Deglycosylation as a Mechanism of Inducible Antibiotic Resistance Revealed Using a Global Relational Tree for One-Component Regulators

Abstract

The ligands that interact with the vast majority of small-molecule binding transcription factors are unknown, a significant gap in our understanding of sensory perception by cells. TetR-family regulators (TFRs) are found in most prokaryotes and are involved in regulating virtually every aspect of prokaryotic life however only a few TFRs have been characterized. We report the application of phylogenomics to the identification of cognate ligands for TFRs. Using phylogenomics we identify a TFR, KijR, that responds to the antibiotic kijanimicin. We go on to show that KijR represses a gene, kijX, which confers resistance to kijanimicin. Finally we show that KijX inactivates kijanimicin by the hydrolytic removal of sugar residues. This is a demonstration of antibiotic resistance by deglycosylation.

The TetR Family of Regulators

“…Most sequenced bacterial genomes encode at least one TFR (14,25). In the over 200 genomes that we examined, 23, from 8 genera, did not encode TFRs.…”

“…Bacteria with large genomes tend to encode more TFRs (Fig. 3) (25). While in some instances this may be a function of the fact that bacteria with large genomes tend to encode a higher number of regulatory proteins, in other instances the situation may be more complex and indicate a preference for TFRs over other families of regulators.…”

“…We have employed phylogenomics as a tool to predict ligands for TFRs of unknown function (25). Using this approach, we successfully identified the antibiotic kijanimicin as the inducing ligand for a previously uncharacterized TFR, KijR from Streptomyces coelicolor.…”

“…Our phylogenomics analyses coupled with additional database searches identify numerous TFRs sharing high similarity to SCO4099 in other actinomycetes; however, no ligands have been identified for any of them (Fig. 6) (25). These homologs are transcribed divergently from additional gene products implicated in resistance to streptogramin antibiotics (e.g., vgaA and vgbA) as well as gene products known to be involved in antibiotic resistance but not specifically in streptogramin resistance (e.g., mgtA/oleD and ereA).…”

“…Of these, six TFRs, i.e., ActR, KijA8, LanK, PhlF, SimR, and VarR, have been shown to bind the products of the biosynthetic pathways in which they are encoded (25,(75)(76)(77)(78)(79). These TFRs primarily regulate the expression of efflux pumps required for antibiotic export but may also regulate the expression of late-stage biosynthetic genes.…”