Long-term imaging of intranuclear Mg2+ dynamics during mitosis using a localized fluorescent probe.

A novel fluorescent Mg2+ probe was developed based on a small molecule-protein hybrid. This probe enables subcellular targeting, long-term imaging, and high selectivity for Mg2+ over Ca2+. Using ratiometric fluorescence microscopy with a co-localized standard fluorophore, the variations in intranuclear Mg2+ concentrations during mitosis could be visualized.

Zinc homeostasis governed by Golgi-resident ZnT family members regulates ERp44-mediated proteostasis at the ER-Golgi interface.

Many secretory enzymes acquire essential zinc ions (Zn2+) in the Golgi complex. ERp44, a chaperone operating in the early secretory pathway, also binds Zn2+ to regulate its client binding and release for the control of protein traffic and homeostasis. Notably, three membrane transporter complexes, ZnT4, ZnT5/ZnT6 and ZnT7, import Zn2+ into the Golgi lumen in exchange with protons. To identify their specific roles, we here perform quantitative Zn2+ imaging using super-resolution microscopy and Zn2+-probes targeted in specific Golgi subregions. Systematic ZnT-knockdowns reveal that ZnT4, ZnT5/ZnT6 and ZnT7 regulate labile Zn2+ concentration at the distal, medial, and proximal Golgi, respectively, consistent with their localization. Time-course imaging of cells undergoing synchronized secretory protein traffic and functional assays demonstrates that ZnT-mediated Zn2+ fluxes tune the localization, trafficking, and client-retrieval activity of ERp44. Altogether, this study provides deep mechanistic insights into how ZnTs control Zn2+ homeostasis and ERp44-mediated proteostasis along the early secretory pathway.

Arylazopyrazole-Based Photoswitchable Inhibitors Selective for Escherichia coli Dihydrofolate Reductase.

Selective inhibitors of Escherichia coli dihydrofolate reductase (eDHFR) are crucial chemical biology tools that have widespread clinical applications. We developed a set of eDHFR-selective photoswitchable inhibitors by derivatizing the structure of our previously reported methotrexate (MTX) azolog, azoMTX. Substitution of the skeletal p-phenylene group of azoMTX with bulky bis-alkylated arylazopyrazole moieties significantly increased its selectivity toward eDHFR over human DHFR. Owing to the physical properties of arylazopyrazoles, the new ligands exhibited nearly complete Z-to-E photoconversion and high thermostability of Z-isomers. In addition, real-time photoreversible control of eDHFR activity was achieved by alternatively switching the illumination light wavelengths.

Flexible Target Recognition of the Intrinsically Disordered DNA-Binding Domain of CytR Monitored by Single-Molecule Fluorescence Spectroscopy.

The intrinsically disordered DNA-binding domain of cytidine repressor (CytR-DBD) folds in the presence of target DNA and regulates the expression of multiple genes in E. coli. To explore the conformational rearrangements in the unbound state and the target recognition mechanisms of CytR-DBD, we carried out single-molecule Förster resonance energy transfer (smFRET) measurements. The smFRET data of CytR-DBD in the absence of DNA show one major and one minor population assignable to an expanded unfolded state and a compact folded state, respectively. The population of the folded state increases and decreases upon titration with salt and denaturant, respectively, in an apparent two-state manner. The peak FRET efficiencies of both the unfolded and folded states change continuously with denaturant concentration, demonstrating the intrinsic flexibility of the DNA-binding domain and the deviation from a strict two-state transition. Remarkably, the CytR-DBD exhibits a compact structure when bound to both the specific and nonspecific DNA; however, the peak FRET efficiencies of the two structures are slightly but consistently different. The observed conformational heterogeneity highlights the potential structural changes required for CytR to bind variably spaced operator sequences.

Clip to Click: Controlling Inverse Electron-Demand Diels-Alder Reactions with Macrocyclic Tetrazines.

A universal strategy to control tetrazine reactivity in the inverse electron-demand Diels-Alder (IEDDA) reaction was developed as "Clip to Click". Incorporating a chemical bridge into 3,6-diphenyl-1,2,4,5-tetrazine (macrocyclic tetrazine) rendered it unreactive toward trans-cyclooctene. A computational study revealed that the unreactive property of macrocyclic tetrazines is mainly due to the high distortion energy of tetrazine. We demonstrated that the cleavage ("Clip") of the macrocyclic linker can activate the tetrazine moiety for the IEDDA reaction ("Click").

Organelle-Level Labile Zn2+ Mapping Based on Targetable Fluorescent Sensors.

Although many Zn2+ fluorescent probes have been developed, there remains a lack of consensus on the labile Zn2+ concentrations ([Zn2+]) in several cellular compartments, as the fluorescence properties and zinc affinity of the fluorescent probes are greatly affected by the pH and redox environments specific to organelles. In this study, we developed two turn-on-type Zn2+ fluorescent probes, namely, ZnDA-2H and ZnDA-3H, with low pH sensitivity and suitable affinity (Kd = 5.0 and 0.16 nM) for detecting physiological labile Zn2+ in various cellular compartments, such as the cytosol, nucleus, ER, and mitochondria. Due to their sufficient membrane permeability, both probes were precisely localized to the target organelles in HeLa cells using HaloTag labeling technology. Using an in situ standard quantification method, we identified the [Zn2+] in the tested organelles, resulting in the subcellular [Zn2+] distribution as [Zn2+]ER < [Zn2+]mito < [Zn2+]cyto ∼ [Zn2+]nuc.

Long-Term Mg2+ Imaging in Live Cells with a Targetable Fluorescent Probe.

Living cells dynamically change their morphology and function according to the cell cycle. Long-term observations of living cells are privileged when we spy the unique, cell cycle-driven molecular events, which cannot be obtained from short-term ones. Mg2+, a metal ion abundant in cells, has been shown to be involved in a variety of physiological phenomena by noninvasive cellular observation using fluorescence microscopy. However, long-term observation of Mg2+ in cells has been a great challenge. Herein, we present a protocol for the long-term microscopic imaging of intracellular Mg2+ levels using a small molecule-protein hybrid fluorescent probe we developed.

Protocol for synthesis and use of a turn-on fluorescent probe for quantifying labile Zn2+ in the Golgi apparatus in live cells.

Quantitative analysis using a turn-on fluorescent probe is inherently difficult due to the dependency of the fluorescence intensity on the probe concentration. To overcome this limitation, we developed an in situ quantification method using a turn-on fluorescent probe and a standard fluorophore, which are colocalized by protein tag technology. This protocol describes the synthesis of a Zn2+ probe, named ZnDA-1H, and the procedure to quantify the labile Zn2+ concentration in the Golgi of live HeLa cells by confocal fluorescence microscopy. For complete details on the use and execution of this protocol, please refer to Kowada et al. (2020).

Optical Manipulation of Subcellular Protein Translocation Using a Photoactivatable Covalent Labeling System.

The photoactivatable chemically induced dimerization (photo-CID) technique for tag-fused proteins is one of the most promising methods for regulating subcellular protein translocations and protein-protein interactions. However, light-induced covalent protein dimerization in living cells has yet to be established, despite its various advantages. Herein, we developed a photoactivatable covalent protein-labeling technology by applying a caged ligand to the BL-tag system, a covalent protein labeling system that uses mutant ß-lactamase. We further developed CBHD, a caged protein dimerizer, using caged BL-tag and HaloTag ligands, and achieved light-induced protein translocation from the cytoplasm to subcellular regions. In addition, this covalent photo-CID system enabled quick protein translocation to a laser-illuminated microregion. These results indicate that the covalent photo-CID system will expand the scope of CID applications in the optical manipulation of cellular functions.

Quantitative Imaging of Labile Zn2+ in the Golgi Apparatus Using a Localizable Small-Molecule Fluorescent Probe.

Fluorescent Zn2+ probes used for the quantitative analysis of labile Zn2+ concentration ([Zn2+]) in target organelles are crucial for understanding the role of Zn2+ in biological processes. Although several fluorescent Zn2+ probes have been developed to date, there is still a lack of consensus concerning the [Zn2+] in intracellular organelles. In this study, we describe the development of ZnDA-1H, a small-molecule fluorescent probe for Zn2+, which exhibits less pH sensitivity, high Zn2+ selectivity, and large fluorescence enhancement upon binding to Zn2+. Through protein labeling technology, ZnDA-1H was precisely targeted in various intracellular organelles, such as the nucleus, mitochondria, endoplasmic reticulum, and Golgi apparatus. ZnDA-1H exhibited a reversible fluorescence response toward labile Zn2+ in these organelles in live cells. Using this probe, the [Zn2+] in the Golgi apparatus was estimated to be 25 ± 1 nM, suggesting that labile Zn2+ plays a physiological role in the secretory pathway.

Exploring the Condensation Reaction between Aromatic Nitriles and Amino Thiols To Optimize In†Situ Nanoparticle Formation for the Imaging of Proteases and Glycosidases in Cells.

The condensation reaction between 6-hydroxy-2-cyanobenzothiazole (CBT) and cysteine has been shown for various applications such as site-specific protein labelling and in vivo cancer imaging. This report further expands the substrate scope of this reaction by varying the substituents on aromatic nitriles and amino thiols and testing their reactivity and ability to form nanoparticles for cell imaging. The structure-activity relationship study leads to the identification of the minimum structural requirement for the macrocyclization and assembly process in forming nanoparticles. One of the scaffolds made of 2-pyrimidinecarbonitrile and cysteine joined by a benzyl linker was applied to design fluorescent probes for imaging caspase-3/7 and ß-galactosidase activity in live cells. These results demonstrate the generality of this system for imaging hydrolytic enzymes.

Light-Wavelength-Based Quantitative Control of Dihydrofolate Reductase Activity by Using a Photochromic Isostere of an Inhibitor.

Photopharmacology has attracted research attention as a new tool for achieving optical control of biomolecules, following the methods of caged compounds and optogenetics. We have developed an efficient photopharmacological inhibitor-azoMTX-for Escherichia coli dihydrofolate reductase (eDHFR) by replacing some atoms of the original ligand, methotrexate, to achieve photoisomerization properties. This fine molecular design enabled quick structural conversion between the active "bent" Z isomer of azoMTX and the inactive "extended" E isomer, and this property afforded quantitative control over the enzyme activity, depending on the wavelength of irradiating light applied. Real-time photoreversible control over enzyme activity was also achieved.

Real-time intravital imaging of pH variation associated with osteoclast activity.

Intravital imaging by two-photon excitation microscopy (TPEM) has been widely used to visualize cell functions. However, small molecular probes (SMPs), commonly used for cell imaging, cannot be simply applied to intravital imaging because of the challenge of delivering them into target tissues, as well as their undesirable physicochemical properties for TPEM imaging. Here, we designed and developed a functional SMP with an active-targeting moiety, higher photostability, and a fluorescence switch and then imaged target cell activity by injecting the SMP into living mice. The combination of the rationally designed SMP with a fluorescent protein as a reporter of cell localization enabled quantitation of osteoclast activity and time-lapse imaging of its in vivo function associated with changes in cell deformation and membrane fluctuations. Real-time imaging revealed heterogenic behaviors of osteoclasts in vivo and provided insights into the mechanism of bone resorption.

[Frontiers in Live Bone Imaging Researches. Development of fluorescent pH probe for imaging osteoclast activation].

For the clinical diagnosis of osteoporosis, X-ray CT and biochemical bone metabolism markers, however, there is no method to monitor osteoclast activity in the living system. We have developed the fluorescent probe to monitor osteoclast activity, by the combination of pH sensitive fluorescent dye with bisphosphonate which is delivered to the bone surface by its high affinity to hydroxyl apatite, which is named BAp-E. In vivo mouse imaging of activated osteoclast was successfully demonstrated using two photon excitation laser microscope.

BODIPY-based probes for the fluorescence imaging of biomolecules in living cells.

Fluorescence imaging techniques have been widely used to visualize biological molecules and phenomena. In particular, several studies on the development of small-molecule fluorescent probes have been carried out, because their fluorescence properties can be easily tuned by synthetic chemical modification. For this reason, various fluorescent probes have been developed for targeting biological components, such as proteins, peptides, amino acids, and ions, to the interior and exterior of cells. In this review, we cover advances in the development of 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY)-based fluorescent probes for biological studies over the past decade.

Electron-rich carbon nanorings as macrocyclic hosts for fullerenes.

Electron-rich cycloparaphenyleneacetylenes as well as their twin "glasses-like" conjugates form stable complexes with fullerenes.

Dynamic visualization of RANKL and Th17-mediated osteoclast function.

Osteoclasts are bone resorbing, multinucleate cells that differentiate from mononuclear macrophage/monocyte-lineage hematopoietic precursor cells. Although previous studies have revealed important molecular signals, how the bone resorptive functions of such cells are controlled in vivo remains less well characterized. Here, we visualized fluorescently labeled mature osteoclasts in intact mouse bone tissues using intravital multiphoton microscopy. Within this mature population, we observed cells with distinct motility behaviors and function, with the relative proportion of static - bone resorptive (R) to moving - nonresorptive (N) varying in accordance with the pathophysiological conditions of the bone. We also found that rapid application of the osteoclast-activation factor RANKL converted many N osteoclasts to R, suggesting a novel point of action in RANKL-mediated control of mature osteoclast function. Furthermore, we showed that Th17 cells, a subset of RANKL-expressing CD4+ T cells, could induce rapid N-to-R conversion of mature osteoclasts via cell-cell contact. These findings provide new insights into the activities of mature osteoclasts in situ and identify actions of RANKL-expressing Th17 cells in inflammatory bone destruction.

In vivo fluorescence imaging of bone-resorbing osteoclasts.

Osteoclasts are giant polykaryons responsible for bone resorption. Because an enhancement or loss of osteoclast function leads to bone diseases such as osteoporosis and osteopetrosis, real-time imaging of osteoclast activity in vivo can be of great help for the evaluation of drugs. Herein, pH-activatable chemical probes BAp-M and BAp-E have been developed for the detection of bone-resorbing osteoclasts in vivo. Their acid dissociation constants (pK(a)) were determined as 4.5 and 6.2 by fluorometry in various pH solutions. These pK(a) values should be appropriate to perform selective imaging of bone-resorbing osteoclasts, because synthesized probes cannot fluoresce intrinsically at physiological pH and the pH in the resorption pit is lowered to about 4.5. Furthermore, BAp-M and BAp-E have a bisphosphonate moiety that enabled the probes to localize on bone tissues. The hydroxyapatite (HA) binding assay in vitro was, therefore, performed to confirm the tight binding of the probes to the bone tissues. Our probes showed intense fluorescence at low pH values but no fluorescence signal under physiological pH conditions on HA. Finally, we applied the probes to in vivo imaging of osteoclasts by using intravital two-photon microscopy. As expected, the fluorescence signals of the probes were locally observed between the osteoclasts and bone tissues, that is, in resorption pits. These results indicate that our pH-activatable probes will prove to be a powerful tool for the selective detection of bone-resorbing osteoclasts in vivo, because this is the first instance where in vivo imaging has been conducted in a low-pH region created by bone-resorbing osteoclasts.

Synthesis of strained pyridine-containing cyclyne via reductive aromatization.

The Sonogashira-Hagihara coupling reactions of 2,6-diiodopyridine and cis-3,6-diethynyl-3,6-dimethoxycyclohexa-1,4-diene or cis-9,10-diethynyl-9,10-dimethoxy-9,10-dihydroanthracene gave macrocyclic compounds having alternating 2,6-diethynylpyridine and 3,6-dimethoxycyclohexa-1,4-diene segments. Transformation of the C(3)-symmetric 2,6-diethynylpyridine-based cyclotrimer was efficiently achieved using tin-mediated reductive aromatization under mild conditions.