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EP1325148A1 - Procede et ensemble permettant de detecter des interactions proteine membranaire-proteine - Google Patents

Procede et ensemble permettant de detecter des interactions proteine membranaire-proteine

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Publication number
EP1325148A1
EP1325148A1 EP00962148A EP00962148A EP1325148A1 EP 1325148 A1 EP1325148 A1 EP 1325148A1 EP 00962148 A EP00962148 A EP 00962148A EP 00962148 A EP00962148 A EP 00962148A EP 1325148 A1 EP1325148 A1 EP 1325148A1
Authority
EP
European Patent Office
Prior art keywords
protein
gene
host cell
membrane
test
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Withdrawn
Application number
EP00962148A
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German (de)
English (en)
Inventor
Igor Stagljar
Christine Buerki
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Zurich Universitaet Institut fuer Medizinische Virologie
Original Assignee
Zurich Universitaet Institut fuer Medizinische Virologie
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Zurich Universitaet Institut fuer Medizinische Virologie filed Critical Zurich Universitaet Institut fuer Medizinische Virologie
Publication of EP1325148A1 publication Critical patent/EP1325148A1/fr
Withdrawn legal-status Critical Current

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6897—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids involving reporter genes operably linked to promoters

Definitions

  • the present invention is concerned with a method for detecting membrane protein - protein interactions with an in vivo genetic system based in yeast, bacterial or mammalian cells. Furthermore, the invention provides a kit for detecting the interactions between a first membrane test protein and a second test protein using reconstitution of the split ubiquitin protein.
  • the reconstitution of split ubiquitin makes use of chimeric genes, which express hybrid proteins.
  • Proteins are complex macromolecules made up of covalently linked chains of amino acids. Each protein assumes a unique three-dimensional shape principally determined by its sequence of amino acids. Many proteins consist of smaller units called domains, which are continuous stretches of amino acids able to fold independently from the rest of the protein (e.g. ⁇ -helices, ⁇ -sheets) .
  • BESTATIGUNGSKOPIE pramolecular structures of ribosomes, filaments and viruses A special and specific role can be attributed to membrane proteins. They are involved in the transport of molecules; in the interaction of receptors on the cell surface with growth fac- tors and hormones; membrane bound oncogene products can give rise to neoplastic transformation through protein-protein interactions with proteins called kinases whose enzymatic activity on cellular target proteins leads to a cancerous state. Other examples of a protein-protein interaction in membranes occur when virus infects a cell by recognizing a protein (receptor) on the surface, and this interaction has been used to design antiviral agents.
  • Type I transmembrane proteins have their C-terminus in the cytoplasm
  • Type II transmembrane proteins have their C-terminus outside the cell (or in the inner part of some other organelle, for example in the lumen of the endoplas- mic reticulum) .
  • Protein-protein interactions have been generally studied in the past ten years by using biochemical techniques such as cross- linking, co-immunoprecipitation and co-fractionation by chroma- tography.
  • Biochemical methods have the disadvantage that interacting proteins are generally known as bands of a particular mobility on a polyacrylamide gel. To progress from these bands to cloned genes is often a very tedious process.
  • yeast two-hybrid system is based on reconstitution of a transcrip- tional activator and transcriptional activation of reporter genes.
  • the yeast two-hybrid system is a powerful method in the in vivo analysis of the protein-protein interaction, but is naturally limited to the analysis of soluble proteins or soluble domains of membrane proteins, i.e. interactions between integral membrane proteins cannot be studied.
  • the hybrid proteins are targeted to the nucleus where the interac- tions take place. Thus, the interactions that are dependent on post-translational modifications that take place within ER, such as glycosylation and disulfide bond formation, may not occur.
  • the split-ubiquitin system represents an alternative assay for the in vivo analysis of protein interactions. It was developed in 1994 by Niels Johnsson and Alexander Varshavsky [Johnsson, N. and Varshavsky, A., Proc. Natl. Acad. Sci. USA 91, 10340- 10344 (1994)] for the detection of interactions between soluble proteins ( Figure 1) .
  • Ubiquitin (Ub) is a 76 amino acid residue, single domain protein that is present in cells either free or covalently linked to other proteins. Ubiquitin plays a role in a number of processes primarily through routes that involve protein degradation.
  • Ub fusions are rapidly cleaved by ubiquitin specific proteases (UBPs) after the last residue of Ub at the Ub-polypeptide junction.
  • UBPs ubiquitin specific proteases
  • the cleavage of a UB fusion by UBPs requires the folded conformation of Ub.
  • Cub C-terminal fragment of ubiquitin
  • Nub N-terminal fragment of Ubiquitin
  • a further object of the present invention is a method for the identification of new genes by screening libraries fused to the N-terminal domain of Ubiquitin (Nub) .
  • Another object of this invention is to provide a method by which a multiplicity of proteins, such as those encoded by the entire genome of a cell, can be simultaneously tested for in- teraction with a known protein.
  • Yet another object of the present invention is to provide a method which can be used in the design of peptides to be used therapeutically.
  • a still further object of this invention is to provide a method for testing affinity reagents for protein purification.
  • the present invention also provides kits for carrying out each of the above mentioned objects.
  • the present invention provides a method and a kit for detecting interactions between either two membrane proteins or one membrane and one cytosolic protein.
  • the reconstitution of split ubiquitin makes use of chimeric genes, which express hybrid proteins.
  • Two types of hybrid proteins are prepared. The first hybrid contains a membrane protein of interest (bait) fused to the Cub-PLV module
  • the second hybrid protein contains an N-terminal domain of ubiquitin fused to the second test protein.
  • the prey protein can be either a membrane protein or a soluble cytoplasmic pro- tein. If two test proteins are able to interact, they reconstitute two separate ubiquitin domains into an active ubiquitin leading to the cleavage of the transcriptional activator and activation of the yeast reporter system.
  • a multiplicity of membrane proteins can be simultaneously tested to determine whether any interact with a known protein.
  • a DNA fragment encoding the membrane protein of interest (bait) is fused to a DNA fragment encoding the Cub-Protein A-LexA-VP16 fusion.
  • This hybrid is introduced into the host cell (yeast, bacterial or mammalian cells) carrying marker genes.
  • a library of plasmids can be constructed which may include, for example, total human complementary DNA (cDNA) fused to the DNA sequence encoding the N-terminal domain of Ubiquitin (NubG) .
  • This library is introduced into the yeast cells carrying bait protein. If any individual plasmid from the library encodes a protein that is capable of interacting with the membrane bait protein, a positive signal will be obtained. In addition, when an interaction between proteins occurs, the gene for the newly identified protein is available.
  • the system can be of value in the identification of new genes. For example, membrane bound receptors may be identified that interact with a known membrane protein. Proteins that interact with oncogene-encoded membrane proteins may be discovered, and these proteins will be of therapeutic value.
  • the system can be used in the design of peptide inhibitors. For example, peptides that interact with membrane bound growth factor receptors can be identified and then tested in other sys- terns for their ability to inhibit the signal transduction. Peptides that bind to bacterial or viral membrane proteins can be identified and then tested in other systems for their ability to inhibit these bacteria or viruses.
  • the system can be used to test affinity reagents for protein purification. Peptides or protein domains can be identified that interact with the known membrane protein of interest and these may then be used in a purification protocol for the known protein.
  • a method for detecting the interaction between a first test membrane protein and a second test (membrane or soluble) pro- tein is provided in accordance to the present invention.
  • the method is set up in yeast, preferably in Schizosaccharomyces pombe, most preferably in the budding yeast Saccharomyces cere- visiae, but can be set up as well in bacteria such as Es- cherichia coli and mammalian cell systems.
  • the host cell con- tains a detectable gene having a binding site for a transcriptional activator, preferably PLV (for Protein A-LexA-VP16) , such that the detectable gene expresses a detectable protein when the detectable gene is transcriptionally activated.
  • PLV for Protein A-LexA-VP16
  • the first chimeric gene is provided which is capable of being expressed in the host cell.
  • the first chimeric gene contains a DNA coding for a first test membrane protein fused to the transcriptional activator called PLV (for Protein A-LexA-VP16) . This protein is then tested for interaction with a second test protein or protein fragment.
  • a second chimeric gene is provided which is capable of being expressed in the hosr. cell.
  • the second chimeric gene contains a DNA sequence that encodes a second hybrid protein.
  • the second hybrid protein contains an N-terminal domain of Ubiquitin (NubG) .
  • the second hybrid protein also contains a second test protein or a protein fragment which is to be tested for interaction with the first test protein or protein fragment.
  • the second hybrid protein may be encoded in a library of plasmids that contain genomic, cDNA or synthetically generated DNA se- quences fused to the DNA sequence encoding the N-terminal domain of Ubiquitin (NubG) .
  • the interaction between the first test membrane protein and the second test protein in the host cell therefore, causes the cleavage of the transcriptional activator that activates transcription of the reporter genes.
  • the method is carried out by introducing the first chimeric gene and the second chimeric gene into the yeast reporter strain.
  • the host cell is subjected to conditions under which the first membrane test protein and the second test protein are expressed in sufficient quantity for the reporter gene to be activated.
  • the cells are then tested for their expression of the detectable gene to a greater degree than in the absence of an interaction between the first test protein and the second test protein.
  • the first test membrane protein may be derived from a bacterial membrane protein, a viral membrane protein, an oncogene-encoded membrane protein, a growth-factor receptor or any eukaryotic membrane protein.
  • the second test protein may be derived from a library of plasmids as described above.
  • the method of the present invention may be practiced using a kit for detecting interaction between a first test membrane protein and a second test protein.
  • the kit includes a con- tainer, six vectors and a host cell.
  • the vectors for the membrane based yeast two-hybrid system are schematically shown in Figure 2.
  • the first vector that allows to assay any Type I transmembrane protein (Y) , contains a weak yeast promoter selected from the group consisting of the ADH pro- moter, Cycl promoter and TEF promoter, followed by the unique restriction sites for inserting a DNA sequence encoding a test membrane protein in such a manner that the first test protein is expressed as a fusion to the Cub-Protein A-LexA-VPl ⁇ portion.
  • the first vector also contains a terminator sequence which is necessary to terminate the transcription of a given test membrane protein.
  • the first vector does not include the sequence that allows its replication in yeast. This vector is an integrative vector that has to be stable integrated in the yeast genome.
  • a first marker gene (LEU2), the expression of which in the host cell permits selection of cells containing the first marker gene from cells that do not contain the first marker gene.
  • the second vector that allows to assay any Type II transmembrane protein (Y) , contains a weak yeast promoter selected from the group consisting of the ADH promoter, Cycl promoter and TEF promoter, followed by the unique restriction site for inserting a DNA sequence encoding a test membrane protein in such a manner that the first test protein is expressed as a fusion to Protein A-LexA-VPl ⁇ -Cub portion ( Figure 2) . Note that there is an inverted orientation of the transcription factor fused to the PLV portion.
  • the second vector also contains a terminator sequence which is necessary to terminate the transcription of a given test membrane protein.
  • the second vector does not include the sequence that allows its replication in yeast.
  • this vector is an integrative- vector that has to be stable integrated in the yeast genome. Also included on the second vector is a marker gene (LEU2), the expression of which in the host cell permits selection of cells containing the first marker gene from cells that do not contain the first marker gene.
  • LEU2 marker gene
  • the third vector allows the cloning of the prey protein (X) that may be a transmembrane protein or soluble (cyto- plasmic) protein ( Figure 2).
  • the test protein may be encoded in a library of plasmids that contain genomic, cDNA or synthetically generated DNA sequences fused to the NubG domain.
  • the third vector also includes a promoter selected from the group consisting of the ADH promoter, Cycl promoter and TEF promoter, and does include a transcription termination signal to direct transcription. It also includes a DNA sequence that encodes the N-terminal domain of Ubiquitin (NubG) and a unique restriction site to insert a DNA sequence encoding the second test protein or protein fragment into the vector.
  • the third vector allows the cloning of the test protein as an N-terminal fusion to the NubG domain.
  • the third vector further includes a means for replicating itself in the host cell, i.e. yeast or bacteria. It also includes a second marker gene (TRP1), the expression of which in the host cell permits selection of cells containing the second marker gene from cells that do not contain the second marker gene.
  • TRP1 second marker gene
  • the fourth vector allows the cloning of the prey protein (X) , a transmembrane protein or soluble (cytoplasmic) protein, as a C-terminal fusion to the NubG domain ( Figure 2) .
  • the fourth vector also includes a promoter selected from the group consisting of the ADH promoter, Cycl promoter and TEF promoter, and transcription termination signal to direct transcription. It also includes a DNA sequence that encodes the N-terminal domain of ubiquitin (NubG) and a unique restriction site to insert a DNA sequence encoding the second test protein or protein fragment into the vector.
  • the fourth vector further includes a means for replicating itself in the host cell and in bacteria. It also includes a second marker gene (TRP1), the expression of which in the host cell permits selection of cells containing the second marker gene from cells that do not contain the sec- ond marker gene.
  • TRP1 second marker gene
  • the fifth (pNubl-X) and the sixth (pX-Nubl) vector ' serve as the control vectors of the membrane based yeast two-hybrid system. They are identical to the pNubG-X and pX-NubG vectors, respec- tively, with the only difference that they contain the wild type Nub domain (Nubl) . Thus, any in frame fusion of a second test protein to these two vectors will result in a positive signal using the yeast host cell.
  • the kit includes a host cell, a yeast or bacterial strain that contains the detectable gene having binding sites for the artificial transcription factor Protein A-Cub-PLV.
  • the binding site is positioned so that the reporter gene expresses a reporter protein when two proteins interact in this system.
  • the host cell by itself, is incapable of expressing a protein having a function of the first marker gene (LEU2), the second marker gene (TRP1), the Cub-PLV portion, or the NubG domain.
  • the basic strategy of the testing method is shown in Figure 1.
  • the method is based on the previously developed split-ubiquitin technique.
  • the split-ubiquitin technique is based on the ability of Nub and Cub, the N- and C-terminal halves of Ub, to assemble into quasi-native Ubiquitin.
  • Ubiquitin-specific proteases Ubiquitin-specific proteases (UBPs), which are present in all eukaryotic cells, recognize the reconstituted Ubiquitin, but not its halves, and cleave the Ubiquitin moiety off a reporter protein that had been linked to the C terminus of Cub. Quite in analogy to the two-hybrid system, the liberation of the reporter serves as a readout indicating the reconstruction of Ubiquitin.
  • the assay is designed in a way that prevents efficient association of Nub and Cub by themselves, but allows it if the two Ubiquitin halves are separately linked to proteins that interact in vivo.
  • the first chimeric protein contains the Type I transmembrane bait protein Y fused to the Cub-PLV portion resulting in Y-Cub-PLV protein.
  • the second chimeric protein contains a second interacting protein X (here depicted as a membrane protein) fused to the NubG domain called X-NubG. Neither of these proteins, Y-Cub-PLV and X-NubG, is able to activate transcription.
  • the interaction of proteins Y and X results in formation of the split-ubiquitin het- erodimer.
  • the heterodimer is recognized and cleaved by the Ubiquitin specific proteases (UBPs) (open scissors), liberating PLV.
  • UBPs Ubiquitin specific proteases
  • the PLV can enter the nucleus by diffusion and bind to the LexA-binding sites leading to activation of transcription of the lacZ and HIS3 reporter genes. This results in blue cells in the presence of X-gal and growth of the cells on agar plates lacking histidine.
  • Figure 3c schematically illustrates interaction between a Type II transmembrane protein (Y) and a cytoplasmic protein (X) .
  • the first chimeric protein contains the bait protein Y fused to the PLV-Cub portion resulting in PLV-Cub-Y protein.
  • the second chimeric protein contains a second interacting protein X (here depicted as a cytoplasmic protein) fused to the NubG domain called NubG-X. Neither of these proteins, PLV-Cub-Y and NubG-X, is able to activate transcription.
  • Y and X results in formation of the split-ubiquitin heterodimer.
  • the heterodimer is recognized and cleaved by the Ubiquitin specific proteases (UBPs) (open scissors), liberating PLV-Cub.
  • UBPs Ubiquitin specific proteases
  • the PLV-Cub can enter the nucleus by diffusion and bind to the LexA-binding sites leading to activation of transcription of the lacZ and HIS3 reporter genes. This results in blue cells in the presence of X-gal and growth of the cells on agar plates lacking histidine.
  • the system is dependent on a number of conditions to properly carry out the method of this invention.
  • the first interacting mecanicbait "The first interacting mecanicbait" protein must be a membrane protein.
  • the bait protein carrying Cub-PLV may not be overexpressed since overexpression would result in false-positives.
  • the bait fusion protein has to be anchored to the lipid bilayer in order to test for interactions. Soluble proteins of interest might be tested by fusing them to a membrane protein anchor.
  • the Cub-PLV and NubG domains must be located in the cytoplasm, otherwise the cleavage of the PLV portion cannot occur since UBPs are located only in the cytoplasm of the yeast cell.
  • Cub-Protein A-LexA-VP16 reporter protein is fused to the C-terminal tail of the target bait transmembrane protein (Y) , resulting in the bait construct Y-Cub-PLV.
  • the other candidate protein, the "prey" (X) is fused to the NubG as either a N- or C- terminal fusion creating NubG-X or X-NubG.
  • the bait plasmid encoding Y-Cub-PLV is linearized and inte- grated into the yeast genome LEU2 locus following the transformation of the "prey" construct (X-NubG or NubG-X) . Transfer- ants are selected and assayed for the production of ⁇ - galactosidase.
  • the expression of ⁇ -galactosidase indicates that the two hybrid proteins interact and reconstitute a functional ubiquitin molecule.
  • Transformed cells are selected on the appropriate selective plates (dropout plates omitting leucine) .
  • This strain is transformed with the "prey" plas id (X-NubG or NubG-X) or a cDNA library fused to NubG (Example 2) .
  • the transformed cells are plated on dropout media lacking uracil and leucine and incubated at 30 ⁇ C. 3.
  • the transformants for ⁇ -galactosidase activity are tested.
  • the transformants can be streaked out in the form of patches and tested using the filter test assay (Ex- ample 3).
  • Transformants expressing Nubl/NubA or relevant interacting proteins will turn blue after the filter test assay.
  • the ⁇ -galactosidase activity can be quantified by using the liquid assay (Example 4).
  • Another control experiment is the analysis of the interaction mediated cleavage of the PLV portion in vivo by Western blot analysis and probing with peroxidase-IgG (Example 5) .
  • All plasmids to be used in the membrane protein applicable two- hybrid system are shuttle vectors, which replicate autonomously in both E.coli and S. cerevisiae.
  • the available vectors and yeast strains are published in Stagljar, I. et al., Proc. Natl. Acad. Sci. USA, 95, pp. 5187-5192 (1998). It is advisable to integrate the fusion gene encoding the bait protein into the chromosome. Expression of the protein fusion from episomal or CEN/ARS plasmids might result in overexpression and false positives.
  • Example 3 Filter assay for the detection of ⁇ -galactosidase activity.
  • the yeast expressing Y-Cub-PLV are grown together with Nub- fusion proteins for two days at 30°C on sterile Whatman filters on drop-out agar plates lacking leucine and tryptophan.
  • the drop-out-medium is used because cells tend to grow poorly in standard minimal medium.
  • the filter is transferred and dipped into liquid nitrogen for 3 min and allowed to thaw at room temperature.
  • the filters are overlaid with 1.5% agarose in 0.1 M NaP0 4 - buffer (pH 7.0) containing 0.4 mg/ml X-gal .
  • the filters are incubated at 30 °C for 0.4-24 hours.
  • Yeast transformants expressing Y-Cub-PLV are inoculated together with Nub-fusion proteins into 3 ml of liquid drop-out medium lacking uracil, leucine and tryptophan.
  • Yeast cells expressing Y-Cub-PLV together with Nub-fusion proteins are grown at 30°C to an OD 546 of 0.3-1.2 in drop-out liquid medium lacking leucine and tryptophan.
  • the cells are pelleted and resuspended in 50 ⁇ l 1.85 M NaOH per 3 OD units of cells, and incubated on ice for 10 min.
  • the membranes are probed with peroxidase-IgG at 1:5000 dilu- tion. Protein A-fusion proteins are detected by enhanced che i- luminescence (Pierce of Amersham) .

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Abstract

La présente invention concerne un procédé et un ensemble permettant de détecter une interaction entre une première protéine d'essai membranaire ou un fragment de celle-ci et une seconde protéine d'essai ou un fragment de celle-ci qui est soit membranaire, soit soluble, à l'aide d'un système génétique in vivo, dans des levures, des bactéries ou des cellules mammifères. Ce système met en oeuvre la reconstitution de la protéine d'ubiquitine divisée.
EP00962148A 2000-09-29 2000-09-29 Procede et ensemble permettant de detecter des interactions proteine membranaire-proteine Withdrawn EP1325148A1 (fr)

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PCT/CH2000/000534 WO2002027020A1 (fr) 2000-09-29 2000-09-29 Procede et ensemble permettant de detecter des interactions proteine membranaire-proteine

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ATE348190T1 (de) * 2002-03-28 2007-01-15 Dualsystems Biotech Ag Verfahren zum nachweis von protein- proteininteraktionen in membranen
KR20070051257A (ko) 2004-06-21 2007-05-17 프로겐라 인코포레이티드 단백질 가수분해 활성과 관련된 진단과 스크리닝 방법 및키트
WO2008025564A2 (fr) 2006-08-31 2008-03-06 Nexigen Gmbh Moyens et procédés de détection d'interactions protéine-peptide
DK3008213T3 (da) 2013-06-10 2020-08-24 Governing Council Univ Toronto Detektion af protein-til-protein-interaktioner
GB201909491D0 (en) * 2019-07-01 2019-08-14 Governing Council Of The Univ Of Toronto Detection of protein to protein interactions

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US5503977A (en) * 1994-04-22 1996-04-02 California Institute Of Technology Split ubiquitin protein sensor
DE19737562A1 (de) * 1997-08-28 1999-05-06 Otogene Biotechnologische Fors Verfahren zur Identifizierung von Wechselwirkungen zwischen Proteinen bzw. Peptiden
AU757637B2 (en) * 1998-04-24 2003-02-27 Yale University A method of detecting drug-receptor and protein-protein interactions

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WO2002027020A1 (fr) 2002-04-04

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