| 1. |
- Garre, Elena, 1978, et al.
(författare)
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The Lsm1-7/Pat1 complex binds to stress-activated mRNAs and modulates the response to hyperosmotic shock.
- 2018
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Ingår i: PLoS Genetics. - : Public Library of Science (PLoS). - 1553-7390 .- 1553-7404. ; 14:7
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Tidskriftsartikel (refereegranskat)abstract
- RNA-binding proteins (RBPs) establish the cellular fate of a transcript, but an understanding of these processes has been limited by a lack of identified specific interactions between RNA and protein molecules. Using MS2 RNA tagging, we have purified proteins associated with individual mRNA species induced by osmotic stress, STL1 and GPD1. We found members of the Lsm1-7/Pat1 RBP complex to preferentially bind these mRNAs, relative to the non-stress induced mRNAs, HYP2 and ASH1. To assess the functional importance, we mutated components of the Lsm1-7/Pat1 RBP complex and analyzed the impact on expression of osmostress gene products. We observed a defect in global translation inhibition under osmotic stress in pat1 and lsm1 mutants, which correlated with an abnormally high association of both non-stress and stress-induced mRNAs to translationally active polysomes. Additionally, for stress-induced proteins normally triggered only by moderate or high osmostress, in the mutants the protein levels rose high already at weak hyperosmosis. Analysis of ribosome passage on mRNAs through co-translational decay from the 5' end (5P-Seq) showed increased ribosome accumulation in lsm1 and pat1 mutants upstream of the start codon. This effect was particularly strong for mRNAs induced under osmostress. Thus, our results indicate that, in addition to its role in degradation, the Lsm1-7/Pat1 complex acts as a selective translational repressor, having stronger effect over the translation initiation of heavily expressed mRNAs. Binding of the Lsm1-7/Pat1p complex to osmostress-induced mRNAs mitigates their translation, suppressing it in conditions of weak or no stress, and avoiding a hyperresponse when triggered.
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| 2. |
- Garre, Elena, 1978, et al.
(författare)
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Yeast mRNA cap-binding protein Cbc1/Sto1 is necessary for the rapid reprogramming of translation after hyperosmotic shock
- 2012
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Ingår i: Molecular Biology of the Cell. - 1059-1524. ; 23:1, s. 137-150
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Tidskriftsartikel (refereegranskat)abstract
- In response to osmotic stress, global translation is inhibited, but the mRNAs encoding stress-protective proteins are selectively translated to allow cell survival. To date, the mechanisms and factors involved in the specific translation of osmostress-responsive genes in Saccharomyces cerevisiae are unknown. We find that the mRNA cap-binding protein Cbc1 is important for yeast survival under osmotic stress. Our results provide new evidence supporting a role of Cbc1 in translation initiation. Cbc1 associates with polysomes, while the deletion of the CBC1 gene causes hypersensitivity to the translation inhibitor cycloheximide and yields synthetic “sickness” in cells with limiting amounts of translation initiator factor eIF4E. In cbc1Δ mutants, translation drops sharply under osmotic stress, the subsequent reinitiation of translation is retarded, and “processing bodies” containing untranslating mRNAs remain for long periods. Furthermore, osmostress-responsive mRNAs are transcriptionally induced after osmotic stress in cbc1Δ cells, but their rapid association with polysomes is delayed. However, in cells containing a thermosensitive eIF4E allele, their inability to grow at 37ºC is suppressed by hyperosmosis, and Cbc1 relocalizes from nucleus to cytoplasm. These data support a model in which eIF4E-translation could be stress-sensitive, while Cbc1-mediated translation is necessary for the rapid translation of osmostress-protective proteins under osmotic stress.
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| 3. |
- Gorschek, Tony, et al.
(författare)
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A Model for Technology Transfer in Practice
- 2006
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Ingår i: IEEE Software. - : IEEE. - 0740-7459 .- 1937-4194. ; 23:6, s. 88-95
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Tidskriftsartikel (refereegranskat)abstract
- Technology transfer, and thus industry-relevant research, involves more than merely producing research results and delivering them in publications and technical reports. It demands close cooperation and collaboration between industry and academia throughout the entire research process. During research conducted in a partnership between Blekinge Institute of Technology and two companies, Danaher Motion Saro AB (DHR) and ABB, we devised a technology transfer model that embodies this philosophy. We initiated this partnership to conduct industry-relevant research in requirements engineering and product management. Technology transfer in this context is a prerequisite: it validates academic research results in a real setting, and it provides a way to improve industry development and business processes
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| 4. |
- Gorschek, Tony, et al.
(författare)
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Industry Evaluation of the Requirements Abstraction Model
- 2007
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Ingår i: Requirements Engineering. - London : Springer. - 0947-3602 .- 1432-010X. ; 12:3, s. 163-190
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Tidskriftsartikel (refereegranskat)abstract
- Software requirements are often formulated on different levels and hence they are difficult to compare to each other. To address this issue, a model that allows for placing requirements on different levels has been developed. The model supports both abstraction and refinement of requirements, and hence requirements can both be compared with each other and to product strategies. Comparison between requirements will allow for prioritization of requirements, which in many cases is impossible if the requirements are described on different abstraction levels. Comparison to product strategies will enable early and systematic acceptance or dismissal of requirements, minimizing the risk for overloading. This paper presents an industrial evaluation of the model. It has been evaluated in two different companies, and the experiences and findings are presented. It is concluded that the requirements abstraction model provides helpful improvements to the industrial requirements engineering process.
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| 5. |
- Gorschek, Tony, et al.
(författare)
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Industry evaluation of the Requirements Abstraction Model
- 2008
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Ingår i: Requirements Engineering Journal. - : Springer Science and Business Media LLC. - 0947-3602 .- 1432-010X. ; 12:3, s. 163-190
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Tidskriftsartikel (refereegranskat)abstract
- Software requirements are often formulated on different levels and hence they are difficult to compare to each other. To address this issue, a model that allows for placing requirements on different levels has been developed. The model supports both abstraction and refinement of requirements, and hence requirements can both be compared with each other and to product strategies. Comparison between requirements will allow for prioritization of requirements, which in many cases is impossible if the requirements are described on different abstraction levels. Comparison to product strategies will enable early and systematic acceptance or dismissal of requirements, minimizing the risk for overloading. This paper presents an industrial evaluation of the model. It has been evaluated in two different companies, and the experiences and findings are presented. It is concluded that the requirements abstraction model provides helpful improvements to the industrial requirements engineering process.
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| 6. |
- Li, Tianlu, 1988, et al.
(författare)
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The mRNA cap-binding protein Cbc1 is required for high and timely expression of genes by promoting the accumulation of gene-specific activators at promoters
- 2016
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Ingår i: Biochimica et Biophysica Acta. Gene Regulatory Mechanisms. - : Elsevier BV. - 1874-9399 .- 1876-4320. ; 1859:2, s. 405-419
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Tidskriftsartikel (refereegranskat)abstract
- The highly conserved Saccharomyces cerevisiae cap-binding protein Cbc1/Sto1 binds mRNA co-transcriptionally and acts as a key coordinator of mRNA fate. Recently, Cbc1 has also been implicated in transcription elongation and pre-initiation complex (PIC) formation. Previously, we described Cbc1 to be required for cell growth under osmotic stress and to mediate osmostress-induced translation reprogramming. Here, we observe delayed global transcription kinetics in cbc1Δ during osmotic stress that correlates with delayed recruitment of TBP and RNA polymerase II to osmo-induced promoters. Interestingly, we detect an interaction between Cbc1 and the MAPK Hog1,which controls most gene expression changes during osmostress, and observe that deletion of CBC1 delays the accumulation of the activator complex Hot1–Hog1 at osmostress promoters. Additionally, CBC1 deletion specifically reduces transcription rates of highly transcribed genes under non-stress conditions, such as ribosomal protein (RP) genes, while having low impact on transcription of weakly expressed genes. For RP genes, we show that recruitment of the specific activator Rap1, and subsequently TBP, to promoters is Cbc1-dependent. Altogether, our results indicate that binding of Cbc1 to the cappedmRNAs is necessary for the accumulation of specific activators as well as PIC components at the promoters of genes whose expression requires high and rapid transcription.
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| 7. |
- Statello, Luisa, et al.
(författare)
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Identification of RNA-binding proteins in exosomes capable of interacting with different types of RNA: RBP-facilitated transport of RNAs into exosomes.
- 2018
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Ingår i: PLoS One. - : Public Library of Science (PLoS). - 1932-6203. ; 13:4
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Tidskriftsartikel (refereegranskat)abstract
- The RNA that is packaged into exosomes is termed as exosomal-shuttle RNA (esRNA); however, the players, which take this subset of RNA (esRNA) into exosomes, remain largely unknown. We hypothesized that RNA binding proteins (RBPs) could serve as key players in this mechanism, by making complexes with RNAs and transporting them into exosomes during the biosynthesis of exosomes. Here, we demonstrate the presence of 30 RBPs in exosomes that were shown to form RNA-RBP complexes with both cellular RNA and exosomal-RNA species. To assess the involvement of these RBPs in RNA-transfer into exosomes, the gene transcripts encoding six of the proteins identified in exosomes (HSP90AB1, XPO5, hnRNPH1, hnRNPM, hnRNPA2B1, and MVP) were silenced by siRNA and subsequent effect on esRNA was assessed. A significant reduction of total esRNA was observed by post-transcriptional silencing of MVP, compared to other RBPs. Furthermore, to confirm the binding of MVP with esRNA, a biotinylated-MVP was transiently expressed in HEK293F cells. Higher levels of esRNA were recovered from MVP that was eluted from exosomes of transfected cells, as compared to those of non-transfected cells. Our data indicate that these RBPs could end up in exosomes together with RNA molecules in the form of RNA-ribonucleoprotein complexes, which could be important for the transport of RNAs into exosomes and the maintenance of RNAs inside exosomes. This type of maintenance may favor the shuttling of RNAs from exosomes to recipient cells in the form of stable complexes.
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| 8. |
- Yang, Xiaoxue, et al.
(författare)
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Stress granule-defective mutants deregulate stress responsive transcripts
- 2014
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Ingår i: PLoS Genetics. - : Public Library of Science (PLoS). - 1553-7390 .- 1553-7404. ; 10:11
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Tidskriftsartikel (refereegranskat)abstract
- To reduce expression of gene products not required under stress conditions, eukaryotic cells form large and complex cytoplasmic aggregates of RNA and proteins (stress granules; SGs), where transcripts are kept translationally inert. The overall composition of SGs, as well as their assembly requirements and regulation through stress-activated signaling pathways remain largely unknown. We have performed a genome-wide screen of S. cerevisiae gene deletion mutants for defects in SG formation upon glucose starvation stress. The screen revealed numerous genes not previously implicated in SG formation. Most mutants with strong phenotypes are equally SG defective when challenged with other stresses, but a considerable fraction is stress-specific. Proteins associated with SG defects are enriched in low-complexity regions, indicating that multiple weak macromolecule interactions are responsible for the structural integrity of SGs. Certain SG-defective mutants, but not all, display an enhanced heat-induced mutation rate. We found several mutations affecting the Ran GTPase, regulating nucleocytoplasmic transport of RNA and proteins, to confer SG defects. Unexpectedly, we found stress-regulated transcripts to reach more extreme levels in mutants unable to form SGs: stress-induced mRNAs accumulate to higher levels than in the wild-type, whereas stress-repressed mRNAs are reduced further in such mutants. Our findings are consistent with the view that, not only are SGs being regulated by stress signaling pathways, but SGs also modulate the extent of stress responses. We speculate that nucleocytoplasmic shuttling of RNA-binding proteins is required for gene expression regulation during stress, and that SGs modulate this traffic. The absence of SGs thus leads the cell to excessive, and potentially deleterious, reactions to stress.
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| 9. |
- Zörgö, Enikö, 1968, et al.
(författare)
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Ancient Evolutionary Trade-Offs between Yeast Ploidy States
- 2013
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Ingår i: Plos Genetics. - : Public Library of Science (PLoS). - 1553-7404. ; 9:3
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Tidskriftsartikel (refereegranskat)abstract
- The number of chromosome sets contained within the nucleus of eukaryotic organisms is a fundamental yet evolutionarily poorly characterized genetic variable of life. Here, we mapped the impact of ploidy on the mitotic fitness of baker's yeast and its never domesticated relative Saccharomyces paradoxus across wide swaths of their natural genotypic and phenotypic space. Surprisingly, environment-specific influences of ploidy on reproduction were found to be the rule rather than the exception. These ploidy–environment interactions were well conserved across the 2 billion generations separating the two species, suggesting that they are the products of strong selection. Previous hypotheses of generalizable advantages of haploidy or diploidy in ecological contexts imposing nutrient restriction, toxin exposure, and elevated mutational loads were rejected in favor of more fine-grained models of the interplay between ecology and ploidy. On a molecular level, cell size and mating type locus composition had equal, but limited, explanatory power, each explaining 12.5%–17% of ploidy–environment interactions. The mechanism of the cell size–based superior reproductive efficiency of haploids during Li+ exposure was traced to the Li+ exporter ENA. Removal of the Ena transporters, forcing dependence on the Nha1 extrusion system, completely altered the effects of ploidy on Li+ tolerance and evoked a strong diploid superiority, demonstrating how genetic variation at a single locus can completely reverse the relative merits of haploidy and diploidy. Taken together, our findings unmasked a dynamic interplay between ploidy and ecology that was of unpredicted evolutionary importance and had multiple molecular roots.
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