Biology subjects

Hasebe, M.

Publications and source records attributed to Hasebe, M..

5 recordsLinked to original sources

bioRxiv2025

A moss N-Acetyltransferase-MAPK protein controls 2D to 3D developmental transition via acetylation and phosphorylation changes

Post-translational modifications (PTMs) finetune plant responses to developmental and environmental cues by impacting protein activity, stability, localization and interaction landscape. In this study we identified a moss specific protein which combines two common PTMs: acetylation and phosphorylation. This protein originated from the fusion of a MAPK with an N-acetyltransferase, for which we named it Rosetta NATD-MAPK 1 (RAK1). Using biochemical methods, we demonstrated that RAK1 has acetyltransferase activity that is enhanced by activation of its MAPK domain. Phenotypical studies of rak1 knockout mutants revealed a role for RAK1 in the regulation of the 2D-to-3D growth transition. Through Mass Spectrometry we verified that defective 2D-to-3D transition in the mutants was caused by differentially regulated acetylation and phosphorylation events associated to metabolic reprogramming and 3D differentiation. Collectively, this study uncovers a previously unknown multidomain protein and provides insights into the interplay of PTMs during developmental reprogramming. TeaserAcetylation and phosphorylation changes modulate the 2D to 3D developmental transition in Physcomitrium patens.

plant biology↗

bioRxiv2022

Chemical screen of Arabidopsis zygote and proteomics in tobacco BY-2 cells identify general plant cell division inhibitors

Cell division is essential for growth and development and involves events such as spindle assembly, chromosome separation, and cell plate formation. In plants, the tools used to control these events at the desired time are still poor because the genetic approach is ineffective owing to a high redundancy and lethality, as well as harmful side effects. Accordingly, we screened cell division-affecting compounds, with a focus on Arabidopsis thaliana zygotes, which individually develop in maternal ovules; the cell division was reliably traceable without time-lapse observations. We then identified the target events of the identified compounds using tobacco BY-2 cells for live-cell imaging and proteomics. As a result, we isolated two compounds, PD-180970 and PP2. PD-180970 disrupts microtubule (MT) organization and, thus, nuclear separation, presumably by inhibiting MT-associated proteins (MAP70). PP2 affected class II Kinesin-12 localization at the phragmoplast emerging site and impaired cytokinesis. Moreover, neither chemical caused irreversible damage to viability but they were effective in multiple plant species such as cucumber (Cucumis sativus) and moss (Physcomitrium patens). We propose that the combination of chemical screening based on Arabidopsis zygotes and target event specification focusing on tobacco BY-2 cells can be used to effectively identify novel tools and transiently control specific cell division events that are conserved in diverse plant species.

plant biology↗

bioRxiv2022

Genome sequence of 12 Vigna species as a knowledge base of stress tolerance and resistance

Harnessing plant genetic resources including wild plants enables exploitation of agronomically unfavorable lands to secure food in the future. The genus Vigna, family Fabaceae, consists of many species of such kind, as they are often adapted to harsh environments including marine beach, arid sandy soil, acidic soil, limestone karst and marshes. Here we report long-read assemblies of 12 Vigna species, achieving 95% or higher BUSCO scores. The comparative analyses discovered a new class of WUSCHEL-related homeobox (WOX) transcription factor superfamily that are incorporated into LTR retrotransposons and have dramatically amplified in some species of the genus Vigna. Except WOX transcription factors, however, gene contents are highly conserved among Vigna species with few copy number variations. On the other hand, transcriptome data provided some insights that transcriptional alterations played more important roles in evolution of stress tolerance in the genus Vigna. The whole genome sequences presented in this study will facilitate understanding genetic mechanisms of stress tolerance and application for developing new crops that are adapted to unfavorable environments.

genomics↗

bioRxiv2020

Chloroplast acquisition without the gene transfer in kleptoplastic sea slugs

Some sea slugs sequester chloroplasts from algal food in their intestinal cells and photosynthesize for months. This phenomenon, kleptoplasty, poses a question of how the chloroplast retains its activity without the algal nucleus. There have been debates on the horizontal transfer of algal genes to the animal nucleus. To settle the arguments, this study reported the genome of a kleptoplastic sea slug Plakobranchus ocellatus and found no evidence of photosynthetic genes encoded on the nucleus. Nevertheless, it was confirmed that light illumination prolongs the life of mollusk under starvation. These data presented a paradigm that a complex adaptive trait, as typified by photosynthesis, can be transferred between eukaryotic kingdoms by a unique organelle transmission without nuclear gene transfer. Our phylogenomic analysis showed that genes for proteolysis and immunity undergo gene expansion and are up-regulated in chloroplast-enriched tissue, suggesting that these molluskan genes are involved in the DNA-independent phenotype acquisition.

evolutionary biology↗

bioRxiv2018

Single-cell transcriptome analysis of Physcomitrella leaf cells during reprogramming using microcapillary manipulation

BackgroundNext-generation sequencing technologies have made it possible to carry out transcriptome analysis at the single-cell level. Single-cell RNA-sequencing (scRNA-seq) data provide insights into cellular dynamics, including intercellular heterogeneity as well as inter- and intra-cellular fluctuations in gene expression that cannot be studied using populations of cells. The utilization of scRNA-seq is, however, restricted to specific types of cells that can be isolated from their original tissues, and it can be difficult to obtain precise positional information for these cells in situ.\n\nResultsHere, we established single cell-digital gene expression (1cell-DGE), a method of scRNA-seq that uses micromanipulation to extract the contents of individual living cells in intact tissue while recording their positional information. Furthermore, we employed a unique molecular identifier to reduce amplification bias in the cDNA libraries. With 1cell-DGE, we could detect differentially expressed genes (DEGs) during the reprogramming of leaf cells into stem cells in excised tissues of the moss Physcomitrella patens, identifying 6,382 DEGs between cells at 0 h and 24 h after excision. We found substantial variations in both the transcript levels of previously reported reprogramming factors and the overall expression profiles between cells, which appeared to be related to their different reprogramming abilities or the estimated states of the cells according to the pseudotime based on the transcript profiles.\n\nConclusionsWe developed 1cell-DGE with microcapillary manipulation, a technique that can be used to analyze the gene expression of individual cells without detaching them from their tightly associated tissues, enabling us to retain positional information and investigate cell-cell interactions.

plant biology↗