{"_buckets": {"deposit": "bea26120-cdb7-4b33-9bfe-d81cad87187e"}, "_deposit": {"created_by": 21, "id": "1445", "owners": [21], "pid": {"revision_id": 0, "type": "depid", "value": "1445"}, "status": "published"}, "_oai": {"id": "oai:ir.soken.ac.jp:00001445", "sets": ["20"]}, "author_link": ["0", "0", "0"], "item_1_biblio_info_21": {"attribute_name": "書誌情報（ソート用）", "attribute_value_mlt": [{"bibliographicIssueDates": {"bibliographicIssueDate": "2009-03-24", "bibliographicIssueDateType": "Issued"}, "bibliographic_titles": [{}]}]}, "item_1_creator_2": {"attribute_name": "著者名", "attribute_type": "creator", "attribute_value_mlt": [{"creatorNames": [{"creatorName": "大栁, 一"}], "nameIdentifiers": [{"nameIdentifier": "0", "nameIdentifierScheme": "WEKO"}]}]}, "item_1_creator_3": {"attribute_name": "フリガナ", "attribute_type": "creator", "attribute_value_mlt": [{"creatorNames": [{"creatorName": "オオヤナギ, ハジメ"}], "nameIdentifiers": [{"nameIdentifier": "0", "nameIdentifierScheme": "WEKO"}]}]}, "item_1_date_granted_11": {"attribute_name": "学位授与年月日", "attribute_value_mlt": [{"subitem_dategranted": "2009-03-24"}]}, "item_1_degree_grantor_5": {"attribute_name": "学位授与機関", "attribute_value_mlt": [{"subitem_degreegrantor": [{"subitem_degreegrantor_name": "総合研究大学院大学"}]}]}, "item_1_degree_name_6": {"attribute_name": "学位名", "attribute_value_mlt": [{"subitem_degreename": "博士（理学）"}]}, "item_1_description_1": {"attribute_name": "ID", "attribute_value_mlt": [{"subitem_description": "2009802", "subitem_description_type": "Other"}]}, "item_1_description_12": {"attribute_name": "要旨", "attribute_value_mlt": [{"subitem_description": "　It is believed that primordial eukaryotes were derived from prokaryotes, acquiring\u003cbr /\u003enucleus.　A number of attempts have been made to reveal the early evolution of\u003cbr /\u003eeukaryotes, and some hypotheses for the emergence of the early eukaryotes are\u003cbr /\u003eproposed so far. However, the evolutionary process of early eukaryotes is still a\u003cbr /\u003econtroversial issue and remains one of the biggest questions in current biology. In this\u003cbr /\u003estudy, with the eventual goal toward elucidation of the evolutionary origin and process\u003cbr /\u003eof early eukaryotes, I conducted molecular evolutionary analyses of transporter proteins\u003cbr /\u003eof ribosomes between the nucleus and the cytoplasm, called ribosome export factors\u003cbr /\u003e(REFs).\u003cbr /\u003e　This　thesis consists of four chapters and an appendix. In \u003cb\u003eChapter 1\u003c/b\u003e, I described the\u003cbr /\u003eresearch background for this study, with particular emphasis on the molecular function\u003cbr /\u003eof the REFs. The ribosome, one of the largest complexes in eukaryotic cells, is to be\u003cbr /\u003eexported from the nucleus to the cytoplasm through nuclear pores. As discovered in\u003cbr /\u003erecent years, the kinetic steps in this nucleocytoplasmic transport pathway are\u003cbr /\u003estimulated by the REFs. The REFs would be worth focusing on because they can be\u003cbr /\u003econsidered as one of the components in the eukaryotic core system, translation, and as\u003cbr /\u003eone of the key genes in the evolutionary process of early eukaryotes for maintaining the\u003cbr /\u003emobility of the ribosomes under the existence of nuclear membrane in the\u003cbr /\u003ethen-emerging eukaryotic cells. \u003cbr /\u003e　In \u003cb\u003eChapter 2\u003c/b\u003e, with the aim of revealing the functional significance of the REFs in\u003cbr /\u003ethe process of eukaryotic evolution, I examined the functional constraints of the entire\u003cbr /\u003etranslation system, the ribosomal proteins and the REF proteins. Estimating the relative\u003cbr /\u003eevolutionary rates of the yeast REF proteins, I found that, although not as much as the\u003cbr /\u003eribosomal proteins, the REF proteins do slowly evolve. More interestingly, the\u003cbr /\u003eevolutionary rates of the REFs can be classified into two groups. In order to explain this\u003cbr /\u003edifference in evolutionary rates between the two groups, I considered two subcategories\u003cbr /\u003efor the REFs, according to the steps in which the REFs are involved. Those two\u003cbr /\u003esubcategories are non-membranous REFs (non-mREFs) and membranous REFs\u003cbr /\u003e(mREFs). Interestingly, this categorization was coincided with the evolutionary rate\u003cbr /\u003edifference: Namely, the rapidly evolving REFs were the non-mREFs while the slowly\u003cbr /\u003eevolving REFs were the mREFs. These results show that the mREF proteins evolve\u003cbr /\u003eslower than the non-mREF proteins, suggesting the functional importance of mREFs in\u003cbr /\u003ethe evolutionary process of eukaryotes. \u003cbr /\u003e　In \u003cb\u003eChapter 3\u003c/b\u003e, I examined the evolutionary origin of the eukaryotic nucleus by\u003cbr /\u003econducting the ortholog detection analysis of the REFs in prokaryotic lineages. The\u003cbr /\u003eevolutionary origin of the nucleus is still unclear, although a number of hypotheses have\u003cbr /\u003ebeen proposed so far. I searched for the origin of the REFs in archaeal and eubacterial\u003cbr /\u003elineages by the method of PSI-BLAST. The results obtained showed that the\u003cbr /\u003enon-mREFs originated exclusively from eubacterial proteins whereas the mREFs were\u003cbr /\u003efrom both archaeal and eubacterial proteins. Thus, the REFs working inside the nuclear\u003cbr /\u003emembrane (\u003ci\u003ei.e.\u003c/i\u003enon-mREFs) are derived only from eubacteria, while alternatively, the\u003cbr /\u003eREFs shuttling between the nucleus and the cytoplasm (\u003ci\u003ei.e.\u003c/i\u003e mREFs) are from both\u003cbr /\u003earchaea and eubacteria. If we assume that the early nucleus has parsimoniously\u003cbr /\u003eemployed intranuclear proteins as the intranuclear transporters (\u003ci\u003ei.e.\u003c/i\u003e non-mREFs), these\u003cbr /\u003edata suggest that the structure of the nucleus may be a descendant of the eubacterial cell. \u003cbr /\u003eAt least, it is suggested that the nucleus arose in a cell that contained chromosomes\u003cbr /\u003epossessing a substantial fraction of eubacterial genes. Therefore, from the viewpoint of\u003cbr /\u003eribosome transport, it is plausible that the nuclear structure is not originated from\u003cbr /\u003earchaea, but from eubacteria. \u003cbr /\u003e　Lastly, in \u003cb\u003eChapter 4\u003c/b\u003e,I provided a summary and conclusions for the present study. I\u003cbr /\u003ehave shown that the REFs evolve slowly, in addition, the mREFs evolve more slowly, \u003cbr /\u003esuggesting that the entire eukaryotic translation system is under the functional\u003cbr /\u003econstraints, and in particular, that the mREFs are functionally important in the process\u003cbr /\u003eof eukaryotic evolution. Moreover, from the prokaryotic origin of the REFs, it is\u003cbr /\u003esuggested that the nucleus is rather a descendant of the eubacterial cell, not the archaeal cell. \u003cbr /\u003e　In \u003cb\u003eAppendix\u003c/b\u003e, I made particular mention to the biological database projects for\u003cbr /\u003eeukaryotes, in which I have been involved. Comprehensive annotations of model\u003cbr /\u003eeukaryotes and integrated databases for such annotations are becoming more and more important in the current post-genome era. Moreover, such databases are useful for the study of early evolution of eukaryotes that is the main aim of the present study. Such\u003cbr /\u003edatabases are also invaluable for comprehensive access to the information resources, \u003cbr /\u003eand will stimulate the comparative evolutionary genomics. With the eventual goal to\u003cbr /\u003eknow the early evolution of eukaryotes, here I refer to three eukaryotic database projects\u003cbr /\u003ein which I have been involved, \u003cu\u003ethe Molecular Database of \u003ci\u003eHydra\u003c/i\u003e Cells\u003c/u\u003e, \u003cu\u003ethe Rice\u003cbr /\u003eAnnotation Project Database (RAP-DB)\u003c/u\u003e, and \u003cu\u003ethe H-Invitational Database (H-InvDB)\u003c/u\u003e. \u003cbr /\u003e　The Molecular Database of \u003ci\u003eHydra\u003c/i\u003e Cells includes the invaluable data of expression\u003cbr /\u003epatterns of cell type-specific genes in \u003ci\u003eHydra\u003c/i\u003e, a member of phylum Cnidaria, which\u003cbr /\u003ebranched more than 500 million years ago from the main stem leading to all bilaterian\u003cbr /\u003eanimals. The database framework was developed by myself, and it serves a unique\u003cbr /\u003eopportunity for graphically browsing more than 100 cell type-specific genes in \u003ci\u003eHydra.\u003c/i\u003e \u003cbr /\u003eAll of the resources can be accessed through http://hydra.lab.nig.ac.jp/hydra/.\u003cbr /\u003e　The RAP-DB is a database for \u003ci\u003eOryza sativa\u003c/i\u003e ssp. \u003ci\u003eJaponica\u003c/i\u003e, one of the model\u003cbr /\u003eeukaryotes, and has been developed in order to comprehensively house all the\u003cbr /\u003eannotations produced by the RAP (Rice Annotation Project), which is internationally\u003cbr /\u003eorganized with the aim of providing standardized and highly accurate annotations of the\u003cbr /\u003erice genome. The latest version of the RAP-DB contains 3l,439 genes validated by\u003cbr /\u003ecDNAs. The RAP-DB has been also developed by myself, and employed in the analyses\u003cbr /\u003ewithin \u003cb\u003eChapter 2\u003c/b\u003e. The RAP-DB is available at http://rapdb.lab.nig.ac.jp/.\u003cbr /\u003e　The H-Invitational Database (H-InvDB) was originally developed as an integrated\u003cbr /\u003edatabase of the human transcriptome that was based on extensive annotation of large\u003cbr /\u003esets of full-length cDNA (FLcDNA) clone. I participated in the Annotation Meeting of\u003cbr /\u003eGenome Information Integration Project for the further development of the human\u003cbr /\u003egenome annotations. Now, the database provides annotation for 175,537 human\u003cbr /\u003etranscripts and 120,558 human mRNAs extracted from the public DNA databank, in\u003cbr /\u003eaddition to 54,978 human FLcDNA, in the latest release, H-InvDB_4.3. The H-InvDB\u003cbr /\u003eis available at http://www.h-invitational jp/.\u003cbr /\u003e　The three projects in which I have been involved produced comprehensive\u003cbr /\u003einformation for the model eukaryotes. Each database provides a nice implementation for\u003cbr /\u003eeach biological resource and will stimulate the further exploration in the early evolution\u003cbr /\u003eof eukaryotes.", "subitem_description_type": "Other"}]}, "item_1_description_18": {"attribute_name": "フォーマット", "attribute_value_mlt": [{"subitem_description": "application/pdf", "subitem_description_type": "Other"}]}, "item_1_description_7": {"attribute_name": "学位記番号", "attribute_value_mlt": [{"subitem_description": "総研大乙第191号", "subitem_description_type": "Other"}]}, "item_1_select_14": {"attribute_name": "所蔵", "attribute_value_mlt": [{"subitem_select_item": "有"}]}, "item_1_select_16": {"attribute_name": "複写", "attribute_value_mlt": [{"subitem_select_item": "複写不可"}]}, "item_1_select_17": {"attribute_name": "公開状況", "attribute_value_mlt": [{"subitem_select_item": "全文公開可"}]}, "item_1_select_8": {"attribute_name": "研究科", "attribute_value_mlt": [{"subitem_select_item": "生命科学研究科"}]}, "item_1_select_9": {"attribute_name": "専攻", "attribute_value_mlt": [{"subitem_select_item": "18 遺伝学専攻"}]}, "item_1_text_10": {"attribute_name": "学位授与年度", "attribute_value_mlt": [{"subitem_text_value": "2008"}]}, "item_creator": {"attribute_name": "著者", "attribute_type": "creator", "attribute_value_mlt": [{"creatorNames": [{"creatorName": "OHYANAGI, Hajime", "creatorNameLang": "en"}], "nameIdentifiers": [{"nameIdentifier": "0", "nameIdentifierScheme": "WEKO"}]}]}, "item_files": {"attribute_name": "ファイル情報", "attribute_type": "file", "attribute_value_mlt": [{"accessrole": "open_date", "date": [{"dateType": "Available", "dateValue": "2016-02-17"}], "displaytype": "simple", "download_preview_message": "", "file_order": 0, "filename": "乙191_要旨.pdf", "filesize": [{"value": "344.7 kB"}], "format": "application/pdf", "future_date_message": "", "is_thumbnail": false, "licensetype": "license_11", "mimetype": "application/pdf", "size": 344700.0, "url": {"label": "要旨・審査要旨", "url": "https://ir.soken.ac.jp/record/1445/files/乙191_要旨.pdf"}, "version_id": "5572ae14-d5c1-4b15-922f-6d8972946890"}, {"accessrole": "open_date", "date": [{"dateType": "Available", "dateValue": "2016-02-17"}], "displaytype": "simple", "download_preview_message": "", "file_order": 1, "filename": "乙191_本文.pdf", "filesize": [{"value": "5.1 MB"}], "format": "application/pdf", "future_date_message": "", "is_thumbnail": false, "licensetype": "license_11", "mimetype": "application/pdf", "size": 5100000.0, "url": {"label": "本文", "url": "https://ir.soken.ac.jp/record/1445/files/乙191_本文.pdf"}, "version_id": "cde2b546-d5f5-45a0-9636-94174c57b430"}]}, "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": "thesis", "resourceuri": "http://purl.org/coar/resource_type/c_46ec"}]}, "item_title": "The early evolution of eukaryotes with special reference to ribosome export factors", "item_titles": {"attribute_name": "タイトル", "attribute_value_mlt": [{"subitem_title": "The early evolution of eukaryotes with special reference to ribosome export factors"}, {"subitem_title": "The early evolution of eukaryotes with special reference to ribosome export factors", "subitem_title_language": "en"}]}, "item_type_id": "1", "owner": "21", "path": ["20"], "permalink_uri": "https://ir.soken.ac.jp/records/1445", "pubdate": {"attribute_name": "公開日", "attribute_value": "2010-03-24"}, "publish_date": "2010-03-24", "publish_status": "0", "recid": "1445", "relation": {}, "relation_version_is_last": true, "title": ["The early evolution of eukaryotes with special reference to ribosome export factors"], "weko_shared_id": -1}