rifamycin inactivating phosphotransferase family shared by environmental and pathogenic bacteria

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 111; no. 19; pp. 7102 - 7107
• Main Authors: Spanogiannopoulos, Peter, Waglechner, Nicholas, Koteva, Kalinka, Wright, Gerard D.
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 13.05.2014; National Acad Sciences
• Subjects: Actinobacteria - genetics; Actinomycetes; Anti-Bacterial Agents - chemistry; Anti-Bacterial Agents - pharmacology; Antibiotic resistance; Antibiotics; Bacillus cereus; Bacillus cereus - enzymology; Bacillus cereus - genetics; Bacillus cereus - pathogenicity; Bacteria; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Base Sequence; Biological Sciences; Conserved Sequence; Drug Design; Drug resistance; Drug Resistance, Bacterial - genetics; Enzymes; evolution; gene expression; Genes; Genomes; heterologous gene expression; Listeria monocytogenes; Listeria monocytogenes - enzymology; Listeria monocytogenes - genetics; Listeria monocytogenes - pathogenicity; Molecular Sequence Data; multiple drug resistance; Nucleotides; Open reading frames; Pathogens; Phosphotransferases - genetics; Phosphotransferases - metabolism; Protein expression; Proteins; rifampicin; Rifamycins; Rifamycins - chemistry; Rifamycins - pharmacology; Soil Microbiology; Streptomycetaceae - enzymology; Streptomycetaceae - genetics; Streptomycetaceae - pathogenicity; varietal resistance; silent resistome; drug inactivation; gene regulation; phosphorylation
• ISSN: 0027-8424; 1091-6490; 1091-6490
• DOI: 10.1073/pnas.1402358111

Many environmental bacteria are multidrug-resistant and represent a reservoir of ancient antibiotic resistance determinants, which have been linked to genes found in pathogens. Exploring the environmental antibiotic resistome, therefore, reveals the diversity and evolution of antibiotic resistance and also provides insight into the vulnerability of clinically used antibiotics. In this study, we describe the identification of a highly conserved regulatory motif, the rifampin (RIF) -associated element (RAE), which is found upstream of genes encoding RIF-inactivating enzymes from a diverse collection of actinomycetes. Using gene expression assays, we confirmed that the RAE is involved in RIF-responsive regulation. By using the RAE as a probe for new RIF-associated genes in several actinomycete genomes, we identified a heretofore unknown RIF resistance gene, RIF phosphotransferase (rph). The RPH enzyme is a RIF-inactivating phosphotransferase and represents a new protein family in antibiotic resistance. RPH orthologs are widespread and found in RIF-sensitive bacteria, including Bacillus cereus and the pathogen Listeria monocytogenes . Heterologous expression and in vitro enzyme assays with purified RPHs from diverse bacterial genera show that these enzymes are capable of conferring high-level resistance to a variety of clinically used rifamycin antibiotics. This work identifies a new antibiotic resistance protein family and reinforces the fact that the study of resistance in environmental organisms can serve to identify resistance elements with relevance to pathogens.