Biology subjects

Shimazu, T.

Publications and source records attributed to Shimazu, T..

4 recordsLinked to original sources

bioRxiv2021

METTL18-mediated histidine methylation on RPL3 modulates translation elongation for proteostasis maintenance

Protein methylation occurs predominantly on lysine and arginine residues, but histidine also serves as a substrate for the modification. However, a limited number of enzymes responsible for this modification have been reported. Moreover, the biological role of histidine methylation has remained poorly understood. Here, we report that human METTL18 is a histidine methyltransferase for the ribosomal protein RPL3 and that the modification specifically slows ribosome traverse on tyrosine codons, allowing the proper folding of synthesized proteins. By performing an in vitro methylation assay with a methyl donor analog and quantitative mass spectrometry, we found that His245 of RPL3 is methylated at the {tau}-N position by METTL18. Structural comparison of the modified and unmodified ribosomes showed stoichiometric modification and suggested a role in translation tuning. Indeed, genome-wide ribosome profiling revealed suppressed ribosomal translocation at tyrosine codons by RPL3 methylation. Because the slower elongation provides enough time for nascent protein folding, RPL3 methylation protects cells from the cellular aggregation of Tyr-rich proteins. Our results reveal histidine methylation as an example of a "ribosome code" that ensures proteome integrity in cells.

molecular biology↗

bioRxiv2021

Visualization of Arabidopsis root system architecture in 3D by refraction-contrast X-ray micro-computed tomography

Plant roots change their morphological traits in order to adapt themselves to different environmental conditions, resulting in alteration of the root system architecture. To understand this mechanism, it is essential to visualize morphology of the entire root system. To reveal effects of long-term alteration of gravity environment on root system development, we have performed an experiment in the International Space Station using Arabidopsis (Arabidopsis thaliana (L.) Heynh.) plants and obtained dried root systems grown in rockwool slabs (mineral wool substrate). X-ray computer tomography (CT) technique using an industrial X-ray scanner has been introduced for the purpose to visualize root system architecture of crop species grown in soil in 3D non-invasively. In the case of the present study, however, root system of Arabidopsis is composed of finer roots compared with typical crop plants and rockwool is also composed of fibers having similar dimension to that of the roots. A higher spatial resolution imaging method is required for distinguishing roots from rockwool. Therefore, in the present study, we tested refraction-contrast X-ray micro-CT using coherent X-ray optics available at the beamline BL20B2 of the synchrotron radiation facility SPring-8. Using this technique, both the primary and the secondary roots were successfully identified in the tomographic slices, clearly distinguished from the individual rockwool fibers and resulting in successful tracing of these roots from their basal regions. This newly-developed technique should contribute to elucidate the effect of microgravity on Arabidopsis root system architecture in space.

plant biology↗

bioRxiv2020

Life cycle of arabidopsis in the international space station - Growth direction of the inflorescence stems in the presence of light under microgravity

In the "Space Seed" experiment performed in Kibo module of the International Space Station, growth direction of the inflorescence stem of arabidopsis was examined under space 1 G, G, and ground 1 G conditions in the presence of light. The stems grew almost upright (vertical to the surface of seedbed) under ground 1 G. Although the stems were primarily upright both under space 1 G and G, they tilted slightly. The tilting of the stems under space 1 G was indicated to be due to tilting of the artificial gravitational acceleration vectors produced on the centrifuge. The tilting of the stems under G was suggested to be due to the pressure of directional airflow produced by ventilation.

plant biology↗

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↗