Amyloid formation as a protective mechanism and a new Alzheimer's disease model

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 2011.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Cataloged from student submitted PDF version of thesis.Includes bibliographical references.Numerous neurodegenerative diseases are pathologically characterized by idiosyncratic protein amyloid inclusions. Not surprisingly amyloid fibrils have long been proposed to be the toxic protein species in these neurodegenerative diseases. However, more recent work has begun to suggest that the formation of ordered inclusions serves a protective role and that soluble oligomers on pathway to amyloid formation cause neuronal death. In that regard, ordered protein inclusions, such as aggresomes, have also been shown to facilitate the asymmetric inheritance of protein damage during the mitoses of cells ranging from E. coli to human stem cells. Yeast prion proteins are another group of proteins capable of adapting an amyloid conformation. The self-templating amyloid fold allows yeast prions to act as non-Mendelian elements of inheritance. We have shown that yeast prion amyloid fibrils, especially upon prion protein overexpression, localize to the IPOD (insoluble protein deposit), an ordered inclusion proximal to the vacuole, and that the majority of the prion amyloid is asymmetrically inherited upon cell division. I used the yeast prion Rnq1 to investigate how amyloid formation contributes to proteotoxicity. Ectopic overexpression of Rnq1 was extremely toxic, but only if the endogenous Rnq1 protein had adopted its amyloid conformation. The Hsp40 co-chaperone Sis1 was able to counteract the Rnq1-induced toxicity when co-overexpressed. In collaboration with Doug Cyr's lab I showed that Sis1-mediated amyloid formation was cytoprotective and that disordered non-amyloid aggregates induced toxicity. These results provide evidence that the formation of ordered inclusions can be cytoprotective. I further characterized Rnq1 toxicity, conducted two genome-ide screens for modifiers and found that Rnq1 induced a G2/M cell cycle arrest. Rnq1 overexpression resulted in the mislocalization of the core spindle pole body component Spc42 to the IPOD and an unduplicated spindle pole body. In mammalian cells aggresomes localize to centrosomes, the mammalian equivalent of the yeast spindle pole body. The finding that a yeast prion can interact with a spindle pole body component represents a new connection between the IPOD and aggresomes. Lastly, I studied a yeast model of A[beta] 1-42 toxicity. Accumulation of the amyloid beta peptide is thought to be causal in both sporadic and familial Alzheimer's disease. In collaboration with Kent Matlack I developed a yeast model that expressed A[beta] 1-42 in a manner recapitulating mammalian A[beta] 1-42 generation and that was amenable to screens for genetic modifiers of A[beta] 1-42 toxicity. The screen identified the yeast homolog of PICALM, a known Alzheimer's disease risk factor. I showed that A[beta] 1-42 expression resulted in a defect in endocytosis that could be reverted by several of the genetic suppressors. In collaboration with the Caldwell lab, we showed that the genetic modifiers also modulated A[beta] 1-42 toxicity in a neuronal setting, C. elegans glutamatergic neurons. Finally, we showed that PICALM could protect primary rat cortical neuron cultures from A[beta] oligomer toxicity.by Sebastian Treusch.Ph.D

Amyloid Deposits: Protection Against Toxic Protein Species?

Neurodegenerative diseases ranging from Alzheimer’s disease and polyglutamine diseases to transmissible spongiform encephalopathies are associated with the aggregation and accumulation of misfolded proteins. In several cases the intracellular and extracellular protein deposits contain a fibrillar protein species called amyloid. However while amyloid deposits are hallmarks of numerous neurodegenerative diseases, their actual role in disease progression remains unclear. Especially perplexing is the often poor correlation between protein deposits and other markers of neurodegeneration. As a result the question remains whether amyloid deposits are the disease causing species, the consequence of cellular disease pathology or even the result of a protective cellular response to misfolded protein species. Here we highlight studies that suggest that accumulation and sequestration of misfolded protein in amyloid inclusion bodies and plaques can serve a protective function. Furthermore, we discuss how exceeding the cellular capacity for protective deposition of misfolded proteins may contribute to the formation of toxic protein species

Genetic interactions contribute less than additive effects to quantitative trait variation in yeast.

Genetic mapping studies of quantitative traits typically focus on detecting loci that contribute additively to trait variation. Genetic interactions are often proposed as a contributing factor to trait variation, but the relative contribution of interactions to trait variation is a subject of debate. Here we use a very large cross between two yeast strains to accurately estimate the fraction of phenotypic variance due to pairwise QTL-QTL interactions for 20 quantitative traits. We find that this fraction is 9% on average, substantially less than the contribution of additive QTL (43%). Statistically significant QTL-QTL pairs typically have small individual effect sizes, but collectively explain 40% of the pairwise interaction variance. We show that pairwise interaction variance is largely explained by pairs of loci at least one of which has a significant additive effect. These results refine our understanding of the genetic architecture of quantitative traits and help guide future mapping studies

Rare variants contribute disproportionately to quantitative trait variation in yeast.

How variants with different frequencies contribute to trait variation is a central question in genetics. We use a unique model system to disentangle the contributions of common and rare variants to quantitative traits. We generated ~14,000 progeny from crosses among 16 diverse yeast strains and identified thousands of quantitative trait loci (QTLs) for 38 traits. We combined our results with sequencing data for 1011 yeast isolates to show that rare variants make a disproportionate contribution to trait variation. Evolutionary analyses revealed that this contribution is driven by rare variants that arose recently, and that negative selection has shaped the relationship between variant frequency and effect size. We leveraged the structure of the crosses to resolve hundreds of QTLs to single genes. These results refine our understanding of trait variation at the population level and suggest that studies of rare variants are a fertile ground for discovery of genetic effects

Genetics of single-cell protein abundance variation in large yeast populations

Many DNA sequence variants influence phenotypes by altering gene expression. Our understanding of these variants is limited by sample sizes of current studies and by measurements of mRNA rather than protein abundance. We developed a powerful method for identifying genetic loci that influence protein expression in very large populations of the yeast Saccharomyes cerevisiae. The method measures single-cell protein abundance through the use of green-fluorescent-protein tags. We applied this method to 160 genes and detected many more loci per gene than previous studies. We also observed closer correspondence between loci that influence protein abundance and loci that influence mRNA abundance of a given gene. Most loci cluster at hotspot locations that influence multiple proteins - in some cases, more than half of those examined. The variants that underlie these hotspots have profound effects on the gene regulatory network and provide insights into genetic variation in cell physiology between yeast strains

An intrinsically disordered yeast prion arrests the cell cycle by sequestering a spindle pole body component

Intrinsically disordered proteins play causative roles in many human diseases. Their overexpression is toxic in many organisms, but the causes of toxicity are opaque. In this paper, we exploit yeast technologies to determine the root of toxicity for one such protein, the yeast prion Rnq1. This protein is profoundly toxic when overexpressed but only in cells carrying the endogenous Rnq1 protein in its [RNQ[superscript +]] prion (amyloid) conformation. Surprisingly, toxicity was not caused by general proteotoxic stress. Rather, it involved a highly specific mitotic arrest mediated by the Mad2 cell cycle checkpoint. Monopolar spindles accumulated as a result of defective duplication of the yeast centrosome (spindle pole body [SPB]). This arose from selective Rnq1-mediated sequestration of the core SPB component Spc42 in the insoluble protein deposit (IPOD). Rnq1 does not normally participate in spindle pole dynamics, but it does assemble at the IPOD when aggregated. Our work illustrates how the promiscuous interactions of an intrinsically disordered protein can produce highly specific cellular toxicities through illicit, yet highly specific, interactions with the proteome

Jitter-correction for IR/UV-XUV pump-probe experiments at the FLASH free-electron laser

In pump-probe experiments employing a free-electron laser (FEL) in combination with a synchronized optical femtosecond laser, the arrival-time jitter between the FEL pulse and the optical laser pulse often severely limits the temporal resolution that can be achieved. Here, we present a pump-probe experiment on the UV-induced dissociation of 2,6-difluoroiodobenzene (C6H3F2I) molecules performed at the FLASH FEL that takes advantage of recent upgrades of the FLASH timing and synchronization system to obtain high-quality data that are not limited by the FEL arrival-time jitter. We discuss in detail the necessary data analysis steps and describe the origin of the time-dependent effects in the yields and kinetic energies of the fragment ions that we observe in the experiment

Alignment, orientation, and Coulomb explosion of difluoroiodobenzene studied with the pixel imaging mass spectrometry (PImMS) camera

Citation: Amini, K., Boll, R., Lauer, A., Burt, M., Lee, J. W. L., Christensen, L., . . . Rolles, D. (2017). Alignment, orientation, and Coulomb explosion of difluoroiodobenzene studied with the pixel imaging mass spectrometry (PImMS) camera. Journal of Chemical Physics, 147(1). doi:10.1063/1.4982220Laser-induced adiabatic alignment and mixed-field orientation of 2,6-difluoroiodobenzene (C6H3F2I) molecules are probed by Coulomb explosion imaging following either near-infrared strong-field ionization or extreme-ultraviolet multi-photon inner-shell ionization using free-electron laser pulses. The resulting photoelectrons and fragment ions are captured by a double-sided velocity map imaging spectrometer and projected onto two position-sensitive detectors. The ion side of the spectrometer is equipped with a pixel imaging mass spectrometry camera, a time-stamping pixelated detector that can record the hit positions and arrival times of up to four ions per pixel per acquisition cycle. Thus, the time-of-flight trace and ion momentum distributions for all fragments can be recorded simultaneously. We show that we can obtain a high degree of one-and three-dimensional alignment and mixed-field orientation and compare the Coulomb explosion process induced at both wavelengths. © 2017 Author(s)

Alternatives to vitamin B 1 uptake revealed with discovery of riboswitches in multiple marine eukaryotic lineages

Vitamin B 1 (thiamine pyrophosphate, TPP) is essential to all life but scarce in ocean surface waters. In many bacteria and a few eukaryotic groups thiamine biosynthesis genes are controlled by metabolite-sensing mRNA-based gene regulators known as riboswitches. Using available genome sequences and transcriptomes generated from ecologically important marine phytoplankton, we identified 31 new eukaryotic riboswitches. These were found in alveolate, cryptophyte, haptophyte and rhizarian phytoplankton as well as taxa from two lineages previously known to have riboswitches (green algae and stramenopiles). The predicted secondary structures bear hallmarks of TPP-sensing riboswitches. Surprisingly, most of the identified riboswitches are affiliated with genes of unknown function, rather than characterized thiamine biosynthesis genes. Using qPCR and growth experiments involving two prasinophyte algae, we show that expression of these genes increases significantly under vitamin B 1 -deplete conditions relative to controls. Pathway analyses show that several algae harboring the uncharacterized genes lack one or more enzymes in the known TPP biosynthesis pathway. We demonstrate that one such alga, the major primary producer Emiliania huxleyi, grows on 4-amino-5-hydroxymethyl-2-methylpyrimidine (a thiamine precursor moiety) alone, although long thought dependent on exogenous sources of thiamine. Thus, overall, we have identified riboswitches in major eukaryotic lineages not known to undergo this form of gene regulation. In these phytoplankton groups, riboswitches are often affiliated with widespread thiamine-responsive genes with as yet uncertain roles in TPP pathways. Further, taxa with 'incomplete' TPP biosynthesis pathways do not necessarily require exogenous vitamin B 1, making vitamin control of phytoplankton blooms more complex than the current paradigm suggests. © 2014 International Society for Microbial Ecology. All rights reserved