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Identification of new members of the MAPK gene family in plants shows diverse conserved domains and novel activation loop variants.

Mohanta TK, Arora PK, Mohanta N, Parida P, Bae H - BMC Genomics (2015)

Bottom Line: The MAPK cascade plays an indispensible role in the growth and development of plants, as well as in biotic and abiotic stress responses.Phylogenetic analysis of all predicted MAPKs were clustered into six different groups (group A, B, C, D, E and F), and all predicted MAPKs were assigned with specific names based on their orthology based evolutionary relationships with Arabidopsis or Oryza MAPKs.Our study showed the presence of several new activation loop motifs and diverse conserved domains in MAPKs.

View Article: PubMed Central - PubMed

Affiliation: School of Biotechnology, Yeungnam University, Daehak Gyeongsan, Gyeonsangbook, 712749, Republic of Korea. nostoc.tapan@gmail.com.

ABSTRACT

Background: Mitogen Activated Protein Kinase (MAPK) signaling is of critical importance in plants and other eukaryotic organisms. The MAPK cascade plays an indispensible role in the growth and development of plants, as well as in biotic and abiotic stress responses. The MAPKs are constitute the most downstream module of the three tier MAPK cascade and are phosphorylated by upstream MAP kinase kinases (MAPKK), which are in turn are phosphorylated by MAP kinase kinase kinase (MAPKKK). The MAPKs play pivotal roles in regulation of many cytoplasmic and nuclear substrates, thus regulating several biological processes.

Results: A total of 589 MAPKs genes were identified from the genome wide analysis of 40 species. The sequence analysis has revealed the presence of several N- and C-terminal conserved domains. The MAPKs were previously believed to be characterized by the presence of TEY/TDY activation loop motifs. The present study showed that, in addition to presence of activation loop TEY/TDY motifs, MAPKs are also contain MEY, TEM, TQM, TRM, TVY, TSY, TEC and TQY activation loop motifs. Phylogenetic analysis of all predicted MAPKs were clustered into six different groups (group A, B, C, D, E and F), and all predicted MAPKs were assigned with specific names based on their orthology based evolutionary relationships with Arabidopsis or Oryza MAPKs.

Conclusion: We conducted global analysis of the MAPK gene family of plants from lower eukaryotes to higher eukaryotes and analyzed their genomic and evolutionary aspects. Our study showed the presence of several new activation loop motifs and diverse conserved domains in MAPKs. Advance study of newly identified activation loop motifs can provide further information regarding the downstream signaling cascade activated in response to a wide array of stress conditions, as well as plant growth and development.

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Multiple sequence alignment of plant MAPKs. A. The figure shows presence of N-terminal TEY, TDY, SEY and SDY motifs (in red). The SEY and SDY motifs are aligned with TEY and TDY motifs and very specific to group D MAP kinase genes. Activation loop TDY motifs are marked in blue and indicated inside the box. Conserved signature consensus sequences present within MAP kinases domain of MAPK proteins are marked in maroon. C-terminal conserved motifs are marked in green and presented inside box. All eleven sub-domains are also indicated in the figure. B. Molecular structure of AtMPK1 (group C) and SiMPK20-1 (group D). In AtMPK1, the arrow mark shows presence of TEY motif in the activation loop region. Similarly, in the group D MAP kinase (SiMPK20-1), the conserved N-terminal TEY motif and activation loop TDY motifs are indicated by different arrows.
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Fig1: Multiple sequence alignment of plant MAPKs. A. The figure shows presence of N-terminal TEY, TDY, SEY and SDY motifs (in red). The SEY and SDY motifs are aligned with TEY and TDY motifs and very specific to group D MAP kinase genes. Activation loop TDY motifs are marked in blue and indicated inside the box. Conserved signature consensus sequences present within MAP kinases domain of MAPK proteins are marked in maroon. C-terminal conserved motifs are marked in green and presented inside box. All eleven sub-domains are also indicated in the figure. B. Molecular structure of AtMPK1 (group C) and SiMPK20-1 (group D). In AtMPK1, the arrow mark shows presence of TEY motif in the activation loop region. Similarly, in the group D MAP kinase (SiMPK20-1), the conserved N-terminal TEY motif and activation loop TDY motifs are indicated by different arrows.

Mentions: The MAPKs are characterized by the presence of a conserved T-E-Y/T-D-Y motif in the activation loop region. Despite having the activation loop T-E-Y/T-D-Y motif in MAPKs, in this study, we found that several MAPKs shared conserved N-terminal T-E-Y, T-D-Y, S-D-Y and S-E-Y motifs (Figure 1A, 1B, Table 2, Additional file 4). These N-terminal conserved motifs are only shared by group D MAPKs. In total, 182 genes shared the N-terminal conserved motifs. Among them, 11 genes shared the S-D-Y motif, 27 shared the S-E-Y motif, six shared the T-D-Y motif and the remaining138 genes shared the T-E-Y motif (Additional file 4). Chlamydomonas and Volvox share a common A-V-H motif instead of the S-E-Y/S-D-Y/T-E-Y and T-D-Y motif (Additional file 4). Several other group specific conserved motifs are also present in the N-terminal region of MAPKs. They includes A-K-Y, N-K-Y (group A), S-K-Y, R-K-Y (group B), T-K-Y (group C) and S-Q-Y, N-R-Y, S-R-Y (group D) (Figure 2, Table 2). These motifs are present immediately after the N-terminal T-E-Y, T-D-Y, S-D-Y and S-E-Y motifs. The MAPK sequences sharing different numbers of motifs are A-K-Y (70), N-K-Y (13), S-K-Y (74), R-K-Y (42), T-K-Y (81), S-Q-Y (36), N-R-Y (98), and S-R-Y (91) (Additional file 4). In addition to the presence of conserved motifs, the N-terminal region of MAPKs also contained conserved amino acid consensus sequences including I-G-x-G-x-Y-G-x-V, I-K-K-I-x3-F, D-A-x-R-x-L-R-E, F-x-D-I-Y-x3-E-L-M, D-L-x2-V-I, D-x-L-x2-E-H, Q-x-L-R-x-L-K-Y-x-H, H-R-D-L-K-P-x-N, and L-x-L-x-N-C-x-L-K-I-x-D-F-G-L-A-R (Figure 1A, Table 3).Figure 1


Identification of new members of the MAPK gene family in plants shows diverse conserved domains and novel activation loop variants.

Mohanta TK, Arora PK, Mohanta N, Parida P, Bae H - BMC Genomics (2015)

Multiple sequence alignment of plant MAPKs. A. The figure shows presence of N-terminal TEY, TDY, SEY and SDY motifs (in red). The SEY and SDY motifs are aligned with TEY and TDY motifs and very specific to group D MAP kinase genes. Activation loop TDY motifs are marked in blue and indicated inside the box. Conserved signature consensus sequences present within MAP kinases domain of MAPK proteins are marked in maroon. C-terminal conserved motifs are marked in green and presented inside box. All eleven sub-domains are also indicated in the figure. B. Molecular structure of AtMPK1 (group C) and SiMPK20-1 (group D). In AtMPK1, the arrow mark shows presence of TEY motif in the activation loop region. Similarly, in the group D MAP kinase (SiMPK20-1), the conserved N-terminal TEY motif and activation loop TDY motifs are indicated by different arrows.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4363184&req=5

Fig1: Multiple sequence alignment of plant MAPKs. A. The figure shows presence of N-terminal TEY, TDY, SEY and SDY motifs (in red). The SEY and SDY motifs are aligned with TEY and TDY motifs and very specific to group D MAP kinase genes. Activation loop TDY motifs are marked in blue and indicated inside the box. Conserved signature consensus sequences present within MAP kinases domain of MAPK proteins are marked in maroon. C-terminal conserved motifs are marked in green and presented inside box. All eleven sub-domains are also indicated in the figure. B. Molecular structure of AtMPK1 (group C) and SiMPK20-1 (group D). In AtMPK1, the arrow mark shows presence of TEY motif in the activation loop region. Similarly, in the group D MAP kinase (SiMPK20-1), the conserved N-terminal TEY motif and activation loop TDY motifs are indicated by different arrows.
Mentions: The MAPKs are characterized by the presence of a conserved T-E-Y/T-D-Y motif in the activation loop region. Despite having the activation loop T-E-Y/T-D-Y motif in MAPKs, in this study, we found that several MAPKs shared conserved N-terminal T-E-Y, T-D-Y, S-D-Y and S-E-Y motifs (Figure 1A, 1B, Table 2, Additional file 4). These N-terminal conserved motifs are only shared by group D MAPKs. In total, 182 genes shared the N-terminal conserved motifs. Among them, 11 genes shared the S-D-Y motif, 27 shared the S-E-Y motif, six shared the T-D-Y motif and the remaining138 genes shared the T-E-Y motif (Additional file 4). Chlamydomonas and Volvox share a common A-V-H motif instead of the S-E-Y/S-D-Y/T-E-Y and T-D-Y motif (Additional file 4). Several other group specific conserved motifs are also present in the N-terminal region of MAPKs. They includes A-K-Y, N-K-Y (group A), S-K-Y, R-K-Y (group B), T-K-Y (group C) and S-Q-Y, N-R-Y, S-R-Y (group D) (Figure 2, Table 2). These motifs are present immediately after the N-terminal T-E-Y, T-D-Y, S-D-Y and S-E-Y motifs. The MAPK sequences sharing different numbers of motifs are A-K-Y (70), N-K-Y (13), S-K-Y (74), R-K-Y (42), T-K-Y (81), S-Q-Y (36), N-R-Y (98), and S-R-Y (91) (Additional file 4). In addition to the presence of conserved motifs, the N-terminal region of MAPKs also contained conserved amino acid consensus sequences including I-G-x-G-x-Y-G-x-V, I-K-K-I-x3-F, D-A-x-R-x-L-R-E, F-x-D-I-Y-x3-E-L-M, D-L-x2-V-I, D-x-L-x2-E-H, Q-x-L-R-x-L-K-Y-x-H, H-R-D-L-K-P-x-N, and L-x-L-x-N-C-x-L-K-I-x-D-F-G-L-A-R (Figure 1A, Table 3).Figure 1

Bottom Line: The MAPK cascade plays an indispensible role in the growth and development of plants, as well as in biotic and abiotic stress responses.Phylogenetic analysis of all predicted MAPKs were clustered into six different groups (group A, B, C, D, E and F), and all predicted MAPKs were assigned with specific names based on their orthology based evolutionary relationships with Arabidopsis or Oryza MAPKs.Our study showed the presence of several new activation loop motifs and diverse conserved domains in MAPKs.

View Article: PubMed Central - PubMed

Affiliation: School of Biotechnology, Yeungnam University, Daehak Gyeongsan, Gyeonsangbook, 712749, Republic of Korea. nostoc.tapan@gmail.com.

ABSTRACT

Background: Mitogen Activated Protein Kinase (MAPK) signaling is of critical importance in plants and other eukaryotic organisms. The MAPK cascade plays an indispensible role in the growth and development of plants, as well as in biotic and abiotic stress responses. The MAPKs are constitute the most downstream module of the three tier MAPK cascade and are phosphorylated by upstream MAP kinase kinases (MAPKK), which are in turn are phosphorylated by MAP kinase kinase kinase (MAPKKK). The MAPKs play pivotal roles in regulation of many cytoplasmic and nuclear substrates, thus regulating several biological processes.

Results: A total of 589 MAPKs genes were identified from the genome wide analysis of 40 species. The sequence analysis has revealed the presence of several N- and C-terminal conserved domains. The MAPKs were previously believed to be characterized by the presence of TEY/TDY activation loop motifs. The present study showed that, in addition to presence of activation loop TEY/TDY motifs, MAPKs are also contain MEY, TEM, TQM, TRM, TVY, TSY, TEC and TQY activation loop motifs. Phylogenetic analysis of all predicted MAPKs were clustered into six different groups (group A, B, C, D, E and F), and all predicted MAPKs were assigned with specific names based on their orthology based evolutionary relationships with Arabidopsis or Oryza MAPKs.

Conclusion: We conducted global analysis of the MAPK gene family of plants from lower eukaryotes to higher eukaryotes and analyzed their genomic and evolutionary aspects. Our study showed the presence of several new activation loop motifs and diverse conserved domains in MAPKs. Advance study of newly identified activation loop motifs can provide further information regarding the downstream signaling cascade activated in response to a wide array of stress conditions, as well as plant growth and development.

Show MeSH
Related in: MedlinePlus