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Cheng C, Lu D, Sun H, Zhang K, Yin L, Luan G, Liu Y, Ma H, Lu X. Structural insight into the functional regulation of Elongation factor Tu by reactive oxygen species in Synechococcus elongatus PCC 7942. Int J Biol Macromol 2024; 277:133632. [PMID: 38971279 DOI: 10.1016/j.ijbiomac.2024.133632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 06/24/2024] [Accepted: 07/01/2024] [Indexed: 07/08/2024]
Abstract
In cyanobacteria, Elongation factor Tu (EF-Tu) plays a crucial role in the repair of photosystem II (PSII), which is highly susceptible to oxidative stress induced by light exposure and regulated by reactive oxygen species (ROS). However, the specific molecular mechanism governing the functional regulation of EF-Tu by ROS remains unclear. Previous research has shown that a mutated EF-Tu, where C82 is substituted with a Ser residue, can alleviate photoinhibition, highlighting the important role of C82 in EF-Tu photosensitivity. In this study, we elucidated how ROS deactivate EF-Tu by examining the crystal structures of EF-Tu in both wild-type and mutated form (C82S) individually at resolutions of 1.7 Å and 2.0 Å in Synechococcus elongatus PCC 7942 complexed with GDP. Specifically, the GDP-bound form of EF-Tu adopts an open conformation with C82 located internally, making it resistant to oxidation. Coordinated conformational changes in switches I and II create a tunnel that positions C82 for ROS interaction, revealing the vulnerability of the closed conformation of EF-Tu to oxidation. An analysis of these two structures reveals that the precise spatial arrangement of C82 plays a crucial role in modulating EF-Tu's response to ROS, serving as a regulatory element that governs photosynthetic biosynthesis.
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Affiliation(s)
- Chen Cheng
- School of Chemical Engineering, Marine and Life Sciences, Dalian University of Technology, Panjin 124221, China; Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Songling Rd 189, Qingdao 266101, China
| | - Di Lu
- School of Chemical Engineering, Marine and Life Sciences, Dalian University of Technology, Panjin 124221, China; Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Songling Rd 189, Qingdao 266101, China
| | - Huili Sun
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Songling Rd 189, Qingdao 266101, China; Shandong Energy Institute, Songling Rd 189, Qingdao 266101, China; Qingdao New Energy Shandong Laboratory, Songling Rd 189, Qingdao 266101, China
| | - Keke Zhang
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Songling Rd 189, Qingdao 266101, China; Shandong Energy Institute, Songling Rd 189, Qingdao 266101, China; Qingdao New Energy Shandong Laboratory, Songling Rd 189, Qingdao 266101, China
| | - Lei Yin
- School of Chemical Engineering, Marine and Life Sciences, Dalian University of Technology, Panjin 124221, China
| | - Guodong Luan
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Songling Rd 189, Qingdao 266101, China; Shandong Energy Institute, Songling Rd 189, Qingdao 266101, China; Qingdao New Energy Shandong Laboratory, Songling Rd 189, Qingdao 266101, China
| | - YaJun Liu
- School of Chemical Engineering, Marine and Life Sciences, Dalian University of Technology, Panjin 124221, China.
| | - Honglei Ma
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Songling Rd 189, Qingdao 266101, China; Shandong Energy Institute, Songling Rd 189, Qingdao 266101, China; Qingdao New Energy Shandong Laboratory, Songling Rd 189, Qingdao 266101, China.
| | - Xuefeng Lu
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Songling Rd 189, Qingdao 266101, China; Shandong Energy Institute, Songling Rd 189, Qingdao 266101, China; Qingdao New Energy Shandong Laboratory, Songling Rd 189, Qingdao 266101, China
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2
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Christin O, Roulland E. Optimizing the Synthesis Strategy of the Chlorinated Chain Characteristic to the Enacyloxin Series Using Models. J Org Chem 2024; 89:7210-7215. [PMID: 38709622 DOI: 10.1021/acs.joc.4c00626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
In this paper are presented the results of the preliminary studies conducted on two model substrates that allowed the testing of various strategies and set the proper conditions that thereafter culminated in the synthesis of the C1-C23 chain of enacyloxin-IIa and its congeners. Innovative strategic options were explored on each model allowing the stereochemical control of the following two elements: (a) the 2E, 4E, 6E, 8E, and 10Z chlorinated undecapentaenoic chain, thanks to Z-selective Kaneda's alkyne allylchlorination and an E-selective Pd/Cu allene-alkyne coupling and (b) the unusual syn-anti -OH/-Cl/-OCONH2 C17-C19 triad, thanks to a highly diastereoselective Mukaiyama aldol reaction.
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Affiliation(s)
- Orane Christin
- CNRS, CiTCoM, Faculté de Pharmacie, Université Paris Cité, 4, avenue de l'Observatoire, F-75006 Paris, France
| | - Emmanuel Roulland
- CNRS, CiTCoM, Faculté de Pharmacie, Université Paris Cité, 4, avenue de l'Observatoire, F-75006 Paris, France
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3
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Gonzales M, Jacquet P, Gaucher F, Chabrière É, Plener L, Daudé D. AHL-Based Quorum Sensing Regulates the Biosynthesis of a Variety of Bioactive Molecules in Bacteria. JOURNAL OF NATURAL PRODUCTS 2024; 87:1268-1284. [PMID: 38390739 DOI: 10.1021/acs.jnatprod.3c00672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Bacteria are social microorganisms that use communication systems known as quorum sensing (QS) to regulate diverse cellular behaviors including the production of various secreted molecules. Bacterial secondary metabolites are widely studied for their bioactivities including antibiotic, antifungal, antiparasitic, and cytotoxic compounds. Besides playing a crucial role in natural bacterial niches and intermicrobial competition by targeting neighboring organisms and conferring survival advantages to the producer, these bioactive molecules may be of prime interest to develop new antimicrobials or anticancer therapies. This review focuses on bioactive compounds produced under acyl homoserine lactone-based QS regulation by Gram-negative bacteria that are pathogenic to humans and animals, including the Burkholderia, Serratia, Pseudomonas, Chromobacterium, and Pseudoalteromonas genera. The synthesis, regulation, chemical nature, biocidal effects, and potential applications of these identified toxic molecules are presented and discussed in light of their role in microbial interactions.
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Affiliation(s)
- Mélanie Gonzales
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille 13288, France
- Gene&GreenTK, Marseille 13005, France
| | | | | | - Éric Chabrière
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille 13288, France
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4
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Alzamami A, Alturki NA, Khan K, Basharat Z, Mashraqi MM. Screening inhibitors against the Ef-Tu of Fusobacterium nucleatum: a docking, ADMET and PBPK assessment study. Mol Divers 2024:10.1007/s11030-024-10815-x. [PMID: 38457020 DOI: 10.1007/s11030-024-10815-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 01/21/2024] [Indexed: 03/09/2024]
Abstract
The oral pathogen Fusobacterium nucleatum has recently been associated with an elevated risk of colorectal cancer (CRC), endometrial metastasis, chemoresistance, inflammation, metastasis, and DNA damage, along with several other diseases. This study aimed to explore the disruption of protein machinery of F. nucleatum via inhibition of elongation factor thermo unstable (Ef-Tu) protein, through natural products. No study on Ef-Tu inhibition by natural products or in Fusobacterium spp. exists till todate. Ef-Tu is an abundant specialized drug target in bacteria that varies from human Ef-Tu. Elfamycins target Ef-Tu and hence, Enacyloxin IIa was used to generate pharmacophore for virtual screening of three natural product libraries, Natural Product Activity and Species Source (NPASS) (n = 30000 molecules), Tibetan medicinal plant database (n = 54 molecules) and African medicinal plant database (n > 6000 molecules). Peptaibol Septocylindrin B (NPC141050), Hirtusneanoside, and ZINC95486259 were prioritized from these libraries as potential therapeutic candidates. ADMET profiling was done for safety assessment, physiological-based pharmacokinetic modeling in human and mouse for getting insight into drug interaction with body tissues and molecular dynamics was used to assess stability of the best hit NPC141050 (Septocylindrin B). Based on the promising results, we propose further in vitro, in vivo and pharmacokinetic testing on the lead Septocylindrin B, for possible translation into therapeutic interventions.
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Affiliation(s)
- Ahmad Alzamami
- Clinical Laboratory Science Department, College of Applied Medical Sciences, Shaqra University, 11961, Al-Quwayiyah, Saudi Arabia
| | - Norah A Alturki
- Clinical Laboratory Science Department, College of Applied Medical Sciences, King Saud University, 11433, Riyadh, Saudi Arabia
| | - Kanwal Khan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Zarrin Basharat
- Alpha Genomics (Private) Limited, Islamabad, 45710, Pakistan.
| | - Mutaib M Mashraqi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, 61441, Najran, Saudi Arabia.
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5
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Christin O, Roulland E. Advancements in Enacyloxins Total Synthesis: Access to the Chlorinated Polyunsaturated Chain Peculiar to this Promising Family of Antibiotics. Org Lett 2023; 25:6869-6874. [PMID: 37676860 DOI: 10.1021/acs.orglett.3c02477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
The first synthesis of the protected chain specific to the enacyloxin antibiotic family is reported. The noticeable features are (a) the construction of the chlorinated undecapentaenoic moiety implementing the sequence Tsuji's alkyne syn allyl-chlorination, E-selective Pd/Cu-catalyzed allene-alkyne coupling, Horner-Wadsworth-Emmons olefination, dehydration; (b) control of the C18 chlorinated stereogenic center by organo-catalyzed aldehyde α-chlorination; and (c) the assemblage of this aldehyde with the C1-C16 ketone using a highly diastereoselective Mukaiyama aldol.
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Affiliation(s)
- Orane Christin
- CiTCoM, UMR 8038, CNRS-Université Paris Cité, Faculté de Pharmacie, 4, avenue de l'Observatoire, 75006 Paris, France
| | - Emmanuel Roulland
- CiTCoM, UMR 8038, CNRS-Université Paris Cité, Faculté de Pharmacie, 4, avenue de l'Observatoire, 75006 Paris, France
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6
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Shanbhag C, Saraogi I. Bacterial GTPases as druggable targets to tackle antimicrobial resistance. Bioorg Med Chem Lett 2023; 87:129276. [PMID: 37030567 DOI: 10.1016/j.bmcl.2023.129276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 04/08/2023]
Abstract
Small molecules as antibacterial agents have contributed immensely to the growth of modern medicine over the last several decades. However, the emergence of drug resistance among bacterial pathogens has undermined the effectiveness of the existing antibiotics. Thus, there is an exigency to address the antibiotic crisis by developing new antibacterial agents and identifying novel drug targets in bacteria. In this review, we summarize the importance of guanosine triphosphate hydrolyzing proteins (GTPases) as key agents for bacterial survival. We also discuss representative examples of small molecules that target bacterial GTPases as novel antibacterial agents, and highlight areas that are ripe for exploration. Given their vital roles in cell viability, virulence, and antibiotic resistance, bacterial GTPases are highly attractive antibacterial targets that will likely play a vital role in the fight against antimicrobial resistance.
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7
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Compilation of the Antimicrobial Compounds Produced by Burkholderia Sensu Stricto. Molecules 2023; 28:molecules28041646. [PMID: 36838633 PMCID: PMC9958762 DOI: 10.3390/molecules28041646] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/26/2023] [Accepted: 01/28/2023] [Indexed: 02/11/2023] Open
Abstract
Due to the increase in multidrug-resistant microorganisms, the investigation of novel or more efficient antimicrobial compounds is essential. The World Health Organization issued a list of priority multidrug-resistant bacteria whose eradication will require new antibiotics. Among them, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacteriaceae are in the "critical" (most urgent) category. As a result, major investigations are ongoing worldwide to discover new antimicrobial compounds. Burkholderia, specifically Burkholderia sensu stricto, is recognized as an antimicrobial-producing group of species. Highly dissimilar compounds are among the molecules produced by this genus, such as those that are unique to a particular strain (like compound CF66I produced by Burkholderia cepacia CF-66) or antimicrobials found in a number of species, e.g., phenazines or ornibactins. The compounds produced by Burkholderia include N-containing heterocycles, volatile organic compounds, polyenes, polyynes, siderophores, macrolides, bacteriocins, quinolones, and other not classified antimicrobials. Some of them might be candidates not only for antimicrobials for both bacteria and fungi, but also as anticancer or antitumor agents. Therefore, in this review, the wide range of antimicrobial compounds produced by Burkholderia is explored, focusing especially on those compounds that were tested in vitro for antimicrobial activity. In addition, information was gathered regarding novel compounds discovered by genome-guided approaches.
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8
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Lu P, Ji X, Xue J, Dong Y, Chen X. Proteomic Analysis Revealed Metabolic Inhibition and Elongation Factor Tu Deamidation by p-Coumaric Acid in Cronobacter sakazakii. Front Microbiol 2022; 13:888103. [PMID: 35615519 PMCID: PMC9125189 DOI: 10.3389/fmicb.2022.888103] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/29/2022] [Indexed: 11/16/2022] Open
Abstract
Screening drugs and compounds to fight against Cronobacter sakazakii (C. sakazakii), one of the most common pathogens that can cause fatal necrotizing enterocolitis, septicema and meningitis, is still needed. We found that p-coumaric acid (pCA) has an inhibitory effect on C. sakazakii in vitro and in vivo. Proteomic changes of C. sakazakii BAA-894 exposed to pCA were studied to reveal the antibacterial mechanisms involved. A total of 1,553 proteins were identified in C. sakazakii BAA-894 by label-free proteomics analysis. Fuzzy cluster analysis showed that 33 were up-regulated, and 110 were down-regulated with pCA treatment. Gene Ontology (GO) analysis concluded that pCA caused the change of metabolic state of bacteria and generally in the state of metabolic inhibition. KEGG Enrichment Analysis (KEGG) analysis showed that pCA inhibited energy metabolism and distorted the balance of amino acid metabolism. Posttranslational modification analysis showed that pCA affected the deamidation of three proteins, including Elongation factor Tu, one of the vital proteins in bacteria. Molecular docking suggested the hydrogen bond between the pCA carboxyl group and Elongation factor Tu Asn-64 might contribute to deamidation. Overall, we found that pCA interfered with cellular energy and amino acid metabolism and promoted elongation factor Tu deamidation, suggesting that pCA can be an effective natural substitute to control C. sakazakii.
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Affiliation(s)
- Ping Lu
- Tianjin Key Laboratory of Ophthalmology and Visual Science, Tianjin Eye Institute, Tianjin Eye Hospital, Tianjin, China
- Nankai University Affiliated Eye Hospital, Nankai University, Tianjin, China
- Clinical College of Ophthalmology, Tianjin Medical University, Tianjin, China
| | - Xuemeng Ji
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin, China
| | - Juan Xue
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Yinping Dong
- Institute of Radiation Medicine, Chinese Academy of Medical Science, Peking Union Medical College, Tianjin, China
| | - Xi Chen
- Tianjin Key Laboratory of Ophthalmology and Visual Science, Tianjin Eye Institute, Tianjin Eye Hospital, Tianjin, China
- Nankai University Affiliated Eye Hospital, Nankai University, Tianjin, China
- Clinical College of Ophthalmology, Tianjin Medical University, Tianjin, China
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
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9
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Bach E, Passaglia LMP, Jiao J, Gross H. Burkholderia in the genomic era: from taxonomy to the discovery of new antimicrobial secondary metabolites. Crit Rev Microbiol 2021; 48:121-160. [PMID: 34346791 DOI: 10.1080/1040841x.2021.1946009] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Species of Burkholderia are highly versatile being found not only abundantly in soil, but also as plants and animals' commensals or pathogens. Their complex multireplicon genomes harbour an impressive number of polyketide synthase (PKS) and nonribosomal peptide-synthetase (NRPS) genes coding for the production of antimicrobial secondary metabolites (SMs), which have been successfully deciphered by genome-guided tools. Moreover, genome metrics supported the split of this genus into Burkholderia sensu stricto (s.s.) and five new other genera. Here, we show that the successful antimicrobial SMs producers belong to Burkholderia s.s. Additionally, we reviewed the occurrence, bioactivities, modes of action, structural, and biosynthetic information of thirty-eight Burkholderia antimicrobial SMs shedding light on their diversity, complexity, and uniqueness as well as the importance of genome-guided strategies to facilitate their discovery. Several Burkholderia NRPS and PKS display unusual features, which are reflected in their structural diversity, important bioactivities, and varied modes of action. Up to now, it is possible to observe a general tendency of Burkholderia SMs being more active against fungi. Although the modes of action and biosynthetic gene clusters of many SMs remain unknown, we highlight the potential of Burkholderia SMs as alternatives to fight against new diseases and antibiotic resistance.
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Affiliation(s)
- Evelise Bach
- Departamento de Genética and Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Luciane Maria Pereira Passaglia
- Departamento de Genética and Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Junjing Jiao
- Department for Pharmaceutical Biology, Pharmaceutical Institute, University of Tübingen, Tübingen, Germany
| | - Harald Gross
- Department for Pharmaceutical Biology, Pharmaceutical Institute, University of Tübingen, Tübingen, Germany
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10
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Yarlagadda V, Medina R, Johnson TA, Koteva KP, Cox G, Thaker MN, Wright GD. Resistance-Guided Discovery of Elfamycin Antibiotic Producers with Antigonococcal Activity. ACS Infect Dis 2020; 6:3163-3173. [PMID: 33164482 DOI: 10.1021/acsinfecdis.0c00467] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The rise of bacterial antibiotic resistance coupled with a diminished antibiotic drug pipeline underlines the importance of developing rational strategies to discover new antimicrobials. Microbially derived natural products are the basis for most of the antibiotic arsenal available to modern medicine. Here, we demonstrate a resistance-based approach to identify producers of elfamycins, an under-explored class of natural product antibiotics that target the essential translation factor EF-Tu. Antibiotic producers carry self-resistance genes to avoid suicide. These genes are often found within the same biosynthetic gene cluster (BGC) responsible for making the antibiotic, and we exploited this trait to identify members of the kirromycin class of elfamycin producers. Genome mining of Streptomyces spp. led to the identification of three isolates that harbor kirromycin-resistant EF-Tu (EF-TuKirR) within predicted natural product BGCs. Activity-guided purification on extracts of one of the Streptomyces isolates, which was not known to produce an elfamycin, identified it as a producer of phenelfamycin B, a linear polyketide. Phenelfamycin B demonstrates impressive antibacterial activity (MIC ∼ 1 μg/mL) against multidrug-resistant Neisseria gonorrhoeae, a clinically important Gram negative pathogen. The antigonococcal activity of phenelfamycin was shown to be the result of inhibition of protein biosynthesis by binding to EF-Tu. These results indicate that a resistance-based approach of identifying elfamycin producers is translatable to other antibiotic classes that can identify new and overlooked antibiotics necessary to address the antibiotic crisis.
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Affiliation(s)
- Venkateswarlu Yarlagadda
- David Braley Center for Antibiotic Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Ricardo Medina
- Department of Microbiology, Chemical Bioactive Center, Central University Marta Abreu de las Villas, Santa Clara 54830, Villa Clara, Cuba
| | - Timothy A. Johnson
- Department of Animal Sciences, Purdue University College of Agriculture, West Lafayette, Indiana 47907, United States
| | - Kalinka P. Koteva
- David Braley Center for Antibiotic Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Georgina Cox
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Maulik N. Thaker
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Gerard D. Wright
- David Braley Center for Antibiotic Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
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Kiyota H. Synthetic studies of biologically active natural products contributing to pesticide development. JOURNAL OF PESTICIDE SCIENCE 2020; 45:177-183. [PMID: 32913421 PMCID: PMC7453299 DOI: 10.1584/jpestics.j20-03] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 07/01/2020] [Indexed: 06/11/2023]
Abstract
Natural product research, including total synthesis, is becoming increasingly important for the discovery of pesticide seeds and leads. Synthetic studies of biologically active compounds such as antibiotics (enacyloxins, polynactin, pamamycins, spirofungin A and B, glutarimides and antimycins), phytopathogenic toxins (pyricuol, pyriculariol, tabtoxinine-β-lactam, gigantenone, phomenone and phaseolinone), marine derived products (pteroenone, β-D-Asp-Gly, didemniselinolipid B, cortistatin A, sanctolide A and gizzerosine), POPs (dieldrin, endosulfan, HCB), plant hormones (abscisic acid and jasmonic acid), insect pheromones (endo-brevicomin etc.), especially using a variety of biotransformation are described.
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Affiliation(s)
- Hiromasa Kiyota
- Grad. Sch. Environmental & Life Science, Okayama University, 1–1–1 Tsushima-Naka, Kita, Okayama 700–8530, Japan
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12
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Warias M, Grubmüller H, Bock LV. tRNA Dissociation from EF-Tu after GTP Hydrolysis: Primary Steps and Antibiotic Inhibition. Biophys J 2020; 118:151-161. [PMID: 31711607 PMCID: PMC6950810 DOI: 10.1016/j.bpj.2019.10.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 09/25/2019] [Accepted: 10/22/2019] [Indexed: 11/25/2022] Open
Abstract
In each round of ribosomal translation, the translational GTPase elongation factor Tu (EF-Tu) delivers a transfer RNA (tRNA) to the ribosome. After successful decoding, EF-Tu hydrolyzes GTP, which triggers a conformational change that ultimately results in the release of the tRNA from EF-Tu. To identify the primary steps of these conformational changes and how they are prevented by the antibiotic kirromycin, we employed all-atom explicit-solvent molecular dynamics simulations of the full ribosome-EF-Tu complex. Our results suggest that after GTP hydrolysis and Pi release, the loss of interactions between the nucleotide and the switch 1 loop of EF-Tu allows domain D1 of EF-Tu to rotate relative to domains D2 and D3 and leads to an increased flexibility of the switch 1 loop. This rotation induces a closing of the D1-D3 interface and an opening of the D1-D2 interface. We propose that the opening of the D1-D2 interface, which binds the CCA tail of the tRNA, weakens the crucial EF-Tu-tRNA interactions, which lowers tRNA binding affinity, representing the first step of tRNA release. Kirromycin binds within the D1-D3 interface, sterically blocking its closure, but does not prevent hydrolysis. The resulting increased flexibility of switch 1 explains why it is not resolved in kirromycin-bound structures.
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Affiliation(s)
- Malte Warias
- Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Helmut Grubmüller
- Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Lars V Bock
- Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
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13
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A dual transacylation mechanism for polyketide synthase chain release in enacyloxin antibiotic biosynthesis. Nat Chem 2019; 11:906-912. [PMID: 31548673 PMCID: PMC6774797 DOI: 10.1038/s41557-019-0309-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 07/12/2019] [Indexed: 01/24/2023]
Abstract
Polyketide synthases assemble diverse natural products with numerous important applications. The thioester intermediates in polyketide assembly are covalently tethered to acyl carrier protein domains of the synthase. Several mechanisms for polyketide chain release are known, contributing to natural product structural diversification. Here we report a dual transacylation mechanism for chain release from the enacyloxin polyketide synthase, which assembles an antibiotic with promising activity against Acinetobacter baumannii. A non-elongating ketosynthase domain transfers the polyketide chain from the final acyl carrier protein domain of the synthase to a separate carrier protein and a nonribosomal peptide synthetase condensation domain condenses it with (1S, 3R, 4S)-3, 4-dihydroxycyclohexane carboxylic acid. Molecular dissection of this process reveals that non-elongating ketosynthase domain-mediated transacylation circumvents the inability of the condensation domain to recognize the acyl carrier protein domain. Several 3, 4-dihydroxycyclohexane carboxylic acid analogues can be employed for chain release, suggesting a promising strategy for producing enacyloxin analogues.
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14
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Rudorf S. Efficiency of protein synthesis inhibition depends on tRNA and codon compositions. PLoS Comput Biol 2019; 15:e1006979. [PMID: 31369559 PMCID: PMC6692046 DOI: 10.1371/journal.pcbi.1006979] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 08/13/2019] [Accepted: 07/15/2019] [Indexed: 11/19/2022] Open
Abstract
Regulation and maintenance of protein synthesis are vital to all organisms and are thus key targets of attack and defense at the cellular level. Here, we mathematically analyze protein synthesis for its sensitivity to the inhibition of elongation factor EF-Tu and/or ribosomes in dependence of the system’s tRNA and codon compositions. We find that protein synthesis reacts ultrasensitively to a decrease in the elongation factor’s concentration for systems with an imbalance between codon usages and tRNA concentrations. For well-balanced tRNA/codon compositions, protein synthesis is impeded more effectively by the inhibition of ribosomes instead of EF-Tu. Our predictions are supported by re-evaluated experimental data as well as by independent computer simulations. Not only does the described ultrasensitivity render EF-Tu a distinguished target of protein synthesis inhibiting antibiotics. It may also enable persister cell formation mediated by toxin-antitoxin systems. The strong impact of the tRNA/codon composition provides a basis for tissue-specificities of disorders caused by mutations of human mitochondrial EF-Tu as well as for the potential use of EF-Tu targeting drugs for tissue-specific treatments. We predict and analyze the response of differently composed protein synthesis systems to the inhibition of elongation factor EF-Tu and/or ribosomes. The study reveals a strong interdependency of a protein synthesis system’s composition and its susceptibility to inhibition. This interdependency defines a generic mechanism that provides a common basis for a variety of seemingly unrelated phenomena including, for example, persister cell formation and tissue-specificity of certain mitochondrial diseases. The described mechanism applies to simple artificial translation systems as well as to complex protein synthesis in vivo.
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Affiliation(s)
- Sophia Rudorf
- Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- * E-mail:
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15
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Abstract
Burkholderia bacteria are multifaceted organisms that are ecologically and metabolically diverse. The Burkholderia genus has gained prominence because it includes human pathogens; however, many strains are nonpathogenic and have desirable characteristics such as beneficial plant associations and degradation of pollutants. The diversity of the Burkholderia genus is reflected within the large genomes that feature multiple replicons. Burkholderia genomes encode a plethora of natural products with potential therapeutic relevance and biotechnological applications. This review highlights Burkholderia as an emerging source of natural products. An overview of the taxonomy of the Burkholderia genus, which is currently being revised, is provided. We then present a curated compilation of natural products isolated from Burkholderia sensu lato and analyze their characteristics in terms of biosynthetic class, discovery method, and bioactivity. Finally, we describe and discuss genome characteristics and highlight the biosynthesis of a select number of natural products that are encoded in unusual biosynthetic gene clusters. The availability of >1000 Burkholderia genomes in public databases provides an opportunity to realize the genetic potential of this underexplored taxon for natural product discovery.
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Affiliation(s)
- Sylvia Kunakom
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Alessandra S. Eustáquio
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
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16
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Abstract
Many antibiotics available in the clinic today directly inhibit bacterial translation. Despite the past success of such drugs, their efficacy is diminishing with the spread of antibiotic resistance. Through the use of ribosomal modifications, ribosomal protection proteins, translation elongation factors and mistranslation, many pathogens are able to establish resistance to common therapeutics. However, current efforts in drug discovery are focused on overcoming these obstacles through the modification or discovery of new treatment options. Here, we provide an overview for common mechanisms of resistance to translation-targeting drugs and summarize several important breakthroughs in recent drug development.
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Affiliation(s)
- Anne Witzky
- 1 Department of Molecular Genetics, Ohio State University , Columbus, OH 43210 , USA.,2 Center for RNA Biology, Ohio State University , Columbus, OH 43210 , USA
| | - Rodney Tollerson
- 2 Center for RNA Biology, Ohio State University , Columbus, OH 43210 , USA.,3 Department of Microbiology, Ohio State University , Columbus, OH 43210 , USA
| | - Michael Ibba
- 2 Center for RNA Biology, Ohio State University , Columbus, OH 43210 , USA.,3 Department of Microbiology, Ohio State University , Columbus, OH 43210 , USA
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17
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Johansen JS, Kavaliauskas D, Pfeil SH, Blaise M, Cooperman BS, Goldman YE, Thirup SS, Knudsen CR. E. coli elongation factor Tu bound to a GTP analogue displays an open conformation equivalent to the GDP-bound form. Nucleic Acids Res 2019; 46:8641-8650. [PMID: 30107565 PMCID: PMC6144822 DOI: 10.1093/nar/gky697] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 08/07/2018] [Indexed: 11/12/2022] Open
Abstract
According to the traditional view, GTPases act as molecular switches, which cycle between distinct ‘on’ and ‘off’ conformations bound to GTP and GDP, respectively. Translation elongation factor EF-Tu is a GTPase essential for prokaryotic protein synthesis. In its GTP-bound form, EF-Tu delivers aminoacylated tRNAs to the ribosome as a ternary complex. GTP hydrolysis is thought to cause the release of EF-Tu from aminoacyl-tRNA and the ribosome due to a dramatic conformational change following Pi release. Here, the crystal structure of Escherichia coli EF-Tu in complex with a non-hydrolysable GTP analogue (GDPNP) has been determined. Remarkably, the overall conformation of EF-Tu·GDPNP displays the classical, open GDP-bound conformation. This is in accordance with an emerging view that the identity of the bound guanine nucleotide is not ‘locking’ the GTPase in a fixed conformation. Using a single-molecule approach, the conformational dynamics of various ligand-bound forms of EF-Tu were probed in solution by fluorescence resonance energy transfer. The results suggest that EF-Tu, free in solution, may sample a wider set of conformations than the structurally well-defined GTP- and GDP-forms known from previous X-ray crystallographic studies. Only upon binding, as a ternary complex, to the mRNA-programmed ribosome, is the well-known, closed GTP-bound conformation, observed.
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Affiliation(s)
- Jesper S Johansen
- Department of Molecular Biology & Genetics, University of Aarhus, Gustav Wieds Vej 10 C, DK-8000 Aarhus C, Denmark
| | - Darius Kavaliauskas
- Department of Molecular Biology & Genetics, University of Aarhus, Gustav Wieds Vej 10 C, DK-8000 Aarhus C, Denmark
| | - Shawn H Pfeil
- Department of Physics, West Chester University, West Chester, PA 19383, USA
| | - Mickaël Blaise
- Department of Molecular Biology & Genetics, University of Aarhus, Gustav Wieds Vej 10 C, DK-8000 Aarhus C, Denmark
| | - Barry S Cooperman
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yale E Goldman
- Pennsylvania Muscle Institute, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Søren S Thirup
- Department of Molecular Biology & Genetics, University of Aarhus, Gustav Wieds Vej 10 C, DK-8000 Aarhus C, Denmark
| | - Charlotte R Knudsen
- Department of Molecular Biology & Genetics, University of Aarhus, Gustav Wieds Vej 10 C, DK-8000 Aarhus C, Denmark
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18
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Girodat D, Mercier E, Gzyl KE, Wieden HJ. Elongation Factor Tu's Nucleotide Binding Is Governed by a Thermodynamic Landscape Unique among Bacterial Translation Factors. J Am Chem Soc 2019; 141:10236-10246. [PMID: 31058500 DOI: 10.1021/jacs.9b01522] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Molecular switches such as GTPases are powerful devices turning "on" or "off" biomolecular processes at the core of critical biological pathways. To develop molecular switches de novo, an intimate understanding of how they function is required. Here we investigate the thermodynamic parameters that define the nucleotide-dependent switch mechanism of elongation factor (EF) Tu as a prototypical molecular switch. EF-Tu alternates between GTP- and GDP-bound conformations during its functional cycle, representing the "on" and "off" states, respectively. We report for the first time that the activation barriers for nucleotide association are the same for both nucleotides, suggesting a guanosine nucleoside or ribose-first mechanism for nucleotide association. Additionally, molecular dynamics (MD) simulations indicate that enthalpic stabilization of GDP binding compared to GTP binding originates in the backbone hydrogen bonding network of EF-Tu. In contrast, binding of GTP to EF-Tu is entropically driven by the liberation of bound water during the GDP- to GTP-bound transition. GDP binding to the apo conformation of EF-Tu is both enthalpically and entropically favored, a feature unique among translational GTPases. This indicates that the apo conformation does not resemble the GDP-bound state. Finally, we show that antibiotics and single amino acid substitutions can be used to target specific structural elements in EF-Tu to redesign the thermodynamic landscape. These findings demonstrate how, through evolution, EF-Tu has fine-tuned the structural and dynamic features that define nucleotide binding, providing insight into how altering these properties could be exploited for protein engineering.
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Affiliation(s)
- Dylan Girodat
- Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry and Biochemistry , University of Lethbridge , 4401 University Drive West , Lethbridge , Alberta T1K 3M4 , Canada
| | - Evan Mercier
- Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry and Biochemistry , University of Lethbridge , 4401 University Drive West , Lethbridge , Alberta T1K 3M4 , Canada
| | - Katherine E Gzyl
- Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry and Biochemistry , University of Lethbridge , 4401 University Drive West , Lethbridge , Alberta T1K 3M4 , Canada
| | - Hans-Joachim Wieden
- Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry and Biochemistry , University of Lethbridge , 4401 University Drive West , Lethbridge , Alberta T1K 3M4 , Canada
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19
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Lant JT, Berg MD, Heinemann IU, Brandl CJ, O'Donoghue P. Pathways to disease from natural variations in human cytoplasmic tRNAs. J Biol Chem 2019; 294:5294-5308. [PMID: 30643023 DOI: 10.1074/jbc.rev118.002982] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Perfectly accurate translation of mRNA into protein is not a prerequisite for life. Resulting from errors in protein synthesis, mistranslation occurs in all cells, including human cells. The human genome encodes >600 tRNA genes, providing both the raw material for genetic variation and a buffer to ensure that resulting translation errors occur at tolerable levels. On the basis of data from the 1000 Genomes Project, we highlight the unanticipated prevalence of mistranslating tRNA variants in the human population and review studies on synthetic and natural tRNA mutations that cause mistranslation or de-regulate protein synthesis. Although mitochondrial tRNA variants are well known to drive human diseases, including developmental disorders, few studies have revealed a role for human cytoplasmic tRNA mutants in disease. In the context of the unexpectedly large number of tRNA variants in the human population, the emerging literature suggests that human diseases may be affected by natural tRNA variants that cause mistranslation or de-regulate tRNA expression and nucleotide modification. This review highlights examples relevant to genetic disorders, cancer, and neurodegeneration in which cytoplasmic tRNA variants directly cause or exacerbate disease and disease-linked phenotypes in cells, animal models, and humans. In the near future, tRNAs may be recognized as useful genetic markers to predict the onset or severity of human disease.
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Affiliation(s)
| | | | | | | | - Patrick O'Donoghue
- From the Departments of Biochemistry and .,Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
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20
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Neuwald AF, Aravind L, Altschul SF. Inferring joint sequence-structural determinants of protein functional specificity. eLife 2018; 7. [PMID: 29336305 PMCID: PMC5770160 DOI: 10.7554/elife.29880] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 12/22/2017] [Indexed: 01/05/2023] Open
Abstract
Residues responsible for allostery, cooperativity, and other subtle but functionally important interactions remain difficult to detect. To aid such detection, we employ statistical inference based on the assumption that residues distinguishing a protein subgroup from evolutionarily divergent subgroups often constitute an interacting functional network. We identify such networks with the aid of two measures of statistical significance. One measure aids identification of divergent subgroups based on distinguishing residue patterns. For each subgroup, a second measure identifies structural interactions involving pattern residues. Such interactions are derived either from atomic coordinates or from Direct Coupling Analysis scores, used as surrogates for structural distances. Applying this approach to N-acetyltransferases, P-loop GTPases, RNA helicases, synaptojanin-superfamily phosphatases and nucleases, and thymine/uracil DNA glycosylases yielded results congruent with biochemical understanding of these proteins, and also revealed striking sequence-structural features overlooked by other methods. These and similar analyses can aid the design of drugs targeting allosteric sites.
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Affiliation(s)
- Andrew F Neuwald
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, United States.,Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, United States
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - Stephen F Altschul
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
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21
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Prezioso SM, Brown NE, Goldberg JB. Elfamycins: inhibitors of elongation factor-Tu. Mol Microbiol 2017; 106:22-34. [PMID: 28710887 DOI: 10.1111/mmi.13750] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2017] [Indexed: 01/26/2023]
Abstract
Elfamycins are a relatively understudied group of antibiotics that target the essential process of translation through impairment of EF-Tu function. For the most part, the utility of these compounds has been as laboratory tools for the study of EF-Tu and the ribosome, as their poor pharmacokinetic profile and solubility has prevented implementation as therapeutic agents. However, due to the slowing of the antibiotic pipeline and the rapid emergence of resistance to approved antibiotics, this group is being reconsidered. Some researchers are using screens for novel naturally produced variants, while others are making directed, systematic chemical improvements on publically disclosed compounds. As an example of the latter approach, a GE2270 A derivative, LFF571, has completed phase 2 clinical trials, thus demonstrating the potential for elfamycins to become more prominent antibiotics in the future.
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Affiliation(s)
- Samantha M Prezioso
- Microbiology and Molecular Genetics Program, Graduate Division of Biological and Biomedical Sciences, Emory University School of Medicine, Atlanta, GA 30322, USA.,Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis and Sleep, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Nicole E Brown
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Joanna B Goldberg
- Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis and Sleep, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA.,Emory+Children's Center for Cystic Fibrosis and Airway Disease Research, Emory University School of Medicine, Atlanta, GA 30322, USA
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22
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Masschelein J, Jenner M, Challis GL. Antibiotics from Gram-negative bacteria: a comprehensive overview and selected biosynthetic highlights. Nat Prod Rep 2017. [PMID: 28650032 DOI: 10.1039/c7np00010c] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: up to 2017The overwhelming majority of antibiotics in clinical use originate from Gram-positive Actinobacteria. In recent years, however, Gram-negative bacteria have become increasingly recognised as a rich yet underexplored source of novel antimicrobials, with the potential to combat the looming health threat posed by antibiotic resistance. In this article, we have compiled a comprehensive list of natural products with antimicrobial activity from Gram-negative bacteria, including information on their biosynthetic origin(s) and molecular target(s), where known. We also provide a detailed discussion of several unusual pathways for antibiotic biosynthesis in Gram-negative bacteria, serving to highlight the exceptional biocatalytic repertoire of this group of microorganisms.
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Affiliation(s)
- J Masschelein
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| | - M Jenner
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| | - G L Challis
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
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23
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Mistranslation: from adaptations to applications. Biochim Biophys Acta Gen Subj 2017; 1861:3070-3080. [PMID: 28153753 DOI: 10.1016/j.bbagen.2017.01.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/23/2017] [Accepted: 01/24/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND The conservation of the genetic code indicates that there was a single origin, but like all genetic material, the cell's interpretation of the code is subject to evolutionary pressure. Single nucleotide variations in tRNA sequences can modulate codon assignments by altering codon-anticodon pairing or tRNA charging. Either can increase translation errors and even change the code. The frozen accident hypothesis argued that changes to the code would destabilize the proteome and reduce fitness. In studies of model organisms, mistranslation often acts as an adaptive response. These studies reveal evolutionary conserved mechanisms to maintain proteostasis even during high rates of mistranslation. SCOPE OF REVIEW This review discusses the evolutionary basis of altered genetic codes, how mistranslation is identified, and how deviations to the genetic code are exploited. We revisit early discoveries of genetic code deviations and provide examples of adaptive mistranslation events in nature. Lastly, we highlight innovations in synthetic biology to expand the genetic code. MAJOR CONCLUSIONS The genetic code is still evolving. Mistranslation increases proteomic diversity that enables cells to survive stress conditions or suppress a deleterious allele. Genetic code variants have been identified by genome and metagenome sequence analyses, suppressor genetics, and biochemical characterization. GENERAL SIGNIFICANCE Understanding the mechanisms of translation and genetic code deviations enables the design of new codes to produce novel proteins. Engineering the translation machinery and expanding the genetic code to incorporate non-canonical amino acids are valuable tools in synthetic biology that are impacting biomedical research. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.
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24
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Créchet JB, Malosse C, Hountondji C. EF-Tu from the enacyloxin producing Frateuria W-315 strain: Structure/activity relationship and antibiotic resistance. Biochimie 2016; 127:59-69. [PMID: 27126073 DOI: 10.1016/j.biochi.2016.04.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 04/20/2016] [Indexed: 10/21/2022]
Abstract
In this report, we have demonstrated that the poly(U)-dependent poly(Phe) synthesis activity of elongator factor Tu (EF-Tu) from the enacyloxin producing strain Frateuria sp. W-315 is inhibited by the antibiotic similarly to that of Escherichia coli EF-Tu. The inhibitory effect of enacyloxin observed in a purified system was the same as that obtained with an S30 extract from E. coli or Frateuria sp. W-315, respectively, suggesting that antibiotic resistance of enacyloxin producing Frateuria sp. W-315 is not due neither to EF-Tu nor to other components of the translation machinery but to a still unknown mechanism. The EF-Tu gene, as PCR amplified from Frateuria W-315 genomic DNA and sequenced represented an ORF of 1191 nucleotides corresponding to 396 amino acids. This protein is larger than the product of tufA from E. coli by only two amino acid residues. Alignment of the amino acid sequence of EF-Tu from E. coli with those of Frateuria and Ralstonia solanacearum indicates on average 80% identical amino acid residues and 9.7% conservative replacements between EF-Tu Frateuria and EF-Tu E. coli, on one hand, and 97% identity and 1.7% conservative replacement between EF-Tu Frateuria and EF-Tu Ralstonia solanacearum, on the other hand. These strong primary structure similarities between EF-Tu from different origins are consistent with the fact that this factor is essential for the translation process in all kingdoms of life. Comparison of the effects of antibiotics on EF-Tu Frateuria and EF-Tu E. coli revealed that enacyloxin, kirromycin and pulvomycin exert a stronger stimulation of the GDP dissociation rate on EF-Tu Frateuria, while the effects of the antibiotics on the GDP association rate were comparable for the two EF-Tu species. Different mutants of EF-Tu E. coli were constructed with the help of site directed mutagenesis by changing one or several residues of EF-Tu E. coli by the corresponding residues of EF-Tu Frateuria. The single A45K substitution did not modify the intrinsic GTPase activity of EF-Tu E. coli. In contrast, a 2-3 fold stimulation of the intrinsic GTPase activity was observed with the single A42E, F46Y, Q48E and the double F46Y/Q48E substitution. Finally, up to a 7 fold stimulation was observed with the quadruple substitution (mutant A42E/A45K/F46Y/Q48E.
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Affiliation(s)
| | - Christian Malosse
- Institut Pasteur, Département de Biologie Structurale et Chimie, Unité Spectrométrie de Masse Structurale et Protéomique, CNRS UMR 3528, 28 rue du Dr Roux, 75724 PARIS Cedex 15 France
| | - Codjo Hountondji
- Sorbonne Universités UPMC Univ Paris 06, Unité de Recherche UPMC UR6 "Enzymologie de l'ARN", 4, Place Jussieu, F-75252 Paris Cedex 05, France
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25
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Helfrich EJN, Piel J. Biosynthesis of polyketides by trans-AT polyketide synthases. Nat Prod Rep 2016; 33:231-316. [DOI: 10.1039/c5np00125k] [Citation(s) in RCA: 230] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This review discusses the biosynthesis of natural products that are generated bytrans-AT polyketide synthases, a family of catalytically versatile enzymes that represents one of the major group of proteins involved in the production of bioactive polyketides.
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Affiliation(s)
- Eric J. N. Helfrich
- Institute of Microbiology
- Eidgenössische Technische Hochschule (ETH) Zurich
- 8093 Zurich
- Switzerland
| | - Jörn Piel
- Institute of Microbiology
- Eidgenössische Technische Hochschule (ETH) Zurich
- 8093 Zurich
- Switzerland
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26
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Saito A, Igarashi W, Furukawa H, Hoshikawa H, Yamada T, Kuwahara S, Kiyota H. Synthetic Studies of Enacyloxins: A Series of Antibiotics Isolated from Frateuria sp. W-315: C1′-C8′ and C9′-C15′ Fragments. Nat Prod Commun 2015. [DOI: 10.1177/1934578x1501000429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Synthetic studies of enacyloxins (ENXs), a series of yellow-colored, polyene-polyol antibiotics produced by Frateuria sp. W-315, are described. The C1′-C8′ polyene fragments were prepared using successive Wittig reactions. The C9′-C15′ and C10′-C15′ fragments were constructed from ( S)-isopropylideneglyceraldehyde using Yamaguchi's nucleophilic substitution reaction of acetylide to epoxide, and/or Marshall's allenylindium mediated reaction as the key steps.
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Affiliation(s)
- Aki Saito
- Graduate School of Agricultural Science, Tohoku University, Sendai 981-8555, Japan
| | - Wataru Igarashi
- Graduate School of Agricultural Science, Tohoku University, Sendai 981-8555, Japan
| | - Hiroyuki Furukawa
- Graduate School of Agricultural Science, Tohoku University, Sendai 981-8555, Japan
| | - Hiroki Hoshikawa
- Graduate School of Agricultural Science, Tohoku University, Sendai 981-8555, Japan
| | - Teiko Yamada
- Graduate School of Agricultural Science, Tohoku University, Sendai 981-8555, Japan
| | - Shigefumi Kuwahara
- Graduate School of Agricultural Science, Tohoku University, Sendai 981-8555, Japan
| | - Hiromasa Kiyota
- Graduate School of Environmental & Life Sciences, Okayama University, Okayama 700-8530, Japan
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27
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Yanagisawa T, Ishii R, Hikida Y, Fukunaga R, Sengoku T, Sekine SI, Yokoyama S. A SelB/EF-Tu/aIF2γ-like protein from Methanosarcina mazei in the GTP-bound form binds cysteinyl-tRNA(Cys.). JOURNAL OF STRUCTURAL AND FUNCTIONAL GENOMICS 2015; 16:25-41. [PMID: 25618148 PMCID: PMC4329189 DOI: 10.1007/s10969-015-9193-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 01/10/2015] [Indexed: 11/15/2022]
Abstract
The putative translation elongation factor Mbar_A0971 from the methanogenic archaeon Methanosarcina barkeri was proposed to be the pyrrolysine-specific paralogue of EF-Tu ("EF-Pyl"). In the present study, the crystal structures of its homologue from Methanosarcina mazei (MM1309) were determined in the GMPPNP-bound, GDP-bound, and apo forms, by the single-wavelength anomalous dispersion phasing method. The three MM1309 structures are quite similar (r.m.s.d. < 0.1 Å). The three domains, corresponding to domains 1, 2, and 3 of EF-Tu/SelB/aIF2γ, are packed against one another to form a closed architecture. The MM1309 structures resemble those of bacterial/archaeal SelB, bacterial EF-Tu in the GTP-bound form, and archaeal initiation factor aIF2γ, in this order. The GMPPNP and GDP molecules are visible in their co-crystal structures. Isothermal titration calorimetry measurements of MM1309·GTP·Mg(2+), MM1309·GDP·Mg(2+), and MM1309·GMPPNP·Mg(2+) provided dissociation constants of 0.43, 26.2, and 222.2 μM, respectively. Therefore, the affinities of MM1309 for GTP and GDP are similar to those of SelB rather than those of EF-Tu. Furthermore, the switch I and II regions of MM1309 are involved in domain-domain interactions, rather than nucleotide binding. The putative binding pocket for the aminoacyl moiety on MM1309 is too small to accommodate the pyrrolysyl moiety, based on a comparison of the present MM1309 structures with that of the EF-Tu·GMPPNP·aminoacyl-tRNA ternary complex. A hydrolysis protection assay revealed that MM1309 binds cysteinyl (Cys)-tRNA(Cys) and protects the aminoacyl bond from non-enzymatic hydrolysis. Therefore, we propose that MM1309 functions as either a guardian protein that protects the Cys moiety from oxidation or an alternative translation factor for Cys-tRNA(Cys).
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Affiliation(s)
- Tatsuo Yanagisawa
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
- RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
| | - Ryohei Ishii
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Yasushi Hikida
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
- RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Ryuya Fukunaga
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
- Present Address: Department of Biochemistry, School of Medicine, Johns Hopkins University, 725 N. Wolfe Street, 521A Physiology Bldg., Baltimore, MD 21205 USA
| | - Toru Sengoku
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
- RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Shun-ichi Sekine
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
- RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Shigeyuki Yokoyama
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
- RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
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28
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Abstract
Transfer RNAs (tRNAs) are central players in the protein translation machinery and as such are prominent targets for a large number of natural and synthetic antibiotics. This review focuses on the role of tRNAs in bacterial antibiosis. We will discuss examples of antibiotics that target multiple stages in tRNA biology from tRNA biogenesis and modification, mature tRNAs, aminoacylation of tRNA as well as prevention of proper tRNA function by small molecules binding to the ribosome. Finally, the role of deacylated tRNAs in the bacterial “stringent response” mechanism that can lead to bacteria displaying antibiotic persistence phenotypes will be discussed.
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Ross C, Opel V, Scherlach K, Hertweck C. Biosynthesis of antifungal and antibacterial polyketides byBurkholderia gladioliin coculture withRhizopus microsporus. Mycoses 2014; 57 Suppl 3:48-55. [DOI: 10.1111/myc.12246] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 03/03/2014] [Accepted: 03/14/2014] [Indexed: 12/17/2022]
Affiliation(s)
- Claudia Ross
- Leibniz Institute for Natural Product Research and Infection Biology; Hans Knöll Institute (HKI); Jena Germany
| | - Viktoria Opel
- Leibniz Institute for Natural Product Research and Infection Biology; Hans Knöll Institute (HKI); Jena Germany
| | - Kirstin Scherlach
- Leibniz Institute for Natural Product Research and Infection Biology; Hans Knöll Institute (HKI); Jena Germany
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology; Hans Knöll Institute (HKI); Jena Germany
- Friedrich Schiller University; Jena Germany
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30
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Scotti JS, Leung IKH, Ge W, Bentley MA, Paps J, Kramer HB, Lee J, Aik W, Choi H, Paulsen SM, Bowman LAH, Loik ND, Horita S, Ho CH, Kershaw NJ, Tang CM, Claridge TDW, Preston GM, McDonough MA, Schofield CJ. Human oxygen sensing may have origins in prokaryotic elongation factor Tu prolyl-hydroxylation. Proc Natl Acad Sci U S A 2014; 111:13331-6. [PMID: 25197067 PMCID: PMC4169948 DOI: 10.1073/pnas.1409916111] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The roles of 2-oxoglutarate (2OG)-dependent prolyl-hydroxylases in eukaryotes include collagen stabilization, hypoxia sensing, and translational regulation. The hypoxia-inducible factor (HIF) sensing system is conserved in animals, but not in other organisms. However, bioinformatics imply that 2OG-dependent prolyl-hydroxylases (PHDs) homologous to those acting as sensing components for the HIF system in animals occur in prokaryotes. We report cellular, biochemical, and crystallographic analyses revealing that Pseudomonas prolyl-hydroxylase domain containing protein (PPHD) contain a 2OG oxygenase related in structure and function to the animal PHDs. A Pseudomonas aeruginosa PPHD knockout mutant displays impaired growth in the presence of iron chelators and increased production of the virulence factor pyocyanin. We identify elongation factor Tu (EF-Tu) as a PPHD substrate, which undergoes prolyl-4-hydroxylation on its switch I loop. A crystal structure of PPHD reveals striking similarity to human PHD2 and a Chlamydomonas reinhardtii prolyl-4-hydroxylase. A crystal structure of PPHD complexed with intact EF-Tu reveals that major conformational changes occur in both PPHD and EF-Tu, including a >20-Å movement of the EF-Tu switch I loop. Comparison of the PPHD structures with those of HIF and collagen PHDs reveals conservation in substrate recognition despite diverse biological roles and origins. The observed changes will be useful in designing new types of 2OG oxygenase inhibitors based on various conformational states, rather than active site iron chelators, which make up most reported 2OG oxygenase inhibitors. Structurally informed phylogenetic analyses suggest that the role of prolyl-hydroxylation in human hypoxia sensing has ancient origins.
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Affiliation(s)
- John S Scotti
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Ivanhoe K H Leung
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Wei Ge
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom; Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Michael A Bentley
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Jordi Paps
- Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom
| | - Holger B Kramer
- Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom; and
| | - Joongoo Lee
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - WeiShen Aik
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Hwanho Choi
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Steinar M Paulsen
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Lesley A H Bowman
- Department of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Nikita D Loik
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Shoichiro Horita
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom; Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom; and
| | - Chia-hua Ho
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Nadia J Kershaw
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Christoph M Tang
- Department of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Timothy D W Claridge
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Gail M Preston
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Michael A McDonough
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom;
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31
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Saito A, Igarashi W, Furukawa H, Yamada T, Kuwahara S, Kiyota H. Facile synthesis of the cyclohexane fragment of enacloxins, a series of antibiotics isolated from Frateuria sp. W-315. Biosci Biotechnol Biochem 2014; 78:766-9. [PMID: 25035977 DOI: 10.1080/09168451.2014.905192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
An efficient and good yield synthesis of the cyclohexane moiety of enacyloxins, a series of antibiotics isolated from Frateuria sp. W-315, was achieved from d-quinic acid using a successive Barton-McCombie deoxygenation.
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Affiliation(s)
- Aki Saito
- a Graduate School of Agricultural Science , Tohoku University , Aoba-ku , Japan
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32
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Fabbretti A, Giuliodori AM. Inhibitors of Bacterial Elongation Factor EF-Tu. Antibiotics (Basel) 2013. [DOI: 10.1002/9783527659685.ch18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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33
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Gross S, Nguyen F, Bierschenk M, Sohmen D, Menzel T, Antes I, Wilson DN, Bach T. Amythiamicin D and related thiopeptides as inhibitors of the bacterial elongation factor EF-Tu: modification of the amino acid at carbon atom C2 of ring C dramatically influences activity. ChemMedChem 2013; 8:1954-62. [PMID: 24106106 DOI: 10.1002/cmdc.201300323] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Indexed: 11/12/2022]
Abstract
Three analogues of amythiamicin D, which differ in the substitution pattern at the methine group adjacent to C2 of the thiazole ring C, were prepared by de novo total synthesis. In amythiamicin D, this carbon atom is (S)-isopropyl substituted. Two of the new analogues carry a hydroxymethyl in place of the isopropyl group, one at an S- (compound 3 a) and the other at an R-configured stereogenic center (3 b). The third analogue, 3 c, contains a benzyloxymethyl group at an S-configured stereogenic center. Compounds 3 b and 3 c showed no inhibitory effect toward various bacterial strains, nor did they influence the translation of firefly luciferase. In stark contrast, compound 3 a inhibited the growth of Gram-positive bacteria Staphylococcus aureus (strains NCTC and Mu50) and Listeria monocytogenes EGD. In the firefly luciferase assay it proved more potent than amythiamicin D, and rescue experiments provided evidence that translation inhibition is due to binding to the bacterial elongation factor Tu (EF-Tu). The results were rationalized by structural investigations and by molecular dynamics simulations of the free compounds in solution and bound to the EF-Tu binding site. The low affinity of compound 3 b was attributed to the absence of a critical hydrogen bond, which stabilizes the conformation required for binding to EF-Tu. Compound 3 c was shown not to comply with the binding properties of the binding site.
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Affiliation(s)
- Stefan Gross
- Lehrstuhl für Organische Chemie I, Technische Universität München, Lichtenbergstr. 4, 85747 Garching (Germany)
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34
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Grøftehauge MK, Therkelsen MØ, Taaning R, Skrydstrup T, Morth JP, Nissen P. Identifying ligand-binding hot spots in proteins using brominated fragments. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1060-5. [PMID: 23989163 PMCID: PMC3758163 DOI: 10.1107/s1744309113018551] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 07/04/2013] [Indexed: 11/10/2022]
Abstract
High-quality crystals of Thermus thermophilus EF-Tu in the GTP-bound conformation at 1.7-2.7 Å resolution were used to test 18 small organic molecules, all brominated for confident identification in the anomalous difference maps. From this relatively small collection, it was possible to identify a small molecule bound in the functionally important tRNA CCA-end binding pocket. The antibiotic GE2270 A is known to interact with the same pocket in EF-Tu and to disrupt the association with tRNA. Bromide could be located from peaks in the anomalous map in data truncated to very low resolution without refining the structure. Considering the speed with which diffraction data can be collected today, it is proposed that it is worthwhile to collect the extra data from fragment screens while crystals are at hand to increase the knowledge of biological function and drug binding in an experimental structural context.
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Affiliation(s)
| | - Martin Ø. Therkelsen
- Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark
| | - Rolf Taaning
- Center for Insoluble Protein Structures (inSPIN), Department of Chemistry and the Interdisciplinary Nanoscience Center, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Troels Skrydstrup
- Center for Insoluble Protein Structures (inSPIN), Department of Chemistry and the Interdisciplinary Nanoscience Center, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - J. Preben Morth
- Centre for Molecular Medicine Norway, University of Oslo, Forskningsparken, 0349 Oslo, Norway
| | - Poul Nissen
- Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark
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35
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Bavi RS, Sambhare SB, Sonawane KD. MD simulation studies to investigate iso-energetic conformational behaviour of modified nucleosides m(2)G and m(2) 2G present in tRNA. Comput Struct Biotechnol J 2013; 5:e201302015. [PMID: 24688708 PMCID: PMC3962230 DOI: 10.5936/csbj.201302015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 05/16/2013] [Accepted: 05/19/2013] [Indexed: 11/28/2022] Open
Abstract
Modified nucleic acid bases are most commonly found in tRNA. These may contain modifications from simple methylation to addition of bulky groups. Methylation of the four canonical nucleotide bases at a wide variety of positions is particularly prominent among the known modification. Methylation of N2 group of guanine is a relatively common modification in tRNA and rRNA. N2-methylguanosine (m2G) is the second most often encountered nucleoside in E. coli tRNAs. N2, N2- dimethylguanosine (m22G) is found in the majority of eukaryotic tRNAs and involved in forming base pair interactions with adjacent bases. Hence, in order to understand the structural significance of these methylated nucleic acid bases we have carried out molecular dynamics simulation to see the salvation effect. The results obtained shows iso-energetic conformational behaviors for m2G and m22G. The simulation trajectory of m2G shows regular periodical fluctuations suggesting that m2G is equally stable as either s-cis or s-trans rotamers. The two rotamers of m2G may interact canonically or non-canonically with opposite base as s-trans m2G26:C/A/U44 and s-cis m2G26:A/U44. The free rotations around the C-N bond could be the possible reason for these iso-energetic conformations. Dimethylation of G has almost no influence on base pairing with either A or U. Thus, these results reveal that modified nucleosides m2G and m22G may play an important role to prevent tRNA from adopting the unusual mitochondrial like conformation.
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Affiliation(s)
- Rohit S Bavi
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur 416 004, Maharashtra, India
| | - Susmit B Sambhare
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur 416 004, Maharashtra, India
| | - Kailas D Sonawane
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur 416 004, Maharashtra, India ; Department of Microbiology, Shivaji University, Kolhapur 416 004, Maharashtra, India
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36
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Kumbhar NM, Kumbhar BV, Sonawane KD. Structural significance of hypermodified nucleic acid base hydroxywybutine (OHyW) which occur at 37th position in the anticodon loop of yeast tRNA(Phe). J Mol Graph Model 2012; 38:174-85. [PMID: 23073221 DOI: 10.1016/j.jmgm.2012.07.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 07/18/2012] [Accepted: 07/20/2012] [Indexed: 10/28/2022]
Abstract
Conformational preferences of hypermodified nucleic acid base hydroxywybutine (OHyW) have been studied using quantum chemical single point semi-empirical PM3 method. Automated geometry optimization using semi-empirical RM1, molecular mechanics force field (MMFF) along with ab-initio HF-SCF (6-31G** basis set) and DFT (B3LYP/6-31G** basis set) calculations have also been made to compare the salient features. Molecular electrostatic potentials (MEPs) depict the polarities of hydroxywybutine (OHyW) side chain. Another conformational study showed that hydroxywybutosine side chain interacts with adjacent bases within the anticodon loop of tRNA(Phe). The solvent accessible surface area (SASA) calculations revealed the structural role of hydroxywybutine in anticodon loop. Explicit molecular dynamics (MD) simulation has been done over the PM3 most stable structure of OHyW. The hydroxywybutine side chain prefers 'distal' conformation i.e. spreads away from the cyclic five membered imidazole moiety of modified tricyclic guanine base. The predicted preferred conformation of hydroxywybutine may prevent extended Watson-Crick base pairing during protein biosynthesis process. This conformation of OHyW stabilized by intramolecular interactions between O(6)⋯HO(16), O(6)⋯HC(15) and O(20)⋯HC(17). Further stabilization is also expected from interactions between O(22)⋯HC(16) and O(23)⋯HC(15). Explicit molecular dynamics (MD) simulation over the PM3 most stable structure of OHyW support the preferred geometry by preserving the 'distal' orientation of hydroxywybutine side chain and intramolecular hydrogen bonding interactions. MD simulation study revealed the role of hydroxyl group of OHyW to avoid fluctuations and prevent multiple iso-energetic conformations of hydroxywybutine side chain as compared to wybutine (yW).
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Affiliation(s)
- Navanath M Kumbhar
- Department of Biotechnology, Shivaji University, Kolhapur 416004, Maharashtra-MS, India
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37
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Kavaliauskas D, Nissen P, Knudsen CR. The busiest of all ribosomal assistants: elongation factor Tu. Biochemistry 2012; 51:2642-51. [PMID: 22409271 DOI: 10.1021/bi300077s] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
During translation, the nucleic acid language employed by genes is translated into the amino acid language used by proteins. The translator is the ribosome, while the dictionary employed is known as the genetic code. The genetic information is presented to the ribosome in the form of a mRNA, and tRNAs connect the two languages. Translation takes place in three steps: initiation, elongation, and termination. After a protein has been synthesized, the components of the translation apparatus are recycled. During each phase of translation, the ribosome collaborates with specific translation factors, which secure a proper balance between speed and fidelity. Notably, initiation, termination, and ribosomal recycling occur only once per protein produced during normal translation, while the elongation step is repeated a large number of times, corresponding to the number of amino acids constituting the protein of interest. In bacteria, elongation factor Tu plays a central role during the selection of the correct amino acids throughout the elongation phase of translation. Elongation factor Tu is the main subject of this review.
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Affiliation(s)
- Darius Kavaliauskas
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark
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38
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Conformational preferences of modified nucleoside N(2)-methylguanosine (m(2)G) and its derivative N(2), N(2)-dimethylguanosine (m(2)(2)G) occur at 26th position (hinge region) in tRNA. Cell Biochem Biophys 2012; 61:507-21. [PMID: 21735129 DOI: 10.1007/s12013-011-9233-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Conformational preferences of the modified nucleosides N(2)-methylguanosine (m(2)G) and N(2), N(2)-dimethylguanosine (m(2)(2)G) have been studied theoretically by using quantum chemical perturbative configuration interaction with localized orbitals (PCILO) method. Automated complete geometry optimization using semiempirical quantum chemical RM1, along with ab initio molecular orbital Hartree-Fock (HF-SCF), and density functional theory (DFT) calculations has also been made to compare the salient features. Single-point energy calculation studies have been made on various models of m(2)G26:C/A/U44 and m(2)(2)G26:C/A/U44. The glycosyl torsion angle prefers "syn" (χ = 286°) conformation for m(2)G and m(2)(2)G molecules. These conformations are stabilized by N(3)-HC2' and N(3)-HC3' by replacing weak interaction between O5'-HC(8). The N(2)-methyl substituent of (m(2)G26) prefers "proximal" or s-trans conformation. It may also prefer "distal" or s-cis conformation that allows base pairing with A/U44 instead of C at the hinge region. Thus, N(2)-methyl group of m(2)G may have energetically two stable s-trans m(2)G:C/A/U or s-cis m(2)G:A/U rotamers. This could be because of free rotations around C-N bond. Similarly, N(2), N(2)-dimethyl substituent of (m(2)(2)G) prefers "distal" conformation that may allow base pairing with A/U instead of C at 44th position. Such orientations of m(2)G and m(2)(2)G could play an important role in base-stacking interactions at the hinge region of tRNA during protein biosynthesis process.
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Enacyloxins Are Products of an Unusual Hybrid Modular Polyketide Synthase Encoded by a Cryptic Burkholderia ambifaria Genomic Island. ACTA ACUST UNITED AC 2011; 18:665-77. [DOI: 10.1016/j.chembiol.2011.01.020] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Revised: 01/24/2011] [Accepted: 01/26/2011] [Indexed: 11/22/2022]
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40
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Berisio R, Ruggiero A, Vitagliano L. Elongation Factors EFIA and EF-Tu: Their Role in Translation and Beyond. Isr J Chem 2010. [DOI: 10.1002/ijch.201000005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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41
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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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42
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Schuette JC, Murphy FV, Kelley AC, Weir JR, Giesebrecht J, Connell SR, Loerke J, Mielke T, Zhang W, Penczek PA, Ramakrishnan V, Spahn CMT. GTPase activation of elongation factor EF-Tu by the ribosome during decoding. EMBO J 2009; 28:755-65. [PMID: 19229291 PMCID: PMC2666022 DOI: 10.1038/emboj.2009.26] [Citation(s) in RCA: 162] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2008] [Accepted: 01/14/2009] [Indexed: 11/09/2022] Open
Abstract
We have used single-particle reconstruction in cryo-electron microscopy to determine a structure of the Thermus thermophilus ribosome in which the ternary complex of elongation factor Tu (EF-Tu), tRNA and guanine nucleotide has been trapped on the ribosome using the antibiotic kirromycin. This represents the state in the decoding process just after codon recognition by tRNA and the resulting GTP hydrolysis by EF-Tu, but before the release of EF-Tu from the ribosome. Progress in sample purification and image processing made it possible to reach a resolution of 6.4 A. Secondary structure elements in tRNA, EF-Tu and the ribosome, and even GDP and kirromycin, could all be visualized directly. The structure reveals a complex conformational rearrangement of the tRNA in the A/T state and the interactions with the functionally important switch regions of EF-Tu crucial to GTP hydrolysis. Thus, the structure provides insights into the molecular mechanism of signalling codon recognition from the decoding centre of the 30S subunit to the GTPase centre of EF-Tu.
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Affiliation(s)
- Jan-Christian Schuette
- Institut für Medizinische Physik und Biophysik, Charite-Universitätsmedizin Berlin, Berlin, Germany
| | - Frank V Murphy
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Ann C Kelley
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - John R Weir
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Jan Giesebrecht
- Institut für Medizinische Physik und Biophysik, Charite-Universitätsmedizin Berlin, Berlin, Germany
| | - Sean R Connell
- Institut für Medizinische Physik und Biophysik, Charite-Universitätsmedizin Berlin, Berlin, Germany
| | - Justus Loerke
- UltraStrukturNetzwerk, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Thorsten Mielke
- UltraStrukturNetzwerk, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Wei Zhang
- Department of Biochemistry and Molecular Biology, The University of Texas—Houston Medical School, Houston, TX, USA
| | - Pawel A Penczek
- Department of Biochemistry and Molecular Biology, The University of Texas—Houston Medical School, Houston, TX, USA
| | - V Ramakrishnan
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Christian M T Spahn
- Institut für Medizinische Physik und Biophysik, Charite-Universitätsmedizin Berlin, Berlin, Germany
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Furukawa H, Kiyota H, Yamada T, Yaosaka M, Takeuchi R, Watanabe T, Kuwahara S. Stereochemistry of Enacyloxins. Part 4. Chem Biodivers 2007; 4:1601-4. [PMID: 17638342 DOI: 10.1002/cbdv.200790140] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The absolute configurations of the enacyloxins, a series of polyhydroxylated polyene antibiotics from Frateuria species, were determined. The so far elusive (13'R,14'R,15'S)-configuration was assigned to enacycloxin IVa (1) by means of 'J-resolved HMBC-1' and NOESY NMR methods.
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Affiliation(s)
- Hiroyuki Furukawa
- Laboratory of Applied Bioorganic Chemistry, Division of Life Science, Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiya, Aoba-ku, Sendai 981-8555, Japan
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44
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Olsthoorn-Tieleman LN, Palstra RJTS, van Wezel GP, Bibb MJ, Pleij CWA. Elongation factor Tu3 (EF-Tu3) from the kirromycin producer Streptomyces ramocissimus Is resistant to three classes of EF-Tu-specific inhibitors. J Bacteriol 2007; 189:3581-90. [PMID: 17337575 PMCID: PMC1855904 DOI: 10.1128/jb.01810-06] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2006] [Accepted: 02/21/2007] [Indexed: 11/20/2022] Open
Abstract
The antibiotic kirromycin inhibits prokaryotic protein synthesis by immobilizing elongation factor Tu (EF-Tu) on the elongating ribosome. Streptomyces ramocissimus, the producer of kirromycin, contains three tuf genes. While tuf1 and tuf2 encode kirromycin-sensitive EF-Tu species, the function of tuf3 is unknown. Here we demonstrate that EF-Tu3, in contrast to EF-Tu1 and EF-Tu2, is resistant to three classes of EF-Tu-targeted antibiotics: kirromycin, pulvomycin, and GE2270A. A mixture of EF-Tu1 and EF-Tu3 was sensitive to kirromycin and resistant to GE2270A, in agreement with the described modes of action of these antibiotics. Transcription of tuf3 was observed during exponential growth and ceased upon entry into stationary phase and therefore did not correlate with the appearance of kirromycin in stationary phase; thus, it is unlikely that EF-Tu3 functions as a resistant alternative for EF-Tu1. EF-Tu3 from Streptomyces coelicolor A3(2) was also resistant to kirromycin and GE2270A, suggesting that multiple antibiotic resistance is an intrinsic feature of EF-Tu3 species. The GE2270A-resistant character of EF-Tu3 demonstrated that this divergent elongation factor is capable of substituting for EF-Tu1 in vivo.
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Kondrashov FA, Gurbich TA, Vlasov PK. Selection for functional uniformity of tuf duplicates in gamma-proteobacteria. Trends Genet 2007; 23:215-8. [PMID: 17383049 DOI: 10.1016/j.tig.2007.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2006] [Revised: 02/14/2007] [Accepted: 03/07/2007] [Indexed: 10/23/2022]
Abstract
Having an extra copy of a gene is thought to provide some functional redundancy, which results in a higher rate of evolution in duplicated genes. In this article, we estimate the impact of gene duplication on the selection of tuf paralogs, and we find that in the absence of gene conversion, tuf paralogs have evolved significantly slower than when gene conversion has been a factor in their evolution. Thus, tuf gene copies evolve under a selective pressure that ensures their functional uniformity, and gene conversion reduces selection against amino acid substitutions that affect the function of the encoded protein, EF-Tu.
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Affiliation(s)
- Fyodor A Kondrashov
- Section on Ecology, Behavior and Evolution, Division of Biological Sciences, University of California at San Diego, 2218 Muir Biology Building, La Jolla, CA 92093, USA.
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Jonák J. Bacterial elongation factors EF-Tu, their mutants, chimeric forms, and domains: isolation and purification. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 849:141-53. [PMID: 17197255 DOI: 10.1016/j.jchromb.2006.11.053] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2006] [Revised: 11/14/2006] [Accepted: 11/20/2006] [Indexed: 11/24/2022]
Abstract
Prokaryotic elongation factors EF-Tu form a family of homologous, three-domain molecular switches catalyzing the binding of aminoacyl-tRNAs to ribosomes during the process of mRNA translation. They are GTP-binding proteins, or GTPases. Binding of GTP or GDP regulates their conformation and thus their activity. Because of their particular structure and regulation, various activities (also outside of the translation system) and a relative abundance they represent attractive tools for studies of many basic but still not fully understood mechanisms both of the translation process, the structure-function relationships in EF-Tu molecules themselves and proteins and energy transduction mechanisms in general. The review critically summarizes procedures for the isolation and purification of native and engineered eubacterial elongation factors EF-Tu and their mutants on a large as well as small scale. Current protocols for the purification of both native and polyHis-tagged or glutathione-S-transferase (GST)-tagged EF-Tu proteins and their variants using conventional procedures and the Ni-NTA-Agarose or Glutathione Sepharose are presented.
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Affiliation(s)
- J Jonák
- Department of Gene Expression, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 37 Prague 6, Czech Republic.
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Abstract
For the past five decades, the need for new antibiotics has been met largely by semisynthetic tailoring of natural product scaffolds discovered in the middle of the 20(th) century. More recently, however, advances in technology have sparked a resurgence in the discovery of natural product antibiotics from bacterial sources. In particular, efforts have refocused on finding new antibiotics from old sources (for example, streptomycetes) and new sources (for example, other actinomycetes, cyanobacteria and uncultured bacteria). This has resulted in several newly discovered antibiotics with unique scaffolds and/or novel mechanisms of action, with the potential to form a basis for new antibiotic classes addressing bacterial targets that are currently underexploited.
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Affiliation(s)
- Jon Clardy
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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Parmeggiani A, Nissen P. Elongation factor Tu-targeted antibiotics: four different structures, two mechanisms of action. FEBS Lett 2006; 580:4576-81. [PMID: 16876786 DOI: 10.1016/j.febslet.2006.07.039] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2006] [Revised: 07/07/2006] [Accepted: 07/11/2006] [Indexed: 10/24/2022]
Abstract
Elongation factor Tu (EF-Tu), the carrier of aa-tRNA to the mRNA-programmed ribosome, is the target of four families of antibiotics of unrelated structure, of which the action is supported by two basic mechanisms. Kirromycin and enacyloxin block EF-Tu.GDP on the ribosome; pulvomycin and GE2270 A inhibit the interaction of EF-Tu.GTP with aa-tRNA. The crystallographic analysis has unveiled the structural background of their actions, explaining how antibiotics of unrelated structures and binding modes and sites can employ similar mechanism of action. The selective similarities and differences of their binding sites and the induced EF-Tu conformations make understand how nature can affect the activities of a complex regulatory enzyme by means of low-molecular compounds, and have proposed a suitable approach for drug design.
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Affiliation(s)
- Andrea Parmeggiani
- Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10 C, DK-8000 Aarhus C, Denmark.
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Parmeggiani A, Krab IM, Okamura S, Nielsen RC, Nyborg J, Nissen P. Structural Basis of the Action of Pulvomycin and GE2270 A on Elongation Factor Tu,. Biochemistry 2006; 45:6846-57. [PMID: 16734421 DOI: 10.1021/bi0525122] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pulvomycin inhibits protein synthesis by preventing the formation of the ternary complex between elongation factor Tu (EF-Tu) x GTP and aa-tRNA. In this work, the crystal structure of Thermus thermophilus EF-Tu x pulvomycin in complex with the GTP analogue guanylyl imino diphosphate (GDPNP) at 1.4 A resolution reveals an antibiotic binding site extending from the domain 1-3 interface to domain 2, overlapping the domain 1-2-3 junction. Pulvomycin binding interferes with the binding of the 3'-aminoacyl group, the acceptor stem, and 5' end of tRNA. Only part of pulvomycin overlaps the binding site of GE2270 A, a domain 2-bound antibiotic of a structure unrelated to pulvomycin, which also hinders aa-tRNA binding. The structure of the T. thermophilus EF-Tu x GDPNP x GE2270 A complex at 1.6 A resolution shows that GE2270 A interferes with the binding of the 3'-aminoacyl group and part of the acceptor stem of aa-tRNA but not with the 5' end. Both compounds, pulvomycin more markedly, hinder the correct positioning of domain 1 over domains 2 and 3 that characterizes the active form of EF-Tu, while they affect the domain 1 switch regions that control the EF-Tu x GDP/GTP transitions in different ways. This work reveals how two antibiotics with different structures and binding modes can employ a similar mechanism of action.
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Affiliation(s)
- Andrea Parmeggiani
- Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10 C, DK-8000 Aarhus C, Denmark.
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