Skip to main content
SpringerLink
Log in

In Silico Evaluation of Osmoprotectants in Eucalyptus Transcriptome

  • Conference paper
Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB 2008)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 5488))

Abstract

The synthesis of osmoprotectants is one of the main mechanisms to dribble harmful effects caused by abiotic stresses. In the present work, osmoprotectant genes were selected and used in a search for orthologs in the FORESTs database using in silico procedures. The studied genes were here analyzed for the first time in Eucalyptus, including 51 identified orthologs from nine gene families (P5CS=3, P5CR=4, TPS1=10, TPPB=8, SAT=6, OASTL=13, CMO=1, BADH=3 and INPS1=3). In general, the most represented genes were those involved in the trehalose and cysteine synthesis, probably due to their vital importance in the maintenance of cellular homeostasis. Overall expression pattern revealed significant amounts of reads in most libraries. Dendrograms based on analysis of selected genes from other flowering plants revealed no clear separation between mono and dicots, since diversity regarding the evolution and diversity in gene signatures may be more related to fitness and adaptation, than evolutionary patterns.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Lemcoff, J.H., Guarnaschelli, A.B., Garau, A.M., Bascialli, M.E., Ghersa, C.M.: Osmotic Adjustment and its Use as a Selection Criterion in Eucalyptus Seedlings. Can. J. For. Res. 24(12), 2404–2408 (1994)

    Article  Google Scholar 

  2. Ladiges, P.Y.: Variation in Drought Tolerance in Eucalyptus viminalis Labill. Aust. J. Bot. 22(3), 489–500 (1974)

    Article  Google Scholar 

  3. Paston, G.M., Foyer, C.H.: Common components, Networks, and Pathways of Cross-Tolerance to Stress. The Central Role of Redox and Abscisic Acid-mediated Controls. Plant Physiol. 129, 460–468 (1999)

    Google Scholar 

  4. Elbein, A.D., Pan, Y.T., Pastuszak, I., Carroll, D.: New Insights on Trehalose: a Multifunctional Molecule. Glycobiology 13, 17–27 (2003)

    Article  Google Scholar 

  5. Hegeman, C.E., Good, L.L., Grabau, E.A.: Expression of D-Myo-Inositol-3-Phosphate Synthase in Soybean. Implications for Phytic Acid Biosynthesis. Plant Physiol. 125, 1941–1948 (2001)

    CAS  PubMed  Google Scholar 

  6. Hu, C.A., Delauney, A.J., Verma, D.P.: A Bifunctional Enzyme (Delta 1-Pyrroline-5-Carboxylate Synthetase) Catalyzes the First Two Steps in Proline Biosynthesis in Plants. Proc. Natl. Acad. Sci. USA 89(19), 9354–9358 (1992)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Sirko, A., Blaszczyk, A., Liszewska, F.: Overproduction of SAT and/or OASTL in Transgenic Plants: a Survey of Effects. J. Exp. Bot. 55(404), 1881–1888 (2004)

    Article  CAS  PubMed  Google Scholar 

  8. Sakamoto, A., Murata, N.: The role of Glycine-Betaine in the Protection of Plants from Stress: Clues from Transgenic Plants. Plant Cell Environ. 25(2), 163–171 (2002)

    Article  CAS  PubMed  Google Scholar 

  9. Vicentini, R., Sassaki, F.T., Gimenes, M.A., Maia, I.G., Menossi, M.: In Silico Evaluation of the Eucalyptus Transcriptome. Gen. Mol. Bio. 28(3), 487–495 (2005)

    Article  CAS  Google Scholar 

  10. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J.: Basic Local Alignment Search Tool. J. Mol. Biol. 251, 403–410 (1990)

    Article  Google Scholar 

  11. Thompson, J.D., Higgins, D.G., Gibson, T.J.: CLUSTALX, Multiple Sequence Alignment Program Version 1.63b. EMBO Rep. (1997)

    Google Scholar 

  12. Tamura, K., Dudley, J., Nei, M., Kumar, S.: MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0. Mol. Biol. Evol. 24, 1596–1599 (2007)

    Article  CAS  PubMed  Google Scholar 

  13. Eisen, M.B., Spellman, P.T., Brown, P.O., Botstein, D.: Cluster Analysis and Display of Genome-Wide Expression Patterns. Proc. Natl. Acad. Sci. USA 95, 14863–14868 (1998)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Page, R.D.: Treeview Program Version 161. Comput. Appl. Biosci. 12, 357–358 (1996)

    CAS  PubMed  Google Scholar 

  15. Barbosa-da-Silva, A., Wanderley-Nogueira, A.C., Silva, R.R.M., Berlarmino, L.C., Soares-Cavalcanti, N.M., Benko-Iseppon, A.M.: In Silico Survey of Resistance (R) Genes in Eucalyptus Transcriptome. Gen. Mol. Biol. 28(3), 562–574 (2005)

    Article  CAS  Google Scholar 

  16. Hell, R., Wirtz, F., Berkowitz, O., Droux, M.: The Cysteine Synthase Complex from Plants. Mitochondrial Serine Acetyltransferase from Arabidopsis thaliana Carries a Bifunctional Domain for Catalysis and Protein-protein Interaction. Eur. J. Biochem. 268, 683–686 (2001)

    Google Scholar 

  17. Müller, J., Aeschbacher, R.A., Wingler, A., Boller, T., Wiemken, A.: Trehalose and Trehalase in Arabidopsis. Plant Physiol. 125, 1086–1093 (2001)

    Article  PubMed  PubMed Central  Google Scholar 

  18. Verbruggen, N., Villarroel, R., Montagu, M.V.: Osmoregulation of a Pyrroline-5-Carboxylate Reductase Gene in Arabidopsis thaliana. Plant Physiol. 103, 771–781 (1993)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Marsh, N.R., Adams, M.A.: Decline of Eucalyptus tereticornis near Bairnsdale, Victoria: Insect Herbivory and Nitrogen Fractions in Sap and Foliage. Aust. J. Bot. 43, 39–50 (1995)

    Article  Google Scholar 

  20. Adams, M.A., Richter, A., Hill, A.K., Colmer, T.D.: Salt Tolerance in Eucalyptus spp.: Identity and Response of Putative Osmolytes. Plant Environ. 28, 772–787 (2005)

    Article  CAS  Google Scholar 

  21. Hazen, S.P., Wu, Y., Kreps, J.A.: Gene Expression Profiling of Plant Responses to Abiotic Stress. Funct. Integr. Genomics 3(3), 105–111 (2003)

    Article  CAS  PubMed  Google Scholar 

  22. Weston, D.J., Gunter, L.E., Rogers, A., Wullschleger, S.D.: Connecting Genes, Coexpression Modules and Molecular Signatures to Environmental Stress Phenotypes in Plants. BMC Syst. Biol. 2, 1–17 (2008)

    Article  Google Scholar 

  23. Benko-Iseppon, A.M., Soares-Cavalcanti, N.M., Wanderley-Nogueira, A.C., Berlarmino, L.C., Silva, R.R.M., Almeida, P.M.L., Brunelli, K.R., Kido, L.M.H., Kido, E.A.: Genes Associated to Biotic and Abiotic Stresses in Cowpea [Vigna unguiculata (L.) Walp.] and Other Angiosperms. In: Nogueira, R.J.M.C., Araújo, E.L., Willadino, L.C., Cavalcante, U.M.T. (eds.) Environmental Stresses: Damages and Benefits to Plants, pp. 350–359. UFRPE University Press Recife, Brazil (2005)

    Google Scholar 

  24. Ishitani, M., Arakawa, K., Mizuno, K., Kishitani, S., Takabe, T.: Betaine Aldehyde in Leaves of both Betain-Accumulating and Non-Accumulating Cereal Plants. Plant Cell Physiol. 34, 493–495 (1993)

    CAS  Google Scholar 

  25. Kawashima, C.G., Berkowitz, O., Hell, R., Noji, M., Saito, K.: Characterization and Expression Analysis of a Serine Acetyltransferase Gene Family Involved in a Key Step of the Sulfur Assimilation Pathway in Arabidopsis. Plant Physiol. 137, 220–230 (2005)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Freeman, J.L., Salt, D.E.: The Metal Tolerance Profile of Thlaspi goesingense is Mimicked in Arabidopsis thaliana Heterologously Expressing Serine Acetyl-Transferase. BMC Plant Biol. 7, 63 (2007)

    Article  PubMed  PubMed Central  Google Scholar 

  27. Liu, F., Byung-Chun, Y., Jung-Youn, L., Pan, W., Harmon, A.C.: Calcium-Regulated Phosphorylation of Soybean Serine Acetyltransferase in Response to Oxidative Stress. J. Biol. Chem. 281(37), 27405–27415 (2006)

    Article  CAS  PubMed  Google Scholar 

  28. Saito, K.: Isolation and Characterization of a cDNA that Encodes a Putative Mitochondrion-Localized Isoform of Cysteine Synthase (O-Acetylserine(Thiol)-lyase) from Spinacia oleracea. J. Biol. Chem. 269(28), 187–192 (1994)

    Google Scholar 

  29. Liszewska, F., Gaganidze, D., Sirko, A.: Isolation of Nicotiana plumbaginifolia cDNAs Encoding Isoforms of Serine Acetyltransferase and O-Acetylserine (Thiol)lyase in a Yeast Two-Hybrid System with Escherichia coli CysE and CysK Genes as Baits. Acta Biochim. Pol. 52(1), 117–128 (2005)

    CAS  PubMed  Google Scholar 

  30. González, E.M., Ladrera, R., Larrainzar, E., Arrese-Igor, C.: Response of Medicago truncatula to Drought Stress. In: Mathesius, U., Journet, E.P., Sumner, L.W. (eds.) The Samuel Roberts Noble Foundation, Ardmore, OK, pp. 1–6 (2007)

    Google Scholar 

  31. Chandran, D., Sharopova, N., Ivashuta, S., Gantt, J., VandenBosch, K.A., Samac, D.A.: Transcriptome Profiling Identified Novel Genes Associated with Aluminum Toxicity, Resistance and Tolerance in Medicago truncatula. Planta 228, 151–166 (2008)

    Article  CAS  PubMed  Google Scholar 

  32. Waldren, R.P., Teare, I.D.: Free Proline Accumulation in Drought-Stressed Plants under Laboratory Conditions. Plant Soil 40(3), 689–692 (1974)

    Article  CAS  Google Scholar 

  33. Weiss, E.A. (ed.): Oilseed Crops. Longman, London (1983)

    Google Scholar 

  34. Yoshida, K.T., Wada, T., Koyama, H., Mizobuchi-Fukuoka, R., Naito, S.: Temporal and Spatial Patterns of Accumulation of the Transcript of Myo-Inositol-1-Phosphate Synthase and Phytin-Containing Particles During Seed Development in Rice. Plant Physiol. 119(1), 65–72 (1999)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Kiranmayi, P., Mohan, P.M.: Metal Transportome of Neurospora crassa. Silico Biol. 6(3), 169–180 (2006)

    CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Center for Biological Sciences (CCB), Genetics Department, Laboratory for Plant Genetics and Biotechnology, Universidade Federal de Pernambuco, Av. Prof. Moraes Rêgo s/no., Recife, PE, Brazil

    Petra dos Santos Barros, Nina M. Soares-Cavalcanti, Gabriela S. Vieira-Mello, Ana C. Wanderley-Nogueira, Tercílio Calsa-Junior & Ana M. Benko-Iseppon

Authors
  1. Petra dos Santos Barros
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Nina M. Soares-Cavalcanti
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Gabriela S. Vieira-Mello
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ana C. Wanderley-Nogueira
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Tercílio Calsa-Junior
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Ana M. Benko-Iseppon
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. DISI - Dipartimento di Informatica e Scienze dell’Informazione, Università di Genova, Via Dodecaneso 35, 16146, Genova, Italy

    Francesco Masulli

  2. DMI, Dipartimento di Matematica ed Informatica, Università di Salerno, Via Ponte don Melillo, 84084, Fisciano (Sa), Italy

    Roberto Tagliaferri

  3. Department of Pharmaceutical Chemistry, School of Pharmacy, The University of Kansas, 2095 Constant Ave, Lawrence, 66047, Kansas, USA

    Gennady M. Verkhivker

Rights and permissions

Reprints and permissions

Copyright information

© 2009 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

dos Santos Barros, P., Soares-Cavalcanti, N.M., Vieira-Mello, G.S., Wanderley-Nogueira, A.C., Calsa-Junior, T., Benko-Iseppon, A.M. (2009). In Silico Evaluation of Osmoprotectants in Eucalyptus Transcriptome. In: Masulli, F., Tagliaferri, R., Verkhivker, G.M. (eds) Computational Intelligence Methods for Bioinformatics and Biostatistics. CIBB 2008. Lecture Notes in Computer Science(), vol 5488. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-02504-4_6

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-02504-4_6

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-02503-7

  • Online ISBN: 978-3-642-02504-4

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation