Assessing the precision of high-throughput computational and laboratory approaches for the genome-wide identification of protein subcellular localization in bacteria

[1]  Matthew E Monroe,et al.  Global detection and characterization of hypothetical proteins in Shewanella oneidensis MR‐1 using LC‐MS based proteomics , 2005, Proteomics.

[2]  Martin Ester,et al.  Sequence analysis PSORTb v . 2 . 0 : Expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis , 2004 .

[3]  Christophe G. Lambert,et al.  PSORTdb: a protein subcellular localization database for bacteria , 2004, Nucleic Acids Res..

[4]  I. Henderson,et al.  Type V Protein Secretion Pathway: the Autotransporter Story , 2004, Microbiology and Molecular Biology Reviews.

[5]  Y. Sasaki,et al.  Use of Fluorescent-Protein Tagging To Determine the Subcellular Localization of Mycoplasma pneumoniae Proteins Encoded by the Cytadherence Regulatory Locus , 2004, Journal of bacteriology.

[6]  Continued proteomic analysis of Mycobacterium leprae subcellular fractions , 2004, Proteomics.

[7]  A. Harvey Millar,et al.  Location, location, location: surveying the intracellular real estate through proteomics in plants. , 2004, Functional plant biology : FPB.

[8]  Jenn-Kang Hwang,et al.  Predicting subcellular localization of proteins for Gram‐negative bacteria by support vector machines based on n‐peptide compositions , 2004, Protein science : a publication of the Protein Society.

[9]  P. Démoulin,et al.  Ju n 20 07 Progressive transformation of a flux rope to an ICME Comparative analysis using the direct and fitted expansion methods , 2008 .

[10]  Zhiyong Lu,et al.  Predicting subcellular localization of proteins using machine-learned classifiers , 2004, Bioinform..

[11]  Identification of chromosomally encoded membranal polypeptides of Bacillus anthracis by a proteomic analysis: Prevalence of proteins containing S‐layer homology domains , 2004, Proteomics.

[12]  Richard D. Smith,et al.  Global analysis of the membrane subproteome of Pseudomonas aeruginosa using liquid chromatography-tandem mass spectrometry. , 2004, Journal of proteome research.

[13]  A. Archakov,et al.  Proteomic Technologies in Modern Biomedical Science , 2002, Biochemistry (Moscow).

[14]  F. Reiss-Husson,et al.  Cytoplasmic and outer membranes separation in Rhodopseudomonas sphaeroides , 1975, Archives of Microbiology.

[15]  Elaine Allan,et al.  Genes to genetic immunization: identification of bacterial vaccine candidates. , 2003, Methods.

[16]  Ke Wang,et al.  PSORT-B: improving protein subcellular localization prediction for Gram-negative bacteria , 2003, Nucleic Acids Res..

[17]  L. Huber,et al.  This Review Is Part of a Thematic Series on Proteomics, Which Includes the following Articles: Cardiovascular Proteomics: Evolution and Potential Applied Proteomics: Mitochondrial Proteins and Effect on Function Organelle Proteomics: Implications for Subcellular Fractionation in Proteomics Proteomic , 2022 .

[18]  Sarka Beranova-Giorgianni,et al.  Proteome analysis by two-dimensional gel electrophoresis and mass spectrometry: strengths and limitations , 2003 .

[19]  Richard D. Smith,et al.  Affinity labeling of highly hydrophobic integral membrane proteins for proteome-wide analysis. , 2003, Journal of proteome research.

[20]  Rino Rappuoli,et al.  Reverse vaccinology. , 2000, Current opinion in microbiology.

[21]  S. Cole,et al.  Proteome Analysis of the Plasma Membrane of Mycobacterium Tuberculosis , 2002, Comparative and functional genomics.

[22]  Burkhard Rost,et al.  Sequence conserved for subcellular localization , 2002, Protein science : a publication of the Protein Society.

[23]  S. Cordwell,et al.  Proteomic comparison of membrane and extracellular proteins from invasive (PAO1) and cytotoxic (6206) strains of Pseudomonas aeruginosa , 2002, Proteomics.

[24]  T. Meyer,et al.  Proteome Analysis of Secreted Proteins of the Gastric Pathogen Helicobacter pylori , 2002, Infection and Immunity.

[25]  Darren R Flower,et al.  Bacterial bioinformatics: pathogenesis and the genome. , 2002, Journal of molecular microbiology and biotechnology.

[26]  S. Wikel,et al.  Changes in Temporal and Spatial Patterns of Outer Surface Lipoprotein Expression Generate Population Heterogeneity and Antigenic Diversity in the Lyme Disease Spirochete, Borrelia burgdorferi , 2002, Infection and Immunity.

[27]  F. Yoshimura,et al.  Separation of the outer membrane and identification of major outer membrane proteins from Porphyromonas gingivalis. , 2002, European journal of oral sciences.

[28]  H. Pakrasi,et al.  Proteomics of Synechocystis sp. Strain PCC 6803 , 2000, Molecular & Cellular Proteomics.

[29]  M. Bott,et al.  A high‐resolution reference map for cytoplasmic and membrane‐associated proteins of Corynebacterium glutamicum , 2001, Electrophoresis.

[30]  S. Gygi,et al.  Proteomics: the move to mixtures. , 2001, Journal of mass spectrometry : JMS.

[31]  Jan Maarten van Dijl,et al.  A proteomic view on genome-based signal peptide predictions. , 2001, Genome research.

[32]  A. Jonsson Mass spectrometry for protein and peptide characterisation , 2001, Cellular and Molecular Life Sciences CMLS.

[33]  J R Maddock,et al.  Two‐dimensional electrophoresis and peptide mass fingerprinting of bacterial outer membrane proteins , 2001, Electrophoresis.

[34]  H Sahm,et al.  Proteome analysis of Corynebacterium glutamicum , 2001, Electrophoresis.

[35]  S. Cordwell,et al.  Comparative proteomics of bacterial pathogens , 2001, Proteomics.

[36]  S. Engelmann,et al.  Extracellular proteins of Staphylococcus aureus and the role of SarA and σB , 2001, Proteomics.

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

[38]  S. Dunn,et al.  Specific heterodimer formation by the cytoplasmic domains of the b and b' subunits of cyanobacterial ATP synthase. , 2001, Biochemistry.

[39]  J. Lay,et al.  MALDI-TOF mass spectrometry of bacteria. , 2001, Mass spectrometry reviews.

[40]  J. E. Lawson,et al.  Expression, purification, and structural analysis of the trimeric form of the catalytic domain of the Escherichia coli dihydrolipoamide succinyltransferase , 2008, Protein science : a publication of the Protein Society.

[41]  I. Henderson,et al.  Autotransporter proteins, evolution and redefining protein secretion. , 2000, Trends in microbiology.

[42]  A Yamaguchi,et al.  Molecular construction of a multidrug exporter system, AcrAB: molecular interaction between AcrA and AcrB, and cleavage of the N-terminal signal sequence of AcrA. , 2000, Journal of biochemistry.

[43]  H. Nikaido,et al.  Cross-Linked Complex between Oligomeric Periplasmic Lipoprotein AcrA and the Inner-Membrane-Associated Multidrug Efflux Pump AcrB from Escherichia coli , 2000, Journal of bacteriology.

[44]  S. Dunn,et al.  The second stalk of Escherichia coli ATP synthase. , 2000, Biochimica et biophysica acta.

[45]  A. Gooley,et al.  Proteomic analysis of the Escherichia coli outer membrane. , 2000, European journal of biochemistry.

[46]  A. Das,et al.  Subcellular localization of the Agrobacterium tumefaciens T‐DNA transport pore proteins: VirB8 is essential for the assembly of the transport pore , 2000, Molecular microbiology.

[47]  M. Molloy,et al.  Membrane proteins and proteomics: Un amour impossible? , 2000, Electrophoresis.

[48]  M. Hagemann,et al.  Proteomics of Synechocystis sp. strain PCC 6803. Identification of periplasmic proteins in cells grown at low and high salt concentrations. , 2000, European journal of biochemistry.

[49]  L. Huber,et al.  Subcellular fractionation, electromigration analysis and mapping of organelles. , 1999, Journal of chromatography. B, Biomedical sciences and applications.

[50]  D. Touati,et al.  Coupling 2D SDS-PAGE with CNBr cleavage and MALDI-TOFMS: a strategy applied to the identification of proteins induced by a hypochlorous acid stress in Escherichia coli. , 1998, Analytical chemistry.

[51]  J. Knapp,et al.  Crystal structure of the truncated cubic core component of the Escherichia coli 2-oxoglutarate dehydrogenase multienzyme complex. , 1998, Journal of molecular biology.

[52]  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..

[53]  R. Hancock,et al.  Utilization of alkaline phosphatase fusions to identify secreted proteins, including potential efflux proteins and virulence factors from Helicobacter pylori. , 1997, FEMS microbiology letters.

[54]  K Takeyasu,et al.  Molecular imaging of Escherichia coli F0F1‐ATPase in reconstituted membranes using atomic force microscopy , 1996, FEBS letters.

[55]  R. Fernandez,et al.  Cloning and sequencing of a Bordetella pertussis serum resistance locus , 1994, Infection and immunity.

[56]  A. Darzins Characterization of a Pseudomonas aeruginosa gene cluster involved in pilus biosynthesis and twitching motility: sequence similarity to the chemotaxis proteins of enterics and the gliding bacterium Myxococcus xanthus , 1994, Molecular microbiology.

[57]  K. Poole,et al.  Multiple antibiotic resistance in Pseudomonas aeruginosa: evidence for involvement of an efflux operon , 1993, Journal of bacteriology.

[58]  Joanne I. Yeh,et al.  Three-dimensional structures of the ligand-binding domain of the bacterial aspartate receptor with and without a ligand. , 1995, Science.

[59]  M. Kanehisa,et al.  Expert system for predicting protein localization sites in gram‐negative bacteria , 1991, Proteins.

[60]  W. Page,et al.  Comparison of methods used to separate the inner and outer membranes of cell envelopes of Campylobacter spp. , 1988, Journal of general microbiology.

[61]  Demel Ra,et al.  Outer membranes of gram-negative bacteria. , 1987 .

[62]  R. Doolittle,et al.  A simple method for displaying the hydropathic character of a protein. , 1982, Journal of molecular biology.

[63]  H. Winkler,et al.  Separation of inner and outer membranes of Rickettsia prowazeki and characterization of their polypeptide compositions , 1979, Journal of bacteriology.

[64]  R. Hancock,et al.  Outer membranes of gram-negative bacteria. XIX. Isolation from Pseudomonas aeruginosa PAO1 and use in reconstitution and definition of the permeability barrier , 1978, Journal of bacteriology.

[65]  S. Morse,et al.  The biology of the gonococcus. , 1978, CRC critical reviews in microbiology.