REVIEW Proteomic signatures in antibiotic research Michaela Wenzel and Julia E. Bandow Biology of Microorganisms, Ruhr-University Bochum, Bochum, Germany Received: January 26, 2011 Revised: March 13, 2011 Accepted: March 22, 2011 Antibiotics disturb the physiological homeostasis of bacterial cells by interfering with essential cellular functions or structures. The bacterial proteome adjusts quickly in response to antibiotic challenge. This physiological response is specifically tailored to overcome the inflicted damage and, thus, closely linked to the antibiotic target and mechanism of action. In a way, the proteome mirrors the antibiotic insult. This connection can be exploited to guide the development of novel antibiotics. By using structurally different antibiotics, which cause the same physiological disturbance, proteomic signatures diagnostic of the mechanism of action can be defined. These proteomic signatures inform about mechanism-related differ- ential protein expression as well as about protein modifications. This review recapitulates how antibiotic proteomic signatures are established and highlights areas of antibiotic research benefiting most from proteomic signatures. Antibacterial research programs designed to structurally advance existing antibiotic classes profit from rapid in vivo mechanism of action confirmation. What is more, a comprehensive reference compendium of antibiotic proteomic signatures allows rapid mechanism of action identification of those structurally novel compounds that inhibit known targets. Finally, novel proteomic response profiles indicate unprecedented mechanisms. Here, the proteome profile provides evidence on the nature of the antibiotic-caused physiological disturbance leading to testable hypotheses on the mechanism of action. Keywords: Antibiotics / Drug mechanism of action / Microbiology / Proteomic signature 1 Introduction 1.1 An introduction to antibiotics According to a definition by Selman A. Waksman, anti- biotics are low-molecular-weight compounds that inhibit growth of microorganisms at low concentrations but do not inhibit growth of the producer [1]. Antibiotics occur frequently in nature. Many antibiotics known to date are secondary metabolites of microbes and their ecological functions may range from inhibiting growth of competitors to serving as signaling molecules [2]. Streptomyces species, Gram-positive bacteria living in the soil, are known to produce a wealth of different antibiotics as part of their extensive secondary metabolism. But antibiotic substances are not only produced by microbes, as part of the innate immune system of eukaryotic organisms they contribute to preventing infections. Mammals, for example, produce antibiotic peptides, most prominently defensins [3]. An antibiotic aminosterol, squalamine, was isolated from tissues of the shark Squalus acanthias, where it is present in antibiotic concentrations [4]. Although antibiotics are of great importance as selection tools in molecular biology and biotechnology, without doubt their main benefits to humankind are their therapeutic properties. Comprehensive vaccination programs and improved hygiene in concert with antibiotics led to a revo- lution in medicine [5]. While infectious diseases were the primary cause of death in the pre-antibiotic 19th century, in the 20th century many of the worst infectious diseases were brought under control where access to healthcare was adequate, leading to an increase in life expectancy of about 30 years [6]. Synthetic antibiotic classes, especially orga- noarsenic compounds [7] and sulfonamides [8] played an important role in kick-starting the antibiotic era by Abbreviations: MRSA, methicillin-resistant Staphylococcus aureus Correspondence: Dr. Julia E. Bandow, Ruhr University Bochum, Universit . atsstr. 150, 44801 Bochum, Germany E-mail: julia.bandow@rub.de; julia.bandow@ruhr-uni-bochum.de Fax: 149-234-32-14620 & 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.com 3256 Proteomics 2011, 11, 3256–3268 DOI 10.1002/pmic.201100046