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21498682
Systems biology approach in Chlamydomonas reveals connections between copper nutrition and multiple metabolic steps.

Plant Cell, 2011/4;23(4):1273-92.

Castruita M[1], Casero D, Karpowicz SJ, Kropat J, Vieler A, Hsieh SI, Yan W, Cokus S, Loo JA, Benning C, Pellegrini M, Merchant SS

Affiliations

PMID: 21498682DOI: 10.1105/tpc.111.084400

Impact factor: 12.085

Abstract
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 regulation as a major control mechanism for copper signaling in Chlamydomonas. The impact of copper deficiency on the expression of several O₂-dependent enzymes included steps in lipid modification pathways. Quantitative lipid profiles indicated increased polyunsaturation of fatty acids on thylakoid membrane digalactosyldiglycerides, indicating a global impact of copper deficiency on the photosynthetic apparatus. Discovery of a putative plastid copper chaperone and a membrane protease in the thylakoid suggest a mechanism for blocking copper utilization in the chloroplast. We also found an example of copper sparing in the N assimilation pathway: the replacement of copper amine oxidase by a flavin-dependent backup enzyme. Forty percent of the targets are previously uncharacterized proteins, indicating considerable potential for new discovery in the biology of copper.
MeSH terms
Autotrophic Processes; Base Sequence; Chlamydomonas; Copper; Gene Expression Profiling; Gene Expression Regulation, Plant; Genes, Plant; Genetic Loci; Heterotrophic Processes; Metabolism; Molecular Sequence Data; Nutritional Physiological Phenomena; Oxidation-Reduction; Plant Proteins; Promoter Regions, Genetic; Protein Structure, Tertiary; Proteome; RNA, Messenger; RNA, Plant; Reproducibility of Results; Reverse Transcriptase Polymerase Chain Reaction; Systems Biology
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