The power of the yeast two-hybrid system in the identification of novel drug targets: building and modulating PPP1 interactomes

The development of proximity labeling technology and its applications in mammals, plants, and microorganisms

Protein‒protein, protein‒RNA, and protein‒DNA interaction networks form the basis of cellular regulation and signal transduction, making it crucial to explore these interaction networks to understand complex biological processes. Traditional methods such as affinity purification and yeast two-hybrid assays have been shown to have limitations, as they can only isolate high-affinity molecular interactions under nonphysiological conditions or in vitro. Moreover, these methods have shortcomings for organelle isolation and protein subcellular localization. To address these issues, proximity labeling techniques have been developed. This technology not only overcomes the limitations of traditional methods but also offers unique advantages in studying protein spatial characteristics and molecular interactions within living cells. Currently, this technique not only is indispensable in research on mammalian nucleoprotein interactions but also provides a reliable approach for studying nonmammalian cells, such as plants, parasites and viruses. Given these advantages, this article provides a detailed introduction to the principles of proximity labeling techniques and the development of labeling enzymes. The focus is on summarizing the recent applications of TurboID and miniTurbo in mammals, plants, and microorganisms. Video Abstract.

Whole genome resequencing reveals signatures of rapid selection in a virus-affected commercial fishery

Infectious diseases are recognized as one of the greatest global threats to biodiversity and ecosystem functioning. Consequently, there is a growing urgency to understand the speed at which adaptive phenotypes can evolve and spread in natural populations to inform future management. Here we provide evidence of rapid genomic changes in wild Australian blacklip abalone (Haliotis rubra) following a major population crash associated with an infectious disease. Genome scans on H. rubra were performed using pooled whole genome resequencing data from commercial fishing stocks varying in historical exposure to haliotid herpesvirus-1 (HaHV-1). Approximately 25,000 single nucleotide polymorphism loci associated with virus exposure were identified, many of which mapped to genes known to contribute to HaHV-1 immunity in the New Zealand pāua (Haliotis iris) and herpesvirus response pathways in haliotids and other animal systems. These findings indicate genetic changes across a single generation in H. rubra fishing stocks decimated by HaHV-1, with stock recovery potentially determined by rapid evolutionary changes leading to virus resistance. This is a novel example of apparently rapid adaptation in natural populations of a nonmodel marine organism, highlighting the pace at which selection can potentially act to counter disease in wildlife communities.

The protein phosphatase isoform PP1γ1 substitutes for PP1γ2 to support spermatogenesis but not normal sperm function and fertility†

Four isoforms of serine/threonine phosphatase type I, PP1α, PP1β, PP1γ1, and PP1γ2, are derived from three genes. The PP1γ1 and PP1γ2 isoforms are alternately spliced transcripts of the protein phosphatase 1 catalytic subunit gamma gene (Ppp1cc). While PP1γ1 is ubiquitous in somatic cells, PP1γ2 is expressed exclusively in testicular germ cells and sperm. Ppp1cc knockout male mice (-/-), lacking both PP1γ1 and PP1γ2, are sterile due to impaired sperm morphogenesis. Fertility and normal sperm function can be restored by transgenic expression of PP1γ2 alone in testis of Ppp1cc (-/-) mice. The purpose of this study was to determine whether the PP1γ1 isoform is functionally equivalent to PP1γ2 in supporting spermatogenesis and male fertility. Significant levels of transgenic PP1γ1 expression occurred only when the transgene lacked a 1-kb 3΄UTR region immediately following the stop codon of the PP1γ1 transcript. PP1γ1 was also incorporated into sperm at levels comparable to PP1γ2 in sperm from wild-type mice. Spermatogenesis was restored in mice expressing PP1γ1 in the absence of PP1γ2. However, males from the transgenic rescue lines were subfertile. Sperm from the PP1γ1 rescue mice were unable to fertilize eggs in vitro. Intrasperm localization of PP1γ1 and the association of the protein regulators of the phosphatase were altered in epididymal sperm in transgenic PP1γ1 compared to PP1γ2. Thus, the ubiquitous isoform PP1γ1, not normally expressed in differentiating germ cells, could replace PP1γ2 to support spermatogenesis and spermiation. However, PP1γ2, which is the PP1 isoform in mammalian sperm, has an isoform-specific role in supporting normal sperm function and fertility.

Yeast Two-Hybrid Screening of Photoswitchable Protein-Protein Interaction Libraries

Although widely used in the detection and characterization of protein-protein interactions, Y2H screening has been under-used for the engineering of new optogenetic tools or the improvement of existing tools. Here we explore the feasibility of using Y2H selection and screening to evaluate libraries of photoswitchable protein-protein interactions. We targeted the interaction between circularly permuted photoactive yellow protein (cPYP) and its binding partner binder of PYP dark-state (BoPD) by mutating a set of four surface residues of cPYP that contribute to the binding interface. A library of ~10,000 variants was expressed in yeast together with BoPD in a Y2H format. An initial selection for the cPYP/BoPD interaction was performed using a range of concentrations of the cPYP chromophore. As expected, the majority (>90% of cPYP variants) no longer bound to BoPD. Replica plating was then used to evaluate the photoswitchability of the surviving clones. Photoswitchable cPYP variants with BoPD affinities equal to, or higher than, native cPYP were recovered in addition to variants with altered photocycles and binders that interacted with BoPD as apo-proteins. Y2H results reflected protein-protein interaction affinity, expression, photoswitchability, and chromophore uptake, and correlated well with results obtained both in vitro and in mammalian cells. Thus, by systematic variation of selection parameters, Y2H screens can be effectively used to generate new optogenetic tools for controlling protein-protein interactions for use in diverse settings.

The mammalian two-hybrid system as a powerful tool for high-throughput drug screening

Protein-protein interactions (PPIs) are the backbone of signaling pathways, responsible for the basis of cell communication and, when deregulated, several diseases. Consequently, identifying and modulating PPIs can unravel the pathophysiological mechanisms of diseases. The two-hybrid system, particularly the mammalian two-hybrid system (MTH), is an efficient technique to validate PPIs ex vivo. Combining MTH with high-throughput screening has a huge advantage in biomedical research. In this review, we describe methodologies developed from MTH and the role of these adaptations in PPI discovery. We also highlight the powerful contribution of MTH to the identification of disease-related PPIs and its use in the development of potential new drug screens.

Protein-Protein Interactions in Candida albicans

Despite being one of the most important human fungal pathogens, Candida albicans has not been studied extensively at the level of protein-protein interactions (PPIs) and data on PPIs are not readily available in online databases. In January 2018, the database called "Biological General Repository for Interaction Datasets (BioGRID)" that contains the most PPIs for C. albicans, only documented 188 physical or direct PPIs (release 3.4.156) while several more can be found in the literature. Other databases such as the String database, the Molecular INTeraction Database (MINT), and the Database for Interacting Proteins (DIP) database contain even fewer interactions or do not even include C. albicans as a searchable term. Because of the non-canonical codon usage of C. albicans where CUG is translated as serine rather than leucine, it is often problematic to use the yeast two-hybrid system in Saccharomyces cerevisiae to study C. albicans PPIs. However, studying PPIs is crucial to gain a thorough understanding of the function of proteins, biological processes and pathways. PPIs can also be potential drug targets. To aid in creating PPI networks and updating the BioGRID, we performed an exhaustive literature search in order to provide, in an accessible format, a more extensive list of known PPIs in C. albicans.

Insect Transcription Factors: A Landscape of Their Structures and Biological Functions in Drosophila and beyond

Transcription factors (TFs) play essential roles in the transcriptional regulation of functional genes, and are involved in diverse physiological processes in living organisms. The fruit fly Drosophila melanogaster, a simple and easily manipulated organismal model, has been extensively applied to study the biological functions of TFs and their related transcriptional regulation mechanisms. It is noteworthy that with the development of genetic tools such as CRISPR/Cas9 and the next-generation genome sequencing techniques in recent years, identification and dissection the complex genetic regulatory networks of TFs have also made great progress in other insects beyond Drosophila. However, unfortunately, there is no comprehensive review that systematically summarizes the structures and biological functions of TFs in both model and non-model insects. Here, we spend extensive effort in collecting vast related studies, and attempt to provide an impartial overview of the progress of the structure and biological functions of current documented TFs in insects, as well as the classical and emerging research methods for studying their regulatory functions. Consequently, considering the importance of versatile TFs in orchestrating diverse insect physiological processes, this review will assist a growing number of entomologists to interrogate this understudied field, and to propel the progress of their contributions to pest control and even human health.

General Genetic Strategies

It is difficult to study the genetics and molecular mechanisms of anesthesia in humans. Fortunately, the genetic approaches in model organisms can, and have, led to profound insights as to the targets of anesthetics. In turn, the organization of these putative targets into meaningful pathways has begun to elucidate the mechanisms of action of these agents. However, it is important to first appreciate the strengths, and limitations, of genetic approaches to understand the anesthetic action. Here we compare the commonly used genetic model organisms, various anesthetic endpoints, and different modes of genetic screens. Coupled with the more specific data presented in subsequent chapters, this chapter places those results in a framework with which to analyze the discoveries across organisms and eventually extend the resulting models to humans.

Identification of the interaction and interaction domains of chicken anemia virus VP2 and VP3 proteins

Chicken anemia virus (CAV) is a small, single-stranded DNA virus of Anelloviridae family. Its genome segments encode three proteins, VP1, VP2, and VP3. This study identified an interaction between VP2 and VP3 and mapped the interaction domains. Through the yeast two-hybrid (Y2H) system, VP2 was found to interact with VP3. The presence of the VP2-VP3 complex in CAV-infected chicken cells was confirmed by co-immunoprecipitation. Confocal microscopy showed that VP2 and VP3 were expressed in the cytoplasm in cotransfected Vero cells. In the Y2H system, the interaction domains were identified as being within the N-terminal aa 1-30 and C-terminal aa 17-60 for VP2 and the N-terminal aa 46-60 and C-terminal aa 1-7 for VP3. This study showed the interaction between VP2 and VP3 of CAV and identified multiple independent interactive domains within the two proteins. This provides novel information for investigating the biological functions of these proteins.

Yeast-based assays for detecting protein-protein/drug interactions and their inhibitors

Understanding cellular processes at molecular levels in health and disease requires the knowledge of protein-protein interactions (PPIs). In line with this, identification of PPIs at genome-wide scale is highly valuable to understand how different cellular pathways are interconnected, and it eventually facilitates designing effective drugs against certain PPIs. Furthermore, investigating PPIs at a small laboratory scale for deciphering certain biochemical pathways has been demanded for years. In this regard, yeast two hybrid system (Y2HS) has proven an extremely useful tool to discover novel PPIs, while Y2HS derivatives and novel yeast-based assays are contributing significantly to identification of protein-drug/inhibitor interaction at both large- and small-scale set-ups. These methods have been evolving over time to provide more accurate, reproducible and quantitative results. Here we briefly describe different yeast-based assays for identification of various protein-protein/drug/inhibitor interactions and their specific applications, advantages, shortcomings, and improvements. The broad range of yeast-based assays facilitates application of the most suitable method(s) for each specific need.

Regulating the regulator: Insights into the cardiac protein phosphatase 1 interactome

Reversible phosphorylation of proteins is a delicate yet dynamic balancing act between kinases and phosphatases, the disturbance of which underlies numerous disease processes. While our understanding of protein kinases has grown tremendously over the past decades, relatively little is known regarding protein phosphatases. This may be because protein kinases are great in number and relatively specific in function, and thereby amenable to be studied in isolation, whereas protein phosphatases are much less abundant and more nonspecific in their function. To achieve subcellular localization and substrate specificity, phosphatases depend on partnering with a large number of regulatory subunits, protein scaffolds and/or other interactors. This added layer of complexity presents a significant barrier to their study, but holds the key to unexplored opportunities for novel pharmacologic intervention. In this review we focus on serine/threonine protein phosphatase type-1 (PP1), which plays an important role in cardiac physiology and pathophysiology. Although much work has been done to investigate the role of PP1 in cardiac diseases including atrial fibrillation and heart failure, most of these studies were limited to examining and manipulating the catalytic subunit(s) of PP1 without adequately considering the PP1 interactors, which give specificity to PP1's functions. To complement these studies, three unbiased methods have been developed and applied to the mapping of the PP1 interactome: bioinformatics approaches, yeast two-hybrid screens, and affinity-purification mass spectrometry. The application of these complementary methods has the potential to generate a detailed cardiac PP1 interactome, which is an important step in identifying novel and targeted pharmacological interventions.

Interactions among SARS-CoV accessory proteins revealed by bimolecular fluorescence complementation assay

The accessory proteins (3a, 3b, 6, 7a, 7b, 8a, 8b, 9b and ORF14), predicted unknown proteins (PUPs) encoded by the genes, are considered to be unique to the severe acute respiratory syndrome coronavirus (SARS-CoV) genome. These proteins play important roles in various biological processes mediated by interactions with their partners. However, very little is known about the interactions among these accessory proteins. Here, a EYFP (enhanced yellow fluorescent protein) bimolecular fluorescence complementation (BiFC) assay was used to detect the interactions among accessory proteins. 33 out of 81 interactions were identified by BiFC, much more than that identified by the yeast two-hybrid (Y2H) system. This is the first report describing direct visualization of interactions among accessory proteins of SARS-CoV. These findings attest to the general applicability of the BiFC system for the verification of protein-protein interactions.