Proteome analysis in the study of the bacterial heat‐shock response

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I. Introduction 245 II. Global Regulatory Networks 245 III. Heat‐Shock Response 247 A. Control Elements in Gram‐Positive Bacteria 247 1. Sigma B‐Controlled Genes 247 2. HrcA‐CIRCE Controlled Genes 249 3. Genes Controlled by Additional Repressors 250 B. Control Elements in Gram‐Negative Bacteria 250 1. Sigma 32‐Controlled Genes 250 2. Genes Controlled by Other Minor Sigma Factors 252 3. HrcA‐CIRCE‐Controlled Genes 252 4. Minor Regulatory Elements 252 C. Networks of Positive and Negative Regulators 253 IV. Proteome Studies of Heat‐Shock Regulons 253 V. Mass Spectrometry in The Analysis of Heat‐Shock‐Induced Post‐Translational Modifications of Proteins 256 A. Phosphorylation 256 B. Other Post‐Translational Modifications 258 1. Protein Oxidation 258 2. Sulfoxidation 258 3. Acetylation 258 VI. Potential Significance of Proteome Studies for Analysis of Regulons 258 Acknowledgments 259 References 259 In recent years, it has become clear that, in addition to the regulation of the expression of specific genes, there are global regulatory systems that control the simultaneous expression of a large number of genes in response to a variety of environmental stresses. The first of these global control systems, and of substantial importance, is the heat‐shock response. The heat‐shock response is characterized by the induction of a large set of proteins (heat‐shock proteins—HSPs) upon shifts to higher temperature and upon exposure to conditions in which proteins are denatured (i.e., alcohols, heavy metals). The heat‐shock response is universal and many of the heat‐shock proteins are highly conserved among species. In bacteria, the heat‐shock response has been studied extensively in several Gram‐positive bacteria (Bacillus subtilis) and in the Gram‐negative bacteria (i.e., Escherichia coli, Agrobacterium tumefaciens). The first recognition of the molecular abundance of the bacterial heat‐shock proteins took place with the introduction of high‐resolution two‐dimensional polyacrylamide gels (2D gels) to analyze complex mixtures of cellular proteins. Two‐dimensional gels, followed by mass spectrometry, were used to define the heat‐shock stimulons in several bacteria, and to study the regulatory elements that control the heat‐shock response. Here, we review the heat‐shock response and its regulation in bacteria. The review will emphasize the use of proteome analysis in the study of this response, and will point out those open questions that can be investigated with proteomics, including mass spectrometry techniques. © 2003 Wiley Periodicals, Inc., Mass Spec Rev 21:244–265, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mas.10031