Iron chelation promotes mitophagy through SENP3-mediated deSUMOylation of FIS1

The selective clearance of mitochondria by mitophagy is an important quality control mechanism for maintaining mitochondrial and cellular health. Iron chelation, for example by the compound deferiprone (DFP), leads to a specific form of PINK1-PRKN/Parkin-independent mitophagy; however, the molecular mechanisms underlying this are poorly understood. In our recent paper, we examined the role of the deSUMOylating enzyme SENP3 in DFP-induced mitophagy. We observed that SENP3 levels are enhanced by DFP treatment, and that SENP3 is essential for DFP-induced mitophagy. Furthermore, we identified the mitochondrial protein FIS1, which is also required for DFP-induced mitophagy, as a novel SUMO substrate. Our data demonstrate that SENP3-dependent deSUMOylation of FIS1 enhances FIS1 mitochondrial targeting, to promote mitophagy in response to DFP treatment. These findings offer new insight into the mechanisms underlying mitophagy upon iron chelation, and have relevance to the therapeutic potential of DFP in a number of disorders, including Parkinson disease

The SHAPE of tRNA folding and of the 5'-end of the HIV-1 genome

Most RNAs function only once they fold to form difficult-to-predict base-paired helices and other structural elements. As an RNA forms a preferred secondary or tertiary structure, a characteristic set of nucleotides becomes constrained by base pairing and higher-order interactions, while unconconstrained positions remain flexible. Determining local nucleotide flexibility as a function of nucleotide position in a folded RNA provides important information that enables the sequence and structure of an RNA to be related to its biological function. I have developed a technology, termed selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE), that can be used to interrogate RNA structure under diverse in vitro and in vivo conditions. SHAPE chemistry can be applied to monitor protein binding events and locate promising sites for primer annealing in arbitrary RNA. SHAPE chemistry is based on the discovery that flexible RNA nucleotides preferentially sample conformations that enhance the nucleophilic reactivity of the 2'-hydroxyl group toward electrophiles, such as N-methylisatoic anhydride. Modified sites are detected as stops in an optimized DNA primer extension reaction, followed by sizing of the extension products. SHAPE chemistry scores local flexibility at all four ribonucleotides in a single experiment and discriminates between base-paired versus unconstrained residues with a dynamic range of 20-fold or greater. I have applied SHAPE chemistry to observe equilibrium melting of a model tRNA at single nucleotide resolution. I observed that RNA folding is a complex process involving structural rearrangement and the formation of tertiary structure concurrent with secondary structure. Furthermore, I have employed capillary electrophoresis and sophisticated analysis algorithms to create a high-throughput SHAPE (hSHAPE) experiment that can comprehensively interrogate the flexibility of several hundred nucleotides in a single robust experiment. Using hSHAPE, I analyzed the structure of HIV-1 genomic RNA as a function of 4 different biologically relevant states, including infectious viral particles. Despite many thermodynamically plausible structures, the HIV-1 genome exists in a single conformation. I observed the effects of tRNA primer binding, and the effects of nucleocapsid protein on RNA flexibility. hSHAPE chemistry is a promising, scalable approach that can rapidly and accurately analyze the structure of RNA molecules under biologically relevant conditions

Insulin-dependent GLUT4 trafficking is not regulated by protein SUMOylation in L6 myocytes

Type-II Diabetes Mellitus (T2DM) is one of the fastest growing public health issues today, consuming 12% of worldwide health budgets and affecting an estimated 400 million people. One of the key pathological traits of this disease is insulin resistance at ‘glucose sink’ tissues (mostly skeletal muscle), and this remains one of the features of this disease most intractable to therapeutic intervention. Several lines of evidence have implicated the post-translational modification,SUMOylation, in insulin signalling and insulin resistance in skeletal muscle. In this study, we examined this possibility by manipulation of cellular SUMOylation levels using multiple different tools, and assaying the effect on insulin-stimulated GLUT4 surface expression in differentiated L6 rat myocytes. Although insulin stimulation of L6 myocytes produced a robust decrease in total cellular SUMO1-ylation levels, manipulating cellular SUMOylation had no effect on insulin-responsive GLUT4 surface trafficking using any of the tools we employed. Whilst we cannot totally exclude the possibility that SUMOylation plays a role in the insulin signalling pathway in human health and disease, our data strongly argue that GLUT4 trafficking in response to insulin is not regulated by protein SUMOylation, and that SUMOylation does not therefore represent a viable therapeutic target for the treatment of insulin resistance

Surface biotinylation of primary neurons to monitor changes in AMPA receptor surface expression in response to kainate receptor stimulation

Here, we detail a surface biotinylation technique used to label surface-expressed proteins in primary neuronal cultures. Surface proteins are labeled with membrane-impermeant Sulfo-NHS-SS-biotin, and isolated by pull-down with streptavidin beads followed by western blotting to measure levels of surface expression of the protein of interest under different conditions. We have used this approach extensively to monitor activity-dependent changes in α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) and kainate receptor (KAR) subunits. However, this protocol can be used to investigate any surface-expressed protein. For complete details on the use and execution of this protocol, please refer to Nair et al. (2021)

Mechanisms and roles of mitochondrial localisation and dynamics in neuronal function

Neurons are highly polarised, complex and incredibly energy intensive cells, and their demand for ATP during neuronal transmission is primarily met by oxidative phosphorylation by mitochondria. Thus, maintaining the health and efficient function of mitochondria is vital for neuronal integrity, viability and synaptic activity. Mitochondria do not exist in isolation, but constantly undergo cycles of fusion and fission, and are actively transported around the neuron to sites of high energy demand. Intriguingly, axonal and dendritic mitochondria exhibit different morphologies. In axons mitochondria are small and sparse whereas in dendrites they are larger and more densely packed. The transport mechanisms and mitochondrial dynamics that underlie these differences, and their functional implications, have been the focus of concerted investigation. Moreover, it is now clear that deficiencies in mitochondrial dynamics can be a primary factor in many neurodegenerative diseases. Here, we review the role that mitochondrial dynamics play in neuronal function, how these processes support synaptic transmission and how mitochondrial dysfunction is implicated in neurodegenerative disease

Assembly, Secretory Pathway Trafficking, and Surface Delivery of Kainate Receptors Is Regulated by Neuronal Activity

Summary: Ionotropic glutamate receptor (iGluR) trafficking and function underpin excitatory synaptic transmission and plasticity and shape neuronal networks. It is well established that the transcription, translation, and endocytosis/recycling of iGluRs are all regulated by neuronal activity, but much less is known about the activity dependence of iGluR transport through the secretory pathway. Here, we use the kainate receptor subunit GluK2 as a model iGluR cargo to show that the assembly, early secretory pathway trafficking, and surface delivery of iGluRs are all controlled by neuronal activity. We show that the delivery of de novo kainate receptors is differentially regulated by modulation of GluK2 Q/R editing, PKC phosphorylation, and PDZ ligand interactions. These findings reveal that, in addition to short-term regulation of iGluRs by recycling/endocytosis and long-term modulation by altered transcription/translation, the trafficking of iGluRs through the secretory pathway is under tight activity-dependent control to determine the numbers and properties of surface-expressed iGluRs. : Evans et al. show that secretory pathway trafficking of KARs is highly activity-dependent. This medium-term regulatory mechanism demonstrates how neuronal excitability and network activity are regulated at multiple levels over a range of time courses. Keywords: kainate receptor, retention using selective hooks, RUSH, secretory pathway, ER exit sites, Golgi outposts, AMPA receptors, scaling, Q/R editing, ADAR2, PDZ ligan

No Detectable Fertility Benefit from a Single Additional Mating in Wild Stalk-Eyed Flies

Background: Multiple mating by female insects is widespread, and the explanation(s) for repeated mating by females has been the subject of much discussion. Females may profit from mating multiply through direct material benefits that increase their own reproductive output, or indirect genetic benefits that increase offspring fitness. One particular direct benefit that has attracted significant attention is that of fertility assurance, as females often need to mate multiply to achieve high fertility. This hypothesis has never been tested in a wild insect population.Methodology/Principal Findings: Female Malaysian stalk-eyed flies (Teleopsis dalmanni) mate repeatedly during their lifetime, and have been shown to be sperm limited under both laboratory and field conditions. Here we ask whether receiving an additional mating alleviates sperm limitation in wild females. In our experiment one group of females received a single additional mating, while a control group received an interrupted, and therefore unsuccessful, mating. Females that received an additional mating did not lay more fertilised eggs in total, nor did they lay proportionately more fertilised eggs. Female fertility declined significantly through time, demonstrating that females were sperm limited. However, receipt of an additional mating did not significantly alter the rate of this decline.Conclusions/Significance: Our data suggest that the fertility consequences of a single additional mating were small. We discuss this effect (or lack thereof), and suggest that it is likely to be attributed to small ejaculate size, a high proportion of failed copulations, and the presence of X-linked meiotic drive in this species

Action of earthworms on flint burial – a return to Darwin’s estate

For thirty years, from the early 1840s, Charles Darwin documented the disappearance of flints in the grounds of Down House in Kent, at a location originally known as the “Stony Field”. This site (Great Pucklands Meadow - GPM) was visited in 2007 and an experiment set up in this ungrazed grassland. Locally-sourced flints (either large - 12 cm, or small – 5 cm dia.) were deposited at two densities within sixteen 1 m2 plots in a randomised factorial design. The area selected was distant from public access routes and remained unmown throughout the duration here reported. Fixed point photographs were taken at the outset to enable later photogrammetric analysis. After 6 years, the site was re-examined. The flints had generally been incorporated into the soil. Photographs were re-taken, proportion of buried flints recorded and measurements made of burial depth from a quarter of each plot. Results showed that large flints were more deeply incorporated than smaller (p=0.025), but more of the latter were below the soil surface. A controlled laboratory experiment was also conducted using Aporrectodea longa (the dominant earthworm species in GPM) to assess effects of casting in the absence of other biota. Results suggested that this species has a major influence on flint burial through surface casting. Combined with a long term, but small scale collection of A. longa casts from an area close to GPM, all results were consistent with those provided by Darwin and showed that rate of flint burial was within the range 0.21-0.96 cm y-1