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Sannino C, Borruso L, Mezzasoma A, Turchetti B, Ponti S, Buzzini P, Mimmo T, Guglielmin M. The Unusual Dominance of the Yeast Genus Glaciozyma in the Deeper Layer in an Antarctic Permafrost Core (Adélie Cove, Northern Victoria Land) Is Driven by Elemental Composition. J Fungi (Basel) 2023; 9:jof9040435. [PMID: 37108890 PMCID: PMC10145851 DOI: 10.3390/jof9040435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/24/2023] [Accepted: 03/28/2023] [Indexed: 04/05/2023] Open
Abstract
Rock glaciers are relatively common in Antarctic permafrost areas and could be considered postglacial cryogenic landforms. Although the extensive presence of rock glaciers, their chemical–physical and biotic composition remain scarce. Chemical–physical parameters and fungal community (by sequencing the ITS2 rDNA, Illumina MiSeq) parameters of a permafrost core were studied. The permafrost core, reaching a depth of 6.10 m, was divided into five units based on ice content. The five units (U1–U5) of the permafrost core exhibited several significant (p < 0.05) differences in terms of chemical and physical characteristics, and significant (p < 0.05) higher values of Ca, K, Li, Mg, Mn, S, and Sr were found in U5. Yeasts dominated on filamentous fungi in all the units of the permafrost core; additionally, Ascomycota was the prevalent phylum among filamentous forms, while Basidiomycota was the dominant phylum among yeasts. Surprisingly, in U5 the amplicon sequence variants (ASVs) assigned to the yeast genus Glaciozyma represented about two-thirds of the total reads. This result may be considered extremely rare in Antarctic yeast diversity, especially in permafrost habitats. Based on of the chemical–physical composition of the units, the dominance of Glaciozyma in the deepest unit was correlated with the elemental composition of the core.
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Affiliation(s)
- Ciro Sannino
- Industrial Yeasts Collection DBVPG, Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy
| | - Luigimaria Borruso
- Faculty of Science and Technology, Free University of Bozen-Bolzano, 39100 Bozen-Bolzano, Italy
| | - Ambra Mezzasoma
- Industrial Yeasts Collection DBVPG, Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy
| | - Benedetta Turchetti
- Industrial Yeasts Collection DBVPG, Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy
| | - Stefano Ponti
- Department of Theoretical and Applied Sciences, Insubria University, 21100 Varese, Italy
| | - Pietro Buzzini
- Industrial Yeasts Collection DBVPG, Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy
| | - Tanja Mimmo
- Faculty of Science and Technology, Free University of Bozen-Bolzano, 39100 Bozen-Bolzano, Italy
| | - Mauro Guglielmin
- Department of Theoretical and Applied Sciences, Insubria University, 21100 Varese, Italy
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Gungormus M, Ozdogan MS, Ertem SY, Tulumbaci F, Kara H, Orhan M. Accelerated Calcium Phosphate Mineralization by Peptides with Adjacent Oppositely Charged Residues. ACS Biomater Sci Eng 2020; 6:3791-3798. [DOI: 10.1021/acsbiomaterials.0c00194] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Mustafa Gungormus
- Department of Basic Sciences, School of Dentistry, Ankara Yildirim Beyazit University, Ankara 06760, Turkey
- Department of Biomedical Engineering, School of Engineering and Natural Sciences Ankara Yildirim Beyazit University, Ankara 06760, Turkey
| | - Mahmut Sertac Ozdogan
- Department of Clinical Sciences, School of Dentistry, Ankara Yildirim Beyazit University, Ankara 06760, Turkey
| | - Sinan Yasin Ertem
- Department of Clinical Sciences, School of Dentistry, Ankara Yildirim Beyazit University, Ankara 06760, Turkey
| | - Fatih Tulumbaci
- Department of Clinical Sciences, School of Dentistry, Ankara Yildirim Beyazit University, Ankara 06760, Turkey
| | - Halil Kara
- Department of Medical Pharmacology, School of Medicine, Ankara Yildirim Beyazit University, Ankara 06760, Turkey
| | - Metin Orhan
- Department of Clinical Sciences, School of Dentistry, Ankara Yildirim Beyazit University, Ankara 06760, Turkey
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Calcium-Binding Generates the Semi-Clathrate Waters on a Type II Antifreeze Protein to Adsorb onto an Ice Crystal Surface. Biomolecules 2019; 9:biom9050162. [PMID: 31035615 PMCID: PMC6572318 DOI: 10.3390/biom9050162] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 04/25/2019] [Accepted: 04/25/2019] [Indexed: 01/15/2023] Open
Abstract
Hydration is crucial for a function and a ligand recognition of a protein. The hydration shell constructed on an antifreeze protein (AFP) contains many organized waters, through which AFP is thought to bind to specific ice crystal planes. For a Ca2+-dependent species of AFP, however, it has not been clarified how 1 mol of Ca2+-binding is related with the hydration and the ice-binding ability. Here we determined the X-ray crystal structure of a Ca2+-dependent AFP (jsAFP) from Japanese smelt, Hypomesus nipponensis, in both Ca2+-bound and -free states. Their overall structures were closely similar (Root mean square deviation (RMSD) of Cα = 0.31 Å), while they exhibited a significant difference around their Ca2+-binding site. Firstly, the side-chains of four of the five Ca2+-binding residues (Q92, D94 E99, D113, and D114) were oriented to be suitable for ice binding only in the Ca2+-bound state. Second, a Ca2+-binding loop consisting of a segment D94–E99 becomes less flexible by the Ca2+-binding. Third, the Ca2+-binding induces a generation of ice-like clathrate waters around the Ca2+-binding site, which show a perfect position-match to the waters constructing the first prism plane of a single ice crystal. These results suggest that generation of ice-like clathrate waters induced by Ca2+-binding enables the ice-binding of this protein.
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Chakraborty S, Jana B. Calcium ion implicitly modulates the adsorption ability of ion-dependent type II antifreeze proteins on an ice/water interface: a structural insight. Metallomics 2019; 11:1387-1400. [DOI: 10.1039/c9mt00100j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Ca2+modulates the dynamics of ion-dependent type II AFP to efficiently adsorb on ice surface with high degree of specificity.
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Affiliation(s)
- Sandipan Chakraborty
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Jadavpur
- Kolkata-700032
- India
| | - Biman Jana
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Jadavpur
- Kolkata-700032
- India
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Abstract
Ice binding proteins (IBPs) are produced by various cold-adapted organisms to protect their body tissues against freeze damage. First discovered in Antarctic fish living in shallow waters, IBPs were later found in insects, microorganisms, and plants. Despite great structural diversity, all IBPs adhere to growing ice crystals, which is essential for their extensive repertoire of biological functions. Some IBPs maintain liquid inclusions within ice or inhibit recrystallization of ice, while other types suppress freezing by blocking further ice growth. In contrast, ice nucleating proteins stimulate ice nucleation just below 0 °C. Despite huge commercial interest and major scientific breakthroughs, the precise working mechanism of IBPs has not yet been unraveled. In this review, the authors outline the state-of-the-art in experimental and theoretical IBP research and discuss future scientific challenges. The interaction of IBPs with ice, water and ions is examined, focusing in particular on ice growth inhibition mechanisms.
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Shaw PL, Kirschner AN, Jardetzky TS, Longnecker R. Characteristics of Epstein-Barr virus envelope protein gp42. Virus Genes 2010; 40:307-19. [PMID: 20162447 PMCID: PMC2854865 DOI: 10.1007/s11262-010-0455-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Accepted: 01/27/2010] [Indexed: 12/21/2022]
Abstract
Epstein-Barr virus (EBV) glycoprotein 42 (gp42) is a membrane protein essential for fusion and entry of EBV into host B-lymphocytes. Gp42 is a member of the protein-fold family C-type lectin or lectin-like domains (CLECT or CTLD) and specifically is classified as a natural-killer receptor (NKR)-like CLECT. Literature review and phylogenetic comparison show that EBV gp42 shares a common structure with other NKR-like CLECTs and possibly with many viral CTLDs, but does not appear to exhibit some common binding characteristics of many CTLDs, such as features required for calcium binding. The flexible N-terminal region adjacent to the CTLD fold is important for binding to other EBV glycoproteins and for a cleavage site that is necessary for infection of host cells. From structural studies of gp42 unbound and bound to receptor and extensive mutational analysis, a general model of how gp42 triggers membrane fusion utilizing both the flexible N-terminal region and the CTLD domain has emerged.
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Affiliation(s)
- Pamela L. Shaw
- Department of Microbiology and Immunology, The Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611
- Galter Health Sciences Library, The Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611
| | - Austin N. Kirschner
- Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, Evanston, Illinois 60208
| | - Theodore S. Jardetzky
- Department of Structural Biology, Stanford University School of Medicine, Stanford California 94305
| | - Richard Longnecker
- Department of Microbiology and Immunology, The Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611
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Nishimiya Y, Kondo H, Takamichi M, Sugimoto H, Suzuki M, Miura A, Tsuda S. Crystal structure and mutational analysis of Ca2+-independent type II antifreeze protein from longsnout poacher, Brachyopsis rostratus. J Mol Biol 2008; 382:734-46. [PMID: 18674542 DOI: 10.1016/j.jmb.2008.07.042] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2008] [Revised: 07/13/2008] [Accepted: 07/16/2008] [Indexed: 10/21/2022]
Abstract
We recently found that longsnout poacher (Brachyosis rostratus) produces a Ca(2+)-independent type II antifreeze protein (lpAFP) and succeeded in expressing recombinant lpAFP using Phichia pastoris. Here, we report, for the first time, the X-ray crystal structure of lpAFP at 1.34 A resolution. The lpAFP structure displayed a relatively planar surface, which encompasses two loop regions (Cys86-Lys89 and Asn91-Cys97) and a short beta-strand (Trp109-Leu112) with three unstructured segments (Gly57-Ile58, Ala103-Ala104, and Pro113-His118). Electrostatic calculation of the protein surface showed that the relatively planar surface was divided roughly into a hydrophobic area (composed of the three unstructured segments lacking secondary structure) and a hydrophilic area (composed of the loops and beta-strand). Site-directed mutation of Ile58 with Phe at the center of the hydrophobic area decreased activity significantly, whereas mutation of Leu112 with Phe at an intermediate area between the hydrophobic and hydrophilic areas retained complete activity. In the hydrophilic area, a peptide-swap mutant in the loops retained 60% activity despite simultaneous mutations of eight residues. We conclude that the epicenter of the ice-binding site of lpAFP is the hydrophobic region, which is centered by Ile58, in the relatively planar surface. We built an ice-binding model for lpAFP on the basis of a lattice match of ice and constrained water oxygen atoms surrounding the hydrophobic area in the lpAFP structure. The model in which lpAFP has been docked to a secondary prism (2-1-10) plane, which is different from the one determined for Ca(2+)-independent type II AFP from sea raven (11-21), appears to explain the results of the mutagenesis analysis.
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Affiliation(s)
- Yoshiyuki Nishimiya
- Functional Protein Research Group, Research Institute of Genome-based Biofactory, National Institute of Advanced Industrial Science and Technology, 2-17-2-1 Tsukisamu-Higashi, Toyohira, Sapporo 062-8517, Japan
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A Ca2+-dependent bacterial antifreeze protein domain has a novel β-helical ice-binding fold. Biochem J 2008; 411:171-80. [DOI: 10.1042/bj20071372] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
AFPs (antifreeze proteins) are produced by many organisms that inhabit ice-laden environments. They facilitate survival at sub-zero temperatures by binding to, and inhibiting, the growth of ice crystals in solution. The Antarctic bacterium Marinomonas primoryensis produces an exceptionally large (>1 MDa) hyperactive Ca2+-dependent AFP. We have cloned, expressed and characterized a 322-amino-acid region of the protein where the antifreeze activity is localized that shows similarity to the RTX (repeats-in-toxin) family of proteins. The recombinant protein requires Ca2+ for structure and activity, and it is capable of depressing the freezing point of a solution in excess of 2 °C at a concentration of 0.5 mg/ml, therefore classifying it as a hyperactive AFP. We have developed a homology-guided model of the antifreeze region based partly on the Ca2+-bound β-roll from alkaline protease. The model has identified both a novel β-helical fold and an ice-binding site. The interior of the β-helix contains a single row of bound Ca2+ ions down one side of the structure and a hydrophobic core down the opposite side. The ice-binding surface consists of parallel repetitive arrays of threonine and aspartic acid/asparagine residues located down the Ca2+-bound side of the structure. The model was tested and validated by site-directed mutagenesis. It explains the Ca2+-dependency of the region, as well its hyperactive antifreeze activity. This is the first bacterial AFP to be structurally characterized and is one of only five hyperactive AFPs identified to date.
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Liu Y, Li Z, Lin Q, Kosinski J, Seetharaman J, Bujnicki JM, Sivaraman J, Hew CL. Structure and evolutionary origin of Ca(2+)-dependent herring type II antifreeze protein. PLoS One 2007; 2:e548. [PMID: 17579720 PMCID: PMC1891086 DOI: 10.1371/journal.pone.0000548] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2007] [Accepted: 05/24/2007] [Indexed: 01/07/2023] Open
Abstract
In order to survive under extremely cold environments, many organisms produce antifreeze proteins (AFPs). AFPs inhibit the growth of ice crystals and protect organisms from freezing damage. Fish AFPs can be classified into five distinct types based on their structures. Here we report the structure of herring AFP (hAFP), a Ca(2+)-dependent fish type II AFP. It exhibits a fold similar to the C-type (Ca(2+)-dependent) lectins with unique ice-binding features. The 1.7 A crystal structure of hAFP with bound Ca(2+) and site-directed mutagenesis reveal an ice-binding site consisting of Thr96, Thr98 and Ca(2+)-coordinating residues Asp94 and Glu99, which initiate hAFP adsorption onto the [10-10] prism plane of the ice lattice. The hAFP-ice interaction is further strengthened by the bound Ca(2+) through the coordination with a water molecule of the ice lattice. This Ca(2+)-coordinated ice-binding mechanism is distinct from previously proposed mechanisms for other AFPs. However, phylogenetic analysis suggests that all type II AFPs evolved from the common ancestor and developed different ice-binding modes. We clarify the evolutionary relationship of type II AFPs to sugar-binding lectins.
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Affiliation(s)
- Yang Liu
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Zhengjun Li
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Qingsong Lin
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Jan Kosinski
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - J. Seetharaman
- X4 Beamline, Brookhaven National Laboratory, Upton, New York, United States of America
| | | | - J. Sivaraman
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- * To whom correspondence should be addressed. E-mail: (JS); (C-LH)
| | - Choy-Leong Hew
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- * To whom correspondence should be addressed. E-mail: (JS); (C-LH)
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Scotter AJ, Kuntz DA, Saul M, Graham LA, Davies PL, Rose DR. Expression and purification of sea raven type II antifreeze protein from Drosophila melanogaster S2 cells. Protein Expr Purif 2006; 47:374-83. [PMID: 16330225 DOI: 10.1016/j.pep.2005.10.028] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2005] [Revised: 10/26/2005] [Accepted: 10/27/2005] [Indexed: 11/19/2022]
Abstract
We present a system for the expression and purification of recombinant sea raven type II antifreeze protein, a cysteine-rich, C-type lectin-like globular protein that has proved to be a difficult target for recombinant expression and purification. The cDNAs encoding the pro- and mature forms of the sea raven protein were cloned into a modified pMT Drosophila expression vector. These constructs produced N-terminally His(6)-tagged pro- and mature forms of the type II antifreeze protein under the control of a metallothionein promoter when transfected into Drosophila melanogaster S2 cells. Upon induction of stable cell lines the two proteins were expressed at high levels and secreted into the medium. The proteins were then purified from the cell medium in a simple and rapid protocol using immobilized metal affinity chromatography and specific protease cleavage by tobacco etch virus protease. The proteins demonstrated antifreeze activity indistinguishable from that of wild-type sea raven antifreeze protein purified from serum as illustrated by ice affinity purification, ice crystal morphology, and their ability to inhibit ice crystal growth. This expression and purification system gave yields of 95 mg/L of fully active mature sea raven type II AFP and 9.6 mg/L of the proprotein. This surpasses all previous attempts to express this protein in Escherichia coli, baculovirus-infected fall armyworm cells and Pichia pastoris and will provide sufficient protein for structural analysis.
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Affiliation(s)
- Andrew J Scotter
- Department of Biochemistry and the Protein Engineering Network Centres of Excellence, Queen's University, Kingston, Ont., Canada.
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Nishimiya Y, Kondo H, Yasui M, Sugimoto H, Noro N, Sato R, Suzuki M, Miura A, Tsuda S. Crystallization and preliminary X-ray crystallographic analysis of Ca2+-independent and Ca2+-dependent species of the type II antifreeze protein. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:538-41. [PMID: 16754975 PMCID: PMC2243089 DOI: 10.1107/s1744309106015570] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2006] [Accepted: 04/28/2006] [Indexed: 11/10/2022]
Abstract
Ca2+-independent and Ca2+-dependent species of the type II antifreeze protein (AFP) were both crystallized using the hanging-drop vapour-diffusion method. It appeared that the crystal of the Ca2+-independent species from Brachyosis rostratus belongs to space group P2(1)2(1)2(1), with unit-cell parameters a = 43.3, b = 48.4, c = 59.7 A, and diffraction data were collected to 1.34 A resolution. For the Ca2+-dependent type II AFP species from Hypomesus nipponensis, crystallization was carried out for its Ca2+-free and Ca2+-bound states. 1.25 A resolution data were collected from the crystal in the Ca(2+)-free state, which exhibited P3(1)21 (or P3(2)21) symmetry, with unit-cell parameters a = b = 66.0, c = 50.3 A. Data collection could be extended to 1.06 A resolution for the crystal in the Ca2+ -bound state, which appeared to be isomorphous to the crystal in the Ca2+-free state (unit-cell parameters a = b = 66.0, c = 49.8 A). These data will allow us to determine the high-resolution structures of the two species of type II AFP.
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Affiliation(s)
- Yoshiyuki Nishimiya
- Functional Protein Research Group, Research Institute of Genome-based Biofactory, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira, Sapporo 062-8517, Japan
| | - Hidemasa Kondo
- Functional Protein Research Group, Research Institute of Genome-based Biofactory, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira, Sapporo 062-8517, Japan
| | - Masanori Yasui
- Functional Protein Research Group, Research Institute of Genome-based Biofactory, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira, Sapporo 062-8517, Japan
- Division of Biological Sciences, Graduate School of Science, Hokkaido University, N8W5, Kita, Sapporo 060-0808, Japan
| | - Hiroshi Sugimoto
- Biometal Science Laboratory, Riken SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Natsuko Noro
- Functional Protein Research Group, Research Institute of Genome-based Biofactory, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira, Sapporo 062-8517, Japan
| | - Ryoko Sato
- Functional Protein Research Group, Research Institute of Genome-based Biofactory, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira, Sapporo 062-8517, Japan
| | - Mamoru Suzuki
- Insititute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Ai Miura
- Functional Protein Research Group, Research Institute of Genome-based Biofactory, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira, Sapporo 062-8517, Japan
| | - Sakae Tsuda
- Functional Protein Research Group, Research Institute of Genome-based Biofactory, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira, Sapporo 062-8517, Japan
- Division of Biological Sciences, Graduate School of Science, Hokkaido University, N8W5, Kita, Sapporo 060-0808, Japan
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