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Genome-wide identification and transcriptional expression analysis of mitogen-activated protein kinase and mitogen-activated protein kinase kinase genes in Capsicum annuum.

Liu Z, Shi L, Liu Y, Tang Q, Shen L, Yang S, Cai J, Yu H, Wang R, Wen J, Lin Y, Hu J, Liu C, Zhang Y, Mou S, He S - Front Plant Sci (2015)

Bottom Line: However, significant divergences were also found.Notably, five members of the pepper MAPKK family were much less conserved than those found in Arabidopsis, and 9 Arabidopsis MAPKs did not have orthologs in pepper.These results will facilitate future functional characterization of MAPK cascades in pepper.

View Article: PubMed Central - PubMed

Affiliation: National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University Fuzhou, China ; College of Plant Protection, Fujian Agriculture and Forestry University Fuzhou, China.

ABSTRACT
The tripartite mitogen-activated protein kinase (MAPK) signaling cascades have been implicated in plant growth, development, and environment adaptation, but a comprehensive understanding of MAPK signaling at genome-wide level is limited in Capsicum annuum. Herein, genome-wide identification and transcriptional expression analysis of MAPK and MAPK kinase (MAPKK) were performed in pepper. A total of 19 pepper MAPK (CaMAPKs) genes and five MAPKK (CaMAPKKs) genes were identified. Phylogenetic analysis indicated that CaMAPKs and CaMAPKKs could be classified into four groups and each group contains similar exon-intron structures. However, significant divergences were also found. Notably, five members of the pepper MAPKK family were much less conserved than those found in Arabidopsis, and 9 Arabidopsis MAPKs did not have orthologs in pepper. Additionally, 7 MAPKs in Arabidopsis had either two or three orthologs in the pepper genome, and six pepper MAPKs and one MAPKK differing in sequence were found in three pepper varieties. Quantitative real-time RT-PCR analysis showed that the majority of MAPK and MAPKK genes were ubiquitously expressed and transcriptionally modified in pepper leaves after treatments with heat, salt, and Ralstonia solanacearum inoculation as well as exogenously applied salicylic acid, methyl jasmonate, ethephon, and abscisic acid. The MAPKK-MAPK interactome was tested by yeast two-hybrid assay, the results showed that one MAPKK might interact with multiple MAPKs, one MAPK might also interact with more than one MAPKKs, constituting MAPK signaling networks which may collaborate in transmitting upstream signals into appropriate downstream cellular responses and processes. These results will facilitate future functional characterization of MAPK cascades in pepper.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic relationship among MAPK genes from pepper and Arabidopsis. The complete amino acid sequences of 19 pepper MAPKs and 20 Arabidopsis MAPKs were aligned using Clustal X, and the Maximum Likelihood tree was constructed using MEGA 6.0 with bootstrapping analysis (1000 replicates). The values above the branches are bootstrap support of 1000 replicates. Groups A–D indicate different gene clusters. To identify the plant species origin for each MAPK, a species acronym is included before the protein name: CaMAPK indicate MAPK from pepper and AtMAPK indicate MAPK from Arabidopsis. The green and red dots before the protein names indicate MAPKs from pepper and Arabidopsis, respectively.
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Figure 3: Phylogenetic relationship among MAPK genes from pepper and Arabidopsis. The complete amino acid sequences of 19 pepper MAPKs and 20 Arabidopsis MAPKs were aligned using Clustal X, and the Maximum Likelihood tree was constructed using MEGA 6.0 with bootstrapping analysis (1000 replicates). The values above the branches are bootstrap support of 1000 replicates. Groups A–D indicate different gene clusters. To identify the plant species origin for each MAPK, a species acronym is included before the protein name: CaMAPK indicate MAPK from pepper and AtMAPK indicate MAPK from Arabidopsis. The green and red dots before the protein names indicate MAPKs from pepper and Arabidopsis, respectively.

Mentions: To analyze the evolutionary relationships between different MAPK and MAPKK family members in pepper and Arabidopsis, full-length amino acid sequences of 19 MAPKs and five MAPKKs from pepper, and 20 MAPKs and 10 MAPKKs from Arabidopsis, were together subjected to a multiple sequence alignment using the MEGA 6.0 program. An unrooted phylogenetic tree was constructed, and the 19 MAPKs were divided into four groups (A, B, C, and D) based on their predicted amino acid sequences (Figure 3). The size of groups A and B appeared to be similar; whereas, the size of group D differed significantly between pepper and Arabidopsis. The group D gene family is the largest subfamily in rice, poplar, tomato, and apple (Chen et al., 2012; Zhang et al., 2013; Wang et al., 2015). The five MAPKKs in the pepper genome were also classified into four groups with the MAPKKs of Arabidopsis. Like the MAPKKs in tomato (Wu et al., 2014), two MAPKKs were classified into group A, and groups B, C, and D each had one MAPKK in pepper (Figure 4). Similar to MAPKs, the number of MAPKKs in group D differed greatly between pepper and Arabidopsis.


Genome-wide identification and transcriptional expression analysis of mitogen-activated protein kinase and mitogen-activated protein kinase kinase genes in Capsicum annuum.

Liu Z, Shi L, Liu Y, Tang Q, Shen L, Yang S, Cai J, Yu H, Wang R, Wen J, Lin Y, Hu J, Liu C, Zhang Y, Mou S, He S - Front Plant Sci (2015)

Phylogenetic relationship among MAPK genes from pepper and Arabidopsis. The complete amino acid sequences of 19 pepper MAPKs and 20 Arabidopsis MAPKs were aligned using Clustal X, and the Maximum Likelihood tree was constructed using MEGA 6.0 with bootstrapping analysis (1000 replicates). The values above the branches are bootstrap support of 1000 replicates. Groups A–D indicate different gene clusters. To identify the plant species origin for each MAPK, a species acronym is included before the protein name: CaMAPK indicate MAPK from pepper and AtMAPK indicate MAPK from Arabidopsis. The green and red dots before the protein names indicate MAPKs from pepper and Arabidopsis, respectively.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4585111&req=5

Figure 3: Phylogenetic relationship among MAPK genes from pepper and Arabidopsis. The complete amino acid sequences of 19 pepper MAPKs and 20 Arabidopsis MAPKs were aligned using Clustal X, and the Maximum Likelihood tree was constructed using MEGA 6.0 with bootstrapping analysis (1000 replicates). The values above the branches are bootstrap support of 1000 replicates. Groups A–D indicate different gene clusters. To identify the plant species origin for each MAPK, a species acronym is included before the protein name: CaMAPK indicate MAPK from pepper and AtMAPK indicate MAPK from Arabidopsis. The green and red dots before the protein names indicate MAPKs from pepper and Arabidopsis, respectively.
Mentions: To analyze the evolutionary relationships between different MAPK and MAPKK family members in pepper and Arabidopsis, full-length amino acid sequences of 19 MAPKs and five MAPKKs from pepper, and 20 MAPKs and 10 MAPKKs from Arabidopsis, were together subjected to a multiple sequence alignment using the MEGA 6.0 program. An unrooted phylogenetic tree was constructed, and the 19 MAPKs were divided into four groups (A, B, C, and D) based on their predicted amino acid sequences (Figure 3). The size of groups A and B appeared to be similar; whereas, the size of group D differed significantly between pepper and Arabidopsis. The group D gene family is the largest subfamily in rice, poplar, tomato, and apple (Chen et al., 2012; Zhang et al., 2013; Wang et al., 2015). The five MAPKKs in the pepper genome were also classified into four groups with the MAPKKs of Arabidopsis. Like the MAPKKs in tomato (Wu et al., 2014), two MAPKKs were classified into group A, and groups B, C, and D each had one MAPKK in pepper (Figure 4). Similar to MAPKs, the number of MAPKKs in group D differed greatly between pepper and Arabidopsis.

Bottom Line: However, significant divergences were also found.Notably, five members of the pepper MAPKK family were much less conserved than those found in Arabidopsis, and 9 Arabidopsis MAPKs did not have orthologs in pepper.These results will facilitate future functional characterization of MAPK cascades in pepper.

View Article: PubMed Central - PubMed

Affiliation: National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University Fuzhou, China ; College of Plant Protection, Fujian Agriculture and Forestry University Fuzhou, China.

ABSTRACT
The tripartite mitogen-activated protein kinase (MAPK) signaling cascades have been implicated in plant growth, development, and environment adaptation, but a comprehensive understanding of MAPK signaling at genome-wide level is limited in Capsicum annuum. Herein, genome-wide identification and transcriptional expression analysis of MAPK and MAPK kinase (MAPKK) were performed in pepper. A total of 19 pepper MAPK (CaMAPKs) genes and five MAPKK (CaMAPKKs) genes were identified. Phylogenetic analysis indicated that CaMAPKs and CaMAPKKs could be classified into four groups and each group contains similar exon-intron structures. However, significant divergences were also found. Notably, five members of the pepper MAPKK family were much less conserved than those found in Arabidopsis, and 9 Arabidopsis MAPKs did not have orthologs in pepper. Additionally, 7 MAPKs in Arabidopsis had either two or three orthologs in the pepper genome, and six pepper MAPKs and one MAPKK differing in sequence were found in three pepper varieties. Quantitative real-time RT-PCR analysis showed that the majority of MAPK and MAPKK genes were ubiquitously expressed and transcriptionally modified in pepper leaves after treatments with heat, salt, and Ralstonia solanacearum inoculation as well as exogenously applied salicylic acid, methyl jasmonate, ethephon, and abscisic acid. The MAPKK-MAPK interactome was tested by yeast two-hybrid assay, the results showed that one MAPKK might interact with multiple MAPKs, one MAPK might also interact with more than one MAPKKs, constituting MAPK signaling networks which may collaborate in transmitting upstream signals into appropriate downstream cellular responses and processes. These results will facilitate future functional characterization of MAPK cascades in pepper.

No MeSH data available.


Related in: MedlinePlus