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Computational prediction and experimental assessment of secreted/surface proteins from Mycobacterium tuberculosis H37Rv
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Vizcaíno, Carolina
Restrepo-Montoya, Daniel
Rodríguez Burbano, Diana Consuelo
Niño, Luis F.
Ocampo, Marisol
Vanegas, Magnolia
Reguero, María T.
Martínez, Nora L.
Patarroyo, Manuel E.
Patarroyo, Manuel A.
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2010
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Abstract
The mycobacterial cell envelope has been implicated in the pathogenicity of tuberculosis and therefore has been a prime target for the identification and characterization of surface proteins with potential application in drug and vaccine development. In this study, the genome of Mycobacterium tuberculosis H37Rv was screened using Machine Learning tools that included feature-based predictors, general localizers and transmembrane topology predictors to identify proteins that are potentially secreted to the surface of M. tuberculosis, or to the extracellular milieu through different secretory pathways. The subcellular localization of a set of 8 hypothetically secreted/surface candidate proteins was experimentally assessed by cellular fractionation and immunoelectron microscopy (IEM) to determine the reliability of the computational methodology proposed here, using 4 secreted/surface proteins with experimental confirmation as positive controls and 2 cytoplasmic proteins as negative controls. Subcellular fractionation and IEM studies provided evidence that the candidate proteins Rv0403c, Rv3630, Rv1022, Rv0835, Rv0361 and Rv0178 are secreted either to the mycobacterial surface or to the extracellular milieu. Surface localization was also confirmed for the positive controls, whereas negative controls were located on the cytoplasm. Based on statistical learning methods, we obtained computational subcellular localization predictions that were experimentally assessed and allowed us to construct a computational protocol with experimental support that allowed us to identify a new set of secreted/surface proteins as potential vaccine candidates. © 2010 Vizcaíno et al.
Palabras clave
Proteína bacteriana , Bacteriana , Linfocito B , Gel de poliacrilamida , Proteína de citoplasma , Proteína de membrana , Vacuna peptídica , Proteína Rv178 , Proteína Rv361 , Proteína Rv43C , Proteína Rv835 , Proteína Rv122 , Proteína Rv36 , Medicamento no clasificado , Anticuerpo bacteriano , Epítopo , Proteína de membrana externa , Péptido , Experimento con animales , Genoma bacteriano , Cepa bacteriana , Fraccionamiento Celular , Predicción por computadora , Estudio controlado , Citoplasma , Identificación de drogas , Aprendizaje automático , Computación Matemática , Estructura de la membrana , Tuberculosis micobacteriana , Localización de proteínas , Secreción de proteínas , Producción de vacunas , Inteligencia artificial , Escherichia Coli , inmunotransferencia , Microscopía inmunoelectrónica , Inmunología , Metabolismo , Metodología , Mycobacterium Smegmatis , Electroforesis en gel de poliacrilamida , Modelo estadístico , Ultrasonido , Tuberculosis micobacteriana , Anticuerpos , Inteligencia artificial , Proteínas de la membrana externa bacteriana , Fraccionamiento Celular , Biología Computacional , Electroforesis , Epítopos , Fracciones subcelulares
Keywords
Subcellular Fractions , Immunoelectron , Electrophoresis , Microscopy , Models , Computational Biology , Epitopes , Cell Fractionation , Bacterial Outer Membrane Proteins , Artificial Intelligence , Antibodies , Mycobacterium Tuberculosis , Ultrasound , Statistical Model , Polyacrylamide Gel Electrophoresis , Methodology , Metabolism , Immunology , Immunoelectron Microscopy , Immunoblotting , Artificial Intelligence , Vaccine Production , Protein Secretion , Protein Localization , Mycobacterium Tuberculosis , Membrane Structure , Mathematical Computing , Machine Learning , Drug Identification , Cytoplasm , Controlled Study , Computer Prediction , Cell Fractionation , Bacterial Strain , Bacterial Genome , Peptide , Animal Experiment , Outer Membrane Protein , Outer Membrane Protein , Bacterium Antibody , Unclassified Drug , Protein Rv363 , Protein Rv122 , Protein Rv43C , Protein Rv835 , Protein Rv361 , Protein Rv178 , Peptide Vaccine , Cytoplasm Protein , Membrane Protein , Polyacrylamide Gel , B-Lymphocyte , Bacterial , Bacterial Protein
