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Series GSE25124 Query DataSets for GSE25124
Status Public on Oct 24, 2011
Title Systems analysis of Chlamydomonas Cu nutrition reveals connections between Cu and multiple O2-dependent metabolic steps
Organism Chlamydomonas reinhardtii
Experiment type Expression profiling by high throughput sequencing
Summary We used digital gene expression (NlaIII sequence tags) and RNA-Seq to compare the transcriptomes of Cu-replete vs. Cu–deficient Chlamydomonas wild-type cells to reveal dozens of mRNAs whose abundance is modified. Half of the corresponding genes are targets of CRR1, a master regulator of nutritional copper sensing, and are associated with candidate CRR1 binding sites. The targets include many plastid-localized proteins, like FDX5 encoding a ferredoxin isoform, and CGL78, encoding a protein conserved in the green lineage, indicative of modified plastid metabolism. Immunoblot analysis and proteome profiles recapitulate the transcriptome profiles. New evidence for Cu sparing is suggested by up-regulation of AOF1 encoding a copper-independent but flavin-dependent amine oxidase and down-regulation of two metal- binding proteins. Genes encoding redox proteins, many of which function in lipid metabolism, are over-represented, which is compatible with the role of Cu in biology. Lipid profiles indicate a CRR1-dependent increase in Cu-deficient cells in the proportion of unsaturated (16:2, 16:3, 16:4, 18:2) fatty acids at the expense of the more saturated (16:0, 16:1, 18:0) precursors, especially on plastid galactolipids, which validates the increased expression of acyl-ACP and plastid-localized w-6 desaturases. CRR1-independent changes in the transcriptome suggest a role for Cu in oxygen sensing in Chlamydomonas.
 
Overall design Sampling of Chlamydomonas CC-1021 (2137) and crr1-2, crr1:CRR1 mutant cells (the mutant is knock-down for the transcription factor crr1, which plays a key role in the transcriptional response to copper levels) cultivated in TAP or minimal medium under Cu-sufficient (control) and Cu-defficient conditions.
poly-A purification, NlaIII digestion/random fragmentation
 
Contributor(s) Castruita M, Casero D, Karpowicz SJ, Kropat J, Vieler A, Hsieh SI, Yan W, Cokus S, Koo JA, Benning C, Pellegrini M, Merchant SS
Citation(s) 21498682, 22403401
Submission date Nov 03, 2010
Last update date May 15, 2019
Contact name Sabeeha Merchant
E-mail(s) merchant@chem.ucla.edu
Phone 310-825-8300
Organization name University of California Los Angeles
Department Department of Chemistry and Biochemistry
Street address 607 Charles E. Young Drive East
City Los Angeles
State/province California
ZIP/Postal code 90095-1569
Country USA
 
Platforms (2)
GPL9100 Illumina Genome Analyzer II (Chlamydomonas reinhardtii)
GPL9152 Illumina Genome Analyzer (Chlamydomonas reinhardtii)
Samples (34)
GSM617187 Chlamydomonas reinhardtii 2137 - Copper deficient - TAP - 1
GSM617188 Chlamydomonas reinhardtii 2137 - Copper deficient - TAP - 2
GSM617189 Chlamydomonas reinhardtii 2137 - Copper deficient - TAP - 3
Relations
SRA SRP005483
BioProject PRJNA134525

Download family Format
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE25124_RAW.tar 239.5 Mb (http)(custom) TAR (of TXT, WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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