| Phenylalanine ammonia lyase(PAL)is one of the fundamental enzymes involved in plant’s secondary metabolism.This enzyme catalyzes the deamination of phenylalanine to cinnamic acid,the first committed step in the phenylpropanoid pathway.This pathway synthesis of natural products functions in plants,including protection against biotic and abiotic stresses,cellular signaling,UV protection mechanical support and response to low levels of nutrients like iron and phosphate,etc.Grains,commonly referred as ‘cereals’ or ‘cereal grains’,are the edible seeds of specific grasses belong to the Poaceae(also known as Gramineae)family,including rice(Oryza sativa),barley(Hordeum vulgar),maize(Zea mays)and wheat Triticum aestivum).In order to explore the evolutionary relationship among the mentioned species,a genome wide study was conducted on PAL gene family.A total of 67 encoding genes for PAL gene members from rice,barley,maize and wheat were identified.In rice,there were 9 PAL genes identified as Os PAL1-Os PAL9.These genes were distributed on chromosome 2,4,5,6,11 12.Barley has 9 PAL genes distributed on chromosome 1,2,3 and 6,which were named as Hv PAL1-Hv PAL9.In maize,these genes were named with Zm PAL1-Zm PAL13 which were distributed on chromosome 1,2,4,5,6,7.In addition,36 TaPAL in wheat were on six chromosomes(Chr 1,2,3,4,5,6).The SMART database’s result indicated that all PAL genes families found in four species mentioned contained a well-conserved aromatic-lyase domain that they belong to PAL family.The number of introns and exons per gene varied from one to four based on gene structure analysis of PAL genes in Rice,Barley,Maize and Wheat.These results showed that they were closely related.In the phylogenetic tree shown that the PAL genes with the same exon–intron structure were grouped in the same terminal branches.The Gene Structure and Motif Organization were found to be notably conserved over the distinct phylogenetic groups,showing the evolutionary significant role of each PAL in different species.The phylogenetic analysis places 67 PAL genes from Oryza sativa,Hordeum vulgar,Zea mays and Triticum aestivum.along with 4 PAL genes from Arabidopsis thaliana into 4 groups and it concluded that wheat has a closer relationship with barley than maize and rice,while maize had a closer relationship with rice than barley and wheat.The Plant-CARE database with default parameters for the identification of the important stress and hormone responsive.cis-regulatory elements identified in this study Me-JA are the most abundant elements with 24% of the total cis-regulatory elements present in PAL families.Furthermore,the Light stress-(G-box)and wounding stress-(WUN-motif)related elements are found to be,respectively,the most and least(41% and0.1%).The Gene Ontology(GO)results showed that 67 were involved in GO functional annotation.In relation to the MF,the following GO functional annotation was noted:phenylalanine ammonia-lyase activity(GO:0045548),ammonia-lyase activity(GO:0016841).In BP,the following functional annotations were found: phenylalanine catabolic process(GO:0006559),phenylpropanoid metabolic process(GO:0009698).In CC,the locations relative to cellular structures in which a PAL genes product performs a function were found in cytoplasm.The predicted mi RNAs show that one mi RNA can target more than one PAL genes.For instance,osa-mi R6246 targets four Os PAL genes,hvu-mi R6189 targets three Hv PAL genes,whereas zma-mi R395 and zma-mi R171 both target 2 Zm PAL,and tae-mi R1119 targets thirteen Ta PAL(Fig.4.6).In addition,Os PAL 2,Hv PAL4,Zm PAL3,Ta PAL36 were also found as the most-targeted PAL genes in each species.These predicted mi RNAs were determined to be involved in cleaving of target genes and translational inhibition... |
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