Materials and Reagents

Fly vials (e.g., VWR, catalog number: 734-2254 )
Fly vial plugs (e.g., Carl Roth, catalog number: PK13.1 )
Gal4 activator strains of choice (e.g., C57-Gal4 for muscle-specific expression [from Ulrich Thomas, Magdeburg, Germany], elav^C155-Gal4 for pan-neuronal expression [from Bloomington stock center, Bloomington, Indiana, USA], repo-Gal4 for glial expression [from Christian Klämbt, Münster, Germany])
UAS-dMetRS^L262G effector strains [available at request from Daniela C. Dieterich & Ulrich Thomas]. As described in Erdmann et al. (2015) various lines expressing dMetRS^L262G either tagged with 3xmyc or EGFP are available
Note: We traditionally use ONM. The standard corn meal medium has also been successfully used in Niehues et al. (2015) for ANL labeling, thus, we anticipate that other media can be used as well without any limitations.
Otto-normal-medium (ONM, see Recipes)

Agar-Agar (Carl Roth, catalog number: 5210 )
Semolina (local food store)
Mashed raisins (local food store)
Baker’s yeast (local food store)
Sugar beet sirup (local food store)
Honey (local food store)
Tap water
20% (w/v) Nipagin (see Recipes)

Methyl-4-hydroxybenzoate (Merck, catalog number: 106757 )
Propyl-4-hydroxybenzoate (Merck, catalog number: 107427 )
100 % ethanol (Th. Geyer, catalog number: 2246 )

200 mM ANL stock solution (for the synthesis of ANL see [Link et al., 2007; Ngo et al., 2009; Erdmann et al., 2015]) (see Recipes)

Equipment

Beaker (kitchen/household grade)
Immersion blender (kitchen/household grade)
Paintbrush (art supplies)
Fly incubator (e.g., SANYO, model: MIR-553 )
Hotplate (kitchen/household grade)
Pot (kitchen/household grade)
Tablespoon (kitchen/household grade)

Procedure

Preparation of ANL-containing fly food medium (Figure 1)
1. Thaw baker’s yeast.
2. Add semolina and Agar-Agar to 0.33 L water. Stir from time to time until swelling is completed.
3. Heat mashed raisins, yeast, sugar beet syrup and honey in 0.66 L water. Boil the mixture for 5 min while stirring constantly.
4. Add the semolina-Agar-Agar-mixture and boil once again. Don’t forget to stir constantly, as the mixture might braise at the bottom of the pot.
5. Cool down the ONM to 50 °C. Stir every 15-20 min for 1 min.
6. Add the Nipagin and stir for at least 1 min until the Nipagin is homogenously distributed in the food.
7. Add 2 ml of ANL stock solution to 100 ml ONM in a beaker for a final concentration of 4 mM ANL. Mix for 1 min using an immersion blender.
8. Aliquot ANL-containing ONM (2-4 ml) into fly vials and let cool down completely at room temperature.
9. Plug the vials.
10. ANL-containing ONM can be stored for approximately two weeks at 4 °C. Discard vials once the ONM detaches from the vial wall.
  
  Figure 1. Preparation of ANL-containing fly food medium. A. Ingredients for ONM are shown: R (mashed raisins); S (semolina); BS (sugar beet syrup); H (honey). B. Semolina and Agar-Agar are added to water and allowed to swell, SAA. C. Raisins and Baker’s yeast (Y), sugar beet syrup (BS), and honey (H), are added into water and boiled for 5 min. D. Afterwards, the SAA mixture is added and boiled once more. After cooling down to 50 °C with stirring from time to time, Nigapin and ANL are added and mixed thoroughly. E and F. Media is then aliquoted and allowed to cool down completely before storage at 4 °C.
Cell type-specific expression of dMetRS^L262G-variants in Drosophila larvae and flies
1. Collect virgin female flies of the respective activator strain.
  Note: The number of flies and hence the number of offspring depends on your experimental design including the type of analysis (e.g., MS/MS) and the effectiveness and degree of cell selectivity of the Gal4-activator in use.
2. Cross virgin female flies of the activator strain to male flies of a UAS-dMetRS^L262G-effector strain (Erdmann et al., 2015).
  Note: Crosses can as well be set up reciprocally, that is, you may use virgin female flies of a UAS-dMetRS^L262G-effector strain and cross them to males of your activator strain.
Cell type-specific labeling of proteins with ANL–examples
1. Long-term labeling of proteins in larval body wall muscles:
  1. Raise appropriate crosses on ANL-containing ONM such that ANL is present during all developmental stages of the progeny.
  2. Mid- to late 3^rd larval stage is reached after approximately 5 days when crosses are raised at 25 °C and after approximately 10-12 days when kept at 18 °C.
  3. Perform dissection of larval body walls according to ‘Click Chemistry (CuAAC) and detection of tagged de novo synthesized proteins’. See also Bellen and Budnik (2000).
    Note: Biochemical approaches on whole larval extracts have proven difficult to perform time and again, perhaps due to lytic activities. We therefore recommend separating body walls (mainly comprising muscles, epithelia, cuticle, trachea and sensory neurons) from all other tissues.
2. Long-term labeling of proteins in fly heads (e.g., if dMetRS^L262G is expressed in the CNS, compound eyes and/or antenna):
  1. Raise crosses on ANL-containing ONM so that ANL is present throughout development of the progeny.
  2. Remove parental flies before eclosure of the offspring.
  3. Prepare fly heads from adult progeny according to ‘Click Chemistry (CuAAC) and detection of tagged de novo synthesized proteins’.
3. Short-term labeling of proteins in larval body wall muscles or brains:
  1. Raise crosses on ANL-free ONM for 1-2 days at 25 °C.
  2. Transfer parental flies onto fresh ANL-free ONM for 4-6 h. Remove parental flies.
  3. Keep vials for 72 ± 2 h at 25 °C.
  4. Wash early 3^rd instar larvae out of the food with warm tap water and rinse them into a mesh basket.
  5. Transfer 3^rd instar larvae onto ANL-containing ONM using a paintbrush.
  6. Keep larvae at 25 °C for 24 h.
  7. Prepare the larval body walls or larval brains according to ‘Click Chemistry (CuAAC) and detection of tagged de novo synthesized proteins’.
4. Short-term labeling of proteins in fly heads:

Data analysis

ANL incorporation into fly or larval proteins can be analyzed after performing copper-catalyzed azide-alkyne cycloaddition (CuAAC, ‘click chemistry’) as described in Erdmann et al. (2015) and the accompanying bio-protocol. General fly and larvae viabilities upon ANL incorporation can be analyzed by assessing e.g., locomotor behavior and/or hatching rates as described in Erdmann et al. (2015).

Notes

Reproducibility and variability: Uptake of ANL and thus subsequent labeling efficiency may vary when heterogeneous animal numbers are raised in the vials, as the food will be differently mashed through depending on the number of larvae. Also of note, larvae will show in general stronger ANL incorporation compared to adult flies.
ANL-containing ONM is used best within two weeks after preparation to yield reproducible results.

Recipes

20% (w/v) Nipagin
150 g methyl-4-hydroxybenzoate
50 g propyl-4-hydroxybenzoate
Dissolve in 100% (abs) ethanol
Otto-normal-medium (ONM)
8.3 g Agar-Agar
50 g semolina
40 g mashed raisins
2 cubes of yeast ( 42 g each)
1 tablespoon sugar beet syrup
1 tablespoon honey
6.6 ml 20% (w/v) Nipagin
200 mM ANL stock solution
34.4 mg per 1 ml ddH₂O

Acknowledgments

This work was supported by the German Research Foundation (DFG) with an SFB 779 grant to D.C.D., SFB 854 grants to U.T. and D.C.D. and a Leibniz Society PAKT grant (LGS SynaptoGenetics) to D.C.D. and U.T. This protocol was adapted from Erdmann et al., 2015.

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