In silico Analysis of osr40c1 Promoter Sequence Isolated from Indica Variety Pokkali
Received date: 2016-09-10
Accepted date: 2016-11-28
Online published: 2017-04-28
The promoter region of a drought and abscisic acid (ABA) inducible gene, osr40c1, was isolated from a salt-tolerant indica rice variety Pokkali, which is 670 bp upstream of the putative translation start codon. In silico promoter analysis of resulted sequence showed that at least 15 types of putative motifs were distributed within the sequence, including two types of common promoter elements, TATA and CAAT boxes. Additionally, several putative cis-acing regulatory elements which may be involved in regulation of osr40c1 expression under different conditions were found in the 5′-upstream region of osr40c1. These are ABA-responsive element, light-responsive elements (ATCT-motif, Box I, G-box, GT1-motif, Gap-box and Sp1), myeloblastosis oncogene response element (CCAAT-box), auxin responsive element (TGA-element), gibberellin-responsive element (GARE-motif) and fungal-elicitor responsive elements (Box E and Box-W1). A putative regulatory element, required for endosperm-specific pattern of gene expression designated as Skn-1 motif, was also detected in the Pokkali osr40c1 promoter region. In conclusion, the bioinformatic analysis of osr40c1 promoter region isolated from indica rice variety Pokkali led to the identification of several important stress-responsive cis-acting regulatory elements, and therefore, the isolated promoter sequence could be employed in rice genetic transformation to mediate expression of abiotic stress induced genes.
Key words： osr40c1; promoter; cis-acting regulatory element; rice
S. I. de Silva W., M. N. Perera M., L. N. S. Perera K., M. Wickramasuriya A., A. U. Jayasekera G. . In silico Analysis of osr40c1 Promoter Sequence Isolated from Indica Variety Pokkali[J]. Rice Science, 2017 , 24(4) : 32 -40 . DOI: 10.1016/j.rsci.2016.11.002
| 1 | Ansari M U R, Shaheen T, Bukhari S, Husnain T.2015. Genetic improvement of rice for biotic and abiotic stress tolerance.Turk J Bot, 39(6): 911-919. |
| 2 | Borghi L.2010. Inducible gene expression systems for plants. In: Hennig L, Köhler C. Plant Developmental Biology. Totowa: Humana Press: 65-75. |
| 3 | Chen L, Jiang B J, Wu C X, Sun S, Hou W S, Han T F.2015. The characterization of GmTIP, a root-specific gene from soybean, and the expression analysis of its promoter.Plant Cell Tiss Organ Cult, 121(2): 259-274. |
| 4 | Doyle J J, Doyle J L.1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue.Phytochem Bull, 19: 11-15. |
| 5 | Furtado A, Henry R J.2005. The wheat Em promoter drives reporter gene expression in embryo and aleurone tissue of transgenic barley and rice.Plant Biotechnol J, 3(4): 421-434. |
| 6 | Hanahan D.1983. Studies on transformation of Escherichia coli with plasmids.J Mol Biol, 166(4): 557-580. |
| 7 | Hernandez-Garcia C M, Finer J J.2014. Identification and validation of promoters and cis-acting regulatory elements.Plant Sci, 217/218: 109-119. |
| 8 | Hsieh T H, Lee J T, Charng Y Y, Chan M T.2002. Tomato plants ectopically expressing Arabidopsis CBF1 show enhanced resistance to water deficit stress.Plant Physiol, 130(2): 618-626. |
| 9 | Huda K M K, Banu M S A, Pathi K M, Tuteja N.2013. Reproductive organ and vascular specific promoter of the rice plasma membrane Ca2+ ATPase mediates environmental stress responses in plants.PLoS One, 8: e57803. |
| 10 | International Rice Genome Sequencing Project.2005. The map-based sequence of the rice genome.Nature, 436: 793-800. |
| 11 | Jeon J S, Chung Y Y, Lee S, Yi G H, Oh B G, An G.1999. Isolation and characterization of an anther-specific gene, RA8, from rice (Oryza sativa L.).Plant Mol Biol, 39(1): 35-44. |
| 12 | Jiang C, Iu B, Singh J.1996. Requirement of a CCGAC cis-acting element for cold induction of the BN115 gene from winter Brassica napus.Plant Mol Biol, 30(3): 679-684. |
| 13 | Kasuga M, Liu Q, Miura S, Yamaguchi-Shinozaki K, Shinozaki K.1999. Improving plant drought, salt, and freezing tolerance by gene transfer of a single stress-inducible transcription factor.Nat Biotechnol, 17(3): 287-291. |
| 14 | Kasuga M, Miura S, Shinozaki K, Yamaguchi-Shinozaki K.2004. A combination of the Arabidopsis DREB1A gene and stress-inducible rd29A promoter improved drought- and low- temperature stress tolerance in tobacco by gene transfer.Plant Cell Physiol, 45(3): 346-350. |
| 15 | Kawahara Y, de la Bastide M, Hamilton J P, Kanamori H, McCombie W R, Ouyang S, Schwartz D C, Tanaka T, Wu J Z, Zhou S G, Childs K L, Davidson R M, Lin H N, Quesada-Ocampo L, Vaillancourt B, Sakai H, Lee S S, Kim J, Numa H, Itoh T, Buell C R, Matsumoto T.2013. Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data.Rice, 6: 1-10. |
| 16 | Khush G S.2001. Green revolution: The way forward.Nat Rev Genet, 2: 815-822. |
| 17 | Lan T, Gao J, Zeng Q Y.2013. Genome-wide analysis of the LEA (late embryogenesis abundant) protein gene family in Populus trichocarpa.Tree Genet Genom, 9(1): 253-264. |
| 18 | Langridge P, Fleury D.2011. Making the most of ‘omics’ for crop breeding.Trends Biotechnol, 29(1): 33-40. |
| 19 | Lata C, Yadav A, Prasad M.2011. Role of plant transcription factors in abiotic stress tolerance. In: Shanker A K, Venkateswarlu B. Abiotic Stress Response in Plants: Physiological, Biochemical and Genetic Perspectives. Croatia: InTech: 269-296. |
| 20 | Lescot M, Dehais P, Thijs G, Marchal K, Moreau Y, van de Peer Y, Rouze P, Rombauts S.2002. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences.Nucl Acids Res, 30(1): 325-327. |
| 21 | Mittler R.2006. Abiotic stress, the field environment and stress combination.Trends Plant Sci, 11(1): 15-19. |
| 22 | Moons A, Gielen J, vandekerckhove J, van der Straeten D, Gheysen G, van Montagu M.1997. An abscisic-acid- and salt-stress- responsive rice cDNA from a novel plant gene family.Planta, 202(4): 443-454. |
| 23 | Nakagawa H, Ohmiya K, Hattori T.1996. A rice bZIP protein, designated OSBZ8, is rapidly induced by abscisic acid.Plant J, 9(2): 217-227. |
| 24 | Nantel A, Quatrano R S.1996. Characterization of three rice basic/leucine zipper factors, including two inhibitors of EmBP-1 DNA binding activity.J Biol Chem, 271: 31296-31305. |
| 25 | Pan Y L, Ma X, Liang H W, Zhao Q, Zhu D Y, Yu J J.2015. Spatial and temporal activity of the foxtail millet (Setaria italica) seed-specific promoter pF128.Planta, 241(1): 57-67. |
| 26 | Shah S H, Jan S A, Ahmad N, Khan S U, Kumar T, Iqbal A, Nasir F, Noman M, Ali U A.2015. Use of different promoters in transgenic plant development: Current challenges and future perspectives.Am Eur J Agric Environ Sci, 15(4): 664-675. |
| 27 | Sundheep R, Arul L, Nagarajan P, Balasubramanian P.2008. Sprome: A database on promoters of abiotic stress inducible genes in rice.Int J Integr Biol, 2: 153-156. |
| 28 | Uno Y, Furihata T, Abe H, Yoshida R, Shinozaki K, Yamaguchi-Shinozaki K.2000. Arabidopsis basic leucine zipper transcription factors involved in an abscisic acid-dependent signal transduction pathway under drought and high-salinity conditions.Proc Natl Acad Sci USA, 97: 11632-11637. |
| 29 | Wani S H, Sah S K.2014. Biotechnology and abiotic stress tolerance in rice.J Rice Res, 2: e105. |
| 30 | Yamaguchi-Shinozaki K, Shinozaki K.1994. A novel cis-acting element in an Arabidopsis gene is involved in responsiveness to drought, low-temperature, or high-salt stress.Plant Cell, 6(2): 251-264. |
| 31 | Yamaguchi-Shinozaki K, Shinozaki K.2006. Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses.Annu Rev Plant Biol, 57: 781-803. |
| 32 | Youm J W, Jeon J H, Choi D, Yi S Y, Joung H, Kim H S.2008. Ectopic expression of pepper CaPF1 in potato enhances multiple stresses tolerance and delays initiation of in vitro tuberization.Planta, 228(4): 701-708. |
| 33 | Yu J, Hu S N, Wang J, Wong G K, Li S G, Liu B, Deng Y J, Dai L, Zhou Y, Zhang X Q, Cao M L, Liu J, Sun J D, Tang J B, Chen Y J, Huang X B, Lin W, Ye C, Tong W, Cong L J, Geng J N, Han Y J, Li L, Li W, Hu G Q, Huang X G, Li W J, Li J, Liu Z W, Li L, Liu J P, Qi Q H, Liu J S, Li L, Li T, Wang X G, Lu H, Wu T T, Zhu M, Ni P X, Han H, Dong W, Ren X Y, Feng X L, Cui P, Li X R, Wang H, Xu X, Zhai W X, Xu Z, Zhang J S, He S J, Zhang J G, Xu J C, Zhang K L, Zheng X W, Dong J H, Zeng W Y, Tao L, Ye J, Tan J, Ren X D, Chen X W, He J, Liu D F, Tian W, Tian C G, Xia H A, Bao Q Y, Li G, Gao H, Cao T, Wang J, Zhao W M, Li P, Chen W, Wang X D, Zhang Y, Hu J F, Wang J, Liu S, Yang J, Zhang G Y, Xiong Y Q, Li Z J, Mao L, Zhou C S, Zhu Z, Chen R S, Hao B L, Zheng W M, Chen S Y, Guo W, Li G J, Liu S Q, Tao M, Wang J, Zhu L H, Yuan L P, Yang H M.2002. A draft sequence of the rice genome (Oryza sativa L. ssp. indica).Science, 296: 79-92. |
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