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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.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.

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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Related in: MedlinePlus

The N-terminal conserved motifs of plant MAPKs. These motifs are immediately followed by presence of N-terminal SEY, SDY, TEY, TDY motifs of group D MAPKs. This picture is a pictorial representation of different motifs taken from different groups of MAPKs. For details, please see Table 2 and Additional file 4.
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Fig2: The N-terminal conserved motifs of plant MAPKs. These motifs are immediately followed by presence of N-terminal SEY, SDY, TEY, TDY motifs of group D MAPKs. This picture is a pictorial representation of different motifs taken from different groups of MAPKs. For details, please see Table 2 and Additional file 4.

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)

The N-terminal conserved motifs of plant MAPKs. These motifs are immediately followed by presence of N-terminal SEY, SDY, TEY, TDY motifs of group D MAPKs. This picture is a pictorial representation of different motifs taken from different groups of MAPKs. For details, please see Table 2 and Additional file 4.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4363184&req=5

Fig2: The N-terminal conserved motifs of plant MAPKs. These motifs are immediately followed by presence of N-terminal SEY, SDY, TEY, TDY motifs of group D MAPKs. This picture is a pictorial representation of different motifs taken from different groups of MAPKs. For details, please see Table 2 and Additional file 4.
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.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.

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