sensing Domain (VSD) in their N-terminus. The VSD of Ci-VSP shares high homology with those from voltage-gated channels and confers voltage sensitivity to these enzymes. The catalytic domain of Ci-VSP displays extraordinary structural and functional similarities to PTEN. This latter protein is encoded by the Phosphatase and Tensin homolog deleted from chromosome 10 gene, thus its name, and it is known as a tumor suppressor. The resemblance between these proteins has prompted the use of PTEN as a template for the study of Ci-VSP and produced a rapid advance in our understanding of the mechanism of activity of Ci-VSP. This review will be focused on discussing recent advances in the understanding of the activation mechanism for these molecules known as electrochemical coupling.
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Hobiger K, Utesch T, Mroginski MA, Friedrich T. Coupling of Ci-VSP modules requires a combination of structure and electrostatics within the linker. Biophys J 2012; 102:1313-22. [PMID: 22455914 DOI: 10.1016/j.bpj.2012.02.027] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2011] [Revised: 02/01/2012] [Accepted: 02/08/2012] [Indexed: 11/26/2022] Open
Abstract
The voltage-sensitive phosphatase Ci-VSP consists of an intracellular phosphatase domain (PD) coupled to a transmembrane voltage-sensor domain (VSD). Depolarization triggers the selective dephosphorylation of phosphoinositides. However, the molecular mechanisms of coupling are still elusive. To clarify the role of the VSD-PD linker as a putative partner for electrostatic interactions with the membrane, we carried out a cysteine-scanning mutagenesis of the whole motif M240-K257. Upon coexpression with PI(4,5)P(2)-sensitive KCNQ2/KCNQ3 channels in Xenopus oocytes, we identified four positions (A242C, R245C, K252C, and Y255C) with a completely abrogated PD activity. Because the mutation effect occurred periodically, we hypothesize that α-helical elements exist within the linker, with a gap near position S249. The combination of these results with the analysis of transient sensing currents of the VSD revealed distinct roles for the N-terminal (M240-S249) and C-terminal (Q250-K257) linker motifs in the VSD-PD coupling. According to our functional results, the computational structure prediction of the Q239-D258 fragment confirmed α-helical structures within the linker, with a short β-turn around S249 in the activated conformation. Remarkably, the position K252 may be a candidate for interacting with the PD rather than for binding to the membrane. This provides the first insight (to our knowledge) into the direct intervention of the linker in the VSD-PD coupling process.
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Affiliation(s)
- Kirstin Hobiger
- Berlin Institute of Technology, Institute of Chemistry, Max-Volmer-Laboratory of Biophysical Chemistry, Berlin, Germany.
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