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Comparative analysis of the conserved functions of Arabidopsis DRL1 and yeast KTI12.

Jun SE, Cho KH, Hwang JY, Abdel-Fattah W, Hammermeister A, Schaffrath R, Bowman JL, Kim GT - Mol. Cells (2014)

Bottom Line: In a previous study, we showed that the DRL1 gene, which encodes a homolog of the Elongator-associated protein KTI12 of yeast, acts as a positive regulator of adaxial leaf patterning and shoot meristem activity.To determine the evolutionally conserved functions of DRL1, we performed a comparison of the deduced amino acid sequence of DRL1 and its yeast homolog, KTI12, and found that while overall homology was low, well-conserved domains were presented.Our results provide insight into the communication network between the SAM and leaf primordia required for the establishment of leaf polarity by mediating histone acetylation or through other mechanisms.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biotechnology, Dong-A University, Busan 604-714, Korea.

ABSTRACT
Patterning of the polar axis during the early leaf developmental stage is established by cell-to-cell communication between the shoot apical meristem (SAM) and the leaf primordia. In a previous study, we showed that the DRL1 gene, which encodes a homolog of the Elongator-associated protein KTI12 of yeast, acts as a positive regulator of adaxial leaf patterning and shoot meristem activity. To determine the evolutionally conserved functions of DRL1, we performed a comparison of the deduced amino acid sequence of DRL1 and its yeast homolog, KTI12, and found that while overall homology was low, well-conserved domains were presented. DRL1 contained two conserved plant-specific domains. Expression of the DRL1 gene in a yeast KTI12-deficient yeast mutant suppressed the growth retardation phenotype, but did not rescue the caffeine sensitivity, indicating that the role of Arabidopsis Elongator-associated protein is partially conserved with yeast KTI12, but may have changed between yeast and plants in response to caffeine during the course of evolution. In addition, elevated expression of DRL1 gene triggered zymocin sensitivity, while overexpression of KTI12 maintained zymocin resistance, indicating that the function of Arabidopsis DRL1 may not overlap with yeast KTI12 with regards to toxin sensitivity. In this study, expression analysis showed that class-I KNOX genes were downregulated in the shoot apex, and that YAB and KAN were upregulated in leaves of the Arabidopsis drl1-101 mutant. Our results provide insight into the communication network between the SAM and leaf primordia required for the establishment of leaf polarity by mediating histone acetylation or through other mechanisms.

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Amino acid sequence alignment and homology analysis of DRL1. (A) Amino acid sequence alignment. Conserved domains include an ATP/GTP-binding motif and two CaM-binding motifs (thin line), two plant-specific sequences (thick lines). The functions of the plant-specific motifs are unknown. Amino acid sequences of DRL1 and its homologs used in the alignment were retrieved from the NCBI GenBank database. The Gen-Bank accession numbers of the amino acid sequences are NP_172840 (Arabidopsis thaliana), NP_001145516 (Zea mays), XP_003528855 (Glycine max), BAH-95225 (Oryza sativa), XP_643511 (Dictyostelium discoideum), NP_594556 (Schizosaccharomyces pombe), NP_012812 (Saccharomyces cerevisiae), NP_001119890 (Danio rerio), and NP_612426 (Homo sapiens). (B) A portion of the overall alignment containing plant-specific sequences I (box). (C) A portion of the overall alignment containing plant-specific sequences II (box). (D) Amino acid sequence homologies of DRL1 homologs from plants, animals, protozoa and yeasts to Arabidopsis DRL1.
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f1-molcell-38-3-243: Amino acid sequence alignment and homology analysis of DRL1. (A) Amino acid sequence alignment. Conserved domains include an ATP/GTP-binding motif and two CaM-binding motifs (thin line), two plant-specific sequences (thick lines). The functions of the plant-specific motifs are unknown. Amino acid sequences of DRL1 and its homologs used in the alignment were retrieved from the NCBI GenBank database. The Gen-Bank accession numbers of the amino acid sequences are NP_172840 (Arabidopsis thaliana), NP_001145516 (Zea mays), XP_003528855 (Glycine max), BAH-95225 (Oryza sativa), XP_643511 (Dictyostelium discoideum), NP_594556 (Schizosaccharomyces pombe), NP_012812 (Saccharomyces cerevisiae), NP_001119890 (Danio rerio), and NP_612426 (Homo sapiens). (B) A portion of the overall alignment containing plant-specific sequences I (box). (C) A portion of the overall alignment containing plant-specific sequences II (box). (D) Amino acid sequence homologies of DRL1 homologs from plants, animals, protozoa and yeasts to Arabidopsis DRL1.

Mentions: DRL1 was reported previously to encode a homolog of the yeast Elongator-associated protein, KTI12 (Cho et al., 2007; Nelissen et al., 2003). To examine the evolutionary history and structural features of the DRL1 protein, we aligned the Arabidopsis DRL1 sequence with the sequences of DRL1 homologs from various other species. Alignment of the amino acid sequences of DRL1 homologs from plants (Arabidopsis thaliana, Oryza sativa, Zea mays, and Glycine max), yeast (S. cerevisiae and Schizosaccharomyces pombe), protozoa (Dictyostelium discoideum), and animals (Danio rerio and Homo sapiens) revealed the presence of conserved domains including an ATP/GTP-binding motif in the N-terminus, two calmodulin (CaM)-binding motifs in the N- and C-terminal regions, and domains specific to plant species (plant-specific sequences I and II) (Fig. 1A). The Arabidopsis DRL1 amino acid sequence exhibited the highest similarity to the sequences of other plant DRL1 homologs with similarities of 58.55, 72.52, and 66.11% to the DRL1 homologs of O. sativa, G. max, and Z. mays, respectively, and the lowest similarity to the yeast DRL1 homologs from S. cerevisiae (28.15%; Fig. 1D). Based on an amino acid alignment and functional site prediction analyses, we identified a conserved sequence, KTQ(R)DVR(K) designated plant-specific sequence I, in the central region that could form a short α-helix and may have WD40 repeat-binding motif (Fig. 1B; Dinkel et al., 2013). We also identified a second invariant sequence, GQS(Y/T)SL designated plant-specific sequence II, in the C-terminal region that was conserved among dicot plants; could form a shorter α-helix than in the yeast proteins and may have NEK2 phosphorylation motif (Fig. 1C; Dinkel et al., 2013). Among the genes examined in this study, the H. sapiens DRL1 homolog encoded the longest amino acid sequence (Fig. 1A). A protein secondary structure prediction analysis of the full amino acid sequences of Arabidopsis (DRL1) and S. cerevisiae (KTI12) using the PHYRE2 program (www.sbg.bio.ic.ac.uk/phyre2/) showed that the structure of both proteins was very similar (Supplementary Fig. S1). The DRL1 protein contained 13 α-helices and 6 β-sheets, while the KTI12 protein had 11 α-helices and 5 β-sheets (Supplementary Figs. S1A–S1D). Based on hydropathy and transmembrane prediction analysis using TMpred and SPLIT programs, the DRL1 and KTI12 proteins apparently lack any transmembrane domains (Supplementary Figs. S1E and S1F).


Comparative analysis of the conserved functions of Arabidopsis DRL1 and yeast KTI12.

Jun SE, Cho KH, Hwang JY, Abdel-Fattah W, Hammermeister A, Schaffrath R, Bowman JL, Kim GT - Mol. Cells (2014)

Amino acid sequence alignment and homology analysis of DRL1. (A) Amino acid sequence alignment. Conserved domains include an ATP/GTP-binding motif and two CaM-binding motifs (thin line), two plant-specific sequences (thick lines). The functions of the plant-specific motifs are unknown. Amino acid sequences of DRL1 and its homologs used in the alignment were retrieved from the NCBI GenBank database. The Gen-Bank accession numbers of the amino acid sequences are NP_172840 (Arabidopsis thaliana), NP_001145516 (Zea mays), XP_003528855 (Glycine max), BAH-95225 (Oryza sativa), XP_643511 (Dictyostelium discoideum), NP_594556 (Schizosaccharomyces pombe), NP_012812 (Saccharomyces cerevisiae), NP_001119890 (Danio rerio), and NP_612426 (Homo sapiens). (B) A portion of the overall alignment containing plant-specific sequences I (box). (C) A portion of the overall alignment containing plant-specific sequences II (box). (D) Amino acid sequence homologies of DRL1 homologs from plants, animals, protozoa and yeasts to Arabidopsis DRL1.
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f1-molcell-38-3-243: Amino acid sequence alignment and homology analysis of DRL1. (A) Amino acid sequence alignment. Conserved domains include an ATP/GTP-binding motif and two CaM-binding motifs (thin line), two plant-specific sequences (thick lines). The functions of the plant-specific motifs are unknown. Amino acid sequences of DRL1 and its homologs used in the alignment were retrieved from the NCBI GenBank database. The Gen-Bank accession numbers of the amino acid sequences are NP_172840 (Arabidopsis thaliana), NP_001145516 (Zea mays), XP_003528855 (Glycine max), BAH-95225 (Oryza sativa), XP_643511 (Dictyostelium discoideum), NP_594556 (Schizosaccharomyces pombe), NP_012812 (Saccharomyces cerevisiae), NP_001119890 (Danio rerio), and NP_612426 (Homo sapiens). (B) A portion of the overall alignment containing plant-specific sequences I (box). (C) A portion of the overall alignment containing plant-specific sequences II (box). (D) Amino acid sequence homologies of DRL1 homologs from plants, animals, protozoa and yeasts to Arabidopsis DRL1.
Mentions: DRL1 was reported previously to encode a homolog of the yeast Elongator-associated protein, KTI12 (Cho et al., 2007; Nelissen et al., 2003). To examine the evolutionary history and structural features of the DRL1 protein, we aligned the Arabidopsis DRL1 sequence with the sequences of DRL1 homologs from various other species. Alignment of the amino acid sequences of DRL1 homologs from plants (Arabidopsis thaliana, Oryza sativa, Zea mays, and Glycine max), yeast (S. cerevisiae and Schizosaccharomyces pombe), protozoa (Dictyostelium discoideum), and animals (Danio rerio and Homo sapiens) revealed the presence of conserved domains including an ATP/GTP-binding motif in the N-terminus, two calmodulin (CaM)-binding motifs in the N- and C-terminal regions, and domains specific to plant species (plant-specific sequences I and II) (Fig. 1A). The Arabidopsis DRL1 amino acid sequence exhibited the highest similarity to the sequences of other plant DRL1 homologs with similarities of 58.55, 72.52, and 66.11% to the DRL1 homologs of O. sativa, G. max, and Z. mays, respectively, and the lowest similarity to the yeast DRL1 homologs from S. cerevisiae (28.15%; Fig. 1D). Based on an amino acid alignment and functional site prediction analyses, we identified a conserved sequence, KTQ(R)DVR(K) designated plant-specific sequence I, in the central region that could form a short α-helix and may have WD40 repeat-binding motif (Fig. 1B; Dinkel et al., 2013). We also identified a second invariant sequence, GQS(Y/T)SL designated plant-specific sequence II, in the C-terminal region that was conserved among dicot plants; could form a shorter α-helix than in the yeast proteins and may have NEK2 phosphorylation motif (Fig. 1C; Dinkel et al., 2013). Among the genes examined in this study, the H. sapiens DRL1 homolog encoded the longest amino acid sequence (Fig. 1A). A protein secondary structure prediction analysis of the full amino acid sequences of Arabidopsis (DRL1) and S. cerevisiae (KTI12) using the PHYRE2 program (www.sbg.bio.ic.ac.uk/phyre2/) showed that the structure of both proteins was very similar (Supplementary Fig. S1). The DRL1 protein contained 13 α-helices and 6 β-sheets, while the KTI12 protein had 11 α-helices and 5 β-sheets (Supplementary Figs. S1A–S1D). Based on hydropathy and transmembrane prediction analysis using TMpred and SPLIT programs, the DRL1 and KTI12 proteins apparently lack any transmembrane domains (Supplementary Figs. S1E and S1F).

Bottom Line: In a previous study, we showed that the DRL1 gene, which encodes a homolog of the Elongator-associated protein KTI12 of yeast, acts as a positive regulator of adaxial leaf patterning and shoot meristem activity.To determine the evolutionally conserved functions of DRL1, we performed a comparison of the deduced amino acid sequence of DRL1 and its yeast homolog, KTI12, and found that while overall homology was low, well-conserved domains were presented.Our results provide insight into the communication network between the SAM and leaf primordia required for the establishment of leaf polarity by mediating histone acetylation or through other mechanisms.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biotechnology, Dong-A University, Busan 604-714, Korea.

ABSTRACT
Patterning of the polar axis during the early leaf developmental stage is established by cell-to-cell communication between the shoot apical meristem (SAM) and the leaf primordia. In a previous study, we showed that the DRL1 gene, which encodes a homolog of the Elongator-associated protein KTI12 of yeast, acts as a positive regulator of adaxial leaf patterning and shoot meristem activity. To determine the evolutionally conserved functions of DRL1, we performed a comparison of the deduced amino acid sequence of DRL1 and its yeast homolog, KTI12, and found that while overall homology was low, well-conserved domains were presented. DRL1 contained two conserved plant-specific domains. Expression of the DRL1 gene in a yeast KTI12-deficient yeast mutant suppressed the growth retardation phenotype, but did not rescue the caffeine sensitivity, indicating that the role of Arabidopsis Elongator-associated protein is partially conserved with yeast KTI12, but may have changed between yeast and plants in response to caffeine during the course of evolution. In addition, elevated expression of DRL1 gene triggered zymocin sensitivity, while overexpression of KTI12 maintained zymocin resistance, indicating that the function of Arabidopsis DRL1 may not overlap with yeast KTI12 with regards to toxin sensitivity. In this study, expression analysis showed that class-I KNOX genes were downregulated in the shoot apex, and that YAB and KAN were upregulated in leaves of the Arabidopsis drl1-101 mutant. Our results provide insight into the communication network between the SAM and leaf primordia required for the establishment of leaf polarity by mediating histone acetylation or through other mechanisms.

Show MeSH
Related in: MedlinePlus