Abstract
Rice waxy gene is one of the major genes, which determines the amylose content of a rice grain. The expression of this gene is regulated by various stimuli such as temperature, light, drought and diseases. Promoter region of a gene is responsible for changing the level of expression with the help of transcription factors and their binding sites, cis-acting regulatory elements found in the promoter region ranging from 2000 bp upstream and 500 bp downstream relative to the transcription start site. Present study investigated the putative transcription factor binding sites in the promoter region and possible expression regulation stimuli using five Sri Lankan rice varieties, two glutinous rice varieties, Arabidopsis thaliana and potato. The promoter regions of the plants were extracted either after mapping selected varieties from rice 3000 genome project or from promoter databases. Signal scan was carried out to capture putative signal sequences, and kappa incidence of coincidence vs guanine cytosine content, guanine cytosine skew, and multiple sequence alignment were also performed. The results revealed that rice Wx promoter could be a TATA-less promoter with a putative pyrimidine patch, and categorized under ATCG middle class of promoters. The possible transcription regulation stimuli of waxy gene include dehydration, light, temperature, and hormones. There were signal sequences related to mesophyll, root nodule, seed and root specific regulation of expression.
Highlights
Rice grain is mainly composed of starch (90%) deposited in the endosperm
Plant cis-acting regulatory DNA elements (PLACE) results for the rice Wx promoter region (2.5 kb, -2 kb and + 0.5 kb relative to transcription start site (TSS)), consisted of a total of 591 transcription factor binding sites (TFBS), out of which 283 in the forward strand and 308 in the reverse strand
Core promoter region and common TFBS There were 22 TFBS in the rice Wx core promoter with two initiator element (INR) elements at +10 and +88 positions and no TATA boxes were found from signal scan
Summary
Rice grain is mainly composed of starch (90%) deposited in the endosperm. The amount of starch content varies with genetic and environmental factors. Digestion rate and time of ingested rice vary with the amylose: amylopectin ratio, grain processing, physicochemical properties, size of the particles and amount of lipid-amylose complex (Hu et al, 2004). The most influential character is amylose: amylopectin ratio. Lower the stickiness of cooked rice and lower the gelatinous nature of rice floor. If the ratio is higher, glucose intake to the blood becomes slower and time taken to empty the gastrointestinal tract is increased, helping to regulate glucose level in blood (Behall et al, 1988)
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