Structural, functional, and phylogenetic characterization of phosphoenolpyruvate carboxylase (PEPC) in C₄ and CAM plants

ABSTRACT

Phosphoenolpyruvate carboxylase (PEPC; EC 4.1.1.31) is an enzyme in the family of carboxylyases found in plants and some bacteria, but not in fungi or animals. In this study, bioinformatic characterization of PEPC enzyme was performed in protein sequences of 34 C₄ and CAM plants of 14 different families. In protein–protein interactions analysis by STRING 10 tool, 10 functional partners and enriched pathways were identified in Zea mays and other species. The functional and structural analyses were investigated by ProDom, ProtParam, SOPMA, Predotar 1.03, SignalP 4.1, TargetP 1.1, and TMHMM 2.0 tools in ExPASy database. Fifteen ProDom domains were common in selected plants while there was not any transmembrane helix in PEPC proteins. Tertiary structure was predicted by Phyre2 and TM-score servers, then their qualities were verified by SuperPose, PROCHECK, and ProSA-web servers. All the tertiary structure samples were estimated using “c1jqoA” model, with 100% confidence. In MEME and MAST analyses, four common conserved motifs were obtained in all C₄ and CAM plants. The protein sequences gwere aligned with ClustalW algorithm by MEGA 6.06 software and phylogenetic tree was constructed using the neighbor-joining (NJ) method and the bootstrap test carried out with 1000 replicates. Based on the phylogenetic relationships, PEPCs were divided into seven groups. According to the results, there is a high identity of PEPC in different species of C₄ and CAM plants so that they should be derived from a common ancestor. The results provide background of bioinformatic studies for the function and evolution of PEPC in other plants.

KEYWORDS:

• Bioinformatics
• phylogenetic analysis
• protein-protein interaction
• phosphoenolpyruvate carboxylase (PEPC)
• structural analysis

Disclosure statement

No potential conflict of interest was reported by the authors.