Bacterial Cell Wall Homeostasis: Methods and Protocols

ISBN-13: 9781493936748 / Angielski / Twarda / 2016 / 288 str.

Hee-Jeon Hong

Spis treści

Part I Analyzing Physical Properties of the Bacterial Cell Wall

1.   Atomic Force Microscopic Analysis of Bacterial Cell Wall Peptidoglycan Architecture       Robert D. Turner, Jamie K. Hobbs, and Simon J. Foster               

2.   Ultra-Sensitive High Throughput Analytical Methods to Identify Novel Components Involved in Cell Wall Biology and to Study Bacterial Cell Wall Dynamics
Laura Alvarez, Sara B. Hernandez, Miguel A. de Pedro, and Felipe Cava

Part II Genome-Wide Approaches for the Identification of Gene Products with Roles in Cell Wall Homeostasis

3.   Microarray Analysis to Monitor Bacterial Cell Wall Homeostasis
Hee-Jeon Hong and Andy Hesketh

4.   Cell Shaving and False Positive Control Strategies Coupled to Novel Statistical Tools to Profile Gram-Positive Bacterial Surface ProteomesNestor Solis and Stuart J. Cordwell

5.   Differential Proteomics Based on Multidimensional Protein Identification Technology to Understand the Biogenesis of Outer Membrane of Escherichia coli
Alessandra M. Martorana, Sara Motta, Paola Sperandeo, Pierluigi Mauri, and Alessandra Polissi

6.   Random Transposon Mutagenesis for Cell-Envelope Resistant to Phage Infection              Ruth Reyes-Cortés, Emma S. Arguijo-Hernández, Marco A. Carballo-Ontiveros, Eva Martínez-Peñafiel and Luis Kameyama

Part III Functional Analysis of Cell-Wall Associated Proteins

7.   Zymographic Techniques for the Analysis of Bacterial Cell Wall in Bactillus
Tatsuya Fukushima and Junichi Sekiguchi

8.   Liquid Chromatography-Tandem Mass Spectrometry to Define Sortase Cleavage Products
Andrew Duong, Kalinka Koteva, Danielle L. Sexton, and Marie A. Elliot

9.   Genetics and Cell Morphology Analyses of the Actinomyces oris srtA Mutant
Chenggang Wu, Melissa Elizabeth Reardon-Robinson, and Hung Ton-That

Part IV Reporter Assays for Cell Wall Stress

10. Construction of a Bioassay System to Identify Extracellular Agents Targeting Bacterial Cell Envelope
Hee-Jeon Hong                            

11. Luciferase Reporter Gene System to Detect Cell Wall Stress Stimulon Induction in Staphylococcus aureus
Vanina Dengler and Nadine McCallum

Part V Analysis of the Non-Protein Components of the Cell Wall

12. Extraction and Analysis of Peptidoglycan Cell Wall Precursors
Elisa Binda, Lùcia Carrano, Giorgia Letizia Marcone, and Flavia Marinelli

13. Continuous Fluorescence Assay for Peptidoglycan Glycosyltransferases
Alexander J. F. Egan and Waldemar Vollmer

14. Analysis of Peptidoglycan Fragment Release                                                   
Ryan E. Schaub, Jonathan D. Lenz, and Joseph P. Dillard

15. Analysis of Cell Wall Teichoic Acids in Staphylococcus aureus                                  
Gonçalo Covas, Filipa Vaz, Gabriela Henriques, Mariana G. Pinho, and Sérgio R. Filipe

16. Analysis of Bacterial Cell Surface Chemical Composition Using Cryogenic X-Ray Photoelectron Spectroscopy
Madeleine Ramstedt and Andrey Shchukarev

Part VI Bioinformatics and Computational Biology Based Approaches

17. Biophysical Measurements of Bacterial Cell Shape
Jeffrey P. Nguyen, Benjamin P. Bratton, and Joshua W. Shaevitz

18. Coarse-Grained Molecular Dynamics Simulations of the Bacterial Cell Wall
Lam T. Nguyen, James C. Gumbart, and Grant J. Jensen

19. Structural Comparison and Simulation of Pneumococcal Peptidoglycan Hydrolase LytB
Xiao-Hui Bai, Qiong Li, Yong-Liang Jiang, Jing-Ren Zhang, Yuxing Chen, and Cong-Zhao Zhou        

Blurb

This volume brings together the most widely used and important protocols currently being employed in researching and understanding bacterial cell wall homeostasis. Chapters in Bacterial Cell Wall Homeostasis cover a variety of subjects, such as: modern microscopy techniques and other biophysical methods used to characterize the subcellular structure of the bacterial cell wall; high-throughput approaches that can be used to identify all the genes and proteins that participate in the correct functioning of an organism’s cell wall; protocols for assaying individual gene products for specific cell wall functions or identify chemicals with inhibitory activity against the cell wall; and methods for analyzing the non-protein components of the cell wall and the increasing use of computational approaches for predicting and modeling cell wall related functions and processes. Written in the highly successful Methods in Molecular Biology series format, chapters include introduction to their respective topics, lists of the necessary material and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Thorough and cutting-edge, Bacterial Cell Wall Homeostasis: Methods and Protocols emphasizes the diversity of the research taking place in bacterial cell wall homeostasis, and explains how the integration of information from across multiple disciplines is going to be essential if a holistic understanding of this important process is to be obtained.