To make
experiments with transgenic plants, the researchers commonly need to arrange
specific genetic constructions providing certain expression pattern of the
transgene(s). Selection of a promoter with appropriate characteristics is often
problematic and demands preliminary information on the pattern of its
transcriptional activity (transcriptional level, tissue- and stage-specificity,
etc.). Despite the set of very well-characterized promoters is rather small,
published experimental investigations of many plant genes frequently included
characterization of promoter regions and provided some details on the
transcriptional activities of related promoter regions and their segments. We
designed a special database (TransGene Promoters, TGP) containing data on the
transcriptional activities of plant promoter regions verified in experiments
with transgenic plants. TGP was built on the SRS platform and contains three
cross-indexed tables with information on the related genes, promoters and their
nucleotide sequences. The TGP format allows users to select DNA fragments with
experimentally verified promoter activity on the basis of various search
parameters: inducibility, specificity, etc (58 endogenous and exogenous
inducers were annotated). We believe that this information resource can be
useful both for the researchers dealing with transgenic plants as models for
fundamental research and for the specialists in plant biotechnology.
Current release of the
database comprises 318 entries including 127 promoters, 66 genes and 127
sequences of 22 plant species.
Species representation
(22)
TGP database compiles the
information on promoters of a large variety of plant species: Arabidopsis
thaliana (mouse-ear cress), Avena
sativa (oat), Capsicum annuum (pepper), Catharanthus
roseus (Madagascar periwinkle),
Dianthus caryophyllus (clove pink), Hordeum vulgare (barley), Ipomeae batatas (sweet potato), Glycine max (soybean), Lemna gibba (swollen duckweed), Lycopersicon esculentum (tomato), Medicago
sativa (alfalfa), Nicotiana plumbaginifolia (curled-leaved tobacco), Nicotiana tabacum (tobacco), Oryza sativa (rice),
Petroselinum crispum (parsley), Pisum sativum (pea), Populus trichocarpa x Populus deltoids, Solanum commersonii
(Commerson's wild potato), Solanum tuberosum (potato), Triticum aestivum
(wheat), Vicia faba (fava bean), Zea mays (maize)
Inducer representation
(58)
Auxin, cytokinin,
gibberellin A3, methyl jasmonate (MeJa), salicylic acid,
ethylene, ethephon, abscisic acid (
red light, far-red light, white light,
UV light, high light, gamma irradiation,
sucrose, glucose, mannitol, sugar
deprivation, sugar,
low temperature (cold), heat shock,
Heat Stress transcription Factor (HsfA2)
fungal infection, beta-megaspermin, pathogen, glycol, chitin, Ca2+-ionophore
A23187,
wounding, elicitor, infection, tobacco mosaic virus (TMV), Rhizobium, chitin, glucan,
pectin,
anaerobic condition, hydrogen peroxide
(H2O2), paraquat, methyl viologen,
rose bengal, mitomycin C (MMC), actinomycin
D (ActD), etoposide, senescence,
heavy metal, cadmium, copper, cobalt,
salt, NaCl, HgCl2, iron,
water, dehydration, drought, flooding
Transgenic
organisms (12)
TGP
database compiles information on following transgene promoter recipients: alfalfa, Arabidopsis, barley, swollen duckweed, parsley, potato, rice, soybean, tobacco, tomato, Vicia hirsute, maize
Links to other plant
promoter resource
TRRD (http://www.bionet.nsc.ru/trrd/)
PLACE (http://www.dna.affrc.go.jp/PLACE/)
PlantPromDB (http://www.softberry.com/berry.phtml?topic=plantprom&group=data&subgroup=plantprom)
RARGE (http://rarge.gsc.riken.jp/cdna/promoter/index.pl)
PPDB (http://www.ppdb.gene.nagoya-u.ac.jp)
AGRIS (http://arabidopsis.med.ohio-state.edu/)
DATF (http://datf.cbi.pku.edu.cn/)
ICiG group (Institute of Cytology and Genetics, Novosibirsk, Russia)
Olga G.
Alex V. Kochetov
Please send comments,
corrections and requests for additional information to
Dr. Olga G.
Fax to +7(383) 333 12 78
Dr. Olga G.
Prospekt Lavrentyeva 10
630090
We would like to thank Dmitry
Grigorovich for his contribution, construction and improvement of this database,
Dmitry Rasskazov for his updates and maintenance of this database, and
This work was supported by the
Program of Russian Academy of Sciences "Dynamics of Gene Pools". We also
thank the SD RAS Complex Integration Program (no. 5.3) for a partial support.