title: Comparative and evolutionary analysis of α-amylase gene across monocots and dicots.
abstract: α-amylase is an important enzyme involved in starch degradation to provide energy to the germinating seedling. The present study was conducted to reveal structural and functional evolution of this gene among higher plants. Discounting polyploidy, most plant species showed only a single copy of the gene making multiple isoforms in different tissues and developmental stages. Genomic length of the gene ranged from 1472 bp in wheat to 2369 bp in soybean, and the size variation was mainly due to differences in the number and size of introns. In spite of this variation, the intron phase distribution and insertion sites were mostly conserved. The predicted protein size ranged from 414 amino acid (aa) in soybean to 449aa in Brachypodium. Overall, the protein sequence similarity among orthologs ranged from 56.4 to 97.4 %. Key motifs and domains along with their relative distances were conserved among plants although several species, genera, and class specific motifs were identified. The glycosyl hydrolase superfamily domain length varied from 342aa in soybean to 384aa in maize and sorghum while length of the C-terminal β-sheet domain was highly conserved with 61aa in all monocots and Arabidopsis but was 59aa in soybean and Medicago. Compared to rice, 3D structure of the proteins showed 89.8 to 91.3 % similarity among the monocots and 72.7 to 75.8 % among the dicots. Sequence and relative location of the five key aa required for the ligand binding were highly conserved in all species except rice.
authors.affiliation: Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India.
authors.forename: Sorabh
authors.initials: S
authors.lastname: Sethi
authors.affiliation: Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India. joharsingh@pau.edu.
authors.forename: Johar S
authors.initials: JS
authors.lastname: Saini
authors.affiliation: Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA.
authors.forename: Amita
authors.initials: A
authors.lastname: Mohan
authors.affiliation: Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India.
authors.forename: Navreet K
authors.initials: NK
authors.lastname: Brar
authors.affiliation: Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India.
authors.forename: Shabda
authors.initials: S
authors.lastname: Verma
authors.affiliation: Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India.
authors.forename: Navraj K
authors.initials: NK
authors.lastname: Sarao
authors.affiliation: Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA.
authors.forename: Kulvinder S
authors.initials: KS
authors.lastname: Gill
mesh_terms: D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics; D018506:Gene Expression Regulation, Plant / Q000235:genetics*; D007438:Introns / Q000235:genetics; D019684:Magnoliopsida / Q000145:classification / Q000235:genetics; D005810:Multigene Family / Q000235:genetics*; D012275:Oryza / Q000235:genetics; D010802:Phylogeny; D013025:Glycine max / Q000235:genetics; D014908:Triticum / Q000235:genetics; D003313:Zea mays / Q000235:genetics; D000516:alpha-Amylases / Q000145:classification / Q000235:genetics*
chemical_list: D000516:alpha-Amylases
keywords: 3D protein structure; Comparative analysis; Gene structure; Intron evolution; Ligand binding; α-amylase