• PNAS Streamlines Submission
  • Sign-up for PNAS eTOC Alerts

Resistance to ketolide antibiotics by coordinated expression of rRNA methyltransferases in a bacterial producer of natural ketolides

  1. Alexander S. Mankina,2
  1. aCenter for Pharmaceutical Biotechnology, University of Illinois, Chicago, IL 60607;
  2. bLife Sciences Institute, University of Michigan, Ann Arbor, MI 48109;
  3. cDepartment of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense, Denmark;
  4. dDepartment of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109;
  5. eDepartment of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109;
  6. fDepartment of Chemistry, University of Michigan, Ann Arbor, MI 48109

  1. Edited by Chaitan Khosla, Stanford University, Stanford, CA, and accepted by the Editorial Board September 4, 2015 (received for review June 22, 2015)

Significance

Studies of antibiotic resistance are usually initiated in earnest only after resistance has become established in clinical pathogens. Here, we forewarn of a resistance mechanism to the novel antibiotics ketolides, which are only coming into broad medical practice. We show that the balanced activities and coordinated expression of two genes, pikR1 and pikR2, provide efficient protection to Streptomyces venezuelae, a bacterial producer of natural ketolides. Expression of the more potent gene, pikR2, is supported by pikR1 and specifically induced by ketolides. The resistance mechanism remains fully functional when pikR1 and pikR2 are transferred to other bacterial species and affords protection against clinical ketolides. These findings emphasize the need for the preemptive development of antibiotics that can overcome this resistance mechanism.

Abstract

Ketolides are promising new antimicrobials effective against a broad range of Gram-positive pathogens, in part because of the low propensity of these drugs to trigger the expression of resistance genes. A natural ketolide pikromycin and a related compound methymycin are produced by Streptomyces venezuelae strain ATCC 15439. The producer avoids the inhibitory effects of its own antibiotics by expressing two paralogous rRNA methylase genes pikR1 and pikR2 with seemingly redundant functions. We show here that the PikR1 and PikR2 enzymes mono- and dimethylate, respectively, the N6 amino group in 23S rRNA nucleotide A2058. PikR1 monomethylase is constitutively expressed; it confers low resistance at low fitness cost and is required for ketolide-induced activation of pikR2 to attain high-level resistance. The regulatory mechanism controlling pikR2 expression has been evolutionary optimized for preferential activation by ketolide antibiotics. The resistance genes and the induction mechanism remain fully functional when transferred to heterologous bacterial hosts. The anticipated wide use of ketolide antibiotics could promote horizontal transfer of these highly efficient resistance genes to pathogens. Taken together, these findings emphasized the need for surveillance of pikR1/pikR2-based bacterial resistance and the preemptive development of drugs that can remain effective against the ketolide-specific resistance mechanism.

Footnotes

  • ↵1Present address: Pharmacognosy Department, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia.

  • ↵2To whom correspondence should be addressed. Email: shura{at}uic.edu.

  • Author contributions: A.S.M. designed research; M.M.A. and S.R. performed research; S.R.P. and D.A.H. contributed new reagents/analytic tools; M.M.A., N.V.-L., S.D., D.H.S., and A.S.M. analyzed data; and M.M.A., S.D., D.H.S., and A.S.M. wrote the paper.

  • The authors declare no conflict of interest.

  • This article is a PNAS Direct Submission. C.K. is a guest editor invited by the Editorial Board.

  • This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1512090112/-/DCSupplemental.

Online Impact