Simple database to select promoters for plant transgenesis

Transgenic Research - Tập 21 - Trang 429-437 - 2011
Olga G. Smirnova1, Salmaz S. Ibragimova1, Alex V. Kochetov1,2
1Institute of Cytology and Genetics, Novosibirsk, Russia
2Novosibirsk State University, Novosibirsk, Russia

Tóm tắt

The experiments with transgenic plants frequently demand selection of promoters providing appropriate transcription patterns. The set of promoters commonly used in vectors and genetic constructs is very limited, and these promoters provide only a few variants of gene expression patterns. Moreover, identical promoters in a complex construct can induce transgene silencing. This problem can be solved using a variety of plant gene promoters with experimentally verified characteristics. However, this requires a time-consuming analysis of literature data. Here, we describe a database of plant promoters (TransGene Promoters, TGP; http://wwwmgs.bionet.nsc.ru/mgs/dbases/tgp/home.html ). TGP contains the information on genomic DNA segments providing certain expression patterns of reporter genes in experiments with transgenic plants. TGP was constructed on the SRS platform, and its interface allows users to search for the promoters with particular characteristics.

Tài liệu tham khảo

Baker SS, Wilhelm KS, Thomashow MF (1994) The 5′-region of Arabidopsis thaliana cor15a has cis-acting elements that confer cold-, drought- and ABA-regulated gene expression. Plant Mol Biol 24:701–713 Bate N, Twell D (1998) Functional architecture of a late pollen promoter: pollen-specific transcription is developmentally regulated by multiple stage-specific and co-dependent activator elements. Plant Mol Bio 37:859–869 Bülow L, Brill Y, Hehl R (2010) AthaMap-assisted transcription factor target gene identification in Arabidopsis thaliana. Database (Oxford) 2010: baq034 Chang WC, Lee TY, Huang HD, Huang HY, Pan RL (2008) PlantPAN: plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups. BMC Genomics 9:561 Eskelin K, Ritala A, Suntio T, Blumer S, Holkeri H, Wahlström EH, Baez J, Mäkinen K, Maria NA (2009) Production of a recombinant full-length collagen type I alpha-1 and of a 45-kDa collagen type I alpha-1 fragment in barley seeds. Plant Biotechnol J 7:657–672 Furtado A, Henry RJ, Takaiwa F (2008) Comparison of promoters in transgenic rice. Plant Biotechnol J 6:679–693 Furtado A, Henry RJ, Pellegrineschi A (2009) Analysis of promoters in transgenic barley and wheat. Plant Biotechnol J 7:240–253 Hettiarachchi GH, Reddy MK, Sopory SK, Chattopadhyay S (2005) Regulation of TOP2 by various abiotic stresses including cold and salinity in pea and transgenic tobacco plants. Plant Cell Physiol 46:1154–1160 Hettiarachchi GH, Yadav V, Reddy MK, Chattopadhyay S, Sopory SK (2003) Light-mediated regulation defines a minimal promoter region of TOP2. Nucleic Acids Res 31:5256–5265 Higo K, Ugawa Y, Iwamoto M, Korenaga T (1999) Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res 27:297–300 Jones HD, Sparks CA (2009) Promoter sequences for defining transgene expression. Methods Mol Biol 478:171–184 Kim TW, Goo YM, Lee CH, Lee BH, Bae JM, Lee SW (2009) The sweet potato ADP-glucose pyrophosphorylase gene (ibAGP1) promoter confers high-level expression of the GUS reporter gene in the potato tuber. C R Biol 332:876–885 Morris RT, O’Connor TR, Wyrick JJ (2008) Osiris: an integrated promoter database for Oryza sativa L. Bioinformatics 24:2915–2917 O’Connor TR, Dyreson C, Wyrick JJ (2005) Athena: a resource for rapid visualization and systematic analysis of Arabidopsis promoter sequences. Bioinformatics 21:4411–4413 Peremarti A, Twyman RM, Gymez-Galera S, Naqvi S, Farrй G, Sabalza M, Miralpeix B, Dashevskaya S, Yuan D, Ramessar K, Christou P, Zhu C, Bassie L, Capell T (2010) Promoter diversity in multigene transformation. Plant Mol Biol 73:363–378 Potenza C, Aleman L, Sengupta-Gopalan C (2004) Targeting transgene expression in research, agricultural, and environmental applications: promoters used in plant transformation. In Vitro Cell Dev Biol Plant 40:1–22 Qu le Q, Xing YP, Liu WX, Xu XP, Song YR (2008) Expression pattern and activity of six glutelin gene promoters in transgenic rice. J Exp Bot 59:2417–2424 Qu LQ, Takaiwa F (2004) Evaluation of tissue specificity and expression strength of rice seed component gene promoters in transgenic rice. Plant Biotechnol J 2:113–125 Reddy MK, Nair S, Tewari KK, Mudgil Y, Yadav BS, Sopory SK (1999) Cloning and characterization of a cDNA encoding topoisomerase II in pea and analysis of its expression in relation to cell proliferation. Plant Mol Biol 41:125–137 Shahmuradov IA, Gammerman AJ, Hancock JM, Bramley PM, Solovyev VV (2003) PlantProm: a database of plant promoter sequences. Nucleic Acids Res 31:114–117 Tittarelli A, Santiago M, Morales A, Meisel LA, Silva H (2009) Isolation and functional characterization of cold-regulated promoters, by digitally identifying peach fruit cold-induced genes from a large EST dataset. BMC Plant Biol 9:121 Tiwari S, Spielman M, Day RC, Scott RJ (2006) Proliferative phase endosperm promoters from Arabidopsis thaliana. Plant Biotechnol J 4:393–407 Vickers CE, Xue G, Gresshoff PM (2006) A novel cis-acting element, ESP, contributes to high-level endosperm-specific expression in an oat globulin promoter. Plant Mol Biol 62:195–214 Xiao YL, Redman JC, Monaghan EL, Zhuang J, Underwood BA, Moskal WA, Wang W, Wu HC, Town CD (2010) High throughput generation of promoter reporter (GFP) transgenic lines of low expressing genes in Arabidopsis and analysis of their expression patterns. Plant Methods 6:18 Yamaguchi-Shinozaki K, Shinozaki K (1993) Characterization of the expression of a desiccation-responsive rd29 gene of Arabidopsis thaliana and analysis of its promoter in transgenic plants. Mol Gen Genet 236:331–340 Yamamoto YY, Obokata J (2008) ppdb: a plant promoter database. Nucleic Acids Res 36:D977–D981 Yang W, Liu XD, Chi XJ, Wu CA, Li YZ, Song LL, Liu XM, Wang YF, Wang FW, Zhang C, Liu Y, Zong JM, Li HY (2011) Dwarf apple MbDREB1 enhances plant tolerance to low temperature, drought, and salt stress via both ABA-dependent and ABA-independent pathways. Planta 233:219–229 Yilmaz A, Mejia-Guerra MK, Kurz K, Liang X, Welch L, Grotewold E (2011) AGRIS: the arabidopsis gene regulatory information server, an update. Nucleic Acids Res 39(Database issue):D1118–D1122