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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

Phylogenetic tree of MAPK gene family in plants. Unrooted phylogenetic tree of MAPKs show presence of six different groups with well supported bootstrap values. We named them as group A (red), B (blue), C (pink), D (purple), E (teal) and F (green). The group E MAPKs are present at towards the end of the phylogenetic tree and group F present at the mid of the phylogenetic tree. Group E and F MAPKs are derived from lower plants of algae, pteridophytes and gymnosperm. Different MAPK genes falls in different groups are; group A (MPK3, MPK6, MPK10), group B (MPK4, MPK5, MPK11, MPK12, MPK13), group C (MPK1, MPK2, MPK7, MPK14), group D (MPK8, MPK9, MPK16, MPK17, MPK18, MPK19, MPK20 and MPK21), group E (CreinMPK7, CsubMPK3, PaMPK10, PaMPK7-2, PaMPK5, PaMPK14, CsubMPK7, MpMPK13, SmMPK10, VcMPK5) and group F (CreinMPK4-1, VcMPK4-1, OlMPK6, MpMPK4). The ERK1, ERK2, AtPIN1 (auxin efflux carrier) and AtCBL1 (calcineurin B like protein) were used as out group. Different statistical parameters used to constrcut the phylogenetic tree was: statistical method- maximum likelihood, test of phylogeny-boot strap method, no. of bootsrap replicate-2000, model/method-Jones-Taylor-Thornton (JTT) model, site coverage cutoff-95%, and branch swap filter-very strong. Phylogenetic tree was constructed using MEGA6 software.
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Fig5: Phylogenetic tree of MAPK gene family in plants. Unrooted phylogenetic tree of MAPKs show presence of six different groups with well supported bootstrap values. We named them as group A (red), B (blue), C (pink), D (purple), E (teal) and F (green). The group E MAPKs are present at towards the end of the phylogenetic tree and group F present at the mid of the phylogenetic tree. Group E and F MAPKs are derived from lower plants of algae, pteridophytes and gymnosperm. Different MAPK genes falls in different groups are; group A (MPK3, MPK6, MPK10), group B (MPK4, MPK5, MPK11, MPK12, MPK13), group C (MPK1, MPK2, MPK7, MPK14), group D (MPK8, MPK9, MPK16, MPK17, MPK18, MPK19, MPK20 and MPK21), group E (CreinMPK7, CsubMPK3, PaMPK10, PaMPK7-2, PaMPK5, PaMPK14, CsubMPK7, MpMPK13, SmMPK10, VcMPK5) and group F (CreinMPK4-1, VcMPK4-1, OlMPK6, MpMPK4). The ERK1, ERK2, AtPIN1 (auxin efflux carrier) and AtCBL1 (calcineurin B like protein) were used as out group. Different statistical parameters used to constrcut the phylogenetic tree was: statistical method- maximum likelihood, test of phylogeny-boot strap method, no. of bootsrap replicate-2000, model/method-Jones-Taylor-Thornton (JTT) model, site coverage cutoff-95%, and branch swap filter-very strong. Phylogenetic tree was constructed using MEGA6 software.

Mentions: An unrooted phylogenetic tree was constructed to infer group specific relationships of MAPKs. Upon phylogenetic analysis, all studied MAPK genes are fell into six different clusters, that are named according to the MAPK grouping of A. thaliana. In A. thaliana, MAPK genes are classified into four different groups (A, B, C, and D) based on their evolutionary relationship and presence of the T-D-Y and T-E-Y phosphorylation motif. In this study, MAPKs are categorized into six different groups namely group A (red), B (blue), C (pink), D (purple), E (teal) and F (green) (Figure 5, Additional file 5). Two new group of MAPK (group E and F) are generated during this analysis. The new group E and F are mainly shared by MAPKs of lower eukaryotic and gymnosperm plants such as CsubMPK7, MpMPK13, SmMPK10, CreinMPK7, VcMPK5, CsubMPK3, PaMPK10, PaMPK7-2, PaMPK5, PaMPK14, CreinMPK4-1, VcMPK4-1, OlMPK6, MpMPK4. The phylogenetic analysis revealed that 89, 128, 100, 258, 10 and 4 MAPKs fall into group A, B, C, D, E, and F respectively (Additional file 5, Table 5). The average overall phylogenetic mean distance of plant MAPK is 0.54 (standard error 0.029). During phylogenetic distance estimation, all the positions with less than 95% site coverage are eliminated. That is, fewer than 5% alignment gaps. The missing data and ambiguous bases are allowed at any position.Figure 5


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)

Phylogenetic tree of MAPK gene family in plants. Unrooted phylogenetic tree of MAPKs show presence of six different groups with well supported bootstrap values. We named them as group A (red), B (blue), C (pink), D (purple), E (teal) and F (green). The group E MAPKs are present at towards the end of the phylogenetic tree and group F present at the mid of the phylogenetic tree. Group E and F MAPKs are derived from lower plants of algae, pteridophytes and gymnosperm. Different MAPK genes falls in different groups are; group A (MPK3, MPK6, MPK10), group B (MPK4, MPK5, MPK11, MPK12, MPK13), group C (MPK1, MPK2, MPK7, MPK14), group D (MPK8, MPK9, MPK16, MPK17, MPK18, MPK19, MPK20 and MPK21), group E (CreinMPK7, CsubMPK3, PaMPK10, PaMPK7-2, PaMPK5, PaMPK14, CsubMPK7, MpMPK13, SmMPK10, VcMPK5) and group F (CreinMPK4-1, VcMPK4-1, OlMPK6, MpMPK4). The ERK1, ERK2, AtPIN1 (auxin efflux carrier) and AtCBL1 (calcineurin B like protein) were used as out group. Different statistical parameters used to constrcut the phylogenetic tree was: statistical method- maximum likelihood, test of phylogeny-boot strap method, no. of bootsrap replicate-2000, model/method-Jones-Taylor-Thornton (JTT) model, site coverage cutoff-95%, and branch swap filter-very strong. Phylogenetic tree was constructed using MEGA6 software.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Fig5: Phylogenetic tree of MAPK gene family in plants. Unrooted phylogenetic tree of MAPKs show presence of six different groups with well supported bootstrap values. We named them as group A (red), B (blue), C (pink), D (purple), E (teal) and F (green). The group E MAPKs are present at towards the end of the phylogenetic tree and group F present at the mid of the phylogenetic tree. Group E and F MAPKs are derived from lower plants of algae, pteridophytes and gymnosperm. Different MAPK genes falls in different groups are; group A (MPK3, MPK6, MPK10), group B (MPK4, MPK5, MPK11, MPK12, MPK13), group C (MPK1, MPK2, MPK7, MPK14), group D (MPK8, MPK9, MPK16, MPK17, MPK18, MPK19, MPK20 and MPK21), group E (CreinMPK7, CsubMPK3, PaMPK10, PaMPK7-2, PaMPK5, PaMPK14, CsubMPK7, MpMPK13, SmMPK10, VcMPK5) and group F (CreinMPK4-1, VcMPK4-1, OlMPK6, MpMPK4). The ERK1, ERK2, AtPIN1 (auxin efflux carrier) and AtCBL1 (calcineurin B like protein) were used as out group. Different statistical parameters used to constrcut the phylogenetic tree was: statistical method- maximum likelihood, test of phylogeny-boot strap method, no. of bootsrap replicate-2000, model/method-Jones-Taylor-Thornton (JTT) model, site coverage cutoff-95%, and branch swap filter-very strong. Phylogenetic tree was constructed using MEGA6 software.
Mentions: An unrooted phylogenetic tree was constructed to infer group specific relationships of MAPKs. Upon phylogenetic analysis, all studied MAPK genes are fell into six different clusters, that are named according to the MAPK grouping of A. thaliana. In A. thaliana, MAPK genes are classified into four different groups (A, B, C, and D) based on their evolutionary relationship and presence of the T-D-Y and T-E-Y phosphorylation motif. In this study, MAPKs are categorized into six different groups namely group A (red), B (blue), C (pink), D (purple), E (teal) and F (green) (Figure 5, Additional file 5). Two new group of MAPK (group E and F) are generated during this analysis. The new group E and F are mainly shared by MAPKs of lower eukaryotic and gymnosperm plants such as CsubMPK7, MpMPK13, SmMPK10, CreinMPK7, VcMPK5, CsubMPK3, PaMPK10, PaMPK7-2, PaMPK5, PaMPK14, CreinMPK4-1, VcMPK4-1, OlMPK6, MpMPK4. The phylogenetic analysis revealed that 89, 128, 100, 258, 10 and 4 MAPKs fall into group A, B, C, D, E, and F respectively (Additional file 5, Table 5). The average overall phylogenetic mean distance of plant MAPK is 0.54 (standard error 0.029). During phylogenetic distance estimation, all the positions with less than 95% site coverage are eliminated. That is, fewer than 5% alignment gaps. The missing data and ambiguous bases are allowed at any position.Figure 5

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