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Gygi lab defines the ways in which genetic variants affect global protein abundance - Jun 29, 2016

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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. 

Spiegelman Lab identifies new signaling mechanism that regulates thermogenic activity of “healthy” fat - May 26, 2016

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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. 

Brugge lab uncovers important role for transaminases in proliferating cells - May 10, 2016

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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.

Yang Shi elected to the American Academy of Arts and Sciences, 2016 Class - Apr 27, 2016

Yang Shi

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.

Rapoport lab determines structure of the active translocon - Mar 23, 2016

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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.

Rapoport Lab clarifies mechanism of a bacterial O-glycosyltransferase - Feb 24, 2016

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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.

Liao Lab determines high-resolution cryo-EM structures of synaptic RAG1-RAG2 complex to reveal the molecular mechanism of V(D)J recombination - Feb 24, 2016

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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.

Spiegelman Lab identifies Slit2-C as secreted protein that regulates adipose tissue thermogenesis - Feb 24, 2016

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This new work, by Katrin Svensson in the Spiegelman Lab and recently published in Cell Metabolism, has found a new function for Slit2, a protein secreted from beige cells. Slit2-C, a C-terminal cleaved fragment of Slit2 circulates in plasma and improves glucose homeostasis in mice by activating a thermogenic gene expression program and the classical PKA signaling pathway in fat cells. These findings establish a previously unknown peripheral role for a Slit2 fragment that has therapeutic potential for the treatment of diabetes and other metabolic disorders.

Näär Lab identifies compound that prevents multidrug-resistant fungi from pumping out drugs - Feb 22, 2016

Anders Näär

An international team led by researchers at Harvard Medical School and Massachusetts General Hospital has devised a new way to approach the problem of multidrug-resistant fungal infections that can be life-threatening to people with weakened immune systems. The Näär Lab and Gerhard Wagner's lab identified this compound from a library of 150,000 small molecules. To learn more, see here.

Anders Näär receives Research to Prevent Blindness Stein Innovation Award - Dec 09, 2015

Anders Näär

RPB Stein Innovation Awards provide funds to researchers in the ophthalmology department and to basic science or other relevant vision researchers outside of the ophthalmology department (but within the institution) with a common goal of understanding the visual system and the diseases that compromise its function. These awards are intended to provide seed money to proposed high-risk/high-gain vision science research which is innovative, cutting-edge, and demonstrates out-of-the-box thinking.

Congrats to Anders!