Dynamic visualization of signaling activities in living cells

A gene-encoded FRET fluorescent sensor designed for detecting asymmetric dimethylation levels in vitro and in living cells

Arginine methylation is involved in many important biological processes. PRMT1 is a major arginine methyltransferase in mammalian cells and is highly conserved in eukaryotes. It catalyzes the methylation of various of substrates, including histones, and PRMT1 has been reported to be overexpressed in many cancers, indicating that it is a potential therapeutic target. No tool for efficient methylation level detection in living cells has been available to date. In this work, we designed and constructed a gene-encoded fluorescence resonance energy transfer (FRET) fluorescent sensor for detecting dimethylation levels in living cells and evaluated its functional efficiency both in vitro and in living cells. Both site-directed mutagenesis and PRMT1 inhibition experiments verified that the fluorescent sensor responded to changes in PRMT1 activity and to different PRMT1-induced methylation levels in vitro. Finally, we verified that this optimized methyl sensor responded sensitively to changes in methylation levels in living cells by overexpressing and inhibiting PRMT1, which makes it a useful tool for real-time imaging of arginine methylation. As a new tool for detecting arginine dimethylation levels in living cells, the designed FRET sensor is very important for posttranslational studies and may show a wide range of applications.

Integrated Strategies to Gain a Systems-Level View of Dynamic Signaling Networks

In order to survive and function properly in the face of an ever changing environment, cells must be able to sense changes in their surroundings and respond accordingly. Cells process information about their environment through complex signaling networks composed of many discrete signaling molecules. Individual pathways within these networks are often tightly integrated and highly dynamic, allowing cells to respond to a given stimulus (or, as is typically the case under physiological conditions, a combination of stimuli) in a specific and appropriate manner. However, due to the size and complexity of many cellular signaling networks, it is often difficult to predict how cellular signaling networks will respond under a particular set of conditions. Indeed, crosstalk between individual signaling pathways may lead to responses that are nonintuitive (or even counterintuitive) based on examination of the individual pathways in isolation. Therefore, to gain a more comprehensive view of cell signaling processes, it is important to understand how signaling networks behave at the systems level. This requires integrated strategies that combine quantitative experimental data with computational models. In this chapter, we first examine some of the progress that has recently been made toward understanding the systems-level regulation of cellular signaling networks, with a particular emphasis on phosphorylation-dependent signaling networks. We then discuss how genetically targetable fluorescent biosensors are being used together with computational models to gain unique insights into the spatiotemporal regulation of signaling networks within single, living cells.

EMBO conference series: Chemical Biology 2014

Around 300 people from 18 countries took part in the fourth biennial Chemical Biology conference at The European Molecular Biology Laboratory (EMBL) in Heidelberg, from August 20 to 23, 2014. Many advances in the field of chemical biology were presented in talks and poster sessions. Picture: Petra Riedinger (EMBL).

Optimizing targeted cancer therapy: towards clinical application of systems biology approaches

In cancer, genetic and epigenetic alterations ultimately culminate in discordant activation of signal transduction pathways driving the malignant process. Pharmacological or biological inhibition of such pathways holds significant promise with respect to devising rational therapy for cancer. Thus, technical concepts pursuing robust characterization of kinase activity in tissue samples from cancer patients have been subject of investigation. In the present review we provide a comprehensive overview of these techniques and discuss their advantages and disadvantages for systems biology approaches to identify kinase targets in oncological disease. Recent advances in the development and application of array-based peptide-substrate kinase activity screens show great promise in overcoming the discrepancy between the evaluation of aberrant cell signaling in specific malignancies or even individual patients and the currently available ensemble of highly specific targeted treatment strategies. These developments have the potential to result in a more effective selection of kinase inhibitors and thus optimize mechanism-based patient-specific therapeutic strategies. Given the results from current research on the tumor kinome, generating network views on aberrant tumor cell signaling is critical to meet this challenge.

Cell-cycle markers and biosensors

Since the first schematic illustrations of dividing cells, we have come a long way in characterising eukaryotic cells and defining their cell-cycle status thanks to a number of complementary approaches. Although most of these approaches rely on cell-fixation procedures to identify molecular components in cell lysates, cultured cells or tissues, the development of GFP technology has enabled visualisation of virtually any fusion protein in cellulo and in vivo, and the exploitation of functional elements with well-defined spatiotemporal characteristics has enabled the development of genetically encoded fluorescent markers of cell-cycle phases, thus providing novel means of characterising the status of living cells in real time with high resolution. Together with technological advances in fluorescence chemistry and imaging approaches, the more recent development of fluorescent biosensors has provided direct means of probing cell-cycle regulators and of studying their dynamics with high spatial and temporal resolution. Here we review classical approaches that rely on cell fixation to characterise the cell-cycle status and its regulatory enzymes, and we describe the more recent development of cell-cycle markers based on genetically encoded fusions of fluorescent proteins with characteristic cell-cycle features, and of fluorescent biosensor technology to probe cell-cycle regulators in living cells. Biosensors not only provide a means of characterising the behaviour of cell-cycle regulators in their natural environment, they are also very useful for comparative studies of biological processes in healthy and pathological conditions, and can be further applied to diagnostic approaches to assess the status of a specific target, and to monitor response to therapeutic intervention.

Fluorescent biosensors of intracellular targets from genetically encoded reporters to modular polypeptide probes

With the escalation of drug discovery programmes, it has become essential to visualize and monitor biological activities in healthy and pathological cells, with high spatial and temporal resolution. To this aim, the development of probes and sensors, which can report on the levels and activities of specific intracellular targets, has become essential. Together with the discovery of the Green Fluorescent Protein (GFP), and the development of GFP-based reporters, recent advances in the synthesis of small molecule fluorescent probes, and the explosion of fluorescence-based imaging technologies, the biosensor field has witnessed a dramatic expansion of fluorescence-based reporters which can be applied to complex biological samples, living cells and tissues to probe protein/protein interactions, conformational changes and posttranslational modifications. Here, we review recent developments in the field of fluorescent biosensor technology. We describe different varieties and categories of fluorescent biosensors together with an overview of the technologies commonly employed to image biosensors in cellulo and in vivo. We discuss issues and strategies related to the choice of synthetic fluorescent probes, labelling, quenching, caging and intracellular delivery of biosensors. Finally, we provide examples of some well-characterized genetically encoded FRET reporter systems, peptide and protein biosensors and describe biosensor applications in a wide variety of fields.

Green light to illuminate signal transduction events

When cells are exposed to hormones that act on cell surface receptors, information is processed through the plasma membrane into the cell interior via second messengers generated in the inner leaflet of the plasma membrane. Individual biochemical steps along this cascade have been characterized from ligand binding to receptors through to activation of guanine nucleotide binding proteins and their downstream effectors such as adenylate cyclase or phospholipase C. However, the complexity of temporal and spatial integration of these molecular events requires that they are studied in intact cells. The great expansion of fluorescent techniques and improved imaging technologies such as confocal and TIRF microscopy combined with genetically-engineered protein modules has provided a completely new approach to signal transduction research. Spatial definition of biochemical events followed with real-time temporal resolution has become a standard goal, and several new techniques are now breaking the resolution barrier of light microscopy.