title: Transcriptomics as a tool to discover new antibacterial targets.
abstract: The emergence of antibiotic-resistant pathogens, multiple drug-resistance, and extremely drug-resistant strains demonstrates the need for improved strategies to discover new drug-based compounds. The development of transcriptomics, proteomics, and metabolomics has provided new tools for global studies of living organisms. However, the compendium of expression profiles produced by these methods has introduced new scientific challenges into antimicrobial research. In this review, we discuss the practical value of transcriptomic techniques as well as their difficulties and pitfalls. We advocate the construction of new databases of transcriptomic data, using standardized formats in addition to standardized models of bacterial and yeast similar to those used in systems biology. The inclusion of proteomic and metabolomic data is also essential, as the resulting networks can provide a landscape to rationally predict and exploit new drug targets and to understand drug synergies.
authors.affiliation: Department of Microbiology and Genetics, Universidad de Salamanca, Plaza de los Drs. de la Reina s/n, 37007, Salamanca, Spain. ado@usal.es.
authors.forename: Ángel
authors.initials: Á
authors.lastname: Domínguez
authors.affiliation: Department of Cell Biology & Pathology, Universidad de Salamanca, Salamanca, Spain.
authors.forename: Elisa
authors.initials: E
authors.lastname: Muñoz
authors.affiliation: Department of Microbiology and Genetics, Universidad de Salamanca, Plaza de los Drs. de la Reina s/n, 37007, Salamanca, Spain.
authors.forename: M Carmen
authors.initials: MC
authors.lastname: López
authors.affiliation: Department of Medicine, Universidad de Salamanca, Salamanca, Spain.
authors.forename: Miguel
authors.initials: M
authors.lastname: Cordero
authors.affiliation: Department of Microbiology & Ecology, Universitat de Valencia/Estudi General (UVEG), Valencia, Spain.
authors.forename: José Pedro
authors.initials: JP
authors.lastname: Martínez
authors.affiliation: Department of Pathology and Experimental Therapeutics, Universitat de Barcelona, Barcelona, Spain.
authors.forename: Miguel
authors.initials: M
authors.lastname: Viñas
mesh_terms: D000900:Anti-Bacterial Agents; D001419:Bacteria / Q000187:drug effects / Q000235:genetics / Q000378:metabolism; D016503:Drug Delivery Systems; D024881:Drug Resistance, Bacterial; D005658:Fungi / Q000187:drug effects / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling; D020411:Oligonucleotide Array Sequence Analysis; D017423:Sequence Analysis, RNA
chemical_list: D000900:Anti-Bacterial Agents
keywords: Antibiotic resistance; Expression profiles; Microarrays; RNA-seq; Transcriptomics