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Identification of genes and pathways associated with aluminum stress and tolerance using transcriptome profiling of wheat near-isogenic lines.

Houde M, Diallo AO - BMC Genomics (2008)

Bottom Line: The stress-associated genes include important enzymes such as pyruvate dehydrogenase, alternative oxidase, and galactonolactone oxidase, ABC transporter and ascorbate oxido-reducatase.In this survey, we identified stress- and tolerance-associated genes that may be involved in the detoxification of Al and reactive oxygen species.The Al tolerance-associated genes may be key factors that regulate these pathways.

View Article: PubMed Central - HTML - PubMed

Affiliation: Centre TOXEN, Département des Sciences biologiques, Université du Québec à Montréal, C.P. 8888, Succ. Centre-ville, Montréal QC, H3C 3P8, Canada. houde.mario@uqam.ca

ABSTRACT

Background: Aluminum is considered the most limiting factor for plant productivity in acidic soils, which cover large areas of the world's potential arable lands. The inhibition of root growth is recognized as the primary effect of Al toxicity. To identify genes associated with Al stress and tolerance, transcriptome analyses of four different wheat lines (2 Al-tolerant and 2 Al sensitive) that differ in their response to Al were performed.

Results: Microarray expression profiling revealed that 83 candidate genes are associated with Al stress and 25 are associated with tolerance. The stress-associated genes include important enzymes such as pyruvate dehydrogenase, alternative oxidase, and galactonolactone oxidase, ABC transporter and ascorbate oxido-reducatase. The Al tolerance-associated genes include the ALMT-1 malate transporter, glutathione S-transferase, germin/oxalate oxidase, fructose 1,6-bisphosphatase, cysteine-rich proteins, cytochrome P450 monooxygenase, cellulose synthase, zinc finger transcription factor, disease resistance response protein and F-box containing domain protein.

Conclusion: In this survey, we identified stress- and tolerance-associated genes that may be involved in the detoxification of Al and reactive oxygen species. Alternative pathways could help maintain the supply of important metabolites (H2O2, ascorbate, NADH, and phosphate) needed for Al tolerance and root growth. The Al tolerance-associated genes may be key factors that regulate these pathways.

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Related in: MedlinePlus

Putative gene function in ascorbate homeostasis and Al tolerance. Al tolerance-associated genes are represented by white numbers* in the dark blue boxes (numbers in black are other genes of the same type associated with Al stress). Genes associated with Al stress responses are in black boxes. Box 1) The normal process of cell wall loosening is promoted by the production of hydroxyl radicals (•OH) to break glycosidic linkages (sugar-sugar). The hydroxyl radicals are produced non-enzymatically by the Fenton chemistry in the presence of Cu2+, H2O2 and ascorbate which serves as electron donor (the three molecules are in grey boxes). In the apoplasm, ascorbate (ASC) is transformed to monodehydroascorbate (MDHA + e-) and a free electron is used to reduce the Cu2+ to Cu+ (needed for the Fenton reaction). An ascorbate oxido-reductase (ASC ox-red), or other plasma membrane transporters may be involved in the regeneration of apoplasmic ASC. Cytoplasmic ASC and NADH are needed to maintain the level of ASC in both compartments. Al (red box) was shown to block a redox reaction (electron transfer) [34] suggesting that it interferes either with the electron transfer from the cytoplasm to ASC (regeneration) or from ascorbate to Cu2+ (utilization). The diverted electron may generate different ROS molecules that will cause oxidative stress and trigger a redox response and the induction of various genes. Box 2) A slower regeneration of ASC could lead to its degradation and to the accumulation of oxalate. The induction of oxalate oxidase can use this oxalate to maintain the production of H2O2 and support the Fenton reaction. If the apoplasmic ASC concentration decreases too much, H2O2 may not be used efficiently in the cell wall loosening process and will accumulate. This ROS can cause the oxidation of several targets including different cysteine-rich proteins associated with Al tolerance. GSTs associated with Al stress or tolerance can participate in the protection or repair of oxidized targets. Box 3) Mobilisation of phloem sugars and reduction in phosphate availability (Low Pi in green) caused by Al can also participate in gene regulation and stimulate alternative pathways to increase the availability of important metabolite precursors such as NADPH (in light grey) through the pentose-P pathway (G6P: Glucose-6 phosphate; G6PDH: glucose 6 phosphate dehydrogenase); and phosphate (F1,6BP, Fructose 1,6 bisphosphatase; PPi PFK: pyrophosphosphate dependent phosphofructokinase). Other alternative pathways are activated to maintain the Krebs cycle (PDH: pyruvate dehydrogenase, AOX: alternative oxidase) and to stimulate malate production (PEPC: phosphoenol pyruvate carboxylase; MDH: malate dehydrogenase). UDP-glucose can be used to generate ASC and NADH (arabinonolactone oxidase). Other genes such as ALMT1 or ABC transporters may be involved in Al chelation and transport to exclude Al. *: the numbers represent genes identified in this work; see Table 1 and Table 2. o: genes, enzyme activities or metabolite changes identified in other studies. For references, see text.
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Figure 3: Putative gene function in ascorbate homeostasis and Al tolerance. Al tolerance-associated genes are represented by white numbers* in the dark blue boxes (numbers in black are other genes of the same type associated with Al stress). Genes associated with Al stress responses are in black boxes. Box 1) The normal process of cell wall loosening is promoted by the production of hydroxyl radicals (•OH) to break glycosidic linkages (sugar-sugar). The hydroxyl radicals are produced non-enzymatically by the Fenton chemistry in the presence of Cu2+, H2O2 and ascorbate which serves as electron donor (the three molecules are in grey boxes). In the apoplasm, ascorbate (ASC) is transformed to monodehydroascorbate (MDHA + e-) and a free electron is used to reduce the Cu2+ to Cu+ (needed for the Fenton reaction). An ascorbate oxido-reductase (ASC ox-red), or other plasma membrane transporters may be involved in the regeneration of apoplasmic ASC. Cytoplasmic ASC and NADH are needed to maintain the level of ASC in both compartments. Al (red box) was shown to block a redox reaction (electron transfer) [34] suggesting that it interferes either with the electron transfer from the cytoplasm to ASC (regeneration) or from ascorbate to Cu2+ (utilization). The diverted electron may generate different ROS molecules that will cause oxidative stress and trigger a redox response and the induction of various genes. Box 2) A slower regeneration of ASC could lead to its degradation and to the accumulation of oxalate. The induction of oxalate oxidase can use this oxalate to maintain the production of H2O2 and support the Fenton reaction. If the apoplasmic ASC concentration decreases too much, H2O2 may not be used efficiently in the cell wall loosening process and will accumulate. This ROS can cause the oxidation of several targets including different cysteine-rich proteins associated with Al tolerance. GSTs associated with Al stress or tolerance can participate in the protection or repair of oxidized targets. Box 3) Mobilisation of phloem sugars and reduction in phosphate availability (Low Pi in green) caused by Al can also participate in gene regulation and stimulate alternative pathways to increase the availability of important metabolite precursors such as NADPH (in light grey) through the pentose-P pathway (G6P: Glucose-6 phosphate; G6PDH: glucose 6 phosphate dehydrogenase); and phosphate (F1,6BP, Fructose 1,6 bisphosphatase; PPi PFK: pyrophosphosphate dependent phosphofructokinase). Other alternative pathways are activated to maintain the Krebs cycle (PDH: pyruvate dehydrogenase, AOX: alternative oxidase) and to stimulate malate production (PEPC: phosphoenol pyruvate carboxylase; MDH: malate dehydrogenase). UDP-glucose can be used to generate ASC and NADH (arabinonolactone oxidase). Other genes such as ALMT1 or ABC transporters may be involved in Al chelation and transport to exclude Al. *: the numbers represent genes identified in this work; see Table 1 and Table 2. o: genes, enzyme activities or metabolite changes identified in other studies. For references, see text.

Mentions: The identification of stress-regulated genes provide new tools to reduce Al stress, as shown by the ectopic overexpression of some Al stress-regulated genes [23-26]. Among the 83 candidate genes regulated by Al stress (Table 1), several could play a role in alleviating phosphate deficiency and provide energy to fight oxidative stress. Nutrient deficiency, and especially phosphate, occurs in the presence of Al due to the precipitation of Al-phosphate [47]. Under phosphate deficiency, several pathways are hindered due to the reduced availability of ATP and related nucleoside phosphates. These imbalances lead to the induction of alternative pathways of glycolysis to maintain energy and carbon skeletons for key metabolic processes [48]. The fructose-1,6-bisphosphatase (gene # 101) associated with Al tolerance (Table 2) is normally inhibited by phosphate but is stimulated under low phosphate availability (Fig. 3, Box 3). This activity produces fructose-6-P and liberates Pi. The glycolytic alternative enzyme pyrophosphate phosphofructokinase is stimulated by low phosphate and can resynthesise fructose-1,6-bisphosphate and liberate more Pi. This apparently futile cycle is useful to conserve ATP and recycle Pi that is readily available in the pyrophosphate molecule [48]. Furthermore, since sucrose is the most abundant photosynthate available in the phloem sap, fructose (from sucrose) is readily available and will enter the glycolytic pathway at the level of fructose-6-P thereby maintaining a stable supply of this metabolite. The high availability of fructose-6-P (and other hexose-P) can provide sufficient metabolites to support both the pentose phosphate pathway and organic acid synthesis (Fig. 3, Box 3). Al-tolerant rye was found to maintain a higher content of glucose-6-phosphate than Al-sensitive wheat in response to Al exposure [49]. This metabolite is an important precursor of the pentose phosphate pathway (with glucose-6-phosphate dehydrogenase (G6PDH) as the first enzyme) and is an important source of NADPH production. The importance of energy metabolism in modulating Al tolerance is exemplified in Pseudomonas fluorescens where G6PDH was shown to play a pivotal role in enhancing NADPH production and protecting against ROS toxicity [50]. The up-regulation of pyruvate dehydrogenase (gene # 65) and alternative oxidase (gene # 72) supports the involvement of an alternative pathway to maintain energy production (Fig. 3, Box 3) [48]. Members of the alternative oxidase gene family were found to be highly responsive to oxidative stress and to reduce mitochondrial ROS production while maintaining NADH supply [51,52]. In Al tolerant plants, a higher NADH supply (and NADPH through the pentose phosphate pathway) would provide reducing power to regenerate ascorbate and glutathione to fight oxidative stress (Fig. 3, Box 3).


Identification of genes and pathways associated with aluminum stress and tolerance using transcriptome profiling of wheat near-isogenic lines.

Houde M, Diallo AO - BMC Genomics (2008)

Putative gene function in ascorbate homeostasis and Al tolerance. Al tolerance-associated genes are represented by white numbers* in the dark blue boxes (numbers in black are other genes of the same type associated with Al stress). Genes associated with Al stress responses are in black boxes. Box 1) The normal process of cell wall loosening is promoted by the production of hydroxyl radicals (•OH) to break glycosidic linkages (sugar-sugar). The hydroxyl radicals are produced non-enzymatically by the Fenton chemistry in the presence of Cu2+, H2O2 and ascorbate which serves as electron donor (the three molecules are in grey boxes). In the apoplasm, ascorbate (ASC) is transformed to monodehydroascorbate (MDHA + e-) and a free electron is used to reduce the Cu2+ to Cu+ (needed for the Fenton reaction). An ascorbate oxido-reductase (ASC ox-red), or other plasma membrane transporters may be involved in the regeneration of apoplasmic ASC. Cytoplasmic ASC and NADH are needed to maintain the level of ASC in both compartments. Al (red box) was shown to block a redox reaction (electron transfer) [34] suggesting that it interferes either with the electron transfer from the cytoplasm to ASC (regeneration) or from ascorbate to Cu2+ (utilization). The diverted electron may generate different ROS molecules that will cause oxidative stress and trigger a redox response and the induction of various genes. Box 2) A slower regeneration of ASC could lead to its degradation and to the accumulation of oxalate. The induction of oxalate oxidase can use this oxalate to maintain the production of H2O2 and support the Fenton reaction. If the apoplasmic ASC concentration decreases too much, H2O2 may not be used efficiently in the cell wall loosening process and will accumulate. This ROS can cause the oxidation of several targets including different cysteine-rich proteins associated with Al tolerance. GSTs associated with Al stress or tolerance can participate in the protection or repair of oxidized targets. Box 3) Mobilisation of phloem sugars and reduction in phosphate availability (Low Pi in green) caused by Al can also participate in gene regulation and stimulate alternative pathways to increase the availability of important metabolite precursors such as NADPH (in light grey) through the pentose-P pathway (G6P: Glucose-6 phosphate; G6PDH: glucose 6 phosphate dehydrogenase); and phosphate (F1,6BP, Fructose 1,6 bisphosphatase; PPi PFK: pyrophosphosphate dependent phosphofructokinase). Other alternative pathways are activated to maintain the Krebs cycle (PDH: pyruvate dehydrogenase, AOX: alternative oxidase) and to stimulate malate production (PEPC: phosphoenol pyruvate carboxylase; MDH: malate dehydrogenase). UDP-glucose can be used to generate ASC and NADH (arabinonolactone oxidase). Other genes such as ALMT1 or ABC transporters may be involved in Al chelation and transport to exclude Al. *: the numbers represent genes identified in this work; see Table 1 and Table 2. o: genes, enzyme activities or metabolite changes identified in other studies. For references, see text.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
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Figure 3: Putative gene function in ascorbate homeostasis and Al tolerance. Al tolerance-associated genes are represented by white numbers* in the dark blue boxes (numbers in black are other genes of the same type associated with Al stress). Genes associated with Al stress responses are in black boxes. Box 1) The normal process of cell wall loosening is promoted by the production of hydroxyl radicals (•OH) to break glycosidic linkages (sugar-sugar). The hydroxyl radicals are produced non-enzymatically by the Fenton chemistry in the presence of Cu2+, H2O2 and ascorbate which serves as electron donor (the three molecules are in grey boxes). In the apoplasm, ascorbate (ASC) is transformed to monodehydroascorbate (MDHA + e-) and a free electron is used to reduce the Cu2+ to Cu+ (needed for the Fenton reaction). An ascorbate oxido-reductase (ASC ox-red), or other plasma membrane transporters may be involved in the regeneration of apoplasmic ASC. Cytoplasmic ASC and NADH are needed to maintain the level of ASC in both compartments. Al (red box) was shown to block a redox reaction (electron transfer) [34] suggesting that it interferes either with the electron transfer from the cytoplasm to ASC (regeneration) or from ascorbate to Cu2+ (utilization). The diverted electron may generate different ROS molecules that will cause oxidative stress and trigger a redox response and the induction of various genes. Box 2) A slower regeneration of ASC could lead to its degradation and to the accumulation of oxalate. The induction of oxalate oxidase can use this oxalate to maintain the production of H2O2 and support the Fenton reaction. If the apoplasmic ASC concentration decreases too much, H2O2 may not be used efficiently in the cell wall loosening process and will accumulate. This ROS can cause the oxidation of several targets including different cysteine-rich proteins associated with Al tolerance. GSTs associated with Al stress or tolerance can participate in the protection or repair of oxidized targets. Box 3) Mobilisation of phloem sugars and reduction in phosphate availability (Low Pi in green) caused by Al can also participate in gene regulation and stimulate alternative pathways to increase the availability of important metabolite precursors such as NADPH (in light grey) through the pentose-P pathway (G6P: Glucose-6 phosphate; G6PDH: glucose 6 phosphate dehydrogenase); and phosphate (F1,6BP, Fructose 1,6 bisphosphatase; PPi PFK: pyrophosphosphate dependent phosphofructokinase). Other alternative pathways are activated to maintain the Krebs cycle (PDH: pyruvate dehydrogenase, AOX: alternative oxidase) and to stimulate malate production (PEPC: phosphoenol pyruvate carboxylase; MDH: malate dehydrogenase). UDP-glucose can be used to generate ASC and NADH (arabinonolactone oxidase). Other genes such as ALMT1 or ABC transporters may be involved in Al chelation and transport to exclude Al. *: the numbers represent genes identified in this work; see Table 1 and Table 2. o: genes, enzyme activities or metabolite changes identified in other studies. For references, see text.
Mentions: The identification of stress-regulated genes provide new tools to reduce Al stress, as shown by the ectopic overexpression of some Al stress-regulated genes [23-26]. Among the 83 candidate genes regulated by Al stress (Table 1), several could play a role in alleviating phosphate deficiency and provide energy to fight oxidative stress. Nutrient deficiency, and especially phosphate, occurs in the presence of Al due to the precipitation of Al-phosphate [47]. Under phosphate deficiency, several pathways are hindered due to the reduced availability of ATP and related nucleoside phosphates. These imbalances lead to the induction of alternative pathways of glycolysis to maintain energy and carbon skeletons for key metabolic processes [48]. The fructose-1,6-bisphosphatase (gene # 101) associated with Al tolerance (Table 2) is normally inhibited by phosphate but is stimulated under low phosphate availability (Fig. 3, Box 3). This activity produces fructose-6-P and liberates Pi. The glycolytic alternative enzyme pyrophosphate phosphofructokinase is stimulated by low phosphate and can resynthesise fructose-1,6-bisphosphate and liberate more Pi. This apparently futile cycle is useful to conserve ATP and recycle Pi that is readily available in the pyrophosphate molecule [48]. Furthermore, since sucrose is the most abundant photosynthate available in the phloem sap, fructose (from sucrose) is readily available and will enter the glycolytic pathway at the level of fructose-6-P thereby maintaining a stable supply of this metabolite. The high availability of fructose-6-P (and other hexose-P) can provide sufficient metabolites to support both the pentose phosphate pathway and organic acid synthesis (Fig. 3, Box 3). Al-tolerant rye was found to maintain a higher content of glucose-6-phosphate than Al-sensitive wheat in response to Al exposure [49]. This metabolite is an important precursor of the pentose phosphate pathway (with glucose-6-phosphate dehydrogenase (G6PDH) as the first enzyme) and is an important source of NADPH production. The importance of energy metabolism in modulating Al tolerance is exemplified in Pseudomonas fluorescens where G6PDH was shown to play a pivotal role in enhancing NADPH production and protecting against ROS toxicity [50]. The up-regulation of pyruvate dehydrogenase (gene # 65) and alternative oxidase (gene # 72) supports the involvement of an alternative pathway to maintain energy production (Fig. 3, Box 3) [48]. Members of the alternative oxidase gene family were found to be highly responsive to oxidative stress and to reduce mitochondrial ROS production while maintaining NADH supply [51,52]. In Al tolerant plants, a higher NADH supply (and NADPH through the pentose phosphate pathway) would provide reducing power to regenerate ascorbate and glutathione to fight oxidative stress (Fig. 3, Box 3).

Bottom Line: The stress-associated genes include important enzymes such as pyruvate dehydrogenase, alternative oxidase, and galactonolactone oxidase, ABC transporter and ascorbate oxido-reducatase.In this survey, we identified stress- and tolerance-associated genes that may be involved in the detoxification of Al and reactive oxygen species.The Al tolerance-associated genes may be key factors that regulate these pathways.

View Article: PubMed Central - HTML - PubMed

Affiliation: Centre TOXEN, Département des Sciences biologiques, Université du Québec à Montréal, C.P. 8888, Succ. Centre-ville, Montréal QC, H3C 3P8, Canada. houde.mario@uqam.ca

ABSTRACT

Background: Aluminum is considered the most limiting factor for plant productivity in acidic soils, which cover large areas of the world's potential arable lands. The inhibition of root growth is recognized as the primary effect of Al toxicity. To identify genes associated with Al stress and tolerance, transcriptome analyses of four different wheat lines (2 Al-tolerant and 2 Al sensitive) that differ in their response to Al were performed.

Results: Microarray expression profiling revealed that 83 candidate genes are associated with Al stress and 25 are associated with tolerance. The stress-associated genes include important enzymes such as pyruvate dehydrogenase, alternative oxidase, and galactonolactone oxidase, ABC transporter and ascorbate oxido-reducatase. The Al tolerance-associated genes include the ALMT-1 malate transporter, glutathione S-transferase, germin/oxalate oxidase, fructose 1,6-bisphosphatase, cysteine-rich proteins, cytochrome P450 monooxygenase, cellulose synthase, zinc finger transcription factor, disease resistance response protein and F-box containing domain protein.

Conclusion: In this survey, we identified stress- and tolerance-associated genes that may be involved in the detoxification of Al and reactive oxygen species. Alternative pathways could help maintain the supply of important metabolites (H2O2, ascorbate, NADH, and phosphate) needed for Al tolerance and root growth. The Al tolerance-associated genes may be key factors that regulate these pathways.

Show MeSH
Related in: MedlinePlus