This article is part of the supplement: Seventh International Conference on Bioinformatics (InCoB2008)

Open Access Research

Predicted mouse peroxisome-targeted proteins and their actual subcellular locations

Yumi Mizuno1, Igor V Kurochkin23, Marlis Herberth24, Yasushi Okazaki1* and Christian Schönbach25*

Author Affiliations

1 Division of Functional Genomics and Systems Medicine, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama 350-1241, Japan

2 Immunoinformatics Team, Advanced Genome Information Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Kanagawa 230-0045, Japan

3 RIKEN Advanced Science Institute (ASI), MetaSystems Research Team, Yokohama, Kanagawa 230-0045, Japan

4 Cambridge Centre for Neuropsychiatric Research (CCNR), Institute of Biotechnology, University of Cambridge, Cambridge CB2 1QT, UK

5 Division of Genomics and Genetics, School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore

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BMC Bioinformatics 2008, 9(Suppl 12):S16  doi:10.1186/1471-2105-9-S12-S16

Published: 12 December 2008



The import of most intraperoxisomal proteins is mediated by peroxisome targeting signals at their C-termini (PTS1) or N-terminal regions (PTS2). Both signals have been integrated in subcellular location prediction programs. However their present performance, particularly of PTS2-targeting did not seem fitting for large-scale screening of sequences.


We modified an earlier reported PTS1 screening method to identify PTS2-containing mouse candidates using a combination of computational and manual annotation. For rapid confirmation of five new PTS2- and two previously identified PTS1-containing candidates we developed the new cell line CHO-perRed which stably expresses the peroxisomal marker dsRed-PTS1. Using CHO-perRed we confirmed the peroxisomal localization of PTS1-targeted candidate Zadh2. Preliminary characterization of Zadh2 expression suggested non-PPARα mediated activation. Notably, none of the PTS2 candidates located to peroxisomes.


In a few cases the PTS may oscillate from "silent" to "functional" depending on its surface accessibility indicating the potential for context-dependent conditional subcellular sorting. Overall, PTS2-targeting predictions are unlikely to improve without generation and integration of new experimental data from location proteomics, protein structures and quantitative Pex7 PTS2 peptide binding assays.