Abstract
Gene duplication is a source of genetic materials and evolutionary changes, and has been associated with gene family expansion. Functional divergence of duplicated genes is strongly directed by natural selections such as organism diversification and novel feature acquisition. We show that, plant α-amylase gene family (AMY) is comprised of six subfamilies (AMY1-AMY6) that fell into two ancient phylogenetic lineages (AMY3 and AMY4). Both AMY1 and AMY2 are grass-specific and share a single-copy ancestor, which is derived from grass AMY3 genes that have undergone massive tandem and whole-genome duplications during evolution. Ancestral features of AMY4 and AMY5/AMY6 genes have been retained among four green algal sequences (Chrein_08.g362450, Vocart_0021s0194, Dusali_0430s00012 and Monegl_16464), suggesting a gene duplication event following Chlorophyceae diversification. The observed horizontal gene transfers between plant and bacterial AMYs, and chromosomal locations of AMY3 and AMY4 genes in the most ancestral green body (C. reinhardtii), provide evidences for the monophyletic origin of plant AMYs. Despite subfamily-specific sequence divergence driven by natural selections, the active site and SBS1 are well-conserved across different AMY isoforms. The differentiated electrostatic potentials and hydrogen bands-forming residue polymorphisms, further imply variable digestive abilities for a broad substrates in particular tissues or subcellular localizations.
Highlights
As the best known and most deeply studied amylolytic enzyme[1,2,3,4,5,6], α-amylase (AMY, α-1,4-glucan-4glucanohydrolases, EC 3.2.1.1) is an ubiquitous hydrolase synthesized by plants, animals and microorganisms, catalyzing the cleavage of internal α-(1–4)-glycosidic linkages in starch, glycogen and other related oligosaccharides with a retaining endo-acting mechanism
Subsequent phylogenetic inference indicated that cereal amylase gene family (AMY) genes fell into two classes: AmyA (AMY1 and AMY2) and AmyB (AMY3), and they should be derived from a duplication event of the common ancestor of monocot and dicot AMY genes[34]
AMY3, AMY4 and AMY5 genes were widely distributed across the entire green lineage, while both AMY1 and AMY2 were grass-specific
Summary
As the best known and most deeply studied amylolytic enzyme[1,2,3,4,5,6], α-amylase (AMY, α-1,4-glucan-4glucanohydrolases, EC 3.2.1.1) is an ubiquitous hydrolase synthesized by plants, animals and microorganisms, catalyzing the cleavage of internal α-(1–4)-glycosidic linkages in starch, glycogen and other related oligosaccharides with a retaining endo-acting mechanism. Under the sequence-based classification rules of carbohydrate-active enzymes (CAZy database, http://www.cazy.org/index.html), AMYs are classified as the main representative of the glycoside hydrolase (GH) family 13, and probably present in families GH57, GH119 and GH1265–7. Among Drosophila species, the AMY gene family of D. ananassae is believed to be the most complicated situation in animals, because its seven copies are distributed on the different chromosomes, and mainly organized as two genetically distinct clusters; and two copies of them, Amyrel and Amyc[1], shows strong sequence divergence with the two classical paralogous clusters[24,25]. Wegrzyn et al.[36] isolated an apple AMY gene (AMY8W), which showed most similar to a gene (GenBank accession M79328) from potato These two genes lacked the standard signal peptides, and formed a distantly separate branch, which appeared to have diverged prior to the split of monocot and dicot plants. The active site and starch granule binding surface site (SBS1) are conserved in most reported enzymes; and the surface binding site of domain C (SBS2) is unique in low-pI AMY242
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