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Reck-Peterson Lab describes dynein-driven spatial organization of protein aggregates in fungal model system - Apr 20, 2015

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Organisms across the evolutionary spectrum have evolved mechanisms to maintain the integrity of the cellular proteome. Among these mechanisms are spatial protein quality control pathways in which damaged and misfolded cellular proteins are actively sequestered at unique subcellular structures in response to acute stress. This mitigates the deleterious effects of these aberrant protein species, which can include advanced cellular aging and cytotoxicity leading to cell death. Despite the universal importance of such spatial control of the proteome, there is considerable mechanistic diversity throughout the evolutionary scale regarding how this control is achieved. In a recent publication in Cell Reports (Egan and McClintock et al., PMID 25865884) the Reck-Peterson Lab expanded on the known evolutionary diversity of spatial quality control mechanisms by examining the subcellular organization of heat-induced protein aggregates in filamentous fungi, which are of substantial health and economic importance and serve as a model for transport processes in other polarized eukaryotic cells. Using Aspergillus nidulans, the Reck-Peterson group found that protein aggregates are actively organized at periodic subcellular structures in a process dependent on microtubules and their associated motor dynein. In addition, they found that sustained stress and increased burdening of this spatial quality control pathway can lead to defects in other microtubule-based transport processes. Given the significance of protein aggregation and polarized transport in neurodegenerative disorders, as well as the pathogenicity of many filamentous fungi, this work suggests several avenues of further investigation for understanding and combating disease.

Pellman Lab shows that whole genome duplication can accelerate evolutionary adaptation - Mar 26, 2015

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Doubling the compete sets of chromosomes, or tetraploidy, occurs commonly during organismal evolution and also is frequent in disease states, such as cancer.  Theory suggests that increased chromosome sets might promote evolutionary adaptation, especially if many available beneficial mutations are dominant. Whole genome duplications can also alter cell physiology in poorly understood ways.  For example, whole genome duplications often cause genetic instability.  Using in vitro evolution of yeast, the Pellman group demonstrates that tetraploidy can increase the rate of evolutionary adaptation when cells are grown in a poor nutrient environment (published recently in Nature).  Two different mathematical modeling approaches (collaborations with Franziska Michor’s and Roy Kishony’s labs) suggest that tetraploids have an increased rate of adaptive mutations and these mutations have stronger fitness effects.  Whole genome sequencing of multiple evolved clones verified increased frequencies of mutations and chromosome rearrangements in tetraploids.  A class of mutations was discovered that provide a fitness advantage only to the tetraploid strains.  Together, these results provide quantitative analysis of the long discussed role of polyploidy in evolutionary adaptation.

Figure legend:

Evolution experiments were performed by batch culture of genetically identical strains, differing only by ploidy.  The experiment starts with a 50:50 mix of otherwise identical YFP and CFP-labeled cells.  Deviation from 50% YFP cells indicates adaptation.

Shi Lab uncovers a molecular program that specifies early neuronal morphology - Mar 11, 2015

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Neurons are among the most polarized cells in nature, having emerged more than a half-billion years ago in metazoans to receive, process, and transmit information. The basic instructions to polarize a neuron appear to be intrinsically encoded, but what drives neurons to their extreme morphology is largely unknown. In a recent article in Genes and Development, the Shi Lab describes a molecular program that induces the early morphology of neurons through a deeply conserved, metazoan-specific zinc finger protein Unkempt. They find that ectopic expression of Unkempt confers neuronal-like morphology to cells of different nonneuronal lineages, while its depletion in mouse embryonic brain disrupts the shape of migrating neurons. The authors show that Unkempt functions as a sequence-specific RNA-binding protein that targets coding regions of a defined set of ubiquitously expressed messages linked to protein metabolism and regulation of the cytoskeleton. They further demonstrate that RNA binding is required for Unkempt-induced remodeling of cellular shape and is directly coupled to a reduced production of the encoded proteins. Thus, during embryonic development, Unkempt controls a translationally regulated cell morphology program to ensure proper structuring of the nervous system.

Moazed Lab uncovers a cellular safeguard that prevents the assembly of inactive Argonaute complexes - Mar 09, 2015

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Small RNA molecules are familiar as negative regulators of endogenous protein-coding genes, but their more deeply conserved function is to ensure genomic stability by keeping repetitive and parasitic elements in check. In the fission yeast Schizosaccharomyces pombe, small RNAs accomplish this task by guiding heterochromatin formation at DNA regions flanking the centromere of each chromosome. The small RNA effector complex that targets the heterochromatin machinery to pericentromeric domains, called RITS, includes an Argonaute protein and a subunit bearing glycine-tryptophan (GW) repeats. The GW motif is a feature of Argonaute-interacting proteins that is conserved across several kingdoms of life and in silencing pathways both nuclear and cytoplasmic. A recent publication from the Moazed Lab has now uncovered a mechanism of ordered assembly for the GW protein-containing RITS complex that prevents Argonautes not yet programmed with a guide RNA from associating with GW repeat-containing proteins. In addition, they show that the poorly characterized fungal protein Arb1 is essential for loading small RNAs onto the S. pombe Argonaute in vitro and for RITS assembly in vivo. Altogether, the results demonstrate that a GW protein can act as a sensor of an Argonaute’s small RNA loading state. Finally, the work suggests that GW proteins play an evolutionarily conserved role in restricting the recruitment of downstream silencing machineries as varied as RNA deadenylases and chromatin-modifying enzymes exclusively to mature, competent Argonaute complexes.

(Holoch and Moazed, Nat. Struct. Mol. Biol., PMID 25730778)

Five members of the Cell Bio community profiled in the Dimensions of HMS exhibit - Mar 09, 2015

Van Vactor

The Dimensions of Harvard Medical School, in the Transit Gallery of Gordon Hall, is a collection of photographs and profiles that captures a wide representation of the HMS community.  Featured are 5 members of the Cell Biology community: faculty members Joan Brugge, Tomas Kirchhausen, and Davie Van Vactor; Nikon Imaging Center Director Jennifer Waters; and Research Operations Manager Karen Easley. Their profiles are on display until April 7th.

Gygi Lab develops methods to identify and quantify thousands of proteins in non-standard model organisms - Mar 09, 2015

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Mass spectrometry-based proteomics enables the global identification and quantification of proteins and their posttranslational modifications in complex biological samples. However, proteomic analysis requires a complete and accurate reference set of proteins and is therefore largely restricted to model organisms with sequenced genomes. In collaboration, the Gygi and Kirschner labs demonstrated the feasibility of deep genome-free proteomics by using a reference proteome derived from heterogeneous mRNA data. They identify more than 11,000 proteins from the egg of the African clawed frog and estimate each protein's abundance with approximately 2-fold precision. To facilitate proteomics in nonmodel organisms, the researchers made their platform available as an online resource that converts heterogeneous mRNA data into a protein reference set.  This work was published in Current Biology.

Figure: Xenopus laevis ovary

Danial Lab probes the utility of phospho-BAD BH3 mimicry in restoring functional β-cell mass in diabetes - Feb 19, 2015

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Autoimmune destruction of insulin-producing β-cells leaves individuals with type 1 diabetes (T1D) insulin dependent for life. Strategies that replace or regenerate β-cells, including islet transplantation and β-cell generation from non-β-cell precursors are potential therapies in T1D. However, insufficient β-cell proliferation, survival, and insulin secretory response to glucose can limit the benefits of these strategies. As such, molecular pathways or strategies that simultaneously enhance β-cell mass and glucose signaling are of therapeutic interest. The Danial Lab has identified such strategy. Previous work showed that the BCL-2 family protein BAD stimulates the β-cell glucose response and insulin secretion through phosphorylation of a defined residue within an amphipathic α-helix known as the BCL-2 Homology (BH)-3 domain. This modification neutralizes BAD’s apoptotic function by preventing its capacity to bind and inactivate pro-survival BCL-2, BCL-XL and BCL-w proteins, and simultaneously triggers its ability to directly activate the glucose-metabolizing enzyme glucokinase (GK). However, whether beyond neutralizing BAD’s apoptotic activity, BAD phosphorylation has active, cell autonomous effects on b-cell survival was not known. In the February 2015 issue of Cell Reports, new findings from the Danial Lab show that genetic and pharmacologic approaches to mimic BAD phosphorylation within its BH3 helix not only stimulate insulin secretion but protect β-cells from death induced by T1D-related stress stimuli, including inflammatory, ER and oxidative stress. β-cell survival in this setting is not merely due to the inability of phospho-BAD to suppress pro-survival BCL-2 proteins but requires its activation of GK. Strikingly, the β-cell-autonomous benefits of phospho-BAD mimicry lead to improved donor islet engraftment in transplanted diabetic mice, increased β-cell viability in islet grafts, restoration of insulin release, and diabetes reversal. These findings highlight the utility of BAD phospho-BH3 mimetic approaches in augmenting functional β-cell mass in diabetes.  

Rapoport Lab recapitulates retro-translocation of misfolded proteins with purified components - Dec 11, 2014

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Proteins that are translocated into the endoplasmic reticulum (ER) undergo quality control so that only correctly folded proteins are moved on in the secretory pathway. If a protein cannot reach its native folded state, it is ultimately transported back into the cytosol, poly-ubiquitinated, and degraded by the proteasome, a process called ER-associated protein degradation (ERAD). How proteins are retro-translocated across the ER membrane and moved into the cytosol is only poorly understood. Previous work demonstrated that the ubiquitin ligase Hrd1p is the only membrane component needed for a basic ERAD process. Now, the Rapoport group shows that key steps of basic ERAD can be recapitulated with purified components (Stein et al., Cell 158, 1375-1388). Hrd1p binds misfolded protein substrates, discriminating them from folded proteins. Subsequently, both Hrd1p and substrate are poly-ubiquitinated. Next, the Cdc48p ATPase complex binds and uses the energy of ATP hydrolysis to release substrate from Hrd1p. Finally, ubiquitin chains are trimmed by the de-ubiquitinating enzyme Otu1p, which is recruited and activated by the Cdc48p complex. The Cdc48-dependent extraction of poly-ubiquitinated proteins from the membrane can be reproduced with reconstituted proteoliposomes. These results provide a major step forward towards the goal to recapitulate ERAD with purified components and to elucidate the molecular mechanism of the process.

Rapoport Lab outlines a theoretical model that explains nearly all observed ER morphologies - Dec 11, 2014

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The endoplasmic reticulum (ER) is an important membrane-bound organelle in all eukaryotic cells. Depending on cell type and functional state, the ER membrane can adopt different morphologies, including a network of interconnected tubules, and sheets that can contain fenestrations or be stacked on top of each other.  How these different morphologies are generated is unclear. A collaboration of different groups, including the Rapoport group, resulted in a recent paper that presents a comprehensive theoretical model, which explains the formation and interconversion of virtually all known ER morphologies (Shemesh et al., 2014, Proc. Natl. Acad. Sci. USA PMID:25404289). The model is based on two types of membrane-shaping proteins (R- and S-type proteins), exemplified by the reticulons and lunapark, which both stabilize the high membrane curvature in cross-sections of tubules and sheet edges, but favor straight or concave sheet edges, respectively. Dependent on the concentrations of R- and S-type proteins, membrane morphologies can be generated that consist of tubules, sheets, sheet fenestrations, and sheet stacks with helicoidal connections. In a tubular ER network, lunapark stabilizes three-way junctions, i.e. small triangular sheets with concave edges. The model agrees with experimental observations and explains how curvature-stabilizing proteins determine ER morphology.