Transcriptomics

Dataset Information

302

Systems analysis of Chlamydomonas Cu nutrition reveals connections between Cu and multiple O2-dependent metabolic steps


ABSTRACT: 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. 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

ORGANISM(S): Chlamydomonas reinhardtii  

SUBMITTER: Shawn Cokus   Weihong Yan  Sabeeha S Merchant  Sabeeha Merchant  Janette Kropat  Matteo Pellegrini  Joseph A Koo  Astrid Vieler  David Casero  Christoph Benning  Scott I Hsieh  Madeli Castruita  Steven J Karpowicz 

PROVIDER: E-GEOD-25124 | ArrayExpress | 2011-10-23

SECONDARY ACCESSION(S): SRP005483GSE25124PRJNA134525

REPOSITORIES: GEO, ArrayExpress, ENA

altmetric image

Publications

Systems biology approach in Chlamydomonas reveals connections between copper nutrition and multiple metabolic steps.

Castruita Madeli M   Casero David D   Karpowicz Steven J SJ   Kropat Janette J   Vieler Astrid A   Hsieh Scott I SI   Yan Weihong W   Cokus Shawn S   Loo Joseph A JA   Benning Christoph C   Pellegrini Matteo M   Merchant Sabeeha S SS  

The Plant cell 20110415 4


In this work, we query the Chlamydomonas reinhardtii copper regulon at a whole-genome level. Our RNA-Seq data simulation and analysis pipeline validated a 2-fold cutoff and 10 RPKM (reads per kilobase of mappable length per million mapped reads) (~1 mRNA per cell) to reveal 63 CRR1 targets plus another 86 copper-responsive genes. Proteomic and immunoblot analyses captured 25% of the corresponding proteins, whose abundance was also dependent on copper nutrition, validating transcriptional regulat  ...[more]

Similar Datasets

2011-10-24 | GSE25124 | GEO
2013-10-14 | E-GEOD-24696 | ArrayExpress
2011-09-07 | E-GEOD-26331 | ArrayExpress
| GSE104916 | GEO
2011-09-08 | GSE26331 | GEO
2012-10-31 | E-GEOD-41899 | ArrayExpress
2013-12-31 | E-GEOD-47662 | ArrayExpress
2016-02-20 | E-GEOD-78133 | ArrayExpress
2013-05-03 | E-GEOD-41096 | ArrayExpress
| GSE24696 | GEO