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Genome-wide microarray analysis of tomato roots showed defined responses to iron deficiency.

Zamboni A, Zanin L, Tomasi N, Pezzotti M, Pinton R, Varanini Z, Cesco S - BMC Genomics (2012)

Bottom Line: These transcripts are related to the physiological responses of tomato roots to the nutrient stress resulting in an improved iron uptake, including regulatory aspects, translocation, root morphological modification and adaptation in primary metabolic pathways, such as glycolysis and TCA cycle.Other genes play a role in flavonoid biosynthesis and hormonal metabolism.The transcriptional characterization confirmed the presence of the previously described mechanisms to adapt to iron starvation in tomato, but also allowed to identify other genes potentially playing a role in this process, thus opening new research perspectives to improve the knowledge on the tomato root response to the nutrient deficiency.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biotechnology, University of Verona, via delle Grazie 15, 37134 Verona, Italy.

ABSTRACT

Background: Plants react to iron deficiency stress adopting different kind of adaptive responses. Tomato, a Strategy I plant, improves iron uptake through acidification of rhizosphere, reduction of Fe3+ to Fe2+ and transport of Fe2+ into the cells. Large-scale transcriptional analyses of roots under iron deficiency are only available for a very limited number of plant species with particular emphasis for Arabidopsis thaliana. Regarding tomato, an interesting model species for Strategy I plants and an economically important crop, physiological responses to Fe-deficiency have been thoroughly described and molecular analyses have provided evidence for genes involved in iron uptake mechanisms and their regulation. However, no detailed transcriptome analysis has been described so far.

Results: A genome-wide transcriptional analysis, performed with a chip that allows to monitor the expression of more than 25,000 tomato transcripts, identified 97 differentially expressed transcripts by comparing roots of Fe-deficient and Fe-sufficient tomato plants. These transcripts are related to the physiological responses of tomato roots to the nutrient stress resulting in an improved iron uptake, including regulatory aspects, translocation, root morphological modification and adaptation in primary metabolic pathways, such as glycolysis and TCA cycle. Other genes play a role in flavonoid biosynthesis and hormonal metabolism.

Conclusions: The transcriptional characterization confirmed the presence of the previously described mechanisms to adapt to iron starvation in tomato, but also allowed to identify other genes potentially playing a role in this process, thus opening new research perspectives to improve the knowledge on the tomato root response to the nutrient deficiency.

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Related in: MedlinePlus

Functional categories distribution of differentially expressed transcripts. Distribution in main functional categories according to the GO "biological process" terms of the 75 up-regulated (A) and 22 down-regulated (B) transcripts in roots of Fe-deficient relative to Fe-sufficient plants. Percentage of transcripts is reported for each functional category.
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Figure 3: Functional categories distribution of differentially expressed transcripts. Distribution in main functional categories according to the GO "biological process" terms of the 75 up-regulated (A) and 22 down-regulated (B) transcripts in roots of Fe-deficient relative to Fe-sufficient plants. Percentage of transcripts is reported for each functional category.

Mentions: Manually curated annotation of the 97 differentially expressed transcripts was based on results of BlastP analysis against UniProt [26] database (Figure 3; Additional file 1) using terms of biological process of Gene Ontology (GO) [27]. Sequence grouping in functional categories according to the GO terms revealed that the most abundant functional category was "metabolic process" both for up-regulated and down-regulated transcripts (35% and 45% respectively; Figure 3). Other up-regulated transcripts belonged to "establishment of localization" (12%) and "cell wall organization and biogenesis" (8%), while for the down-regulated transcripts "response to stimulus" (9%) was one of the most representative main functional categories (Figure 3). Only up-regulated transcripts are present in the "secondary metabolic process" category (Table 2). Transcripts encoding proteins with no sequence homology to known proteins were defined as "no hits found" (12% and 5% for up-regulated and down-regulated transcripts respectively), while a similar percentage of transcripts showed homology to proteins involved in "unknown" biological process (24% and 23% respectively). A selection of differentially expressed and discussed in relation to Fe deficiency is reported in Table 2. The up-regulation and down-regulation of six differentially expressed transcripts in response to Fe deficiency were confirmed through Real-time RT-PCR experiments (Table 3).


Genome-wide microarray analysis of tomato roots showed defined responses to iron deficiency.

Zamboni A, Zanin L, Tomasi N, Pezzotti M, Pinton R, Varanini Z, Cesco S - BMC Genomics (2012)

Functional categories distribution of differentially expressed transcripts. Distribution in main functional categories according to the GO "biological process" terms of the 75 up-regulated (A) and 22 down-regulated (B) transcripts in roots of Fe-deficient relative to Fe-sufficient plants. Percentage of transcripts is reported for each functional category.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3368770&req=5

Figure 3: Functional categories distribution of differentially expressed transcripts. Distribution in main functional categories according to the GO "biological process" terms of the 75 up-regulated (A) and 22 down-regulated (B) transcripts in roots of Fe-deficient relative to Fe-sufficient plants. Percentage of transcripts is reported for each functional category.
Mentions: Manually curated annotation of the 97 differentially expressed transcripts was based on results of BlastP analysis against UniProt [26] database (Figure 3; Additional file 1) using terms of biological process of Gene Ontology (GO) [27]. Sequence grouping in functional categories according to the GO terms revealed that the most abundant functional category was "metabolic process" both for up-regulated and down-regulated transcripts (35% and 45% respectively; Figure 3). Other up-regulated transcripts belonged to "establishment of localization" (12%) and "cell wall organization and biogenesis" (8%), while for the down-regulated transcripts "response to stimulus" (9%) was one of the most representative main functional categories (Figure 3). Only up-regulated transcripts are present in the "secondary metabolic process" category (Table 2). Transcripts encoding proteins with no sequence homology to known proteins were defined as "no hits found" (12% and 5% for up-regulated and down-regulated transcripts respectively), while a similar percentage of transcripts showed homology to proteins involved in "unknown" biological process (24% and 23% respectively). A selection of differentially expressed and discussed in relation to Fe deficiency is reported in Table 2. The up-regulation and down-regulation of six differentially expressed transcripts in response to Fe deficiency were confirmed through Real-time RT-PCR experiments (Table 3).

Bottom Line: These transcripts are related to the physiological responses of tomato roots to the nutrient stress resulting in an improved iron uptake, including regulatory aspects, translocation, root morphological modification and adaptation in primary metabolic pathways, such as glycolysis and TCA cycle.Other genes play a role in flavonoid biosynthesis and hormonal metabolism.The transcriptional characterization confirmed the presence of the previously described mechanisms to adapt to iron starvation in tomato, but also allowed to identify other genes potentially playing a role in this process, thus opening new research perspectives to improve the knowledge on the tomato root response to the nutrient deficiency.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biotechnology, University of Verona, via delle Grazie 15, 37134 Verona, Italy.

ABSTRACT

Background: Plants react to iron deficiency stress adopting different kind of adaptive responses. Tomato, a Strategy I plant, improves iron uptake through acidification of rhizosphere, reduction of Fe3+ to Fe2+ and transport of Fe2+ into the cells. Large-scale transcriptional analyses of roots under iron deficiency are only available for a very limited number of plant species with particular emphasis for Arabidopsis thaliana. Regarding tomato, an interesting model species for Strategy I plants and an economically important crop, physiological responses to Fe-deficiency have been thoroughly described and molecular analyses have provided evidence for genes involved in iron uptake mechanisms and their regulation. However, no detailed transcriptome analysis has been described so far.

Results: A genome-wide transcriptional analysis, performed with a chip that allows to monitor the expression of more than 25,000 tomato transcripts, identified 97 differentially expressed transcripts by comparing roots of Fe-deficient and Fe-sufficient tomato plants. These transcripts are related to the physiological responses of tomato roots to the nutrient stress resulting in an improved iron uptake, including regulatory aspects, translocation, root morphological modification and adaptation in primary metabolic pathways, such as glycolysis and TCA cycle. Other genes play a role in flavonoid biosynthesis and hormonal metabolism.

Conclusions: The transcriptional characterization confirmed the presence of the previously described mechanisms to adapt to iron starvation in tomato, but also allowed to identify other genes potentially playing a role in this process, thus opening new research perspectives to improve the knowledge on the tomato root response to the nutrient deficiency.

Show MeSH
Related in: MedlinePlus