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  • 1. Broach, James R
    et al.
    Bharatula, Vasudha
    Chereji, Razvan
    Elfving, Nils
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Björklund, Stefan
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Morozov, Alexandre
    The Msn2 mediated stress response: Survival based on "hedging your bet" and a dynamic interplay of transcription factor binding and nucleosome occupancy2015Inngår i: Yeast, ISSN 0749-503X, E-ISSN 1097-0061, Vol. 32, nr Suppl. 1, s. S221-S222Artikkel i tidsskrift (Annet vitenskapelig)
    Abstract [en]

    Yeast cell subjected to many different stresses elicit an acute transcriptional stress response mediated by the Msn2 transcription factor, which alters expression of both a stress specific-cohort of genes as well as a common cohort of genes that changes expression in a stereotypic fashion upon exposure to any of a wide variety of stresses. We have shown by dynamic single cell analysis that stresses regulate Msn2 activity through cytoplasm to nuclear relocalization but do so in an unusual way: stresses induce increased frequency of bursts of short-lived, recurrent periods of Msn2 nuclear localization with different stresses eliciting different patterns of bursts. Moreover, genetically identical cells subject to an identical stress can behave quite differently, with some cells mounting a robust nuclear occupancy of Msn2 while others show no nuclear localization at all. We have proposed that this idiosyncratic behavior allows populations of cells to “hedge their bet” as to what will be the optimum strategy for surviving the ensuing stress. We have used computational modeling and single cell analysis to determine that bursting is a consequence of noise in the stress signaling pathways amplified by the small number of Msn2 molecules in the cell. Moreover, we have applied genome wide chromatin immunoprecipitation and nucleosome profiling to address how different stresses determine where Msn2 binds under a particular stressful conditions, and thus what genes are regulated by that stress, and how that binding affects, and is affected by, nucleosome positioning and other transcription factor binding. These results provide in vivo validation of Widon's model of indirect cooperativity of transcription factor binding, mediated by partial unwinding of nucleosomes by one transcription factor to allow access for a second transcription factor to a previously occluded binding site. Finally, we have addressed the “bet hedging” hypothesis by showing that persistence of the Msn2-mediated stress response yields cell growth arrest and have identified the targets responsible for that growth arrest. We have applied experimental evolution paradigms to address the relative fitness of cells exhibiting stochastic stress responses versus those with a uniform response. In short, our results indicate that the stress response is complex and that complexity is critical for cell survival.

  • 2. Earp, Caroline
    et al.
    Rowbotham, Samuel
    Marjavaara, Lisette
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Chabes, Andrei
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Cha, Rita S
    Acute sensitivity of DNA replication to reduction in dNTP pools following Mec1ATR inactivation2015Inngår i: Yeast, ISSN 0749-503X, E-ISSN 1097-0061, Vol. 32, nr Suppl. 1, s. S56-S56Artikkel i tidsskrift (Annet vitenskapelig)
    Abstract [en]

    Inactivation of Mec1, the budding yeast ATR, results in a permanent S phase arrest followed by a fatal mitotic catastrophe. The mec1 S phase arrest was proposed to stem from a defect in the Mec1-Rad53-Dun1 dependent removal of Sml1, a conserved inhibitor of ribonucleotide reductase (RNR), at the onset of S phase: According to this view, Sml1 removal and the ensuing RNR activation would promote the dNTP production necessary for genome duplication. In support for this view, dNTP levels in hypomorphic mec1 or rad53 mutants and a dun1∆ strain were shown to be reduced by as much as 46% compared to a MEC1 control strain. Notably however, nearly all analyses on a lethal mec1 allele (e.g. mec1∆ or mec1-kd [kinase dead]) have been performed in a strain background that was either deleted for SML1 or over-expressing RNR1, a requirement for maintaining viability of a mutant lacking Mec1's essential function. As a result, while it is clear that absence of Mec1 causes dNTP pool to decrease, the true extent of the reduction and whether it would be sufficient to account for the replication arrest remain elusive. Here, we addressed these questions utilizing a temperature sensitive mutant, mec1-4, which maintains its viability at permissive temperature in an otherwise wild-type background, circumventing the need to exogenously manipulate Sml1 and/or RNR activity. Results show that Mec1 inactivation leads to an S phase arrest and a ~17% reduction in dNTP pool; expression of a novel suppressor, GIS2 (glucose inhibition of gluconeogenic growth suppressor 2), rescues the arrest and partially restores the dNTP pool to ~ 93% of a control. Unexpectedly modest effects of mec1 and GIS2 on dNTP levels demonstrate that the arrest does result from a severe depletion of dNTP pool as assumed, but a heightened sensitivity to its availability

  • 3.
    Jonsson, Leif
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Wu, Guochao
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Xu, Zixiang
    Saccharomyces cerevisiae transcription factors involved in multidrug resistance2013Inngår i: Yeast, ISSN 0749-503X, E-ISSN 1097-0061, Vol. 30, nr Supplement: 1, s. 158-158Artikkel i tidsskrift (Annet vitenskapelig)
  • 4. Kuzmenko, Anton
    et al.
    Derbikova, Ksenia
    Hauryliuk, Vasili
    Umeå universitet, Medicinska fakulteten, Institutionen för molekylärbiologi (Medicinska fakulteten). Insitute of Technology, Tartu University, Tartu, Estonia.
    Kamenski, Piotr
    Aim23 is an yeast mitochondrial translation initiation factor 3 which is unnecessary for protein synthesis2015Inngår i: Yeast, ISSN 0749-503X, E-ISSN 1097-0061, Vol. 32, nr Suppl. 1, s. S192-S193Artikkel i tidsskrift (Annet vitenskapelig)
    Abstract [en]

    Mitochondria are essential organelles of virtually all eukaryotic cells. They have their own genome and are able to transcribe and translate their genetic material. The system of mitochondrial protein synthesis is organized in a manner close to that of prokaryotes. However, mitochondrial DNA contains just a few protein-coded genes (9 in yeast, 13 in humans), so the mitochondrial translation system deals with a limited number of mRNAs. The mitochondrial translation machinery is also somewhat lineage-specific, with various components being gained and lost in different taxonomic groups. The classical bacterial initiation factors (IFs) IF1, IF2 and IF3 are universal in prokaryotes, but only IF2 is universal in mitochondria (mIF2). No IF1 has been identified in mitochondria of any organism. An insertion in mIF2 has been suggested to functionally compensate for the absence of mIF1. Mitochondrial IF3 (mIF3), although known to be present in various eukaryotes, has not been identified for many years in budding yeast Saccharomyces cerevisiae, the model organism for studying mitochondrial translation in vivo. In 2012, we have proven that IF3 does present in yeast mitochondria, and it is Aim23 protein. In the present study, we have characterized the effects of AIM23 gene deletion on yeast mitochondrial function. One could suggest that such a deletion would lead to a complete loss of respiration, translation and other molecular processes in mitochondria. However, this was not the case: the growth of AIM23∆ yeast on clycerol-containing media was suppressed in first 1-2 days only and reached the levels of wild-type in 3-4 days. AIM23∆ cells also were able to respire. Interestingly, we observed a very unusual pattern of mitochondrially-synthesized proteins in the ΔAIM23 strain. The amount of several proteins is decreased in the mutants compared to the wild-type but the amount of some others is increased. We conclude that the yeast cells are able to adapt somehow to the absence of Aim23p.

  • 5. Mountain, Harry A
    et al.
    Byström, Anders S
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för molekylärbiologi (Teknisk-naturvetenskaplig fakultet).
    Larsen, J T
    Korch, C
    Four major transcriptional responses in the methionine/threonine biosynthetic pathway of Saccharomyces cerevisiae1991Inngår i: Yeast, ISSN 0749-503X, E-ISSN 1097-0061, Vol. 7, nr 8, s. 781-803Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Genes encoding enzymes in the threonine/methionine biosynthetic pathway were cloned and used to investigate their transcriptional response to signals known to affect gene expression on the basis of enzyme specific-activities. Four major responses were evident: strong repression by methionine of MET3, MET5 and MET14, as previously described for MET3, MET2 and MET25; weak repression by methionine of MET6; weak stimulation by methionine but no response to threonine was seen for THR1, HOM2 and HOM3; no response to any of the signals tested, for HOM6 and MES1. In a BOR3 mutant, THR1, HOM2 and HOM3 mRNA levels were increased slightly. The stimulation of transcription by methionine for HOM2, HOM3 and THR1 is mediated by the GCN4 gene product and hence these genes are under the general amino acid control. In addition to the strong repression by methionine, MET5 is also regulated by the general control.

  • 6. Shiriaeva, Anna
    et al.
    Zhuk, Anna
    Andreychuck, Yulia
    Umeå universitet.
    Stepchenkova, Elena
    Inge-Vechtomov, Sergey
    The alpha-test: defining the nature of mating type switching alpha -> a in heterotallic yeast S. cerevisiae2013Inngår i: Yeast, ISSN 0749-503X, E-ISSN 1097-0061, Vol. 30, nr Supplement: 1, s. 140-140Artikkel i tidsskrift (Annet vitenskapelig)
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