PXD002377

PXD002377 is an original dataset announced via ProteomeXchange.

Title	The response of Chlamydomonas reinhardtii to nitrogen deprivation: a systems biology analysis
Description	Drastic alteration in macronutrients causes large changes in gene expression in the photosynthetic unicellular alga Chlamydomonas reinhardtii. Preliminary data suggested that cells follow a biphasic response to this change hinging on the initiation of lipid accumulation, and we hypothesized that drastic repatterning of metabolism also followed this biphasic modality. To test this hypothesis, transcriptomic, proteomic, and metabolite changes that occur under nitrogen (N) deprivation were analyzed. Eight sampling times were selected covering the progressive slowing of growth and induction of oil synthesis between 4 and 6 h after N deprivation. Results of the combined, systems-level investigation indicated that C. reinhardtii cells sense and respond on a large scale within 30 min to a switch to N-deprived conditions turning on a largely gluconeogenic metabolic state, which then transitions to a glycolytic stage between 4 and 6 h after N depletion. This nitrogen-sensing system is transduced to carbon- and nitrogen-responsive pathways, leading to down-regulation of carbon assimilation and chlorophyll biosynthesis, and an increase in nitrogen metabolism and lipid biosynthesis. For example, the expression of nearly all the enzymes for assimilating nitrogen from ammonium, nitrate, nitrite, urea, formamide/acetamide, purines, pyrimidines, polyamines, amino acids and proteins increased significantly. Although arginine biosynthesis enzymes were also rapidly up-regulated, arginine pool size changes and isotopic labeling results indicated no increased flux through this pathway.
HostingRepository	PRIDE
AnnounceDate	2015-06-17
AnnouncementXML	Submission_2015-06-17_03:44:42.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD002377
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Evan McConnell
SpeciesList	scientific name: Chlamydomonas reinhardtii; NCBI TaxID: 3055;
ModificationList	Oxidation; iTRAQ4plex; Acetyl; Carbamidomethyl; Deamidated
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2015-06-16 06:29:42	ID requested
⏵ 1	2015-06-17 03:44:44	announced

Park JJ, Wang H, Gargouri M, Deshpande RR, Skepper JN, Holguin FO, Juergens MT, Shachar-Hill Y, Hicks LM, Gang DR, The response of Chlamydomonas reinhardtii to nitrogen deprivation: a systems biology analysis. Plant J, 81(4):611-24(2015) [pubmed]

curator keyword: Biological

submitter keyword: proteomics, Chlamydomonas reinhardtii, systems biology, nitrogen deprivation, technical advance

Leslie M. Hicks
contact affiliation	Assistant Professor, Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
contact email	lmhicks@email.unc.edu
lab head
Evan McConnell
contact affiliation	Graduate Research Assistant
contact email	evanmcc@live.unc.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD002377
     1. Label: PRIDE project
     2. Name: The response of Chlamydomonas reinhardtii to nitrogen deprivation: a systems biology analysis