Biology subjects

Miyazaki, I.

Publications and source records attributed to Miyazaki, I..

3 recordsLinked to original sources

bioRxiv2026

A StayGold-based calcium ion indicator

Genetically encoded calcium ion (Ca2+) indicators (GECIs) enable visualization of Ca2+ dynamics in living systems but often suffer from limited photostability during prolonged imaging. The recent discovery of StayGold, a green fluorescent protein (FP) with exceptional brightness and photostability, opened the possibility of addressing this longstanding challenge. Here, we sought to establish whether a monomeric variant of StayGold (mStayGold) could be converted into a single FP-based GECI. Through extensive protein engineering, we generated a functional mStayGold-based GECI, HiCaRI (Highly intensiometric Ca2+ Responsive Indicator) by fusing Calmodulin (CaM) and the ckkap binding peptide from K-GECO1 into mStayGold(J). HiCaRI exhibits a large Ca2+-dependent inverse fluorescence response ({Delta}F/Fmin = -15) while retaining high brightness and improved photostability relative to previously reported GFP-based GECIs. Although the current variant represents a first-generation prototype with shortcomings in terms of Ca2+ affinity and photostability (relative to StayGold and mStayGold(J)), this work demonstrates the feasibility of constructing single FP-based GECIs from a highly photostable fluorescent protein.

bioengineering↗

bioRxiv2026

A unified pipeline for discovering previously unknown enzyme activities

Enzymes catalyze diverse chemical transformations and offer a sustainable approach to both breaking and making chemical bonds. However, finding an enzyme capable of performing a specific chemical reaction remains a challenge. We developed a new framework, Enzyme-toolkit (Enzyme-tk), that integrates 23 open-source tools to enable the discovery of enzymes that have activity toward a specific target reaction. Additionally, we introduce two new methods to facilitate enzyme discovery: (1) Func-e, an ML tool that searches large databases for enzymes that potentially catalyze a specific chemical transformation and (2) Oligopoolio, a gene assembly approach that reduces the cost of accessing protein sequences and thus the barrier to their experimental validation. We applied Enzyme-tk to find enzymes for chemical degradation of two man-made pollutants, di-(2-ethylhexyl) phthalate (DEHP) and triphenyl phosphate (TPP). We demonstrate that new, previously unannotated enzymes with favorable characteristics, such as high thermostability, can be identified using Enzyme-tk for reactions that are dissimilar to the training set.

biochemistry↗

bioRxiv2024

Synthesis and application of a photocaged L-lactate

O_SCPLOWLC_SCPLOW-Lactate, once considered a metabolic waste product of glycolysis, is now recognized as a vitally important metabolite and signaling molecule in multiple biological pathways. However, exploring O_SCPLOWLC_SCPLOW-lactates emerging intra- and extra-cellular roles is hindered by a lack of tools to locally perturb O_SCPLOWLC_SCPLOW-lactate concentration intracellularly and extracellularly. Photocaged compounds are a powerful way to introduce bioactive molecules with spatial and temporal precision using illumination. Here, we report the development of a photocaged derivative of O_SCPLOWLC_SCPLOW-lactate, 4-methoxy-7-nitroindolinyl O_SCPLOWLC_SCPLOW-lactate (MNI-O_SCPLOWLC_SCPLOW-lac), that releases O_SCPLOWLC_SCPLOW-lactate upon UV illumination. We validated MNI-O_SCPLOWLC_SCPLOW-lac in cell culture by demonstrating that the photorelease of O_SCPLOWLC_SCPLOW-lactate elicits a response from genetically encoded extra- and intracellular O_SCPLOWLC_SCPLOW-lactate biosensors. These results indicate that MNI-O_SCPLOWLC_SCPLOW-lac may be useful for perturbing the concentration of endogenous O_SCPLOWLC_SCPLOW-lactate in order to investigate O_SCPLOWLC_SCPLOW-lactates roles in metabolism and signaling pathways.

biochemistry↗