Triana Amen

Phosphorylation modulates clearance of alpha-synuclein inclusions in a yeast model of Parkinson's disease.

Alpha-synuclein (aSyn) is the main component of proteinaceous inclusions known as Lewy bodies (LBs), the typical pathological hallmark of Parkinsons disease (PD) and other synucleinopathies. Although aSyn is phosphorylated at low levels under physiological conditions, it is estimated that ∼90% of aSyn in LBs is phosphorylated at S129 (pS129). Nevertheless, the significance of pS129 in the biology of aSyn and in PD pathogenesis is still controversial. Here, we harnessed the power of budding yeast in order to assess the implications of phosphorylation on aSyn cytotoxicity, aggregation and sub-cellular distribution. We found that aSyn is phosphorylated on S129 by endogenous kinases. Interestingly, phosphorylation reduced aSyn toxicity and the percentage of cells with cytosolic inclusions, in comparison to cells expressing mutant forms of aSyn (S129A or S129G) that mimic the unphosphorylated form of aSyn. Using high-resolution 4D imaging and fluorescence recovery after photobleaching (FRAP) in live cells, we compared the dynamics of WT and S129A mutant aSyn. While WT aSyn inclusions were very homogeneous, inclusions formed by S129A aSyn were larger and showed FRAP heterogeneity. Upon blockade of aSyn expression, cells were able to clear the inclusions formed by WT aSyn. However, this process was much slower for the inclusions formed by S129A aSyn. Interestingly, whereas the accumulation of WT aSyn led to a marked induction of autophagy, cells expressing the S129A mutant failed to activate this protein quality control pathway. The finding that the phosphorylation state of aSyn on S129 can alter the ability of cells to clear aSyn inclusions provides important insight into the role that this posttranslational modification may have in the pathogenesis of PD and other synucleinopathies, opening novel avenues for investigating the molecular basis of these disorders and for the development of therapeutic strategies.

Dynamic JUNQ inclusion bodies are asymmetrically inherited in mammalian cell lines through the asymmetric partitioning of vimentin

Significance We show, for the first time to our knowledge, that vimentin intermediate filaments establish mitotic polarity in dividing mammalian cell lines. By confining damaged, misfolded, and aggregated proteins in JUNQ inclusion bodies, vimentin mediates their asymmetric partitioning during division. We also, to our knowledge, provide the first direct evidence of active proteasomal degradation in dynamic JUNQ inclusion bodies. This work sheds light on an important rejuvenation mechanism in mammalian cells and provides new biological insight into the role of inclusion bodies in regulating aggregation, toxicity, and aging. Aging is associated with the accumulation of several types of damage: in particular, damage to the proteome. Recent work points to a conserved replicative rejuvenation mechanism that works by preventing the inheritance of damaged and misfolded proteins by specific cells during division. Asymmetric inheritance of misfolded and aggregated proteins has been shown in bacteria and yeast, but relatively little evidence exists for a similar mechanism in mammalian cells. Here, we demonstrate, using long-term 4D imaging, that the vimentin intermediate filament establishes mitotic polarity in mammalian cell lines and mediates the asymmetric partitioning of damaged proteins. We show that mammalian JUNQ inclusion bodies containing soluble misfolded proteins are inherited asymmetrically, similarly to JUNQ quality-control inclusions observed in yeast. Mammalian IPOD-like inclusion bodies, meanwhile, are not always inherited by the same cell as the JUNQ. Our study suggests that the mammalian cytoskeleton and intermediate filaments provide the physical scaffold for asymmetric inheritance of dynamic quality-control JUNQ inclusions. Mammalian IPOD inclusions containing amyloidogenic proteins are not partitioned as effectively during mitosis as their counterparts in yeast. These findings provide a valuable mechanistic basis for studying the process of asymmetric inheritance in mammalian cells, including cells potentially undergoing polar divisions, such as differentiating stem cells and cancer cells.

Lipid Droplets Are Essential for Efficient Clearance of Cytosolic Inclusion Bodies

Exposing cells to folding stress causes a subset of their proteins to misfold and accumulate in inclusion bodies (IBs). IB formation and clearance are both active processes, but little is known about their mechanism. To shed light on this issue, we performed a screen with over 4,000 fluorescently tagged yeast proteins for co-localization with a model misfolded protein that marks IBs during folding stress. We identified 13 proteins that co-localize to IBs. Remarkably, one of these IB proteins, the uncharacterized and conserved protein Iml2, exhibited strong physical interactions with lipid droplet (LD) proteins. Indeed, we here show that IBs and LDs are spatially and functionally linked. We further demonstrate a mechanism for IB clearance via a sterol-based metabolite emanating from LDs. Our findings therefore uncover a function for Iml2 and LDs in regulating a critical stage of cellular proteostasis.

Dynamic droplets: the role of cytoplasmic inclusions in stress, function, and disease

Neurodegenerative diseases and other proteinopathies constitute a class of several dozen illnesses etiologically linked to pathological protein misfolding and aggregation. Because of this strong association with disease pathology, cell death, and aging, accumulation of proteins in aggregates or aggregation-associated structures (inclusions) has come to be regarded by many as a deleterious process, to be avoided if possible. Recent work has led us to see inclusion structures and disordered aggregate-like protein mixtures (which we call dynamic droplets) in a new light: not necessarily as a result of a pathological breakdown of cellular order, but as an elaborate cellular architecture regulating function and stress response. In this review, we discuss what is currently known about the role of inclusion structures in cellular homeostasis, stress response, toxicity, and disease. We will focus on possible mechanisms of aggregate toxicity, in contrast to the homeostatic function of several inclusion structures.

Asymmetric Inheritance of Aggregated Proteins and Age Reset in Yeast Are Regulated by Vac17-Dependent Vacuolar Functions

Summary Age can be reset during mitosis in both yeast and stem cells to generate a young daughter cell from an aged and deteriorated one. This phenomenon requires asymmetry-generating genes (AGGs) that govern the asymmetrical inheritance of aggregated proteins. Using a genome-wide imaging screen to identify AGGs in Saccharomyces cerevisiae, we discovered a previously unknown role for endocytosis, vacuole fusion, and the myosin-dependent adaptor protein Vac17 in asymmetrical inheritance of misfolded proteins. Overproduction of Vac17 increases deposition of aggregates into cytoprotective vacuole-associated sites, counteracts age-related breakdown of endocytosis and vacuole integrity, and extends replicative lifespan. The link between damage asymmetry and vesicle trafficking can be explained by a direct interaction between aggregates and vesicles. We also show that the protein disaggregase Hsp104 interacts physically with endocytic vesicle-associated proteins, such as the dynamin-like protein, Vps1, which was also shown to be required for Vac17-dependent sequestration of protein aggregates. These data demonstrate that two physiognomies of aging—reduced endocytosis and protein aggregation—are interconnected and regulated by Vac17.

Dynamic Sumoylation of a Conserved Transcription Corepressor Prevents Persistent Inclusion Formation during Hyperosmotic Stress

Cells are often exposed to physical or chemical stresses that can damage the structures of essential biomolecules. Stress-induced cellular damage can become deleterious if not managed appropriately. Rapid and adaptive responses to stresses are therefore crucial for cell survival. In eukaryotic cells, different stresses trigger post-translational modification of proteins with the small ubiquitin-like modifier SUMO. However, the specific regulatory roles of sumoylation in each stress response are not well understood. Here, we examined the sumoylation events that occur in budding yeast after exposure to hyperosmotic stress. We discovered by proteomic and biochemical analyses that hyperosmotic stress incurs the rapid and transient sumoylation of Cyc8 and Tup1, which together form a conserved transcription corepressor complex that regulates hundreds of genes. Gene expression and cell biological analyses revealed that sumoylation of each protein directs distinct outcomes. In particular, we discovered that Cyc8 sumoylation prevents the persistence of hyperosmotic stress-induced Cyc8-Tup1 inclusions, which involves a glutamine-rich prion domain in Cyc8. We propose that sumoylation protects against persistent inclusion formation during hyperosmotic stress, allowing optimal transcriptional function of the Cyc8-Tup1 complex.

Structural Basis for Modulation of Quality Control Fate in a Marginally Stable Protein

Summary The human von Hippel-Lindau (VHL) tumor suppressor is a marginally stable protein previously used as a model substrate of eukaryotic refolding and degradation pathways. When expressed in the absence of its cofactors, VHL cannot fold and is quickly degraded by the quality control machinery of the cell. We combined computational methods with in vivo experiments to examine the basis of the misfolding propensity of VHL. By expressing a set of randomly mutated VHL sequences in yeast, we discovered a more stable mutant form. Subsequent modeling suggested the mutation had caused a conformational change affecting cofactor and chaperone interaction, and this hypothesis was then confirmed by additional knockout and overexpression experiments targeting a yeast cofactor homolog. These findings offer a detailed structural basis for the modulation of quality control fate in a model misfolded protein and highlight burial mode modeling as a rapid means to detect functionally important conformational changes in marginally stable globular domains.

Integrative modules for efficient genome engineering in yeast

We present a set of vectors containing integrative modules for efficient genome integration into the commonly used selection marker loci of the yeast Saccharomyces cerevisiae. A fragment for genome integration is generated via PCR with a unique set of short primers and integrated into HIS3, URA3, ADE2, and TRP1 loci. The desired level of expression can be achieved by using constitutive (TEF1p, GPD1p), inducible (CUP1p, GAL1/10p), and daughter-specific (DSE4p) promoters available in the modules. The reduced size of the integrative module compared to conventional integrative plasmids allows efficient integration of multiple fragments. We demonstrate the efficiency of this tool by simultaneously tagging markers of the nucleus, vacuole, actin, and peroxisomes with genomically integrated fluorophores. Improved integration of our new pDK plasmid series allows stable introduction of several genes and can be used for multi-color imaging. New bidirectional promoters (TEF1p-GPD1p, TEF1p-CUP1p, and TEF1p-DSE4p) allow tractable metabolic engineering.

Yeast screening platform identifies FDA-approved drugs that reduce Aβ oligomerization

The older the average person alive today becomes, the more instances of neurodegeneration are observed worldwide. Alzheimers disease is the most common neurodegenerative disorder preferentially affecting older individuals with 26.6 million cases recorded in 2006. It is estimated that worldwide prevalence will rise to 100 million cases by 2050 [1]. There is currently no effective treatment nor preventative therapy for Alzheimers disease, and no definitive diagnosis besides post-mortem pathology. Diagnosis is based on the presence of intracellular inclusions of hyperphosphorylated microtubule associated protein tau and extracellular plaques consisting of amyloid beta (Aβ) peptide [2]. Aβ is a small peptide 40-42 aa in length, formed via amyloid precursor protein (APP) cleavage that results in Aβ release into the extracellular space. Aβ is normally observed circulating in the cerebrospinal fluid of mammals, and is produced mostly in the central nervous system [3]. Although Aβ aggregates are the major pathological hallmark of Alzheimer’s disease, the mechanisms of Aβ induced neurotoxicity is not well understood, and even less is known about the physiological function of Aβ peptide. Absence of APP results in embryonic development defects due to irregular migration of cerebral cortex neurons [4]. Recent work also indicates that Aβ peptide concentrations in the CNS modulate synaptic transmission and synaptic hyperactivity via direct binding to APP [5]. In addition to the pathological connection between Aβ deposition and Alzheimer’s, a genetic connection has been mapped as well. Multiple mutations in APP and its cleaving enzymes increase the risk of Alzheimer disease onset [6-8]. Some mutations alter the cleavage of APP, resulting in a shifted ratio of Aβ1-42 to Aβ1-40, thus increasing the proportion of the more aggregation-prone species. Other mutations affect the aggregation propensity of the Aβ1-40/42 peptide itself [9]. As with another aggregation-prone disease associated protein, α-synuclein in Parkinson’s disease, an increase in Aβ production results in its aggregation and the early onset of Alzheimer’s disease [10]. While most models of Aβ cellular pathology assume that toxicity stems from its aggregation propensity [11], there has been vigorous debate about whether the toxicity stems mostly from extracellular high-molecular weight amyloid plaques, or mostly from the low molecular weight oligomers [12-14]. Aβ can be re-incorporated into the cytoplasm after extra-cellular cleavage, and much evidence has accumulated over the past several years that favors the small intracellular oligomers as the toxic aggregate species [15]. Particularly convincing are seminal studies in simple models of disease: C. elegans and mice, demonstrating a link between aging, insulin signaling, and toxicity driven by low molecular weight oligomers of Aβ [16-18]. Another study, modeling Alzheimers disease in mice, showed that cognitive impairment precedes mature fibrillar deposits [19]. Due to the multifaceted and multifactorial nature of Alzheimer’s physiology, no single model can fully recapitulate disease. Mice are currently the model system that most closely resembles human beings while still being capable of exhibiting features of aging on a time-scale in line with the duration of a typical PhD or postdoc. Mice can also be scored for learning and memory defects, as well as motor neuron function. However, it is equally the case that a mouse that is artificially expressing extremely high amounts of Aβ in its brain will not accurately recapitulate the memory neuronal circuits of a 75-year-old human being. At the same time, mammalian models are sometimes less tractable and may offer less molecular and cellular detail of pathology and toxic events. Simpler models of Aβ toxicity have been exploited with tremendous success towards greatly improving our understanding of the cellular pathology of molecular events associated with Alzheimer’s, as well as other neurodegenera-