Nakamura, Yuki

中村友輝
Nakamura, Yuki
Associate Research Fellow

 

2015-present: Associate Research Fellow, IPMB, Academia Sinica, Taiwan

2015-present: EMBO Young Investigator

2016-present: Adjunct Associate Professor, Taiwan International Graduate Program (TIGP), National Chun-Hsing Univ., Taiwan

 

2014-2016: Adjunct Assistant Professor, Taiwan International Graduate Program (TIGP), National Chun-Hsing Univ., Taiwan

2011-2015: Assistant Research Fellow, IPMB, Academia Sinica, Taiwan

2011-2014: PRESTO, Japan Science and Technology Agency (JST), Japan

2010-2011: A. von Humboldt Research Fellow, Max-Planck-Institute of Plant Breeding Research, Cologne, Germany; Univ. Bonn, Germany

2009-2010: Research Fellow, National University of Singapore

2007-2009: JSPS Research Fellow, Temasek Life Sciences Laboratory, Singapore

2007: Ph.D. Tokyo Institute of Technology, Japan

TEL: 

+886-2-2787-1130 (Lab)

CONCEPTS:

~Lipids to understand plant life

Lipids are the most predominant yet diverse biological molecule. Apart from being essential cellular membranes or energy storage components, lipids have now emerged as dynamic signal mediators. Using the seed plant Arabidopsis and the microalgae Chlamydomonas as model systems, our research group investigates how lipids interact with key signaling modules to coordinate their crucial life events. Our findings will not only help resolve outstanding or totally unknown questions in plant sciences, but also provide industry with potential candidates to future development.

FOCUSES:

~Think with lipids whenever an unresolved biological issue appears

Lipids interact with other molecules to fulfill their roles. Our primary focus is "lipid-protein interaction" in the signaling cascades. As below, our ongoing projects all aim to unravel the interplay between lipids and key components of signaling modules in various aspects of plant development.

Circadian-controlled lipid levels and flowering time control

Lipids are circadian-controlled. This rhythmic oscillation resonates with well-established environmental inputs, such as light, temperature and plant hormones, to coordinate proper flowering time. This project focuses on the specific interaction between lipids and the key components that control flowering time.

Organ patterning and stem cell regulation by lipids

Lipids contribute to the beauty of plant body. This is because of their tight association with stem cell maintenance. Hence, malfunctions in this regulatory network collapse the organ's positioning mechanism, resulting in odd-shaped plants. Our collection of funny-looking lipid mutants demonstrate their key role in maintaining a plant's shapely form.

Inter-organelle logistics of lipid deposition in seed maturation

Lipids are deposited as an energy source during seed maturation. This project focuses on understanding how lipid accumulation is initiated, how lipids are allocated to specific sites and how they are deposited as a lipid droplet. We aim to uncover the inter-organelle dynamism of lipid trafficking and will eventually apply this work to agriculture.

 

TECHNOLOGIES:

~"Metabolic Switching System", a technical innovation in lipid studies

Lipids are not genetically encoded. Hence, changing lipid levels in vivo is not easily achieved by gene manipulation. Our "Metabolic Switching Systems" is a novel technical platform that enables us to alter site-specific lipid levels by transiently altering the lipid metabolic flow. We are developing this system to observe the spatiotemporal effects of altered lipid levels in tissue function.

STRATEGY:

~Tempered approaches from cutting-edge omics to established biochemistry

Lipids are to be investigated multilaterally. The experimental approach should not limit the project's expansion, but should be chosen in accordance with the scientific goal. Hence, we encompass a wide range of experimental techniques from modern systems approaches to established biochemistry. We keep acquiring new skills so that we can always apply the best approach to given scientific questions.

APPLICATION:

~Green innovation by algal biofuel production

Lipids have the potential to save the world. Our Metabolic Switching System is now being applied to algal cells to switch the metabolic flow toward triglyceride biosynthesis. This vigorous "green micro-factory" will mass-produce a source of biodiesel with given quality, thereby contributing to bioenergy creation and other oil industries.

 

コンセプト

~脂質で考える植物の生き様

脂質は最も主要な生体分子であり、多様な構造と機能を持っています。生体膜の構成成分やエネルギー貯蔵の役割はもとより、脂質は今日、重要なシグナルメディエーターとしても知られるようになっています。我々の研究室では種子植物のシロイヌナズナと真核緑藻のクラミドモナスを用いて、植物のライフサイクルの様々な場面において脂質がどのような重要な役割を果たしているかを研究しています。

視点

~植物科学の難問を脂質で解く

脂質は他の分子と相互作用することにより、その役割を果たします。我々のグループの主な視点は、シグナル伝達における「脂質―タンパク質相互作用」です。以下のように、現在進行している研究プロジェクトはいずれも、植物の生長や発生における著名なシグナル伝達モジュールと脂質とのクロストークを明らかにすることを目的としています。

脂質代謝の概日リズムと開花制御
脂質代謝は概日リズムにより変動し、環境シグナルとして知られる光、温度や植物ホルモンなどと共鳴することにより開花時期の制御に関わっていると考えられます。この研究プロジェクトでは、脂質代謝の概日変動と開花制御の関係について明らかにしていきます。

脂質シグナルによる器官発生のパターン制御およびメリステム維持の機構
脂質はメリステム機能の維持に関わることにより植物の美しい形づくりに貢献しています。この研究プロジェクトでは、様々な形態の異常を来たした脂質関連のミュータントを解析することにより、植物の形づくりにおける脂質の役割を明らかにしていきます。

種子の成熟における貯蔵脂質の細胞間輸送システム
脂質は種子の成熟に従って、貯蔵物質として蓄積します。この研究プロジェクトでは、貯蔵脂質の蓄積がどのように開始され、どのように細胞間を輸送され、特定の部位に蓄積されていくか、そのメカニズムを明らかにしていきます。

 

技術

~独自技術「代謝スイッチング」を用いた脂質研究の新展開

脂質はタンパク質と異なり、遺伝子に直接コードされた産物ではありません。したがって、遺伝子操作により植物体の脂質レベルを改変することは必ずしも容易ではありません。我々が開発中の「代謝スイッチング」技術では、特定の組織における脂質代謝フローを一過的に変えることにより、脂質レベルと組織の機能の関係を時空間的に研究する新しい方法論の確立を目指しています。

戦略

~生化学からオミクスまで、自在の研究戦略

我々は、各研究プロジェクトの戦略に則り、常に最適な実験手法を選択します。持ち合わせの実験技術が研究プロジェクトの展開を妨げることのないよう、広範な実験技術を維持するとともに、常に新たな手法を習得し続けることを心がけています。

応用

~藻類バイオ燃料の創製によるグリーンイノベーションへの貢献

藻類バイオ燃料は、地球を救う次世代のエネルギー技術として期待されています。我々は、植物脂質科学の研究により得る知見と、独自の「代謝スイッチング」技術を緑藻で生かすことにより、緑藻内に油脂を大量蓄積させる「グリーンミクロファクトリー」の創出を目指しています。このことにより、我々の基礎研究と技術基盤が、人類と地球の未来に貢献できることを願っています。

All publication list

 

Selected publication list

 

Original articles (* corresponding author)

  • 29. Artik Elisa Angkawijaya and Yuki Nakamura* (2017) Arabidopsis PECP1 and PS2 are phosphate starvation-inducible phosphocholine phosphatases. Biochem. Biophys. Res. Commun. 494:397-401.
  • 28. Artik Elisa Angkawijaya, Van Cam Nguyen, and Yuki Nakamura* (2017) Enhanced root growth in phosphate-starved Arabidopsis by stimulating
        de novophospholipid biosynthesis through the overexpression of LYSOPHOSPHATIDIC ACID ACYLTRANSFERASE 2 (LPAT2). Plant Cell Environ.
         In press DOI: 10.1111/pce.12988. 
  • 27. Takashi Hirashima, Masakazu Toyoshima, Takashi Moriyama, Yuki Nakamura, and Naoki Sato (2017) Characterization of phosphoethanolamine-
         N-methyltransferases in green algae. Biochem. Biophys. Res. Commun. 488(1):141-146.
  • 26. Yueh Cho, Chao-Yuan Yu, Yuki Nakamura, and Kazue Kanehara* (2017) Arabidopsis dolichol kinase AtDOK1 is involved in flowering time control.
         J. Exp. Bot. In press DOI: 10.1093/jxb/erx095
  • 25. Ying-Chen Lin, Koichi Kobayashi, Chun-Hsien Hung, Hajime Wada, and Yuki Nakamura* (2016) Arabidopsis PHOSPHATIDYLGL
         YCEROPHOSPHATE PHOSPHATASE1 (PGPP1) involved in phosphatidylglycerol biosynthesis and photosynthetic function. Plant J., 88:1022-1037
  • 24. Ian Sofian Yunus, Yu-chi Liu, and Yuki Nakamura* (2016) The importance of SERINE DECARBOXYLASE1 (SDC1) and ethanolamine
          biosynthesis during embryogenesis of Arabidopsis thaliana. Plant J., 88:559-569
  • 23. Chun-Hsien Hung, Kazue Kanehara, and Yuki Nakamura*(2016) Isolation and characterization of a mutant defective in triacylglycerol
          accumulation in nitrogen-starved Chlamydomonas reinhardtii. Biochimica. Biophysica. Acta, 1861:1282-1293
  • 22. Chun-Hsien Hung, Kazue Kanehara, and Yuki Nakamura*(2016) In vivo reconstitution of algal triacylglycerol production in
          Saccharomyces cerevisiae. Front. Microbiol., 7:70. DOI: 10.3389/fmicb.2016.00070
  • 21. Chun-Hsien Hung, Koichi Kobayashi, Hajime Wada, and Yuki Nakamura*(2016) Functional specificity of cardiolipin synthase
          revealed by the identification of a cardiolipin synthase CrCLS1 in Chlamydomonas reinhardtii. Front. Microbiol.,
          6:1542. DOI: 10.3389/fmicb.2015.01542
  • 20. Kazue Kanehara*, Chao-Yuan Yu, Yueh Cho, Wei-Fun Cheong, Federico Torta, Guanghou Shui, Markus R Wenk, and Yuki Nakamura
          (2015)  Arabidopsis AtPLC2 is a primary phosphoinositide-specific phospholipase C in phosphoinositide metabolism and
          the endoplasmic reticulum stress response. PLOS Genet., DOI:10.1371/journal.pgen.1005511
  • 19. Chun-Hsien Hung, Kaichiro Endo, Koichi Kobayashi, Yuki Nakamura*, and Hajime Wada (2015) Characterization of Chlamydomonas
          reinhardtii
    phosphatidylglycerophosphate synthase in Synechocystis sp. PCC 6803. Front. Microbiol., 6:842.
          DOI: 10.3389/fmicb.2015.00842
  • 18. Ian Sofian Yunus, Amaury Cazenave-Gassiot, Yu-chi Liu, Ying-Chen Lin, Markus R. Wenk and Yuki Nakamura* (2015)
          Phosphatidic acid is a major phospholipid class in reproductive organs of Arabidopsis thaliana. Plant Signal. Behav.,
          DOI:10.1080/15592324.2015.1049790
  • 17. Ying-Chen Lin, Yu-chi Liu, Yuki Nakamura*. (2015) The choline/ethanolamine kinase family in Arabidopsis: Essential role of CEK4 in
          phospholipid biosynthesis and embryo development. Plant Cell, 27:1497-1511.
          [cover issue:  http://www.plantcell.org/content/27/5.cover-expansion]
  • 16. Chun-Hsien Hung, Koichi Kobayashi, Hajime Wada, Yuki Nakamura*. (2015) Isolation and characterization of a phosphatodylglycerol-
          phosphate phosphatase1, PGPP1, in Chlamydomonas reinhardtii. Plant Physiol. Biochem., 92:56-61.
  • 15. Kazue Kanehara*, Yueh Cho, Ying-Chen Lin, Chia-En Chen, Chao-Yuan Yu and Yuki Nakamura. (2015) Arabidopsis DOK1 encodes a
          functional dolichol kinase involved in reproduction, Plant J., 81:292-303.
  • 14. Sho Fujii, Koichi Kobayashi*, Yuki Nakamura* and Hajime Wada. (2014) Inducible knockdown of
          MONOGALACTOSYLDIACYLGLYCEROL SYNTHASE1 reveals roles of galactolipids in organelle differentiation
          in Arabidopsis cotyledons. Plant Physiol., 166:1436-1449.
  • 13. Yuki Nakamura*, Fernando Andrés, Kazue Kanehara, Yu-chi Liu, George Coupland and Peter Dörmann. (2014) Diurnal and circadian
          expression profiles of glycerolipid biosynthetic genes in Arabidopsis. Plant Signal. Behav., e29715 doi:10.4161/psb.29715.
  • 12. Yuki Nakamura*, Yu-chi Liu and Ying-Chen Lin. (2014) Floral glycerolipid profiles in homeotic mutants of Arabidopsis thaliana.
          Biochem. Biophys. Res. Commu., 450:1272-1275.
  • 11. Yuki Nakamura*, Fernando Andrés, Kazue Kanehara, Yu-chi Liu, Peter Dörmann and George Coupland. (2014) Arabidopsis florigen
          FT binds to diurnally oscillating phospholipids that accelerate flowering. Nat. Commun., 5:3553 doi: 10.1038/ncomms4553.
  • 10. Yuki Nakamura*, Norman Z. W. Teo, Guanghou Shui, Christine H.L. Chua, Wei-Fun Cheong, Sriram Parameswaran, Ryota Koizumi,
          Hiroyuki Ohta, Markus R. Wenk and Toshiro Ito*. (2014) Transcriptomic and lipidomic profiles of glycerolipids during Arabidopsis
          flower development. New Phytol., 203:310-322.
  • 9. Chun-Hsien Hung, Ming-Yang Ho, Kazue Kanehara and Yuki Nakamura*. (2013) Functional study of diacylglycerol acyltransferase
        type 2 family in Chlamydomonas reinhardtii. FEBS Lett., 587:2364-2370.
  • 8. Yuki Nakamura, Ryota Koizumi, Guanghou Shui, Mie Shimojima, Markus R. Wenk, Toshiro Ito and Hiroyuki Ohta*. (2009) Arabidopsis
        lipins mediate eukaryotic pathway of lipid metabolism and cope critically with phosphate starvation. Proc. Natl. Acad. Sci. USA,
        106:20978-83.
  • 7. Yuki Nakamura, Koichi Kobayashi and Hiroyuki Ohta*. (2009) Activation of Galactolipid Biosynthesis in Development of Pistils and
        Pollen tubes. Plant Physiol. Biochem. 47:535-539.
  • 6. Nicole Gaude, Yuki Nakamura, Wolf-Rudiger Scheible, Hiroyuki Ohta and Peter Dörmann* (2008) Phospholipase C5 (NPC5) is involved
        in galactolipid accumulation during phosphate limitation in leaves of Arabidopsis. Plant J. 56:28-39.
  • 5. Yuki Nakamura and Hiroyuki Ohta* (2007) The diacylglycerol forming pathways differ among floral organs of Petunia hybrida.
        FEBS Lett. 581:5475-5479.
  • 4. Yuki Nakamura, Mami Tsuchiya and Hiroyuki Ohta* (2007) Plastidic phosphatidic acid phosphatases identified in a distinct subfamily of
        lipid phosphate phosphatases with prokaryotic origin. J. Biol. Chem. 282:29013-29021.
  • 3. Koichiro Awai, Takatoshi Kakimoto, Chie Awai, Takakazu Kaneko, Yuki Nakamura, Ken-ichiro Takamiya, Hajime Wada and Hiroyuki
        Ohta*.(2006) Comparative genomic analysis revealed a gene for monoglucosyldiacylglycerol synthase, an enzyme for photosynthetic
        membrane lipid synthesis in cyanobacteria. Plant Physiol. 141:1120-1127.
  • 2. Yuki Nakamura, Koichiro Awai, Tatsuru Masuda, Yasushi Yoshioka, Ken-ichiro Takamiya and Hiroyuki Ohta*. (2005) A novel
        phosphatidylcholine-hydrolyzing phospholipase C induced by phosphate starvation in Arabidopsis. J. Biol. Chem.
        280:7469-7476. [Recommended by Faculty1000]
  • 1. Yuki Nakamura, Hitomi Arimitsu, Yoshiki Yamaryo, Koichiro Awai, Tatsuru Masuda, Hiroshi Shimada, Ken-ichiro Takamiya and Hiroyuki
        Ohta*. (2003) Digalactosyldiacylglycerol is a major glycolipid in floral organs of Petunia hybrida. Lipids 38:1107-1112

 

Review articles / book chapters

  • 13. Yuki Nakamura*. (2017) Plant phospholipid diversity: Emerging functions in metabolism and protein-lipid interactions. Trends Plant Sci.
           22(12):1027-1040.

     
  • 12. Takashi Osanai*, Youn-Il Park* and Yuki Nakamura*. (2017) Editorial: Biotechnology of Microalgae, Based on Molecular Biology and
          Biochemistry of Eukaryotic Algae and Cyanobacteria. Front. Microbiol. 8:118. doi: 10.3389/fmicb.2017.00118
  • 11. Yonghua Li-Beisson*, Yuki Nakamura and John Harwood. (2016) Lipids: From Chemical Structures, Biosynthesis, and Analyses to
          Industrial Applications. In “Lipids in Plant and Algae Development (Y Nakamura and Y Li-Beisson eds)” Subcellular Biochemistry
          86:1-18, Springer.
  • 10. Yuki Nakamura*. (2015) Function of polar glycerolipids in flower development in Arabidopsis thaliana. Prog. Lipid. Res. 60:17-29.
  • 9. Yuki Nakamura*. (2014) NPC: non-specific phospholipase Cs in plant functions. In “Phospholipases in Plant Signaling (Wang, X ed)
        Singaling and Communication in Plants 8094:55-68, Springer.
  • 8. Yuki Nakamura*. (2013) Galactolipid biosynthesis in flowers. Botanical Studies, 54:29.
  • 7. Yuki Nakamura*. (2013) Assaying Plant Phosphatidic Acid Phosphatase Activity. In "Plant Lipid Signaling Protocols (Munnik T and
        Heilmann I, eds)" Methods in Molecular Biology 1009:233-240, Springer.
  • 6. Yuki Nakamura*. (2013) Phosphate starvation and membrane lipid remodeling in seed plants. Prog. Lipid. Res. 52:43-50.
  • 5. Yuki Nakamura and Hiroyuki Ohta*. (2011) Phosphatidic Acid Phosphatases in Seed Plants ~ Involvement in Membrane Lipid
        Biosynthesis and Signal Transduction. Seikagaku (Biochemistry) 82:1137-40 [Review in Japanese]
  • 4. Yuki Nakamura, Koichi Kobayashi, Mie Shimojima and Hiroyuki Ohta*. (2010) Biosynthesis and Function of
        Monogalactosyldiacylglycerol, the Signature Lipid of Chloroplasts. In "The Chloroplast (Rebeiz, CA ed)
       " Advances in Photosynthesis and Respiration 31:185-202, Springer.
  • 3. Mie Shimojima*, Hiroyuki Ohta and Yuki Nakamura. (2010) Biosynthesis and Function of Chloroplast Lipids. In "Lipids
        in Photosynthesis
    (Wada, H. and Murata, N eds)" Advances in Photosynthesis and Respiration 30:35-55, Springer.
  • 2. Yuki Nakamura and Hiroyuki Ohta*. (2010) Phosphatidic acid phosphatases in seed plants. In "Lipid Singaling in Plants
        (Munnik T, ed)", Plant Cell Monographs 16:131-141, Springer.
  • 1. Koichi Kobayashi, Yuki Nakamura and Hiroyuki Ohta*. (2009) Type A and type B monogalactosyldiacylglycerol synthases are spatially
        and functionally separated in plastids of higher plants. Plant Physiol. Biochem. 47:518-525.
 

Artik Elisa Angkawijaya

Postdoctoral Fellow

   

Farrel Gunawan

Research Assistant

   

 

Ying-Chen Lin

PhD Student (TIGP)

   

Yu-chi Liu

Technical Specialist

   

Hai Anh Ngo

PhD Student (TIGP)

   

Cam Van Nguyen

PhD Student (TIGP)

   

Lab Alumni

Ming-Yang Ho (Sep 2012 - Jun 2013)
Ph.D. student, Penn. State Univ. USA

Ian Sofian Yunus (Jul 2014-Sep 2015)
Ph.D. student, Imperial College London

Chun-Hsien Hung (Dec 2011-Dec 2015) 

Panadda Kungwon (Jan-Dec 2017)