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Comprehensive study on transcriptional network system in the photoautotrophic cyanobacteria Synechococcusstrains

Research Project

Project/Area Number 13206027
Research Category

Grant-in-Aid for Scientific Research on Priority Areas

Allocation TypeSingle-year Grants
Review Section Biological Sciences
Research InstitutionNagoya University

Principal Investigator

SUGITA Mamoru  Nagoya University, Center for Gene Research, Professor, 遺伝子実験施設, 教授 (70154474)

Co-Investigator(Kenkyū-buntansha) OMATA Tatsuo  Nagoya University, Grad.Sc. Bioagricultural Sciences, Professor, 生命農学研究科, 教授 (50175270)
IWASAKI Hideo  Nagoya University, Graduate School of Sciences, Assistant Prof., 理工学術院・電気・情報生命工学科, 助手 (00324393)
續 伯彦  愛知学院大学, 情報社会政策学部, 教授 (60064896)
Project Period (FY) 2001 – 2004
Project Status Completed (Fiscal Year 2004)
Budget Amount *help
¥58,300,000 (Direct Cost: ¥58,300,000)
Fiscal Year 2004: ¥14,400,000 (Direct Cost: ¥14,400,000)
Fiscal Year 2003: ¥14,400,000 (Direct Cost: ¥14,400,000)
Fiscal Year 2002: ¥13,500,000 (Direct Cost: ¥13,500,000)
Fiscal Year 2001: ¥16,000,000 (Direct Cost: ¥16,000,000)
Keywordscyanobacteria / transcription network / two-component regulatory system / nitrate transport system / DNA chip / photoautotroph / circadian rhythm / clock gene / ゲノム / 光合成遺伝子 / 炭酸水素イオン能動輸送体 / Synechococcus 6301株 / Synechococcus 7942株 / Synechocystis 6803株 / Synechococcus6301株 / Synechococcus7942株 / Synechocystis6803株
Research Abstract

(1) The entire genome of a unicellular cyanobacterium, Synechococcus sp. strain PCC 6301, was sequenced. The genome consisted of a circular chromosome 2,696,255 bp long. A total of 2525 potential protein-encoding genes, two sets of rRNA genes, 45 tRNA genes representing 42 tRNA species and several genes, for small structural RNAs were assigned to the chromosome. Thirty-seven genes for the proteins involved in two-component regulatory system were also annotated. Ten percent of all the protein genes lacked significant similarity to genes for predicted proteins in the public, indicating the genes unique to Synechococcus PCC6301. We constructed high-density DNA microarrays (Affimetrix Gene Chip) of Synechococcus PCC6301 as a tool for comprehensive analysis of transcriptional network in cyanobacteria.
(2) We identified three genes responsible for the latent transport activity for nitrate: ltnA, which encodes a response regulator with no effector domain; ltnB, which encodes a hybrid histidine kinase with two receiver domains; and ltnT, which encodes a sulfate permease-like protein with a putative cyclic nucleoside monophosphate (cNMP)-binding domain.
(3) Circadian clock of cyanobacteria was considered to be composed of negative feedback regulation of kaiBC expression. We demonstrated that KaiC phosphorylation state oscillated even without kaiBC messenger RNA accumulation under continuous dark conditions. Moreover, kinetic profiles in the ratio of KaiC autophosphorylation-dephosphorylation were also temperature compensated in vitro. Thus, the cyanobacterial clock can keep time independent of de novo transcription and translation processes. Furthermore, we have reconstituted the self-sustainable oscillation of KaiC phosphorylation in vitro. The period of the in vitro oscillation was stable and the circadian periods observed in vivo in KaiC mutant strains were consistent with those measured in vitro.

Report

(5 results)
  • 2004 Annual Research Report   Final Research Report Summary
  • 2003 Annual Research Report
  • 2002 Annual Research Report
  • 2001 Annual Research Report
  • Research Products

    (34 results)

All 2006 2005 2004 Other

All Journal Article (12 results) Book (1 results) Publications (21 results)

  • [Journal Article] Latent nitrate transport activity of a novel sulfate permease-like protein of the cyanobacterium Synechococcus elongatus.2006

    • Author(s)
      Maeda, S., Sugita, C., Sugita.M., Omata, T.
    • Journal Title

      Journal of Biological Chemistry 281

      Pages: 5869-5876

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Latent nitrate transport activity of a novel sulfate permease-like protein of the cyanobacterium Synechococcus elongatus.2006

    • Author(s)
      Maeda, S., Sugita, C., Sugita, M., Omata, T.
    • Journal Title

      Journal of Biological Chemistry 281

      Pages: 5869-5876

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] No transcription-translation feedback in circadian rhythm of KaiC phosphorylation.2005

    • Author(s)
      Tomita, J., Nakajima, M, Kondo, T, Iwasaki, H.
    • Journal Title

      Science 307

      Pages: 251-254

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Annual Research Report 2004 Final Research Report Summary
  • [Journal Article] Reconstitution of circadian oscillation of cyanobacterial KaiC phosphorylation in vitro.2005

    • Author(s)
      Nakajima, M., Imai, K., Ito, H., Nishiwaki, T., Murayama, Y., Iwasaki, H., Oyama, T., Kondo, T.
    • Journal Title

      Science 308

      Pages: 414-415

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Reconstitution of circadian oscillation of cyanobacterial KaiC phosphorylation in vitro.2005

    • Author(s)
      Nakajima, M., Imai, K., Ito, H., Nishiwaki, T..Murayama, Y., Iwasaki, H., Oyama, T., Kondo, T.
    • Journal Title

      Science 308

      Pages: 415-415

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Plastid transformation reveals that moss tRNA^<Arg>-CCG is not essential for plastid function.2004

    • Author(s)
      Sugiura, C., Sugita, M.
    • Journal Title

      The Plant Journal 40

      Pages: 314-321

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Chloroplast phylogeny indicates that bryophytes are monophyletic.2004

    • Author(s)
      Nishiyama, T., Wolf, P.G., Kugita, M., Sinclair, R.B., Sugita, M., et al.
    • Journal Title

      Molecular Biology and Evolution 21

      Pages: 1813-1819

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Roles of CmpR, a LysR family transcriptional regulator, in acclimation of the cyanobacterium Synechococcus sp. strain PCC 7942 to low-CO2 and high-light conditions.2004

    • Author(s)
      Takahashi, Y., Yamaguchi, O., Omata, T.
    • Journal Title

      Molecular Microbiology 52

      Pages: 837-845

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Roles of CmpR, a LysR family transcriptional regulator, in acclimation of the cyanobacterium Synechococcus sp. strain PCC 7942 to low-CO2 and high-light conditions.2004

    • Author(s)
      Takahashi, Y., Yamaguchi, 0., Omata, T.
    • Journal Title

      Molecular Microbiology 52

      Pages: 837-845

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Plastid transformation reveals that moss tRNA ^<Arg>-CCG is not essential for plastid function.2004

    • Author(s)
      Sugiura, C., Sugita, M.
    • Journal Title

      The Plant Journal 40

      Pages: 314-321

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Chloroplast phylogeny indicates that bryophytes are monophyletic.2004

    • Author(s)
      Nishiyama, T., Wolf, P.G., Kugita, M., Sinclair, R.B., Sugita, M., et al.
    • Journal Title

      Molecul Biology and Evolution 21

      Pages: 1813-1819

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Roles of CmpR, a LysR family transcriptional regulator, in acclimation of the cyanobacterium Synechococcus sp.strain PCC 7942 to low-CO2 and high-light conditions.2004

    • Author(s)
      Takahashi, Y., Yamaguchi, O., Omata, T.
    • Journal Title

      Mol.Microbiol. 52

      Pages: 837-845

    • Related Report
      2004 Annual Research Report
  • [Book] シアノバクテリア(ゲノムミクス・プロテオミクスの新展開)(今中忠行監修)2004

    • Author(s)
      杉田 護, 杉田千恵子
    • Total Pages
      1158
    • Publisher
      エヌ・ティ・エス出版
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Publications] Atanassova.A., Sugita, M., Sugiura, M., Pajpanova, T., Ivanov, I.: "Molecular cloning, expression and characterization of three distinctive genes encoding methionine aminopeptidases in cyanobacterium Synechocystis sp. strain PCC6803."Arch.Mirobiol.. 180. 185-193 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Sugiura, C., Kobayashi, Y., Aoki, T., Sugita, C, Sugita, M.: "Complete chloroplast DNA sequence of the moss Physcomitrella patens reveals loss of rpoA from the chloroplast genome : evidence for the loss and relocation of rpoA from the chloroplast to the nucleus."Nucleic Acids Res.. 31. 5324-5331 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Maeda, S., Omata.T.: "A novel gene (narM) required for expression of nitrate reduction activity in the cyanobacterium Synechococcus elongatus strain PCC 7942"J.Bacteriol.. 186. 2107-2114 (2004)

    • Related Report
      2003 Annual Research Report
  • [Publications] Takahashi, Y., Yamaguchi, O., Omata, T.: "Roles of CmpR, a LysR family transcriptional regulator, in acclimation of the cyanobacterium Synechoccocus sp. strain PCC 7942 to low-CO_2 and high-light conditions."Mol.Microbiol.. 180(in press). (2004)

    • Related Report
      2003 Annual Research Report
  • [Publications] Kitayama, Y., Iwasaki, H., Nishiwaki, M., Kondo, T.: "KaiB functions as an attenuator of KaiC phosphorylation in the cyanobacterial clock system."EMBO J.. 22. 2127-2134 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Nakahira, Y., Katayama, M., Miyashita, H., Kutsuna, S., Iwasaki.H., Oyama, Y., Kondo, T.: "Global gene repression by KaiC as a master process of prokaryotic circadian system."Proc.Natl.Acad.Sci.USA.. 101. 881-885 (2004)

    • Related Report
      2003 Annual Research Report
  • [Publications] 杉田 護, 杉田千恵子: "ゲノミクス・プロテオミクスの新展開(今中忠行監修)"エヌ・テイー・エス(株)(印刷中). (2004)

    • Related Report
      2003 Annual Research Report
  • [Publications] Sugiura, C., Kobayashi, Y., Aoki, T., Sugita, C, Sugita, M: "Complete chloroplast DNA sequence of the moss Physcomitrella patens reveals loss of rpoA from the chloroplast genome"Nucleic Acids Res.. (in press).

    • Related Report
      2002 Annual Research Report
  • [Publications] Miyata, Y., Sugiura, C., Kobayashi, Y.Hagiwara, M.Sugita, M.: "Chloroplast ribosomal S14 protein transcript is edited to create a translation initiation codon in the moss Physcomitrella patens"Biochim.Biophys.Acta. 1576. 346-349 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Kobayashi, Y., Dokiya, Y., Kumazawa, Y., Sugita, M.: "Non-AUG translation initiation of mRNA encoding plastid-targeted phage-type RNA polymerase in Nicotiana sylvestris"Biochem.Biophys.Res.Commun.. 299. 57-61 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Price, G.D., Maeda, S., Omata, T., Badger, M.R.: "Modes of active inorganic carbon uptake in the cyanobacterium, Synechococcus sp. PCC7942"Functional Plant Biol.. 29. 131-149 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Omata, T., Takahashi, Y., Yamaguchi, O., Nishimura, T.: "Structure, function and regulation of the cyanobacterial high-affinity bicarbonate transporter BCT1."Functional Plant Biol.. 29. 151-159 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Tanigawa, R., Shirokane, M., Maeda, S., Omata, T., Tanaka, K., Takahashi, H.: "Transcriptional activation of NtcA-dependent promoters of Synechococcus sp. PCC 7942 by 2-oxoglutarate in vitro"Proc. Natl. Acad. Sci. USA.. 99. 4251-4255 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Yamaguchi, K., Mayfield, S.P., Sugita, M.: "Transcriptional and translational regulation in biosynthesis and repair. In : Photosystem II : The water/plastoquinone oxido-reductase in photosynthesis"Kluwer Publications (in press).

    • Related Report
      2002 Annual Research Report
  • [Publications] Omata, T., Gohta, S., Takahashi, Y., Harano, Y., Maeda, S.: "Involvement of a CbbR homolog in low CO2 induced activation of the bicarbonate transporter operon in cyanobacteria"J.Bacteriol.. 183. 1891-1898 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] Aichi, M., Takatani, N., Omata, T.: "Role of NtcB in activation of the nitrate assimilation genes in the cyanobacterium Synechocystis sp. strain PCC6803"J.Bacteriol.. 183. 5840-5847 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] Kobayashi, Y., Dokiya, Y., Sugita, M.: "Dual targeting of phage-type RNA polymerase to both mitochondria and plastids is due to alternative translation initiation in single transcripts"Biochem. Biophys. Res. Commun.. 289. 1106-1113 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] Kobayashi, Y., Dokiya, Y., Sugiura, M., Niwa, Y., Sugita, M.: "Genomic organization and organ-specific expression of a nuclear gene encoding phage-type RNA polymerase in Nicotiana sylvestris"Gene. 279. 33-40 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] Hara, K., Sugita, M., Aoki, S.: "Cloning and characterization of the cDNA for a plastid sigma factor from the moss Physcomitrella patens"Biochim.Biophys.Acta. 1517. 302-306 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] Tsudzuki, T., Wakasugi, T., Sugiura, M.: "Comparative analysis of RNA editing sites in higher plant chloroplasts"J.Mol.Evol.. 53. 327-332 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] Sugita, M., Tsudzuki, T., Sugita, C., Ishiura, M., Ogata, K., Jikuya, H., Takano, J., Sugiura, M.: "Genome analysis of Synechococcus sp. strain PCC6301. PS2001:Proceedings:12th International Congress on Photosynthesis"CSIRO PUBLISHING(印刷中). (2002)

    • Related Report
      2001 Annual Research Report

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Published: 2001-04-01   Modified: 2018-03-28  

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