1
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Vogel U, Beerens K, Desmet T. Nucleotide sugar dehydratases: Structure, mechanism, substrate specificity, and application potential. J Biol Chem 2022; 298:101809. [PMID: 35271853 PMCID: PMC8987622 DOI: 10.1016/j.jbc.2022.101809] [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: 11/12/2021] [Revised: 02/24/2022] [Accepted: 02/28/2022] [Indexed: 11/14/2022] Open
Abstract
Nucleotide sugar (NS) dehydratases play a central role in the biosynthesis of deoxy and amino sugars, which are involved in a variety of biological functions in all domains of life. Bacteria are true masters of deoxy sugar biosynthesis as they can produce a wide range of highly specialized monosaccharides. Indeed, deoxy and amino sugars play important roles in the virulence of gram-positive and gram-negative pathogenic species and are additionally involved in the biosynthesis of diverse macrolide antibiotics. The biosynthesis of deoxy sugars relies on the activity of NS dehydratases, which can be subdivided into three groups based on their structure and reaction mechanism. The best-characterized NS dehydratases are the 4,6-dehydratases that, together with the 5,6-dehydratases, belong to the NS-short-chain dehydrogenase/reductase superfamily. The other two groups are the less abundant 2,3-dehydratases that belong to the Nudix hydrolase superfamily and 3-dehydratases, which are related to aspartame aminotransferases. 4,6-Dehydratases catalyze the first step in all deoxy sugar biosynthesis pathways, converting nucleoside diphosphate hexoses to nucleoside diphosphate-4-keto-6-deoxy hexoses, which in turn are further deoxygenated by the 2,3- and 3-dehydratases to form dideoxy and trideoxy sugars. In this review, we give an overview of the NS dehydratases focusing on the comparison of their structure and reaction mechanisms, thereby highlighting common features, and investigating differences between closely related members of the same superfamilies.
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Affiliation(s)
- Ulrike Vogel
- Centre for Synthetic Biology (CSB) - Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Koen Beerens
- Centre for Synthetic Biology (CSB) - Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Tom Desmet
- Centre for Synthetic Biology (CSB) - Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium.
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2
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Price NPJ, Jackson MA, Hartman TM, Brändén G, Ek M, Koch AA, Kennedy PD. Branched Chain Lipid Metabolism As a Determinant of the N-Acyl Variation of Streptomyces Natural Products. ACS Chem Biol 2021; 16:116-124. [PMID: 33411499 DOI: 10.1021/acschembio.0c00799] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Branched-chain fatty acids (BCFA) are encountered in Gram-positive bacteria, but less so in other organisms. The bacterial BCFA in membranes are typically saturated, with both odd- and even-numbered carbon chain lengths, and with methyl branches at either the ω-1 (iso) or ω-2 (anteiso) positions. The acylation with BCFA also contributes to the structural diversity of microbial natural products and potentially modulates biological activity. For the tunicamycin (TUN) family of natural products, the toxicity toward eukaryotes is highly dependent upon N-acylation with trans-2,3-unsaturated BCFA. The loss of the 2,3-unsaturation gives modified TUN with reduced eukaryotic toxicity but crucially with retention of the synergistic enhancement of the β-lactam group of antibiotics. Here, we infer from genomics, mass spectrometry, and deuterium labeling that the trans-2,3-unsaturated TUN variants and the saturated cellular lipids found in TUN-producing Streptomyces are derived from the same pool of BCFA metabolites. Moreover, non-natural primers of BCFA metabolism are selectively incorporated into the cellular lipids of TUN-producing Streptomyces and concomitantly produce structurally novel neo-branched TUN N-acyl variants.
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Affiliation(s)
- Neil P. J. Price
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, 1815 N. University St., Peoria, Illinois 61604, United States
| | - Michael A. Jackson
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, 1815 N. University St., Peoria, Illinois 61604, United States
| | - Trina M. Hartman
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, 1815 N. University St., Peoria, Illinois 61604, United States
| | - Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Margareta Ek
- Structure, Biophysics & FBLG, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Aaron A. Koch
- Cayman Chemical, 1180 E. Ellsworth Rd., Ann Arbor, Michigan 48108, United States
| | - Paul D. Kennedy
- Cayman Chemical, 1180 E. Ellsworth Rd., Ann Arbor, Michigan 48108, United States
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3
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McErlean M, Liu X, Cui Z, Gust B, Van Lanen SG. Identification and characterization of enzymes involved in the biosynthesis of pyrimidine nucleoside antibiotics. Nat Prod Rep 2021; 38:1362-1407. [PMID: 33404015 DOI: 10.1039/d0np00064g] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: up to September 2020 Hundreds of nucleoside-based natural products have been isolated from various microorganisms, several of which have been utilized in agriculture as pesticides and herbicides, in medicine as therapeutics for cancer and infectious disease, and as molecular probes to study biological processes. Natural products consisting of structural modifications of each of the canonical nucleosides have been discovered, ranging from simple modifications such as single-step alkylations or acylations to highly elaborate modifications that dramatically alter the nucleoside scaffold and require multiple enzyme-catalyzed reactions. A vast amount of genomic information has been uncovered the past two decades, which has subsequently allowed the first opportunity to interrogate the chemically intriguing enzymatic transformations for the latter type of modifications. This review highlights (i) the discovery and potential applications of structurally complex pyrimidine nucleoside antibiotics for which genetic information is known, (ii) the established reactions that convert the canonical pyrimidine into a new nucleoside scaffold, and (iii) the important tailoring reactions that impart further structural complexity to these molecules.
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Affiliation(s)
- M McErlean
- Department of Pharmaceutical Science, College of Pharmacy, University of Kentucky, USA.
| | - X Liu
- Department of Pharmaceutical Science, College of Pharmacy, University of Kentucky, USA.
| | - Z Cui
- Department of Pharmaceutical Science, College of Pharmacy, University of Kentucky, USA.
| | - B Gust
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, Germany
| | - S G Van Lanen
- Department of Pharmaceutical Science, College of Pharmacy, University of Kentucky, USA.
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4
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Baş L, Otur Ç, Kurt-Kızıldoğan A. Enhanced Tunicamycin Biosynthesis in BldG Overexpressed Streptomyces clavuligerus. APPL BIOCHEM MICRO+ 2020. [DOI: 10.1134/s000368382004002x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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5
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McLean TC, Lo R, Tschowri N, Hoskisson PA, Al Bassam MM, Hutchings MI, Som NF. Sensing and responding to diverse extracellular signals: an updated analysis of the sensor kinases and response regulators of Streptomyces species. MICROBIOLOGY-SGM 2020; 165:929-952. [PMID: 31334697 DOI: 10.1099/mic.0.000817] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Streptomyces venezuelae is a Gram-positive, filamentous actinomycete with a complex developmental life cycle. Genomic analysis revealed that S. venezuelae encodes a large number of two-component systems (TCSs): these consist of a membrane-bound sensor kinase (SK) and a cognate response regulator (RR). These proteins act together to detect and respond to diverse extracellular signals. Some of these systems have been shown to regulate antimicrobial biosynthesis in Streptomyces species, making them very attractive to researchers. The ability of S. venezuelae to sporulate in both liquid and solid cultures has made it an increasingly popular model organism in which to study these industrially and medically important bacteria. Bioinformatic analysis identified 58 TCS operons in S. venezuelae with an additional 27 orphan SK and 18 orphan RR genes. A broader approach identified 15 of the 58 encoded TCSs to be highly conserved in 93 Streptomyces species for which high-quality and complete genome sequences are available. This review attempts to unify the current work on TCS in the streptomycetes, with an emphasis on S. venezuelae.
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Affiliation(s)
- Thomas C McLean
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
| | - Rebecca Lo
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
| | - Natalia Tschowri
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Paul A Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
| | - Mahmoud M Al Bassam
- Department of Paediatrics, Division of Host-Microbe Systems and Therapeutics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Matthew I Hutchings
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
| | - Nicolle F Som
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
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6
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Tancos MA, Sechler AJ, Davis EW, Chang JH, Schroeder BK, Murray TD, Rogers EE. The Identification and Conservation of Tunicaminyluracil-Related Biosynthetic Gene Clusters in Several Rathayibacter Species Collected From Australia, Africa, Eurasia, and North America. Front Microbiol 2020; 10:2914. [PMID: 31998251 PMCID: PMC6965331 DOI: 10.3389/fmicb.2019.02914] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 12/03/2019] [Indexed: 01/12/2023] Open
Abstract
Tunicaminyluracil antibiotics are a novel class of toxigenic glycolipids that are synthesized by several soil-associated Actinomycetes. The acquisition of a tunicaminyluracil biosynthetic gene cluster (TGC) in Rathayibacter toxicus has led to the emergence of the only described, naturally occurring tunicaminyluracil-associated mammalian disease, annual ryegrass toxicity of livestock. Endemic to Australia, R. toxicus is obligately vectored by Anguinid seed gall nematodes to the developing seedheads of forage grasses, in which the bacteria synthesize tunicaminyluracils that may subsequently be consumed by livestock and result in high rates of mortality and morbidity. The potential impact of R. toxicus on U.S. agriculture has led the U.S. Department of Agriculture - Animal and Plant Health Inspection Service to list R. toxicus as a Plant Pathogen Select Agent. R. toxicus is the only characterized phytopathogenic bacterium to produce tunicaminyluracils, but numerous R. toxicus-like livestock poisonings outside Australia suggest additional bacterial sources of tunicaminyluracils may exist. To investigate the conservation of the TGC in R. toxicus and whether the TGC is present in other Rathayibacter species, we analyzed genome sequences of members of the Rathayibacter genus. Putative TGCs were identified in genome sequences of R. toxicus, R. iranicus, R. agropyri, and an undescribed South African Rathayibacter species. In the latter three species, the putative TGCs have homologs of tunicaminyluracil-related genes essential for toxin production, but the TGCs differ in gene number and order. The TGCs appear at least partially functional because in contrast to atoxigenic species, TGC-containing Rathayibacter species were each able to tolerate exogenous applications of tunicamycin from Streptomyces chartreusis. The North American R. agropyri TGC shows extensive diversity among the sequenced isolates, with presense/absense polymorphisms in multiple genes or even the whole TGC. R. agropyri TGC structure does not appear to correlate with date or location of isolate collection. The conservation and identification of tunicaminyluracil-related gene clusters in three additional Rathayibacter species isolated from South Africa, the Middle East, and the United States, suggests a wider global distribution of potentially neurotoxigenic plant-associated bacteria. This potential for additional endemic and exotic toxigenic Rathayibacter species could have widespread and severe implications for agriculture.
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Affiliation(s)
- Matthew A. Tancos
- Foreign Disease-Weed Science Research Unit, United States Department of Agriculture-Agricultural Research Service, Frederick, MD, United States
| | - Aaron J. Sechler
- Foreign Disease-Weed Science Research Unit, United States Department of Agriculture-Agricultural Research Service, Frederick, MD, United States
| | - Edward W. Davis
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Jeff H. Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Brenda K. Schroeder
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, ID, United States
| | - Timothy D. Murray
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | - Elizabeth E. Rogers
- Foreign Disease-Weed Science Research Unit, United States Department of Agriculture-Agricultural Research Service, Frederick, MD, United States
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7
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Homologous expression of lysA encoding diaminopimelic acid (DAP) decarboxylase reveals increased antibiotic production in Streptomyces clavuligerus. Braz J Microbiol 2019; 51:547-556. [PMID: 31833007 DOI: 10.1007/s42770-019-00202-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 11/27/2019] [Indexed: 10/25/2022] Open
Abstract
lysA gene encoding meso-diaminopimelic acid (DAP) decarboxylase enzyme that catalyzes L-lysine biosynthesis in the aspartate pathway in Streptomyces clavuligerus was overexpressed, and its effects on cephamycin C (CephC), clavulanic acid (CA), and tunicamycin productions were investigated. Multicopy expression of lysA gene under the control of glpF promoter (glpFp) in S. clavuligerus pCOlysA led to higher expression levels ranging from 2- to 6-fold increase at both lysA gene and CephC biosynthetic gene cluster at T36 and T48 of TSBG fermentation. These results accorded well with CephC production. Thus, 1.86- and 3.14-fold higher volumetric as well as 1.26- and 1.71-fold increased specific CephC yields were recorded in S. clavuligerus pCOlysA in comparison with the wild-type and its control strain, respectively, at 48th h. Increasing the expression of lysA provided 4.3 times more tunicamycin yields in the recombinant strain. These findings suggested that lysA overexpression in S. clavuligerus made the strain more productive for CephC and tunicamycin. The results also supported the presence of complex interactions among antibiotic biosynthesis pathways in S. clavuligerus.
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8
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Recent advances in the biosynthesis of nucleoside antibiotics. J Antibiot (Tokyo) 2019; 72:913-923. [PMID: 31554958 DOI: 10.1038/s41429-019-0236-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 08/24/2019] [Accepted: 09/07/2019] [Indexed: 01/27/2023]
Abstract
Nucleoside antibiotics are a diverse class of natural products with promising biomedical activities. These compounds contain a saccharide core and a nucleobase. Despite the large number of nucleoside antibiotics that have been reported, biosynthetic studies on these compounds have been limited compared with those on other types of natural products such as polyketides, peptides, and terpenoids. Due to recent advances in genome sequencing technology, the biosynthesis of nucleoside antibiotics has rapidly been clarified. This review covering 2009-2019 focuses on recent advances in the biosynthesis of nucleoside antibiotics.
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9
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Mechanism of action of nucleoside antibacterial natural product antibiotics. J Antibiot (Tokyo) 2019; 72:865-876. [DOI: 10.1038/s41429-019-0227-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/02/2019] [Accepted: 07/31/2019] [Indexed: 01/09/2023]
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10
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Dong YY, Wang H, Pike ACW, Cochrane SA, Hamedzadeh S, Wyszyński FJ, Bushell SR, Royer SF, Widdick DA, Sajid A, Boshoff HI, Park Y, Lucas R, Liu WM, Lee SS, Machida T, Minall L, Mehmood S, Belaya K, Liu WW, Chu A, Shrestha L, Mukhopadhyay SMM, Strain-Damerell C, Chalk R, Burgess-Brown NA, Bibb MJ, Barry Iii CE, Robinson CV, Beeson D, Davis BG, Carpenter EP. Structures of DPAGT1 Explain Glycosylation Disease Mechanisms and Advance TB Antibiotic Design. Cell 2019; 175:1045-1058.e16. [PMID: 30388443 PMCID: PMC6218659 DOI: 10.1016/j.cell.2018.10.037] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 08/01/2018] [Accepted: 10/15/2018] [Indexed: 12/24/2022]
Abstract
Protein N-glycosylation is a widespread post-translational modification. The first committed step in this process is catalysed by dolichyl-phosphate N-acetylglucosamine-phosphotransferase DPAGT1 (GPT/E.C. 2.7.8.15). Missense DPAGT1 variants cause congenital myasthenic syndrome and disorders of glycosylation. In addition, naturally-occurring bactericidal nucleoside analogues such as tunicamycin are toxic to eukaryotes due to DPAGT1 inhibition, preventing their clinical use. Our structures of DPAGT1 with the substrate UDP-GlcNAc and tunicamycin reveal substrate binding modes, suggest a mechanism of catalysis, provide an understanding of how mutations modulate activity (thus causing disease) and allow design of non-toxic “lipid-altered” tunicamycins. The structure-tuned activity of these analogues against several bacterial targets allowed the design of potent antibiotics for Mycobacterium tuberculosis, enabling treatment in vitro, in cellulo and in vivo, providing a promising new class of antimicrobial drug. Structures of DPAGT1 with UDP-GlcNAc and tunicamycin reveal mechanisms of catalysis DPAGT1 mutations in patients with glycosylation disorders modulate DPAGT1 activity Structures, kinetics and biosynthesis reveal role of lipid in tunicamycin Lipid-altered, tunicamycin analogues give non-toxic antibiotics against TB
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Affiliation(s)
- Yin Yao Dong
- Structural Genomics Consortium, University of Oxford, Oxford, OX3 7DQ, UK
| | - Hua Wang
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Ashley C W Pike
- Structural Genomics Consortium, University of Oxford, Oxford, OX3 7DQ, UK
| | - Stephen A Cochrane
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK; School of Chemistry and Chemical Engineering, Queen's University, Belfast, UK
| | - Sadra Hamedzadeh
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Filip J Wyszyński
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Simon R Bushell
- Structural Genomics Consortium, University of Oxford, Oxford, OX3 7DQ, UK
| | - Sylvain F Royer
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - David A Widdick
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Andaleeb Sajid
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Helena I Boshoff
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Yumi Park
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Ricardo Lucas
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Wei-Min Liu
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Seung Seo Lee
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Takuya Machida
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Leanne Minall
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | | | - Katsiaryna Belaya
- Neurosciences Group, Nuffield Department of Clinical Neuroscience, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Wei-Wei Liu
- Neurosciences Group, Nuffield Department of Clinical Neuroscience, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Amy Chu
- Structural Genomics Consortium, University of Oxford, Oxford, OX3 7DQ, UK
| | - Leela Shrestha
- Structural Genomics Consortium, University of Oxford, Oxford, OX3 7DQ, UK
| | | | | | - Rod Chalk
- Structural Genomics Consortium, University of Oxford, Oxford, OX3 7DQ, UK
| | | | - Mervyn J Bibb
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Clifton E Barry Iii
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | | | - David Beeson
- Neurosciences Group, Nuffield Department of Clinical Neuroscience, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Benjamin G Davis
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK.
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11
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Yamamoto K, Ichikawa S. Tunicamycin: chemical synthesis and biosynthesis. J Antibiot (Tokyo) 2019; 72:924-933. [PMID: 31235901 DOI: 10.1038/s41429-019-0200-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/20/2019] [Accepted: 05/27/2019] [Indexed: 11/09/2022]
Abstract
Tunicamycins are nucleoside natural products and show antibacterial, antiviral and antitumor activities, which are attributed to their inhibition of enzymatic reactions between polyisoprenyl phosphate and UDP-GlcNAc or UDP-MurNAc-pentapeptide. Because of their various intriguing biological activities, tunicamycins have potential as therapeutic agents for infectious diseases or cancers. Structurally, tunicamycins have a unique structure composed of an undecodialdose skeleton, a lipid chain and a GlcNAc fragment linked by a 1,1-β,α-trehalose-type glycosidic bond. In this mini review, we summarize the total chemical syntheses and biosynthetic studies of tunicamycins.
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Affiliation(s)
- Kazuki Yamamoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Satoshi Ichikawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan. .,Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan.
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12
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Martínez-Burgo Y, Santos-Aberturas J, Rodríguez-García A, Barreales EG, Tormo JR, Truman AW, Reyes F, Aparicio JF, Liras P. Activation of Secondary Metabolite Gene Clusters in Streptomyces clavuligerus by the PimM Regulator of Streptomyces natalensis. Front Microbiol 2019; 10:580. [PMID: 30984130 PMCID: PMC6448028 DOI: 10.3389/fmicb.2019.00580] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/06/2019] [Indexed: 11/13/2022] Open
Abstract
Expression of non-native transcriptional activators may be a powerful general method to activate secondary metabolites biosynthetic pathways. PAS-LuxR regulators, whose archetype is PimM, activate the biosynthesis of polyene macrolide antifungals and other antibiotics, and have been shown to be functionally preserved across multiple Streptomyces strains. In this work we show that constitutive expression of pimM in Streptomyces clavuligerus ATCC 27064 significantly affected its transcriptome and modifies secondary metabolism. Almost all genes in three secondary metabolite clusters were overexpressed, including the clusters responsible for the biosynthesis of the clinically important clavulanic acid and cephamycin C. In comparison to a control strain, this resulted in 10- and 7-fold higher production levels of these metabolites, respectively. Metabolomic and bioactivity studies of S. clavuligerus::pimM also revealed deep metabolic changes. Antifungal activity absent in the control strain was detected in S. clavuligerus::pimM, and determined to be the result of a fivefold increase in the production of the tunicamycin complex.
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Affiliation(s)
| | | | - Antonio Rodríguez-García
- Microbiology Section, Department of Molecular Biology, University of León, León, Spain.,Institute of Biotechnology of León, INBIOTEC, León, Spain
| | - Eva G Barreales
- Microbiology Section, Department of Molecular Biology, University of León, León, Spain
| | - José Rubén Tormo
- Centre of Excellence for Research into Innovative Medicine, Health Sciences Technology, MEDINA, Granada, Spain
| | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Fernando Reyes
- Centre of Excellence for Research into Innovative Medicine, Health Sciences Technology, MEDINA, Granada, Spain
| | - Jesús F Aparicio
- Microbiology Section, Department of Molecular Biology, University of León, León, Spain
| | - Paloma Liras
- Microbiology Section, Department of Molecular Biology, University of León, León, Spain
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13
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Shiraishi T, Nishiyama M, Kuzuyama T. Biosynthesis of the uridine-derived nucleoside antibiotic A-94964: identification and characterization of the biosynthetic gene cluster provide insight into the biosynthetic pathway. Org Biomol Chem 2019; 17:461-466. [PMID: 30570639 DOI: 10.1039/c8ob02765j] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The natural product A-94964 is a uridine-derived nucleoside antibiotic isolated from Streptomyces sp. SANK 60404. In this study, we propose a biosynthetic pathway for A-94964 using gene deletion experiments coupled with in silico analysis of the biosynthetic gene cluster. This study provides insights into the unique biosynthetic pathway for A-94964.
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Affiliation(s)
- Taro Shiraishi
- Biotechnology Research Center and Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8567, Japan.
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14
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Razzak MA, Lee J, Lee DW, Kim JH, Yoon HS, Hwang I. Expression of seven carbonic anhydrases in red alga Gracilariopsis chorda and their subcellular localization in a heterologous system, Arabidopsis thaliana. PLANT CELL REPORTS 2019; 38:147-159. [PMID: 30446790 DOI: 10.1007/s00299-018-2356-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 11/07/2018] [Indexed: 05/07/2023]
Abstract
Red alga, Gracilariopsis chorda, contains seven carbonic anhydrases that can be grouped into α-, β- and γ-classes. Carbonic anhydrases (CAHs) are metalloenzymes that catalyze the reversible hydration of CO2. These enzymes are present in all living organisms and play roles in various cellular processes, including photosynthesis. In this study, we identified seven CAH genes (GcCAHs) from the genome sequence of the red alga Gracilariopsis chorda and characterized them at the molecular, cellular and biochemical levels. Based on sequence analysis, these seven isoforms were categorized into four α-class, one β-class, and two γ-class isoforms. RNA sequencing revealed that of the seven CAHs isoforms, six genes were expressed in G. chorda in light at room temperature. In silico analysis revealed that these seven isoforms localized to multiple subcellular locations such as the ER, mitochondria and cytosol. When expressed as green fluorescent protein fusions in protoplasts of Arabidopsis thaliana leaf cells, these seven isoforms showed multiple localization patterns. The four α-class GcCAHs with an N-terminal hydrophobic leader sequence localized to the ER and two of them were further targeted to the vacuole. GcCAHβ1 with no noticeable signal sequence localized to the cytosol. The two γ-class GcCAHs also localized to the cytosol, despite the presence of a predicted presequence. Based on these results, we propose that the red alga G. chorda also employs multiple CAH isoforms for various cellular processes such as photosynthesis.
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Affiliation(s)
- Md Abdur Razzak
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, 37673, South Korea
| | - JunMo Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Dong Wook Lee
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, 37673, South Korea
| | - Jeong Hee Kim
- Department of Biochemistry and Molecular Biology, College of Dentistry, Kyung Hee University, Seoul, 130-701, South Korea
- Department of Life and Nanopharmaceutical Sciences, Graduate School, Kyung Hee University, Seoul, 130-701, South Korea
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Inhwan Hwang
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, 37673, South Korea.
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, South Korea.
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Generation of a cluster-free Streptomyces albus chassis strains for improved heterologous expression of secondary metabolite clusters. Metab Eng 2018; 49:316-324. [DOI: 10.1016/j.ymben.2018.09.004] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 08/26/2018] [Accepted: 09/05/2018] [Indexed: 12/19/2022]
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Analysis of the Tunicamycin Biosynthetic Gene Cluster of Streptomyces chartreusis Reveals New Insights into Tunicamycin Production and Immunity. Antimicrob Agents Chemother 2018; 62:AAC.00130-18. [PMID: 29844049 PMCID: PMC6105854 DOI: 10.1128/aac.00130-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 05/10/2018] [Indexed: 11/20/2022] Open
Abstract
The tunicamycin biosynthetic gene cluster of Streptomyces chartreusis consists of 14 genes (tunA to tunN) with a high degree of apparent translational coupling. Transcriptional analysis revealed that all of these genes are likely to be transcribed as a single operon from two promoters, tunp1 and tunp2. In-frame deletion analysis revealed that just six of these genes (tunABCDEH) are essential for tunicamycin production in the heterologous host Streptomyces coelicolor, while five (tunFGKLN) with likely counterparts in primary metabolism are not necessary, but presumably ensure efficient production of the antibiotic at the onset of tunicamycin biosynthesis. Three genes are implicated in immunity, namely, tunI and tunJ, which encode a two-component ABC transporter presumably required for export of the antibiotic, and tunM, which encodes a putative S-adenosylmethionine (SAM)-dependent methyltransferase. Expression of tunIJ or tunM in S. coelicolor conferred resistance to exogenous tunicamycin. The results presented here provide new insights into tunicamycin biosynthesis and immunity.
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Schwarz PN, Buchmann A, Roller L, Kulik A, Gross H, Wohlleben W, Stegmann E. The Immunosuppressant Brasilicardin: Determination of the Biosynthetic Gene Cluster in the Heterologous HostAmycolatopsis japonicum. Biotechnol J 2017; 13. [DOI: 10.1002/biot.201700527] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 10/05/2017] [Indexed: 12/28/2022]
Affiliation(s)
- Paul N. Schwarz
- Microbiology/Biotechnology; Interfaculty Institute of Microbiology and Infection Medicine (IMIT); Eberhard Karls University of Tübingen; Tübingen Germany
| | - Anina Buchmann
- Department of Pharmaceutical Biology; Pharmaceutical Institute; Eberhard Karls University of Tübingen; Tübingen Germany
| | - Luisa Roller
- Microbiology/Biotechnology; Interfaculty Institute of Microbiology and Infection Medicine (IMIT); Eberhard Karls University of Tübingen; Tübingen Germany
| | - Andreas Kulik
- Microbiology/Biotechnology; Interfaculty Institute of Microbiology and Infection Medicine (IMIT); Eberhard Karls University of Tübingen; Tübingen Germany
| | - Harald Gross
- Department of Pharmaceutical Biology; Pharmaceutical Institute; Eberhard Karls University of Tübingen; Tübingen Germany
- German Centre for Infection Research (DZIF); Partner Site Tübingen; Tübingen Germany
| | - Wolfgang Wohlleben
- Microbiology/Biotechnology; Interfaculty Institute of Microbiology and Infection Medicine (IMIT); Eberhard Karls University of Tübingen; Tübingen Germany
- German Centre for Infection Research (DZIF); Partner Site Tübingen; Tübingen Germany
| | - Evi Stegmann
- Microbiology/Biotechnology; Interfaculty Institute of Microbiology and Infection Medicine (IMIT); Eberhard Karls University of Tübingen; Tübingen Germany
- German Centre for Infection Research (DZIF); Partner Site Tübingen; Tübingen Germany
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Selective catalytic hydrogenation of the N-acyl and uridyl double bonds in the tunicamycin family of protein N-glycosylation inhibitors. J Antibiot (Tokyo) 2017; 70:1122-1128. [DOI: 10.1038/ja.2017.141] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 09/29/2017] [Accepted: 10/02/2017] [Indexed: 02/04/2023]
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Sechler AJ, Tancos MA, Schneider DJ, King JG, Fennessey CM, Schroeder BK, Murray TD, Luster DG, Schneider WL, Rogers EE. Whole genome sequence of two Rathayibacter toxicus strains reveals a tunicamycin biosynthetic cluster similar to Streptomyces chartreusis. PLoS One 2017; 12:e0183005. [PMID: 28796837 PMCID: PMC5552033 DOI: 10.1371/journal.pone.0183005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 07/27/2017] [Indexed: 11/20/2022] Open
Abstract
Rathayibacter toxicus is a forage grass associated Gram-positive bacterium of major concern to food safety and agriculture. This species is listed by USDA-APHIS as a plant pathogen select agent because it produces a tunicamycin-like toxin that is lethal to livestock and may be vectored by nematode species native to the U.S. The complete genomes of two strains of R. toxicus, including the type strain FH-79, were sequenced and analyzed in comparison with all available, complete R. toxicus genomes. Genome sizes ranged from 2,343,780 to 2,394,755 nucleotides, with 2079 to 2137 predicted open reading frames; all four strains showed remarkable synteny over nearly the entire genome, with only a small transposed region. A cluster of genes with similarity to the tunicamycin biosynthetic cluster from Streptomyces chartreusis was identified. The tunicamycin gene cluster (TGC) in R. toxicus contained 14 genes in two transcriptional units, with all of the functional elements for tunicamycin biosynthesis present. The TGC had a significantly lower GC content (52%) than the rest of the genome (61.5%), suggesting that the TGC may have originated from a horizontal transfer event. Further analysis indicated numerous remnants of other potential horizontal transfer events are present in the genome. In addition to the TGC, genes potentially associated with carotenoid and exopolysaccharide production, bacteriocins and secondary metabolites were identified. A CRISPR array is evident. There were relatively few plant-associated cell-wall hydrolyzing enzymes, but there were numerous secreted serine proteases that share sequence homology to the pathogenicity-associated protein Pat-1 of Clavibacter michiganensis. Overall, the genome provides clear insight into the possible mechanisms for toxin production in R. toxicus, providing a basis for future genetic approaches.
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Affiliation(s)
- Aaron J Sechler
- Foreign Disease/Weed Science Research Unit, Agricultural Research Service, U.S. Dept. of Agriculture, Frederick, Maryland, United States of America
| | - Matthew A Tancos
- Foreign Disease/Weed Science Research Unit, Agricultural Research Service, U.S. Dept. of Agriculture, Frederick, Maryland, United States of America
| | - David J Schneider
- Emerging Pests and Pathogens Research Unit, Agricultural Research Service, U.S. Dept. of Agriculture, Ithaca, New York, United States of America
| | - Jonas G King
- Foreign Disease/Weed Science Research Unit, Agricultural Research Service, U.S. Dept. of Agriculture, Frederick, Maryland, United States of America
| | - Christine M Fennessey
- Foreign Disease/Weed Science Research Unit, Agricultural Research Service, U.S. Dept. of Agriculture, Frederick, Maryland, United States of America
| | - Brenda K Schroeder
- Dept. of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, Idaho, United States of America
| | - Timothy D Murray
- Dept. of Plant Pathology, Washington State University, Pullman, Washington, United States of America
| | - Douglas G Luster
- Foreign Disease/Weed Science Research Unit, Agricultural Research Service, U.S. Dept. of Agriculture, Frederick, Maryland, United States of America
| | - William L Schneider
- Foreign Disease/Weed Science Research Unit, Agricultural Research Service, U.S. Dept. of Agriculture, Frederick, Maryland, United States of America
| | - Elizabeth E Rogers
- Foreign Disease/Weed Science Research Unit, Agricultural Research Service, U.S. Dept. of Agriculture, Frederick, Maryland, United States of America
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Murray TD, Schroeder BK, Schneider WL, Luster DG, Sechler A, Rogers EE, Subbotin SA. Rathayibacter toxicus, Other Rathayibacter Species Inducing Bacterial Head Blight of Grasses, and the Potential for Livestock Poisonings. PHYTOPATHOLOGY 2017; 107:804-815. [PMID: 28414631 DOI: 10.1094/phyto-02-17-0047-rvw] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Rathayibacter toxicus, a Select Agent in the United States, is one of six recognized species in the genus Rathayibacter and the best known due to its association with annual ryegrass toxicity, which occurs only in parts of Australia. The Rathayibacter species are unusual among phytopathogenic bacteria in that they are transmitted by anguinid seed gall nematodes and produce extracellular polysaccharides in infected plants resulting in bacteriosis diseases with common names such as yellow slime and bacterial head blight. R. toxicus is distinguished from the other species by producing corynetoxins in infected plants; toxin production is associated with infection by a bacteriophage. These toxins cause grazing animals feeding on infected plants to develop convulsions and abnormal gate, which is referred to as "staggers," and often results in death of affected animals. R. toxicus is the only recognized Rathayibacter species to produce toxin, although reports of livestock deaths in the United States suggest a closely related toxigenic species may be present. A closely related but undescribed species, Rathayibacter sp. EV, originally isolated from Ehrharta villosa var. villosa in South Africa, is suspected of producing toxin. Many of the diseases caused by Rathayibacter species occur in arid areas and the extracellular polysaccharide they produce is believed to aid in their survival between crops. For example, R. "agropyri" was isolated from infected plant material after being stored for 50 years in a herbarium. Similarly, the anguinid vectors associated with these bacteria form seed galls in infected plants and are capable of surviving for very long periods of time under dry conditions. The addition of R. toxicus to the list of Select Agents has raised concern over its potential introduction and a realization that current diagnostic methods are inadequate to distinguish among Rathayibacter species. In addition, little is known about the Rathayibacter species and their seed gall nematode vectors present in the United States.
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Affiliation(s)
- Timothy D Murray
- First author: Department of Plant Pathology, Washington State University, Pullman, WA 99164; second author: Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, ID 83844; third, fourth, fifth, and sixth authors: U.S. Department of Agriculture, Agricultural Research Service, Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD 21702; and seventh author: California Department of Food and Agriculture, 3294, Meadowview Road, Sacramento, CA 95832-1448
| | - Brenda K Schroeder
- First author: Department of Plant Pathology, Washington State University, Pullman, WA 99164; second author: Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, ID 83844; third, fourth, fifth, and sixth authors: U.S. Department of Agriculture, Agricultural Research Service, Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD 21702; and seventh author: California Department of Food and Agriculture, 3294, Meadowview Road, Sacramento, CA 95832-1448
| | - William L Schneider
- First author: Department of Plant Pathology, Washington State University, Pullman, WA 99164; second author: Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, ID 83844; third, fourth, fifth, and sixth authors: U.S. Department of Agriculture, Agricultural Research Service, Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD 21702; and seventh author: California Department of Food and Agriculture, 3294, Meadowview Road, Sacramento, CA 95832-1448
| | - Douglas G Luster
- First author: Department of Plant Pathology, Washington State University, Pullman, WA 99164; second author: Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, ID 83844; third, fourth, fifth, and sixth authors: U.S. Department of Agriculture, Agricultural Research Service, Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD 21702; and seventh author: California Department of Food and Agriculture, 3294, Meadowview Road, Sacramento, CA 95832-1448
| | - Aaron Sechler
- First author: Department of Plant Pathology, Washington State University, Pullman, WA 99164; second author: Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, ID 83844; third, fourth, fifth, and sixth authors: U.S. Department of Agriculture, Agricultural Research Service, Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD 21702; and seventh author: California Department of Food and Agriculture, 3294, Meadowview Road, Sacramento, CA 95832-1448
| | - Elizabeth E Rogers
- First author: Department of Plant Pathology, Washington State University, Pullman, WA 99164; second author: Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, ID 83844; third, fourth, fifth, and sixth authors: U.S. Department of Agriculture, Agricultural Research Service, Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD 21702; and seventh author: California Department of Food and Agriculture, 3294, Meadowview Road, Sacramento, CA 95832-1448
| | - Sergei A Subbotin
- First author: Department of Plant Pathology, Washington State University, Pullman, WA 99164; second author: Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, ID 83844; third, fourth, fifth, and sixth authors: U.S. Department of Agriculture, Agricultural Research Service, Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD 21702; and seventh author: California Department of Food and Agriculture, 3294, Meadowview Road, Sacramento, CA 95832-1448
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21
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Bugg TDH. Nucleoside Natural Product Antibiotics Targetting Microbial Cell Wall Biosynthesis. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/7355_2017_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
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22
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Nature's combinatorial biosynthesis and recently engineered production of nucleoside antibiotics in Streptomyces. World J Microbiol Biotechnol 2017; 33:66. [PMID: 28260195 DOI: 10.1007/s11274-017-2233-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 02/22/2017] [Indexed: 10/20/2022]
Abstract
Modified nucleosides produced by Streptomyces and related actinomycetes are widely used in agriculture and medicine as antibacterial, antifungal, anticancer and antiviral agents. These specialized small-molecule metabolites are biosynthesized by complex enzymatic machineries encoded within gene clusters in the genome. The past decade has witnessed a burst of reports defining the key metabolic processes involved in the biosynthesis of several distinct families of nucleoside antibiotics. Furthermore, genome sequencing of various Streptomyces species has dramatically increased over recent years. Potential biosynthetic gene clusters for novel nucleoside antibiotics are now apparent by analysis of these genomes. Here we revisit strategies for production improvement of nucleoside antibiotics that have defined mechanisms of action, and are in clinical or agricultural use. We summarize the progress for genetically manipulating biosynthetic pathways for structural diversification of nucleoside antibiotics. Microorganism-based biosynthetic examples are provided and organized under genetic principles and metabolic engineering guidelines. We show perspectives on the future of combinatorial biosynthesis, and present a working model for discovery of novel nucleoside natural products in Streptomyces.
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23
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Quinovosamycins: new tunicamycin-type antibiotics in which the α, β-1″,11′-linked N-acetylglucosamine residue is replaced by N-acetylquinovosamine. J Antibiot (Tokyo) 2016; 69:637-46. [DOI: 10.1038/ja.2016.49] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/22/2016] [Accepted: 04/03/2016] [Indexed: 02/06/2023]
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24
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Next Generation Sequencing of Actinobacteria for the Discovery of Novel Natural Products. Mar Drugs 2016; 14:md14040078. [PMID: 27089350 PMCID: PMC4849082 DOI: 10.3390/md14040078] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 04/01/2016] [Accepted: 04/06/2016] [Indexed: 12/17/2022] Open
Abstract
Like many fields of the biosciences, actinomycete natural products research has been revolutionised by next-generation DNA sequencing (NGS). Hundreds of new genome sequences from actinobacteria are made public every year, many of them as a result of projects aimed at identifying new natural products and their biosynthetic pathways through genome mining. Advances in these technologies in the last five years have meant not only a reduction in the cost of whole genome sequencing, but also a substantial increase in the quality of the data, having moved from obtaining a draft genome sequence comprised of several hundred short contigs, sometimes of doubtful reliability, to the possibility of obtaining an almost complete and accurate chromosome sequence in a single contig, allowing a detailed study of gene clusters and the design of strategies for refactoring and full gene cluster synthesis. The impact that these technologies are having in the discovery and study of natural products from actinobacteria, including those from the marine environment, is only starting to be realised. In this review we provide a historical perspective of the field, analyse the strengths and limitations of the most relevant technologies, and share the insights acquired during our genome mining projects.
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25
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Natural and engineered biosynthesis of nucleoside antibiotics in Actinomycetes. ACTA ACUST UNITED AC 2016; 43:401-17. [DOI: 10.1007/s10295-015-1636-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 05/15/2015] [Indexed: 12/18/2022]
Abstract
Abstract
Nucleoside antibiotics constitute an important family of microbial natural products bearing diverse bioactivities and unusual structural features. Their biosynthetic logics are unique with involvement of complex multi-enzymatic reactions leading to the intricate molecules from simple building blocks. Understanding how nature builds this family of antibiotics in post-genomic era sets the stage for rational enhancement of their production, and also paves the way for targeted persuasion of the cell factories to make artificial designer nucleoside drugs and leads via synthetic biology approaches. In this review, we discuss the recent progress and perspectives on the natural and engineered biosynthesis of nucleoside antibiotics.
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27
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A Modular Approach to the Total Synthesis of Tunicamycins. Angew Chem Int Ed Engl 2015; 54:6618-21. [DOI: 10.1002/anie.201501890] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Indexed: 01/31/2023]
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Singh R, Reynolds KA. Characterization of FabG and FabI of theStreptomyces coelicolorDissociated Fatty Acid Synthase. Chembiochem 2015; 16:631-40. [DOI: 10.1002/cbic.201402670] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Indexed: 12/16/2022]
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29
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Niu G, Tan H. Nucleoside antibiotics: biosynthesis, regulation, and biotechnology. Trends Microbiol 2015; 23:110-9. [DOI: 10.1016/j.tim.2014.10.007] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 10/15/2014] [Accepted: 10/22/2014] [Indexed: 11/30/2022]
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30
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Ma G, Liu Y. The reaction mechanism of UDP-GlcNAc 5,6-dehydratase: a quantum mechanical/molecular mechanical (QM/MM) study. Theor Chem Acc 2014. [DOI: 10.1007/s00214-014-1524-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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31
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Hiratsuka T, Suzuki H, Kariya R, Seo T, Minami A, Oikawa H. Biosynthesis of the Structurally Unique Polycyclopropanated Polyketide-Nucleoside Hybrid Jawsamycin (FR-900848). Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402623] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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32
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Hiratsuka T, Suzuki H, Kariya R, Seo T, Minami A, Oikawa H. Biosynthesis of the Structurally Unique Polycyclopropanated Polyketide-Nucleoside Hybrid Jawsamycin (FR-900848). Angew Chem Int Ed Engl 2014; 53:5423-6. [DOI: 10.1002/anie.201402623] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Indexed: 02/06/2023]
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33
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Heterologous expression of natural product biosynthetic gene clusters in Streptomyces coelicolor: from genome mining to manipulation of biosynthetic pathways. ACTA ACUST UNITED AC 2014; 41:425-31. [DOI: 10.1007/s10295-013-1348-5] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 09/12/2013] [Indexed: 12/22/2022]
Abstract
Abstract
Heterologous gene expression is one of the main strategies used to access the full biosynthetic potential of actinomycetes, as well as to study the metabolic pathways of natural product biosynthesis and to create unnatural pathways. Streptomyces coelicolor A3(2) is the most studied member of the actinomycetes, bacteria renowned for their prolific capacity to synthesize a wide range of biologically active specialized metabolites. We review here the use of strains of this species for the heterologous production of structurally diverse actinomycete natural products.
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Abstract
Actinomycetes are prolific producers of natural products with a wide range of biological activities. Many of the compounds that they make (and derivatives thereof) are used extensively in medicine, most notably as clinically important antibiotics, and in agriculture. Moreover, these organisms remain a source of novel and potentially useful molecules, but maximizing their biosynthetic potential requires a better understanding of natural product biosynthesis. Recent developments in genome sequencing have greatly facilitated the identification of natural product biosynthetic gene clusters. In the present article, I summarize the recent contributions of our laboratory in applying genomic technologies to better understand and manipulate natural product biosynthesis in a range of different actinomycetes.
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Makitrynskyy R, Ostash B, Tsypik O, Rebets Y, Doud E, Meredith T, Luzhetskyy A, Bechthold A, Walker S, Fedorenko V. Pleiotropic regulatory genes bldA, adpA and absB are implicated in production of phosphoglycolipid antibiotic moenomycin. Open Biol 2013; 3:130121. [PMID: 24153004 PMCID: PMC3814723 DOI: 10.1098/rsob.130121] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Unlike the majority of actinomycete secondary metabolic pathways, the biosynthesis of peptidoglycan glycosyltransferase inhibitor moenomycin in Streptomyces ghanaensis does not involve any cluster-situated regulators (CSRs). This raises questions about the regulatory signals that initiate and sustain moenomycin production. We now show that three pleiotropic regulatory genes for Streptomyces morphogenesis and antibiotic production—bldA, adpA and absB—exert multi-layered control over moenomycin biosynthesis in native and heterologous producers. The bldA gene for tRNALeuUAA is required for the translation of rare UUA codons within two key moenomycin biosynthetic genes (moe), moeO5 and moeE5. It also indirectly influences moenomycin production by controlling the translation of the UUA-containing adpA and, probably, other as-yet-unknown repressor gene(s). AdpA binds key moe promoters and activates them. Furthermore, AdpA interacts with the bldA promoter, thus impacting translation of bldA-dependent mRNAs—that of adpA and several moe genes. Both adpA expression and moenomycin production are increased in an absB-deficient background, most probably because AbsB normally limits adpA mRNA abundance through ribonucleolytic cleavage. Our work highlights an underappreciated strategy for secondary metabolism regulation, in which the interaction between structural genes and pleiotropic regulators is not mediated by CSRs. This strategy might be relevant for a growing number of CSR-free gene clusters unearthed during actinomycete genome mining.
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Affiliation(s)
- Roman Makitrynskyy
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho st. 4, Lviv 79005, Ukraine
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Kwon SY, Kwon HJ. The Possible Role of SCO3388, a tmrB-like Gene of Streptomyces coelicolor, in Germination and Stress Survival of Spores. ACTA ACUST UNITED AC 2013. [DOI: 10.3839/jabc.2013.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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37
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Lin CI, McCarty RM, Liu HW. The biosynthesis of nitrogen-, sulfur-, and high-carbon chain-containing sugars. Chem Soc Rev 2013; 42:4377-407. [PMID: 23348524 PMCID: PMC3641179 DOI: 10.1039/c2cs35438a] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Carbohydrates serve many structural and functional roles in biology. While the majority of monosaccharides are characterized by the chemical composition (CH2O)n, modifications including deoxygenation, C-alkylation, amination, O- and N-methylation, which are characteristic of many sugar appendages of secondary metabolites, are not uncommon. Interestingly, some sugar molecules are formed via modifications including amine oxidation, sulfur incorporation, and "high-carbon" chain attachment. Most of these unusual sugars have been identified over the past several decades as components of microbially produced natural products, although a few high-carbon sugars are also found in the lipooligosaccharides of the outer cell walls of Gram-negative bacteria. Despite their broad distribution in nature, these sugars are considered "rare" due to their relative scarcity. The biosynthetic steps that underlie their formation continue to perplex researchers to this day and many questions regarding key transformations remain unanswered. This review will focus on our current understanding of the biosynthesis of unusual sugars bearing oxidized amine substituents, thio-functional groups, and high-carbon chains.
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Affiliation(s)
| | | | - Hung-wen Liu
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712
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Biosynthesis of the tunicamycin antibiotics proceeds via unique exo-glycal intermediates. Nat Chem 2012; 4:539-46. [DOI: 10.1038/nchem.1351] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 04/03/2012] [Indexed: 11/08/2022]
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Genome sequences of three tunicamycin-producing Streptomyces Strains, S. chartreusis NRRL 12338, S. chartreusis NRRL 3882, and S. lysosuperificus ATCC 31396. J Bacteriol 2012; 193:7021-2. [PMID: 22123769 DOI: 10.1128/jb.06262-11] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We announce the sequencing of Streptomyces chartreusis NRRL 12338 and NRRL 3882 and Streptomyces lysosuperificus ATCC 31396. These are producers of tunicamycins, chartreusins, cephalosporins, holomycins, and calcimycin. The announced genomes, together with the published Streptomyces clavuligerus genome, will facilitate data mining of these secondary metabolites.
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Yang Z, Unrine J, Nonaka K, Van Lanen SG. Fe(II)-dependent, uridine-5'-monophosphate α-ketoglutarate dioxygenases in the synthesis of 5'-modified nucleosides. Methods Enzymol 2012; 516:153-68. [PMID: 23034228 PMCID: PMC3831618 DOI: 10.1016/b978-0-12-394291-3.00031-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Several nucleoside antibiotics from various actinomycetes contain a high-carbon sugar nucleoside that is putatively derived via C-5'-modification of the canonical nucleoside. Two prominent examples are the 5'-C-carbamoyluridine- and 5'-C-glycyluridine-containing nucleosides, both families of which were discovered using screens aimed at finding inhibitors of bacterial translocase I involved in the assembly of the bacterial peptidoglycan cell wall. A shared open reading frame was identified whose gene product is similar to enzymes of the nonheme, Fe(II)-, and α-ketoglutarate-dependent dioxygenases. The enzyme LipL from the biosynthetic pathway for A-90289, a 5'-C-glycyluridine-containing nucleoside, was functionally characterized as an UMP:α-ketoglutarate dioxygenase, providing the enzymatic imperative for the generation of a nucleoside-5'-aldehdye that serves as a downstream substrate for an aldol or aldol-type reaction leading to the high-carbon sugar scaffold. The functional assignment of LipL and the homologous enzymes-including bioinformatic analysis, iron detection and quantification, and assay development for biochemical characterization-is presented herein.
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Affiliation(s)
- Zhaoyong Yang
- Key Laboratory of Biotechnology of Antibiotics, Ministry of Health, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Jason Unrine
- Department of Plant and Soil Sciences, College of Agriculture, University of Kentucky, Lexington, KY 40536, USA
| | - Koichi Nonaka
- Biopharmaceutical Research Group I, Biopharmaceutical Technology Research Laboratories, Pharmaceutical Technology Division, Daiichi Sankyo Co., Ltd., 2716-1, Kurakake, Akaiwa, Chiyoda-machi, Ohra-gun, Gunma 370-0503, Japan
| | - Steven G. Van Lanen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 S. Limestone, Lexington, KY 40536, USA
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Wang J, Xiong Z, Meng H, Wang Y, Wang Y. Synthetic biology triggers new era of antibiotics development. Subcell Biochem 2012; 64:95-114. [PMID: 23080247 DOI: 10.1007/978-94-007-5055-5_5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
As a discipline to design and construct organisms with desired properties, synthetic biology has generated rapid progresses in the last decade. Combined synthetic biology with the traditional process, a new universal workflow for drug development has been becoming more and more attractive. The new methodology exhibits more efficient and inexpensive comparing to traditional methods in every aspect, such as new compounds discovery & screening, process design & drug manufacturing. This article reviews the application of synthetic biology in antibiotics development, including new drug discovery and screening, combinatorial biosynthesis to generate more analogues and heterologous expression of biosynthetic gene clusters with systematic engineering the recombinant microbial systems for large scale production.
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Affiliation(s)
- Jianfeng Wang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
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Gomez-Escribano JP, Song L, Bibb MJ, Challis GL. Posttranslational β-methylation and macrolactamidination in the biosynthesis of the bottromycin complex of ribosomal peptide antibiotics. Chem Sci 2012. [DOI: 10.1039/c2sc21183a] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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