The Theodore Bücher lecture. Investigating signal transduction with genetically encoded fluorescent probes

Disruption of Intracellular Calcium Homeostasis as a Therapeutic Target Against Trypanosoma cruzi

There is no effective cure for Chagas disease, which is caused by infection with the arthropod-borne parasite, Trypanosoma cruzi. In the search for new drugs to treat Chagas disease, potential therapeutic targets have been identified by exploiting the differences between the mechanisms involved in intracellular Ca²⁺ homeostasis, both in humans and in trypanosomatids. In the trypanosomatid, intracellular Ca²⁺ regulation requires the concerted action of three intracellular organelles, the endoplasmic reticulum, the single unique mitochondrion, and the acidocalcisomes. The single unique mitochondrion and the acidocalcisomes also play central roles in parasite bioenergetics. At the parasite plasma membrane, a Ca²⁺-⁻ATPase (PMCA) with significant differences from its human counterpart is responsible for Ca²⁺ extrusion; a distinctive sphingosine-activated Ca²⁺ channel controls Ca²⁺ entrance to the parasite interior. Several potential anti-trypansosomatid drugs have been demonstrated to modulate one or more of these mechanisms for Ca²⁺ regulation. The antiarrhythmic agent amiodarone and its derivatives have been shown to exert trypanocidal effects through the disruption of parasite Ca²⁺ homeostasis. Similarly, the amiodarone-derivative dronedarone disrupts Ca²⁺ homeostasis in T. cruzi epimastigotes, collapsing the mitochondrial membrane potential (ΔΨ_m), and inducing a large increase in the intracellular Ca²⁺ concentration ([Ca²⁺]_i) from this organelle and from the acidocalcisomes in the parasite cytoplasm. The same general mechanism has been demonstrated for SQ109, a new anti-tuberculosis drug with potent trypanocidal effect. Miltefosine similarly induces a large increase in the [Ca²⁺]_i acting on the sphingosine-activated Ca²⁺ channel, the mitochondrion and acidocalcisomes. These examples, in conjunction with other evidence we review herein, strongly support targeting Ca²⁺ homeostasis as a strategy against Chagas disease.

Measurement of intracellular ions by flow cytometry

Using flow cytometry, single-cell measurements of calcium can be made on isolated populations identified by one or more phenotypic characteristics. Most earlier techniques for measuring cellular activation parameters determined the mean value for a population of cells, which did not permit optimal resolution of the responses. The flow cytometer is particularly useful for this purpose because it can measure ion concentrations in large numbers of single cells and thereby allows ion concentration to be correlated with other parameters such as immunophenotype and cell cycle stage. A limitation of flow cytometry, however, is that it does not permit resolution of certain complex kinetic responses such as cellular oscillatory responses. This unit describes the preparation of cells, including labeling with antibodies and with calcium probes, and discusses the principles of data analysis and interpretation.

Investigating second messenger signaling in vivo

All known second messengers are small molecules without complex structural features. However, each of them can mediate different, very specific cellular responses upon arrival of distinct extracellular cues in one and the same cell. From this follows the question of how signal specificity is achieved in space and time. Recent work showed that three factors play major roles in determining signal specificity: intensity, pattern, and compartmentalization of signals. Thus, for understanding the signaling in any specific context, generic information on the involvement of second messenger pathway(s) is insufficient and only the precise, time- and space-resolved monitoring of these processes will lead to meaningful insights. Even more demanding, many second messenger-based signaling events can only occur using tissue-specific morphological arrangements (e.g., striated organization of muscle and synaptic specializations in neurons), making the visualization of intact tissue mandatory. Finally, to appreciate the physiological relevance of second messenger signals, multiparametric readouts are generally needed. This chapter illustrates modes of multiparametric analysis of signaling in live mouse skeletal muscle and briefly discusses possible applications of the technique in other tissues including heart and brain.

Design of fluorescent fusion protein probes

Many fluorescent probes depend on the fluorescence resonance energy transfer (FRET) between fluorescent protein pairs. The efficiency of energy transfer becomes altered by conformational changes of a fused sensory protein in response to a cellular event. A structure-based approach can be taken to design probes better with improved dynamic ranges by computationally modeling conformational changes and predicting FRET efficiency changes of candidate biosensor constructs. FRET biosensors consist of at least three domains fused together: the donor protein, the sensory domain, and the acceptor protein. To more efficiently subclone fusion proteins containing multiple domains, a cassette-based system can be used. Generating a cassette library of commonly used domains facilitates the rapid subcloning of future fusion biosensor proteins. FRET biosensors can then be used with fluorescence microscopy for real-time monitoring of cellular events within live cells by tracking changes in FRET efficiency. Stimulants can be used to trigger a range of cellular events including Ca(2+) signaling, apoptosis, and subcellular translocations.

Plasmodium in the postgenomic era: new insights into the molecular cell biology of malaria parasites

In this review, we bring together some of the approaches toward understanding the cellular and molecular biology of Plasmodium species and their interaction with their host red blood cells. Considerable impetus has come from the development of new methods of molecular genetics and bioinformatics, and it is important to evaluate the wealth of these novel data in the context of basic cell biology. We describe how these approaches are gaining valuable insights into the parasite-host cell interaction, including (1) the multistep process of red blood cell invasion by the merozoite; (2) the mechanisms by which the intracellular parasite feeds on the red blood cell and exports parasite proteins to modify its cytoadherent properties; (3) the modulation of the cell cycle by sensing the environmental tryptophan-related molecules; (4) the mechanism used to survive in a low Ca(2+) concentration inside red blood cells; (5) the activation of signal transduction machinery and the regulation of intracellular calcium; (6) transfection technology; and (7) transcriptional regulation and genome-wide mRNA studies in Plasmodium falciparum.

A Computational Tool for Designing FRET Protein Biosensors by Rigid-Body Sampling of Their Conformational Space

Biosensors relying on the fluorescence resonance energy transfer (FRET) between fluorescent proteins have been used for live-cell imaging of cellular events including Ca(2+) signaling. The efficiency of energy transfer between the donor and acceptor fluorescent proteins depends on the relative distance and orientation between them, which become altered by conformational changes of a fused sensory protein caused by a cellular event. In this way, changes in FRET efficiency of Ca(2+) biosensors can be correlated with Ca(2+) concentrations. The design of these FRET biosensors can be improved by modeling conformational changes before and after a cellular event. Hence, a computational tool called FPMOD was developed to predict FRET efficiency changes by constructing FRET biosensors and sampling their conformational space through rigid-body rotation. We showed with FPMOD that our computational modeling approach can qualitatively predict the FRET efficiencies of a range of biosensors, which had strong agreement with experimental results.

Pharmacology of intracellular signalling pathways

This article provides a brief and somewhat personalized review of the dramatic developments that have occurred over the last 45 years in our understanding of intracellular signalling pathways associated with G-protein-coupled receptor activation. Signalling via cyclic AMP, the phosphoinositides and Ca(2+) is emphasized and these systems have already been revealed as new pharmacological targets. The therapeutic benefits of most of such targets are, however, yet to be realized, but it is certain that the discipline of pharmacology needs to widen its boundaries to meet these challenges in the future.

Calcium signalling: Past, present and future

Ca2+ is a universal second messenger controlling a wide variety of cellular reactions and adaptive responses. The initial appreciation of Ca2+ as a universal signalling molecule was based on the work of Sydney Ringer and Lewis Heilbrunn. More recent developments in this field were critically influenced by the invention of the patch clamp technique and the generation of fluorescent Ca2+ indicators. Currently the molecular Ca2+ signalling mechanisms are being worked out and we are beginning to assemble a reasonably complete picture of overall Ca2+ homeostasis. Furthermore, investigations of organellar Ca2+ homeostasis have added complexity to our understanding of Ca2+ signalling. The future of the Ca2+ signalling field lies with detailed investigations of the integrative function in vivo and clarification of the pathology associated with malfunctions of Ca2+ signalling cascades.

Modified DNA analogues that sense light exposure with color changes

We report the discovery of a new class of light-sensing molecules. These light sensors are composed of fluorophore oligomers assembled on a DNA backbone. A combinatorial library of tetrafluorophores consisting of over 14 000 compounds was synthesized and screened for rapid responses toward light exposure. Among the most light-sensitive molecules, at least three tetramers were found to respond to light exposure with apparent color changes, rather than simple photobleaching.

Examining intracellular organelle function using fluorescent probes: from animalcules to quantum dots

Fluorescence microscopy imaging has become one of the most useful techniques to assess the activity of individual cells, subcellular trafficking of signals to and between organelles, and to appreciate how organelle function is regulated. The past 2 decades have seen a tremendous advance in the rational design and development in the nature and selectivity of probes to serve as reporters of the intracellular environment in live cells. These probes range from small organic fluorescent molecules to fluorescent biomolecules and photoproteins ingeniously engineered to follow signaling traffic, sense ionic and nonionic second messengers, and report various kinase activities. These probes, together with recent advances in imaging technology, have enabled significantly enhanced spatial and temporal resolution. This review summarizes some of these developments and their applications to assess intracellular organelle function.

Measurement of intracellular ions by flow cytometry

The recent development of a number of new fluorescent probes makes it possible to measure the concentrations of various intracellular free ions in single living cells. Among these ions are calcium, magnesium, sodium, potassium, and hydrogen (pH). This unit describes flow cytometric protocols using the dyes Indo-1 AM, Fluo-3, and Fura Red AM to measure intracellular calcium concentration. Support protocols detail the use of calcium buffers to calibrate a flow cytometric calcium assay, and methods to facilitate dye loading; an alternate protocol describes the use of a spectrofluorimeter to measure intracellular calcium for those investigators without access to a flow cytometer.

Mitochondrial pH monitored by a new engineered green fluorescent protein mutant

We here describe a new molecularly engineered green fluorescent protein chimera that shows a high sensitivity to pH in the alkaline range. This probe was named mtAlpHi, for mitochondrial alkaline pH indicator, and possesses several key properties that render it optimal for studying the dynamics of mitochondrial matrix pH, e.g. it has an apparent pK(a) (pK(a)') around 8.5, it shows reversible and large changes in fluorescence in response to changes in pH (both in vitro and in intact cells), and it is selectively targeted to the mitochondrial matrix. Using mtAlpHi we could monitor pH changes that occur in the mitochondrial matrix in a variety of situations, e.g. treatment with uncouplers or Ca(2+) ionophores, addition of drugs that interfere with ATP synthesis or electron flow in the respiratory chain, weak bases or acids, and receptor activation. We observed heterogeneous pH increases in the mitochondrial matrix during Ca(2+) accumulation by this organelle. Finally, we demonstrate that Ca(2+) mobilization from internal stores induced by ionomycin and A23187 cause a dramatic acidification of the mitochondrial matrix.