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The transcript for SUFB, a key component of the plastid iron\u2013sulfur (Fe\u2013S) assembly pathway is down-regulated early after Fe deficiency, and prior to down-regulation of mRNAs encoding abundant chloroplast Fe containing proteins, which should economize the use of Fe. What controls this system is unclear. We utilized RNA-seq. aimed to identify differentially expressed transcripts that are co-regulated with SUFB after Fe deficiency in leaves. To distinguish if lack of Fe or lack of Fe\u2013S cofactors and associated loss of enzymatic and photosynthetic activity trigger transcriptome reprogramming, WT plants on low Fe were compared with an inducible sufb-RNAi knockdown. Fe deficiency targeted a limited set of genes and predominantly affected transcripts for chloroplast localized proteins. A set of glutaredoxin transcripts was concertedly down-regulated early after Fe deficiency, however when these same genes were down-regulated by RNAi the effect on known chloroplast Fe deficiency marker proteins was minimal. In promoters of differentially expressed genes, binding motifs for AP2\/ERF transcription factors were most abundant and three AP2\/ERF transcription factors were also differentially expressed early after low Fe treatment. Surprisingly, Fe deficiency in a WT on low Fe and a sufb-RNAi knockdown presented very little overlap in differentially expressed genes. sufb-RNAi produced expression patterns expected for Fe excess and up-regulation of a transcript for another Fe\u2013S assembly component not affected by low Fe. These findings indicate that Fe scarcity, not Fe utilization, triggers reprogramming of the transcriptome in leaves.<\/jats:p>","DOI":"10.1039\/d0mt00175a","type":"journal-article","created":{"date-parts":[[2020,10,13]],"date-time":"2020-10-13T09:31:04Z","timestamp":1602581464000},"page":"1748-1764","update-policy":"https:\/\/doi.org\/10.1039\/rsc_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["Iron deficiency and the loss of chloroplast iron\u2013sulfur cluster assembly trigger distinct transcriptome changes in Arabidopsis rosettes"],"prefix":"10.1093","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7107-4803","authenticated-orcid":false,"given":"Gretchen Elizabeth","family":"Kroh","sequence":"first","affiliation":[{"name":"Biology Department, Colorado State University, 2515 W. Pitkin Street, Fort Collins, CO 80523-1878, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9922-5039","authenticated-orcid":false,"given":"Marinus","family":"Pilon","sequence":"additional","affiliation":[{"name":"Biology Department, Colorado State University, 2515 W. 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