Phenylalanine Ammonia-lyase Family Research Articles

Genome-Wide Identification and Expression Profile Analysis of the Phenylalanine Ammonia-Lyase Gene Family in Hevea brasiliensis.

The majority of the world's natural rubber comes from the rubber tree (Hevea brasiliensis). As a key enzyme for synthesizing phenylpropanoid compounds, phenylalanine ammonia-lyase (PAL) has a critical role in plant satisfactory growth and environmental adaptation. To clarify the characteristics of rubber tree PAL family genes, a genome-wide characterization of rubber tree PALs was conducted in this study. Eight PAL genes (HbPAL1-HbPAL8), which spread over chromosomes 3, 7, 8, 10, 12, 13, 14, 16, and 18, were found to be present in the genome of H. brasiliensis. Phylogenetic analysis classified HbPALs into groups I and II, and the group I HbPALs (HbPAL1-HbPAL6) displayed similar conserved motif compositions and gene architectures. Tissue expression patterns of HbPALs quantified by quantitative real-time PCR (qPCR) proved that distinct HbPALs exhibited varying tissue expression patterns. The HbPAL promoters contained a plethora of cis-acting elements that responded to hormones and stress, and the qPCR analysis demonstrated that abiotic stressors like cold, drought, salt, and H2O2-induced oxidative stress, as well as hormones like salicylic acid, abscisic acid, ethylene, and methyl jasmonate, controlled the expression of HbPALs. The majority of HbPALs were also regulated by powdery mildew, anthracnose, and Corynespora leaf fall disease infection. In addition, HbPAL1, HbPAL4, and HbPAL7 were significantly up-regulated in the bark of tapping panel dryness rubber trees relative to that of healthy trees. Our results provide a thorough comprehension of the characteristics of HbPAL genes and set the groundwork for further investigation of the biological functions of HbPALs in rubber trees.

Genome-wide identification and expression analysis of phenylalanine ammonia-lyase (PAL) family in rapeseed (Brassica napus L.)

BackgroundPhenylalanine ammonia-lyase (PAL), as a key enzyme in the phenylalanine metabolism pathway in plants, plays an important role in the response to environmental stress. However, the PAL family responding to abiotic stress has not been fully characterized in rapeseed.ResultsIn this study, we conducted a genome-wide study of PAL family, and analyzed their gene structure, gene duplication, conserved motifs, cis-acting elements and response to stress treatment. A total of 17 PALs were identified in the rapeseed genome. Based on phylogenetic analysis, the BnPALs were divided into four clades (I, II, IV, and V). The prediction of protein structure domain presented that all BnPAL members contained a conservative PAL domain. Promoter sequence analysis showed that the BnPALs contain many cis-acting elements related to hormone and stress responses, indicating that BnPALs are widely involved in various biological regulatory processes. The expression profile showed that the BnPALs were significantly induced under different stress treatments (NaCl, Na2CO3, AlCl3, and PEG), suggesting that BnPAL family played an important role in response to abiotic stress.ConclusionsTaken together, our research results comprehensively characterized the BnPAL family, and provided a valuable reference for revealing the role of BnPALs in the regulation of abiotic stress responses in rapeseed.

Genome-wide identification and expression analyses of phenylalanine ammonia-lyase gene family members from tomato (Solanum lycopersicum) reveal their role in root-knot nematode infection.

Phenylalanine ammonia-lyase (PAL) is a key enzyme and rate-limiting enzyme of phenylpropanoid metabolism, which is a very important pathway in plants, and the secondary products it produces play an important role in plant growth and development, disease resistance, and stress resistance responses. However, PALs still lack systematic characterization in tomato. Based on a bioinformatics methods, PAL family genes were identified and characterized from tomato. qRT-PCR was used to study the expression of PAL genes in cultivated tomato after root-knot nematode infection. In this study, 14 and 11 PAL genes were identified in cultivated and wild tomatoes, and phylogenetic analysis classified them into three subfamilies, with different subfamilies of PAL proteins evolving in different directions in monocotyledonous and dicotyledonous plants. The extensive presence of stress, growth, hormone, and light response elements in the promoter sequences of SlPAL (Solanum lycopersicum) and SpenPAL (Solanum pennellii) genes suggests that this family has a critical role in abiotic stress. Collinearity indicates that members of the tomato and Arabidopsis PAL genes family are from the same ancestor, and the SlPAL10 gene is directly homologous to monocotyledonous rice and maize, suggesting that the SlPAL10 gene was present before monocotyledonous differentiation. Two co-expressed gene modules containing PAL genes were screened by WGCNA, and the core genes in the network were mined and functionally annotated by calculating the connectivity of genes within the modules. In addition, the expression of some genes changed significantly after root-knot nematode infection, with up-regulation of 4 genes and down-regulation of 3 genes. This result provides a data reference for the study of PAL family gene functions in tomato, and also provides a potential application for the subsequent selection of PAL genes in tomato for root-knot nematode resistance.

Genomewide Identification and Expression Analyses of <i>PAL</i> Genes in Different Color Radish

Phenylalanine ammonia-lyase (PAL) is the first step key enzyme of the flavonoid biosynthesis pathway which played an essential role in plant anthocyanin accumulation. Five PAL family gene members were identified in the radish ( Raphanus sativus  L.) genome name RsPAL1~5. Specific primers were designed to amplify the open reading frame in red radish ‘Hongxin No.1’ and then sequenced. Real-time PCR was used to analysis the expression pattern of 5  RsPALs  in four different tissues including leaf, petiole, taproot flesh and skin form five different color type radishes, including red skin and red flesh ‘Shaguan’ and ‘Hongxin No.1’, red skin and white flesh ‘Shaguan No.1’ and ‘Mantanghong’, white skin and white flesh ‘Chunbulao’. The results showed that the length of open read frame of RsPAL1~5 were 2 160, 2 166, 2 163, 2 124 and 2 109 bp encoding for 719, 721, 720, 707 and 702 amino acid residues respectively. Sequence alignment analysis showed that MIO motif (Ala-Gly-Ser) was conserved among the five RsPALs proteins. RsPAL1~4 were clustered with Arabidopsis AtPAL1 and AtPAL2, RsPAL5 was clustered with AtPAL4 in the phylogenetic tree. Real-time PCR results suggested that  RsPAL4  was expressed only in the tissue accumulate anthocyanin, and the expression of  RsPAL4  was significantly correlated with anthocyanin content. These results indicating that  RsPAL4  may specifically involved in anthocyanin biosynthesis in radish. However, no obvious expression pattern of other  RsPALs  members was found in this study, suggesting that they may participate in other secondary metabolites biosynthesis of phenylpropane metabolism pathway. This study would provide scientific basis for further study on the function of radish  PAL .

Genome-wide identification and characterisation of phenylalanine ammonia-lyase gene family in grapevine

ABSTRACT Phenylalanine ammonia-lyase (PAL) is a rate-limiting enzyme of phenylpropanoid biosynthesis in plants that synthesise many ubiquitous key compounds, including phenolic acids, flavonoids, lignins, and stilbenes. The first draft of the full grape genome assembly was released, but systematic analysis of the PAL family has not been completed in detail. In this study, 15 PALs were identified in the grape genome. Grape PALs are distributed on 6 chromosomes, and 9 PALs are distributed on chromosome 16, in which most of the 2 downstream genes, including chalcone synthase (CHS) and stilbene synthase (STS). Promoter analysis revealed that there were many cis-acting elements in the promoter regions to respond to light, phytohormone, and stress. According to transcriptome-data analysis, VvPALs have extensive expression patterns in various tissues and developmental stages in response to various stresses. Dynamic expression patterns of PAL1/2/3/5 were observed in different developmental stages of 4 grape varieties on the basis of qRT-PCR analysis, and suggested that PALs are involved in a complex mechanism to modulate in anthocyanin biosynthesis. Comprehensive analysis of PALs offers a basis for further understanding the physiological functions of PALs during grape development and their potential role to respond the various stimuli.

Overexpression of RgPAL family genes involved in phenolic biosynthesis promotes the replanting disease development in Rehmannia glutinosa

Rehmannia glutinosa production is affected by the replanting disease, which involves autotoxic harm mediated by specific endogenous allelochemicals in root exudates. Many phenolics that act as allelochemical agents are mostly phenylpropanoid products of secondary metabolism in plants. Phenylalanine ammonia-lyase (PAL) is the first enzyme that catalyses the deamination of l-phenylalanine for entrance into the phenylpropanoid pathway. PAL family genes have been isolated and functionally characterized in many plant species. However, PAL family genes involved in phenolic biosynthesis remain largely uncharacterized in R. glutinosa. Here, we identified and characterized four PAL family genes (RgPAL2 to RgPAL5) in the species whose sequences exhibited highly conserved domains of PALs according to in silico analysis, implying their potential function in phenolic biosynthesis. Overexpression of RgPALs in R. glutinosa enhanced phenolic production, verifying that RgPAL family genes participate in phenolic biosynthesis pathways. Moreover, we found that the release of several allelopathic phenolics from the roots of RgPAL-overexpressing transgenic R. glutinosa increased, implying that the RgPALs positively promote their release. Importantly, under continuous monoculture stress, we found that the RgPAL transgenic plants exhibited more significant autotoxic harm than did non-transgenic (WT) plants by activating the phenolics/phenylpropanoid pathway, indicating that RgPAL family genes function as positive regulators of the replanting disease development in R. glutinosa. This study revealed that RgPAL family genes are involved in the biosynthesis and release of several phenolics and positively control the replanting disease development in R. glutinosa, laying a foundation for further clarification of the molecular mechanisms underlying the disease formation.

Cloning, characterization and expression of a phenylalanine ammonia-lyase gene (CcPAL) from cumin (Cuminum cyminum L.)

Phenylalanine ammonia-lyase (PAL) that functions a substantial role in defense mechanisms, growth, and development of the plant, is situated at branching point from primary to secondary metabolism. In this study, using highly conserved sequences of plant PALs registered in GenBank, a partial cDNA clone of cumin (Cuminum cyminum) PAL gene (designated as CcPAL) was isolated. The relative transcript levels of CcPAL gene, its enzyme activity, and accumulation of total phenolics were also analyzed in shoots in response to different stresses. The isolated CcPAL had 414 bp in length with a maximum open reading frame (ORF) of 351 bp and encodes a peptide with 116 amino acids. The deduced peptide sequence of CcPAL has classical PAL domains and is a stable protein. Results of multiple sequence alignment indicate that CcPAL had high similarity with other plant PALs available in the GenBank. Analysis of the phylogenetic tree indicated that CcPAL categorized in the angiosperm-type PAL family and dicotyledon subfamily and clustered together with other PAL from Apiaceae species. Transcription analysis indicated that CcPAL expressed in all tested tissues, but more highly in shoots. Moreever, the expression of CcPAL was found to be induced by cadmium, wounding, salicylic acid (SA) and cold treatments. A positive correlation was found between transcript levels of CcPAL and total phenolics accumulation of cumin shoots in response to different stresses. These results suggest that the CcPAL and phenylpropanoid pathway may play a great role in the biosynthesis of the bioactive compounds and counteracting various stresses in C. cyminum.

Comparative genomic analysis of the PAL genes in five Rosaceae species and functional identification of Chinese white pear.

Phenylalanine ammonia lyase (PAL) plays an important role in the biosynthesis of secondary metabolites regulating plant growth response. To date, the evolutionary history of the PAL family in Rosaceae plants remains unclear. In this study, we identified 16 PAL homologous genes in five Rosaceae plants (Pyrus bretschneideri, Fragaria vesca, Prunus mume, Prunus persica, and Malus × domestica). We classified these PALs into three categories based on phylogenetic analysis, and all PALs were distributed on 13 chromosomes. We tracked gene duplication events and performed sliding window analysis. These results revealed the evolution of PALs in five Rosaceae plants. We predicted the promoter of the PbPALs by PLANT CARE online software, and found that the promoter region of both PbPAL1 and PbPAL3 have at least one AC element. The results of qRT-PCR analysis found that PbPAL1 and PbPAL2 were highly expressed in the stems and roots, while expression level of PbPAL3 was relatively low in different tissues. The expression of PbPAL1 and PbPAL2 increased firstly and then decreased at different developmental periods of pear fruit. Among them, the expression of PbPAL1 reached the highest level 55 days after flowering. Three PbPALs were induced by abiotic stress to varying degrees. We transfected PbPAL1 and PbPAL2 into Arabidopsis thaliana, which resulted in an increase in lignin content and thickening of the cell walls of intervascular fibres and xylem cells. In summary, this research laid a foundation for better understanding the molecular evolution of PALs in five Rosaceae plants. Furthermore, the present study revealed the role of PbPALs in lignin synthesis, and provided basic data for regulating lignin synthesis and stone cells development in pear plants.

Phenylalanine ammonia-lyase family is closely associated with response to phosphate deficiency in rice

Phenylalanine ammonia-lyase (PAL) catalyzes the first step in the biosynthetic phenylpropanoid pathway (PPP) via deamination of phenylalanine to trans-cinnamic acid, a precursor for the lignin and flavonoid biosynthetic pathways. Although its role is well-established in various plants, the functional significance of PAL genes in rice remains poorly understood. This study aims to find out the global feature of rice PAL genes associated with phosphate use efficiency. To identify the biological functions of individual rice PAL genes, we performed meta-expression profiling analysis based on phylogenomics of rice PAL genes and confirmed the expression patterns using Quantitative real-time PCR (qPCR). We identified nine genes that were remarkably up-regulated during long-term phosphate (Pi) starvation and recovery processes through RNA-Seq data analysis. Expression patterns of the nine rice PAL genes under Pi starvation were further confirmed by qPCR, indicating that the function of PAL genes is strongly associated with Pi starvation response in rice. Our study reports the functional significance of rice PAL genes involved in adaptation to low Pi growth conditions and provides useful information to improve Pi use efficiency in crop plant.

Effect of nitrous oxide against Botrytis cinerea and phenylpropanoid pathway metabolism in table grapes

Nitrous oxide (N2O) was investigated for the potential use on inhibiting the postharvest decay of the grape. In this study, 50 μL L−1 N2O gas was used for fumigating the ‘Munage’ grape which was used as the test material at room temperature for 6 h. Results indicated that N2O had no direct effect on the Botrytis cinerea inhibition. But N2O can promote the accumulation of total phenolic, flavonoids and lignin, as well as increase the activities of phenylalanine ammonia-lyase (PAL), cinnamate-4-hydroxylase (C4H), and 4-coumarate CoA ligase (4CL), which were the key enzymes in the metabolism of phenylpropanol. N2O also induced PAL family genes expression in a short time at the molecular level. Thereby the N2O significantly reduced the lesion diameter and incidence of the grape fruit inoculated with Botrytis cinerea. These results suggested that N2O participated in enhancement of disease resistance by improving the phenylpropanoid pathway metabolism of the grape fruit and it could be a promising strategy to suppress postharvest disease.