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Aryal et al, 2011, metabolic labelling of Cyanothece protein synthesis

Aryal et al, 2011, metabolic labelling of Cyanothece protein synthesis

Quantitative proteomic analysis of Cyanothece ATCC51142 grown in 12L:12D light:dark cycles, using partial metabolic labeling and LC-MS analysis.

SEEK ID: https://fairdomhub.org/assays/632

Class: Experimental Assay

Contributor: Daniel Seaton

Projects: Millar group, TiMet

Investigation: Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism

Study: Proteome and translation rate data for the Ostreococcus alga and for cyanobacteria

Assay type: Proteomics

Technology type: Mass Spectrometry

Organisms: No organisms

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Created: 14th Jan 2018 at 23:37

Last updated: 20th Feb 2018 at 23:03

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Projects (2)
Investigations (1)
Studies (1)
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Daniel Seaton

Projects: Millar group, TiMet, Regulation of flowering time in natural conditions

Institutions: University of Edinburgh

https://orcid.org/0000-0002-5222-3893

Millar group

Andrew Millar's research group, University of Edinburgh

Programme: SynthSys

Public web page: http://www.amillar.org

Organisms: Escherichia coli, Arabidopsis thaliana, Ostreococcus tauri

TiMet

EU FP7 collaborative project TiMet, award number 245143. Funded 2010-2015.
"TiMet assembles world leaders in experimental and theoretical plant systems biology to advance understanding of the regulatory interactions between the circadian clock and plant metabolism, and their emergent effects on whole-plant growth and productivity."

Programme: SynthSys

Public web page: http://timing-metabolism.eu/

Organisms: Arabidopsis thaliana, Ostreococcus tauri

Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism

Millar group, TiMet

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Andrew Millar

Daniel Seaton

Katja Baerenfaller

Click on Snapshot 2 to download data, models and analysis for Daniel Seaton et al.
biorXiv 2017 https://doi.org/10.1101/182071 and
Molecular Systems Biology, accepted Jan 2018, https://doi.org/10.15252/msb.20177962.
Note that the published paper cannot be fully linked into this record as the DOI above was not live when we made the Research Object from this Investigation on FAIRDOMHub.

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.investigation.163.2

Studies: Modelling and analysis of translational coincidence, Photoperiod-specific proteome data for Arabidopsis, Proteome and translation rate data for the Ostreococcus alga and for cya..., Rhythmic and photoperiod-specific transcriptome datasets for Arabidopsis

Assays: Aryal et al, 2011, metabolic labelling of Cyanothece protein synthesis, Blasing et al, 2005, diurnal microarray in 12L:12D, Estimation of rates of translation and turnover from proteomics datasets, Martin et al, 2012, Ostreococcus N15 labelling proteomics data, Photoperiod proteomics, Stitt lab, TiMet photoperiod microarrays, Translational coincidence model

Created: 16th Nov 2017 at 13:04, Last updated: 18th Sep 2018 at 09:48

Proteome and translation rate data for the Ostreococcus alga and for cyanobacteria

Millar group, TiMet

All contributors

Andrew Millar

Literature data and associated scripts analysed in the Seaton et al. 2017 study; data processing by Daniel Seaton.

Person responsible: Andrew Millar

Snapshots: No snapshots

Investigation: Photoperiodic control of the Arabidopsis proteo...

Assays: Aryal et al, 2011, metabolic labelling of Cyanothece protein synthesis, Estimation of rates of translation and turnover from proteomics datasets, Martin et al, 2012, Ostreococcus N15 labelling proteomics data

Created: 16th Nov 2017 at 13:20, Last updated: 20th Feb 2018 at 23:03

Aryal et al, 2011, metabolic labelling of Cyanothece protein synthesis

Millar group

All contributors

Daniel Seaton

Andrew Millar

Quantitative proteomic analysis of Cyanothece ATCC51142 grown in 12L:12D light:dark cycles, using partial metabolic labeling and LC-MS analysis.

Creators: Daniel Seaton, Andrew Millar

Contributor: Daniel Seaton

Relationship type: Not specified

Investigations: Photoperiodic control of the Arabidopsis proteo...

Studies: Proteome and translation rate data for the Ostr...

Assays: Aryal et al, 2011, metabolic labelling of Cyano..., Estimation of rates of translation and turnover...

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Created: 14th Jan 2018 at 23:37, Last updated: 20th Feb 2018 at 23:03

Dynamic proteomic profiling of a unicellular cyanobacterium Cyanothece ATCC51142 across light-dark diurnal cycles.

Millar group

Abstract (Expand)

BACKGROUND: Unicellular cyanobacteria of the genus Cyanothece are recognized for their ability to execute nitrogen (N2)-fixation in the dark and photosynthesis in the light. An understanding of these … mechanistic processes in an integrated systems context should provide insights into how Cyanothece might be optimized for specialized environments and/or industrial purposes. Systems-wide dynamic proteomic profiling with mass spectrometry (MS) analysis should reveal fundamental insights into the control and regulation of these functions. RESULTS: To expand upon the current knowledge of protein expression patterns in Cyanothece ATCC51142, we performed quantitative proteomic analysis using partial ("unsaturated") metabolic labeling and high mass accuracy LC-MS analysis. This dynamic proteomic profiling identified 721 actively synthesized proteins with significant temporal changes in expression throughout the light-dark cycles, of which 425 proteins matched with previously characterized cycling transcripts. The remaining 296 proteins contained a cluster of proteins uniquely involved in DNA replication and repair, protein degradation, tRNA synthesis and modification, transport and binding, and regulatory functions. Functional classification of labeled proteins suggested that proteins involved in respiration and glycogen metabolism showed increased expression in the dark cycle together with nitrogenase, suggesting that N2-fixation is mediated by higher respiration and glycogen metabolism. Results indicated that Cyanothece ATCC51142 might utilize alternative pathways for carbon (C) and nitrogen (N) acquisition, particularly, aspartic acid and glutamate as substrates of C and N, respectively. Utilization of phosphoketolase (PHK) pathway for the conversion of xylulose-5P to pyruvate and acetyl-P likely constitutes an alternative strategy to compensate higher ATP and NADPH demand. CONCLUSION: This study provides a deeper systems level insight into how Cyanothece ATCC51142 modulates cellular functions to accommodate photosynthesis and N2-fixation within the single cell.

Authors: U. K. Aryal, J. Stockel, R. K. Krovvidi, M. A. Gritsenko, M. E. Monroe, R. J. Moore, D. W. Koppenaal, R. D. Smith, H. B. Pakrasi, J. M. Jacobs

Date Published: No date defined

Journal: BMC Syst Biol

PubMed ID: 22133144

Citation: BMC Syst Biol. 2011 Dec 1;5:194. doi: 10.1186/1752-0509-5-194.

Created: 14th Jan 2018 at 23:38