Bacterial Secretion Systems

Methods and Protocols

Laure Journet, Eric Cascales (Herausgeber)

Buch | Hardcover

613 Seiten

2023 | Second Edition 2024
Springer-Verlag New York Inc.
978-1-0716-3444-8 (ISBN)

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lt;p>This second edition details new and updated protocols that cover techniques used to study secretion systems. Chapters focus on identifying and localizing the different subunits, defining interactions within subunits, monitoring conformational changes, purifying and imaging of large complexes, defining the assembly pathway by fluorescence microscopy and the role of energy during assembly and/or secretion, identifying secreted effectors as well as using reporters to follow effector transport. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls.

Authoritative and cutting-edge, Bacterial Secretion Systems: Methods and Protocols- Second Edition aims to be a useful and practical guide to new researchers and experts looking to expand their knowledge.

lt;p>1 Identification of protein secretion systems in bacterial genomes using MacSyFinder version 2

Sophie S Abby, Rémi Denise, and Eduardo PC Rocha

2 Protein sorting prediction

Henrik Nielsen

3 Cell fractionation

Melissa Petiti, Laetitia Houot, and Denis Duché

4 Components sub-cellular localization: identification of lipoproteins using globomycin and radioactive palmitate

Nienke Buddelmeijer

5 Components sub-cellular localization: identification of lipoproteins using alkyne fatty acids and click-chemistry

Karine Nozeret, and Nienke Buddelmeijer

6 Defining membrane protein localization by isopycnic density gradients

Rhys A. Dunstan, Iain D. Hay, and Trevor Lithgow

7 Components sub-cellular localization: Cell surface exposure

Anna Konovalova

8 Probing protein topology and conformation by limited proteolysis

Maïalène Chabalier, Thierry Doan, and Eric Cascales

9 Exploring uniform, dual and dynamic topologies of membrane proteins by substituted cysteine accessibility method (SCAM^TM)

Mikhail Bogdanov

10 Preparation of uniformly oriented inverted inner (cytoplasmic) membrane vesicles from Gram-negative bacterial cells

Mikhail Bogdanov

11 Defining membrane protein topology using pho-lac reporter fusions

Gouzel Karimova, and Daniel Ladant

12 Measure of peptidoglycan degradation activity

Yoann G. Santin, and Eric Cascales

13 Protein-protein interaction: Bacterial Two-Hybrid

Gouzel Karimova, Emilie Gauliard, Maryline Davi, Scot P. Oulelette, and Daniel Ladant

14 Protein-protein interactions: oxidative Bacterial Two-Hybrid

Callypso Pellegri, Emmanuelle Bouveret, and Laetitia Houot

15 Protein-protein interactions: Yeast two-hybrid

Jer-Sheng Lin, and Erh-Min Lai

16 Protein-protein interactions: Bimolecular Fluorescence Complementation and Cytology two-hybrid

Dvuti Purkait, Mohd Ilyas, and Krishnamohan Atmakuri

17 Bacterial one- and two-hybrid assays to monitor transmembrane helix interactions

Abdelrahim Zoued, Jean-Pierre Duneau, and Eric Cascales

18 Protein-protein interactions: Co-immunoprecipitation

Jer-Sheng Lin, Jemal Ali, and Erh-Min Lai

19 Protein-protein interaction: Tandem Affinity Purification in bacteria

Julie P. M. Viala, and Emmanuelle Bouveret

20 In vivo site-directed and time-resolved photocrosslinking of envelope proteins

Yassin A. Abuta'a, Anne Caumont-Sarcos, Cécile Albenne, and Raffaele Ieva

21 Identification of protein partners by APEX2 proximity labeling

Ophélie Remy, and Yoann G. Santin

22 Blue native PAGE analysis of bacterial secretion complexes

Susann Zilkenat, Eunjin Kim, Tobias Dietsche, Julia V. Monjaràs Feria, Claudia E. Torres-Vargas, Mehari Tesfazgi Mebrhatu, and Samuel Wagner

23 Surface Plasmon Resonance: a sensitive tool to study protein-protein interactions

Badreddine Douzi

24 Defining assembly pathways by fluorescence microscopy

Andreas Diepold

25 Large complexes: cloning strategy, production and purification

Samira Zouhir, Wiem Abidi, and Petya V. Krasteva

26 Starting with an integral membrane protein project for structural biology: production, purification, detergent quantification and buffer optimization - case study of the exporter CntI from Pseudomonas aeruginosa.

Maxime Mégret-Cavalier, Alexandre Pozza, Quentin Cece, Françoise Bonneté, Isabelle Broutin, and Gilles Phan

27 Structural analysis of protein complexes by cryo electron microscopy

Athanasios Ignatiou, Kévin Macé, Adam Redzej, Tiago R. D. Costa, Gabriel Waksman, and Elena V. Orlova

28 CryoEM data analysis of membrane proteins. Practical considerations on amphipathic belts, ligands and variability analysis

Alexia Gobet, Loïck Moissonnier, and Vincent Chaptal

29 Structural analyses of bacterial effectors by X-ray crystallography

Chloé Dugelay, Virginie Gueguen-Chaignon, and Laurent Terradot

30 Structural analysis of proteins from bacterial secretion systems and their assemblies by NMR spectroscopy

Gisele Cardoso de Amorim, Benjamin Bardiaux, and Nadia Izadi-Pruneyre

31 Quantifying substrate protein secretion via the type-III secretion system of the bacterial flagellum

Rosa Einenkel, Manuel Halte, and Marc Erhardt

32 Use of Bastion for the identification of secreted substrates

Jiawei Wang, Jiahui Li, and Christopher J. Stubenrauch

33 Identification of effectors: Precipitation of supernatant material

Nicolas Flaugnatti, and Laure Journet

34 Metabolic labelling: snapshot of the effect of toxins on the key cellular processes

Dukas Jur nas

35 Effector translocation assay: differential solubilization

Irina S. Franco, Sara V. Pais, Nuno Charro, and Luís Jaime Mota

36 Monitoring effector translocation with the TEM-1 beta-lactamase reporter system: from endpoint to time course analysis

Julie Allombert, Anne Vianney, and Xavier Charpentier

37 Quantitative determination of anti-bacterial activity during bacterial co-culture

Juliana Alcoforado Diniz, Christopher Earl, Ruth E. Hernandez, Birte Hollmann, and Sarah J. Coulthurst

38 Investigating secretion systems and effectors on Galleria mellonella

Antonia Habich, and Daniel Unterweger

Erscheinungsdatum	08.11.2023
Reihe/Serie	Methods in Molecular Biology
Zusatzinfo	97 Illustrations, color; 23 Illustrations, black and white; XVI, 613 p. 120 illus., 97 illus. in color.
Verlagsort	New York, NY
Sprache	englisch
Maße	178 x 254 mm
Themenwelt	Naturwissenschaften ► Biologie ► Mikrobiologie / Immunologie
Schlagworte	Cell fractionation • Fluorescence Microscopy • Isopycnic Density Gradients • Lipoprotein Localisation • Proteolysis
ISBN-10	1-0716-3444-5 / 1071634445
ISBN-13	978-1-0716-3444-8 / 9781071634448
Zustand	Neuware