Browse
Submit Data
Databases
API
Help

Dataset Information

462 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteome of Saccharomyces cerevisiae extracellular matrix

ABSTRACT: Proteomic analysis of the extracellular matrix of Saccharomyces cerevisiae W303-1A Wt and the isogenic mutant strain gup1Δ during the development of multicellular overlays.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: Fábio Faria-Oliveira

LAB HEAD: Cândida Manuel Ribeiro Simões Lucas

PROVIDER: PXD001133 | Pride | 2015-11-30

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	AmiSOL13-86_FabioFariaSPSaccarocere2miss.prot.xml	Xml
	LIQ13-86_FabioFariaSPSaccarocere2miss.prot.xml	Xml
	W303-1A_Mutant_Batch.mgf	Mgf
	W303-1A_Mutant_Batch.msf	Msf
	W303-1A_Mutant_Batch.raw	Raw

Items per page:

1 - 5 of 16

Publications

Quantitative differential proteomics of yeast extracellular matrix: there is more to it than meets the eye.

Faria-Oliveira Fábio F Carvalho Joana J Ferreira Célia C Hernáez Maria Luisa ML Gil Concha C Lucas Cândida C

BMC microbiology 20151125

<h4>Background</h4>Saccharomyces cerevisiae multicellular communities are sustained by a scaffolding extracellular matrix, which provides spatial organization, and nutrient and water availability, and ensures group survival. According to this tissue-like biology, the yeast extracellular matrix (yECM) is analogous to the higher Eukaryotes counterpart for its polysaccharide and proteinaceous nature. Few works focused on yeast biofilms, identifying the flocculin Flo11 and several members of the HSP ...[more]

PMID: 26608260

Similar Datasets

Differential scaling between G1 protein production and cell size dynamics promotes commitment to the cell division cycle in budding yeast

Project description:In the unicellular eukaryote Saccharomyces cerevisiae, Cln3–cyclin-dependent kinase activity enables Start, the irreversible commitment to the cell division cycle. However, the concentration of Cln3 has been paradoxically considered to remain constant during G1, due to the presumed scaling of its production rate with cell size dynamics. Measuring metabolic and biosynthetic activity during cell cycle progression in single cells, we found that cells exhibit pulses in their protein production rate. Rather than scaling with cell size dynamics, these pulses follow the intrinsic metabolic dynamics, peaking around Start. Using a viral- based bicistronic construct and targeted proteomics to measure Cln3 at the single-cell and population levels, we show that the differential scaling between protein production and cell size leads to a temporal increase in Cln3 concentration, and passage through Start. This differential scaling causes Start in both daughter and mother cells across growth conditions. Thus, uncou- pling between two fundamental physiological parameters drives cell cycle commitment.

2022-05-16 | PXD029959 | Pride

Minimization of proteome reallocation explains metabolic shift in response to hierarchical utilization of mixed carbon sources

Project description:Protein expression levels were measured at different stages of the fermentation process

2023-09-15 | PXD045169 | Pride

Fission yeast NDR/LATS kinase Orb6 regulates exocytosis via phosphorylation of exocyst complex

Project description:NDR/LATS kinases regulate multiple aspects of cell polarity and morphogenesis from yeast to mammals, but few of their substrates are known. Fission yeast NDR/LATS kinase Orb6 has been proposed to control cell polarity via spatial regulation of Gef1, a guanine nucleotide exchange factor for the small GTPase Cdc42. Here we show that Orb6 plays a critical role as a positive regulator of exocytosis, independent of Gef1. Through Orb6 inhibition in vivo and quantitative global phosphoproteomics, we identify several proteins involved in membrane trafficking as Orb6 targets, and we confirm Sec3 and Sec5, conserved components of the exocyst complex, as substrates of Orb6 both in vivo and in vitro. Our results suggest that Orb6 kinase activity is crucial for exocyst localization to actively-growing cell tips and for exocyst activity during septum dissolution after cytokinesis. We further show that Orb6 phosphorylation of Sec3 serine-201 contributes to exocyst function in parallel with exocyst protein Exo70. We propose that Orb6 contributes to polarized growth by regulating membrane trafficking at multiple levels.

2019-01-31 | PXD009408 | Pride

Heat shock: genomic run-on (GRO) analysis

Project description:This SuperSeries is composed of the following subset Series: GSE24483: TR heat-shock GSE24484: RA heat-shock Refer to individual Series

2011-04-19 | E-GEOD-24488 | biostudies-arrayexpress

Profiling of free and polysome-bound mRNA from exponential and stationary growth phase cultures of Haloferax volcanii to identify growth phase dependent translational regulation

Project description:Growth phase dependent translational regulation of Hf. volcanii was analyzed on a genome-wide scale. The relative amounts of free versus polysome-bound mRNA (separated by gradient centrifugation) were quantified in exponential as well as stationary growth phase by the use of shotgun DNA microarrays.

2007-10-31 | E-MEXP-1191 | biostudies-arrayexpress

RA heat-shock

Project description:Within a GRO experiment, samples for mRNA amount (RA) were taken at 0, 4, 11, 16, 26 and 40 minutes after heat stress (from 25ºC to 37ºC). Analysis was done in filters also used for Transcription rate (TR) analysis of aliquots from the same cultures. The analysis includes 3 repeats of stress treatment of the W3030-1a strain. The same times were used for sampling in each repeat of the experiment. A single genomic DNA hybridization on every one of the filters is used for normalization between gene probes.

2011-04-19 | E-GEOD-24484 | biostudies-arrayexpress

Environmental interactions and epistasis are revealed in the proteomic responses to complex stimuli

Project description:Ultimately, the genotype of a cell and its interaction with the environment determine the cell’s biochemical state. While the cell’s response to a single stimulus has been studied extensively, a conceptual framework to model the effect of multiple environmental stimuli applied concurrently is not as well developed. In this study, we developed the concepts of environmental interactions and epistasis to explain the responses of the S. cerevisiae proteome to simultaneous environmental stimuli. We hypothesize that, as an abstraction, environmental stimuli can be treated as analogous to genetic elements. This would allow modeling of the effects of multiple stimuli using the concepts and tools developed for studying gene interactions. Mirroring gene interactions, our results show that environmental interactions play a critical role in determining the state of the proteome. We show that individual and complex environmental stimuli behave similarly to genetic elements in regulating the cellular responses to stimuli, including the phenomena of dominance and suppression. Interestingly, we observed that the effect of a stimulus on a protein is dominant over other stimuli if the response to the stimulus involves the protein. Using publicly available transcriptomic data, we find that environmental interactions and epistasis regulate transcriptomic responses as well.

2015-07-20 | PXD002371 | Pride

Escherichia coli LC-MS/MS treated by tavaborole

Project description:E.coli ATCC 25922 was overnight grown in 10 ml LB and passaged for 3 h with 1:50 dilution in fresh LB. Treated with tavaborole alone (80 μg/ml, labeled ‘A’) or tavaborole plus amikacin (80 μg/ml +40 μg/ml, labeled ‘AK’) for 6 h, cells were washed in PBS and harvested by centrifugation at 4,000 g, 8 min. After liquid nitrogen flash freezing, cells were stored at -80 °C and transported to company for following experiments

2023-03-10 | PXD033907 | Pride

Bioplatforms Australia: Antibiotic Resistant Sepsis Pathogens Framework Initiative - Staphylococcus aureus

Project description:The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies. The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. This submission pertains to Staphylococcus aureus strains BPH2760, BPH2819, BPH2900, BPH2947 and BPH2986.

2021-07-05 | PXD016504 | Pride

Replication Timing in Yeast: CGH microarrays: S vs G1 cells in various stress conditions

Project description:Replication timing in Saccharomyces cerevisiae in various replication stress conditions using CGH microarrays of S vs G1 cells. Replication of the eukaryotic genomes follows a characteristic temporal program, with different regions replicating at different times in S phase. We describe a stochastic model of DNA replication that naturally explains the replication profiles of a dozen of S. cerevisiae mutants. Each profile is described by a single parameter that differ between the mutants: the ratio between the fork velocity and the typical initiation rate (the “replicon length”), while all other origin-specific parameters remain unchanged. We devise an analytical method to infer the replicon lengths from the available data, and predicted its value in different mutant backgrounds. Further experiments verified model’s predictions. Our study supports a stochastic model of DNA replication in S. cerevisiae and explains the apparent robustness of this profile to perturbations that extend S phase. DNA from FACS-sorted cells was extracted, labeled with Cy dyes, hybridized to the CGH microarray and scanned. 18 strains were used, with variable biological repeats number.

2011-09-08 | E-GEOD-32002 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data