title: Quantitative proteome analysis of an antibiotic resistant Escherichia coli exposed to tetracycline reveals multiple affected metabolic and peptidoglycan processes.
abstract: Tetracyclines are among the most commonly used antibiotics administrated to farm animals for disease treatment and prevention, contributing to the worldwide increase in antibiotic resistance in animal and human pathogens. Although tetracycline mechanisms of resistance are well known, the role of metabolism in bacterial reaction to antibiotic stress is still an important assignment and could contribute to the understanding of tetracycline related stress response. In this study, spectral counts-based label free quantitative proteomics has been applied to study the response to tetracycline of the environmental-borne Escherichia coli EcAmb278 isolate soluble proteome. A total of 1484 proteins were identified by high resolution mass spectrometry at a false discovery rate threshold of 1%, of which 108 were uniquely identified under absence of tetracycline whereas 126 were uniquely identified in presence of tetracycline. These proteins revealed interesting difference in e.g. proteins involved in peptidoglycan-based cell wall proteins and energy metabolism. Upon treatment, 12 proteins were differentially regulated showing more than 2-fold change and p<0.05 (p value corrected for multiple testing). This integrated study using high resolution mass spectrometry based label-free quantitative proteomics to study tetracycline antibiotic response in the soluble proteome of resistant E. coli provides novel insight into tetracycline related stress.
  
  
  
  The lack of new antibiotics to fight infections caused by multidrug resistant microorganisms has motivated the use of old antibiotics, and the search for new drug targets. The evolution of antibiotic resistance is complex, but it is known that agroecosystems play an important part in the selection of antibiotic resistance bacteria. Tetracyclines are still used as phytopharmaceutical agents in crops, selecting resistant bacteria and changing the ecology of farm soil. Little is known about the metabolic response of genetically resistant populations to antibiotic exposure. Indeed, to date there are no quantitative tetracycline resistance studies performed with the latest generation of high resolution mass spectrometers allowing high mass accuracy in both MS and MS/MS scans. Here, we report the proteome profiling of a soil-borne Escherichia coli upon tetracycline stress, so that this new perspective could provide a broaden understanding of the metabolic responses of E. coli to a widely used antibiotic.
authors.affiliation: National Reference Laboratory of Antibiotic Resistances and Heathcare Associated Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal; Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, Oporto University, Oporto, Portugal.
authors.forename: Daniela
authors.initials: D
authors.lastname: Jones-Dias
authors.affiliation: Computational and Experimental Biology Group, Department of Health Promotion and Chronic Diseases, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal.
authors.forename: Ana Sofia
authors.initials: AS
authors.lastname: Carvalho
authors.affiliation: National Reference Laboratory of Antibiotic Resistances and Heathcare Associated Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal; Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, Oporto University, Oporto, Portugal.
authors.forename: Inês Barata
authors.initials: IB
authors.lastname: Moura
authors.affiliation: National Reference Laboratory of Antibiotic Resistances and Heathcare Associated Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal; Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, Oporto University, Oporto, Portugal.
authors.forename: Vera
authors.initials: V
authors.lastname: Manageiro
authors.affiliation: Functional Genomics and Proteomics Unit, Department of Genetic and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal; UCIBIO-REQUIMTE, Faculty of Science and Technology, New University of Lisbon, Monte da Caparica, Portugal.
authors.forename: Gilberto
authors.initials: G
authors.lastname: Igrejas
authors.affiliation: National Reference Laboratory of Antibiotic Resistances and Heathcare Associated Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal. Electronic address: manuela.canica@insa.min-saude.pt.
authors.forename: Manuela
authors.initials: M
authors.lastname: Caniça
authors.affiliation: Computational and Experimental Biology Group, Department of Health Promotion and Chronic Diseases, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal.
authors.forename: Rune
authors.initials: R
authors.lastname: Matthiesen
mesh_terms: D024881:Drug Resistance, Bacterial; D004926:Escherichia coli / Q000187:drug effects / Q000378:metabolism / Q000502:physiology*; D055442:Metabolome / Q000187:drug effects*; D010457:Peptidoglycan / Q000187:drug effects*; D020543:Proteome / Q000032:analysis / Q000187:drug effects*; D012988:Soil Microbiology; D012989:Soil Pollutants / Q000494:pharmacology; D053719:Tandem Mass Spectrometry; D013752:Tetracycline / Q000494:pharmacology*
chemical_list: D010457:Peptidoglycan; D020543:Proteome; D012989:Soil Pollutants; D013752:Tetracycline
keywords: Antibiotic resistance; Escherichia coli; Metabolism; Proteome; Tetracycline