2002 Fiscal Year Annual Research Report

細胞システム解明に向けたゲノム生物学の新展開

Research Project

Project/Area Number	12205001
Research Institution	Nara Institute of Science and Technology
Principal Investigator	小笠原直毅奈良先端科学技術大学院大学, 情報科学研究科, 教授 (10110553)
Co-Investigator(Kenkyū-buntansha)	藤田泰太郎福山大学, 工学部, 教授 (40115506) 西岡孝明京都大学, 農学研究科, 教授 (80026559) 久原哲九州大学, 農学研究院, 教授 (00153320) 大森正之東京大学, 総合文化研究科, 教授 (80013580) 田仲可昌筑波大学, 生物科学系, 教授 (80091908)
Keywords	ゲノム生物 / メタボローム解析 / 発現ポルファイル解析 / 変異株バンク / 枯草菌 / シアノバクテリア / 細胞性粘膜 / 原始紅藻
Research Abstract	本領域は、微生物を主要な研究対象として、(1)ゲノム機能の細胞レベルの体系的な解析、(2)モデル微生物のゲノム機能のシステマチックな研究、(3)様々な細胞機能を司る遺伝子システムやゲノム構造に関する実験的及び情報学的な研究を進めることを目的としている。平成14年度は、計画研究、公募研究あわせて71の課題が設定され、以下のような研究の進捗・成果が得られた。 (1)215基礎代謝物質の濃度測定が可能であるメタボローム解析技術の開発。約1,300種類の分裂酵母蛋白質の発現の同定。出芽酵母の転写因子遺伝子破壊株の発現プロファイル解析による、階層的な遺伝子発現調節ネットワークの推定。 (2)約3,000の枯草菌未解析遺伝子の変異株バンクの完成と全増殖必須遺伝子271の同定。108新規枯草菌遺伝子の特異的機能の解明。DNAアレー解析による枯草菌の発現情報収集と転写制御ネットワークの解明。平均20kbの大腸菌欠失変異株の作製による、16個の新規必須遺伝子の同定。大腸菌2成分制御系の網羅的アレー解析。 (3)シアノバクテリSynechocystisの約550種の遺伝子破壊株の作製と約65遺伝子の機能の同定。光応答、乾燥・浸透圧等のストレス応答のDNAアレー解析。細胞性粘菌のcDNA解析による6,743遺伝子の同定。発生過程での遺伝子発現プロファイル解析。in situ hybridizationによる空間的な発現プロファイル解析。原始紅藻ゲノム16.4Mbpの配列決定と約5500の遺伝子の完全長cDNAの単離。病原細菌ウエルシュ菌・大腸菌O157の病原性関連遺伝子と基本転写制御遺伝子の変異株作製と発現解析による機能解析。全ゲノムPCRスキャンニング法による原性大腸菌O157株のゲノム比較解析。

Research Products

(18 results)

All Other

All Publications (18 results)

[Publications] Aburatani, S.: "Discovery of novel transcription control relationships with gene regulatory networks generated from multiple-disruption full genome expression libraries"DNA Res. (印刷中). (2003)
[Publications] Soga, T.: "Simultaneous determination of anionic intermediates for Bacillus subtilis metabolic pathways by capillary electrophoresis electrospray ionization mass spectrometry"Anal Chem. 74. 2233-22396 (2002)
[Publications] Oyama, T.: "Extraction of knowledge on protein-protein interaction by association rule discovery"Bioinformatics. 18. 705-714 (2002)
[Publications] Hashimoto, M.: "Indispensability of the Escherichia coli carbonic anhydrases YadF and CynT in cell proliferation at a low CO2 partial pressure"Biosci Biotech Biochem. (印刷中). (2003)
[Publications] Kobayashi, K.: "Essential Bacillus subtilis genes"Proc Natl Acad Sci USA. (印刷中). (2003)
[Publications] Ogura, M.: "Whole-genome analysis of genes regulated by the Bacillus subtilis competence transcription factor ComK"J Bacteriol. 184. 2344-2351 (2002)
[Publications] Asai, K.: "DNA microarray analysis of Bacillus subtilis sigma factors of extracytoplasmic function family"FEMS Microbiol Lett. (印刷中). (2003)
[Publications] Hosoya, S.: "Mutation in yaaT leads to significant inhibition of phosphorelay during sporulation in Bacillus subtilis"J Bacteriol. 184. 5545-5553 (2002)
[Publications] Kuwana, R.: "Proteomics characterization of novel spore proteins of Bacillus subtilis"Microbiology. 148. 3971-3982 (2002)
[Publications] Fukushima, T.: "Polysaccharide deacetylase gene (pdaA) is required for germination and for production of muramic-delta-lactam residues in the spore cortex of Bacillus subtilis"J Bacteriol. 184. 6007-6015 (2002)
[Publications] Kamei, A.: "Biochemical examination of the potential eukaiyotic-type protein kinase genes in the complete genome of the unicellular cyanobacterium Synechocystis sp. PCC6803"DAN Res. 9. 71-78 (2002)
[Publications] Shibata, M.: "Genes essential to sodium-dependent bicarbonate transport in cyanobacteria : function and phylogenetic analysis"J Biol Chem. 277. 18658-18664 (2002)
[Publications] Tanigawa, R.: "Transcriptional activation of NtcA-dependent promoters of Synechococcus sp. PCC7942 by 2-oxoglutarate in vitro"Proc Natl Acad Sci USA. 99. 4251-4255 (2002)
[Publications] Nishimura, Y.: "mt+ gamete specific nuclease that targets mt-chioroplasts during the sexual reproduction in Chlamydomonas reinhardtii"Genes Develop. 16. 1116-1128 (2002)
[Publications] Nishida, K.: "Dynamic recruitment of Dynamin for final mitochondrial severance in a red alga"Proc Natl Acad Sci USA. 100. 2146-2151 (2003)
[Publications] Nozaki, H.: "The phylogenetic position of red algae revealed by multiple nucler genes from mitochondria-contain ing eukaiyotes and an alternative hypothesis on the origin of plastids"J Bacteriol. 184. 6007-6015 (2002)
[Publications] Driessche, N.V.: "A transcriptional profile of multicellular development in Dictyostelium discoideum"Development. 129. 1543-1552 (2002)
[Publications] Maeda, M.: "Changing patterns of gene expression in prestalk cell subtypes of Dictyostelium recognized by in situ hybridization with genes from microarray analyses"Eukaryotic Cell. (印刷中). (2003)

2002 Fiscal Year Annual Research Report

細胞システム解明に向けたゲノム生物学の新展開

Principal Investigator

小笠原 直毅 奈良先端科学技術大学院大学, 情報科学研究科, 教授 (10110553)

Research Products

[Publications] Aburatani, S.: "Discovery of novel transcription control relationships with gene regulatory networks generated from multiple-disruption full genome expression libraries"DNA Res. (印刷中). (2003)

[Publications] Soga, T.: "Simultaneous determination of anionic intermediates for Bacillus subtilis metabolic pathways by capillary electrophoresis electrospray ionization mass spectrometry"Anal Chem. 74. 2233-22396 (2002)

[Publications] Oyama, T.: "Extraction of knowledge on protein-protein interaction by association rule discovery"Bioinformatics. 18. 705-714 (2002)

[Publications] Hashimoto, M.: "Indispensability of the Escherichia coli carbonic anhydrases YadF and CynT in cell proliferation at a low CO2 partial pressure"Biosci Biotech Biochem. (印刷中). (2003)

[Publications] Kobayashi, K.: "Essential Bacillus subtilis genes"Proc Natl Acad Sci USA. (印刷中). (2003)

[Publications] Ogura, M.: "Whole-genome analysis of genes regulated by the Bacillus subtilis competence transcription factor ComK"J Bacteriol. 184. 2344-2351 (2002)

[Publications] Asai, K.: "DNA microarray analysis of Bacillus subtilis sigma factors of extracytoplasmic function family"FEMS Microbiol Lett. (印刷中). (2003)

[Publications] Hosoya, S.: "Mutation in yaaT leads to significant inhibition of phosphorelay during sporulation in Bacillus subtilis"J Bacteriol. 184. 5545-5553 (2002)

[Publications] Kuwana, R.: "Proteomics characterization of novel spore proteins of Bacillus subtilis"Microbiology. 148. 3971-3982 (2002)

[Publications] Fukushima, T.: "Polysaccharide deacetylase gene (pdaA) is required for germination and for production of muramic-delta-lactam residues in the spore cortex of Bacillus subtilis"J Bacteriol. 184. 6007-6015 (2002)

[Publications] Kamei, A.: "Biochemical examination of the potential eukaiyotic-type protein kinase genes in the complete genome of the unicellular cyanobacterium Synechocystis sp. PCC6803"DAN Res. 9. 71-78 (2002)

[Publications] Shibata, M.: "Genes essential to sodium-dependent bicarbonate transport in cyanobacteria : function and phylogenetic analysis"J Biol Chem. 277. 18658-18664 (2002)

[Publications] Tanigawa, R.: "Transcriptional activation of NtcA-dependent promoters of Synechococcus sp. PCC7942 by 2-oxoglutarate in vitro"Proc Natl Acad Sci USA. 99. 4251-4255 (2002)

[Publications] Nishimura, Y.: "mt+ gamete specific nuclease that targets mt-chioroplasts during the sexual reproduction in Chlamydomonas reinhardtii"Genes Develop. 16. 1116-1128 (2002)

[Publications] Nishida, K.: "Dynamic recruitment of Dynamin for final mitochondrial severance in a red alga"Proc Natl Acad Sci USA. 100. 2146-2151 (2003)

[Publications] Nozaki, H.: "The phylogenetic position of red algae revealed by multiple nucler genes from mitochondria-contain ing eukaiyotes and an alternative hypothesis on the origin of plastids"J Bacteriol. 184. 6007-6015 (2002)

[Publications] Driessche, N.V.: "A transcriptional profile of multicellular development in Dictyostelium discoideum"Development. 129. 1543-1552 (2002)

[Publications] Maeda, M.: "Changing patterns of gene expression in prestalk cell subtypes of Dictyostelium recognized by in situ hybridization with genes from microarray analyses"Eukaryotic Cell. (印刷中). (2003)

小笠原直毅奈良先端科学技術大学院大学, 情報科学研究科, 教授 (10110553)