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Abiotic stress and genome dynamics: specific genes and transposable elements response to iron excess in rice

BACKGROUND: Iron toxicity is a root related abiotic stress, occurring frequently in flooded soils. It can affect the yield of rice in lowland production systems. This toxicity is associated with high concentrations of reduced iron (Fe(2+)) in the soil solution. Although the first interface of the el...

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Autores principales: Finatto, Taciane, de Oliveira, Antonio Costa, Chaparro, Cristian, da Maia, Luciano C, Farias, Daniel R, Woyann, Leomar G, Mistura, Claudete C, Soares-Bresolin, Adriana P, Llauro, Christel, Panaud, Olivier, Picault, Nathalie
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer US 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4385019/
https://www.ncbi.nlm.nih.gov/pubmed/25844118
http://dx.doi.org/10.1186/s12284-015-0045-6
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author Finatto, Taciane
de Oliveira, Antonio Costa
Chaparro, Cristian
da Maia, Luciano C
Farias, Daniel R
Woyann, Leomar G
Mistura, Claudete C
Soares-Bresolin, Adriana P
Llauro, Christel
Panaud, Olivier
Picault, Nathalie
author_facet Finatto, Taciane
de Oliveira, Antonio Costa
Chaparro, Cristian
da Maia, Luciano C
Farias, Daniel R
Woyann, Leomar G
Mistura, Claudete C
Soares-Bresolin, Adriana P
Llauro, Christel
Panaud, Olivier
Picault, Nathalie
author_sort Finatto, Taciane
collection PubMed
description BACKGROUND: Iron toxicity is a root related abiotic stress, occurring frequently in flooded soils. It can affect the yield of rice in lowland production systems. This toxicity is associated with high concentrations of reduced iron (Fe(2+)) in the soil solution. Although the first interface of the element is in the roots, the consequences of an excessive uptake can be observed in several rice tissues. In an original attempt to find both genes and transposable elements involved in the response to an iron toxicity stress, we used a microarray approach to study the transcriptional responses of rice leaves of cv. Nipponbare (Oryza sativa L. ssp. japonica) to iron excess in nutrient solution. RESULTS: A large number of genes were significantly up- or down-regulated in leaves under the treatment. We analyzed the gene ontology and metabolic pathways of genes involved in the response to this stress and the cis-regulatory elements (CREs) present in the promoter region of up-regulated genes. The majority of genes act in the pathways of lipid metabolic process, carbohydrate metabolism, biosynthesis of secondary metabolites and plant hormones. We also found genes involved in iron acquisition and mobilization, transport of cations and regulatory mechanisms for iron responses, and in oxidative stress and reactive oxygen species detoxification. Promoter regions of 27% of genes up-regulated present at least one significant occurrence of an ABA-responsive CRE. Furthermore, and for the first time, we were able to show that iron stress triggers the up-regulation of many LTR-retrotransposons. We have established a complete inventory of transposable elements transcriptionally activated under iron excess and the CREs which are present in their LTRs. CONCLUSION: The short-term response of Nipponbare seedlings to iron excess, includes activation of genes involved in iron homeostasis, in particular transporters, transcription factors and ROS detoxification in the leaves, but also many transposable elements. Our data led to the identification of CREs which are associated with both genes and LTR-retrotransposons up-regulated under iron excess. Our results strengthen the idea that LTR-retrotransposons participate in the transcriptional response to stress and could thus confer an adaptive advantage for the plant. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12284-015-0045-6) contains supplementary material, which is available to authorized users.
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spelling pubmed-43850192015-04-04 Abiotic stress and genome dynamics: specific genes and transposable elements response to iron excess in rice Finatto, Taciane de Oliveira, Antonio Costa Chaparro, Cristian da Maia, Luciano C Farias, Daniel R Woyann, Leomar G Mistura, Claudete C Soares-Bresolin, Adriana P Llauro, Christel Panaud, Olivier Picault, Nathalie Rice (N Y) Research BACKGROUND: Iron toxicity is a root related abiotic stress, occurring frequently in flooded soils. It can affect the yield of rice in lowland production systems. This toxicity is associated with high concentrations of reduced iron (Fe(2+)) in the soil solution. Although the first interface of the element is in the roots, the consequences of an excessive uptake can be observed in several rice tissues. In an original attempt to find both genes and transposable elements involved in the response to an iron toxicity stress, we used a microarray approach to study the transcriptional responses of rice leaves of cv. Nipponbare (Oryza sativa L. ssp. japonica) to iron excess in nutrient solution. RESULTS: A large number of genes were significantly up- or down-regulated in leaves under the treatment. We analyzed the gene ontology and metabolic pathways of genes involved in the response to this stress and the cis-regulatory elements (CREs) present in the promoter region of up-regulated genes. The majority of genes act in the pathways of lipid metabolic process, carbohydrate metabolism, biosynthesis of secondary metabolites and plant hormones. We also found genes involved in iron acquisition and mobilization, transport of cations and regulatory mechanisms for iron responses, and in oxidative stress and reactive oxygen species detoxification. Promoter regions of 27% of genes up-regulated present at least one significant occurrence of an ABA-responsive CRE. Furthermore, and for the first time, we were able to show that iron stress triggers the up-regulation of many LTR-retrotransposons. We have established a complete inventory of transposable elements transcriptionally activated under iron excess and the CREs which are present in their LTRs. CONCLUSION: The short-term response of Nipponbare seedlings to iron excess, includes activation of genes involved in iron homeostasis, in particular transporters, transcription factors and ROS detoxification in the leaves, but also many transposable elements. Our data led to the identification of CREs which are associated with both genes and LTR-retrotransposons up-regulated under iron excess. Our results strengthen the idea that LTR-retrotransposons participate in the transcriptional response to stress and could thus confer an adaptive advantage for the plant. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12284-015-0045-6) contains supplementary material, which is available to authorized users. Springer US 2015-02-25 /pmc/articles/PMC4385019/ /pubmed/25844118 http://dx.doi.org/10.1186/s12284-015-0045-6 Text en © Finatto et al.; licensee Springer. 2015 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.
spellingShingle Research
Finatto, Taciane
de Oliveira, Antonio Costa
Chaparro, Cristian
da Maia, Luciano C
Farias, Daniel R
Woyann, Leomar G
Mistura, Claudete C
Soares-Bresolin, Adriana P
Llauro, Christel
Panaud, Olivier
Picault, Nathalie
Abiotic stress and genome dynamics: specific genes and transposable elements response to iron excess in rice
title Abiotic stress and genome dynamics: specific genes and transposable elements response to iron excess in rice
title_full Abiotic stress and genome dynamics: specific genes and transposable elements response to iron excess in rice
title_fullStr Abiotic stress and genome dynamics: specific genes and transposable elements response to iron excess in rice
title_full_unstemmed Abiotic stress and genome dynamics: specific genes and transposable elements response to iron excess in rice
title_short Abiotic stress and genome dynamics: specific genes and transposable elements response to iron excess in rice
title_sort abiotic stress and genome dynamics: specific genes and transposable elements response to iron excess in rice
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4385019/
https://www.ncbi.nlm.nih.gov/pubmed/25844118
http://dx.doi.org/10.1186/s12284-015-0045-6
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