Distance-Matched Tagging Sequence Optimizes Live-Cell Protein Labeling by a Biarsenical Fluorescent Reagent AsCy3_E

Selective fluorescent labeling of cellular proteins and its biological applications

Proteins, which are ubiquitous in cells and critical to almost all cellular functions, are indispensable for life. Fluorescence imaging of proteins is key to understanding their functions within their native milieu, as it provides insights into protein localization, dynamics, and trafficking in living systems. Consequently, the selective labeling of target proteins with fluorophores has emerged as a highly active research area, encompassing bioorganic chemistry, chemical biology, and cell biology. Various methods for selectively labeling proteins with fluorophores in cells and tissues have been established and are continually being developed to visualize and characterize proteins. This review highlights research findings reported since 2018, with a focus on the selective labeling of cellular proteins with small organic fluorophores and their biological applications in studying protein-associated biological events. We also discuss the strengths and weaknesses of each labeling approach for their utility in living systems.

Biarsenical fluorescent probes for multifunctional site-specific modification of proteins applicable in life sciences: an overview and future outlook

Fluorescent modification of proteins of interest (POI) in living cells is desired to study their behaviour and functions in their natural environment. In a perfect setting it should be easy to perform, inexpensive, efficient and site-selective. Although multiple chemical and biological methods have been developed, only a few of them are applicable for cellular studies thanks to their appropriate physical, chemical and biological characteristics. One such successful system is a tetracysteine tag/motif and its selective biarsenical binders (e.g. FlAsH and ReAsH). Since its discovery in 1998 by Tsien and co-workers, this method has been enhanced and revolutionized in terms of its efficiency, formed complex stability and breadth of application. Here, we overview the whole field of knowledge, while placing most emphasis on recent reports. We showcase the improvements of classical biarsenical probes with various optical properties as well as multifunctional molecules that add new characteristics to proteins. We also present the evolution of affinity tags and motifs of biarsenical probes demonstrating much more possibilities in cellular applications. We summarize protocols and reported observations so both beginners and advanced users of biarsenical probes can troubleshoot their experiments. We address the concerns regarding the safety of biarsenical probe application. We showcase examples in virology, studies on receptors or amyloid aggregation, where application of biarsenical probes allowed observations that previously were not possible. We provide a summary of current applications ranging from bioanalytical sciences to allosteric control of selected proteins. Finally, we present an outlook to encourage more researchers to use these magnificent probes.

Dual-fluorescent bacterial two-hybrid system for quantitative Protein-Protein interaction measurement via flow cytometry

Characterization of protein-protein interactions (PPIs) is essential for understanding cellular signal transduction pathways. However, quantitative measurement of the binding strength remains challenging. Building upon the classical bacterial adenylate cyclase two-hybrid (BACTH) system, we previously demonstrated that the relative reporter protein expression (RRPE), defined as the level of reporter expression normalized to that of the interacting protein, is an intrinsic characteristic associated with the binding strength between the two interacting proteins. In this study, we inserted fluorescent protein tdTomato in the chromosome as the reporter protein by CRISPR/Cas9 technology and employed a 12-amino acid tetracysteine (TC) to tag one of the interacting proteins, which can be further labeled by a membrane-permeable biarsenical dye. The combined use of tdTomato and TC-tag offers rapid and high-throughput analysis of the expression levels of both the reporter protein and one of the interacting proteins at the single-cell level by multicolor flow cytometry, which simplifies the quantitative measurement of PPI. The use of the as-developed RRPE-tdTomato-TC-BACTH approach was demonstrated in three demanding applications. First, binding affinities could be correctly ranked for discriminating interaction strengths with a tenfold difference or of the same order of magnitude. We demonstrate that the method is sensitive enough to discriminate affinities with a small difference of 1.4-fold. Moreover, residues involved in PPI can be easily mapped and ranked. Lastly, protein interaction inhibitors can be rapidly screened.

Deciphering the Antitoxin-Regulated Bacterial Stress Response via Single-Cell Analysis

Bacterial toxin-antitoxin (TA) systems, which are diverse and widespread among prokaryotes, are responsible for tolerance to drugs and environmental stresses. However, the low abundance of toxin and antitoxin proteins renders their quantitative measurement in single bacteria challenging. Employing a laboratory-built nano-flow cytometer (nFCM) to monitor a tetracysteine (TC)-tagged TA system labeled with the biarsenical dye FlAsH, we here report the development of a sensitive method that enables the detection of basal-level expression of antitoxin. Using the Escherichia coli MqsR/MqsA as a model TA system, we reveal for the first time that under its native promoter and in the absence of environmental stress, there exist two populations of bacteria with high or low levels of antitoxin MqsA. Under environmental stress, such as bile acid stress, heat shock, and amino acid starvation, the two populations of bacteria responded differently in terms of MqsA degradation and production. Subsequently, resumed production of MqsA after amino acid stress was observed for the first time. Taking advantage of the multiparameter capability of nFCM, bacterial growth rate and MqsA production were analyzed simultaneously. We found that under environmental stress, the response of bacterial growth was consistent with MqsA production but with an approximate 60 min lag. Overall, the results of the present study indicate that stochastic elevation of MqsA level facilitates bacterial survival, and the two populations with distinct phenotypes empower bacteria to deal with fluctuating environments. This analytical method will help researchers gain deeper insight into the heterogeneity and fundamental role of TA systems.