Immediate-early and delayed cytokinin response genes of Arabidopsis thaliana identified by genome-wide expression profiling reveal novel cytokinin-sensitive processes and suggest cytokinin action through transcriptional cascades

• Published in: The Plant journal : for cell and molecular biology 2005-10, Vol.44 (2), p.314-333
• Main Authors: Brenner, W.G, Romanov, G.A, Kollmer, I, Burkle, L, Schmulling, T
• Format: Article
• Language: English
• Subjects: Arabidopsis - drug effects; Arabidopsis - genetics; Arabidopsis - metabolism; Arabidopsis Proteins - genetics; Arabidopsis Proteins - metabolism; Arabidopsis thaliana; biochemical pathways; Biological Transport - drug effects; Biological Transport - genetics; cytokinin; cytokinin dehydrogenase; cytokinin oxidase; cytokinins; Cytokinins - pharmacology; Flowers & plants; Gene expression; Gene Expression Profiling; gene expression regulation; Gene Expression Regulation, Plant - drug effects; Gene Expression Regulation, Plant - genetics; Genes, Immediate-Early - genetics; Genes, Plant - genetics; genome; Genome, Plant; genomics; Hormones; immediate‐early genes; messenger RNA; molecular sequence data; Nia; nucleotide sequences; oxidoreductases; plant biochemistry; plant genetics; plant hormones; plant proteins; plant response; response genes; RNA, Messenger - analysis; RNA, Messenger - genetics; seedlings; Signal transduction; Signal Transduction - drug effects; Signal Transduction - genetics; transcription (genetics); transcription factors; Transcription, Genetic - drug effects; Transcription, Genetic - genetics; transcriptome analysis; transgenes; transgenic plants
• ISSN: 0960-7412; 1365-313X
• DOI: 10.1111/j.1365-313x.2005.02530.x

Cytokinins are hormones that regulate many developmental and physiological processes in plants. Recent work has revealed that the cytokinin signal is transduced by two-component systems to the nucleus where target genes are activated. Most of the rapid transcriptional responses are unknown. We measured immediate-early and delayed cytokinin responses through genome-wide expression profiling with the Affymetrix ATH1 full genome array (Affymetrix Inc., Santa Clara, CA, USA). Fifteen minutes after cytokinin treatment of 5-day-old Arabidopsis seedlings, 71 genes were upregulated and 11 genes were downregulated. Immediate-early cytokinin response genes include a high portion of transcriptional regulators, among them six transcription factors that had previously not been linked to cytokinin. Five plastid transcripts were rapidly regulated as well, indicating a rapid transfer of the signal to plastids or direct perception of the cytokinin signal by plastids. After 2 h of cytokinin treatment genes coding for transcriptional regulators, signaling proteins, developmental and hormonal regulators, primary and secondary metabolism, energy generation and stress reactions were over-represented. A significant number of the responding genes are known to regulate light (PHYA, PSK1, CIP8, PAT1, APRR), auxin (Aux/IAA), ethylene (ETR2, EIN3, ERFs/EREBPs), gibberellin (GAI, RGA1, GA20 oxidase), nitrate (NTR2, NIA) and sugar (STP1, SUS1) dependent processes, indicating intense crosstalk with environmental cues, other hormones and metabolites. Analysis of cytokinin-deficient 35S:AtCKX1 transgenic seedlings has revealed additional, long-lasting cytokinin-sensitive changes of transcript abundance. Comparative overlay-analysis with the software tool mapman identified previously unknown cytokinin-sensitive metabolic genes, for example in the metabolism of trehalose-6-phosphate. Taken together, we present a genome-wide view of changes in cytokinin-responsive transcript abundance of genes that might be functionally relevant for the many biological processes that are governed by cytokinins.