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Maleckis M, Wibowo M, Gren T, Jarmusch SA, Sterndorff EB, Booth T, Henriksen NNSE, Whitford CM, Jiang X, Jørgensen TS, Ding L, Weber T. Biosynthesis of the Azoxy Compound Azodyrecin from Streptomyces mirabilis P8-A2. ACS Chem Biol 2024; 19:641-653. [PMID: 38340355 DOI: 10.1021/acschembio.3c00632] [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: 02/12/2024]
Abstract
Azoxy compounds are a distinctive group of bioactive secondary metabolites characterized by a unique RN═N+(O-)R moiety. The azoxy moiety is present in various classes of metabolites that exhibit various biological activities. The enzymatic mechanisms underlying azoxy bond formation remain enigmatic. Azodyrecins are cytotoxic azoxy metabolites produced by Streptomyces mirabilis P8-A2. Here, we cloned and confirmed the putative azd biosynthetic gene cluster through CATCH cloning followed by expression and production of azodyrecins in two heterologous hosts, S. albidoflavus J1074 and S. coelicolor M1146, respectively. We explored the function of 14 enzymes in azodyrecin biosynthesis through gene knockout using CRISPR-Cas9 base editing in the native producer, S. mirabilis P8-A2. The key intermediates were analyzed in the mutants through MS/MS fragmentation studies, revealing azoxy bond formation via the conversion of hydrazine to an azo compound followed by further oxygenation. Enzymes involved in modifications of the precursor could be postulated based on their predicted function and the intermediates identified in the knockout strains. Moreover, the distribution of the azoxy biosynthetic gene clusters across Streptomyces spp. genomes is explored, highlighting the presence of these clusters in over 20% of the Streptomyces spp. genomes and revealing that azoxymycin and valanimycin are scarce, while azodyrecin and KA57A-like clusters are widely distributed across the phylogenetic tree.
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Affiliation(s)
- Matiss Maleckis
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Mario Wibowo
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark, Søltofts Plads, Building 221, 2800 Kgs. Lyngby, Denmark
| | - Tetiana Gren
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Scott A Jarmusch
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark, Søltofts Plads, Building 221, 2800 Kgs. Lyngby, Denmark
| | - Eva B Sterndorff
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Thomas Booth
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Nathalie N S E Henriksen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark, Søltofts Plads, Building 221, 2800 Kgs. Lyngby, Denmark
| | - Christopher M Whitford
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Xinglin Jiang
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Tue S Jørgensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Ling Ding
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark, Søltofts Plads, Building 221, 2800 Kgs. Lyngby, Denmark
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, 2800 Kgs. Lyngby, Denmark
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Zheng Z, Xiong J, Bu J, Ren D, Lee YH, Yeh YC, Lin CI, Parry R, Guo Y, Liu HW. Reconstitution of the Final Steps in the Biosynthesis of Valanimycin Reveals the Origin of Its Characteristic Azoxy Moiety. Angew Chem Int Ed Engl 2024; 63:e202315844. [PMID: 37963815 PMCID: PMC10843709 DOI: 10.1002/anie.202315844] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/11/2023] [Accepted: 11/14/2023] [Indexed: 11/16/2023]
Abstract
Valanimycin is an azoxy-containing natural product isolated from the fermentation broth of Streptomyces viridifaciens MG456-hF10. While the biosynthesis of valanimycin has been partially characterized, how the azoxy group is constructed remains obscure. Herein, the membrane protein VlmO and the putative hydrazine synthetase ForJ from the formycin biosynthetic pathway are demonstrated to catalyze N-N bond formation converting O-(l-seryl)-isobutyl hydroxylamine into N-(isobutylamino)-l-serine. Subsequent installation of the azoxy group is shown to be catalyzed by the non-heme diiron enzyme VlmB in a reaction in which the N-N single bond in the VlmO/ForJ product is oxidized by four electrons to yield the azoxy group. The catalytic cycle of VlmB appears to begin with a resting μ-oxo diferric complex in VlmB, as supported by Mössbauer spectroscopy. This study also identifies N-(isobutylamino)-d-serine as an alternative substrate for VlmB leading to two azoxy regioisomers. The reactions catalyzed by the kinase VlmJ and the lyase VlmK during the final steps of valanimycin biosynthesis are established as well. The biosynthesis of valanimycin was thus fully reconstituted in vitro using the enzymes VlmO/ForJ, VlmB, VlmJ and VlmK. Importantly, the VlmB-catalyzed reaction represents the first example of enzyme-catalyzed azoxy formation and is expected to proceed by an atypical mechanism.
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Affiliation(s)
- Ziyang Zheng
- Department of Chemistry, University of Texas at Austin, Austin, TX-78712, USA
| | - Jin Xiong
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA-15213, USA
| | - Junling Bu
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX-78712, USA
| | - Daan Ren
- Department of Chemistry, University of Texas at Austin, Austin, TX-78712, USA
| | - Yu-Hsuan Lee
- Department of Chemistry, University of Texas at Austin, Austin, TX-78712, USA
| | - Yu-Cheng Yeh
- Department of Chemistry, University of Texas at Austin, Austin, TX-78712, USA
| | - Chia-I Lin
- Department of Chemistry, University of Texas at Austin, Austin, TX-78712, USA
| | - Ronald Parry
- Department of Chemistry, Rice University, Houston, TX-77005, USA
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA-15213, USA
| | - Hung-Wen Liu
- Department of Chemistry, University of Texas at Austin, Austin, TX-78712, USA
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX-78712, USA
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3
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Shi J, Zang X, Zhao Z, Shen Z, Li W, Zhao G, Zhou J, Du YL. Conserved Enzymatic Cascade for Bacterial Azoxy Biosynthesis. J Am Chem Soc 2023; 145:27131-27139. [PMID: 38018127 DOI: 10.1021/jacs.3c12018] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
Azoxy compounds exhibit a wide array of biological activities and possess distinctive chemical properties. Although there has been considerable interest in the biosynthetic mechanisms of azoxy metabolites, the enzymatic basis responsible for azoxy bond formation has remained largely enigmatic. In this study, we unveil the enzyme cascade that constructs the azoxy bond in valanimycin biosynthesis. Our research demonstrates that a pair of metalloenzymes, comprising a membrane-bound hydrazine synthase and a nonheme diiron azoxy synthase, collaborate to convert an unstable pathway intermediate to an azoxy product through a hydrazine-azo-azoxy pathway. Additionally, by characterizing homologues of this enzyme pair from other azoxy metabolite pathways, we propose that this two-enzyme cascade could represent a conserved enzymatic strategy for azoxy bond formation in bacteria. These findings provide significant mechanistic insights into biological N-N bond formation and should facilitate the targeted isolation of bioactive azoxy compounds through genome mining.
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Affiliation(s)
- Jingkun Shi
- Department of Microbiology, and Department of Pharmacy of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xin Zang
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Zhijie Zhao
- Department of Microbiology, and Department of Pharmacy of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Zhuanglin Shen
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Wei Li
- Department of Microbiology, and Department of Pharmacy of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Guiyun Zhao
- Department of Microbiology, and Department of Pharmacy of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Jiahai Zhou
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yi-Ling Du
- Department of Microbiology, and Department of Pharmacy of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
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4
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Rietmeyer L, Li De La Sierra-Gallay I, Schepers G, Dorchêne D, Iannazzo L, Patin D, Touzé T, van Tilbeurgh H, Herdewijn P, Ethève-Quelquejeu M, Fonvielle M. Amino-acyl tXNA as inhibitors or amino acid donors in peptide synthesis. Nucleic Acids Res 2022; 50:11415-11425. [PMID: 36350642 PMCID: PMC9723616 DOI: 10.1093/nar/gkac1023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 10/17/2022] [Accepted: 10/21/2022] [Indexed: 11/10/2022] Open
Abstract
Xenobiotic nucleic acids (XNAs) offer tremendous potential for synthetic biology, biotechnology, and molecular medicine but their ability to mimic nucleic acids still needs to be explored. Here, to study the ability of XNA oligonucleotides to mimic tRNA, we synthesized three L-Ala-tXNAs analogs. These molecules were used in a non-ribosomal peptide synthesis involving a bacterial Fem transferase. We compared the ability of this enzyme to use amino-acyl tXNAs containing 1',5'-anhydrohexitol (HNA), 2'-fluoro ribose (2'F-RNA) and 2'-fluoro arabinose. L-Ala-tXNA containing HNA or 2'F-RNA were substrates of the Fem enzyme. The synthesis of peptidyl-XNA and the resolution of their structures in complex with the enzyme show the impact of the XNA on protein binding. For the first time we describe functional tXNA in an in vitro assay. These results invite to test tXNA also as substitute for tRNA in translation.
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Affiliation(s)
| | | | - Guy Schepers
- Laboratory of Medicinal Chemistry, Rega Institute for Biomedical Research, KU Leuven, Herestraat 49, Box 1041, 3000 Leuven, Belgium
| | - Delphine Dorchêne
- INSERM UMR-S 1138, Centre de Recherche des Cordeliers, Sorbonne Université, Université Paris Cité, F-75006 Paris, France
| | - Laura Iannazzo
- Université Paris Cité, CNRS UMR 8601, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, F-75006Paris, France
| | - Delphine Patin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay 91198, Gif-sur-Yvette, France
| | - Thierry Touzé
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay 91198, Gif-sur-Yvette, France
| | - Herman van Tilbeurgh
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay 91198, Gif-sur-Yvette, France
| | - Piet Herdewijn
- Laboratory of Medicinal Chemistry, Rega Institute for Biomedical Research, KU Leuven, Herestraat 49, Box 1041, 3000 Leuven, Belgium
| | - Mélanie Ethève-Quelquejeu
- Université Paris Cité, CNRS UMR 8601, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, F-75006Paris, France
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5
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Choirunnisa AR, Arima K, Abe Y, Kagaya N, Kudo K, Suenaga H, Hashimoto J, Fujie M, Satoh N, Shin-ya K, Matsuda K, Wakimoto T. New azodyrecins identified by a genome mining-directed reactivity-based screening. Beilstein J Org Chem 2022; 18:1017-1025. [PMID: 36051562 PMCID: PMC9379638 DOI: 10.3762/bjoc.18.102] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/29/2022] [Indexed: 11/23/2022] Open
Abstract
Only a few azoxy natural products have been identified despite their intriguing biological activities. Azodyrecins D–G, four new analogs of aliphatic azoxides, were identified from two Streptomyces species by a reactivity-based screening that targets azoxy bonds. A biological activity evaluation demonstrated that the double bond in the alkyl side chain is important for the cytotoxicity of azodyrecins. An in vitro assay elucidated the tailoring step of azodyrecin biosynthesis, which is mediated by the S-adenosylmethionine (SAM)-dependent methyltransferase Ady1. This study paves the way for the targeted isolation of aliphatic azoxy natural products through a genome-mining approach and further investigations of their biosynthetic mechanisms.
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Affiliation(s)
| | - Kuga Arima
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Yo Abe
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Noritaka Kagaya
- Technology Research Association for Next Generation Natural Products Chemistry, Tokyo 135-0064, Japan
| | - Kei Kudo
- National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan
| | - Hikaru Suenaga
- National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium (JBIC), Tokyo 135-0064, Japan
| | - Manabu Fujie
- Okinawa Institute of Science and Technology Graduate University, Okinawa, 904-0495, Japan
| | - Noriyuki Satoh
- Okinawa Institute of Science and Technology Graduate University, Okinawa, 904-0495, Japan
| | - Kazuo Shin-ya
- National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan
| | - Kenichi Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
- Global Station for Biosurfaces and Drug Discovery, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo 060-0812, Japan
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
- Global Station for Biosurfaces and Drug Discovery, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo 060-0812, Japan
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6
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Biosynthesis and Chemical Synthesis of Albomycin Nucleoside Antibiotics. Antibiotics (Basel) 2022; 11:antibiotics11040438. [PMID: 35453190 PMCID: PMC9032320 DOI: 10.3390/antibiotics11040438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/21/2022] [Accepted: 03/21/2022] [Indexed: 11/17/2022] Open
Abstract
The widespread emergence of antibiotic-resistant bacteria highlights the urgent need for new antimicrobial agents. Albomycins are a group of naturally occurring sideromycins with a thionucleoside antibiotic conjugated to a ferrichrome-type siderophore. The siderophore moiety serves as a vehicle to deliver albomycins into bacterial cells via a “Trojan horse” strategy. Albomycins function as specific inhibitors of seryl-tRNA synthetases and exhibit potent antimicrobial activities against both Gram-negative and Gram-positive bacteria, including many clinical pathogens. These distinctive features make albomycins promising drug candidates for the treatment of various bacterial infections, especially those caused by multidrug-resistant pathogens. We herein summarize findings on the discovery and structure elucidation, mechanism of action, biosynthesis and immunity, and chemical synthesis of albomcyins, with special focus on recent advances in the biosynthesis and chemical synthesis over the past decade (2012–2022). A thorough understanding of the biosynthetic pathway provides the basis for pathway engineering and combinatorial biosynthesis to create new albomycin analogues. Chemical synthesis of natural congeners and their synthetic analogues will be useful for systematic structure–activity relationship (SAR) studies, and thereby assist the design of novel albomycin-derived antimicrobial agents.
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7
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He HY, Niikura H, Du YL, Ryan KS. Synthetic and biosynthetic routes to nitrogen-nitrogen bonds. Chem Soc Rev 2022; 51:2991-3046. [PMID: 35311838 DOI: 10.1039/c7cs00458c] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The nitrogen-nitrogen bond is a core feature of diverse functional groups like hydrazines, nitrosamines, diazos, and pyrazoles. Such functional groups are found in >300 known natural products. Such N-N bond-containing functional groups are also found in significant percentage of clinical drugs. Therefore, there is wide interest in synthetic and enzymatic methods to form nitrogen-nitrogen bonds. In this review, we summarize synthetic and biosynthetic approaches to diverse nitrogen-nitrogen-bond-containing functional groups, with a focus on biosynthetic pathways and enzymes.
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Affiliation(s)
- Hai-Yan He
- Department of Chemistry, University of British Columbia, Vancouver, Canada. .,Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Haruka Niikura
- Department of Chemistry, University of British Columbia, Vancouver, Canada.
| | - Yi-Ling Du
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
| | - Katherine S Ryan
- Department of Chemistry, University of British Columbia, Vancouver, Canada.
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8
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Recent Advances in the Heterologous Biosynthesis of Natural Products from Streptomyces. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11041851] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Streptomyces is a significant source of natural products that are used as therapeutic antibiotics, anticancer and antitumor agents, pesticides, and dyes. Recently, with the advances in metabolite analysis, many new secondary metabolites have been characterized. Moreover, genome mining approaches demonstrate that many silent and cryptic biosynthetic gene clusters (BGCs) and many secondary metabolites are produced in very low amounts under laboratory conditions. One strain many compounds (OSMAC), overexpression/deletion of regulatory genes, ribosome engineering, and promoter replacement have been utilized to activate or enhance the production titer of target compounds. Hence, the heterologous expression of BGCs by transferring to a suitable production platform has been successfully employed for the detection, characterization, and yield quantity production of many secondary metabolites. In this review, we introduce the systematic approach for the heterologous production of secondary metabolites from Streptomyces in Streptomyces and other hosts, the genome analysis tools, the host selection, and the development of genetic control elements for heterologous expression and the production of secondary metabolites.
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9
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Abstract
The aminoacylation reaction is one of most extensively studied cellular processes. The so-called "canonical" reaction is carried out by direct charging of an amino acid (aa) onto its corresponding transfer RNA (tRNA) by the cognate aminoacyl-tRNA synthetase (aaRS), and the canonical usage of the aminoacylated tRNA (aa-tRNA) is to translate a messenger RNA codon in a translating ribosome. However, four out of the 22 genetically-encoded aa are made "noncanonically" through a two-step or indirect route that usually compensate for a missing aaRS. Additionally, from the 22 proteinogenic aa, 13 are noncanonically used, by serving as substrates for the tRNA- or aa-tRNA-dependent synthesis of other cellular components. These nontranslational processes range from lipid aminoacylation, and heme, aa, antibiotic and peptidoglycan synthesis to protein degradation. This chapter focuses on these noncanonical usages of aa-tRNAs and the ways of generating them, and also highlights the strategies that cells have evolved to balance the use of aa-tRNAs between protein synthesis and synthesis of other cellular components.
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Ott E, Kawaguchi Y, Özgen N, Yamagishi A, Rabbow E, Rettberg P, Weckwerth W, Milojevic T. Proteomic and Metabolomic Profiling of Deinococcus radiodurans Recovering After Exposure to Simulated Low Earth Orbit Vacuum Conditions. Front Microbiol 2019; 10:909. [PMID: 31110498 PMCID: PMC6501615 DOI: 10.3389/fmicb.2019.00909] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/10/2019] [Indexed: 01/26/2023] Open
Abstract
The polyextremophile, gram-positive bacterium Deinococcus radiodurans can withstand harsh conditions of real and simulated outer space environment, e.g., UV and ionizing radiation. A long-term space exposure of D. radiodurans has been performed in Low Earth Orbit (LEO) in frames of the Tanpopo orbital mission aiming to investigate the possibility of interplanetary life transfer. Space vacuum (10-4–10-7 Pa) is a harmful factor, which induces dehydration and affects microbial integrity, severely damaging cellular components: lipids, carbohydrates, proteins, and nucleic acids. However, the molecular strategies by which microorganisms protect their integrity on molecular and cellular levels against vacuum damage are not yet understood. In a simulation experiment, we exposed dried D. radiodurans cells to vacuum (10-4–10-7 Pa), which resembles vacuum pressure present outside the International Space Station in LEO. After 90 days of high vacuum exposure, survival of D. radiodurans cells was 2.5-fold lower compared to control cells. To trigger molecular repair mechanisms, vacuum exposed cells of D. radiodurans were recovered in complex medium for 3 and 6 h. The combined approach of analyzing primary metabolites and proteins revealed important molecular activities during early recovery after vacuum exposure. In total, 1939 proteins covering 63% of D. radiodurans annotated protein sequences were detected. Proteases, tRNA ligases, reactive oxygen species (ROS) scavenging proteins, nucleic acid repair proteins, TCA cycle proteins, and S-layer proteins are highly abundant after vacuum exposure. The overall abundance of amino acids and TCA cycle intermediates is reduced during the recovery phase of D. radiodurans as they are needed as carbon source. Furthermore, vacuum exposure induces an upregulation of Type III histidine kinases, which trigger the expression of S-layer related proteins. Along with the highly abundant transcriptional regulator of FNR/CRP family, specific histidine kinases might be involved in the regulation of vacuum stress response. After repair processes are finished, D. radiodurans switches off the connected repair machinery and focuses on proliferation. Combined comparative analysis of alterations in the proteome and metabolome helps to identify molecular key players in the stress response of D. radiodurans, thus elucidating the mechanisms behind its extraordinary regenerative abilities and enabling this microorganism to withstand vacuum stress.
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Affiliation(s)
- Emanuel Ott
- Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
| | - Yuko Kawaguchi
- Planetary Exploration Research Center (PERC), Chiba Institute of Technology (CIT), Chiba, Japan
| | - Natalie Özgen
- Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
| | - Akihiko Yamagishi
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta, Yokohama, Japan
| | - Elke Rabbow
- Department of Radiation Biology, Institute of Aerospace Medicine, German Aerospace Center, Cologne, Germany
| | - Petra Rettberg
- Department of Radiation Biology, Institute of Aerospace Medicine, German Aerospace Center, Cologne, Germany
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria.,Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Tetyana Milojevic
- Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
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11
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Matsuda K, Tomita T, Shin-ya K, Wakimoto T, Kuzuyama T, Nishiyama M. Discovery of Unprecedented Hydrazine-Forming Machinery in Bacteria. J Am Chem Soc 2018; 140:9083-9086. [DOI: 10.1021/jacs.8b05354] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Kenichi Matsuda
- Biotechnology Research Center, The University of Tokyo, Tokyo 113-8657, Japan
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Takeo Tomita
- Biotechnology Research Center, The University of Tokyo, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8657, Japan
| | - Kazuo Shin-ya
- Biotechnology Research Center, The University of Tokyo, Tokyo 113-8657, Japan
- National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Tomohisa Kuzuyama
- Biotechnology Research Center, The University of Tokyo, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8657, Japan
| | - Makoto Nishiyama
- Biotechnology Research Center, The University of Tokyo, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8657, Japan
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12
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Almabruk KH, Dinh LK, Philmus B. Self-Resistance of Natural Product Producers: Past, Present, and Future Focusing on Self-Resistant Protein Variants. ACS Chem Biol 2018; 13:1426-1437. [PMID: 29763292 DOI: 10.1021/acschembio.8b00173] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Nature is a prolific producers of bioactive natural products with an array of biological activities and impact on human and animal health. But with great power comes great responsibility, and the organisms that produce a bioactive compound must be resistant to its biological effects to survive during production/accumulation. Microorganisms, particularly bacteria, have developed different strategies to prevent self-toxicity. Here, we review a few of the major mechanisms including the mechanism of resistance with a focus on self-resistant protein variants, target proteins that contain amino acid substitutions to reduce the binding of the bioactive natural product, and therefore its inhibitory effects are highlighted in depth. We also try to identify some future avenues of research and challenges that need to be addressed.
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Affiliation(s)
- Khaled H. Almabruk
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon 97331, United States
| | - Linh K. Dinh
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon 97331, United States
| | - Benjamin Philmus
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon 97331, United States
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13
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Ogasawara Y, Dairi T. Biosynthesis of Oligopeptides Using ATP-Grasp Enzymes. Chemistry 2017; 23:10714-10724. [PMID: 28488371 DOI: 10.1002/chem.201700674] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Indexed: 11/08/2022]
Abstract
Peptides are biologically occurring oligomers of amino acids linked by amide bonds and are indispensable for all living organisms. Many bioactive peptides are used as antibiotics, antivirus agents, insecticides, pheromones, and food preservatives. Nature employs several different strategies to form amide bonds. ATP-grasp enzymes that catalyze amide bond formation (ATP-dependent carboxylate-amine ligases) utilize a strategy of activating carboxylic acid as an acylphosphate intermediate to form amide bonds and are involved in many different biological processes in both primary and secondary metabolisms. The recent discovery of several new ATP-dependent carboxylate-amine ligases has expanded the diversity of this group of enzymes and showed their usefulness for generating oligopeptides. In this review, an overview of findings on amide bond formation catalyzed by ATP-grasp enzymes in the past decade is presented.
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Affiliation(s)
- Yasushi Ogasawara
- Division of Applied Chemistry, Graduate School of Engineering, Hokkaido University, Sapporo, Hokkaido, 060-8628, Japan
| | - Tohru Dairi
- Division of Applied Chemistry, Graduate School of Engineering, Hokkaido University, Sapporo, Hokkaido, 060-8628, Japan
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14
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Waldman AJ, Ng TL, Wang P, Balskus EP. Heteroatom-Heteroatom Bond Formation in Natural Product Biosynthesis. Chem Rev 2017; 117:5784-5863. [PMID: 28375000 PMCID: PMC5534343 DOI: 10.1021/acs.chemrev.6b00621] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Natural products that contain functional groups with heteroatom-heteroatom linkages (X-X, where X = N, O, S, and P) are a small yet intriguing group of metabolites. The reactivity and diversity of these structural motifs has captured the interest of synthetic and biological chemists alike. Functional groups containing X-X bonds are found in all major classes of natural products and often impart significant biological activity. This review presents our current understanding of the biosynthetic logic and enzymatic chemistry involved in the construction of X-X bond containing functional groups within natural products. Elucidating and characterizing biosynthetic pathways that generate X-X bonds could both provide tools for biocatalysis and synthetic biology, as well as guide efforts to uncover new natural products containing these structural features.
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Affiliation(s)
- Abraham J. Waldman
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Tai L. Ng
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Peng Wang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Emily P. Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
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15
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Moutiez M, Belin P, Gondry M. Aminoacyl-tRNA-Utilizing Enzymes in Natural Product Biosynthesis. Chem Rev 2017; 117:5578-5618. [DOI: 10.1021/acs.chemrev.6b00523] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Mireille Moutiez
- Institute for Integrative Biology of the
Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France
| | - Pascal Belin
- Institute for Integrative Biology of the
Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France
| | - Muriel Gondry
- Institute for Integrative Biology of the
Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France
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16
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Ulrich EC, van der Donk WA. Cameo appearances of aminoacyl-tRNA in natural product biosynthesis. Curr Opin Chem Biol 2016; 35:29-36. [PMID: 27599269 PMCID: PMC5161580 DOI: 10.1016/j.cbpa.2016.08.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 08/22/2016] [Indexed: 11/19/2022]
Abstract
The breadth of unprecedented enzymatic reactions performed during the formation of microbial natural products has continued to expand as new biosynthetic gene clusters are unearthed by genome mining. Enzymes that use aminoacyl-tRNA (aa-tRNA) outside of the translation machinery have been known for decades, and accounts of their use in natural product biosynthesis are just beginning to accumulate. This review will highlight the recent discoveries and advances in our mechanistic understanding of aa-tRNA-dependent enzymes that play key roles in the biosynthesis of a growing number of microbial natural products.
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Affiliation(s)
- Emily C Ulrich
- Department of Chemistry and the Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, USA
| | - Wilfred A van der Donk
- Department of Chemistry and the Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, USA.
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17
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Shepherd J, Ibba M. Bacterial transfer RNAs. FEMS Microbiol Rev 2015; 39:280-300. [PMID: 25796611 DOI: 10.1093/femsre/fuv004] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 01/21/2015] [Indexed: 11/14/2022] Open
Abstract
Transfer RNA is an essential adapter molecule that is found across all three domains of life. The primary role of transfer RNA resides in its critical involvement in the accurate translation of messenger RNA codons during protein synthesis and, therefore, ultimately in the determination of cellular gene expression. This review aims to bring together the results of intensive investigations into the synthesis, maturation, modification, aminoacylation, editing and recycling of bacterial transfer RNAs. Codon recognition at the ribosome as well as the ever-increasing number of alternative roles for transfer RNA outside of translation will be discussed in the specific context of bacterial cells.
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Affiliation(s)
- Jennifer Shepherd
- Department of Microbiology and the Center for RNA Biology, Ohio State University, Columbus, Ohio 43210, USA
| | - Michael Ibba
- Department of Microbiology and the Center for RNA Biology, Ohio State University, Columbus, Ohio 43210, USA
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18
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Giessen TW, Marahiel MA. The tRNA-dependent biosynthesis of modified cyclic dipeptides. Int J Mol Sci 2014; 15:14610-31. [PMID: 25196600 PMCID: PMC4159871 DOI: 10.3390/ijms150814610] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 08/01/2014] [Accepted: 08/18/2014] [Indexed: 01/28/2023] Open
Abstract
In recent years it has become apparent that aminoacyl-tRNAs are not only crucial components involved in protein biosynthesis, but are also used as substrates and amino acid donors in a variety of other important cellular processes, ranging from bacterial cell wall biosynthesis and lipid modification to protein turnover and secondary metabolite assembly. In this review, we focus on tRNA-dependent biosynthetic pathways that generate modified cyclic dipeptides (CDPs). The essential peptide bond-forming catalysts responsible for the initial generation of a CDP-scaffold are referred to as cyclodipeptide synthases (CDPSs) and use loaded tRNAs as their substrates. After initially discussing the phylogenetic distribution and organization of CDPS gene clusters, we will focus on structural and catalytic properties of CDPSs before turning to two recently characterized CDPS-dependent pathways that assemble modified CDPs. Finally, possible applications of CDPSs in the rational design of structural diversity using combinatorial biosynthesis will be discussed before concluding with a short outlook.
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Affiliation(s)
- Tobias W Giessen
- Department of Chemistry/Biochemistry and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Hans-Meerwein-Strasse-4, 35032 Marburg, Germany.
| | - Mohamed A Marahiel
- Department of Chemistry/Biochemistry and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Hans-Meerwein-Strasse-4, 35032 Marburg, Germany.
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19
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Gao J, Ju KS, Yu X, Velásquez JE, Mukherjee S, Lee J, Zhao C, Evans BS, Doroghazi JR, Metcalf WW, van der Donk WA. Use of a phosphonate methyltransferase in the identification of the fosfazinomycin biosynthetic gene cluster. Angew Chem Int Ed Engl 2014; 53:1334-7. [PMID: 24376039 PMCID: PMC3927463 DOI: 10.1002/anie.201308363] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 11/16/2013] [Indexed: 12/19/2022]
Abstract
Natural product discovery has been boosted by genome mining approaches, but compound purification is often still challenging. We report an enzymatic strategy for "stable isotope labeling of phosphonates in extract" (SILPE) that facilitates their purification. We used the phosphonate methyltransferase DhpI involved in dehydrophos biosynthesis to methylate a variety of phosphonate natural products in crude spent medium with a mixture of labeled and unlabeled S-adenosyl methionine. Mass-guided fractionation then allowed straightforward purification. We illustrate its utility by purifying a phosphonate that led to the identification of the fosfazinomycin biosynthetic gene cluster. This unusual natural product contains a hydrazide linker between a carboxylic acid and a phosphonic acid. Bioinformatic analysis of the gene cluster provides insights into how such a structure might be assembled.
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Affiliation(s)
- Jiangtao Gao
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West, Gregory Drive, Urbana, Illinois 61801, USA
| | - Kou-San Ju
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West, Gregory Drive, Urbana, Illinois 61801, USA
| | - Xiaomin Yu
- Department of Microbiology, 601 South Goodwin Avenue, Urbana, Illinois 61801, USA
| | - Juan E. Velásquez
- Howard Hughes Medical Institute and Department of Chemistry, University of Illinois at Urbana-Champaign, 600, South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Subha Mukherjee
- Howard Hughes Medical Institute and Department of Chemistry, University of Illinois at Urbana-Champaign, 600, South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Jaeheon Lee
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West, Gregory Drive, Urbana, Illinois 61801, USA
| | - Changming Zhao
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West, Gregory Drive, Urbana, Illinois 61801, USA
| | - Bradley S. Evans
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West, Gregory Drive, Urbana, Illinois 61801, USA
| | - James R. Doroghazi
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West, Gregory Drive, Urbana, Illinois 61801, USA
| | - William W. Metcalf
- Department of Microbiology, 601 South Goodwin Avenue, Urbana, Illinois 61801, USA
| | - Wilfred A. van der Donk
- Howard Hughes Medical Institute and Department of Chemistry, University of Illinois at Urbana-Champaign, 600, South Mathews Avenue, Urbana, Illinois 61801, USA
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20
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Maršavelski A, Lesjak S, Močibob M, Weygand-Đurašević I, Tomić S. A single amino acid substitution affects the substrate specificity of the seryl-tRNA synthetase homologue. ACTA ACUST UNITED AC 2014; 10:3207-16. [DOI: 10.1039/c4mb00416g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recently described and characterizedBradyrhizobium japonicumglycine:[carrier protein] ligase 1 (Bj Gly:CP ligase 1), a homologue of methanogenic type seryl-tRNA synthetase (SerRS) is an intriguing enzyme whose physiological role is not yet known.
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Affiliation(s)
| | - Sonja Lesjak
- Department of Chemistry
- Faculty of Science
- University of Zagreb
- Zagreb, Croatia
| | - Marko Močibob
- Department of Chemistry
- Faculty of Science
- University of Zagreb
- Zagreb, Croatia
| | | | - Sanja Tomić
- Department of Physical Chemistry
- Rudjer Boskovic Institute
- Zagreb, Croatia
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21
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Gao J, Ju KS, Yu X, Velásquez JE, Mukherjee S, Lee J, Zhao C, Evans BS, Doroghazi JR, Metcalf WW, van der Donk WA. Use of a Phosphonate Methyltransferase in the Identification of the Fosfazinomycin Biosynthetic Gene Cluster. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201308363] [Citation(s) in RCA: 4] [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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22
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Shepherd J, Ibba M. Direction of aminoacylated transfer RNAs into antibiotic synthesis and peptidoglycan-mediated antibiotic resistance. FEBS Lett 2013; 587:2895-904. [PMID: 23907010 DOI: 10.1016/j.febslet.2013.07.036] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 07/17/2013] [Indexed: 12/30/2022]
Abstract
Prokaryotic aminoacylated-transfer RNAs often need to be efficiently segregated between translation and other cellular biosynthetic pathways. Many clinically relevant bacteria, including Streptococcus pneumoniae, Staphylococcus aureus, Enterococcus faecalis and Pseudomonas aeruginosa direct some aminoacylated-tRNA species into peptidoglycan biosynthesis and/or membrane phospholipid modification. Subsequent indirect peptidoglycan cross-linkage or change in membrane permeability is often a prerequisite for high-level antibiotic resistance. In Streptomycetes, aminoacylated-tRNA species are used for antibiotic synthesis as well as antibiotic resistance. The direction of coding aminoacylated-tRNA molecules away from translation and into antibiotic resistance and synthesis pathways are discussed in this review.
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Affiliation(s)
- Jennifer Shepherd
- Department of Microbiology and Center for RNA Biology, Ohio State University, Columbus, OH 43210-1292, USA
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23
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Mocibob M, Ivic N, Luic M, Weygand-Durasevic I. Adaptation of Aminoacyl-tRNA Synthetase Catalytic Core to Carrier Protein Aminoacylation. Structure 2013; 21:614-26. [DOI: 10.1016/j.str.2013.02.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 02/01/2013] [Accepted: 02/11/2013] [Indexed: 10/27/2022]
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24
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Chang AT, Nikonowicz EP. Solution nuclear magnetic resonance analyses of the anticodon arms of proteinogenic and nonproteinogenic tRNA(Gly). Biochemistry 2012; 51:3662-74. [PMID: 22468768 DOI: 10.1021/bi201900j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Although the fate of most tRNA molecules in the cell is aminoacylation and delivery to the ribosome, some tRNAs are destined to fulfill other functional roles. In addition to their central role in translation, tRNA molecules participate in processes such as regulation of gene expression, bacterial cell wall biosynthesis, viral replication, antibiotic biosynthesis, and suppression of alternative splicing. In bacteria, glycyl-tRNA molecules with anticodon sequences GCC and UCC exhibit multiple extratranslational functions, including transcriptional regulation and cell wall biosynthesis. We have determined the high-resolution structures of three glycyl-tRNA anticodon arms with anticodon sequences GCC and UCC. Two of the tRNA molecules are proteinogenic (tRNA(Gly,GCC) and tRNA(Gly,UCC)), and the third is nonproteinogenic (np-tRNA(Gly,UCC)) and participates in cell wall biosynthesis. The UV-monitored thermal melting curves show that the anticodon arm of tRNA(Gly,UCC) with a loop-closing C-A(+) base pair melts at a temperature 10 °C lower than those of tRNA(Gly,GCC) and np-tRNA(Gly,UCC). U-A and C-G pairs close the loops of the latter two molecules and enhance stem stability. Mg(2+) stabilizes the tRNA(Gly,UCC) anticodon arm and reduces the T(m) differential. The structures of the three tRNA(Gly) anticodon arms exhibit small differences among one another, but none of them form the classical U-turn motif. The anticodon loop of tRNA(Gly,GCC) becomes more dynamic and disordered in the presence of multivalent cations, whereas metal ion coordination in the anticodon loops of tRNA(Gly,UCC) and np-tRNA(Gly,UCC) establishes conformational homogeneity. The conformational similarity of the molecules is greater than their functional differences might suggest. Because aminoacylation of full-length tRNA molecules is accomplished by one tRNA synthetase, the similar structural context of the loop may facilitate efficient recognition of each of the anticodon sequences.
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Affiliation(s)
- Andrew T Chang
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77251-1892, United States
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25
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Schrader JM, Uhlenbeck OC. Is the sequence-specific binding of aminoacyl-tRNAs by EF-Tu universal among bacteria? Nucleic Acids Res 2011; 39:9746-58. [PMID: 21893586 PMCID: PMC3239215 DOI: 10.1093/nar/gkr641] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Three base pairs in the T-stem are primarily responsible for the sequence-specific interaction of tRNA with Escherichia coli and Thermus thermophilus EF-Tu. While the amino acids on the surface of EF-Tu that contact aminoacyl-tRNA (aa-tRNA) are highly conserved among bacteria, the T-stem sequences of individual tRNA are variable, making it unclear whether or not this protein–nucleic acid interaction is also sequence specific in other bacteria. We propose and validate a thermodynamic model that predicts the ΔG° of any tRNA to EF-Tu using the sequence of its three T-stem base pairs. Despite dramatic differences in T-stem sequences, the predicted ΔG° values for the majority of tRNA classes are similar in all bacteria and closely match the ΔG° values determined for E. coli tRNAs. Each individual tRNA class has evolved to have a characteristic ΔG° value to EF-Tu, but different T-stem sequences are used to achieve this ΔG° value in different bacteria. Thus, the compensatory relationship between the affinity of the tRNA body and the affinity of the esterified amino acid is universal among bacteria. Additionally, we predict and validate a small number of aa-tRNAs that bind more weakly to EF-Tu than expected and thus are candidates for acting as activated amino acid donors in processes outside of translation.
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Affiliation(s)
- Jared M Schrader
- Department of Molecular Biosciences, Northwestern University, Hogan 2-100, Evanston, IL 60208, USA
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26
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tRNA-dependent peptide bond formation by the transferase PacB in biosynthesis of the pacidamycin group of pentapeptidyl nucleoside antibiotics. Proc Natl Acad Sci U S A 2011; 108:12249-53. [PMID: 21746899 DOI: 10.1073/pnas.1109539108] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pacidamycins are a family of uridyl tetra/pentapeptide antibiotics with antipseudomonal activities through inhibition of the translocase MraY in bacterial cell wall assembly. The biosynthetic gene cluster for pacidamycins has recently been identified through genome mining of the producer Streptomyces coeruleorubidus, and the highly dissociated nonribosomal peptide assembly line for the uridyl tetrapeptide scaffold of pacidamycin has been characterized. In this work a hypothetical protein PacB, conserved in known uridyl peptide antibiotics gene clusters, has been characterized by both genetic deletion and enzymatic analysis of the purified protein. PacB catalyzes the transfer of the alanyl residue from alanyl-tRNA to the N terminus of the tetrapeptide intermediate yielding a pentapeptide on the thio-templated nonribosomal peptide synthetase (NRPS) assembly line protein PacH. PacB thus represents a new group of tRNA-dependent peptide bond-forming enzymes in secondary metabolite biosynthesis in addition to the recently identified cyclodipeptide synthases. The characterization of PacB completes the assembly line reconstitution of pacidamycin pentapeptide antibiotic scaffolds, bridging the primary and secondary metabolic pathways by hijacking an aminoacyl-tRNA to the antibiotic biosynthetic pathway.
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27
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Biosynthesis of the RNA polymerase inhibitor streptolydigin in Streptomyces lydicus: tailoring modification of 3-methyl-aspartate. J Bacteriol 2011; 193:2647-51. [PMID: 21398531 DOI: 10.1128/jb.00108-11] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The asparaginyl-tRNA synthetase-like SlgZ and methyltransferase SlgM enzymes are involved in the biosynthesis of the tetramic acid streptolydigin in Streptomyces lydicus. Inactivation of slgZ led to a novel streptolydigin derivative. Overexpression of slgZ, slgM, or both in S. lydicus led to a considerable increase in streptolydigin production.
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28
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Helaly SE, Pesic A, Fiedler HP, Süssmuth RD. Elaiomycins B and C: Alkylhydrazide Antibiotics from Streptomyces sp. BK 190. Org Lett 2011; 13:1052-5. [DOI: 10.1021/ol1031014] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Soleiman E. Helaly
- Institut für Chemie, Technische Universität Berlin, 10623 Berlin, Germany, Mikrobiologisches Institut, Universität Tübingen, 72076 Tübingen, Germany, and Department of Chemistry, Faculty of Science, South Valley University, Aswan 81528, Egypt
| | - Alexander Pesic
- Institut für Chemie, Technische Universität Berlin, 10623 Berlin, Germany, Mikrobiologisches Institut, Universität Tübingen, 72076 Tübingen, Germany, and Department of Chemistry, Faculty of Science, South Valley University, Aswan 81528, Egypt
| | - Hans-Peter Fiedler
- Institut für Chemie, Technische Universität Berlin, 10623 Berlin, Germany, Mikrobiologisches Institut, Universität Tübingen, 72076 Tübingen, Germany, and Department of Chemistry, Faculty of Science, South Valley University, Aswan 81528, Egypt
| | - Roderich D. Süssmuth
- Institut für Chemie, Technische Universität Berlin, 10623 Berlin, Germany, Mikrobiologisches Institut, Universität Tübingen, 72076 Tübingen, Germany, and Department of Chemistry, Faculty of Science, South Valley University, Aswan 81528, Egypt
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29
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Brown MV, Reader JS, Tzima E. Mammalian aminoacyl-tRNA synthetases: Cell signaling functions of the protein translation machinery. Vascul Pharmacol 2010; 52:21-6. [DOI: 10.1016/j.vph.2009.11.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Revised: 11/20/2009] [Accepted: 11/29/2009] [Indexed: 12/01/2022]
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30
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Francklyn CS, Minajigi A. tRNA as an active chemical scaffold for diverse chemical transformations. FEBS Lett 2009; 584:366-75. [PMID: 19925795 DOI: 10.1016/j.febslet.2009.11.045] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Revised: 11/11/2009] [Accepted: 11/11/2009] [Indexed: 10/20/2022]
Abstract
During protein synthesis, tRNA serves as the intermediary between cognate amino acids and their corresponding RNA trinucleotide codons. Aminoacyl-tRNA is also a biosynthetic precursor and amino acid donor for other macromolecules. AA-tRNAs allow transformations of acidic amino acids into their amide-containing counterparts, and seryl-tRNA(Ser) donates serine for antibiotic synthesis. Aminoacyl-tRNA is also used to cross-link peptidoglycan, to lysinylate the lipid bilayer, and to allow proteolytic turnover via the N-end rule. These alternative functions may signal the use of RNA in early evolution as both a biological scaffold and a catalyst to achieve a wide variety of chemical transformations.
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Affiliation(s)
- Christopher S Francklyn
- Cell and Molecular Biology Program, University of Vermont, Burlington, VT 05405, United States.
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31
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tRNAs: cellular barcodes for amino acids. FEBS Lett 2009; 584:387-95. [PMID: 19903480 DOI: 10.1016/j.febslet.2009.11.013] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2009] [Revised: 10/29/2009] [Accepted: 11/05/2009] [Indexed: 01/06/2023]
Abstract
The role of tRNA in translating the genetic code has received considerable attention over the last 50 years, and we now know in great detail how particular amino acids are specifically selected and brought to the ribosome in response to the corresponding mRNA codon. Over the same period, it has also become increasingly clear that the ribosome is not the only destination to which tRNAs deliver amino acids, with processes ranging from lipid modification to antibiotic biosynthesis all using aminoacyl-tRNAs as substrates. Here we review examples of alternative functions for tRNA beyond translation, which together suggest that the role of tRNA is to deliver amino acids for a variety of processes that includes, but is not limited to, protein synthesis.
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32
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Garg RP, Parry RJ. Regulation of valanimycin biosynthesis in Streptomyces viridifaciens: characterization of VlmI as a Streptomyces antibiotic regulatory protein (SARP). MICROBIOLOGY-SGM 2009; 156:472-483. [PMID: 19892763 DOI: 10.1099/mic.0.033167-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Streptomyces antibiotic regulatory proteins (SARPs) have been shown to activate transcription by binding to a tandemly arrayed set of heptameric direct repeats located around the -35 region of their cognate promoters. Experimental evidence is presented here showing that vlmI is a regulatory gene in the valanimycin biosynthetic gene cluster of Streptomyces viridifaciens and encodes a protein belonging to the SARP family. The organization of the valanimycin biosynthetic gene cluster suggests that the valanimycin biosynthetic genes are located on three potential transcripts, vlmHORBCD, vlmJKL and vlmA. Disruption of vlmI abolished valanimycin biosynthesis. Western blot analyses showed that VlmR and VlmA are absent from the vlmI mutant and that the production of VlmK is severely diminished. These results demonstrate that the expression of these genes from the three potential transcripts is under the positive control of VlmI. The vlmA-vlmH and vlmI-vlmJ intergenic regions both exhibit a pattern of heptameric direct repeats. Gel shift assays with VlmI overproduced in Escherichia coli as a C-terminal FLAG-tagged protein clearly demonstrated that VlmI binds to DNA fragments from both regions that contain these heptameric repeats. When a high-copy-number vlmI expression plasmid was introduced into Streptomyces coelicolor M512, which contains mutations in the undecylprodigiosin and actinorhodin activators redD and actII-orf4, undecylprodigiosin production was restored, showing that vlmI can complement a redD mutation. Introduction of the same vlmI expression plasmid into an S. viridifaciens vlmI mutant restored valanimycin production to wild-type levels.
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Affiliation(s)
- Ram P Garg
- Department of Chemistry, Rice University, Houston, TX 77005, USA
| | - Ronald J Parry
- Department of Chemistry, Rice University, Houston, TX 77005, USA
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33
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Garg RP, Alemany LB, Moran S, Parry RJ. Identification, characterization, and bioconversion of a new intermediate in valanimycin biosynthesis. J Am Chem Soc 2009; 131:9608-9. [PMID: 19548668 DOI: 10.1021/ja901243p] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The antibiotic valanimycin is a naturally occurring azoxy compound isolated from Streptomyces viridifaciens. Detailed investigations have shown that valanimycin is derived from L-valine and L-serine via the intermediacy of O-(L-seryl)isobutylhydroxylamine. Sequence analysis of the valanimycin biosynthetic genes provides relatively few clues concerning the nature of the later stages of the pathway. Two exceptions are provided by the vlmJ and vlmK genes. The translation product of vlmJ exhibits similarity to diacylglycerol kinases, while the translation product of vlmK exhibits a weak similarity to the MmgE/PrpD superfamily of proteins. This superfamily includes 2-methylcitrate dehydratase. This communication describes the isolation and structure elucidation of valanimycin hydrate from vlmJ and vlmK mutants of S. viridifaciens. Additional studies have shown that the conversion of valanimycin hydrate into valanimycin by S. viridifaciens requires both the vlmJ and vlmK genes and that VlmJ catalyzes the ATP-dependent phosphorylation of the hydroxyl group of valanimycin hydrate prior to VlmK-catalyzed dehydration.
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Affiliation(s)
- Ram P Garg
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, USA
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Characterization of two seryl-tRNA synthetases in albomycin-producing Streptomyces sp. strain ATCC 700974. Antimicrob Agents Chemother 2009; 53:4619-27. [PMID: 19721072 DOI: 10.1128/aac.00782-09] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Trojan horse antibiotic albomycin, produced by Streptomyces sp. strain ATCC 700974, contains a thioribosyl nucleoside moiety linked to a hydroxamate siderophore through a serine residue. The seryl nucleoside structure (SB-217452) is a potent inhibitor of seryl-tRNA synthetase (SerRS) in the pathogenic bacterium Staphylococcus aureus, with a 50% inhibitory concentration (IC(50)) of approximately 8 nM. In the albomycin-producing Streptomyces sp., a bacterial SerRS homolog (Alb10) was found to be encoded in a biosynthetic gene cluster in addition to another serRS gene (serS1) at a different genetic locus. Alb10, named SerRS2 herein, is significantly divergent from SerRS1, which shows high homology to the housekeeping SerRS found in other Streptomyces species. We genetically and biochemically characterized the two genes and the proteins encoded. Both genes were able to complement a temperature-sensitive serS mutant of Escherichia coli and allowed growth at a nonpermissive temperature. serS2 was shown to confer albomycin resistance, with specific amino acid residues in the motif 2 signature sequences of SerRS2 playing key roles. SerRS1 and SerRS2 are comparably efficient in vitro, but the K(m) of serine for SerRS2 measured during tRNA aminoacylation is more than 20-fold higher than that for SerRS1. SB-217452 was also enzymatically generated and purified by two-step chromatography. Its IC(50) against SerRS1 was estimated to be 10-fold lower than that against SerRS2. In contrast, both SerRSs displayed comparable inhibition kinetics for serine hydroxamate, indicating that SerRS2 was specifically resistant to SB-217452. These data suggest that mining Streptomyces genomes for duplicated aminoacyl-tRNA synthetase genes could provide a novel approach for the identification of natural products targeting aminoacyl-tRNA synthetases.
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Winter JM, Jansma AL, Handel TM, Moore BS. Formation of the pyridazine natural product azamerone by biosynthetic rearrangement of an aryl diazoketone. Angew Chem Int Ed Engl 2009; 48:767-70. [PMID: 19072974 DOI: 10.1002/anie.200805140] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jaclyn M Winter
- Scripps Institution of Oceanography, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0204, USA
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Winter J, Jansma A, Handel T, Moore B. Formation of the Pyridazine Natural Product Azamerone by Biosynthetic Rearrangement of an Aryl Diazoketone. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200805140] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Chen K, Cole RB, Santa Cruz V, Blakeney EW, Kanz MF, Dugas TR. Characterization of biliary conjugates of 4,4'-methylenedianiline in male versus female rats. Toxicol Appl Pharmacol 2008; 232:190-202. [PMID: 18692083 DOI: 10.1016/j.taap.2008.06.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2008] [Accepted: 06/20/2008] [Indexed: 11/18/2022]
Abstract
4,4'-Methylenedianiline (4,4'-diaminodiphenylmethane; DAPM) is an aromatic diamine used in the production of numerous polyurethane foams and epoxy resins. Previous studies in rats revealed that DAPM initially injures biliary epithelial cells of the liver, that the toxicity is greater in female than in male rats, and that the toxic metabolites of DAPM are excreted into bile. Since male and female rats exhibit differences in the expression of both phase I and phase II enzymes, our hypothesis was that female rats either metabolize DAPM to more toxic metabolites or have a decreased capacity to conjugate metabolites to less toxic intermediates. Our objective was thus to isolate, characterize, and quantify DAPM metabolites excreted into bile in both male and female bile duct-cannulated Sprague Dawley rats. The rats were gavaged with [(14)C]-DAPM, and the collected bile was subjected to reversed-phase HPLC with radioisotope detection. Peaks eluting from HPLC were collected and analyzed using electrospray MS and NMR spectroscopy. HPLC analysis indicated numerous metabolites in both sexes, but male rats excreted greater amounts of glutathione and glucuronide conjugates than females. Electrospray MS and NMR spectra of HPLC fractions revealed that the most prominent metabolite found in bile of both sexes was a glutathione conjugate of an imine metabolite of a 4'-nitroso-DAPM. Seven other metabolites were identified, including acetylated, cysteinyl-glycine, glutamyl-cysteine, glycine, and glucuronide conjugates. While our prior studies demonstrated increased covalent binding of DAPM in the liver and bile of female compared to male rats, in these studies, SDS-PAGE with autoradiography revealed 4-5 radiolabeled protein bands in the bile of rats treated with [(14)C]-DAPM. In addition, these bands were much more prominent in female than in male rats. These studies thus suggest that a plausible mechanism for the increased sensitivity of female rats to DAPM toxicity may be decreased conjugation of reactive DAPM metabolites, leading to greater levels of protein adduct formation.
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Affiliation(s)
- Kan Chen
- Department of Chemistry, University of New Orleans, New Orleans, LA, USA
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Investigations of valanimycin biosynthesis: elucidation of the role of seryl-tRNA. Proc Natl Acad Sci U S A 2008; 105:6543-7. [PMID: 18451033 DOI: 10.1073/pnas.0708957105] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The antibiotic valanimycin is a naturally occurring azoxy compound produced by Streptomyces viridifaciens MG456-hF10. Precursor incorporation experiments showed that valanimycin is derived from l-valine and l-serine via the intermediacy of isobutylamine and isobutylhydroxylamine. Enzymatic and genetic investigations led to the cloning and sequencing of the valanimycin biosynthetic gene cluster, which was found to contain 14 genes. A novel feature of the valanimycin biosynthetic gene cluster is the presence of a gene (vlmL) that encodes a class II seryl-tRNA synthetase. Previous studies suggested that the role of this enzyme is to provide seryl-tRNA for the valanimycin biosynthetic pathway. Here, we report the results of investigations to elucidate the role of seryl-tRNA in valanimycin biosynthesis. A combination of enzymatic and chemical studies has revealed that the VlmA protein encoded by the valanimycin biosynthetic gene cluster catalyzes the transfer of the seryl residue from seryl-tRNA to the hydroxyl group of isobutylhydroxylamine to produce the ester O-seryl-isobutylhydroxylamine. These findings provide an example of the involvement of an aminoacyl-tRNA in an antibiotic biosynthetic pathway.
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