Genome-Wide Characterization and Expression Analysis of CsPALs in Cucumber ( L.) Reveal Their Potential Roles in Abiotic Stress and Aphid Stress Tolerance

Overview

Journal Plants (Basel)

Date 2024 Sep 28

PMID 39339512

Authors

Jieni Gu

Hamza Sohail

Lei Qiu

Chaoyan Chen

Haoyu Yue

Ziyi Li

Xiaodong Yang

Lili Zhang

Affiliations

Soon will be listed here.

Abstract

Phenylalanine ammonia lyase (PAL) is a pivotal enzyme in the phenylalanine metabolic pathway in plants and has a crucial role in the plant's response to environmental stress. Although the PAL family has been widely studied in many plant species, limited is known about its particular role in cucumbers under stress. We investigated the physicochemical properties, gene structure, gene duplication events, conserved motifs, cis-acting elements, protein interaction networks, stress-related transcriptome data, and quantitatively validated key stress-related genes. The main results indicated that 15 genes were grouped into four clades: I, II, and III when arranged in a phylogenetic tree of genes in angiosperms. The analysis of the promoter sequence revealed the presence of multiple cis-acting elements related to hormones and stress responses in the cucumber genes (). The analysis of protein interaction networks suggested that CsPAL1 interacts with eight other members of the PAL family through CsELI5 and CsHISNA, and directly interacts with multiple proteins in the 4CL family. Further investigation into the expression patterns of genes in different tissues and under various stress treatments (NaCl, Cu, Zn, PEG6000, aphids) demonstrated significant differential expression of across cucumber tissues. In summary, our characterization of the family offers valuable insights and provides important clues regarding the molecular mechanisms of in managing abiotic and biotic stress interactions in cucumbers.

References

Gho Y, Kim S, Jung K . Phenylalanine ammonia-lyase family is closely associated with response to phosphate deficiency in rice. Genes Genomics. 2019; 42(1):67-76. DOI: 10.1007/s13258-019-00879-7. View

Jun S, Sattler S, Cortez G, Vermerris W, Sattler S, Kang C . Biochemical and Structural Analysis of Substrate Specificity of a Phenylalanine Ammonia-Lyase. Plant Physiol. 2017; 176(2):1452-1468. PMC: 5813539. DOI: 10.1104/pp.17.01608. View

Deng Y, Li C, Li H, Lu S . Identification and Characterization of Flavonoid Biosynthetic Enzyme Genes in Salvia miltiorrhiza (Lamiaceae). Molecules. 2018; 23(6). PMC: 6099592. DOI: 10.3390/molecules23061467. View

Weisshaar B, Jenkins G . Phenylpropanoid biosynthesis and its regulation. Curr Opin Plant Biol. 1999; 1(3):251-7. DOI: 10.1016/s1369-5266(98)80113-1. View

Huang J, Gu M, Lai Z, Fan B, Shi K, Zhou Y . Functional analysis of the Arabidopsis PAL gene family in plant growth, development, and response to environmental stress. Plant Physiol. 2010; 153(4):1526-38. PMC: 2923909. DOI: 10.1104/pp.110.157370. View

Huang S, Li R, Zhang Z, Li L, Gu X, Fan W . The genome of the cucumber, Cucumis sativus L. Nat Genet. 2009; 41(12):1275-81. DOI: 10.1038/ng.475. View

Ohl S, Hedrick S, Chory J, Lamb C . Functional properties of a phenylalanine ammonia-lyase promoter from Arabidopsis. Plant Cell. 1990; 2(9):837-48. PMC: 159934. DOI: 10.1105/tpc.2.9.837. View

He J, Liu Y, Yuan D, Duan M, Liu Y, Shen Z . An R2R3 MYB transcription factor confers brown planthopper resistance by regulating the phenylalanine ammonia-lyase pathway in rice. Proc Natl Acad Sci U S A. 2019; 117(1):271-277. PMC: 6955232. DOI: 10.1073/pnas.1902771116. View

Khakdan F, Alizadeh H, Ranjbar M . Molecular cloning, functional characterization and expression of a drought inducible phenylalanine ammonia-lyase gene (ObPAL) from Ocimum basilicum L. Plant Physiol Biochem. 2018; 130:464-472. DOI: 10.1016/j.plaphy.2018.07.026. View

10.

Dixon R, Paiva N . Stress-Induced Phenylpropanoid Metabolism. Plant Cell. 1995; 7(7):1085-1097. PMC: 160915. DOI: 10.1105/tpc.7.7.1085. View

11.

Costa M, Bedgar D, Moinuddin S, Kim K, Cardenas C, Cochrane F . Characterization in vitro and in vivo of the putative multigene 4-coumarate:CoA ligase network in Arabidopsis: syringyl lignin and sinapate/sinapyl alcohol derivative formation. Phytochemistry. 2005; 66(17):2072-91. DOI: 10.1016/j.phytochem.2005.06.022. View

12.

Xu X, Liu M, Hu Q, Yan W, Pan J, Yan Y . A CsEIL3-CsARN6.1 module promotes waterlogging-triggered adventitious root formation in cucumber by activating the expression of CsPrx5. Plant J. 2023; 114(4):824-835. DOI: 10.1111/tpj.16172. View

13.

Gou C, Zhu P, Meng Y, Yang F, Xu Y, Xia P . Evaluation and Genetic Analysis of Parthenocarpic Germplasms in Cucumber. Genes (Basel). 2022; 13(2). PMC: 8872377. DOI: 10.3390/genes13020225. View

14.

Shang Q, Li L, Dong C . Multiple tandem duplication of the phenylalanine ammonia-lyase genes in Cucumis sativus L. Planta. 2012; 236(4):1093-105. DOI: 10.1007/s00425-012-1659-1. View

15.

Cesarino I . Structural features and regulation of lignin deposited upon biotic and abiotic stresses. Curr Opin Biotechnol. 2019; 56:209-214. DOI: 10.1016/j.copbio.2018.12.012. View

16.

Gharibi S, Sayed Tabatabaei B, Saeidi G, Talebi M, Matkowski A . The effect of drought stress on polyphenolic compounds and expression of flavonoid biosynthesis related genes in Achillea pachycephala Rech.f. Phytochemistry. 2019; 162:90-98. DOI: 10.1016/j.phytochem.2019.03.004. View

17.

Koukol J, Conn E . The metabolism of aromatic compounds in higher plants. IV. Purification and properties of the phenylalanine deaminase of Hordeum vulgare. J Biol Chem. 1961; 236:2692-8. View

18.

Zhang X, Liu C . Multifaceted regulations of gateway enzyme phenylalanine ammonia-lyase in the biosynthesis of phenylpropanoids. Mol Plant. 2015; 8(1):17-27. DOI: 10.1016/j.molp.2014.11.001. View

19.

Yang L, Zhang S, Chu D, Wang X . Exploring the evolution of gene family in plants. Front Genet. 2024; 15:1368358. PMC: 11091334. DOI: 10.3389/fgene.2024.1368358. View

20.

Cochrane F, Davin L, Lewis N . The Arabidopsis phenylalanine ammonia lyase gene family: kinetic characterization of the four PAL isoforms. Phytochemistry. 2004; 65(11):1557-64. DOI: 10.1016/j.phytochem.2004.05.006. View