At KEPLR, we host seminars aimed at fostering connections among participants from our partner research labs. The first seminar was organized by HigashiyamaG and took place at the University of Tokyo Hongo Campus. Following the seminar, a tour of the research facilities was conducted for the attendees.

日経新聞に、清水健太郎教授の寄稿記事が掲載されました。
An article contributed by Professor Kentaro Shimizu was published in the Nikkei newspaper. (May 16, 2023).

A seminar by Professor Wolf B. Frommer is being held at the University of Tokyo 'Biological Science Seminar'

Prof. Wolf B. Frommer（ITbM, Nagoya University; Heinrich Heine University, Düsseldorf; Max Planck Institute for Plant Breeding Research, Cologne）

1470th Biological Science Seminar / Dec. 8, 2023

We have worked on key questions regarding the uptake and distribution of nutrients and signaling molecules in plants with an emphasis on transport processes. These involve highly specialized proteins that are embedded into the cell membranes and interact with their substrates to move them in or out of the cells or to neighboring cells. In plants this also involves a unique and highly complex structure, the plasmodesmata which consist of multiple membranes with properties similar to size exclusion chromatography systems. My lab identified many of the key transporter genes in plants (ammonium, urea, ureides, amino acids, sucrose (SUTs and SWEETs) and is studying their role and regulation. My lab also developed genetically encoded Förster Resonance Energy and Matryoshka sensors that enable quantification of the dynamics of metabolites and hormones, as well as the activity of transporters in vivo. Along the way we discovered that pathogens hijack the sugar transport systems, and through genome editing, we can prevent multiplication of bacterial blight-causing bacteria and blast causing fungi and are now at the point that we can provide resistant elite varieties to India and Kenya. These discoveries were only possible through interdisciplinary approaches and increasingly involve chemistry: 1. Implementation of covalent protein labeling (SNAP tagging) in plants to enable studies of transporter endocytosis, and ultimately to generate hybrid sensors that include chemical reporters. 2. Characterization of the selectivity of transporters using MD simulations- why a transporter can recognize a lot of compounds but does not necessarily use them. 3. The use of synthetic hormone analogs together with modified hormone receptors to control hormone signals by chemicals in specific cell types. 4. Screens of chemical libraries to identify transport inhibitors as potential new pesticides
References:
1. Luu et al (2023) eLife in press; 2. Isoda et al (2022) PNAS 119: e2207558119; 3. Iwatate et al (2020) Plant Cell 32:3081-3094; 4. Ast et al (2017) Nat Commun 8:431; 5. Latorraca et al (2017) Cell 169, 96-107; 6. Jones et al (2014) eLife 3: e01741; 7. Ho et al (2014) eLife 3: e01917; 8. Lanquar et al (2014) New Phytol 202:198-208; 9. De Michele et al (2022) eLife 2: e00800; 10. Chen et al (2012) Science 335: 207-211; 11. Kaper et al. (2007) PLoS Biol 5:e257; 12. Loqué et al (2007) Nature 446, 195198. 13. Fehr et al (2002) PNAS 99, 9846-9851.

Prof. Benjamin Podbilewicz（Department of Biology, Technion - Israel Institute of Technology）

2023年09月05日(火) 13:30-15:00 理学部2号館223号室及びZoom

Fusion between gametes is essential for sexual reproduction. It is widely accepted that sex is an ancient trait of eukaryotes and was probably present in their last common ancestor. Archaea (prokaryotes without nuclei) are the progenitors of the eukaryotic nucleocytoplasm and current evidence suggests that cell fusion probably originated in archaea. Indeed, sex-like exchange of genetic material via fusion is known to occur in archaea from the Dead and Mediterranean seas. These archaea can form cytoplasmic bridges visible by electron microscopy that then enable large-scale eukaryotic-like recombination. However, neither molecular nor cellular mechanisms of cell fusion have been described in archaea. A few types of protein machineries that are both necessary and sufficient to fuse eukaryotic cells (fusogens) have been identified and studied. Our lab discovered the first two, EFF-1 and AFF-1 from C. elegans, that are now known to be a member of a diverse protein family1,2. In eukaryotes, sexual reproduction depends on the GCS1(HAP2) plasma membrane protein that is necessary in plants and protists for gamete fusion3,4. GCS1 is related to class II viral glycoproteins (e.g. from Zika and Dengue viruses) and have structural and functional similarity to fusion proteins from animals (e.g. EFF-1 and AFF-1)5-8. We named this family of fusogens from gametes, enveloped viruses, and somatic cells Fusexins: fusion proteins essential for sexual reproduction and exoplasmic merger of plasma membranes6. More recently we found fusexins in archaea and determined the crystal structure of the prokaryotic Fsx19. Moreover, Fsx1 can fuse heterologous mammalian cells demonstrating that they are fusogens9. To understand the origin of eukaryotic sexual reproduction we study the functions and evolutionary history of Fsx1 and we also found that the mouse sperm adhesion protein IZUMO110 is also a fusogen that is unrelated to fusexins11. Thus, different families of fusogens can fuse gamete plasma membranes essential for sexual reproduction, using different mechanisms.
References:
1. Mohler et al (2002) Dev Cell 2(3):355–362; 2. Sapir et al (2007) Dev Cell 12(5):683–698; 3. Mori et al., (2006) Nat Cell Biol 8(1):64–71; 4. Johnson et al., (2004) Genetics 168(2):971–98; 5. Perez-Vargas et al., (2014) Cell 157, 407-419; 6. Valansi, Moi et al (2017) J Cell Biol 216(3):571–581; 7. Fedry et al (2017) Cell 168(5):904-915.e10; 8. Pinello et al (2017) Curr Biol 27(5):651–660; 9. Moi, Nishio. Li. et al. (2022) Nat Commun. 13: 3880; 10. Inoue et al., (2005) Nature 434: 234–238; 11. Brukman, Nakajima et al. (2023) J Cell Biol 222 (2): e202207147

Contact： Higashiyama Lab 生物科学専攻・東山研究室

清水健太郎　教授（チューリッヒ大学進化生物学・環境学研究所）

2023年01月06日(金) 17:05-18:35 Zoomによるweb講義

倍数体種は野生植物にも栽培植物にも多くみられ、その長所と短所は長く議論されてきた。これまでよく研究されてきたのは、一方で古代ゲノム重複であり、もう一方は合成倍数体にしばしばみられるゲノムワイドな遺伝子発現やエピゲノムの変化であり、大規模な変化は「ゲノムショック」と呼ばれてきた。しかしゲノムの複雑さのため、倍数体種のゲノムレベルの解析は遅れていた。近年、ゲノミクスの進歩に加え、野外環境in naturaでの機械学習を用いた植物画像解析などの進歩により、倍数体種の長所と短所が分子レベルから明らかになってきた。まず、倍数体種のRNA-seq解析や野外画像解析から、両親種の環境応答を受け継いで組み合わせることにより、倍数体種が広い環境に適応する能力、つまり環境頑健性を得たことが示唆された。また、コムギ10+ゲノムプロジェクトやシロイヌナズナ属倍数体ミヤマハタザオなどを用いたDNA多型解析から、両親から多型を受け継ぎ、同祖遺伝子による突然変異頑健性によって進化可能性が高まったことが示唆された。どちらも、倍数体化以前に二倍体種で蓄えられた環境適応や多型を組み合わせることが倍数体化の重要な長所であることを示唆する。言い換えれば、倍数体の特徴は、ゲノムショックなどの突然のゲノムワイド変化ではなく、環境適応などに貢献する比較的少数の遺伝子群の組みあわせによると考えられる。このことは倍数体の長所を他種に移す合成生物学的アプローチの可能性を拓く。

参考文献
Akiyama et al. PlantServation: time-series phenotyping using machine learning revealed seasonal pigment fluctuation in diploid and polyploid Arabidopsis. bioRxiv, https://doi.org/10.1101/2022.11.21.517294, 2022
Shimizu, K.K. Robustness and the generalist niche of polyploid species: genome shock or gradual evolution? Current Opinion in Plant Biology, 69: 102292.
Walkowiak et al. Multiple wheat genomes reveal global variation in modern breeding. Nature, 588, 277–283, 2020.

担当：　東京大学大学院理学系研究科・生物科学専攻・発生細胞生物学研究室