RIKEN Plant Science Center

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1 RIKEN Plant Science Center Evaluation of the RIKEN Plant Science Center in Phase 2 (PSC2) This report is based on a mail review conducted in 2005 to evaluate the Strategic Research Report provided by PSC Director Prof. Dr. Kazuo Shinozaki and on a site visit of the Chair of the RIKEN Plant Science Center Advisory Council from April 19-21, The report summarizes the statements of the Advisory Council members and addresses the PSC Strategic Research Plan that was discussed during the site visit. The full reports of the individual Advisory Council members are included with this report. The Advisory Council members will have opportunities for site visits of the RIKEN Yokohama Campus during The next meeting of the full PSC Advisory Council is planned during the second half of PSC2. Members of the RIKEN PSC Advisory Council Prof., Chair ETH Zurich (Swiss Federal Institute of Technology) Prof. Peter McCourt University of Toronto, Canada Prof. Naoto Shibuya Meiji University Dr. Yoshikazu Tanaka Suntory Limited General comments The RIKEN Plant Science Center Phase 2 (PSC2) continues as the premier plant research institution of Japan that enjoys strong international visibility. Research in PSC2 focuses on improving plant productivity using front line technologies and approaches, including gene discovery, comparative genomics and systems biology. A new focus has been developed in metabolomics, which builds on the tradition of RIKEN s excellent plant biochemistry and the current strength in NMR technologies. PSC2 is well positioned to become one of the internationally leading institutions in structural and functional metabolomics. The PSC2 research plan has a concise focus for the funding period. It also outlines a clear and important long-term vision for the transfer of research results to applications in developing sustainable agricultural production systems that will be of high impact for human health and nutrition. PSC2 has made impressive progress since the appointment of Director Kazuo Shinozaki.

2 Research plan in the second phase of the Plant Science Center (PSC2) In their 2 nd review of the PSC (2004), the previous PSC Advisory Council had expressed concern about the unresolved future of the PSC and strongly recommended that RIKEN continue funding of PSC to promote plant science for the future. The RIKEN Advisory Council (RAC) shared this concern in their 2004 report. With the appointment of Professor Kazuo Shinozaki as the new PSC Director, the RIKEN President and the Government of Japan have sent clear signals for the continuation of PSC and the importance of plant science research for Japan. The Advisory Council welcomes the positive development for the PSC, which will also be appreciated in the international plant science community. While the first phase of RIKEN PSC (PSC1) had a strong focus on the development of technologies and model organisms, PCS2 now provides an opportunity to focus on key plant models and exploit functional genomics technology platforms to understand the molecular mechanisms of plant production. This refocusing is consistent with the new national initiative Green-Techno Plan (Green Technology for the Future of Human Beings), which was launched by leading Japanese plant scientists. With the new focus PSC2 is well positioned to contribute solutions to important and longer-term problems that impact human well-being and food security. In addition, PSC2 research will continue to make increasing contributions to the Life Sciences. Director Shinozaki is leading PSC2 by focusing the research on plant metabolic systems and its applications. This new direction promises to provide important insights into plant functions that will help to improve the productivity of crops and trees. The research plan as outlined in 2005 report is well structured, ambitious but realistic, and forward looking. The research will be carried out by expert scientists with the support of established technologies and new infrastructure platforms. Until new research projects and infrastructure platforms have been fully established and will be in operation, however, it is difficult to provide more detailed comments or suggestions on their effectiveness and productivity. Recommendation: PSC should convene a meeting of the Advisory Council in the near future to provide advice on PSC2 research programs, strategic affiliations and development of technology platforms (including IT and bioinformatics), and to provide guidance to Director Shinozaki and the research groups on strategic directions. Research organization of PSC2 In the past, the Advisory Council expressed concerns about the part-time appointment of PSC1 group directors, several of whom maintained significant research activities at their home Universities. Director Shinozaki has now made important changes to the operation of PSC2 research groups, with group directors expected to have full RIKEN appointments and to provide full-time leadership to the research groups. At present, PSC2 has five major research groups, which are made up of smaller research teams directed by team leaders. Only Dr. Yuji Kamiya was appointed as 2

3 group director from PSC1, which is consistent with his strong research program relevant to plant metabolic systems, his excellent international visibility, and his effort in training young scientists. A new director will be appointed in 2006 to lead the Plant Productivity Systems Research Group. The Metabolomics Research Group is headed by Dr. Kazuki Saito, who is also leading the Metabolomics Function Research Group. The Advisory Committee sees a strategic advantage that Dr. Saito is leading both groups during the build-up phase of the metabolomics platform. It is important that both groups closely interact during this build-up phase, which can be best accomplished through the coordination of both groups by Dr. Saito. But since the Metabolic Function Research Group will likely assume important integrating functions of PSC2 research activities in the future, PSC should consider to appoint individual Group Directors for both groups. PSC Director Shinozaki functions as Deputy Director for the Metabolomics Research Group. Following RAC advice, the position of Center Directors should be strengthened and entrepreneurship of Directors should be encouraged. With broader administrative and leadership responsibilities for Director Shinozaki in the future, PSC should consider to appoint an additional Deputy Research Director for the Metabolomics Research Group, who can facilitate interactions with other groups. Most PSC2 Team Leaders were transferred from PSC1 to provide a certainly level of continuity of research activities. The Advisory Council feels that this was a sensible strategy, but also recommends that efforts should be made to attract additional young and innovative scientists to lead creative research teams. The organization of PSC2 follows the established RIKEN administrative management structure, with larger research groups consisting of smaller research teams. While this organization has functioned well in the past, PSC2 should consider new organizational structures that provide additional career opportunities for promising young scientists to lead independent research groups, especially for woman scientists. These could include career tracks equivalent to independent assistant professor positions (even if non-tenure track) at U.S. or some European Universities. Recommendation: The organizational development of PSC2 should be facilitated to meet the goals of the national Green-Techno Plan. PSC2 Group Directors should review current team leader appointments and promote the appointment of additional promising young scientists (including foreign scientists) to build strong and effective research teams around the central PSC2 research theme. Consideration should be given to the development of additional and/or new career tracks for young scientists to foster their independent growth. 3

4 Research groups and outline of their research subjects 1) Metabolomics Research Group (Group Director: Kazuki Saito; Group Deputy Director: Kazuo Shinozaki) The Metabolomics Research Group was newly established with the arrival of PSC Director Shinozaki. The primary focus of the group will be on gene expression and metabolite profiling to understand gene function and networks. The Research Plan provides information on the general direction of this group. The Advisory Council looks forward to provide feedback on more detailed research plans and strategic goals. Prof. Kazuki Saito is expert in metabolite research and maintains close links with leading metabolomics research groups in Europe (especially MPI Golm) and Japan. The Advisory Council expects that Prof. Saito will be able to build an advanced metabolomics infrastructure platform that will also support the PSC research groups and collaborations with other researchers in Japan and at the international level. Unit leaders Dr. Masami Hirai, Dr. Jun Kikuchi and Dr. Tetsuya Sakurai are excellent appointments. Their strong expertise in transcriptomics, metabolomics and NMR technologies will be critical for PSC2 to become an internationally leading center for plant gene network analysis. 2) Gene Discovery Research Group (Group Director: Kazuo Shinozaki) The Gene Discovery Research Group consists of four teams. The Gene Discovery Research Team headed by Director Shinozaki is well established and internationally recognized. The other three teams, which are headed by Ken Matsuoka, Tatsuya Sakai and Takuji Wada, were transferred from PSC1. They have ambitious research programs, but from the brief outline it is difficult see how these three teams will contribute to the PSC2 central goal of discovering novel genes involved in plant productivity and abiotic stress resistance. The Advisory Council recommended in 2003 that Dr. Wada should consider screening for mutants in cell-to-cell movement. It is appreciated that this screen is now part of his research program. The Advisory Council had previously suggested that Dr. Sakai should focus his research program on central problems in blue light signaling. The Advisory Council looks forward to learn how Dr. Sakai will contribute to the central goal of the Group. The Advisory Council had also recommended that Dr. Matsuoka should focus his research program. From his recent publications it appears that he in now concentrating on specific problems in the secretory pathway 3) Growth Regulation Research Group (Group Director: Yuji Kamiya) This Group continues frontier research in hormone metabolism and signaling, and their relationship to secondary metabolite synthesis. The three teams, headed by Dr. Yuji 4

5 Kamiya, Dr. Eiji Nambara and Dr. Shinjiro Yamaguchi, have aligned their research programs such that they form strongly complementary efforts, mainly focusing on the hormones gibberelline and abscisic acid. Their research programs are fully consistent with the mission of PSC2. As a new effort they will develop a highly sensitive and highthroughput hormone analysis program that will also be offered as an international service program. The three team leaders have excellent track records and are internationally recognized in their fields. The Advisory Council looks forward to learn more about their detailed research programs and strategic goals. 4) Metabolic Function Research Group (Group Director: Kazuki Saito) The group consists of three teams with broad research programs ranging from the identification of novel useful genes from medicinal and unexplored plants to sulfur and nitrogen metabolism. This research breadth is in part the result of the appointments of PSC1 team leaders Dr. Toshiya Muranaka and Dr. Hideki Takahashi, who have both developed strong independent research programs. The Director Dr. Kazuki Saito brings a new research component to the team. Although the broad program of this Group is generally consistent with the overall goal of PSC2, the Advisory Council is looking forward to learn how the research will be integrated to reach the stated objectives. Also, it will be important to explain how in the longer term this Group distinguishes itself from the Metabolomics Research Group, for which Dr. Saito is also the Group Director. 5) Plant Productivity Systems Research Group (Group Director: Kazuo Shinozaki) This group is made up of two teams headed by the PSC1 team leaders Dr. Hitoshi Sakakibara and Dr. Taku Demura. Both bring strong research programs to the Group that in PSC2 will become more focused on applications to grain yield in rice and wood production in poplar. These are interesting efforts, although it must be noted that strong consortia in Europe and the U.S. have also developed key functional genomics tools to address wood formation using poplar as model system. Importantly, to remain competitive it will become increasingly important to develop novel assays for poplar genes identified from gene expression analysis of xylem tissue to understand their function in wood production. Similarly, strong efforts are underway in the U.S. and China to develop functional genomics platforms for rice. It will be key for PSC2 to participate in these international efforts and focus on problems that are not already being addressed by other laboratories. 6) Plant Immunity Research Group (Group Director: Ken Shirasu, since 10/2005) The preliminary research plan of this group focuses on work that Dr. Shirasu initiated with Paul Schulze-Lefert and in collaboration with Jeff Dangl. Dr. Shirasu has a strong track record, and it can be expected that he will build a strong research group to focus on disease resistance mechanisms. Based on his long-term research in Germany and the U.K., Dr. Shirasu brings a welcome international flavor to PSC2. The Advisory 5

6 Council looks forward to learn more about the detailed research programs and strategic goals once this group is established and additional team leaders have been identified. Collaboration with other institutes, universities and companies Because of his international leadership, Dr. Shinozaki enjoys wide recognition and the interest of national and international laboratories in collaborations with PSC. The 2005 report includes a list of current and planned collaborations. While this list is very impressive, it is also clear that collaborations must be fully compatible with PSC2 goals, integrated with the PSC2 research program, and supported by PSC2 researchers. Most important is the collaboration with researchers at MPI Golm to share and develop technologies in metabolite profiling. Management of research projects in PSC2 The Advisory Council previously noted that the productivity of PSC research groups was generally good but could further benefit from facilitating communication among the scientists. As noted in the 2005 report, Director Shinozaki has started discussions in PSC2 on research strategies, research plans and project proposals. This positive development will allow PSC2 to achieve excellence and maintain groundbreaking research programs. The Advisory Council welcomed the establishment of the Director s Special Fund and recommended to restrict its use to support new ideas from young PSC2 researchers. It is an excellent idea to use such a special fund for promoting interactions and collaborations among the research groups. Training of young scientists in PSC2 PSC2 will place particular emphasis on the recruitment and training of young scientists, including women scientists and foreign researchers. The Advisory Council welcomes this proactive staff recruitment plan, which assures that PSC2 will develop a dynamic scientific workforce of highly motivated young researchers who will be guided by more senior team leaders and group directors. Attraction of international scientists The Advisory Council welcomes RIKEN s efforts to attract international scientists and scholars to work on their campuses. Considering the location of the Yokohama campus, however, the Advisory Council remains concerned about the lack of housing facilities to accommodate international scientists. This will make it difficult for PSC2 to attract foreign PhD and postdoctoral students. It also constrains the housing of international 6

7 collaborators and scientists, who have to be accommodated in hotels away from the campus. The Advisory Council strongly recommends finding solutions to this problem. Appropriateness of the research theme, objectives and research plan and potential for future development The RIKEN PSC was established in 2000 as part of the Millennium Project that was launched by the Japanese Government to promote science and technology. The research activities during the first phase of the PSC (PSC2) were broadly focused on a molecular understanding of plant functions and the utilization of plants to improve living and eating. The mission of PSC2, which started in 2005 under the leadership of Director Kazuo Shinozaki, focuses on the discovery of new plant functions and their applications to improve plant productivity. In general, the problem of plant productivity is central to the future of agricultural production worldwide. Therefore it is appropriate and important for PSC2 to develop and implement research programs that will contribute to the improvement of plant productivity, food quality, and the transfer of knowledge from model plants to important crops, trees and medicinal plants. The mission of PSC2 is generally consistent with the Green Techno Plan in Japan as well as comparable initiatives in the U.S., Europe and China. In 2000 the U.S. launched the NSF Arabidopsis 2010 Project, and new crop genomics programs have been initiated in the last two years. Plant function and productivity has also been recognized as a major topic in the European Union. In 2005, the EU launched the Technology Platform 2025 Plants for the Future, which includes an ambitious research program in plant genomics and biotechnology that will receive significant financial support during Framework Program 7. Similar initiatives are underway in China, where a strong focus has been developed on functional genomcis and engineering of crop plants. Recommendation: The research theme and objectives of PSC2 are timely and fully aligned with other international initiatives. The PSC2 research plan has significant potential for the development of sustainable agricultural production in Japan and for the improvement of human health and nutrition through novel plant products. It is clear that the ambitious PSC2 research program and its application to crop plants cannot be accomplished during a single 5-year period. The Advisory Council recommends to support the 15-year road map of the RIKEN PSC to translate important plant discoveries into agricultural products. Achievement of research plan Since the appointment of Director Kazuo Shinozaki in early 2005, PSC2 has already developed a strong new profile of plant research at RIKEN and has begun with the implementation of the strategic research plan. Most notably, during 2005 Director Shinozaki was instrumental in the smooth transition from PSC1 to PSC2 and the sensible continuation of specific and highly successful PSC1 research activities. He 7

8 started a new research group in metabolomics research. Most importantly, he strengthened gene discovery and extension of applications to crop plants through the transfer of the Plant Functional Genomcis group from the Genome Science Center to PSC2. Director Shinozaki facilitated communication and cooperation among the PSC2 research groups and helped them to network with other internal RIKEN groups. Innovative and cutting edge discovery research must be supported by strong technology platforms. To implement the strategic research plan, PSC2 is building new state-of-theart metabolomics platform that will also be accessible for other researchers in Japan. A novel high-throughput hormone analysis platform is under construction that will be open for the international plant research community to measure hormones with unprecedented sensitivity and spatial resolution. These new platforms complement the existing transcriptomics and functional genomics platforms. A new proteomics platform is planned that will focus on the analysis of protein complexes and protein modifications. The Advisory Council recommends that PSC researchers should exploit the technology platforms not only for data collection, but also consider how technological limits can be pushed further to understand the molecular details of plant function. Transferring basic discoveries to applications requires considerable greenhouse infrastructure and access to field space. Both aspects are difficult to realize for PSC2 on the RIKEN Yokohama campus. The Advisory Council strongly recommends that RIKEN should find ways to expand the existing greenhouse facilities to support the strategic research in crop plants. Director Shinozaki has already made efforts to develop links with the Kihara Institute for Biological Research of Yokohama City University, which has accessible field space for wheat breeding and crop genomics. The Advisory Council sees the collaboration with Kihara Institute as an important and valuable asset to PSC2 that allows RIKEN plant researchers to expand into agricultural crop biotechnology. Further collaborations with NAIST (metabolomics), NIAS (rice genomics), and selected companies fit well into the PSC2 strategic plan, but as mentioned earlier in the report they must remain focused and compatible with the PSC2 research goals. The Advisory Council previously recommended that database management and bioinformatics needed specific attention to cope with the data flow and to interpret largescale datasets in their appropriate biological context. It recommended to develop training programs in bioinformatics and to establish central computational facilities in which researchers from different programs can meet, exchange ideas and collaborate to develop tools for modelling biological processes. PSC2 plans to employ many scientists in bioinformatics and provide training courses in bioinformatics, but no further details were provided. Strong bioinformatics components are still in the build-up phase, and PSC2 has started two bioinformatics teams in the Metabolomics Research Group. Dr. Shinozaki has also established a collaboration with Dr. Toyoda in GSC on tiling array analysis and Dr. Kanaya at NAIST and Dr. Arita at the University of Tokyo on bioinformatics tools for metabolomics. It will still be useful for PSC2 to develop a comprehensive plan for bioinformatics and computational biology support. Recommendation: It will be important during the next 12 months to further shape the research themes and objectives. Since several Team Leaders of PSC2 were transferred 8

9 from PSC1, it will be imperative that they share and support the research themes and vision of Director Shinozaki. They must contribute to the central and longer-term goal of PSC2 to achieve the research plan. Special efforts should be made to recruit excellent and high-profile young Group and Team Leaders from outside RIKEN. Director Shinozaki should also consider promoting excellent PSC2 Team Leaders with proven track records to Group Leaders. Connection and balance between the planned work, research results and subsequent publications Research excellence is measured by publications in high-ranking journals, and therefore Team Leaders should be encouraged to promote the most innovative discovery research in their groups. Since January 2005 PSC2 has published already over 130 papers, of which more than two-thirds appears in journals with impact factor 5 and higher. Although many of these papers report work accomplished during PSC1, this nevertheless represents a strong productivity that compares very favourably with the publication records of other leading plant research centers such as the MPI Golm. The Advisory Council feels that the rate and quality of publications reflect a good balance between the implementation of work plans and their effectiveness to produce results and subsequent publications. Excellence can also be achieved through translational research, especially in applied plant sciences and biotechnology, if it derives an economic benefit. RIKEN PSC2 is in a strong position to become the leading research center in Japan for agricultural innovation and food improvement. With the appointment of Director Shinozaki PSC has also established internal interactions with the BioResource Center (BRC) at Tsukuba Institute. BRC is an important strategic link for RIKEN to provide research products to the international plant science community. Recommendation: The Advisory Council supports Director Shinozaki s decision to facilitate the transfer of basic research results into applied crop biotechnology. This pipeline will require ongoing monitoring of activities to assure that the research remains focused on the longer-term goals of PSC2. Appropriateness of methodology for defined research To support the new focus on plant productivity improvement, PSC2 exploits the newest technologies and instrumentation. Already in PSC1 RIKEN plant scientists contributed high-throughput transcriptome data to the community (AtGeneExpress) that had high impact in gene discovery research. The decision of Director Shinozaki to expand research activities into metabolite analysis and proteomics are logical and consistent with the strategic plan. 9

10 Recommendation: The Advisory Council strongly supports the development of new methodologies, but also cautions that they must remain closely connected to the biological questions and applied problems. Uniqueness and effectiveness of the research method and management system (particularly regarding staff and budget) The strategic research goal of PSC2 to contribute to the improvement of plant productivity for more and better food and materials is consistent with the strategies of other nations who support leading plant research institutions. But PSC2 is in a unique position to develop integrated research and technology platforms that support basic discoveries and facilitate their transfer into applications. As a logical step to reach this goal, Director Shinozak has established a Director s Fund to support innovative research activities and investments into new technology platforms. He has also accomplished the transfer of the Plant Functional Genomics Group (PFG) from the Genomics Science Center to PSC. The PFG group under the leadership of Dr. Minami Matsui has an excellent record of research accomplishments that has provided the group a high international visibility. The technology platform and functional genomics tools that have been developed by the PFG group will become a cornerstone of the PSC strategic plan and provide critical support to the PSC research groups. The Advisory Council therefore supports Director Shinozaki s decision to integrate the PFG group into PSC2 and to allocate PSC2 funds to establish new technology platforms. At the same time the Advisory Council is concerned about the erosion of the PSC2 budget, which has significantly decreased compared to the funding that was available for PSC1. The increase in funding for 2006 essentially reflects the transfer of funds for the PFG group, but not new money to support strategic initiatives. The available budget requires tight management of resources and competitive allocation of research funds. Recommendation: The Advisory Council supports Director Shinozaki s decision to establish a Director s Fund. This discretionary fund should be invested into new strategic initiatives and used for the development of technology platforms to achieve the stated goals. The Advisory Council also strongly supports the transfer of the PFG group to the PSC, as this adds important research and technology capacities to reach strategic goals. Summary Under the guidance of Director Shinozaki and together with the RIKEN leadership, PSC2 can realize the vision of an organization with a strong international reputation for excellence as Japan s leader in plant research. The Advisory Council is convinced that PSC2 is on the right track and looks forward to review the implementation of the longterm strategic research plan and progress towards the 5-year goals during its next meeting. 10