Comparable autophagic flux in the IECs of <i>tti^s450</i> larvae and WT larvae treated with rapamycin.

<p>(A–F) Transverse sections (200 µm) through the intestinal bulb region of untreated WT (A) and <i>tti^s450</i> (B) larvae at 120 hpf or larvae previously treated for 14 h with rapamycin and/or chloroquine (C–F) stained with rhodamine phalloidin to detect F-actin (<i>red</i>), Hoechst 33342 to detect DNA (<i>blue</i>) and the LC3B antibody to detect LC3II–containing autophagosomes (<i>green puncta</i>). (G) The numbers of autophagosomes are increased in chloroquine-treated WT and <i>tti^s450</i> larvae compared to the corresponding untreated larvae. Chloroquine-treated <i>tti^s450</i> larvae contain significantly more puncta than chloroquine-treated WT larvae and similar numbers to WT larvae treated with rapamycin and chloroquine. Rapamycin and chloroquine-treated <i>tti^s450</i> larvae contain significantly more puncta per IEC than the IECs in chloroquine-treated <i>tti^s450</i> larvae and chloroquine and rapamycin-treated WT larvae. Puncta were counted in 20 cells from 3 independent sections using Metamorph. (H) Representative Western blot analysis of whole cell lysates of WT and <i>tti^s450</i> larvae (96 hpf) previously treated for 14 h with rapamycin (10 µM) and/or chloroquine (2.5 µM) using antibodies to LC3B and Actin (loading control). (I) Graphical representation of the data shown in H and two independent analyses. The LC3II signals were quantitated by densitometry. <i>tti^s450</i> larvae treated with chloroquine contain more LC3II than their chloroquine-treated WT siblings and comparable levels to WT larvae treated with rapamycin and chloroquine. Data are represented as mean +/− SD, *p&lt;0.05.</p

<i>tti^s450</i> larvae exhibit elevated levels of Torc1 activity.

<p>(A) Western blot analysis of RPS6, p-RPS6 and Actin (loading control) in whole cell lysates of WT and <i>tti^s450</i> larvae between 72–120 hpf. (B) Graphical representation of the data shown in A combined with two additional experiments (each bar represents the mean +/− SD, *p&lt;0.05). <i>tti^s450</i> larvae exhibit increased levels of p-RPS6 at 96–120 hpf and decreased levels of total RPS6 between 72–120 hpf compared to WT siblings. (C) Immunohistochemical analysis of transverse sections of <i>tti^s450</i> and WT larvae at 96 hpf reveals robust p-RPS6 expression in the digestive organs. Scale bars = 50 µM. (D) The persistent expression of p-RPS6 expression in <i>tti^s450</i> larvae at 96 hpf compared to WT is due entirely to up-regulated Torc1 activity as shown by the disappearance of the p-RPS6 signal when larvae are pre-treated with rapamycin. (E) Inhibiting the Tor pathway in <i>tti^s450</i> larvae with rapamycin in the presence of chloroquine reduces p-RPS6 expression and at the same time increases autophagic flux as shown by the increase in LC3II level. In the graphical representation of the data, each bar represents the mean +/− SD (n = 3), *p&lt;0.05.</p

Positional cloning reveals that <i>pwp2h</i> is the mutated gene in <i>tti^s450</i>.

<p>(A) Physical map of chromosome 1 in the region encompassing the <i>tti^s450</i> locus. Analysis of recombinants from 7376 meioses narrowed the genetic interval containing the mutation to a region flanked by 2 BACs (green boxes) and encompassed by 2 scaffolds zv945445 and zv945446 (blue bars) containing 5 genes (arrows). (B) Schematic representation of the <i>pwp2h</i> gene and the location of the sequence variation in intron 9. (C) The nucleotide sequence of <i>pwp2h</i> cDNA from <i>tti^s450</i> larvae contains an A→T transversion. Wholemount <i>in situ</i> hybridization (WISH) reveals the <i>pwp2h</i> mRNA expression pattern from 4–144 hpf in WT larvae (D–L). <i>pwp2h</i> expression is ubiquitous from 4–12 hpf (D–F), restricted to the retina at 24 hpf (G; <i>black arrow</i>) and encompasses the pharyngeal cartilages <i>(black arrowhead)</i>, liver <i>(white arrow)</i>, intestine <i>(bracket)</i> and pancreas <i>(white arrowhead)</i> at 48 hpf (H), 72 hpf (I) and 96 hpf (J). From 120–144 hpf <i>pwp2h</i> expression is restricted to the pancreas (K–L; <i>white arrowhead</i>). <i>pwp2h</i> expression is barely detectable at 24 hpf (M) and 72 hpf (N) in <i>tti^s450</i> larvae. Staining is absent in the sense control at 72 hpf (O) and at all other time points (data not shown).</p

Autophagy in <i>tti^s450</i> larvae is not due to Tp53 activation.

<p>(A) Western blot analysis of Tp53 protein in whole cell lysates of WT <i>(lane 1)</i> and <i>tti^s450 (lane 2)</i> larvae at 96 hpf reveals up-regulation of Tp53 expression in <i>tti^s450</i>. Larvae treated with roscovotine (ROS; <i>lane 3</i>) to induce Tp53 protein expression or untreated larvae (<i>lane 4</i>) are positive and negative controls, respectively. The Actin signal provides a loading control. (B–E) Relative expression of <i>ΔN113p53</i> (B), <i>mdm2</i> (C), <i>cyclinG1</i> (D) and <i>p21</i> (E) mRNAs in WT, <i>tti^s450 (pwp2h^−/−)</i>, <i>tp53^M214K/M214K</i> (<i>tp53^−/−</i>) and <i>tti^s450;tp53^M214K/M214K</i> (<i>pwp2h^−/−;tp53^−/−</i>) larvae at 96 hpf (n = 3) demonstrates that the expression of Tp53 target genes is increased in <i>tti^s450</i> compared to WT larvae (compare first 2 bars in all graphs). The Tp53 response is diminished on the <i>tp53^M214K/M214K</i> background, as expected (compare 2^nd and 4^th bars). Data were normalised by reference to Elongation factor alpha (Elf-α) expression. (F) Western blot analysis of LC3 in whole cell lysates of <i>tp53</i>-mutant (<i>tp53^M214K/M214K</i>) and <i>tti^s450;tp53^M214K/M214K</i> larvae at 96 hpf. The elevated autophagic flux in <i>tti^s450</i> larvae due to ribosomal stress is not diminished on a <i>tp53</i>-mutant background. (G) Graphical representation of the data shown in F and two additional experiments. Bars represent the mean +/− SD (n = 3), *p&lt;0.05. (H) Transmission electron micrographs of IECs of <i>tti^s450;tp53^M214K/M214K</i> larvae at 120 hpf (<i>right panel</i>) reveal electron dense vesicles, resembling autolysosomes (<i>white arrowhead</i>), in comparable numbers to those found in <i>tti^s450</i> larvae with WT Tp53 expression (<i>left panel</i>).</p

The intestinal epithelial cells (IECS) in <i>tti^s450</i> larvae contain autophagosome- and autolysome-like structures.

<p>(A–H) Transmission electron micrographs of WT and <i>tti^s450</i> larvae at 96 hpf (A, B), 120 hpf (C–F) and 144 hpf (G, H). Sections are transverse through the yolk in the region of the intestinal bulb. WT IECs demonstrate well-developed apicobasal polarity as evidenced by basally positioned nuclei (n) and the elaboration of microvilli (mv) projecting from the apical surface into the intestinal lumen. Mitochondria (m) are abundant and plasma membranes (pm) are well defined. The intestinal epithelium in <i>tti^s450</i> is highly disorganized, with shorter and relatively sparse apical microvilli compared to WT. Vesicles resembling autophagosomes (<i>white arrowhead</i> in B) are present in the intestinal epithelial cells of <i>tti^s450</i> larvae (B′ [boxed area in B], H″ [boxed area in H]) but not in WT (A, A′ [boxed area in A] and G). At 120 hpf, electron-dense structures, likely to correspond to autolysosomes, are present in <i>tti^s450</i> larvae (<i>white arrowheads</i> in D, D′ [boxed area in D]), but not WT (C, C′ [boxed area in C]). When <i>tti^s450</i> larvae are treated with chloroquine to block the fusion of autophagosomes with lysosomes, the electron-dense structures are no longer apparent at 120 hpf; instead vesicles more typical of autophagosomes are found (<i>white arrowheads</i> in F). The boxed areas in F (F′ and F″) show vesicles containing debris, including one (white arrow in F″), with a clear double membrane. Scale bars = 10 µm (A–H) and 1 µm (all insets).</p

<i>tti^s450</i> larvae display defects in ribosome biogenesis.

<p>(A) Northern analysis of RNA isolated from WT and <i>tti^s450</i> larvae at 120 hpf using 5′ETS, ITS1, and ITS2 probes to detect precursor forms of rRNA. Elf1α is a loading control. a–d correspond to the rRNA intermediates depicted in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003279#pgen-1003279-g003" target="_blank">Figure 3B</a>. (B) Schematic diagram showing the rRNA processing pathway in zebrafish <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003279#pgen.1003279-Azuma1" target="_blank">[60]</a>. The sites of hybridization of the 5′ETS, ITS1 and ITS2 probes are indicated. (C) Representative E-Bioanalyser analysis of total RNA isolated from WT and <i>tti^s450</i> larvae at 120 hpf demonstrates a reduction in the 18S peak in <i>tti^s450</i> larvae resulting in an elevated 28S/18S rRNA ratio in <i>tti^s450</i> (D). Graphical representation of the experiment shown in C. Data are represented as mean +/− SD (n = 5). (E) Representative polysome fractionation analysis performed on WT and <i>tti^s450</i> larvae at 96 hpf demonstrates reduced levels of 40S ribosomal subunits and 80S monosomes and an increase in free 60S subunits in <i>tti^s450</i> larvae compared to WT. (F) Graphical representation of the experiment shown in E. Data are represented as mean +/− SD (n = 5) *p&lt;0.05.</p

Disrupting autophagy in <i>tti^s450</i> larvae results in the death of IECs and a reduced lifespan.

<p>(A) Western blot analysis of lysates of <i>tti^s450</i> larvae (72 hpf) that had been injected at the 1–4 cell stage with an antisense morpholino oligonucleotide (MO) targeted to the start codon of <i>atg5</i> mRNA reveals decreased levels of LC3II compared to untreated and vehicle controls, both in the presence and absence of chloroquine. Data are represented as mean +/− SD, *p&lt;0.05. (B) Survival curve of untreated WT and <i>tti^s450</i> larvae compared to WT and <i>tti^s450</i> larvae that had been injected at the 1–4 cell stage with vehicle or <i>atg5</i> MO (n&gt;85 larvae per group). The lifespan of WT embryos/larvae is completely unaffected by injection with the <i>atg5</i> MO since all three groups of WT larvae (untreated, vehicle-treated and <i>atg5</i> MO-treated) progress normally through the first 10 days of development, when the experiment was terminated. The horizontal line represents untreated WT embryos (maroon squares), vehicle-injected WT embryos (green triangles) and <i>atg5</i> MO-injected WT embryos (blue triangles). In contrast, <i>tti^s450</i> embryos respond to microinjection of the <i>atg5</i> MO by impaired survival. Whereas all untreated (yellow diamonds) or vehicle-injected (purple circles) <i>tti^s450</i> larvae are still alive at 7 dpf, all the <i>atg5</i> MO-injected <i>tti^s450</i> larvae are dead at this time-point (red squares). Indeed, 20% of the <i>atg5</i> MO-injected <i>tti^s450</i> larvae have already succumbed by 3 dpf. (C–F) TEMs of WT (C) and <i>tti^s450</i> larvae at 120 hpf (D–F), injected at the 1–4 cell stage with the <i>atg5</i>-targeted MO. Inhibiting autophagy in <i>tti^s450</i> larvae results in the appearance of detached and shrunken IECs in the intestinal lumen (black arrow in D, E and F [boxed area in D]) but has no impact on WT IECs (C). Scale bars = 10 µm.</p