Biology subjects

Yoshimi, Y.

Publications and source records attributed to Yoshimi, Y..

10 recordsLinked to original sources

bioRxiv2026

Preserving Native Cellulose-Xylan Architecture Enables Structure-Property Control in Holocellulose Nanofibrils and High-Performance Sustainable Materials

The hierarchical organization of cellulose microfibrils and their intimate interactions with hemicelluloses such as xylan underpin the exceptional mechanical performance of plant cell walls. However, translating these biological design principles into sustainable nanocellulosic materials remains limited by conventional cellulose nanofibril production routes, which rely on harsh chemical treatments that disrupt the native cellulose-hemicellulose architecture. Here, we present an optimized isolation strategy for holocellulose nanofibrils (hCNFs) that preserves native cellulose structure, xylan substitution and conformation, and cellulose-xylan interactions. Using wild-type Arabidopsis thaliana, a xylan glucuronidation-deficient gux1/2 mutant, and Brassica napus straw as model systems, we systematically elucidate how xylan content and substitution pattern govern nanofibril isolation, interfacial interactions, and macroscopic properties. Two-dimensional 13C magic-angle spinning NMR demonstrates retention of native cellulose glucosyl environments, the presence of two-fold and three-fold helical xylan conformations, and cellulose-associated two-fold helical xylan. Cryogenic transmission electron microscopy reveals fibril widths of [~]3 nm, consistent with elementary cellulose I{beta} microfibrils. We show that xylan glucuronidation regulates colloidal stability, hydration behavior, and interfibrillar cohesion, whereas xylan content controls nanofibrillation efficiency. These multiscale structural features translate directly into moisture sorption, thermal behavior, and mechanical performance. Notably, Brassica napus hCNF films exhibit exceptional strength and extensibility, surpassing many chemically modified CNF systems. This work demonstrates that preserving the native cellulose-hemicellulose architecture enables high-performance, sustainable nanocellulosic materials without chemical reconstruction.

biochemistry↗

bioRxiv2025

An interplay between cytoplasmic flow and cell morphology during cytokinesis simulated by the moving-particle semi-implicit method

Cells are composite mechanical systems: a viscoelastic cytoplasm enclosed by a deformable cell cortex. These two components exchange forces continuously--fluid motion deforms the cortex, and cortical deformation in turn redirects intracellular flow. Yet most cellular mechanics simulations treat either the fluid or the cortex in isolation, leaving their mechanical interplay largely unexplored. To address this gap, we developed a fluid-structure interaction framework based on the moving-particle semi-implicit (MPS) method that solves the coupled dynamics of cytoplasmic flow, internal pressure, and cortical elasticity. We applied this framework to cytokinesis, focusing on how the cleavage plane is positioned. While the mitotic spindle is known to specify the furrow site, prior work has emphasized biochemical cues emanating from the spindle, whereas a direct mechanical cue has been difficult to interrogate. Our simulations show that spindle elongation generates cytoplasmic flows that create a pressure minimum near the spindle midzone; when the cortex is modeled as an elastic shell, this pressure landscape drives a localized cortical invagination at that site. We therefore propose that spindle-driven cytoplasmic flow provides a mechanical positional cue for cleavage-furrow initiation. Author SummaryDividing cells exhibit two contrasting properties: dynamic state changes and the maintenance of homeostasis. During cell division, a dividing cell breaks its identity while successful daughter cells inherit a certain set of its components for survival. Heterogeneous physical properties such as cell shape, cytoplasmic flow, and internal pressure interact to maintain an appropriate range of cellular conditions. The interaction of such physical components is highly dynamic; therefore, simulation studies play an important role in understanding the mechanisms. We constructed a model based on the moving-particle semi-implicit method that recapitulates the behavior of highly dynamic physical objects such as cytoplasmic fluid with practical computational time. The simulation showed that the change in cell shape is caused by internal cell pressure, which is evoked by cytoplasmic flow during elongation of spindle microtubules. The developed simulation platform provided a tool to integrate physical measurements to understand the mechanisms that balance physical dynamics during cell division. Such quantitative simulation combined with the data from molecular or genetic experiments may predict how internal dynamics maintain homeostasis during drastic changes in the cell state.

systems biology↗

bioRxiv2025

GT61 β-1,2-xylosyltransferases define a conserved xylan modification in gymnosperm and Arabidopsis primary cell walls

Plant primary and secondary cell walls differ in molecular composition, structure, and mechanical properties. While secondary wall xylan has been extensively characterised, the structure of xylan in primary walls remains less well understood, particularly in gymnosperms. Here, we identify a previously uncharacterised {beta}-1,2-linked xylosyl side chain in conifer and Arabidopsis thaliana xylan. Using enzymatic fingerprinting, NMR, and mass spectrometry, we show that this structure is positioned two xylose residues away from glucuronic acid substitutions, forming an evenly patterned substituted xylan. This spacing pattern is consistent with xylan-cellulose interaction, suggesting a structural role in primary wall architecture. This modification, found in primary wall-rich tissues of diverse conifer species, including needles and pro-embryogenic mass (PEM), is also present in Arabidopsis callus. We demonstrate that conifer Group III GT61 glycosyltransferases introduce this modification with consistent positional specificity. In Arabidopsis, three closely related GT61 enzymes act redundantly to generate the same structure, and their combined loss results in its complete absence. These findings uncover a conserved primary wall xylan modification in seed plants and define the GT61 enzymes responsible for its biosynthesis, opening new avenues to explore how xylan structure contributes to primary wall function. Significance StatementXylan structure is well characterised in secondary walls, but its primary wall counterpart remains poorly understood. We identified a conserved {beta}-1,2-xylosyl modification on xylan in the primary walls of conifers and Arabidopsis. This side chain is positioned at a defined position from a glucuronic acid substitution and is introduced by GT61 glycosyltransferases that cluster in one phylogenetic subclade. Our findings revealed a previously unrecognised xylan structural pattern and the biosynthetic enzymes responsible for its addition. This work expands the current understanding of primary wall architecture across seed plants.

plant biology↗

bioRxiv2025

Atypical endo-β-1,4-mannannases are necessary for normal glucomannan synthesis in Arabidopsis

The molecular mechanisms underlying the synthesis of large cell wall polysaccharides in plant cells are not fully understood. Here we report that two atypical endo-{beta}-1,4-mannanases (MANs), which are not secreted and do not degrade glucomannan in the cell wall, play a novel role in glucomannan synthesis. Among the six MANs in Arabidopsis, AtMAN2 and AtMAN5 contain a transmembrane domain at their N-terminal region instead of a signal peptide. Subcellular localization using MAN protein fused with fluorescent protein demonstrated that AtMAN2 localizes to the endomembrane system including the Golgi apparatus in xylem and interfascicular fiber cells. We found that an Arabidopsis man2 man5 double mutant lost 65% of glucomannan in the cell walls of the inflorescence stem. Immunostaining and immunoelectron microscopic observation also revealed that the man2 man5 double mutant lost glucomannan in the cell walls to about the same extent as the csla2 csla9 double mutant, which lacks major glucomannan synthases. Gene complementation experiments showed that the enzymatic activities of AtMAN2 and AtMAN5 are important for the function in synthesis of glucomannan for the cell wall. Arabidopsis possesses another atypical MAN, AtMAN6, with an HDEL retention signal at its C-terminus. However, mutation of AtMAN6 did not affect glucomannan content in the cell walls, suggesting distinct functions for these MANs. This study has identified AtMAN2 and AtMAN5 as novel factors necessary for the normal glucomannan synthesis in Arabidopsis, along with GDP-mannose generating enzymes and CslAs, and suggests that the glucomannan hydrolysis by these MANs contributes to the maintenance of glucomannan synthesis.

plant biology↗

bioRxiv2024

Glucomannan engineering highlights the role of galactosyl modification in fine-tuning cellulose-glucomannan interaction in Arabidopsis cell walls

Widely found in most plant lineages, {beta}-mannans are structurally diverse polysaccharides that can bind to cellulose fibrils to form the complex polysaccharide architecture of the cell wall. Glucomannan backbones acquire variable patterns of galactosyl substitutions, depending on plant developmental stage and species. How the changes in polysaccharide structure influence its cell wall solubility or promote appropriate interaction with cellulose fibrils is poorly understood. Here, we show that fine-tuning of galactosyl modification on glucomannans is achieved by the differing acceptor recognition of mannan -galactosyltransferases (MAGTs). Biochemical analysis and 13C solid-state nuclear magnetic resonance spectroscopy of Arabidopsis with cell wall glucomannan engineered by MAGTs revealed that the degree of galactosylation strongly affects the interaction with cellulose. The findings indicate that plants tailor galactosyl modification on glucomannans for constructing an appropriate cell wall architecture, paving the way to convert properties of lignocellulosic biomass for better use.

bioengineering↗

bioRxiv2024

New insights into the structure of cellulose in plant cell walls

The structure of plant cellulose microfibrils remains elusive, despite the abundance of cellulose and its utility in industry. Using 2D solid-state NMR of 13C labelled never-dried plants, six major glucose environments are resolved which are common to the cellulose of softwood, hardwood and grasses. These environments are maintained in isolated holo-cellulose nanofibrils, allowing more detailed microfibril characterisation. We show there are only two glucose environments that reside within the microfibril interior. These have the same NMR 13C chemical shifts as tunicate cellulose I{beta} centre and origin chains, with no cellulose I being detected. The third major glucose site with a carbon 4 chemical shift near 89 ppm, previously assigned to the crystalline microfibril interior, is now shown to be one of four surface glucose environments. The NMR peak widths of all four surface glucose environments are similar to those of the core indicating that their glucose local order is comparable; there is no significant amorphous cellulose in the microfibrils. Consequently, the ratio of the carbon 4 peaks at [~]89 and [~]84 ppm, which has often provided a sample cellulose crystallinity index, is not a meaningful measure of crystallinity or the interior to surface ratio. The revised ratio for poplar wood microfibrils is estimated to be 1:2, which is consistent with a cellulose I{beta} 18-chain microfibril having 6 core and 12 surface chains, although other microfibril sizes are possible. These advances change substantially both the interpretation of solid-state NMR studies of cellulose and the understanding of cellulose microfibril structure and crystallinity.

biochemistry↗

bioRxiv2024

Convergent Acquisition of Glucomannan β-galactosyltransferases in Asterids and Rosids

{beta}-Galactoglucomannan ({beta}-GGM) is a primary cell wall polysaccharide in rosids and asterids. The {beta}-GGM polymer has a backbone of repeating glucose and mannose, usually with mono- or di-galactosyl sidechains on the mannosyl residues. CELLULOSE SYNTHASE-LIKE 2 (CSLA2), MANNAN -GALACTOSYLTRANSFERASE (MAGT), and MANNAN {beta}-GALACTOSYLTRANSFERASE (MBGT) are required for {beta}-GGM synthesis in Arabidopsis thaliana. The single MBGT identified so far, AtMBGT1, lies in glycosyltransferase family 47A subclade VII, and was identified in Arabidopsis. However, despite the presence of {beta}-GGM, an orthologous gene is absent in tomato (Solanum lycopersicum), a model asterid. In this study, we screened candidate MBGT genes from the tomato genome, functionally tested the activities of encoded proteins, and identified the tomato MBGT (SlMBGT1) in GT47A-III. Interestingly therefore, AtMBGT1 and SlMBGT1 are located in different GT47A subclades. Further, phylogenetic and glucomannan structural analysis from different species raised the possibility that various asterids possess conserved MBGTs in GT47A-III, indicating that MBGT activity has been acquired convergently among asterids and rosids. Although functional convergence was observed, the acquired amino acid substitutions among the two MBGT groups were not shared, suggesting different evolutionary pathways to achieve the same biochemical outcome. The present study highlights the promiscuous emergence of donor and acceptor preference in GT47A enzymes, and suggests an adaptive advantage for eudicots to acquire {beta}-GGM {beta}-galactosylation.

plant biology↗

bioRxiv2023

Differing structures of galactoglucomannan in eudicots and non-eudicot angiosperms

The structures of cell wall mannan hemicelluloses have changed during plant evolution. Recently, a new structure called {beta}-galactoglucomannan ({beta}-GGM) was discovered in eudicot plants. This galactoglucomannan has {beta}-(1,2)-Gal--(1,6)-Gal disaccharide branches on some mannosyl residues of the strictly alternating Glc-Man backbone. Studies in Arabidopsis revealed {beta}-GGM is related in structure, biosynthesis and function to xyloglucan. However, when and how plants acquired {beta}-GGM remains elusive. Here, we studied mannan structures in many sister groups of eudicots. All glucomannan structures were distinct from {beta}-GGM. In addition, we searched for candidate mannan {beta}-galactosyltransferases (MBGT) in non-eudicot angiosperms. Candidate AtMBGT1 orthologues from rice and Amborella did not show MBGT activity in vivo. However, the AtMBGT1 orthologue from rice showed MUR3-like xyloglucan galactosyltransferase activity in complementation analysis using Arabidopsis. Further, reverse genetic analysis revealed that the enzyme contributes to proper root growth in rice. Together, gene duplication and diversification of GT47A-VII in eudicot evolution may have been involved in the acquisition of mannan {beta}-galactosyltransferase activity. Our results indicate that {beta}-GGM is likely to be a eudicot-specific mannan.

biochemistry↗

bioRxiv2022

Eudicot primary cell wall glucomannan is related in synthesis, structure and function to xyloglucan

The functional differences between plant cell wall hemicelluloses such as glucomannan, xylan and xyloglucan (XyG) remain unclear. These polysaccharides influence assembly and properties of the wall, perhaps by interacting with cellulose to affect the deposition and bundling of the fibrils. As the most abundant hemicellulose, XyG is considered important in eudicot primary cell walls (PCWs), but plants devoid of XyG show relatively mild phenotypes. We report here that a patterned {beta}-galactoglucomannan ({beta}-GGM) is widespread in PCW of eudicots and shows remarkable similarities to XyG. The sugar linkages forming the backbone and side chains of {beta}-GGM are analogous to those that make up XyG, and moreover, these linkages are formed by glycosyltransferases from the same CAZy families. Solid-state NMR indicated that {beta}-GGM shows low mobility in the cell wall, consistent with interaction with cellulose. Although Arabidopsis {beta}-GGM synthesis mutants show no obvious growth defects, genetic crosses between {beta}-GGM and XyG mutants produce exacerbated phenotypes compared to XyG mutants. These findings demonstrate a related role of these two similar but distinct classes of hemicelluloses in PCWs. This work will provide new avenues to study the roles of both {beta}-GGM and XyG in PCWs. One sentence summaryPatterned {beta}-GGM resembles xyloglucan in structure, biosynthesis and function.

plant biology↗

bioRxiv2021

The Mechanism of Neurite Outgrowth Induction by Novel Synthetic Retinobenzoic Acids

Retinoids are a family of vitamin A-derived molecules and include the biologically active metabolite, retinoic acid (RA). RA acts as a specific modulator of neuronal differentiation and proliferation. However, teratogenicity and a large excess of RA have been found in animal studies. Thus, development of effective and stable retinoids is desirable. In this study, we showed that treatment with novel synthetic retinobenzoic acids promotes neurite outgrowth in a selected subpopulation of the human neuroblastoma cell line SK-N-SH. Furthermore, we found that, although acting via a different mechanism, retinobenzoic acids have the same neurite outgrowth-inducing effect as RA. Retinoids, including RA, bind to nuclear retinoic acid receptors (RARs). Therefore, we examined the expression of RARs in retinobenzoic acid-treated cells. Similar to already known retinoids, novel synthetic retinobenzoic acids promote the upregulation of RAR{beta} and have no effect on RAR or {gamma}. These results suggest that retinobenzoic acids act via RAR{beta} during neurite outgrowth. Moreover, stimulation with RA or retinobenzoic acids significantly increased the phosphorylation levels of both ERK1/2 and mTOR. ERK1/2 and mTOR inhibition blocked the retinobenzoic acid-induced increase in neurite outgrowth, suggesting that retinobenzoic acids promoted neurite outgrowth by activating the ERK1/2 and mTOR signaling pathways. Notably, the RA-induced increase in neurite outgrowth was blocked by the ERK1/2 inhibitor U0126, but not by the mTOR inhibitor rapamycin. In addition, ERK1/2 inhibition blocked the upregulation of RAR{beta} promoted by RA and retinobenzoic acids. In contrast, mTOR inhibition had no effect on upregulation of RAR{beta}. Our results show that novel synthetic retinobenzoic acids induce neurite outgrowth by a different mechanism than RA. These findings suggest that activation of both ERK1/2, which results in downstream regulation of RAR{beta}, and mTOR, are responsible for the novel synthetic retinobenzoic acid-induced neurite outgrowth in human neuroblastoma cells.

cell biology↗