Biology subjects

Yagi-Utsumi, M.

Publications and source records attributed to Yagi-Utsumi, M..

5 recordsLinked to original sources

bioRxiv2022

The double-layered structure of amyloid-β assemblage on GM1-containing membranes catalytically promotes fibrillization

Alzheimers disease (AD) is associated with progressive accumulation of amyloid-{beta} (A{beta}) cross-{beta} fibrils in the brain. A{beta} species tightly associated with GM1 ganglioside, a glycosphingolipid abundant in neuronal membranes, promote amyloid fibril formation; therefore, they could be attractive clinical targets. However, the active conformational state of A{beta} in GM1-containing lipid membranes is still unknown. The present solid-state nuclear magnetic resonance study revealed a nonfibrillar A{beta} assemblage characterized by a double-layered antiparallel {beta}-structure specifically formed on GM1 ganglioside clusters. Our data show that this unique assemblage was not transformed into fibrils on GM1-containing membranes, but could promote conversion of monomeric A{beta} into fibrils, suggesting that a solvent-exposed hydrophobic layer provides a catalytic surface evoking A{beta} fibril formation. Our findings will offer structural clues for designing drugs targeting catalytically active A{beta} conformational species for the development of anti-AD therapeutics.

biophysics↗

bioRxiv2021

Desiccation-induced fibrous condensation of CAHS protein from an anhydrobiotic tardigrade

Anhydrobiosis is one of the most extensively studied forms of cryptobiosis that is induced in certain organisms as a response to desiccation. Anhydrobiotic species has been hypothesized to produce substances that can protect their biological components and/or cell membranes without water. In extremotolerant tardigrades, highly hydrophilic and heat-soluble protein families, cytosolic abundant heat-soluble (CAHS) proteins, have been identified, which are postulated to be integral parts of the tardigrades response to desiccation. However, the molecular mechanisms underlying these protein functions remain to be fully elucidated. In this study, we perfomed in vitro and in vivo characterizations of the self-assembling property of CAHS1 protein, a major isoform of CAHS proteins from Ramazzottius varieornatus, using a series of spectroscopic and microscopic techniques. Our in vitro observations showed that CAHS1 proteins homo-oligomerized via the C-terminal -helical region and formed a hydrogel as their concentration increased, and that these molecular assembling processes were reversible. Furthermore, our in vivo observations demonstrated that the overexpressed CAHS1 proteins formed condensates under desiccation-mimicking conditions. These data strongly suggested that, upon drying, the CAHS1 proteins form oligomers and eventually underwent sol-gel transition in tardigrade cytosols. Thus, it is proposed that the CAHS1 proteins form the cytosolic fibrous condensates, which presumably have variable mechanisms for the desiccation tolerance of tardigrades. These findings provide insights into the protective mechanisms involved in the anhydrobiosis of tardigrades.

biochemistry↗

bioRxiv2020

Multiomics study of a heterotardigrade, Echinisicus testudo, suggests convergent evolution of anhydrobiosis-related proteins in Tardigrada

Many limno-terrestrial tardigrades can enter an ametabolic state upon desiccation, in which the animals can withstand extreme environments. To date, studies of the molecular mechanism have predominantly investigated the class Eutardigrada, and that in the Heterotardigrada, remains elusive. To this end, we report a multiomics study of the heterotardigrade Echiniscus testudo, which is one of the most desiccation-tolerant species. None of the previously identified tardigrade-specific anhydrobiosis-related genes was conserved, while the loss and expansion of existing pathways were partly shared. Furthermore, we identified two families of novel abundant heat-soluble proteins and the proteins exhibited structural changes from random coil to -helix as the water content decreased in vitro. These characteristics are analogous to those of anhydrobiosis-related protein in eutardigrades, while there is no conservation at the sequence level. Our results suggest that Heterotardigrada have partly shared but distinct anhydrobiosis machinery compared with Eutardigrada, possibly due to convergent evolution within Tardigrada.

genomics↗

bioRxiv2020

Characterization of amyloid β fibril formation under microgravity conditions

Amyloid fibrils are self-assembled and ordered proteinaceous supramolecules structurally characterized by the cross-{beta} spine. Amyloid formation is known to be related to various diseases typified by neurogenerative disorders and involved in a variety of functional roles. Whereas common mechanisms for amyloid formation have been postulated across diverse systems, the mesoscopic morphology of the fibrils is significantly affected by the type of solution condition in which it grows. Amyloid formation is also thought to share a phenomenological similarity with protein crystallization. While many studies have demonstrated the effect of gravity on protein crystallization, its effect on amyloid formation has not been reported. In this study, we conducted an experiment at the International Space Station (ISS) to characterize fibril formation of 40-residue amyloid {beta} (A{beta}(1-40)) under microgravity conditions. Our comparative analyses revealed that the A{beta}(1-40) fibrilization progresses much more slowly on the ISS than on the ground, similarly to protein crystallization. Furthermore, microgravity promoted the formation of distinct morphologies of A{beta}(1-40) fibrils. Our findings demonstrate that the ISS provides an ideal experimental environment for detailed investigations of amyloid formation mechanisms by eliminating the conventionally uncontrollable factors derived from gravity.

biophysics↗

bioRxiv2018

Residual Structure of Unfolded Ubiquitin as Revealed by Hydrogen/Deuterium-Exchange 2D NMR

The characterization of residual structures persistent in unfolded proteins in concentrated denaturant solution is currently an important issue in studies of protein folding, because the residual structure present, if any, in the unfolded state may form a folding initiation site and guide the subsequent folding reactions. Here, we thus studied the hydrogen/deuterium (H/D)-exchange behavior of unfolded ubiquitin in 6.0 M guanidinium chloride at pH 2.6 and 20{degrees}C. We employed a dimethylsulfoxide (DMSO)-quenched H/D-exchange NMR technique with the use of spin desalting columns, which allowed us to make a quick medium exchange from 6.0 M guanidinium chloride to a quenching DMSO solution. The technique is particularly effective for studies of the H/D-exchange kinetics of unfolded proteins in concentrated denaturant. By the backbone resonance assignment of the hetero-nuclear single quantum coherence spectrum of 15N-labeled ubiquitin in the DMSO solution, we successfully investigated the H/D-exchange kinetics of 27 identified peptide amide groups in the ubiquitin sequence. Although most of these amide groups were not protected, the four amide groups of Ile3, Val5, Ile13 and Leu73 were weakly but significantly protected with a protection factor of 2.5-3.0, indicating that there were residual structures in unfolded ubiquitin and that these amide groups were 60-67% hydrogen-bonded by the residual structures. We show that the first native {beta}-hairpin, composed of residues 2-16 in the native ubiquitin structure, is partially structured even in 6.0 M guanidinium chloride and that the amide group of Leu73 is protected by a nonnative hydrogen-bonding interaction. From comparison with the previous folding studies of ubiquitin, it is concluded that the residual native {beta}-hairpin in unfolded ubiquitin forms a folding initiation site and guides the subsequent folding reactions of the protein.

biophysics↗