Retrieval from vacuolar/endosomal compartments underpinning neofunctionalization of SNARE in plants

Retrieval from vacuolar/endosomal compartments underpinning neofunctionalization of SNARE in plants | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Article Retrieval from vacuolar/endosomal compartments underpinning neofunctionalization of SNARE in plants Takashi Ueda, Yihong Feng, Kazuo Ebine, Yoko Ito, Takehiko Kanazawa, and 4 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-5274462/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 03 Oct, 2025 Read the published version in Nature Plants → Version 1 posted You are reading this latest preprint version Abstract The distinctive protein and lipid composition underlies the distinct function of each organelle, regulated by balanced anterograde and retrograde membrane trafficking. The vacuole, the largest plant organelle, is pivotal in various plant functions, with its protein composition tightly regulated by bidirectional trafficking. However, the existence of retrograde transport from the plant vacuole remained unverified. In this study, we demonstrate retrograde trafficking from the vacuole in Arabidopsis. We observed retrieval of VAMP727, a plant-unique vacuolar membrane fusion machinery, from the vacuolar membrane. VAMP727 retrieval is facilitated by SORTING NEXIN proteins, which were independently diversified between plant and non-plant systems. Furthermore, we show that the core retromer complex and SORTING NEXINs act independently in distinct retrograde transport events with specific cargos. Thus, plant cells have elaborated a unique retrieval mechanism from the vacuole, underpinning the neofunctionalization of VAMP727 during plant evolution. Biological sciences/Plant sciences/Plant cell biology/Protein trafficking in plants Biological sciences/Plant sciences/Plant evolution Full Text Additional Declarations There is NO Competing Interest. Supplementary Files SupplementalTable.xlsx Supplementary Table SupplementaryInformation.pdf ExtendedDataMovie1.avi Extended Data Movie1 ExtendedDataMovie2.avi Extended Data Movie2 ExtendedDataMovie3.avi Extended Data Movie3 ExtendedDataMovie4.avi Extended Data Movie4 Cite Share Download PDF Status: Published Journal Publication published 03 Oct, 2025 Read the published version in Nature Plants → Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-5274462","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":371429954,"identity":"ef807c4d-d6e1-44eb-983c-069b9312ccb6","order_by":0,"name":"Takashi Ueda","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAAuklEQVRIiWNgGAWjYJACCYYKBh4DCTCbjbByHrCWMyRrYWxjYIBqIQLYSyQfvPFz3h0Zc+kGxg8/GPjyCNsikZZs2bvtGY/lnAPMkj0MbMVEaMkxk+DddpjH4EYCgzTQL4kNhLXkf5P8Oweshfk3kVpy2KR5G8Ba2Ii05cwzY2uZY4eBfjnYZtljQIRf2NuTH958U3PY3ly6+fCNHxXHCIcYEmAEOsngWAIpWsCghnQto2AUjIJRMOwBAAnqNkN8YiKfAAAAAElFTkSuQmCC","orcid":"https://orcid.org/0000-0002-5190-892X","institution":"National Institute for Basic Biology","correspondingAuthor":true,"prefix":"","firstName":"Takashi","middleName":"","lastName":"Ueda","suffix":""},{"id":371429955,"identity":"7fffceb5-11ba-44ab-86e4-bb2d3c0c7a8d","order_by":1,"name":"Yihong Feng","email":"","orcid":"","institution":"National Institute for Basic Biology","correspondingAuthor":false,"prefix":"","firstName":"Yihong","middleName":"","lastName":"Feng","suffix":""},{"id":371429956,"identity":"38148e44-357b-4669-bec8-dc1858d090d4","order_by":2,"name":"Kazuo Ebine","email":"","orcid":"","institution":"National Institute for Basic Biology","correspondingAuthor":false,"prefix":"","firstName":"Kazuo","middleName":"","lastName":"Ebine","suffix":""},{"id":371429957,"identity":"2fed2e61-f30d-44d4-be69-00b8d553f3b9","order_by":3,"name":"Yoko Ito","email":"","orcid":"https://orcid.org/0000-0002-9877-1596","institution":"Ochanomizu University","correspondingAuthor":false,"prefix":"","firstName":"Yoko","middleName":"","lastName":"Ito","suffix":""},{"id":371429958,"identity":"be0bee0d-40c4-4a83-ab61-c4e6b65369a8","order_by":4,"name":"Takehiko Kanazawa","email":"","orcid":"https://orcid.org/0000-0003-0472-2273","institution":"National Institute for Basic Biology","correspondingAuthor":false,"prefix":"","firstName":"Takehiko","middleName":"","lastName":"Kanazawa","suffix":""},{"id":371429959,"identity":"dae2f65e-7780-41ce-8097-d81985d279a1","order_by":5,"name":"Tatsuya Sawasaki","email":"","orcid":"","institution":"Ehime Univeristy","correspondingAuthor":false,"prefix":"","firstName":"Tatsuya","middleName":"","lastName":"Sawasaki","suffix":""},{"id":371429960,"identity":"82da5fb2-d4a5-408f-b222-0c0894fcf9e0","order_by":6,"name":"Akira Nozawa","email":"","orcid":"https://orcid.org/0000-0003-4886-0213","institution":"Ehime University","correspondingAuthor":false,"prefix":"","firstName":"Akira","middleName":"","lastName":"Nozawa","suffix":""},{"id":371429961,"identity":"cea7e68f-a1ec-4587-a149-9c8c398a73ee","order_by":7,"name":"Tomohiro Uemura","email":"","orcid":"https://orcid.org/0000-0001-7270-7986","institution":"Ochanomizu University","correspondingAuthor":false,"prefix":"","firstName":"Tomohiro","middleName":"","lastName":"Uemura","suffix":""},{"id":371429962,"identity":"5b9d41a3-dd48-4d9f-b05d-5ac5fea5e09f","order_by":8,"name":"Akihiko Nakano","email":"","orcid":"https://orcid.org/0000-0003-3635-548X","institution":"Live Cell Super-Resolution Imaging Research Team, RIKEN Center for Advanced Photonics","correspondingAuthor":false,"prefix":"","firstName":"Akihiko","middleName":"","lastName":"Nakano","suffix":""}],"badges":[],"createdAt":"2024-10-16 09:15:34","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-5274462/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-5274462/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1038/s41477-025-02115-5","type":"published","date":"2025-10-03T04:00:00+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":92761834,"identity":"ae0457d0-6815-4b01-85ff-ec53b4e2e5bc","added_by":"auto","created_at":"2025-10-04 07:09:55","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":3268309,"visible":true,"origin":"","legend":"","description":"","filename":"manuscrip.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5274462/v1_covered_0a4a0d04-8bae-45e3-8815-e3b24764442f.pdf"},{"id":67806948,"identity":"096f5223-97d3-4b10-b61f-d14a7297c3a9","added_by":"auto","created_at":"2024-10-30 01:42:57","extension":"xlsx","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":16204,"visible":true,"origin":"","legend":"Supplementary Table","description":"","filename":"SupplementalTable.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-5274462/v1/0723c43114901d32179605f5.xlsx"},{"id":67806952,"identity":"d6b5b061-a4f5-422f-aac3-cecd56c11344","added_by":"auto","created_at":"2024-10-30 01:42:58","extension":"pdf","order_by":2,"title":"","display":"","copyAsset":false,"role":"supplement","size":7189194,"visible":true,"origin":"","legend":"","description":"","filename":"SupplementaryInformation.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5274462/v1/d56850c79dbc954a328ebf31.pdf"},{"id":67807255,"identity":"7a65dbd9-6e57-4bbc-895b-c2bc206d8de6","added_by":"auto","created_at":"2024-10-30 01:50:57","extension":"avi","order_by":3,"title":"","display":"","copyAsset":false,"role":"supplement","size":5832442,"visible":true,"origin":"","legend":"\u003cp\u003eExtended Data Movie1\u003c/p\u003e","description":"","filename":"ExtendedDataMovie1.avi","url":"https://assets-eu.researchsquare.com/files/rs-5274462/v1/f349a199a9a34e288a907c1a.avi"},{"id":67806949,"identity":"40719adf-4dff-4e6b-ba16-128258791953","added_by":"auto","created_at":"2024-10-30 01:42:57","extension":"avi","order_by":4,"title":"","display":"","copyAsset":false,"role":"supplement","size":3056358,"visible":true,"origin":"","legend":"\u003cp\u003eExtended Data Movie2\u003c/p\u003e","description":"","filename":"ExtendedDataMovie2.avi","url":"https://assets-eu.researchsquare.com/files/rs-5274462/v1/d4a1e86de4ef49f3a9699915.avi"},{"id":67806951,"identity":"657fa00b-d453-4822-9270-9fb50092ef7b","added_by":"auto","created_at":"2024-10-30 01:42:57","extension":"avi","order_by":5,"title":"","display":"","copyAsset":false,"role":"supplement","size":4111186,"visible":true,"origin":"","legend":"\u003cp\u003eExtended Data Movie3\u003c/p\u003e","description":"","filename":"ExtendedDataMovie3.avi","url":"https://assets-eu.researchsquare.com/files/rs-5274462/v1/4f99335c450c51b6d743f61e.avi"},{"id":67807256,"identity":"5162cc0f-dfd4-4019-96ec-286b4bdf5258","added_by":"auto","created_at":"2024-10-30 01:50:58","extension":"avi","order_by":6,"title":"","display":"","copyAsset":false,"role":"supplement","size":3117112,"visible":true,"origin":"","legend":"\u003cp\u003eExtended Data Movie4\u003c/p\u003e","description":"","filename":"ExtendedDataMovie4.avi","url":"https://assets-eu.researchsquare.com/files/rs-5274462/v1/75492204c925ff527268965c.avi"}],"financialInterests":"There is \u003cb\u003eNO\u003c/b\u003e Competing Interest.","formattedTitle":"Retrieval from vacuolar/endosomal compartments underpinning neofunctionalization of SNARE in plants","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"nature-portfolio","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"","title":"Nature Portfolio","twitterHandle":"","acdcEnabled":false,"dfaEnabled":false,"editorialSystem":"ejp","reportingPortfolio":"","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"","lastPublishedDoi":"10.21203/rs.3.rs-5274462/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-5274462/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"The distinctive protein and lipid composition underlies the distinct function of each organelle, regulated by balanced anterograde and retrograde membrane trafficking. The vacuole, the largest plant organelle, is pivotal in various plant functions, with its protein composition tightly regulated by bidirectional trafficking. However, the existence of retrograde transport from the plant vacuole remained unverified. In this study, we demonstrate retrograde trafficking from the vacuole in Arabidopsis. We observed retrieval of VAMP727, a plant-unique vacuolar membrane fusion machinery, from the vacuolar membrane. VAMP727 retrieval is facilitated by SORTING NEXIN proteins, which were independently diversified between plant and non-plant systems. Furthermore, we show that the core retromer complex and SORTING NEXINs act independently in distinct retrograde transport events with specific cargos. Thus, plant cells have elaborated a unique retrieval mechanism from the vacuole, underpinning the neofunctionalization of VAMP727 during plant evolution.","manuscriptTitle":"Retrieval from vacuolar/endosomal compartments underpinning neofunctionalization of SNARE in plants","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2024-10-30 01:42:52","doi":"10.21203/rs.3.rs-5274462/v1","editorialEvents":[],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"nature-plants","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"nplants","sideBox":"Learn more about [Nature Plants](http://www.nature.com/nplants/)","snPcode":"","submissionUrl":"","title":"Nature Plants","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"ejp","reportingPortfolio":"Nature Research","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"bfc4fdd8-996e-43d3-b7d7-40db698092b5","owner":[],"postedDate":"October 30th, 2024","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[{"id":39527272,"name":"Biological sciences/Plant sciences/Plant cell biology/Protein trafficking in plants"},{"id":39527273,"name":"Biological sciences/Plant sciences/Plant evolution"}],"tags":[],"updatedAt":"2025-10-04T07:09:48+00:00","versionOfRecord":{"articleIdentity":"rs-5274462","link":"https://doi.org/10.1038/s41477-025-02115-5","journal":{"identity":"nature-plants","isVorOnly":false,"title":"Nature Plants"},"publishedOn":"2025-10-03 04:00:00","publishedOnDateReadable":"October 3rd, 2025"},"versionCreatedAt":"2024-10-30 01:42:52","video":"","vorDoi":"10.1038/s41477-025-02115-5","vorDoiUrl":"https://doi.org/10.1038/s41477-025-02115-5","workflowStages":[]},"version":"v1","identity":"rs-5274462","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-5274462","identity":"rs-5274462","version":["v1"]},"buildId":"qtupq5eGEP_6zYnWcrvyt","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}