Expression data from Saccharomyces cerevisiae
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ABSTRACT:
ORGANISM(S): Schizosaccharomyces pombe Saccharomyces cerevisiae
PROVIDER: GSE49025 | GEO | 2016/01/01
SECONDARY ACCESSION(S): PRJNA212702
REPOSITORIES: GEO
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Project description:In this study, we characterize the protein uptake and degradation pathways of S. cerevisiae to better understand its impact on protein secretion titers. We do find that S. cerevisiae can consume significant (g/L) quantities of whole proteins. Characterizing the systems with metabolomics and transcriptomics, we identify metabolic and regulatory markers that are consistent with uptake of whole proteins by endocytosis, followed by intracellular degradation and catabolism of substituent amino acids. Uptake and degradation of recombinant protein products may be common in S. cerevisiae protein secretion systems, and the current data should help formulate strategies to mitigate product loss. Saccharomyces cerevisiae strains at different cultivation conditions were selected at early glucose phase in batch fermentations for RNA extraction and hybridization on Affymetrix microarrays. Biological triplicates were applied, and strains growing at normal conditions (with no BSA supplemented) were used as the control strain.
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2015-04-20 | ST000399 | MetabolomicsWorkbench
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2016-05-13 | ST000400 | MetabolomicsWorkbench
Project description:The ever-increasing size and scale of biological information have created a need for systems-level tools that synthesize large quantities of dispersed and distinct data and inform decision- and hypothesis-making processes in basic and translational sciences. To address this need, we have created KiRNet, an kinase-centered method designed to integrate results of functional screens with interactome or other protein-protein interaction data, as well as additional molecular data to generate functional network-level models. These network models can be further optimized and refined to identify small, differentially regulated subnetworks, even in the absence of large-scale datasets. As a proof of concept, we applied KiRNet to liver cancer cells driven by Fzd2, a gene known to cause epithelial-mesenchymal transition and cancer metastasis and identified a subnetwork of 166 proteins that regulate this cell state. The KiRNet derived information can be used to formulate high-value predictions for future testing and thus accelerate basic and translational discoveries.
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Project description:Membrane protein and phospholipid (PL) compositions change in response to environmental cues and during infections. Covalent modification (e.g., unsaturation and cyclopropanation) and remodeling the acyl chain length of PLs is an important bacterial adaptation mechanism. However, little is known about which bacterial pathways are regulated in response to the alteration of PL composition. Here, we show that P. aeruginosa PlaF, which modulates membrane PL composition, is important for biofilm biogenesis, and we performed whole-cell quantitative proteomics of P. aeruginosa wild-type and ∆plaF biofilms to identify pathways regulated by PlaF. The results revealed profound alterations in the abundance of 14 two-component systems (TCS), including the PprA-PprB, which controls the transition to biofilm. Activation of PprA-the PprB system observed by proteomics was confirmed by mRNA quantification. Furthermore, we have observed a unique phosphorylation pattern of transcriptional regulators, transporters and metabolic enzymes, and differential production of nine proteases in ∆plaF, indicating that PlaF-mediated virulence adaptation involves complex transcriptional and post-transcriptional regulation. Moreover, proteomics revealed that the pyoverdin-mediated iron uptake pathway proteins were depleted in ∆plaF, which agrees with decreased concentrations of extracellular pyoverdine and intracellular iron in ∆plaF and is likely responsible for its prolonged lag phase due to reduced iron uptake. Conversely, the accumulation of proteins from alternative iron-uptake systems in ∆plaF suggests that PlaF may function as a switch between different iron-acquisition pathways. The observation that ∆plaF accumulates PL-acyl chain modifying enzymes and PlsX, an initiator of de novo PL synthesis, reveals novel insights into the relationship between degradation, covalent modification and biosynthesis of PLs for membrane homeostasis. Although the precise mechanism by which PlaF simultaneously affects multiple pathways remains to be elucidated, we suggest that PlaF-catalyzed degradation of PLs is a signal which is amplified by proteins of TCS, phosphorylation and proteolytic degradation systems to elicit the global adaptive response in P. aeruginosa.
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Project description:Abstract: Proteins contribute to a major part of the organic nitrogen in forest soils. This nitrogen is mobilized and becomes available to trees as a result of the depolymerizing activities of symbiotic ectomycorrhizal fungi. The mechanisms by which these fungi depolymerize proteins and assimilate the released nitrogen are poorly characterized. Biochemical analysis and transcriptome profiling were performed to examine the proteolytic machinery and the uptake system of the ectomycorrhizal basidiomycete Paxillus involutus during the assimilation of organic nitrogen from various protein sources and extracts of organic matter. All substrates induced secretion of peptidase activity with an acidic pH optimum, mostly contributed by aspartic peptidases. The peptidase activity was transiently repressed by ammonium. Transcriptional analysis revealed a large number of extracellular endo- and exopeptidases. The expression levels of these peptidases were regulated in parallel with transporters and enzymes involved in the assimilation and metabolism of the released peptides and amino acids. For the first time the molecular components of the protein degradation pathways of an ectomycorrhizal fungus are described. The data suggest that the transcripts encoding these components are regulated in response to the chemical properties and the availability of the protein substrates. Firoz Shah, Francois Rineau, Björn Canbäck, Tomas Johansson and Anders Tunlid (2013) The molecular components of the extracellular protein-degradation pathways of the ectomycorrhizal fungus Paxillus involutus (submitted) A one-chip study (data from 9 subarrays collected from a 12-plex Nimblegen microarray (ID: 461228)) using total RNA recovered from glass-bead cultures of Paxillus involutus (ATCC200175) after amendments of 3 different substrates (3 replicates of each).
2013-09-01 | E-GEOD-47838 | biostudies-arrayexpress
Project description:Investigation of whole genome gene expression level changes in Ashbya gossypii VTT D-101398 secreting recombinant endoglucanase I (EGI) from Trichoderma ressei (Ribeiro et al. 2010 - PMID: 20422178), compared to the its corresponding empty vector control strain and to conditions where VTT D-101398 EGI secreting cultures were treated with dithiothreitol (DTT). Background: Ashbya gossypii is a filamentous Saccharomycete used for the industrial production of riboflavin that has been recently explored as a host system for recombinant protein production. To gain insight into the protein secretory pathway of this biotechnologically relevant fungus, we undertook genome-wide analyses to explore its secretome and its transcriptional responses to protein secretion stress. Results: A computational pipeline was used to predict the inventory of proteins putatively secreted by A. gossypii via the general secretory pathway. The proteins actually secreted by this fungus into the supernatants of submerged cultures in minimal and rich medium were mapped by two-dimensional gel electrophoresis, revealing that most of the A. gossypii secreted proteins have an isoelectric point between 4 and 6, and a molecular mass above 25 kDa. These analyses together indicated that 1-4% of A. gossypii proteins are likely to be secreted, of which less than 33% are putative hydrolases. Furthermore, transcriptomic analyses carried out in A. gossypii cells under recombinant protein secretion conditions and dithiothreitol-induced secretion stress unexpectedly revealed that a conventional unfolded protein response (UPR) was not activated in any of the conditions, as the expression levels of several well-known UPR target genes (e.g. IRE1, KAR2, HAC1 and PDI1 homologs) remained unaffected. However, several other genes involved in protein unfolding, endoplasmatic reticulum-associated degradation, proteolysis, vesicle trafficking, vacuolar protein sorting, secretion and mRNA degradation were up-regulated by dithiothreitol-induced secretion stress. Conversely, the transcription of several genes encoding secretory proteins, such as components of the glycosylation pathway, was severely repressed by dithiothreitol Conclusions: This study provides the first insights into the secretion stress response of A. gossypii, as well as a basic understanding of its protein secretion potential, which is more similar to that of yeast than to that of other filamentous fungi. Contrary to what has been widely described for yeast and fungi, a conventional UPR was not observed in A. gossypii, but alternative protein quality control mechanisms enabled it to cope with secretion stress. These data will help provide strategies for improving heterologous protein secretion in A. gossypii.
2014-10-16 | GSE62366 | GEO
Project description:We used microarray analyses in adult female zebrafish (Danio rerio) to identify metabolic pathways regulated by starvation in two key organs that 1) serve biosynthetic and energy mobilizing functions (liver) and 2) consume energy and direct behavioral responses (brain). Starvation affected the expression of 574 transcripts in the liver, indicating an overall decrease in metabolic activity, reduced lipid metabolism, protein biosynthesis and proteolysis, and cellular respiration, and increased gluconeogenesis. Starvation also regulated expression of many components of the Unfolded Protein Response, the first such report in a species other than yeast (Saccharomyces cerevisiae) and mice (Mus musculus). The response of the zebrafish hepatic transcriptome to starvation was strikingly similar to that of rainbow trout (Oncorhynchus mykiss), but very different from common carp (Cyprinus carpio) and mouse. The transcriptome of zebrafish whole brain was much less affected than the liver, with only two differentially expressed genes, both down-regulated. Down-regulation of one of these genes, matrix metalloproteinase 9 (mmp9), suggests increased inhibition of apoptosis (neuroprotection) and decreased restructuring of the extracellular matrix in the brain of starved zebrafish. The low level of response in the transcriptome of whole zebrafish brain agrees with observations that the brain is metabolically protected compared to the rest of the body. Keywords: starvation study
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