Predicted mouse peroxisome-targeted proteins and their actual subcellular locations

Abstract

BackgroundThe 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.ResultsWe 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.ConclusionIn 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.

Glyoxylate Reductase Isoform 1 is Localized in the Cytosol and Not Peroxisomes in Plant Cells

“…Nevertheless, results obtained in the past few years from various bioinformatics studies and proteome analyses of isolated peroxisomes have revealed that the PTS1 is far more diverse and complex than just a C‐terminal SKL tripeptide motif (Brocard and Hartig 2006; Mizuno et al 2008; Palma et al 2009; Ghosh and Berg 2010; Reumann 2011). For instance, in a recent survey of all known Arabidopsis peroxisomal proteins, as well as their putative orthologs and homologous ESTs from other diverse plant species, over 23 new PTS1 tripeptides were identified, many of which possessed amino acid residues that differ considerably from those originally defined by the SKL motif (Lingner et al 2011).…”

“…Furthermore, most, if not all, PTS1‐containing proteins, especially those that possess non‐canonical PTS1, appear to rely on so‐called ‘accessory’ or ‘auxiliary’ residues that lie just upstream of their C termini and function to contextually enhance the efficiency of peroxisomal targeting (Brocard and Hartig 2006). There is also growing appreciation that changes in the overall conformation of a protein, for instance, in response to a certain cellular cue, can influence the accessibility of its PTS1; hence, a protein that contains a PTS1 that, on its own is sufficient for targeting to peroxisomes, may in some cases be localized to the cytosol or some other subcellular compartment (Eisenhaber and Eisenhaber 2007; Mizuno et al 2008; Reumann 2011). Taken together, this means that the current criteria by which a C‐terminal tripeptide is predicted and/or experimentally confirmed to be a bona fide PTS1 must take into consideration not only the ever‐expanding flexibility of functional residues within the PTS1 tripeptide motif, but also the structural/sequence‐related context in which the tripeptide normally exists.…”

“…It is also notable that GLYR1 possesses a C‐terminal tripeptide, ‐SRE, that resembles a type 1 peroxisomal targeting signal (PTS1) motif, albeit a divergent PTS1 (reviewed in Lanyon‐Hogg et al 2010; refer also to Lingner et al 2011 and references therein), and, thus, the previously reported localization of GLYR1‐GFP to the cytosol in tobacco cells (Simpson et al 2008) may have been a consequence of the C‐terminal‐appended GFP sterically blocking GLYR1's putative peroxisomal targeting information. There is also the possibility that, similar to some other proteins (Mizuno et al 2008; Jung et al 2010; Kataya and Reumann 2010; Lu et al 2010; Meyer et al 2011), GLYR1 is localized to both peroxisomes and the cytosol, but that its distribution in these two compartments varies depending on the species/tissue/cell‐type and/or in response to an environmental cue(s), such as abiotic stress.…”

Peroxisomal localisation of the final steps of the mevalonic acid pathway in planta

“…This shows that the presence of a canonical PTS2 motif is not necessary suYcient to target the protein to peroxisome. Indeed, Mizuno et al (2008) showed that of Wve mouse proteins containing conserved PTS2 motifs identiWed by bioinformatic approaches, none located to peroxisome. The authors pointed out the poor performance of computer-aided predictions of PTS2-containing proteins.…”

Identification of a novel isoform of DHRS4 protein with a nuclear localization signal

“…APE1 contains dual targeting signals and preferentially resides in the nuclei with conditional distribution in the mitochondria. Conditional subcellular sorting was also found for the PTS, where it may oscillate from silent to functional depending on its surface accessibility (Dinur-Mills et al, 2008;Mizuno et al, 2008). Similar to the NRDR protein, which harbors a putative MTS and PTS (Fig.…”