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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.<\/jats:p>","DOI":"10.1105\/tpc.111.084400","type":"journal-article","created":{"date-parts":[[2011,4,16]],"date-time":"2011-04-16T07:36:56Z","timestamp":1302939416000},"page":"1273-1292","source":"Crossref","is-referenced-by-count":202,"title":["Systems Biology Approach in <i>Chlamydomonas<\/i> Reveals Connections between Copper Nutrition and Multiple Metabolic Steps\n\u00a0\n\u00a0"],"prefix":"10.1093","volume":"23","author":[{"given":"Madeli","family":"Castruita","sequence":"first","affiliation":[{"name":"Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Casero","sequence":"additional","affiliation":[{"name":"Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095"},{"name":"Institute of Genomics and Proteomics, University of California, Los Angeles, California 90095"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steven J.","family":"Karpowicz","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Janette","family":"Kropat","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Astrid","family":"Vieler","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Scott I.","family":"Hsieh","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weihong","family":"Yan","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shawn","family":"Cokus","sequence":"additional","affiliation":[{"name":"Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joseph A.","family":"Loo","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095"},{"name":"Institute of Genomics and Proteomics, University of California, Los Angeles, California 90095"},{"name":"Department of Biological Chemistry, University of California, Los Angeles, California 90095"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christoph","family":"Benning","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matteo","family":"Pellegrini","sequence":"additional","affiliation":[{"name":"Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095"},{"name":"Institute of Genomics and Proteomics, University of California, Los Angeles, California 90095"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sabeeha S.","family":"Merchant","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095"},{"name":"Institute of Genomics and Proteomics, University of California, Los Angeles, California 90095"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2011,4,1]]},"reference":[{"key":"2021040622135670100_b1","doi-asserted-by":"crossref","first-page":"1233","DOI":"10.1105\/tpc.104.030452","article-title":"Two P-type ATPases are required for copper delivery in Arabidopsis thaliana chloroplasts","volume":"17","author":"Abdel-Ghany","year":"2005","journal-title":"Plant Cell"},{"key":"2021040622135670100_b2","doi-asserted-by":"crossref","first-page":"15932","DOI":"10.1074\/jbc.M801406200","article-title":"MicroRNA-mediated systemic down-regulation of copper protein expression in response to low copper availability in Arabidopsis","volume":"283","author":"Abdel-Ghany","year":"2008","journal-title":"J. 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