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Yoshioka D, Fukushima S, Koteishi H, Okuno D, Ide T, Matsuoka S, Ueda M. Single-molecule imaging of PI(4,5)P 2 and PTEN in vitro reveals a positive feedback mechanism for PTEN membrane binding. Commun Biol 2020; 3:92. [PMID: 32111929 PMCID: PMC7048775 DOI: 10.1038/s42003-020-0818-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 02/10/2020] [Indexed: 01/21/2023] Open
Abstract
PTEN, a 3-phosphatase of phosphoinositide, regulates asymmetric PI(3,4,5)P3 signaling for the anterior-posterior polarization and migration of motile cells. PTEN acts through posterior localization on the plasma membrane, but the mechanism for this accumulation is poorly understood. Here we developed an in vitro single-molecule imaging assay with various lipid compositions and use it to demonstrate that the enzymatic product, PI(4,5)P2, stabilizes PTEN's membrane-binding. The dissociation kinetics and lateral mobility of PTEN depended on the PI(4,5)P2 density on artificial lipid bilayers. The basic residues of PTEN were responsible for electrostatic interactions with anionic PI(4,5)P2 and thus the PI(4,5)P2-dependent stabilization. Single-molecule imaging in living Dictyostelium cells revealed that these interactions were indispensable for the stabilization in vivo, which enabled efficient cell migration by accumulating PTEN posteriorly to restrict PI(3,4,5)P3 distribution to the anterior. These results suggest that PI(4,5)P2-mediated positive feedback and PTEN-induced PI(4,5)P2 clustering may be important for anterior-posterior polarization.
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Affiliation(s)
- Daisuke Yoshioka
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 565-0043, Japan
- Center for Biosystems Dynamics Research (BDR), RIKEN, Suita, Osaka, 565-0874, Japan
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Seiya Fukushima
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 565-0043, Japan
- Center for Biosystems Dynamics Research (BDR), RIKEN, Suita, Osaka, 565-0874, Japan
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Hiroyasu Koteishi
- Center for Biosystems Dynamics Research (BDR), RIKEN, Suita, Osaka, 565-0874, Japan
| | - Daichi Okuno
- Center for Biosystems Dynamics Research (BDR), RIKEN, Suita, Osaka, 565-0874, Japan
| | - Toru Ide
- Graduate School of Natural Science and Technology, Okayama University, Okayama-shi, Okayama, 700-8530, Japan
| | - Satomi Matsuoka
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 565-0043, Japan.
- Center for Biosystems Dynamics Research (BDR), RIKEN, Suita, Osaka, 565-0874, Japan.
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan.
| | - Masahiro Ueda
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 565-0043, Japan.
- Center for Biosystems Dynamics Research (BDR), RIKEN, Suita, Osaka, 565-0874, Japan.
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan.
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Fukuda Y, Koteishi H, Yoneda R, Tamada T, Takami H, Inoue T, Nojiri M. Structural and functional characterization of the Geobacillus copper nitrite reductase: involvement of the unique N-terminal region in the interprotein electron transfer with its redox partner. Biochim Biophys Acta 2014; 1837:396-405. [PMID: 24440558 DOI: 10.1016/j.bbabio.2014.01.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 12/19/2013] [Accepted: 01/07/2014] [Indexed: 11/28/2022]
Abstract
The crystal structures of copper-containing nitrite reductase (CuNiR) from the thermophilic Gram-positive bacterium Geobacillus kaustophilus HTA426 and the amino (N)-terminal 68 residue-deleted mutant were determined at resolutions of 1.3Å and 1.8Å, respectively. Both structures show a striking resemblance with the overall structure of the well-known CuNiRs composed of two Greek key β-barrel domains; however, a remarkable structural difference was found in the N-terminal region. The unique region has one β-strand and one α-helix extended to the northern surface of the type-1 copper site. The superposition of the Geobacillus CuNiR model on the electron-transfer complex structure of CuNiR with the redox partner cytochrome c551 in other denitrifier system led us to infer that this region contributes to the transient binding with the partner protein during the interprotein electron transfer reaction in the Geobacillus system. Furthermore, electron-transfer kinetics experiments using N-terminal residue-deleted mutant and the redox partner, Geobacillus cytochrome c551, were carried out. These structural and kinetics studies demonstrate that the region is directly involved in the specific partner recognition.
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Affiliation(s)
- Yohta Fukuda
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Department of Materials Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan; Molecular Biology Research Center, Quantum Beam Science Directorate, Japan Atomic Energy Agency, Tokai, Ibaraki 319-1195, Japan
| | - Hiroyasu Koteishi
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Ryohei Yoneda
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Taro Tamada
- Molecular Biology Research Center, Quantum Beam Science Directorate, Japan Atomic Energy Agency, Tokai, Ibaraki 319-1195, Japan
| | - Hideto Takami
- Microbial Genome Research Group, Japan Agency of Marine-Earth Science and Technology, Yokosuka, Kanagawa 237-0061, Japan
| | - Tsuyoshi Inoue
- Department of Materials Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Masaki Nojiri
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan.
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Hiruma Y, Hass MA, Kikui Y, Liu WM, Ölmez B, Skinner SP, Blok A, Kloosterman A, Koteishi H, Löhr F, Schwalbe H, Nojiri M, Ubbink M. The Structure of the Cytochrome P450cam–Putidaredoxin Complex Determined by Paramagnetic NMR Spectroscopy and Crystallography. J Mol Biol 2013; 425:4353-65. [DOI: 10.1016/j.jmb.2013.07.006] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 07/03/2013] [Accepted: 07/08/2013] [Indexed: 11/27/2022]
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Tsuda A, Ishikawa R, Koteishi H, Tange K, Fukuda Y, Kobayashi K, Inoue T, Nojiri M. Structural and mechanistic insights into the electron flow through protein for cytochrome c-tethering copper nitrite reductase. J Biochem 2013; 154:51-60. [PMID: 23543476 DOI: 10.1093/jb/mvt023] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Copper-containing nitrite reductases (CuNiRs), which catalyse the reversible one-electron reduction of nitrite to nitric oxide, are members of a large family of multi-copper enzymes that require an interprotein electron transfer (ET) reaction with redox partner proteins. Here, we show that the naturally fused type of CuNiR tethering a cytochrome c (Cyt c) at the C-terminus folds as a unique trimeric domain-swapped structure and has a self-sufficient electron flow system. The C-terminal Cyt c domain is located at the surface of the type 1 copper (T1Cu) site in the N-terminal CuNiR domain from the adjacent subunit, the heme-to-Cu distance (10.6 Å) of which is comparable to the transient ET complex of normal CuNiR with Cyt c. The structural aspects for the domain-domain interface and the ET kinetics indicate that the Cyt c-CuNiR domain interaction should be highly transient. The further electrochemical analysis of the interprotein ET reaction with a cognate redox partner protein suggested that an electron is directly transferred from the partner to the T1Cu. Structural and mechanistic comparisons of Cyt c-CuNiR with another cupredoxin-tethering CuNiR highlight the behaviours of extra domains on the fusion types of CuNiRs required for ET through proteins.
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Affiliation(s)
- Aiko Tsuda
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
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Nojiri M, Koteishi H, Nakagami T, Kobayashi K, Inoue T, Yamaguchi K, Suzuki S. Structural basis of inter-protein electron transfer for nitrite reduction in denitrification. Nature 2009; 462:117-20. [DOI: 10.1038/nature08507] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Accepted: 09/14/2009] [Indexed: 11/10/2022]
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Koteishi H, Nojiri M, Nakagami T, Yamaguchi K, Suzuki S. Cytochromec551Is a Mediator of Electron Transfer between Copper-Containing Nitrite Reductase and Azurin in a Denitrifying Bacterium,Achromobacter xylosoxidans. BCSJ 2009. [DOI: 10.1246/bcsj.82.1003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Nojiri M, Koteishi H, Tsuda A, Yamaguchi K, Suzuki S. Inter- and intra-molecular complex structures of Cu-containing nitrite reductase with cytochrome c. Acta Crystallogr A 2008. [DOI: 10.1107/s0108767308090752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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