Tropical Plant Biology

, Volume 6, Issue 2–3, pp 131–137 | Cite as

Secretome Prediction and Analysis in Sacred Lotus (Nelumbo nucifera Gaertn.)

  • Gengkon Lum
  • Robert VanBuren
  • Ray Ming
  • Xiang Jia Min


Sacred lotus, Nelumbo nucifera (Gaertn.), is a basal eudicot with agricultural and medicinal importance. The secretome and proteins in some other subcellular locations including endoplasmic reticulum (ER), mitochondrion, chloroplast, and membrane of sacred lotus were predicted using a set of computational tools. The distribution of proteins in each subcellular location in sacred lotus was compared with proteins in five other plant species. Plant proteomes contained approximately 6–9 % of secreted proteins, 13–15 % membrane proteins, 12–20 % mitochondrial or chloroplast proteins, respectively. Plant secreted proteins consist of a large number of hydrolases and peroxidases which may contribute to cell wall formation, rhizome development and seed germination regulation. The information of secretome and other protein subcellular locations in sacred lotus and other species can be accessed at the PlantSecKB website (


Secreted protein Secretome Subcellular locations Hydrolase Peroxidase 



Basic local alignment search tool


Endoplasmic reticulum


Gene ontology




Reads Per Kilobase of exon model per Million mapped reads


Reversed position specific BLAST



The work was supported by the University of Illinois at Urbana-Champaign to RM and the Ohio Plant Biotechnology Consortium and Youngstown State University (YSU) Research Council to XJM.

Supplementary material

12042_2013_9121_MOESM1_ESM.xls (3.4 mb)
Supplementary Table 1 Subcellular location prediction of Lotus proteome (XLS 3523 kb)
12042_2013_9121_MOESM2_ESM.xls (92 kb)
Supplementary Table 2 Pfam analysis of secretomes in three species (XLS 92 kb)
12042_2013_9121_MOESM3_ESM.xls (51 kb)
Supplementary Table 3 RNA-seq expression levels of identified highly genes coding for secreted proteins (XLS 51 kb)


  1. Agrawal GK, Jwa NS, Lebrun MH, Job D, Rakwal R (2010) Plant secretome: unlocking secrets of the secreted proteins. Proteomics 10:799–827PubMedCrossRefGoogle Scholar
  2. Andrews J, Adams SR, Burton KS, Evered CE (2002) Subcellular localization of peroxidase in tomato fruit skin and the possible implications for the regulation of fruit growth. J Exp Bot 53:2185–2191PubMedCrossRefGoogle Scholar
  3. Bendtsen JD, Nielsen H, von Heijne G, Brunak S (2004) Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340:783–795PubMedCrossRefGoogle Scholar
  4. Borner GH, Sherrier DJ, Stevens TJ, Arkin IT, Dupree P (2002) Prediction of glycosylphosphatidylinositol-anchored proteins in Arabidopsis. A genomic analysis. Plant Physiol 129:486–499PubMedCrossRefGoogle Scholar
  5. Borner GH, Lilley KS, Stevens TJ, Dupree P (2003) Identification of glycosylphosphatidylinositol-anchored proteins in Arabidopsis. A proteomic and genomic analysis. Plant Physiol 132:568–577PubMedCrossRefGoogle Scholar
  6. Boudart G, Minic Z, Albenne C, Canut H, Jamet E, Pont-Lezica R (2007) Cell wall proteome. In: Samaj S, Thelen J (eds) Plant Proteomics. Springer, pp. 169–185Google Scholar
  7. Cho WK, Chen XY, Chu H, Rim Y, Kim S, Kim ST et al (2009) Proteomic analysis of the secretome of rice calli. Physiol Plant 135:331–341PubMedCrossRefGoogle Scholar
  8. de Castro E, Sigrist CJ, Gattiker A, Bulliard V, Langendijk-Genevaux PS, Gasteiger E et al (2006) ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. Nucleic Acids Res 34:W362–W365, Web Server issuePubMedCrossRefGoogle Scholar
  9. De-la-Peña C, Badri DV, Lei Z, Watson BS, Brandão MM, Silva-Filho MC, Sumner LW, Vivanco JM (2010) Root secretion of defense-related proteins is development-dependent and correlated with flowering time. J Biol Chem 285:30654–30665PubMedCrossRefGoogle Scholar
  10. Emanuelsson O, Brunak S, von Heijne G, Nielsen H (2007) Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc 2:953–971PubMedCrossRefGoogle Scholar
  11. Finnie C, Andersen B, Shahpiri A, Svensson B (2011) Proteomes of the barley aleurone layer: A model system for plant signalling and protein secretion. Proteomics 11:1595–1605PubMedCrossRefGoogle Scholar
  12. Foresti O, Denecke J (2008) Intermediate organelles of the plant secretory pathway: identity and function. Traffic 9:1599–1612PubMedCrossRefGoogle Scholar
  13. Gillmor CS, Lukowitz W, Brininstool G, Sedbrook JC, Hamann T, Poindexter P et al (2005) Glycosylphosphatidylinositol-anchored proteins are required for cell wall synthesis and morphogenesis in Arabidopsis. Plant Cell 17:1128–1140PubMedCrossRefGoogle Scholar
  14. Hathout Y (2007) Approaches to the study of the cell secretome. Expert Rev Proteomics 4:239–248PubMedCrossRefGoogle Scholar
  15. Isaacson T, Rose JKC (2006) The plant cell wall proteome, or secretome. In: Finnie C (ed) Plant Proteomics. Annual Plant Reviews Series. Blackwell Publishing 28: 185–209Google Scholar
  16. Jones RL, Robinson DG (1989) Protein secretion in plants. Tansley Review No. 17. New Phytol 111:567–597CrossRefGoogle Scholar
  17. Jung YH, Jeong SH, Kim SH, Singh R, Lee JE, Cho YS et al (2008) Systematic secretome analyses of rice leaf and seed callus suspension-cultured cells: workflow development and establishment of high-density two-dimensional gel reference maps. J Proteome Res 7:5187–5210PubMedCrossRefGoogle Scholar
  18. Käll L, Krogh A, Sonnhammer EL (2004) A combined transmembrane topology and signal peptide prediction method. J Mol Biol 338:1027–1036PubMedCrossRefGoogle Scholar
  19. Kamoun S (2009) The secretome of plant-associated fungi and oomycetes. In: Deising VH (ed) Plant relationships. The mycota, 2nd edn. Springer, Berlin, pp 173–180CrossRefGoogle Scholar
  20. Krogh A, Larsson B, von Heijne G, Sonnhammer ELL (2001) Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J Mol Biol 305:567–580PubMedCrossRefGoogle Scholar
  21. Lopez-Casado G, Urbanowicz BR, Damasceno CM, Rose JK (2008) Plant glycosyl hydrolases and biofuels: a natural marriage. Curr Opin Plant Biol 11:329–337PubMedCrossRefGoogle Scholar
  22. Lum G, Min XJ (2011a) FunSecKB: the fungal secretome knowledgebase. Database - J Biol Database Curation. doi: 10.1093/database/bar001 Google Scholar
  23. Lum G, Min XJ (2011b) Plant secretomes: Current status and future perspectives. Plant Omics J 4:114–119Google Scholar
  24. Lum G, Min XJ (2013) Bioinformatic protocols and the knowledge − base for secretomes in fungi. In: Gupta VK, Tuohy MG, Ayyachamy M, Turner KM, O’Donovan A (eds) Laboratory protocols in fungal biology: current methods in fungal biology. Springer, pp. 545–557Google Scholar
  25. Marchler-Bauer A, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH et al (2009) CDD: specific functional annotation with the Conserved Domain Database. Nucleic Acids Res 37:D205–D210PubMedCrossRefGoogle Scholar
  26. McCarthy FM, Wang N, Magee GB, Nanduri B, Lawrence ML, Camon EB et al (2006) AgBase: a functional genomics resource for agriculture. BMC Genomics 7:229PubMedCrossRefGoogle Scholar
  27. Min XJ (2010) Evaluation of computational methods for secreted protein prediction in different eukaryotes. J Proteomics Bioinform 3:143–147Google Scholar
  28. Ming R, VanBuren R, Liu Y, et al (2013) Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biology: 14:R41Google Scholar
  29. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621–628PubMedCrossRefGoogle Scholar
  30. Oh IS, Park AR, Bae MS, Kwon SJ, Kim YS, Lee JE et al (2005) Secretome analysis reveals an Arabidopsis lipase involved in defense against Alternaria brassicicola. Plant Cell 17:2832–2847PubMedCrossRefGoogle Scholar
  31. Poisson G, Chauve C, Chen X, Bergeron A (2007) FragAnchor a large scale all Eukaryota predictor of Glycosylphosphatidylinositol-anchor in protein sequences by qualitative scoring. Genomics Proteomics Bioinform 5:121–130CrossRefGoogle Scholar
  32. Ranki H, Sopanen T (1984) Secretion of alpha-amylase by the aleurone layer and the scutellum of germinating barley grain. Plant Physiol 75:710–715PubMedCrossRefGoogle Scholar
  33. Rose JK, Lee SJ (2010) Straying off the highway: trafficking of secreted plant proteins and complexity in the plant cell wall proteome. Plant Physiol 153:433–436PubMedCrossRefGoogle Scholar
  34. Shen-Miller J, Schopf JW, Harbottle G, Cao RJ, Ouyang S, Zhou KS, Southon JR, Liu GH (2002) Long-living lotus: germination and soil g-irradiation of centuries-old fruits, and cultivation, growth, and phenotypic abnormalities of offspring. Am J Bot 89:236–247PubMedCrossRefGoogle Scholar
  35. Shinano T, Komatsu S, Yoshimura T, Tokutake S, Kong FJ, Watanabe T et al (2011) Proteomic analysis of secreted proteins from aseptically grown rice. Phytochemistry 72:312–320PubMedCrossRefGoogle Scholar
  36. Sigrist CJA, Cerutti L, de Casro E, Langendijk-Genevaux PS, Bulliard V, Bairoch A et al (2010) PROSITE, a protein domain database for functional characterization and annotation. Nucleic Acids Res 38:161–166CrossRefGoogle Scholar
  37. Simpson C, Thomas C, Findlay K, Bayer E, Maule AJ (2009) An Arabidopsis GPI-anchor plasmodesmal neck protein with callose binding activity and potential to regulate cell-to-cell trafficking. Plant Cell 21:581–594PubMedCrossRefGoogle Scholar
  38. The UniProt Consortium (2011) Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res 39:D214–D219CrossRefGoogle Scholar
  39. Tran HT, Plaxton WC (2008) Proteomic analysis of alterations in the secretome of Arabidopsis thaliana suspension cells subjected to nutritional phosphate deficiency. Proteomics 8:4317–4326PubMedCrossRefGoogle Scholar
  40. VanBuren R, Walters B, Ming R, Min XJ (2013) Analysis of expressed sequence tags and alternative splicing genes in sacred lotus (Nelumbo nucifera Gaertn.). Plant Omics J (in press)Google Scholar
  41. Veitch NC (2004) Structural determinants of plant peroxidase function. Phytochem Rev 3:3–18CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  • Gengkon Lum
    • 1
    • 3
  • Robert VanBuren
    • 2
  • Ray Ming
    • 2
  • Xiang Jia Min
    • 1
  1. 1.Center for Applied Chemical Biology, Department of Biological SciencesYoungstown State UniversityYoungstownUSA
  2. 2.Department of Plant BiologyUniversity of Illinois at Urbana-ChampaignUrbanaUSA
  3. 3.Department of Computational & Systems Biology, School of MedicineUniversity of PittsburghPittsburghUSA

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