Monitoring protein-protein interactions in intact eukaryotic cells by beta-galactosidase complementation

Structure-guided design of a reversible fluorogenic reporter of protein-protein interactions

A reversible green fluorogenic protein-fragment complementation assay was developed based on the crystal structure of UnaG, a recently discovered fluorescent protein. In living mammalian cells, the nonfluorescent fragments complemented and rapidly became fluorescent upon rapamycin-induced FKBP and Frb protein interaction, and lost fluorescence when the protein interaction was inhibited. This reversible fluorogenic reporter, named uPPI [UnaG-based protein-protein interaction (PPI) reporter], uses bilirubin (BR) as the chromophore and requires no exogenous cofactor. BR is an endogenous molecule in mammalian cells and is not fluorescent by itself. uPPI may have many potential applications in visualizing spatiotemporal dynamics of PPIs.

Mechanisms of JAK/STAT pathway negative regulation by the short coreceptor Eye Transformer/Latran

The short receptor Et/Lat negatively regulates Drosophila JAK/STAT signaling. It binds to intracellular components and the Domeless receptor but cannot bind ligands, thus generating a signaling-incompetent complex. Et/Lat is also more stable than Dome. The study provides insights into how short receptors negatively regulate signaling.

Transmembrane receptors interact with extracellular ligands to transduce intracellular signaling cascades, modulate target gene expression, and regulate processes such as proliferation, apoptosis, differentiation, and homeostasis. As a consequence, aberrant signaling events often underlie human disease. Whereas the vertebrate JAK/STAT signaling cascade is transduced via multiple receptor combinations, the Drosophila pathway has only one full-length signaling receptor, Domeless (Dome), and a single negatively acting receptor, Eye Transformer/Latran (Et/Lat). Here we investigate the molecular mechanisms underlying Et/Lat activity. We demonstrate that Et/Lat negatively regulates the JAK/STAT pathway activity and can bind to Dome, thus reducing Dome:Dome homodimerization by creating signaling-incompetent Dome:Et/Lat heterodimers. Surprisingly, we find that Et/Lat is able to bind to both JAK and STAT92E but, despite the presence of putative cytokine-binding motifs, does not detectably interact with pathway ligands. We find that Et/Lat is trafficked through the endocytic machinery for lysosomal degradation but at a much slower rate than Dome, a difference that may enhance its ability to sequester Dome into signaling-incompetent complexes. Our data offer new insights into the molecular mechanism and regulation of Et/Lat in Drosophila that may inform our understanding of how short receptors function in other organisms.

Split protein biosensor assays in molecular pharmacological studies

Cellular signalling is commonly mediated through dynamic protein-protein interactions (PPIs). When pivotal PPIs are deregulated, cellular signalling can be altered; it is therefore attractive to monitor regulated PPIs to understand their role in health and disease. Genetically encoded biosensors that rely on protein fragment complementation have made it feasible to monitor PPIs in living cells precisely and robustly. In particular, split protein biosensors using fluorescent proteins or luciferases are frequently applied. Further, split TEV and split ubiquitin biosensor platforms flexibly allow using readouts of choice, including transcriptional barcode reporters that are amenable to multiplexed high-throughput formats and next-generation sequencing. Combining these technologies will enable assessing drug target activities and cellular response profiles in parallel, thereby opening up new avenues in drug discovery.

Studying Cellular Signal Transduction with OMIC Technologies

In the gulf between genotype and phenotype exists proteins and, in particular, protein signal transduction systems. These systems use a relatively limited parts list to respond to a much longer list of extracellular, environmental, and/or mechanical cues with rapidity and specificity. Most signaling networks function in a highly non-linear and often contextual manner. Furthermore, these processes occur dynamically across space and time. Because of these complexities, systems and "OMIC" approaches are essential for the study of signal transduction. One challenge in using OMIC-scale approaches to study signaling is that the "signal" can take different forms in different situations. Signals are encoded in diverse ways such as protein-protein interactions, enzyme activities, localizations, or post-translational modifications to proteins. Furthermore, in some cases, signals may be encoded only in the dynamics, duration, or rates of change of these features. Accordingly, systems-level analyses of signaling may need to integrate multiple experimental and/or computational approaches. As the field has progressed, the non-triviality of integrating experimental and computational analyses has become apparent. Successful use of OMIC methods to study signaling will require the "right" experiments and the "right" modeling approaches, and it is critical to consider both in the design phase of the project. In this review, we discuss common OMIC and modeling approaches for studying signaling, emphasizing the philosophical and practical considerations for effectively merging these two types of approaches to maximize the probability of obtaining reliable and novel insights into signaling biology.

Intermonomer Interactions in Hemagglutinin Subunits HA1 and HA2 Affecting Hemagglutinin Stability and Influenza Virus Infectivity

Influenza virus hemagglutinin (HA) mediates virus entry by binding to cell surface receptors and fusing the viral and endosomal membranes following uptake by endocytosis. The acidic environment of endosomes triggers a large-scale conformational change in the transmembrane subunit of HA (HA2) involving a loop (B loop)-to-helix transition, which releases the fusion peptide at the HA2 N terminus from an interior pocket within the HA trimer. Subsequent insertion of the fusion peptide into the endosomal membrane initiates fusion. The acid stability of HA is influenced by residues in the fusion peptide, fusion peptide pocket, coiled-coil regions of HA2, and interactions between the surface (HA1) and HA2 subunits, but details are not fully understood and vary among strains. Current evidence suggests that the HA from the circulating pandemic 2009 H1N1 influenza A virus [A(H1N1)pdm09] is less stable than the HAs from other seasonal influenza virus strains. Here we show that residue 205 in HA1 and residue 399 in the B loop of HA2 (residue 72, HA2 numbering) in different monomers of the trimeric A(H1N1)pdm09 HA are involved in functionally important intermolecular interactions and that a conserved histidine in this pair helps regulate HA stability. An arginine-lysine pair at this location destabilizes HA at acidic pH and mediates fusion at a higher pH, while a glutamate-lysine pair enhances HA stability and requires a lower pH to induce fusion. Our findings identify key residues in HA1 and HA2 that interact to help regulate H1N1 HA stability and virus infectivity.

IMPORTANCE

Influenza virus hemagglutinin (HA) is the principal antigen in inactivated influenza vaccines and the target of protective antibodies. However, the influenza A virus HA is highly variable, necessitating frequent vaccine changes to match circulating strains. Sequence changes in HA affect not only antigenicity but also HA stability, which has important implications for vaccine production, as well as viral adaptation to hosts. HA from the pandemic 2009 H1N1 influenza A virus is less stable than other recent seasonal influenza virus HAs, but the molecular interactions that contribute to HA stability are not fully understood. Here we identify molecular interactions between specific residues in the surface and transmembrane subunits of HA that help regulate the HA conformational changes needed for HA stability and virus entry. These findings contribute to our understanding of the molecular mechanisms controlling HA function and antigen stability.

Sensing of biomolecular interactions using fluorescence complementing systems in living cells

Sensing biomolecule interactions in living cells allows for a deeper understanding of the mechanisms governing biological processes, and has increasing significance for improvements in clinical diagnosis. It is now possible by using molecular biosensors. One method involving molecular biosensors is called molecular fluorescence complementation, usually referred to as BiFC (bimolecular fragment/fluorescence complementary/complementation) or TriFC (trimolecular fragment complementary/complementation). This complementation method is based on the principle that two non-fluorescent fragments of a fluorescent protein are brought into sufficient lyclose proximity, upon which they are reconstructed so that fluorescence is re-established. This process relies on the interaction between the two fusion partners, which normally are proteins. This method is simple, noninvasive, sensitive, and does not require specialized tools, hence being available to most standard laboratories. Here, we selectively describe three relevant examples, although many other molecular interactions have been shown to work with this method. Recent developments of this method include multicolor BiFC, which allows for simultaneous detection of multi-biomolecule interactions, RNA-protein interactions, far red and near infrared sensing systems for deep tissue imaging. Challenges in the utilization of this method are discussed. Given the current rate of technological advancements, we believe that fluorescence fragment complementing systems have the potential to be utilized across a wide range of areas, including in routine research and clinical diagnosis.

Monitoring β-arrestin recruitment via β-lactamase enzyme fragment complementation: purification of peptide E as a low-affinity ligand for mammalian bombesin receptors

Identification of cognate ligands for G protein-coupled receptors (GPCRs) provides a starting point for understanding novel regulatory mechanisms. Although GPCR ligands have typically been evaluated through the activation of heterotrimeric G proteins, recent studies have shown that GPCRs signal not only through G proteins but also through β-arrestins. As such, monitoring β-arrestin signaling instead of G protein signaling will increase the likelihood of identifying currently unknown ligands, including β-arrestin-biased agonists. Here, we developed a cell-based assay for monitoring ligand-dependent GPCR-β-arrestin interaction via β-lactamase enzyme fragment complementation. Inter alia, β-lactamase is a superior reporter enzyme because of its cell-permeable fluorescent substrate. This substrate makes the assay non-destructive and compatible with fluorescence-activated cell sorting (FACS). In a reporter cell, complementary fragments of β-lactamase (α and ω) were fused to β-arrestin 2 and GPCR, respectively. Ligand stimulation initiated the interaction of these chimeric proteins (β-arrestin-α and GPCR-ω), and this inducible interaction was measured through reconstituted β-lactamase activity. Utilizing this system, we screened various mammalian tissue extracts for agonistic activities on human bombesin receptor subtype 3 (hBRS3). We purified peptide E as a low-affinity ligand for hBRS3, which was also found to be an agonist for the other two mammalian bombesin receptors such as gastrin-releasing peptide receptor (GRPR) and neuromedin B receptor (NMBR). Successful purification of peptide E has validated the robustness of this assay. We conclude that our newly developed system will facilitate the discovery of GPCR ligands.

Combining random gene fission and rational gene fusion to discover near-infrared fluorescent protein fragments that report on protein-protein interactions

Gene fission can convert monomeric proteins into two-piece catalysts, reporters, and transcription factors for systems and synthetic biology. However, some proteins can be challenging to fragment without disrupting function, such as near-infrared fluorescent protein (IFP). We describe a directed evolution strategy that can overcome this challenge by randomly fragmenting proteins and concomitantly fusing the protein fragments to pairs of proteins or peptides that associate. We used this method to create libraries that express fragmented IFP as fusions to a pair of associating peptides (IAAL-E3 and IAAL-K3) and proteins (CheA and CheY) and screened for fragmented IFP with detectable near-infrared fluorescence. Thirteen novel fragmented IFPs were identified, all of which arose from backbone fission proximal to the interdomain linker. Either the IAAL-E3 and IAAL-K3 peptides or CheA and CheY proteins could assist with IFP fragment complementation, although the IAAL-E3 and IAAL-K3 peptides consistently yielded higher fluorescence. These results demonstrate how random gene fission can be coupled to rational gene fusion to create libraries enriched in fragmented proteins with AND gate logic that is dependent upon a protein-protein interaction, and they suggest that these near-infrared fluorescent protein fragments will be suitable as reporters for pairs of promoters and protein-protein interactions within whole animals.

Quenching resonance energy transfer (QRET): a single-label technique for inhibitor screening and interaction studies

The increased number of therapeutic targets has led to a growing need for screening methods enabling possible inhibitor compound selection. Information for new therapeutic targets has been found mostly from sequencing of the human genome but this knowledge cannot be directly converted into clinically relevant drug molecules. After target identification, the multistep drug development process takes many years and hundreds of millions of dollars are spent without certainty of the outcome. The first and the most critical step in the drug development process is hit selection. The optimal high throughput screening method should provide the highest possible number of true positive hits for further studies and lead discovery. The result should be achieved with low material consumption in a rapid and automated process. Radioactive label based methods are sensitive, but due to the problems arising from the radioactivity, luminescence-based methods have become increasingly popular in screening. In this review, the time-resolved luminescence based quenching resonance energy transfer (QRET) technique is discussed for primary screening.

Stoichiometry of the α-complementation reaction of Escherichia coli β-galactosidase as revealed through single-molecule studies

The α-complementation reaction of β-galactosidase was studied at single-molecule resolution using arrays of femtoliter-sized wells. Single molecules of the complementation species were observed to be stable for long periods of time, demonstrating that the α-complementation reaction is irreversible. By directly counting the number of active molecules formed in the complementation reaction when different concentrations of enzyme acceptor (EA) and enzyme donor (ED) are used, we deduce that the EA:ED ratio in the complementation species is 4:1.

Mapping biochemical networks with protein fragment complementation assays

Cellular biochemical machineries, what we call pathways, consist of dynamically assembling and disassembling macromolecular complexes. Although our models for the organization of biochemical machines are derived largely from in vitro experiments, do they reflect their organization in intact, living cells? We have developed a general experimental strategy that addresses this question by allowing the quantitative probing of molecular interactions in intact, living cells. The experimental strategy is based on Protein fragment Complementation Assays (PCA), a method whereby protein interactions are coupled to refolding of enzymes from cognate fragments where reconstitution of enzyme activity acts as the detector of a protein interaction. A biochemical machine or pathway is defined by grouping interacting proteins into those that are perturbed in the same way by common factors (hormones, metabolites, enzyme inhibitors, etc.). In this chapter we review some of the essential principles of PCA and provide details and protocols for applications of PCA, particularly in mammalian cells, based on three PCA reporters, dihydrofolate reductase, green fluorescent protein, and β-lactamase.

Influenza virus M2 protein ion channel activity helps to maintain pandemic 2009 H1N1 virus hemagglutinin fusion competence during transport to the cell surface

The influenza virus hemagglutinin (HA) envelope protein mediates virus entry by first binding to cell surface receptors and then fusing viral and endosomal membranes during endocytosis. Cleavage of the HA precursor (HA0) into a surface receptor-binding subunit (HA1) and a fusion-inducing transmembrane subunit (HA2) by host cell enzymes primes HA for fusion competence by repositioning the fusion peptide to the newly created N terminus of HA2. We previously reported that the influenza virus M2 protein enhances pandemic 2009 influenza A virus [(H1N1)pdm09] HA-pseudovirus infectivity, but the mechanism was unclear. In this study, using cell-cell fusion and HA-pseudovirus infectivity assays, we found that the ion channel function of M2 was required for enhancement of HA fusion and HA-pseudovirus infectivity. The M2 activity was needed only during HA biosynthesis, and proteolysis experiments indicated that M2 proton channel activity helped to protect (H1N1)pdm09 HA from premature conformational changes as it traversed low-pH compartments during transport to the cell surface. While M2 has previously been shown to protect avian influenza virus HA proteins of the H5 and H7 subtypes that have polybasic cleavage motifs, this study demonstrates that M2 can protect HA proteins from human H1N1 strains that lack a polybasic cleavage motif. This finding suggests that M2 proton channel activity may play a wider role in preserving HA fusion competence among a variety of HA subtypes, including HA proteins from emerging strains that may have reduced HA stability.

IMPORTANCE

Influenza virus infects cells when the hemagglutinin (HA) surface protein undergoes irreversible pH-induced conformational changes after the virus is taken into the cell by endocytosis. HA fusion competence is primed when host cell enzymes cleave the HA precursor. The proton channel function of influenza virus M2 protein has previously been shown to protect avian influenza virus HA proteins that contain a polybasic cleavage site from pH-induced conformational changes during biosynthesis, but this effect is less well understood for human influenza virus HA proteins that lack polybasic cleavage sites. Using assays that focus on HA entry and fusion, we found that the M2 protein also protects (H1N1)pdm09 influenza A virus HA from premature conformational changes as it transits low-pH compartments during biosynthesis. This work suggests that M2 may play a wider role in preserving HA function in a variety of influenza virus subtypes that infect humans and may be especially important for HA proteins that are less stable.

Desired alteration of protein affinities: competitive selection of protein variants using yeast signal transduction machinery

Molecules that can control protein-protein interactions (PPIs) have recently drawn attention as new drug pipeline compounds. Here, we report a technique to screen desirable affinity-altered (affinity-enhanced and affinity-attenuated) protein variants. We previously constructed a screening system based on a target protein fused to a mutated G-protein γ subunit (Gγcyto) lacking membrane localization ability. This ability, required for signal transmission, is restored by recruiting Gγcyto into the membrane only when the target protein interacts with an artificially membrane-anchored candidate protein, thereby allowing interacting partners (Gγ recruitment system) to be searched and identified. In the present study, the Gγ recruitment system was altered by integrating the cytosolic expression of a third protein as a competitor to set a desirable affinity threshold. This enabled the reliable selection of both affinity-enhanced and affinity-attenuated protein variants. The presented approach may facilitate the development of therapeutic proteins that allow the control of PPIs.

Luciferase fragment complementation imaging in preclinical cancer studies

The luciferase fragment complementation assay (LFCA) enables molecular events to be non-invasively imaged in live cells in vitro and in vivo in a comparatively cheap and safe manner. It is a development of previous enzyme complementation assays in which reporter genes are split into two, individually enzymatically inactive, fragments that are able to complement one another upon interaction. This complementation can be used to externally visualize cellular activities. In recent years, the number of studies which have used LFCAs to probe questions relevant to cancer have increased, and this review summarizes the most significant and interesting of these. In particular, it focuses on work conducted on the epidermal growth factor, nuclear and chemokine receptor families, and intracellular signaling pathways, including IP3, cAMP, Akt, cMyc, NRF2 and Rho GTPases. LFCAs which have been developed to image DNA methylation and detect RNA transcripts are also discussed.

Structural complementation of the catalytic domain of pseudomonas exotoxin A

The catalytic moiety of Pseudomonas exotoxin A (domain III or PE3) inhibits protein synthesis by ADP-ribosylation of eukaryotic elongation factor 2. PE3 is widely used as a cytocidal payload in receptor-targeted protein toxin conjugates. We have designed and characterized catalytically inactive fragments of PE3 that are capable of structural complementation. We dissected PE3 at an extended loop and fused each fragment to one subunit of a heterospecific coiled coil. In vitro ADP-ribosylation and protein translation assays demonstrate that the resulting fusions-supplied exogenously as genetic elements or purified protein fragments-had no significant catalytic activity or effect on protein synthesis individually but, in combination, catalyzed the ADP-ribosylation of eukaryotic elongation factor 2 and inhibited protein synthesis. Although complementing PE3 fragments are catalytically less efficient than intact PE3 in cell-free systems, co-expression in live cells transfected with transgenes encoding the toxin fusions inhibits protein synthesis and causes cell death comparably as intact PE3. Complementation of split PE3 offers a direct extension of the immunotoxin approach to generate bispecific agents that may be useful to target complex phenotypes.

Fluorescent protein-based biosensors and their clinical applications

Green fluorescent protein and its relatives have shed their light on a wide range of biological problems. To date, with a color palette consisting of fluorescent proteins with different spectra, researchers can "paint" living cells as they desire. Moreover, sophisticated biosensors engineered to contain single or multiple fluorescent proteins, including FRET-based biosensors, spatiotemporally unveil molecular mechanisms underlying physiological processes. Although such molecules have contributed considerably to basic research, their abilities to be used in applied life sciences have yet to be fully explored. Here, we review the molecular bases of fluorescent proteins and fluorescent protein-based biosensors and focus on approaches aimed at applying such proteins to the clinic.

Protein fragment bimolecular fluorescence complementation analyses for the in vivo study of protein-protein interactions and cellular protein complex localizations

The analyses of protein-protein interactions are crucial for understanding cellular processes including signal transduction, protein trafficking, and movement. Protein fragment complementation assays are based on the reconstitution of protein function when non-active protein fragments are brought together by interacting proteins that were genetically fused to these protein fragments. Bimolecular fluorescence complementation (BiFC) relies on the reconstitution of fluorescent proteins and enables both the analysis of protein-protein interactions and the visualization of protein complex formations in vivo. Transient expression of proteins is a convenient approach to study protein functions in planta or in other organisms and minimizes the need for time-consuming generation of stably expressing transgenic organisms. Here we describe protocols for BiFC analyses in Nicotiana benthamiana and Arabidopsis thaliana leaves transiently transformed by Agrobacterium infiltration. Further, we discuss different BiFC applications and provide examples for proper BiFC analyses in planta.

Fluorescent biphenyl derivatives of phenylalanine suitable for protein modification

In a recent study, we demonstrated that structurally compact fluorophores incorporated into the side chains of amino acids could be introduced into dihydrofolate reductase from Escherichia coli (ecDHFR) with minimal disruption of protein structure or function, even when the site of incorporation was within a folded region of the protein. The modified proteins could be employed for FRET measurements, providing sensitive monitors of changes in protein conformation. The very favorable results achieved in that study encouraged us to prepare additional fluorescent amino acids of potential utility for studying protein dynamics. Presently, we describe the synthesis and photophysical characterization of four positional isomers of biphenyl-phenylalanine, all of which were found to exhibit potentially useful fluorescent properties. All four phenylalanine derivatives were used to activate suppressor tRNA transcripts and incorporated into multiple positions of ecDHFR. All phenylalanine derivatives were incorporated with good efficiency into position 16 of ecDHFR and afforded modified proteins that consumed NADPH at rates up to about twice the rate measured for wild type. This phenomenon has been noted on a number of occasions previously and shown to be due to an increase in the off-rate of tetrahydrofolate from the enzyme, altering a step that is normally rate limiting. When introduced into sterically accessible position 49, the four phenylalanine derivatives afforded DHFRs having catalytic function comparable to wild type. The four phenylalanine derivatives were also introduced into position 115 of ecDHFR, which is known to be a folded region of the protein less tolerant of structural alteration. As anticipated, significant differences were noted in the catalytic efficiencies of the derived proteins. The ability of two of the sizable biphenyl-phenylalanine derivatives to be accommodated at position 115 with minimal perturbation of DHFR function is attributed to rotational flexibility about the biphenyl bonds.

A new protein-protein interaction sensor based on tripartite split-GFP association

Monitoring protein-protein interactions in living cells is key to unraveling their roles in numerous cellular processes and various diseases. Previously described split-GFP based sensors suffer from poor folding and/or self-assembly background fluorescence. Here, we have engineered a micro-tagging system to monitor protein-protein interactions in vivo and in vitro. The assay is based on tripartite association between two twenty amino-acids long GFP tags, GFP10 and GFP11, fused to interacting protein partners, and the complementary GFP1-9 detector. When proteins interact, GFP10 and GFP11 self-associate with GFP1-9 to reconstitute a functional GFP. Using coiled-coils and FRB/FKBP12 model systems we characterize the sensor in vitro and in Escherichia coli. We extend the studies to mammalian cells and examine the FK-506 inhibition of the rapamycin-induced association of FRB/FKBP12. The small size of these tags and their minimal effect on fusion protein behavior and solubility should enable new experiments for monitoring protein-protein association by fluorescence.

In Vitro Anti-diabetic Activity of Sclerocarya Birrea and Ziziphus Mucronata

Type 2 diabetes mellitus is on the increase worldwide. Current treatments possess undesirable side-effects and therefore investigations into alternative remedies, which may be cost-effective and devoid of such side-effects, are on-going. Aqueous and methanol extracts of the bark of Sclerocarya birrea (A. Rich.) Hochst. subsp. caffra (Sond.) Kokwaro (Anacardiaceae) and Ziziphus mucronata Willd. subsp. mucronata (Rhamnaceae) were subjected to testing in order to assess their in vitro anti-diabetic activity. Total polyphenolic content and antioxidant activity, as well as the effect on α-amylase, α-glucosidase and cytotoxicity, were measured. Furthermore, glucose uptake was evaluated in C2C12 myotubes, 3T3-L1 adipocytes and HepG2 hepatocarcinoma cells, and insulin secretion in RIN-m5F rat pancreatic β-cells. The extracts of both plants inhibited the activities of α-amylase and α-glucosidase in a concentration dependent manner, with results being comparable with the positive control, acarbose. All the extracts contained antioxidant activity, with the methanol extracts of S. birrea displaying the strongest free radical scavenging capacity (IC50 = 2.16 μg/mL). Most of the extracts were not cytotoxic to the cell lines with IC50 values > 100 μg/mL. Extracts of both plants significantly increased glucose uptake in C2C12, 3T3-L1 and HepG2 cells. However, insulin secretion from RIN-m5F cells was not altered. This study provides evidence that the plants possess in vitro anti-diabetic properties.

Design and semisynthesis of photoactivable split-GFP by incorporation of photocleavable functionality

The design of proteins whose structure and function can be manipulated by the external stimuli has been of great interest in the field of protein engineering. In particular, caged proteins which can be activated by photo-irradiation become powerful tools for investigating a variety of biological events. Although protein caging is straightforward to render light-responsive protein functions, this approach mostly have difficulties based on the preparation of caged proteins in which amino acid residues required for biological activities must be specifically modified with synthetic photolabile groups. The synthetic peptide-based strategy for photoactivation of protein function may expand the versatility of protein caging approaches since the photolabile protecting group can be easily introduced into the peptide by means of standard solid-phase methods in a site-specific manner. In this study, we designed a new photoactivable green fluorescent protein (GFP), in which a relatively short C-terminal fragment (residues 214-230) of a dissected protein was modified with 7-diethylamino-4-hydroxymethylcoumarin (DECM) as a photoresponsive-protecting group. The introduced DECM unit completely inhibited the reconstitution with the GFP N-terminal fragment (residues 2-214). However, irradiation of visible light (>400 nm) resulted in efficient cleavage of DECM group, leading to acceleration of protein reassembly and concomitant GFP fluorescence recovery. These results demonstrated direct control of protein structure and function by application of the synthetic photocleavable functionality to a fragmented protein. The combined system of fragmented proteins and synthetic photocleavable elements will provide the useful and potentially wide applicable strategy for the regulation of protein structure and function by the light in a temporal and spacial manner.

Multiparametric homogeneous method for identification of ligand binding to G protein-coupled receptors: receptor-ligand binding and β-arrestin assay

Two homogeneous assay systems have been combined to provide a new cell-based functional assay. The assay can be used to identify ligand binding to β(2)-adrenergic receptors, but also the downstream response can be determined in the same assay. Both the quenching resonance energy transfer (QRET) and the DiscoveRx PathHunter assay formats allow the use of intact cells. The homogeneous QRET technique is a single-label approach based on nonspecific quenching of the time-resolved luminescence, enabling agonist and antagonist receptor binding measurements. The commercial PathHunter assay is in turn based on enzyme fragment complementation, which can be detected on the basis of chemiluminescence signal. In the PathHunter technology the enzyme complementation is recorded immediately downstream of agonist-induced receptor activation. The new multiparametric detection technology combines these two assay methods enabling the identification of agonist, and antagonist binding to the receptor, and the agonist-induced response. Using the QRET and the PathHunter methods a panel of β(2)-adrenergic receptor ligands (epinephrine, terbutaline, metaproterenol, salmeterol, propranolol, alprenolol, bisoprolol, ICI 118,551, and bucindolol) was tested to prove the assay performance. The signal-to-background ratio for tested ligands ranged from 5 to 11 and from 6 to 18 with QRET and PathHunter, respectively. Combined homogeneous assay technique can provide an informative method for screening purposes and an efficient way to monitor receptor-ligand interaction, thus separating agonist from antagonist.

Proteomics Defines Protein Interaction Network of Signaling Pathways

Protein interactions play fundamental roles in signaling transduction. Analysis of protein–protein interaction (PPI) has contributed numerous insights to the understanding of the regulation of signal pathways. Different approaches have been used to discover PPI and characterize protein complexes. In addition to conventional PPI methods, such as yeast two-hybrid (YTH), affinity purification coupled with mass spectrometry (AP-MS) is emerging as an important and popular tool to unravel protein complex and elucidate protein function through the interaction partners. With the AP-MS method, protein complexes are prepared first by affinity purification directly from cell lysates, followed by characterization of their components by mass spectrometry. In contrast to most PPI methods, AP-MS reflects PPI under near physiological conditions in the relevant organism and cell type. AP-MS is also able to probe dynamic PPI dependent on protein posttranslational modifications, which is common for signal transduction. AP-MS mapping protein interaction network of various signal pathways has dramatically increased in recent years. Here, I’ll present the strategies toward obtaining an interactome map of signal pathway and the methodology, detailed protocols, and perspectives of AP-MS.

Interactome mapping for analysis of complex phenotypes: insights from benchmarking binary interaction assays

Protein interactions mediate essentially all biological processes and analysis of protein-protein interactions using both large-scale and small-scale approaches has contributed fundamental insights to the understanding of biological systems. In recent years, interactome network maps have emerged as an important tool for analyzing and interpreting genetic data of complex phenotypes. Complementary experimental approaches to test for binary, direct interactions, and for membership in protein complexes are used to explore the interactome. The two approaches are not redundant but yield orthogonal perspectives onto the complex network of physical interactions by which proteins mediate biological processes. In recent years, several publications have demonstrated that interactions from high-throughput experiments can be equally reliable as the high quality subset of interactions identified in small-scale studies. Critical for this insight was the introduction of standardized experimental benchmarking of interaction and validation assays using reference sets. The data obtained in these benchmarking experiments have resulted in greater appreciation of the limitations and the complementary strengths of different assays. Moreover, benchmarking is a central element of a conceptual framework to estimate interactome sizes and thereby measure progress toward near complete network maps. These estimates have revealed that current large-scale data sets, although often of high quality, cover only a small fraction of a given interactome. Here, I review the findings of assay benchmarking and discuss implications for quality control, and for strategies toward obtaining a near-complete map of the interactome of an organism.

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.

Split-superpositive GFP reassembly is a fast, efficient, and robust method for detecting protein-protein interactions in vivo

Split-GFP reassembly is an operationally simple in vivo technique used to identify and study interactions involving proteins and/or peptides. However, the instability of split-GFP fragments and their susceptibility to aggregation place limitations on the broader use of split-GFP reassembly. Supercharged proteins, including supercharged GFP, are variants with high theoretical negative or positive charge that are resistant to aggregation. We show that a split-superpositive GFP (split-spGFP) variant reassembles faster and more efficiently than previously reported split-sg100 GFP and split-folding-reporter GFP (split-frGFP) systems. In addition, interaction-dependent split-spGFP reassembly is efficient at physiological temperature. The increased efficiency and robustness of split-spGFP reassembly make this reporter system ideal for identifying and studying interactions involving proteins and/or peptides in vivo, and may be particularly useful for identifying or studying interactions involving proteins or peptides that are themselves susceptible to aggregation.

A split luciferase complementation assay for studying in vivo protein-protein interactions in filamentous ascomycetes

Protein-protein interactions play important roles in controlling many cellular events. To date, several techniques have been developed for detection of protein-protein interactions in living cells, among which split luciferase complementation has been applied in animal and plant cells. Here, we examined whether the split luciferase assay could be used in filamentous ascomycetes, such as Gibberella zeae and Cochliobolus heterostrophus. The coding sequences of two strongly interacting proteins (the F-box protein, FBP1, and its partner SKP1) in G. zeae, under the control of the cryparin promoter from Cryphonectria parasitica, were translationally fused to the C- and N-terminal fragments of firefly luciferase (luc), respectively. Each fusion product inserted into a fungal transforming vector carrying the gene for resistance to either geneticin or hygromycin B, was transformed into both fungi. We detected complementation of split luciferase proteins driven by interaction of the two fungal proteins with a high luminescence intensity-to-background ratio only in the fungal transformants expressing both N-luc and C-luc fusion constructs. Using this system, we also confirmed a novel protein interaction between transcription factors, GzMCM1 and FST12 in G. zeae, which could hardly be proven by the yeast two-hybrid method. This is the first study demonstrating that monitoring of split luciferase complementation is a sensitive and efficient method of studying in vivo protein-protein interactions in filamentous ascomycetes.

LUCIFERASES FOR THE STUDY OF PROTEIN–PROTEIN INTERACTIONS IN LIVE CELLS AND ANIMALS

Many imaging technologies based on luminescent proteins have proven useful for detecting protein–protein interactions, tracking cells in mice, and monitoring transcriptional regulation of specific genes. Especially, novel bioluminescent proteins have advanced the study of induced protein interactions and protein modification in live cells and animals. This review focuses on recent developments of bioluminescent probes for quantitative evaluation of specific protein–protein interactions and their spatio-temporal imaging by means of split luciferase complementation techniques. From the comparison between fluorescent and bioluminescent proteins, advantages and drawbacks of the bioluminescence techniques are described.

Overview of high-throughput screening

High-throughput screening (HTS) is a key process used in drug discovery to identify hits from compound libraries that may become leads for medicinal chemistry optimization. This updated overview discusses the utilization of compound libraries, compounds derived from combinatorial and parallel synthesis campaigns and natural product sources; creation of mother and daughter plates; and compound storage, handling, and bar coding in HTS. The unit also presents an overview of established and emerging assay technologies (i.e., time-resolved fluorescence, fluorescence polarization, fluorescence-correlation spectroscopy, functional whole cell assays, and high-content assays) and their integration in automation hardware and IT systems. This revised unit provides updated descriptions of state-of-the-art instrumentation and technologies in this rapidly changing environment. The section on assay methodologies now also covers enzyme complementation assays and methods for high-throughput screening of ion channel activities. Finally, a section on criteria for assay robustness is included discussing the Z'-factor, which is now a widely accepted criterion for evaluation and validation of high throughput screening assays.

Analysis of protein-protein interactions using high-throughput yeast two-hybrid screens

The yeast two-hybrid (Y2H) system is a powerful tool to identify binary protein-protein interactions. Here, we describe array-based two-hybrid methods that use defined libraries of open reading frames (ORFs) and pooled prey library screenings that use random genomic or cDNA libraries. The array-based Y2H system is well-suited for interactome studies of existing ORFeomes or subsets thereof, preferentially in a recombination-based cloning system. Array-based Y2H screens efficiently reduce false positives by using built-in controls, retesting, and evaluation of background activation. Hands-on time and the amount of used resources grow exponentially with the number of tested proteins; this is a disadvantage for large genome sizes. For large genomes, random library screen may be more efficient in terms of time and resources, but not as comprehensive as array screens, and it requires significant sequencing capacity. Furthermore, multiple variants of the Y2H vector systems detect markedly different subsets of interactions in the same interactome. Hence, only multiple variations of the Y2H systems ensure comprehensive coverage of an interactome.

Ribosome display: a perspective

Ribosome display is an in vitro evolution technology for proteins. It is based on in vitro translation, but prevents the newly synthesized protein and the mRNA encoding it from leaving the ribosome. It thereby couples phenotype and genotype. Since no cells need to be transformed, very large libraries can be used directly in selections, and the in vitro amplification provides a very convenient integration of random mutagenesis that can be incorporated into the procedure. This review highlights concepts, mechanisms, and different variations of ribosome display and compares it to related methods. Applications of ribosome display are summarized, e.g., the directed evolution of proteins for higher binding affinity, for higher stability or other improved biophysical parameters and enzymatic properties. Ribosome display has developed into a robust technology used in academia and industry alike, and it has made the cell-free Darwinian evolution of proteins over multiple generations a reality.

A cell-based protein-protein interaction method using a permuted luciferase reporter

We have developed a novel cell-based protein-protein interaction assay method. The method relies on conversion of an inactive permuted luciferase containing a Tobacco Etch Virus protease (TEV) cleavage sequence fused onto protein (A) to an active luciferase upon interaction and cleavage by another protein (B) fused with the TEV protease. We demonstrate assay applicability for ligand-induced protein-protein interactions including G-protein coupled receptors, receptor tyrosine kinases and nuclear hormone receptors.

Selection with a peptide fusion inhibitor corresponding to the first heptad repeat of HIV-1 gp41 identifies two genetic pathways conferring cross-resistance to peptide fusion inhibitors corresponding to the first and second heptad repeats (HR1 and HR2) of gp41

We generated four HIV-1 cultures that are resistant to a peptide fusion inhibitor corresponding to the first heptad repeat of gp41 in order to study mechanisms of resistance and gain insights into envelope glycoprotein-mediated membrane fusion. Two genetic pathways emerged that were defined by acquisition of a specific mutation in either the first or second heptad repeat region of gp41 (HR1 or the HR2, respectively). Each pathway was enriched in mutations that clustered in either HR2 and V3 or in HR1 and residues in or near CD4 contact sites. The gp41 mutations in both pathways not only accounted for resistance to the selecting HR1 peptide but also conferred cross-resistance to HR2 peptide fusion inhibitors and enhanced the stability of the six-helix bundle formed by the self-assembly of HR1 and HR2. The gp120 mutations alone enhanced fusion but did not appear to directly contribute to resistance. The implications of these findings for resistance mechanisms and regulation of envelope-mediated fusion are discussed.

Recent developments of biological reporter technology for detecting gene expression

Reporter gene assay is an invaluable tool for both biomedical and pharmaceutical researches to monitor cellular events associated with gene expression, regulation and signal transduction. On the basis of the alternations in reporter gene activities mediated by attaching response elements to these reporter genes, one sensitive, reliable and convenient assay can be provided to efficiently report the activation of particular messenger cascades and their effects on gene expression and regulations inside cells or living subjects. In this review, we introduce the current status of several commonly used reporter genes such as chloramphenicol acetyltransferase (CAT), alkaline phosphatase (AP), β-galactosidase (β-gal), luciferases, green fluorescent protein (GFP), and β-lactamase. Their applications in monitoring gene expression and regulations in vitro and in vivo will be summarized. With the development of advanced technology in gene expression and optical imaging modalities, reporter genes will become increasingly important in real-time detection of the gene expression at the single-cell level. This synergy will make it possible to understand the molecular basis of diseases, track the effectiveness of pharmaceuticals, monitor the response to therapies and evaluate the development process of new drugs.

Detection of protein-protein interactions in bacteria by GFP-fragment reconstitution

Protein-protein interaction is one of the most pivotal roles of proteins in living organisms. Association/dissociation of proteins reflects responses to intrinsic or extrinsic perturbations of signaling pathways, involved in gene expression, cell division, cell differentiation, and apoptosis. For further understanding of the biological processes, it is important to monitor protein-protein interactions in model organisms. In particular, Escherichia coli-based methods are suitable to assess large libraries of proteins. Many of these proteins cannot be used in yeast due to toxicity or poor expression. Herein we describe a general method based on an intein-mediated protein reconstitution system (PRS) to detect protein-protein interactions in bacterial cells. The PRS-based approach requires no other agents including enzymes, substrates, and ATP. Another advantage is that matured green fluorescent protein (GFP) accumulates in a targeted cell till degraded. These allow highly sensitive screening of protein-protein interactions.

A short receptor downregulates JAK/STAT signalling to control the Drosophila cellular immune response

Regulation of JAK/STAT signalling by a short, nonsignalling receptor in Drosophila modulates response to specific immune challenges such as parasitoid infestations.

The posterior signalling centre (PSC), a small group of specialised cells, controls hemocyte (blood cell) homeostasis in the Drosophila larval hematopoietic organ, the lymph gland. This role of the PSC is very reminiscent of the “niche,” the micro-environment of hematopoietic stem cells in vertebrates. We have recently shown that the PSC acts in a non–cell-autonomous manner to maintain janus tyrosine kinase/signal transducers and activators of transcription (JAK/STAT) signalling in hematopoietic progenitors (prohemocytes), thereby preserving the multipotent character necessary for their differentiation into lamellocytes, a cryptic and dedicated immune cell type required to fight specific immune threats such as wasp parasitism. In this report, on the basis of a knock out generated by homologous recombination, we show that a short type I cytokine-related receptor CG14225/Latran is required for switching off JAK/STAT signalling in prohemocytes. This is a prerequisite to massive differentiation of lamellocytes upon wasp parasitisation. In vivo and cell culture assays indicate that Latran forms heteromers with Domeless, the Drosophila type I cytokine signalling receptor related to mammalian GP130, and antagonises Domeless activity in a dose-dependent manner. Our analysis further shows that a primary immune response to wasp parasitism is a strong decrease in cytokine mRNA levels in the lymph gland, followed by an increase in the latran/domeless ratio. We propose that this sequence of events culminates in the complete inhibition of residual JAK/STAT signalling by Latran. JAK/STAT activity has been associated with several human diseases including leukaemia while knock-out studies in mice point to a central role of this pathway in hematopoiesis and regulation of immune functions. The specific function of Drosophila Latran is, to our knowledge, the first in vivo example of a role for a nonsignalling receptor in controlling a dedicated immune response, and thus raises the question of whether short, nonsignalling receptors also control specific aspects of vertebrate cellular immunity.

A specific microenvironment termed the “niche” supports long term maintenance of hematopoietic stem cells in vertebrates. A small group of specialised cells called the posterior signalling center (PSC) controls hemocyte (blood cell) homeostasis in the Drosophila larval hematopoietic tissue and thus fulfills a similar function to the vertebrate niche. The PSC acts at a distance to maintain JAK/STAT signalling in hematopoietic progenitors (prohemocytes), thereby ensuring their multipotent character. We report here that a short cytokine receptor encoded by CG14225/latran is required to extinguish JAK/STAT signalling in prohemocytes and thereby ensures their mass differentiation into lamellocytes, an immune cell type required to fight specific threats such as wasp parasitism. Domeless, a related receptor in Drosophila, was previously the only known cytokine receptor that signals through the JAK/STAT pathway. We show that Latran lacks the intracellular domains required for signal transduction and acts instead by antagonizing the function of Domeless in a dose-dependent manner. The role of Drosophila Latran in the repression of JAK/STAT signalling under specific immune conditions raises the question of whether short, nonsignalling receptors that antagonize full-length receptors could also control specific aspects of vertebrate immunity.

A proximity ligation assay using transiently transfected, epitope-tagged proteins: application for in situ detection of dimerized receptor tyrosine kinases

The development of small molecule and antibody inhibitors targeting the interaction of receptor tyrosine kinases (RTKs), such as epidermal growth factor receptor (EGFR), is of high pharmacological and biological interest. Unfortunately, conventional biochemical techniques using cell or tissue lysates and co-immunoprecipitation experiments to investigate EGFR dimerization are not always conclusive. Here we describe a series of technical and biological validation experiments demonstrating the utility of a proximity ligation assay (PLA)-based methodology for in situ visualization and quantification of ligand-dependent EGFR receptor dimerization in intact cells. Using the PLA approach combined with a universally applicable epitope tagging strategy, we detected EGFR dimers in cells transiently co-expressing FLAG-tagged and MYC-tagged human EGFRs. Our data strongly suggest that PLA can be used to detect ligand-dependent EGFR dimerization and this signal is generated in a protein interaction-based manner, rather than solely due to proximity of target proteins. This application represents a generalized RTK expression strategy for protein-interaction analysis in a transient expression system where antibody epitopes are not known or not unique enough to discriminate between interaction partners. This assay also holds promise as a general RTK dimerization screening tool in tissue specimens to identify potential dimerization inhibitors with clinical relevance.

Dynamic culture of droplet-confined cell arrays

Responding to the need of creating an accurate and controlled microenvironment surrounding the cell while meeting the requirements for biological processes or pharmacological screening tests, we aimed at designing and developing a microscaled culture system suitable for analyzing the synergic effects of extracellular matrix proteins and soluble environments on cell phenotype in a high-throughput fashion. We produced cell arrays deposing micrometer-scale protein islands on hydrogels using a robotic DNA microarrayer, constrained the culture media in a droplet-like volume and developed a suitable perfusion system. The droplet-confined cell arrays were used either with conventional culture methods (batch operating system) or with automated stable and constant perfusion (steady-state operating system). Mathematical modeling assisted the experimental design and assessed efficient mass transport and proper fluidodynamic regimes. Cells cultured on arrayed islands (500 mum diameter) maintained the correct phenotype both after static and perfused conditions, confirmed by immunostaining and gene expression analyses through total RNA extraction. The mathematical model, validated using a particle tracking experiment, predicted the constant value of velocities over the cell arrays (less than 10% variation) ensuring the same mass transport regime. BrdU analysis on an average of 96 cell spots for each experimental condition showed uniform expression inside each cell island and low variability in the data (average of 13%). Perfused arrays showed longer doubling times when compared with static cultures. In addition, perfused cultures showed a reduced variability in the collected data, allowing to detect statistically significant differences in cell behavior depending on the spotted ECM protein.

Expanding the utility of beta-galactosidase complementation: piece by piece

The ability to image and quantify multiple biomarkers in disease necessitates the development of split reporter fragment platforms. We have divided the beta-galactosidase enzyme into unique, independent polypeptides that are able to reassemble and complement enzymatic activity in bacteria and in mammalian cells. We created two sets of complementing pairs that individually have no enzymatic activity. However, when brought into close geometric proximity, the complementing pairs associated resulting in detectable enzymatic activity. We then constructed a stable ligand complex composed of reporter fragment, linker, and targeting moiety. The targeting moiety, in this case a ligand, allowed cell surface receptor targeting in vitro. Further, we were able to simultaneously visualize two cell surface receptors implicated in cancer development, epidermal growth factor receptor and transferrin receptor, using complementing pairs of the ligand-reporter fragment complex.

Bimolecular fluorescence complementation: lighting up seven transmembrane domain receptor signalling networks

There is increasing complexity in the organization of seven transmembrane domain (7TM) receptor signalling pathways, and in the ability of their ligands to modulate and direct this signalling. Underlying these events is a network of protein interactions between the 7TM receptors themselves and associated effectors, such as G proteins and beta-arrestins. Bimolecular fluorescence complementation, or BiFC, is a technique capable of detecting these protein-protein events essential for 7TM receptor function. Fluorescent proteins, such as those from Aequorea victoria, are split into two non-fluorescent halves, which then tag the proteins under study. On association, these fragments refold and regenerate a mature fluorescent protein, producing a BiFC signal indicative of complex formation. Here, we review the experimental criteria for successful application of BiFC, considered in the context of 7TM receptor signalling events such as receptor dimerization, G protein and beta-arrestin signalling. The advantages and limitations of BiFC imaging are compared with alternative resonance energy transfer techniques. We show that the essential simplicity of the fluorescent BiFC measurement allows high-content and advanced imaging applications, and that it can probe more complex multi-protein interactions alone or in combination with resonance energy transfer. These capabilities suggest that BiFC techniques will become ever more useful in the analysis of ligand and 7TM receptor pharmacology at the molecular level of protein-protein interactions.

Visualization of molecular interactions using bimolecular fluorescence complementation analysis: characteristics of protein fragment complementation

Investigations of the molecular processes that sustain life must include studies of these processes in their normal cellular environment. The bimolecular fluorescence complementation (BiFC) assay provides an approach for the visualization of protein interactions and modifications in living cells. This assay is based on the facilitated association of complementary fragments of a fluorescent protein that are fused to interaction partners. Complex formation by the interaction partners tethers the fluorescent protein fragments in proximity to each other, which can facilitate their association. The BiFC assay enables sensitive visualization of protein complexes with high spatial resolution. The temporal resolution of BiFC analysis is limited by the time required for fluorophore formation, as well as the stabilization of complexes by association of the fluorescent protein fragments. Many modifications and enhancements to the BiFC assay have been developed. The multicolor BiFC assay enables simultaneous visualization of multiple protein complexes in the same cell, and can be used to investigate competition among mutually exclusive interaction partners for complex formation in cells. The ubiquitin-mediated fluorescence complementation (UbFC) assay enables visualization of covalent ubiquitin family peptide conjugation to substrate proteins in cells. The BiFC assay can also be used to visualize protein binding to specific chromatin domains, as well as other molecular scaffolds in cells. BiFC analysis therefore provides a powerful approach for the visualization of a variety of processes that affect molecular proximity in living cells. The visualization of macromolecular interactions and modifications is of great importance owing to the central roles of proteins, nucleic acids and other macromolecular complexes in the regulation of cellular functions. This tutorial review describes the BiFC assay, and discusses the advantages and disadvantages of this experimental approach. The review will be of interest to scientists interested in the investigation of macromolecular interactions or modifications who need exquisite sensitivity for the detection of their complexes or conjugates of interest.