Studies on the antagonistic effect of rhizobacteria against soilborne Phytophthora species on strawberry

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Yeast as a Model System to Study Tau Biology

Hyperphosphorylated and aggregated human protein tau constitutes a hallmark of a multitude of neurodegenerative diseases called tauopathies, exemplified by Alzheimer's disease. In spite of an enormous amount of research performed on tau biology, several crucial questions concerning the mechanisms of tau toxicity remain unanswered. In this paper we will highlight some of the processes involved in tau biology and pathology, focusing on tau phosphorylation and the interplay with oxidative stress. In addition, we will introduce the development of a human tau-expressing yeast model, and discuss some crucial results obtained in this model, highlighting its potential in the elucidation of cellular processes leading to tau toxicity

Histone H2B ubiquitylation represses gametogenesis by opposing RSC-dependent chromatin remodeling at the ste11 master regulator locus.

In fission yeast, the ste11 gene encodes the master regulator initiating the switch from vegetative growth to gametogenesis. In a previous paper, we showed that the methylation of H3K4 and consequent promoter nucleosome deacetylation repress ste11 induction and cell differentiation (Materne et al., 2015) but the regulatory steps remain poorly understood. Here we report a genetic screen that highlighted H2B deubiquitylation and the RSC remodeling complex as activators of ste11 expression. Mechanistic analyses revealed more complex, opposite roles of H2Bubi at the promoter where it represses expression, and over the transcribed region where it sustains it. By promoting H3K4 methylation at the promoter, H2Bubi initiates the deacetylation process, which decreases chromatin remodeling by RSC. Upon induction, this process is reversed and efficient NDR (nucleosome depleted region) formation leads to high expression. Therefore, H2Bubi represses gametogenesis by opposing the recruitment of RSC at the promoter of the master regulator ste11 gene. DOI: http://dx.doi.org/10.7554/eLife.13500.00

Regulation of entry into gametogenesis by Ste11: the endless game

Abstract Sexual reproduction is a fundamental aspect of eukaryotic cells, and a conserved feature of gametogenesis is its dependency on a master regulator. The ste11 gene was isolated more than 20 years ago by the Yamamoto laboratory as a suppressor of the uncontrolled meiosis driven by a pat1 mutant. Numerous studies from this laboratory and others have established the role of the Ste11 transcription factor as the master regulator of the switch between proliferation and differentiation in fission yeast. The transcriptional and post-transcriptional controls of ste11 expression are intricate, but most are not redundant. Whereas the transcriptional controls ensure that the gene is transcribed at a high level only when nutrients are rare, the post-transcriptional controls restrict the ability of Ste11 to function as a transcription factor to the G 1 -phase of the cell cycle from where the differentiation programme is initiated. Several feedback loops ensure that the cell fate decision is irreversible. The complete panel of molecular mechanisms operating to warrant the timely expression of the ste11 gene and its encoded protein basically mirrors the advances in the understanding of the numerous ways by which gene expression can be modulated

Perturbations of Transcription and Gene Expression-Associated Processes Alter Distribution of Cell Size Values in Saccharomyces cerevisiae

The question of what determines whether cells are big or small has been the focus of many studies because it is thought that such determinants underpin the coupling of cell growth with cell division. In contrast, what determines the overall pattern of how cell size is distributed within a population of wild type or mutant cells has received little attention. Knowing how cell size varies around a characteristic pattern could shed light on the processes that generate such a pattern and provide a criterion to identify its genetic basis. Here, we show that cell size values of wild type Saccharomyces cerevisiae cells fit a gamma distribution, in haploid and diploid cells, and under different growth conditions. To identify genes that influence this pattern, we analyzed the cell size distributions of all single-gene deletion strains in Saccharomyces cerevisiae. We found that yeast strains which deviate the most from the gamma distribution are enriched for those lacking gene products functioning in gene expression, especially those in transcription or transcription-linked processes. We also show that cell size is increased in mutants carrying altered activity substitutions in Rpo21p/Rpb1, the largest subunit of RNA polymerase II (Pol II). Lastly, the size distribution of cells carrying extreme altered activity Pol II substitutions deviated from the expected gamma distribution. Our results are consistent with the idea that genetic defects in widely acting transcription factors or Pol II itself compromise both cell size homeostasis and how the size of individual cells is distributed in a population

Uncoupling Transcription from Covalent Histone Modification

<div><p>It is widely accepted that transcriptional regulation of eukaryotic genes is intimately coupled to covalent modifications of the underlying chromatin template, and in certain cases the functional consequences of these modifications have been characterized. Here we present evidence that gene activation in the silent heterochromatin of the yeast <i>Saccharomyces cerevisiae</i> can occur in the context of little, if any, covalent histone modification. Using a SIR-regulated heat shock-inducible transgene, <i>hsp82-2001</i>, and a natural drug-inducible subtelomeric gene, <i>YFR057w</i>, as models we demonstrate that substantial transcriptional induction (>200-fold) can occur in the context of restricted histone loss and negligible levels of H3K4 trimethylation, H3K36 trimethylation and H3K79 dimethylation, modifications commonly linked to transcription initiation and elongation. Heterochromatic gene activation can also occur with minimal H3 and H4 lysine acetylation and without replacement of H2A with the transcription-linked variant H2A.Z. Importantly, absence of histone modification does not stem from reduced transcriptional output, since <i>hsp82-ΔTATA</i>, a euchromatic promoter mutant lacking a TATA box and with threefold lower induced transcription than heterochromatic <i>hsp82-2001</i>, is strongly hyperacetylated in response to heat shock. Consistent with negligible H3K79 dimethylation, <i>dot1Δ</i> cells lacking H3K79 methylase activity show unimpeded occupancy of RNA polymerase II within activated heterochromatic promoter and coding regions. Our results indicate that large increases in transcription can be observed in the virtual absence of histone modifications often thought necessary for gene activation.</p></div

Heterochromatic gene activation occurs in the context of minimal transcription-linked H3 methylation and is unimpaired by ablation of Dot1.

<p>(a) H3K56ac ChIP analysis of <i>hsp82-2001</i> in <i>sir4Δ</i> or <i>SIR⁺</i> cells subjected to an instantaneous 30° to 39°C thermal upshift for the times indicated. Quantification was done using Real Time qPCR. The acetylated H3K56/Myc-H4 quotient of the non-induced <i>sir4Δ</i> sample was set to 1.0 for each amplicon. PTM-specific and Myc-H4 signals at the heat shock transgene were normalized to those measured at <i>PMA1</i> and <i>ARS504</i>, respectively. Shown are means ± S.D. (N = 2; qPCR = 4). (b) H3K36me3 ChIP analysis of <i>hsp82-2001</i> conducted as in A. (c) H3K4me3 ChIP analysis of <i>hsp82-2001</i> in <i>sir4Δ</i> or <i>SIR⁺</i> cells subjected to an instantaneous 30° to 39°C thermal upshift for the times indicated. Quantification and scaling were done as in A, except H3K4me3/H3 quotients are depicted, and both PTM-specific and H3 signals were normalized to those measured at <i>ARS504</i>. Shown are means ± S.D. (N = 2; qPCR = 4). (d) H3K79me2 ChIP analysis of <i>hsp82-2001</i> in <i>sir4Δ</i> or <i>SIR⁺</i> cells as in C. (e) Pol II ChIP analysis of heterochromatic <i>hsp82-2001</i> in <i>DOT1⁺</i> and <i>dot1Δ</i> strains subjected to heat shock as above. Pol II occupancy was determined using ChIP-qPCR as in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004202#pgen-1004202-g003" target="_blank">Figure 3A</a>. Shown are means ± S.D. (N = 2; qPCR = 4).</p

Retention of the Sir protein complex and increased nucleosome density and stability at the heat shock-induced <i>hsp82-2001</i> transgene.

<p>(a) <i>In vivo</i> crosslinking analysis of Sir3 at the promoter, ORF and 3′-UTR of <i>hsp82-201</i>, <i>hsp82-1001</i> and <i>hsp82-2001</i>. Crosslinked chromatin, sheared to a mean size of ∼0.5 kb, was isolated from cells cultivated at 30°C and either maintained at that temperature or subjected to a 20 min 39°C heat shock (HS) (− and +, respectively). Following immunoprecipitation, crosslinks were reversed and purified DNA was subjected to quantitative multiplex PCR in the presence of [α-³²P] dATP using primers specific for the five loci indicated. A gel analysis of multiplex PCR products is presented on the left, while a summary of three independent experiments (means ± S.E.) is presented on the right. Input sample (lane 1), derived from strain EAS2011, represents 4% of soluble chromatin used in the corresponding IP (lane 2). In the histogram, Sir3 occupancy at each <i>hsp82</i> transgene was normalized to its occupancy at <i>HMRa1</i>. prom, promoter. (b) ChIP analysis of Sir3 at <i>hsp82-2001</i> as in A, except that cells were subjected to the indicated heat shock time course and quantification of Sir3 abundance was performed using Real Time qPCR. Sir3 abundance at the indicated regions was normalized to its occupancy at <i>HMRa2</i>; illustrated are means ± S.D. (N = 2; qPCR = 4). (c) Histone H3 abundance at the promoter, ORF and 3′-UTR of <i>hsp82-2001</i> in <i>sir4Δ</i> and <i>SIR⁺</i> contexts as indicated, normalized to its occupancy at <i>ARS504</i>. Cultures were maintained at 30°C (0 min) or subjected to an instantaneous 39°C upshift for the times indicated. Quantification performed as in B; depicted are means ± S.D.; N = 2, qPCR = 4.</p

Yeast strains.

<p>Yeast strains.</p