title: Characterization, prediction and evolution of plant peroxisomal targeting signals type 1 (PTS1s).
abstract: Our knowledge of the proteome of plant peroxisomes and their functional plasticity is far from being complete, primarily due to major technical challenges in experimental proteome research of the fragile cell organelle. Several unexpected novel plant peroxisome functions, for instance in biotin and phylloquinone biosynthesis, have been uncovered recently. Nevertheless, very few regulatory and membrane proteins of plant peroxisomes have been identified and functionally described up to now. To define the matrix proteome of plant peroxisomes, computational methods have emerged as important powerful tools. Novel prediction approaches of high sensitivity and specificity have been developed for peroxisome targeting signals type 1 (PTS1) and have been validated by in vivo subcellular targeting analyses and thermodynamic binding studies with the cytosolic receptor, PEX5. Accordingly, the algorithms allow the correct prediction of many novel peroxisome-targeted proteins from plant genome sequences and the discovery of additional organelle functions. In this review, we provide an overview of methodologies, capabilities and accuracies of available prediction algorithms for PTS1 carrying proteins. We also summarize and discuss recent quantitative, structural and mechanistic information of the interaction of PEX5 with PTS1 carrying proteins in relation to in vivo import efficiency. With this knowledge, we develop a model of how proteins likely evolved peroxisomal targeting signals in the past and still nowadays, in which order the two import pathways might have evolved in the ancient eukaryotic cell, and how the secondary loss of the PTS2 pathway probably happened in specific organismal groups.
authors.affiliation: Department of Plant Biochemistry and Infection Biology, Biocentre Klein Flottbek, University of Hamburg, D-22609 Hamburg, Germany; Centre for Organelle Research, University of Stavanger, N-4036 Stavanger, Norway. Electronic address: sigrun.reumann@uni-hamburg.de.
authors.forename: S
authors.initials: S
authors.lastname: Reumann
authors.affiliation: Centre for Organelle Research, University of Stavanger, N-4036 Stavanger, Norway; KIIT School of Biotechnology, Campus XI, KIIT University, I-751024 Bhubaneswar, India. Electronic address: gopal.chowdhary@uis.no.
authors.forename: G
authors.initials: G
authors.lastname: Chowdhary
authors.affiliation: Department of Bioinformatics, Institute for Microbiology and Genetics, D-37077 Goettingen, Germany. Electronic address: thomas.lingner@biologie.uni-goettingen.de.
authors.forename: T
authors.initials: T
authors.lastname: Lingner
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism; D019143:Evolution, Molecular; D018506:Gene Expression Regulation, Plant; D019697:Onions / Q000235:genetics / Q000378:metabolism; D000074437:Peroxisomal Targeting Signal 2 Receptor; D000074435:Peroxisome-Targeting Signal 1 Receptor; D020675:Peroxisomes / Q000737:chemistry / Q000378:metabolism*; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D021382:Protein Sorting Signals; D021381:Protein Transport; D018160:Receptors, Cytoplasmic and Nuclear / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D015398:Signal Transduction; D014026:Nicotiana / Q000235:genetics / Q000378:metabolism
chemical_list: D000074437:Peroxisomal Targeting Signal 2 Receptor; D000074435:Peroxisome-Targeting Signal 1 Receptor; D010940:Plant Proteins; D021382:Protein Sorting Signals; D018160:Receptors, Cytoplasmic and Nuclear
keywords: Evolution; PEX5; Peroxisome; Peroxisome targeting signal type 1; Proteome