Phenylalanine ammonia-lyase (PAL) is the core branch-point enzyme connecting plant primary aromatic amino acid metabolism to the phenylpropanoid pathway, which determines carbon flux redistribution between growth and defense and is essential for plant adaptation to various environments. Extensive research has clarified PAL’s conserved homotetrameric structure, MIO cofactor-dependent catalytic mechanism, and its roles in plant growth, development, and stress responses. However, there is a lack of comprehensive review studies focusing on PAL-mediated carbon metabolic flux redistribution, specifically covering its structural and evolutionary foundations, the links between this flux regulation and plant growth/development, its multi-layered regulatory network, and its roles in stress adaptation, limiting a comprehensive understanding of its evolutionary and functional diversity. This review systematically covers four core aspects: first, the molecular foundation, encompassing PAL’s structural features and catalytic specificity governed by the MIO cofactor; second, evolutionary diversity spanning from algae to angiosperms, with emphasis on unique regulatory mechanisms and evolutionary significance across lineages; third, the multi-layered regulatory network, integrating transcriptional control, post-translational modifications, epigenetic regulation, and functional crosstalk with phytohormones; and fourth, functional dynamics, which elaborate PAL’s roles in organ development, including root lignification, stem mechanical strength, leaf photoprotection, flower and fruit quality formation, and lifecycle-wide dynamic expression, as well as its mediated stress adaptations and regulatory networks under combined stresses. These insights provide a theoretical basis for targeted manipulation of PAL to optimize crop carbon allocation, thus improving growth performance, enhance stress resilience, and promote sustainable agriculture.

Background: Ca²⁺ played as a ubiquitous secondary messenger involved in plant growth, development, and responses to various environmental stimuli. Calcium-dependent protein kinases (CDPK) were important Ca²⁺ sensors, which could directly translate Ca²⁺ signals into downstream phosphorylation signals. Considering the importance of CDPKs as Ca²⁺ effectors for regulation of plant stress tolerance and few studies on Brachypodium distachyon were available, it was of interest for us to isolate CDPKs from B. distachyon. Results: A systemic analysis of 30 CDPK family genes in B. distachyon was performed. Results showed that all BdCDPK family members contained conserved catalytic Ser/Thr protein kinase domain, autoinhibitory domain, and EF-hand domain, and a variable N-terminal domain, could be divided into four subgroup (I-IV), based upon sequence homology. Most BdCDPKs had four EF-hands, in which EF2 and EF4 revealed high variability and strong divergence from EF-hand in AtCDPKs. Synteny results indicated that large number of syntenic relationship events existed between rice and B. distachyon, implying their high conservation. Expression profiles indicated that most of BdCDPK genes were involved in phytohormones signal transduction pathways and regulated physiological process in responding to multiple environmental stresses. Moreover, the co-expression network implied that BdCDPKs might be both the activator and the repressor involved in WRKY transcription factors or MAPK cascade genes mediated stress response processes, base on their complex regulatory network. Conclusions: BdCDPKs might play multiple function in WRKY or MAPK mediated abiotic stresses response and phytohormone signaling transduction in B. distachyon. Our genomics analysis of BdCDPKs could provide fundamental information for further investigation the functions of CDPKs in integrating Ca²⁺ signalling pathways in response to environments stresses in B. distachyon.

WRKY transcription factors (TFs), which are plant-specific TFs, play significant roles in plant defense. Here, a pathogen-induced WRKY gene, named AktWRKY12, which was the homologous gene of AtWRKY12, was isolated from Akebia trifoliata. The AktWRKY12 gene has a total length of 645 nucleotides and an open reading frame (ORF) encoding 214 amino acid polypeptides. The characterizations of AktWRKY12 were subsequently performed with the ExPASy online tool Compute pI/Mw, PSIPRED and SWISS-MODEL softwares. The AktWRKY12 could be classified as a member of WRKY group II-c TFs based on sequence alignment and phylogenetic analysis. The results of tissue-specific expression analysis revealed that the AktWRKY12 gene was expressed in all the tested tissues, and the highest expression level was detected in A. trifoliata leaves. Subcellular localization analysis showed that AktWRKY12 was a nuclear protein. Results showed that the expression level of AktWRKY12 significantly increased in A. trifoliata leaves with pathogen infection. Furthermore, heterologous over-expression of AktWRKY12 in tobacco resulted in suppressed expression of lignin synthesis key enzyme genes. Based on our results, we speculate that AktWRKY12 might play a negative role in A. trifoliata responding to biotic stress by regulating the expression of lignin synthesis key enzyme genes during pathogen infection.

GT factors play critical roles in plant growth and development and in response to various environmental stimuli. Considering the new functions of GT factors on the regulation of plant stress tolerance and seeing as few studies on Brachypodium distachyon were available, we identified GT genes in B. distachyon, and the gene characterizations and phylogenies were systematically analyzed. Thirty-one members of BdGT genes were distributed on all five chromosomes with different densities. All the BdGTs could be divided into five subfamilies, including GT-1, GT-2, GTγ, SH4, and SIP1, based upon their sequence homology. BdGTs exhibited considerably divergent structures among each subfamily according to gene structure and conserved functional domain analysis, but the members within the same subfamily were relatively structure-conserved. Synteny results indicated that a large number of syntenic relationship events existed between rice and B. distachyon. Expression profiles indicated that the expression levels of most of BdGT genes were changed under abiotic stresses and hormone treatments. Moreover, the co-expression network exhibited a complex regulatory network between BdGTs and BdWRKYs as well as that between BdGTs and BdMAPK cascade gene. Results showed that GT factors might play multiple functions in responding to multiple environmental stresses in B. distachyon and participate in both the positive and negative regulation of WRKY- or MAPK-mediated stress response processes. The genome-wide analysis of BdGTs and the co-regulation network under multiple stresses provide valuable information for the further investigation of the functions of BdGTs in response to environment stresses.

The tea geometrid (Ectropis grisescens) is a significant pest in Chinese tea plantations. Although Metarhizium anisopliae serves as an environmentally friendly biocontrol agent against E. grisescens, the molecular mechanisms underlying the insect’s immune response remain unclear. This study investigates changes in immunity-related genes and metabolites in E. grisescens larvae infected with a virulent strain of M. anisopliae through transcriptome sequencing and metabolome analysis. We identified 2409 differentially expressed genes (DEGs) at 48 h post-infection, with 1611 genes up-regulated. GO analysis revealed that 119 DEGs were significantly enriched in immune-related processes. Additionally, 1860 differentially accumulated metabolites (DAMs) were detected, including 652 up-regulated and 1208 down-regulated metabolites, with 236 significantly enriched in 82 KEGG pathways. These findings indicate the activation of immunity-related and detoxifying enzyme-related genes, providing new insights into the physiological and biochemical responses of insects to biopesticides and potential targets for controlling tea geometrid.

Chrysanthemum morifolium, a perennial herb of the genus Chrysanthemum (Asteraceae), is highly valued for its ornamental, edible and medicinal properties, primarily attributed to its abundant flavonoids. Phenylalanine ammonia-lyase (PAL) is the rate-limiting enzyme initiating the phenylpropanoid pathway, which synthesizes lignin, flavonoids, and phytoalexins, key metabolites for plant growth, development, and stress adaptation. Despite the availability of the chromosome-level C. morifolium genome, the PAL gene family remains insufficiently characterized. Specifically, the expression patterns of CmPAL genes across floral developmental stages, floret types, and various abiotic stresses have not been elucidated. In this study, 19 CmPAL genes were identified from C. morifolium. Systematic analyses of their molecular evolutionary characteristics, including gene/protein structures, chromosomal localization, phylogenetic relationships, and genome-wide synteny were performed. CmPAL genes were found to be unevenly distributed across 8 of 27 chromosomes, and phylogenetically clustered members exhibited similar gene/protein structures, reflecting evolutionary conservation and functional importance. Expression profiles revealed that CmPAL genes were preferentially expressed in ray florets and at the color-emerging/blooming stages, indicating their involvement in floral pigmentation. Additionally, several CmPALs were significantly upregulated/downregulated under cold, salt, drought, and heavy metal stresses, suggesting roles in abiotic stress responses. This study provides a comprehensive characterization and expression profiles of the C. morifolium PAL gene family. These findings provide a valuable genomic resource for functional studies of CmPAL genes, as well as identify candidate genes for molecular breeding to improving flower quality and environmental adaptability of chrysanthemums. Specifically, CmPAL1, 6, 11, and 13 are prioritized as major candidate genes for floral pigmentation, while CmPAL3, 5, 9, 10, and 15 are highlighted for their broad-spectrum stress adaptation roles.