Volume 26, Issue 3, Pages 393-402 (May 2007) The Site of Action of Oxazolidinone Antibiotics in Living Bacteria and in Human Mitochondria  Karen L. Leach, Steven M. Swaney, Jerry R. Colca, William G. McDonald, James R. Blinn, Lisa M. Thomasco, Robert C. Gadwood, Dean Shinabarger, Liqun Xiong, Alexander S. Mankin  Molecular Cell  Volume 26, Issue 3, Pages 393-402 (May 2007) DOI: 10.1016/j.molcel.2007.04.005 Copyright © 2007 Elsevier Inc. Terms and Conditions

Figure 1 Structures of Oxazolidinone Antibiotics (A) Linezolid, a clinically approved antibiotic. (B) Photoreactive oxazolidinones used in the study. The photoreactive azido groups are circled, and radiolabeled atoms are indicated by asterisks. (C) Nonphotoreactive competitors. Molecular Cell 2007 26, 393-402DOI: (10.1016/j.molcel.2007.04.005) Copyright © 2007 Elsevier Inc. Terms and Conditions

Figure 2 Mapping the Sites of Crosslinking of [3H]-XL2 and [125I]-XL3 to S. aureus and Human rRNA (A) RNase H mapping of the S. aureus 23S rRNA segment crosslinked to antibiotic. rRNA extracted from cells crosslinked with radiolabeled photoreactive antibiotics was treated with RNase H in the absence (K) or in the presence of oligonucleotides A and B. Resulting rRNA fragments were fractionated on a polyacrylamide gel, and radioactive bands were revealed by fluorography ([3H]-XL2) or autoradiography ([125I]-XL3). The positions of the RNA size markers are shown by the dots. The diagram at the bottom shows the position of 23S rRNA sequences complementary to oligonucleotides A and B and the sizes (nt) of the fragments released by RNase H. rRNA fragments carrying crosslinked radiolabeled antibiotic are indicated by thick lines. (B and C) Primer-extension analysis of S. aureus 23S rRNA extracted from the cells crosslinked with XL2 (B) or XL3 (C). Lanes on the gels are marked as follows: K, rRNA isolated from control nonirradiated cells; UV, rRNA from cells irradiated with UV light in the absence of antibiotics; and X, rRNA from cells irradiated with UV light after incubation with photoreactive compounds in the absence (−) or presence (+) of the competitor eperezolid. C, U, A, and G are sequencing lanes. The crosslinked nucleotides are indicated by the arrows. (D and E) Primer-extension analysis of (D) mitochondrial or (E) cytoplasmic large ribosomal subunit rRNA extracted from the human K562 cells crosslinked with XL2. Lanes on the gels are marked as in (B) and (C). The nucleotides crosslinked in mitochondrial rRNA are indicated by the arrows; in (E), arrows mark the equivalent positions in cytoplasmic rRNA. Molecular Cell 2007 26, 393-402DOI: (10.1016/j.molcel.2007.04.005) Copyright © 2007 Elsevier Inc. Terms and Conditions

Figure 3 Oxazolidinones in Their Binding Site in the Bacterial Ribosome (A–C) Modeled placement of photoreactive oxazolidinones XL1 (A), XL2 (B), and XL3 (C) in the PTC of the bacterial (E. coli) ribosome. The photoreactive compounds are shown in salmon, and the aryl-azido group participating in the crosslinking reaction is shown in red. The nucleotides crosslinked by the probe are shown in olive. (D) The model of linezolid in its binding site. The nucleotides interacting with the drug are shown in gray. The drug molecule is shown in salmon (carbon atoms), red (oxygens), blue (nitrogens), and light blue (fluorine). (E) Position of the linezolid binding site in the bacterial ribosome relative to the tRNA substrates bound in the P site (light brown) and A site (light blue). Molecular Cell 2007 26, 393-402DOI: (10.1016/j.molcel.2007.04.005) Copyright © 2007 Elsevier Inc. Terms and Conditions

Figure 4 The Structures of the Central Loop of Domain V or Large Ribosomal Subunit rRNA of S. aureus, Human Mitochondria, and Human Cytoplasm Nucleotide positions crosslinked to photoreactive linezolid derivatives XL1, XL2, and XL3 (this work) are indicated by arrows (A and B). The nucleotide positions of 23S rRNA, whose mutations are implicated in linezolid resistance in bacteria and archaea, are circled (A). Positions that are similar between bacterial (S. aureus) and human mitochondrial rRNA but different in human cytoplasmic rRNA are boxed in (C). Asterisks indicate positions that coincide with the known antibiotic resistance mutations. Molecular Cell 2007 26, 393-402DOI: (10.1016/j.molcel.2007.04.005) Copyright © 2007 Elsevier Inc. Terms and Conditions