Biology subjects

Kitaguchi, T.

Publications and source records attributed to Kitaguchi, T..

7 recordsLinked to original sources

bioRxiv2026

Green genetically encoded IP3 biosensor for hierarchical analysis of its signaling network

Inositol 1,4,5-trisphosphate (IP3) is a key second messenger that regulates diverse physiological processes. Visualization of IP3 dynamics in living cells is therefore important for understanding its signaling processes. In this study, we developed genetically encoded green fluorescent IP3 biosensors named Green iPenguins with distinct half-maximal effective concentrations (EC50) for IP3, enabling detection of IP3 signals over a range of concentrations. The biosensors displayed more than a 4-fold increase in fluorescence intensity upon IP3 and showed high specificity for IP3 over structurally related molecules. When expressed in HEK293T cells, the biosensors enabled visualization of IP3 dynamics involved in different signaling pathways. They were also compatible with dual-color imaging, allowing simultaneous monitoring of IP3 together with cAMP or Ca2+ signals. In addition, the hierarchical relationship between IP3 and Ca2+ signaling was visualized, providing insight into the temporal relationship between these two second messengers. The biosensors are expected to facilitate future studies of physiological processes involving IP3 signaling networks.

bioengineering↗

bioRxiv2025

SMART platform for enzyme engineering: A novel single-molecule display approach for evolution and functional studies of D-amino acid oxidase

This study introduces SMART (Single Molecule Assay on Ribonucleic Acid by Translated Product), an innovative in vitro platform integrating mRNA display, next-generation sequencing, and bioinformatics to address several key challenges in enzyme engineering. The characteristic feature of SMART is its auxiliary unit, attached to the mRNA-displayed enzyme library to mediate the biotinylation of reactive enzyme variants and enable their enrichment by streptavidin beads pull-down. The unit comprises a hairpin single-stranded DNA that hybridizes with the mRNA and anchors a DNA-binding protein, single-chain Cro, which carries functional auxiliary molecules specific to the enzyme of interest. Here, we report on the establishment of SMART for the engineering of oxidases, specifically D-amino acid oxidase (DAAO) from Schizosaccharomyces pombe, with engineered ascorbate peroxidase 2 as its auxiliary enzyme. In a single selection round of a DAAO library with randomized catalytic residue Y232 and D-Alanine as the substrate, we identified several catalytically active enzyme variants with altered substrate specificity in a matter of days. This surpasses traditional enzyme engineering methods in speed, cost, library capacity, and precision. This research underscores the potential of SMART for the engineering of various oxidases, and other enzymes after the corresponding adjustment of the auxiliary unit.

bioengineering↗

bioRxiv2023

qMaLioffG: A single green fluorescent protein FLIM indicator enabling quantitative imaging of endogenous ATP

The widespread use of fluorescence lifetime imaging microscopy (FLIM) for quantitative imaging is hindered by the limited availability of a FLIM-based genetically encoded indicator using a conventional 488 nm laser. Here, we present qMaLioffG, a single green fluorescent protein FLIM indicator showing a fluorescence lifetime change in ATP concentration within the physiological range. This allows quantitative imaging of endogenous ATP to investigate cellular energy status of different cell types.

biophysics↗

bioRxiv2022

Exocytotic dynamics of glucagon-like peptide-1 from enteroendocrine L cell line is regulated by actin polymerization

Stimulus-secretion coupling of glucagon-like peptide-1 (GLP-1) from enteroendocrine L cells is important for glucose homeostasis. Although intracellular second messengers including Ca2+ and cAMP, and cellular structures including actin cytoskeleton play roles in induction of exocytosis of GLP-1 granules, little is known about the specific part in the process of exocytosis in which they are involved. Here we explored the role of those molecules by live-cell imaging with mouse L cell line GLUTag cells, and used two stimuli: deoxycholic acid (DCA) and high K+. DCA increased both intracellular Ca2+ and cAMP levels, while high K+ only increased Ca2+. We next monitored a single exocytosis of GLP-1 granules and found that, during the first 10 minutes of stimulation, both stimuli mainly induced the exocytosis from the predocked granules with the plasma membrane before stimulation or granules immediately fused to the plasma membrane without docking. Furthermore, inhibition of actin polymerization suppressed the proportion of exocytosis by the predocked granules. These results suggest that the exocytotic process of GLP-1 granules is determined by interaction with F-actin upon the increase of either Ca2+ or cAMP. Summary statementExocytotic process of glucagon-like peptide-1 granules from a mouse enteroendocrine L cell line is regulated by actin polymerization immediately after elevation of intracellular Ca2+ or cAMP levels.

cell biology↗

bioRxiv2022

Creating a thermostable beta-glucuronidase switch for homogeneous immunoassay by disruption of conserved salt bridges at diagonal interfaces

The Escherichia coli beta-glucuronidase (GUS) has been used as a reporter enzyme in molecular biology and has been engineered to enzyme switches for the development of homogeneous biosensors. Here, we developed a thermostable GUS enzyme switch from a thermostable GUS mutant TR3337 by disrupting a conserved salt bridge (H514-E523) between the diagonal subunits of its homotetramer. A combinatorial library (240 variants) was screened by a novel high-throughput strategy, and a mutant DLW (H514D/M516L/Y517W) was found to be a functional enzyme switch in a caffeine-recognizing immunosensor. The molecular dynamics simulations were performed to predict the topology change around position 514, and the sidechain flip of D514 (repulsion with E523) was observed in the DLW mutant. Up to 1.8-fold of the signal-to-background ratio was confirmed when measured at 45 {degrees}C, which makes the DLW mutant a versatile tool for developing the thermostable immunosensors for in vitro and in cellulo applications. Table of contents graphic O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

bioengineering↗

bioRxiv2021

Photothermal Dye-based Subcellular-sized Heat Spot Enabling the Modulation of Local Cellular Activities

Thermal engineering at microscale such as the control and measurement of temperature is a key technology in basic biological research and biomaterials development, which remains challenge yet. Here, we engineered the polymeric nanoparticle, in which a fluorescent temperature sensory dye and a photothermal dye were embedded in its polymer matrices, termed nanoHT. When a near infrared laser at 808 nm is illuminated to the particle, it enables to create the subcellular-sized heat spot in a live cell, where fluorescence thermometry allows the read out of the temperature increment concurrently at individual heat spots. Owing to the controlled local heating, we found that the cell death of HeLa cells was induced at the certain temperature at rate of a few seconds. It should be also noted that the cell death was triggered from the very local heat spot at subcellular level. Furthermore, nanoHT was applied for the induction of muscle contraction of the C2C12 myotube by heat. We successfully showed that the heat-induced contraction took place at the limited area of a single myotube according to the alteration of protein-protein interactions related to the contraction event. These studies demonstrated that even a single heat spot provided by a photothermal material could be very effective in altering cellular functions, paving the way for novel photothermal therapies.

bioengineering↗

bioRxiv2021

The molecular basis of ubiquitin-specific protease 8 autoinhibition by the WW-like domain

Ubiquitin-specific protease 8 (USP8) is a deubiquitinating enzyme involved in multiple membrane trafficking pathways. The enzyme activity is inhibited by binding to 14-3-3 proteins, and mutations of the 14-3-3 binding motif in USP8 are related to Cushings disease. However, the molecular basis of USP8 enzyme activity regulation remains unclear. Here, we identified amino acids 645-684 of USP8 as an autoinhibitory region, which our pull-down and single-molecule FRET assay results suggested interacts with the catalytic USP domain. In silico modelling indicated that the region forms a WW-like domain structure, plugs the catalytic cleft, and narrows the entrance to the ubiquitin-binding pocket. Furthermore, 14-3-3 was found to inhibit USP8 enzyme activity partly by enhancing the interaction between the WW-like and USP domains. These findings provide the molecular basis of USP8 autoinhibition via the WW-like domain. Moreover, they suggest that the release of autoinhibition may underlie Cushings disease caused by USP8 mutations.

biochemistry↗