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Genome-wide identification and expression analysis of the IQD gene family in moso bamboo (Phyllostachys edulis).

Wu M, Li Y, Chen D, Liu H, Zhu D, Xiang Y - Sci Rep (2016)

Bottom Line: We surveyed the putative promoter regions of the PeIQD genes, which showed that largely stress-related cis-elements existed in these genes.The expression profiles of the IQD genes shed light on their functional divergence.Additionally, a yeast two-hybrid assay proved that PeIQD8 can interact with PeCaM2 and that IQ or I in the IQ motif is required for PeIQD8 to combine with CaM2.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.

ABSTRACT
Members of the plant-specific IQ67-domain (IQD) protein family are involved in various aspects of normal plant growth and developmental processes as well as basal defence response. Although hundreds of IQD proteins have been identified, only a small number of IQDs have been functionally characterized. Moreover, no systematic study has been performed on moso bamboo. In this study, we performed for the first time a genome-wide identification and expression analysis of the IQD gene family in moso bamboo. We identified 29 non-redundant PeIQD encoding genes. Analysis of the evolutionary patterns and divergence revealed that the IQD genes underwent a large-scale event around 12 million years ago and the division times of IQD family genes between moso bamboo and rice, and, between moso bamboo and Brachypodium, were found to be 20-35 MYA and 25-40 MYA, respectively. We surveyed the putative promoter regions of the PeIQD genes, which showed that largely stress-related cis-elements existed in these genes. The expression profiles of the IQD genes shed light on their functional divergence. Additionally, a yeast two-hybrid assay proved that PeIQD8 can interact with PeCaM2 and that IQ or I in the IQ motif is required for PeIQD8 to combine with CaM2.

No MeSH data available.


Schematic representation of the 10 conserved motifs in PeIQD proteins.Motifs of the PeIQD proteins were identified using the online MEME program. Different coloured boxes represent different motifs, with their names in the centre of the boxes. The coloured boxes were ordered manually according to the results of the MEME analysis. The length of each box in the figure does not represent the actual motif size.
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f3: Schematic representation of the 10 conserved motifs in PeIQD proteins.Motifs of the PeIQD proteins were identified using the online MEME program. Different coloured boxes represent different motifs, with their names in the centre of the boxes. The coloured boxes were ordered manually according to the results of the MEME analysis. The length of each box in the figure does not represent the actual motif size.

Mentions: We further searched for the conserved motifs in PeIQD proteins by MEME program to obtain more insights into the diversity of motif compositions among PeIQDs. As shown in Fig. 3, a total of 10 conserved motifs designated as motif 1 to motif 10 were identified. The details of the 10 putative motifs were referred in Table S2. Motif 1 was found to encode the IQ domain, while motif 2 encoded proteins of unknown function (DUF4005). The specific motifs of the other subfamilies have not been functionally annotated. As expected, most of the closely related members had common motif compositions, suggesting functional similarities among IQD proteins within the same subfamily (Fig. 3). The most common motif is motif 1, found in all 29 moso bamboo IQD genes (Fig. 3). To predict calmodulin-binding sites, we searched the Calmodulin Target Database, which provides various structural and biophysical parameters for the 29 PeIQD protein sequences. Consecutive strings of amino acid residues with high values of ≥7 indicated the locations of the putative binding sites. The search results showed that all of the predicted PeIQD proteins contained at least one CaM-binding site. These CaM-binding sites are described in Table 2.


Genome-wide identification and expression analysis of the IQD gene family in moso bamboo (Phyllostachys edulis).

Wu M, Li Y, Chen D, Liu H, Zhu D, Xiang Y - Sci Rep (2016)

Schematic representation of the 10 conserved motifs in PeIQD proteins.Motifs of the PeIQD proteins were identified using the online MEME program. Different coloured boxes represent different motifs, with their names in the centre of the boxes. The coloured boxes were ordered manually according to the results of the MEME analysis. The length of each box in the figure does not represent the actual motif size.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4837358&req=5

f3: Schematic representation of the 10 conserved motifs in PeIQD proteins.Motifs of the PeIQD proteins were identified using the online MEME program. Different coloured boxes represent different motifs, with their names in the centre of the boxes. The coloured boxes were ordered manually according to the results of the MEME analysis. The length of each box in the figure does not represent the actual motif size.
Mentions: We further searched for the conserved motifs in PeIQD proteins by MEME program to obtain more insights into the diversity of motif compositions among PeIQDs. As shown in Fig. 3, a total of 10 conserved motifs designated as motif 1 to motif 10 were identified. The details of the 10 putative motifs were referred in Table S2. Motif 1 was found to encode the IQ domain, while motif 2 encoded proteins of unknown function (DUF4005). The specific motifs of the other subfamilies have not been functionally annotated. As expected, most of the closely related members had common motif compositions, suggesting functional similarities among IQD proteins within the same subfamily (Fig. 3). The most common motif is motif 1, found in all 29 moso bamboo IQD genes (Fig. 3). To predict calmodulin-binding sites, we searched the Calmodulin Target Database, which provides various structural and biophysical parameters for the 29 PeIQD protein sequences. Consecutive strings of amino acid residues with high values of ≥7 indicated the locations of the putative binding sites. The search results showed that all of the predicted PeIQD proteins contained at least one CaM-binding site. These CaM-binding sites are described in Table 2.

Bottom Line: We surveyed the putative promoter regions of the PeIQD genes, which showed that largely stress-related cis-elements existed in these genes.The expression profiles of the IQD genes shed light on their functional divergence.Additionally, a yeast two-hybrid assay proved that PeIQD8 can interact with PeCaM2 and that IQ or I in the IQ motif is required for PeIQD8 to combine with CaM2.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.

ABSTRACT
Members of the plant-specific IQ67-domain (IQD) protein family are involved in various aspects of normal plant growth and developmental processes as well as basal defence response. Although hundreds of IQD proteins have been identified, only a small number of IQDs have been functionally characterized. Moreover, no systematic study has been performed on moso bamboo. In this study, we performed for the first time a genome-wide identification and expression analysis of the IQD gene family in moso bamboo. We identified 29 non-redundant PeIQD encoding genes. Analysis of the evolutionary patterns and divergence revealed that the IQD genes underwent a large-scale event around 12 million years ago and the division times of IQD family genes between moso bamboo and rice, and, between moso bamboo and Brachypodium, were found to be 20-35 MYA and 25-40 MYA, respectively. We surveyed the putative promoter regions of the PeIQD genes, which showed that largely stress-related cis-elements existed in these genes. The expression profiles of the IQD genes shed light on their functional divergence. Additionally, a yeast two-hybrid assay proved that PeIQD8 can interact with PeCaM2 and that IQ or I in the IQ motif is required for PeIQD8 to combine with CaM2.

No MeSH data available.