Characterization of an ?-amylase multigene cluster in rice

Sutliff, Thomas D.; Huang, Ning; Litts, James C.; Rodriguez, Raymond L.

doi:10.1007/bf00023423

Cited by 45 publications

(25 citation statements)

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“…One of the wheat Amy3 genes, Amy3/33, is only expressed at low levels in immature seeds and no orthologous gene has been detected in barley (14). Our studies indicate that 6 of the 10 rice a-amylase genes belong to the Amy3 subfamily (8,9,21). Unlike the wheat Amy3 gene, however, members of this gene subfamily in rice are expressed in germinating seeds as well as in other tissues of the plant (8).…”

Section: Resultsmentioning

confidence: 74%

“…Subsequently, Huang et al (20) used DNA-DNA hybridization to classify 30 rice genomic clones into five hybridization groups. These five groups were eventually consolidated into three subfamilies (Amyl, Amy2, and Amy3) on the basis of protein comparisons to other wheat and barley a-amylase genes (8,(20)(21)(22). Other investigators have used the high and low pI nomenclature to describe their cloned rice a-amylase genes (23,24).…”

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confidence: 99%

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Classification and evolution of alpha-amylase genes in plants.

Huang

Stebbins

Rodriguez

1992

Proc. Natl. Acad. Sci. U.S.A.

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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

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Section: Resultsmentioning

confidence: 74%

mentioning

confidence: 99%

Classification and evolution of alpha-amylase genes in plants.

Huang

Stebbins

Rodriguez

1992

Proc. Natl. Acad. Sci. U.S.A.

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“…1B) were synthesized and used as primers. The primer extension analysis was performed according to Sutliff et al (38).…”

Section: Methodsmentioning

confidence: 99%

Sugar Response Sequence in the Promoter of a Rice α-Amylase Gene Serves as a Transcriptional Enhancer

Lu¹,

Lim²,

Yu³

1998

Journal of Biological Chemistry

162

163

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Expression of ␣-amylase genes in both rice suspension cells and germinating embryos is repressed by sugars and the mechanism involves transcriptional regulation. The promoter of a rice ␣-amylase gene ␣Amy3 was analyzed by both loss-and gain-of-function studies and the major sugar response sequence (SRS) was located between 186 and 82 base pairs upstream of the transcription start site. The SRS conferred sugar responsiveness to a minimal promoter in an orientation-independent manner. It also converted a sugar-insensitive rice actin gene promoter into a sugar-sensitive promoter in a dosedependent manner. Linker-scan mutation studies identified three essential motifs: the GC box, the G box, and the TATCCA element, within the SRS. Sequences containing either the GC box plus G box or the TATCCA element each mediated sugar response, however, they acted synergistically to give a high level glucose starvation-induced expression. Nuclear proteins from rice suspension cells binding to the TATCCA element in a sequence-specific and sugar-dependent manner were identified. The TATCCA element is also an important component of the gibberellin response complex of the ␣-amylase genes in germinating cereal grains, suggesting that the regulation of ␣-amylase gene expression by sugar and hormone signals may share common regulatory machinery.Sugar repression of gene expression is a fundamental and ubiquitous regulatory system for adjusting to changes in nutrient availability in both prokaryotic and eukaryotic cells. In microorganisms, glucose or other rapidly metabolizable carbon sources repress the expression of genes that code for enzymes related to the metabolism of other carbon sources. Our understanding of the mechanisms of sugar repression has been based largely on studies of microorganisms. In the case of Escherichia coli, a model to explain at the molecular level, the mechanism of sugar repression has been determined (1, 2). The mechanism of glucose repression in yeast is more complicated and is less understood than it is in E. coli (3-5). Studies using Saccharomyces cerevisiae mutants have revealed many of the components involved in the response to carbon catabolite repression (5), but it is still unclear how all of these components interact to regulate transcription. A universal signaling pathway which leads to the regulation of all glucose-repressible genes has yet to be determined.As in microorganisms, sugar repression of gene expression also allows plant cells to cope effectively with changes in the carbon sources present in their environment. However, in multicellular plants, feedback repression by excess sugars provides an additional mechanism for maintaining an economical balance between supply (source) and demand (sink) for carbohydrate allocation and utilization among tissues and organs (6 -8). Despite the fact that sugar repression of gene expression is likely a central control mechanism mediating energy homeostasis and carbohydrate distribution in plants, the molecular mechanism of sugar feedback regulation remain...

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“…Previously, mRNA of RAmy3B and RAmy3C has been detected in both embryo and aleurone layer of germinating rice seed. 7,11) This study demonstrated the native forms of these gene products. The degree of amino acid sequence similarity among RAmy1A, RAmy3B/3C, and RAmy3E was calculated to be 83.7 to 90.4%.…”

Section: Discussionmentioning

confidence: 66%