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
Article

Abstract

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 (http://proteomics.ysu.edu/secretomes/plant.php).

Keywords

Secreted protein Secretome Subcellular locations Hydrolase Peroxidase 

Abbreviations

BLAST

Basic local alignment search tool

ER

Endoplasmic reticulum

GO

Gene ontology

GPI

Glycosylphosphatidylinositol

RPKM

Reads Per Kilobase of exon model per Million mapped reads

rpsBLAST

Reversed position specific BLAST

Supplementary material

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

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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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