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Identification of Protein Secretion Systems in Bacterial Genomes Using MacSyFinder

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Bacterial Protein Secretion Systems

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1615))

Abstract

Protein secretion systems are complex molecular machineries that translocate proteins through the outer membrane, and sometimes through multiple other barriers. They have evolved by co-option of components from other envelope-associated cellular machineries, making them sometimes difficult to identify and discriminate. Here, we describe how to identify protein secretion systems in bacterial genomes using MacSyFinder. This flexible computational tool uses the knowledge stemming from experimental studies to identify homologous systems in genome data. It can be used with a set of predefined models—“TXSScan”—to identify all major secretion systems of diderm bacteria (i.e., with inner and with LPS-containing outer membranes). For this, it identifies and clusters colocalized components of secretion systems using sequence similarity searches with hidden Markov model protein profiles. Finally, it checks whether the genetic content and organization of clusters satisfy the constraints of the model. TXSScan models can be customized to search for variants of known systems. The models can also be built from scratch to identify novel systems. In this chapter, we describe a complete pipeline of analysis, including the identification of a reference set of experimentally studied systems, the identification of components and the construction of their protein profiles, the definition of the models, their optimization, and, finally, their use as tools to search genomic data.

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Author information

Authors and Affiliations

  1. Microbial Evolutionary Genomics, Institut Pasteur, 25-28 rue Dr Roux, Paris, 75015, France

    Sophie S. Abby & Eduardo P. C. Rocha

  2. CNRS, UMR3525, 25-28 rue Dr. Roux, Paris, 75015, France

    Sophie S. Abby & Eduardo P. C. Rocha

  3. Université Grenoble Alpes, Laboratoire Techniques de l’Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble (TIMC-IMAG), F-38000 Grenoble, France ; Centre National de la Recherche Scientifique (CNRS), TIMC-IMAG, F-38000, Grenoble, France

    Sophie S. Abby

Authors
  1. Sophie S. Abby
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  2. Eduardo P. C. Rocha
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Corresponding author

Correspondence to Sophie S. Abby .

Editor information

Editors and Affiliations

  1. Institut de Microbiologie de la Méditerranée, Aix-Marseille Univ - CNRS, Marseille, France

    Laure Journet

  2. Institut de Microbiologie de la Méditerranée, Aix-Marseille Univ - CNRS, Marseille, France

    Eric Cascales

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Abby, S.S., Rocha, E.P.C. (2017). Identification of Protein Secretion Systems in Bacterial Genomes Using MacSyFinder. In: Journet, L., Cascales, E. (eds) Bacterial Protein Secretion Systems. Methods in Molecular Biology, vol 1615. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7033-9_1

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  • DOI: https://doi.org/10.1007/978-1-4939-7033-9_1

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7031-5

  • Online ISBN: 978-1-4939-7033-9

  • eBook Packages: Springer Protocols

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