1
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Fang N, Wu L, Duan S, Li J. The Structural and Molecular Mechanisms of Mycobacterium tuberculosis Translational Elongation Factor Proteins. Molecules 2024; 29:2058. [PMID: 38731549 PMCID: PMC11085428 DOI: 10.3390/molecules29092058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/19/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
Targeting translation factor proteins holds promise for developing innovative anti-tuberculosis drugs. During protein translation, many factors cause ribosomes to stall at messenger RNA (mRNA). To maintain protein homeostasis, bacteria have evolved various ribosome rescue mechanisms, including the predominant trans-translation process, to release stalled ribosomes and remove aberrant mRNAs. The rescue systems require the participation of translation elongation factor proteins (EFs) and are essential for bacterial physiology and reproduction. However, they disappear during eukaryotic evolution, which makes the essential proteins and translation elongation factors promising antimicrobial drug targets. Here, we review the structural and molecular mechanisms of the translation elongation factors EF-Tu, EF-Ts, and EF-G, which play essential roles in the normal translation and ribosome rescue mechanisms of Mycobacterium tuberculosis (Mtb). We also briefly describe the structure-based, computer-assisted study of anti-tuberculosis drugs.
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Affiliation(s)
- Ning Fang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai 200438, China; (N.F.); (L.W.)
| | - Lingyun Wu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai 200438, China; (N.F.); (L.W.)
| | - Shuyan Duan
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai 200438, China; (N.F.); (L.W.)
- College of Food Science and Pharmaceutical Engineering, Zaozhuang University, Zaozhuang 277160, China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai 200438, China; (N.F.); (L.W.)
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2
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Fellner M, Walsh A, Dela Ahator S, Aftab N, Sutherland B, Tan EW, Bakker AT, Martin NI, van der Stelt M, Lentz CS. Biochemical and Cellular Characterization of the Function of Fluorophosphonate-Binding Hydrolase H (FphH) in Staphylococcus aureus Support a Role in Bacterial Stress Response. ACS Infect Dis 2023; 9:2119-2132. [PMID: 37824340 PMCID: PMC10644348 DOI: 10.1021/acsinfecdis.3c00246] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Indexed: 10/14/2023]
Abstract
The development of new treatment options for bacterial infections requires access to new targets for antibiotics and antivirulence strategies. Chemoproteomic approaches are powerful tools for profiling and identifying novel druggable target candidates, but their functions often remain uncharacterized. Previously, we used activity-based protein profiling in the opportunistic pathogen Staphylococcus aureus to identify active serine hydrolases termed fluorophosphonate-binding hydrolases (Fph). Here, we provide the first characterization of S. aureus FphH, a conserved, putative carboxylesterase (referred to as yvaK in Bacillus subtilis) at the molecular and cellular level. First, phenotypic characterization of fphH-deficient transposon mutants revealed phenotypes during growth under nutrient deprivation, biofilm formation, and intracellular survival. Biochemical and structural investigations revealed that FphH acts as an esterase and lipase based on a fold well suited to act on a small to long hydrophobic unbranched lipid group within its substrate and can be inhibited by active site-targeting oxadiazoles. Prompted by a previous observation that fphH expression was upregulated in response to fusidic acid, we found that FphH can deacetylate this ribosome-targeting antibiotic, but the lack of FphH function did not infer major changes in antibiotic susceptibility. In conclusion, our results indicate a functional role of this hydrolase in S. aureus stress responses, and hypothetical functions connecting FphH with components of the ribosome rescue system that are conserved in the same gene cluster across Bacillales are discussed. Our atomic characterization of FphH will facilitate the development of specific FphH inhibitors and probes to elucidate its physiological role and validity as a drug target.
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Affiliation(s)
- Matthias Fellner
- Biochemistry
Department, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Annabel Walsh
- Biochemistry
Department, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Stephen Dela Ahator
- Research
Group for Host-Microbe Interactions, Department of Medical Biology
and Centre for New Antibacterial Strategies (CANS) UiT, The Arctic University of Norway, 9037 Tromsø, Norway
| | - Nadia Aftab
- Research
Group for Host-Microbe Interactions, Department of Medical Biology
and Centre for New Antibacterial Strategies (CANS) UiT, The Arctic University of Norway, 9037 Tromsø, Norway
| | - Ben Sutherland
- Department
of Chemistry, Division of Sciences, University
of Otago, Dunedin 9054, New Zealand
| | - Eng W. Tan
- Department
of Chemistry, Division of Sciences, University
of Otago, Dunedin 9054, New Zealand
| | - Alexander T. Bakker
- Department
of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands
| | - Nathaniel I. Martin
- Biological
Chemistry Group, Institute of Biology Leiden, Leiden University, 2333
BE Leiden, The Netherlands
| | - Mario van der Stelt
- Department
of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands
| | - Christian S. Lentz
- Research
Group for Host-Microbe Interactions, Department of Medical Biology
and Centre for New Antibacterial Strategies (CANS) UiT, The Arctic University of Norway, 9037 Tromsø, Norway
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3
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Fitzgerald BA, Wadud A, Slimak Z, Slonczewski JL. Enterococcus faecalis OG1RF Evolution at Low pH Selects Fusidate-Sensitive Mutants in Elongation Factor G and at High pH Selects Defects in Phosphate Transport. Appl Environ Microbiol 2023; 89:e0046623. [PMID: 37272807 PMCID: PMC10304957 DOI: 10.1128/aem.00466-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/15/2023] [Indexed: 06/06/2023] Open
Abstract
Enterococcus bacteria inhabit human and soil environments that show a wide range of pH values. Strains include commensals as well as antibiotic-resistant pathogens. We investigated the adaptation to pH stress in E. faecalis OG1RF by conducting experimental evolution under acidic (pH 4.8), neutral pH (pH 7.0), and basic (pH 9.0) conditions. A serial planktonic culture was performed for 500 generations and in a high-pH biofilm culture for 4 serial bead transfers. Nearly all of the mutations led to nonsynonomous codons, indicating adaptive selection. All of the acid-adapted clones from the planktonic culture showed a mutation in fusA (encoding elongation factor G). The acid-adapted fusA mutants had a trade-off of decreased resistance to fusidic acid (fusidate). All of the base-adapted clones from the planktonic cultures as well as some from the biofilm-adapted cultures showed mutations that affected the Pst phosphate ABC transporter (pstA, pstB, pstB2, pstC) and pyrR (pyrimidine biosynthesis regulator/uracil phosphoribosyltransferase). The biofilm cultures produced small-size colonies on brain heart infusion agar. These variants each contained a single mutation in pstB2, pstC, or pyrR. The pst and pyrR mutants outgrew the ancestral strain at pH 9.2, with a trade-off of lower growth at pH 4.8. Additional genes that had a mutation in multiple clones that evolved at high pH (but not at low pH) include opp1BCDF (oligopeptide ABC transporter), ccpA (catabolite control protein A), and ftsZ (septation protein). Overall, the experimental evolution of E. faecalis showed a strong pH dependence, favoring the fusidate-sensitive elongation factor G modification at low pH and the loss of phosphate transport genes at high pH. IMPORTANCE E. faecalis bacteria are found in dental biofilms, where they experience low pH as a result of fermentative metabolism. Thus, the effect of pH on antibiotic resistance has clinical importance. The loss of fusidate resistance is notable for OG1RF strains in which fusidate resistance is assumed to be a stable genetic marker. In endodontal infections, enterococci can resist calcium hydroxide therapy that generates extremely high pH values. In other environments, such as the soil and plant rhizosphere, enterococci experience acidification that is associated with climate change. Thus, the pH modulation of natural selection in enterococci is important for human health as well as for understanding soil environments.
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Affiliation(s)
| | - Ayman Wadud
- Department of Biology, Kenyon College, Gambier, Ohio, USA
| | - Zachary Slimak
- Department of Biology, Kenyon College, Gambier, Ohio, USA
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4
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Santos KR, Souza FN, Ramos-Sanchez EM, Batista CF, Reis LC, Fotoran WL, Heinemann MB, Cunha AF, Rocha MC, Faria AR, Andrade HM, Cerqueira MMOP, Gidlund M, Goto H, Della Libera AMMP. Staphylococcus aureus-Cure-Associated Antigens Elicit Type 3 Immune Memory T Cells. Antibiotics (Basel) 2022; 11:1831. [PMID: 36551488 PMCID: PMC9774748 DOI: 10.3390/antibiotics11121831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/20/2022] [Accepted: 11/22/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Staphylococcus aureus is one of the most frequently major mastitis pathogens that cause clinical and subclinical mastitis worldwide. Current antimicrobial treatments are usually ineffective, and the commercially available vaccines lack proven effectiveness. The immunological response elicited by the recombinant S. aureus-cure-associated proteins phosphoglycerate kinase (PGK), enolase (ENO), and elongation factor-G (EF-G) in combination with the granulocyte-macrophage colony-stimulating factor (GM-CSF) DNA vaccination was studied in this work. METHODS Here, twenty-three C57BL/6 mice were divided into four groups and vaccinated with: G1: none (control); G2: GM-CSF DNA plasmid DNA vaccine; G3: the combination of EF-G+ENO+PGK; and G4: the combinations of EF-G+ENO+PGK proteins plus GM-CSF plasmid DNA vaccine. After 44 days, spleen cells were collected for immunophenotyping and lymphocyte proliferation evaluation by flow cytometry upon S. aureus stimulus. RESULTS Immunization with the three S. aureus recombinant proteins alone resulted in a higher percentage of IL-17A+ cells among CD8+ T central memory cells, as well as the highest intensity of IL-17A production by overall lymphocytes indicating that the contribution of the combined lymphocyte populations is crucial to sustaining a type 3 cell immunity environment. CONCLUSION The immunization with three S. aureus-cure-associated recombinant proteins triggered type 3 immunity, which is a highly interesting path to pursue an effective bovine S. aureus mastitis vaccine.
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Affiliation(s)
- Kamila R. Santos
- Veterinary Clinical Immunology Research Group, Departamento de Clínica Médica, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo 05508-270, Brazil
| | - Fernando N. Souza
- Veterinary Clinical Immunology Research Group, Departamento de Clínica Médica, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo 05508-270, Brazil
- Programa de Pós-Graduação em Ciência Animal, Universidade Federal da Paraíba, Areia 58397-000, Brazil
| | - Eduardo M. Ramos-Sanchez
- Programa de Pós-Graduação em Ciência Animal, Universidade Federal da Paraíba, Areia 58397-000, Brazil
- Laboratório de Soroloepidemiologia e Imunobiologia, Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, Brazil
- Departamento de Salud Publica, Facultad de Ciencias de La Salud, Universidad Nacional Torino Rodriguez de Mendonza de Amazonas, Chachapoyas 01001, Peru
| | - Camila F. Batista
- Veterinary Clinical Immunology Research Group, Departamento de Clínica Médica, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo 05508-270, Brazil
| | - Luiza C. Reis
- Laboratório de Soroloepidemiologia e Imunobiologia, Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Wesley L. Fotoran
- Laboratório de Genética, Instituto Butantã, Universidade de São Paulo, São Paulo 05503-900, Brazil
| | - Marcos B. Heinemann
- Departamento de Medicina Veterinária Preventiva e Saúde Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo 05508-270, Brazil
| | - Adriano F. Cunha
- Departamento de Tecnologia e Inspeção de Produtos de Origem Animal, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte 31270-010, Brazil
| | - Mussya C. Rocha
- Laboratório de Soroloepidemiologia e Imunobiologia, Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Angélica R. Faria
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
- Laboratório de Parasitologia Clínica, Faculdade de Ciências Farmacêuticas, Universidade Federal de Alfenas, Alfenas 37130-000, Brazil
| | - Hélida M. Andrade
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Mônica M. O. P. Cerqueira
- Departamento de Tecnologia e Inspeção de Produtos de Origem Animal, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte 31270-010, Brazil
| | - Magnus Gidlund
- Departamento de Imunologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo 05508-900, Brazil
| | - Hiro Goto
- Laboratório de Soroloepidemiologia e Imunobiologia, Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, Brazil
- Departamento de Medicina Preventiva, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246-903, Brazil
| | - Alice Maria M. P. Della Libera
- Veterinary Clinical Immunology Research Group, Departamento de Clínica Médica, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo 05508-270, Brazil
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5
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Transcriptomic and Metabolomic Analysis of a Fusidic Acid-Selected fusA Mutant of Staphylococcus aureus. Antibiotics (Basel) 2022; 11:antibiotics11081051. [PMID: 36009920 PMCID: PMC9405211 DOI: 10.3390/antibiotics11081051] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 11/17/2022] Open
Abstract
Physiological experimentation, transcriptomics, and metabolomics were engaged to compare a fusidic acid-resistant Staphylococcus aureus mutant SH10001st-2 to its parent strain SH1000. SH10001st-2 harbored a mutation (H457Y) in the gene fusA which encodes the fusidic acid target, elongation factor G, as well as mutations in a putative phage gene of unknown function. SH10001st-2 grew slower than SH1000 at three temperatures and had reduced coagulase activity, two indicators of the fitness penalty reported for fusA-mediated fusidic acid- resistance in the absence of compensatory mutations. Despite the difference in growth rates, the levels of O2 consumption and CO2 production were comparable. Transcriptomic profiling revealed 326 genes were upregulated and 287 were downregulated in SH10001st-2 compared to SH1000. Cell envelope and transport and binding protein genes were the predominant functional categories of both upregulated and downregulated genes in SH10001st-2. Genes of virulence regulators, notably the agr and kdp systems, were highly upregulated as were genes encoding capsule production. Contrary to what is expected of mid-exponential phase cells, genes encoding secreted virulence factors were generally upregulated while those for adhesion-associated virulence factors were downregulated in SH10001st-2. Metabolomic analysis showed an overall increase in metabolite pools in SH10001st-2 compared to SH1000, mostly for amino acids and sugars. Slowed growth and metabolite accumulation may be byproducts of fusA mutation-mediated protein synthesis impairment, but the overall results indicate that SH10001st-2 is compensating for the H457Y fitness penalty by repurposing its virulence machinery, in conjunction with increasing metabolite uptake capacity, in order to increase nutrient acquisition.
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6
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Ero R, Yan XF, Gao YG. Ribosome Protection Proteins-"New" Players in the Global Arms Race with Antibiotic-Resistant Pathogens. Int J Mol Sci 2021; 22:5356. [PMID: 34069640 PMCID: PMC8161019 DOI: 10.3390/ijms22105356] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/12/2021] [Accepted: 05/14/2021] [Indexed: 01/07/2023] Open
Abstract
Bacteria have evolved an array of mechanisms enabling them to resist the inhibitory effect of antibiotics, a significant proportion of which target the ribosome. Indeed, resistance mechanisms have been identified for nearly every antibiotic that is currently used in clinical practice. With the ever-increasing list of multi-drug-resistant pathogens and very few novel antibiotics in the pharmaceutical pipeline, treatable infections are likely to become life-threatening once again. Most of the prevalent resistance mechanisms are well understood and their clinical significance is recognized. In contrast, ribosome protection protein-mediated resistance has flown under the radar for a long time and has been considered a minor factor in the clinical setting. Not until the recent discovery of the ATP-binding cassette family F protein-mediated resistance in an extensive list of human pathogens has the significance of ribosome protection proteins been truly appreciated. Understanding the underlying resistance mechanism has the potential to guide the development of novel therapeutic approaches to evade or overcome the resistance. In this review, we discuss the latest developments regarding ribosome protection proteins focusing on the current antimicrobial arsenal and pharmaceutical pipeline as well as potential implications for the future of fighting bacterial infections in the time of "superbugs."
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Affiliation(s)
- Rya Ero
- Department of Molecular Biology, Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore;
| | - Xin-Fu Yan
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore;
| | - Yong-Gui Gao
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore;
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore 639798, Singapore
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7
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Abstract
Antibiotic resistance is mediated through several distinct mechanisms, most of which are relatively well understood and the clinical importance of which has long been recognized. Until very recently, neither of these statements was readily applicable to the class of resistance mechanism known as target protection, a phenomenon whereby a resistance protein physically associates with an antibiotic target to rescue it from antibiotic-mediated inhibition. In this Review, we summarize recent progress in understanding the nature and importance of target protection. In particular, we describe the molecular basis of the known target protection systems, emphasizing that target protection does not involve a single, uniform mechanism but is instead brought about in several mechanistically distinct ways.
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8
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Wang YT, Lin YT, Wan TW, Wang DY, Lin HY, Lin CY, Chen YC, Teng LJ. Distribution of antibiotic resistance genes among Staphylococcus species isolated from ready-to-eat foods. J Food Drug Anal 2019; 27:841-848. [PMID: 31590755 PMCID: PMC9306985 DOI: 10.1016/j.jfda.2019.05.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/17/2019] [Accepted: 05/17/2019] [Indexed: 12/30/2022] Open
Abstract
We investigated antibiotic resistance of staphylococci isolated from 1128 samples of high-circulating RTE foods in Taiwan. A total of 111 Staphylococcus aureus and 709 coagulase-negative staphylococci (CoNS) comprising 23 species were isolated. The prevalence of S. aureus differed in various category of RTE foods, highest in fresh-cut fruits/vegetables (20.5%) and lowest in low-water activity (LWA) foods (0.7%). The overall staphylococcal contamination was highest in fresh-cut fruits/vegetables (62.2%), in which multiple isolates (up to 10) or species (up to 6) in single sample were frequently found. Distinct distribution of species contributed to unique feature in each category. Prevalence of antibiotic-resistant S. aureus was higher in fresh-cut fruits/vegetables samples (14.2% in 127) compared to other food categories (0–7.1%). A total of 4 MRSA carrying SCCmec type IV or VT were identified (3.6% in 111), in which 3 belonged to sequence type ST59 and one was ST5. Among CoNS, S. epidermidis and S. warneri exhibited higher non-intrinsic antibiotic resistance than other species. Of 41 methicillin-resistant CoNS (5.8% in 709) isolates, SCCmec type IV (n = 16) and type VT (n = 6) were most frequent. Isolates of S. saprophyticus, S. xylosus and S. sciuri displayed high rates of resistance to fusidic acid. Novel fusB-family determinants were identified in S. xylosus, S. sciuri and S. kloosii, which may contribute to their intrinsic resistance to fusidic acid. Compared to other food categories, fresh-cut fruits/vegetables were more contaminated by staphylococci carrying non-intrinsic resistance determinants including methicillin resistance. This nation-wide study demonstrated that some categories may have potential risk for transmitting antibiotic resistance, in which S. epidermidis and S. warneri should be gotten more attention.
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Affiliation(s)
- Yu-Ting Wang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan; Division of Research and Analysis, Food and Drug Administration, Ministry of Health and Welfare, Taipei, Taiwan
| | - Yu-Tzu Lin
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Tsai-Wen Wan
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Der-Yuan Wang
- Division of Research and Analysis, Food and Drug Administration, Ministry of Health and Welfare, Taipei, Taiwan
| | - Hsu-Yang Lin
- Division of Food Safety, Food and Drug Administration, Ministry of Health and Welfare, Taipei, Taiwan
| | - Che-Yang Lin
- Division of Research and Analysis, Food and Drug Administration, Ministry of Health and Welfare, Taipei, Taiwan
| | - Yu-Chih Chen
- Division of Research and Analysis, Food and Drug Administration, Ministry of Health and Welfare, Taipei, Taiwan
| | - Lee-Jene Teng
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan.
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9
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Lashkov AA, Rubinsky SV, Eistrikh-Heller PA. Application of the DBSCAN Algorithm to Detect Hydrophobic Clusters in Protein Structures. CRYSTALLOGR REP+ 2019. [DOI: 10.1134/s1063774519030179] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Abstract
The sheer molecular scale of the ribosome is intimidating to the traditional drug designer. By analyzing the ribosome as a series of 12 key target sites, this review seeks to make the ribosome ligand design process more manageable. Analysis of recently evaluated ribosomal structures, particularly those with bound antibiotics, indicates where the ligand target sites are located. This review employs current research data to map antibiotic binding across the ribosome. A number of neighboring ligand-binding sites are often contiguous and can be combined. Ligands that bind in close proximity can be combined into hybrid structures. The different ways antibiotics disrupt ribosomal function are also discussed. Antibiotics tend to inhibit conformational changes that are essential to the ribosomal mechanism.
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11
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Borg A, Pavlov M, Ehrenberg M. Mechanism of fusidic acid inhibition of RRF- and EF-G-dependent splitting of the bacterial post-termination ribosome. Nucleic Acids Res 2016; 44:3264-75. [PMID: 27001509 PMCID: PMC4838388 DOI: 10.1093/nar/gkw178] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 03/07/2016] [Indexed: 01/13/2023] Open
Abstract
The antibiotic drug fusidic acid (FA) is commonly used in the clinic against gram-positive bacterial infections. FA targets ribosome-bound elongation factor G (EF-G), a translational GTPase that accelerates both messenger RNA (mRNA) translocation and ribosome recycling. How FA inhibits translocation was recently clarified, but FA inhibition of ribosome recycling by EF-G and ribosome recycling factor (RRF) has remained obscure. Here we use fast kinetics techniques to estimate mean times of ribosome splitting and the stoichiometry of GTP hydrolysis by EF-G at varying concentrations of FA, EF-G and RRF. These mean times together with previous data on uninhibited ribosome recycling were used to clarify the mechanism of FA inhibition of ribosome splitting. The biochemical data on FA inhibition of translocation and recycling were used to model the growth inhibitory effect of FA on bacterial populations. We conclude that FA inhibition of translocation provides the dominant cause of bacterial growth reduction, but that FA inhibition of ribosome recycling may contribute significantly to FA-induced expression of short regulatory open reading frames, like those involved in FA resistance.
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Affiliation(s)
- Anneli Borg
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Michael Pavlov
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Måns Ehrenberg
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, 75124 Uppsala, Sweden
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12
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Tomlinson JH, Thompson GS, Kalverda AP, Zhuravleva A, O'Neill AJ. A target-protection mechanism of antibiotic resistance at atomic resolution: insights into FusB-type fusidic acid resistance. Sci Rep 2016; 6:19524. [PMID: 26781961 PMCID: PMC4725979 DOI: 10.1038/srep19524] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 12/09/2015] [Indexed: 11/09/2022] Open
Abstract
Antibiotic resistance in clinically important bacteria can be mediated by proteins that physically associate with the drug target and act to protect it from the inhibitory effects of an antibiotic. We present here the first detailed structural characterization of such a target protection mechanism mediated through a protein-protein interaction, revealing the architecture of the complex formed between the FusB fusidic acid resistance protein and the drug target (EF-G) it acts to protect. Binding of FusB to EF-G induces conformational and dynamic changes in the latter, shedding light on the molecular mechanism of fusidic acid resistance.
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Affiliation(s)
- Jennifer H Tomlinson
- School of Molecular and Cellular Biology, Garstang Building, University of Leeds, Leeds, UK, LS2 9JT.,Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK, LS2 9JT
| | - Gary S Thompson
- School of Molecular and Cellular Biology, Garstang Building, University of Leeds, Leeds, UK, LS2 9JT.,Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK, LS2 9JT
| | - Arnout P Kalverda
- School of Molecular and Cellular Biology, Garstang Building, University of Leeds, Leeds, UK, LS2 9JT.,Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK, LS2 9JT
| | - Anastasia Zhuravleva
- School of Molecular and Cellular Biology, Garstang Building, University of Leeds, Leeds, UK, LS2 9JT.,Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK, LS2 9JT
| | - Alex J O'Neill
- School of Molecular and Cellular Biology, Garstang Building, University of Leeds, Leeds, UK, LS2 9JT.,Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK, LS2 9JT
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13
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Fernandes P. Fusidic Acid: A Bacterial Elongation Factor Inhibitor for the Oral Treatment of Acute and Chronic Staphylococcal Infections. Cold Spring Harb Perspect Med 2016; 6:a025437. [PMID: 26729758 DOI: 10.1101/cshperspect.a025437] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Fusidic acid is an oral antistaphylococcal antibiotic that has been used in Europe for more than 40 years to treat skin infections as well as chronic bone and joint infections. It is a steroidal antibiotic and the only marketed member of the fusidane class. Fusidic acid inhibits protein synthesis by binding EF-G-GDP, which results in the inhibition of both peptide translocation and ribosome disassembly. It has a novel structure and novel mode of action and, therefore, there is little cross-resistance with other known antibiotics. Many mutations can occur in the FusA gene that codes for EF-G, and some of these mutations can result in high-level resistance (minimum inhibitory concentration [MIC] > 64 mg/L), whereas others result in biologically unfit staphylococci that require compensatory mutations to survive. Low-level resistance (<8 mg/L) is more common and is mediated by fusB, fusC, and fusD genes that code for small proteins that protect EF-G-GDP from binding fusidic acid. The genes for these proteins are spread by plasmids and can be selected mostly by topical antibiotic use. Reports of resistance have led to combination use of fusidic acid with rifampin, which is superseded by the development of a new dosing regimen for fusidic acid that can be used in monotherapy. It consists of a front-loading dose to decrease the potential for resistance development followed by a maintenance dose. This dosing regimen is now being used in clinical trials in the United States for skin and refractory bone and joint infections.
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Hung WC, Chen HJ, Lin YT, Tsai JC, Chen CW, Lu HH, Tseng SP, Jheng YY, Leong KH, Teng LJ. Skin Commensal Staphylococci May Act as Reservoir for Fusidic Acid Resistance Genes. PLoS One 2015; 10:e0143106. [PMID: 26581090 PMCID: PMC4651549 DOI: 10.1371/journal.pone.0143106] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 10/30/2015] [Indexed: 11/18/2022] Open
Abstract
We analyzed the occurrence and mechanisms of fusidic acid resistance present in staphylococci isolated from 59 healthy volunteers. The fingers of the volunteers were screened for the presence of staphylococci, and the collected isolates were tested for resistance to fusidic acid. A total of 34 fusidic acid resistant staphylococcal strains (all were coagulase-negative) were isolated from 22 individuals (22/59, 37.3%). Examination of the resistance genes revealed that acquired fusB or fusC was present in Staphylococcus epidermidis, Staphylococcus capitis subsp. urealyticus, Staphylococcus hominis subsp. hominis, Staphylococcus warneri and Staphylococcus haemolyticus. Resistance islands (RIs) carrying fusB were found in S. epidermidis and S. capitis subsp. urealyticus, while staphylococcal chromosome cassette (SCC)-related structures harboring fusC were found in S. hominis subsp. hominis. Genotypic analysis of S. epidermidis and S. hominis subsp. hominis indicated that the fus elements were disseminated in diverse genetic strain backgrounds. The fusC elements in S. hominis subsp. hominis strains were highly homologous to SCCfusC in the epidemic sequence type (ST) 239/SCCmecIII methicillin-resistant S. aureus (MRSA) or the pseudo SCCmec in ST779 MRSA. The presence of acquired fusidic acid resistance genes and their genetic environment in commensal staphylococci suggested that the skin commensal staphylococci may act as reservoir for fusidic acid resistance genes.
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Affiliation(s)
- Wei-Chun Hung
- Department of Microbiology and Immunology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Hsiao-Jan Chen
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yu-Tzu Lin
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Jui-Chang Tsai
- Center for Optoelectronic Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
- Division of Neurosurgery, Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | | | | | - Sung-Pin Tseng
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yao-Yu Jheng
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Kin Hong Leong
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Lee-Jene Teng
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
- * E-mail:
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Zhang D, Yan K, Zhang Y, Liu G, Cao X, Song G, Xie Q, Gao N, Qin Y. New insights into the enzymatic role of EF-G in ribosome recycling. Nucleic Acids Res 2015; 43:10525-33. [PMID: 26432831 PMCID: PMC4666400 DOI: 10.1093/nar/gkv995] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 09/19/2015] [Indexed: 12/30/2022] Open
Abstract
During translation, elongation factor G (EF-G) plays a catalytic role in tRNA translocation and a facilitative role in ribosome recycling. By stabilizing the rotated ribosome and interacting with ribosome recycling factor (RRF), EF-G was hypothesized to induce the domain rotations of RRF, which subsequently performs the function of splitting the major intersubunit bridges and thus separates the ribosome into subunits for recycling. Here, with systematic mutagenesis, FRET analysis and cryo-EM single particle approach, we analyzed the interplay between EF-G/RRF and post termination complex (PoTC). Our data reveal that the two conserved loops (loop I and II) at the tip region of EF-G domain IV possess distinct roles in tRNA translocation and ribosome recycling. Specifically, loop II might be directly involved in disrupting the main intersubunit bridge B2a between helix 44 (h44 from the 30S subunit) and helix 69 (H69 from the 50S subunit) in PoTC. Therefore, our data suggest a new ribosome recycling mechanism which requires an active involvement of EF-G. In addition to supporting RRF, EF-G plays an enzymatic role in destabilizing B2a via its loop II.
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Affiliation(s)
- Dejiu Zhang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kaige Yan
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yiwei Zhang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Guangqiao Liu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xintao Cao
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guangtao Song
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Qiang Xie
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Ning Gao
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yan Qin
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing 100049, China
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den Heijer CDJ, van Bijnen EME, Paget WJ, Stobberingh EE. Fusidic acid resistance in Staphylococcus aureus nasal carriage strains in nine European countries. Future Microbiol 2015; 9:737-45. [PMID: 25046521 DOI: 10.2217/fmb.14.36] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM To evaluate fusidic acid resistance pheno- and geno-typically in nasal carriage Staphylococcus aureus isolated from general practice patients in nine European countries. MATERIALS & METHODS Phenotypic fusidic acid resistance was determined by disc diffusion and MIC values, and genotypically by a PCR detecting fusA-E genes. The main analysis was performed on methicillin-susceptible S. aureus strains, because methicillin-resistant S. aureus isolates were scarce. RESULTS Overall S. aureus fusidic acid resistance was low (<10%). fusC was the predominant mechanism of resistance and associations were found between resistance genes and specific spa types. CONCLUSION S. aureus strains showed low resistance to fusidic acid, making this antibiotic an appropriate choice in the treatment of methicillin-susceptible S. aureus skin infections in general practice patients in the nine participating European countries.
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Affiliation(s)
- Casper D J den Heijer
- Department of Medical Microbiology, Maastricht University Medical Centre/CAPHRI, Maastricht, The Netherlands
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Chen HJ, Hung WC, Lin YT, Tsai JC, Chiu HC, Hsueh PR, Teng LJ. A novel fusidic acid resistance determinant, fusF, in Staphylococcus cohnii. J Antimicrob Chemother 2014; 70:416-9. [DOI: 10.1093/jac/dku408] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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Starosta AL, Lassak J, Jung K, Wilson DN. The bacterial translation stress response. FEMS Microbiol Rev 2014; 38:1172-201. [PMID: 25135187 DOI: 10.1111/1574-6976.12083] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 07/18/2014] [Accepted: 08/07/2014] [Indexed: 11/30/2022] Open
Abstract
Throughout their life, bacteria need to sense and respond to environmental stress. Thus, such stress responses can require dramatic cellular reprogramming, both at the transcriptional as well as the translational level. This review focuses on the protein factors that interact with the bacterial translational apparatus to respond to and cope with different types of environmental stress. For example, the stringent factor RelA interacts with the ribosome to generate ppGpp under nutrient deprivation, whereas a variety of factors have been identified that bind to the ribosome under unfavorable growth conditions to shut-down (RelE, pY, RMF, HPF and EttA) or re-program (MazF, EF4 and BipA) translation. Additional factors have been identified that rescue ribosomes stalled due to stress-induced mRNA truncation (tmRNA, ArfA, ArfB), translation of unfavorable protein sequences (EF-P), heat shock-induced subunit dissociation (Hsp15), or antibiotic inhibition (TetM, FusB). Understanding the mechanism of how the bacterial cell responds to stress will not only provide fundamental insight into translation regulation, but will also be an important step to identifying new targets for the development of novel antimicrobial agents.
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Affiliation(s)
- Agata L Starosta
- Gene Center, Department for Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany; Center for integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Munich, Germany
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Abstract
The ribosome is one of the main antibiotic targets in the bacterial cell. Crystal structures of naturally produced antibiotics and their semi-synthetic derivatives bound to ribosomal particles have provided unparalleled insight into their mechanisms of action, and they are also facilitating the design of more effective antibiotics for targeting multidrug-resistant bacteria. In this Review, I discuss the recent structural insights into the mechanism of action of ribosome-targeting antibiotics and the molecular mechanisms of bacterial resistance, in addition to the approaches that are being pursued for the production of improved drugs that inhibit bacterial protein synthesis.
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Mutagenesis mapping of the protein-protein interaction underlying FusB-type fusidic acid resistance. Antimicrob Agents Chemother 2013; 57:4640-4. [PMID: 23836182 PMCID: PMC3811445 DOI: 10.1128/aac.00198-13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
FusB-type proteins represent the predominant mechanism of resistance to fusidic acid in staphylococci and act by binding to and modulating the function of the drug target (elongation factor G [EF-G]). To gain further insight into this antibiotic resistance mechanism, we sought to identify residues important for the interaction of FusB with EF-G and thereby delineate the binding interface within the FusB–EF-G complex. Replacement with alanine of any one of four conserved residues within the C-terminal domain of FusB (F156, K184, Y187, and F208) abrogated the ability of the protein to confer resistance to fusidic acid; the purified mutant proteins also lost the ability to bind S. aureus EF-G in vitro. E. coli EF-G, which is not ordinarily able to bind FusB-type proteins, was rendered competent for binding to FusB following deletion of a 3-residue tract (529SNP531) from domain IV of the protein. This study has identified key regions of both FusB and EF-G that are important for the interaction between the proteins, findings which corroborate our previous in silico prediction for the architecture of the complex formed between the resistance protein and the drug target (G. Cox, G. S. Thompson, H. T. Jenkins, F. Peske, A. Savelsbergh, M. V. Rodnina, W. Wintermeyer, S. W. Homans, T. A. Edwards, and A. J. O'Neill, Proc. Natl. Acad. Sci. U. S. A. 109:2102-2107, 2012).
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Koripella RK, Chen Y, Peisker K, Koh CS, Selmer M, Sanyal S. Mechanism of elongation factor-G-mediated fusidic acid resistance and fitness compensation in Staphylococcus aureus. J Biol Chem 2012; 287:30257-67. [PMID: 22767604 DOI: 10.1074/jbc.m112.378521] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Antibiotic resistance in bacteria is often associated with fitness loss, which is compensated by secondary mutations. Fusidic acid (FA), an antibiotic used against pathogenic bacteria Staphylococcus aureus, locks elongation factor-G (EF-G) to the ribosome after GTP hydrolysis. To clarify the mechanism of fitness loss and compensation in relation to FA resistance, we have characterized three S. aureus EF-G mutants with fast kinetics and crystal structures. Our results show that a significantly slower tRNA translocation and ribosome recycling, plus increased peptidyl-tRNA drop-off, are the causes for fitness defects of the primary FA-resistant mutant F88L. The double mutant F88L/M16I is three to four times faster than F88L in both reactions and showed no tRNA drop-off, explaining its fitness compensatory phenotype. The M16I mutation alone showed hypersensitivity to FA, higher activity, and somewhat increased affinity to GTP. The crystal structures demonstrate that Phe-88 in switch II is a key residue for FA locking and also for triggering interdomain movements in EF-G essential for its function, explaining functional deficiencies in F88L. The mutation M16I loosens the hydrophobic core in the G domain and affects domain I to domain II contact, resulting in improved activity both in the wild-type and F88L background. Thus, FA-resistant EF-G mutations causing fitness loss and compensation operate by affecting the conformational dynamics of EF-G on the ribosome.
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Affiliation(s)
- Ravi Kiran Koripella
- Department of Cell and Molecular Biology, Uppsala University, 75124 Uppsala, Sweden
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