Genome-wide analysis of the pectin acetylesterase (PAE) gene family in tomato and SlPAE16 functional characterization associated with pedicel abscission.
The identified SlPAE genes were classified phylogenetically into three conserved subfamilies, with branch members sharing domain architectures, motifs, and genomic structure, providing a much-needed framework for future research into their specific biological roles in tomatoes.
Abstract
Pectin acetylesterase (PAE) regulates pectin acetylation, which affects plant growth, development, and stress tolerance. While their functions are well-defined in models like Arabidopsis, we still know surprisingly little about how they operate in tomatoes (Solanum lycopersicum). We identified 17 SlPAE genes using tomato genome-wide analysis. These genes were classified phylogenetically into three conserved subfamilies, with branch members sharing domain architectures, motifs, and genomic structure. Promoter cis-element analysis identified multiple motifs related to hormone signaling, light response, and stress response. Spatiotemporal expression patterns obtained via qRT-PCR revealed the functional roles of SlPAE genes. Notably, silencing SlPAE16 effectively retarded pedicel abscission, a process mediated by the inhibition of TAPG1/2/4 expression. These findings clarify the functional diversity within the PAE gene family, providing a much-needed framework for future research into their specific biological roles in tomatoes.
Together, these findings provide a foundation for functional characterization and useful information for future research on the role of SlPHD family members in plant abiotic stress tolerance.
Tayeb Muhammad, Tao Yang, Haitao Yang et al.· Planta· 0 citations
BACKGROUND
AINTEGUMENTA-LIKE (AIL) transcription factors belong to the APETALA2/ethylene-responsive factor (AP2/ERF) superfamily and play critical roles in plant growth and development. Although their functions have been characterized in several model and crop species, systematic knowledge of the AIL family in maize remains limited.
RESULTS
Here, we performed a genome-wide identification of the maize AIL family and uncovered nine ZmAIL genes. These genes are asymmetrically distributed across six chromosomes and exhibit highly conserved gene and protein structures. Phylogenetic analysis grouped them into two clades: the ZmANT clade (ZmANT1-4) and the ZmAIL clade (ZmAIL1-5). Synteny analysis revealed that ZmAIL genes are more closely related to AIL genes from monocots than to those from dicots. Analysis of promoter cis-acting elements and expression profiles indicated that ZmAIL genes respond to environmental, hormonal, and developmental cues. Their expression patterns fall into two main categories: constitutively expressed and tissue-specific. Phenotypic analysis of a zmant1 mutant showed that ZmANT1 negatively regulates maize leaf length. Further experiments demonstrated that ZmANT1 directly binds to a specific cis-acting element in the promoters of target genes and regulates their expression, including four other ZmAIL members, thereby influencing multiple developmental pathways.
CONCLUSION
Overall, this study systematically identifies the maize AIL family and suggests a role for ZmANT1 in restricting leaf elongation. Our results provide a resource for future AIL functional studies and offer insights into the genetic mechanisms of leaf development in maize.
Dusheng Lu, Xitong Xu, Yancui Wang et al.· BMC Plant Biology· 0 citations
Clubroot, caused by the obligate biotrophic protist Plasmodiophora brassicae (P. brassicae), is a destructive soil-borne disease that severely threatens the production of radish (Raphanus sativus L.). Although chitinases are known to execute critical defense functions by degrading pathogen chitin, a comprehensive genome-wide characterization of the radish chitinase (RsChi) gene family and its specific role in clubroot resistance remains lacking. Here, we systematically identified 24 RsChi genes in the radish genome, characterizing their chromosomal distribution, structural organization, and promoter regulatory networks. These genes are unevenly distributed across seven chromosomes and cluster into four subfamilies, with tandem duplication driving family expansion, particularly on Chromosome 3. Promoter analysis revealed a significant enrichment of jasmonic acid- and abscisic acid-responsive cis-elements, implicating RsChi genes in hormone-mediated defense signaling. Using qRT-PCR to profile expression dynamics during P. brassicae infection across contrasting radish lines, we identified strong genotype- and stage-specific transcriptional responses. Notably, TRs0x1c000780 remained transcriptionally silent prior to infection but was specifically induced over 10-fold in the resistant line at 28 days post-inoculation. This infection-triggered induction positions TRs0x1c000780 as a promising candidate defense gene. Together, these findings provide structural and functional insights into the RsChi family and highlight candidate targets for breeding clubroot-resistant radish cultivars.
Zhi-Jie Liu, T. Hu, Min-Yan Mai et al.· International Journal of Mol...· 0 citations
Sucrose non-fermenting-1-related protein kinase (SnRK) is a plant serine/threonine kinase that mediates stress signaling, yet its function in the mangrove Avicennia marina remains unexplored. In this study, we identified 46 SnRK genes in A. marina, classifying them into three subfamilies with high phylogenetic conservation. Family expansion occurred mainly through 20 segmental duplication events under purifying selection (Ka/Ks < 1). Promoter regions were enriched in stress- and hormone-responsive elements, and expression profiling showed distinct tissue-specific and stress-responsive patterns. Our study specifically focused on the functional characterization of AmSnRK2.7. AmSnRK2.7-overexpressed Arabidopsis thaliana increases salt tolerance by altering the expression of ion transport genes and mediating Na+ efflux from the roots. Further investigation revealed that AmSnRK2.7 interacts with and phosphorylates AmENO2 (enolase, a key enzyme in the glycolysis pathway). Meanwhile, measurements of ATP content in wild type, AmSnRK2.7-overexpressed Arabidopsis lines and the atsnrk2.6 (homologous gene of AmSnRK2.7 in A. thaliana) mutant confirm that the AmSnRK2.7-AmENO2 module can affect the energy-driven Na+ efflux. Our findings provide key insights into the role of SnRK gene family in mangrove adaptation to saline intertidal habitat, and suggest AmSnRK2.7-AmENO2 module plays a role in salt tolerance.
Jin-Yu Liu, Yudan Xiang, Lingyu Song et al.· Plant, Cell and Environment· 0 citations
GDSL esterase/lipases (GELPs) are important regulators of plant growth and development, lipid metabolism, and stress responses. However, their genomic characteristics and expression patterns have not been systematically characterized for Juglans mandshurica, a woody oil crop species of significant ecological and economic value. Here, we identified 61 JmGELP genes in J. mandshurica through genome-wide analysis. Phylogenetic analysis classified them into seven major clades, and variations in gene structure and conserved motifs suggested potential functional divergence. Promoter cis-acting element analysis revealed widespread enrichment of motifs responsive to light, phytohormones, and abiotic stresses. Transcriptomic sequencing and qRT-PCR validation revealed distinct tissue-specific and seed development stage-specific expression patterns of JmGELP members, as well as their differential responses to various stress and hormone treatments. Gene Ontology (GO) annotation and protein–protein interaction (PPI) network analyses further supported their involvement in lipid metabolism. In silico analyses of transcription factor binding sites, miRNA targets, and molecular docking predicted that JmGELP-3, -38, and -41 have distinct transcriptional and post-transcriptional regulatory networks and potentially divergent substrate preferences. This study provides the first comprehensive characterization of the GELP family in J. mandshurica, identifying candidate genes that may inform future germplasm improvement and stress-resistance breeding in Juglans species.
Meng Dang, Rui Wang, Zhenlin Shen et al.· International Journal of Mol...· 0 citations
BACKGROUND
Fusarium wilt is among the most destructive diseases threatening global banana production and severely undermines the industry's sustainability. GDSL-type esterase/lipase proteins (GELPs) are lipid-hydrolyzing enzymes with diverse substrate specificities that catalyze the generation and transduction of lipid-derived signals, playing key roles in plant defense responses.
RESULTS
Here, we systematically identified members of the GELP gene family in the banana genome and conducted an integrated analysis of their phylogeny, gene structures, and promoter cis-elements. After manual correction of incorrectly annotated gene structures, a total of 92 MaGELP genes were identified and found to be unevenly distributed across 11 chromosomes, with most located near chromosome ends. Phylogenetic analysis combined with collinearity evidence indicated that the family is evolutionarily conserved. Promoter analysis revealed an enrichment of cis-elements associated with light responsiveness and MeJA-mediated signaling. Expression profiling showed that MaGELP81 is strongly up-regulated (fold change > 1.5) by infection with Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) and by SA, JA, and ET treatments, with pronounced differential expression between resistant and susceptible cultivars (fold change > 1.6). Subcellular localization assays demonstrated that MaGELP81 resides at the vacuolar membrane. When MaGELP81 was overexpressed in Arabidopsis thaliana, three independent high-expression lines exhibited better growth after Foc TR4 inoculation and significantly reduced disease incidence, severity scores, and disease index compared with the wild type, suggesting that MaGELP81 may be associated with enhanced resistance to Foc TR4.
CONCLUSION
Collectively, this study provides a comprehensive view of the composition and evolutionary features of the banana GELP family, elucidates their potential roles in responses to Foc TR4 stress, and pinpoints MaGELP81 as a key candidate gene. These findings offer foundational insight into the molecular interplay between lipid metabolism and plant immune signaling and provide valuable genetic resources for the molecular breeding of Foc TR4-resistant banana.
