A split enhanced green fluorescent protein-based reporter in yeast two-hybrid system

Ste2p Under the Microscope: the Investigation of Oligomeric States of a Yeast G Protein-Coupled Receptor

Oligomerization of G protein-coupled receptors (GPCRs) may play important roles in maturation, internalization, signaling, and pharmacology of these receptors. However, the nature and extent of their oligomerization is still under debate. In our study, Ste2p, a yeast mating pheromone GPCR, was tagged with enhanced green fluorescent protein (EGFP), mCherry, and with split florescent protein fragments at the receptor C-terminus. The Förster resonance energy transfer (FRET) technique was used to detect receptors' oligomerization by calculating the energy transfer from EGFP to mCherry. Stimulation of Ste2p oligomers with the receptor ligand did not result in any significant change on observed FRET values. The bimolecular fluorescence complementation (BiFC) assay was combined with FRET to further investigate the tetrameric complexes of Ste2p. Our results suggest that in its quiescent (nonligand-activated) state, Ste2p is found at least as a tetrameric complex on the plasma membrane. Intriguingly, receptor tetramers in their active form showed a significant increase in FRET. This study provides a direct in vivo visualization of Ste2p tetramers and the pheromone effect on the extent of the receptor oligomerization.

Detecting In-Situ oligomerization of engineered STIM1 proteins by diffraction-limited optical imaging

Several signaling proteins require self-association of individual monomer units to be activated for triggering downstream signaling cascades in cells. Methods that allow visualizing their underlying molecular mechanisms will immensely benefit cell biology. Using enhanced Green Fluorescent Protein (eGFP) complementation, here I present a functional imaging approach for visualizing the protein-protein interaction in cells. Activation mechanism of an ER (endoplasmic reticulum) resident Ca²⁺ sensor, STIM1 (Stromal Interaction Molecule 1) that regulates store-operated Ca²⁺ entry in cells is considered as a model system. Co-expression of engineered full-length human STIM1 (ehSTIM1) with N-terminal complementary split eGFP pairs in mammalian cells fluoresces to form ‘puncta’ upon a drop in ER lumen Ca²⁺ concentration. Quantization of discrete fluorescent intensities of ehSTIM1 molecules at a diffraction-limited resolution revealed a diverse set of intensity levels not exceeding six-fold. Detailed screening of the ehSTIM1 molecular entities characterized by one to six fluorescent emitters across various in-plane sections shows a greater probability of occurrence for entities with six emitters in the vicinity of the plasma membrane (PM) than at the interior sections. However, the number density of entities with six emitters was lesser than that of others localized close to the PM. This finding led to hypothesize that activated ehSTIM1 dimers perhaps oligomerize in bundles ranging from 1–6 with an increased propensity for the occurrence of hexamers of ehSTIM1 dimer units close to PM even when its partner protein, ORAI1 (PM resident Ca²⁺ channel) is not sufficiently over-expressed in cells. The experimental data presented here provide direct evidence for luminal domain association of ehSTIM1 monomer units to trigger activation and allow enumerating various oligomers of ehSTIM1 in cells.

The yeast Ste2p G protein-coupled receptor dimerizes on the cell plasma membrane

Dimerization of G protein-coupled receptors (GPCR) may play an important role in maturation, internalization, signaling and/or pharmacology of these receptors. However, the location where dimerization occurs is still under debate. In our study, variants of Ste2p, a yeast mating pheromone GPCR, were tagged with split EGFP (enhanced green fluorescent protein) fragments inserted between transmembrane domain seven and the C-terminus or appended to the C-terminus. Bimolecular Fluorescence Complementation (BiFC) assay was used to determine where receptor dimerization occurred during protein trafficking by monitoring generation of EGFP fluorescence, which occurred upon GPCR dimerization. Our results suggest that these tagged receptors traffic to the membrane as monomers, undergo dimerization or higher ordered oligomerization predominantly on the plasma membrane, and are internalized as dimers/oligomers. This study is the first to provide direct in vivo visualization of GPCR dimerization/oligomerization, during trafficking to and from the plasma membrane.

Mapping Protein-Protein Interaction Using High-Throughput Yeast 2-Hybrid

A tremendous asset to the analysis of protein-protein interactions is the yeast-2-hybrid (Y2H) method. The Y2H assay is a heterologous system that is expanding network biology knowledge via in vivo investigations of binary protein-protein interactions. Traditionally, the Y2H protocol entails the mating or co-transformation of yeast in solid agar media followed by visual analysis for diploid selection. Having played a key role in identifying protein-protein interactions for nearly three decades in a wide range of biological systems, the Y2H system assays the interaction between two proteins of interest which results in a reconstituted and/or activation of transcription factor allowing a reporter gene to be transcribed. Overall, the Y2H method takes advantage of two factors: (1) the auxotrophic yeast requires expression of the reporter gene to grow in media purposefully designed to lack one or more essential amino acids, and (2) the DNA-binding (DB) domain of transcription factor GAL4 is unable to initiate transcription unless it is physically associated with an activating domain (AD), which, together, DBs and ADs are fused to proteins of interest that must interact with each other to reconstitute the transcription factor and activate the reporter gene. The applications of Y2H are broad, entailing fields such as drug discovery, clinical trials for human disease including cancer and neurodegenerative disease, and extend even into synthetic biology applications and cellular engineering. This chapter begins with an introduction to the fundamental mechanics of Y2H utilizing a genetically engineered strain of yeast and proceeds with an in-depth look at the different types of Y2H and turn our focus particularly to the GAL4-based Y2H system to map protein-protein interactions. We will then provide a step-by-step protocol for the Y2H experimentation preceded by a materials listing while simultaneously including key notes throughout the entire experimental process of biological-mechanistic and historical understandings of the steps.

Two-hybrid-based systems: powerful tools for investigation of membrane traffic machineries

Protein-protein interactions regulate biological processes and are fundamental for cell functions. Recently, efforts have been made to define interactomes, which are maps of protein-protein interactions that are useful for understanding biological pathways and networks and for investigating how perturbations of these networks lead to diseases. Therefore, interactomes are becoming fundamental for establishing the molecular basis of human diseases and contributing to the discovery of effective therapies. Interactomes are constructed based on experimental data present in the literature and computational predictions of interactions. Several biochemical, genetic and biotechnological techniques have been used in the past to identify protein-protein interactions. The yeast two-hybrid system has beyond doubt represented a revolution in the field, being a versatile tool and allowing the immediate identification of the interacting proteins and isolation of the cDNA coding for the interacting peptide after in vivo screening. Recently, variants of the yeast two-hybrid assay have been developed, including high-throughput systems that promote the rapidly growing field of proteomics. In this review we will focus on the role of this technique in the discovery of Rab interacting proteins, highlighting the importance of high-throughput two-hybrid screening as a tool to study the complexity of membrane traffic machineries.

An eYFP reporter gene for the yeast two-hybrid system

The yeast two-hybrid system is a powerful tool for detecting binary protein interactions, widely used in large-scale interactome mapping. We modified two yeast strains commonly used in yeast two-hybrid experiments by integrating into their genomes a new reporter gene encoding the enhanced yellow fluorescent protein eYFP. The suitability of this reporter gene for interaction screening was evaluated by fluorescence microscopy and fluorescence-activated cell sorting analysis. The gene shows good potential as a two-hybrid reporter gene for detecting strong interactions. Gal4 transcriptional activation gives rise to sufficient fluorescence for detection with a flow cytometer, but the eYFP reporter is not sensitive enough for detecting weak or moderate interactions. This study highlights the advantages of a fluorescent reporter gene in yeast two-hybrid screening.

Diversity in genetic in vivo methods for protein-protein interaction studies: from the yeast two-hybrid system to the mammalian split-luciferase system

The yeast two-hybrid system pioneered the field of in vivo protein-protein interaction methods and undisputedly gave rise to a palette of ingenious techniques that are constantly pushing further the limits of the original method. Sensitivity and selectivity have improved because of various technical tricks and experimental designs. Here we present an exhaustive overview of the genetic approaches available to study in vivo binary protein interactions, based on two-hybrid and protein fragment complementation assays. These methods have been engineered and employed successfully in microorganisms such as Saccharomyces cerevisiae and Escherichia coli, but also in higher eukaryotes. From single binary pairwise interactions to whole-genome interactome mapping, the self-reassembly concept has been employed widely. Innovative studies report the use of proteins such as ubiquitin, dihydrofolate reductase, and adenylate cyclase as reconstituted reporters. Protein fragment complementation assays have extended the possibilities in protein-protein interaction studies, with technologies that enable spatial and temporal analyses of protein complexes. In addition, one-hybrid and three-hybrid systems have broadened the types of interactions that can be studied and the findings that can be obtained. Applications of these technologies are discussed, together with the advantages and limitations of the available assays.

Allosteric regulation of human liver pyruvate kinase by peptides that mimic the phosphorylated/dephosphorylated N-terminus

An advantage of studying allosteric regulation over covalent modification is that allostery allows the experimentalist to vary the concentration of effector, thereby allowing independent quantification of effector binding and allosteric coupling. In turn, this capacity allows the use of effector analogues to determine which regions of the effector contribute to effector binding and which contribute to allosteric regulation. Like many other proteins, human liver pyruvate kinase (hL-PYK) is regulated by phosphorylation. The phosphorylation of hL-PYK occurs on Ser12 of the N-terminus. Phosphorylation appears to interrupt an interaction (distant from the active site) between the N-terminus and the main body of the protein. Since this interaction increases the affinity of hL-PYK for the substrate (phosphoenolpyruvate, PEP), phosphorylation-dependent interruption of the N-terminus/main-body interaction results in an antagonism of PEP binding. Due to the advantages of studying an allosteric system, we detail a protocol to express and purify N-terminal peptides of hL-PYK using a SUMO-fusion system. We further demonstrate that these peptides act as allosteric regulators that modulate the affinity of hL-PYK for PEP.

The GAL genetic switch: visualisation of the interacting proteins by split-EGFP bimolecular fluorescence complementation

A split-EGFP bimolecular fluorescence complementation assay was used to visualise and locate three interacting pairs of proteins from the GAL genetic switch of the budding yeast, Saccharomyces cerevisiae. Both the Gal4p-Gal80p and Gal80p-Gal3p pairs were found to be located in the nucleus under inducing conditions. However, the Gal80p-Gal1p complex was located throughout the cell. These results support recent work establishing an initial interaction between Gal3p and Gal80p occurring in the nucleus. Labelling of all three protein pairs impaired the growth of the yeast strains and resulted in reduced galactokinase activity in cell extracts. The most likely cause of this impairment is decreased dissociation rates of the complexes, caused by the essentially irreversible reassembly of the EGFP fragments. This suggests that a fully functional GAL genetic switch requires dynamic interactions between the protein components. These results also highlight the need for caution in the interpretation of in vivo split-EGFP experiments.

A molecularly engineered split reporter for imaging protein-protein interactions with positron emission tomography

Improved techniques to non-invasively image protein-protein interactions (PPIs) are essential. We molecularly engineered a positron emission tomography (PET)-based split reporter (herpes simplex virus type 1 thymidine kinase [TK]), split between Thr265 and Ala266, and used this in a protein-fragment complementation assay (PCA) to quantitatively measure PPIs in mammalian cells and to microPET image them in living mice. An introduced point mutation (V119C) significantly enhanced TK complementation in PCAs based on rapamycin modulation of FRB (FKBP12-rapamycin-binding domain) and FKBP12 (FK506 binding protein), on interaction of hypoxia-inducible factor-1α and the von Hippel-Lindau tumor suppressor, and in an estrogen receptor intramolecular protein folding assay. Applications of this novel split TK are potentially far-reaching, including for example considerably more accurate monitoring of immune and stem cell therapies, allowing unprecedented fully quantitative and tomographic PET localization of PPIs in pre-clinical small and large animal models of disease.

Split-EGFP screens for the detection and localisation of protein-protein interactions in living yeast cells

Proteomics aims to identify and classify the proteins present in a particular cell or tissue. However, we know that proteins rarely function alone and knowledge of which proteins interact with which other proteins is vital if we wish to understand how cells work. The budding yeast, Saccharomyces cerevisiae, is a well-established model for studying protein-protein interactions, and a number of methods have been developed to do this. A method for the in vivo detection and localisation of interacting pairs of proteins in living yeast cells is presented. The method relies on the ability of fragments of enhanced green fluorescent protein (EGFP) to reassemble if brought into close proximity. The reassembled EGFP regains the ability to fluoresce, and this fluorescence can be detected providing evidence of interaction and information about its location. S. cerevisiae is an ideal organism to apply this method to due to the relative ease with which its genome can be manipulated. The method described enables the modification of S. cerevisiae genes at the 3'-end with DNA encoding fragments of EGFP. Consequently, the expression levels of the proteins are unlikely to be affected and thus the method is unlikely to result in false positives. In addition to the protocol for labelling and detection of interacting pairs of yeast proteins, methods for simple tests for the effects of the labelling on the organism's function are presented.

A dual function for Pex3p in peroxisome formation and inheritance

Pex3p interacts with peroxisome retention factor Inp1p at the peroxisomal membrane and functions in the organelle’s segregation in addition to its biogenesis.

Saccharomyces cerevisiae Pex3p has been shown to act at the ER during de novo peroxisome formation. However, its steady state is at the peroxisomal membrane, where its role is debated. Here we show that Pex3p has a dual function: one in peroxisome formation and one in peroxisome segregation. We show that the peroxisome retention factor Inp1p interacts physically with Pex3p in vitro and in vivo, and split-GFP analysis shows that the site of interaction is the peroxisomal membrane. Furthermore, we have generated PEX3 alleles that support peroxisome formation but fail to support recruitment of Inp1p to peroxisomes, and as a consequence are affected in peroxisome segregation. We conclude that Pex3p functions as an anchor for Inp1p at the peroxisomal membrane, and that this function is independent of its role at the ER in peroxisome biogenesis.

A surface display yeast two-hybrid screening system for high-throughput protein interactome mapping

Despite the wide acceptance of yeast two-hybrid (Y2H) system for protein-protein interaction analysis and discovery, conventional Y2H assays are not well suited for high-throughput screening of the protein interaction network ("interactome") on a genomic scale due to several limitations, including labor-intensive agar plating and colony selection methods associated with the use of nutrient selection markers, complicated reporter analysis methods associated with the use of LacZ enzyme reporters, and incompatibility of the liquid handling robots. We recently reported a robust liquid culture Y2H system based on quantitative analysis of yeast-enhanced green fluorescent protein (yEGFP) reporters that greatly increased the analysis throughput and compatibility with liquid handling robots. To further advance its utility in high-throughput complementary DNA (cDNA) library screening, we report the development of a novel surface display Y2H (sdY2H) library screening system with uniquely integrated surface display hemagglutination (sdHA) antigen and yEGFP reporters. By introduction of a surface reporter sdHA into the yEGFP-based Y2H system, positive Y2H targets are quickly isolated from library cells by a simple magnetic separation without a large plating effort. Moreover, the simultaneous scoring of multiple reporters, including sdHA, yEGFP, and conventional nutrient markers, greatly increased the specificity of the Y2H assay. The feasibility of the sdY2H assay on large cDNA library screening was demonstrated by the successful recovery of positive P53/T interaction pairs at a target-to-background ratio of 1:1,000,000. Together with the massive parallel DNA sequencing technology, it may provide a powerful proteomic tool for high-throughput interactome mapping on a genomic scale.

Development and implementation of split-GFP-based bimolecular fluorescence complementation (BiFC) assays in yeast

BiFC (bimolecular fluorescence complementation) is a tool for investigating interactions between proteins. Non-fluorescent fragments of, for example, GFP (green fluorescent protein) are fused to the interacting partners. The interaction brings the fragments together, which then fold, reassemble and fluoresce. This process can be carried out in living cells and provides information both on the interaction and its subcellular location. We have developed a split-GFP-based BiFC assay for use in the budding yeast Saccharomyces cerevisiae in which the modifications are carried out at the genomic level, thus resulting in the tagged yeast proteins being expressed at wild-type levels. The system is capable of detecting interactions in all subcellular compartments tested (the cytoplasm, mitochondria and nucleus) and makes a valuable addition to techniques for the investigation of protein-protein interactions in this model organism.

Bimolecular fluorescence complementation (BiFC) analysis as a probe of protein interactions in living cells

Protein interactions are a fundamental mechanism for the generation of biological regulatory specificity. The study of protein interactions in living cells is of particular significance because the interactions that occur in a particular cell depend on the full complement of proteins present in the cell and the external stimuli that influence the cell. Bimolecular fluorescence complementation (BiFC) analysis enables direct visualization of protein interactions in living cells. The BiFC assay is based on the association between two nonfluorescent fragments of a fluorescent protein when they are brought in proximity to each other by an interaction between proteins fused to the fragments. Numerous protein interactions have been visualized using the BiFC assay in many different cell types and organisms. The BiFC assay is technically straightforward and can be performed using standard molecular biology and cell culture reagents and a regular fluorescence microscope or flow cytometer.