Autophagy-independent function of Atg1 for apoptosis-induced compensatory proliferation
© Li et al. 2016
Received: 15 May 2016
Accepted: 8 August 2016
Published: 19 August 2016
ATG1 belongs to the Uncoordinated-51-like kinase protein family. Members of this family are best characterized for roles in macroautophagy and neuronal development. Apoptosis-induced proliferation (AiP) is a caspase-directed and JNK-dependent process which is involved in tissue repair and regeneration after massive stress-induced apoptotic cell loss. Under certain conditions, AiP can cause tissue overgrowth with implications for cancer.
Here, we show that Atg1 in Drosophila (dAtg1) has a previously unrecognized function for both regenerative and overgrowth-promoting AiP in eye and wing imaginal discs. dAtg1 acts genetically downstream of and is transcriptionally induced by JNK activity, and it is required for JNK-dependent production of mitogens such as Wingless for AiP. Interestingly, this function of dAtg1 in AiP is independent of its roles in autophagy and in neuronal development.
In addition to a role of dAtg1 in autophagy and neuronal development, we report a third function of dAtg1 for AiP.
Autophagy-related gene 1 (Atg1) in yeast, dAtg1 in Drosophila, uncoordinated-51 (unc-51) in C. elegans, and Unc-51-like kinase 1 and 2 (ULK1/2) in mammals are members of the evolutionary conserved Uncoordinated-51-like kinase (ULK) protein kinase family that play critical roles in macroautophagy (referred to as autophagy) and neuronal development (reviewed in [1, 2]). Autophagy is a catabolic process engaged under starvation and other stress conditions . A critical step in autophagy is the formation of autophagosomes which trap cytosolic cargo for degradation after fusion with lysosomes . Genetic studies in yeast identified Atg1 as an essential gene required for the initiation of autophagy [3–5]. This function of ULK proteins is conserved in evolution [6–9]. For this process, ATG1 forms a protein complex composed of ATG1/ULK1, ATG13, and ATG17 (FIP200), and in mammalian cells also ATG101 [10–15]. The ATG1/ULK complex phosphorylates several substrates including ATG9 [16, 17] and the Myosin light chain kinase (ZIP kinase in mammals, Sqa in Drosophila) , which are required for the formation of autophagosomes. Activation of the ATG1/ULK complex is also required for the recruitment of the ATG6/Beclin protein complex to the pre-autophagosomal structure (PAS) . The ATG6/Beclin complex is composed of ATG6 (Beclin-1 in mammals), the type III PI3-K VPS34, as well as ATG14 and VPS15. Maturation of the PAS to autophagosomes requires lipidation of the ubiquitin-like ATG8/LC3 protein, which is mediated by two ubiquitin-like conjugation systems, ATG12 and ATG8/LC3 . Critical components in these ubiquitin-like conjugation systems are ATG7 (E1), ATG10 and ATG3 (E2s), as well as another protein complex, ATG5-ATG12-ATG16, which serves as an E3 ligase for ATG8/LC3 lipidation [3, 19–21]. Finally, autophagosomes fuse with lysosomes for degradation of cargo.
In addition to a critical role in autophagy, ATG1 also has functions outside of autophagy, most notably in neuronal development. This was initially observed in mutants of the ULK ortholog unc-51 in C. elegans, which display uncoordinated movement with an underlying axonal defect [22–28]. A neuronal function of ULK orthologs was subsequently also reported in Drosophila, zebrafish and mammals [27, 29–33]. This autophagy-independent function of ULK proteins does not appear to involve other canonical autophagy proteins, including components of the ATG1/ULK protein complex such as ATG13 and FIP200 [34, 35]. Instead, the neuronal function of ULK proteins is dependent on different sets of proteins that include – depending on the organism analyzed – UNC-14, VAB-8 and PP2A (C. elegans), UNC-76 (Drosophila), and Syntenin and SynGAP (mammals) several of which are phosphorylated by ULKs [26–28, 33, 36–41]. Thus, the two known functions of ULK proteins in autophagy and neuronal processes involve different sets of proteins.
Apoptosis-induced proliferation (AiP) is a specialized form of compensatory proliferation that occurs after massive cell loss due to stress-induced apoptosis [42–45]. Initially described in Drosophila where it can compensate for the apoptotic loss of up to 60 % of imaginal disc cells , AiP has since been observed in many organisms, including classical regeneration models such as hydra, planarians, zebrafish, xenopus, and mouse [47–50]. Interestingly, AiP is directly dependent on a non-apoptotic function of caspases that otherwise execute the apoptotic program in the dying cell. In Drosophila, the initiator caspase Dronc triggers activation of Jun-N-terminal kinase (JNK) signaling, which leads to the production of mitogens including Wingless (Wg), Decaplentaplegic (Dpp), and the EGF ligand Spitz for AiP [51–59].
The second type of AiP models does not involve the use of p35 and has been referred to as genuine or regenerative AiP [43, 52, 60, 61, 63]. These models take advantage of Gal80ts, a temperature-sensitive inhibitor of Gal4, which allows temporal control of UAS-transgene expression by a temperature shift to 29 °C . Because these AiP models are p35-independent, cells complete the apoptotic program and we score the ability of the affected tissue to regenerate the lost cells by new proliferation. In our genuine/regenerative AiP model, we express the pro-apoptotic factor hid for 12 h under control of dorsal-eye-Gal4  (referred to as DE ts -hid) in eye imaginal discs during second or early third larval instar . This treatment causes massive tissue loss which is regenerated by AiP within 72 h after tissue loss.
Here, we report the identification of dAtg1 as a suppressor of the overgrowth phenotype of the undead ey > hid-p35 AiP model. dAtg1 is also required for complete regeneration in the DE ts -hid AiP model. Furthermore, we show that dAtg1 is genetically acting downstream of JNK activation, but upstream of mitogen production such as Wg. Consistently, dAtg1 is transcriptionally induced by JNK activity during AiP. Interestingly, the involvement of dAtg1 in AiP is independent of other dAtg genes, including dAtg13, dAtg17/Fip200, dAtg6, vps15, vps34, dAtg7, and dAtg8. These findings suggest that dAtg1 has an autophagy-independent function in AiP. Finally, dAtg1 is not employing the mechanism used during neuronal development as targeting unc-76 did not affect AiP. Therefore, in addition to a role of dAtg1 in autophagy and neuronal development, we define a third function of dAtg1 for AiP.
dAtg1 is a suppressor of apoptosis-induced proliferation
AiP phenotypes of ey > hid-p35 animals vary from mild to moderate to severe overgrowth of head capsules characterized by pattern duplications of ocelli, bristles, and sometimes entire antennae (moderate) as well as deformed heads with amorphic tissue (severe) (Fig. 1a–d) . To identify genes required for AiP, we are screening for suppressors of the ey > hid-p35-induced overgrowth phenotypes. For follow-up characterization of identified suppressors, we are using undead and regenerative (p35-independent) AiP models in eye and wing imaginal discs.
Using this approach, we identified dAtg1 as a strong AiP suppressor of ey > hid-p35 by RNAi (Fig. 1f–h). The percentage of ey > hid-p35 animals with severe and moderate AiP phenotypes is strongly reduced upon dAtg1 knock-down (Fig. 1f–h; quantified in Fig. 1i). No effect was scored on control (ey > p35) animals (Fig. 1e). Although dAtg1 RNAi results in significant loss of dATG1 mRNA and protein levels (Additional file 1: Figure S1A–B’) and no off-targets have been reported, we tested additional reagents for an involvement of dAtg1 in AiP. Expression of a dominant negative dAtg1 transgene also suppressed ey > hid-p35-induced overgrowth (Fig. 1i). Furthermore, increased expression of dAtg1, which does not alter apoptosis (Additional file 2: Figure S2), enhances the AiP phenotype and generates many animals with severe AiP phenotype (Fig. 1i). We therefore conclude that dAtg1 is required for tissue overgrowth in the undead AiP model.
dATG1 is required for regenerative apoptosis-induced proliferation
dAtg1 is required for AiP downstream of Dronc in undead eye and wing imaginal discs
We also characterized the involvement of dAtg1 in AiP in undead wing imaginal discs. Expression of hid and p35 under nub-Gal4 control (nub > hid-p35) causes strong overgrowth of the wing imaginal disc compared to nub > p35 control discs (Fig. 3g, h). dAtg1 RNAi suppresses the overgrowth of nub > hid-p35 wing discs, but leaves cCasp3 activity intact (Fig. 3i, k). To further confirm these data obtained by RNAi, we conducted mosaic analysis using dAtg1 null mutants in wing imaginal discs because homozygous dAtg1 mutants are early larval lethal in the ey > hid-p35 genetic background. Consistent with RNAi results, dAtg1 mutants do not alter cCasp3 labeling induced by co-expression of hid and p35 in MARCM clones (Additional file 3: Figure S3A–C). Similarly, dAtg1 mutant clones or RNAi do not suppress GMR-hid-induced apoptosis in the eye (Additional file 3: Figure S3D–F). Together, these data further confirm that loss of dAtg1 does not affect apoptosis and that dAtg1 controls AiP downstream of caspase (Dronc) activation.
dAtg1 is required for AiP downstream of JNK, but upstream of wingless in undead eye and wing imaginal discs
Next, because JNK is an important mediator of AiP [43, 52, 56, 57], we determined the position of dAtg1 relative to JNK in the AiP pathway. The JNK activity reporter puc-lacZ is strongly induced in AiP models compared to controls (Fig. 3a’, c’; arrows) [52, 54, 56, 57]. The morphology of the discs is severely disrupted, which correlates with signal intensity of puc-lacZ, especially in overgrown areas. In response to dAtg1 RNAi, overgrowth and disc morphology, as judged by ELAV labeling, is restored to almost normal (Fig. 3e). Nevertheless, despite the rescue of disc morphology, puc-lacZ expression is not significantly reduced (Fig. 3e’; arrows). These data suggest that dAtg1 acts downstream of or in parallel to JNK activity in the AiP pathway.
Finally, we determined the position of dAtg1 relative to wingless (wg), another marker in the AiP pathway [54–56]. Wg and its orthologs are critical mediators of AiP in regenerative responses in many animals (reviewed by [43, 45]). In undead eye discs, inappropriate wg expression is induced compared to controls (Fig. 3b, b’, d, d’; arrows). dAtg1 knockdown normalizes wg expression in the disc (Fig. 3f, f’). In addition, in undead nub > hid-p35 wing imaginal discs, wg expression is strongly induced (arrows in Fig. 3h’). However, similar to undead eye discs, co-expression of dAtg1 RNAi in nub > hid-p35 discs suppresses overgrowth (Fig. 3i) and normalizes the wg pattern (Fig. 3i’). Together, these analyses suggest that dAtg1 acts genetically downstream of Dronc and either downstream of or in parallel to JNK, but upstream of Wg, in the AiP network.
Because dAtg1 is required for wg expression in AiP, we tested if dAtg1 was also sufficient for expression of AiP markers including wg, dpp, and kekkon1 (kek), the latter being a marker of EGFR activity [51, 52, 54–56, 70]. However, while expression of hid in the DE ts > hid model is sufficient to induce wg, dpp, and kek expression (Additional file 4: Figure S4A–B’, D–E’, G–H’), expression of dAtg1 alone under the same conditions (DE ts > Atg1) is not (Additional file 4: Figure S4C, C’, F, F’, I, I’). These observations suggest that, in addition to dAtg1 expression, additional caspase-dependent events have to occur in order to induce AiP.
dAtg1 is transcriptionally induced for AiP in a JNK-dependent manner
Because dAtg1 acts genetically downstream of or in parallel to JNK (Figs. 3 and 4) and because JNK can induce dAtg1 expression under oxidative stress conditions and by ectopic activation of JNK , we tested if the transcriptional induction of dAtg1 in the AiP models is also dependent on JNK. The Drosophila JNK homolog is encoded by the gene basket (bsk) [73, 74]. Indeed, while bsk RNAi does not affect dAtg1 expression in control discs (Fig. 5c, c’), it suppresses the accumulation of dATG1 protein in undead and dAtg1 transcripts in regenerative wing discs (Fig. 5d, d’, j). Consistent with a previous report , ectopic JNK activation by expression of a constitutively active JNKK transgene (hep CA ) for a short pulse of 6 h with 6 h recovery at 18 °C (TS6hR6h) is sufficient to induce dAtg1 expression in wing imaginal discs (Fig. 5l). However, expression of the pro-apoptotic gene hid under the same conditions (TS6hR6h) cannot induce dAtg1 expression (Fig. 5k). Combined, these data suggest that dAtg1 expression is under direct control of JNK signaling, while it is far downstream of Hid expression.
Undead tissue produces autophagosome-like particles which do not contribute to apoptosis-induced proliferation
dAtg1 acts upstream in the autophagy pathway and its activation can induce autophagy [6, 10, 17]. Oxidative stress or ectopic activation of JNK has been previously reported to induce expression of multiple dAtg genes, including dAtg1, as well as autophagy in midgut and fat body cells . We therefore examined if autophagy is induced in undead disc tissue and whether it contributes to AiP. Because dATG8 is an essential part of autophagosomes, fusion proteins of dATG8 with fluorescent proteins such as GFP or mCherry are used as markers for formation of autophagosomes . Moreover, because GFP is stable in autophagosomes, but unstable in autolysosomes, whereas mCherry is stable in both compartments, the tandem fusion protein GFP-mCherry-dATG8a is used as marker for the maturation of autophagosomes into autolysosomes, indicating autophagic flux [75, 76]. Indeed, as shown in Additional file 6: Figure S6, undead ey > hid-p35-expressing tissue accumulates large quantities of GFP-mCherry-dATG8a-containing particles. However, it is unclear if these particles are classical autophagosomes. While the GFP signals are weaker compared to the mCherry signals, which may be an indicator of autophagic flux, there are clearly GFP-only particles which do not display mCherry fluorescence (compare Additional file 6: Figure S6b’ and S6b”). This observation is inconsistent with the concept of autophagic flux . Furthermore, even though dAtg1 RNAi suppresses AiP, it does not suppress the formation of the GFP-mCherry-dATG8a particles (Additional file 6: Figure S6C–C”). This result suggests that the ectopic expression of dAtg1 in undead tissue does not induce the formation of the GFP-mCherry-dATG8a-containing particles. Furthermore, and more importantly, these particles do not contribute to the overgrowth of undead tissue nor, thus, to AiP.
Other dAtg genes mediating autophagy and unc-76 are not required for apoptosis-induced proliferation
In addition to targeting essential autophagy components by RNAi, we also tested homozygous dAtg13 and dAtg7 mutants which can survive to pupal or adult stages, respectively, for suppression of AiP. dAtg13 encodes a component of the ATG1/ULK protein complex, while dAtg7 encodes the E1-conjugating enzyme for autophagosome maturation. However, dAtg13 and dAtg7 mutants fail to suppress the abnormal morphology of ey > hid-p35 discs as visualized by ELAV labeling and the ectopic Wg expression (Fig. 6b, c). These results suggest that the tested dAtg genes, except dAtg1, are not required for AiP. An involvement of dAtg1 in AiP is further confirmed by expression of a kinase dead form of TOR (TOR TED ) , which activates dAtg1 , or RNAi knockdown of Raptor, an adaptor protein required for TOR activation , both of which enhance AiP (Fig. 6a).
Finally, we also examined the possibility that dAtg1 uses the same mechanism in AiP that it uses during neuronal development. However, RNAi targeting unc-76, which is an important mediator of the function of dAtg1 during neuronal development , does not suppress the overgrowth phenotype of the undead ey > hid-p35 AiP model (Fig. 6a). Three independent RNAi lines gave consistent results. Therefore, in addition to autophagy and neuronal development, our data define a third function of dAtg1 for AiP.
In this paper, we show that the sole ULK ortholog in Drosophila, dAtg1, is required for AiP both in undead and regenerative models. We demonstrated that dAtg1 acts downstream of JNK activity in AiP and is transcriptionally induced by JNK, consistent with a previous study on oxidation response . Furthermore, dAtg1 is required for the expression of Wg, a mitogen associated with AiP [51, 52, 54–56, 81]. Finally, our data provide evidence that the role of dAtg1 in AiP is independent on its role in canonical autophagy.
It is generally assumed that the secreted mitogens Wg, Dpp, and Spitz promote the proliferation of surviving cells during AiP [43, 45]. The expression of these genes is under control of JNK activity. Until recently, it was unknown how JNK signaling promotes expression of these genes. However, very recently, it was reported that an enhancer element in the wg gene that drives expression of wg under regenerative conditions contains three AP-1 binding sites required for regeneration . AP-1 is composed of the transcription factors Jun and Fos (Kayak in Drosophila), which are controlled by JNK activity. This observation suggests a direct way of wg expression by JNK-dependent AP-1.
How does dATG1 fit into the AiP network? Our genetic data suggest that dAtg1 acts downstream of or in parallel to JNK. Furthermore, we placed dAtg1 genetically upstream of wg expression. Therefore, dAtg1 may act in at least two different ways in the AiP network. It may directly modulate the activity of the AP-1 transcriptional complex. An indirect mode of action is also possible in which dATG1 provides a permissive environment for AP-1 activity. However, dAtg1 does not control all AP-1 activities. Expression of puc-lacZ and MMP-1 are not affected by dAtg1 RNAi and dAtg1 mutants, respectively (Figs. 3 and 4). In contrast, wg expression is suppressed under these conditions. Therefore, of the known transcriptional targets of JNK and AP-1 during AiP (puc-lacZ, MMP-1, dAtg1, and wg), dAtg1 affects only wg expression. Future work will address the mechanistic role of dATG1 for the control of AiP.
Although dAtg1 is required for AiP, it is not sufficient. Overexpression of dAtg1 using DE ts -Gal4 for 12 h followed by 24 h recovery does not trigger AiP markers such as wg-lacZ, dpp-lacZ, or kek-lacZ (Additional file 4: Figure S4). Expression of hid under the same conditions is able to induce these markers ectopically. These observations suggest that, in addition to dAtg1 expression, apoptotic signaling triggers an additional activity required for wg expression and AiP.
The best characterized function of dATG1 and of ULKs in general is the initiation of autophagy under starvation or stress conditions [1, 2, 5, 10, 72]. Autophagy requires a total of 36 Atg genes . Although we did not test all 36 dAtg genes for a role in AiP, we tested several genes which are critical for autophagy, including dAtg3, dAtg6, dAtg7, dAtg8, dAtg9, dAtg13, dAtg17, and vps34. dAtg13 and dAtg17 (aka Fip200) encode subunits of the ATG1/ULK complex [10–12]. ATG6 and VPS34 are subunits of the ATG6/Beclin complex, which is activated by ATG1 during autophagy. Phosphorylation of ATG9, the mammalian ortholog of dATG9, by ULK1 is required for autophagy [16, 17]. Finally, lipidation of ATG8, which is essential for formation of autophagosomes requires the function of ATG3 and ATG7 [3, 20, 21]. In contrast to dAtg1, inactivation of any of these genes does not suppress the overgrowth phenotype of ey > hid-p35 animals. Furthermore, although we detect the formation of ATG8a-containing particles in undead eye imaginal discs, these particles are not dependent on dAtg1 and do not contribute to AiP and overgrowth (Additional file 6: Figure S6). Combined, these data suggest that dATG1 does not trigger canonical autophagy in an AiP context.
In addition to autophagy, ULK proteins have also been implicated in neuronal development, most notably axon guidance and axonal growth [27, 30]. However, we also exclude a neuronal function of dAtg1 in AiP because inactivation of unc-76, a mediator of dAtg1 for neuronal development , does not suppress overgrowth induced by ey > hid-p35.
We revealed a third function of dAtg1 in Drosophila for the control of regenerative proliferation after massive apoptotic cell loss. Future work will address if this role of dAtg1 in regenerative proliferation is also conserved in other organisms, the molecular mechanism of this function, and whether it is potentially misregulated in pathological conditions such as cancer.
Fly strains and the ey > hid-p35 assay
UAS-dAtg1 [KQ#5B] or UAS-dAtg1 [K38Q] were used to express an dAtg1 kinase-dead mutant that functions as a dominant negative . Either UAS-dAtg1 6B or UAS-dAtg1 GS10797 were used to express wildtype dAtg1 . Both constructs gave similar results under the control of Gal4 lines tested in this study. Dorsal Eye-Gal4 (DE-Gal4) , dronc I29 , dAtg1 Δ3D , dAtg13 Δ7 , dAtg7 d14 , dAtg7 d77 , dAtg8a::GFP-mCherry-dAtg8a , and eyeful (ey-Gal4 > UAS-delta, GS88A8 UAS-lola and UAS-pipsqueak)  were as described. puc-lacZ E69 , wg-lacZ, dpp-lacZ, kek-lacZ, ey-Gal4, hh-Gal4, nub-Gal4, GMR-Gal4, tub-Gal80 ts , UAS-p35, UAS-hid, UAS-hep CA , UAS-GFP, and UAS-TOR TED were obtained from the Bloomington Stock Center. UAS-based RNAi stocks of the following genes were obtained from Bloomington, VDRC or NIG-FLY stock centers: bsk (BL 32977, V34138), dAtg1 (BL26731), dAtg3 (BL34359, V101364), dAtg6 (V22122, V110197), dAtg8a (V43076, V43097), dAtg8b (V17097), dAtg9 (V10045), dAtg17 (V106176), Vps15 (V110706, NIG9746R-2), Vps34 (V100296), raptor (BL34814, BL41912), and unc-76 (V20721, V20722, V40495). Comparable results were obtained from multiple RNAi lines targeting the same gene. Functionality of BL26731, V101364, V43097 and V17097 was tested on inhibition of starvation-induced autophagy  (Additional file 7: Figure S7). The exact genotype of ey > hid-p35 is either UAS-hid; ey-Gal4 UAS-p35 (UAS-hid on X; ey-Gal4 UAS-p35 on second chromosome) or UAS-hid; ey-Gal4 UAS-p35 (UAS-hid on X; ey-Gal4 UAS-p35 on third chromosome; only used in Fig. 6c, c’). For analysis of ey > hid-p35 adult hyperplastic phenotype, three categories, weak (W), moderate (M) and severe (S), were used as previously described . Each screen analysis was repeated at least twice at 25 °C, or at room temperature (RT, 22 °C) if strong lethality was caused by expressing RNAi or dominant-negative mutant constructs at 25 °C in the background of ey > hid-p35, with scoring more than 50 ey > hid-p35/(RNAi or mutant) adult flies.
Temperature-sensitive regenerative assays and statistical analysis
Larvae of the following genotypes (1) DE ts > hid (UAS-hid/+; UAS-GFP/+; DE-Gal4 tub-Gal80 ts /+); (2) DE ts > dAtg1 RNAi (UAS-GFP/+; DE-Gal4 tub-Gal80 ts /UAS-dAtg1 RNAi ); (3) DE ts > hid-dAtg1 RNAi (UAS-hid/+; UAS-GFP/+; DE-Gal4 tub-Gal80 ts /UAS-dAtg1 RNAi ); (4) DE ts > dAtg1 DN (UAS-GFP/+; DE-Gal4 tub-Gal80 ts /UAS-dAtg1 DN ); (5) DE ts > hid-dAtg1 DN (UAS-hid/+; UAS-GFP/+; DE-Gal4 tub-Gal80 ts /UAS-dAtg1 DN ) were raised at 18 °C. Expression of UAS-constructs (GFP, hid, dAtg1 RNAi , dAtg1 DN ) was induced by a temporal temperature shift to 29 °C for 12 h. After a 72 h recovery period at 18 °C, late third instar eye discs were dissected and analyzed as indicated in the panels (Fig. 2). Full details of the DE ts > hid assay have been described previously . At least three independent experimental repeats were done for each genotype and the results were consistent. For statistical analysis shown in Fig. 2d, at least 10 eye discs from each of the following genotypes, DE ts > hid; DE ts > dAtg1 RNAi ; DE ts > hid-dAtg1 RNAi ; DE ts > dAtg1 DN ; and DE ts > hid-dAtg1 DN , were measured for their sizes of dorsal versus ventral half of discs using the “histogram” function in Adobe Photoshop CS6. For such measurement, location of the optic stalk at the center of the posterior edge of eye disc was used as a landmark to horizontally divide eye discs into dorsal versus ventral halves. The dorsal/ventral size ratio was then calculated for each genotype. The statistical significance was evaluated through a one-way ANOVA with Bonferroni multiple comparison test (at least P < 0.01). For the developing wing tissue (Fig. 5), hh-Gal4 tub-Gal80 ts (hh ts ) was used to temporally control expression of UAS-constructs in the posterior compartment of wing discs.
For mosaic analysis with “undead” cell clones in larval discs (Fig. 4), the 3 L-MARCM assay was used . Mid second instar (32–40 h post-hatching) larvae of the following genotypes were heat shocked for 1 h at 37 °C, raised at 25 °C, and analyzed at the late third instar larval stage. (1) Generation of hid and p35 co-expressing “undead” clones: hs-FLP tub-GAL4 UAS-GFP/UAS-hid; UAS-p35/+; tub-GAL80 FRT80B/FRT80B. (2) Generation of hid and p35 co-expressing dronc mutant clones: hs-FLP tub-GAL4 UAS-GFP/UAS-hid; UAS-p35/+; tub-GAL80 FRT80B/dronc I29 FRT80B. (3) Generation of hid and p35 co-expressing dAtg1 mutant clones: hs-FLP tub-GAL4 UAS-GFP/UAS-hid; UAS-p35/+; tub-GAL80 FRT80B/dAtg1 Δ3D FRT80B. (4) Generation of dAtg1 mutant clones in GMR-hid eye discs: ey-FLP/+; GMR-hid/+; dAtg1 Δ3D FRT80B/ubi-GFP FRT80B. The mosaic assay in starving fat body (Additional file 7: Figure S7) was done according to Neufeld . UAS-RNAi lines targeting dAtg1, dAtg3, dAtg8a, and dAtg8b were crossed to yw hs-FLP; r4-mCherry-Atg8a Act > CD2 > Gal4 UAS-GFPnls  and incubated at 25 °C. Offspring were starved for 3 h on 20 % sucrose solution before dissection.
Immunohistochemistry and quantification of cCasp3 labeling intensity
Imaginal discs were dissected from late third instar larvae and stained using standard protocols . Antibodies to the following primary antigens were used: anti-cleaved Caspase-3 (Cell Signaling), β-GAL, ELAV, MMP1 (3B8D12 and 5H7B1 used as a 1:1 cocktail), and Wg (all DHSB). dATG1 antibodies were kindly provided by Jun Hee Lee . Secondary antibodies were donkey Fab fragments conjugated to FITC, Cy3 or Cy5 from Jackson ImmunoResearch. For the dATG1 labeling, HRP-labeled secondary antibodies were used and amplified with Tyramide Signal Amplification (TSA, PerkinElmer). Fluorescent images were taken with a Zeiss confocal microscope. Adult fly images were taken using a Zeiss stereomicroscope equipped with an AxioCam ICC1 camera.
For quantification of cCasp3 labeling intensity in eye or wing discs (Fig. 3j, k and Additional file 3: Figure S3C), the average cCasp3 signal intensities in certain disc areas were acquired through Adobe Photoshop CS6 and normalized to the corresponding background level of cCasp3 labeling in the same disc. The background cCasp3 labeling intensity was obtained from the antenna discs for measurement in eye discs (Fig. 3j), the notum regions for measurement in wing discs (Fig. 3k), and the non-clonal areas for the Additional file 3: Figure S3C. At least five representative discs of each genotype were used for such quantification. The statistical significance was evaluated through either a one-way ANOVA with Bonferroni multiple comparison test (at least P < 0.01, Fig. 3j, k) or a two-tailed, unpaired Student’s t test (Additional file 3: Figure S3C).
In situ hybridization
For in situ hybridization to detect dAtg1 transcripts, Drosophila cDNA clone LD18893 (Berkeley Drosophila Genome Project expressed sequence tags, Drosophila Genomic Resource Center) was used as a template to generate digoxigenin-labeled sense and antisense RNA probes (Roche). Labeled probes were detected with a TSA Cy3 kit (PerkinElmer) as previously described .
Quantitative real-time PCR (qPCR)
Total RNA was isolated from 100 eye discs collected from either the control ey-GAL4 or ey-GAL4 UAS-Atg1RNAi (ey > dAtg1 RNAi ) third instar larvae using the TRIzol Reagent (Thermo Fisher Scientific). cDNA was then generated from 1 μg of total RNA with the GoScript™ Reverse Transcription System (Promega). This is followed by the real-time PCR using the SensiFAST SYBR Hi-Rox kit (BIOLINE) with a ABI Prism7000 system (Life technologies). dAtg1 mRNA levels were normalized to the reference gene ribosomal protein L32 (RPL32) by using the ΔΔCt analysis. Three independent biological repeats were analyzed. The following primers suggested by the FlyPrimerBank  were used: dAtg1 Fw, CGTCAGCCTGGTCATGGAGTA; dAtg1 Rv, TAACGGTATCCTCGCTGAG; RPL32 Fw, AGCATACAGGCCCAAGATCG; RPL32 Rv, TGTTGTCGATACCCTTGGGC.
We would like to thank Eric Baehrecke, Georg Halder, Anne-Claire Jacomin, Ioannis Nezis, Jun Hee Lee, the Bloomington Stock Center, the Drosophila Genomics Resource Center in Indiana, the VDRC stock center in Vienna, the NIG-FLY stock center in Kyoto and the Developmental Studies Hybridoma Bank (DSHB) in Iowa for fly stocks and reagents.
ML is supported by the China Scholarship Council (CSC)-Birmingham joint PhD program. AB is supported by MIRA grant R35 GM118330 from the National Institute of General Medicine Science (NIGMS), USA. YF is supported by Marie Curie Career Integration Grant (CIG) 630846 from the European Union’s Seventh Framework Programme (FP7) and Grant BB/M010880/1 from the Biotechnology and Biological Sciences Research Council (BBSRC), UK. The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Availability of data and materials
All data generated or analyzed during this study are included in this published article (and its supplementary information files). Requests for material should be made to the corresponding authors.
ML, JL, EP and YF carried out the experiments. ML, AB and YF discussed and interpreted the results. AB and YF supervised the project and wrote the manuscript. All authors read and approved the final manuscript.
The authors declare that they have no competing interests.
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