Comparing transcriptomes of wild-type, hyperfilamentous, and hypofilamentous biofilms in S. cerevisiae
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ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE115657 | GEO | 2018/06/13
REPOSITORIES: GEO
Similar Datasets
Project description:Cellular processes are subject to variability, or noise, yet mechanisms that promote cell-to-cell uniformity are poorly understood. We have identified such a role for Dig1, a redundant (with Dig2) MAPK-responsive inhibitor of the S. cerevisiae mating pathway transcription factor Ste12. Cells lacking Dig1, but not Dig2, exhibited increased variability in outputs of the mating pathway. dig1∆ mutants also displayed a Ste12-dependent defect in growth in the absence of mating pheromone and a quantitative defect in the process of mating, itself. In cells expressing two reporter genes driven by the same promoter, both intrinsic/uncorrelated and extrinsic/correlated noise were found to increase. Remarkably, the extrinsic noise phenotype in cells lacking Dig1 correlates with the aggregation of target genes: we observed subnuclear foci of Ste12 specifically in dig1∆ cells and, using a newly-developed method to immunoprecipitate a single locus from crosslinked chromatin, we found that Dig1 inhibits long-range interactions between Ste12 target genes in vivo. Dig1 may shield binding surfaces on Ste12 whose unmasking leads to inappropriate gene associations and increased gene expression noise. These studies reveal how investigations of variability modulation mechanisms can yield unexpected biological insights.
2010-12-15 | GSE17583 | GEO
Project description:Cellular processes are subject to variability, or noise, yet mechanisms that promote cell-to-cell uniformity are poorly understood. We have identified such a role for Dig1, a redundant (with Dig2) MAPK-responsive inhibitor of the S. cerevisiae mating pathway transcription factor Ste12. Cells lacking Dig1, but not Dig2, exhibited increased variability in outputs of the mating pathway. dig1∆ mutants also displayed a Ste12-dependent defect in growth in the absence of mating pheromone and a quantitative defect in the process of mating, itself. In cells expressing two reporter genes driven by the same promoter, both intrinsic/uncorrelated and extrinsic/correlated noise were found to increase. Remarkably, the extrinsic noise phenotype in cells lacking Dig1 correlates with the aggregation of target genes: we observed subnuclear foci of Ste12 specifically in dig1∆ cells and, using a newly-developed method to immunoprecipitate a single locus from crosslinked chromatin, we found that Dig1 inhibits long-range interactions between Ste12 target genes in vivo. Dig1 may shield binding surfaces on Ste12 whose unmasking leads to inappropriate gene associations and increased gene expression noise. These studies reveal how investigations of variability modulation mechanisms can yield unexpected biological insights. The FUS1 locus is tagged with an array of lac operators. Wild type and dig1∆ cells containing this tagged FUS1 locus and expressing a mCherry-LacI were grown up for ChIP-chip. The FUS1 locus was selectively immunoprecipitated using an anti-DsRed antibody.
2010-12-15 | E-GEOD-17583 | biostudies-arrayexpress
Project description:The purpose of this experiment was to determine the genes directly regulated by Ste12 in K. lactis. The experiment was performed in a cells to determine if the a-specific genes were bound by Ste12. Ste12 was tagged with c-myc and was immunoprecipitated with a c-myc antibody. Cells were starved in SD media lacking phosphate for 2 hours, then treated with 10µg/mL K. lactis alpha factor for 2 hours before harvesting. A control untagged strain was processed in parallel. The experiment was repeated 3 times, and sequenced on an Illumina HiSeq 2500.
2015-07-06 | GSE65792 | GEO
Project description:The purpose of this experiment was to determine the genes directly regulated by Ste12 in K. lactis. The experiment was performed in a cells to determine if the a-specific genes were bound by Ste12. Ste12 was tagged with c-myc and was immunoprecipitated with a c-myc antibody. Cells were starved in SD media lacking phosphate for 2 hours, then treated with 10µg/mL K. lactis alpha factor for 2 hours before harvesting. A control untagged strain was processed in parallel. The experiment was repeated 3 times, and sequenced on an Illumina HiSeq 2500. K. lactis Ste12-myc vs. untagged control under pheromone response condition with 3 technical replicates done on different days
2015-07-06 | E-GEOD-65792 | biostudies-arrayexpress
Project description:Legionella pneumophila is a Gram-negative, environmental bacterium, which causes the life-threatening pneumonia Legionnaires’ disease. The facultative intracellular bacterium forms biofilms and employs the Icm/Dot type IV secretion system (T4SS) to replicate in amoebae and macrophages. The Legionella quorum sensing (Lqs) system and the transcription factor LvbR form a regulatory network controlling various traits, including bacterial motility, virulence and biofilm architecture. Here we show by comparative proteomics that in biofilms formed by L. pneumophila mutant strains lacking LvbR or the response regulator LqsR, proteins encoded by the 133 kb fitness island and components of the flagellum (FlaA) are downregulated. Confocal microscopy revealed that the ∆lqsR or ∆flaA mutant strains formed biofilms of the same patchy morphology as the parental strain JR32, while the ∆lvbR mutant forms a mat-like biofilm as previously shown. Acanthamoeba castellanii amoebae migrated more slowly through biofilms formed by the ∆lvbR, ∆lqsR or ∆flaA mutant strains, and amoebae migration was impaired in biofilms formed by L. pneumophila lacking a functional Icm/Dot T4SS (∆icmT) or the secreted effector proteins LegG1 and PpgA. Amoebae migrating through biofilms formed by JR32, ∆lvbR or ∆icmT were decorated by clusters of bacteria, while amoebae in ∆lqsR or ∆flaA biofilms were not. Taken together, the Lqs system, LvbR, FlaA and the Icm/Dot T4SS regulate migration of A. castellanii through L. pneumophila biofilms, and – with the exception of the T4SS – also regulate bacterial cluster formation on the amoeba. Hence, amoebae migration through L. pneumophila biofilms is regulated by bacterial quorum sensing, virulence and motility.
2022-06-08 | PXD030337 | Pride
Project description:Transcription profile of Escherichia coli cells in biofilms under static batch culture was compared to that of E. coli cells in planktonic cultures. Both E. coli biofilm and planktonic cultures were cultivated for 18 h in 10% Luria-Bertani broth at room temperature (20 degree Celsius). Biofilms were grown in static batch culture in petri dishes. Both planktonic culture and biofilms were homogenized and run through a separated protocol.
2013-12-30 | GSE24914 | GEO
Project description:This model is from the article:
Positive roles for negative regulators in the mating response of yeast.
Houser JR, Ford E, Nagiec MJ, Errede B, Elston TC. Mol Syst Biol
2012 June 5;8:586 22669614
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Abstract:
All cells must detect and respond to changes in their environment, often through changes in gene expression. The yeast pheromone pathway has been extensively characterized, and is an ideal system for studying transcriptional regulation. Here we combine computational and experimental approaches to study transcriptional regulation mediated by Ste12, the key transcription factor in the pheromone response. Our mathematical model is able to explain multiple counterintuitive experimental results and led to several novel findings. First, we found that the transcriptional repressors Dig1 and Dig2 positively affect transcription by stabilizing Ste12. This stabilization through protein-protein interactions creates a large pool of Ste12 that is rapidly activated following pheromone stimulation. Second, we found that protein degradation follows saturating kinetics, explaining the long half-life of Ste12 in mutants expressing elevated amounts of Ste12. Finally, our model reveals a novel mechanism for robust perfect adaptation through protein-protein interactions that enhance complex stability. This mechanism allows the transcriptional response to act on a shorter time scale than upstream pathway activity.
2005-01-01 | MODEL1204040000 | BioModels
Project description:Biofilm formation by microorganisms is a major cause of recurring infections and removal of biofilms has proven to be extremely difficult given their inherent drug resistance. Understanding the biological processes that underlie biofilm formation is thus extremely important and could lead to the development of more effective drug therapies, resulting in better infection outcomes. Using the yeast S. cerevisiae as a biofilm model, overexpression screens identified DIG1, SFL1, HEK2, TOS8, SAN1 and ROF1/YHR177W as regulators of biofilm formation. Subsequent RNA-seq analysis of biofilm and non-biofilm forming strains revealed that all of the overexpression strains, other than DIG1 and TOS8, were adopting a single differential expression profile, although induced to varying degrees. TOS8 adopted a separate profile, while the expression profile of DIG1 reflected the common pattern seen in most of the strains, plus substantial DIG1-specific expression changes. We interpret the existence of the common transcriptional pattern seen across multiple, unrelated overexpression strains as reflecting a real transcriptional state, that the yeast cell can access through regulatory signaling mechanisms, allowing an adaptive morphological change between biofilm-forming and non-biofilm states.
2017-04-25 | GSE98079 | GEO