Browse
Submit Data
Databases
API
Help

Dataset Information

344 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Systems-level organisation of yeast methylotrophic lifestyle

ABSTRACT: Changes in the proteome of Pichia pastoris cultures either grown on glucose or methanol were analysed using a 2D-chromatography based TMT labeling LC-ESI-MS workflow. Three biological replicates, with two technical replicates each, had been analyzed leading to six replicate data sets of both growth conditions.

OTHER RELATED OMICS DATASETS IN: PRJNA280698

INSTRUMENT(S): maXis

ORGANISM(S): Komagataella Pastoris Dsmz 70382

TISSUE(S): Cell Suspension Culture

SUBMITTER: Clemens Grünwald-Gruber

LAB HEAD: Friedrich Altmann

PROVIDER: PXD002036 | Pride | 2015-10-01

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Systems-level organization of yeast methylotrophic lifestyle.

Rußmayer Hannes H Buchetics Markus M Gruber Clemens C Valli Minoska M Grillitsch Karlheinz K Modarres Gerda G Guerrasio Raffaele R Klavins Kristaps K Neubauer Stefan S Drexler Hedda H Steiger Matthias M Troyer Christina C Al Chalabi Ali A Krebiehl Guido G Sonntag Denise D Zellnig Günther G Daum Günther G Graf Alexandra B AB Altmann Friedrich F Koellensperger Gunda G Hann Stephan S Sauer Michael M Mattanovich Diethard D Gasser Brigitte B

BMC biology 20150923

<h4>Background</h4>Some yeasts have evolved a methylotrophic lifestyle enabling them to utilize the single carbon compound methanol as a carbon and energy source. Among them, Pichia pastoris (syn. Komagataella sp.) is frequently used for the production of heterologous proteins and also serves as a model organism for organelle research. Our current knowledge of methylotrophic lifestyle mainly derives from sophisticated biochemical studies which identified many key methanol utilization enzymes suc ...[more]

PMID: 26400155

Similar Datasets

Systems-level organisation of yeast methylotrophic lifestyle - organelle preparation

Project description:Changes in the proteome of Pichia pastoris cultures either grown on glucose or methanol were analysed using a 2D-chromatography based TMT labeling LC-ESI-MS workflow. Three biological replicates, with two technical replicates each, had been analyzed leading to six replicate data sets of both growth conditions. The data is supported by peroxisomal protein data.

2015-10-01 | PXD002831 | Pride

Pichia pastoris Glucose/Methanol comparison

2015-08-31 | GSE67690 | GEO

Pichia pastoris Glucose/Methanol comparison

Project description:Comparison of transcription profile of Pichia pastoris cells grown on Glucose medium with Pichia pastoris cells grown on Methanol/Glycerol medium, the fermentations were done in a chemostat. 2 color experiment in reference design. Pichia pastoris reference mix [mixed pool of Pichia pastoris cells sampled from various conditions including cells grown on glycerine, glucose and methanol, on full andminimal medium, in stationary and exponential growth phase, and in different stress states]

2015-08-31 | E-GEOD-67690 | biostudies-arrayexpress

To identify novel targets of Mxr1p in Pichia pastoris cultured in methanol

Project description:Pichia pastoris (Komagataella phaffi) transcription factor Mxr1p is known to regulate multiple metabolic pathways by binding to Mxr1p response elements of target genes. Mxr1p possesses a transactivation domain within the N-terminal 400 amino acids (Mxr1N400) which is functional during methanol metabolism. (Parua et al; 2012) Studies from our lab have shown that delta_mxr1 complemented with Mxr1N400 fails to reverse the growth defect of delta_mxr1 cultured in a medium containing methanol suggesting that region beyond N-terminal 400 amino acids has an essential function. We employed DNA microarray to identify genes whose expression is regulated by Mxr1N400 and full length Mxr1 during methanol metabolism. Pichia pastoris 14-3-3 regulates transcriptional activity of the methanol inducible transcription factor Mxr1 by direct interaction. Pabitra K. Parua, Paul M. Ryan and Elton T. Young. Molecular microbiology, 2012

2021-09-22 | GSE146829 | GEO

To identify novel targets of a histone acetyltransferase Gcn5, and Snf1 kinase complex in Pichia pastoris in YNBM

Project description:The regulation of gene expression in Pichia pastoris has so far involved study of transcription factors. However, there are factors other than transcription factors affecting mRNA synthesis such as coactivators, enhancers, and chromatin modifiers. This study is a first ever report on epigenetic regulation in Pichia pastoris where, a histone acetyltransferase is reported to regulate transcription of genes involved in utilization of alternate carbon sources. We employed RNA Seq to identify new targets of Gcn5 in methanol medium.

2022-09-28 | GSE186300 | GEO

To identify novel targets of a histone acetyltransferase Gcn5 in Pichia pastoris

2022-12-31 | GSE150467 | GEO

Comparison of gene expression profile among Pichia pastoris strain with a different gene dosage

Project description:Pichia pastoris is a widely used yeast platform for heterologous protein production. Although increasing gene dosage is a powerful strategy to improve recombinant protein production, an excess in the number of gene copies often leads to decreased product yields and increased metabolic burden. In order to find the bottlenecks of this strategy, here we present a transcriptome profile comparison of a series of Pichia pastoris strains carrying a different gene dosage of the Rhizopus oryzae lipase (Rol) as a model protein. Cells were grown on a mixture of glycerol:methanol in chemostat cultures. 2 color experiment in reference design.

2017-02-22 | E-MTAB-4582 | biostudies-arrayexpress

Komagataella phaffii CBS 7435

Project description:Pichia pastoris Glucose/Methanol comparison

| PRJNA280698 | ENA

Project description:Methanol-free Pichia pastoris for protein expression

| PRJNA433717 | ENA

Catabolite repression of phosphoenolpyruvate carboxykinase by a zinc finger protein under biotin- and pyruvate carboxylase-deficient conditions in Pichia pastoris

Project description:We have identified a methanol- and biotin-starvation-inducible zinc finger protein named ROP [repressor of phosphoenolpyruvate carboxykinase (PEPCK)] in the methylotrophic yeast Pichia pastoris. When P.pastoris strain GS115 (wild-type, WT) is cultured in biotin-deficient, glucose ammonium (Bio-) medium, growth is suppressed due to the inhibition of anaplerotic synthesis of oxaloacetate, catalysed by the biotin-dependent enzyme pyruvate carboxylase (PC). Deletion of ROP results in a strain (∆ROP) that can grow under biotin-deficient conditions due to derepression of a biotin- and PC-independent pathway of anaplerotic synthesis of oxaloacetate. Northern analysis as well as microarray expression profiling of RNA isolated from WT and ∆ROP strains cultured in Bio(-) medium indicate that expression of the phosphoenolpyruvate carboxykinase gene (PEPCK) is induced in ∆ROP during biotin- or PC-deficiency even under glucose-abundant conditions. There is an excellent correlation between PEPCK expression and growth of ∆ROP in Bio(-) medium, suggesting that ROP-mediated regulation of PEPCK may have a crucial role in the biotin- and PC-independent growth of the ∆ROP strain. To our knowledge, ROP is the first example, of a zinc finger transcription factor involved in the catabolite repression of PEPCK in yeast cells cultured under biotin- or PC-deficient and glucose-abundant conditions. Agilent one-color experiment,Organism: Pichia pastoris ,Custom Pichia pastoris Gene Expression 8x15k array designed by Genotypic Technology Pvt. Ltd. (Agilent -AMADID: 25088 ) , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

2011-10-13 | E-GEOD-32948 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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