Browse
Submit Data
Databases
API
Help

Dataset Information

265 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Synechocystis 6803 LC-MS/MS - Systematically Ranking the Tightness of Membrane Association for Peripheral Membrane Proteins

ABSTRACT: Identification of the membrane and the soluble proteins in Synechocystis sp. PCC6803

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Synechocystis Sp. Pcc 6803

SUBMITTER: Yingchun Wang

LAB HEAD: Yingchun Wang

PROVIDER: PXD001246 | Pride | 2015-01-16

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Systematically ranking the tightness of membrane association for peripheral membrane proteins (PMPs).

Gao Liyan L Ge Haitao H Huang Xiahe X Liu Kehui K Zhang Yuanya Y Xu Wu W Wang Yingchun Y

Molecular & cellular proteomics : MCP 20141213 2

Large-scale quantitative evaluation of the tightness of membrane association for nontransmembrane proteins is important for identifying true peripheral membrane proteins with functional significance. Herein, we simultaneously ranked more than 1000 proteins of the photosynthetic model organism Synechocystis sp. PCC 6803 for their relative tightness of membrane association using a proteomic approach. Using multiple precisely ranked and experimentally verified peripheral subunits of photosynthetic ...[more]

PMID: 25505158

Similar Datasets

Synechocystis spatial proteome LC-MS/MS

Project description:We treated a unicellular photosynthetic model cyanobacterium, Synechocystis sp. PCC 6803, with five different types of abiotic stresses including nitrogen starvation, iron deficiency, cold, heat, and darkness, and systematically identified proteins showing stress-induced differential expression and/or redistribution between the membrane and the soluble compartments using a quantitative proteomics approach.

2023-03-20 | PXD035771 | Pride

Proteomic comparison of HliD and Ycf39 protein abundances in FLAG-tagged chlorophyll synthase co-immunoprecipitation assays of control and CrtR/CruF (carotenoid biosynthesis) knockout strains of Synechocystis sp. PCC 6803.

Project description:Chlorophyll a synthase (ChlG) is the enzyme responsible for attaching either a geranygeranyl or phytyl group to the chlorophyllide macrocycle during chlorophyll biosynthesis. Previous co-immunoprecipitation assays using FLAG-tagged ChlG identified the high light inducible protein HliD and the photosystem II assembly factor Ycf39 among the interaction partners. Non-protein components of this complex are the carotenoids zeaxanthin and myxoxanthophyll. To elucidate the function of these carotenoids in the association of ChlG/HliD/Ycf39, knockout strains of Synechocystis were produced to disrupt carotenoid biosynthesis. The abundances of HliD and Ycf39 relative to FLAG-tagged ChlG were compared in the different strains by proteomic analysis.

2022-08-18 | PXD020471 | Pride

Phosphoproteome of the cyanobacterium Synechocystis sp. PCC 6803 and its dynamics during nitrogen starvation

Project description:Cyanobacteria have shaped the earth’s biosphere as the first oxygenic photoautotrophs and still play an important role in many ecosystems. The ability to adapt to changing environmental conditions is an essential characteristic in order to ensure survival. To this end, numerous studies have shown that bacteria use protein post-translational modifications such as Ser/Thr/Tyr phosphorylation in cell signalling, adaptation and regulation. Nevertheless, our knowledge of cyanobacterial phosphoproteomes and their dynamic response to environmental stimuli is relatively limited. In this study, we applied gel-free methods and high accuracy mass spectrometry towards the unbiased detection of Ser/Thr/Tyr phosphorylation events in the model cyanobacterium Synechocystis sp. PCC 6803. We could identify over 300 phosphorylation events in cultures grown on nitrate as exclusive nitrogen source. Chemical dimethylation labelling was applied to investigate proteome and phosphoproteome dynamics during nitrogen starvation. Our dataset describes the most comprehensive (phospho)proteome of Synechocystis to date, identifying 2,382 proteins and 183 phosphorylation events and quantifying 2,111 proteins and 148 phosphorylation events during nitrogen starvation. Global protein phosphorylation levels were increased in response to nitrogen depletion after 24 hours. Among the proteins with increased phosphorylation, the PII signalling protein showed the highest fold-change, serving as positive control. Other proteins with increased phosphorylation levels comprised functions in photosynthesis and in carbon and nitrogen metabolism. This study reveals dynamics of Synechocystis phosphoproteome in response to environmental stimuli and suggests an important role of protein Ser/Thr/Tyr phosphorylation in fundamental mechanisms of homeostatic control in cyanobacteria.

2016-05-09 | PXD001831 | Pride

Synechocystis sp. PCC 6803 WT and Δhik33 (sll0698) proteomic research, proteomic data of normal culture conditions.

Project description:In this study, by using shotgun LC-MS/MS approach with the Tandem Mass Tag (TMTs) isobaric labelling technique we show that proteins in photosystem, inorganic carbon uptake and CO2 fixation systems are significantly changed in Δhik33 cells compared with WT cells.This is the normal culture condition proteomic data.

2017-05-19 | PXD005085 | Pride

Proximity labeling facilitates defining neighborhood proteome of photosystem II oxygen evolution complex in a model cyanobacterium

Project description:APEX2-based proximity labeling coupled with mass spectrometry have great potential for spatiotemporal identification of proteins proximal to a protein complex of interest. Using this approach it is feasible to define the proteome neighborhood of important protein complexes in a popular photosynthetic model cyanobacterium Synechocystis sp. PCC6803 (hereafter named as Synechocystis). To this end, we developed a robust workflow for APEX2-based proximity labeling in Synechocystis, and used the workflow to identify proteins proximal to the photosystem II (PS II) oxygen evolution complex (OEC) through fusion APEX2 with a luminal OEC subunit, PsbO.

2023-02-17 | PXD036113 | Pride

Absolute quantification of cellular levels of photosynthesis-related proteins in Synechocystis sp. PCC 6803

Project description:We quantified proteins in the model cyanobacterium Synechocystis sp. PCC 6803 given the general importance of cyanobacteria for global photosynthesis, for synthetic biology and biotechnology research, and their ancestral relationship to the chloroplasts of plants. Four mass spectrometry methods were used to quantify 97 cellular components involved in the biosynthesis of chlorophyll, carotenoid and bilin pigments, membrane assembly, the light reactions of photosynthesis, fixation of carbon dioxide and nitrogen, and hydrogen and sulfur metabolism. One quantification method was calibrated with artificial 15N-labelled proteins comprising concatenated proteotypic tryptic peptides and the other three methods were label-free (DDA-iBAQ, DDA-Top3, DIA-Top3) calibrated with the Sigma UPS2 standard protein mixture. As expected, the quantification methods gave individual distributions of abundance levels for each target protein that, for statistical validity, were not combined into single central tendency and variation metrics. Instead, overlapping distributions were merged to provide consensus abundance ranges. Quantification, expressed as copy numbers per cell (cpc), spanned four orders of magnitude, representing the complete abundance range from <1000 to >100,000 cpc of the proteins representing the complexes and pathways that were the focus of this study.

2023-01-04 | PXD035632 | Pride

Synechocystis sp. PCC 6803

Project description:Synechocystis PCC6803 time course responses to H2O2 3mM.

| PRJNA94289 | ENA

Synechocystis sp. PCC 6803

Project description:Synechocystis PCC6803 dose responses to iron starvation (96h).

| PRJNA94299 | ENA

Synechocystis sp. PCC 6803

Project description:Synechocystis PCC6803 time course responses to 50 µM cadmium

| PRJNA94287 | ENA

Comparison of wild-type Synechocystis sp. PCC 6803 with strains overexpressing wild-type or 5’-sensing-deficient RNase E

Project description:We compared transcriptomic changes, 5'-triphosphorylated (TSS) and 5'-monophosphorylated (PSS) RNA ends of different strains of the cyanobacterium Synechocystis sp. PCC6803. Comparison encompassed wild-type Synechocystis (WT), a strain overexpressing RNase E and RNase HII (rne(WT)) and a strain overexpressing 5’-sensing-deficient RNase E and RNase HII (rne(5p)). Analysis of changing 5'-monophosphorylated ends revealed 5’ sensing depedent processing sites on a transcriptome-wide level.

2023-01-20 | GSE184824 | GEO

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