Motif refinement of the peroxisomal targeting signal 1 and evaluation of taxon-specific differences.

Eukaryote peroxisomes, plant glyoxysomes and trypanosomal glycosomes belong to the microbody family of organelles that compartmentalise a variety of biochemical processes. The interaction between the PTS1 signal and its cognate receptor Pex5 initiates the major import mechanism for proteins into the matrix of these organelles. Relying on the analysis of amino acid sequence variability of known PTS1-targeted proteins and PTS1-containing peptides that interact with Pex5 in the yeast two-hybrid assay, on binding site studies of the Pex5-ligand complex crystal structure, 3D models and sequences of Pex5 proteins from various taxa, we derived the requirements for a C-terminal amino acid sequence to interact productively with Pex5. We found evidence that, at least the 12 C-terminal residues of a given substrate protein are implicated in PTS1 signal recognition. This motif can be structurally and functionally divided into three regions: (i) the C-terminal tripeptide, (ii) a region interacting with the surface of Pex5 (about four residues further upstream), and (iii) a polar, solvent-accessible and unstructured region with linker function (the remaining five residues). Specificity differences are confined to taxonomic subgroups (metazoa and fungi) and are connected with amino acid type preferences in region 1 and deviating hydrophobicity patterns in region 2.

[1]  P Bork,et al.  Sequence properties of GPI-anchored proteins near the omega-site: constraints for the polypeptide binding site of the putative transamidase. , 1998, Protein engineering.

[2]  T. Yoshihara,et al.  Localization of Cytosolic NADP-dependent Isocitrate Dehydrogenase in the Peroxisomes of Rat Liver Cells , 2001, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society.

[3]  Sebastian Maurer-Stroh,et al.  N-terminal N-myristoylation of proteins: refinement of the sequence motif and its taxon-specific differences. , 2002, Journal of molecular biology.

[4]  P. Argos,et al.  Incorporation of non-local interactions in protein secondary structure prediction from the amino acid sequence. , 1996, Protein engineering.

[5]  H. Scheraga,et al.  Statistical mechanical treatment of protein conformation. II. A three-state model for specific-sequence copolymers of amino acids. , 1976, Macromolecules.

[6]  P. Ponnuswamy,et al.  Hydrophobic packing and spatial arrangement of amino acid residues in globular proteins. , 1980, Biochimica et biophysica acta.

[7]  Maria Jesus Martin,et al.  The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 , 2003, Nucleic Acids Res..

[8]  U. Hobohm,et al.  Selection of representative protein data sets , 1992, Protein science : a publication of the Protein Society.

[9]  L. Kier,et al.  Amino acid side chain parameters for correlation studies in biology and pharmacology. , 2009, International journal of peptide and protein research.

[10]  K Nishikawa,et al.  The amino acid composition is different between the cytoplasmic and extracellular sides in membrane proteins , 1992, FEBS letters.

[11]  T. Tsukamoto,et al.  Characterization of the signal peptide at the amino terminus of the rat peroxisomal 3-ketoacyl-CoA thiolase precursor. , 1994, The Journal of biological chemistry.

[12]  M. Levitt.  A simplified representation of protein conformations for rapid simulation of protein folding. , 1976, Journal of molecular biology.

[13]  S. Subramani,et al.  A novel, cleavable peroxisomal targeting signal at the amino‐terminus of the rat 3‐ketoacyl‐CoA thiolase. , 1991, The EMBO journal.

[14]  S Subramani,et al.  A conserved tripeptide sorts proteins to peroxisomes , 1989, The Journal of cell biology.

[15]  M. Vihinen,et al.  Accuracy of protein flexibility predictions , 1994, Proteins.

[16]  N. Guex,et al.  SWISS‐MODEL and the Swiss‐Pdb Viewer: An environment for comparative protein modeling , 1997, Electrophoresis.

[17]  S. Gould,et al.  Identification of a peroxisomal targeting signal at the carboxy terminus of firefly luciferase , 1987, The Journal of cell biology.

[18]  F. Kragler,et al.  Two independent peroxisomal targeting signals in catalase A of Saccharomyces cerevisiae , 1993, The Journal of cell biology.

[19]  P Argos,et al.  Protein secondary structure. Studies on the limits of prediction accuracy. , 2009, International journal of peptide and protein research.

[20]  M. Sternberg,et al.  Prediction of protein secondary structure and active sites using the alignment of homologous sequences. , 1987, Journal of molecular biology.

[21]  S. Rackovsky,et al.  Hydrophobicity, hydrophilicity, and the radial and orientational distributions of residues in native proteins. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[22]  M. Levitt.  Conformational preferences of amino acids in globular proteins. , 1978, Biochemistry.

[23]  R. Erdmann,et al.  Protein translocation machineries of peroxisomes , 2001, FEBS letters.

[24]  J. M. Zimmerman,et al.  The characterization of amino acid sequences in proteins by statistical methods. , 1968, Journal of theoretical biology.

[25]  A. D. McLachlan,et al.  Solvation energy in protein folding and binding , 1986, Nature.

[26]  B. Geisbrecht,et al.  The Human PICD Gene Encodes a Cytoplasmic and Peroxisomal NADP+-dependent Isocitrate Dehydrogenase* , 1999, The Journal of Biological Chemistry.

[27]  Jaap Heringa,et al.  OBSTRUCT: a program to obtain largest cliques from a protein sequence set according to structural resolution and sequence similarity , 1992, Comput. Appl. Biosci..

[28]  P. Argos,et al.  Structural prediction of membrane-bound proteins. , 2005, European journal of biochemistry.

[29]  K Nishikawa,et al.  Distinct character in hydrophobicity of amino acid compositions of mitochondrial proteins , 1990, Proteins.

[30]  P. Karplus,et al.  Prediction of chain flexibility in proteins , 1985, Naturwissenschaften.

[31]  John C. Wootton,et al.  Statistics of Local Complexity in Amino Acid Sequences and Sequence Databases , 1993, Comput. Chem..

[32]  M. Fransen,et al.  The Difference in Recognition of Terminal Tripeptides as Peroxisomal Targeting Signal 1 between Yeast and Human Is Due to Different Affinities of Their Receptor Pex5p to the Cognate Signal and to Residues Adjacent to It* , 1998, The Journal of Biological Chemistry.

[33]  R. Wanders,et al.  Biochemistry of peroxisomes. , 1992, Annual review of biochemistry.

[34]  P. Argos,et al.  Seventy‐five percent accuracy in protein secondary structure prediction , 1997, Proteins.

[35]  S. Rackovsky,et al.  Characterization of multiple bends in proteins , 1980, Biopolymers.

[36]  H. Moser,et al.  Human PEX7 encodes the peroxisomal PTS2 receptor and is responsible for rhizomelic chondrodysplasia punctata , 1997, Nature Genetics.

[37]  P. Bork,et al.  Prediction of potential GPI-modification sites in proprotein sequences. , 1999, Journal of molecular biology.

[38]  H. Scheraga,et al.  Analysis of Conformations of Amino Acid Residues and Prediction of Backbone Topography in Proteins , 1974 .

[39]  S. Fields,et al.  Protein-peptide interactions analyzed with the yeast two-hybrid system. , 1995, Nucleic acids research.

[40]  T Hashimoto,et al.  Amino-terminal presequence of the precursor of peroxisomal 3-ketoacyl-CoA thiolase is a cleavable signal peptide for peroxisomal targeting. , 1991, Biochemical and biophysical research communications.

[41]  S. Sunyaev,et al.  PSIC: profile extraction from sequence alignments with position-specific counts of independent observations. , 1999, Protein engineering.

[42]  M. Skoneczny,et al.  Rhizomelic chondrodysplasia punctata is caused by deficiency of human PEX7, a homologue of the yeast PTS2 receptor , 1997, Nature Genetics.

[43]  J. Kirkwood,et al.  Proteins, amino acids and peptides as ions and dipolar ions , 1943 .

[44]  M. Marzioch,et al.  The import receptor for the peroxisomal targeting signal 2 (PTS2) in Saccharomyces cerevisiae is encoded by the PAS7 gene. , 1996, The EMBO journal.

[45]  J. Gibrat,et al.  Secondary structure prediction: combination of three different methods. , 1988, Protein engineering.

[46]  M. Kendall,et al.  The advanced theory of statistics , 1945 .

[47]  R. Grantham.  Amino Acid Difference Formula to Help Explain Protein Evolution , 1974, Science.

[48]  H. Cid,et al.  Hydrophobicity and structural classes in proteins. , 1992, Protein engineering.

[49]  C. Brees,et al.  Identification and Characterization of the Putative Human Peroxisomal C-terminal Targeting Signal Import Receptor (*) , 1995, The Journal of Biological Chemistry.

[50]  Jeremy M. Berg,et al.  Molecular dynamics simulations of biomolecules , 2002, Nature Structural Biology.

[51]  H. Tabak,et al.  Saccharomyces cerevisiae Acyl-CoA Oxidase Follows a Novel, Non-PTS1, Import Pathway into Peroxisomes That Is Dependent on Pex5p* , 2002, The Journal of Biological Chemistry.

[52]  H. Miziorko,et al.  3-Hydroxy-3-methylglutaryl-CoA lyase is present in mouse and human liver peroxisomes. , 1994, The Journal of biological chemistry.

[53]  S Subramani,et al.  Mutagenesis of the amino targeting signal of Saccharomyces cerevisiae 3-ketoacyl-CoA thiolase reveals conserved amino acids required for import into peroxisomes in vivo. , 1994, The Journal of biological chemistry.

[54]  Manuel C. Peitsch,et al.  Protein Modeling by E-mail , 1995, Bio/Technology.

[55]  F. Kragler,et al.  The tetratricopeptide repeat-domain of the PAS10 protein of Saccharomyces cerevisiae is essential for binding the peroxisomal targeting signal-SKL. , 1994, Biochemical and biophysical research communications.

[56]  D. Eisenberg,et al.  Correlation of sequence hydrophobicities measures similarity in three-dimensional protein structure. , 1983, Journal of molecular biology.

[57]  T. D. Schneider,et al.  Sequence logos: a new way to display consensus sequences. , 1990, Nucleic acids research.

[58]  H. Tabak,et al.  Peroxisomal and mitochondrial carnitine acetyltransferases of Saccharomyces cerevisiae are encoded by a single gene. , 1995, The EMBO journal.

[59]  Sebastian Maurer-Stroh,et al.  N-terminal N-myristoylation of proteins: prediction of substrate proteins from amino acid sequence. , 2002, Journal of molecular biology.

[60]  M C Peitsch,et al.  Protein modelling for all. , 1999, Trends in biochemical sciences.

[61]  M. Kanehisa,et al.  Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins. , 1996, Protein engineering.

[62]  H Nielsen,et al.  Machine learning approaches for the prediction of signal peptides and other protein sorting signals. , 1999, Protein engineering.

[63]  D. Eisenberg.  Three-dimensional structure of membrane and surface proteins. , 1984, Annual review of biochemistry.