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Mendel-ESTS: Database of Plant ESTs in dbEST Annotated with Gene Family Numbers and Gene Family Names

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Abstract

The rapid expansion of gene sequencing has led to an exponential increase in the number of genes being deposited in the sequence databases. Associated with this is the proliferation of idiosyncratic gene names. The DE field descriptions in closely related sequences, whether they be from the same or different species, particularly in the EMBL and TrEMBL databases are often inconsistent and sometimes incorrect and misleading (Galperin and Koonin 1998). In an attempt to unify gene nomenclature and DE field descriptions, initially within the plants, two databases have been created: Mendel-GFDb (genes arranged into gene families) and Mendel-ESTS (plant EST and STS sequences related to genes in Mendel-GFDb by gene family numbers). The database web addresses are:

Mendel-GFDb and Mendel-ESTS: http://www.mendel.ac.uk/

US Mirror: http://genome.cornell.edu/

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References

  1. Ausubel F, Brent R, Kingston RE, Moore DD, Seidmann JG, Smith JA, Struhl K: Current Protocols in Molecular Biology, vol. 1. John Wiley, New York (1987–1997).

    Google Scholar 

  2. Barkla BJ, Pantoja O: Physiology of ion transport across the tonoplast of higher plants. Annu Rev Plant Physiol Plant Mol Biol 47: 159–184(1996).

    Google Scholar 

  3. Barkla BJ, Zingarelli L, Blumwald E, Smith JAC: Tonoplast NaC/HC antiport activity and its energization by the vacuolar HC-ATPase in the halophytic plant Mesembryanthemum crystallinum L. Plant Physiol 109: 549–556(1995).

    Google Scholar 

  4. Binzel ML, Dunlap JR: Abscisic acid does not mediate NaCl-induced accumulation of 70 kDa subunit tonoplast HCATPase message in tomato. Planta 197: 563–568(1995).

    Google Scholar 

  5. Binzel ML: NaCl-induced accumulation of tonoplast and plasma membrane HC-ATPase message in tomato. Physiol Plant 94: 722–728(1995).

    Google Scholar 

  6. Blumwald E, Poole RJ: NaC/HC antiport in isolated tonoplast vesicles from storage tissue of Beta vulgaris. Plant Physiol 78: 163–167(1985).

    Google Scholar 

  7. Blumwald E, Poole RJ: Salt tolerance in suspension cultured cells of sugar beet: induction of NaC/HC antiport activity at the tonoplast by growth in salt. Plant Physiol 83: 884–887 (1987).

    Google Scholar 

  8. Bowman EA, Tenney K, Bowman BJ: Isolation of genes encoding the Neurospora crassa vacuolar ATPase. J Biol Chem 263: 13994–14001(1988).

    Google Scholar 

  9. Callis J, Fromm M, Walbot V: Introns increase gene expression in cultured maize cells. Gene Dev 1: 1183–1200 (1987)

    Google Scholar 

  10. Chanson A: Active transport of protons and calcium in higher plant cells. Plant Physiol Biochem 31: 943–955(1993).

    Google Scholar 

  11. Cushman JC, Bohnert HJ: Salt stress alters A/T-rich DNAbinding factor interactions within the phosphoenolpyruvate carboxylase promoter from Mesembryanthemum crystallinum. Plant Mol Biol 20: 411–424(1992).

    Google Scholar 

  12. De Vetten NC, Ferl RJ: Transcriptional regulation of environmentally inducible genes in plants by an evolutionary conserved family of G-box binding factors. Int J Biochem 26: 1055–1068(1994).

    Google Scholar 

  13. DuPont FM: Salt-induced changes in ion transport: regulation of primary pumps and secondary transporters. In: Cooke DT, Clarkson D (eds) Transport and receptor proteins of plant membranes, pp. 91–100. Plenum, New York (1992).

    Google Scholar 

  14. Enjuto M, Lumbreras V, Marin C, Boronat A: Expression of the Arabidopsis HMG2 gene, encoding 3-hydroxy-3-methylglutaryl coenzyme A reductase, is restricted to meristematic and floral tissues. Plant Cell 7: 517–527(1995).

    Google Scholar 

  15. Gelli A, Blumwald E: Calcium retrieval from vacuolar pools: characterization of a vacuolar calcium channel. Plant Physiol 102: 1139–1146(1993).

    Google Scholar 

  16. Gogarten JP, Fichmann J, Braun Y, Morgan L, Styles P, Taiz SL, DeLapp K, Taiz L: The use of antisense mRNA to inhibit the tonoplast HCATPase in carrot. Plant Cell 4: 851–864 (1992).

    Google Scholar 

  17. Hasebe M, Hanada H, Moriyama Y, Maeda M, Futai M: Vacuolar type HC-ATPase genes: Presence of four genes including pseudogenes for the 16-kDa proteolipid subunit in the human genome. Biochem Biophys Res Comm 183: 856–863 (1992).

    Google Scholar 

  18. Hasenfratz M, Tsou C, Wilkins TA: Expression of two related vacuolar HC-ATPase 16-kDa proteolipid genes is differentially regulated in a tissue-specific manner. Plant Physiol 108: 1395–1404(1995).

    Google Scholar 

  19. Kirsch M, An Zhigang, Viereck R, Löw R, Rausch T: Salt stress induces an increased expression of V-type HC-ATPase in mature sugar beet leaves. Plant Mol Biol 32: 543–547 (1996).

    Google Scholar 

  20. Logemann J, Schell J, Willmitzer L: Improved method for the isolation of RNA from plant tissues. Anal Biochem 163: 16–20 (1987).

    Google Scholar 

  21. Löw R, Rausch T: In suspension-cultured Daucus carota cells salt stress stimulates HC transport but not ATP hydrolysis of the V-ATPase. J Exp Bot 47: 1725–1732(1996).

    Google Scholar 

  22. Löw R, Rausch T: Detection of nucleic acids with biotinylated PCR-amplified probes. In: Meier T, Fahrenholz F (eds) A Laboratory Guide to Biotin-Labelling in Biomolecule Analysis pp. 201–213. Birkhäuser Verlag, Basel (1996).

    Google Scholar 

  23. Löw R, Rockel B, Kirsch M, Ratajczak R, Hörtensteiner S, Martinoia E, Lüttge U, Rausch T: Early salt stress effects on the differential expression of vacuolar HC-ATPase genes in roots and leaves of Mesembryanthemum crystallinum. Plant Physiol 110: 259–265(1996).

    Google Scholar 

  24. Manolson MF, Quelette BFF, Filion M, Poole RJ: cDNA sequence and homologies of the ‘57 kDa’ nucleotide-binding subunit of the vacuolar ATPase from Arabidopsis. J Biol Chem 263: 17987–17994(1988).

    Google Scholar 

  25. Miller AJ, Smith SJ: Nitrate transport and compartmentation in cereal root cells. J Exp Bot 47: 843–854(1996).

    Google Scholar 

  26. Murray MG, Thompson WF: Rapid isolation of high molecular weight plant DNA. Nucl Acids Res 8: 4321–4325 (1980).

    Google Scholar 

  27. Narasimhan ML, Binzel ML, Perez-Prat E, Chen Z, Nelson DE, Singh NK, Bressan RA, Hasegawa PM: NaCl regulation of tonoplast ATPase 70-kDa subunit mRNA in tobacco cells. Plant Physiol 97: 562–568(1991).

    Google Scholar 

  28. Palmer JD, Logsdon JM: The recent origins of introns. Curr Opin Genet Dev 1: 470–477(1991).

    Google Scholar 

  29. Perera IY, Li X, Sze H: Several distinct genes encode nearly identical 16 kDa proteolipids of the vacuolar HC-ATPase from Arabidopsis thaliana. Plant Mol Biol 29: 227–244(1995).

    Google Scholar 

  30. Ratajczak R, Richter J, Lüttge U: Adaptation of the tonoplast V-type HC-APase of Mesembryanthemum cristallinum to salt stress, C3-CAM transition and plant age. Plant Cell Environ 17: 1101-1112(1994).

    Google Scholar 

  31. Rausch T, Kirsch M, Löw R, Lehr A, Viereck R, An Zhigang: Salt stress responses of higher plants: The role of proton pumps and NaC/HC antiporters. J Plant Physiol 148: 425–433 (1996).

    Google Scholar 

  32. Rea PA, Sanders D: Tonoplast energetization: two HC pumps, one membrane. Physiol Plant 71: 131–141(1987).

    Google Scholar 

  33. Schledzewski K, Mendel RR: Quantitative transient gene expression: comparison of the promoters of maize polyubiquitin1, rice actin1, maize-derived Emu and CaMV 35S in cells of barley, maize, and tobacco. Transgen Res 3: 249–255(1994).

    Google Scholar 

  34. Shen Q, Ho T-HD: Functional dissection of an abscisic acid (ABA)-inducible gene reveals two independent ABAresponsive complexes each containing a G-box and a novel cis-acting element. Plant Cell 7: 295–307(1995).

    Google Scholar 

  35. Sista H, Wechser M, Bowman BJ: The proteolipid subunit of the Neurospora crassa vacuolar ATPase: isolation of the protein and the vma-3 gene. Mol Gen Genet 243: 82–90 (1994).

    Google Scholar 

  36. Starke T, Gogarten JP: A conserved intron in the V-ATPase A subunit genes of plants and algae. FEBS Lett 315: 252–258 (1993).

    Google Scholar 

  37. Stomp AM: Histochemical localization of _-glucuronidase. In: Gallagher SR (ed) GUS Protocols, pp. 103–113. Academic Press, San Diego (1992).

    Google Scholar 

  38. Struve I, Rausch T, Bernasconi P, Taiz L: Structure and function of the promoter of the carrot V-type HC-ATPase catalytic subunit gene. J Biol Chem 265: 7927–7932(1990).

    Google Scholar 

  39. Sze H, Ward JM, Lai S: Vacuolar HC-translocating ATPases from plants: Structure, function, and isoforms. J Bioenerg Biomembr 24: 371–381(1992).

    Google Scholar 

  40. Timmermanns MCP, Maliga P, Vieira J, Messing J: The pFF plasmids: cassettes utilising CaMW sequences for expression of foreign genes in plants. J Biotechnol 14: 333–344(1990).

    Google Scholar 

  41. Toyama R, Goldstein DJ, Schlegel R, Dhar R: A genomic sequence of the Schizosaccharomyces pombe 16 kDa vacuolar HC-ATPase. Yeast 7: 989–991(1991).

    Google Scholar 

  42. Tsiantis M, Bartholomew DM, Smith JAC: Salt regulation of transcript levels for the c subunit of a leaf vacuolar HC-ATPase in the halophyte Mesembryanthemum crystallinum. Plant J 9: 729–726(1996).

    Google Scholar 

  43. Viereck R, Kirsch M, Löw R, Rausch T: Down-regulation of plant V-type HC-ATPase genes after light-induced inhibition of growth. FEBS Lett 384: 285–288(1996).

    Google Scholar 

  44. Wechser M, Bowman BJ: Regulation of the expression of three housekeeping genes encoding subunits of the Neurospora crassa vacuolar ATPase. Mol Gen Genet 249: 317–327 (1995).

    Google Scholar 

  45. Wilkins TA, Wan CY, Lu CC: Ancient origin of the vacuolar HC-ATPase 69-kilodalton subunit superfamily. Theor Appl Genet 89: 514–524(1994).

    Google Scholar 

  46. Zhen RG, Koyro HW, Leigh RA, Tomos AD, Miller AJ: Compartmental nitrate concentrations in barley root cells measured with nitrate-selective microelectrodes and by single-cell sap sampling. Planta 185: 356–361(1991).

    Google Scholar 

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Authors and Affiliations

  1. Mendel Bioinformatics Group, John Innes Centre, Colney, Norwich, NR4 7UH, UK

    David Lonsdale, Benjamin Arnold & Benedict Arnold

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  1. David Lonsdale
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  2. Benjamin Arnold
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Lonsdale, D., Arnold, B. & Arnold, B. Mendel-ESTS: Database of Plant ESTs in dbEST Annotated with Gene Family Numbers and Gene Family Names. Plant Molecular Biology Reporter 17, 239–247 (1999). https://doi.org/10.1023/A:1007610917444

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