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Detection of in vivo Protein Interactions in All Bacterial Compartments by Förster Resonance Energy Transfer with the Superfolder mTurquoise2 ox-mNeongreen FRET Pair

利用超折叠mTurquoise2 ox-mNeongreen荧光分子共振能量转移法检测细菌体内蛋白相互作用

Nils Y. Meiresonne Nils Y. Meiresonne
EC Elisa Consoli
LM Laureen M.Y. Mertens
TB Tanneke den Blaauwen

发布: 2019年12月05日第9卷第23期 DOI: 10.21769/BioProtoc.3448 浏览次数: 7261

评审: Gal Haimovich

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Cover of Molecular Microbiology, featuring study using the protocol.

Apr 2019

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Abstract

This protocol was developed to qualitatively and quantitatively detect protein-protein interactions in all compartments of Escherichia coli by Förster Resonance Energy Transfer (FRET) using the Superfolder mTurquoise2 ox-mNeonGreen FRET pair (sfTq2ox-mNG). This FRET pair has more than twice the detection range for FRET interaction studies in the cytoplasm or periplasm of E. coli compared to other pairs to date. These protein-interaction studies can be performed in vivo because fluorescent proteins can be genetically encoded as fusions to proteins of interest and expressed in the cell. sfTq2ox and mNG fluorescent protein fusions are co-expressed in bacterial cells and the fluorescence emission spectra are measured. By also measuring reference spectra for the background, sfTq2ox-only and mNG-only samples, expected emission spectra can be calculated. Sensitized emission for mNG above the expected spectrum can be attributed to FRET and quantified by spectral unmixing. This bio-protocol discusses the sfTq2ox-mNG FRET pair and provides a practical guide in preparing the protein fusions, setting up and running the FRET experiments, measuring fluorescence spectra and gives the tools to analyze the collected data.

Keywords: Bacteria (细菌) search Protein interactions (蛋白相互作用) search FRET (FRET) search Cytoplasm (细胞质) search Periplasm (周质) search sfTq2ox (sfTq2ox) search mNG (mNG) search

Background

Determining how and which proteins interact to sustain life is at the core of molecular biology research. Many in vitro methods exist but may result in false positives as the interactions are taken out of their biological context. An in vivo method is crucial for the verification of in vitro obtained results. Moreover, in vivo methods allow for the observation of the often, dynamic processes that take place in the cell. Fluorescent proteins (FP)s are ideal for in vivo experiments as they can be fused to proteins of interest, making it possible to microscopically track the localization and dynamics of the fused proteins in living cells. Energy can be transferred between FPs by Förster Resonance Energy Transfer (FRET) provided they have compatible physical properties. The emission spectrum of a donor FP must overlap with the excitation spectrum of an acceptor FP and the physical distance between the chromophores within the folded FPs should be less than 10 nm. The larger the spectral overlap and the smaller the distance between the donor and acceptor FP the more FRET can occur. The stringent distance dependence for FRET is ideal to detect direct protein-protein interactions as they also occur in the nanometer range, whereas indirect protein interactions are usually on a larger distance scale and not detectable by FRET. For this reason, it gives very few false positives but due to the physical requirements of the involved fluorophores, negative results could be false negatives. The advantage of using FPs for FRET measurements is that the chromophore is enclosed in a protein barrel and therefore much better protected from the environment than chemical chromophores. The fluorescence of the latter is extremely sensitive to environmental changes such as pH, salt, and solvents. Consequently, they often cannot be used reliably to measure FRET in a complicated environment like the living cell. A drawback of the 3-4 nm in diameter protein-barrel that encloses the chromophore in FPs is that it reduces the detectable distance between proteins to 1-6 nm. Since 5-7 nm is the typical size of proteins, it usually does not pose a problem, but can again result in false negatives. For a recent perspective on FRET as a biomolecular research tool see Alger et al. (2019). We have used a spectroscopy based FRET method to analyze the interaction between proteins in the cytoplasm and in the periplasm of Escherichia coli (Alexeeva et al., 2010; Fraipont et al., 2011; van der Ploeg et al., 2013 and 2015; Meiresonne et al., 2017 and 2019) and showed that the technique is suitable for mode of action studies of antibiotics (van der Ploeg et al., 2015) and medium throughput screening (Meiresonne et al., 2017 and 2019) using various FP FRET pairs. Building on our experience with bacterial FRET and fluorescent proteins in challenging compartments, we preferentially use the FRET-pair that gives the highest rates of energy transfer in the cytoplasm as well as in the periplasm.

This bio-protocol describes how to perform our sfTq2ox-mNG FRET assay in bacteria to determine protein-protein interactions by spectrally unmixing fluorescence signal into its individual components. Although this protocol is written for E. coli, the method of spectral unmixing is suitable for any organism, provided fusion proteins can be expressed in the species and fluorescence spectra can be collected. The protocol describes how to perform FRET experiments by 2 approaches; 1) Measurements on fixed cell using a fluorometer, the initial determination of protein interactions. 2) Measurements on fixed cells in the plate reader for the faster detection of already confirmed protein interactions that provide clear fluorescence signals.

Materials and Reagents

  1. Sterile straight neck culturing flasks (DWK Life Sciences, DURAN, catalog number: 2177124) with aluminum anodized metal blue cap (DWK Life Sciences, DURAN, catalog number: 2901324)
  2. 50 ml sterile Falcon tubes (SARSTEDT, catalog number: 62.657.254)
  3. 2 ml sterile Eppendorf tubes (Greiner Bio One International, catalog number: 623201)
  4. 1.5 ml sterile Eppendorf tubes (Greiner Bio One International, catalog number: 616201)
  5. Disposable pipet tips 200 µl (Ultratip, Greiner Bio One International, catalog number: 739290)
  6. Disposable pipet tips 1,000 µl (Ultratip, Greiner Bio One International, catalog number: 686290)
  7. Wash bottles (Thermo Fisher Scientific, Thermo ScientificTM, catalog number: 2401-0500)
  8. Glass-bottomed black walled 96 wells plate (Porvair Sciences, catalog number: 324002)
  9. Black walled clear bottomed 96 wells plastic plate (Greiner Bio One International, catalog number: 675096)
  10. Stirred Quartz cuvettes (Hellma, catalog number: 119004F-10-40)
  11. Lens cleaning tissue (Fischer Scientific, FisherbrandTM, catalog number: 10605955)
    Note: This product has been discontinued.
  12. Filtropur S 0.2 µm filter (SARSTEDT, catalog number: 83.1826.001)
  13. Plasmids containing cytosolic and periplasmic controls for the sfTq2ox-mNG FRET pair as well as additional information are available on: https://www.addgene.org/browse/article/28196682/
  14. Ethanol 70% in lab wash bottle (VWR, Technisolv®, catalog number: 83801.360)
  15. Ethanol 96% in lab wash bottle (VWR, Technisolv®, catalog number: 83804.360)
  16. H2O in lab wash bottle
  17. 1 M β-D-1-thiogalactopyranoside (IPTG) (Duchefa Biochemie, catalog number: I1401)
  18. Hellmanex III (Hellma, catalog number: 9-307-011-4-507)
  19. Bacto tryptone (Duchefa Biochemie, catalog number: T1332)
  20. Yeast extract (Duchefa Biochemie, catalog number: Y1333)
  21. Sodium chloride (NaCl) (Merck, catalog number: 106404)
  22. Glucose (Duchefa Biochemie, catalog number: G0802)
  23. Thiamine hydrochloride (Sigma-Aldrich, catalog number: T4625-25G)
  24. L-Lysine monohydrochloride (Sigma-Aldrich, catalog number: L8662)
  25. Ampicillin stock solution 100 mg/ml (Sigma-Aldrich, catalog number: A9518) in 50% ethanol
  26. Chloramphenicol stock solution 25 mg/ml (Duchefa Biochemie, catalog number: C0113) in 50% ethanol
  27. di-Potassium hydrogen phosphate (K2HPO4·3H2O) (VWR, catalog number: 26932.290)
  28. Potassium dihydrogen phosphate (KH2PO4) (Merck, catalog number: 104873)
  29. Ammonium sulfate, (NH4)2SO4 (Sigma-Aldrich, catalog number: A4418)
  30. Magnesium sulfate heptahydrate (MgSO4·7H2O) (Carl Roth, catalog number: T888.1)
  31. Iron(II) sulfate heptahydrate (FeSO4·7H2O) (Sigma-Aldrich, catalog number: 215422)
  32. Calcium nitrate tetrahydrate, Ca(NO3)2·4H2O (Sigma-Aldrich, catalog number: C1396)
  33. L-Arginine (Sigma-Aldrich, catalog number: A8094)
  34. L-Glutamine (Sigma-Aldrich, catalog number: G8540)
  35. Thymidine (Sigma-Aldrich, catalog number: T1895)
  36. Uracil (Sigma-Aldrich, catalog number: U1128)
  37. Potassium chloride (KCl) (VWR, catalog number: 71003-522)
  38. di-Sodium hydrogen phosphate dihydrate (Na2HPO4·2H2O) (Merck, catalog number: 106580)
  39. Glutaraldehyde 25% (Merck, catalog number: 1042390250)
  40. Formaldehyde ≥ 36.0% (Sigma-Aldrich, catalog number: 47608)
  41. Lysine (Sigma-Aldrich, catalog number: L8662)
  42. PBS buffer (pH 7.2)
  43. TY medium (see Recipes)
  44. 20% glucose solution (see Recipes)
  45. GB1 medium (see Recipes)
  46. Stock solution (see Recipes)
    1. MM1-10x
    2. MM2-10x
    3. MM3-100x
    4. MM4-100x
    5. Vitamin B1 stock solution (4 mg/ml)
    6. Lysine stock solution (20 mg/ml)
  47. Phosphate buffered saline (PBS 1x) (see Recipes)
  48. Formaldehyde and glutaraldehyde (FAGA) (see Recipes)

Equipment

  1. P20, P200 & P1,000 Pipetman pipettes (Gilson, catalog number: F167300)
  2. Gyrotory water bath shaker Model G76 (Eppendorf, New Brunswick Scientific, model: Model G76 or GFL-Gesellschaft für Labortechnik, catalog number: 1092) with holders for culturing flasks 
  3. Photospectrometer (Biochrom, model: Libra S22)
  4. Compressed air source
  5. Water purification system (Purelab flex with ELGA LC197-Biofilter from ELGA LabWater, Laner End, HP14 3BY, UK)
    Note: All H2O in the protocol indicates water of at least 18.0 MΩ from Water purification system.
  6. Centrifuge for 50 ml Falcon tubes (Eppendorf, model: 5804 R)
  7. Centrifuge for 1.5 and 2.0 ml Eppendorf tubes (Eppendorf, model: 5424 R)
  8. Spectrofluorometer Quantamaster 2000-4 (Photon Technology International, NJ) with a red-optimized set-up: R928P PMT tube (185-900 nm), 500 nm blaze (1,200 lines/mm) both excitation and emission gratings
    Note: A Photomultiplier tube (PMT) that will reliably detect fluorescence spectra up until 700 nm will be suitable for the described protocol.
  9. Optical filters
  10. 500/10 nm BrightLine® single-band bandpass filter (Semrock, catalog number: FF01-500/10)
  11. ET510LP (Chroma, catalog number: ET510lp)
  12. 435/40 nm BrightLine® single-band bandpass filter (Semrock, catalog number: FF02-435/40)
  13. 458LP EdgeBasic™ best-value long-pass edge filter (Semrock, catalog number: BLP01-458R)
  14. Fluorescence scanning plate reader (BioTek Instruments, model: SynergyTM Mx, catalog number: SMATBC)
  15. Autoclave (Sanyo, catalog number: MLS-3780)

Software

  1. Fluorescence spectrophotometer software (PTI acquisition software FeliX32 version 1.2 Build 56)
  2. Microplate reader software Gen5 version 2.00 (Biotek)
  3. Excel (Microsoft)

Procedure

English
中文翻译

文章信息

版权信息

© 2019 The Authors; exclusive licensee Bio-protocol LLC.

如何引用

Meiresonne, N. Y., Consoli, E., Mertens, L. M. and den Blaauwen, T. (2019). Detection of in vivo Protein Interactions in All Bacterial Compartments by Förster Resonance Energy Transfer with the Superfolder mTurquoise2 ox-mNeongreen FRET Pair. Bio-protocol 9(23): e3448. DOI: 10.21769/BioProtoc.3448.

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分类

微生物学 > 体内实验模型 > 细菌

生物化学 > 蛋白质 > 相互作用 > 蛋白质-蛋白质相互作用

分子生物学 > 蛋白质 > 蛋白质-蛋白质相互作用

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