Skip to main content
SpringerLink
Log in

Identification and Expression of Early Nodulin in Sugarcane Transcriptome Revealed by in Silico Analysis

  • Conference paper
Book cover Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB 2010)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 6685))

Abstract

Nodulin genes have been defined as plant genes that are induced during nodule formation in legumes. Many studies, however, revealed a number of nodulins in non-legumes, including monocot plants, suggesting that these genes play additional roles besides nodulation. The presence and expression profile of the early nodulin genes (Annexin, DMI3, NIN, NORK, CCS52A, and ENOD8) was evaluated in the sugarcane transcriptome (237,954 ESTs) using in silico procedures. 129 sugarcane clusters were identified (out of 1,476 transcripts) and their expression profile was evaluated. Higher expression was observed in libraries of flowers, roots and normalized mix of tissues, confirming their multi-function character besides the plant-bacteria endophytic interaction in sugarcane. The multiple alignments revealed high homology among sugarcane sequences and respective proteins from other plants, mainly monocots, revealing a relatively conserved genetic structure among species, probably regarding ancient genetic processes.

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. Nogueira, E.M., Vinagre, F., Masuda, H.P., Vargas, C., Padua, V.L.M., Silva, F.R., Santos, R.V., Baldani, J.I., Ferreira, P.C.G., Hemerly, A.S.: Expression of Sugarcane Genes Induced by Inoculation With Gluconacetobacter diazotrophicus and Herbaspirillum rubrisubalbicans. Gen. and Mol. Biol. 24, 199–206 (2001)

    Article  Google Scholar 

  2. Serrato, R.V., Sassaki, G.L., Cruz, L.M., Carlson, R.W., Muszynski, A., Monteiro, R.A., Pedrosa, F.O., Souza, E.M., Iacomini, M.: Chemical Composition of Lipopolysaccharides Isolated From Various Endophytic Nitrogen-fixing Bacteria of the Genus Herbaspirillum. Can. J. Microbiol. 56, 342–347 (2010)

    Article  Google Scholar 

  3. Kouchi, H., Takane, K., So, R.B., Ladha, J.K., Reddy, P.M.: Rice ENOD40: Isolation and Expression Analysis in Rice and Transgenic Soybean Root Nodules. Plant J. 18, 121–129 (1999)

    Article  Google Scholar 

  4. Reddy, P.M., Aggarwal, R.K., Ramos, M.C., Ladha, J.K., Brar, D.S., Kouchi, K.: Widespread Occurrence of the Homologs of the Early Nodulin (ENOD) Genes in Oryza Species, Related Grasses. Bioch. and Bioph. Res. Com. 258, 148–154 (1999)

    Article  Google Scholar 

  5. Vargas, C., Padua, V.L.M., Nogueira, E.M., Vinagre, F., Masuda, H.P., Da Silva, L.: Signaling Pathways Mediating the Association Between Sugarcane and Endophytic Diazotrophic Bacteria: A Genomic Approach. Symb. 35, 159–180 (2003)

    Google Scholar 

  6. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, M., Lipman, D.J.: Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Programs. Nucl. Acid Res. 25, 3389–3402 (1997)

    Article  Google Scholar 

  7. Eisen, M.B., Spellman, P.T., Brown, P.O., Botstein, D.: Cluster Analysis and Display of Genomic-wide Expression Pattern. PNAS 95, 14863–14868 (1998)

    Article  Google Scholar 

  8. Page, R.D.: Treeview Program Version 161. Com. App. Biosc. 12, 357–358 (1996)

    Google Scholar 

  9. Tamura, K., Dudley, J., Nei, M., Kumar, S.: Mega4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0. Mol. Biol. and Evol. 24, 1596–1599 (2004)

    Article  Google Scholar 

  10. Morgan, R.O., Martin-Almedina, S., Iglesias, J.M., Gonzalez-Florez, M.I., Fernandez, M.P.: Evolutionary Perspective on Annexin Calcium-binding Domains. Bioch. Bioph. Acta 1742, 133–140 (2004)

    Article  Google Scholar 

  11. Niebel, F.C., Lescure, N., Cullimore, J.V., Gamas, P.: The Medicago truncatula MtAnn1 Gene Encoding an Annexin is Induced by Nod Factors and During the Symbiotic Interaction With Rhizobium meliloti. Mol. Plant-Microbe Interac. 1, 504–513 (1998)

    Article  Google Scholar 

  12. Laohavisit, A., Mortimer, J.C., Demidchik, V., Coxon, K.M., Stancombe, A.M., Macpherson, N., Brownlee, C., Hofmann, A., Webb, A.A.R., Miedema, H., Battey, N.H., Davies, J.M.: Zea mays Annexins Modulate Cytosolic Free Ca2 +  and Generate a Ca2 + -Permeable Conductance. The Plant Cell 21, 479–493 (2009)

    Article  Google Scholar 

  13. Messinese, E., Mun, J.-H., Yeun, L.H., Jayaraman, D., Rouge, P., Barre, A., Lougnon, G., Schornack, S., Bono, J.-J., Cook, D.R., Ane, J.-M.: A Novel Nuclear Protein Interacts With the Symbiotic DMI3 Calcium- and Calmodulin-dependent Protein Kinase of Medicago truncatula. Mol. Plant-Microbe Interac. 20, 912–921 (2007)

    Article  Google Scholar 

  14. Yang, T., Poovaiah, B.W.: Calcium/calmodulin-mediated Signal Network in Plants. Trends in Plant Sci. 8, 505–512 (2003)

    Article  Google Scholar 

  15. Cebolla, A., Vinardell, J.M., Kiss, E., Olah, B., Roudier, F., Kondorosi, A., Kondorosi, E.: The Mitotic Inhibitor ccs52 is Required for Endoreduplication and Ploidy-dependent Cell Enlargement in Plants. Europ. Mol. Biol. J. 18, 4476–4484 (1999)

    Article  Google Scholar 

  16. Foucher, F., Kondorosi, A.: Cell Cycle Regulation in Course of Nodule Organogenesis in Medicago. Plant Mol. Biol. 43, 773–786 (2000)

    Article  Google Scholar 

  17. Gonzalez-Sama, A., de la Peña, T.C., Kevei, Z., Mergaert, P., Lucas, M.M., Felipe, M.R., Kondorosi, E., Pueyo, J.J.: Nuclear DNA Endoreduplication and Expression of the Mitotic Inhibitor CCS52 Associated to Determinate and Lupinoid Nodule Organogenesis. Mol. Plant-Microbe Interac. 19, 173–180 (2006)

    Article  Google Scholar 

  18. Riechman, J.L., Heard, J., Martin, G., Reuber, L., Keddie, C.Z.J., Pineda, L.A.O., Ratcliffe, O.J., Samaha, R.R., Creelman, R., Pilgrim, M., Broun, P., Zhang, J.Z., Ghandehari, D., Sherman, B.K., Yu, G.L.: Arabidopsis Transcription Factors: Genome-wide Comparative Analysis Among Eukaryotes. Sci. 290, 2105–2110 (2000)

    Article  Google Scholar 

  19. Schauser, L., Wieloch, W., Stougaard, J.: Evolution of NIN-Like Proteins in Arabidopsis, Rice, and Lotus japonicas. J. Mol. Evol. 60, 229–237 (2005)

    Article  Google Scholar 

  20. Endre, G., Kereszt, A., Kevei, Z., Mihacea, S., Kalo, P., Kiss, G.B.: A receptor Kinase Gene Regulating Symbiotic Nodule Development. Nature 417, 962–966 (2002)

    Article  Google Scholar 

  21. Shiu, S.H., Karlowski, W.M., Pan, R., Tzeng, Y.H., Mayer, K.F.X., Li, W.-H.: Comparative Analysis of the Receptor-like Kinase Family in Arabidopsis and Rice. The Plant Cell 16, 1220–1234 (2004)

    Article  Google Scholar 

  22. Morillo, S.A., Tax, F.E.: Functional Analysis of Receptor-like Kinases in Monocots and Dicots. Cur. Op. in Plant Biol. 9, 460–469 (2006)

    Article  Google Scholar 

  23. Vinagre, F., Vargas, C., Schwarcz, K., Cavalcante, J., Nogueira, E.M., Baldani, J.I., Ferreira, P.C.G., Hemerly, A.S.: SHR5: A Novel Plant Receptor Kinase Involved in Plant-N2-fixing Endophytic Bacteria Association. J. Exp. Bot. 57, 559–569 (2006)

    Article  Google Scholar 

  24. Gyorgyey, J., Vaubert, D., Jimenez-Zurdo, J.I., Charon, C., Troussard, T., Kondorosi, A., Kondorosi, E.: Analysis of Medicago truncatula Nodule Expressed Tags. Mol. Plant-Microbe Interac. 13, 62–71 (2000)

    Article  Google Scholar 

  25. Ruppert, M., Woll, J., Giritch, A., Genady, E., Ma, X., Stockigt, J.: Functional Expression of an Ajmaline Pathway-specific Esterase From Rauvolfia in a Novel Plant-virus Expression System. Planta 222, 888–898 (2005)

    Article  Google Scholar 

  26. Ruttink, T.: ENOD40 Affects Phytohormone Cross-talk. PhD Thesis, Wageningen University (2003) ISBN:9058089797

    Google Scholar 

  27. Compaan, B., Ruttinka, T., Albrecht, C., Meeley, R.: Identification and Characterization of a Zea mays Line Carrying a Transposon-tagged ENOD40. Bioch. Bioph. Acta 1629, 84–91 (2003)

    Google Scholar 

  28. Charon, C., Sousa, C., Crespi, M., Kondorosi, A.: Alteration of enod40 Expression Modifies Medicago truncatula Root Nodule Development Induced by Sinorhizobium meliloti. The Plant Cell 11, 1953–1966 (1999)

    Google Scholar 

  29. Sinvany, G., Kapulnik, Y., Wininger, S., Badani, H., Jurkevitch, E.: The Early Nodulin ENOD40 is Induced by, And Also Promotes Arbuscular Mycorrhizal Root Colonization. Physiol. Mol. Plant Pathol. 60, 103–109 (2002)

    Article  Google Scholar 

  30. Ling, H., Zhao, J., Zuo, K., Qiu, C., Yao, H., Qin, J., Sun, X., Tang, K.: Isolation and Expression Analysis of a GDSL-like lipase Gene From Brassica napus L. J. Bioch. Mol. Biol. 39, 297–303 (2006)

    Google Scholar 

  31. Miyao, A., Iwasaki, Y., Kitano, H., Itoh, J., Maekawa, M., Murata, K., Yatou, O., Nagato, Y., Hirochika, H.: A Large-scale Collection of Phenotypic Data Describing an Insertional Mutant Population to Facilitate Functional Analysis of Rice Genes. Plant Mol. Biol. 63, 625–635 (2007)

    Article  Google Scholar 

  32. Andersson, C., Ostergaard Jensen, E., Llewellyn, D., Dennis, E., Peacock, W.J.: A New Hemoglobin Gene From Soybean: a Role for Hemoglobin in all Plants. PNAS 93, 5682–5687 (1996)

    Article  Google Scholar 

  33. Kawahara, H., Chonan, N.: Studies on Morphogenesis in Rice Plants. Histological Observation on the Maturing Process of Vascular Bundles in Culm. Japan J. Crop Sci. 37, 399–410 (1968)

    Article  Google Scholar 

  34. Proust, J., Houlne, G., Schantz, M.-L., Schantz, R.: Characterization and Gene Expression of an Annexin During Fruit Development in Capsicum annum. FEBS Letters 383, 208–212 (1996)

    Article  Google Scholar 

  35. Smallwood, M.F., Gurr, S.J., McPherson, M.J., Roberts, K., Bowles, D.J.: The Pattern of Plant Annexin Gene Expression. Bioch. 281, 501–505 (1992)

    Article  Google Scholar 

  36. Carroll, A.D., Moyen, C., Van Kesteren, P., Tooke, F., Battey, N.H., Brownlee, C.: Ca(2 + ), Annexins, and GTP Modulate Exocytosis From Maize Root Cap Protoplasts. The Plant Cell 10, 1267–1276 (1998)

    Google Scholar 

  37. Peng, T., Dickstein, R.: Regulation of Plant Nodule-specific Genes Expressed in Alfalfa Nodules Arrested at an Early Stage of Development. Plant Sci. 101, 65–73 (1994)

    Article  Google Scholar 

  38. Heckmann, A.B., Lombardo, F., Miwa, H., Perry, J.A., Bunnewell, S., Parniske, M., Wang, T.L., Downie, A.: Lotus japonicas Nodulation Requires two GRAS Domain Regulators, One of Which is Functionally Conserved in a Non-legume. Plant Physiol. 142, 1739–1750 (2006)

    Article  Google Scholar 

  39. Catalano, C.M., Lane, W.S., Sherrier, D.J.: Biochemical Characterization of Symbiosome Membrane Proteins From Medicago truncatula Root Nodules. Electroph. 25, 519–531 (2004)

    Article  Google Scholar 

  40. Doyle, J.J., Luckow, M.A.: The Rest of the Iceberg. Legume Diversity in a Phylogenetic Context. Plant Physiol. 131, 900–910 (2003)

    Article  Google Scholar 

  41. Morgan, S.O., Fernandez, M.P.: Distinct Annexin Subfamilies in Plants and Protists Diverged Prior to Animal Annexins and From a Common Ancestor. J. Mol. Evol. 44, 178–188 (1997)

    Article  Google Scholar 

  42. Moss, S.E.: Annexins. Trends in Cell Biol. 7, 87–89 (1997)

    Article  Google Scholar 

  43. Clark, G.B., Roux, S.J.: Annexins of Plant Cells. Plant Physiol. 109, 1133–1139 (1995)

    Article  Google Scholar 

  44. Andrawis, A., Solomon, M., Delmer, D.P.: Cotton Fiber Annexins: A Potential Role in the Regulation of Callose Synthase. The Plant J.: for Cell and Mol. Biol. 18, 763–772 (1993)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Genetics, Laboratory of Plant Genetics and Biotechnology, Universidade Federal de Pernambuco, Center of Biological Sciences, R. Prof. Moraes Rêgo 1235, CEP 50670-420, Recife, PE, Brazil

    Gabriela Souto Vieira-de-Mello, Petra Barros dos Santos, Nina da Mota Soares-Cavalcanti & Ana Maria Benko-Iseppon

Authors
  1. Gabriela Souto Vieira-de-Mello
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Petra Barros dos Santos
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Nina da Mota Soares-Cavalcanti
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ana Maria Benko-Iseppon
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. ICAR-CNR, Consiglio Nazionale delle Ricerche, 90128, Palermo, Italy

    Riccardo Rizzo

  2. School of Computing and Mathematical Sciences, Liverpool John Moores University, L3 3AF, Liverpool, UK

    Paulo J. G. Lisboa

Rights and permissions

Reprints and permissions

Copyright information

© 2011 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Vieira-de-Mello, G.S., Barros dos Santos, P., da Mota Soares-Cavalcanti, N., Benko-Iseppon, A.M. (2011). Identification and Expression of Early Nodulin in Sugarcane Transcriptome Revealed by in Silico Analysis. In: Rizzo, R., Lisboa, P.J.G. (eds) Computational Intelligence Methods for Bioinformatics and Biostatistics. CIBB 2010. Lecture Notes in Computer Science(), vol 6685. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-21946-7_6

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-21946-7_6

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-21945-0

  • Online ISBN: 978-3-642-21946-7

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation