title: Predicted mouse peroxisome-targeted proteins and their actual subcellular locations.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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-PPARalpha mediated activation. Notably, none of the PTS2 candidates located to peroxisomes.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Division of Functional Genomics and Systems Medicine, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama 350-1241, Japan. yumimi@saitama-med.ac.jp
authors.forename: Yumi
authors.initials: Y
authors.lastname: Mizuno
authors.forename: Igor V
authors.initials: IV
authors.lastname: Kurochkin
authors.forename: Marlis
authors.initials: M
authors.lastname: Herberth
authors.forename: Yasushi
authors.initials: Y
authors.lastname: Okazaki
authors.forename: Christian
authors.initials: C
authors.lastname: Schönbach
mesh_terms: D000426:Alcohol Dehydrogenase / Q000737:chemistry / Q000502:physiology*; D000818:Animals; D016466:CHO Cells; D019295:Computational Biology / Q000379:methods*; D006224:Cricetinae; D003412:Cricetulus; D051379:Mice; D018613:Microscopy, Confocal; D008954:Models, Biological; D047493:PPAR alpha / Q000378:metabolism; D010455:Peptides / Q000737:chemistry; D000074437:Peroxisomal Targeting Signal 2 Receptor; D020675:Peroxisomes / Q000378:metabolism*; D017434:Protein Structure, Tertiary; D018160:Receptors, Cytoplasmic and Nuclear / Q000737:chemistry
chemical_list: D047493:PPAR alpha; D010455:Peptides; D000074437:Peroxisomal Targeting Signal 2 Receptor; D018160:Receptors, Cytoplasmic and Nuclear; D000426:Alcohol Dehydrogenase