In silico Analysis of osr40c1 Promoter Sequence Isolated from Indica Variety Pokkali

doi:10.1016/j.rsci.2016.11.002

Abstract

Abstract:

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.

Figures/Tables 5

References 33

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Species	Gene ID	Gene name	Chromosome	Coding sequence		Gene description
Species	Gene ID	Gene name	Chromosome	Start	End	Gene description
O. sativa ssp. indica	OSINDICA_03G20090	OsIFCC006351	3	13335722	13337061	No description available
	OSINDICA_07G40440	OsIFCC024829	7	27091888	27093301
	OSINDICA_07G40470	OsIFCC024830	7	27114027	27114723
O. sativa ssp. japonica	OS03G21040	LOC_OS03G21040.2	3	11957978	11959491	Stress responsive protein, putative, expressed
	OS07G48490	LOC_OS07G48490.2	7	29004296	29005809
	OS07G48500	LOC_OS07G48500.1	7	29008973	29009669

Species	Gene ID	Gene name	Chromosome	Coding sequence		Gene description
Species	Gene ID	Gene name	Chromosome	Start	End	Gene description
O. sativa ssp. indica	OSINDICA_03G20090	OsIFCC006351	3	13335722	13337061	No description available
	OSINDICA_07G40440	OsIFCC024829	7	27091888	27093301
	OSINDICA_07G40470	OsIFCC024830	7	27114027	27114723
O. sativa ssp. japonica	OS03G21040	LOC_OS03G21040.2	3	11957978	11959491	Stress responsive protein, putative, expressed
	OS07G48490	LOC_OS07G48490.2	7	29004296	29005809
	OS07G48500	LOC_OS07G48500.1	7	29008973	29009669

Stress	Changed fold^a	Gene expression omnibus accession number
Drought stress	18.85	GSE24048
	6.44	GSE25176
	5.64	GSE24048
	4.4	GSE25176
	3.91	GSE26280
Cold stress	7.74	GSE37940
	5.1	GSE37940
	4.54	GSE37940
	3.42	GSE38023
Heat stress	5.5	GSE14275
Photoperiod	2.84	GSE28124
Biotic stress	4.49	GSE36272

Stress	Changed fold^a	Gene expression omnibus accession number
Drought stress	18.85	GSE24048
	6.44	GSE25176
	5.64	GSE24048
	4.4	GSE25176
	3.91	GSE26280
Cold stress	7.74	GSE37940
	5.1	GSE37940
	4.54	GSE37940
	3.42	GSE38023
Heat stress	5.5	GSE14275
Photoperiod	2.84	GSE28124
Biotic stress	4.49	GSE36272

Type	Element	Motif function	Abundance of element
ABA-responsive element	ABRE	cis-acting regulatory element involved in the ABA responsiveness	3
Hormone-responsive element	GARE-motif	Gibberellin-responsive element	1
	TGA-element	Auxin-responsive element	2
Light-responsive element	ATCT-motif	Part of a conserved DNA module involved in light responsiveness	1
	Box I	Light responsive element	1
	G-box like motif	cis-acting regulatory element involved in light responsiveness	3
	GT1-motif	Light responsive element	1
	Gap-box	Part of a light responsive element	1
	Sp1	Light responsive element	2
Stress-responsive element	CCAAT-box	MYBHv1 binding site	1
Fungal elicitor-responsive element	Box-W1	Fungal elicitor responsive element	1
Fungal elicitor-responsive element	Box E	cis-acting regulatory element for induction upon fungal elicitation	1
Tissue-specific element	Skn-1 motif	cis-acting regulatory element required for endosperm expression	1
Core promoter element	CAAT-box	Common cis-acting regulatory element in promoter and enhancer regions	6
	TATA-box	Core promoter element around -30 of transcription start	3