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Comprehensive expression analysis of rice Armadillo gene family during abiotic stress and development.

Sharma M, Singh A, Shankar A, Pandey A, Baranwal V, Kapoor S, Tyagi AK, Pandey GK - DNA Res. (2014)

Bottom Line: Previous studies have confirmed that Armadillo proteins constitute a multigene family in Arabidopsis.Phylogenetic study classified them into several arbitrary groups based on a varying number of non-conserved ARM repeats and accessory domain(s) associated with them.The non-synonymous and synonymous substitutions per site ratios (Ka/Ks) of duplicated gene pairs indicate a purifying selection.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi 110021, India.

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Phylogenetic relationship between Arabidopsis and rice ARM superfamily genes. A phylogeny created with the full-length protein sequences of ARMs in Arabidopsis and O. sativa. The alignment of ARM repeat protein sequences of rice Armadillo genes was done using ClustalX 2.0.12. An unrooted neighbour-joining (NJ) tree was generated using the p-distance substitution model in MEGA 5. Bootstrap analysis was performed with 1000 replicates to obtain a support value for each branch. Based on bootstrap score, the phylogenetic tree is divided into 15 groups. The domain organization and number and position of ARM repeats in rice have been predicted by the sequence analysis in HHpred and Pfam. The domain organization of Arabidopsis ARM proteins has been adapted from Mudgil et al. 2004. The representative domain organization of each gene is shown on the right.
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DST056F1: Phylogenetic relationship between Arabidopsis and rice ARM superfamily genes. A phylogeny created with the full-length protein sequences of ARMs in Arabidopsis and O. sativa. The alignment of ARM repeat protein sequences of rice Armadillo genes was done using ClustalX 2.0.12. An unrooted neighbour-joining (NJ) tree was generated using the p-distance substitution model in MEGA 5. Bootstrap analysis was performed with 1000 replicates to obtain a support value for each branch. Based on bootstrap score, the phylogenetic tree is divided into 15 groups. The domain organization and number and position of ARM repeats in rice have been predicted by the sequence analysis in HHpred and Pfam. The domain organization of Arabidopsis ARM proteins has been adapted from Mudgil et al. 2004. The representative domain organization of each gene is shown on the right.

Mentions: To elucidate the evolutionary significance of ARM proteins across species, comparative phylogenetic analysis was performed using complete protein sequences of OsARMs and their respective Arabidopsis orthologues from previous study by Mudgil et al.14 The result showed that rice ARM repeat proteins coincide with specific ARM gene subtypes in Arabidopsis, signifying that ARM repeats might have co-evolved between the monocots and eudicots (Fig. 1). Additionally, several other accessory functional domains were found to be present in all predicted ARM repeat proteins. As observed in Arabidopsis, the U-box containing ARM repeat proteins (OsPUB-ARM) were found to outline a major group with 47 of 158 ARM repeats proteins in the rice genome. The unique UND region was also recognized based on sequence homology with the Arabidopsis UND/U-box proteins. Interestingly, the number of UND/U-box proteins was found to be equivalent (17) in both rice and Arabidopsis. Moreover, we observed that rice ARM proteins also display similar organization of ARM repeats and other domains when compared with well-characterized orthologues of Arabidopsis ARM family. Other known domains found in rice are five Importin-α proteins with Importin-β-binding (IBB) domain followed by five to seven ARM repeats. A large number of additional motifs were found to be associated within the predicted set of ARM proteins. These included domains implicated in protein–protein interactions such as HEAT and BTB. Again, several domains recognized for their role in protein ubiquitination such as U-box (47), HECT (1), Fes1 (3), and F-box (1) were found in conjunction with ARM domain in rice. In addition, two calcium-dependent phospholipid binding C2 domain responsible for membrane targeting and three microtubule-associated kinesin motor domain proteins were also found to be present. The protein sequence of sole orthologue of Arabidillo-1, 2 in rice (LOC_Os10g41360) derived from RGAP (http://rice.plantbiology.msu.edu) did not contain NLS/F-box N-terminal; however, a BAC clone search (GenBank Accession: AAG60190) in NCBI has confirmed the similar domain organization.Figure 1.


Comprehensive expression analysis of rice Armadillo gene family during abiotic stress and development.

Sharma M, Singh A, Shankar A, Pandey A, Baranwal V, Kapoor S, Tyagi AK, Pandey GK - DNA Res. (2014)

Phylogenetic relationship between Arabidopsis and rice ARM superfamily genes. A phylogeny created with the full-length protein sequences of ARMs in Arabidopsis and O. sativa. The alignment of ARM repeat protein sequences of rice Armadillo genes was done using ClustalX 2.0.12. An unrooted neighbour-joining (NJ) tree was generated using the p-distance substitution model in MEGA 5. Bootstrap analysis was performed with 1000 replicates to obtain a support value for each branch. Based on bootstrap score, the phylogenetic tree is divided into 15 groups. The domain organization and number and position of ARM repeats in rice have been predicted by the sequence analysis in HHpred and Pfam. The domain organization of Arabidopsis ARM proteins has been adapted from Mudgil et al. 2004. The representative domain organization of each gene is shown on the right.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4060948&req=5

DST056F1: Phylogenetic relationship between Arabidopsis and rice ARM superfamily genes. A phylogeny created with the full-length protein sequences of ARMs in Arabidopsis and O. sativa. The alignment of ARM repeat protein sequences of rice Armadillo genes was done using ClustalX 2.0.12. An unrooted neighbour-joining (NJ) tree was generated using the p-distance substitution model in MEGA 5. Bootstrap analysis was performed with 1000 replicates to obtain a support value for each branch. Based on bootstrap score, the phylogenetic tree is divided into 15 groups. The domain organization and number and position of ARM repeats in rice have been predicted by the sequence analysis in HHpred and Pfam. The domain organization of Arabidopsis ARM proteins has been adapted from Mudgil et al. 2004. The representative domain organization of each gene is shown on the right.
Mentions: To elucidate the evolutionary significance of ARM proteins across species, comparative phylogenetic analysis was performed using complete protein sequences of OsARMs and their respective Arabidopsis orthologues from previous study by Mudgil et al.14 The result showed that rice ARM repeat proteins coincide with specific ARM gene subtypes in Arabidopsis, signifying that ARM repeats might have co-evolved between the monocots and eudicots (Fig. 1). Additionally, several other accessory functional domains were found to be present in all predicted ARM repeat proteins. As observed in Arabidopsis, the U-box containing ARM repeat proteins (OsPUB-ARM) were found to outline a major group with 47 of 158 ARM repeats proteins in the rice genome. The unique UND region was also recognized based on sequence homology with the Arabidopsis UND/U-box proteins. Interestingly, the number of UND/U-box proteins was found to be equivalent (17) in both rice and Arabidopsis. Moreover, we observed that rice ARM proteins also display similar organization of ARM repeats and other domains when compared with well-characterized orthologues of Arabidopsis ARM family. Other known domains found in rice are five Importin-α proteins with Importin-β-binding (IBB) domain followed by five to seven ARM repeats. A large number of additional motifs were found to be associated within the predicted set of ARM proteins. These included domains implicated in protein–protein interactions such as HEAT and BTB. Again, several domains recognized for their role in protein ubiquitination such as U-box (47), HECT (1), Fes1 (3), and F-box (1) were found in conjunction with ARM domain in rice. In addition, two calcium-dependent phospholipid binding C2 domain responsible for membrane targeting and three microtubule-associated kinesin motor domain proteins were also found to be present. The protein sequence of sole orthologue of Arabidillo-1, 2 in rice (LOC_Os10g41360) derived from RGAP (http://rice.plantbiology.msu.edu) did not contain NLS/F-box N-terminal; however, a BAC clone search (GenBank Accession: AAG60190) in NCBI has confirmed the similar domain organization.Figure 1.

Bottom Line: Previous studies have confirmed that Armadillo proteins constitute a multigene family in Arabidopsis.Phylogenetic study classified them into several arbitrary groups based on a varying number of non-conserved ARM repeats and accessory domain(s) associated with them.The non-synonymous and synonymous substitutions per site ratios (Ka/Ks) of duplicated gene pairs indicate a purifying selection.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi 110021, India.

Show MeSH
Related in: MedlinePlus