title: Transcriptome analysis of root transporters reveals participation of multiple gene families in the response to cation stress.
abstract: Plant nutrition critically depends on the activity of membrane transporters that translocate minerals from the soil into the plant and are responsible for their intra- and intercellular distribution. Most plant membrane transporters are encoded by multigene families whose members often exhibit overlapping expression patterns and a high degree of sequence homology. Furthermore, many inorganic nutrients are transported by more than one transporter family. These considerations, coupled with a large number of so-far non-annotated putative transporter genes, hamper our progress in understanding how the activity of specific transporters is integrated into a response to fluctuating conditions. We designed an oligonucleotide microarray representing 1096 Arabidopsis transporter genes and analysed the root transporter transcriptome over a 96-h period with respect to 80 mM NaCl, K+ starvation and Ca2+ starvation. Our data show that cation stress led to changes in transcript level of many genes across most transporter gene families. Analysis of transcriptionally modulated genes across all functional groups of transporters revealed families such as V-type ATPases and aquaporins that responded to all treatments, and families - which included putative non-selective cation channels for the NaCl treatment and metal transporters for Ca2+ starvation conditions - that responded to specific ionic environments. Several gene families including primary pumps, antiporters and aquaporins were analysed in detail with respect to the mRNA levels of different isoforms during ion stress. Cluster analysis allowed identification of distinct expression profiles, and several novel putative regulatory motifs were discovered within sets of co-expressed genes.
authors.affiliation: Department of Biology, University of York, PO Box 373, York YO10 5YW, UK.
authors.forename: Frans J M
authors.initials: FJ
authors.lastname: Maathuis
authors.forename: Victor
authors.initials: V
authors.lastname: Filatov
authors.forename: Pawel
authors.initials: P
authors.lastname: Herzyk
authors.forename: Gerard C
authors.initials: GC
authors.lastname: Krijger
authors.forename: Kristian B
authors.initials: KB
authors.lastname: Axelsen
authors.forename: Sixue
authors.initials: S
authors.lastname: Chen
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Green
authors.forename: Yi
authors.initials: Y
authors.lastname: Li
authors.forename: Kathryn L
authors.initials: KL
authors.lastname: Madagan
authors.forename: Rocío
authors.initials: R
authors.lastname: Sánchez-Fernández
authors.forename: Brian G
authors.initials: BG
authors.lastname: Forde
authors.forename: Michael G
authors.initials: MG
authors.lastname: Palmgren
authors.forename: Philip A
authors.initials: PA
authors.lastname: Rea
authors.forename: Lorraine E
authors.initials: LE
authors.lastname: Williams
authors.forename: Dale
authors.initials: D
authors.lastname: Sanders
authors.forename: Anna
authors.initials: A
authors.lastname: Amtmann
mesh_terms: D017360:Arabidopsis / Q000187:drug effects / Q000235:genetics / Q000254:growth & development / Q000502:physiology*; D029681:Arabidopsis Proteins / Q000235:genetics; D001692:Biological Transport; D002118:Calcium / Q000494:pharmacology; D002412:Cations / Q000493:pharmacokinetics*; D017343:Genes, Plant; D016623:Ion Pumps / Q000235:genetics / Q000502:physiology*; D005810:Multigene Family; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D018517:Plant Roots / Q000502:physiology*; D011188:Potassium / Q000494:pharmacology; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012965:Sodium Chloride / Q000494:pharmacology; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D029681:Arabidopsis Proteins; D002412:Cations; D016623:Ion Pumps; D012965:Sodium Chloride; D011188:Potassium; D002118:Calcium