Membrane Yeast Two-Hybrid (MYTH) Mapping of Full-Length Membrane Protein Interactions

Workflow to Select Functional Promoter DNA Baits and Screen Arrayed Gene Libraries in Yeast

The yeast one-hybrid system (Y1H) is used extensively to identify DNA-protein interactions. The generation of large collections of open reading frames (ORFs) to be used as prey in screenings is not a bottleneck nowadays and can be carried out in-house or offered as a service by companies. However, the straightforward use of full gene promoters as baits to identify interacting proteins undermines the accuracy and sensitivity of the assay, especially in the case of multicellular eukaryotes. Therefore, it is paramount to implement procedures for efficient identification of suitable promoter fragments compatible with the Y1H assay. Here, we describe a workflow to identify biologically relevant conserved promoter fragments of Arabidopsis thaliana through simple and robust phylogenetic analyses. Additionally, we describe a manual method and its automated robotized version for rapid and efficient high-throughput Y1H screenings of arrayed ORF libraries with the identified DNA fragments. Moreover, this method can be scaled up or down and used for yeast two-hybrid screenings to search for possible interactors of proteins identified by the Y1H approach or any other protein of interest, altogether underscoring its suitability to build gene regulatory networks. © 2024 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Selection of DNA baits for Y1H screenings Basic Protocol 2: Y1H screenings with arrayed gene libraries Alternate Protocol: Automated screening with a liquid-handling robot.

Caenorhabditis elegans sperm membrane protein interactome

The interaction and organization of proteins in the sperm membrane are important for all aspects of sperm function. We have determined the interactions between 12 known mutationally defined and cloned sperm membrane proteins in a model system for reproduction, the nematode Caenorhabditis elegans. Identification of the interactions between sperm membrane proteins will improve our understanding of and ability to characterize defects in sperm function. To identify interacting proteins, we conducted a split-ubiquitin membrane yeast two-hybrid analysis of gene products identified through genetic screens that are necessary for sperm function and predicted to encode transmembrane proteins. Our analysis revealed novel interactions between sperm membrane proteins known to have roles in spermatogenesis, spermiogenesis, and fertilization. For example, we found that a protein known to play a role in sperm function during fertilization, SPE-38 (a predicted four pass transmembrane protein), interacts with proteins necessary for spermiogenesis and spermatogenesis and could serve as a central organizing protein in the plasma membrane. These novel interaction pairings will provide the foundation for investigating previously unrealized membrane protein interactions during spermatogenesis, spermiogenesis, and sperm function during fertilization.

Screening Arrayed Libraries with DNA and Protein Baits to Identify Interacting Proteins

Molecular interactions are an integral part of the regulatory mechanisms controlling gene expression. The yeast one- and two-hybrid systems (Y1H/Y2H) have been widely used by many laboratories to detect DNA-protein (Y1H) and protein-protein interactions (Y2H). The development of efficient cloning systems have promoted the generation of large open reading frame (ORF) clone collections (libraries) for several organisms. Functional analyses of such large collections require the establishment of adequate protocols. Here, we describe a simple straightforward procedure for high-throughput screenings of arrayed libraries with DNA or protein baits that can be carried out by one person with minimal labor and not requiring robotics. The protocol can also be scaled up or down and is compatible with several library formats. Procedures to make yeast stocks for long-term storage (tube and microplate formats) are also provided.

Discovering cellular protein-protein interactions: Technological strategies and opportunities

The analysis of protein interaction networks is one of the key challenges in the study of biology. It connects genotypes to phenotypes, and disruption often leads to diseases. Hence, many technologies have been developed to study protein-protein interactions (PPIs) in a cellular context. The expansion of the PPI technology toolbox however complicates the selection of optimal approaches for diverse biological questions. This review gives an overview of the binary and co-complex technologies, with the former evaluating the interaction of two co-expressed genetically tagged proteins, and the latter only needing the expression of a single tagged protein or no tagged proteins at all. Mass spectrometry is crucial for some binary and all co-complex technologies. After the detailed description of the different technologies, the review compares their unique specifications, advantages, disadvantages, and applicability, while highlighting opportunities for further advancements.

Features of the Chaperone Cellular Network Revealed through Systematic Interaction Mapping

A comprehensive view of molecular chaperone function in the cell was obtained through a systematic global integrative network approach based on physical (protein-protein) and genetic (gene-gene or epistatic) interaction mapping. This allowed us to decipher interactions involving all core chaperones (67) and cochaperones (15) of Saccharomyces cerevisiae. Our analysis revealed the presence of a large chaperone functional supercomplex, which we named the naturally joined (NAJ) chaperone complex, encompassing Hsp40, Hsp70, Hsp90, AAA+, CCT, and small Hsps. We further found that many chaperones interact with proteins that form foci or condensates under stress conditions. Using an in vitro reconstitution approach, we demonstrate condensate formation for the highly conserved AAA+ ATPases Rvb1 and Rvb2, which are part of the R2TP complex that interacts with Hsp90. This expanded view of the chaperone network in the cell clearly demonstrates the distinction between chaperones having broad versus narrow substrate specificities in protein homeostasis.

Systems analysis of the genetic interaction network of yeast molecular chaperones

Many molecular chaperones were found to be central drivers of the yeast whole genome genetic interaction network topology.

Yeast One- and Two-Hybrid High-Throughput Screenings Using Arrayed Libraries

Since their original description more than 25 years ago, the yeast one- and two-hybrid systems (Y1H/Y2H) have been used by many laboratories to detect DNA-protein (Y1H) and protein-protein interactions (Y2H). These systems use yeast cells (Saccharomyces cerevisiae) as a eukaryotic "test tube" and are amenable for most labs in the world. The development of highly efficient cloning methods has fostered the generation of large collections of open reading frames (ORFs) for several organisms that have been used for yeast screenings. Here, we describe a simple mating based method for high-throughput screenings of arrayed ORF libraries with DNA (Y1H) or protein (Y2H) baits not requiring robotics. One person can easily carry out this protocol in approximately 10 h of labor spread over 5 days. It can also be scaled down to test one-to-one (few) interactions, scaled up (i.e., robotization) and is compatible with several library formats (i.e., 96, 384-well microtiter plates).

Recent advances in understanding hepatic drug transport

Cells need to strictly control their internal milieu, a function which is performed by the plasma membrane. Selective passage of molecules across the plasma membrane is controlled by transport proteins. As the liver is the central organ for drug metabolism, hepatocytes are equipped with numerous drug transporters expressed at the plasma membrane. Drug disposition includes absorption, distribution, metabolism, and elimination of a drug and hence multiple passages of drugs and their metabolites across membranes. Consequently, understanding the exact mechanisms of drug transporters is essential both in drug development and in drug therapy. While many drug transporters are expressed in hepatocytes, and some of them are well characterized, several transporters have only recently been identified as new drug transporters. Novel powerful tools to deorphanize (drug) transporters are being applied and show promising results. Although a large set of tools are available for studying transport in vitro and in isolated cells, tools for studying transport in living organisms, including humans, are evolving now and rely predominantly on imaging techniques, e.g. positron emission tomography. Imaging is an area which, certainly in the near future, will provide important insights into "transporters at work" in vivo.

MYTH Screening: iMYTH and tMYTH Variants

Once a bait has been generated and validated for the membrane yeast two-hybrid (MYTH) assay, it can be used for either high-throughput screening to generate a detailed interaction map (interactome) or in low-throughput experiments to examine interactions with specific targets. Here we describe how to carry out high-throughput MYTH library screening of a validated bait generated using integrated or traditional MYTH. The principles herein can be easily adapted for use in a smaller-scale format if required. A typical MYTH library screen can be completed in ∼3-4 wk.

Generation and Validation of MYTH Baits: iMYTH and tMYTH Variants

Generation of baits for membrane yeast two-hybrid (MYTH) screening differs depending on the nature of the protein(s) being studied. When using native yeast proteins with cytoplasmic carboxyl termini, the integrated form of MYTH (iMYTH) is the method of choice. iMYTH involves endogenous carboxy-terminal tagging of the gene of interest within the yeast chromosome, leaving the gene under the control of its natural promoter. When studying proteins not native to yeast, or native yeast proteins with only cytoplasmic amino termini, traditional MYTH (tMYTH) must be used. In the tMYTH approach, amino- or carboxy-terminally tagged proteins are expressed ectopically from a plasmid. In this protocol, we describe the generation and validation of iMYTH and tMYTH baits. MYTH bait generation can typically be completed in ∼1-2 wk.