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Hennrich O, Weinmann L, Kulik A, Harms K, Klahn P, Youn JW, Surup F, Mast Y. Biotransformation-coupled mutasynthesis for the generation of novel pristinamycin derivatives by engineering the phenylglycine residue. RSC Chem Biol 2023; 4:1050-1063. [PMID: 38033732 PMCID: PMC10685826 DOI: 10.1039/d3cb00143a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 10/06/2023] [Indexed: 12/02/2023] Open
Abstract
Streptogramins are the last line of defense antimicrobials with pristinamycin as a representative substance used as therapeutics against highly resistant pathogenic bacteria. However, the emergence of (multi)drug-resistant pathogens renders these valuable antibiotics useless; making it necessary to derivatize compounds for new compound characteristics, which is often difficult by chemical de novo synthesis due to the complex nature of the molecules. An alternative to substance derivatization is mutasynthesis. Herein, we report about a mutasynthesis approach, targeting the phenylglycine (Phg) residue for substance derivatization, a pivotal component of streptogramin antibiotics. Mutasynthesis with halogenated Phg(-like) derivatives altogether led to the production of two new derivatized natural compounds, as there are 6-chloropristinamycin I and 6-fluoropristinamycin I based on LC-MS/MS analysis. 6-Chloropristinamycin I and 6-fluoropristinamycin I were isolated by preparative HPLC, structurally confirmed using NMR spectroscopy and tested for antimicrobial bioactivity. In a whole-cell biotransformation approach using an engineered E. coli BL21(DE3) pET28-hmo/pACYC-bcd-gdh strain, Phg derivatives were generated fermentatively. Supplementation with the E. coli biotransformation fermentation broth containing 4-fluorophenylglycine to the pristinamycin mutasynthesis strain resulted in the production of 6-fluoropristinamycin I, demonstrating an advanced level of mutasynthesis.
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Affiliation(s)
- Oliver Hennrich
- Department Bioresources for Bioeconomy and Health Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B 38124 Braunschweig Germany
| | - Leoni Weinmann
- Institute of Microbiology, University Stuttgart, Allmandring 31 D-70569 Stuttgart Germany
| | - Andreas Kulik
- Department Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, Faculty of Science, University of Tübingen, Auf der Morgenstelle 28 D-72076 Tübingen Germany
| | - Karen Harms
- Microbial Drugs Department, Helmholtz-Centre for Infection Research 38124 Braunschweig Germany
| | - Philipp Klahn
- Division of Organic and Medicinal Chemistry, Department of Chemistry and Molecular Biology, University of Gothenburg, Kemigården 4 412 96 Göteborg Sweden
- Centre of Antimicrobial Resistance Research in Gothenburg (CARe) Gothenburg Sweden
| | - Jung-Won Youn
- Institute of Microbiology, University Stuttgart, Allmandring 31 D-70569 Stuttgart Germany
| | - Frank Surup
- Microbial Drugs Department, Helmholtz-Centre for Infection Research 38124 Braunschweig Germany
| | - Yvonne Mast
- Department Bioresources for Bioeconomy and Health Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B 38124 Braunschweig Germany
- Technische Universität Braunschweig, Institut für Mikrobiologie, Rebenring 56 38106 Braunschweig Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen Tübingen Germany
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2
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Du X, Zuo X, Meng F, Han C, Ouyang W, Han Y, Gu Y, Zhao X, Xu F, Qin FX. Direct inhibitory effect on viral entry of influenza A and SARS-CoV-2 viruses by azithromycin. Cell Prolif 2020; 54:e12953. [PMID: 33211371 PMCID: PMC7744835 DOI: 10.1111/cpr.12953] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 10/13/2020] [Accepted: 10/21/2020] [Indexed: 12/22/2022] Open
Abstract
Objectives Using strategy of drug repurposing, antiviral agents against influenza A virus (IAV) and newly emerging SARS‐coronavirus 2 (SARS‐CoV‐2, also as 2019‐nCoV) could be quickly screened out. Materials and Methods A previously reported engineered replication‐competent PR8 strain carrying luciferase reporter gene (IAV‐luc) and multiple pseudotyped IAV and SARS‐CoV‐2 virus was used. To specifically evaluate the pH change of vesicles containing IAV, we constructed an A549 cell line with endosomal and lysosomal expression of pHluorin2. Results Here, we identified azithromycin (AZ) as an effective inhibitor against multiple IAV and SARS‐CoV‐2 strains. We found that AZ treatment could potently inhibit IAV infection in vitro. Moreover, using pseudotyped virus model, AZ could also markedly block the entry of SARS‐CoV‐2 in HEK293T‐ACE2 and Caco2 cells. Mechanistic studies further revealed that such effect was independent of interferon signalling. AZ treatment neither impaired the binding and internalization of IAV virions, nor the viral replication, but rather inhibited the fusion between viral and vacuolar membranes. Using a NPC1‐pHluorin2 reporter cell line, we confirmed that AZ treatment could alkalize the vesicles containing IAV virions, thereby preventing pH‐dependent membrane fusion. Conclusions Overall, our findings demonstrate that AZ can exert broad‐spectrum antiviral effects against IAV and SARS‐CoV‐2, and could be served as a potential clinical anti‐SARS‐CoV‐2 drug in emergency as well as a promising lead compound for the development of next‐generation anti‐IAV drugs.
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Affiliation(s)
- Xiaohong Du
- Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, China.,Institute of Clinical Medicine Research, the Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Science and Technology Town Hospital, Suzhou, China
| | - Xiangyang Zuo
- Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, China
| | - Fang Meng
- Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, China
| | - Chenfeng Han
- Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, China
| | - Wei Ouyang
- Department of Infectious Diseases, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Yu Han
- Department of Infectious Diseases, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Yayun Gu
- Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, China
| | - Xin Zhao
- Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, China
| | - Feng Xu
- Department of Infectious Diseases, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Frank Xiaofeng Qin
- Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, China
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3
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Synergy of streptogramin antibiotics occurs independently of their effects on translation. Antimicrob Agents Chemother 2014; 58:5269-79. [PMID: 24957822 DOI: 10.1128/aac.03389-14] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Streptogramin antibiotics are divided into types A and B, which in combination can act synergistically. We compared the molecular interactions of the streptogramin combinations Synercid (type A, dalfopristin; type B, quinupristin) and NXL 103 (type A, flopristin; type B, linopristin) with the Escherichia coli 70S ribosome by X-ray crystallography. We further analyzed the activity of the streptogramin components individually and in combination. The streptogramin A and B components in Synercid and NXL 103 exhibit synergistic antimicrobial activity against certain pathogenic bacteria. However, in transcription-coupled translation assays, only combinations that include dalfopristin, the streptogramin A component of Synercid, show synergy. Notably, the diethylaminoethylsulfonyl group in dalfopristin reduces its activity but is the basis for synergy in transcription-coupled translation assays before its rapid hydrolysis from the depsipeptide core. Replacement of the diethylaminoethylsulfonyl group in dalfopristin by a nonhydrolyzable group may therefore be beneficial for synergy. The absence of general streptogramin synergy in transcription-coupled translation assays suggests that the synergistic antimicrobial activity of streptogramins can occur independently of the effects of streptogramin on translation.
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4
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Wilson D. Peptidyltransferase Inhibitors of the Bacterial Ribosome. Antibiotics (Basel) 2013. [DOI: 10.1002/9783527659685.ch20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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5
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Crystal structure of the synergistic antibiotic pair, lankamycin and lankacidin, in complex with the large ribosomal subunit. Proc Natl Acad Sci U S A 2011; 108:2717-22. [PMID: 21282615 DOI: 10.1073/pnas.1019406108] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The structures of the large ribosomal subunit of Deinococcus radiodurans (D50S) in complex with the antibiotic lankamycin (3.2 Å) and a double antibiotic complex of lankamycin and lankacidin C (3.45 Å) have been determined, in continuation of previous crystallographic studies on lankacidin-D50S complex. These two drugs have been previously reported to inhibit ribosomal function with mild synergistic effect. Lankamycin, a member of the macrolide family, binds in a similar manner to erythromycin. However, when in complex with lankacidin, lankamycin is located so that it can form interactions with lankacidin in the adjacent ribosomal binding site. When compared to the well-documented synergistic antibiotics, Streptogramins A and B, the pair of lankacidin and lankamycin bind in similar sites, the peptidyl transferase center and nascent peptide exit tunnel, respectively. Herein, we discuss the structural basis for antibiotic synergism and highlight the key factors involved in ribosomal inhibition.
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Abstract
Protein synthesis is one of the major targets in the cell for antibiotics. This review endeavors to provide a comprehensive "post-ribosome structure" A-Z of the huge diversity of antibiotics that target the bacterial translation apparatus, with an emphasis on correlating the vast wealth of biochemical data with more recently available ribosome structures, in order to understand function. The binding site, mechanism of action, and modes of resistance for 26 different classes of protein synthesis inhibitors are presented, ranging from ABT-773 to Zyvox. In addition to improving our understanding of the process of translation, insight into the mechanism of action of antibiotics is essential to the development of novel and more effective antimicrobial agents to combat emerging bacterial resistance to many clinically-relevant drugs.
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Affiliation(s)
- Daniel N Wilson
- Gene Center and Department of Chemistry and Biochemistry, University of Munich, LMU, Munich, Germany.
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7
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Bishai WR. Macrolide immunomodulatory effects and symptom resolution in acute exacerbation of chronic bronchitis and acute maxillary sinusitis: a focus on clarithromycin. Expert Rev Anti Infect Ther 2006; 4:405-16. [PMID: 16771618 DOI: 10.1586/14787210.4.3.405] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Bacterial respiratory tract infections are common in the primary care setting and patients often seek the assistance of a healthcare professional in order to achieve resolution of their symptoms. Antibiotic agents that offer rapid symptom relief, in addition to excellent bacteriological and clinical cure, are highly desired. Macrolides have proven to be highly effective in treating acute bacterial exacerbations of chronic bronchitis and acute maxillary sinusitis. In addition, immunomodulatory effects that may contribute to symptom resolution have been reported. This article reviews current literature on symptom resolution in acute bacterial exacerbations of chronic bronchitis and acute maxillary sinusitis, with a focus on clarithromycin, and explores the potential mechanisms that may contribute to this action.
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Affiliation(s)
- William R Bishai
- The Johns Hopkins University School of Medicine, Division of Infectious Diseases, Department of Medicine, 1550 Orleans Street, CRB2-108, Baltimore, MD 21231, USA.
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8
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Abstract
Members of the macrolide class of antibiotics inhibit peptide elongation on the ribosome by binding close to the peptidyltransferase center and blocking the peptide exit tunnel in the large ribosomal subunit. We have studied the modes of action of the macrolides josamycin, with a 16-membered lactone ring, and erythromycin, with a 14-membered lactone ring, in a cell-free mRNA translation system with pure components from Escherichia coli. We have found that the average lifetime on the ribosome is 3 h for josamycin and less than 2 min for erythromycin and that the dissociation constants for josamycin and erythromycin binding to the ribosome are 5.5 and 11 nM, respectively. Josamycin slows down formation of the first peptide bond of a nascent peptide in an amino acid-dependent way and completely inhibits formation of the second or third peptide bond, depending on peptide sequence. Erythromycin allows formation of longer peptide chains before the onset of inhibition. Both drugs stimulate the rate constants for drop-off of peptidyl-tRNA from the ribosome. In the josamycin case, drop-off is much faster than drug dissociation, whereas these rate constants are comparable in the erythromycin case. Therefore, at a saturating drug concentration, synthesis of full-length proteins is completely shut down by josamycin but not by erythromycin. It is likely that the bacterio-toxic effects of the drugs are caused by a combination of inhibition of protein elongation, on the one hand, and depletion of the intracellular pools of aminoacyl-tRNAs available for protein synthesis by drop-off and incomplete peptidyl-tRNA hydrolase activity, on the other hand.
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Affiliation(s)
- Martin Lovmar
- Department of Cell and Molecular Biology, Molecular Biology Program, BMC, Box 596, Uppsala University, S-75124 Uppsala, Sweden
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9
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Tenson T, Lovmar M, Ehrenberg M. The mechanism of action of macrolides, lincosamides and streptogramin B reveals the nascent peptide exit path in the ribosome. J Mol Biol 2003; 330:1005-14. [PMID: 12860123 DOI: 10.1016/s0022-2836(03)00662-4] [Citation(s) in RCA: 263] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The macrolide-lincosamide-streptogramin B class (MLS) of antibiotics contains structurally different but functionally similar drugs, that all bind to the 50S ribosomal subunit. It has been suggested that these compounds block the path by which nascent peptides exit the ribosome. We have studied the mechanisms of action of four macrolides (erythromycin, josamycin, spiramycin and telithromycin), one lincosamide (clindamycin) and one streptogramin B (pristinamycin IA). All these MLS drugs cause dissociation of peptidyl-tRNA from the ribosome. Josamycin, spiramycin and clindamycin, that extend to the peptidyl transferase center, cause dissociation of peptidyl-tRNAs containing two, three or four amino acid residues. Erythromycin, which does not reach the peptidyl transferase center, induces dissociation of peptidyl-tRNAs containing six, seven or eight amino acid residues. Pristinamycin IA causes dissociation of peptidyl-tRNAs with six amino acid residues and telithromycin allows polymerisation of nine or ten amino acid residues before peptidyl-tRNA dissociates. Our data, in combination with previous structural information, suggest a common mode of action for all MLS antibiotics, which is modulated by the space available between the peptidyl transferase center and the drug.
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Affiliation(s)
- Tanel Tenson
- Institute of Technology, Tartu University, Riia 23, Tartu 51010, Estonia.
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10
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Chinali G. Isolation of tRNA isoacceptors by affinity chromatography with immobilized elongation factor Tu from Escherichia coli. JOURNAL OF BIOCHEMICAL AND BIOPHYSICAL METHODS 1997; 34:1-10. [PMID: 9089380 DOI: 10.1016/s0165-022x(96)00028-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Elongation factor Tu (EF-Tu) from E. coli was coupled to activated CH Sepharose 4B. The immobilized EF-Tu maintained most of the guanosine nucleotide binding activity, but its ability to bind aminoacyl-tRNA depended on the type of complex used in the coupling reaction. The EF-Tu.GTP.aminoacyl-tRNA.kirromycin complex yielded an immobilized factor that was much more active in binding aminoacyl-tRNA than that obtained by coupling EF-Tu.GDP or EF-Tu.GDP.kirromycin to CH Sepharose 4B. Like the free factor, the immobilized EF-Tu.GTP did bind aminoacyl-tRNAs, but not unacylated tRNAs or N-acylated-aminoacyl-tRNAs. The antibiotic kirromycin was used to obtain the rapid conversion of EF-Tu.GDP to EF-Tu.GTP and the release of aminoacyl-tRNA from the matrix-bound EF-Tu by GDP. When total tRNA was aminoacylated by one amino acid only, a column of immobilized EF-Tu-GTP.kirromycin allowed the isolation of the aminoacylated tRNA from bulk tRNA. A rapid and nearly quantitative recovery of highly purified tRNA isoacceptors for various amino acids was obtained in one chromatographic step.
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Affiliation(s)
- G Chinali
- Dipartimento de Medicina Clinica e Sperimentale, Facoltà di Medicina e Chirurgia, Università di Napoli Federico II, Italy
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11
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Abstract
Protein synthesis is catalysed by ribosomes and cytoplasmic factors. Bacterial ribosomes (70S) are made up of 2 subunits (50S and 30S) containing ribosomal RNA (rRNA) and ribosomal proteins: the 30S binds messenger RNA and begins the ribosomal cycle (initiation), whereas 50S binds transfer RNA (tRNA) derivatives and controls elongation. The key reaction, peptide bond formation, is promoted by the catalytic centre of 50S (the peptidyl transferase centre), and the growing peptide chain (peptidyl-tRNA) attached at the donor P site undergoes peptide linkage with an aminoacyl-tRNA at the acceptor A site. This reaction is inhibited by several antibiotics, the best known being chloramphenicol, and the macrolide-lincosamide-streptogramin (MLS) group. These inhibitors have a reversible action, except for streptogramins that are composed of A and B components, which are bacteriostatic alone, but bactericidal when combined. The peptidyl transferase centre has been identified at the 50S surface, and the binding sites of inhibitors have been mapped within this domain: some of these sites overlap (e.g. those of macrolides, and type B streptogramins, which compete for binding to ribosomes). Chloramphenicol blocks the catalytic portion, and A streptogramins the substrate sites of the peptidyl transferase centre. Macrolides and type B streptogramins interfere with the formation of long polypeptides and cause a premature detachment of incomplete peptide chains. The synergism between types A and B streptogramins is due to induction by type A streptogramins of an increased ribosome affinity for type B streptogramins. Microbial resistance to antibiotics mainly involves inactivation of inhibitors and modification of targets (mutations of ribosomal proteins or rRNA genes). Alterations of rRNA bases can induce resistance to a single inhibitor or to a group of antibiotics (e.g. MLSB). The impact of resistance in chemotherapy is less important for streptogramins than for other inhibitors, because the synergistic effect of A and B streptogramins also applies to strains resistant to the MLSB group. It is proposed that mutations and modifications of rRNA bases induce conformational ribosomal changes that prevent antibiotics binding to the target. Conformational changes are also triggered by type A streptogramins: they are responsible for their synergism with type B streptogramins.
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Affiliation(s)
- P Vannuffel
- Department of Genetics and Microbiology, Catholic University of Louvain, Brussels, Belgium
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12
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Vannuffel P, Di Giambattista M, Cocito C. Chemical probing of a virginiamycin M-promoted conformational change of the peptidyl-transferase domain. Nucleic Acids Res 1994; 22:4449-53. [PMID: 7971275 PMCID: PMC308478 DOI: 10.1093/nar/22.21.4449] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Previous findings suggest the location of the central loop of domain V of 23S rRNA within the peptidyltransferase domain of ribosomes. This enzymatic activity is inhibited by some antibiotics, including type A (virginiamycin M or VM) and type B (virginiamycin S or VS) synergimycins, antibiotics endowed with a synergistic action in vivo. In the present work, the ability of VM and VS to modify the accessibility of 23S rRNA bases within ribosomes to chemical reagents has been explored. VM afforded a protection of rRNA bases A2037, A2042, G2049 and C2050. Moreover, when ribosomes were incubated with the two virginiamycin components, the base A2062, which was protected by VS alone, became accessible to dimethyl sulphate (DMS). Modified reactivity to chemical reagents of different rRNA bases located either in the central loop of domain V or in its proximity furnishes experimental evidence for conformational ribosome alterations induced by VM binding.
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Affiliation(s)
- P Vannuffel
- Microbiology and Genetics Unit, University of Louvain, Medical School, Brussels, Belgium
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13
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Vannuffel P, Di Giambattista M, Cocito C. The role of rRNA bases in the interaction of peptidyltransferase inhibitors with bacterial ribosomes. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)41974-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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14
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Picking W, Picking WD, Hardesty B. The use of synthetic tRNAs as probes for examining nascent peptides on Escherichia coli ribosomes. Biochimie 1991; 73:1101-7. [PMID: 1742354 DOI: 10.1016/0300-9084(91)90152-q] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The polyuridylic acid-dependent syntheses of polycysteine and polyserine were carried out on Escherichia coli ribosomes using two new synthetic tRNA species. The peptides were initiated with N-acetyl or N-acyl coumarin derivatives of either Ser-tRNA or Phe-tRNA. The properties of the resulting nascent peptides were compared to those of nascent polyphenylalanine chains synthesized under similar conditions. This was accomplished by following changes in the fluorescence properties of the probes covalently linked to the amino-terminus of each of the nascent polypeptides as they were formed on the ribosomes. Nascent polycysteine and polyserine peptides appeared quite different from those of polyphenylalanine, as indicated by the anisotropy of fluorescence from the amino terminal probe. In contrast to serine and cysteine peptides, the synthesis of all the polyphenylalanine peptides was insensitive to inhibition by erythromycin, even though these peptides were initiated with N-acyl serine. The results support the hypothesis that nascent polyphenylalanine peptides have atypical physical and chemical properties and demonstrate the utility of using modified tRNAs to study ribosome function and the synthesis of proteins.
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Affiliation(s)
- W Picking
- Department of Chemistry and Biochemistry, University of Texas, Austin 78712
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15
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Odom OW, Picking WD, Hardesty B. Movement of tRNA but not the nascent peptide during peptide bond formation on ribosomes. Biochemistry 1990; 29:10734-44. [PMID: 1703007 DOI: 10.1021/bi00500a004] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The results from experiments involving nonradiative energy transfer indicate that a fluorescent probe on the 5'-end of tRNA(Phe) moves more than 20 A towards probes on ribosomal protein L1 as a peptide bond is formed during the peptidyl transferase reaction on Escherichia coli ribosomes. The peptide itself moves no more than a few angstroms during peptide bond formation, as judged by the movement of fluorescent probes attached to the phenylalanine amino group of phenylalanyl-tRNA. Other results demonstrate that an analogue of peptidyl-tRNA, deacylated tRNA, and puromycin can be bound simultaneously to the same ribosome, indicating that there are three physically distinct sites to which tRNA is bound during the reaction steps by which peptides are elongated. The results appear to be consistent with the displacement model of peptide elongation.
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Affiliation(s)
- O W Odom
- Department of Chemistry and Biochemistry, University of Texas, Austin 78712
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16
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Di Giambattista M, Nyssen E, Pecher A, Cocito C. Affinity labeling of the virginiamycin S binding site on bacterial ribosome. Biochemistry 1990; 29:9203-11. [PMID: 2125475 DOI: 10.1021/bi00491a014] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Virginiamycin S (VS, a type B synergimycin) inhibits peptide bond synthesis in vitro and in vivo. The attachment of virginiamycin S to the large ribosomal subunit (50S) is competitively inhibited by erythromycin (Ery, a macrolide) and enhanced by virginiamycin M (VM, a type A synergimycin). We have previously shown, by fluorescence energy transfer measurements, that virginiamycin S binds at the base of the central protuberance of 50S, the putative location of peptidyltransferase domain [Di Giambattista et al. (1986) Biochemistry 25, 3540-3547]. In the present work, the ribosomal protein components at the virginiamycin S binding site were affinity labeled by the N-hydroxysuccinimide ester derivative (HSE) of this antibiotic. Evidence has been provided for (a) the association constant of HSE-ribosome complex formation being similar to that of native virginiamycin S, (b) HSE binding to ribosomes being antagonized by erythromycin and enhanced by virginiamycin M, and (c) a specific linkage of HSE with a single region of 50S, with virtually no fixation to 30S. After dissociation of covalent ribosome-HSE complexes, the resulting ribosomal proteins have been fractionated by electrophoresis and blotted to nitrocellulose, and the HSE-binding proteins have been detected by an immunoenzymometric procedure. More than 80% of label was present within a double spot corresponding to proteins L18 and L22, whose Rfs were modified by the affinity-labeling reagent. It is concluded that these proteins are components of the peptidyltransferase domain of bacterial ribosomes, for which a topographical model, including the available literature data, is proposed.
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Affiliation(s)
- M Di Giambattista
- Unit of Microbiology and Genetics, ICP, Medical School, University of Louvain, Brussels, Belgium
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17
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Hardesty B, Picking WD, Odom OW. The extension of polyphenylalanine and polylysine peptides on Escherichia coli ribosomes. BIOCHIMICA ET BIOPHYSICA ACTA 1990; 1050:197-202. [PMID: 2207144 DOI: 10.1016/0167-4781(90)90166-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Fluorescence techniques were used to examine aminoacyl-tRNA binding to Escherichia coli ribosomes and the subsequent extension of polyphenylalanine and polylysine nascent peptides. The results demonstrate that deacylated tRNA, an analogue of peptidyl-tRNA and puromycin (an analogue of aminoacyl-tRNA) can be bound simultaneously to the same ribosome. Moreover, the fluorescence properties of nascent polyphenylalanine and polylysine peptides with a fluorophore attached to their amino termini were determined and found to be quite different. This difference is reflected in the effects that erythromycin has in each case.
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Affiliation(s)
- B Hardesty
- Department of Chemistry and Biochemistry, University of Texas, Austin 78712
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18
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Nyssen E, Di Giambattista M, Cocito C. Analysis of the reversible binding of virginiamycin M to ribosome and particle functions after removal of the antibiotic. BIOCHIMICA ET BIOPHYSICA ACTA 1989; 1009:39-46. [PMID: 2506929 DOI: 10.1016/0167-4781(89)90076-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Type A synergimycins (VM) were shown to act catalytically and to induce two ribosomal alterations: (a) inability to promote polypeptide synthesis; (b) high-affinity binding of type B synergimycins (VS). A claim for irreversible binding of type A synergimycins to ribosomes has promoted the present reinvestigation. Submission of ribosomes from VM-treated bacteria to a purification procedure (supposed to remove the drug, according to a low association constant previously reported) yielded particles still holding residual VM. The formation of VM.ribosome complexes, more stable than previously inferred but without covalent linkage, was deduced from the extractability of complexed VM by organic solvents. Moreover, incubation of these complexes with increasing amounts of anti-VM immunoglobulins progressively restored ribosome activity in protein synthesis. Binding of VS to ribosomes, by fluorimetric titrations in the presence of substoichiometric concentrations of VM, was incompatible with catalytic action of type A synergimycins. Ribosomes from VM-treated bacteria displayed also a higher affinity for VS than did control ribosomes. This property did not disappear when ribosome.VM complexes were incubated with anti-VM IgG, nor when VM-IgG complexes were withdrawn from the reaction mixture by protein A-agarose binding. We can conclude that VM binding produces: (1) an inhibition of ribosome-promoted peptide bond formation, which occurs only in the presence of the drug; and (2) an increase of ribosome affinity for VS, which lasts after VM removal. The linkage of this drug with ribosomes is tight but reversible and its action is stoichiometric.
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Affiliation(s)
- E Nyssen
- Microbiology & Genetics Unit, ICP, University of Lowvain Medical School, Brussels, Belgium
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Chinali G, Nyssen E, Di Giambattista M, Cocito C. Action of erythromycin and virginiamycin S on polypeptide synthesis in cell-free systems. BIOCHIMICA ET BIOPHYSICA ACTA 1988; 951:42-52. [PMID: 3142522 DOI: 10.1016/0167-4781(88)90023-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Erythromycin (a 14-membered macrolide) and virginiamycin S (a type B synergimycin) block protein biosynthesis in bacteria, but are virtually inactive on poly(U)-directed poly(Phe) synthesis. We have recently shown, however, that these antibiotics inhibit the in vitro polypeptide synthesis directed by synthetic copolymers: this effect is analyzed further in the present work. We were unable to find any consistent alteration produced by these antibiotics on coupled and uncoupled EF-G- and EF-Tu-dependent GTPases, on the EF-Tu-directed binding of aminoacyl-tRNA to ribosomes, and on the EF-G- and GTP-mediated translocation of peptidyl-tRNA bound to poly(U,C).ribosome complexes. With these complexes, the peptidyl transfer reaction, as measured by peptidylpuromycin synthesis, was 10-30% inhibited by virginiamycin S and erythromycin. A direct relationship between the virginiamycin S- and erythromycin-promoted inhibition of poly(A,C)-directed polypeptide synthesis, on the one hand, and the EF-G concentration and the rate of the polymerization reaction, on the other hand, was observed, in agreement with a postulated reversible inhibitor action of these antibiotics. The increased inhibitory activity, which was observed during the first 4-6 rounds of elongation, in the presence of virginiamycin S or erythromycin, was suggestive of a specific action of these antibiotics on the correct positioning of peptidyl-tRNA at the P site. The marked stimulation of premature release of peptidyl-tRNA from poly(A,C).ribosome complexes can be referred to an altered interaction of the C-terminal aminoacyl residue of the growing peptidyl chain with the ribosome. We conclude that the action of virginiamycin S and erythromycin entails a template-dependent alteration of the interaction of peptidyl-tRNA with the donor site of peptidyltransferase, which may lead to a transient functional block of the ribosome and in some instances to a premature release of peptidyl-tRNA and termination of the elongation process.
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Affiliation(s)
- G Chinali
- Istituto di Strutture Biologiche ed Ultrastruttura Cellulare, Ila Facoltà di Medicina, Università di Napoli, Italy
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