The ARC1 E3 Ligase Promotes a Strong and Stable Self-Incompatibility Response in Arabidopsis Species: Response to the Nasrallah and Nasrallah Commentary

Following the identification of the male (S-locus Cysteine Rich/S-locus Protein 11) and female (S Receptor kinase [SRK]) factors controlling self-incompatibility in the Brassicaceae, research in this field has focused on understanding the nature of the cellular responses activated by these regulators. We previously identified the ARM Repeat Containing1 (ARC1) E3 ligase as a component of the SRK signaling pathway and demonstrated ARC1’s requirement in the stigma for self-incompatible pollen rejection in Brassica napus, Arabidopsis lyrata, and Arabidopsis thaliana. Here, we discuss our findings on the role of ARC1 in reconstructing a strong and stable A. thaliana self-incompatibility phenotype, in the context of the putative issues outlined in a commentary by Nasrallah and Nasrallah. Additionally, with their proposed standardized strategy for studying self-incompatibility in A. thaliana, we offer our perspective on what constitutes a strong and stable self-incompatibility phenotype in A. thaliana and how this should be investigated and reported to the greater community.With many angiosperms possessing hermaphroditic flowers, self-incompatibility (SI) systems have evolved to avoid the deleterious effects of inbreeding (Figures 1A and 1B). As defined by Charlesworth et al. (2005), “plant SI systems all prevent self-fertilization through recognition and rejection of pollen by pistils expressing ‘cognate’ allelic specificity.” In Brassicaceae species, the allele specificity is conferred by two well-characterized polymorphic genes encoding the female S Receptor kinase (SRK) and the male S-locus Protein 11/S-locus Cysteine Rich (SP11/SCR; hereby referred to as SCR) (reviewed in Iwano and Takayama, 2012). The major outstanding area in this field is identifying the signaling proteins activated by SRK, determining their function at the cellular level, and investigating whether these signaling proteins have conserved functions across the self-incompatible species in the Brassicaceae. Despite strong interest in finding these potential factors by us and other groups, only the Brassica rapa M Locus Protein Kinase (Murase et al., 2004; Kakita et al., 2007a, 2007b) and the ARM Repeat Containing1 (ARC1) E3 ligase have emerged as direct downstream signaling proteins. We demonstrated a conserved role for ARC1 in self-incompatible Brassica napus (Gu et al., 1998; Stone et al., 1999, 2003), self-incompatible Arabidopsis lyrata (Indriolo et al., 2012), and self-incompatible Arabidopsis thaliana expressing A. lyrata SCRb, SRKb, and ARC1 transgenes (Indriolo et al., 2014). The commentary by Nasrallah and Nasrallah (2014) focuses on our proposed role for ARC1 in reconstituting self-incompatibility in transgenic A. thaliana.Open in a separate windowFigure 1.Pathways for Compatible and Self-Incompatible Pollen Responses in A. thaliana.(A) Compatible (arrow) and self-incompatible (bar) pollen-pistil interactions.(B) Criteria for assessing compatible versus self-incompatible pollinations.(C) Model for the basal compatible pollen response. An unknown basal pollen response pathway is activated in the stigmatic papilla under the compatible pollen grain leading to the activation of vesicle secretion. Our research on Brassica and Arabidopsis Exo70A1 revealed a putative role for the exocyst complex in docking secretory vesicles at the stigmatic papillae plasma membrane (Samuel et al., 2009; Safavian and Goring, 2013; Safavian et al., 2014). Exo70A1 is proposed to assemble with the remaining subunits of the exocyst complex to dock secretory vesicles (reviewed in Zárský et al., 2013). SNARE proteins mediate vesicle fusion to the plasma membrane, and unknown cargo (ACA13 as one candidate; Iwano et al., 2014) are released to enable pollen hydration pollen tube entry through the stigmatic papillar cell wall (compatible pollen is accepted).(D) Model for the reconstituted self-incompatibility signaling pathway in the Sha ecotype. Following self-pollination in transgenic SCR-SRK+ARC1 Sha ecotype flowers, the pollen SCR ligand binds to SRK at the stigmatic papillar plasma membrane, resulting in the activation of the downstream signaling pathway. The ARC1 E3 ligase is recruited by SRK and targets Exo70A1 for ubiquitination. Even though the basal compatible pollen response pathway has been also activated, ubiquitinated Exo70A1 is somehow inhibited so that exocyst-mediated vesicle secretion to the self-incompatible pollen grain is blocked. In addition, secretory vesicles are degraded in the vacuole through autophagy. An unknown signaling protein (yellow) also has activity in the Sha ecotype in blocking exocytosis (see Samuel et al. [2009], Safavian and Goring [2013], and Indriolo et al. [2014] for further details and references therein).(E) Transmission electron microscopy image of a self-incompatible pollen-stigmatic papillar interaction at 10 min postpollination from the transgenic SCRb-SRKb+ARC1 Sha ecotype. Pseudocoloring has been added to distinguish the pollen (brown) from the stigmatic papilla (green). Autophagy is detected with the autophagic vacuole in the vacuole (see Rose et al. [2006] and Indriolo et al. [2014] for details). (Figures 1C to 1E adapted from Indriolo et al. [2014], Figures 9 and 10.)     

Nesting Habitat Creation Enhances Recruitment in a Predator‐Free Environment: Malaclemys Nesting at the Paul S. Sarbanes Ecosystem Restoration Project

Aquatic turtles worldwide are plagued with habitat loss due to development and shoreline alteration that destroys the terrestrial–aquatic linkage which they must cross to reproduce successfully. Furthermore, nesting habitat loss can concentrate nesting, increasing nest predator efficiency. We describe how the Paul S. Sarbanes Ecosystem Restoration Project at Poplar Island created nesting habitat for Malaclemys terrapin (Diamondback Terrapin), and document nesting success in response to construction progress and the absence of raccoons and foxes, the primary nest predators. We monitored terrapin nests throughout the nesting seasons from 2002 to 2011 to determine overall and within‐nest survivorship. Female terrapins began nesting on the restoration project within 1 year but planned construction during the study eliminated some nesting areas and opened previously inaccessible areas. Overall, nest survivorship was considerably higher than mainland nesting areas due to the absence of raccoons and foxes on the island and within‐nest survivorship was similar. Egg size, hatchling size, and the frequency of shell scute anomalies were similar to other terrapin populations, suggesting normal developmental conditions on the island. We documented annual variation in hatchling size that correlated negatively with mean air temperature during the incubation season. Our results indicate that restored or created isolated island habitat can be located rapidly by terrapins and can become an important source of recruitment in regions where nesting habitat is limited and predation is high. Poplar Island illustrates how habitat loss and restoration can affect turtle populations by revealing the changes in nesting patterns and success in newly created, predator‐free habitat.     

Separating direct and indirect effects of global change: a population dynamic modeling approach using readily available field data

Two sources of complexity make predicting plant community response to global change particularly challenging. First, realistic global change scenarios involve multiple drivers of environmental change that can interact with one another to produce non‐additive effects. Second, in addition to these direct effects, global change drivers can indirectly affect plants by modifying species interactions. In order to tackle both of these challenges, we propose a novel population modeling approach, requiring only measurements of abundance and climate over time. To demonstrate the applicability of this approach, we model population dynamics of eight abundant plant species in a multifactorial global change experiment in alpine tundra where we manipulated nitrogen, precipitation, and temperature over 7 years. We test whether indirect and interactive effects are important to population dynamics and whether explicitly incorporating species interactions can change predictions when models are forecast under future climate change scenarios. For three of the eight species, population dynamics were best explained by direct effect models, for one species neither direct nor indirect effects were important, and for the other four species indirect effects mattered. Overall, global change had negative effects on species population growth, although species responded to different global change drivers, and single‐factor effects were slightly more common than interactive direct effects. When the fitted population dynamic models were extrapolated under changing climatic conditions to the end of the century, forecasts of community dynamics and diversity loss were largely similar using direct effect models that do not explicitly incorporate species interactions or best‐fit models; however, inclusion of species interactions was important in refining the predictions for two of the species. The modeling approach proposed here is a powerful way of analyzing readily available datasets which should be added to our toolbox to tease apart complex drivers of global change.     

Degradation of Activated K-Ras Orthologue via K-Ras-specific Lysine Residues Is Required for Cytokinesis

Mammalian cells encode three closely related Ras proteins, H-Ras, N-Ras, and K-Ras. Oncogenic K-Ras mutations frequently occur in human cancers, which lead to dysregulated cell proliferation and genomic instability. However, mechanistic role of the Ras isoform regulation have remained largely unknown. Furthermore, the dynamics and function of negative regulation of GTP-loaded K-Ras have not been fully investigated. Here, we demonstrate RasG, the Dictyostelium orthologue of K-Ras, is targeted for degradation by polyubiquitination. Both ubiquitination and degradation of RasG were strictly associated with RasG activity. High resolution tandem mass spectrometry (LC-MS/MS) analysis indicated that RasG ubiquitination occurs at C-terminal lysines equivalent to lysines found in human K-Ras but not in H-Ras and N-Ras homologues. Substitution of these lysine residues with arginines (4KR-RasG) diminished RasG ubiquitination and increased RasG protein stability. Cells expressing 4KR-RasG failed to undergo proper cytokinesis and resulted in multinucleated cells. Ectopically expressed human K-Ras undergoes polyubiquitin-mediated degradation in Dictyostelium, whereas human H-Ras and a Dictyostelium H-Ras homologue (RasC) are refractory to ubiquitination. Our results indicate the existence of GTP-loaded K-Ras orthologue-specific degradation system in Dictyostelium, and further identification of the responsible E3-ligase may provide a novel therapeutic approach against K-Ras-mutated cancers.     

Structures of Human Steroidogenic Cytochrome P450 17A1 with Substrates

The human cytochrome P450 17A1 (CYP17A1) enzyme operates at a key juncture of human steroidogenesis, controlling the levels of mineralocorticoids influencing blood pressure, glucocorticoids involved in immune and stress responses, and androgens and estrogens involved in development and homeostasis of reproductive tissues. Understanding CYP17A1 multifunctional biochemistry is thus integral to treating prostate and breast cancer, subfertility, blood pressure, and other diseases. CYP17A1 structures with all four physiologically relevant steroid substrates suggest answers to four fundamental aspects of CYP17A1 function. First, all substrates bind in a similar overall orientation, rising ∼60° with respect to the heme. Second, both hydroxylase substrates pregnenolone and progesterone hydrogen bond to Asn²⁰² in orientations consistent with production of 17α-hydroxy major metabolites, but functional and structural evidence for an A105L mutation suggests that a minor conformation may yield the minor 16α-hydroxyprogesterone metabolite. Third, substrate specificity of the subsequent 17,20-lyase reaction may be explained by variation in substrate height above the heme. Although 17α-hydroxyprogesterone is only observed farther from the catalytic iron, 17α-hydroxypregnenolone is also observed closer to the heme. In conjunction with spectroscopic evidence, this suggests that only 17α-hydroxypregnenolone approaches and interacts with the proximal oxygen of the catalytic iron-peroxy intermediate, yielding efficient production of dehydroepiandrosterone as the key intermediate in human testosterone and estrogen synthesis. Fourth, differential positioning of 17α-hydroxypregnenolone offers a mechanism whereby allosteric binding of cytochrome b₅ might selectively enhance the lyase reaction. In aggregate, these structures provide a structural basis for understanding multiple key reactions at the heart of human steroidogenesis.     

Nrbf2 Protein Suppresses Autophagy by Modulating Atg14L Protein-containing Beclin 1-Vps34 Complex Architecture and Reducing Intracellular Phosphatidylinositol-3 Phosphate Levels

Autophagy is a tightly regulated lysosomal degradation pathway for maintaining cellular homeostasis and responding to stresses. Beclin 1 and its interacting proteins, including the class III phosphatidylinositol-3 kinase Vps34, play crucial roles in autophagy regulation in mammals. We identified nuclear receptor binding factor 2 (Nrbf2) as a Beclin 1-interacting protein from Becn1^−/−;Becn1-EGFP/+ mouse liver and brain. We also found that Nrbf2-Beclin 1 interaction required the N terminus of Nrbf2. We next used the human retinal pigment epithelial cell line RPE-1 as a model system and showed that transiently knocking down Nrbf2 by siRNA increased autophagic flux under both nutrient-rich and starvation conditions. To investigate the mechanism by which Nrbf2 regulates autophagy, we demonstrated that Nrbf2 interacted and colocalized with Atg14L, suggesting that Nrbf2 is a component of the Atg14L-containing Beclin 1-Vps34 complex. Moreover, ectopically expressed Nrbf2 formed cytosolic puncta that were positive for isolation membrane markers. These results suggest that Nrbf2 is involved in autophagosome biogenesis. Furthermore, we showed that Nrbf2 deficiency led to increased intracellular phosphatidylinositol-3 phosphate levels and diminished Atg14L-Vps34/Vps15 interactions, suggesting that Nrbf2-mediated Atg14L-Vps34/Vps15 interactions likely inhibit Vps34 activity. Therefore, we propose that Nrbf2 may interact with the Atg14L-containing Beclin 1-Vps34 protein complex to modulate protein-protein interactions within the complex, leading to suppression of Vps34 activity, autophagosome biogenesis, and autophagic flux. This work reveals a novel aspect of the intricate mechanism for the Beclin 1-Vps34 protein-protein interaction network to achieve precise control of autophagy.