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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Effects of SFP1 deletion and Sfp1p prionization on transcription in Saccharomyces cerevisiae

ABSTRACT: Sfp1p is known to form the [ISP+] prion in Saccharomyces cerevisiae. Interestingly enough, the consequences and phenotypes of Sfp1p prionization and its absence are quite different. In order to understand the origin of this difference, we compared transcription profiles of an [ISP+], sfp1delta strains against the control strain (SFP1 [isp-]). 3 strains (an [ISP+], [isp-] and sfp1delta derivative of 25-25-2V-P3982, Peterhoff genetic collection), each in quadruplicate (4 biological replicates).

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Polina Drozdova

PROVIDER: E-GEOD-52189 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Effects of SFP1 deletion and Sfp1p prionization on transcription in Saccharomyces cerevisiae

Project description:Sfp1p is known to form the [ISP+] prion in Saccharomyces cerevisiae. Interestingly enough, the consequences and phenotypes of Sfp1p prionization and its absence are quite different. In order to understand the origin of this difference, we compared transcription profiles of an [ISP+], sfp1delta strains against the control strain (SFP1 [isp-]).

2014-09-23 | GSE52189 | GEO

Quantitative global proteomics of yeast PBP1 deletion mutants and their stress responses reveals glucose metabolism, translation and stress granule changes

Project description:The yeast protein PBP1 has been implicated in diverse pathways such as polyadenylation, translation, RNA-DNA hybrid formation, stress granule homeostasis, mitochondrial dysfunction, and TORC1 sequestration. Intriguingly, its deletion mitigates the toxicity of human neurodegeneration factors, but the molecular mechanisms of these effects are poorly understood. Here we performed label-free quantitative global proteomics to identify crucial downstream factors, comparing two PBP1 deletion strains (DB and SM) and two cell stress conditions (heat and NaN3). In all four analyses, downregulations of key bioenergetics enzymes (CIT1, SDH1, MLS1), cell wall mannoproteins (HSP150, PST1) and the prion protein RNQ1 as well as upregulations of the leucine biosynthesis enzyme LEU1 and the transcription factor TAF6 were documented. Consistently for both unstressed PBP1-deleted strains, over 2-fold dysregulations were documented for potential PBP1 interactors such as MKT1 or RPL39 and the stress granule component NRP1. Upregulation of the ribosomal biogenesis factor NOP10 was observed as in the mouse mutant. Consistently for both PBP1 deletion strains, heat stress triggered changes of the stress granule component GIS2 and several of its interactors.

2016-12-23 | PXD003868 | Pride

A proteome-wide screen of Cdc14 interactors in Candida albicans

Project description:The Cdc14 phosphatase plays a key role in organising the intricate choreography of mitosis and cell division. In order to understand the role of Cdc14 in the human fungal pathogen Candida albicans we used quantitative proteomics to identify interacting proteins of CaCdc14. We used an orthogonal approach of a substrate trapping mutant combined with affinity purification-mass spectrometry analysis using stable isotope labelling in cell culture (SILAC). The results identified 126 proteins that interact with Cdc14 of which 80% are novel. These provide further insight into the function of Cdc14, highlighting roles in regulating the attachment of the mitotic spindle to kinetochores, mitotic exit, cytokinesis, licensing of DNA replication by re-activating pre-replication complexes, and DNA repair. Five Cdc14-interacting proteins with previously unknown functions localized to the Spindle Pole Bodies (SPBs). Intriguingly, there was suggestive evidence that Cdc14 substrates may include components of the ergosterol biosynthesis pathway targeted by azole anti-fungal drugs Thus we have greatly expanded the set of known substrates of Cdc14 by which it carries out these roles.

2019-11-12 | PXD009581 | Pride

[URE3] Prion formation by the Candida albicans Ure2p (but not by C. glabrata Ure2p)-CaUre2

Project description:[URE3] is a prion (infectious protein) of the Saccharomyces cerevisiae Ure2p, a regulator of nitrogen catabolism. We find that the Ure2p of Candida albicans and C. glabrata also regulate nitrogen catabolism. Conservation of amino acid sequence within the prion domain of Ure2p has been proposed as evidence that the [URE3] prion helps its host. We show that the C. albicans Ure2p, which does not conserve this sequence, can nonetheless form a [URE3] prion, but the C. glabrata Ure2p, which does have the conserved sequence, cannot form [URE3]. These results suggest that the sequence is not conserved to preserve prion forming ability. Two groups (WT and ure2 mutants) consisted of 4 biological replicates in which a ure2 deleted strain sample was paired with the wild type strain sample. Each group included 1 reciprocally labeled sample.

2012-01-01 | E-GEOD-26613 | biostudies-arrayexpress

Streptomyces secondary metabolism

Project description:This project aims to discover novel bioactive compounds from Streptomyces isolated from the rhizosphere from wild medicinal plants from Hamedan province, Iran. Proteomics is used to assist in discovery and characterization of the compounds. Streptomyces isolates are grown on ISP-4 medium for three days, proteins were extracted and analysed by shotgun proteomics.

2024-01-04 | PXD041994 | Pride

[URE3] Prion formation by the Candida albicans Ure2p (but not by C. glabrata Ure2p)

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2012-01-01 | E-GEOD-26620 | biostudies-arrayexpress

RNA-sequencing of C.elegans isp-1 mutant and superoxide dismutase-isp-1 double mutants

Project description:isp-1;sod double mutants have decreased lifespan, increased resistance to oxidative stress and slow physiologic rates. We performed RNA sequencing to compare gene expression between isp-1 mutants and isp-1;sod-3 and isp-1;sod-5 double mutants

2017-08-30 | GSE95240 | GEO

Essential role of proline synthesis and the one-carbon metabolism pathways for systemic virulence of Streptococcus pneumoniae

Project description:Rapid adaptation to grow within the physiological conditions found in the host environment is an essential but poorly understood virulence requirement for systemic pathogens such as Streptococcus pneumoniae. We have now demonstrated an essential role for the one-carbon metabolism pathway and a conditional role depending on strain background for proline biosynthesis for S. pneumoniae growth in serum or CSF and therefore for systemic virulence. RNAseq data demonstrated that loss of one carbon metabolism or proline biosynthesis both have profound but differing effects on S. pneumoniae metabolism in human serum, identifying the metabolic processes dependent on each pathway during systemic infection. These data provide a more detailed understanding of the adaptations required by systemic bacterial pathogens in order to cause infection, and demonstrate that the requirement for some of these adaptations vary between strains from the same species and could therefore underpin strain variations in virulence potential.

2023-09-10 | E-MTAB-13289 | biostudies-arrayexpress

RNA sequencing of mammary tumors induced in MTB-IGFIR transgenic mice fed 20% ISP, 1% ISP, or 20% Casein

Project description:Epidemiologic studies demonstrate that women from cultures that consume high levels of dietary soy have reduced breast cancer rates compared to women from cultures where soy consumption is typically much lower. The types of soy products consumed can also differ with Asian cultures consuming primarily minimally refined soy products while Western cultures often consume more highly refined soy products such as isolated soy protein (ISP). Our previous work showed that lifetime exposure to a diet containing 20% ISP promoted mammary tumor development in MTB-IGFIR transgenic mice. In this study, lifetime exposure to lower levels of ISP were evaluated (5% ISP and 1% ISP) to determine whether more moderate levels of ISP could protect against mammary tumorigenesis. A standard rodent diet, Teklad 2018 was also included in this study and Teklad 2018 contains a less refined form of soy, namely soybean meal. MTB-IGFIR mice fed ISP diets, independent of the concentration, displayed increased mammary tumor incidence and reduced tumor latency compared to MTB-IGFIR mice fed a 20% casein diet. Unexpectedly, MTB-IGFIR mice fed Teklad 2018 were completely protected against mammary tumor development. Although RNA sequencing of mammary tumors from ISP or casein fed mice did not identified gene expression patterns associated with the ISP diets, the ISP diets consistently promoted the expression of contractile related proteins in pubertal mammary glands. Therefore, lifetime exposure to ISP may alter gene expression in pubertal mammary glands rendering them more susceptible to transformation. Based on these findings women may want to avoid highly refined soy products such as ISP and switch to less refined forms of dietary soy until additional studies can be performed.

2020-07-15 | GSE122294 | GEO

RNA sequencing of PND55 mammary glands of mice fed 20% ISP, 1% ISP, 20% casein or Teklad 2018

2020-07-15 | GSE122271 | GEO

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