ARAMEMNON, a Novel Database for Arabidopsis Integral Membrane Proteins1

A specialized database (DB) for Arabidopsis membrane proteins, ARAMEMNON, was designed that facilitates the interpretation of gene and protein sequence data by integrating features that are presently only available from individual sources. Using several publicly available prediction programs, putative integral membrane proteins were identified among the approximately 25,500 proteins in the Arabidopsis genome DBs. By averaging the predictions from seven programs, approximately 6,500 proteins were classified as transmembrane (TM) candidate proteins. Some 1,800 of these contain at least four TM spans and are possibly linked to transport functions. The ARAMEMNON DB enables direct comparison of the predictions of seven different TM span computation programs and the predictions of subcellular localization by eight signal peptide recognition programs. A special function displays the proteins related to the query and dynamically generates a protein family structure. As a first set of proteins from other organisms, all of the approximately 700 putative membrane proteins were extracted from the genome of the cyanobacterium Synechocystis sp. and incorporated in the ARAMEMNON DB. The ARAMEMNON DB is accessible at the URL http://aramemnon.botanik.uni-koeln.de.

[1]  K. Fischer,et al.  Analysis of the Plastidic phosphate translocator Gene Family in Arabidopsis and Identification of New phosphate translocator-Homologous Transporters, Classified by Their Putative Substrate-Binding Site1 , 2003, Plant Physiology.

[2]  Huanming Yang,et al.  A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica) , 2002, Science.

[3]  W. Frommer,et al.  Conservation of amino acid transporters in fungi, plants and animals. , 2002, Trends in biochemical sciences.

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

[5]  Ulf-Ingo Flügge,et al.  The Plastidic Pentose Phosphate Translocator Represents a Link between the Cytosolic and the Plastidic Pentose Phosphate Pathways in Plants1 , 2002, Plant Physiology.

[6]  John B. Anderson,et al.  MMDB: Entrez's 3D-structure database , 2002, Nucleic Acids Res..

[7]  Rolf Apweiler,et al.  Erratum: Evaluation of methods for the prediction of membrane spanning regions , 2002, Bioinform..

[8]  A. Oliphant,et al.  A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). , 2002, Science.

[9]  I. Small,et al.  Dual targeting to mitochondria and chloroplasts. , 2001, Biochimica et biophysica acta.

[10]  G von Heijne,et al.  Prediction of organellar targeting signals. , 2001, Biochimica et biophysica acta.

[11]  S. Luan,et al.  A Novel Family of Magnesium Transport Genes in Arabidopsis Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.010352. , 2001, The Plant Cell Online.

[12]  István Simon,et al.  The HMMTOP transmembrane topology prediction server , 2001, Bioinform..

[13]  L. Ungar,et al.  Chloroplast transit peptide prediction: a peek inside the black box. , 2001, Nucleic acids research.

[14]  B. André,et al.  A genomic view of yeast membrane transporters. , 2001, Current opinion in cell biology.

[15]  J F Harper,et al.  Phylogenetic relationships within cation transporter families of Arabidopsis. , 2001, Plant physiology.

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

[17]  John M. Ward,et al.  Identification of novel families of membrane proteins from the model plant Arabidopsis thaliana , 2001, Bioinform..

[18]  Masami Ikeda,et al.  Transmembrane topology prediction methods: A re-assessment and improvement by a consensus method using a dataset of experimentally-characterized transmembrane topology , 2001, Silico Biol..

[19]  P E Bourne,et al.  The Protein Data Bank. , 2002, Nucleic acids research.

[20]  G von Heijne,et al.  Consensus predictions of membrane protein topology , 2000, FEBS letters.

[21]  The Arabidopsis Genome Initiative.  Analysis of the genome sequence of the flowering plant Arabidopsis thaliana , 2000, Nature.

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

[23]  T. Stevens,et al.  Do more complex organisms have a greater proportion of membrane proteins in their genomes? , 2000, Proteins.

[24]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[25]  T. Hirokawa,et al.  Proportion of membrane proteins in proteomes of 15 single-cell organisms analyzed by the SOSUI prediction system. , 1999, Biophysical chemistry.

[26]  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.

[27]  M H Saier,et al.  A functional‐phylogenetic system for the classification of transport proteins , 1999, Journal of cellular biochemistry.

[28]  Yanli Wang,et al.  MMDB: Entrez's 3D-structure database , 2003, Nucleic Acids Res..

[29]  G. Tusnády,et al.  Principles governing amino acid composition of integral membrane proteins: application to topology prediction. , 1998, Journal of molecular biology.

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

[31]  Erik L. L. Sonnhammer,et al.  A Hidden Markov Model for Predicting Transmembrane Helices in Protein Sequences , 1998, ISMB.

[32]  G. Heijne,et al.  Genome‐wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms , 1998, Protein science : a publication of the Protein Society.

[33]  Shigeki Mitaku,et al.  SOSUI: classification and secondary structure prediction system for membrane proteins , 1998, Bioinform..

[34]  J. Thompson,et al.  The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. , 1997, Nucleic acids research.

[35]  Søren Brunak,et al.  A Neural Network Method for Identification of Prokaryotic and Eukaryotic Signal Peptides and Prediction of their Cleavage Sites , 1997, Int. J. Neural Syst..

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

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

[38]  B. Rost,et al.  Topology prediction for helical transmembrane proteins at 86% accuracy–Topology prediction at 86% accuracy , 1996, Protein science : a publication of the Protein Society.

[39]  Patrick Argos,et al.  Topology prediction of membrane proteins , 1996, Protein science : a publication of the Protein Society.

[40]  Sayaka,et al.  Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. , 1996, DNA research : an international journal for rapid publication of reports on genes and genomes.

[41]  W. Pearson.  Effective protein sequence comparison. , 1996, Methods in enzymology.

[42]  Y. Nakamura,et al.  Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions (supplement). , 1996, DNA research : an international journal for rapid publication of reports on genes and genomes.

[43]  B. André,et al.  An overview of membrane transport proteins in Saccharomyces cerevisiae , 1995, Yeast.

[44]  J. Huelsenbeck.  The robustness of two phylogenetic methods: four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining. , 1995, Molecular biology and evolution.

[45]  W. Frommer.  Heterologous Expression of Genes in Bacterial, Fungal, Animal, and Plant Cells , 1995 .

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

[47]  P Argos,et al.  Prediction of transmembrane segments in proteins utilising multiple sequence alignments. , 1994, Journal of molecular biology.

[48]  Kay Hofmann,et al.  Tmbase-A database of membrane spanning protein segments , 1993 .

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

[50]  G. Heijne.  Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule. , 1992, Journal of molecular biology.

[51]  G von Heijne,et al.  Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule. , 1992, Journal of molecular biology.

[52]  D. Lipman,et al.  Improved tools for biological sequence comparison. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[53]  D. Eisenberg,et al.  Analysis of membrane and surface protein sequences with the hydrophobic moment plot. , 1984, Journal of molecular biology.

[54]  Robert R. Sokal,et al.  A statistical method for evaluating systematic relationships , 1958 .