LEC–BiFC: a new method for rapid assay of protein interaction

Rational engineering and synthetic applications of a high specificity BiFC probe derived from Springgreen-M

A high signal-to-noise (S/N) ratio BiFC assay was developed for efficient detection and flexible visualization of protein–protein interactions under physiological conditions in live cells.

Bimolecular Fluorescence Complementation: Quantitative Analysis of In Cell Interaction of Nuclear Transporter Importin α with Cargo Proteins

Bimolecular fluorescence complementation utilizes the ability of two complementary nonfluorescent fragments to reconstitute and emit fluorescence when brought together through specific interaction of attached protein fragments of interest. It has been used in several different contexts to study protein-protein interaction. Here we apply the method for the first time to study interaction of the nuclear transporter importin α and its cargoes in a cellular context. By using image analysis to quantify the extent of nuclear complexation, it is possible to gain insight into the strength of interaction in cells.

Bimolecular Fluorescence Complementation to Assay the Interactions of Ubiquitylation Enzymes in Living Yeast Cells

Ubiquitylation is a versatile posttranslational protein modification catalyzed through the concerted action of ubiquitin-conjugating enzymes (E2s) and ubiquitin ligases (E3s). These enzymes form transient complexes with each other and their modification substrates and determine the nature of the ubiquitin signals attached to their substrates. One challenge in the field of protein ubiquitylation is thus to identify the E2-E3 pairs that function in the cell. In this chapter, we describe the use of bimolecular fluorescence complementation to assay E2-E3 interactions in living cells, using budding yeast as a model organism.

Three-Fragment Fluorescence Complementation Coupled with Photoactivated Localization Microscopy for Nanoscale Imaging of Ternary Complexes

Many cellular processes are governed by molecular machineries that involve multiple protein interactions. However, visualizing and identifying multiprotein complexes such as ternary complexes inside cells is always challenging, particularly in the subdiffraction cellular space. Here, we developed a three-fragment fluorescence complementation system (TFFC) based on the splitting of a photoactivatable fluorescent protein, mIrisFP, for the imaging of ternary complexes inside living cells. Using a combination of TFFC and photoactivated localization microscopy (PALM), namely, the TFFC-PALM technique, we are able to identify the multi-interaction of a ternary complex with nanometer-level spatial resolution and single-molecule sensitivity. The TFFC-PALM system has been further applied to the analysis of the Gs ternary complex, which is composed of αs, β1, and γ2 subunits, providing further insights into the subcellular localization and function of G protein subunits at the single-molecule level. The TFFC-PALM represents a valuable method for the visualization and identification of ternary complexes inside cells at the nanometer scale.

Stress-mediated translational control in cancer cells

Tumor cells are continually subjected to diverse stress conditions of the tumor microenvironment, including hypoxia, nutrient deprivation, and oxidative or genotoxic stress. Tumor cells must evolve adaptive mechanisms to survive these conditions to ultimately drive tumor progression. Tight control of mRNA translation is critical for this response and the adaptation of tumor cells to such stress forms. This proceeds though a translational reprogramming process which restrains overall translation activity to preserve energy and nutrients, but which also stimulates the selective synthesis of major stress adaptor proteins. Here we present the different regulatory signaling pathways which coordinate mRNA translation in the response to different stress forms, including those regulating eIF2α, mTORC1 and eEF2K, and we explain how tumor cells hijack these pathways for survival under stress. Finally, mechanisms for selective mRNA translation under stress, including the utilization of upstream open reading frames (uORFs) and internal ribosome entry sites (IRESes) are discussed in the context of cell stress. This article is part of a Special Issue entitled: Translation and Cancer.

Significant reduction of BiFC non-specific assembly facilitates in planta assessment of heterotrimeric G-protein interactors

Protein networks and signaling cascades are key mechanisms for intra- and intercellular signal transduction. Identifying the interacting partners of a protein can provide vital clues regarding its physiological role. The bimolecular fluorescence complementation (BiFC) assay has become a routine tool for in vivo analysis of protein-protein interactions and their subcellular location. Although the BiFC system has improved since its inception, the available options for in planta analysis are still subject to very low signal-to-noise ratios, and a systematic comparison of BiFC confounding background signals has been lacking. Background signals can obscure weak interactions, provide false positives, and decrease confidence in true positives. To overcome these problems, we performed an extensive in planta analysis of published BiFC fragments used in metazoa and plants, and then developed an optimized single vector BiFC system which utilizes monomeric Venus (mVenus) split at residue 210, and contains an integrated mTurquoise2 marker to precisely identify transformed cells in order to distinguish true negatives. Here we provide our streamlined double ORF expression (pDOE) BiFC system, and show that our advance in BiFC methodology functions even with an internally fused mVenus210 fragment. We illustrate the efficacy of the system by providing direct visualization of Arabidopsis MLO1 interacting with a calmodulin-like (CML) protein, and by showing that heterotrimeric G-protein subunits Gα (GPA1) and Gβ (AGB1) interact in plant cells. We further demonstrate that GPA1 and AGB1 each physically interact with PLDα1 in planta, and that mutation of the so-called PLDα1 'DRY' motif abolishes both of these interactions.

Low false-positives in an mLumin-based bimolecular fluorescence complementation system with a bicistronic expression vector

The simplicity and sensitivity of the bimolecular fluorescence complementation (BiFC) assay make it a powerful tool to investigate protein-protein interactions (PPIs) in living cells. However, non-specific association of the fluorescent protein fragments in a BiFC system can complicate evaluation of PPIs. Here, we introduced a bicistronic expression vector, pBudCE4.1, into an mLumin-based BiFC system, denoted as the BEVL-BiFC system. The BEVL-BiFC system achieved a 25-fold contrast in BiFC efficiency between positive (Fos/Jun) and negative (ΔFos/Jun) PPIs. The high BiFC efficiency was due to a low false-positive rate, where less than 2% of cells displayed BiFC in the negative control. K-Ras and its interactive proteins, Ras binding domain (RBD) of Raf-1 and Grb2 were used to confirm the accuracy of the BEVL-BiFC system. The results also provide direct evidence in individual cells that post-translational modification of K-Ras and its localization at the plasma membrane (PM) were not essential for the interaction of K-Ras and Raf-1, whereas the interaction of Grb2 and K-Ras did depend on the PM localization of K-Ras. Taken together, the BEVL-BiFC system was developed to reduce the false-positive phenomenon in BiFC assays, resulting in more robust and accurate measurement of PPIs in living cells.

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.

Bimolecular fluorescence complementation (BiFC): a 5-year update and future perspectives

Over the past decade, bimolecular fluorescence complementation (BiFC) has emerged as a key technique to visualize protein-protein interactions in a variety of model organisms. The BiFC assay is based on reconstitution of an intact fluorescent protein when two complementary non-fluorescent fragments are brought together by a pair of interacting proteins. While the originally reported BiFC method has enabled the study of many protein-protein interactions, increasing demands to visualize protein-protein interactions under various physiological conditions have not only prompted a series of recent BiFC technology improvements, but also stimulated interest in developing completely new approaches. Here we review current BiFC technology, focusing on the development and improvement of BiFC systems, the understanding of split sites in fluorescent proteins, and enhancements in the signal-to-noise ratio. In addition, we provide perspectives on possible future improvements of the technique.

Bimolecular fluorescence complementation analysis of G protein-coupled receptor dimerization in living cells

Emerging evidence indicates that G protein-coupled receptor (GPCR) signaling is mediated by receptor-receptor interactions at multiple levels. Thus, understanding the biochemistry and pharmacology of those receptor complexes is an important part of delineating the fundamental processes associated with GPCR-mediated signaling in human disease. A variety of experimental approaches have been used to explore these complexes, including bimolecular fluorescence complementation (BiFC) and multicolor BiFC (mBiFC). BiFC approaches have recently been used to explore the composition, cellular localization, and drug modulation of GPCR complexes. The basic methods for applying BiFC and mBiFC to study GPCRs in living cells are the subject of the present chapter.

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.

Structural basis of cytotoxicity mediated by the type III secretion toxin ExoU from Pseudomonas aeruginosa

The type III secretion system (T3SS) is a complex macromolecular machinery employed by a number of Gram-negative pathogens to inject effectors directly into the cytoplasm of eukaryotic cells. ExoU from the opportunistic pathogen Pseudomonas aeruginosa is one of the most aggressive toxins injected by a T3SS, leading to rapid cell necrosis. Here we report the crystal structure of ExoU in complex with its chaperone, SpcU. ExoU folds into membrane-binding, bridging, and phospholipase domains. SpcU maintains the N-terminus of ExoU in an unfolded state, required for secretion. The phospholipase domain carries an embedded catalytic site whose position within ExoU does not permit direct interaction with the bilayer, which suggests that ExoU must undergo a conformational rearrangement in order to access lipids within the target membrane. The bridging domain connects catalytic domain and membrane-binding domains, the latter of which displays specificity to PI(4,5)P₂. Both transfection experiments and infection of eukaryotic cells with ExoU-secreting bacteria show that ExoU ubiquitination results in its co-localization with endosomal markers. This could reflect an attempt of the infected cell to target ExoU for degradation in order to protect itself from its aggressive cytotoxic action.

Pseudomonas aeruginosa is a leading cause of nosocomial infections and is a particular threat for cystic fibrosis and immunodepressed patients. One of the most aggressive toxins in its arsenal is ExoU, injected directly into target cells by a needle-like complex located on the surface of the bacterium, the type III secretion system. P. aeruginosa strains that express ExoU cause rapid cell death as a consequence of the membrane-destruction (phospholipase) potential of the toxin. In this work, we report the three-dimensional structure of ExoU in complex with a partner molecule, SpcU. ExoU contains three distinct regions, and the fold suggests how ExoU binds to the membrane or other molecules within the target cell and becomes activated. In addition, we also show that once it is translocated into the cell, ExoU co-localizes with intracellular organelles of the endosomal pathway, potentially in an attempt of the target cell to destroy the toxin. This work provides new insight into the cellular destruction mechanism of this aggressive toxin and could be a basis for the development of new inhibitors of P. aeruginosa pathogenesis.