2‐D Gel‐Based Proteomic Approaches to Antibiotic Drug Discovery

Nadja Raatschen1, Julia Elisabeth Bandow1

1 Ruhr University Bochum, Bochum, Germany
Publication Name:  Current Protocols in Microbiology
Unit Number:  Unit 1F.2
DOI:  10.1002/9780471729259.mc01f02s26
Online Posting Date:  August, 2012
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Abstract

The global analysis of changes in the protein composition of bacterial cells in response to treatment with antibiotic agents grants insights into the physiological response of cells to inhibition of vital cellular functions. This unit gives an overview of how global proteomic studies can impact antibacterial drug discovery by identifying or validating compound mechanism of action and by increasing the confidence in the value of genes with unknown function as potential new targets. It describes the design and function of a reference compendium of proteomic responses to inhibition of vital cellular functions through antibacterial agents or genetic down‐regulation of potential target genes. An overview of the workflow for two‐dimensional gel electrophoresis‐based experiments is also presented. Curr. Protoc. Microbiol. 26:1F.2.1‐1F.2.16. © 2012 by John Wiley & Sons, Inc.

Keywords: antibiotics; two‐dimensional gel electrophoresis; two‐dimensional polyacrylamide gel; peptide mass fingerprinting; PMF; proteomics; mechanism of action; conditional mutants; stress response

     
 
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Table of Contents

  • Introduction
  • What is Proteomics?
  • Use and Design of the Reference Compendium of Proteomic Responses
  • Experimental Design and Workflow
  • Literature Cited
  • Figures
     
 
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Materials

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Figures

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Literature Cited

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Key References
   Brötz‐Oesterhelt and Sass, 2010. See above.
  Describes recent and current efforts in antibacterial drug discovery.
   Wenzel and Bandow, 2011.
  Reviews the use of the most comprehensive reference compendium of bacterial proteomic responses to antibiotics.
   Freiberg, C., Brötz‐Oesterhelt, H., and Labischinski, H. 2004. The impact of transcriptome and proteome analyses on antibiotic drug discovery. Curr. Opin. Microbiol. 7:451‐459.
  Reviews proteome and transcriptome approaches to antibacterial drug discovery.
   Görg et al., 2004. See above.
  Provides an overview on 2‐D gel‐based proteomic technologies.
Internet Resources
  http://cmr.jcvi.org/tigr‐scripts/CMR/CmrHomePage.cgi
  Provides an updated list of bacterial species with fully sequenced genomes.
  http://world‐2dpage.expasy.org/swiss‐2dpage/
  Provide proteome maps for several species.
  http://eecoli.kaist.ac.kr/main.html
  Source of proteomics tools.
  http://microbio1.biologie.uni‐greifswald.de/csp/bio/login.csp
  http://world‐2dpage.expasy.org/portal/
  http://www.decodon.com/
  http://www.nonlinear.com/
  http://www.bio‐rad.com/
  http://www.genebio.com/
  http://www.syngene.com/
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