Axonal degeneration is frequently observed before the death of neuronal cell bodies in patients with neurodegenerative disorders including ALS and contributes significantly to neurological disability. While blocking axonal degeneration may represent an important therapeutic goal, the mechanism of axonal degeneration is unclear. In a recent paper published in Science by Yuan lab, Ito et al. investigated the role of RIPK1 in Optn-/- mice. Loss-of-function mutations in the Optineurin (Optn) gene have been implicated in both familial and sporadic cases of ALS. The authors demonstrated that optineurin actively suppressed RIPK1-dependent signaling by regulating its turnover. Loss-of-Optn led to progressive dysmyelination and axonal degeneration through engagement of necroptotic machinery, including RIPK1, RIPK3 and MLKL, in the CNS. Furthermore, RIPK1/RIPK3-mediated axonal pathology was commonly observed in SOD1G93A transgenic mice and pathological samples from human ALS. Thus, RIPK1/RIPK3 plays a critical role in mediating progressive axonal degeneration and inhibiting RIPK1 kinase may provide an axonal protective strategy for the treatment of ALS and other human degenerative diseases characterized by axonal degeneration.
To initiate an immune response against pathogens, a small number of T cells within the polyclonal repertoire need to proliferate rapidly to generate large numbers of effector cells that can clear pathogens. To generate the precursors required for macromolecular synthesis, energy and stress response, the T cells activate anabolic metabolism that is coupled with increased mitochondrial mass. In a recent publication in Cell Metabolism, the Haigis Lab uses T cell activation to address a fundamental question in mitochondrial biology: Does biogenesis merely replicates existing mitochondria, or generates a distinct population of mitochondria with specialized functions? Noga Ron-Harel and co-workers, in collaboration with the Gygi and Sharpe labs, show that naïve T cell activation induces a unique program of synchronized mitochondrial biogenesis and proteome remodeling, giving rise to mitochondria with a distinct proteomic signature that drives one-carbon (1C) metabolism. They demonstrate for the first time that mitochondrial 1C metabolism is important for de-novo purine biosynthesis and redox control in T cells. Genetic inhibition of mitochondrial 1C metabolism impaired antigen-specific T cell proliferation and survival in vitro and in vivo. In sum, this study identifies 1C metabolism as an early and essential metabolic signature of naïve T cell activation, and shows that mitochondrial proliferation gives rise to a new population of organelles with distinct and specialized functions.
The vagus nerve is a key body-brain connection that monitors the respiratory, cardiovascular, and digestive systems. Within the gastrointestinal tract, vagal sensory neurons detect a diversity of stimuli including nutrients, nausea-inducing toxins, and mechanical stretch of the stomach and intestine. In a recent publication in Cell, the Liberles Lab identified two classes of vagal gut-to-brain neurons that exert powerful and opposing effects on digestion. Genetically guided anatomical mapping reveals that vagal GPR65 neurons densely innervate intestinal villi near the pyloric sphincter, vagal GLP1R neurons instead target the stomach, and both neuron types innervate dedicated brainstem subnuclei. Optogenetic stimulation of vagal GPR65 neurons selectively blocks gastric contractions without impacting breathing or heart rate, and in vivo ganglion imaging reveals that GPR65 and GLP1R neurons differentially respond to intestinal food and stomach stretch. Delineating gut-to-brain sensory neurons provides a needed foundation for understanding neural control of gastrointestinal physiology.
Harnessing natural genetic variants is a powerful tool for introducing genetic perturbations into a model organism. At the Jackson laboratories a cohort of genetic diverse mice known as the diversity outbred mice was created for the purpose of genetic mapping. The mice harbor millions of genetic variants which creates system-wide genetic perturbations in a single population. The Gygi lab, in collaboration with the Jackson laboratories, explored this model to better understand how variants influence protein expression (Chick et al., Nature, 2016). The results from study show that local genetic regulation is mostly dictated by the central dogma. However, distant regulation was almost exclusively through post-transcriptional mechanisms. Their analysis was able to link the abundance of one protein to one or many other proteins revealing many novel protein-protein associations. This approach has a distinct advantage of interactions maps because the association isn’t always dependent on physical interaction.
Reactive oxygen species (ROS) are thought of as toxic byproducts that cause injury to our tissues and drive pathologies associated with aging. However, recent evidence is emerging showing that under certain conditions ROS can be important signals in healthy tissue. In this study, the Spiegelman Lab examined these ROS signals in brown adipose tissue, which contain cells that have the specialized ability to burn stored fats as heat and combat obesity and diabetes. They found that increases in ROS levels in brown adipose supported thermogenesis in living mouse models. Moreover, they demonstrated that ROS signals involved the direct modification by ROS of key functional targets including the critical thermogenic protein uncoupling protein 1 (UCP1). These findings suggest that modification of ROS processes and this newfound signaling site on UCP1 provide new and unexpected ways of manipulating thermogenesis to combat obesity and diabetes.
In order to proliferate, cells must reproduce their biomass by acquiring nutrients from their environment and using them to synthesize macromolecules. Using a 3D tissue culture model combined with quantitative metabolomics and proteomics, members of the Brugge and Gygi labs have identified a mechanism by which proliferating cells use glutamate to support the biosynthesis of other non-essential amino acids (Coloff et al, Cell Metabolism, 2016). In proliferating cells, transaminases that make use of both the carbon and nitrogen from glutamate are utilized to generate amino acids and to fuel the TCA cycle. When cells exit the cell cycle, they reduce transaminase expression and induce an alternative enzyme, glutamate dehydrogenase, which no longer makes use of glutamate-derived nitrogen, thereby reducing amino acid biosynthesis. Importantly, this pathway appears to be used by rapidly proliferating cells from a variety of tissues and organisms, as well as by most rapidly proliferating tumor cells. This work highlights the importance of achieving a detailed understanding of the mechanisms by which cells utilize nutrients if we hope to target the aberrant metabolism observed in cancer cells as cancer therapy.
We congratulate faculty member Yang Shi, one of four members of the Harvard Medical School community who are part of this year’s class of national and international leaders elected to the American Academy of Arts and Sciences.
Founded in 1780, AAAS is one of the country’s oldest and most prestigious honorary societies and independent policy research centers, convenes leaders from the academic, business and government sectors to respond to the challenges facing the nation and the world.
To see the other members of the 2016 class, click here.
A recent paper by Li et al. (Rapoport lab, with help from Hidde Ploegh’s lab at the MIT), reports a crystal structure of the active protein translocation channel, which had been a “holy grail” in the field. Previously, the Rapoport lab had reported crystal structures of the idle channel (van den Berg, B. et al. Nature 427, 36-44 (2004)) and of a complex of the channel with the translocation ATPase SecA (Zimmer et al. Nature 455, 936-943 (2008)). Structures of the idle channel show that the largest subunit, SecY, consists of two halves that form an hourglass-shaped pore and a lateral gate that faces lipid. The constriction in the middle of the membrane is formed from six pore ring residues. The cytoplasmic funnel is empty, while the extracellular funnel is filled with a plug domain. When SecA binds to the channel, it inserts a two-helix finger into the cytoplasmic opening of the channel and partially opens the lateral gate. The new structure now contains the SecY channel, SecA, and a short segment of a secretory protein fused into the two-helix finger of SecA. This segment inserts into the channel as a loop, displacing the plug domain. The hydrophobic core of the signal sequence forms a helix that sits in a groove outside the lateral gate, while the following polypeptide segment intercalates into the gate. The C-terminal section of the polypeptide loop is located in the channel, surrounded by four pore ring residues. The structure shows that the hydrophobic regions of signal sequences exit the lateral gate and partition into the lipid phase, explaining their diversity in sequence and length. A comparison with other structures shows that this mechanism of signal sequence recognition is universal, regardless of the organism and mode of translocation, and also applies to bilayer-spanning domains of nascent membrane proteins.
Many proteins are glycosylated on Ser or Thr residues, but the mechanism of O-glycosylation is only poorly understood. A recent study by Chen et al. (Rapoport Lab, in collaboration with Paul Sullam’s lab at San Francisco Veteran Affairs Medical Center) reports on the mechanism by which the cytosolic O-glycosyltransferase GtfA/B of Streptococcus gordonii modifies the Ser/Thr-rich repeats of adhesin, a protein that mediates the attachment of the bacterium to host cells. Crystal structures and biochemical experiments indicate that, during a first phase of glycosylation, the conformation of GtfB is restrained by GtfA to bind substrate with unmodified Ser/Thr residues. In a slow second phase, GtfB recognizes residues that are already modified with N-acetylglucosamine by converting into a relaxed conformation. These results explain how the glycosyltransferase modifies a progressively changing substrate molecule.
Diverse repertoires of antigen-receptor genes that result from combinatorial splicing of V(D)J gene segments are hallmarks of vertebrate immunity. The (RAG1-RAG2)2 recombinase precisely recognizes and cleaves two different recombination signal sequences (12-RSS and 23-RSS), and forms synaptic complexes only with one 12-RSS and one 23-RSS, a dogma known as the 12/23 rule that governs the recombination fidelity. As described in a recent paper in Cell, the Liao Lab (in collaboration with Dr. Hao Wu's lab at Boston Children's Hospital) used single-particle cryo-electron microscopy (cryo-EM) to determine the structures of synaptic RAG1-RAG2 complexes at up to 3.4 Å resolution. These structures reveal an RSS-induced closed conformation that activates catalysis and uncovers the molecular basis for the 12/23 rule.