Death Associated Protein Kinase (DAPK) -mediated neurodegenerative mechanisms in nematode excitotoxicity

Excitotoxicity (the toxic overstimulation of neurons by the excitatory transmitter Glutamate) is a central process in widespread neurodegenerative conditions such as brain ischemia and chronic neurological diseases. Many mechanisms have been suggested to mediate excitotoxicity, but their significance across diverse excitotoxic scenarios remains unclear. Death Associated Protein Kinase (DAPK), a critical molecular switch that controls a range of key signaling and cell death pathways, has been suggested to have an important role in excitotoxicity. However, the molecular mechanism by which DAPK exerts its effect is controversial. A few distinct mechanisms have been suggested by single (sometimes contradicting) studies, and a larger array of potential mechanisms is implicated by the extensive interactome of DAPK. Here we analyze a well-characterized model of excitotoxicity in the nematode C. elegans to show that DAPK is an important mediator of excitotoxic neurodegeneration across a large evolutionary distance. We further show that some proposed mechanisms of DAPK’s action (modulation of synaptic strength, involvement of the DANGER-related protein MAB-21, and autophagy) do not have a major role in nematode excitotoxicity. In contrast, Pin1/PINN-1 (a DAPK interaction-partner and a peptidyl-prolyl isomerase involved in chronic neurodegenerative conditions) suppresses neurodegeneration in our excitotoxicity model. Our studies highlight the prominence of DAPK and Pin1/PINN-1 as conserved mediators of cell death processes in diverse scenarios of neurodegeneration.


Background
Excitotoxicity is a neurodegenerative process believed to be the central mediator of brain damage in acute conditions such as brain ischemia and traumatic injury, and an important contributor to a range of chronic neurodegenerative diseases [1][2][3][4]. In excitotoxicity, the malfunction of Glutamate (Glu) Transporters (GluTs) [5][6][7] causes accumulation of Glu in excitatory synapses and exaggerated stimulation of postsynaptic Glu receptors (GluRs) [8]. The excessive influx of ions (especially Ca 2+ ) into the postsynaptic neurons leads to their cell death via a spectrum of mechanisms that range from necrosis (at the core of the ischemic damage) to apoptosis or even recovery (at the penumbra). Despite our familiarity with the first few steps in excitotoxicity, our understanding of the steps following Ca 2+ influx is very limited. Clinical trials using GluRs antagonists ended with disappointment, and recent data suggests that using antagonists to block GluR functions might be counterproductive, because Glu signaling includes both neurotoxic and pro-survival cascades [9,10]. These complications emphasize the need to illuminate cell-deathspecific signaling cascades in excitotoxicity downstream of GluRs. A considerable number of such excitotoxic mechanisms have been suggested, but in many cases the data that supports a given suggestion is limited to specific excitotoxic paradigms.
One suggested mediator of excitotoxicity implicated in multiple experimental setups is the CaM-dependent Death Associated Protein Kinase (DAPK) [11][12][13][14]. Originally identified by an unbiased screen for mediators of interferon-induced cell death [15], DAPK was later recognized as a molecular switch that controls the choice between cell death processes such as apoptosis and autophagy [16,17]. Moreover, an elaborate web of biochemical interactions and functional connections has been revealed, placing DAPK in a key position at the center of many critical signaling cascades [11,18]. A considerable body of evidence suggests that DAPK also contributes to cell death in excitotoxicity [19], and its inhibition reduces neuronal loss in models of brain ischemia [20]. Several mechanisms have been suggested to explain DAPK's involvement in excitotoxicity, but the issue remains controversial. One possible mechanism involves DAPK's regulation of autophagy [17], a process that modulates some neurodegenerative conditions [21]. Alternatively, an intriguing study suggests the involvement of DANGER, a protein that contains a region of homology to the nematode protein MAB-21 and functions as a regulator of the IP 3 R [22]. Indeed DANGER was found to also interact with and inhibit the activity of DAPK [23]. The most cited suggestion in the field attributes the involvement of DAPK in excitotoxicity to the potentiation of Ca 2+ currents through NR2B/GluN2B subunit-containing complexes of the NMDA-receptor (NMDA-Rs) family of GluRs [24]. This suggestion fits well with a proposed leading role for extrasynaptic NR2B/GluN2B -containing NMDA-Rs in excitotoxicity [25]. However, recently the proposed unique significance of NR2B/GluN2B -containing extrasynaptic NMDA-Rs in excitotoxicity has been brought into question [26][27][28]. Moreover, an earlier study suggests that in some mammalian neurons DAPK knockout provides protection from excitotoxicity that is not dependent on NMDA-Rs [29]. Indeed, some cases of excitotoxicity are mediated by another family of GluRs, the Ca 2+ -Permeable AMPA Receptors (CPARs) [30][31][32]. These observations suggest that if DAPK is widely involved in excitotoxicity, including in cases where NR2B/GluN2B is not a main determinant of neurodegeneration, it might act through additional mechanisms to exert its effect.
We hypothesize that many signaling cascades might be involved in specific cases of excitotoxicity, depending on the exact scenario being used to induce it. However, the key features that constitute the core of the excitotoxic process might be conserved across differences in cell death scenarios and large evolutionary distances, as is the case in apoptosis [33,34] and autophagy [35,36]. We therefore set out to study the role of DAPK in excitotoxicity in our model of CPAR-mediated neurodegeneration in C. elegans [37], where GluR-dependent necrosis of central neurons postsynaptic to Glu connections is triggered by knockout (ko) of the GluT gene glt-3 [38] in a sensitized background (nuIs5 [39]). Indeed, this model has proven effective in identifying core processes that are conserved between nematode and mammalian excitotoxicity [37,40,41]. DAPK is particularly well conserved in C. elegans (in 52% sequence homology, presenting all of DAPK's functional domains, and in its involvement in a number of signaling cascades [42][43][44]). The nematode DAPK-1 is widely expressed (including in neurons [42]), allowing us to test its involvement in nematode excitotoxicity and to study its mechanism of action. In this study we establish the central role of DAPK in Glu-triggered neurodegeneration in C. elegans, suggesting that its function is conserved across evolution and excitotoxic scenarios. We find little or no support for the views that DAPK's regulation of excitotoxicity is mediated through the modulation of synaptic strength, MAB-21, or autophagy. Instead, we identify PINN-1, the nematode homolog of the DAPK-interaction-partner and phosphorylation-dependent peptidyl-prolyl isomerase Pin1, as an important factor in nematode excitotoxicity.

DAPK-1 has a central role in nematode excitotoxicity
To test the involvement of DAPK in nematode excitotoxicity we combined our excitotoxicity strain (glt-3;nuIs5) with a deletion allele of the nematode homolog of DAPK, dapk-1(gk219), a gene knockout that was used to confirm the effect of the (ubiquitously expressed) nematode DAPK in autophagy and innate immunity [42,45]. In our previously described model of neurodegeneration we use the sensitizing transgenic modification nuIs5, where hyperactive Gαs and GFP are expressed under the glr-1 promoter in~30 neurons [39] and cause GluR-independent stochastic degeneration of~1 of these at-risk neurons per animal. When we add the KO of the GluT gene glt-3 we observe that more of these at-risk neurons degenerate [37]. The GluT-KO-triggered exacerbated necrosis in glt-3;nuIs5 is GluR-dependent, and therefore qualifies as nematode excitotoxicity. Nematode excitotoxicity causes neuronal swelling and death that is manifested with characteristic kinetics as gradually and stochastically appearing vacuole-like structures in some of the at-risk postsynaptic neurons. These vacuole-like structures become more abundant during larval development as the Glu signaling system matures (usually reaching up to~4.5 head neurons/animal at L3), and then decline due to removal of cell corpses by engulfment [37]. We now observe that adding dapk-1 ko to this excitotoxicity strain causes a strong and statistically significant suppression of neurodegeneration throughout development ( Figure 1A, an additional independent cross gave very similar results, not shown). To further confirm the contribution of dapk-1 to nematode excitotoxicity, we overexpressed the wt dapk-1 cDNA from an extra-chromosomal transgenic construct under a heat-shock promoter [42]. Since heat-shock might affect susceptibility to neurodegeneration, we took special care to compare an exact match of treated animals, without or with the dapk-1 overexpression transgene. To that end we took advantage of the fact that the random and partial segregation of the non-integrated overexpression construct allows us to compare transgenic and non-transgenic animals on the same plate exposed to the same conditions. We observed that dapk-1 overexpression resulted in a strong and statistically significant potentiation of necrotic neurodegeneration in postsynaptic neurons in all developmental stages ( Figure 1B). Together, our data indicate that DAPK is an important mediator of excitotoxicity in C. elegans, suggesting that diverse scenarios of excitotoxicity share a common mechanism that assigns a central role to DAPK.
dapk-1 ko does not alter presynaptic release or postsynaptic Glu response We used two main guidelines in trying to track the mechanism by which dapk-1 regulates excitotoxic neurodegeneration in the nematode: 1) we looked at previous reports suggesting specific mechanisms for DAPK's involvement in mammalian excitotoxicity; 2) we inferred from the general map of DAPK's connectome in other cell processes [18] which additional proteins are plausible candidates for mediating DAPK's effect in nematode excitotoxicity. One line of evidence suggests that DAPK interacts with, and may regulate the function of, Syntaxin 1A [46]. Syntaxin is part of the general mechanism of vesicular neurotransmitter release, a mechanism that is shared among all neurotransmitters [47]. Therefore, an effect of dapk-1 ko on any component of the synaptic vesicle release could lead to DAPK-mediated changes in excitotoxicity levels. However, given the ubiquitous expression of this gene, such an effect of DAPK on the common synaptic vesicle release mechanism will affect the dynamics of neurotransmitter release in all synapses. The study of synaptic vesicle release is very well developed in the nematode, and aldicarb is routinely used in C. elegans to identify mutations that cause even modest changes to the general synaptic release mechanism [48]. As aldicarb suppresses the degradation of Acetylcholine in the neuro-muscular junction, it causes animal paralysis with a typical dynamics. Mutations that reduce the activity of the general, common vesicle release mechanism (such as rab-3 [48]) cause a pronounced resistance to aldicarb (shifting the time-dependent paralysis curve to the right, Figure 2A), while mutations that enhance synaptic release (such as the ko of cpx-1, which encodes the synaptic vesicle release regulator complexin [49]) cause increased sensitivity to aldicarb (shifting the paralysis curve to the left, Figure 2A). We observed that the sensitivity of dapk-1 animals to aldicarb is indistinguishable from that of WT animals, suggesting that dapk-1 ko does not modify the synaptic release mechanism, as would have been expected of an effect on syntaxin ( Figure 2A).
We next asked if DAPK modifies the extent of postsynaptic response in the glutamatergic synapses where excitotoxicity occurs (as reported in mammals, where DAPK was suggested to modify synaptic strength [24]). Two behavioral assays have proven very effective in detecting even small changes in the activity level of glutamatergic A) Dynamics of neurodegeneration in nematode excitotoxicity during development (using the glt-3;nuIs5 excitotoxicity model). dapk-1 ko mutation suppresses neurodegeneration in all developmental stages, but does not bring it down to background levels. B) Overexpression of wt dapk-1 from a heat-shock promoter enhances neurodegeneration compared to matched controls. In all bar graphs, error bars represent SE. Statistical significance is calculated using z score. *p < 0.05; ***p < 0.01. synapses in C. elegans. These are the Nose Touch (NOT) assay, and the duration of spontaneous forward mobility assay. Therefore, if dapk-1 ko causes changes in the specific Glu packaging mechanism in synaptic vesicles (e.g., by affecting vGluTs), or changes the number or activity-level of GluRs in the synapse, this should be reflected in behavioral changes in these assays. In the particular case of dapk-1, a secondary phenotype of this mutation, namely overgrowth of cuticle on the animal's nose [42], makes the nose-touch assay less informative. However, the duration of spontaneous forward mobility depends on the internal balance between forward and backward circuits, and should not be affected by the cuticle aberration. This assay is very reliable in detecting both under-activity and over-activity of the relevant Glu synapses [50][51][52], allowing us to use it as a proxy measure for Glu synaptic strength. We did not observe any changes in spontaneous mobility triggered by dapk-1 ko, either in WT background or in the background of each of the two components (glt-3 or nuIs5) used in our excitotoxicity model to trigger the intensified Glu signaling ( Figure 2B). These observations suggest that dapk-1 has no strong effect on synaptic release or the overall strength of signaling in Glu synapses in C. elegans. Figure 2 The effect of dapk-1 does not correlate with several proposed mechanisms. A) Aldicarb assay measures the overall activity of the common mechanism of synaptic vesicle release. Complexin (cpx-1) mutant is used as example of an oversensitive mutant (where synaptic release is exaggerate), while rab-3 serves as an example of aldicarb resistant mutant (where synaptic release is abnormally low). dapk-1 mutants do not show oversensitivity or resistance, suggesting their level of synaptic release is roughly normal. B) Duration of forward runs during spontaneous mobility is a sensitive reporter of the overall strength of Glu synapses that control this parameter. Even small changes in the activity or number of GluRs typically modify this behavior. dapk-1 mutants are not different from normal counterparts in either a WT background, in an excessive Glu stimulation background (glt-3), or in the sensitized background (nuIs5) used in our excitotoxicity model. These three conditions by themselves do not cause excessive command neuron loss, a loss that might otherwise render the assay uninformative as it is suppressible by dapk-1. C) A mutation in the gene encoding the DANGER-related protein MAB-21 does not affect nematode excitotoxicity. D) A mutation in the gene encoding the nematode homolog of CaMKK does not affect nematode excitotoxicity.
The DANGER-related protein MAB-21 and the CaMKK CKK-1 do not exert strong regulation of nematode excitotoxicity The characterization of DAPK as a CaM-dependent kinase is particularly intriguing to us, since Ca 2+ signaling is critical to excitotoxicity in both mammals and nematodes. We therefore examined DAPK-partners that might also be involved in Ca 2+ signaling. DANGER is a mammalian DAPK inhibitor that regulates Ca 2+ release from the ER [22,23]. There is no direct, full-length homolog of DANGER in the worm genome, but the core of the mammalian protein is thought to be homologous to the nematode protein MAB-21 [53]. It is therefore reasonable to assume that mab-21 will be essential to the role of a hypothetic DANGER-like complex in C. elegans. However, a mutation in mab-21 had no effect on nematode excitotoxicity ( Figure 2C). Another important protein that binds mammalian DAPK and is involved in Ca 2+ signaling is CaMKK. However, again, a mutation in the only CaMKK gene in the worm, ckk-1 [54], had no effect on excitotoxicity ( Figure 2D). These results suggest that these two putative Ca 2+ signaling regulators and DAPK-interactionpartners do not have a large contribution to nematode excitotoxicity.
We also considered the many other proteins that are known to interact with DAPK [18] as possible modulators of excitotoxicity, but we could not assign to many of them high priority because either there was no immediate obvious connection to neurodegeneration (e.g., tropomyosin), there is no clear nematode homolog (e.g., NFκB), the nematode homolog is not known to be active in C. elegans neurons (e.g., p53), or the process in which this protein is involved has been shown by us to be not involved in nematode excitotoxicity (e.g., apoptosis [41]). However, DAPK is also known to interact with Beclin1, a key regulator of the evolutionary conserved process of autophagy, suggesting that autophagy-mediated cell death could potentially be an avenue for DAPK to regulate nematode excitotoxicity.

Autophagy has a minor role in nematode excitotoxicity
The interaction between mammalian DAPK and Beclin1 is considered a major avenue for DAPK's ability to regulate autophagy [11,16,17,55]. Autophagy has been suggested to be an important factor in some neurodegenerative conditions [21,56,57], and has also been shown to be a major contributor to degenerin-mediated neurodegeneration in the nematode [58][59][60] (where necrotic neurodegeneration is triggered by a constitutively open channel of the DEG/ ENaC family [61]). Moreover, dapk-1 regulates autophagy in C. elegans [43]. We therefore set out to determine the role of autophagy in nematode excitotoxicity, using some of the same reagents used to demonstrate autophagy's role in degenerin-induced neurodegeneration in the worm [58,60,62]. One such reagent is the red fluorescent labeled LC3 -homolog LGG-1 (originally created by the Tavernarakis lab [62], for the current study assigned the strain name IMN21). This reporter indicates elevated autophagy by both the appearance of intracellular puncta and by an overall increase in cellular fluorescence. We crossed IMN21 with our excitotoxicity strain glt-3;nuIs5. Since the red fluorescence can appear in any body cell that triggers autophagy, we used the P glr-1 ::GFP marker expressed in our excitotoxicity strains to focus our attention on the postsynaptic neurons that are at risk for neurodegeneration. If autophagy is a strong component of excitotoxicity, we would expect at-risk neurons (labeled with GFP) to express autophagy marker (DsRed) upon exposure to high concentrations of Glu (triggered by the glt-3 ko). We counted the number of at-risk neurons that show LGG-1 puncta and measured the overall intensity of DsRed::LGG-1 signal in these neurons. Since autophagy was reported to have a role in the low-level neurodegeneration caused by nuIs5 alone [60], we concentrated on the added effect of excitotoxicity by comparing DsRed::LGG-1 signals in animals that express only the sensitizing construct nuIs5 to those of animals in which neurons are subjected to the full excitotoxic insult (glt-3;nuIs5). We found that excitotoxicity resulted in only a small and statistically-insignificant increase in LGG-1 puncta, and no change in overall LGG-1 intensity in at-risk neurons ( Figure 3A and B).
To further study the possible involvement of autophagy in nematode excitotoxicity we examined the effect of inhibiting autophagy by genetic and chemical means. While a number of mutations and drugs have been used in the past, not all of them are available to us here. For example, bec-1 ko was previously used to monitor the requirement of this autophagy regulator for mec-4(d) -induced necrosis in early development [58]. However, the lethal effect of this mutation in later development, when most of the nematode excitotoxic necrosis occurs, prevents us from using this approach. Similarly, the vacuolar-type ATPase inhibitor bafilomycin is commonly used to block autophagy by elevating lysosomal pH [63]. However, the same V-ATPase is used in neurons to acidify synaptic vesicles as a means to provide the driving force for neurotransmitter loading [64][65][66], and therefore using bafilomycin can be expected to reduce neurotransmitter release. We therefore turned to use other means of intervention that are more compatible with our system: a mutation in the autophagy regulator unc-51 (using the e369 allele) and the chemical inhibitor 3MA (both used previously to show that degenerin-triggered neurodegeneration in C. elegans depends strongly on autophagy [58,60]). We noticed only a moderate effect for these two factors, evident in some developmental stages ( Figure 4A and B). Such a moderate effect is in line with the reported effect of unc-51 on nuIs5 alone [60] (see discussion). We then used an independent set of experiments and epistasis analysis to determine if this moderate effect works independently of dapk-1 or in the same pathway. We noticed that the effect of blocking autophagy on the extent of excitotoxicity is reproducible only in one developmental stage (L3). Trying to determine if dapk-1 and 3MA work in the same pathway, we compared their observed combined effect (in the dapk-1 + 3MA combination) to the calculated expected effect if these two processes were completely independent. However, given the moderate size of the 3MA effect and the inherent variability in our experiments, it is currently difficult to determine if dapk-1 and autophagy work in the same pathway or independently. Nonetheless, the fact that the effect of autophagy is much more limited in size and duration than that of dapk-1 supported a continued search for other mechanisms by which dapk-1 might regulate excitotoxicity.
The DAPK interaction-partner and phosphorylationdependent peptidyl-prolyl isomerase Pin1/PINN-1 is a conserved suppressor of neurodegeneration Pin1 is an isomerase that changes the conformation of proline residues located next to phosphorylated Ser or Thr residues, thus changing overall protein conformation and controlling the activity of many phosphoproteins [67,68]. In recent years this protein has gained recognition as a major regulator of many signaling cascades, involved in both normal cell physiology, pathology, and in neurodegenerative diseases [67,[69][70][71]. Pin1 is expressed in dendrites, its activity is modulated by Glu signaling, and it regulates PKCζ and PKMζ [72,73]. Pin1 is also known for its regulation of neuronal cytoskeleton and Tau protein phosphorylation, and for modulating neurodegeneration [69,74,75]. Recently, Pin1 was shown to functionally interact with DAPK [76]. We find that pinn-1 ko [77] causes increased neurodegeneration in nematode excitotoxicity ( Figure 5). Like dapk-1 ko, the effect of pinn-1 ko is seen in all developmental stages ( Figure 5A), and does not seem to involve a change in Glu synaptic strength ( Figure 5B and C), suggesting that they influence cell-death processes subsequent to-(and not at the level of-) GluR.
We wished to confirm that the effects of dapk-1 and pinn-1 on the dynamics of vacuolar appearance (as seen in Figures 1A and 5A) translate to ultimate survival of specific neurons in adult animals. Given the stochastic nature of neurodegeneration in glt-3;nuIs5 animals, it is usually difficult to identify which of the~30 at-risk head neurons are degenerating in different animals. To circumvent this difficulty, we address the survival of specific neurons by focusing on the easily identifiable RIG neurons. The RIG neurons are part of the group of atrisk head neurons, they show only very minor levels of neurodegeneration in nuIs5 alone, and they are sensitive to all the treatments that modify total head neuron degeneration analyzed in our previous studies [37,40,41]. Indeed, RIG neurons exhibit inverse correlation between the number of vacuole-like structures they show during development (as observed by Nomarski) and the number of GFP-labeled RIG neurons surviving in the adult [37]. We now confirm that the number of degenerating RIG neurons during development is reduced by dapk-1 ko and increased by pinn-1 ko (data not shown). Importantly, we find that the number of GFP-labeled RIG neurons that survive to adulthood is increased by dapk-1 ko and decreased by pinn-1 ko ( Figure 6B). These observations suggest that the effects of dapk-1 and pinn-1 on vacuolar appearance during development indeed translate to changes in ultimate survival of identified neurons.
Finally, we wanted to determine if dapk-1 (where a KO causes decreased neurodegeneration) and pinn-1 (where a KO causes increased neurodegeneration) work in the same or separate pathways. Mammalian studies suggest that DAPK is acting upstream of Pin1 to inhibit its function [76], so that KO of pinn-1 could be expected to exert its death-stimulating effect regardless of whether dapk-1 is present or not. Instead, using epistasis analysis ( Figure 6A), we observe that the double knockout dapk-1 ; pinn-1 exhibited suppression of excitotoxicity. We tried to further determine if the effect of dapk-1; pinn-1 double knockout reflects an intermediate outcome (in line with Figure 4 Treatments that block autophagy (and dramatically reduce neurodegeneration in other forms of necrotic neurodegeneration in C. elegans) have a reproducible but small effect in nematode excitotoxicity. A) A mutation in unc-51 shows a moderate effect on nematode excitotoxicity. *p < 0.05 ; ***p < 0.01 B) Treatment with the autophagy-blocking drug 3MA has a moderate effect on nematode excitotoxicity. ***p < 0.01 C) Independent repetition of the experiment shown in B with the addition of epistasis analysis. The data shows that the only reproducible effect of autophagy blockade is in L3. Although at this stage the combined effect of autophagy blockade and dapk-1 correlates with a model of independent action of these two factors, the moderate extent of effects limits the strength of such a conclusion. an independent, parallel effect of these two factors) or a dapk-1 ko -only-like outcome (in line with an obligatory sequential effect, where the dapk-1 mutation-induced decrease in neurodegeneration completely masks the ability of pinn-1 mutation to increase neurodegeneration). To that end we calculated what would be the effect of these two factors acting in parallel, to predict their cumulative independent effect ( Figure 6A). Unfortunately, the small difference between the observed effect of dapk-1 alone and the calculated independent cumulative effects of dapk-1 and pinn-1, together with the variability in our data, do not allow us to discriminate with confidence between these two options. We therefore limit our conclusion to say that dapk-1 acts either downstream or in parallel to-(but not upstream of-) pinn-1 in nematode excitotoxicity.

Discussion
Mammalian studies have generated a plethora of proposed mechanisms in excitotoxicity, and some of these studies include suggested pathways for the involvement of DAPK in critical cell death events. However, the significance of these proposed mechanisms across divergent excitotoxic conditions remains unclear. In our study we focused on a glutamate-dependent neuronal death in C. elegans and examined a set of candidate mechanisms to define those that might be conserved through a large evolutionary distance. We previously found that some core constitutes of excitotoxicity are well conserved in our nematode model of GluT KOtriggered and CPAR-mediated neuronal necrosis. These include both death-promoting factors (such as release of Ca 2+ from the ER [37]), and neuroprotective factors (such as cell stress resistance to insults, resistance that is conferred by FoxO/DAF-16 [40,41]). We now report that DAPK is also a highly conserved regulator of excitotoxicity ( Figure 1A and B), though we note that dapk-1 ko does not bring neurodegeneration all the way down to background levels. We find no evidence for dapk-1mediated regulation of synaptic strength, as defined by the spontaneous mobility assay ( Figure 2B), suggesting that the effect of DAPK on mammalian NR2B/GluN2B, though probably very important, does not extend to all forms of excitotoxicity. We also found no role for the DANGER-related protein MAB-21 in nematode excitotoxicity (though DANGER is a much larger protein than MAB-21, suggesting it might have additional functions not tested here).
Although dapk-1 is an important regulator of autophagy in C. elegans, we find only a minor role for autophagy in the neurodegenerative condition we study in glt-3;nuIs5 animals. We find that blocking autophagy has a relatively small neurodegeneration-reducing effect (~0.5-1 dying neuron/animal, Figure 4). This effect is smaller than the neurodegeneration-suppressing effect of dapk-1 ko (a decrease of~2.5 dying neurons/animal, three independent isolates counted in Figures 1A, 4C, and 6A). Therefore, even if related, autophagy cannot account for the majority of DAPK's effect in glt-3;nuIs5 animals. The minor effect of autophagy on neurodegeneration in glt-3;nuIs5 is in sharp contrast to the major effect that autophagy has on degenerin-mediated neurodegeneration, where it suppresses neurodegeneration by 75-90% [60]. We further note that these previous studies have demonstrated that blocking autophagy decreases the extent of low-level neurodegeneration triggered by nuIs5 alone [60]. Since neurodegeneration by nuIs5 alone (independent of excitotoxicity) is part of the total number of degenerating neurons we count in our assay (accounting for~1 dying neuron/animal [37]), the small effect of autophagy seen in the current study can be attributed to its documented effect of nuIs5 alone. Indeed, we see no significant difference in labeling of fluorescent autophagy reporter when comparing nuIs5 to glt-3;nuIs5 animals ( Figure 3). The results of epistasis analysis are not conclusive, but put together with the difference in size and timing of the effects of dapk-1 and autophagy on nematode excitotoxicity, our observations cause us Figure 6 dapk-1 might cooperate with pinn-1 to regulate nematode excitotoxicity. A) Epistasis analysis testing the involvement of dapk-1 and pinn-1 in nematode excitotoxicity. Since the combined mutant shows strong suppression of neurodegeneration compared to the starting strain, these observations strongly suggest that pinn-1 is not downstream of dapk-1 (though the data is not conclusive enough to choose between the possibilities of pinn-1 acting upstream or independently of dapk-1). B) Verification that the effects of dapk-1 and pinn-1 mutations on the dynamics of overall neurodegeneration in head neurons translates to survival of identified neurons in the adult (counting surviving GFP-labeled RIG neurons in young adult animals). C) One of the likely models that can account for our observations on the role of DAPK-1, PINN-1, and autophagy in nematode excitotoxicity. to favor one of the possible models in which autophagy has only a minor role in nematode excitotoxicity in parallel to the role of DAPK-1 ( Figure 6C). We emphasize that the parallel action of DAPK and autophagy is preferred by us in the specific scenario of nematode excitotoxic stress, while other stresses might include DAPK and autophagy in other pathway configurations.
The observation that the DAPK-interaction-partner Pin1/PINN-1 is a significant regulator of excitotoxicity is particularly intriguing and novel. In addition to its involvement in cancer [71] and stress response [78], Pin1 has been shown to be a critical regulator of dendritic Glu responses [72,73] and of neurodegeneration in Alzheimer disease [69,74,75]. The results of our epistasis analysis do not seem to support a role for Pin1/PINN-1 as an obligatory step downstream of DAPK/DAPK-1, as might be inferred from mammalian cancer studies [76]. Instead, our data supports that PINN-1 acts in parallel or upstream of DAPK-1 ( Figure 6A and C).

Conclusions
Put together, our study suggests that nematode excitotoxicity can be an important tool to sift through many proposed mechanisms of excitotoxicity, allowing us to identify conserved mechanisms that might be at the core of neurodegenerative processes common across divergent excitotoxic scenarios. Furthermore, our studies now illuminate DAPK/DAPK-1 and Pin1/PINN-1 as two such factors, important for excitotoxicity mechanisms across a large evolutionary distance. We can now further use this system to decipher DAPK-1 and PINN-1 -related mechanisms in nematode excitotoxicity, with the hope that such understanding might help us to continue uncovering conserved core mechanisms in this important form of neurodegeneration.

Neurodegeneration analysis
The level of necrotic neurodegeneration in head neurons was monitored using an inverted scope and Nomarski Differential Interference Contrast (DIC). Animals with no anesthetics were examined on a fresh chunk of agar of nematode culture flipped upside down over a slide. Swollen "vacuolated-looking" cells located in the area of the nerve ring were counted as head neurons undergoing necrosis, as described previously [37,41]. Briefly, we use freshly growing mixed-stage animals, and we record the developmental stage and the number of "vacuolated" dying neurons of each animal that we see while scanning through the agar chunk, thus creating a "snap-shot" of the transitory number of dying neurons exhibited by the population of animals at the time of analysis. As mentioned above, in the excitotoxicity strain the number of "vacuolated" cells observed at each developmental stage typically goes up until L3 (with the maturation of Glu signaling in the worm), and then declines with the engulfment of cell copses. This analysis is repeated several times, with several isolates of each strain. For confirmation of suspected effects in new mutant combinations, a representative part of the analysis is done blindly by independent observers. Similar numbers of control and test animals are recorded in each session. Records from all these sessions is pooled together to calculate average neurodegeneration from large number of animals in each strain and each stage  in each data bar). We occasionally confirmed these dying neurons as neurons postsynaptic to Glu connections by verifying their labeling with the GFP coexpressed in nuIs5 animals under the glr-1 promoter. For heat-shock-induced overexpression of DAPK-1, animals carrying [P hsp16 ::DAPK-1; P ttx-3 ::RFP] were placed in a 35°C incubator for 2 hours to induce activation of heat shock promoter, left to rest for about 30 minutes and scored regularly for two days for the extent of swollen degenerating neurons (protocol & strains coordinated with the Chisholm group, UCSD [42]). Experimental animals (animals with extrachromosomal array) and control animals (animals lacking extrachromosomal array) were obtained, identified and scored on the same day from the same pool of heat-shocked animals. For epistasis analysis between given excitotoxicity-modifying mutations X and Y, we calculated the effect of each mutation for each developmental stage as: Fold effect of X = (the average number of dying head neuron in the excitotoxicity strain in the presence of mutation X)/(the average number of dying head neuron in the starting excitotoxicity strain), with a similar calculation for mutation Y. The expected cumulative fold effect of mutations X and Y when working independently in parallel pathways is (fold effect of X) * (fold effect of Y). The calculated expected number of dying neurons presented on the graphs in Figures 4 and 6 is (the average number of dying head neuron in the starting excitotoxicity strain) * (fold effect of X) * (fold effect of Y). Error bars represent SE. Statistical significance of difference between control groups and experimental groups was analyzed using z-test score (as the significance of these differences is calculated for large populations of~100 animals in each group).

Fluorescence microscopy analysis of autophagy
Animals carrying Ex [P lgg-1 :: DsRed:: LGG-1; P myo-2 :: GFP]; glt-3(bz34) IV; nuIs5 V and Ex [P lgg-1 :: DsRed:: LGG-1; P myo-2 :: GFP]; nuIs5 V were analyzed for the extent to which glr-1 expressing command interneuron (labeled with GFP) were undergoing autophagy (i.e., show DsRed punca or increased DsRed intensity). Animals were mounted on a 2% agar pad. To compare average DsRed intensity between worms we identified the cell with the highest DsRed intensity as 100% and then compared the other neurons to this cell (following the procedure used by the Tavernarakis lab, who developed this DsRed::LGG-1 marker [62]). A few cells were analyzed in each animal and the average intensity from a total from 20-25 animals was calculated. We also counted the average of the number of green-labeled neurons showing DsRed puncta as another indication of neurons undergoing autophagy and compared control (nuIs5 only) versus experimental (glt-3; nuIs5) groups.

Behavioral assays
Behavioral assays on nematode locomotion and worm paralysis were performed blindly following standard methods of behavioral analysis. For duration of Gluregulated spontaneous forward mobility we followed the protocol of the Maricq group (U Utah) [79]. We did not measure mobility in strains that show excitotoxic neurodegeneration because the degeneration or rescue of command interneurons can change the results of this assay. For aldicarb assays we followed the Nonet lab protocol (Washington U) [48]. Briefly, we soaked worm plates with aldicarb to a final concentration of 0.5 mM and added food. We placed~30 freshly growing young adult animal onto these plates. The percentages of paralyzed worms were recorded every 15 minutes for a period of 2 hours.