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

Abstract

Summary 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.

Transcription Analysis of Arabidopsis Membrane Transporters and Hormone Pathways during Developmental and Induced Leaf Senescence

“…Of two phosphorelay mediators and 11 B-type ARRs on the array, only AtARR1 seems to be weakly (2.6-to 3.4-fold) up-regulated. Several A-type ARRs are rapidly induced by CK (Rashotte et al, 2003;Brenner et al, 2005;Kiba et al, 2005). Consistent with a depletion of CK during senescence progression, four of those are down-regulated in NS, DIS, and DET (Fig.…”

“…The expression profiles of genes involved in CK homeostasis are mostly consistent with a depletion of this hormone during senescence. However, the expression of CK-signaling genes indicates a more complex picture, as about 20% of the immediate CK-response genes (Brenner et al, 2005) are up-regulated during NS, among them the A-type response regulator AtARR16. In the JA pathway, the senescence-type specificity of some genes is striking.…”

“…Recently 71 up-regulated and 11 down-regulated immediate CK-response genes of Arabidopsis were identified (Brenner et al, 2005). From a simplistic viewpoint, one would expect that these genes are not regulated or down-regulated during senescence, if the CK level decreases.…”

GeBP and GeBP-Like Proteins Are Noncanonical Leucine-Zipper Transcription Factors That Regulate Cytokinin Response in Arabidopsis

“…Gels were stained with ethidium bromide, digitally scanned under UV light under exposing conditions that provided nonsaturating signals, and the integrated density of each band was measured with Image J software (http://rsb.info.nih.gov/ij/) and subtracted from the background below and above each band. Transcript levels of response genes other than type-A ARRs, such as an AP2-related gene (At3g16770; Brenner et al, 2005), a zinc finger gene (At4g26150; Brenner et al, 2005), senescence-associated protein gene (At1g53885; Rashotte et al, 2006), and the steroid sulfotransferase SST1 (At1g13420; To et al, 2004), genes were also measured using the same approach except SST1 for which real-time PCR was used.…”

Overexpression of the Trehalase Gene AtTRE1 Leads to Increased Drought Stress Tolerance in Arabidopsis and Is Involved in Abscisic Acid-Induced Stomatal Closure

“…Trehalase expression and activity are higher in flowers, green siliques, and developing seeds than in other parts of the plant, indicating a role for trehalase in flower development (Müller et al, 2001a). Transcriptional profiles and microarray data sets show that AtTRE1 expression is increased in vegetative tissues during senescence and is induced by auxin, cytokinin, sugar availability, and abiotic stresses such as drought (Müller et al, 2001b;Zimmermann et al, 2004;Brenner et al, 2005;Rolland et al, 2006). An important role for trehalase has been proposed during plant-microbe interactions in plants hosting trehalose-producing microorganisms, such as arbuscular mycorrhizal fungi, rhizobia, and the clubroot disease-inducing pathogen Plasmodiophora brassicae (Müller et al, 1994;Schubert and Wyss, 1995;Brodmann et al, 2002).…”