title: Identification of New Fungal Peroxisomal Matrix Proteins and Revision of the PTS1 Consensus.
abstract: The peroxisomal targeting signal type 1 (PTS1) is a seemingly simple peptide sequence at the C-terminal end of most peroxisomal matrix proteins. PTS1 can be described as a tripeptide with the consensus motif [S/A/C] [K/R/H] L. However, this description is neither necessary nor sufficient. It does not cover all cases of PTS1 proteins, and some proteins in accordance with this consensus do not target to the peroxisome. In order to find new PTS proteins in yeast and to arrive at a more complete description of the PTS1 consensus motif, we developed a machine learning approach that involves orthologue expansion of the set of known peroxisomal proteins. We performed a genome-wide in silico screen, characterised several PTS1-containing peptides and identified two new peroxisomal matrix proteins, which we named Pxp1 (Yel020c) and Pxp2 (Yjr111c). Based on these in silico and in vivo analyses, we revised the yeast PTS1 consensus which now includes all known PTS1 proteins.
authors.affiliation: Department of Child and Adolescent Health, University Medical Center, University of Göttingen, Göttingen, Germany.|Current address: Program in Biochemistry and Structural Biology, Cell and Developmental Biology, and Molecular Biology, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA.
authors.forename: Christopher
authors.initials: C
authors.lastname: Nötzel
authors.affiliation: Department of Bioinformatics, Institute for Microbiology and Genetics, University of Göttingen, Göttingen, Germany.|Current address: Microarray and Deep Sequencing Core Facility, University Medical Center, University of Göttingen, Göttingen, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Lingner
authors.affiliation: Department of Bioinformatics, Institute for Microbiology and Genetics, University of Göttingen, Göttingen, Germany.
authors.forename: Heiner
authors.initials: H
authors.lastname: Klingenberg
authors.affiliation: Department of Child and Adolescent Health, University Medical Center, University of Göttingen, Göttingen, Germany. sven.thoms@med.uni-goettingen.de.
authors.forename: Sven
authors.initials: S
authors.lastname: Thoms
mesh_terms: D020816:Amino Acid Motifs; D016384:Consensus Sequence; D030541:Databases, Genetic; D016681:Genome, Fungal; D055106:Genome-Wide Association Study; D000069550:Machine Learning; D000074435:Peroxisome-Targeting Signal 1 Receptor; D020675:Peroxisomes / Q000235:genetics / Q000378:metabolism*; D021382:Protein Sorting Signals / Q000235:genetics; D018160:Receptors, Cytoplasmic and Nuclear / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: D000074435:Peroxisome-Targeting Signal 1 Receptor; D021382:Protein Sorting Signals; C000622497:Pxp1 protein, S cerevisiae; C000622498:Pxp2 protein, S cerevisiae; D018160:Receptors, Cytoplasmic and Nuclear; D029701:Saccharomyces cerevisiae Proteins
keywords: PTS1; Pxp1; Pxp2; Yel020c; Yjr111c; amino acid analysis; machine learning; organelle targeting; peroxisomal targeting signal 1; peroxisome