Increased mitochondrial biogenesis preserves intestinal stem cell homeostasis and contributes to longevity in Indy mutant flies

Aging increases Indy mRNA levels in the midgut of control flies

In Drosophila, INDY is predominantly expressed in the basolateral membrane of the midgut epithelia, fat body and oenocytes [10]. To identify a relationship between Indy expression and aging in midgut tissue, we measured Indy mRNA levels in control yellow-white (yw) flies at 10 and 40 days. Indy transcript levels increase by approximately 89% in female yw flies, whereas Indy²⁰⁶/+ and Indy²⁰⁶/Indy²⁰⁶ mutants show decreased Indy mRNA levels at all ages following 10 generations of backcrossing into yw background (Fig. 1A, S1A). Consistently, exposure to 20 mM paraquat, an agent known to induce free radical production and mimic aging, upregulates Indy mRNA and protein levels in young control flies to levels similar to those that are observed in aged flies (Fig. 1B, S1B, S1C) [5, 19].

Figure 1.

Indy reduction is associated with increased dPGC-1 levels and mitochondrial biogenesis. (A) Indy mRNA levels in the midgut of yw control, Indy²⁰⁶/+ and Indy²⁰⁶/Indy²⁰⁶ female flies at 10 and 40 days determined by qPCR. Controls show an age-related increase in Indy mRNA, which is absent in the mutant midgut (n=3, 25 guts per replicate. p<0.001, p<0.0001, t test, error bars represent SEM). (B) Indy mRNA levels in yw control flies on a regular diet, after overnight exposure to paraquat, HC and CR, and Indy²⁰⁶/+ and Indy²⁰⁶/Indy²⁰⁶ mutant flies at 20 days. Paraquat and HC significantly increases and CR significantly reduces Indy transcript levels in the midgut of control female flies (n=3, 25 guts per replicate p<0.01, p<0.05, p<0.001, error bars represent SEM). (C) dPGC-1 mRNA levels in female yw control, Indy²⁰⁶/+ and Indy²⁰⁶/Indy²⁰⁶ mutant midguts at 10, 20 and 40 days. There is a significant age-related decrease in dPGC-1 mRNA in control flies by 40 days (p <0.05, t test) that is absent in heterozygous and homozygous Indy²⁰⁶ mutants, which show increased dPGC-1 mRNA levels compared to controls at all ages (p<0.01, p<0.001, p<0.0001, t test. n=3, 25 guts per replicate, error bars represent SEM). (D) Mitochondrial (COI) and nuclear (GAPDH) DNA ratio determined by qPCR. Indy²⁰⁶/+ and Indy²⁰⁶/Indy²⁰⁶ mutant females show significant increases in mitochondrial DNA copy number, compared to yw control or Indy²⁰⁶/dPGC-1^KG08646 mutant flies (p<0.01, p<0.001, p<0.0001, n=3, 25 guts per replicate) (E) Electron micrographs of control, Indy²⁰⁶/+ and Indy²⁰⁶/Indy²⁰⁶ midguts at 20 days imaged at 10,000x. Scale bar represents 11μm. (F) Mitochondrial density (mitochondrial number/counted cell volume X100) as assessed by point counting in Image J. There is a significant increase in mitochondrial number in Indy²⁰⁶/+ and Indy²⁰⁶/Indy²⁰⁶ mutant midgut tissue at 20 days (p<0.05, p<0.001, t test. n> 25 cells per guts). (G) Indy²⁰⁶/+ and Indy²⁰⁶/Indy²⁰⁶ mutants have significantly smaller mitochondria at 20 days in midgut tissue assessed by point counting in Image J. (p<0.001, n>25 cells per gut). (H) Quantification of l(2)neo, Pdsw encoding components of complex I and Cytochrome C oxidase encoding a component of complex IV are increased in the midgut of Indy²⁰⁶/+ and Indy²⁰⁶/Indy²⁰⁶ mutant flies determined by qPCR. (p<0.05, p<0.01, p<0.001, n=3, 25 guts per replicate).

To investigate the relationship between Indy mRNA and nutrient availability in the midgut, we measured Indy mRNA levels in female yw control, Indy²⁰⁶/+ and Indy²⁰⁶/Indy²⁰⁶ flies on a normal, high caloric (HC) and CR diets at 20 days. Indy mRNA levels nearly doubled in yw flies on a HC diet, whereas a 50% reduction in transcript was observed in both yw flies on a CR diet and Indy²⁰⁶/+ flies on a regular diet (Fig. 1B). Diet-induced changes in Indy mRNA levels support a role for Indy as a physiological regulator, whose expression changes to modulate intermediate metabolism in response to nutrient availability.

Indy reduction is associated with increased dPGC-1 levels in the midgut

dPGC-1 increases mitochondrial biogenesis in response to CR and decreases as a consequnce of normal aging [2, 3, 6, 7, 16]. Consistently, we found a significant age-related decrease in dPGC-1 mRNA levels in the midgut of yw females between 20 and 40 days (Fig. 1C). Our observation that Indy levels decrease in response to CR (Fig. 1B), led us to investigate whether INDY reduction is sufficient to upregulate dPGC-1 in the fly midgut and rescue the age-associated decline in expression levels. We found significantly higher dPGC-1 mRNA levels compared yw controls at all ages in both Indy²⁰⁶/+ and Indy²⁰⁶/Indy²⁰⁶ mutant females, with a similar increase observed in Indy²⁰⁶/+ male flies at age 40 (Fig. 1C, S2A). This trend is consistent through out lifespan, as demonstrated by the absence of any age-associated changes in both Indy and dPGC-1 mRNA levels in Indy mutant midguts (Fig. 1A, 1C).

To further examine the relationship between Indy and dPGC-1 mRNA levels, we used the TIGS2-geneswitch driver (TIGS2-GS) to drive gut specific Indy-RNAi mediated silencing. dPGC-1 mRNA levels increase in response to a small reduction of Indy mRNA levels in the midguts of TIGS2-GS; Indy-RNAi male and female flies at 20 days (Fig. S2B-E). Together, these data suggest that there is an inverse relationship between Indy and dPGC-1 mRNA levels in the midgut.

Reduced Indy increases dPGC-1 medited mitochondrial biogenesis

We next examined whether dPGC-1 upregulation in the midgut of Indy mutant flies was sufficient to increase mitochondrial biogenesis by measuring mitochondrial density. The ratio of mitochondrial DNA to nuclear DNA in the midgut of Indy²⁰⁶/+ and Indy²⁰⁶/Indy²⁰⁶ mutant flies is significantly increased compared to control at 40 days (Fig. 1D). Using double mutant flies with the Indy²⁰⁶ mutant allele and a hypomorphic dPGC-1 allele (Indy²⁰⁶/dPGC-1^KG08646), we determined that the observed increase in mitochondrial DNA copy number, which depends on increased dPGC-1 levels. These flies have mitochondrial DNA copy numbers similar to those observed in control flies at 40 days (Fig. 1D). Increased mitochondrial biogenesis in enterocytes residing in the anterior midgut of Indy mutant was confirmed by electron microscopy and the point counting method. Enterocytes comprise ~90% of the midgut cell populations; therefore thery represent the majority of cell types and can be used to indicate overal mitochondrial density in the midgut. Electron micrographs of Indy²⁰⁶/+ and Indy²⁰⁶/Indy²⁰⁶ mutant midgut tissue show a clear increase in mitochondrial density and significantly smaller size by 20 days compared to controls (Fig. 1E-G).

In addition to higher mitochondrial biogenesis, Indy²⁰⁶/+ and Indy²⁰⁶/Indy²⁰⁶ female midguts have increases in mitochondrial electron transport chain complex I (ETC) gene expression (Figure 1H). While l(3)neo18 and Pdsw mRNA levels are elevated in both Indy²⁰⁶/+ and Indy²⁰⁶/Indy²⁰⁶, we also observed significant increases in ND23, ND42, ND75 mRNA levels in the midgut of Indy²⁰⁶/Indy²⁰⁶ mutant flies by 20 days (Fig. S2F). Furthermore, mRNA levels of ETC complex IV component, Cytochrome C oxidase I (COI), were also significantly increased in aged Indy²⁰⁶/+ and Indy²⁰⁶/Indy²⁰⁶ female flies (Fig. 1H).

Indy mutants have enhanced mitochondrial activity and reduced ROS levels in the midgut

High mitochondrial membrane potential is associated with preserved mitochondrial physiology and efficiency. We determined the status of mitochondrial membrane potential in Indy²⁰⁶/+ and Indy²⁰⁶/Indy²⁰⁶ mutant midgut tissue by using positively charged JC-1, which fluoresces green as a monomer in cytoplasm but forms red aggregates upon entering the mitochondrial matrix as a result of high membrane potential. The red:green ratio in aged Indy mutant midguts is significantly greater in both Indy²⁰⁶/+ and Indy²⁰⁶/Indy²⁰⁶ mutants compared to controls (Fig 2A,B). Moreover, the ratio for Indy²⁰⁶/dPGC-1^KG08646 double mutants is strikingly similar to that observed in controls suggesting that dPGC-1 mediates changes in mitochondrial physiology observed in Indy mutants (Fig. 2A,B).

Figure 2.

Indy mutants have reduced ROS levels and increased oxidative stress resistance. (A) Visualization of JC-1 dye in female yw control, Indy²⁰⁶/+, Indy²⁰⁶/Indy²⁰⁶ and Indy²⁰⁶/dPGC-1^KG08646 mutant flies at 40 days. Indy mutant flies show increased mitochondrial membrane potential compared to controls and Indy²⁰⁶/dPGC-1^KG08646 mutants. Scale bar represents 1μm (B) Ratio of red JC-aggregates to green JC-1 monomer. Indy²⁰⁶/+ and Indy²⁰⁶/Indy²⁰⁶ mutant flies have increased mitochondrial membrane potential shown by increased red:green JC-1 ratiocompared to control and Indy²⁰⁶/dPGC-1^KG08646 mutants (p<0.01, p<0.001, n>10 guts per genotype, compared by Mann-Whitney U test) (C) Positive DHE staining for ROS in compressed Z-stack of female control, Indy²⁰⁶/+, Indy²⁰⁶/Indy²⁰⁶ and Indy²⁰⁶/dPGC-1^KG08646 mutant midgut flies at 40 days. Scale bar represents 1μm. (D) Mean DHE intensity in compressed Z-stack of female control, Indy²⁰⁶/+, Indy²⁰⁶/Indy²⁰⁶ and Indy²⁰⁶/dPGC-1^KG08646 mutant midguts at 40 days. (p<0.001, p<0.0001, n>15 guts per genotype; Scale bar represents 1μm). (E) Levels of GstE1 and GstD5 mRNA in female yw control, Indy²⁰⁶/+, Indy²⁰⁶/Indy²⁰⁶ and Indy²⁰⁶/dPGC-1^KG08646 mutant midgut tissue determined by qPCR. There is a significant increase (p<0.05, p<0.001, p< 0001 n=3, 25 guts per replicate) in levels of both gene mRNA levels in Indy²⁰⁶ mutant midgut tissue at 20 days compared to control and Indy²⁰⁶/dPGC-1^KG08646. Survival curves for female (F) and male (G) yw control, Indy²⁰⁶/+ and Indy²⁰⁶/Indy²⁰⁶ flies on 20mM paraquat. Indy²⁰⁶ mutants have increased resistance to oxidative stress compared to control.

Increased levels of mitochondrial ROS production and oxidative damage are associated with decreased mitochondrial function and considered hallmarks of aging across species [2, 4, 23, 24]. Dihydroethidium (DHE) fluoresces red when it reacts with superoxide and was used to measure changes in the total redox environment in the midgut of female Indy²⁰⁶ mutants, Indy²⁰⁶/dPGC-1^KG08646 double mutants and control flies at 40 days. Both Indy²⁰⁶/+ and Indy²⁰⁶/Indy²⁰⁶ mutants had significantly decreased red fluorescence when compared to controls indicating lower levels of ROS (Fig. 2C,D). Indy²⁰⁶/dPGC-1^KG08646 show partial protection against ROS accumulation as shown by intermediate levels of DHE intensity, which is likely due to the effects of Indy reduction on the wild-type copy of dPGC-1 (Fig. 2D).

Indy mutant flies have increased resistance to oxidative stress

We next examined whether Indy mutations affect fly oxidative stress resistance. ROS-detoxification factors Glutathione S transferase E1 (GstE1) and Glutathione S transferase D5 (GstD5) mRNA were significantly increased in Indy²⁰⁶/+ and Indy²⁰⁶/Indy²⁰⁶ mutant midgut tissue at 40 days compared to yw controls (Fig. 2E). Levels were not significantly altered in Indy²⁰⁶/dPGC-1^KG08646 flies compared to controls, suggesting that both copies of wild type dPGC-1 are necessary to modulate ROS detoxification in Indy mutants (Fig. 2E). Additionally, male and female Indy²⁰⁶ mutant flies have increased oxidative stress resistance when exposed to 20 mM paraquat compared to yw controls at 20 days (Fig. 2F, 2G, Table S1). Increased resistance in Indy²⁰⁶/+ flies compared to Indy²⁰⁶/Indy²⁰⁶ flies can be atributed to enhanced mitochondrial physiology and decreased ROS levels found in Indy²⁰⁶/+(Fig. 2A-2E).

Indy mutations preserve ISC homeostasis and intestinal integrity

Robust INDY expression in the midgut suggests that transporting metabolites across the midgut epithelia is one of the main functions of INDY. The midgut is maintained by multipotent ISCs, which divide asymmetrically giving rise to an identical daughter ISC and an immature progenitor enteroblast cell (EB) with differentiation potential. Elevated levels of ROS disrupt ISC proliferation patterns by inducing division at a rate that surpasses EB differentiation, which leads to accumulation of polyploid aggregates, decreased intestinal integrity and accelerated mortality [5, 17, 18, 25]. The effect of decreased Indy expression on intestinal homeostasis was examined using the Indy^YC0030 mutant fly line, which has a fluorescent protein (GFP) tag inserted in the Indy gene region and was backcrossed 10 generations into the yw background [26]. Indy^YC0030/+ mutant flies have reduced Indy transcript in the midgut at levels similar to those observed in Indy²⁰⁶/+ mutants. These flies also demonstrate significant longevity extension, with a 58.3% and 42.2% increases in median life span in males and females, respectively (Fig. S3A-D, Table S2).

Both the ISC and the progenitor EB express the transcription factor escargot (esg); therefore esg- positive cells represent undifferentiated cells [20, 21]. The number of undifferentiated cells in the midgut was assessed using esgLacZ flies, which express βgal under an esg reporter and were backcrossed 10 generations into the yw genetic background. Quantification of βgal-positive cells in aging male and female control esgLacZ/+ and esgLacZ;Indy^YC0030/+ mutant midgut tissue show significantly fewer βgal-positive cells in Indy^YC0030/+ flies compared to control flies at 40 days (Fig. 3A,B, S4A,B).

Figure 3.

Indy mutations preserve ISC homeostasis. (A) Immunostaining for INDY (red) DAPI (blue nuclear) and β-galactosidase (green) in the midgut of female control (esgLacZ/+) and Indy mutant (esgLacZ;Indy^YC0030/+) flies at 20 days at 40X. Scale bar represents 1μm. (B) Quantification shows reduced number of esg-positive cells in the esgLacZ; Indy^YC0030/+ mutant female midgut throughout lifespan (p<0.0001, n>20). (C) Immunostaining for β-galactosidase activity (green), nuclear (blue) and pH3-positive cells (red) in control (esgLacZ/+) and the Indy mutant (esgLacZ/+;Indy^YC0030/+) midgut tissue at 40 days. β-gal- positive cells represent ISC/EB populations and pH3-positive cells represent dividing cells. Scale bar represents 1μm. (D) Quantification of pH3-positive cells in the midgut of control (esgLacZ/+) and Indy (esgLacZ;Indy^YC0030/+) mutant flies. There is increased cell division in female control midgut tissue throughout lifespan that is largely absent in esgLacZ; Indy^YC0030/+ mutant females (p<0.01, p<0.0001, n>20). Error bars represent SEM. (E) Quantification of dividing cells in the midgut determined by the presence of pH3-positive immunostaining. There is increased cell division in female control midgut tissue throughout lifespan that is largely absent in esgLacZ; Indy^YC0030/+ mutant females (p<0.05, p<0.0001, n>20). Error bars represent SEM. See Figures S4, S5 and Table S2. (F) Quantification of pH3- postive cells in the midgut of yw control, Indy²⁰⁶/+ mutant and Indy^206/+/dPGC-1^KG08646 female flies at 40 days. There are reduced dividing cells in the midgut of Indy mutant flies compared to control and Indy²⁰⁶/dPGC-1^KG08646 midgut (p<0.0001, n>15). Error bars represent SEM.

Phosphorylation of histone 3 (pH3) occurs during mitosis and marks active cell proliferation [27]. esgLacZ;Indy^YC0030/+ mutant flies have significantly fewer pH3-positive cells in midgut tissue compared to control esgLacZ/+ flies at 40 days (Fig. 3C,D, S4B). Moreover, the number of pH3-positive cells is steady from 20-40 days in Indy mutant flies, indicating preserved ISC proliferative homeostasis (Fig. 3E). Using double mutant Indy²⁰⁶/dPGC-1^KG08646 flies, we determined that two copies of dPGC-1 are required to maintain low numbers of pH3-positive cells in aged Indy²⁰⁶ mutants. Unlike Indy²⁰⁶/+ mutants, double mutant Indy²⁰⁶/dPGC-1^KG08646 midguts have significantly more pH3-positive cells, suggesting dPGC-1 mediates downstream effect of Indy reduction (Fig. 3F).

ISCs maintain intestinal architecture by replacing damaged cells that comprise the barrier between lumen and hemolymph in the midgut. Age-related accumulation of aggregates and regions of disjoined cells compromises intestinal integrity and can be observed in the midgut of control flies; however, Indy²⁰⁶/Indy²⁰⁶ midguts retain cellular architecture (Fig. 4A,B). To assess the state of intestinal integrity in aged Indy mutants, we added 2.5% w/v non-absorbable FD&C blue dye #1 to fly food and quantified the percentage of flies displaying total tissue staining [17]. About 40% of aged controls show loss of intestinal integrity as measured by total staining throughout the body after feeding (Fig. 4C). In contrast, only about 10% of Indy²⁰⁶/+ and Indy²⁰⁶/Indy²⁰⁶ mutant flies were completely blue, with most retaining blue dye in the digestive tract and proboscis similarly to young flies (Fig. 4C). Furthermore, we observed about 30% of Indy²⁰⁶/dPGC-1^KG08646 flies with total blue staining, which further supports a role for dPGC-1 as a downstream mediator of beneficial effects of Indy mutations.

Figure 4.

Indy mutations preserve intestinal integrity. (A) Electron micrograph of yw control (left) and Indy²⁰⁶/Indy²⁰⁶ (right) midgut imaged at 1000x. Arrow shows damaged tissue and asterisks mark ISCs. Scale bar represents 1 μm. (B) Quantitative analysis of blue staining of female control and Indy²⁰⁶/Indy²⁰⁶ flies fed food containing 2.5% w/v FD&C blue dye for 150 minutes at 40 days. Blue coloring throughout body indicates loss of intestinal integrity. Control and Indy²⁰⁶/dPGC-1^KG08646 flies have a significantly higher number of blue flies compared to Indy²⁰⁶/+ and Indy²⁰⁶/Indy²⁰⁶ mutants (p<0.01, n>50).

Indy-longevity is mediated by dPGC-1

Decreased Indy expression and restricted upregulation of dPGC-1 in midgut stem and progenitor cells extends lifespan in flies [12, 13, 17]. As described above, Indy mutants have significantly increased dPGC-1 mRNA levels in the midgut throughout lifespan (Fig. 1C); therefore we investigated whether these two longevity pathways share a similar mechanism. We used the esgGAL4/UASdPGC-1(Spargel^EY05931) system to overexpress dPGC-1 in stem and progenitor cells of the digestive tract [17, 28]. To avoid any effects of genetic background, all flies were backcrossed to yw background for 10 generations. Although esgGal4 is also expressed in stem cells of malpighian tubules, the testis and in salivary glands, we focus our attention on the effects of overexpressing dPGC-1 on midgut physiology due to its importance in healhy aging [25]. We censored the first 9 days following eclosion to reduce the influence of early, non-age associated death on longevity studies. Female and male esgGal4;UAS-dPGC1 flies have increased median lifespan by 19.9% and 35.1%, respectively, compared to control esgGal4/yw flies (Fig. 5A,B, Table 3). If Indy and dPGC-1 longevity pathways overlap, we would not expect that overexpression of dPGC-1 in esg-positive cells of Indy²⁰⁶ mutant flies (esgGal4;Indy²⁰⁶/UAS-dPGC-1) to further extend longevity of Indy mutant flies. Compared to controls, these flies have median lifespan extension of 27.7% and 40.6%, in females and males, respectively. As predicted, they do not experience additional increase in lifespan compared to esgGal;UAS-dPGC-1 (Fig. 5A,B, S5A, Table 3).

Figure 5.

Indy and dPGC-1 longevity pathways overlap. (A) Lifespan curves of female esgGal4;Indy²⁰⁶/UAS-dPGC1 (magenta), esgGal4;UAS-dPGC-1 (purple) and genetic controls (esgGal4/+) (blue) flies. esgGal4;UAS-dPGC-1 females overexpressing dPGC-1 in esg-positive cells, and Indy mutant females with dPGC-1 overexpression in the esg-positive cells have 19.9%, and 27.7% increase in median longevity compared to genetic controls (esgGal4/+) flies, respectively. (B) Lifespan curves of male esgGal4;Indy²⁰⁶/UAS-dPGC1 (black), esgGal4;UAS-dPGC-1 (green) and genetic controls (esgGal4/+) (blue). esgGal4;UAS-dPGC-1 males overexpressing dPGC-1 in esg-positive cells, and Indy mutant male with dPGC-1 overexpression in the esg-positive cells have 35.1% and 40.6% increase in median longevity compared to genetic controls (esgGal4/+), respectively. (C) Lifespan curves of female Indy²⁰⁶ mutants with a hypomorphic allele for dPGC-1 (esgGal4;Indy²⁰⁶/UAS-dPGC1) (gray), Indy mutant flies with one copy of the dPGC-1UAS construct (esgGal4;Indy²⁰⁶/UAS-dPGC1) (yellow) and genetic controls (UAS-dPGC1/+) (maroon). esgGal4;Indy²⁰⁶/UAS-dPGC1 flies show similar longevity compared to controls and esgGal4;Indy²⁰⁶/UAS-dPGC1 females show 22.5% median longevity extension. (D) Lifespan curves of male Indy²⁰⁶ mutant with a hypomorphic allele for dPGC-1 (esgGal4;Indy²⁰⁶/UAS-dPGC1) (red), Indy mutant flies with one copy of the dPGC-1UAS construct (esgGal4;Indy²⁰⁶/UAS-dPGC1) (blue) and genetic controls (UAS-dPGC1/+) (green). esgGal4;Indy²⁰⁶/UAS-dPGC1 flies show similar longevity compared to controls and esgGal4;Indy²⁰⁶/UAS-dPGC1 males show 23.5% median longevity extension. See Figure S6, Table 3. n>170 for all lifespan studies.

Flies heterozygous for the Indy²⁰⁶ allele with one copy of the UAS-dPGC-1 construct (Indy²⁰⁶/UAS-dPGC-1) have median lifespan extension compared to the survivorship of UAS-dPGC-1/yw flies with 22.5% and 23.5% increases in female and male flies respectively (Fig. 5C, D, Table 3). Furthermore longevity extension was not observed in double mutant Indy²⁰⁶/dPGC-1^KG08646 flies compared to genetic control (UAS-dPGC-1/yw) and was signifcantly shorter compared to Indy²⁰⁶/UAS-dPGC-1, suggesting that the longevity extension observed in Indy²⁰⁶ mutant flies with one copy of Indy²⁰⁶ chromosome, is most likely mediated by increased levels of dPGC-1 (Fig. 5C, D, Table 3). This conclusion is supported by findings that dPGC-1 mRNA levels found in the midgut of Indy mutant flies are the same as those found in flies overexpressing dPGC-1 in esg-positive cells in Indy mutants or flies with wild type INDY (Fig. S5). Together, the data support a model for Indy-mediated longevity that is mediated by downstream activation of dPGC-1 and its effect on mitochondrial physiology.

Fly Strains

The Indy^YC0030 line was obtained from Lynn Cooley [26]. The esgGal4 (y¹w;esgGAL4/Cyo)(#26816), esgLacZ (y¹w^67c23;esgLacZ/Cyo) (#10359), UAS-dPGC-1 (yw; Spargel ^EY05931) (#2009), y¹;P{SUPor-P}Spargel^KG08646ry⁵⁰⁶/TM3,Sb¹Ser¹(#14965) and yellow-white (yw) flies were obtained from the Bloomington Stock Center at Indiana University. The Indy²⁰⁶ line was obtained from Tim Tully [38]. The TIGS-2 Gene-Switch driver line was provided by Scott Pletcher and the UAS-Indy^RNAI (w¹¹¹⁸;P{GD2712}v9981) line was obtained from the Vienna Drosophila RNAi Center [39].

Fly Maintenance and Lifespan Studies

Flies were collected within 24 hours after eclosion and maintained in plastic vials containing standard food medium and kept in a humidified, temperature-controlled incubator with 12/12-h on/off light cycle at 25 °C. All strains were backcrossed 10x to yellow-white (yw) background and reared on food containing 25 mg/mL tetracycline for 3 generations to eliminate Wolbachia, followed by several generations in tetracycline-free food. Lifespan studies were performed using 10 groups of 25 male and 25 female flies, which were collected within 24 hours following eclosion as described above and maintained in plastic vials containing standard, high or low calorie food medium and kept in a humidified, temperature-controlled incubator with 12/12-h on/off light cycle at 25 °C. Flies were transferred to fresh food every other day for the first 30 days and then every day until no flies remained alive. The number of dead flies was scored after each passage. Flies requiring gene-switch induction were grown on food containing 200 μM RU486 and controls on EtOH. Approximately 20 females and 20 males flies are kept together in each vial and passed to fresh vials every 2 days for aging studies.

Longevity data were censored for early mortality (1-9 Days) and analyzed by long-rank tests using the JMP 10 program.

Oxidative Stress Resistance Studies

Oxidative stress resistance studies were conducted by keeping 20 flies in a vial containing filter paper soaked with 300 μL of 20 mM paraquat following initial starvation for 6 hours. The number of dead flies was counted hourly during the day and twice overnight until no flies remained alive. Stress resistance data were analyzed by long-rank tests using the JMP 10 program. Total number of flies per experiment is listed in Table 1.

Quantitative PCR (qPCR)

Total RNA was isolated from the midguts of 3 biological replicates with more than 25 flies in each replicates using Trizol as described [14]. qPCR was performed following cDNA synthesis and changes in gene expression patterns were determined using a 7500 Fast Real-Time PCR System (Applied Biosystems) and TaqMan Master Mix (Applied Biosystems). Gene specific TaqMan primers for Indy, dPGC-1, Pdsw, l(3)neo18, COI, ND23, ND42, ND75, GstD5 and GstD1 were obtained from the Invitrogen. All experiments were run in triplicate. Ankryn was used as an endogeneous controls in all q-PCR experiments.

Mitochondrial DNA Measurement

Total DNA from the midguts of more than 25 flies was isolated at 40 days using the Invitrogen DNA blood and tissue isolation kit (Life technologies). DNA copy number was determined using qPCR as described above. Mitochondrial DNA content was determined by the ratio of the mitochondrial gene for COI to a nuclear gene, GAPDH [6]. Rpl1140 was used as an endogenous control.

Electron Microscopy and Mitochondrial Quantification

Flies were fixed in 2% glutaraldehyde in 0.1 M sodium cacodylate buffer as described [21]. A minimum of 15 electron micrographs of midgut sections of each sample were taken at 10,000-15,000x, using an unbiased sampling method. Images were processed and analyzed in Adobe Photoshop. Post-fixation was conducted for 1 hr in 1% osmium tetroxide-0.8% potassium ferricyanide. Samples were stained in block with 1% aqueous uranyl acetate, dehydrated in a graded ethanol series, and embedded in Spurr low-viscosity epoxy resin. Thin sections of areas containing midgut were stained with uranyl acetate and lead citrate, and examined in a Hitachi H7650. Mitochondria were counted by using the point counting method by using a grid system to count the number of mitochondria present in a given image relative to cytoplasmic volume [7]. Size was determined by measuring the grid overlays per mitochondria and expressed relative to cytoplasmic volume.

Immunostaining, Quantification of ISCs/EBs and pH3+ Cells

Midguts were dissected from flies at 10, 20 and 40 days, fixed in 4% paraformaldehyde and stained as described [17]. Following washing, samples were mounted and imaged using the Leica camera attachment using LAS V4.1 software, or the Zeiss 780 combined confocal/FCS/NLO system, mounted on an inverted Axio Observer Z1. Fixed tissue was incubated overnight with mouse anti-gal 1:500 (Invitrogen); rabbit anti-pH3 1:300 (Invitrogen) or rabbit anti-INDY 1:300 [10] primary antibodies diluted in PBT [0.1%Triton X-100 in phosphate-buffered saline (PBS)] at 4°C. Following washing and blocking, tissue was incubated with the goat anti-rabbit Cy3 1:300 (Jackson) or goat anti-mouse FITC 1:300 (Jackson) secondary antibodies and DAPI 1:1000 (Invitrogen) diluted in PBT and 2% donkey serum for 1 hour at room temperature. Images were analyzed using Adobe Photoshop or Image J. Variability between different regions of the gut was reduced by quantifying images from the same designated region for each genotype in a 0.06x 0.02cm area. Cells were counted, values averaged and standard deviation calculated separately.

Dihydroethidium Staining

ROS levels were assessed in live whole midgut tissue as described [17, 18]. Tissue was dissected directly in Schneider's medium and incubated for 7 minutes in 60 mM dihydroethidium (DHE) (Invitrogen Molecular Probes) in Schneider's medium and 1:1000 4',6-diamidino-2-phenylindole (DAPI) nuclear stain in 0.1% PBT 2% donkey serum. Midguts were washed in Schneider's medium at room temperature, mounted in 70% glycerol and imaged using a Zeiss 780 combined confocal/FCS/NLO system, mounted on an inverted Axio Observer Z1. 2 μm Z stacks of regions 200-500 μm anterior to the pylorus were measured for mean signal intensity at 568 nm in Image J. Pixel intensities of Z stacks, spanning from the basal to apical cell layers, for at least 15 midguts per genotype were used for each of the quantifications.

JC-1 Analysis

JC-1 analysis was performed as described [17]. Whole midguts were dissected from female flies at 40 days directly into 5 μM JC-1 (Molecular Probes) in DMSO containing 1:1000 DAPI (Invitrogen) and incubated in the dark for 30 minutes at room temperature. Midguts were washed 2 times for 5 minutes each and mounted in PBS. Images were taken of midguts approximately 300 μm from the anterior pylorus in the 568 nm channel using the Zeiss 780 combined confocal/FCS/NLO system and analyzed in Image J. Mean pixel intensities for J-aggregates were averaged, and significant differences between means were determined with a Mann-Whitney U test.

Intestinal Integrity

Quantification of intestinal integrity was done as described [17]. More than 50 female flies were transferred to standard lab food containing 2.5% w/v FD&C blue dye #1 for 150 minutes beginning at 7am. The percentage of blue flies per population was quantified and represented as mean averages ± SE values.

Statistical analysis

Significance was determined using a two-tailed, unpaired t-test from at least three independent experiments and expressed as P values, with the exception of longevity studies and JC-1 aggregation analysis. Error bars represent SEM, t test, P values are specifically indicated in each figure.