Abstract
Phosphoenolpyruvate carboxylase (PEPC) genes have multiple potential roles in plant metabolism such as regulation and accumulation of organic acids in fruits, movement of guard cells and stress tolerance, etc. However, the systematic identification and characterization of PEPC genes in Rosaceae species i.e., loquat, apple, peach, strawberry, and pear are yet to be performed. In present study, 27 putative PEPC genes (loquat 4, apple 6, peach 3, strawberry 9, and pear 5) were identified. To further investigate the role of those PEPC genes, comprehensive bioinformatics and expression analysis were performed. In bioinformatic analysis, the physiochemical properties, conserved domains, gene structure, conserved motif, phylogenetic and syntenic analysis of PEPC genes were performed. The result revealed that the PEPcase superfamily domain was conserved in all examined PEPC proteins. Most of the PEPC proteins were predicted to be localized in cytonuclear. Genomic structural and motif analysis showed that the exon and motif number of each PEPC gene ranged dramatically, from 8 to 20, and 7 to 10, respectively. Syntenic analysis indicated that the segmental or whole-genome duplication played a vital role in extension of PEPC gene family in Rosacea species. The Ka and Ks values of duplicated genes depicted that PEPC genes have undergone a strong purifying selection. Furthermore, the expression analysis of PEPC genes in root, mature leaf, stem, full-bloom flower, and ripened fruit of loquat, apple, peach, strawberry, and pear was performed. Some genes were differentially expressed in aforementioned plant tissues, signifying their role in plant metabolism. This study provides the first genome-wide identification, characterization, and expression profiling of PEPC gene family in Rosaceae species, and provides the foundation for further functional analysis.
Highlights
Phosphoenolpyruvate (PEP) carboxylase (PEPC) enzyme can be widely found among bacteria, archaea, green algae, cyanobacteria, protozoa, and vascular plants, while absent in animals and fungi cells [1,2]
We characterized the general information of 27 PEPCs in Table 3, which shows the biochemical and physiological characteristics of respective proteins
27 PEPC genes were identified in five Rosaceae species i.e., loquat, apple, peach, strawberry, and pear
Summary
Phosphoenolpyruvate (PEP) carboxylase (PEPC) enzyme can be widely found among bacteria, archaea, green algae, cyanobacteria, protozoa, and vascular plants, while absent in animals and fungi cells [1,2]. PEPC is used in the primary fixation reaction for photosynthetic CO2 assimilation in C4 photosynthesis as well as crassulacean acid metabolism (CAM); which take place in mesophyll cells in the presence of bicarbonate (HCO3−) and Mg2+ to catalyze an irreversible β-carboxylation reaction of PEP to produce oxaloacetate (OAA) and inorganic phosphate (Pi) [1]. Besides its central role in atmospheric CO2 fixation during photosynthesis, PEPC is known to have a wide range of non-photosynthetic activities, such as carbon-nitrogen interaction support and fruit ripening [2], seed germination and formation [2,3], and controlling guard cell metabolism for better stomatal functioning [4]. The metabolic functions of PEPC gene family have rarely been reported in the Rosaceae
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