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Recent Faculty Promotion: Adrian Salic - Jul 21, 2017

Adrian Salic

Congratulations to Adrian Salic on his promotion to Professor of Cell Biology!

Adrian uses biochemistry, cell, and chemical biology to elucidate how vertebrate cells send and respond to Hedgehog signals. Two key aspects his lab is currently investigating are the activation of the secreted Hedgehog protein and the regulated proteolysis of Gli, the transcriptional effector of the Hedghog pathway. 

Rapoport and Liao labs determine the cryo-EM structure of the ERAD Hrd1/Hrd3 complex - Jul 19, 2017

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A conserved pathway called “endoplasmic reticulum associated protein degradation (ERAD) is responsible for the disposal of misfolded ER proteins. Previous work from the Rapoport lab indicated that the multi-spanning ubiquitin ligase Hrd1 is a key component of ERAD; Hrd1 allows misfolded luminal and membrane proteins to move from the ER into the cytosol. However, it remained unclear whether Hrd1 forms a protein-conducting channel. In a paper recently published in Nature, the Rapoport and Liao labs teamed up to determine a single particle cryo-EM structure of Hrd1 together with its luminal binding partner Hrd3. The Hrd1/Hrd3 complex structure at ~4 Å shows that Hrd1 forms a dimer inside the membrane with two Hrd3 molecules forming a luminal arch above the dimer. Each Hrd1 molecule has a large hydrophilic cavity extending from the cytosol almost to the ER lumen. A trans-membrane segment of the other Hrd1 molecule forms a lateral seal of the cavity. Both the cavity and the lateral gate are reminiscent of other protein-conducting conduits, such as the Sec61/SecY channel or the YidC protein, which allow proteins to move in the other direction, i.e. from the cytosol into the membrane. These results indicate that the thinning of the lipid bilayer may be a general principle employed by protein-conducting conduits to lower the energetic barrier for moving hydrophobic segments in or out of the membrane.

Liao lab discovers key steps in CRISPR’s mechanism of action - Jul 06, 2017

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Scientists in the Liao lab and Cornell University have produced near-atomic resolution snapshots of CRISPR that reveal key steps in its mechanism of action. The findings, published in Cell on June 29, provide the structural data necessary for efforts to improve the efficiency and accuracy of CRISPR for biomedical applications. You can read more at HMS News, Science Newsline, Phys.org, and Science Daily

New study by Reed lab reveals how RNA splicing errors may cause the development of ALS and a specific form of dementia - Jun 13, 2017

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The most frequent genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) may stem from errors in RNA splicing, an intermediary and critical step for translating genetic instructions into functional proteins. In a recent study published in Cell Reports on June 13, the Reed lab shows that toxic peptides produced by mutation of the C9ORF72 gene can prevent accurate assembly of the spliceosome—the molecular machine responsible for RNA splicing.

For more information, please read the article here.

BioPlex 2.0 project from Harper & Gygi labs sheds new light on protein interaction networks - Jun 01, 2017

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The most recent project from the Harper & Gygi labs, BioPlex 2.0 (Biophysical Interactions of ORFeome-derived complexes), was featured in Nature and uses affinity purification-mass spectrometry to elucidate protein interaction networks and co-complexes nucleated by more than 25% of protein-coding genes from the human genome. It is currently the largest such network assembled, consisting of 56,000 candidate interactions and more than 29,000 previously unknown co-associations.  You can read further about this project here.

Recent Faculty Promotion: Steve Liberles - May 11, 2017

Steve Liberles

Congratulations to Steve Liberles on his promotion to Professor of Cell Biology!

Steve's research focuses on understanding how the brain processes external sensory and internal homeostatic signals that initiate behavioral and physiological responses. Most recently, his lab’s publication in Nature elucidated the mechanisms of respiratory control and its implications in sleep apnoea.

Junying Yuan elected to the National Academy of Sciences - May 03, 2017

The National Academy of Sciences recently announced the election of 84 new members and 21 foreign associates in recognition of their distinguished and continuing achievements in original research (NAS press release here, HMS release here). Among this list is Junying Yuan, Professor of Cell Biology.

The National Academy of Sciences is a private, non-profit society of distinguished scholars. Established by an Act of Congress, signed by President Abraham Lincoln in 1863, the NAS is charged with providing independent, objective advice to the nation on matters related to science and technology. Scientists are elected by their peers to membership in the NAS for outstanding contributions to research.  Congrats, Junying!

Rapoport Lab clarifies mechanism of Cdc48 ATPase - Apr 21, 2017

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The ubiquitin-proteasome system is responsible for regulated destruction of a wide variety of proteins in eukaryotic cells. Some targets, such as proteins embedded in membranes or stable macromolecular complexes, require prior processing by an ATPase known as Cdc48 in yeast, or p97 in higher organisms. The function of Cdc48/p97 and its cofactors Ufd1 and Npl4 (UN complex) is best understood in the case of endoplasmic reticulum-associated degradation (ERAD), in which Cdc48 extracts proteins from the ER membrane before they are degraded in the cytoplasm. Cdc48/p97 consists of an N-terminal domain that binds UN and two stacked hexameric ATPase rings (D1 and D2) surrounding a central pore. How exactly Cdc48/p97 processes its substrates has been unknown.

In a recent paper in Cell, Bodnar and Rapoport analyze the mechanism of Cdc48/p97. In vitro reconstitution of Cdc48 function with purified yeast components shows that the ATPase cooperates with UN to unfold its polyubiquitinated targets by passing them through its central pore. Translocation requires ATP hydrolysis in the D2 ring, whereas ATP hydrolysis in the D1 ring is required for substrate release from the ATPase complex. Substrate release also requires deubiquitination. Surprisingly, the ubiquitin chain is not completely removed; rather, the remaining oligoubiquitin chain is also translocated through the pore. These results lead to a new paradigm for Cdc48 function in diverse cellular systems.

Rapoport Lab identifies the minimal system needed to generate and maintain the tubular ER network - Mar 02, 2017

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How organelle shape is generated and maintained is a fundamental question in cell biology. The endoplasmic reticulum (ER) is particularly intriguing, as it consists of morphologically distinct domains, including the nuclear envelope and the peripheral ER. A major feature of the peripheral ER is a polygonal network of tubules. Previous work has identified proteins involved in ER network formation, the reticulon and REEP/Yop1 families that stabilize the high membrane curvature of tubules in cross-section, and membrane-bound GTPases that fuse ER membranes (the atlastins in metazoans and Sey1p/RHD3 in yeast and plants). In a recent paper in Nature, the Rapoport Lab has determined the minimal components needed to generate the tubular ER network. Reconstitution of S. cerevisiae Sey1p and Yop1p into liposomes yielded a tubular network upon addition of GTP. Maintenance of this network required continuous GTP hydrolysis, as the tubules quickly fragmented upon inhibition of Sey1p. The Yop1p protein could be substituted by a variety of other curvature-stabilizing proteins including those from the reticulon protein family. Interestingly, atlastin could generate a GTP-dependent network all by itself, serving both as a fusogen and curvature-stabilizing protein. These results lead to a model in which the tubular ER network can be generated with a surprisingly small set of membrane proteins that mediate membrane fusion and stabilize curvature. The network corresponds to a steady state balance of continuous membrane fusion and fragmentation.

Shao et al. show how new tail-anchored membrane proteins are given protected time for biosynthesis before being degraded - Jan 26, 2017

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Protein biosynthesis and quality control must be precisely balanced to give new proteins an opportunity to mature before degrading failed intermediates that can cause disease. New work from Shao et al., published in Science, shows how a complex of three chaperones (TRC40, BAG6, and SGTA) triages a class of membrane proteins between biosynthesis and degradation. To do this, they biochemically rebuilt the triage reaction in a test tube with purified proteins and measured the kinetics of substrate flux through the complex. SGTA is the fastest at capturing new substrates to keep them uncommitted from any fate. Priority to biosynthesis is achieved by a ‘private’ and very fast substrate transfer reaction from SGTA to TRC40, which delivers substrates to the endoplasmic reticulum (ER). This transfer is analogous to a baton transfer between two runners in a relay race. Otherwise, BAG6 picks up substrates released from SGTA that have failed transfer to TRC40 and routes them for degradation. This is analogous to a relay race monitor removing a baton dropped because one of the runners was unavailable or out of place. Thus, how long SGTA can hold onto substrates (~20 sec) limits how long they have to mature. Because TRC40 and BAG6 hold onto substrates 15-30 times longer than SGTA, transfer to these chaperones effectively commits substrates to ER targeting or quality control, respectively. This work introduces molecular concepts that are generally applicable to numerous protein triage processes that are crucial for preventing the accumulation of faulty protein by-products linked to various neurodegenerative and aging diseases.

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