Transcriptomics

Dataset Information

420

Systems and trans-system level analysis identifies conserved Fe-deficiency responses in the plant lineage


ABSTRACT: We used RNA-Seq to compare the transcriptomes of Fe-replete vs. Fe-deficient vs. Fe-limited Chlamydomonas wild-type cells. Our RNA-Seq data revealed 90 and 49 genes to be specifically expressed under hetero-phototrophic and phototrophic conditions, respectively. Around 30 genes represent putative Fe-deficiency targets, independent of the carbon source used. Many of these Fe-specific responses are conserved between Chlamydomonas and land plants. We identified several transporters (NRAMP4, a CCC1-like proteins and a ferroportin homologue) all of them most likely being involved in intracellular Fe redistribution. RNA-seq of Chlamydomonas Fe-deficient and limited cells indicated that about 40% of differentially expressed genes represent proteins of unknown functions. Whereas Fe-deficiency gave us insides into putative Fe-specific responses, Fe-limitation revealed responses related to increased oxidative stress. Quantitative proteomics on the soluble Chlamydomonas extracts indicated a fair correlation between changes we detected at mRNA levels compared to changes in protein levels in Fe-deficient and Fe-limited Chlamydomonas. We found that Fe-deficient and Fe-limited cells have increased ascorbate levels, a major antioxidant molecule in plants. Ascorbate levels appear to be elevated by de novo synthesis via the L-Galactose pathway and recycling by monodehydroascorbate reductase. Fe-limited cells showed increased transcript and protein levels of enzymatic antioxidant components of the ascorbate-glutathione scavenging system (MSD3, MDAR1 or GSH1). Fe-limited cells showed the increase of several proteases indicative of elevated proteolitic activity under these severe nutrient limitation conditions. Sampling of Chlamydomonas CC-1021 (2137) cells cultivated photoheterotrophically (TAP) or phototrophically (minimal) under Fe-replete (20mM), Fe-deficient (1 mM) and Fe-limited (0.25 mM) conditions.

ORGANISM(S): Chlamydomonas reinhardtii  

SUBMITTER: Eugen I Urzica   Sabeeha S Merchant  Lital N Adler  Sabeeha Merchant  Joseph A Loo  David Casero  Hiroaki Yamasaki  Scott I Hsieh  Steven G Clarke  Steven J Karpowicz  Matteo Pellegrini 

PROVIDER: E-GEOD-35305 | ArrayExpress | 2012-06-18

SECONDARY ACCESSION(S): SRP010563GSE35305PRJNA150735

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas.

Boyle Nanette R NR   Page Mark Dudley MD   Liu Bensheng B   Blaby Ian K IK   Casero David D   Kropat Janette J   Cokus Shawn J SJ   Hong-Hermesdorf Anne A   Shaw Johnathan J   Karpowicz Steven J SJ   Gallaher Sean D SD   Johnson Shannon S   Benning Christoph C   Pellegrini Matteo M   Grossman Arthur A   Merchant Sabeeha S SS  

The Journal of biological chemistry 20120308 19


Algae have recently gained attention as a potential source for biodiesel; however, much is still unknown about the biological triggers that cause the production of triacylglycerols. We used RNA-Seq as a tool for discovering genes responsible for triacylglycerol (TAG) production in Chlamydomonas and for the regulatory components that activate the pathway. Three genes encoding acyltransferases, DGAT1, DGTT1, and PDAT1, are induced by nitrogen starvation and are likely to have a role in TAG accumul  ...[more]

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