The zebrafish secretome

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

The secretome is a functionally rich proteome subset, including cellular membrane and extracellular proteins processed through the secretory pathway. In this study, Danio rerio and Homo sapiens RefSeq proteins were analyzed with SignalP, TargetP, Phobius, and pTarget algorithms. About 16.5% of the zebrafish proteome and 17.0% of the human proteome possessed predicted N-terminal signal sequences. Nearly half of these proteins were subsequently classified as soluble, as they lacked predicted transmembrane domains. The soluble proteins were further subclassified, predicting 1345 (3.8%) zebrafish and 1207 (3.2%) human proteins as extracellular. Comparison of the zebrafish and human soluble secretome proteins identified 372 as orthologs, on the basis of reciprocal BLAST best hits. The computational characterization of the zebrafish proteins found many more members of the secretome than annotated in the SwissProt database. Only 180 of the 2078 zebrafish SwissProt protein entries, and 995 of the 19,294 human SwissProt protein entries were annotated with secreted protein locales. A specific investigation of the fibroblast growth factor and matrix metalloproteinase (MMP) protein families confirmed the prediction data and generated annotation of three additional putative MMP zebrafish proteins. This study presents the first known published description of the zebrafish secretome since the completion of the zebrafish genome sequencing project.

Original languageEnglish (US)
Pages (from-to)131-138
Number of pages8
JournalZebrafish
Volume5
Issue number2
DOIs
StatePublished - Jun 1 2008

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Zebrafish
Danio rerio
Zebrafish Proteins
protein
Protein Databases
Proteins
Proteome
proteins
proteome
Matrix Metalloproteinases
metalloproteinases
Fibroblast Growth Factors
Secretory Pathway
Protein Sorting Signals
fibroblast growth factors
Membrane Proteins
matrix
Genome
Databases
signal peptide

ASJC Scopus subject areas

  • Developmental Biology
  • Molecular Biology
  • Aquatic Science

Cite this

The zebrafish secretome. / Klee, Eric W.

In: Zebrafish, Vol. 5, No. 2, 01.06.2008, p. 131-138.

Research output: Contribution to journalArticle

Klee, Eric W. / The zebrafish secretome. In: Zebrafish. 2008 ; Vol. 5, No. 2. pp. 131-138.
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