Kazuki Saito

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Short Biography

Professor Kazuki Saito graduated from the Faculty of Pharmaceutical Sciences, the University of Tokyo, Japan, in 1977, and then obtained his Ph.D. for bio-organic chemistry/biochemistry from the University of Tokyo in 1982. After staying at Keio University in Japan and Ghent University in Belgium (Prof. Marc Van Montagu’s laboratory), he became a faculty member at the Graduate School of Pharmaceutical Sciences, Chiba University, Japan. There he has been appointed as a full professor from 1995 until 2020. He is currently entitled as a Professor Emeritus at Chiba University and holds the part-time Director position at Plant Molecular Science Center. Since April 2005, he has been additionally appointed as a group director at RIKEN Plant Science Center, currently at RIKEN Center for Sustainable Resource Science (CSRS), to direct Metabolomics Research Group. Since April 2020, he also holds the post of Director of the RIKEN CSRS. He was awarded The Medal with Purple Ribbon by Japanese Government; The Prize for Science and Technology by the Minister of Education, Culture, Science and Technology, Japan; JSPP Award by the Japanese Society of Plant Physiologists; The Pharmaceutical Society of Japan Award; and Lifetime Honorary Fellowship of The Metabolomics Society. He has been selected one of ‘Highly Cited Researchers’ in the 'Plant & Animal Science' field for 2014-2020, and an ASPB Top Author. His research interests are metabolome-based functional genomics, biochemistry, molecular biology and biotechnology of primary and secondary metabolism in plants. In particular, he is engaging in the biosynthetic studies of sulfur compounds, flavonoids, terpenoids and alkaloids by means of metabolomics. He further pursues the establishment of a new field of 'Sustainable Resource Science'.

Expert Opinion

1. When and why did you start using metabolomics in your investigations?

The initiation of my metabolomics research goes back to the late 1990s. That time was just the dawn of the coming genomic era. The draft assembly of the human genome was just going on from 1991, expecting the completion by the new millennium. In the plant science field, the international team was tackling the genome sequencing of a model plant species, Arabidopsis thaliana. We, plant scientists, were all very enthusiastic about completing the first revealed genome sequence of a plant species. As the consequence of the genome sequence, one can easily expect tremendous progress in holistic gene expression (transcriptomics) and protein accumulation (proteomics), since these pieces of downstream biological information can be deduced from the genome by the Central Dogma of molecular biology. However, the study on the entire accumulation of metabolites (metabolomics) is not necessarily straightforward as transcriptomics and proteomics even after decoding the genome sequence. From the early days of my scientific career, I have been so much fascinated with the chemical diversity of plants – why and how those diversified chemical compounds are synthesized in plants. To address these grand questions, before the completion of genome sequencing of A. thaliana in 2000, I was fully convinced that I should start plant metabolomics research, which looked like a promising new research area in the post-genome era worth challenging. I dreamed that we would connect each gene in the genome to each metabolite in a one-by-one manner in the genome-decoded A. thaliana. Fortunately, at the same time, in 2000, Japan Science Technology Agency (JST) called proposals for a large-amount grant (CREST) specifically for plant science. I have applied a multi-omics research proposal on model plants (Arabidopsis and rice) to this call together with several expert colleagues. Our proposal was luckily accepted, and we got started the metabolomics-based functional genomics project in 2000. In 2001, I organized the first international plant metabolomics symposium entitled 'Metabolomics Approach in Plant Functional Genomics in the Post-genome Eras' in Kisarazu, Chiba, Japan. Invited speakers included Lothar Willmitzer, Rick Dixon, Dirk Inze, Kirsi-Marja Oksman-Caldentey, Malcolm Hawkesford, and Dayan Goodenowe.

2. What have you been working on recently?

Our group has been dealing with functional genomics in A. thaliana through the integration of genomics, transcriptomics, and metabolomics. Omics-data have been acquired from Arabidopsis plants under a variety of conditions: ectopically expressed of regulatory and key metabolic genes, subjected to abiotic stresses (drought, heat, and nutrition depletion), or of natural variants. From those omics data, we can generate hypotheses regarding the relations of genes/transcripts to metabolites. These testable hypotheses can be validated by the reverse genetics approach in Arabidopsis, thanks to the availability of research resources such as a panel of knockout lines of almost all genes, the full-length cDNA collections, and bioinformatics tools. Two recent examples of such studies are published in the papers for the identification of a heat-mitigating gene (Higashi et al., 2018) and biosynthetic genes for seed-protective neolignane (Yonekura-Sakakibara et al, 2021). We are also exploring the metabolomics of major crops, e.g., rice, soybean, and tomato. These crop investigations aim to elucidate genes' function, metabolic physiology for crop performance, and evaluation of biotechnological modification. The metabolomic study of medicinal plants is another main subject of our research. What we are looking forward to is not only the identification of novel bioactive metabolites but functional identification of genes or genome regions for the production of medicinal compounds in given medicinal plants, as exemplified in the latest paper (Rai et al., 2021). Technology development of metabolomics is also one of the major topics of our research group. The combination of utilizing fully stable-isotope-labeled plant materials and cutting-edge chemoinformatics is a powerful strategy for reliable annotation of LC-MS-based plant metabolomics (Tsugawa et al., 2019). If imaging mass spectrometry is applied, new findings on metabolite accumulation and biosynthetic consideration can be obtained (Nakabayashi et al., 2020).

• Yasuhiro Higashi, Yozo Okazaki, Kouji Takano, Fumiyoshi Myouga, Kazuo Shinozaki, Eva Knoch, Atsushi Fukushima, Kazuki Saito: HEAT INDUCIBLE LIPASE1 remodels chloroplastic monogalactosyldiacylglycerol by liberating α-linolenic acid in Arabidopsis leaves under heat stress. Plant Cell., 30, 1887-1905, doi: 10.1105/tpc.18.00347 (2018) • Keiko Yonekura-Sakakibara, Masaomi Yamamura, Fumio Matsuda, Eiichiro Ono, Ryo Nakabayashi, Satoko Sugawara, Tetsuya Mori, Yuki Tobimatsu, Toshiaki Umezawa, Kazuki Saito: Seed-coat protective neolignans are produced by the dirigent protein AtDP1 and the laccase AtLAC5 in Arabidopsis. Plant Cell, in press, https://doi.org/10.1093/plcell/koaa014 (2021) • Amit Rai, Hideki Hirakawa, Ryo Nakabayashi, Shinji Kikuchi, Koki Hayashi, Megha Rai, Hiroshi Tsugawa, Taiki Nakaya, Tetsuya Mori, Hideki Nagasaki, Runa Fukushi, Yoko Kusuya, Hiroki Takahashi, Hiroshi Uchiyama, Atsushi Toyoda, Shoko Hikosaka, Eiji Goto, Kazuki Saito, Mami Yamazaki: Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis: Nature Commun., in press, https://doi.org/10.1038/s41467-020-20508-2 (2021) • Hiroshi Tsugawa, Ryo Nakabayashi, Tetsuya Mori, Yutaka Yamada, Mikiko Takahashi, Amit Rai, Ryosuke Sugiyama, Hiroyuki Yamamoto, Taiki Nakaya, Mami Yamazaki, Rik Kooke, Johanna A. Bac-Molenaar, Nihal Oztolan-Erol, Joost J.B. Keurentjes, Masanori Arita, Kazuki Saito: A cheminformatics approach to characterize metabolomes in stable-isotope-labeled organisms. Nature Methods, 16, 295–298, https://doi.org/10.1038/s41592-019-0358-2 (2019) • Ryo Nakabayashi, Tetsuya Mori, Noriko Takeda, Kiminori Toyooka, Hiroshi Sudo, Hiroshi Tsugawa, Kazuki Saito: Metabolomics with 15N labeling for characterizing missing monoterpene indole alkaloids in plants. Anal. Chem., 92, 5670-5675 https://doi.org/10.1021/acs.analchem.9b03860 (2020)

3. As one of the pioneers in the field of plant metabolomics, what are the main challenges for developing high-throughput analytical techniques for plant metabolomics?

As repeatedly mentioned in the scientific community, the biggest challenge in plant metabolomics is still metabolites' peak annotation. While a significant improvement in reliable peak annotation has been achieved by a magnificent effort of the community, mostly by the chemo/bioinformatic specialists working with experimental biologists, there is still room for advancements in the annotation of unknown metabolites, which is required prior to unequivocal identification of those peaks with synthetic or natural standard compounds. However, if you adopt the fully 13C-labelled plant materials, which are readily available for certain plant species by growing plants under a 13C-CO2 atmosphere or 13C-glucose as the sole carbon source, annotation reliability is dramatically improved. Collection of standard mass spectra of plant products in non-profit public databases, such as MassBank <http://www.massbank.jp/>, should be continued by a community effort for the better peak annotation without any obstacles. To maximize the coverage of chemical space by metabolomic analysis, metabolite analysis is often carried out by a combination of multiple mass-spec platforms in parallel, e.g., GC-MS, LC-MS (polar and non-polar), and CE-MS (positive and negative). Integration of metabolomics data from such multiple platforms is also challenging. Related to this point, absolute quantification of known metabolites is also highly required to obtain deeper insights into plant metabolic physiology under a given condition.

4. What are the main obstacles for integrating metabolomics and genomics?

The speed, quality, and price of genome sequencing have been dramatically improved in the last few years, thanks to the development of new technology. We can expect a substantial number of diversified plant genomes are decoded in the coming years. Sequence diversification obtained by such studies is not only of a species-wide but natural-variant-wide with species- or variant-specific metabolite patterns. By integrating such diversified genome information with precise metabolomics, we will be able to find novel associations of genes to metabolites in a relatively easy manner. These associations provide excellent hints for the function of genes responsible for the production of specific metabolites. However, to verify the genes' function to produce specific metabolites, a reverse genetics approach with loss-of-function and gain-of-function experiments must be taken. While a great advancement has been seen in gene-editing technology represented by CRISPER/Cas9 system in the last several years, experimental protocols for each plant must still be established, in particular, in non-model plants (most of the medicinal plants and some local crops). These tissue-culture-based studies are a kind of tedious works with repeated trials and errors. From a physiological viewpoint, the accumulation of plant metabolites is highly cell-type specific, and the sites of storage are often different from those of biosynthesis. Therefore, a highly sophisticated transport mechanism is well organized for the efficient storage of plant metabolites. The insights on this transport/localization issue are not necessarily easily obtained from the genomics lying some gaps but not in a straightforward manner. We need to take biochemical and physiological approaches to tackle this issue.

5. How do you think the understanding of plant metabolism through genomic and post-genomic approaches can be applied into healthcare?

To answer this question, we have to consider two different folds – direct application or indirect application into healthcare. Understanding of plant metabolism can be directly applied to human healthcare through medicines. In human history, humankind has received a tremendous benefit from novel plant products for curing and preventing diseases. One of the best representative examples is the finding of artemisinin from Artemisia annua as an anti-malaria agent, which was laureated as The Nobel Prize in Physiology and Medicine of 2015. In fact, Royal Botanical Garden Kew Report in 2016 <https://stateoftheworldsplants.org/2016/> says the largest number of plant species used in each category is for medicines over food, materials, and others. However, mankind has investigated only a small part of the huge chemical diversity of all plant species on earth. There are still hidden rich veins of gold of medicinal compounds in unexplored plant species. Genomics and metabolomics should be an excellent way to mine those hidden gold veins for our future healthcare. Indirectly, knowledge of plant metabolism can be applied to healthcare through nutritious and sustainable food, which is owed to the sustainable and resilient production of crops under environmental stresses. Besides food security, a decrease in the level of greenhouse gas, CO2, also depends on the metabolic activity of plants to some extent. These global issues, such as hunger and climate crisis connected to human healthcare, are all concerned with plant metabolism consequently. The study on plant metabolism thus takes a huge responsibility for keeping our planet sustainable and humanity improved.

6. What would your advice be for early career researchers working in the field of plant metabolomics?

The field of plant metabolomics is really an open area – still, a lot of secrets await to be discovered. Without any doubt, you can be fully convinced that the study on plant metabolomics is worthwhile to be enthusiastic about. I hope you can join us to take an endeavor!

See also