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Oversized ubiquinones as molecular probes for structural dynamics of the ubiquinone reaction site in mitochondrial respiratory complex I.

Identifieur interne : 000022 ( Main/Exploration ); précédent : 000021; suivant : 000023

Oversized ubiquinones as molecular probes for structural dynamics of the ubiquinone reaction site in mitochondrial respiratory complex I.

Auteurs : Shinpei Uno [Japon] ; Takahiro Masuya [Japon] ; Kyoko Shinzawa-Itoh [Japon] ; Jonathan Lasham [Finlande] ; Outi Haapanen [Finlande] ; Tomoo Shiba [Japon] ; Daniel Ken Inaoka [Japon] ; Vivek Sharma [Finlande] ; Masatoshi Murai [Japon] ; Hideto Miyoshi [Japon]

Source :

RBID : pubmed:31953326

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English descriptors

Abstract

NADH-quinone oxidoreductase (complex I) couples electron transfer from NADH to quinone with proton translocation across the membrane. Quinone reduction is a key step for energy transmission from the site of quinone reduction to the remotely located proton-pumping machinery of the enzyme. Although structural biology studies have proposed the existence of a long and narrow quinone-access channel, the physiological relevance of this channel remains debatable. We investigated here whether complex I in bovine heart submitochondrial particles (SMPs) can catalytically reduce a series of oversized ubiquinones (OS-UQs), which are highly unlikely to transit the narrow channel because their side chain includes a bulky "block" that is ∼13 Å across. We found that some OS-UQs function as efficient electron acceptors from complex I, accepting electrons with an efficiency comparable with ubiquinone-2. The catalytic reduction and proton translocation coupled with this reduction were completely inhibited by different quinone-site inhibitors, indicating that the reduction of OS-UQs takes place at the physiological reaction site for ubiquinone. Notably, the proton-translocating efficiencies of OS-UQs significantly varied depending on their side-chain structures, suggesting that the reaction characteristics of OS-UQs affect the predicted structural changes of the quinone reaction site required for triggering proton translocation. These results are difficult to reconcile with the current channel model; rather, the access path for ubiquinone may be open to allow OS-UQs to access the reaction site. Nevertheless, contrary to the observations in SMPs, OS-UQs were not catalytically reduced by isolated complex I reconstituted into liposomes. We discuss possible reasons for these contradictory results.

DOI: 10.1074/jbc.RA119.012347
PubMed: 31953326
PubMed Central: PMC7039553


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<term>Alkynes (metabolism)</term>
<term>Animals (MeSH)</term>
<term>Cattle (MeSH)</term>
<term>Computer Simulation (MeSH)</term>
<term>Electron Transport (MeSH)</term>
<term>Electron Transport Complex I (metabolism)</term>
<term>Membrane Potential, Mitochondrial (MeSH)</term>
<term>Mitochondria, Heart (metabolism)</term>
<term>Mitochondrial Proteins (metabolism)</term>
<term>Models, Molecular (MeSH)</term>
<term>Molecular Probes (metabolism)</term>
<term>NAD (metabolism)</term>
<term>Oxidoreductases (metabolism)</term>
<term>Plant Proteins (metabolism)</term>
<term>Protein Subunits (metabolism)</term>
<term>Proteolipids (metabolism)</term>
<term>Protons (MeSH)</term>
<term>Submitochondrial Particles (metabolism)</term>
<term>Ubiquinone (chemistry)</term>
<term>Ubiquinone (metabolism)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr">
<term>Alcynes (métabolisme)</term>
<term>Animaux (MeSH)</term>
<term>Bovins (MeSH)</term>
<term>Complexe I de la chaîne respiratoire (métabolisme)</term>
<term>Mitochondries du myocarde (métabolisme)</term>
<term>Modèles moléculaires (MeSH)</term>
<term>NAD (métabolisme)</term>
<term>Oxidoreductases (métabolisme)</term>
<term>Particules submitochondriales (métabolisme)</term>
<term>Potentiel de membrane mitochondriale (MeSH)</term>
<term>Protons (MeSH)</term>
<term>Protéines mitochondriales (métabolisme)</term>
<term>Protéines végétales (métabolisme)</term>
<term>Protéolipides (métabolisme)</term>
<term>Simulation numérique (MeSH)</term>
<term>Sondes moléculaires (métabolisme)</term>
<term>Sous-unités de protéines (métabolisme)</term>
<term>Transport d'électrons (MeSH)</term>
<term>Ubiquinones (composition chimique)</term>
<term>Ubiquinones (métabolisme)</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en">
<term>Ubiquinone</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en">
<term>Alkynes</term>
<term>Electron Transport Complex I</term>
<term>Mitochondrial Proteins</term>
<term>Molecular Probes</term>
<term>NAD</term>
<term>Oxidoreductases</term>
<term>Plant Proteins</term>
<term>Protein Subunits</term>
<term>Proteolipids</term>
<term>Ubiquinone</term>
</keywords>
<keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr">
<term>Ubiquinones</term>
</keywords>
<keywords scheme="MESH" qualifier="metabolism" xml:lang="en">
<term>Mitochondria, Heart</term>
<term>Submitochondrial Particles</term>
</keywords>
<keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr">
<term>Alcynes</term>
<term>Complexe I de la chaîne respiratoire</term>
<term>Mitochondries du myocarde</term>
<term>NAD</term>
<term>Oxidoreductases</term>
<term>Particules submitochondriales</term>
<term>Protéines mitochondriales</term>
<term>Protéines végétales</term>
<term>Protéolipides</term>
<term>Sondes moléculaires</term>
<term>Sous-unités de protéines</term>
<term>Ubiquinones</term>
</keywords>
<keywords scheme="MESH" xml:lang="en">
<term>Animals</term>
<term>Cattle</term>
<term>Computer Simulation</term>
<term>Electron Transport</term>
<term>Membrane Potential, Mitochondrial</term>
<term>Models, Molecular</term>
<term>Protons</term>
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<keywords scheme="MESH" xml:lang="fr">
<term>Animaux</term>
<term>Bovins</term>
<term>Modèles moléculaires</term>
<term>Potentiel de membrane mitochondriale</term>
<term>Protons</term>
<term>Simulation numérique</term>
<term>Transport d'électrons</term>
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<front>
<div type="abstract" xml:lang="en">NADH-quinone oxidoreductase (complex I) couples electron transfer from NADH to quinone with proton translocation across the membrane. Quinone reduction is a key step for energy transmission from the site of quinone reduction to the remotely located proton-pumping machinery of the enzyme. Although structural biology studies have proposed the existence of a long and narrow quinone-access channel, the physiological relevance of this channel remains debatable. We investigated here whether complex I in bovine heart submitochondrial particles (SMPs) can catalytically reduce a series of oversized ubiquinones (OS-UQs), which are highly unlikely to transit the narrow channel because their side chain includes a bulky "block" that is ∼13 Å across. We found that some OS-UQs function as efficient electron acceptors from complex I, accepting electrons with an efficiency comparable with ubiquinone-2. The catalytic reduction and proton translocation coupled with this reduction were completely inhibited by different quinone-site inhibitors, indicating that the reduction of OS-UQs takes place at the physiological reaction site for ubiquinone. Notably, the proton-translocating efficiencies of OS-UQs significantly varied depending on their side-chain structures, suggesting that the reaction characteristics of OS-UQs affect the predicted structural changes of the quinone reaction site required for triggering proton translocation. These results are difficult to reconcile with the current channel model; rather, the access path for ubiquinone may be open to allow OS-UQs to access the reaction site. Nevertheless, contrary to the observations in SMPs, OS-UQs were not catalytically reduced by isolated complex I reconstituted into liposomes. We discuss possible reasons for these contradictory results.</div>
</front>
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<Month>10</Month>
<Day>14</Day>
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<Year>2020</Year>
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<Month>02</Month>
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</JournalIssue>
<Title>The Journal of biological chemistry</Title>
<ISOAbbreviation>J Biol Chem</ISOAbbreviation>
</Journal>
<ArticleTitle>Oversized ubiquinones as molecular probes for structural dynamics of the ubiquinone reaction site in mitochondrial respiratory complex I.</ArticleTitle>
<Pagination>
<MedlinePgn>2449-2463</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.1074/jbc.RA119.012347</ELocationID>
<Abstract>
<AbstractText>NADH-quinone oxidoreductase (complex I) couples electron transfer from NADH to quinone with proton translocation across the membrane. Quinone reduction is a key step for energy transmission from the site of quinone reduction to the remotely located proton-pumping machinery of the enzyme. Although structural biology studies have proposed the existence of a long and narrow quinone-access channel, the physiological relevance of this channel remains debatable. We investigated here whether complex I in bovine heart submitochondrial particles (SMPs) can catalytically reduce a series of oversized ubiquinones (OS-UQs), which are highly unlikely to transit the narrow channel because their side chain includes a bulky "block" that is ∼13 Å across. We found that some OS-UQs function as efficient electron acceptors from complex I, accepting electrons with an efficiency comparable with ubiquinone-2. The catalytic reduction and proton translocation coupled with this reduction were completely inhibited by different quinone-site inhibitors, indicating that the reduction of OS-UQs takes place at the physiological reaction site for ubiquinone. Notably, the proton-translocating efficiencies of OS-UQs significantly varied depending on their side-chain structures, suggesting that the reaction characteristics of OS-UQs affect the predicted structural changes of the quinone reaction site required for triggering proton translocation. These results are difficult to reconcile with the current channel model; rather, the access path for ubiquinone may be open to allow OS-UQs to access the reaction site. Nevertheless, contrary to the observations in SMPs, OS-UQs were not catalytically reduced by isolated complex I reconstituted into liposomes. We discuss possible reasons for these contradictory results.</AbstractText>
<CopyrightInformation>© 2020 Uno et al.</CopyrightInformation>
</Abstract>
<AuthorList CompleteYN="Y">
<Author ValidYN="Y">
<LastName>Uno</LastName>
<ForeName>Shinpei</ForeName>
<Initials>S</Initials>
<AffiliationInfo>
<Affiliation>Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Masuya</LastName>
<ForeName>Takahiro</ForeName>
<Initials>T</Initials>
<AffiliationInfo>
<Affiliation>Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Shinzawa-Itoh</LastName>
<ForeName>Kyoko</ForeName>
<Initials>K</Initials>
<AffiliationInfo>
<Affiliation>Department of Life Science, Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Lasham</LastName>
<ForeName>Jonathan</ForeName>
<Initials>J</Initials>
<AffiliationInfo>
<Affiliation>Department of Physics, University of Helsinki, FI-00014 Helsinki, Finland.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Haapanen</LastName>
<ForeName>Outi</ForeName>
<Initials>O</Initials>
<AffiliationInfo>
<Affiliation>Department of Physics, University of Helsinki, FI-00014 Helsinki, Finland.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Shiba</LastName>
<ForeName>Tomoo</ForeName>
<Initials>T</Initials>
<Identifier Source="ORCID">0000-0001-9312-1298</Identifier>
<AffiliationInfo>
<Affiliation>Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto 606-8585, Japan.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Inaoka</LastName>
<ForeName>Daniel Ken</ForeName>
<Initials>DK</Initials>
<AffiliationInfo>
<Affiliation>Department of Molecular Infection Dynamics, Institute of Tropical Medicine (NEKKEN).</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki 852-8523, Japan.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Sharma</LastName>
<ForeName>Vivek</ForeName>
<Initials>V</Initials>
<AffiliationInfo>
<Affiliation>Department of Physics, University of Helsinki, FI-00014 Helsinki, Finland.</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Murai</LastName>
<ForeName>Masatoshi</ForeName>
<Initials>M</Initials>
<Identifier Source="ORCID">0000-0001-6601-2854</Identifier>
<AffiliationInfo>
<Affiliation>Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Miyoshi</LastName>
<ForeName>Hideto</ForeName>
<Initials>H</Initials>
<Identifier Source="ORCID">0000-0002-1792-554X</Identifier>
<AffiliationInfo>
<Affiliation>Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan miyoshi@kais.kyoto-u.ac.jp.</Affiliation>
</AffiliationInfo>
</Author>
</AuthorList>
<Language>eng</Language>
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<DataBank>
<DataBankName>PDB</DataBankName>
<AccessionNumberList>
<AccessionNumber>5LC5</AccessionNumber>
</AccessionNumberList>
</DataBank>
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<PublicationType UI="D016428">Journal Article</PublicationType>
<PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType>
</PublicationTypeList>
<ArticleDate DateType="Electronic">
<Year>2020</Year>
<Month>01</Month>
<Day>17</Day>
</ArticleDate>
</Article>
<MedlineJournalInfo>
<Country>United States</Country>
<MedlineTA>J Biol Chem</MedlineTA>
<NlmUniqueID>2985121R</NlmUniqueID>
<ISSNLinking>0021-9258</ISSNLinking>
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<Chemical>
<RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D000480">Alkynes</NameOfSubstance>
</Chemical>
<Chemical>
<RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D024101">Mitochondrial Proteins</NameOfSubstance>
</Chemical>
<Chemical>
<RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D015335">Molecular Probes</NameOfSubstance>
</Chemical>
<Chemical>
<RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance>
</Chemical>
<Chemical>
<RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D021122">Protein Subunits</NameOfSubstance>
</Chemical>
<Chemical>
<RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D011510">Proteolipids</NameOfSubstance>
</Chemical>
<Chemical>
<RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D011522">Protons</NameOfSubstance>
</Chemical>
<Chemical>
<RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="C020485">proteoliposomes</NameOfSubstance>
</Chemical>
<Chemical>
<RegistryNumber>0U46U6E8UK</RegistryNumber>
<NameOfSubstance UI="D009243">NAD</NameOfSubstance>
</Chemical>
<Chemical>
<RegistryNumber>1339-63-5</RegistryNumber>
<NameOfSubstance UI="D014451">Ubiquinone</NameOfSubstance>
</Chemical>
<Chemical>
<RegistryNumber>EC 1.-</RegistryNumber>
<NameOfSubstance UI="D010088">Oxidoreductases</NameOfSubstance>
</Chemical>
<Chemical>
<RegistryNumber>EC 1.-</RegistryNumber>
<NameOfSubstance UI="C088813">alternative oxidase</NameOfSubstance>
</Chemical>
<Chemical>
<RegistryNumber>EC 7.1.1.2</RegistryNumber>
<NameOfSubstance UI="D042967">Electron Transport Complex I</NameOfSubstance>
</Chemical>
</ChemicalList>
<CitationSubset>IM</CitationSubset>
<MeshHeadingList>
<MeshHeading>
<DescriptorName UI="D000480" MajorTopicYN="N">Alkynes</DescriptorName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D002417" MajorTopicYN="N">Cattle</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D003198" MajorTopicYN="N">Computer Simulation</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D004579" MajorTopicYN="N">Electron Transport</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D042967" MajorTopicYN="N">Electron Transport Complex I</DescriptorName>
<QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D053078" MajorTopicYN="N">Membrane Potential, Mitochondrial</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D008929" MajorTopicYN="N">Mitochondria, Heart</DescriptorName>
<QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D024101" MajorTopicYN="N">Mitochondrial Proteins</DescriptorName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D008958" MajorTopicYN="N">Models, Molecular</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D015335" MajorTopicYN="N">Molecular Probes</DescriptorName>
<QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D009243" MajorTopicYN="N">NAD</DescriptorName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D010088" MajorTopicYN="N">Oxidoreductases</DescriptorName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D010940" MajorTopicYN="N">Plant Proteins</DescriptorName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D021122" MajorTopicYN="N">Protein Subunits</DescriptorName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D011510" MajorTopicYN="N">Proteolipids</DescriptorName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D011522" MajorTopicYN="N">Protons</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D013367" MajorTopicYN="N">Submitochondrial Particles</DescriptorName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
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<MeshHeading>
<DescriptorName UI="D014451" MajorTopicYN="N">Ubiquinone</DescriptorName>
<QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName>
<QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName>
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</MeshHeadingList>
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<Keyword MajorTopicYN="Y">bioenergetics</Keyword>
<Keyword MajorTopicYN="Y">chemical biology</Keyword>
<Keyword MajorTopicYN="Y">complex I</Keyword>
<Keyword MajorTopicYN="Y">mitochondria</Keyword>
<Keyword MajorTopicYN="Y">proton pump</Keyword>
<Keyword MajorTopicYN="Y">respiratory chain</Keyword>
<Keyword MajorTopicYN="Y">ubiquinone</Keyword>
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<Month>12</Month>
<Day>19</Day>
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<Year>2020</Year>
<Month>01</Month>
<Day>15</Day>
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<Year>2021</Year>
<Month>02</Month>
<Day>21</Day>
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<Month>1</Month>
<Day>19</Day>
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<Citation>Biochim Biophys Acta. 2011 Sep;1807(9):1170-6</Citation>
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<ArticleId IdType="pubmed">21616052</ArticleId>
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<Reference>
<Citation>Cell. 2017 Sep 7;170(6):1247-1257.e12</Citation>
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<li>Helsinki</li>
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<li>Université d'Helsinki</li>
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<name sortKey="Shiba, Tomoo" sort="Shiba, Tomoo" uniqKey="Shiba T" first="Tomoo" last="Shiba">Tomoo Shiba</name>
<name sortKey="Shinzawa Itoh, Kyoko" sort="Shinzawa Itoh, Kyoko" uniqKey="Shinzawa Itoh K" first="Kyoko" last="Shinzawa-Itoh">Kyoko Shinzawa-Itoh</name>
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