Transcriptome analysis of root transporters reveals participation of multiple gene families in the response to cation stress

@article{citeulike:3014333, 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 2013 which included putative non-selective cation channels for the NaCl treatment and metal transporters for Ca2+ starvation conditions 2013 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.}, address = {Department of Biology, University of York, PO Box 373, York YO10 5YW, UK,; SHWFGF, IBLS, Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK,; School of Biological Sciences, University of Southampton, Biomedical Sciences Building, Bassett Crescent East, Southampton SO16 7PX, UK,; Department of Plant Biology, Royal Veterinary and Agricultural University, 40 Thorsvaldsenvej, 1871 Frederiksberg C, Copenhagen, Denmark,; Department of Biology, 3800 Hamilton Walk, University of Pennsylvania, Philadelphia, PA 19104-6018, USA,; CNAP, Department of Biology, University of York, PO Box 373, York YO10 5YW, UK,; Department of Biological Sciences, Lancaster University, Lancaster LA1 4YQ, UK, and; Plant Sciences Group, IBLS, Bower Building, University of Glasgow, Glasgow G12 8QQ, UK}, author = {Maathuis, Frans J. M. and Filatov, Victor and Herzyk, Pawel and Krijger, Gerard C. and Axelsen, Kristian B. and Chen, Sixue and Green, Brian J. and Li, Yi and Madagan, Kathryn L. and S\'{a}nchez-Fern\'{a}ndez, Roc\'{i}o and Forde, Brian G. and Palmgren, Michael G. and Rea, Philip A. and Williams, Lorraine E. and Sanders, Dale and Amtmann, Anna }, citeulike-article-id = {3014333}, doi = {10.1046/j.1365-313X.2003.01839.x}, journal = {The Plant Journal}, number = {6}, pages = {675--692}, posted-at = {2008-07-17 14:22:58}, priority = {2}, title = {Transcriptome analysis of root transporters reveals participation of multiple gene families in the response to cation stress}, url = {http://dx.doi.org/10.1046/j.1365-313X.2003.01839.x}, volume = {35}, year = {2003} }

TY - JOUR ID - citeulike:3014333 L3 - citeulike-article-id:3014333 TI - Transcriptome analysis of root transporters reveals participation of multiple gene families in the response to cation stress JF - The Plant Journal VL - 35 IS - 6 SP - 675 EP - 692 AD - Department of Biology, University of York, PO Box 373, York YO10 5YW, UK,; SHWFGF, IBLS, Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK,; School of Biological Sciences, University of Southampton, Biomedical Sciences Building, Bassett Crescent East, Southampton SO16 7PX, UK,; Department of Plant Biology, Royal Veterinary and Agricultural University, 40 Thorsvaldsenvej, 1871 Frederiksberg C, Copenhagen, Denmark,; Department of Biology, 3800 Hamilton Walk, University of Pennsylvania, Philadelphia, PA 19104-6018, USA,; CNAP, Department of Biology, University of York, PO Box 373, York YO10 5YW, UK,; Department of Biological Sciences, Lancaster University, Lancaster LA1 4YQ, UK, and; Plant Sciences Group, IBLS, Bower Building, University of Glasgow, Glasgow G12 8QQ, UK N2 - 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 2013 which included putative non-selective cation channels for the NaCl treatment and metal transporters for Ca2+ starvation conditions 2013 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. AU - Maathuis, Frans AU - Filatov, Victor AU - Herzyk, Pawel AU - Krijger, Gerard AU - Axelsen, Kristian AU - Chen, Sixue AU - Green, Brian AU - Li, Yi AU - Madagan, Kathryn AU - Sánchez-Fernández, Rocío AU - Forde, Brian AU - Palmgren, Michael AU - Rea, Philip AU - Williams, Lorraine AU - Sanders, Dale AU - Amtmann, Anna PY - 2003/// UR - http://dx.doi.org/10.1046/j.1365-313X.2003.01839.x ER -