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Related Experiment Videos

The zebrafish secretome.

Eric W Klee1

  • 1Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA. klee.eric@mayo.edu

Zebrafish
|June 17, 2008
PubMed
Summary
This summary is machine-generated.

This study computationally characterizes the zebrafish secretome, identifying significantly more secreted proteins than previously annotated. It provides the first comprehensive description of the zebrafish secretome post-genome sequencing.

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Comparative Genomics

Background:

  • The secretome, comprising proteins processed via the secretory pathway, plays crucial roles in cellular communication and function.
  • Understanding the secretome is vital for deciphering biological processes and disease mechanisms.

Purpose of the Study:

  • To computationally identify and characterize the secretome of Danio rerio (zebrafish) and Homo sapiens (human).
  • To compare the predicted secretomes of zebrafish and humans and identify orthologs.
  • To provide the first comprehensive description of the zebrafish secretome.

Main Methods:

  • Analysis of Danio rerio and Homo sapiens RefSeq proteins using SignalP, TargetP, Phobius, and pTarget algorithms.
  • Prediction of N-terminal signal sequences, transmembrane domains, and extracellular localization.

Related Experiment Videos

  • Ortholog identification using reciprocal BLAST best hits.
  • Comparison with existing SwissProt annotations.

    • Main Results:

    • Approximately 16.5% of the zebrafish proteome and 17.0% of the human proteome were predicted to have signal sequences.
    • Over 1300 zebrafish and 1200 human soluble extracellular proteins were identified.
    • 372 orthologous proteins were found between zebrafish and human secretomes.
    • The study identified substantially more secretome members in zebrafish than currently annotated in SwissProt.
    • Three additional putative matrix metalloproteinase (MMP) zebrafish proteins were annotated.

    Conclusions:

    • Computational analysis significantly expands the known zebrafish secretome compared to SwissProt annotations.
    • This work provides a foundational description of the zebrafish secretome, enabling further functional studies.
    • The findings highlight conserved aspects of secretome composition between zebrafish and humans.