Phenylalanine Ammonia-Lyase (PAL) Genes Family in Wheat (Triticum aestivum L.): Genome-Wide Characterization and Expression Profiling

Amber Afroz,Muhammad Kashif Naeem,Muhammad Ramzan Khan,Muhammad Uzair,Fatima Rasool,Nazia Rehman,Hussain Shah

doi:10.3390/agronomy11122511

Amber Afroz, Muhammad Kashif Naeem + Show 5 more

Open Access

https://doi.org/10.3390/agronomy11122511

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Journal: Agronomy	Publication Date: Dec 10, 2021
Citations: 28	License type: CC BY 4.0

Affiliation: University of Gujrat, Quaid-i-Azam University

Abstract

Phenylalanine ammonia-lyase (PAL) is the first enzyme in the phenylpropanoid pathway and plays a vital role in adoption, growth, and development in plants but in wheat its characterization is still not very clear. Here, we report a genome-wide identification of TaPAL genes and analysis of their transcriptional expression, duplication, and phylogeny in wheat. A total of 37 TaPAL genes that cluster into three subfamilies have been identified based on phylogenetic analysis. These TaPAL genes are distributed on 1A, 1B, 1D, 2A, 2B, 2D, 4A, 5B, 6A, 6B, and 6D chromosomes. Gene structure, conserved domain analysis, and investigation of cis-regulatory elements were systematically carried out. Chromosomal rearrangements and gene loss were observed by evolutionary analysis of the orthologs among Triticum urartu, Aegilops tauschii, and Triticum aestivum during the origin of bread wheat. Gene ontology analysis revealed that PAL genes play a role in plant growth. We also identified 27 putative miRNAs targeting 37 TaPAL genes. The high expression level of PAL genes was detected in roots of drought-tolerant genotypes compared to drought-sensitive genotypes. However, very low expressions of TaPAL10, TaPAL30, TaPAL32, TaPAL3, and TaPAL28 were recorded in all wheat genotypes. Arogenate dehydratase interacts with TaPAL29 and has higher expression in roots. The analysis of all identified genes in RNA-seq data showed that they are expressed in roots and shoots under normal and abiotic stress. Our study offers valuable data on the functioning of PAL genes in wheat.

Highlights

Phenylalanine ammonia-lyase (PAL) produces precursors of various secondary metabolites, including lignin, phytoalexin, and phenolic compounds
The results evidenced that the 37 sequences containing PAL-histidine ammonia lyase (HAL) domains belonged to the PAL gene family (Supplementary File S1)
The PAL-gene family, including Z. mays, A. thaliana, O. sativa, H. vulgare, and T. urartu plant species, contained all the conserved domains indicating that the PAL-gene family remained highly conserved during evolution and took long-term speciation and duplication events to evolve; the results demonstrated its importance in antiretroviral effects

Summary

Introduction

Phenylalanine ammonia-lyase (PAL) produces precursors of various secondary metabolites, including lignin, phytoalexin, and phenolic compounds. This gene family is associated with the production of the first enzyme of the phenylpropanoid pathway [1,2,3]. PAL genes have a molecular mass in the range of 270–330 kilodalton (kDa) and are present in higher plants, yeast, some bacteria, and fungi. These genes are not found in animals because they have another histidine ammonia lyase (HAL) [4]. PAL activity is induced dramatically in reply to various stimuli such as tissue wounding, pathogenic attack, light, low temperature, and hormonal triggers [5,11]

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