Tropical Plant Biology

, Volume 9, Issue 3, pp 161–175

Genome-Wide Identification and Analysis of Genes Encoding Proteolytic Enzymes in Pineapple

  • Ching Man Wai
  • Brian Powell
  • Ray Ming
  • Xiang Jia Min

DOI: 10.1007/s12042-016-9172-5

Cite this article as:
Wai, C.M., Powell, B., Ming, R. et al. Tropical Plant Biol. (2016) 9: 161. doi:10.1007/s12042-016-9172-5


Pineapple, Ananas comosus, is an economically important fruit crop. Recently its genome was completely sequenced and a total of 27,024 protein coding genes were predicted. Using a set of well evaluated bioinformatics tools we have predicted the protein subcellular locations and comparatively analyzed the protein conserved domains of the predicted proteomes in pineapple, Oryza sativa (rice), Sorghum bicolor (sorghum), and Brachypodium distachyson. Our analysis revealed that ~24–26 % of proteins were located in nucleus, 17–21 % in cytosol, 9–11 % in chloroplast, and 8–11 % proteins were secreted in these monocot plants. The secretomes in the four species were analyzed comparatively and a large number of secreted glycosyl hydrolases were identified. As pineapple proteolytic enzymes, knowns as bromelains, have been used for medical treatments, we focused on genome-wide identification and analysis of pineapple genes encoding proteases. A total of 512 pineapple genes encoding putative proteolytic enzymes were identified, with 152 secreted, 74 localized in cytosol, 67 in nucleus, 60 in chloroplast, 18 in mitochondria, and the remaining in other subcellular locations. The top large protease families in pineapple were papain family cysteine protease (62 genes), peptidase S8 family (56 genes), aspartyl protease family (38 genes), and serine carboxypeptidase (33 genes). Gene expression analysis revealed that among 512 protease genes 432 were expressed in various tissues and 72 genes were differentially expressed. The highly expressed protease genes were identified including 7 papain family cysteine proteases. The protease genes with the predicted protein subcellular locations will facilitate the efforts for examining their biological roles in pineapple growth and development and for expressing the recombinant proteases for medical use. The information of protein subcellular location of all plant species can be accessed at the PlantSecKB website (


Bromelain Conserved domain Gene expression Proteolytic enzyme Protease Secreted protein Secretome Subcellular locations 



basic local alignment search tool.


endoplasmic reticulum.


Gene ontology.


Fragments Per Kilobase exon per Million reads mapped.


reversed position specific BLAST.

Supplementary material

12042_2016_9172_MOESM1_ESM.xlsx (17 kb)
Supplementary Table 1Gene Ontology classification of proteomes in four monocot plants (XLSX 17 kb)
12042_2016_9172_MOESM2_ESM.xlsx (405 kb)
Supplementary Table 2Protein family and conserved domain distribution in different plants (XLSX 404 kb)
12042_2016_9172_MOESM3_ESM.xlsx (88 kb)
Supplementary Table 3Summary of conserved protein domain families in the secretomes of different plants (XLSX 87 kb)
12042_2016_9172_MOESM4_ESM.xlsx (24 kb)
Supplementary Table 4Protease family including secreted protein family distribution in different plants (XLSX 23 kb)
12042_2016_9172_MOESM5_ESM.xlsx (29 kb)
Supplementary Table 5Putative proteolytic enzymes with their subcellular locations (XLSX 29 kb)
12042_2016_9172_MOESM6_ESM.xlsx (63 kb)
Supplementary Table 6Differentially expressed genes in ripening fruits of pineapple (XLSX 62 kb)
12042_2016_9172_MOESM7_ESM.xlsx (29 kb)
Supplementary Table 7Gene expression of pineapple protease coding genes (XLSX 29 kb)

Funding information

Funder NameGrant NumberFunding Note
University of Illinois at Urbana-Champaign
    Youngstown State University (YSU) Research Council

      Copyright information

      © Springer Science+Business Media New York 2016

      Authors and Affiliations

      • Ching Man Wai
        • 1
      • Brian Powell
        • 2
      • Ray Ming
        • 1
      • Xiang Jia Min
        • 3
      1. 1.Department of Plant BiologyUniversity of Illinois at Urbana-ChampaignUrbanaUSA
      2. 2.Department of Computer Science and Information SystemsYoungstown State UniversityYoungstownUSA
      3. 3.Department of Biological Sciences, Center for Applied Chemical BiologyYoungstown State UniversityYoungstownUSA

      Personalised recommendations