Construction and evaluation of a whole genome microarray of Chlamydomonas reinhardtii
Ontology highlight
ABSTRACT:
ORGANISM(S): Chlamydomonas reinhardtii
SUBMITTER: Jörg Toepel
PROVIDER: E-GEOD-33042 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Comparison of gene expression for chlamydomonas cells grown for 24 h, 48 h 72 h, 96 h in sulfur depleted media against Two-condition experiment, 3 different Chlamydomonas wt strains plus npq 4 mutant (3 pooled biological samples)
2011-10-18 | E-GEOD-33040 | biostudies-arrayexpress
Project description:Testing for labeling efficiency and Replication effeciency of the microarray (Chlamydomonas cells grown for 24 h under sulfur starvation) Two-condition experiment, 3 Biological replicates
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Project description:Comparison of gene expression for Chlamydomonas cells grown for 0h, 48h, 72h, 96h in sulfur depleted media
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Project description:Phosphorus (P) is an essential nutrient that is limiting in many environments. When P is scarce organisms employ strategies for conservation of internal stores, and to efficiently scavenge P from their external surroundings. In this study we investigated the acclimation response of Chlamydomonas reinhardtii to P deficiency, comparing the transcriptional profiles of P starved wild-type cells to the P replete condition. RNA was prepared from P-containing or P-deprived logarithmic growth phase cells and subjected to RNA-Seq analysis. During the 24 hours after the imposition of P starvation we observed that from the 407 significantly changing genes (> 2 fold change, corrected p-value < 0.05) in the wild-type 317 genes were up-regulated, in average 8.36-fold, and 90 genes were down-regulated by 3.43-fold, in average. Many of the upregulated genes encoded enzymes involved in specific responses to P starvation, including PHOX, encoding the major secreted alkaline phosphatase, and multiple putative, high-efficiency phosphate transporter genes. More general responses included the up-regulation of genes involved in photoprotective processes (LHCSR3, LHCSR1, LHCBM9, PTOX1) and genes involved in protein modification and degradation. Down-regulated mRNAs indicated an early stage of the reduction of chloroplast ribosomal proteins, which are considered to be a reservoir for P in the cell. Chlamydomonas reinhardtii strain 21 gr (CC1690, wild-type) grown in TAP medium (Harris 1989) in a rotary incubator (200 rpm) at 25 M-BM-0C in continuous light (70 M-BM-5mol m-2 s-1). For 24 hours, either 1.1 mM phosphate or 0 mM were provided with the growth media. P deprivation was achieved by washing cells twice in midlogarithmic growth phase with liquid TAP medium without P (TAP-P) and cells were resuspended at a density of 2.5 mg/ml Chlorophyll in TAP or TAP-P. Cell aliquots were collected for mRNA isolation 24 h after being transferred either to TAP or TAP-P medium.
2014-04-05 | E-GEOD-56505 | biostudies-arrayexpress
Project description:Systems analysis reveals that Chlamydomonas reinhardtii responds rapidly and flexibly to an increase in light intensity. Rising metabolite levels and post-translation regulation facilitate a rapid increase in the rate of carbon fixation and a slightly delayed increase in the rate of growth, and slower changes in protein abundance adjust allocation and minimize bottlenecks in the new conditions. Gene expression was measured from samples of Chlamydomonas reinhardtii cell cultures at four time points (two under low, four under high light) under either low (41 µmol) or high (145 µmol) light conditions in two separate bioreactors. Three biological replicate time series were sampled.
2014-04-30 | E-GEOD-56800 | biostudies-arrayexpress
Project description:We used Chlamydomonas microarray v2.0 to compare the time course expression profiles of two Chlamydomonas reinhardtii strains: wild-type WT and the high hydrogen producing mutant Stm6Glc4 during sulfur starvation induced hydrogen production. Major cellular reorganizations in photosynthetic apparatus, sulfur and carbon metabolism upon H2 production were confirmed as common to both strains. More importantly, our results pointed out factors which lead to the higher hydrogen production in the mutant including higher light sensitivity and lower competitions with hydrogenase by alternative electron sinks. Under S-starvation induced H2 producing conditions the induction of LHCSR3, a chlorophyll binding protein involving in non photochemical quenching, was significantly lower in Stm6Glc4 resulting in significant higher photodamage to photosystem II. Consequently, Stm6Glc4 had a shorter aerobic phase, consumed less starch reserves, and produced H2 earlier at higher rates than WT. We also showed that the loss of mitochondrial DNA-binding protein MOC1 in both knockdown and knockout mutant resulted in higher light sensitivity and improved H2 yield. Furthermore, by comparing our data with previously published ‘omics’ data, we were able to identify genes that responded specifically to either sulfur starvation, anaerobiosis or hydrogen production as well as to provide a more complete picture of S-deprived H2 production in the green alga C. reinhardtii. A total of 33 microarray hydridizations were performed covering samples taken during the course of S deprivation induced H2 producction. The samples included 4 time points in the high hydrogen producing mutant Stm6Glc4 (taken at 16, 28, 52 and 76h) and 6 time points in the wildtype CC-406 (taken at 16, 28, 52, 68, 92, 116h). Samples from each time point were compared directly with the sample taken prior to S starvation from the corresponding strain. Three biological replicates were tested at each time point.
2011-11-30 | E-GEOD-30252 | biostudies-arrayexpress
Project description:C. reinhardtii cells exposed to abiotic stresses (e.g. iron-, nitrogen-, zinc- or phosphorus-deficiency) accumulate TAGs which are stored in lipid droplets. Here, we report that iron starvation leads to formation of lipids bodies and accumulation of TAGs. This occurs between 12 and 24 h of iron-starvation. C. reinhardtii cells deprived for iron have more saturated FA, due to the loss of functional FA desaturases, which are diiron enzymes. The abundance of a plastid ACP-acyl desaturase (FAB2) is significantly decreased to the same degree as observed for ferredoxin, which is a substrate of the desaturases. The increase in saturated FA (C16:0 and C18:0) is concomitant with the decrease in saturated FA (C16:4, C18:3 or C18:4). This pattern was observed for MGDG, DGTS or DGDG. When we monitored the absolute levels of glycerolipids, MGDG content dropped significantly after only 2 h of iron-starvation. On the other hand, DGTS and DGDG contents gradually decrease until a minimum is reached after 24-48 h of iron-deprivation. RNA-Seq analysis of iron-starved C. reinhardtii cells revealed significant changes in many transcripts coding for enzymes involved in FA metabolism. The mRNA abundances of genes coding for components involved in TAG accumulation (DGAT or MLDP) are increased. A more dramatic increase at the transcript level has been observed for many lipases, suggesting that a major remodeling of lipid membranes occurs during iron-starvation in C. reinhardtii. Sampling of Chlamydomonas CC-4532 (2137) cells cultivated photoheterotrophically (TAP) under iron-starvation condition (0 uM Fe-EDTA). Samples were collected from biological duplicates after washing in TAP medium lacking Fe at 0, 0.5, 1, 2, 4, 8, 12, 24 and 48 hours.
2014-02-20 | E-GEOD-44611 | biostudies-arrayexpress
Project description:RNA populations in Chlamydomonas reinhardtii Keywords: Highly parallel pyrosequencing
2007-05-16 | GSE7308 | GEO
Project description:Phosphorus (P) is an essential nutrient that is limiting in many environments. When P is scarce organisms employ strategies for conservation of internal stores, and to efficiently scavenge P from their external surroundings. In this study we investigated the acclimation response of Chlamydomonas reinhardtii to P deficiency, comparing the transcriptional profiles of P starved wild-type cells to the P replete condition. RNA was prepared from P-containing or P-deprived logarithmic growth phase cells and subjected to RNA-Seq analysis. During the 24 hours after the imposition of P starvation we observed that from the 407 significantly changing genes (> 2 fold change, corrected p-value < 0.05) in the wild-type 317 genes were up-regulated, in average 8.36-fold, and 90 genes were down-regulated by 3.43-fold, in average. Many of the upregulated genes encoded enzymes involved in specific responses to P starvation, including PHOX, encoding the major secreted alkaline phosphatase, and multiple putative, high-efficiency phosphate transporter genes. More general responses included the up-regulation of genes involved in photoprotective processes (LHCSR3, LHCSR1, LHCBM9, PTOX1) and genes involved in protein modification and degradation. Down-regulated mRNAs indicated an early stage of the reduction of chloroplast ribosomal proteins, which are considered to be a reservoir for P in the cell.
2014-04-05 | GSE56505 | GEO