International Webinar Series ”From Cellular Dynamics to Morphology”

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Fri 27. Nov. 17:00-19:00 JST (UTC+9)
Chair: Keiji Nakajima (NAIST)The last step is the hardest – lignin and suberin formationin the cell wall
Niko Geldner (University of Lausanne)

Chair: Motomu Endo (NAIST)

Mechanisms of auxin-regulated lateral root formation
Hidehiro Fukaki (Kobe University)

Tue 8. Dec. 10:00-12:00 JST (UTC+9)
Chair: Hirokazu Tsukaya (Univ Tokyo)

Orienting asymmetric divisions in the Arabidopsis epidermis
Dominique Bergmann (Stanford University)

Chair: Takashi Ueda (NIBB)

Spatiotemporal dynamics of axis formation in Arabidopsis embryos
Minako Ueda (Tohoku University)

Fri 11. Dec. 17:00-19:00 JST (UTC+9)
Chair: Atsushi Mochizuki (Kyoto Univ)

Human time vs. Mouse time with recapitulated systems
Miki Ebisuya (EMBL Barcelona)

Chair: Minako Ueda (Tohoku Univ)

Actual time-series of single-cell transcriptomics reveals circadianclocks as key regulators of cell differentiation in Arabidopsis
Motomu Endo (NARA Institute of Science and Technology)

1International Webinar Series ”From Cellular Dynamics to Morphology”

Tue 15. Dec. 17:00-19:00 JST (UTC+9)
Chair: Takayuki Kohchi (Kyoto Univ)

Convergence of cell polarity stems across multicellular kingdoms
Dolf Weijers (Wageningen University)

Chair: Hidehiro Fukaki (Kobe Univ)

Molecular basis of cell wall patterning in xylem vessels
Yoshihisa Oda (National Institute of Genetics)

Thu 17. Dec. 10:00-12:00 JST (UTC+9)
Chair: Motomu Endo (NAIST)

Painting chromosomes at the nanoscale: a preview
into the internal genome organization
Hiroshi Sasaki (Harvard University)

Chair: Takayuki Kohchi (Kyoto Univ)

How plants acquired new organelles -Lessons from Marchantia
Takashi Ueda (National Institute for Basic Biology)

Mon 21. Dec 17:00-19:00 JST (UTC+9)
Chair: Hidehiro Fukaki (Kobe Univ)

Evolution and functional regulation of plant glutamate receptors
José Feijó (University of Maryland)
Chair: Yoshihisa Oda (NIG)

Regulation of sexual reproduction and sex differentiationin gametophyte generation
Takayuki Kohchi (Kyoto University)2International Webinar Series ”From Cellular Dynamics to Morphology”

Nov. 27 (Fri) 17:00-19:00 JST; 9:00-11:00 CETThe last step is the hardest - lignin andsuberin formation in the cell wall
Niko Geldner
University of Lausanne
Lignin and suberin are omnipresent polymers, used by humans since the dawn ofcivilisation. They are the defining components of wood and cork, but the occurrence andimportance of these two polymers is much more widespread and diverse. This isespecially evident for the overall little amount of lignin and suberin deposited in the root
endodermis, where absence of lignified Casparian strips or suberised secondary cell walls
has a profound impact on root permeability and stress resistance. Beyond its direct
physiological importance, the endodermis is therefore an interesting model system tostudy the cell biology of lignification and suberisation. A protracted problem in lignin andsuberin research have been the crucial last steps of monomer delivery to, andpolymerisation within, the cell wall. Here, I will report on our efforts to generate highorder CRISPR/Cas9-induced mutants of suberin and lignin biosynthetic enzymes, which
provide strong evidence for the function of GDSL lipases and peroxidases in suberin andlignin polymerisation, respectively. I will also describe overlooked subcellular structuresthat are strongly associated with suberin deposition in the endodermis and could be
involved in delivery of suberin precursor to the cell walls.

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International Webinar Series ”From Cellular Dynamics to Morphology”

Nov. 27 (Fri) 17:00-19:00 JST; 9:00-11:00 CET

Mechanisms of auxin-regulated lateralroot formation
Hidehiro Fukaki
Kobe University
In vascular plants, lateral root (LR) formation contribute to the establishment of the rootsystem architecture. In most eudicot plants, LR formation is initiated by asymmetric
division of LR founder cells in the xylem pole of the existing roots, followed bycoordinated cell proliferation and differentiation for patterning new LR primordia. The
sequential developmental processes of LR formation are triggered by a localized auxin
response. In Arabidopsis, LATERAL ORGAN BOUNDARIES‐DOMAIN 16 (LBD16),
an auxin-inducible transcription factor, is one of the key regulators linking auxin response
to LR initiation. We have identified the LBD16-regulated genes that positively or
negatively regulate LR formation. I will discuss recent results on the mechanisms of
auxin/LBD16-regulated LR initiation and lateral inhibition of LR founder cell formation.

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International Webinar Series ”From Cellular Dynamics to Morphology”

Dec. 8 (Tue) 10:00-12:00 JST; 7 Mon 17:00-19:00 PST

Orienting asymmetric divisions in the
Arabidopsis epidermis
Dominique Bergmann
Stanford University
The creation and organization of diverse tissues often relies on asymmetric cell divisions.
These divisions that create cells of different sizes and compositions can also be oriented
relative to other tissue landmarks. Using the Arabidopsis stomatal lineage, in which
multipotent progenitor cells undergo iterative rounds of asymmetric stem-cell likedivisions, we have delved into how subcellular reorganization of the cytoskeleton, guided
by the polarity protein BASL, leads to oriented cell divisions. Through genetic
manipulations and quantitative imaging, we show how BASL acts with the actin andmicrotubule cytoskeletons before and after cell divisions to ensure the coordination ofdivision plane placement, the inheritance of polarity factors, and stem-cell proliferative
capacity.

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International Webinar Series ”From Cellular Dynamics to Morphology”

Dec. 8 (Tue) 10:00-12:00 JST; 7 Mon 17:00-19:00 PST

Spatiotemporal dynamics of axis
formation in Arabidopsis embryos
Minako Ueda
Tohoku University
Most flowering plants develop from a single-celled zygote. In Arabidopsis thaliana, theapical-basal body axis is initiated by asymmetric cell division of the polarized zygote,
which possesses the nucleus at the apical cell tip and large vacuoles at the basal end.
Despite the obvious asymmetry, the real-time dynamics of the zygote polarization steps
was poorly understood. By combining live-cell imaging system of the zygote with various
fluorescent reporters and specific inhibitors, we assessed the spatiotemporal dynamics ofintracellular structures during zygote polarization. For example, we recently found thatthe mitochondria associated with the longitudinal array of actin filaments and werepolarly distributed along the apical-basal axis. The mitochondria were then temporally
fragmented during zygotic division, resulting in unequal segregation into two daughter
cells. Based on these results, we would like to discuss various spatiotemporal regulations
underlying plant axis formation.

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International Webinar Series ”From Cellular Dynamics to Morphology”

Dec. 11 (Fri) 17:00-19:00 JST; 9:00-11:00 CET

Human time vs. Mouse time withrecapitulated systems
Miki Ebisuya
EMBL Barcelona
Different animal species have different tempos of development: larger species tend togrow more slowly than smaller species. My group has been trying to understand themolecular basis of this interspecies difference in developmental time, using thesegmentation clock as a model system.
The segmentation clock is the oscillatory gene expressions that regulate thetiming of body segment formation during early embryogenesis. We have recently
succeeded in recapitulating the segmentation clock from both human and mousepluripotent stem cells, detecting oscillations and traveling waves in vitro. Interestingly,
the oscillation period of human segmentation clock was 5-6 hours while that of mousewas 2-3 hours. Taking advantage of our in vitro system and simple mathematical models,
we have been comparing the genome sequences and molecular processes of thesegmentation clock between human and mouse to explain the interspecies difference inthe oscillation period.
Refs.
- Matsuda et al., “Species-specific segmentation clock periods are due to differential
biochemical reaction speeds”, Science, 369 (2020)- Matsuda et al., “Recapitulating the human segmentation clock with pluripotent stem
cells”, Nature, 580 (2020)7

International Webinar Series ”From Cellular Dynamics to Morphology”

Dec. 11 (Fri) 17:00-19:00 JST; 9:00-11:00 CET

Actual time-series of single-celltranscriptomics reveals circadianclocks as key regulators of celldifferentiation in Arabidopsis
Motomu Endo
NARA Institute of Science and Technology
The basis of toti/pluripotency is elaborate regulation of cell-cycle progression and cellfate determination. Circadian clocks are involved in this process, but the underlying
mechanisms have not been studied due to technical limitations. In particular, there is alack of research on the universality of cell differentiation mechanisms in multicellularorganisms using plants with high cell-fate plasticity. Here, exploiting in vivo single-cell
RNA sequencing and a new actual time reconstitution method, PeakMacth, we analyzed
actual time-series of cell reprogramming and differentiation processes at single-cellresolution, and found that the circadian clock modulates cell differentiation via BES1mediated GSK3 signaling, which has a β-catenin-like function in Arabidopsis. In thispathway, the clock gene LUX in meristematic stem cells directly targets the CYCD and
RETINOBLASTOMA-RELATED (RBR) genes, which are commonly involved in cellcycle progression and cell-fate determination in plants and animals. In addition, therhythmicity of the circadian clock was associated with cell state, and the establishment of
the circadian rhythm preceded cell differentiation. Thus, our study not only reveals theinvolvement of the circadian clock in the differentiation of plant stem cells but also
demonstrates functionally analogous features in the regulatory system of celldifferentiation across species.

8International Webinar Series ”From Cellular Dynamics to Morphology”

Dec. 15 (Tue) 17:00-19:00 JST; 9:00-11:00 CETConvergence of cell polarity stems
across multicellular kingdoms
Dolf Weijers
Wageningen University
Cells in multicellular organisms organise along body and tissue axes. Cellular processes,
such as division plane orientation, must be aligned with these polarity axes to generatefunctional 3-dimensional morphology, particularly in plants, where cell walls prevent cell
migration. While some polarly localized plant proteins are known, molecular mechanismsof polarity establishment or its translation to division orientation are elusive, in part
because regulators in animals and fungi appear to be missing from plant genomes. Cellpolarity is first established in the embryo, but this has long been an intractable
experimental model. In the past years, genetic and imaging tools have been developedthat allow using the early Arabidopsis embryo as a model for understanding themechanisms that drive cell polarity and oriented cell divisions, I will present our recent
work, focusing on the identification of a novel, deeply conserved polarity system.

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International Webinar Series ”From Cellular Dynamics to Morphology”

Dec. 15 (Tue) 17:00-19:00 JST; 9:00-11:00 CET

Molecular basis of cell wall patterningin xylem vessels
Yoshihisa Oda
National Institute of Genetics
Polarity establishment is essential for cellular development, behavior, and function. Yet,
how multiple polarity is initiated and organized in a cellular space is poorly understood.
Plant xylem vessel cells deposit cell walls in beautiful patterns such as annular, spiral,
reticulate, and pitted patterns, directed by multiple domains of microtubule array. We
revealed that the small G protein ROP is locally activated on the plasma membrane,disassembles microtubules, and thereby directs formation of pitted cell walls. The local
activation of ROP is cell-autonomously triggered through the action of ROP regulators.
Microtubules laterally confine the localization of ROP along the plasma membrane tofine-tune the shape of cell wall pits. We also found that ROP locally assembles actin
microfilaments to promote cell wall deposition specifically at the edge of cell wall pits.
We will discuss how multiple polarity is generated and transformed into the distinct cellwall pattern in xylem vessels.

10International Webinar Series ”From Cellular Dynamics to Morphology”

Dec. 17 (Thu) 10:00-12:00 JST; 16 Wed 20:00-22:00 ESTPainting chromosomes at thenanoscale: a preview into the internal
genome organization
Hiroshi Sasaki
Harvard University
Eukaryotic cells package a genome with a linear length of meters into a nucleus that is amere 10 µm in diameter. Despite this dramatic difference in length scales, theorganization of DNA within the nucleus is non-random and plays an important role inmany nuclear processes such as transcription, duplication, and repair. The recent
introduction of super-resolution chromatin imaging methods, in combination withfluorescence in situ hybridization (FISH), has transformed our view on basicorganizational features of the genome in individual cells. However, our mechanistic
understanding of how the genome works is far from complete due to technical limitations,
as it remains challenging to image chromatin on the order of tens of nanometers, a scalethat could reveal rich structural detail about the genome organization. We introduce arobust and multiplexed super-resolution FISH approach leveraging our super-resolution
imaging method called ‘DNA-PAINT’ and signal-amplification method ‘SABER’ forquantitative chromatin imaging at a spatial resolution close to the nucleosome scale witha simple and easy-to-implement optical set-up. We have applied our approach to sampling
the ultrastructure of the human X chromosomes. Contrary to the prevailing view that theinactive X chromosomes consist of facultative heterochromatin, we have found nodifference in the apparent compaction level between the active and inactive X
chromosomes. Our approach will enable researchers to perform a molecular-level
analysis of nuclear organization and architecture in individual cells that we expect to bebroadly applicable to a wide range of biological questions.

11International Webinar Series ”From Cellular Dynamics to Morphology”

Dec. 17 (Thu) 10:00-12:00 JST; 16 Wed 20:00-22:00 EST

How plants acquired new organelles Lessons from Marchantia
Takashi Ueda
National Institute of Basic Biology"The membrane trafficking system responsible for transporting proteins, lipids, andpolysaccharides plays pivotal roles in various plant functions including development,
defense responses, intercellular communication, and cell wall biogenesis. This system
involves evolutionarily conserved machinery components such as SNARE proteins,which execute membrane fusion between transport vesicles and destination membranes.
The number of genes for SNARE proteins has been increased during land plant evolution,
which should be associated with diversification of membrane trafficking pathways and/or
acquisition of new organelles. For insights into diversification of the membranetrafficking system during land plant evolution, we are conducting comparative analysesof membrane trafficking pathways between Arabidopsis thaliana and Marchantia
polymorpha. We systematically identified SNARE proteins in M. polymorpha, whose
expression patterns, subcellular localizations, and molecular functions were investigated.
We discovered that a SNARE member belonging to the SYP1 family, which generally
mediates membrane fusion at the plasma membrane (PM), localizes to the membrane ofa liverwort-specific organelle, the oil body, suggesting that the oil body membrane shares
similar properties with the PM. We also found that the luminal space of the oil body is
topologically equivalent to the extracellular space. These lines of evidence indicated thatthe oil body is formed by redirection of the secretory pathway from outward to inward
the cell. Furthermore, we identified a master regulator of oil body formation, under which
expression of a set of oil body-related factors including the SYP1 member are regulated.
We propose that the direction of the secretory pathway is periodically reoriented
depending on transition of cellular states in oil body cells, as observed in cell plate
formation in mitotic cells.

12International Webinar Series ”From Cellular Dynamics to Morphology”

Dec. 21 (Mon) 17:00-19:00 JST; 8:00-10:00 WET

Evolution and functional regulation ofplant glutamate receptors
José Feijó
University of Maryland
Ionotropic glutamate receptors (iGluRs) in the animal Central Nervous System are vitalfor high fidelity synaptic transmission. Glutamate, the principal neurotransmitter, binds
to an extracellular ligand-binding domain to open the transmembrane ion channel. Thisaction drives a depolarization of the postsynaptic membrane and promotes Ca2+; transport.
GLutamate Receptor-like channels (GLRs) are the plant homologs of iGluRs and are also
associated with electrical and Ca2+; signaling to participate in essential mechanisms,
including developmental processes, responses to (a)biotic stress, sexual reproduction, andsystemic signaling. The evolutionary relationship between iGluRs and GLRs was recently
verified, finding structural homology in the extracellular ligand-binding domain (LBD)— yet the structure-function relationships of GLRs are only emerging. I'll present anddiscuss data on the characterization of GLRs expressed in moss protonema andheterologous systems, demonstrating the requirements for functional ion channel
operation and the channel properties that distinguish GLRs from iGluRs. With astructurally conserved ligand-binding domain, albeit conferring different ligand-gating
properties, we show the GLR ion channel pore plays a direct role in ion channel gating
and ion selectivity. We further address the conservation of these properties in Arabidopsis
GLRs, and address the vexing problem created by the diversification and strong
expansion of GLRs in flowering plants. These results aim to enlighten the molecular
evolution of plant glutamate receptors shaping the ion channel properties that ultimately
conserve a role in Ca2+; and electrical signaling and have strong implications in ourcurrent interpretation and understanding of GLRs biological functions.

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International Webinar Series ”From Cellular Dynamics to Morphology”

Dec. 21 (Mon) 17:00-19:00 JST; 8:00-10:00 WETRegulation of sexual reproduction andsex differentiation in gametophyte
generation
Takayuki Kohchi
Kyoto University
Bryophytes occupy a basal position in the monophyletic evolution of land plants and havea life cycle in which the gametophyte generation dominates over the sporophyte
generation. We recently showed that BONOBO, a member of the bHLH transcription
factors regulates reproductive development including germ cell differentiation in theliverwort Marchantia polymorpha and generative cell specification in Arabidopsis. We
also reported that MpFGMYB shares functions in female gametophyte development withthe ortholog in Arabidopsis. As above, many orthologs of angiosperm transcription
factors play key roles in bryophyte sexual reproduction processes, including germline cell
specification and differentiation, gamete formation, and haploid-to-diploid transition,suggesting that the land plant reproductive systems has have conserved the core molecularmechanisms despite significant differences in morphology. In this seminar, we would also
like to discuss unique sex determination system mediated by cis-acting lncRNA and‘Feminizer’ encoded in the sex chromosome in M. polymorpha.

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