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.
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.
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!
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.
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.
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.
Joan Brugge was awarded the American Cancer Society Medal of Honor for Basic Research for her influential contributions to the identification of the protein encoded by the Src oncogene, as well as elucidating the fundamental aspects of events involved in the initiation and progression of cancer. The Medal of Honor is awarded to those who have made the most valuable contributions and impact in saving more lives from cancer through basic research, clinical research, and cancer control. For more information, please see the press release here. Congratulations, Joan!
In a recent article in the Journal of Cell Biology, Jennifer Waters & Talley Lambert from the Nikon Imaging Center (NIC@HMS) review the current practical limitations and compromises that must be made when designing a super-resolution microscopy experiment. They also provide information and resources to help biologists navigate through common pitfalls in specimen preparation and optimization of image acquisition, and discuss errors and artifacts that may compromise the reproducibility of super-resolution microscopy data.
Gene regulatory networks are pivotal for many biological processes. In mouse embryonic stem cells (mESCs), the transcriptional network can be divided into three functionally distinct modules: Polycomb, Core, and Myc. The Polycomb module represses developmental genes, while the Myc module is associated with proliferative functions, and its mis-regulation is linked to cancer development. New work from the Shi lab, published in Molecular Cell (see also the Preview in the same issue), showed that, in mESCs, the Polycomb repressive complex 2 (PRC2)-associated protein EPOP/C17orf96 co-localizes at chromatin with members of the Myc and Polycomb module. EPOP interacts with the transcription elongation factor Elongin BC and the H2B deubiquitinase USP7 to modulate transcriptional processes in mESCs similar to MYC. EPOP is commonly upregulated in human cancer, and its loss impairs the proliferation of several human cancer cell lines. These findings establish EPOP as a transcriptional modulator, which impacts both Polycomb and active gene transcription in mammalian cells, and a possible involvement of EPOP in human cancerogenesis.
The Cell Biology Microscopy Facility (CBMF) is proud to announce that their new lattice light sheet microscope is up and running! This state-of-the art instrument, designed by the lab of Nobel Prize winner Eric Betzig (Janelia Research Campus), provides unprecedented spatiotemporal resolution for imaging live samples in 3-D over time, while minimizing photo-toxicity and photobleaching. We invite you to check it out! Thanks to Talley Lambert of the CBMF for all his work in bringing this instrument to life!