Optimizing Luciferase Protein Fragment Complementation for Bioluminescent Imaging of Protein–Protein Interactions in Live Cells and Animals

protein2vec: Predicting Protein-Protein Interactions Based on LSTM

The semantic similarity of gene ontology (GO) terms is widely used to predict protein-protein interactions (PPIs). The traditional semantic similarity measures are based mainly on manually crafted features, which may ignore some important hidden information of the gene ontology. Moreover, those methods usually obtain the similarity between proteins from similarity between GO terms by some simple statistical rules, such as MAX and BMA (best-match average), oversimplifying the possible complex relationship between the proteins and the GO terms annotated with them. To overcome the two deficiencies, we propose a new method named protein2vec, which characterizes a protein with a vector based on the GO terms annotated to it and combines the information of both the GO and known PPIs. We firstly try to apply the network embedding algorithm on the GO network to generate feature vectors for each GO term. Then, Long Short-Time Memory (LSTM) encodes the feature vectors of the GO terms annotated with a protein into another vector (called protein vector). Finally, two protein vectors are forwarded into a feedforward neural network to predict the interaction between the two corresponding proteins. The experimental results show that protein2vec outperforms almost all commonly used traditional semantic similarity methods.

Bioluminescence Imaging Applications in Cancer: A Comprehensive Review

Bioluminescence imaging (BLI), an optical preclinical imaging modality, is an invaluable imaging modality due to its low-cost, high throughput, fast acquisition times, and functional imaging capabilities. BLI is being extensively used in the field of cancer imaging, especially with the recent developments in genetic-engineering, stem cell, and gene therapy treatments. The purpose of this paper is to provide a comprehensive review of the principles, developments, and current status of BLI in cancer research. This paper covers the fundamental BLI concepts including BLI reporters and enzyme-substrate systems, data acquisition, and image characteristics. It reviews the studies discussing the use of BLI in cancer research such as imaging tumor-characteristic phenomena including tumorigenesis, metastasis, cancer metabolism, apoptosis, hypoxia, and angiogenesis, and response to cancer therapy treatments including chemotherapy, radiotherapy, immunotherapy, gene therapy, and stem cell therapy. The key advantages and disadvantages of BLI compared to other common imaging modalities are also discussed.

Molecular and Biochemical Techniques for Deciphering p53-MDM2 Regulatory Mechanisms

The p53 and Mouse double minute 2 (MDM2) proteins are hubs in extensive networks of interactions with multiple partners and functions. Intrinsically disordered regions help to adopt function-specific structural conformations in response to ligand binding and post-translational modifications. Different techniques have been used to dissect interactions of the p53-MDM2 pathway, in vitro, in vivo, and in situ each having its own advantages and disadvantages. This review uses the p53-MDM2 to show how different techniques can be employed, illustrating how a combination of in vitro and in vivo techniques is highly recommended to study the spatio-temporal location and dynamics of interactions, and to address their regulation mechanisms and functions. By using well-established techniques in combination with more recent advances, it is possible to rapidly decipher complex mechanisms, such as the p53 regulatory pathway, and to demonstrate how protein and nucleotide ligands in combination with post-translational modifications, result in inter-allosteric and intra-allosteric interactions that govern the activity of the protein complexes and their specific roles in oncogenesis. This promotes elegant therapeutic strategies that exploit protein dynamics to target specific interactions.

Monitoring Interactions Between S100B and the Dopamine D2 Receptor Using NMR Spectroscopy

S100B is a dimeric EF-hand protein that undergoes a calcium-induced conformational change and interacts with a wide range of proteins to modulate their functions. The dopamine D2 receptor is one potential S100B binding partner that may play a key role in neurological processing. In this chapter, we describe the use of NMR spectroscopy to examine the interaction between calcium-bound S100B and the third intracellular loop (IC3) from the dopamine D2 receptor. We provide details that allow the strength of the interaction (K _d) between the two proteins to be determined and the IC3 site of interaction on the structure of S100B to be identified. Both these characteristics can be identified from a single series of nondestructive experiments.

Biophysical validation of serotonin 5-HT2A and 5-HT2C receptor interaction

The serotonin (5-HT) 5-HT_2A receptor (5-HT_2AR) and 5-HT_2C receptor (5-HT_2CR) in the central nervous system are implicated in a range of normal behaviors (e.g., appetite, sleep) and physiological functions (e.g., endocrine secretion) while dysfunctional 5-HT_2AR and/or 5-HT_2CR are implicated in neuropsychiatric disorders (e.g., addiction, obesity, schizophrenia). Preclinical studies suggest that the 5-HT_2AR and 5-HT_2CR may act in concert to regulate the neural bases for behavior. Here, we utilize three distinct biophysical and immunocytochemistry-based approaches to identify and study this receptor complex in cultured cells. Employing a split luciferase complementation assay (LCA), we demonstrated that formation of the 5-HT_2AR:5-HT_2CR complex exists within 50 nm, increases proportionally to the 5-HT_2CR:5-HT_2AR protein expression ratio, and is specific to the receptor interaction and not due to random complementation of the luciferase fragments. Using a proximity ligation assay (PLA), we found that cells stably expressing both the 5-HT_2AR and 5-HT_2CR exhibit 5-HT_2AR:5-HT_2CR heteroreceptor complexes within 40 nm of each other. Lastly, bioluminescence resonance energy transfer (BRET) analyses indicates the formation of a specific and saturable 5-HT_2AR:5-HT_2CR interaction, suggesting that the 5-HT_2AR and 5-HT_2CR form a close interaction within 10 nm of each other in intact live cells. The bioengineered receptors generated for the LCA and the BRET exhibit 5-HT-mediated intracellular calcium signaling as seen for the native receptors. Taken together, this study validates a very close 5-HT_2AR:5-HT_2CR interaction in cultured cells.

Induction of α-synuclein aggregate formation by CSF exosomes from patients with Parkinson's disease and dementia with Lewy bodies

Extracellular α-synuclein has been proposed as a crucial mechanism for induction of pathological aggregate formation in previously healthy cells. In vitro, extracellular α-synuclein is partially associated with exosomal vesicles. Recently, we have provided evidence that exosomal α-synuclein is present in the central nervous system in vivo. We hypothesized that exosomal α-synuclein species from patients with α-synuclein related neurodegeneration serve as carriers for interneuronal disease transmission. We isolated exosomes from cerebrospinal fluid from patients with Parkinson's disease, dementia with Lewy bodies, progressive supranuclear palsy as a non-α-synuclein related disorder that clinically overlaps with Parkinson's disease, and neurological controls. Cerebrospinal fluid exosome numbers, α-synuclein protein content of cerebrospinal fluid exosomes and their potential to induce oligomerization of α-synuclein were analysed. The quantification of cerebrospinal fluid exosomal α-synuclein showed distinct differences between patients with Parkinson's disease and dementia with Lewy bodies. In addition, exosomal α-synuclein levels correlated with the severity of cognitive impairment in cross-sectional samples from patients with dementia with Lewy bodies. Importantly, cerebrospinal fluid exosomes derived from Parkinson's disease and dementia with Lewy bodies induce oligomerization of α-synuclein in a reporter cell line in a dose-dependent manner. Our data suggest that cerebrospinal fluid exosomes from patients with Parkinson's disease and dementia with Lewy bodies contain a pathogenic species of α-synuclein, which could initiate oligomerization of soluble α-synuclein in target cells and confer disease pathology.

Holocarboxylase synthetase interacts physically with nuclear receptor co-repressor, histone deacetylase 1 and a novel splicing variant of histone deacetylase 1 to repress repeats

HLCS (holocarboxylase synthetase) is a nuclear protein that catalyses the binding of biotin to distinct lysine residues in chromatin proteins. HLCS-dependent epigenetic marks are over-represented in repressed genomic loci, particularly in repeats. Evidence is mounting that HLCS is a member of a multi-protein gene repression complex, which determines its localization in chromatin. In the present study we tested the hypothesis that HLCS interacts physically with N-CoR (nuclear receptor co-repressor) and HDAC1 (histone deacetylase 1), thereby contributing toward the removal of H3K9ac (Lys⁹-acetylated histone H3) gene activation marks and the repression of repeats. Physical interactions between HLCS and N-CoR, HDAC1 and a novel splicing variant of HDAC1 were confirmed by co-immunoprecipitation, limited proteolysis and split luciferase complementation assays. When HLCS was overexpressed, the abundance of H3K9ac marks decreased by 50% and 68% in LTRs (long terminal repeats) 15 and 22 respectively in HEK (human embryonic kidney)-293 cells compared with the controls. This loss of H3K9ac marks was linked with an 83% decrease in mRNA coding for LTRs. Similar patterns were seen in pericentromeric alpha satellite repeats in chromosomes 1 and 4. We conclude that interactions of HLCS with N-CoR and HDACs contribute towards the transcriptional repression of repeats, presumably increasing genome stability.

New researches and application progress of commonly used optical molecular imaging technology

Optical molecular imaging, a new medical imaging technique, is developed based on genomics, proteomics and modern optical imaging technique, characterized by non-invasiveness, non-radiativity, high cost-effectiveness, high resolution, high sensitivity and simple operation in comparison with conventional imaging modalities. Currently, it has become one of the most widely used molecular imaging techniques and has been applied in gene expression regulation and activity detection, biological development and cytological detection, drug research and development, pathogenesis research, pharmaceutical effect evaluation and therapeutic effect evaluation, and so forth, This paper will review the latest researches and application progresses of commonly used optical molecular imaging techniques such as bioluminescence imaging and fluorescence molecular imaging.

Novel split-luciferase-based genetically encoded biosensors for noninvasive visualization of Rho GTPases

Rho family GTPases are critical regulators of many important cellular processes and the dysregulation of their activities is implicated in a variety of human diseases including oncogenesis and propagation of malignancy. The traditional methods, such as “pull-down” or two-hybrid procedures, are poorly suited to dynamically evaluate the activity of Rho GTPases, especially in living mammalian cells. To provide a novel alternative approach to analyzing Rho GTPase-associated signaling pathways in vivo, we developed a series of bioluminescent biosensors based on the genetically engineered firefly luciferase. These split-luciferase-based biosensors enable non-invasive visualization and quantification of the activity of Rho GTPases in living subjects. The strategy is to reasonably split the gene of firefly luciferase protein into two inactive fragments and then respectively fuse the two fragments to Rho GTPase and the GTPase-binding domain (GBD) of the specific effector. Upon Rho GTPase interacting with the binding domain in a GTP-dependent manner, these two luciferase fragments are brought into close proximity, leading to luciferase reconstitution and photon production in the presence of the substrate. Using these bimolecular luminescence complementation (BiLC) biosensors, we successfully visualized and quantified the activities of the three best characterized Rho GTPases by measuring the luminescence in living cells. We also experimentally investigated the sensitivity of these Rho GTPase biosensors to upstream regulatory proteins and extracellular ligands without lysing cells and doing labor-intensive works. By virtue of the unique functional characteristics of bioluminescence imaging, the BiLC-based biosensors provide an enormous potential for in vivo imaging of Rho GTPase signaling pathways and high-throughput screening of therapeutic drugs targeted to Rho GTPases and (or) upstream molecules in the near future.

Plant protein interactomes

Protein-protein interactions are a critical element of biological systems, and the analysis of interaction partners can provide valuable hints about unknown functions of a protein. In recent years, several large-scale protein interaction studies have begun to unravel the complex networks through which plant proteins exert their functions. Two major classes of experimental approaches are used for protein interaction mapping: analysis of direct interactions using binary methods such as yeast two-hybrid or split ubiquitin, and analysis of protein complexes through affinity purification followed by mass spectrometry. In addition, bioinformatics predictions can suggest interactions that have evaded detection by other methods or those of proteins that have not been investigated. Here we review the major approaches to construct, analyze, use, and carry out quality control on plant protein interactome networks. We present experimental and computational approaches for large-scale mapping, methods for validation or smaller-scale functional studies, important bioinformatics resources, and findings from recently published large-scale plant interactome network maps.

Molecular imaging in tumor angiogenesis and relevant drug research

Molecular imaging, including fluorescence imaging (FMI), bioluminescence imaging (BLI), positron emission tomography (PET), single-photon emission-computed tomography (SPECT), and computed tomography (CT), has a pivotal role in the process of tumor and relevant drug research. CT, especially Micro-CT, can provide the anatomic information for a region of interest (ROI); PET and SPECT can provide functional information for the ROI. BLI and FMI can provide optical information for an ROI. Tumor angiogenesis and relevant drug development is a lengthy, high-risk, and costly process, in which a novel drug needs about 10–15 years of testing to obtain Federal Drug Association (FDA) approval. Molecular imaging can enhance the development process by understanding the tumor mechanisms and drug activity. In this paper, we focus on tumor angiogenesis, and we review the characteristics of molecular imaging modalities and their applications in tumor angiogenesis and relevant drug research.

Applications of molecular imaging

Today molecular imaging technologies play a central role in clinical oncology. The use of imaging techniques in early cancer detection, treatment response, and new therapy development is steadily growing and has already significantly impacted on clinical management of cancer. In this chapter, we overview three different molecular imaging technologies used for the understanding of disease biomarkers, drug development, or monitoring therapeutic outcome. They are (1) optical imaging (bioluminescence and fluorescence imaging), (2) magnetic resonance imaging (MRI), and (3) nuclear imaging (e.g., single-photon emission computed tomography (SPECT) and positron emission tomography (PET)). We review the use of molecular reporters of biological processes (e.g., apoptosis and protein kinase activity) for high-throughput drug screening and new cancer therapies, diffusion MRI as a biomarker for early treatment response and PET and SPECT radioligands in oncology.

Application of a split luciferase complementation assay for the detection of viral protein-protein interactions

Intraviral protein-protein interactions are critical for virus survival in the host. Discovery of such interactions is important to understand molecular mechanisms of viral replication and pathogenesis. The development of a cell-based assay that can be employed to examine systematically viral protein interactions is described. The method, known as the split luciferase complementation assay (SLCA), is based on the principle that N- and C-terminal domains of luciferase alone do not emit luminescence; however, if fused to interacting proteins the two non-functional halves can be brought into close enough proximity through a specific protein-protein interaction to restore the functions of the enzyme and emit detectable light. The well-studied influenza B polymerase acidic protein (PA) and basic protein 1 (PB1) interaction was used as a model system to develop the assay. Consistent with previous studies, a strong PA-PB1 interaction was demonstrated in the assay. The PA-PB1 interaction was also disrupted by single amino acid mutations in the N-terminal domain of PB1 that is responsible for binding PA. The described SLCA is highly specific and easy to perform, and thus may be useful for studying protein-protein interactions in viral diseases.

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.

Dual-color click beetle luciferase heteroprotein fragment complementation assays

Understanding the functional complexity of protein interactions requires mapping biomolecular complexes within the cellular environment over biologically relevant time scales. Herein, we describe a set of reversible multicolored heteroprotein complementation fragments based on various firefly and click beetle luciferases that utilize the same substrate, D-luciferin. Luciferase heteroprotein fragment complementation systems enabled dual-color quantification of two discrete pairs of interacting proteins simultaneously or two distinct proteins interacting with a third shared protein in live cells. Using real-time analysis of click beetle green and click beetle red luciferase heteroprotein fragment complementation applied to β-TrCP, an E3-ligase common to the regulation of both β-catenin and IκBα, GSK3β was identified as a candidate kinase regulating IκBα processing. These dual-color protein interaction switches may enable directed dynamic analysis of a variety of protein interactions in living cells.

Cell-based assays: fuelling drug discovery

It has been estimated that over a billion dollars in resources can be consumed to obtain clinical approval, and only a few new chemical entities are approved by the US Food and Drug Administration (FDA) each year. Therefore it is of utmost importance to obtain the maximum amount of information about biological activity, toxicological profile, biochemical mechanisms, and off-target interactions of drug-candidate leads in the earliest stages of drug discovery. Cell-based assays, because of their peculiar advantages of predictability, possibility of automation, multiplexing, and miniaturization, seem the most appealing tool for the high demands of the early stages of the drug-discovery process. Nevertheless, cellular screening, relying on different strategies ranging from reporter gene technology to protein fragment complementation assays, still presents a variety of challenges. This review focuses on main advantages and limitations of different cell-based approaches, and future directions and trends in this fascinating field.

Novel molecular imaging platform for monitoring oncological kinases

Recent advances in oncology have lead to identification of a plethora of alterations in signaling pathways that are critical to oncogenesis and propagation of malignancy. Among the biomarkers identified, dysregulated kinases and associated changes in signaling cascade received the lion's share of scientific attention and have been under extensive investigations with goal of targeting them for anti-cancer therapy. Discovery of new drugs is immensely facilitated by molecular imaging technology which enables non-invasive, real time, dynamic imaging and quantification of kinase activity. Here, we review recent development of novel kinase reporters based on conformation dependent complementation of firefly luciferase to monitor kinase activity. Such reporter system provides unique insights into the pharmacokinetics and pharmacodynamics of drugs that modulate kinase signaling and have a huge potential in drug discovery, validation, and drug-target interactions.

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.

Method of bioluminescence imaging for molecular imaging of physiological and pathological processes

Molecular imaging has emerged as a powerful tool in basic, pre-clinical and clinical research for monitoring a variety of molecular and cellular processes in living organisms. Optical imaging techniques, mainly bioluminescence imaging, have extensively been used to study biological processes because of their exquisite sensitivity and high signal-to noise ratio. However, current applications have mainly been limited to small animals due to attenuation and scattering of light by tissues but efforts are ongoing to overcome these hurdles. Here, we focus on bioluminescence imaging by giving a brief overview of recent advances in instrumentation, current available reporter gene-reporter probe systems and applications such as cell trafficking, protein-protein interactions and imaging endogenous processes.

Visualization of protein interactions in living Caenorhabditis elegans using bimolecular fluorescence complementation analysis

The bimolecular fluorescence complementation (BiFC) assay is a powerful tool for visualizing and identifying protein interactions in living cells. This assay is based on the principle of protein-fragment complementation, using two nonfluorescent fragments derived from fluorescent proteins. When two fragments are brought together in living cells by tethering each to one of a pair of interacting proteins, fluorescence is restored. Here, we provide a protocol for a Venus-based BiFC assay to visualize protein interactions in the living nematode, Caenorhabditis elegans. We discuss how to design appropriate C. elegans BiFC cloning vectors to enable visualization of protein interactions using either inducible heat shock promoters or native promoters; transform the constructs into worms by microinjection; and analyze and interpret the resulting data. When expression of BiFC fusion proteins is induced by heat shock, the fluorescent signals can be visualized as early as 30 min after induction and last for 24 h in transgenic animals. The entire procedure takes 2-3 weeks to complete.

Fluorescence complementation: an emerging tool for biological research

Numerous technologies based on utilizing fluorescent proteins have been developed for biological research, and fluorescence complementation (FC) is a recent application for visualization of molecular events in living cells and organisms. Currently, ten fluorescent proteins have been demonstrated to support FC. Over the past five years, FC-based technologies have been developed to visualize a variety of molecular events, such as protein-protein interactions, post-translational modifications, protein folding, conformational changes, RNA-protein interactions, mRNA localization and DNA hybridization. In addition, FC has also been used for drug discovery. These applications are providing fascinating insights into many biological processes. Here, we review the principles and applications of FC technologies, discuss their current challenges and examine prospects for future advances.

Molecular imaging in drug development

Molecular imaging can allow the non-invasive assessment of biological and biochemical processes in living subjects. Such technologies therefore have the potential to enhance our understanding of disease and drug activity during preclinical and clinical drug development, which could aid decisions to select candidates that seem most likely to be successful or to halt the development of drugs that seem likely to ultimately fail. Here, with an emphasis on oncology, we review the applications of molecular imaging in drug development, highlighting successes and identifying key challenges that need to be addressed for successful integration of molecular imaging into the drug development process.

Molecular imaging of the efficacy of heat shock protein 90 inhibitors in living subjects

Heat shock protein 90 alpha (Hsp90 alpha)/p23 and Hsp90 beta/p23 interactions are crucial for proper folding of proteins involved in cancer and neurodegenerative diseases. Small molecule Hsp90 inhibitors block Hsp90 alpha/p23 and Hsp90 beta/p23 interactions in part by preventing ATP binding to Hsp90. The importance of isoform-selective Hsp90 alpha/p23 and Hsp90 beta/p23 interactions in determining the sensitivity to Hsp90 was examined using 293T human kidney cancer cells stably expressing split Renilla luciferase (RL) reporters. Interactions between Hsp90 alpha/p23 and Hsp90 beta/p23 in the split RL reporters led to complementation of RL activity, which was determined by bioluminescence imaging of intact cells in cell culture and living mice using a cooled charge-coupled device camera. The three geldanamycin-based and seven purine-scaffold Hsp90 inhibitors led to different levels of inhibition of complemented RL activities (10-70%). However, there was no isoform selectivity to both classes of Hsp90 inhibitors in cell culture conditions. The most potent Hsp90 inhibitor, PU-H71, however, led to a 60% and 30% decrease in RL activity (14 hr) in 293T xenografts expressing Hsp90 alpha/p23 and Hsp90 beta/p23 split reporters respectively, relative to carrier control-treated mice. Molecular imaging of isoform-specific Hsp90 alpha/p23 and Hsp90 beta/p23 interactions and efficacy of different classes of Hsp90 inhibitors in living subjects have been achieved with a novel genetically encoded reporter gene strategy that should help in accelerating development of potent and isoform-selective Hsp90 inhibitors.

Detection of protein-protein interactions in live cells and animals with split firefly luciferase protein fragment complementation

Protein fragment complementation has emerged as a powerful tool for measuring protein-protein interactions in the context of live cells. The adaptation of this strategy for use with firefly luciferase now allows for the non-invasive, quantitative, real-time readout of protein interactions in lysates, live cells, and whole animals. Bioluminescence provides a robust imaging modality due to its extremely low background signal and large dynamic range. The split luciferase fusion constructs described here are inducible by addition of ligands, small molecules or drugs, in this example, rapamycin, and have been shown to work in vivo.

Split luciferase complementation assay to study protein-protein interactions in Arabidopsis protoplasts

We developed a split luciferase complementation assay to study protein-protein interactions in Arabidopsis protoplasts. In this assay, the N- and C-terminal fragments of Renilla reniforms luciferase are translationally fused to bait and prey proteins, respectively. When the proteins interact, split luciferase becomes activated and emits luminescence that can be measured by a microplate luminometer. Split luciferase activity was measured by first transforming protoplasts with a DNA vector in a 96-well plate. DNA vector expressing both bait and prey genes was constructed through two independent in vitro DNA recombinant reactions, Gateway and Cre-loxP. As proof of concept, we detected the protein-protein interactions between the nuclear histones 2A and 2B, as well as between membrane proteins SYP (syntaxin of plant) 51 and SYP61, in Arabidopsis protoplasts.

An improved bioluminescence resonance energy transfer strategy for imaging intracellular events in single cells and living subjects

Bioluminescence resonance energy transfer (BRET) is currently used for monitoring various intracellular events, including protein-protein interactions, in normal and aberrant signal transduction pathways. However, the BRET vectors currently used lack adequate sensitivity for imaging events of interest from both single living cells and small living subjects. Taking advantage of the critical relationship of BRET efficiency and donor quantum efficiency, we report generation of a novel BRET vector by fusing a GFP(2) acceptor protein with a novel mutant Renilla luciferase donor selected for higher quantum yield. This new BRET vector shows an overall 5.5-fold improvement in the BRET ratio, thereby greatly enhancing the dynamic range of the BRET signal. This new BRET strategy provides a unique platform to assay protein functions from both single live cells and cells located deep within small living subjects. The imaging utility of the new BRET vector is shown by constructing a sensor using two mammalian target of rapamycin pathway proteins (FKBP12 and FRB) that dimerize only in the presence of rapamycin. This new BRET vector should facilitate high-throughput sensitive BRET assays, including studies in single live cells and small living subjects. Applications will include anticancer therapy screening in cell culture and in small living animals.

Current State of Imaging Protein-Protein Interactions In Vivo with Genetically Encoded Reporters

Signaling pathways regulating proliferation, differentiation, and inflammation are commonly mediated through protein-protein interactions as well as reversible modification (e.g., phosphorylation) of proteins. To facilitate the study of regulated protein-protein interactions in cells and living animals, new imaging tools, many based on optical signals and capable of quantifying protein interactions in vivo, have advanced the study of induced protein interactions and their modification, as well as accelerated the rate of acquisition of these data. In particular, use of protein fragment complementation as a reporter strategy can accurately and rapidly dissect protein interactions with a variety of readouts, including absorbance, fluorescence, and bioluminescence. This review focuses on the development and validation of bioluminescent protein fragment complementation reporters that use either Renilla luciferase or firefly luciferase in vivo. Enhanced luciferase complementation provides a platform for near real-time detection and characterization of regulated and small-molecule-induced protein-protein interactions in intact cells and living animals and enables a wide range of novel applications in drug discovery, chemical genetics, and proteomics research.

Molecular imaging using visible light to reveal biological changes in the brain

Advances in imaging have enabled the study of cellular and molecular processes in the context of the living body that include cell migration patterns, location and extent of gene expression, degree of protein-protein interaction, and levels of enzyme activity. These tools, which operate over a range of scales, resolutions, and sensitivities, have opened up broad new areas of investigation where the influence of organ systems and functional circulation is intact. There are a myriad of imaging modalities available, each with its own advantages and disadvantages, depending on the specific application. Among these modalities, optical imaging techniques, including in vivo bioluminescence imaging and fluorescence imaging, use visible light to interrogate biology in the living body. Optimal imaging with these modalities require that the appropriate marker be used to tag the process of interest to make it uniquely visible using a particular imaging technology. For each optical modality, there are various labels to choose from that range from dyes that permit tissue contrast and dyes that can be activated by enzymatic activity, to gene-encoding proteins with optical signatures that can be engineered into specific biological processes. This article provides and overview of optical imaging technologies and commonly used labels, focusing on bioluminescence and fluorescence, and describes several examples of how these tools are applied to biological questions relating to the central nervous system.

Reporter gene imaging of protein-protein interactions in living subjects

In the past few years there has been a veritable explosion in the field of reporter gene imaging, with the aim of determining the location, duration and extent of gene expression within living subjects. An important application of this approach is the molecular imaging of interacting protein partners, which could pave the way to functional proteomics in living animals and might provide a tool for the whole-body evaluation of new pharmaceuticals targeted to modulate protein-protein interactions. Three general methods are currently available for imaging protein-protein interactions in living subjects using reporter genes: a modified mammalian two-hybrid system, a bioluminescence resonance energy transfer (BRET) system, and split reporter protein complementation and reconstitution strategies. In the future, these innovative approaches are likely to enhance our appreciation of entire biological pathway systems and their pharmacological regulation.

Bimolecular fluorescence complementation analysis system forin vivo detection of protein–protein interaction inSaccharomyces cerevisiae

The bimolecular fluorescence complementation (BiFC) assay has been widely accepted for studying in vivo detection of protein-protein interactions in several organisms. To facilitate the application of the BiFC assay to yeast research, we have created a series of plasmids that allow single-step, PCR-based C- or N-terminal tagging of yeast proteins with yellow fluorescent protein fragments for BiFC assay. By examination of several interacting proteins (Sis1-Sis1, Net1-Sir2, Cet1-Cet1 and Pho2-Pho4), we demonstrate that the BiFC assay can be used to reliably analyse the occurrence and subcellular localization of protein-protein interactions in living yeast cells. The sequences for the described plasmids were submitted to the GenBank under Accession Nos: EF210802, pFA6a-VN-His3MX6; EF210803, pFA6a-VC-His3MX6; EF210804, pFA6a-VN-TRP1; EF210807, pFA6a-VC-TRP1; EF210808, pFA6a-VN-kanMX6; EF210809, pFA6a-VC-kanMX6; EF210810, pFA6a-His3MX6-P(GAL1)-VN; EF210805, pFA6a-His3MX6-P(GAL1)-VC; EF210806, pFA6a-TRP1-P(GAL1)-VN; EF210811, pFA6a-TRP1-P(GAL1)-VC; EF210812, pFA6a-kanMX6-P(GAL1)-VN; EF210813, pFA6a-kanMX6-P(GAL1)-VC; EF521883, pFA6a-His3MX6-P(CET1)-VN; EF521884, pFA6a-His3MX6-P(CET1)-VC; EF521885, pFA6a-TRP1-P(CET1)-VN; EF521886, pFA6a-TRP1-P(CET1)-VC; EF521887, pFA6a-kanMX6-P(CET1)-VN; EF521888, pFA6a-kanMX6-P(CET1)-VC.

Identification of new fluorescent protein fragments for bimolecular fluorescence complementation analysis under physiological conditions

Protein-protein interactions play a pivotal role in coordinating many cellular processes. Determination of subcellular localization of interacting proteins and visualization of dynamic interactions in living cells are crucial to elucidate cellular functions of proteins. Using fluorescent proteins, we previously developed a bimolecular fluorescence complementation (BiFC) assay and a multicolor BiFC assay to visualize protein-protein interactions in living cells. However, the sensitivity of chromophore maturation of enhanced yellow fluorescent protein (YFP) to higher temperatures requires preincubation at lower temperatures prior to visualizing the BiFC signal. This could potentially limit their applications for the study of many signaling molecules. Here we report the identification of new fluorescent protein fragments derived from Venus and Cerulean for BiFC and multicolor BiFC assays under physiological culture conditions. More importantly, the newly identified combinations exhibit a 13-fold higher BiFC efficiency than originally identified fragments derived from YFP. Furthermore, the use of new combinations reduces the amount of plasmid required for transfection and shortens the incubation time, leading to a 2-fold increase in specific BiFC signals. These newly identified fluorescent protein fragments will facilitate the study of protein-protein interactions in living cells and whole animals under physiological conditions.

Novel fusion protein approach for efficient high-throughput screening of small molecule-mediating protein-protein interactions in cells and living animals

Networks of protein interactions execute many different intracellular pathways. Small molecules either synthesized within the cell or obtained from the external environment mediate many of these protein-protein interactions. The study of these small molecule-mediated protein-protein interactions is important in understanding abnormal signal transduction pathways in a variety of disorders, as well as in optimizing the process of drug development and validation. In this study, we evaluated the rapamycin-mediated interaction of the human proteins FK506-binding protein (FKBP12) rapamycin-binding domain (FRB) and FKBP12 by constructing a fusion of these proteins with a split-Renilla luciferase or a split enhanced green fluorescent protein (split-EGFP) such that complementation of the reporter fragments occurs in the presence of rapamycin. Different linker peptides in the fusion protein were evaluated for the efficient maintenance of complemented reporter activity. This system was studied in both cell culture and xenografts in living animals. We found that peptide linkers with two or four EAAAR repeat showed higher protein-protein interaction-mediated signal with lower background signal compared with having no linker or linkers with amino acid sequences GGGGSGGGGS, ACGSLSCGSF, and ACGSLSCGSFACGSLSCGSF. A 9 +/- 2-fold increase in signal intensity both in cell culture and in living mice was seen compared with a system that expresses both reporter fragments and the interacting proteins separately. In this fusion system, rapamycin induced heterodimerization of the FRB and FKBP12 moieties occurred rapidly even at very lower concentrations (0.00001 nmol/L) of rapamycin. For a similar fusion system employing split-EGFP, flow cytometry analysis showed significant level of rapamycin-induced complementation.

Noninvasive imaging of protein-protein interactions from live cells and living subjects using bioluminescence resonance energy transfer

This study demonstrates a significant advancement of imaging of a distance-dependent physical process, known as the bioluminescent resonance energy transfer (BRET2) signal in living subjects, by using a cooled charge-coupled device (CCD) camera. A CCD camera-based spectral imaging strategy enables simultaneous visualization and quantitation of BRET signal from live cells and cells implanted in living mice. We used the BRET2 system, which utilizes Renilla luciferase (hRluc) protein and its substrate DeepBlueC (DBC) as an energy donor and a mutant green fluorescent protein (GFP2) as the acceptor. To accomplish this objective in this proof-of-principle study, the donor and acceptor proteins were fused to FKBP12 and FRB, respectively, which are known to interact only in the presence of the small molecule mediator rapamycin. Mammalian cells expressing these fusion constructs were imaged using a cooled-CCD camera either directly from culture dishes or by implanting them into mice. By comparing the emission photon yields in the presence and absence of rapamycin, the specific BRET signal was determined. The CCD imaging approach of BRET signal is particularly appealing due to its capacity to seamlessly bridge the gap between in vitro and in vivo studies. This work validates BRET as a powerful tool for interrogating and observing protein-protein interactions directly at limited depths in living mice.

Bioluminescence imaging in living organisms

Luciferase enzymes catalyze the emission of light from a substrate -- a phenomenon known as bioluminescence -- and have been employed as reporters of many biological functions. Luminescent reporters are much dimmer than fluorescent reporters, and therefore provide relatively modest spatial and temporal resolution. Yet, they are generally more sensitive and less toxic, making them particularly useful for long-term longitudinal studies of living cells, tissues and whole animals. Bioluminescence imaging has proven useful for detecting protein-protein interactions, for tracking cells in vivo, and for monitoring the transcriptional and post-transcriptional regulation of specific genes. Recent applications have included longitudinal monitoring of tumor progression in vivo, and monitoring circadian rhythms with single-cell resolution.

Monitoring proteasome activity in cellulo and in living animals by bioluminescent imaging: technical considerations for design and use of genetically encoded reporters

The ubiquitin-proteasome pathway is the central mediator of regulated proteolysis, instrumental for switching on and off a variety of signaling cascades. Deregulation of proteasomal activity or improper substrate recognition and processing by the ubiquitin-proteasome machinery may lead to cancer, stroke, chronic inflammation, and neurodegenerative diseases. Quantifying total and substrate-specific proteasome activity in intact cells and living animals would enable analysis in vivo of proteasomal regulation and facilitate the screening and validation of potential modulators of the proteasome or its substrates. We discuss examples of tetra-ubiquitin or IkappaBalpha fused to firefly luciferase as genetically encoded reporters for monitoring total and IkappaBalpha-specific proteasomal activity by bioluminescence imaging. Such technology enables repetitive, temporally resolved, and regionally targeted assessment of proteasomal activity in vivo.

Spying on cancer: molecular imaging in vivo with genetically encoded reporters

Genetically encoded imaging reporters introduced into cells and transgenic animals enable noninvasive, longitudinal studies of dynamic biological processes in vivo. The most common reporters include firefly luciferase (bioluminescence imaging), green fluorescence protein (fluorescence imaging), herpes simplex virus-1 thymidine kinase (positron emission tomography), and variants with enhanced spectral and kinetic properties. When cloned into promoter/enhancer sequences or engineered into fusion proteins, imaging reporters allow transcriptional regulation, signal transduction, protein-protein interactions, oncogenic transformation, cell trafficking, and targeted drug action to be spatiotemporally resolved in vivo. Spying on cancer with genetically encoded imaging reporters provides insight into cancer-specific molecular machinery within the context of the whole animal.

Advances in imaging mouse tumour modelsin vivo

Significant progress has been made recently in the variety of ways that cancer can be non-invasively imaged in murine tumour models. The development and continued refinement of specialized hardware for an array of small animal imaging methodologies are only partly responsible. So too has been the development of new imaging techniques and materials that enable specific, highly sensitive and quantitative measurement of a wide range of tumour-related parameters. Included amongst these new materials are imaging probes that selectively accumulate in tumours, or that become activated by tumour-specific molecules in vivo. Other tumour imaging strategies have been developed that rely upon the detection of reporter transgene expression in vivo, and these too have made a significant impact on both the versatility and the specificity of tumour imaging in living mice. The biological implications resulting from these latest advances are presented here, with particular emphasis on those associated with MRI, PET, SPECT, BLI, and fluorescence-based imaging modalities. Taken together, these advances in tumour imaging are set to have a profound impact on our basic understanding of in vivo tumour biology and will radically alter the application of mouse tumour models in the laboratory.