| 1. |
- Cubillos, Francisco A, et al.
(författare)
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High-resolution mapping of complex traits with a four-parent advanced intercross yeast population.
- 2013
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Ingår i: Genetics. - : Oxford University Press (OUP). - 1943-2631. ; 195:3, s. 1141-55
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Tidskriftsartikel (refereegranskat)abstract
- A large fraction of human complex trait heritability is due to a high number of variants with small marginal effects and their interactions with genotype and environment. Such alleles are more easily studied in model organisms, where environment, genetic makeup, and allele frequencies can be controlled. Here, we examine the effect of natural genetic variation on heritable traits in a very large pool of baker's yeast from a multiparent 12th generation intercross. We selected four representative founder strains to produce the Saccharomyces Genome Resequencing Project (SGRP)-4X mapping population and sequenced 192 segregants to generate an accurate genetic map. Using these individuals, we mapped 25 loci linked to growth traits under heat stress, arsenite, and paraquat, the majority of which were best explained by a diverging phenotype caused by a single allele in one condition. By sequencing pooled DNA from millions of segregants grown under heat stress, we further identified 34 and 39 regions selected in haploid and diploid pools, respectively, with most of the selection against a single allele. While the most parsimonious model for the majority of loci mapped using either approach was the effect of an allele private to one founder, we could validate examples of pleiotropic effects and complex allelic series at a locus. SGRP-4X is a deeply characterized resource that provides a framework for powerful and high-resolution genetic analysis of yeast phenotypes and serves as a test bed for testing avenues to attack human complex traits.
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| 2. |
- Ibstedt, Sebastian, 1983
(författare)
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Adaptation and Protein Quality Control Under Metalloid Stress
- 2015
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Toxic metals and metalloids are emerging as major environmental pollutants, having ecological consequences as well as being linked to a broad range of degenerative conditions in animals, plants and humans. While the toxicity of several metalloids is well established, the underlying molecular mechanisms are often not clear. Several human degenerative diseases are linked to misfolding and aggregation of specific proteins. I have shown that many of these proteins have yeast homologs that are particularly prone to misfolding and aggregation during arsenite exposure. The yeast proteins are highly dependent on chaperones for proper folding, whereas arsenite is capable of inhibiting chaperone function as well as causing additional aggregation through a propagating effect. Computational analyses further revealed that aggregation-prone proteins are abundant and have a high translation rate, but are down-regulated when the cell encounters arsenite. The mechanisms behind tellurite toxicity have eluded scientists for over a century. By using a genome-wide phenotypic screen, it was found that tellurite toxicity is linked to accumulation of elemental tellurium. Sulfate metabolism and mitochondrial respiration were found to mediate toxicity. An understanding of cellular function requires knowledge of the evolutionary processes that have formed it. However, distinguishing between adaptive and non-adaptive differentiation remains an extraordinary challenge within evolutionary biology. The last part of this thesis tests a method for exposing the role of natural selection in evolution of stress tolerance. Analysis of concerted optimization of performance in distinct fitness components followed by mapping of the genetic basis for the optimizations, compellingly suggests that the method is able to detect natural selection. The results presented here are likely to be relevant in gaining a better understanding of the mechanisms behind arsenite and tellurite poisoning and cellular defense, and may form a basis for elucidating evolutionary adaptations in other environments and organisms.
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| 3. |
- Ibstedt, Sebastian, 1983, et al.
(författare)
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Concerted Evolution of Life Stage Performances Signals Recent Selection on Yeast Nitrogen Use.
- 2015
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 1537-1719 .- 0737-4038. ; 32:1, s. 153-161
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Tidskriftsartikel (refereegranskat)abstract
- Exposing natural selection driving phenotypic and genotypic adaptive differentiation is an extraordinary challenge. Given that an organism's life stages are exposed to the same environmental variations, we reasoned that fitness components, such as the lag, rate, and efficiency of growth, directly reflecting performance in these life stages, should often be selected in concert. We therefore conjectured that correlations between fitness components over natural isolates, in a particular environmental context, would constitute a robust signal of recent selection. Critically, this test for selection requires fitness components to be determined by different genetic loci. To explore our conjecture, we exhaustively evaluated the lag, rate, and efficiency of asexual population growth of natural isolates of the model yeast Saccharomyces cerevisiae in a large variety of nitrogen-limited environments. Overall, fitness components were well correlated under nitrogen restriction. Yeast isolates were further crossed in all pairwise combinations and coinheritance of each fitness component and genetic markers were traced. Trait variations tended to map to quantitative trait loci (QTL) that were private to a single fitness component. We further traced QTLs down to single-nucleotide resolution and uncovered loss-of-function mutations in RIM15, PUT4, DAL1, and DAL4 as the genetic basis for nitrogen source use variations. Effects of SNPs were unique for a single fitness component, strongly arguing against pleiotropy between lag, rate, and efficiency of reproduction under nitrogen restriction. The strong correlations between life stage performances that cannot be explained by pleiotropy compellingly support adaptive differentiation of yeast nitrogen source use and suggest a generic approach for detecting selection.
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| 4. |
- Ibstedt, Sebastian, 1983, et al.
(författare)
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Dissection of advanced intercross lines provides information on evolution of yeast in shifting metal abundances
- 2012
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Ingår i: Experimental Approaches to Evolution and Ecology using Yeast (EMBO, Heidelberg, October 2012). ; 2012
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Metals can be friends or foes, depending on their chemical reactivity, dose or mode of exposure. Unfortunately, a general perspective on the importance of different processes for maintaining evolutionary flexibility and physiological homeostasis with regard to metal exposure is lacking. In order to understand the processes that contribute to metal toxicity and resistance in natural populations of Saccharomyces cerevisiae, we have analyzed a twelfth generation intercross between geographically and ecologically distinct populations. Large-scale phenotyping of highly recombined segregants allows us to pinpoint causative alleles to narrow intervals and to make inferences about the evolutionary history of complex traits in natural populations with regard to pleiotropy and epistasis. We show that metal detoxification in Saccharomyces cerevisiae is highly dependent on specific stress, while epistasis depends on population-specific alleles. These results are consistent with an evolutionary history of bottle-necks, rapid dispersion into ecologically differing habitats followed by independent evolutionary paths.
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| 5. |
- Ibstedt, Sebastian, 1983, et al.
(författare)
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Global analysis of protein aggregation in Saccharomyces cerevisiae
- 2013
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Ingår i: Yeast. - : Wiley. - 0749-503X. ; 30:S1
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Konferensbidrag (refereegranskat)abstract
- Protein misfolding and aggregation is associated with various neurodegenerative and age-related disorders. In this study, we isolated aggregation-prone proteins from Saccharomyces cerevisiae and identified several physicochemical characteristics that are linked to physiological, arsenite-induced and age-dependent protein aggregation. Protein abundance, translation rate, physical and genetic interactions, and certain structural properties are correlated with increased aggregation propensity. Arsenite lowers the “threshold” for protein aggregation; hence the predisposition to aggregate increases under stress. We show that arsenite-aggregated proteins are enriched for chaperone interactions, substantiating our previous observations that arsenite interferes with chaperone activity in vivo. Our results suggest that the majority of protein aggregation is co-translational and that yeast decrease expression of aggregation-prone proteins during stress, possibly as a mechanism to prevent excessive accumulation of protein aggregates. Finally, we show that several aggregation-prone yeast proteins have human homologs that are implicated in misfolding diseases. Taken together, this study provides novel insights into the rules that govern protein aggregation in yeast cells.
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| 6. |
- Ibstedt, Sebastian, 1983, et al.
(författare)
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Global analysis of protein aggregation in yeast during physiological conditions and arsenite stress.
- 2014
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Ingår i: Biology open. - : The Company of Biologists. - 2046-6390. ; 3:10, s. 913-923
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Tidskriftsartikel (refereegranskat)abstract
- Protein aggregation is a widespread phenomenon in cells and associated with pathological conditions. Yet, little is known about the rules that govern protein aggregation in living cells. In this study, we biochemically isolated aggregation-prone proteins and used computational analyses to identify characteristics that are linked to physiological and arsenite-induced aggregation in living yeast cells. High protein abundance, extensive physical interactions, and certain structural properties are positively correlated with an increased aggregation propensity. The aggregated proteins have high translation rates and are substrates of ribosome-associated Hsp70 chaperones, indicating that they are susceptible for aggregation primarily during translation/folding. The aggregation-prone proteins are enriched for multiple chaperone interactions, thus high protein abundance is probably counterbalanced by molecular chaperones to allow soluble expression in vivo. Our data support the notion that arsenite interferes with chaperone activity and indicate that arsenite-aggregated proteins might engage in extensive aberrant protein-protein interactions. Expression of aggregation-prone proteins is down-regulated during arsenite stress, possibly to prevent their toxic accumulation. Several aggregation-prone yeast proteins have human homologues that are implicated in misfolding diseases, suggesting that similar mechanisms may apply in disease- and non-disease settings.
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| 7. |
- Jacobson, Therese, et al.
(författare)
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Arsenite interferes with protein folding and triggers formation of protein aggregates in yeast.
- 2012
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Ingår i: Journal of cell science. - : The Company of Biologists. - 1477-9137 .- 0021-9533. ; 125:21, s. 5073-83
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Tidskriftsartikel (refereegranskat)abstract
- Several metals and metalloids profoundly affect biological systems, but their impact on the proteome and mechanisms of toxicity are not fully understood. Here, we demonstrate that arsenite causes protein aggregation in Saccharomyces cerevisiae. Various molecular chaperones were found to be associated with arsenite-induced aggregates indicating that this metalloid promotes protein misfolding. Using in vivo and in vitro assays, we show that proteins in the process of synthesis/folding are particularly sensitive to arsenite-induced aggregation, that arsenite interferes with protein folding by acting on unfolded polypeptides, and that arsenite directly inhibits chaperone activity. Thus, folding inhibition contributes to arsenite toxicity in two ways: by aggregate formation and by chaperone inhibition. Importantly, arsenite-induced protein aggregates can act as seeds committing other, labile proteins to misfold and aggregate. Our findings describe a novel mechanism of toxicity that may explain the suggested role of this metalloid in the etiology and pathogenesis of protein folding disorders associated with arsenic poisoning.
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| 8. |
- Ottosson, Lars-Göran, et al.
(författare)
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Sulfate assimilation mediates tellurite reduction and toxicity in Saccharomyces cerevisiae
- 2010
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Ingår i: Eukaryotic Cell. - 1535-9778 .- 1535-9786. ; 9:10, s. 1635-1647
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Tidskriftsartikel (refereegranskat)abstract
- Despite a century of research and increasing environmental and human health concerns, the mechanistic basis of the toxicity of derivatives of the metalloid tellurium, Te, in particular the oxyanion tellurite, Te(IV), remains unsolved. Here, we provide an unbiased view of the mechanisms of tellurium metabolism in the yeast Saccharomyces cerevisiae by measuring deviations in Te-related traits of a complete collection of gene knockout mutants. Reduction of Te(IV) and intracellular accumulation as metallic tellurium strongly correlated with loss of cellular fitness, suggesting that Te(IV) reduction and toxicity are causally linked. The sulfate assimilation pathway upstream of Met17, in particular, the sulfite reductase and its cofactor siroheme, was shown to be central to tellurite toxicity and its reduction to elemental tellurium. Gene knockout mutants with altered Te(IV) tolerance also showed a similar deviation in tolerance to both selenite and, interestingly, selenomethionine, suggesting that the toxicity of these agents stems from a common mechanism. We also show that Te(IV) reduction and toxicity in yeast is partially mediated via a mitochondrial respiratory mechanism that does not encompass the generation of substantial oxidative stress. The results reported here represent a robust base from which to attack the mechanistic details of Te(IV) toxicity and reduction in a eukaryotic organism.
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| 9. |
- Tamás, Markus J., 1970, et al.
(författare)
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Heavy Metals and Metalloids As a Cause for Protein Misfolding and Aggregation
- 2014
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Ingår i: Biomolecules. - : MDPI AG. - 2218-273X. ; 4:1, s. 252-267
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Tidskriftsartikel (refereegranskat)abstract
- While the toxicity of metals and metalloids, like arsenic, cadmium, mercury, lead and chromium, is undisputed, the underlying molecular mechanisms are not entirely clear. General consensus holds that proteins are the prime targets; heavy metals interfere with the physiological activity of specific, particularly susceptible proteins, either by forming a complex with functional side chain groups or by displacing essential metal ions in metalloproteins. Recent studies have revealed an additional mode of metal action targeted at proteins in a non-native state; certain heavy metals and metalloids have been found to inhibit the in vitro refolding of chemically denatured proteins, to interfere with protein folding in vivo and to cause aggregation of nascent proteins in living cells. Apparently, unfolded proteins with motile backbone and side chains are considerably more prone to engage in stable, pluridentate metal complexes than native proteins with their well-defined 3D structure. By interfering with the folding process, heavy metal ions and metalloids profoundly affect protein homeostasis and cell viability. This review describes how heavy metals impede protein folding and promote protein aggregation, how cells regulate quality control systems to protect themselves from metal toxicity and how metals might contribute to protein misfolding disorders.
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| 10. |
- Weids, Alan J, et al.
(författare)
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Distinct stress conditions result in aggregation of proteins with similar properties.
- 2016
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Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Protein aggregation is the abnormal association of proteins into larger aggregate structures which tend to be insoluble. This occurs during normal physiological conditions and in response to age or stress-induced protein misfolding and denaturation. In this present study we have defined the range of proteins that aggregate in yeast cells during normal growth and after exposure to stress conditions including an oxidative stress (hydrogen peroxide), a heavy metal stress (arsenite) and an amino acid analogue (azetidine-2-carboxylic acid). Our data indicate that these three stress conditions, which work by distinct mechanisms, promote the aggregation of similar types of proteins probably by lowering the threshold of protein aggregation. The proteins that aggregate during physiological conditions and stress share several features; however, stress conditions shift the criteria for protein aggregation propensity. This suggests that the proteins in aggregates are intrinsically aggregation-prone, rather than being proteins which are affected in a stress-specific manner. We additionally identified significant overlaps between stress aggregating yeast proteins and proteins that aggregate during ageing in yeast and C. elegans. We suggest that similar mechanisms may apply in disease- and non-disease settings and that the factors and components that control protein aggregation may be evolutionary conserved.
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