{"created":"2023-06-20T13:20:58.521598+00:00","id":1048,"links":{},"metadata":{"_buckets":{"deposit":"6690dc2b-e79f-4df0-935c-5357362ff7e0"},"_deposit":{"created_by":1,"id":"1048","owners":[1],"pid":{"revision_id":0,"type":"depid","value":"1048"},"status":"published"},"_oai":{"id":"oai:ir.soken.ac.jp:00001048","sets":["2:430:20"]},"author_link":["0","0","0"],"item_1_creator_2":{"attribute_name":"著者名","attribute_type":"creator","attribute_value_mlt":[{"creatorNames":[{"creatorName":"宮本, 貴史"}],"nameIdentifiers":[{"nameIdentifier":"0","nameIdentifierScheme":"WEKO"}]}]},"item_1_creator_3":{"attribute_name":"フリガナ","attribute_type":"creator","attribute_value_mlt":[{"creatorNames":[{"creatorName":"ミヤモト, タカシ"}],"nameIdentifiers":[{"nameIdentifier":"0","nameIdentifierScheme":"WEKO"}]}]},"item_1_date_granted_11":{"attribute_name":"学位授与年月日","attribute_value_mlt":[{"subitem_dategranted":"2008-03-19"}]},"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_12":{"attribute_name":"要旨","attribute_value_mlt":[{"subitem_description":" It is well known that transcription elongation and repair of UV－damage is coupled.
In eukaryotes，stalled RNA pol II recruits several repair proteins to from a complex
containing RNA pol II，TFIIH，and the repair proteins．In prokaryotes，stalled RNAP
recruits Mfd protein．Mfd has a domain homologous to the domain in UvrB which
recognizes a wide range of structurally diverse lesions in addition to a domain for
interaction with RNAP．Mfd binds to the DNA segment immediately upstream of the
stalled RNAP and pushes it towards downstream by using the energy of
ATP-hydrolysis to dissociate it from DNA，and speculated to recruit UvrA to perform
the repair similar to the global nuclear excision repair. These mechanisms provide the
concept on the triggering DNA repair rather than that on transcriptional regulation．
Although RNAP tends to stall at all kinds of UV-damages，the efficiency of stallat at
a UV-damage has not been measured．Therefore，it is possible that inhibition of
transcription is carried out by a mechanism other than the stall of RNAP．The stall
could be overcome by a read-through of the damaged base by misincorporation，
slippage，Jump，and switching the template strand．These considerations indicate the
mechanism of coulpling of UV-damages and initiation，because initiation generally has
the largest dynamic range of transcriptional regulation．Irrespective of the efforts to
find specific factors triggering the inhibition in initiation，such factors have not been
found yet, suggesting an alternative possibility that the triggering function has been
already installed in RNAP．
Transcription initiation is biochemically separated into several steps．RNAP in the
form of holoenzyme binds to a promoter and then DNA duplex in the complex is
partially unwound to expose the template strand of DNA by mostly unknown
mechanism. The resultant complex is called open complex and this complex was once
considered to be homogeneous．However，it is now known to involve two or more
conformations which have different catalytic properties，forming branched pathway
mechanism. One branch leads to produce the full-length transcripts（productive
pathway），While another leads to produce only short transcripts iteratively
synthesized by“moribund complex”which is defined as a complex that produces only
abortive but no full-length transcripts（non-productive pathway）.On some promoters，
moribund complex is converted into dead-end complex which still maintains transcript
but lacks elongation activity．Accumulation of dead-end complex cause less
stoichiometric synthesis of the full-length products in a single-round transcription
assay.
To examine the potential coupling and its mechanism，I have studied on the
relationship between transcription initiation and UV-damage by using purified
reconstitution system of E.coli．This well-characterized system allows me to consider
the relationship between the structure and the function．The system is composed of
RNAP holoenzyme，a promoter DNA，and four NTPs as substrates．I selected the T7A1
promoter because little moribund and dead-end complexes are accumulating on this
promoter，simplifying the analysis of the branched pathway. By irradiating the
promoter DNA with UV light，UV damages are generated at adjacent pyrimidine bases
in the promoter region. If the generated damages are up stream from the transcription
start site，such damages are nothing to do with elongation pause and thus their effect
on transcription must be limited to the effect on initiation．
In this study, UV-irradiation of the template DNA was found to enhance abortive
initiation and to induce dead-end complex，namely enhancing the nonproductive
pathway．The positions of UV-damage in the template DNA in moribund and dead-end
complex was compared with those in the binary complex that contains productive
complex．The pyrimidine dimers at several sites in the upstream from the
transcription start site，but not all，were enriched in the moribund and dead-end
complexes．indicating that these UV-damaged pyrimidine bases induce these
complexes. These positions of the damages are on both template and non-template
strands. The induction by the damaged pyrimidine residues are confirmed by the
transcription on DNA fragments which contain single UV-damageds in the upstream
region．Furthermore，I found that adjacent pyrimidine bases are conserved atone or
more positions of those identified on T7A1 promoter among the majority of the E．coli
promoters，suggesting that these positions would be UV-sensor motif in promoters．
","subitem_description_type":"Other"}]},"item_1_description_7":{"attribute_name":"学位記番号","attribute_value_mlt":[{"subitem_description":"総研大甲第1166号","subitem_description_type":"Other"}]},"item_1_select_14":{"attribute_name":"所蔵","attribute_value_mlt":[{"subitem_select_item":"有"}]},"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":"2007"}]},"item_creator":{"attribute_name":"著者","attribute_type":"creator","attribute_value_mlt":[{"creatorNames":[{"creatorName":"MIYAMOTO, Takashi","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","filename":"甲1166_要旨.pdf","filesize":[{"value":"270.9 kB"}],"format":"application/pdf","licensetype":"license_11","mimetype":"application/pdf","url":{"label":"要旨・審査要旨","url":"https://ir.soken.ac.jp/record/1048/files/甲1166_要旨.pdf"},"version_id":"dd385290-e2f5-4420-8df4-e7773081ebce"}]},"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":"UV-sensor motifs in promoters","item_titles":{"attribute_name":"タイトル","attribute_value_mlt":[{"subitem_title":"UV-sensor motifs in promoters"},{"subitem_title":"UV-sensor motifs in promoters","subitem_title_language":"en"}]},"item_type_id":"1","owner":"1","path":["20"],"pubdate":{"attribute_name":"公開日","attribute_value":"2010-02-22"},"publish_date":"2010-02-22","publish_status":"0","recid":"1048","relation_version_is_last":true,"title":["UV-sensor motifs in promoters"],"weko_creator_id":"1","weko_shared_id":-1},"updated":"2023-06-20T16:09:51.574006+00:00"}