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

Abstract

BackgroundMitogen 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.ResultsA 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.ConclusionWe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1244-7) contains supplementary material, which is available to authorized users.

Comprehensive transcriptome analysis provides new insights into nutritional strategies and phylogenetic relationships of chrysophytes

“…Additional signal transduction pathways and pathways from the sensory system (phototransduction) are possibly also engaged in environmental information processing. MAPK family members have been identified in lower eukaryotes such as Chlamydomonas reinhardtii and are known to be important signaling molecules that perceive various signals and transduce them for active responses to changing environmental conditions (Mohanta et al, 2015). We conclude from the presence of orthologous genes from these pathways that similar functions might be performed in heterotrophic chrysophytes and explain the higher motility of heterotrophic chrysophytes that have to sense and find bacterial food.…”

Context Specificity of Stress-activated Mitogen-activated Protein (MAP) Kinase Signaling: The Story as Told by Caenorhabditis elegans

“…1). The TQY motif is unique to nematodes and several plant species (14,15). C. elegans homologs of stress MAPKKs include four groups, those similar to MKK7 (mek-1, jkk-1), MKK4 (mkk-4, sek-3, sek-6), MKK3/6 (sek-1), and MKK3 (sek-4, sek-5).…”

Novel Genomic and Evolutionary Insight of WRKY Transcription Factors in Plant Lineage

“…Therefore, we identified and analysed the WRKY TF gene family members from 43 different plant species. All identified WRKY TFs were assigned a specific name according to the orthology based nomenclature system55565758. Providing a unique name to every gene is necessary for its future identification.…”

“…In general, the sequences that are highly similar tend to fall into the same group as far as orthology-based similarity is concerned5556. The orthology based nomenclature system of WRKY TFs has the potential to overcome this problem; therefore, we developed an unique nomenclature system to all WRKY TFs of 43 species555658. In total, 3035 WRKY TF genes from the 43 species were identified and classified according to the unique naming system (Supplementary Table 1).…”

“…Nomenclature of the WRKY TFs was assigned according to an orthology-based nomenclature system proposed by different researchers555689. In the nomenclature system, names were assigned by considering the first letter of the genus in upper case and the first letter of the species in lower case followed by the WRKY and orthology-based number of A. thaliana or O. sativa .…”