TGP_PROMOTER accumulates the information about functionally active promoters available in the scientific literature and contains the following fields:


PROMOTER_ID: this identifier is unique within the TGP_ PROMOTER database; each ID contains species abbreviation, gene abbreviation, and promoter number;

GENE_ID: the cross-reference to the corresponding GENE_ID in the TGP_GENE table;

TARGET SPECIES: the common and Latin names of transgenic organism used for analysis of the promoter activity;

LOCALIZATION: the field describes the promoter position relative to: (1) the transcription start site (TSS) or translation initiation site (TIS) and (2) according to the GenBank designations;

DESCRIPTION: description of the promoter sequence used in the corresponding transgene construct;

SEQUENCE_ID: the cross-reference to the SEQUENCE_ID in the TGP_SEQUENCE; table (containing the nucleotide sequences of the promoter fragments);

REPORTER: the gene used for evaluation of the promoter activity;

TRANSGENE the gene of interest expressed under the control of the promoter;

STAGE_ORGAN_TISSUE: the developmental stage, organs, tissues, and cells of transgenic organism where the promoter expression has been detected;

REGULATOR: the inductor or repressor influencing the promoter activity; and

COMMENT: information about the regulator-dependent, spatial, and temporal expression pattern of the promoter;

REFERENCE: the bibliographic reference;

PUBMED: the cross-reference to Entrez-PUBMED; and

END: the end of the entry of the TGP_PROMOTER database.

Example:

TGP_PROMOTER:Ps:TOP2_P3

PROMOTER_ID Ps:TOP2_P3

GENE_ID Ps:TOP2

TARGET SPECIES mouse-ear cress (Arabidopsis thaliana),
tobacco (Nicotiana tabacum)

KEYWORDS stress response, white light-induced, cotyledon, cold-induced,
abscisic acid-induced

LOCALIZATION from -362 to +74; GenBank; AF144649; TSS: 609; 247 to 682

DESCRIPTION The regulatory region upstream of the coding part of the reporter gene

included a promoter fragment (362 bp upstream of the transcription start site), 60 bp of the 5'UTR, and 14 bp of the coding sequence of the PsTOP2 gene.

SEQUENCE_ID Ps:TOP2_P3S

REPORTERGUS

STAGE_ORGAN_TISSUE seedling, cotyledon

REGULATOR white light, cold, abscisic acid

COMMENT The minimal TOP2 promoter that is induced by cold.
Transgenic Arabidopsis
The -362 bp TOP2 promoter showed very little stimulation in GUS, if any, in white light,
red light, far-red light and blue light as compared to dark grown Arabidopsis seedlings
(Hettiarachchi et al., 2003).

Transgenic tobacco

The expression of the -362 bp TOP2 promoter was detectable only in the tobacco cotyledons

(Hettiarachchi et al., 2003).

The -362 bp TOP2 promoter showed about a 2-fold higher level of activity at 12 h, with very little induction, if any, up to 4 h of cold treatment of transgenic tobacco seedlings.

The -362 bp TOP2 promoter had no detectable induction by salt or salicylic acid treatment.

The -362 bp TOP2 promoter showed very little induction, if any, at 100 microM abscisic acid and about 2-fold induction at 150 microM abscisic acid (Hettiarachchi et al., 2005).

REFERENCE Hettiarachchi G.H., Yadav V., Reddy M.K., Chattopadhyay S.,
Sopory S.K. Light-mediated regulation defines a minimal promoter region
of TOP2. Nucleic Acids Res., 2003, 31(18), 5256-5265.

PUBMED12954761

REFERENCEHettiarachchi G.H., Reddy M.K., Sopory S.K., Chattopadhyay S.
Regulation of TOP2 by various abiotic stresses including cold and
salinity in pea and transgenic tobacco plants.

Plant Cell Physiol., 2005, 46, 1154-1160.

PUBMED15879449 END

TGP_SEQUENCE accumulates information about the promoter sequences and contains the following fields

SEQUENCE_ID: this identifier is unique within the TGP_PROMOTER database. Each ID contains species abbreviation, gene abbreviation, and promoter number;

PROMOTER_ID: the cross -reference to the corresponding PROMOTER_ID in the TGP_PROMOTER table;

GENE_ID: the cross -reference to the corresponding GENE_ID in the TGP_GENE table;

SEQUENCE: the promoter nucleotide sequence and promoter positions according to the transcription start site or translation initiation site, marked as +1; and

END: the end of the entry to the TGP_SEQUENCE table.

Example:

TGP_SEQUENCE:Ps:TOP2_P3S

 

SEQUENCE_ID Ps:TOP2_P3S

PROMOTER_ID Ps:TOP2_P3

GENE_IDPs:TOP2

SEQUENCE

 -362 ttaa taaccctagt ttgacactat aaatactaaa gatgctggtg aatgaaagaa
gaaaaccaac agatgcctag cgcgtagccc cgaaatgccc tctctcttca ctctccacct
accaacaacc ggataccccc acgtgtagtc caacaaaaac attaaaagac acactgccag
aactgataca acaacacaca ctcacaaaat caccatcctc ctcaccctcc atctctctcc
acctgctccc tccactctca atccgccgaa aaagcaccac gccggcaacc acaaacctaa
tgcttcctca acctccaatc tccacccttc attcttctcc accgttcgtg tttttatcgt
       +1
tgttcgtcCt cacctccacc caacgacacc aaaaatcctg cgagcaaacc ctcaagccgc
cgcaagccca ccatctaccg tc +74
END

TGP_GENE contains general information on the activity and specificity of expression of the genes whose promoters were annotated in TGP. This table contains the following fields:

GENE_ID this identifier is unique within TGP_GENE. Each gene described is marked with genus species abbreviation and gene abbreviation;

DATE data of the last editing, consisting of day, month, and year;

AUTHOR annotator's name;

GENE short, full and synonym names of the gene;

PRODUCT Full, short and synonym names of the gene product;

TAXON Taxonomy classification of the species;

SPECIES the common and Latin names of the organism;

KEYWORD the key words;

ACTIVITY the description of the gene functional activity;

PROMOTER_ID the cross-references to the PROMOTER_ID in the TGP_PROMOTER table;

SEQUENCE_ID the cross-references to the SEQUENCE_ID in the TGP_SEQUENCE table

REFERENCE the bibliographic reference

PUBMED the cross-reference to Entrez-PUBMED; and

END the end of the entry.

Example:

TGP_GENE:Ps:TOP2

 

GENE_ID Ps:TOP2

GENE top2

PRODUCT DNA topoisomerase 2, TOP2, TOPII

TAXON Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids;
eurosids I; Fabales; Fabaceae; Papilionoideae; Vicieae; Pisum.

SPECIES pea (Pisum sativum)

KEYWORDS stress response, salt-induced, cold-induced, abscisic acid-induced,
salicylic acid-induced, white light-induced, red light-induced, far-red light-induced,
blue light-induced, cell proliferation

ACTIVITY The topo II transcript level was maximal in actively growing tissues such as root tips and young leaves from the apical region as compared to the differentiated tissues such as
the upper part of the root and internodal region of the stem of 7- to 10-day old seedlings.
The topo II transcript was also present in the young and mature flower buds and in immature
pods. The topo II transcript was abundant in proliferative tissues. The level of topo II
transcripts could be stimulated by exogenous application of growth factors that induced
proliferation in vitro cultures. The increase in the topo II transcript was seen within an hour
after irradiation of etiolated seedlings (Reddy et al., 1999).

 


The expression of TOP2 was more than 10-fold higher in constant white light grown seedlings
as compared to the darkness. The expression of TOP2 was induced up to 8-fold by a broad
spectrum of light (red, far-red and blue). The rate of blue light-mediated induction of TOP2
was slower when compared to the red light- and far-red light-mediated inductions. The
expression of TOP2 was detected to be at the highest level with about 10-fold more as
compared to dark in 7-day-old plants. The transcript level significantly decreased in 14-day-
old plants and showed only about 3-fold more expression than the dark in 21-day-old plants
(Hettiarachchi et al., 2003).

In 10-day-old pea seedlings 2.5-fold higher expression of TOP2 mRNA was detected in shoots after 2 h of cold treatment and this increased level remained the same up to 12 h exposure to
cold. Although the cold-mediated induction of TOP2 in roots was slower, more than 6-fold
induction was observed in roots after 12 h exposure to cold. TOP2 mRNA is up-regulated by
salinity stress and the response was stronger in roots (7-fold) compared with shoots (3-fold).
The expression of TOP2 was up-regulated in response to exogenous abscisic acid (ABA) and
the maximum level of induction was observed at 150 microM ABA in both root (4-fold) and
shoot (2.5-fold) tissues. Salicylic acid could induce the maximum level of expression of TOP2
at 100 microM in both shoot (2.5-fold) and root (6-fold) tissues. No significant change in the
expression of TOP2 in 10-day-old pea seedlings under dehydration stress was detected
(Hettiarachchi et al., 2005).

PROMOTER_IDPs:TOP2_P1 Ps:TOP2_P2 Ps:TOP2_P3 Ps:TOP2_P4

SEQUENCE_ID Ps:TOP2_P1S Ps:TOP2_P2S Ps:TOP2_P3S Ps:TOP2_P4S

REFERENCE Reddy M.K., Nair S., Tewari K.K., Mudgil Y., Yadav B.S., Sopory S.K.
Cloning and characterization of a cDNA encoding topoisomerase II in pea and analysis of its
expression in relation to cell proliferation. Plant Mol. Biol., 1999, 41(1), 125-137.

PUBMED10561074

REFERENCE Hettiarachchi G.H., Yadav V., Reddy M.K., Chattopadhyay S., Sopory S.K. Light-mediated regulation defines a minimal promoter region of TOP2.

Nucleic Acids Res., 2003, 31(18), 5256-5265.

PUBMED12954761

REFERENCE Hettiarachchi G.H., Reddy M.K., Sopory S.K., Chattopadhyay S. Regulation of
TOP2 by various abiotic stresses including cold and salinity in pea and transgenic tobacco

plants. Plant Cell Physiol., 2005, 46, 1154-1160.

PUBMED 15879449

END