Transport Assays in Aspergillus nidulans

Year prepared: 2013

Transport assays allow the direct kinetic analysis of a specific transporter by measuring apparent Km and Vmax values, and permit the characterization of substrate specificity profiles through competition assays. In this protocol, we describe a rapid and easy method for performing uptake assays in the model filamentous ascomycete Aspergillus nidulans. These assays make use of A. nidulans germinating conidiospores, thus avoiding technical difficulties associated with the use of mycelia. The ease of construction genetic null mutants in this model fungus permits the rigorous characterization of any transporter in the absence of similar transporters with overlapping specificities, a common problem in relevant studies.

Materials and Reagents

  1. p-aminobenzoic acid (Sigma-Aldrich, catalog number: P5669)
  2. d-Biotin (Sigma-Aldrich, catalog number: B4501)
  3. Calcium-D-pantothenate (Sigma-Aldrich, catalog number: 21210)
  4. Riboflavine (Sigma-Aldrich, catalog number: R4500)
  5. Pyridoxine hydrochloride (Sigma-Aldrich, catalog number: P9755)
  6. KCl
  7. MgSO4.7H2O
  8. KH2PO4
  9. Na2B4O7.10H2O
  10. CuSO4.5H2O
  11. FeO4P.4H2O
  12. MnSO4.H2O
  13. Na2MoO4.2H2O
  14. ZnSO4.7H2O
  15. NaOH
  16. Tween 80 (Sigma-Aldrich, catalog number: P1754)
  17. Radiolabelled substrate
    e.g. [8-3H]-xanthine, 22.8 Ci/mmol (Moravek Biochemicals, catalog number: MT537)
    [2,8-3H]-hypoxanthine, 27.7 Ci/mmol (Moravek Biochemicals, catalog number: MT700)
    [5-3H]-uracil, 23 Ci/mmol (Moravek Biochemicals, catalog number: MT610)
  18. Non radiolabelled substrate
    e.g. Xanthine (Sigma-Aldrich, catalog number: X7375)
    Hypoxanthine (Sigma-Aldrich, catalog number: H9377)
    Uracil (Sigma-Aldrich, catalog number: U0750) 
  19. Toluol (AppliChem GmbH, catalog number: A3393)
  20. Triton X-100
  21. 2,5-Diphenyloxazole (PPO) (Sigma-Aldrich, catalog number: D4630)
  22. 1,4-bis (5-phenyloxazol-2-yl) benzene (POPOP) (Sigma-Aldrich, catalog number: P3754)
  23. Complete Media (CM) (see Recipes) 
  24. Minimal Media (MM) (see Recipes)
  25. Scintillation Fluid (see Recipes)

Equipment

  1. Petri dishes
  2. Neubauer counting-chamber slide
  3. Spatula
  4. Orbital shaking incubator
  5. Incubator at 37 °C
  6. Nylon net filter 60 μm (Merck KGaA, catalog number: NY60)
  7. 50 ml Falcon tubes
  8. 1.5 ml centifuge tubes
  9. Centrifuge 
  10. Vortex
  11. Scintillation vials
  12. Scintillation counter
  13. Heat block
  14. Magnetic stirrer
  15. Magnetic strirr bar
  16. pH meter
  17. Pasteur pipette

Software

  1. GraphPad Prism software (Amillis et al., 2004)

Procedure

  1. Inoculate a petri dish of CM with the strain of interest and let it reach full growth at 37 °C for 96 h. 
  2. Using a spatula transfer one quarter of the fully grown colony (~4 cm) in a 50 ml Falcon tube containing 2 ml of 0.01% v/v Tween 80 in water. This amount usually corresponds to 108 conidiospores. The accurate amount of conidiospores can be estimated using a Neubauer counting-chamber slide or by measuring viable conidiospores after standard serial dilutions and plating on CM.
  3. Vortex well the sample for separating the conidiospores. 
  4. Inoculate a 100 ml flask containing 25 ml MM supplemented with appropriate carbon (C) (e.g. Glucose 1% w/v) and nitrogen (N) (e.g. NaNO3 10 mM) sources and necessary vitamins (e.g. D-biotin 0.02 μg/ml) with the conidiospores filtered through a Nylon net filter 60 μΜ. (All necessary supplements and concentrations for A. nidulans strains can be found at www.fgsc.net.)
  5. Incubate for 3-5 h at 37 °C, shaking with 140 rpm, for the germinating conidiospores to reach a stage just before germ tube emergence. The time and temperature of incubation can change depending on the expression profile of the transporter of interest and the auxotrophic requirements of the strain. All transporters studied up to date in our lab (for example the purine/pyrimidine transporters UapA, UapC, AzgA, FcyB, FurD) reach maximum expression before germ tube emergence, driven by an unknown developmental control, irrespectively of the presence or absence of their substrates or other physiological conditions (Amillis et al., 2004; Vlanti and Diallinas, 2008; Amillis et al., 2007). In mycelia, transporter expression is very much dependent on physiological conditions (e.g. induction by substrates or/and N or C catabolite repression).
  6. While conidiospores germinate, prepare the stock solution of radiolabeled (usually 3H or 14C) substrate of interest in water or MM so that for each assay 25 μl of the stock will be used. 
  7. Collect the conidiospores by centrifuging the culture in a 50 ml Falcon tube for 5 min, at 3,000 x g, room temperature.
  8. Discard the supernatant and resuspend the pellet in 5 ml standard MM. 
  9. Distribute the spores in 75 μl aliquots in eppendorf tubes and use as many as needed. Conidiospore suspensions can be kept at 4 °C for at least 24 h without loss of transport activity. 
  10. Incubate conidiospore aliquots at 37 °C in a heat block for 5 min before addition of radiolabeled substrate. 
  11. Radiolabeled substrate is added for different periods of time. Most transporters show linearly increased activities for at least 1 min. For measuring initial uptake rates, which are necessary for determining Km and apparent Vmaxvalues, the proper time of incubation must be defined for each transporter through a time-course experiment. For steady state substrate accumulation a period of 5 min is used. Usual time points are 10, 20, 30, 60 and 120 sec. For each time point, measurements are performed in triplicate. The temperature used for the incubation with the radiolabeled substrate depends on the transporter being studied at each experiment and the experiment being held, temperature for most experiments is 37 °C. The transport reaction is stopped by adding an equal volume (100 μl) of cold unlabeled substrate at 100-1,000 fold excess concentration, related to radiolabelled substrate, and direct transfer of the assay/eppendorf tube in an ice bucket. 
  12. Centrifuge the samples at 11,000 x g for 3 min at 4 °C.
  13. Remove the supernatant through aspiration under vacuum using a Pasteur pipette. It is important to remove all the supernatant without losing any cells.
  14. Wash the pellet of cells once with 1 ml ice cold MM and centrifuge at 11,000 x g for 3 min. Remove the supernatant as before.
  15. Resuspend the pellet in 1 ml of scintillation fluid and put the eppendorf tubes into scintillation vials. Use a scintillation counter to measure substrate accumulation in the cells. 
  16. Analysis of transport measurements is performed using GraphPad Prism software. Radioactive counts should be converted to substrate concentration/min/conidiospores, based on the concentration and specific activity of the stock of radioactive substrate used. 
  17. For Km determination of a transporter, different substrate concentrations should be used, for a fixed incubation time, previously determined to reflect initial uptake rates. This is usually 1 min. The range of concentrations used is determined at first empirically. In the final experiment, at least three concentration points below and above the apparent Km value should be used. For each concentration point measurements are performed in triplicate.
  18. The stock solutions are prepared using a mixture of fixed radiolabeled substrate and increasing concentrations of non-radiolabeled substrate, so that for each assay 25 μl of the stock will be used. 
  19. Terminate transport assays and perform measurements as described above.
  20. For Ki determination of a transporter, the method is identical to the one for Km determination, but stock solutions are prepared using a mixture of fixed radiolabeled substrate and increasing concentrations of non-radiolabeled putative inhibitors. For each concentration point measurements are performed in triplicate.
  21. Km and Vmax determination is carried out using typical Lineweaver-Burk plot analysis that is based on the Michaelis-Menten equation for enzyme kinetics V = Vmax[S]/(Km + [S]), where V is the reaction velocity (the reaction rate), Km is the Michaelis–Menten constant, Vmax is the maximum reaction velocity, and [S] is the substrate concentration. The Lineweaver-Burk plot depicts the linear expression of the previous equation which is transformed to the following: 1/V = (Km/Vmax).(1/[S]) + 1/Vmax. The data obtained by this experiment correspond to the apparent velocity of the transporter for each substrate concentration. Ki measurements are determined by estimating IC50values (inhibitor concentration for obtaining 50% inhibition) of given substrate/inhibitor, using the formula Ki = IC50/1 + [S]/Km, where [S] is the fixed concentration of radiolabeled substrate used. Another way to analyse the data is by using the GraphPad Prism Software through a non linear regression curve fit and sigmoidal dose response analysis. The IC50 value corresponds to the Km/i of the transporter. Quality factors for the analysis result are: R2which should be > 0.99 and the Hill co-efficient which should be approximately -1 for a transporter with one binding site.
  22. The method described can be modified and adapted for most filamentous fungi that produce asexual spores, e.g. A. fumigatus. (Goudela et al., 2008)

Recipes

  1. Complete Media (1 L)
    Vitamin solution from 100x stock solution* 10 ml
    Salt solution from 50x stock solution** 20 ml
    Glucose 10 g
    Peptone 2 g
    Yeast Extract 1 g
    Cas-amino- acids 1 g
    Agar 10 g
    Add water to 1 L final volume
    Adjust the pH to 6.8 using NaOH
    Autoclave for 20 min

    *Vitamin stock solution 
    p-aminobenzoic acid 20 mg
    d-biotin 1 mg
    Calcium-D-pantothenate 50 mg
    Riboflavin 50 mg
    Pyridoxine 50 mg
    Add water to 1 L final volume

    **Salt stock solution 
    KCl 26 g
    MgSO4.7H2O 26 g
    KH2PO4 76 g
    Trace elements 20x stock solution*** 50 ml
    Add water to 1 L final volume

    ***Trace elements stock solution 
    Na2B4O7.10H2O 40 mg
    CuSO4.5H2O 400 mg
    FeO4P.4H2O 714 mg
    MnSO4.H2O 728 mg
    Na2MoO4.2H2O 800 mg
    ZnSO4.7H2O 8 mg
    Add water to 1 L final volume
     

  2. Minimal Media
    Salt solution from 50x stock solution* 20 ml
    Add water until 1 L final volume
    Adjust the pH to 6.8 using NaOH
    Autoclave for 20 min
  3. Scintillation Fluid (1 L)
    Toluol 666 ml
    PPO 2.66 g
    POPOP 0.0066 g
    2 h stirring in RT
    Add Triton-X 100 333 ml
    Overnight stirring

Acknowledgments

This protocol was adapted from the following publications: Diallinas et al. (1995); Koukaki et al. (2005); Meintanis et al. (2000); Tazebay et al. (1997). E.K. works in the laboratory of G.D, and is co-financed by the European Union (European Social Fund-ESF) and Greek national funds through the Operational Program “Education and Lifelong Learning” of the National Strategic Reference Framework (NSRF) – Research Funding Program: Thales, Investing in knowledge society through the European Social Fund.

References

  1. Amillis, S., Cecchetto, G., Sophianopoulou, V., Koukaki, M., Scazzocchio, C. and Diallinas, G. (2004). Transcription of purine transporter genes is activated during the isotropic growth phase of Aspergillus nidulans conidia. Mol Microbiol 52(1): 205-216.
  2. Amillis, S., Hamari, Z., Roumelioti, K., Scazzocchio, C. and Diallinas, G. (2007). Regulation of expression and kinetic modeling of substrate interactions of a uracil transporter in Aspergillus nidulans. Mol Membr Biol 24(3): 206-214.
  3. Diallinas, G., Gorfinkiel, L., Arst, H. N., Jr., Cecchetto, G. and Scazzocchio, C. (1995). Genetic and molecular characterization of a gene encoding a wide specificity purine permease of Aspergillus nidulans reveals a novel family of transporters conserved in prokaryotes and eukaryotes. J Biol Chem 270(15): 8610-8622.
  4. Goudela, S., Reichard, U., Amillis, S. and Diallinas, G. (2008). Characterization and kinetics of the major purine transporters in Aspergillus fumigatus. Fungal Genet Biol 45(4): 459-472. 
  5. GraphPad Prism version 5.00 for Windows, GraphPad Software, San Diego California USA. www.graphpad.com.
  6. Koukaki, M., Vlanti, A., Goudela, S., Pantazopoulou, A., Gioule, H., Tournaviti, S. and Diallinas, G. (2005). The nucleobase-ascorbate transporter (NAT) signature motif in UapA defines the function of the purine translocation pathway. J Mol Biol 350(3): 499-513.
  7. Meintanis, C., Karagouni, A. D. and Diallinas, G. (2000). Amino acid residues N450 and Q449 are critical for the uptake capacity and specificity of UapA, a prototype of a nucleobase-ascorbate transporter family. Mol Membr Biol17(1): 47-57.
  8. Tazebay, U. H., Sophianopoulou, V., Scazzocchio, C. and Diallinas, G. (1997). The gene encoding the major proline transporter of Aspergillus nidulans is upregulated during conidiospore germination and in response to proline induction and amino acid starvation. Mol Microbiol 24(1): 105-117.
  9. Vlanti, A. and Diallinas, G. (2008). The Aspergillus nidulans FcyB cytosine-purine scavenger is highly expressed during germination and in reproductive compartments and is downregulated by endocytosis. Mol Microbiol 68(4): 959-977.

 

How to cite this protocol: Krypotou, E. and Diallinas, G. (2013). Transport Assays in Aspergillus nidulans. Bio-protocol 3(22): e971. http://www.bio-protocol.org/e971 

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