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

Finatto T, de Oliveira AC, Chaparro C, da Maia LC, Farias DR, Woyann LG, Mistura CC, Soares-Bresolin AP, Llauro C, Panaud O, Picault N - Rice (N Y) (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Plant Genomics and Breeding Center, Eliseu Maciel School of Agronomy, Federal University of Pelotas, 96010-610 Pelotas, RS Brazil ; Present address: Universidade Tecnológica Federal do Paraná, Campus Pato Branco, 85503-390 Pato Branco, PR Brazil.

ABSTRACT

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.

No MeSH data available.


Related in: MedlinePlus

Number of up-regulated and down-regulated genes in leaves of 18-day-old rice seedlings (Oryza sativassp.japonicacv. Nipponbare) after four days of iron excess exposure. Gene ontology was generated by GO Slim with Biological Process and Molecular Function level 2 and Cellular Component level 6. A logarithmic scale was used for the number of genes.
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Fig2: Number of up-regulated and down-regulated genes in leaves of 18-day-old rice seedlings (Oryza sativassp.japonicacv. Nipponbare) after four days of iron excess exposure. Gene ontology was generated by GO Slim with Biological Process and Molecular Function level 2 and Cellular Component level 6. A logarithmic scale was used for the number of genes.

Mentions: The cellular component classification after GO analysis (Figure 2) shows the greatest number of gene products are located in an intracellular membrane bound organelle, and most up-regulated gene products are localized in plastids (558) or in mitochondria (428), followed by comparable numbers in the cytosol (101) and vacuole (97). The down-regulated genes have the same distribution, with the exception of the cytosol. Concerning molecular functions, the binding and catalytic activity are the most highly represented with, respectively, 1159 and 1085 genes for those which are up-regulated and 31 and 26 for down-regulated genes. For transporter activity, only up-regulated genes (111) are observed under iron excess. For biological processes, the most frequent are metabolic process with 1187 up-regulated genes which represent more than one-third of genes affected by iron excess, followed by cellular process (996) and response to stimulus (450). The majority of up-regulated genes in the metabolic pathway are involved in lipid metabolic process (184), carbohydrate metabolism (175), biosynthesis of secondary metabolites (113) and biosynthesis of plant hormones (60) (Additional file 2: Table S2). Among the down-regulated genes, methane metabolism (5 genes) is particularly affected. In biological processes, another function with a large number of up-regulated genes is transport with 239 up-regulated genes.Figure 2


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

Finatto T, de Oliveira AC, Chaparro C, da Maia LC, Farias DR, Woyann LG, Mistura CC, Soares-Bresolin AP, Llauro C, Panaud O, Picault N - Rice (N Y) (2015)

Number of up-regulated and down-regulated genes in leaves of 18-day-old rice seedlings (Oryza sativassp.japonicacv. Nipponbare) after four days of iron excess exposure. Gene ontology was generated by GO Slim with Biological Process and Molecular Function level 2 and Cellular Component level 6. A logarithmic scale was used for the number of genes.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4385019&req=5

Fig2: Number of up-regulated and down-regulated genes in leaves of 18-day-old rice seedlings (Oryza sativassp.japonicacv. Nipponbare) after four days of iron excess exposure. Gene ontology was generated by GO Slim with Biological Process and Molecular Function level 2 and Cellular Component level 6. A logarithmic scale was used for the number of genes.
Mentions: The cellular component classification after GO analysis (Figure 2) shows the greatest number of gene products are located in an intracellular membrane bound organelle, and most up-regulated gene products are localized in plastids (558) or in mitochondria (428), followed by comparable numbers in the cytosol (101) and vacuole (97). The down-regulated genes have the same distribution, with the exception of the cytosol. Concerning molecular functions, the binding and catalytic activity are the most highly represented with, respectively, 1159 and 1085 genes for those which are up-regulated and 31 and 26 for down-regulated genes. For transporter activity, only up-regulated genes (111) are observed under iron excess. For biological processes, the most frequent are metabolic process with 1187 up-regulated genes which represent more than one-third of genes affected by iron excess, followed by cellular process (996) and response to stimulus (450). The majority of up-regulated genes in the metabolic pathway are involved in lipid metabolic process (184), carbohydrate metabolism (175), biosynthesis of secondary metabolites (113) and biosynthesis of plant hormones (60) (Additional file 2: Table S2). Among the down-regulated genes, methane metabolism (5 genes) is particularly affected. In biological processes, another function with a large number of up-regulated genes is transport with 239 up-regulated genes.Figure 2

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Plant Genomics and Breeding Center, Eliseu Maciel School of Agronomy, Federal University of Pelotas, 96010-610 Pelotas, RS Brazil ; Present address: Universidade Tecnológica Federal do Paraná, Campus Pato Branco, 85503-390 Pato Branco, PR Brazil.

ABSTRACT

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.

No MeSH data available.


Related in: MedlinePlus