WEKO3
アイテム
{"_buckets": {"deposit": "2312f68e-a3a3-422d-bd40-b0a544ec42e6"}, "_deposit": {"created_by": 33, "id": "2641", "owners": [33], "pid": {"revision_id": 0, "type": "depid", "value": "2641"}, "status": "published"}, "_oai": {"id": "oai:oist.repo.nii.ac.jp:00002641", "sets": ["74"]}, "author_link": ["17114", "17115"], "item_10001_biblio_info_7": {"attribute_name": "Bibliographic Information", "attribute_value_mlt": [{"bibliographicIssueDates": {"bibliographicIssueDate": "2022-04-04", "bibliographicIssueDateType": "Issued"}, "bibliographicIssueNumber": "4", "bibliographicPageStart": "e1010016", "bibliographicVolumeNumber": "18", "bibliographic_titles": [{}, {"bibliographic_title": "PLOS Computational Biology", "bibliographic_titleLang": "en"}]}]}, "item_10001_creator_3": {"attribute_name": "Author", "attribute_type": "creator", "attribute_value_mlt": [{"creatorNames": [{"creatorName": "Pascarelli, Stefano"}], "nameIdentifiers": [{"nameIdentifier": "17114", "nameIdentifierScheme": "WEKO"}]}, {"creatorNames": [{"creatorName": "Laurino, Paola"}], "nameIdentifiers": [{"nameIdentifier": "17115", "nameIdentifierScheme": "WEKO"}]}]}, "item_10001_description_5": {"attribute_name": "Abstract", "attribute_value_mlt": [{"subitem_description": "Connecting protein sequence to function is becoming increasingly relevant since high-throughput sequencing studies accumulate large amounts of genomic data. In order to go beyond the existing database annotation, it is fundamental to understand the mechanisms underlying functional inheritance and divergence. If the homology relationship between proteins is known, can we determine whether the function diverged? In this work, we analyze different possibilities of protein sequence evolution after gene duplication and identify “inter-paralog inversions”, i.e., sites where the relationship between the ancestry and the functional signal is decoupled. The amino acids in these sites are masked from being recognized by other prediction tools. Still, they play a role in functional divergence and could indicate a shift in protein function. We develop a method to specifically recognize inter-paralog amino acid inversions in a phylogeny and test it on real and simulated datasets. In a dataset built from the Epidermal Growth Factor Receptor (EGFR) sequences found in 88 fish species, we identify 19 amino acid sites that went through inversion after gene duplication, mostly located at the ligand-binding extracellular domain. Our work uncovers an outcome of protein duplications with direct implications in protein functional annotation and sequence evolution. The developed method is optimized to work with large protein datasets and can be readily included in a targeted protein analysis pipeline.", "subitem_description_type": "Other"}]}, "item_10001_publisher_8": {"attribute_name": "Publisher", "attribute_value_mlt": [{"subitem_publisher": "Public Library of Science"}]}, "item_10001_relation_13": {"attribute_name": "PubMedNo.", "attribute_value_mlt": [{"subitem_relation_type": "isIdenticalTo", "subitem_relation_type_id": {"subitem_relation_type_id_text": "info:pmid/35377869", "subitem_relation_type_select": "PMID"}}]}, "item_10001_relation_14": {"attribute_name": "DOI", "attribute_value_mlt": [{"subitem_relation_type": "isIdenticalTo", "subitem_relation_type_id": {"subitem_relation_type_id_text": "info:doi/10.1371/journal.pcbi.1010016", "subitem_relation_type_select": "DOI"}}]}, "item_10001_relation_17": {"attribute_name": "Related site", "attribute_value_mlt": [{"subitem_relation_name": [{"subitem_relation_name_text": "Version 1 Uncorrected Proof"}], "subitem_relation_type_id": {"subitem_relation_type_id_text": "https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010016\u0026rev=1", "subitem_relation_type_select": "URI"}}, {"subitem_relation_name": [{"subitem_relation_name_text": "Version 2"}], "subitem_relation_type_id": {"subitem_relation_type_id_text": "https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010016#sec024", "subitem_relation_type_select": "URI"}}]}, "item_10001_rights_15": {"attribute_name": "Rights", "attribute_value_mlt": [{"subitem_rights": "© 2022 Pascarelli, Laurino. "}]}, "item_10001_source_id_9": {"attribute_name": "ISSN", "attribute_value_mlt": [{"subitem_source_identifier": "1553-7358", "subitem_source_identifier_type": "ISSN"}, {"subitem_source_identifier": "1553-734X", "subitem_source_identifier_type": "ISSN"}]}, "item_10001_version_type_20": {"attribute_name": "Author\u0027s flag", "attribute_value_mlt": [{"subitem_version_resource": "http://purl.org/coar/version/c_970fb48d4fbd8a85", "subitem_version_type": "VoR"}]}, "item_files": {"attribute_name": "ファイル情報", "attribute_type": "file", "attribute_value_mlt": [{"accessrole": "open_date", "date": [{"dateType": "Available", "dateValue": "2022-05-19"}], "displaytype": "detail", "download_preview_message": "", "file_order": 0, "filename": "Pascarelli-2022-Inter-paralog amino acid inver.pdf", "filesize": [{"value": "2.8 MB"}], "format": "application/pdf", "future_date_message": "", "is_thumbnail": false, "licensefree": "Creative Commons Attribution 4.0 International (https://creativecommons.org/licenses/by/4.0/)", "licensetype": "license_free", "mimetype": "application/pdf", "size": 2800000.0, "url": {"label": "Pascarelli-2022-Inter-paralog amino acid inver", "url": "https://oist.repo.nii.ac.jp/record/2641/files/Pascarelli-2022-Inter-paralog amino acid inver.pdf"}, "version_id": "f7f0330f-d700-4765-87ef-dd2bd0067268"}]}, "item_language": {"attribute_name": "言語", "attribute_value_mlt": [{"subitem_language": "eng"}]}, "item_resource_type": {"attribute_name": "資源タイプ", "attribute_value_mlt": [{"resourcetype": "journal article", "resourceuri": "http://purl.org/coar/resource_type/c_6501"}]}, "item_title": "Inter-paralog amino acid inversion events in large phylogenies of duplicated proteins", "item_titles": {"attribute_name": "タイトル", "attribute_value_mlt": [{"subitem_title": "Inter-paralog amino acid inversion events in large phylogenies of duplicated proteins", "subitem_title_language": "en"}]}, "item_type_id": "10001", "owner": "33", "path": ["74"], "permalink_uri": "https://oist.repo.nii.ac.jp/records/2641", "pubdate": {"attribute_name": "公開日", "attribute_value": "2022-05-19"}, "publish_date": "2022-05-19", "publish_status": "0", "recid": "2641", "relation": {}, "relation_version_is_last": true, "title": ["Inter-paralog amino acid inversion events in large phylogenies of duplicated proteins"], "weko_shared_id": 33}
Inter-paralog amino acid inversion events in large phylogenies of duplicated proteins
https://oist.repo.nii.ac.jp/records/2641
https://oist.repo.nii.ac.jp/records/264173f12f18-ebfa-4231-b648-985def2dbc75
名前 / ファイル | ライセンス | アクション |
---|---|---|
Pascarelli-2022-Inter-paralog amino acid inver (2.8 MB)
|
Creative Commons Attribution 4.0 International (https://creativecommons.org/licenses/by/4.0/)
|
Item type | 学術雑誌論文 / Journal Article(1) | |||||
---|---|---|---|---|---|---|
公開日 | 2022-05-19 | |||||
タイトル | ||||||
言語 | en | |||||
タイトル | Inter-paralog amino acid inversion events in large phylogenies of duplicated proteins | |||||
言語 | ||||||
言語 | eng | |||||
資源タイプ | ||||||
資源タイプ識別子 | http://purl.org/coar/resource_type/c_6501 | |||||
資源タイプ | journal article | |||||
著者(英) |
Pascarelli, Stefano
× Pascarelli, Stefano× Laurino, Paola |
|||||
書誌情報 |
en : PLOS Computational Biology 巻 18, 号 4, p. e1010016, 発行日 2022-04-04 |
|||||
抄録 | ||||||
内容記述タイプ | Other | |||||
内容記述 | Connecting protein sequence to function is becoming increasingly relevant since high-throughput sequencing studies accumulate large amounts of genomic data. In order to go beyond the existing database annotation, it is fundamental to understand the mechanisms underlying functional inheritance and divergence. If the homology relationship between proteins is known, can we determine whether the function diverged? In this work, we analyze different possibilities of protein sequence evolution after gene duplication and identify “inter-paralog inversions”, i.e., sites where the relationship between the ancestry and the functional signal is decoupled. The amino acids in these sites are masked from being recognized by other prediction tools. Still, they play a role in functional divergence and could indicate a shift in protein function. We develop a method to specifically recognize inter-paralog amino acid inversions in a phylogeny and test it on real and simulated datasets. In a dataset built from the Epidermal Growth Factor Receptor (EGFR) sequences found in 88 fish species, we identify 19 amino acid sites that went through inversion after gene duplication, mostly located at the ligand-binding extracellular domain. Our work uncovers an outcome of protein duplications with direct implications in protein functional annotation and sequence evolution. The developed method is optimized to work with large protein datasets and can be readily included in a targeted protein analysis pipeline. | |||||
出版者 | ||||||
出版者 | Public Library of Science | |||||
ISSN | ||||||
収録物識別子タイプ | ISSN | |||||
収録物識別子 | 1553-7358 | |||||
ISSN | ||||||
収録物識別子タイプ | ISSN | |||||
収録物識別子 | 1553-734X | |||||
PubMed番号 | ||||||
関連タイプ | isIdenticalTo | |||||
識別子タイプ | PMID | |||||
関連識別子 | info:pmid/35377869 | |||||
DOI | ||||||
関連タイプ | isIdenticalTo | |||||
識別子タイプ | DOI | |||||
関連識別子 | info:doi/10.1371/journal.pcbi.1010016 | |||||
権利 | ||||||
権利情報 | © 2022 Pascarelli, Laurino. | |||||
関連サイト | ||||||
識別子タイプ | URI | |||||
関連識別子 | https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010016&rev=1 | |||||
関連名称 | Version 1 Uncorrected Proof | |||||
関連サイト | ||||||
識別子タイプ | URI | |||||
関連識別子 | https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010016#sec024 | |||||
関連名称 | Version 2 | |||||
著者版フラグ | ||||||
出版タイプ | VoR | |||||
出版タイプResource | http://purl.org/coar/version/c_970fb48d4fbd8a85 |