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In silico promoter analysis reveals rice Wx promoter could be a TATA-less promoter with a putative pyrimidine rich region

Authors:

K. R. D. Hemage ,

University of Peradeniya, LK
About K. R. D.
Centre for Education, Research and Training on Kidney Diseases, Faculty of Medicine
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V. A. Sumanasinghe

University of Peradeniya, LK
About V. A.
Department of Agricultural Biology, Faculty of Agriculture
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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.
How to Cite: Hemage, K.R.D. and Sumanasinghe, V.A., 2017. In silico promoter analysis reveals rice Wx promoter could be a TATA-less promoter with a putative pyrimidine rich region. Tropical Agricultural Research, 29(1), pp.32–44. DOI: http://doi.org/10.4038/tar.v29i1.8295
Published on 31 Dec 2017.
Peer Reviewed

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