Predicting Protein Subcellular Localisation From Amino Acid Sequence Information

Predicting the subcellular localisation of proteins is an important part of the elucidation of their functions and interactions. Here, the amino acid sequence motifs that direct proteins to their proper subcellular compartment are surveyed, different methods for localisation prediction are discussed, and some benchmarks for the more commonly used predictors are presented.

[1]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[2]  P. Gans,et al.  A coil-helix instead of a helix-coil motif can be induced in a chloroplast transit peptide from Chlamydomonas reinhardtii. , 1999, European journal of biochemistry.

[3]  A. Krogh,et al.  Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. , 2001, Journal of molecular biology.

[4]  E. Schleiff,et al.  Positively charged residues, the helical conformation and the structural flexibility of the leader sequence of pALDH are important for recognition by hTom20 , 1999, FEBS letters.

[5]  M. Kanehisa,et al.  A knowledge base for predicting protein localization sites in eukaryotic cells , 1992, Genomics.

[6]  G. von Heijne,et al.  Topogenic signals in integral membrane proteins. , 1988, European journal of biochemistry.

[7]  T. Sicheritz-Pontén,et al.  The genome sequence of Rickettsia prowazekii and the origin of mitochondria , 1998, Nature.

[8]  H. Tabak,et al.  Import of proteins into peroxisomes. , 1999, Biochimica et biophysica acta.

[9]  G von Heijne,et al.  Analysis and prediction of mitochondrial targeting peptides. , 2001, Methods in cell biology.

[10]  Rolf Apweiler,et al.  Evaluation of methods for the prediction of membrane spanning regions , 2001, Bioinform..

[11]  Y. Abe.  [Structural basis of presequence recognition by the mitochondrial protein import receptor Tom20]. , 2001, Fukuoka igaku zasshi = Hukuoka acta medica.

[12]  T. Rapoport,et al.  Protein Translocation: Tunnel Vision , 1998, Cell.

[13]  N. Pfanner,et al.  The sorting signal of cytochrome b2 promotes early divergence from the general mitochondrial import pathway and restricts the unfoldase activity of matrix Hsp70. , 1995, The EMBO journal.

[14]  William D. Richardson,et al.  A short amino acid sequence able to specify nuclear location , 1984, Cell.

[15]  H. Ikezawa,et al.  Glycosylphosphatidylinositol (GPI)-anchored proteins. , 2002, Biological & pharmaceutical bulletin.

[16]  P. Gans,et al.  NMR structures of ferredoxin chloroplastic transit peptide from Chlamydomonas reinhardtii promoted by trifluoroethanol in aqueous solution , 1994, FEBS letters.

[17]  M. Sakaguchi,et al.  Eukaryotic protein secretion. , 1997, Current opinion in biotechnology.

[18]  G. Schulz.  β-Barrel membrane proteins , 2000 .

[19]  B. Rost,et al.  Finding nuclear localization signals , 2000, EMBO reports.

[20]  W. Hol,et al.  Structures of type 2 peroxisomal targeting signals in two trypanosomatid aldolases. , 2000, Journal of molecular biology.

[21]  S. Brunak,et al.  SHORT COMMUNICATION Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites , 1997 .

[22]  G von Heijne,et al.  Forced transmembrane orientation of hydrophilic polypeptide segments in multispanning membrane proteins. , 1998, Molecular cell.

[23]  W. Doolittle,et al.  On the prokaryotic nature of red algal chloroplasts. , 1975, Proceedings of the National Academy of Sciences of the United States of America.

[24]  L. Busconi,et al.  Membrane localization of a rice calcium-dependent protein kinase (CDPK) is mediated by myristoylation and palmitoylation. , 2000, The Plant journal : for cell and molecular biology.

[25]  R. Zeller,et al.  A GR-motif functions in nuclear accumulation of the large FGF-2 isoforms and interferes with mitogenic signalling , 1998, Oncogene.

[26]  A. Mant,et al.  Multiple pathways for the targeting of thylakoid proteins in chloroplasts , 1998, Plant Molecular Biology.

[27]  F. Kalousek,et al.  Mitochondrial intermediate peptidase. , 1995, Methods in enzymology.

[28]  J. Soll,et al.  Toc, tic, and chloroplast protein import. , 2001, Biochimica et biophysica acta.

[29]  P Bork,et al.  Wanted: subcellular localization of proteins based on sequence. , 1998, Trends in cell biology.

[30]  E. Glaser,et al.  Interaction of plant mitochondrial and chloroplast signal peptides with the Hsp70 molecular chaperone. , 2002, Trends in plant science.

[31]  G von Heijne,et al.  Species‐specific variation in signal peptide design Implications for protein secretion in foreign hosts , 1989, FEBS letters.

[32]  K. Nakai.  Protein sorting signals and prediction of subcellular localization. , 2000, Advances in protein chemistry.

[33]  Thomas L. Madden,et al.  Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. , 2001, Nucleic acids research.

[34]  M. Gonzalo Claros,et al.  MitoProt, a Macintosh application for studying mitochondrial proteins , 1995, Comput. Appl. Biosci..

[35]  C. Christophe-Hobertus,et al.  Nuclear targeting of proteins: how many different signals? , 2000, Cellular signalling.

[36]  Rolf Apweiler,et al.  The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000 , 2000, Nucleic Acids Res..

[37]  P. Thier,et al.  The origin of red algae and the evolution of chloroplasts , 2022 .

[38]  C. Robinson,et al.  Transport of proteins into chloroplasts. The thylakoidal processing peptidase is a signal-type peptidase with stringent substrate requirements at the -3 and -1 positions. , 1991, The Journal of biological chemistry.

[39]  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.

[40]  Satoru Miyano,et al.  Extensive feature detection of N-terminal protein sorting signals , 2002, Bioinform..

[41]  G von Heijne,et al.  Transcending the impenetrable: how proteins come to terms with membranes. , 1988, Biochimica et biophysica acta.

[42]  J. Deisenhofer,et al.  Crystal structures of mitochondrial processing peptidase reveal the mode for specific cleavage of import signal sequences. , 2001, Structure.

[43]  G. von Heijne.  The signal peptide. , 1990, The Journal of membrane biology.

[44]  K. Cline,et al.  Post-translational protein translocation into thylakoids by the Sec and DeltapH-dependent pathways. , 2001, Biochimica et biophysica acta.

[45]  J. Schneider-Mergener,et al.  Distribution of Binding Sequences for the Mitochondrial Import Receptors Tom20, Tom22, and Tom70 in a Presequence-carrying Preprotein and a Non-cleavable Preprotein* , 1999, The Journal of Biological Chemistry.

[46]  G. von Heijne,et al.  Chloroplast transit peptides the perfect random coil? , 1991, FEBS letters.

[47]  Manuel G. Claros,et al.  TopPred II: an improved software for membrane protein structure predictions , 1994, Comput. Appl. Biosci..

[48]  J. Soll,et al.  Protein translocation into and across the chloroplastic envelope membranes , 1998, Plant Molecular Biology.

[49]  J. Hendrick,et al.  Two mitochondrial matrix proteases act sequentially in the processing of mammalian matrix enzymes. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[50]  G. Schulz.  beta-Barrel membrane proteins. , 2000, Current opinion in structural biology.

[51]  G von Heijne,et al.  Signal sequences. The limits of variation. , 1985, Journal of molecular biology.

[52]  Amos Bairoch,et al.  A Generalized Profile Syntax for Biomolecular Sequence Motifs and its Function in Automatic Sequence Interpretation , 1994, ISMB.

[53]  G von Heijne,et al.  Patterns of amino acids near signal-sequence cleavage sites. , 1983, European journal of biochemistry.

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

[55]  W. Doolittle,et al.  Reconstructing/Deconstructing the Earliest Eukaryotes How Comparative Genomics Can Help , 2001, Cell.

[56]  Peter Roepstorff,et al.  Central Functions of the Lumenal and Peripheral Thylakoid Proteome of Arabidopsis Determined by Experimentation and Genome-Wide Prediction Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.010304. , 2002, The Plant Cell Online.

[57]  R. Hallberg,et al.  Cytochromes c 1 and b 2 are sorted to the intermembrane space of yeast mitochondria by a stop-transfer mechanism , 1992, Cell.

[58]  G. von Heijne,et al.  Domain structure of mitochondrial and chloroplast targeting peptides. , 1989, European journal of biochemistry.

[59]  J U Bowie,et al.  Helix packing in membrane proteins. , 1997, Journal of molecular biology.

[60]  M. Silva-Filho,et al.  Dual targeting properties of the N-terminal signal sequence of Arabidopsis thaliana THI1 protein to mitochondria and chloroplasts , 2001, Plant Molecular Biology.

[61]  Paul Horton,et al.  Better Prediction of Protein Cellular Localization Sites with the it k Nearest Neighbors Classifier , 1997, ISMB.

[62]  M. Gerstein,et al.  A Bayesian system integrating expression data with sequence patterns for localizing proteins: comprehensive application to the yeast genome. , 2000, Journal of molecular biology.

[63]  A. Driessen,et al.  The Sec system. , 1998, Current opinion in microbiology.

[64]  G. Dreyfuss,et al.  A Novel Receptor-Mediated Nuclear Protein Import Pathway , 1996, Cell.

[65]  R. Ellis,et al.  Transport of proteins into chloroplasts. Partial purification of a chloroplast protease involved in the processing of important precursor polypeptides. , 1984, European journal of biochemistry.

[66]  G. Schneider,et al.  Feature‐extraction from endopeptidase cleavage sites in mitochondrial targeting peptides , 1998 .

[67]  Mark C. Field,et al.  Acylation-dependent Protein Export inLeishmania * , 2000, The Journal of Biological Chemistry.

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

[69]  M. Czisch,et al.  The structural flexibility of the preferredoxin transit peptide , 1999, FEBS letters.

[70]  J Lundström,et al.  Pcons: A neural‐network–based consensus predictor that improves fold recognition , 2001, Protein science : a publication of the Protein Society.

[71]  D. Eisenberg,et al.  Localizing proteins in the cell from their phylogenetic profiles. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[72]  G von Heijne,et al.  Differential use of the signal recognition particle translocase targeting pathway for inner membrane protein assembly in Escherichia coli. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[73]  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.

[74]  S. Brunak,et al.  Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. , 2000, Journal of molecular biology.

[75]  N. Pfanner,et al.  Versatility of the mitochondrial protein import machinery , 2001, Nature Reviews Molecular Cell Biology.

[76]  Piero Fariselli,et al.  A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins , 2002, ISMB.

[77]  R. Laskey,et al.  Two interdependent basic domains in nucleoplasmin nuclear targeting sequence: Identification of a class of bipartite nuclear targeting sequence , 1991, Cell.

[78]  Anders Krogh,et al.  Prediction of Signal Peptides and Signal Anchors by a Hidden Markov Model , 1998, ISMB.

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

[80]  G. A. Thompson,et al.  Lipid-linked proteins of plants. , 2000, Progress in lipid research.

[81]  A. Delcour.  Structure and function of pore-forming beta-barrels from bacteria. , 2002, Journal of molecular microbiology and biotechnology.

[82]  A. Bolhuis,et al.  Protein targeting by the twin-arginine translocation pathway , 2001, Nature Reviews Molecular Cell Biology.

[83]  B. Dobberstein,et al.  Common Principles of Protein Translocation Across Membranes , 1996, Science.

[84]  W. Neupert,et al.  Processing of mitochondrial precursor proteins. , 1991, Biomedica biochimica acta.

[85]  R. Hegde,et al.  Membrane Protein Biogenesis: Regulated Complexity at the Endoplasmic Reticulum , 1997, Cell.

[86]  R. Stroud,et al.  The signal recognition particle. , 2001, Annual review of biochemistry.

[87]  P Vincens,et al.  Computational method to predict mitochondrially imported proteins and their targeting sequences. , 1996, European journal of biochemistry.

[88]  N. Pante,et al.  Viruses, microorganisms and scientists meet the nuclear pore Leysin, VD, Switzerland, February 26–March 1, 1998 , 1999, The EMBO journal.

[89]  E V Koonin,et al.  How many genes can make a cell: the minimal-gene-set concept. , 2000, Annual review of genomics and human genetics.

[90]  B. Bruce,et al.  The paradox of plastid transit peptides: conservation of function despite divergence in primary structure. , 2001, Biochimica et biophysica acta.

[91]  Zhirong Sun,et al.  Support vector machine approach for protein subcellular localization prediction , 2001, Bioinform..

[92]  G. Schneider,et al.  Feature-extraction from endopeptidase cleavage sites in mitochondrial targeting peptides. , 1998, Proteins.

[93]  K Nishikawa,et al.  Discrimination of intracellular and extracellular proteins using amino acid composition and residue-pair frequencies. , 1994, Journal of molecular biology.

[94]  G. Vonheijne.  The signal peptide. , 1990 .

[95]  H. Braun,et al.  The mitochondrial processing peptidase. , 1997, The international journal of biochemistry & cell biology.

[96]  Romé Voulhoux,et al.  In vivo dissection of the Tat translocation pathway in Escherichia coli. , 2002, Journal of molecular biology.

[97]  T. Rapoport.  Transport of proteins across the endoplasmic reticulum membrane. , 1992, Science.

[98]  G. Heijne,et al.  ChloroP, a neural network‐based method for predicting chloroplast transit peptides and their cleavage sites , 1999, Protein science : a publication of the Protein Society.

[99]  T. Hubbard,et al.  Using neural networks for prediction of the subcellular location of proteins. , 1998, Nucleic acids research.

[100]  R. Ellis,et al.  The Transport of Proteins into Chloroplasts , 1986 .

[101]  K. Keegstra,et al.  Transport of proteins into chloroplasts , 1988, Photosynthesis Research.

[102]  K. Akashi,et al.  Two birds with one stone: genes that encode products targeted to two or more compartments , 1998, Plant Molecular Biology.

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