1
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Zhang D, Wang Y, Tang Q, Zhang Q, Ji X, Qiu X, Chen D, Liu W. An NADH/NAD +-favored aldo-keto reductase facilitates avilamycin A biosynthesis by primarily catalyzing oxidation of avilamycin C. Appl Environ Microbiol 2024; 90:e0015024. [PMID: 38551341 PMCID: PMC11022570 DOI: 10.1128/aem.00150-24] [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: 01/29/2024] [Accepted: 03/06/2024] [Indexed: 04/18/2024] Open
Abstract
Avilamycins, which possess potent inhibitory activity against Gram-positive bacteria, are a group of oligosaccharide antibiotics produced by Streptomyces viridochromogenes. Among these structurally related oligosaccharide antibiotics, avilamycin A serves as the main bioactive component in veterinary drugs and animal feed additives, which differs from avilamycin C only in the redox state of the two-carbon branched-chain of the terminal octose moiety. However, the mechanisms underlying assembly and modification of the oligosaccharide chain to diversify individual avilamycins remain poorly understood. Here, we report that AviZ1, an aldo-keto reductase in the avilamycin pathway, can catalyze the redox conversion between avilamycins A and C. Remarkably, the ratio of these two components produced by AviZ1 depends on the utilization of specific redox cofactors, namely NADH/NAD+ or NADPH/NADP+. These findings are inspired by gene disruption and complementation experiments and are further supported by in vitro enzymatic activity assays, kinetic analyses, and cofactor affinity studies on AviZ1-catalyzed redox reactions. Additionally, the results from sequence analysis, structure prediction, and site-directed mutagenesis of AviZ1 validate it as an NADH/NAD+-favored aldo-keto reductase that primarily oxidizes avilamycin C to form avilamycin A by utilizing abundant NAD+ in vivo. Building upon the biological function and catalytic activity of AviZ1, overexpressing AviZ1 in S. viridochromogenes is thus effective to improve the yield and proportion of avilamycin A in the fermentation profile of avilamycins. This study represents, to our knowledge, the first characterization of biochemical reactions involved in avilamycin biosynthesis and contributes to the construction of high-performance strains with industrial value.IMPORTANCEAvilamycins are a group of oligosaccharide antibiotics produced by Streptomyces viridochromogenes, which can be used as veterinary drugs and animal feed additives. Avilamycin A is the most bioactive component, differing from avilamycin C only in the redox state of the two-carbon branched-chain of the terminal octose moiety. Currently, the biosynthetic pathway of avilamycins is not clear. Here, we report that AviZ1, an aldo-keto reductase in the avilamycin pathway, can catalyze the redox conversion between avilamycins A and C. More importantly, AviZ1 exhibits a unique NADH/NAD+ preference, allowing it to efficiently catalyze the oxidation of avilamycin C to form avilamycin A using abundant NAD+ in cells. Thus, overexpressing AviZ1 in S. viridochromogenes is effective to improve the yield and proportion of avilamycin A in the fermentation profile of avilamycins. This study serves as an enzymological guide for rational strain design, and the resulting high-performance strains have significant industrial value.
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Affiliation(s)
- Derundong Zhang
- State Key Laboratory of Chemical Biology, Center for Excellence on Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China
- Huzhou Zhongke Center of Bio-Synthetic Innovation, Huzhou, China
| | - Yaotong Wang
- State Key Laboratory of Chemical Biology, Center for Excellence on Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China
| | - Qunyan Tang
- State Key Laboratory of Chemical Biology, Center for Excellence on Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China
| | - Qinglin Zhang
- State Key Laboratory of Chemical Biology, Center for Excellence on Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China
- Huzhou Zhongke Center of Bio-Synthetic Innovation, Huzhou, China
| | - Xiaowei Ji
- Lifecome Biochemistry Co. Ltd., Pucheng, China
| | - Xiangqi Qiu
- Lifecome Biochemistry Co. Ltd., Pucheng, China
| | - Dandan Chen
- State Key Laboratory of Chemical Biology, Center for Excellence on Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China
- Huzhou Zhongke Center of Bio-Synthetic Innovation, Huzhou, China
| | - Wen Liu
- State Key Laboratory of Chemical Biology, Center for Excellence on Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China
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2
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Xiong W, Xia J, Peng X, Tan Y, Chen W, Zhou M, Yang C, Wang W. Novel therapeutic role of Ganoderma Polysaccharides in a septic mouse model - The key role of macrophages. Heliyon 2024; 10:e26732. [PMID: 38449666 PMCID: PMC10915390 DOI: 10.1016/j.heliyon.2024.e26732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 02/17/2024] [Accepted: 02/19/2024] [Indexed: 03/08/2024] Open
Abstract
Ganoderma lucidum polysaccharides (G. PS) have been recognized for their immune-modulating properties. In this study, we investigated the impact of G. PS in a sepsis mouse model, exploring its effects on survival, inflammatory cytokines, Treg cell differentiation, bacterial load, organ dysfunction, and related pathways. We also probed the role of macrophages through chlorphosphon-liposome pretreatment. Using the cecal ligation and puncture (CLP) model, we categorized mice into normal, PBS, and G. PS injection groups. G. PS significantly enhanced septic mouse survival, regulated inflammatory cytokines (TNF-α, IL-17A, IL-6, IL-10), and promoted CD4+Foxp3+ Treg cell differentiation in spleens. Additionally, G. PS reduced bacterial load, mitigated organ damage, and suppressed the NF-κB pathway. In vitro, G. PS facilitated CD4+ T cell differentiation into Treg cells via the p-STAT5 pathway. Chlorphosphon-liposome pretreatment heightened septic mortality, bacterial load, biochemical markers, and organ damage, emphasizing macrophages' involvement. G. PS demonstrated significant protective effects in septic mice by modulating inflammatory responses, enhancing Treg cell differentiation, diminishing bacterial load, and inhibiting inflammatory pathways. These findings illuminate the therapeutic potential of G. PS in sepsis treatment.
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Affiliation(s)
- Wei Xiong
- Chongqing Three Gorges Medical College, Chongqing Key Laboratory of Development and Utilization of Genuine Medicinal Materials in Three Gorges Reservoir Area, Chongqing, 404120, PR China
| | - Jing Xia
- Chongqing Three Gorges Medical College, Chongqing Key Laboratory of Development and Utilization of Genuine Medicinal Materials in Three Gorges Reservoir Area, Chongqing, 404120, PR China
| | - Xiaoyuan Peng
- Chongqing Three Gorges Medical College, Chongqing Key Laboratory of Development and Utilization of Genuine Medicinal Materials in Three Gorges Reservoir Area, Chongqing, 404120, PR China
| | - Ying Tan
- Chongqing Three Gorges Medical College, Chongqing Key Laboratory of Development and Utilization of Genuine Medicinal Materials in Three Gorges Reservoir Area, Chongqing, 404120, PR China
| | - Wansong Chen
- Chongqing Three Gorges Medical College, Chongqing Key Laboratory of Development and Utilization of Genuine Medicinal Materials in Three Gorges Reservoir Area, Chongqing, 404120, PR China
| | - Minghua Zhou
- Chongqing Three Gorges Medical College, Chongqing Key Laboratory of Development and Utilization of Genuine Medicinal Materials in Three Gorges Reservoir Area, Chongqing, 404120, PR China
| | - Ce Yang
- Chongqing Three Gorges Medical College, Chongqing Key Laboratory of Development and Utilization of Genuine Medicinal Materials in Three Gorges Reservoir Area, Chongqing, 404120, PR China
| | - Wenxiang Wang
- Chongqing Three Gorges Medical College, Chongqing Key Laboratory of Development and Utilization of Genuine Medicinal Materials in Three Gorges Reservoir Area, Chongqing, 404120, PR China
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3
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Yñigez-Gutierrez AE, Wurm JE, Froese JT, Rosenthal NE, Bachmann BO. Characterization of Dichloroisoeverninic Acid Biosynthesis and Chemoenzymatic Synthesis of New Orthosomycins. ACS Chem Biol 2024; 19:526-535. [PMID: 38289021 DOI: 10.1021/acschembio.3c00693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
The orthosomycins are highly modified oligosaccharide natural products with a broad spectrum and potent antimicrobial activities. These include everninomicins and avilamycins, which inhibit protein translation by binding a unique site on the bacterial ribosome. Notably, ribosomal bound structures reveal a network of interactions between the 50S subunit and dichloroisoeverninic acid (DCIE), the aromatic A1-ring conserved across orthosomycins, but the relationship of these interactions to their antimicrobial activity remains undetermined. Genetic functional analysis of three genes putatively associated with DCIE biosynthesis in the everninomicin producer Micromonospora carbonacea delineates the native biosynthetic pathway and provides previously unreported advanced biosynthetic intermediates. Subsequent in vitro biochemical analyses demonstrate the complete DCIE biosynthetic pathway and provide access to novel everninomicin analogs. In addition to the orsellinate synthase EvdD3 and a flavin-dependent halogenase EvdD2, our results identified a key acyltransferase, EvdD1, responsible for transferring orsellinate from the acyl carrier protein domain of EvdD3 to a heptasaccharide orthosomycin biosynthetic intermediate. We have also shown that EvdD1 is able to transfer unnatural aryl groups via their N-acyl cysteamine thioesters to the everninomicin scaffold and used this as a biocatalyst to generate a panel of unnatural aryl analogs. The impact of diverse aryl functional group substitution on both ribosome inhibition and antibacterial activities demonstrates the importance of the DCIE moiety in the pharmacology of orthosomycins, notably revealing an uncoupling between ribosomal engagement and antibiotic activity. Control of A1-ring functionality in this class of molecules provides a potential handle to explore and address pharmacological roles of the DCIE ring in this potent and unique class of antibiotics.
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Affiliation(s)
| | - Jennifer E Wurm
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Chemical and Physical Biology Graduate Program, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Jordan T Froese
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Nicholas E Rosenthal
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Brian O Bachmann
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
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4
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Paternoga H, Crowe-McAuliffe C, Bock LV, Koller TO, Morici M, Beckert B, Myasnikov AG, Grubmüller H, Nováček J, Wilson DN. Structural conservation of antibiotic interaction with ribosomes. Nat Struct Mol Biol 2023; 30:1380-1392. [PMID: 37550453 PMCID: PMC10497419 DOI: 10.1038/s41594-023-01047-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 06/26/2023] [Indexed: 08/09/2023]
Abstract
The ribosome is a major target for clinically used antibiotics, but multidrug resistant pathogenic bacteria are making our current arsenal of antimicrobials obsolete. Here we present cryo-electron-microscopy structures of 17 distinct compounds from six different antibiotic classes bound to the bacterial ribosome at resolutions ranging from 1.6 to 2.2 Å. The improved resolution enables a precise description of antibiotic-ribosome interactions, encompassing solvent networks that mediate multiple additional interactions between the drugs and their target. Our results reveal a high structural conservation in the binding mode between antibiotics with the same scaffold, including ordered water molecules. Water molecules are visualized within the antibiotic binding sites that are preordered, become ordered in the presence of the drug and that are physically displaced on drug binding. Insight into RNA-ligand interactions will facilitate development of new antimicrobial agents, as well as other RNA-targeting therapies.
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Affiliation(s)
- Helge Paternoga
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | | | - Lars V Bock
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Timm O Koller
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Martino Morici
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Bertrand Beckert
- Dubochet Center for Imaging at EPFL-UNIL, Batiment Cubotron, Lausanne, Switzerland
| | | | - Helmut Grubmüller
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Jiří Nováček
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.
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5
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Dulin CC, Sharma P, Frigo L, Voehler MW, Iverson TM, Bachmann BO. EvdS6 is a bifunctional decarboxylase from the everninomicin gene cluster. J Biol Chem 2023:104893. [PMID: 37286037 PMCID: PMC10338323 DOI: 10.1016/j.jbc.2023.104893] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/25/2023] [Accepted: 05/29/2023] [Indexed: 06/09/2023] Open
Abstract
The everninomicins are bacterially produced antibiotic octasaccharides characterized by the presence of two interglycosidic spirocyclic ortho-δ-lactone (orthoester) moieties. The terminating G- and H-ring sugars, L-lyxose and C-4 branched sugar β-D-eurekanate, are proposed to be biosynthetically derived from nucleotide diphosphate pentose sugar pyranosides; however, the identity of these precursors and their biosynthetic origin remain to be determined. Herein we identify a new glucuronic acid decarboxylase from Micromonospora belonging to the superfamily of short-chain dehydrogenase/reductase enzymes, EvdS6. Biochemical characterization demonstrated that EvdS6 is an NAD+-dependent bifunctional enzyme that produces a mixture of two products, differing in the sugar C-4 oxidation state. This product distribution is atypical for glucuronic acid decarboxylating enzymes, most of which favor production of the reduced sugar and a minority of which favor release of the oxidized product. Spectroscopic and stereochemical analysis of reaction products revealed that the first product released is the oxidatively produced 4-keto-D-xylose and the second product is the reduced D-xylose. X-ray crystallographic analysis of EvdS6 at 1.51 Å resolution with bound co-factor and TDP demonstrated that the overall geometry of the EvdS6 active site is conserved with other SDR enzymes and enabled studies probing structural determinants for the reductive half of the net neutral catalytic cycle. Critical active site threonine and aspartate residues were unambiguously identified as essential in the reductive step of the reaction and resulted in enzyme variants producing almost exclusively the keto sugar. This work defines potential precursors for the G-ring L-lyxose and resolves likely origins of the H-ring β-D-eurekanate sugar precursor.
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Affiliation(s)
- Callie C Dulin
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Pankaj Sharma
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, USA
| | - Laura Frigo
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, USA
| | - Markus W Voehler
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA; Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - T M Iverson
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, USA; Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Brian O Bachmann
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA; Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
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6
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Zhu M, Wang L, Zhang H, Zhang L, Tan B, Huang Q, Zhu Y, Zhang C. Biosynthesis and Engineered Overproduction of Everninomicins with Promising Activity against Multidrug-Resistant Bacteria. ACS Synth Biol 2023; 12:1520-1532. [PMID: 37084337 DOI: 10.1021/acssynbio.3c00055] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2023]
Abstract
Ribosome-targeting oligosaccharides, everninomicins (EVNs), are promising drug leads with a unique mode of action distinct from that of currently used antibiotics in human therapy. However, the low yields in natural microbial producers hamper an efficient preparation of EVNs for detailed structure-activity relationship analysis. Herein, we enhance the production of EVNs by duplicating the biosynthetic gene cluster (BGC) in Micromonospora sp. SCSIO 07395 and thus obtain multiple EVNs that are sufficient for bioactivity evaluation. EVNs (1-5) are shown to significantly inhibit the growth of multidrug-resistant Gram-positive staphylococcal, enterococcal, and streptococcal strains and Gram-negative pathogens Acinetobacter baumannii and Vibrio cholerae, with micromolar to nanomolar potency, which are comparable or superior to vancomycin, linezolid, and daptomycin. Furthermore, the BGC duplication strategy is proven effective in stepwisely improving titers of the bioactive EVN M (5) from the trace amount to 98.6 mg L-1. Our findings demonstrate the utility of a bioengineering approach for enhanced production and chemical diversification of the medicinally promising EVNs.
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Affiliation(s)
- Mengyi Zhu
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Lijuan Wang
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Haibo Zhang
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Liping Zhang
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Bin Tan
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Qi Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, College of Veterinary Medicine, Wuhan 430070, China
| | - Yiguang Zhu
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
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7
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Mangano K, Marks J, Klepacki D, Saha CK, Atkinson GC, Vázquez-Laslop N, Mankin AS. Context-based sensing of orthosomycin antibiotics by the translating ribosome. Nat Chem Biol 2022; 18:1277-1286. [PMID: 36138139 DOI: 10.1038/s41589-022-01138-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 08/10/2022] [Indexed: 11/09/2022]
Abstract
Orthosomycin antibiotics inhibit protein synthesis by binding to the large ribosomal subunit in the tRNA accommodation corridor, which is traversed by incoming aminoacyl-tRNAs. Structural and biochemical studies suggested that orthosomycins block accommodation of any aminoacyl-tRNAs in the ribosomal A-site. However, the mode of action of orthosomycins in vivo remained unknown. Here, by carrying out genome-wide analysis of antibiotic action in bacterial cells, we discovered that orthosomycins primarily inhibit the ribosomes engaged in translation of specific amino acid sequences. Our results reveal that the predominant sites of orthosomycin-induced translation arrest are defined by the nature of the incoming aminoacyl-tRNA and likely by the identity of the two C-terminal amino acid residues of the nascent protein. We show that nature exploits this antibiotic-sensing mechanism for directing programmed ribosome stalling within the regulatory open reading frame, which may control expression of an orthosomycin-resistance gene in a variety of bacterial species.
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Affiliation(s)
- Kyle Mangano
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA.,Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA.,Amgen Research, Thousand Oaks, CA, USA
| | - James Marks
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA.,Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA.,National Institute of Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD, USA
| | - Dorota Klepacki
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA.,Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Chayan Kumar Saha
- Department of Experimental Medicine, Lund University, Lund, Sweden.,Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Gemma C Atkinson
- Department of Experimental Medicine, Lund University, Lund, Sweden
| | - Nora Vázquez-Laslop
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA. .,Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA.
| | - Alexander S Mankin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA. .,Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA.
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8
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Huang A, Luo X, Xu Z, Huang L, Wang X, Xie S, Pan Y, Fang S, Liu Z, Yuan Z, Hao H. Optimal Regimens and Clinical Breakpoint of Avilamycin Against Clostridium perfringens in Swine Based on PK-PD Study. Front Pharmacol 2022; 13:769539. [PMID: 35281904 PMCID: PMC8908370 DOI: 10.3389/fphar.2022.769539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/14/2022] [Indexed: 11/21/2022] Open
Abstract
Clostridium perfringens causes significant morbidity and mortality in swine worldwide. Avilamycin showed no cross resistance and good activity for treatment of C. perfringens. The aim of this study was to formulate optimal regimens of avilamycin treatment for C. perfringens infection based on the clinical breakpoint (CBP). The wild-type cutoff value (COWT) was defined as 0.25 μg/ml, which was developed based on the minimum inhibitory concentration (MIC) distributions of 120 C. perfringens isolates and calculated using ECOFFinder. Pharmacokinetics–pharmacodynamics (PK-PD) of avilamycin in ileal content were analyzed based on the high-performance liquid chromatography method and WinNonlin software to set up the target of PK/PD index (AUC0–24h/MIC)ex based on sigmoid Emax modeling. The PK parameters of AUC0–24h, Cmax, and Tmax in the intestinal tract were 428.62 ± 14.23 h μg/mL, 146.30 ± 13.41 μg/ml,, and 4 h, respectively. The target of (AUC0–24h/MIC)ex for bactericidal activity in intestinal content was 36.15 h. The PK-PD cutoff value (COPD) was defined as 8 μg/ml and calculated by Monte Carlo simulation. The dose regimen designed from the PK-PD study was 5.2 mg/kg mixed feeding and administrated for the treatment of C. perfringens infection. Five respective strains with different MICs were selected as the infection pathogens, and the clinical cutoff value was defined as 0.125 μg/ml based on the relationship between MIC and the possibility of cure (POC) following nonlinear regression analysis, CART, and “Window” approach. The CBP was set to be 0.25 μg/ml and selected by the integrated decision tree recommended by the Clinical Laboratory of Standard Institute. The formulation of the optimal regimens and CBP is good for clinical treatment and to control drug resistance.
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Affiliation(s)
- Anxiong Huang
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA (Ministry of Agriculture) Key Laboratory for Detection of Veterinary Drug Residues, Wuhan, China.,MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan, China
| | - Xun Luo
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA (Ministry of Agriculture) Key Laboratory for Detection of Veterinary Drug Residues, Wuhan, China.,MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan, China
| | - Zihui Xu
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA (Ministry of Agriculture) Key Laboratory for Detection of Veterinary Drug Residues, Wuhan, China.,MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan, China
| | - Lingli Huang
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA (Ministry of Agriculture) Key Laboratory for Detection of Veterinary Drug Residues, Wuhan, China.,MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan, China
| | - Xu Wang
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA (Ministry of Agriculture) Key Laboratory for Detection of Veterinary Drug Residues, Wuhan, China.,MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan, China
| | - Shuyu Xie
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA (Ministry of Agriculture) Key Laboratory for Detection of Veterinary Drug Residues, Wuhan, China.,MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan, China
| | - Yuanhu Pan
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA (Ministry of Agriculture) Key Laboratory for Detection of Veterinary Drug Residues, Wuhan, China.,MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan, China
| | - Shiwei Fang
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA (Ministry of Agriculture) Key Laboratory for Detection of Veterinary Drug Residues, Wuhan, China.,MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan, China
| | - Zhenli Liu
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA (Ministry of Agriculture) Key Laboratory for Detection of Veterinary Drug Residues, Wuhan, China.,MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan, China
| | - Zonghui Yuan
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA (Ministry of Agriculture) Key Laboratory for Detection of Veterinary Drug Residues, Wuhan, China.,MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan, China
| | - Haihong Hao
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA (Ministry of Agriculture) Key Laboratory for Detection of Veterinary Drug Residues, Wuhan, China.,MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan, China
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9
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Microbial Oligosaccharides with Biomedical Applications. Mar Drugs 2021; 19:md19060350. [PMID: 34205503 PMCID: PMC8234114 DOI: 10.3390/md19060350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/09/2021] [Accepted: 06/16/2021] [Indexed: 11/17/2022] Open
Abstract
Microbial oligosaccharides have been regarded as one of the most appealing natural products attributable to their potent and selective bioactivities, such as antimicrobial activity, inhibition of α-glucosidases and lipase, interference of cellular recognition and signal transduction, and disruption of cell wall biosynthesis. Accordingly, a handful of bioactive oligosaccharides have been developed for the treatment of bacterial infections and type II diabetes mellitus. Given that naturally occurring oligosaccharides have increasingly gained recognition in recent years, a comprehensive review is needed. The current review highlights the chemical structures, biological activities and divergent biosynthetic origins of three subgroups of oligomers including the acarviosine-containing oligosaccharides, saccharomicins, and orthosomycins.
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10
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Cryo-EM Determination of Eravacycline-Bound Structures of the Ribosome and the Multidrug Efflux Pump AdeJ of Acinetobacter baumannii. mBio 2021; 12:e0103121. [PMID: 34044590 PMCID: PMC8263017 DOI: 10.1128/mbio.01031-21] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Antibiotic-resistant strains of the Gram-negative pathogen Acinetobacter baumannii have emerged as a significant global health threat. One successful therapeutic option to treat bacterial infections has been to target the bacterial ribosome. However, in many cases, multidrug efflux pumps within the bacterium recognize and extrude these clinically important antibiotics designed to inhibit the protein synthesis function of the bacterial ribosome. Thus, multidrug efflux within A. baumannii and other highly drug-resistant strains is a major cause of failure of drug-based treatments of infectious diseases. We here report the first structures of the Acinetobacterdrug efflux (Ade)J pump in the presence of the antibiotic eravacycline, using single-particle cryo-electron microscopy (cryo-EM). We also describe cryo-EM structures of the eravacycline-bound forms of the A. baumannii ribosome, including the 70S, 50S, and 30S forms. Our data indicate that the AdeJ pump primarily uses hydrophobic interactions to bind eravacycline, while the 70S ribosome utilizes electrostatic interactions to bind this drug. Our work here highlights how an antibiotic can bind multiple bacterial targets through different mechanisms and potentially enables drug optimization by taking advantage of these different modes of ligand binding.
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11
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Bean-Hodgins L, Kiarie EG. Mandated restrictions on the use of medically important antibiotics in broiler chicken production in Canada: implications, emerging challenges, and opportunities for bolstering gastrointestinal function and health– A review. CANADIAN JOURNAL OF ANIMAL SCIENCE 2021. [DOI: 10.1139/cjas-2021-0015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Chicken Farmers of Canada has been progressively phasing out prophylactic use of antibiotics in broiler chicken production. Consequently, hatcheries, veterinarians, and nutritionists have been mandated to contend with less reliance on use of preventive antibiotics. A topical concern is the increased risk of proliferation of enteric pathogens leading to poor performance, increased mortality and compromised welfare. Moreover, the gut harbors several taxa such as Campylobacter and Salmonella capable of causing significant illnesses in humans via contaminated poultry products. This has created opportunity for research and development of dietary strategies designed to modulate gastrointestinal environment for enhanced performance and food safety. Albeit with inconsistent responses, literature data suggests that dietary strategies such as feed enzymes, probiotics/prebiotics and phytogenic feed additives can bolster gut health and function in broiler chickens. However, much of the efficacy data was generated at controlled research settings that vary significantly with the complex commercial broiler production operations due to variation in dietary, health and environmental conditions. This review will summarize implications of mandated restrictions on the preventative use of antibiotics and emerging Canadian broiler production programs to meet processor specifications. Challenges and opportunities for integrating alternative dietary strategies in commercial broiler production settings will be highlighted.
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Affiliation(s)
- Lisa Bean-Hodgins
- New-Life Mills, A division of Parrish & Heimbecker, Cambridge , Ontario, Canada
- University of Guelph, 3653, Department of Animal Biosciences, Guelph, Ontario, Canada
| | - Elijah G. Kiarie
- University of Guelph, Department of Animal Biosciences, 50 Stone Road East, Guelph, Ontario, Canada, N1G 2W1
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12
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Limbrick EM, Graf M, Derewacz DK, Nguyen F, Spraggins JM, Wieland M, Ynigez-Gutierrez AE, Reisman BJ, Zinshteyn B, McCulloch KM, Iverson TM, Green R, Wilson DN, Bachmann BO. Bifunctional Nitrone-Conjugated Secondary Metabolite Targeting the Ribosome. J Am Chem Soc 2020; 142:18369-18377. [PMID: 32709196 DOI: 10.1021/jacs.0c04675] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Many microorganisms possess the capacity for producing multiple antibiotic secondary metabolites. In a few notable cases, combinations of secondary metabolites produced by the same organism are used in important combination therapies for treatment of drug-resistant bacterial infections. However, examples of conjoined roles of bioactive metabolites produced by the same organism remain uncommon. During our genetic functional analysis of oxidase-encoding genes in the everninomicin producer Micromonospora carbonacea var. aurantiaca, we discovered previously uncharacterized antibiotics everninomicin N and O, comprised of an everninomicin fragment conjugated to the macrolide rosamicin via a rare nitrone moiety. These metabolites were determined to be hydrolysis products of everninomicin P, a nitrone-linked conjugate likely the result of nonenzymatic condensation of the rosamicin aldehyde and the octasaccharide everninomicin F, possessing a hydroxylamino sugar moiety. Rosamicin binds the erythromycin macrolide binding site approximately 60 Å from the orthosomycin binding site of everninomicins. However, while individual ribosomal binding sites for each functional half of everninomicin P are too distant for bidentate binding, ligand displacement studies demonstrated that everninomicin P competes with rosamicin for ribosomal binding. Chemical protection studies and structural analysis of everninomicin P revealed that everninomicin P occupies both the macrolide- and orthosomycin-binding sites on the 70S ribosome. Moreover, resistance mutations within each binding site were overcome by the inhibition of the opposite functional antibiotic moiety binding site. These data together demonstrate a strategy for coupling orthogonal antibiotic pharmacophores, a surprising tolerance for substantial covalent modification of each antibiotic, and a potential beneficial strategy to combat antibiotic resistance.
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Affiliation(s)
- Emilianne M Limbrick
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Michael Graf
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg 20146, Germany
| | - Dagmara K Derewacz
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Fabian Nguyen
- Department of Biochemistry, University of Munich, 81377 Munich, Germany
| | - Jeffrey M Spraggins
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37205, United States.,Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Maximiliane Wieland
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg 20146, Germany
| | | | - Benjamin J Reisman
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Boris Zinshteyn
- Department of Molecular Biology and Genetics, Johns Hopkins University. Baltimore, Maryland 21205, United States
| | - Kathryn M McCulloch
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - T M Iverson
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37205, United States.,Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States.,Vanderbilt Center for Structural Biology, Nashville, Tennessee 37232, United States
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins University. Baltimore, Maryland 21205, United States.,Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Daniel N Wilson
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg 20146, Germany
| | - Brian O Bachmann
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37205, United States.,Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States.,Vanderbilt Institute of Chemical Biology, Nashville, Tennessee 37205, United States
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13
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Limbrick EM, Yñigez-Gutierrez AE, Dulin CC, Derewacz DK, Spraggins JM, McCulloch KM, Iverson TM, Bachmann BO. Methyltransferase Contingencies in the Pathway of Everninomicin D Antibiotics and Analogues. Chembiochem 2020; 21:3349-3358. [PMID: 32686210 DOI: 10.1002/cbic.202000305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/17/2020] [Indexed: 12/11/2022]
Abstract
Everninomicins are orthoester oligosaccharide antibiotics with potent activity against multidrug-resistant bacterial pathogens. Everninomicins act by disrupting ribosomal assembly in a distinct region in comparison to clinically prescribed drugs. We employed microporous intergeneric conjugation with Escherichia coli to manipulate Micromonospora for targeted gene-replacement studies of multiple putative methyltransferases across the octasaccharide scaffold of everninomicin effecting the A1 , C, F, and H rings. Analyses of gene-replacement and genetic complementation mutants established the mutability of the everninomicin scaffold through the generation of 12 previously unreported analogues and, together with previous results, permitted assignment of the ten methyltransferases required for everninomicin biosynthesis. The in vitro activity of A1 - and H-ring-modifying methyltransferases demonstrated the ability to catalyze late-stage modification of the scaffold on an A1 -ring phenol and H-ring C-4' hydroxy moiety. Together these results establish the potential of the everninomicin scaffold for modification through mutagenesis and in vitro modification of advanced biosynthetic intermediates.
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Affiliation(s)
- Emilianne M Limbrick
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Ctr, Nashville, TN 37235, USA.,Department of Chemistry, Mercer University, 1501 Mercer University Drive, Macon, GA 31207, USA
| | | | - Callie C Dulin
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Ctr, Nashville, TN 37235, USA
| | - Dagmara K Derewacz
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Ctr, Nashville, TN 37235, USA
| | - Jeffrey M Spraggins
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Ctr, Nashville, TN 37235, USA.,Department of Biochemistry, Vanderbilt University School of Medicine, 607 Light Hall, Nashville, TN 37205, USA.,Mass Spectrometry Research Center, Vanderbilt University School of Medicine, 465 21st Ave S, Nashville, TN 37240, USA
| | - Kathryn M McCulloch
- Department of Pharmacology, Vanderbilt University 7124 MRBIII, 465 21st Ave S, Nashville, TN 37232, USA.,Department of Chemistry & Biochemistry, California State Polytechnic University, Pomona, 3801 West Temple Ave, Pomona, CA 91768, USA
| | - T M Iverson
- Department of Biochemistry, Vanderbilt University School of Medicine, 607 Light Hall, Nashville, TN 37205, USA.,Department of Pharmacology, Vanderbilt University 7124 MRBIII, 465 21st Ave S, Nashville, TN 37232, USA.,Vanderbilt Institute of Chemical Biology.,Vanderbilt Center for Structural Biology
| | - Brian O Bachmann
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Ctr, Nashville, TN 37235, USA.,Department of Biochemistry, Vanderbilt University School of Medicine, 607 Light Hall, Nashville, TN 37205, USA.,Department of Pharmacology, Vanderbilt University 7124 MRBIII, 465 21st Ave S, Nashville, TN 37232, USA.,Vanderbilt Institute of Chemical Biology
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14
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Elongation factor-Tu can repetitively engage aminoacyl-tRNA within the ribosome during the proofreading stage of tRNA selection. Proc Natl Acad Sci U S A 2020; 117:3610-3620. [PMID: 32024753 PMCID: PMC7035488 DOI: 10.1073/pnas.1904469117] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Elongation factor Tu (EF-Tu) facilitates rapid and accurate selection of aminoacyl-tRNA (aa-tRNA) by the bacterial ribosome during protein synthesis. We show that EF-Tu dissociates from the ribosome as aa-tRNA navigates the accommodation corridor en route to peptide bond formation. We find that EF-Tu’s release from the ribosome during aa-tRNA selection can be reversible. We also demonstrate that new ternary complex formation, accompanied by futile cycles of GTP hydrolysis, can occur on aa-tRNA bound within the ribosome. These findings inform on the decoding mechanism, the contributions of EF-Tu to the fidelity of translation, and the potential consequences of reduced rates of peptide bond formation on cellular physiology. The substrate for ribosomes actively engaged in protein synthesis is a ternary complex of elongation factor Tu (EF-Tu), aminoacyl-tRNA (aa-tRNA), and GTP. EF-Tu plays a critical role in mRNA decoding by increasing the rate and fidelity of aa-tRNA selection at each mRNA codon. Here, using three-color single-molecule fluorescence resonance energy transfer imaging and molecular dynamics simulations, we examine the timing and role of conformational events that mediate the release of aa-tRNA from EF-Tu and EF-Tu from the ribosome after GTP hydrolysis. Our investigations reveal that conformational changes in EF-Tu coordinate the rate-limiting passage of aa-tRNA through the accommodation corridor en route to the peptidyl transferase center of the large ribosomal subunit. Experiments using distinct inhibitors of the accommodation process further show that aa-tRNA must at least partially transit the accommodation corridor for EF-Tu⋅GDP to release. aa-tRNAs failing to undergo peptide bond formation at the end of accommodation corridor passage after EF-Tu release can be reengaged by EF-Tu⋅GTP from solution, coupled to GTP hydrolysis. These observations suggest that additional rounds of ternary complex formation can occur on the ribosome during proofreading, particularly when peptide bond formation is slow, which may serve to increase both the rate and fidelity of protein synthesis at the expense of GTP hydrolysis.
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15
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Dao Duc K, Batra SS, Bhattacharya N, Cate JHD, Song YS. Differences in the path to exit the ribosome across the three domains of life. Nucleic Acids Res 2019; 47:4198-4210. [PMID: 30805621 PMCID: PMC6486554 DOI: 10.1093/nar/gkz106] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 02/22/2019] [Indexed: 01/07/2023] Open
Abstract
The ribosome exit tunnel is an important structure involved in the regulation of translation and other essential functions such as protein folding. By comparing 20 recently obtained cryo-EM and X-ray crystallography structures of the ribosome from all three domains of life, we here characterize the key similarities and differences of the tunnel across species. We first show that a hierarchical clustering of tunnel shapes closely reflects the species phylogeny. Then, by analyzing the ribosomal RNAs and proteins, we explain the observed geometric variations and show direct association between the conservations of the geometry, structure and sequence. We find that the tunnel is more conserved in the upper part close to the polypeptide transferase center, while in the lower part, it is substantially narrower in eukaryotes than in bacteria. Furthermore, we provide evidence for the existence of a second constriction site in eukaryotic exit tunnels. Overall, these results have several evolutionary and functional implications, which explain certain differences between eukaryotes and prokaryotes in their translation mechanisms. In particular, they suggest that major co-translational functions of bacterial tunnels were externalized in eukaryotes, while reducing the tunnel size provided some other advantages, such as facilitating the nascent chain elongation and enabling antibiotic resistance.
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Affiliation(s)
- Khanh Dao Duc
- Computer Science Division, University of California, Berkeley, CA 94720, USA
| | - Sanjit S Batra
- Computer Science Division, University of California, Berkeley, CA 94720, USA
| | | | - Jamie H D Cate
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.,Department of Chemistry, University of California, Berkeley, CA 94720, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yun S Song
- Computer Science Division, University of California, Berkeley, CA 94720, USA.,Department of Statistics, University of California, Berkeley, CA 94720, USA.,Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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16
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Demongeot J, Norris V. Emergence of a "Cyclosome" in a Primitive Network Capable of Building "Infinite" Proteins. Life (Basel) 2019; 9:E51. [PMID: 31216720 PMCID: PMC6617141 DOI: 10.3390/life9020051] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/08/2019] [Accepted: 06/13/2019] [Indexed: 01/02/2023] Open
Abstract
We argue for the existence of an RNA sequence, called the AL (for ALpha) sequence, which may have played a role at the origin of life; this role entailed the AL sequence helping generate the first peptide assemblies via a primitive network. These peptide assemblies included "infinite" proteins. The AL sequence was constructed on an economy principle as the smallest RNA ring having one representative of each codon's synonymy class and capable of adopting a non-functional but nevertheless evolutionarily stable hairpin form that resisted denaturation due to environmental changes in pH, hydration, temperature, etc. Long subsequences from the AL ring resemble sequences from tRNAs and 5S rRNAs of numerous species like the proteobacterium, Rhodobacter sphaeroides. Pentameric subsequences from the AL are present more frequently than expected in current genomes, in particular, in genes encoding some of the proteins associated with ribosomes like tRNA synthetases. Such relics may help explain the existence of universal sequences like exon/intron frontier regions, Shine-Dalgarno sequence (present in bacterial and archaeal mRNAs), CRISPR and mitochondrial loop sequences.
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Affiliation(s)
- Jacques Demongeot
- Faculty of Medicine, Université Grenoble Alpes, AGEIS EA 7407 Tools for e-Gnosis Medical, 38700 La Tronche, France.
| | - Vic Norris
- Laboratory of Microbiology Signals and Microenvironment, Université de Rouen, 76821 Mont-Saint-Aignan CEDEX, France.
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17
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Lin J, Zhou D, Steitz TA, Polikanov YS, Gagnon MG. Ribosome-Targeting Antibiotics: Modes of Action, Mechanisms of Resistance, and Implications for Drug Design. Annu Rev Biochem 2018; 87:451-478. [PMID: 29570352 DOI: 10.1146/annurev-biochem-062917-011942] [Citation(s) in RCA: 161] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genetic information is translated into proteins by the ribosome. Structural studies of the ribosome and of its complexes with factors and inhibitors have provided invaluable information on the mechanism of protein synthesis. Ribosome inhibitors are among the most successful antimicrobial drugs and constitute more than half of all medicines used to treat infections. However, bacterial infections are becoming increasingly difficult to treat because the microbes have developed resistance to the most effective antibiotics, creating a major public health care threat. This has spurred a renewed interest in structure-function studies of protein synthesis inhibitors, and in few cases, compounds have been developed into potent therapeutic agents against drug-resistant pathogens. In this review, we describe the modes of action of many ribosome-targeting antibiotics, highlight the major resistance mechanisms developed by pathogenic bacteria, and discuss recent advances in structure-assisted design of new molecules.
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Affiliation(s)
- Jinzhong Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China;
| | - Dejian Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China;
| | - Thomas A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA; .,Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA.,Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520, USA
| | - Yury S Polikanov
- Department of Biological Sciences, and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois 60607, USA;
| | - Matthieu G Gagnon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA; .,Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520, USA.,Current affiliation: Department of Microbiology and Immunology, and Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555, USA;
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18
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von Loeffelholz O, Natchiar SK, Djabeur N, Myasnikov AG, Kratzat H, Ménétret JF, Hazemann I, Klaholz BP. Focused classification and refinement in high-resolution cryo-EM structural analysis of ribosome complexes. Curr Opin Struct Biol 2017; 46:140-148. [PMID: 28850874 DOI: 10.1016/j.sbi.2017.07.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 07/23/2017] [Accepted: 07/27/2017] [Indexed: 11/17/2022]
Abstract
Cryo electron microscopy (cryo-EM) historically has had a strong impact on the structural and mechanistic analysis of protein synthesis by the prokaryotic and eukaryotic ribosomes. Vice versa, studying ribosomes has helped moving forwards many methodological aspects in single particle cryo-EM, at the level of automated data collection and image processing including advanced techniques for particle sorting to address structural and compositional heterogeneity. Here we review some of the latest ribosome structures, where cryo-EM allowed gaining unprecedented insights based on 3D structure sorting with focused classification and refinement methods helping to reach local resolution levels better than 3Å. Such high-resolution features now enable the analysis of drug interactions with RNA and protein side-chains including even the visualization of chemical modifications of the ribosomal RNA. These advances represent a major breakthrough in structural biology and show the strong potential of cryo-EM beyond the ribosome field including for structure-based drug design.
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Affiliation(s)
- Ottilie von Loeffelholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France
| | - S Kundhavai Natchiar
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France
| | - Nadia Djabeur
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France
| | - Alexander G Myasnikov
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France
| | - Hanna Kratzat
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France
| | - Jean-François Ménétret
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France
| | - Isabelle Hazemann
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France
| | - Bruno P Klaholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France. mailto:
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19
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Affiliation(s)
- Donna Matzov
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel;, ,
| | - Anat Bashan
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel;, ,
| | - Ada Yonath
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel;, ,
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