Programmed cell death (PCD) is a fundamentally important process delicately coordinated throughout an organism’s life cycle. In plants, PCD is an integral part of development, reproduction, and pathogenesis. Numerous types of proteins are involved in regulation of PCD in plants, like phosphatases, metacaspases, and protein kinases. In tomato resistance to the pathogen Pseudomonas syringae pv. tomato (Pst), a Ser/Thr protein kinase, Adi3 (AvrPto-dependent Pto-interacting protein 3), interacts with the pathogen’s avirulence protein AvrPto and the tomato resistance protein Pto. Adi3 is a member of the AGC protein kinase family, a group known to transmit signals via the secondary messengers cAMP, cGMP, and phospholipids. In an unchallenged system, the master regulator of AGC kinases, Pdk1, activates Adi3. Activation of Adi3 enables nuclear localization and cell death suppression – all of which is prevented when challenged by Pst. A BLAST_p search of the Arabidopsis thaliania genome with the amino acid sequence of Adi3 identified a 67% identical match, AGC1-3. Like Adi3, AGC1-3 at its activation-loop serine and another site, by Pdk1. With N-terminal deletions of AGC1-3, Pdk1 was found to phosphorylate AGC1-3 at two serines – one serine conserved among all Arabidopsis AGC kinases, the other a serine on the N-terminus of the kinase domain. The non-activation loop serine in AGC1-3, Ser269, is conserved at Ser212, in Adi3. Phosphorylation at Ser212 does not impact auto-catalytic activity of Adi3. However it does enhance trans-catalytic activity. Analysis of AGC1-4 and AGC1-7, two proteins closely related to AGC1-3, reveals that phosphorylation of non-activation loop residues by Pdk1 is not restricted to AGC1-3 and Adi3. Functional analysis of AGC1-3 in Arabidopsis protoplasts revealed that like Adi3, nuclear localization and activation-loop phosphorylation are essential for cell viability. In an effort to elucidate a signaling network controlled by AGC1-3, the KiC (Kinase-client) assay was employed. In the KiC assay, a 2,100-member peptide library was assayed against AGC1-3 and the constitutively active mutant AGC1-3^(S596D). By MS analysis, AGC1-3 and AGC1-3(S596D) phosphorylated 26 and 19 substrate peptides, respectively. Substrate peptides were mapped to proteins involved in central metabolism, transcription, and protein metabolism. The work presented in this dissertation provides conclusive evidence that Pdk1 phosphorylates AGC1-3 and Adi3 at a non-activation loop residue. The work also supports AGC1-3 as the Arabidopsis homologue of Adi3 and presents novel phosphorylation data of potential AGC1-3 substrates.

Programmed cell death (PCD) is an active process by which organisms coordinate the controlled destruction of cells. In tomato, the protein kinase Adi3 (AvrPto-dependent Pto-interacting kinase 3), acts as a negative regulator of PCD and shares important functional homologies with the mammalian anti-apoptotic AGC kinase PBK/Akt. Adi3 was originally identified as an interactor of the complex formed by the tomato resistance protein Pto and the Pseudomonas syringae pv. tomato (Pst) effector protein AvrPto. The complex formed by AvrPto and Pto causes a resistance response characterized by a rapid form of PCD that limits the spread of Pst and prevents the onset of the tomato bacterial speck disease. In an effort to characterize the mechanisms by which Adi3 regulates PCD, we identified Adi3 interacting partners in a Y2H screen. Here, I describe the interaction of Adi3 with two interacting partners identified: the Sucrose Non-fermenting (SNF1) kinase complex (SnRK) which is a eukaryotic master regulator of energy homeostasis and the E3 RING Ubiquitin ligase AdBiL. Using a combination of in vitro and in vivo approaches I found that AdBiL is an active ubiquitin ligase that ubiquitinates Adi3. Interestingly, Adi3 was found to be degraded in a proteasome-dependent manner suggesting ubiquitination could play a role in its degradation. On the other hand, Adi3 was found to inhibit the SnRK complex by directly interacting with its catalytic subunit as well as by phosphorylating the regulatory subunit SlGal83 at Ser26. SlGal83 is phosphorylated at multiple sites in vivo, and this phosphorylation state, as well as its intracellular localization was found to depend on a myristoylation signal present at its N-terminus. Phosphorylation at Ser26 by Adi3 was found to alter the localization of this subunit in a myristoylation-dependent manner. The interactions studied in this dissertation provide additional evidence on the functional homologies shared by Adi3 and PKB. In addition, the regulatory control of SnRK activity and cellular localization offers a novel connection between pathways involved in energy homeostasis and pathogen-mediated PCD.

Autophagy is a process by which cells re-cycle organelles and macromolecular proteins during cellular stress. Defects in the regulation of autophagy have been associated with various human pathologies including heart failure. In the heart tumor suppressor p53 protein is known to promote apoptotic and autophagic cell death. We found p53 over-expression increased endogenous protein level of the hypoxia-inducible Bcl-2 death gene Bnip3 which leads to loss of mitochondrial membrane potential (ΔΨm). This was accompanied by autophagic flux and cell death. Conversely, loss of function of Bnip3 in cardiac myocytes or Bnip3-/- mouse embryonic fibroblasts prevented mitochondrial targeting of p53 and autophagic cell death. These data provide the first evidence for the dual regulation of autophagic cell death of cardiac myocytes by p53 that is mutually dependent on Bnip3 activation. Hence, our findings may explain how autophagy and cell death are dually regulated during cardiac stress conditions where p53 is activated.

During Drosophila melanogaster pupation, groups of undifferentiated adult cells proliferate and undergo regulated cell shape changes, while larval tissues are eliminated by programmed cell death (PCD). PCD is most commonly associated with apoptosis; however, a growing body of evidence suggests that autophagic cell death represents an alternative form of PCD. In some contexts autophagy can induce caspase-dependent PCD, but the regulatory pathways that link autophagy and apoptosis remain poorly understood. The overexpression of Atg16B induces autophagy-dependent caspase activation in the larval epidermis, and presumptive adult tissues. Also, the overexpression of Atg16B, in tissues specified by pnrGAL4, results in an adult cuticular phenotype that cannot be directly attributed to caspase activity. However, altering the level of Atg16B expression can modulate the adult cuticular phenotype. Therefore, the adult cuticular phenotype was used in a broad based genome-wide screen for dose-dependent modifiers of the regulation of autophagy. To date, 399 chromosomal deficiencies, representing approximately 92% of the 2nd and 3rd chromosomes, and 25 duplications have been tested. Consequently, 42 deficiencies have been identified as dominant enhancers of the Atg16B overexpression phenotype, 24 deficiencies have been identified as dominant modifiers, and 13 deficiencies have been identified as dominant suppressors. Further genetic analysis of these interacting deficiencies was carried out to initiate the process of identifying individual loci associated with the dose-sensitive modification of the Atg16B overexpression phenotype. It is hoped that the identification of these genes will elucidate the genetic pathways regulating autophagy and the autophagic induction of caspase activity.

Autophagy is a process by which cells re-cycle organelles and macromolecular proteins during cellular stress. Defects in the regulation of autophagy have been associated with various human pathologies including heart failure. In the heart tumor suppressor p53 protein is known to promote apoptotic and autophagic cell death. We found p53 over-expression increased endogenous protein level of the hypoxia-inducible Bcl-2 death gene Bnip3 which leads to loss of mitochondrial membrane potential (ΔΨm). This was accompanied by autophagic flux and cell death. Conversely, loss of function of Bnip3 in cardiac myocytes or Bnip3-/- mouse embryonic fibroblasts prevented mitochondrial targeting of p53 and autophagic cell death. These data provide the first evidence for the dual regulation of autophagic cell death of cardiac myocytes by p53 that is mutually dependent on Bnip3 activation. Hence, our findings may explain how autophagy and cell death are dually regulated during cardiac stress conditions where p53 is activated.

Programmed Cell Death (PCD) describes an orderly cellular breakdown that occurs in both plants and animals throughout development and in response to biotic and abiotic stresses. The molecular machinery that functions in the induction and execution of animal PCD has been characterised in great detail. Conversely, few genes and proteins involved in plant PCD have been identified. While certain features of animal PCD may be conserved, the induction and execution of plant PCD is also likely to involve novel proteins and mechanisms. The aim of the work presented in this thesis was to investigate experimental approaches for studying plant PCD and to gain an understanding of the molecular mechanisms involved. To this end, an Arabidopsis thaliana cell suspension system was developed in which PCD could be induced by both a heat treatment (55°C, 10 min) and senescence (13 to 14 days-old). This system allowed for the molecular responses related to programmed cell death to be distinguished from those that were a specific response to the inducing stimulus. The Arabidopsis cell suspension system was utilised for an analysis of transcriptomic and proteomic changes that occur following the induction of PCD. A custom cDNA microarray analysis of ~100 putative cell death-related genes was used to measure the abundance of transcripts of these genes during PCD, and this work was extended to a whole-genome transcriptomic analysis of PCD. A number of candidate genes that may play a role in plant PCD were identified. These included those encoding antioxidant enzymes, cytosolic heat shock proteins, the mitochondrial adenine nucleotide translocase, ion transporters, a two-component response regulator (ARR4), several pathogenesis-related proteins, phospholipases and proteases, extracellular glycoproteins and enzymes (including a subtilisin-like protease, chitinases, and glucanases), and transcriptional regulators such as a homeobox leucine zipper and NAC-domain proteins. The induction and execution of plant PCD is also likely to involve mechanisms that are not transcriptionally regulated. A proteomic analysis of changes in the total cellular protein profile during heat- and senescence-induced PCD was therefore used to identify 12 proteins that are modulated in both systems and may play a PCD-specific role. These included the mitochondrial voltage-dependent anion channel (Athsr2), catalase, mitochondrial superoxide dismutase, an extracellular glycoprotein, and aconitase. Selected genes and proteins identified in the transcriptomic and proteomic analyses were further investigated in an attempt to define their role in plant PCD. Since PCD is difficult to quantitatively analyse at the whole-plant level, initially a strategy of transient expression of genes of interest in Arabidopsis protoplasts was adopted. However, it proved to be technically difficult to accurately quantify the number of dead cells in this system. As an alternative, Arabidopsis T-DNA insertional mutants within genes of interest were investigated for PCD-related phenotypes. Mutants in Senescence-Related Gene 3, the mitochondrial voltage-dependent anion channel (Athsr2), and cytosolic Heat shock protein 70-3 were isolated. The mutant lines were not visibly affected in their development, formation of xylem, onset and progression of senescence, or responses to abiotic and biotic stresses. This indicated that these genes are either not involved in the PCD pathway or that their functional role can be fulfilled by other gene products.

No description available.

Cullin 7 (Cul7) is a member of the cullin protein family that is emerging as a complex anti-apoptotic player in tumourigenesis. We hypothesize that by determining the mechanism through which Cul7 can protect against specific forms of cell death, we will uncover novel molecular pathways important in cancer. We aimed to address mechanism by evaluating which domains within Cul7 are important for its activity. Thus, we have introduced mutations in each of the Cul7 domains and asked whether any of these has an effect on the ability of Cul7 to inhibit cell death. To be able to detect even subtle affects of mutation, we required that mutants be assessed in appropriate experimental systems where ectopic wild-type Cul7 could robustly inhibit death compared to vector controls. We screened multiple cell lines and agonists, and have now indentified conditions in U2OS and SHEP cell lines in which our mutants can be evaluated.

Programmed cell death (PCD) is a highly evolved mechanism of cellular suicide that is aberrantly activated following neural injury. Two fundamental PCD signaling pathways termed the extrinsic (caspase-8-mediated) and intrinsic (caspase-9-mediated) pathways, have been described. While each pathway is initiated by distinct cellular stimuli, both pathways culminate in the activation of downstream executioner caspases. Previous efforts to isolate the in vivo contribution of each pathway have been hindered by the embryonic lethality of casp8 and casp9 null mice. In the present study, I overcame this obstacle to directly assess the contribution of each pathway following two well-characterized forms of acute neural injury; excitotoxic destruction of CA1 pyramidal neurons, and the loss of motor neurons following facial nerve transection. To determine the role of caspase-8, I constructed several lines of mice in which caspase-8 was conditionally ablated within the relevant neuronal populations. The results obtained from these animals definitively demonstrate that caspase-8 is not required by either motor neurons or CA1 pyramidal neurons to undergo PCD following injury. Therefore, these findings have provided the first direct experimental evidence to counter the widely held dogma of caspase-8 as the central effector of death receptor-mediated signaling within neurons. With respect to the intrinsic pathway, several lines of evidence suggest that the apoptosome predominantly regulates the death of motor neurons. I tested this hypothesis by performing facial axotomies in mice containing a point mutation introduced (“knocked in”) into the genomic locus of cytochrome c which abolishes its ability to activate the intrinsic pathway. Homozygous cytochrome c knock-in mice displayed a significant enhancement in motor neuron survival in comparison to control littermates following injury. However, the level of motor neuron protection differed from that previously reported in mice either overexpressing anti-apoptotic or lacking pro-apoptotic members of the Bcl-2 family. Therefore, the results of this study directly demonstrate the influence of the apoptosome on injury-induced neuronal PCD isolated from upstream Bcl-2 family-mediated effects. In addition, my results have provided the first evidence that activation of the apoptosome is required for the release of apoptosis inducing factor (AIF) from the mitochondria of injured motor neurons in vivo.

Cullin 7 (Cul7) is a member of the cullin protein family that is emerging as a complex anti-apoptotic player in tumourigenesis. We hypothesize that by determining the mechanism through which Cul7 can protect against specific forms of cell death, we will uncover novel molecular pathways important in cancer. We aimed to address mechanism by evaluating which domains within Cul7 are important for its activity. Thus, we have introduced mutations in each of the Cul7 domains and asked whether any of these has an effect on the ability of Cul7 to inhibit cell death. To be able to detect even subtle affects of mutation, we required that mutants be assessed in appropriate experimental systems where ectopic wild-type Cul7 could robustly inhibit death compared to vector controls. We screened multiple cell lines and agonists, and have now indentified conditions in U2OS and SHEP cell lines in which our mutants can be evaluated.