Genome-Wide Identification and Analysis of Protease-Coding Genes in Pineapple

  • Xiang Jia MinEmail author
  • Ching Man Wai
  • Brian Powell
  • Ray Ming
Part of the Plant Genetics and Genomics: Crops and Models book series (PGG, volume 22)


Pineapple proteases, commonly known as bromelains, have been used for many years. In this work we identified and analyzed the protease-coding genes and their products in pineapple. A total of 512 genes encoding putative proteases in pineapple were identified. The encoded proteases are predicted to be distributed in different subcellular compartments, with 152 secreted into extracellular space, 74 localized in cytosol, 67 in nucleus, 60 in chloroplast, 18 in mitochondria, and the remaining in other subcellular locations. The proteases are classified using the conserved domain and protein family database as well as the MEROPS protease classification method. 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. Papain family protease (cysteine proteases, bromelain) genes were among the highly expressed genes. Phylogenetic analysis of cysteine proteases showed four large clusters formed among them. The information of identified protease genes with their gene expression profiles along with the predicted subcellular locations of the protease proteins will facilitate the community to further examine their biological roles of proteases in pineapple growth and development and to explore the potential for expressing the recombinant proteases for medical use.


Bromelain Cysteine protease Gene expression Phylogenetic analysis Proteolytic enzyme Protease Subcellular locations 



Fragments per kilobase exon per million reads mapped


Reversed position-specific BLAST



The work was supported by the University of Illinois at Urbana-Champaign to RM and the Youngstown State University (YSU) Research Professorship award to XJM.


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Copyright information

© Springer Nature Switzerland AG 2018

Authors and Affiliations

  • Xiang Jia Min
    • 1
    Email author
  • Ching Man Wai
    • 2
  • Brian Powell
    • 3
  • Ray Ming
    • 2
  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 Computer Science and Information SystemsYoungstown State UniversityYoungstownUSA

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