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

Transcriptome analysis of root transporters reveals participation of multiple gene families in the response to cation stress
Transcriptome analysis of root transporters reveals participation of multiple gene families in the response to cation stress
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.
arabidopsis thaliana, mineral nutrition, abiotic stress, expression profiling, microarray, membrane transporter
0960-7412
675-692
Maathuis, Frans J.M.
75f68506-b28b-4825-9761-9d62069dd38a
Filatov, Victor
da1b6d2b-2b80-4e3c-8443-cf817df049c4
Herzyk, Pawel
cef75f09-fa0b-4da4-9050-37df18da040b
Krijger, Gerard C.
5b7cdf7f-ad85-4db7-94c0-38242eb06ac4
Axelsen, Kristian B.
fe152bbc-2958-46c6-ad2a-74923980f1ca
Chen, Sixue
5385c836-b81c-444b-a107-80cde39d3544
Green, Brian J.
335ad4f6-6195-42bc-9a93-53b9edbbcd84
Li, Yi
76dfac3c-5e81-4b4e-8887-98e9d91dd119
Madagan, Kathryn L.
1840347d-e740-407a-9818-b233c31b7500
Sánchez-Fernández, Rocio
69d157de-0a9f-45fa-b45f-04a4f1cd3dcf
Forde, Brian G.
f29f8add-c346-4286-b1a3-6ed921d0a540
Palmgren, Michael G.
397acbcb-5064-4af1-88c4-a2d2b89a9401
Rea, Philip A.
60e189a3-06ba-4767-b863-37d44b1d3a80
Williams, Lorraine E.
79ee1856-3732-492b-8ac5-239749c85d9e
Sanders, Dale
3b87f2a5-563d-435b-945f-f5bd5a43cc98
Amtmann, Anna
a37286d0-f6a7-4f51-b914-de6edbee1f0a
Maathuis, Frans J.M.
75f68506-b28b-4825-9761-9d62069dd38a
Filatov, Victor
da1b6d2b-2b80-4e3c-8443-cf817df049c4
Herzyk, Pawel
cef75f09-fa0b-4da4-9050-37df18da040b
Krijger, Gerard C.
5b7cdf7f-ad85-4db7-94c0-38242eb06ac4
Axelsen, Kristian B.
fe152bbc-2958-46c6-ad2a-74923980f1ca
Chen, Sixue
5385c836-b81c-444b-a107-80cde39d3544
Green, Brian J.
335ad4f6-6195-42bc-9a93-53b9edbbcd84
Li, Yi
76dfac3c-5e81-4b4e-8887-98e9d91dd119
Madagan, Kathryn L.
1840347d-e740-407a-9818-b233c31b7500
Sánchez-Fernández, Rocio
69d157de-0a9f-45fa-b45f-04a4f1cd3dcf
Forde, Brian G.
f29f8add-c346-4286-b1a3-6ed921d0a540
Palmgren, Michael G.
397acbcb-5064-4af1-88c4-a2d2b89a9401
Rea, Philip A.
60e189a3-06ba-4767-b863-37d44b1d3a80
Williams, Lorraine E.
79ee1856-3732-492b-8ac5-239749c85d9e
Sanders, Dale
3b87f2a5-563d-435b-945f-f5bd5a43cc98
Amtmann, Anna
a37286d0-f6a7-4f51-b914-de6edbee1f0a

Maathuis, Frans J.M., Filatov, Victor, Herzyk, Pawel, Krijger, Gerard C., Axelsen, Kristian B., Chen, Sixue, Green, Brian J., Li, Yi, Madagan, Kathryn L., Sánchez-Fernández, Rocio, Forde, Brian G., Palmgren, Michael G., Rea, Philip A., Williams, Lorraine E., Sanders, Dale and Amtmann, Anna (2003) Transcriptome analysis of root transporters reveals participation of multiple gene families in the response to cation stress. The Plant Journal, 35 (6), 675-692. (doi:10.1046/j.1365-313X.2003.01839.x).

Record type: Article

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.

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More information

Published date: September 2003
Keywords: arabidopsis thaliana, mineral nutrition, abiotic stress, expression profiling, microarray, membrane transporter

Identifiers

Local EPrints ID: 56155
URI: http://eprints.soton.ac.uk/id/eprint/56155
ISSN: 0960-7412
PURE UUID: 19f67456-5d91-4435-aeba-a18c574c18fb

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Date deposited: 07 Aug 2008
Last modified: 15 Mar 2024 11:00

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Contributors

Author: Frans J.M. Maathuis
Author: Victor Filatov
Author: Pawel Herzyk
Author: Gerard C. Krijger
Author: Kristian B. Axelsen
Author: Sixue Chen
Author: Brian J. Green
Author: Yi Li
Author: Kathryn L. Madagan
Author: Rocio Sánchez-Fernández
Author: Brian G. Forde
Author: Michael G. Palmgren
Author: Philip A. Rea
Author: Dale Sanders
Author: Anna Amtmann

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