Preferences of synonymous codons and translational control during the chloroplast genome evolution

2010 Fiscal Year Final Research Report

• Project/Area Number: 21770258
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Single-year Grants
• Research Field: Evolutionary biology
• Research Institution: Nagoya City University
• Principal Investigator: NAKAMURA Masayuki Nagoya City University -> 名古屋市立大学, 大学院・システム自然科学研究科, 研究員 (60322145)
• Project Period (FY): 2009 – 2010
• Keywords: 葉緑体 / 翻訳 / 同義コドン / 進化 / in vitro翻訳系

Research Abstract

In chloroplasts, the translation efficiencies of synonymous codons are not always correlated with their codon usage. Tobacco chloroplast rps2 mRNA contains many codons having efficient translation activity, whereas rps16 mRNA has a lot of inefficient codons. To elucidate whether the codon preference affect the translation efficiencies of these mRNAs, I analyzed the translation efficiencies of rps2 and rps16 mRNAs using the in vitro translation system from tobacco chloroplasts. I found that (1) 5'UTR of rps16 mRNA has less translation activity, (2) protein coding region of rps16 mRNA was translated about 3-times faster than that of rps2 mRNA, and (3) codon substitutions increased that translation efficiency of protein coding region of rps16 mRNA.

Research Products

• [Journal Article] Translation efficiencies of synonymous codons for arginine differ dramatically and are not correlated with codon usage in chloroplasts. (2011)
  • Author(s): Nakamura, M., Sugiura, M.
  • Journal Title: Gene 472 Pages: 50-54
  • Peer Reviewed
• [Journal Article] An organellar maturase associates with multiple group II introns. (2010)
  • Author(s): Zoschke, R., Nakamura, M., Liere, K., Sugiura, M. Borner, T., Schmitz-Linneweber, C.
  • Journal Title: Proc. Natl. Acad. Sci. USA. 107 Pages: 3245-3250
  • Peer Reviewed
• [Presentation] 葉緑体ゲノムに存在するrps16遺伝子は機能しているのか? (2011)
  • Author(s): 中邨真之、杉浦昌弘
  • Organizer: 第52回日本植物生理学会年会
  • Place of Presentation: 仙台
  • Year and Date: 20110320-20110322
• [Presentation] 植物の核ゲノムにはATG開始コドンを介した新規プロモーターの出現メカニズムがある (2011)
  • Author(s): 佐藤壮一郎、松尾充啓、工藤久幸、木村宏、中邨真之、山本義治、小保方潤一
  • Organizer: 第52回日本植物生理学会年会
  • Place of Presentation: 仙台
  • Year and Date: 20110320-20110322
• [Presentation] タバコBY-2細胞におけるアミロプラスト分化制御メカニズムの解析 (2011)
  • Author(s): 本橋典子、江波和彦、小沢友希、中邨真之、田中寛、華岡光正
  • Organizer: 第52回日本植物生理学会年会
  • Place of Presentation: 仙台
  • Year and Date: 20110320-20110322
• [Presentation] Translation efficiency of rps16 mRNA in tobacco chloroplasts (2010)
  • Author(s): 中邨真之、杉浦昌弘
  • Organizer: 第33回日本分子生物学会年会
  • Place of Presentation: 神戸
  • Year and Date: 20101207-20101210
• [Presentation] 構造遺伝子の挿入によるクリプティックプロモーターの活性化機構の解明 (2010)
  • Author(s): 松尾充啓、佐藤壮一郎、工藤久幸、中邨真之、山本義治、小保方潤一
  • Organizer: 第33回日本分子生物学会年会
  • Place of Presentation: 神戸
  • Year and Date: 20101207-20101210
• [Presentation] クリプティックプロモーターの活性化メカニズムと転写領域の新生 (2010)
  • Author(s): 小保方潤一、工藤久幸、松尾充啓、佐藤壮一郎、中邨真之、山本義治、木村宏
  • Organizer: 日本遺伝学会第82回大会
  • Place of Presentation: 札幌
  • Year and Date: 20100920-20100922
• [Presentation] 植物核に挿入されたコード領域はクロマチンのリモデリングと転写領域の新生を引き起こす (2010)
  • Author(s): 工藤久幸、松尾充啓、佐藤壮一郎、木村宏、中邨真之、山本義治、小保方潤一
  • Organizer: 日本植物学会第74回大会
  • Place of Presentation: 春日井
  • Year and Date: 20100909-20100911
• [Presentation] 葉緑体mRNAの同義コドンと翻訳活性 (2010)
  • Author(s): 中邨真之、杉浦昌弘
  • Organizer: 日本植物学会第74回大会
  • Place of Presentation: 春日井
  • Year and Date: 20100909-20100911
• [Presentation] MatK or why keep a chloroplast-encoded splicing factor? (2010)
  • Author(s): Zoschke, R., Neumann, L., Nakamura, M., Liere, K., Sugiura, M., Borner, T., Schmitz-Linneweber, C.
  • Organizer: XIth International Colloquium on Endocytiobiology and Symbiosis
  • Place of Presentation: Tromsφ
  • Year and Date: 20100829-20100903
• [Presentation] Translation activity of rps16 mRNA in tobacco chloroplasts (2010)
  • Author(s): Nakamura, M., Sugiura, M.
  • Organizer: XIth International Colloquium on Endocytobiology and Symbiosis
  • Place of Presentation: Tromsφ
  • Year and Date: 20100829-20100903
• [Presentation] Chloroplast- and nuclear-encoded rps16 genes in tobacco (2010)
  • Author(s): Nakamura, M., Sugiura, M.
  • Organizer: Gordon Research Conferences ; Mitochondria and Chloroplasts
  • Place of Presentation: Lucca
  • Year and Date: 20100710-20100716
• [Presentation] Comparative analysis of the translation efficiencies between rps2 and rps16 mRNAs in tobacco chloroplasts (2010)
  • Author(s): Nakamura, M., Sugiura, M.
  • Organizer: FESPB 2010
  • Place of Presentation: Valencia
  • Year and Date: 20100604-20100609
• [Presentation] 植物核に挿入されたコード領域はヌクレオソームと転写単位の再編成を引き起こす (2010)
  • Author(s): 工藤久幸、松尾充啓、木村宏、中邨真之、山本義治、小保方潤一
  • Organizer: 第51回日本植物生理学会年会
  • Place of Presentation: 熊本
  • Year and Date: 20100318-20100321
• [Presentation] タバコ葉緑体mRNAにおける同義コドンと翻訳効率 (2010)
  • Author(s): 中邨真之、杉浦昌弘
  • Organizer: 第51回日本植物生理学会年会
  • Place of Presentation: 熊本
  • Year and Date: 20100318-20100321
• [Presentation] PolIIの転写開始位置の決定に関わるコード領域の役割 (2009)
  • Author(s): 工藤久幸、山本義治、中邨真之、小保方潤一
  • Organizer: 第32回日本分子生物学会
  • Place of Presentation: 横浜
  • Year and Date: 20091209-20091212
• [Presentation] タバコ葉緑体rps2 mRNAとrps16 mRNAの翻訳効率の比較 (2009)
  • Author(s): 中邨真之、杉浦昌弘
  • Organizer: 第32回日本分子生物学会
  • Place of Presentation: 横浜
  • Year and Date: 20091209-20091212
• [Presentation] An organellar maturase associates with multiple group II introns (2009)
  • Author(s): Zoschke, R., Nakamura, M., Liere, K., Sugiura, M., Borner, T., Schmitz-Linneweber, C.
  • Organizer: LEOPOLDINA-SYMPOSIUM
  • Place of Presentation: Berlin
  • Year and Date: 20090920-20090923
• [Presentation] Translation efficiencies of chloroplast mRNAs are modulated by the selection of synonymous codons (2009)
  • Author(s): Nakamura, M., Sugiura, M.
  • Organizer: LEOPOLDINA-SYMPOSIUM
  • Place of Presentation: Berlin
  • Year and Date: 20090920-20090923
• [Presentation] Correlation between codon usage and translation efficiencies of synonymous codons in tobacco chloroplasts (2009)
  • Author(s): Nakamura, M., Sugiura, M.
  • Organizer: Plant Biology 2009.
  • Place of Presentation: Honolulu
  • Year and Date: 20090718-20090722