Genome-Wide Identification and Expression Analysis of the PME and PMEI Gene Families in Diospyros kaki: A Bioinformatics Study

Abstract

Pectins are major components of cell walls in plants. Pectin methylesterases (PMEs) and pectin methylesterase inhibitors (PMEIs) play crucial roles in pectin synthesis and metabolism. Overall, 28 putative DkPMEs and 29 putative DkPMEIs were identified from the D. kaki genome. According to phylogenetic analysis, DkPME/DkPMEI proteins can be classified into four and five clades, respectively. Motif and gene structure analysis showed that DkPME/DkPMEI are highly conserved in the same clades, which indicates that the function of these DkPME/DkPMEI were similar. Besides, DkPME/DkPMEI genes were distributed unevenly on their corresponding chromosomes. Synteny analysis showed that PME or PMEI gene usually matched with more than one DkPME/DkPMEI in D. oleifera, D. lotus, and A. thaliana, implying that the function of these genes in D. kaki may be diverse. Expression analysis showed that DkPME/DkPMEI from the same clade exhibited diverse expression patterns, indicating that these genes might have diverse functions. Functional protein–protein interaction network analysis showed that DkPMEI21 and DkPMEI15 were core nodes and were, respectively, positive and negative regulators for carbohydrate metabolism, stress responses, and sugar signaling. This study provides a theoretical basis for the functional characteristics, evolutionary relationship, and role of these gene families in developing persimmon fruit.

Pectin-Degrading Enzymes during Soursop (Annona muricata L.) Fruit Ripening: A Bioinformatics Approach

“…On the other hand, due to the dual function of PME, it is important to control their activity in the fruit ripening process; therefore, there are PME inhibitors (PMEis), which bind to PME and regulate its activity [5]. Regarding the PMEis, 39 isoenzymes were found, and these genes have been reported in other plants, such as Arabidopsis thaliana with 78 genes and in white pear (Pyrus bretschneideri) with 42 genes [29,30].…”

“…Pectins are structurally very complex polysaccharides that play an important role in cell adhesion. These are mainly composed of homogalacturonans (HGs), xylogalacturonan (XGA), rhamnogalacturonan-I (RG-I), and rhamnogalacturonan-II (RG-II) [5]. This pectin matrix undergoes modifications that impact the mechanical properties of the cell wall, primarily in HG, in which a group of enzymes is involved [6,7].…”