Mechanisms of core promoter recognition by general transcription factor TFIID

2013 Fiscal Year Final Research Report

• Project/Area Number: 23370077
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Molecular biology
• Research Institution: Yokohama City University
• Principal Investigator: KOKUBO Tetsuro 横浜市立大学, その他の研究科, 教授 (10271587)
• Project Period (FY): 2011-04-01 – 2014-03-31
• Keywords: 転写調節 / 転写因子 / 基本転写因子 / 転写開始 / 出芽酵母 / TFIID / TAF / TBP

Research Abstract

TFIID, the largest GTF composed of TBP and 14 TAFs, plays a critical role in transcription from TATA-less promoters. In metazoans, several core promoter elements (CE) other than the TATA element are thought to be recognition sites for TFIID. However, it is unclear whether functionally homologous elements also exist in TATA-less promoters in yeast.
Here we develop a novel high-throughput screening system to measure gene expression in yeast by using VTC1 as a reporter gene. This method allows us to isolate several active and novel CE by screening a randomized oligonucleotide pool for the CYC1 promoter. The TAF N-terminal domain (TAND) of the TAF1 protein plays a significant role in transcriptional activation. TAND comprises two subdomains, TAND1 and TAND2, which interact with the concave and convex surfaces of TBP, respectively. In collaboration with other groups, we determine the crystal structure of the TAND-TBP complex that provides a novel insight into transcriptional activation.

Research Products

• [Journal Article] High-resolution structure of TBP with TAF1 reveals anchoring patterns in transcriptional regulation (2013)
  • Author(s): Anandapadamanaban M, Andresen C, Helander S, Ohyama Y, Siponen MI, Lundström P, Kokubo T, Ikura M, Moche M, Sunnerhagen M
  • Journal Title: Nat Struct Mol Biol Volume: 20(8) Pages: 1008-14
  • DOI: 10.1038/nsmb.2611
  • Peer Reviewed
• [Journal Article] Identification and recombinant analysis of botrocetin-2, a snake venom cofactor for von Willebrand factor-induced platelet agglutination (2012)
  • Author(s): Yamamoto-Suzuki Y, Sakurai Y, Fujimura Y, Matsumoto M, Hamako J, Kokubo T, Kitagawa H, Kawsar SM, Fujii Y, Ozeki Y, Matsushita F, Matsui T
  • Journal Title: Biochemistry Volume: 51(26) Pages: 5329-38
  • Peer Reviewed
• [Journal Article] Rapid cell division contributes to efficient induction of A/T mutations during Ig gene hypermutation (2011)
  • Author(s): Kano C, Ouchida R, Kokubo T, Wang JY
  • Journal Title: Mol Immunol Volume: 48(15-16) Pages: 1993-9
  • DOI: 10.1016/j.molimm.2011.06.218
  • Peer Reviewed
• [Journal Article] Cell polarity in Saccharomyces cerevisiae depends on proper localization of the Bud9 landmark protein by the EKC/KEOPS complex (2011)
  • Author(s): Kato Y, Kawasaki H, Ohyama Y, Morishita T, Iwasaki H, Kokubo T, Hirano H
  • Journal Title: Genetics Volume: 188(4) Pages: 871-82
  • DOI: 10.1534/genetics.111.128231
  • Peer Reviewed
• [Journal Article] Hmo1 directs pre-initiation complex assembly to an appropriate site on its target gene promoters by masking a nucleosome-free region (2011)
  • Author(s): Kasahara K, Ohyama Y, Kokubo T
  • Journal Title: Nucleic Acids Res Volume: 39(10) Pages: 4136-50
  • DOI: 10.1093/nar/gkq1334
  • Peer Reviewed
• [Presentation] 二種類の異なる機能を持つG1サイクリンCln2pの転写段階での運命決定 (2014)
  • Author(s): 高井直樹, 大山良文, 古久保哲朗
  • Organizer: 転写研究会・転写サイクル・転写代謝システム共催「冬の若手ワークショップ2014」
  • Place of Presentation: 軽井沢
  • Year and Date: 2014-01-31
• [Presentation] リボソーム構成因子の発現調節に関わる酵母Hmo1タンパク質のDNA結合機構 (2013)
  • Author(s): 東野綺子, 雲財悟, 中山理紗, 土屋奈穂, 吉川博文, 古久保哲朗, 笠原浩司
  • Organizer: 日本分子生物学会第36回年会
  • Place of Presentation: 神戸
  • Year and Date: 2013-12-04
• [Presentation] 出芽酵母におけるTFIIDを介したGAL遺伝子群の脱抑制機構 (2013)
  • Author(s): 矢部誠, 大山良文, 高井直樹, 古久保哲朗
  • Organizer: 日本分子生物学会第36回年会
  • Place of Presentation: 神戸
  • Year and Date: 2013-12-03
• [Presentation] 母性mRNAの3'非翻訳領域を標的としたアンチセンスモルフォリノオリゴによるpoly(A)鎖短小化機構の解析 (2012)
  • Author(s): 茂呂華奈子, 古久保哲朗, 和田忠士
  • Organizer: 日本分子生物学会第35回年会
  • Place of Presentation: 福岡
  • Year and Date: 2012-12-14
• [Presentation] 出芽酵母のTFIIDとSAGAは細胞の極成長に関わるRAMシグナル経路と遺伝学的に相互作用する (2012)
  • Author(s): 大山良文, 和田忠士, 古久保哲朗
  • Organizer: 新学術領域研究「転写代謝システム」・転写研究会共催「若手ワークショップ@湯河原」
  • Place of Presentation: 湯河原
  • Year and Date: 2012-02-09
• [Presentation] 出芽酵母における新規ハイスループット型プロモーター活性測定法の開発とその応用 (2012)
  • Author(s): 渡邉清, 矢部誠, 古久保哲朗
  • Organizer: 新学術領域研究「転写代謝システム」・転写研究会共催「若手ワークショップ@湯河原」
  • Place of Presentation: 湯河原
  • Year and Date: 2012-02-09
• [Presentation] 基本転写因子TFIIDの機能発現における天然変性領域の役割 (2012)
  • Author(s): 古久保哲朗
  • Organizer: 新学術領域研究「天然変性タンパク質の分子認識機構と機能発現」第2回公開シンポジウム
  • Place of Presentation: 大阪
  • Year and Date: 2012-01-24
• [Presentation] TFIID and SAGA regulate the fate of CLN2 mRNA cooperatively with the RAM signaling network (2011)
  • Author(s): 大山良文, 和田忠士, 古久保哲朗
  • Organizer: 日本分子生物学会第34回年会
  • Place of Presentation: 横浜
  • Year and Date: 2011-12-15
• [Presentation] Novel regulatory mechanism for transcriptional initiation of ribosomal protein genes in S. cerevisiae (2011)
  • Author(s): 笠原浩司, 大山良文, 古久保哲朗
  • Organizer: 日本分子生物学会第34回年会
  • Place of Presentation: 横浜
  • Year and Date: 2011-12-15
• [Presentation] A novel high-throughput screening system to measure gene expression in Saccharomyces cerevisiae (2011)
  • Author(s): 渡邉清, 古久保哲朗
  • Organizer: 日本分子生物学会第34回年会
  • Place of Presentation: 横浜
  • Year and Date: 2011-12-15
• [Book] Essay; Mechanisms of Transcriptional Activation and Repression (p1210-1217). Definitions; Activation Domain Shielding (p4-6), ATAC (p49-50), Chromatin Helicase DNA binding (CHD) (p402-404), INO80 (p1033-1035), ISWI (p1058-1060), Mammalian HDAC (p1173-1174), PIC Disassembly (p1715), Set3C (p1932-1933), TAND (p2121-2122), Tra1p (p2218-2219) : Encyclopedia ofSystems Biology, W. Dubitzky, O. Wolkenhauer, K. H. Cho, H. Yokota (Eds.) (2013)
  • Author(s): T. Kokubo
  • Publisher: Springer Science + Business Media LLC
• [Book] Essay; Transcription in Eukaryote (p2239-2245). Definitions; Cofactors (p436-437), Core Promoter Elements (p502-504), General Transcription Factors (p813-814), Mediator (p1217-1218), PIC Assembly Pathways (p1714-1715), RNA Polymerase I, II and III (p1862-1863), SAGA (p1890-1891), Type 3 Promoters (p2306-2307) : Encyclopedia of Systems Biology, W. Dubitzky, O. Wolkenhauer, K. H. Cho, H. Yokota (Eds.) (2013)
  • Author(s): T. Kokubo
  • Publisher: Springer Science + Business Media LLC
• [Book] Essay; Transcription Initiation in Eukaryote (p2245-2251). Definitions; Immobilized Template Assay (p989-990), Phosphodiester Bond Formation (p1702-1703), Stalk of RNAPII (p1982-1984), TAF Paralogs (p2120-2121), TFIIA-Like Factor (ALF) (p2163), TRF1 (p2299-2300), TRF2 (p2300-2301), TRF3 (p2301-2302) : Encyclopedia ofSystems Biology, W. Dubitzky, O. Wolkenhauer, K. H. Cho, H. Yokota (Eds.) (2013)
  • Author(s): T. Kokubo
  • Publisher: Springer Science + Business Media LLC
• [Remarks]
  • URL: http://www.tsurumi.yokohama-cu.ac.jp/mcbl/index2.html