Classification and evolution of alpha-amylase genes in plants.

Abstract

The DNA sequences for 17 plant genes for a-amylase (EC 3.2.1.1) were analyzed to determine their phylogenetic relationship. A phylogeny for these genes was obtained using two separate approaches, one based on molecular clock assumptions and the other based on a comparison of sequence polymorphisms (i.e., small and localized insertions) in the a-amylase genes. These polymorphisms are called "ra-amylase signatures" because they are diagnostic of the gene subfamily to which a particular a-amylase gene belongs. Results indicate that the cereal a-amylase genes fall into two major classes: AmyA and AmyB. The AmyA class is subdivided into the Amyl and Amy2 subfamilies previously used to classify a-amylase genes in barley and wheat. The AmyB class includes the Amy3 subfamily to which most of the a-amylase genes of rice belong. Using polymerase chain reaction and oligonucleotide primers that flank one of the two signatu regions, we show that the AmyA and AmyB gene classes are present in approximately equal amounts in all grass species exined except barley. The AmyB (Amy3 subfamily) genes in the latter case are comparatively underrepresented. Additional evidence suggests that the AmyA genes appeared recently and may be confined to the grass family.a-Amylase (EC 3.2.1.1) plays a key role in the metabolism of the plant by hydrolyzing starch in the germinating seed and in other tissues. This is accomplished primarily through the 1,4-a endoglycolytic cleavage of amylose and amylopectin, the principal components of starch granules in plant cells. Because of its importance to cereal seed germination and malting, the genetic basis and biochemical mechanism of this process have been the subject of study for many years (1). More recent descriptions of the biology and biochemistry of plant a-amylases have been reviewed by Akazawa et al. (2) and Fincher (3).Protein sequence comparisons of a-amylases from plants, animals, and microbes reveal four highly conserved domains that correspond to sites necessary for enzyme structure and/or function (4). A subsequent comparison of 11 different cereal a-amylase proteins revealed the same four sites plus three additional sites (5). Two of these correspond to intron splice sites, whereas the third may represent a duplication of the calcium binding site, essential for enzyme stability. These results clearly indicate a common ancestry for the a-amylases and conservation of critical sequences over evolutionary time.Although three a-amylase isozymes have been detected in germinating rice seeds (6, 7), it is now known that a-amylase isozymes are encoded by a family of 10 genes located on five different chromosomes (8-10). Multiple a-amylase genes are also known to exist in barley (11) and wheat (12). In barley, 7 genes encoding a-amylase isozymes with high isoelectric

A novel α‐amylase gene is transiently upregulated during low temperature exposure in apple fruit

“…In addition, our results supported the subdivisions within the monocotyledonous α‐amylases according to Huang et al . [16], and confirmed the placing of the other, less‐divergent α‐amylase sequences from dicotyledonous sources into a separate group from monocotyledon α‐amylases. The structure of the phylogenetic tree generated (Fig.…”

“…ten genes on five different chromosomes in rice [14]. Cross‐hybridization of rice genomic clones [15], and comparison with known wheat and barley sequences [16] revealed the presence of two major families of genes within cereal genomes, one of which separated further into two subfamilies. Cereal α‐amylases share the same intron/exon structure, apart from the loss of an intron in one subfamily.…”

“…Cereal α‐amylases share the same intron/exon structure, apart from the loss of an intron in one subfamily. On the basis of phylogenetic analysis of coding sequence one of these major families is more closely related to the α‐amylase from mung bean [16]. This relationship is supported by the conservation of the complete intron/exon structure of cereal α‐amylases in the genomic sequence from mung bean [8].…”

Interaction between Rice MYBGA and the Gibberellin Response Element Controls Tissue-Specific Sugar Sensitivity of α-Amylase Genes

“…The GARE, therefore, would not only be responsible for GA activation but would also function in preventing the sugar feedback repression of a-amylase genes in endosperms, which would ensure a continuous supply of sugars to embryos during active seedling growth. All a-amylase genes in the monocot lineage are derived from duplication of a single ancestor gene (Huang et al, 1992). The GARE is present in some a-amylase gene promoters but absent in others throughout evolution.…”

Functional dissection of a sugar‐repressed α‐amylase gene (RAmy1A) promoter in rice embryos

“…However, in rice, only two of the ten genes encoding for Kamylase isoforms [2,3] appear to be strongly under the control of sugar level, namely RAmy3D and RAmy3E (also identi¢ed as KAmy3 and KAmy8) [4^9]. While the expression of the RAmy3D gene is restricted to the embryo, the RAmy1A (KAmy7) gene is expressed in both the embryo and aleurone layers.…”