Ribosomal Elongation Factor 4 Promotes Cell Death Associated with Lethal Stress

bWe studied the transcriptomic response of Streptococcus pneumoniae to the fluoroquinolone moxifloxacin at a concentration that inhibits DNA gyrase. Treatment of the wild-type strain R6, at a concentration of 10؋ the MIC, triggered a response involving 132 genes after 30 min of treatment. Genes from several metabolic pathways involved in the production of pyruvate were upregulated. These included 3 glycolytic enzymes, which ultimately convert fructose 6-phosphate to pyruvate, and 2 enzymes that funnel phosphate sugars into the glycolytic pathway. In addition, acetyl coenzyme A (acetyl-CoA) carboxylase was downregulated, likely leading to an increase in acetyl-CoA. When coupled with an upregulation in formate acetyltransferase, an increase in acetyl-CoA would raise the production of pyruvate. Since pyruvate is converted by pyruvate oxidase (SpxB) into hydrogen peroxide (H 2 O 2 ), an increase in pyruvate would augment intracellular H 2 O 2 . Here, we confirm a 21-fold increase in the production of H 2 O 2 and a 55-fold increase in the amount of hydroxyl radical in cultures treated during 4 h with moxifloxacin. This increase in hydroxyl radical through the Fenton reaction would damage DNA, lipids, and proteins. These reactive oxygen species contributed to the lethality of the drug, a conclusion supported by the observed protective effects of an SpxB deletion. These results support the model whereby fluoroquinolones cause redox alterations. The transcriptional response of S. pneumoniae to moxifloxacin is compared with the response to levofloxacin, an inhibitor of topoisomerase IV. Levofloxacin triggers the transcriptional activation of iron transport genes and also enhances the Fenton reaction.

The contribution of reactive oxygen species (ROS) to antimicrobial lethality was examined by treating Escherichia coli with dimethyl sulfoxide (DMSO), an antioxidant solvent frequently used in antimicrobial studies. DMSO inhibited killing by ampicillin, kanamycin, and two quinolones and had little effect on MICs. DMSO-mediated protection correlated with decreased ROS accumulation and provided evidence for ROS-mediated programmed cell death. These data support the contribution of ROS to antimicrobial lethality and suggest caution when using DMSO-dissolved antimicrobials for short-time killing assays. O ne approach to help stem the emergence of new antimicrobial resistance is to kill bacterial pathogens rapidly, thereby quickly reducing bacterial burden and restricting effects of stressinduced mutagenesis (1, 2). Reactive oxygen species (ROS) have been proposed to be key factors in antimicrobial lethality (3-5), and substantial evidence supports this proposition (3-19). However, their role in lethality has been challenged (20, 21). If ROS are indeed integral to antimicrobial-mediated killing, compounds that act as antioxidants and radical scavengers should reduce antimicrobial lethality. We chose to examine this hypothesis using the radical scavenger dimethyl sulfoxide (DMSO) (22, 23), because it is also a popular solvent that is widely used in the pharmaceutical industry and in antimicrobial research due to its (i) low toxicity, (ii) ability to dissolve both organic and inorganic compounds, (iii) ability to remain in a liquid state over a broad temperature range (e.g., from 19°C to 189°C), (iv) ability to enhance cell membrane permeability, and (v) miscibility in water and a wide range of organic solvents. We report here that DMSO interferes with rapid killing of Escherichia coli and Acinetobacter baumannii by members of three antimicrobial classes.E. coli K-12 strains BW25113 and ATCC 25922 and A. baumannii strain ATCC 17978 were grown in Luria-Bertani (LB) broth or on LB agar at 37°C. LB medium, ampicillin, and kanamycin were obtained from Sangon Biotech Co., Ltd. (Shanghai, China). Oxolinic acid, ciprofloxacin, and DMSO were acquired from Sigma-Aldrich Co. (St. Louis, MO). Meropenem (Sumitomo Dainippon Pharma Co. Ltd.) was obtained from Zhongshan Hospital Pharmacy. The fluorescent probe carboxy-H 2 DCFDA [5(6)-carboxy-2=,7=-dichlorodihydrofluorescein diacetate] was purchased from Invitrogen (Grand Island, NY). All chemical stock solutions were dissolved in sterile water (except carboxy-H 2 DCFDA, which was dissolved in DMSO) and stored at Ϫ80°C until use. MICs were assayed by broth dilution according to CLSI protocols (24); exponentially growing cultures were diluted to 10 5 CFU/ml for MIC determinations. To measure rapid bacterial killing, exponentially growing cultures at about 5 ϫ 10 8 CFU/ml were treated with antimicrobials, after which they were serially diluted and plated on drug-free agar. Viable colony counts were determined after an overnight incubation at 37°C; percentage survival rates were calculat...

During translation, a plethora of protein factors bind to the ribosome and regulate protein synthesis. Many of those factors are guanosine triphosphatases (GTPases), proteins that catalyze the hydrolysis of guanosine 5′-triphosphate (GTP) to promote conformational changes. Despite numerous studies, the function of elongation factor 4 (EF-4/LepA), a highly conserved translational GTPase, has remained elusive. Here, we present the crystal structure at 2.6-Å resolution of the Thermus thermophilus 70S ribosome bound to EF-4 with a nonhydrolyzable GTP analog and A-, P-, and E-site tRNAs. The structure reveals the interactions of EF-4 with the A-site tRNA, including contacts between the C-terminal domain (CTD) of EF-4 and the acceptor helical stem of the tRNA. Remarkably, EF-4 induces a distortion of the A-site tRNA, allowing it to interact simultaneously with EF-4 and the decoding center of the ribosome. The structure provides insights into the tRNA-remodeling function of EF-4 on the ribosome and suggests that the displacement of the CCA-end of the A-site tRNA away from the peptidyl transferase center (PTC) is functionally significant.T ranslation of the genetic information requires protein factors that interact with the ribosome sequentially, regulate its activity, and guide it through the protein synthesis cycle in a concerted manner. Many of those factors are guanosine triphosphatases (GTPases), proteins that use energy from guanosine 5′-triphosphate (GTP) to promote conformational changes that lead to transitions between ribosome functional states (1, 2). In bacteria, for instance, initiation of protein synthesis is largely regulated by initiation factor 2 (IF-2), a GTPase that stabilizes the initiator tRNA in the P site of the ribosome (3). Subsequently, the elongation step is catalyzed by two universally conserved GTPases, elongation factor Tu (EF-Tu) and elongation factor G (EF-G). The ternary complex, consisting of EF-Tu, GTP, and the aminoacyl-tRNA, interacts with the ribosome to decode the codon in the A site of the ribosome. Following accommodation of the aminoacyl-tRNA in the A site of the ribosome and subsequent peptide bond formation, the tRNA-mRNA duplex is translocated by one codon-a process catalyzed by EF-G and GTP (4-6). Termination of protein synthesis is triggered when a stop codon is reached, upon which the newly synthesized protein is released with the help of release factor 3 (RF-3), yet another GTPase (7).Elongation factor 4 (EF-4/LepA) is a highly conserved protein structurally similar to EF-G (8) and has a ribosome-dependent GTPase activity (9-13). However, despite numerous studies, its function has remained elusive (9-20). Fast kinetic studies showed that EF-4 competes with EF-G during elongation for binding to the pretranslocation (PRE) ribosome, with tRNAs in the A and P sites (17). Despite this, EF-4 was also shown to increase the rate of protein synthesis at high intracellular ionic strength (16), without any effect on translational accuracy (16, 18). Conversely, EF-4 was also reported...