Hafiz Muhammad Rizwan , Jiayi He , Muhammad Bilal Arshad , Mingfu Wang
{"title":"大豆苯丙氨酸解氨酶基因的鉴定:基因组分析和在非生物胁迫下的表达分析","authors":"Hafiz Muhammad Rizwan , Jiayi He , Muhammad Bilal Arshad , Mingfu Wang","doi":"10.1016/j.stress.2025.100896","DOIUrl":null,"url":null,"abstract":"<div><div>Phenylalanine ammonia-lyase (PAL) is a critical enzyme in the phenylpropanoid pathway, playing essential roles in plant development and responses to environmental stresses. Despite its importance, an inclusive characterization of the <em>PAL</em> gene family in soybean (<em>Glycine</em> max) has yet to be fully explored. This study identified nine <em>PAL</em> genes within the soybean genome, which were randomly distributed across six chromosomes including Gm02, Gm03, Gm10, Gm13, Gm19 and Gm20. All genes comprised of Lyase_aromatic domain with different physicochemical properties. Phylogenetic analysis grouped <em>PAL</em> proteins into three main clades, with closeness to dicots species such as <em>Arabidopsis thaliana, Citrullus lanatus</em> and <em>Vitis vinifera. GmPAL</em> Gene structure analysis revealed 10 conserved motifs and 2 exons across all genes. <em>Cis</em>-regulatory element analysis highlighted key elements associated with plant growth and development (13 %), hormone signaling (36 %), light responsiveness (37 %), and stress responsiveness (14 %). Synteny analyses revealed 11 segmentally duplicated <em>GmPAL</em> genes, which underwent purifying selection. Furthermore, <em>GmPAL</em> collinearity analyses demonstrated significant homology with dicot species, suggesting a shared evolutionary origin and potential functional conservation. Protein-protein interaction and 3D modeling confirmed GmPAL proteins involvement in phenylpropanoid regulation. Furthermore, 89 gma-miRNAs from 32 different families were predicted that targeted all genes. TF analysis revealed significant associations in stress regulation. GO and KEGG analysis linked <em>GmPAL</em> genes to biological processes and the phenylpropanoid pathway. FPKM-based expression profiling revealed tissue-specific and stress-responsive expression patterns for <em>GmPAL</em> genes, under various conditions. Furthermore, qRT-PCR confirmed diverse expression of all <em>GmPAL</em> genes in soybean leaves under abiotic stresses under cold, heat, drought, salinity, metal ion toxicity, and hormone treatments. Notably, <em>GmPAL3/4/5</em> and <em>GmPAL7</em> were significantly upregulated under all stresses, while CdCl₂ uniquely upregulated all <em>GmPAL</em> gene expressions, highlighting their potential for soybean stress resilience studies. This comprehensive study provides valuable insights into the structure, evolution, and functional regulation of <em>GmPAL</em> genes, offering a foundation for future research and their potential application in improving soybean resilience to environmental stresses.</div></div>","PeriodicalId":34736,"journal":{"name":"Plant Stress","volume":"16 ","pages":"Article 100896"},"PeriodicalIF":6.8000,"publicationDate":"2025-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Characterization of phenylalanine ammonia-lyase genes in soybean: genomic insights and expression analysis under abiotic stress tolerance\",\"authors\":\"Hafiz Muhammad Rizwan , Jiayi He , Muhammad Bilal Arshad , Mingfu Wang\",\"doi\":\"10.1016/j.stress.2025.100896\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><div>Phenylalanine ammonia-lyase (PAL) is a critical enzyme in the phenylpropanoid pathway, playing essential roles in plant development and responses to environmental stresses. Despite its importance, an inclusive characterization of the <em>PAL</em> gene family in soybean (<em>Glycine</em> max) has yet to be fully explored. This study identified nine <em>PAL</em> genes within the soybean genome, which were randomly distributed across six chromosomes including Gm02, Gm03, Gm10, Gm13, Gm19 and Gm20. All genes comprised of Lyase_aromatic domain with different physicochemical properties. Phylogenetic analysis grouped <em>PAL</em> proteins into three main clades, with closeness to dicots species such as <em>Arabidopsis thaliana, Citrullus lanatus</em> and <em>Vitis vinifera. GmPAL</em> Gene structure analysis revealed 10 conserved motifs and 2 exons across all genes. <em>Cis</em>-regulatory element analysis highlighted key elements associated with plant growth and development (13 %), hormone signaling (36 %), light responsiveness (37 %), and stress responsiveness (14 %). Synteny analyses revealed 11 segmentally duplicated <em>GmPAL</em> genes, which underwent purifying selection. Furthermore, <em>GmPAL</em> collinearity analyses demonstrated significant homology with dicot species, suggesting a shared evolutionary origin and potential functional conservation. Protein-protein interaction and 3D modeling confirmed GmPAL proteins involvement in phenylpropanoid regulation. Furthermore, 89 gma-miRNAs from 32 different families were predicted that targeted all genes. TF analysis revealed significant associations in stress regulation. GO and KEGG analysis linked <em>GmPAL</em> genes to biological processes and the phenylpropanoid pathway. FPKM-based expression profiling revealed tissue-specific and stress-responsive expression patterns for <em>GmPAL</em> genes, under various conditions. Furthermore, qRT-PCR confirmed diverse expression of all <em>GmPAL</em> genes in soybean leaves under abiotic stresses under cold, heat, drought, salinity, metal ion toxicity, and hormone treatments. Notably, <em>GmPAL3/4/5</em> and <em>GmPAL7</em> were significantly upregulated under all stresses, while CdCl₂ uniquely upregulated all <em>GmPAL</em> gene expressions, highlighting their potential for soybean stress resilience studies. This comprehensive study provides valuable insights into the structure, evolution, and functional regulation of <em>GmPAL</em> genes, offering a foundation for future research and their potential application in improving soybean resilience to environmental stresses.</div></div>\",\"PeriodicalId\":34736,\"journal\":{\"name\":\"Plant Stress\",\"volume\":\"16 \",\"pages\":\"Article 100896\"},\"PeriodicalIF\":6.8000,\"publicationDate\":\"2025-05-18\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Plant Stress\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S2667064X25001642\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"PLANT SCIENCES\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Plant Stress","FirstCategoryId":"1085","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S2667064X25001642","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"PLANT SCIENCES","Score":null,"Total":0}
Characterization of phenylalanine ammonia-lyase genes in soybean: genomic insights and expression analysis under abiotic stress tolerance
Phenylalanine ammonia-lyase (PAL) is a critical enzyme in the phenylpropanoid pathway, playing essential roles in plant development and responses to environmental stresses. Despite its importance, an inclusive characterization of the PAL gene family in soybean (Glycine max) has yet to be fully explored. This study identified nine PAL genes within the soybean genome, which were randomly distributed across six chromosomes including Gm02, Gm03, Gm10, Gm13, Gm19 and Gm20. All genes comprised of Lyase_aromatic domain with different physicochemical properties. Phylogenetic analysis grouped PAL proteins into three main clades, with closeness to dicots species such as Arabidopsis thaliana, Citrullus lanatus and Vitis vinifera. GmPAL Gene structure analysis revealed 10 conserved motifs and 2 exons across all genes. Cis-regulatory element analysis highlighted key elements associated with plant growth and development (13 %), hormone signaling (36 %), light responsiveness (37 %), and stress responsiveness (14 %). Synteny analyses revealed 11 segmentally duplicated GmPAL genes, which underwent purifying selection. Furthermore, GmPAL collinearity analyses demonstrated significant homology with dicot species, suggesting a shared evolutionary origin and potential functional conservation. Protein-protein interaction and 3D modeling confirmed GmPAL proteins involvement in phenylpropanoid regulation. Furthermore, 89 gma-miRNAs from 32 different families were predicted that targeted all genes. TF analysis revealed significant associations in stress regulation. GO and KEGG analysis linked GmPAL genes to biological processes and the phenylpropanoid pathway. FPKM-based expression profiling revealed tissue-specific and stress-responsive expression patterns for GmPAL genes, under various conditions. Furthermore, qRT-PCR confirmed diverse expression of all GmPAL genes in soybean leaves under abiotic stresses under cold, heat, drought, salinity, metal ion toxicity, and hormone treatments. Notably, GmPAL3/4/5 and GmPAL7 were significantly upregulated under all stresses, while CdCl₂ uniquely upregulated all GmPAL gene expressions, highlighting their potential for soybean stress resilience studies. This comprehensive study provides valuable insights into the structure, evolution, and functional regulation of GmPAL genes, offering a foundation for future research and their potential application in improving soybean resilience to environmental stresses.
期刊介绍:
The journal Plant Stress deals with plant (or other photoautotrophs, such as algae, cyanobacteria and lichens) responses to abiotic and biotic stress factors that can result in limited growth and productivity. Such responses can be analyzed and described at a physiological, biochemical and molecular level. Experimental approaches/technologies aiming to improve growth and productivity with a potential for downstream validation under stress conditions will also be considered. Both fundamental and applied research manuscripts are welcome, provided that clear mechanistic hypotheses are made and descriptive approaches are avoided. In addition, high-quality review articles will also be considered, provided they follow a critical approach and stimulate thought for future research avenues.
Plant Stress welcomes high-quality manuscripts related (but not limited) to interactions between plants and:
Lack of water (drought) and excess (flooding),
Salinity stress,
Elevated temperature and/or low temperature (chilling and freezing),
Hypoxia and/or anoxia,
Mineral nutrient excess and/or deficiency,
Heavy metals and/or metalloids,
Plant priming (chemical, biological, physiological, nanomaterial, biostimulant) approaches for improved stress protection,
Viral, phytoplasma, bacterial and fungal plant-pathogen interactions.
The journal welcomes basic and applied research articles, as well as review articles and short communications. All submitted manuscripts will be subject to a thorough peer-reviewing process.