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Genome-wide investigation and expression profiling of AP2/ERF transcription factor superfamily in foxtail millet (Setaria italica L.).

Lata C, Mishra AK, Muthamilarasan M, Bonthala VS, Khan Y, Prasad M - PLoS ONE (2014)

Bottom Line: Comparative physical mapping between foxtail millet AP2/ERF genes and its orthologs of sorghum (18 genes), maize (14 genes), rice (9 genes) and Brachypodium (6 genes) showed the evolutionary insights of AP2/ERF gene family and also the decrease in orthology with increase in phylogenetic distance.The study showed that the genes SiAP2/ERF-069, SiAP2/ERF-103 and SiAP2/ERF-120 may be considered as potential candidate genes for further functional validation as well for utilization in crop improvement programs for stress resistance since these genes were up-regulated under drought and salinity stresses in ABA dependent manner.Altogether the present study provides new insights into evolution, divergence and systematic functional analysis of AP2/ERF gene family at genome level in foxtail millet which may be utilized for improving stress adaptation and tolerance in millets, cereals and bioenergy grasses.

View Article: PubMed Central - PubMed

Affiliation: National Research Centre on Plant Biotechnology, New Delhi, India; CSIR-National Botanical Research Institute, Lucknow, Uttar Pradesh, India.

ABSTRACT
The APETALA2/ethylene-responsive element binding factor (AP2/ERF) family is one of the largest transcription factor (TF) families in plants that includes four major sub-families, namely AP2, DREB (dehydration responsive element binding), ERF (ethylene responsive factors) and RAV (Related to ABI3/VP). AP2/ERFs are known to play significant roles in various plant processes including growth and development and biotic and abiotic stress responses. Considering this, a comprehensive genome-wide study was conducted in foxtail millet (Setaria italica L.). A total of 171 AP2/ERF genes were identified by systematic sequence analysis and were physically mapped onto nine chromosomes. Phylogenetic analysis grouped AP2/ERF genes into six classes (I to VI). Duplication analysis revealed that 12 (∼7%) SiAP2/ERF genes were tandem repeated and 22 (∼13%) were segmentally duplicated. Comparative physical mapping between foxtail millet AP2/ERF genes and its orthologs of sorghum (18 genes), maize (14 genes), rice (9 genes) and Brachypodium (6 genes) showed the evolutionary insights of AP2/ERF gene family and also the decrease in orthology with increase in phylogenetic distance. The evolutionary significance in terms of gene-duplication and divergence was analyzed by estimating synonymous and non-synonymous substitution rates. Expression profiling of candidate AP2/ERF genes against drought, salt and phytohormones revealed insights into their precise and/or overlapping expression patterns which could be responsible for their functional divergence in foxtail millet. The study showed that the genes SiAP2/ERF-069, SiAP2/ERF-103 and SiAP2/ERF-120 may be considered as potential candidate genes for further functional validation as well for utilization in crop improvement programs for stress resistance since these genes were up-regulated under drought and salinity stresses in ABA dependent manner. Altogether the present study provides new insights into evolution, divergence and systematic functional analysis of AP2/ERF gene family at genome level in foxtail millet which may be utilized for improving stress adaptation and tolerance in millets, cereals and bioenergy grasses.

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Predicated structures of SiAP2/ERF proteins.The structures of 12 SiAP2/ERF proteins with greater than 90% confidence level were shown along with its potential active site.
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pone-0113092-g010: Predicated structures of SiAP2/ERF proteins.The structures of 12 SiAP2/ERF proteins with greater than 90% confidence level were shown along with its potential active site.

Mentions: Three dimensional protein models of twelve proteins were constructed by sequence similarity searching against the PDB database using BLASTP. These 12 proteins were selected owing to their higher homology to the known protein sequences in the PDB and Phyre2 was used for homology modeling of their predicted structures. The protein structure of all the 12 SiAP2/ERFs were modelled at 90% confidence and the potential active sites were identified (Figure 10). The 3D structure revealed the presence of conserved AP2/ERF domain of about 60–70 amino acids in all the SiAP2/ERF proteins with a typical three-dimensional conformation ordered into a layer of three antiparallel β-sheets followed by a parallel α-helix. Further examination of the AP2/ERF domain showed the presence of two regions namely YRG and RAYD. The YRG region was 20-amino acid long N-terminal stretch rich in basic and hydrophilic residues and was reported to play a crucial role in establishing direct contact with the DNA [72]. Conversely, RAYD region comprises about 40 amino acids and this region was reported to mediate protein-protein interactions through α-helix. Moreover, reports also indicate that RAYD region is involved in DNA binding through interactions of hydrophobic face of the α-helix with the major groove of DNA [72]. The AP2 sub-family members possess two AP2/ERF domains separated by a linker sequence of 25 amino acids which is responsible for positioning of the DNA-binding domains [73]. The molecular modeling thus proved that all the predicted protein structures were highly consistent and this data would offer a preliminary foundation for comprehending the molecular functions of SiAP2/ERF proteins.


Genome-wide investigation and expression profiling of AP2/ERF transcription factor superfamily in foxtail millet (Setaria italica L.).

Lata C, Mishra AK, Muthamilarasan M, Bonthala VS, Khan Y, Prasad M - PLoS ONE (2014)

Predicated structures of SiAP2/ERF proteins.The structures of 12 SiAP2/ERF proteins with greater than 90% confidence level were shown along with its potential active site.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4237383&req=5

pone-0113092-g010: Predicated structures of SiAP2/ERF proteins.The structures of 12 SiAP2/ERF proteins with greater than 90% confidence level were shown along with its potential active site.
Mentions: Three dimensional protein models of twelve proteins were constructed by sequence similarity searching against the PDB database using BLASTP. These 12 proteins were selected owing to their higher homology to the known protein sequences in the PDB and Phyre2 was used for homology modeling of their predicted structures. The protein structure of all the 12 SiAP2/ERFs were modelled at 90% confidence and the potential active sites were identified (Figure 10). The 3D structure revealed the presence of conserved AP2/ERF domain of about 60–70 amino acids in all the SiAP2/ERF proteins with a typical three-dimensional conformation ordered into a layer of three antiparallel β-sheets followed by a parallel α-helix. Further examination of the AP2/ERF domain showed the presence of two regions namely YRG and RAYD. The YRG region was 20-amino acid long N-terminal stretch rich in basic and hydrophilic residues and was reported to play a crucial role in establishing direct contact with the DNA [72]. Conversely, RAYD region comprises about 40 amino acids and this region was reported to mediate protein-protein interactions through α-helix. Moreover, reports also indicate that RAYD region is involved in DNA binding through interactions of hydrophobic face of the α-helix with the major groove of DNA [72]. The AP2 sub-family members possess two AP2/ERF domains separated by a linker sequence of 25 amino acids which is responsible for positioning of the DNA-binding domains [73]. The molecular modeling thus proved that all the predicted protein structures were highly consistent and this data would offer a preliminary foundation for comprehending the molecular functions of SiAP2/ERF proteins.

Bottom Line: Comparative physical mapping between foxtail millet AP2/ERF genes and its orthologs of sorghum (18 genes), maize (14 genes), rice (9 genes) and Brachypodium (6 genes) showed the evolutionary insights of AP2/ERF gene family and also the decrease in orthology with increase in phylogenetic distance.The study showed that the genes SiAP2/ERF-069, SiAP2/ERF-103 and SiAP2/ERF-120 may be considered as potential candidate genes for further functional validation as well for utilization in crop improvement programs for stress resistance since these genes were up-regulated under drought and salinity stresses in ABA dependent manner.Altogether the present study provides new insights into evolution, divergence and systematic functional analysis of AP2/ERF gene family at genome level in foxtail millet which may be utilized for improving stress adaptation and tolerance in millets, cereals and bioenergy grasses.

View Article: PubMed Central - PubMed

Affiliation: National Research Centre on Plant Biotechnology, New Delhi, India; CSIR-National Botanical Research Institute, Lucknow, Uttar Pradesh, India.

ABSTRACT
The APETALA2/ethylene-responsive element binding factor (AP2/ERF) family is one of the largest transcription factor (TF) families in plants that includes four major sub-families, namely AP2, DREB (dehydration responsive element binding), ERF (ethylene responsive factors) and RAV (Related to ABI3/VP). AP2/ERFs are known to play significant roles in various plant processes including growth and development and biotic and abiotic stress responses. Considering this, a comprehensive genome-wide study was conducted in foxtail millet (Setaria italica L.). A total of 171 AP2/ERF genes were identified by systematic sequence analysis and were physically mapped onto nine chromosomes. Phylogenetic analysis grouped AP2/ERF genes into six classes (I to VI). Duplication analysis revealed that 12 (∼7%) SiAP2/ERF genes were tandem repeated and 22 (∼13%) were segmentally duplicated. Comparative physical mapping between foxtail millet AP2/ERF genes and its orthologs of sorghum (18 genes), maize (14 genes), rice (9 genes) and Brachypodium (6 genes) showed the evolutionary insights of AP2/ERF gene family and also the decrease in orthology with increase in phylogenetic distance. The evolutionary significance in terms of gene-duplication and divergence was analyzed by estimating synonymous and non-synonymous substitution rates. Expression profiling of candidate AP2/ERF genes against drought, salt and phytohormones revealed insights into their precise and/or overlapping expression patterns which could be responsible for their functional divergence in foxtail millet. The study showed that the genes SiAP2/ERF-069, SiAP2/ERF-103 and SiAP2/ERF-120 may be considered as potential candidate genes for further functional validation as well for utilization in crop improvement programs for stress resistance since these genes were up-regulated under drought and salinity stresses in ABA dependent manner. Altogether the present study provides new insights into evolution, divergence and systematic functional analysis of AP2/ERF gene family at genome level in foxtail millet which may be utilized for improving stress adaptation and tolerance in millets, cereals and bioenergy grasses.

Show MeSH
Related in: MedlinePlus