Organelle-Specific Nitric Oxide Detection in Living Cells via HaloTag Protein Labeling

Hybrid Small-Molecule/Protein Fluorescent Probes

Hybrid small-molecule/protein fluorescent probes are powerful tools for visualizing protein localization and function in living cells. These hybrid probes are constructed by diverse site-specific chemical protein labeling approaches through chemical reactions to exogenous peptide/small protein tags, enzymatic post-translational modifications, bioorthogonal reactions for genetically incorporated unnatural amino acids, and ligand-directed chemical reactions. The hybrid small-molecule/protein fluorescent probes are employed for imaging protein trafficking, conformational changes, and bioanalytes surrounding proteins. In addition, fluorescent hybrid probes facilitate visualization of protein dynamics at the single-molecule level and the defined structure with super-resolution imaging. In this review, we discuss development and the bioimaging applications of fluorescent probes based on small-molecule/protein hybrids.

Recent progress in developing fluorescent probes for imaging cell metabolites

Cellular metabolites play a crucial role in promoting and regulating cellular activities, but it has been difficult to monitor these cellular metabolites in living cells and in real time. Over the past decades, iterative development and improvements of fluorescent probes have been made, resulting in the effective monitoring of metabolites. In this review, we highlight recent progress in the use of fluorescent probes for tracking some key metabolites, such as adenosine triphosphate, cyclic adenosine monophosphate, cyclic guanosine 5'-monophosphate, Nicotinamide adenine dinucleotide (NADH), reactive oxygen species, sugar, carbon monoxide, and nitric oxide for both whole cell and subcellular imaging.

HaloFlippers: A General Tool for the Fluorescence Imaging of Precisely Localized Membrane Tension Changes in Living Cells

Tools to image membrane tension in response to mechanical stimuli are badly needed in mechanobiology. We have recently introduced mechanosensitive flipper probes to report quantitatively global membrane tension changes in fluorescence lifetime imaging microscopy (FLIM) images of living cells. However, to address specific questions on physical forces in biology, the probes need to be localized precisely in the membrane of interest (MOI). Herein we present a general strategy to image the tension of the MOI by tagging our newly introduced HaloFlippers to self-labeling HaloTags fused to proteins in this membrane. The critical challenge in the construction of operational HaloFlippers is the tether linking the flipper and the HaloTag: It must be neither too taut nor too loose, be hydrophilic but lipophilic enough to passively diffuse across membranes to reach the HaloTags, and allow partitioning of flippers into the MOI after the reaction. HaloFlippers with the best tether show localized and selective fluorescence after reacting with HaloTags that are close enough to the MOI but remain nonemissive if the MOI cannot be reached. Their fluorescence lifetime in FLIM images varies depending on the nature of the MOI and responds to myriocin-mediated sphingomyelin depletion as well as to osmotic stress. The response to changes in such precisely localized membrane tension follows the validated principles, thus confirming intact mechanosensitivity. Examples covered include HaloTags in the Golgi apparatus, peroxisomes, endolysosomes, and the ER, all thus becoming accessible to the selective fluorescence imaging of membrane tension.

Quantitative measurement of cytosolic penetration using the chloroalkane penetration assay

A major barrier for drug development is ensuring molecules can access intracellular targets. This is especially true for biomolecules, which are notoriously difficult to deliver to the cytosol. Many current methods for measuring the internalization of therapeutic biomolecules are largely indirect and qualitative, and they do not offer information about subcellular localization. We recently reported a new assay, called the ChloroAlkane Penetration Assay (CAPA), that addresses some of the drawbacks of existing methods. CAPA is high-throughput, quantitative, and compartment-specific, and can be used to monitor cytosolic penetration over time and under a variety of culture conditions. We have used CAPA to investigate the cytosolic localization of peptides, proteins, and oligonucleotides. In this chapter, we discuss the materials, protocols, and troubleshooting necessary to perform CAPA and appropriately analyze the data. We end with a discussion about the applications and limitations of CAPA, and we speculate on the potential of the assay and its variations.

Illuminating NAD+ Metabolism in Live Cells and In Vivo Using a Genetically Encoded Fluorescent Sensor

Understanding of NAD⁺ metabolism provides many critical insights into health and diseases, yet highly sensitive and specific detection of NAD⁺ metabolism in live cells and in vivo remains difficult. Here, we present ratiometric, highly responsive genetically encoded fluorescent indicators, FiNad, for monitoring NAD⁺ dynamics in living cells and animals. FiNad sensors cover physiologically relevant NAD⁺ concentrations and sensitively respond to increases and decreases in NAD⁺. Utilizing FiNad, we performed a head-to-head comparison study of common NAD⁺ precursors in various organisms and mapped their biochemical roles in enhancing NAD⁺ levels. Moreover, we showed that increased NAD⁺ synthesis controls morphofunctional changes of activated macrophages, and directly imaged NAD⁺ declines during aging in situ. The broad utility of the FiNad sensors will expand our mechanistic understanding of numerous NAD⁺-associated physiological and pathological processes and facilitate screening for drug or gene candidates that affect uptake, efflux, and metabolism of this important cofactor.

Fluorescent probes for organelle-targeted bioactive species imaging

The dynamic fluctuations of bioactive species in living cells are associated with numerous physiological and pathological phenomena. The emergence of organelle-targeted fluorescent probes has significantly facilitated our understanding on the biological functions of these species. This review describes the design, applications, challenges and potential directions of organelle-targeted bioactive species probes.

Bioactive species, including reactive oxygen species (ROS, including O₂˙^–, H₂O₂, HOCl, ¹O₂, ˙OH, HOBr, etc.), reactive nitrogen species (RNS, including ONOO^–, NO, NO₂, HNO, etc.), reactive sulfur species (RSS, including GSH, Hcy, Cys, H₂S, H₂S_n, SO₂ derivatives, etc.), ATP, HCHO, CO and so on, are a highly important category of molecules in living cells. The dynamic fluctuations of these molecules in subcellular microenvironments determine cellular homeostasis, signal conduction, immunity and metabolism. However, their abnormal expressions can cause disorders which are associated with diverse major diseases. Monitoring bioactive molecules in subcellular structures is therefore critical for bioanalysis and related drug discovery. With the emergence of organelle-targeted fluorescent probes, significant progress has been made in subcellular imaging. Among the developed subcellular localization fluorescent tools, ROS, RNS and RSS (RONSS) probes are highly attractive, owing to their potential for revealing the physiological and pathological functions of these highly reactive, interactive and interconvertible molecules during diverse biological events, which are rather significant for advancing our understanding of different life phenomena and exploring new technologies for life regulation. This review mainly illustrates the design principles, detection mechanisms, current challenges, and potential future directions of organelle-targeted fluorescent probes toward RONSS.

Real-Time Imaging of Nitric Oxide Signals in Individual Cells Using geNOps

Nitric oxide (NO^•) is a versatile signaling molecule which regulates fundamental cellular processes in all domains of life. However, due to the radical nature of NO^• it has a very short half-life that makes it challenging to trace its formation, diffusion, and degradation on the level of individual cells. Very recently, we expanded the family of genetically encoded sensors by introducing a novel class of single fluorescent protein-based NO^• probes-the geNOps. Once expressed in cells of interest, geNOps selectively respond to NO^• by fluorescence quench, which enables real-time monitoring of cellular NO^• signals. Here, we describe detailed methods suitable for imaging of NO^• signals in mammalian cells. This novel approach may facilitate a broad range of studies to (re)investigate the complex NO^• biochemistry in living cells.

Improved Analysis of RNA Localization by Spatially Restricted Oxidation of RNA-Protein Complexes

Recent analysis of transcriptomes has revealed that RNAs perform a myriad of functions beyond encoding proteins. Critical to RNA function is its transport to unique subcellular locations. Despite the importance of RNA localization, it is still very challenging to study in an unbiased manner. We recently described the ability to tag RNA molecules within subcellular locations through spatially restricted nucleobase oxidation. Herein, we describe a dramatic improvement of this protocol through the localized oxidation and tagging of proteins. Isolation of RNA-protein complexes enabled the enrichment of challenging RNA targets on chromatin and presented a considerably optimized protocol for the analysis of RNA subcellular localization within living cells.

Gasotransmitter Heterocellular Signaling

SIGNIFICANCE

The family of gasotransmitter molecules, nitric oxide (NO), carbon monoxide (CO), and hydrogen sulfide (H₂S), has emerged as an important mediator of numerous cellular signal transduction and pathophysiological responses. As such, these molecules have been reported to influence a diverse array of biochemical, molecular, and cell biology events often impacting one another. Recent Advances: Discrete regulation of gasotransmitter molecule formation, movement, and reaction is critical to their biological function. Due to the chemical nature of these molecules, they can move rapidly throughout cells and tissues acting on targets through reactions with metal groups, reactive chemical species, and protein amino acids.

CRITICAL ISSUES

Given the breadth and complexity of gasotransmitter reactions, this field of research is expanding into exciting, yet sometimes confusing, areas of study with significant promise for understanding health and disease. The precise amounts of tissue and cellular gasotransmitter levels and where they are formed, as well as how they react with molecular targets or themselves, all remain poorly understood.

FUTURE DIRECTIONS

Elucidation of specific molecular targets, characteristics of gasotransmitter molecule heterotypic interactions, and spatiotemporal formation and metabolism are all important to better understand their true pathophysiological importance in various organ systems. Antioxid. Redox Signal. 26, 936-960.

Monitoring Nitric Oxide in Subcellular Compartments by Hybrid Probe Based on Rhodamine Spirolactam and SNAP-tag

By connection of O(6)-benzylguanine (BG) to an "o-phenylenediamine-locked" rhodamine spirolactam responsive to nitric oxide (NO), a novel substrate (TMR-NO-BG) of genetically encoded SNAP-tag has been constructed. In living cells, labeling SNAP-tag fused proteins with TMR-NO-BG will in situ generate corresponding probe-protein conjugates (TMR-NO-SNAP) that not only inherit high NO sensitivity from the small-molecule parent but also guarantee the site-specificity to the designated subcellular compartments such as the mitochondrial inner membrane, nucleus, and cytoplasm. In two representative cellular processes, TMR-NO-BG demonstrates its applicability to monitor endogenous subcellular NO in the activated RAW264.7 cells stimulated by lipopolysaccharide and in the apoptotic COS-7 cells induced by etoposide.