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Co-expression analysis identifies putative targets for CBP60g and SARD1 regulation

BACKGROUND: Salicylic acid is a critical signalling component in plant defence responses. In Arabidopsis, isochorismate synthase encoded by SID2 is essential for the biosynthesis of salicylic acid in response to biotic challenges. Recently, both the calmodulin binding protein CBP60g and its closest...

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Autores principales: Truman, William, Glazebrook, Jane
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3511238/
https://www.ncbi.nlm.nih.gov/pubmed/23153277
http://dx.doi.org/10.1186/1471-2229-12-216
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author Truman, William
Glazebrook, Jane
author_facet Truman, William
Glazebrook, Jane
author_sort Truman, William
collection PubMed
description BACKGROUND: Salicylic acid is a critical signalling component in plant defence responses. In Arabidopsis, isochorismate synthase encoded by SID2 is essential for the biosynthesis of salicylic acid in response to biotic challenges. Recently, both the calmodulin binding protein CBP60g and its closest homolog, the non-calmodulin binding SARD1, have been shown to bind to the promoter region of SID2. Loss of both CBP60g and SARD1 severely impacts the plants ability to produce SA in response to bacterial inoculation and renders the plant susceptible to infection. In an electrophoretic mobility shift assay CBP60g and SARD1 were shown to bind specifically to a 10mer oligonucleotide with the sequence GAAATTTTGG. RESULTS: Gene expression profiling on a custom microarray identified a set of genes, like SID2, down-regulated in cbp60g sard1 mutant plants. Co-expression analysis across a defined set of ATH1 full genome microarray experiments expanded this gene set; clustering analysis was then applied to group densely interconnected genes. A stringent threshold for co-expression identified two related calmodulin-like genes tightly associated with SID2. SID2 was found to cluster with genes whose promoter regions were significantly enriched with GAAATT motifs. Genes clustering with SID2 were found to be down-regulated in the cbp60g sard1 double mutant. Representative genes from other clusters enriched with the GAAATT motif were found to be variously down-regulated, unchanged or up-regulated in the double mutant. A previously characterised co-expression between SID2 and WRKY28 was not reproduced in this analysis but was contained within a subset of the experiments where SID2 was co-expressed with CBP60g or SARD1. CONCLUSION: Putative components of the CBP60g SARD1 signalling network have been uncovered by co-expression analysis. In addition to genes whose regulation is similar to that of SID2 some are repressed by CBP60g and SARD1.
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spelling pubmed-35112382012-12-01 Co-expression analysis identifies putative targets for CBP60g and SARD1 regulation Truman, William Glazebrook, Jane BMC Plant Biol Research Article BACKGROUND: Salicylic acid is a critical signalling component in plant defence responses. In Arabidopsis, isochorismate synthase encoded by SID2 is essential for the biosynthesis of salicylic acid in response to biotic challenges. Recently, both the calmodulin binding protein CBP60g and its closest homolog, the non-calmodulin binding SARD1, have been shown to bind to the promoter region of SID2. Loss of both CBP60g and SARD1 severely impacts the plants ability to produce SA in response to bacterial inoculation and renders the plant susceptible to infection. In an electrophoretic mobility shift assay CBP60g and SARD1 were shown to bind specifically to a 10mer oligonucleotide with the sequence GAAATTTTGG. RESULTS: Gene expression profiling on a custom microarray identified a set of genes, like SID2, down-regulated in cbp60g sard1 mutant plants. Co-expression analysis across a defined set of ATH1 full genome microarray experiments expanded this gene set; clustering analysis was then applied to group densely interconnected genes. A stringent threshold for co-expression identified two related calmodulin-like genes tightly associated with SID2. SID2 was found to cluster with genes whose promoter regions were significantly enriched with GAAATT motifs. Genes clustering with SID2 were found to be down-regulated in the cbp60g sard1 double mutant. Representative genes from other clusters enriched with the GAAATT motif were found to be variously down-regulated, unchanged or up-regulated in the double mutant. A previously characterised co-expression between SID2 and WRKY28 was not reproduced in this analysis but was contained within a subset of the experiments where SID2 was co-expressed with CBP60g or SARD1. CONCLUSION: Putative components of the CBP60g SARD1 signalling network have been uncovered by co-expression analysis. In addition to genes whose regulation is similar to that of SID2 some are repressed by CBP60g and SARD1. BioMed Central 2012-11-16 /pmc/articles/PMC3511238/ /pubmed/23153277 http://dx.doi.org/10.1186/1471-2229-12-216 Text en Copyright ©2012 Truman and Glazebrook; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Truman, William
Glazebrook, Jane
Co-expression analysis identifies putative targets for CBP60g and SARD1 regulation
title Co-expression analysis identifies putative targets for CBP60g and SARD1 regulation
title_full Co-expression analysis identifies putative targets for CBP60g and SARD1 regulation
title_fullStr Co-expression analysis identifies putative targets for CBP60g and SARD1 regulation
title_full_unstemmed Co-expression analysis identifies putative targets for CBP60g and SARD1 regulation
title_short Co-expression analysis identifies putative targets for CBP60g and SARD1 regulation
title_sort co-expression analysis identifies putative targets for cbp60g and sard1 regulation
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3511238/
https://www.ncbi.nlm.nih.gov/pubmed/23153277
http://dx.doi.org/10.1186/1471-2229-12-216
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