Abstract
In pectin regulation, polygalacturonases (PGs) and pectin methylesterases (PMEs) are critical components in the transformation, disassembly network, and remodeling of plant primary cell walls. In the current study, we identified 36 PG and 47 PME genes using the available genomic resources of grapevine. Herein, we provide a comprehensive overview of PGs and PMEs, including phylogenetic and collinearity relationships, motif and gene structure compositions, gene duplications, principal component analysis, and expression profiling during developmental stages. Phylogenetic analysis of PGs and PMEs revealed similar domain composition patterns with Arabidopsis. The collinearity analysis showed high conservation and gene duplications with purifying selection. The type of duplications also varied in terms of gene numbers in PGs (10 dispersed, 1 proximal, 12 tandem, and 13 segmental, respectively) and PMEs (23 dispersed, 1 proximal, 16 tandem, and 7 segmental, respectively). The tissue-specific response of PG and PME genes based on the reported transcriptomic data exhibited diverged expression patterns in various organs during different developmental stages. Among PGs, VvPG8, VvPG10, VvPG13, VvPG17, VvPG18, VvPG19, VvPG20, VvPG22, and VvPG23 showed tissue- or organ-specific expression in majority of the tissues during development. Similarly, in PMEs, VvPME3, VvPME4, VvPME5, VvPME6, VvPME19, VvPME21, VvPME23, VvPME29, VvPME31, and VvPME32 suggested high tissue-specific response. The gene ontology (GO), Kyoto Encyclopedia of Genes and Genomics (KEGG) enrichment, and cis-elements prediction analysis also suggested the putative functions of PGs and PMEs in plant development, such as pectin and carbohydrate metabolism, and stress activities. Moreover, qRT-PCR validation of 32 PG and PME genes revealed their role in various organs of grapevines (i.e., root, stem, tendril, inflorescence, flesh, skins, and leaves). Therefore, these findings will lead to novel insights and encourage cutting-edge research on functional characterization of PGs and PMEs in fruit crop species.
Highlights
Plant cell walls are mainly composed of various interacting networks of carbohydrate polymers, such as polymers of cellulose, hemicellulose, and pectins [1]
A total of 36 PG and 47 pectin methylesterases (PMEs) genes were identified from the grapevine genome through orthologues analysis with Arabidopsis (Table S1)
The coding sequence length of these genes varied from 999–3702 bp for PGs and 768–2463 bp for PMEs, while the protein length ranged from 332–1233 aa for PGs and 255–820 aa for PMEs, respectively
Summary
Plant cell walls are mainly composed of various interacting networks of carbohydrate polymers, such as polymers of cellulose, hemicellulose, and pectins [1]. Polygalacturonase (PGs; EC 3.2.1.15) hydrolytic enzymes are involved in plant organ cell separation events, reproductive developments, leaf morphology, and organ shedding [4,5,6,7]. Expression profiling, both at a temporal and spatial level, has revealed that transcript accumulations are responsible for cell wall softening during abscission, ripening, and dehiscence [8]. The softening of fruits is regulated by Pc-PG1 and Pc-PG2 as well as MaPG3 and MaPG4, in an ethylene-dependent pattern [16,17]
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