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Nguyen N, Forstater JH, McIntosh JA. Decarboxylation in Natural Products Biosynthesis. JACS AU 2024; 4:2715-2745. [PMID: 39211618 PMCID: PMC11350588 DOI: 10.1021/jacsau.4c00425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/01/2024] [Accepted: 07/05/2024] [Indexed: 09/04/2024]
Abstract
Decarboxylation reactions are frequently found in the biosynthesis of primary and secondary metabolites. Decarboxylase enzymes responsible for these transformations operate via diverse mechanisms and act on a large variety of substrates, making them appealing in terms of biotechnological applications. This Perspective focuses on the occurrence of decarboxylation reactions in natural product biosynthesis and provides a perspective on their applications in biocatalysis for fine chemicals and pharmaceuticals.
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2
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Kudo F. Biosynthesis of macrolactam antibiotics with β-amino acid polyketide starter units. J Antibiot (Tokyo) 2024; 77:486-498. [PMID: 38816450 PMCID: PMC11284099 DOI: 10.1038/s41429-024-00742-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/04/2024] [Accepted: 05/06/2024] [Indexed: 06/01/2024]
Abstract
Macrolactam antibiotics incorporating β-amino acid polyketide starter units, isolated primarily from Actinomycetes species, show significant biological activities. This review provides a detailed analysis into the biosynthetic studies of vicenistatin, a macrolactam antibiotic with a 3-aminoisobutyrate starter unit, as well as biosynthetic research on related macrolactam compounds. Firstly, the elucidation of a common mechanism for the incorporation of β-amino acid starter units into the polyketide synthase (PKS) is described. Secondly, the unique biosynthetic mechanisms of the β-amino acids that are used to supply the main macrolactam biosynthetic pathways with starter units are discussed. Thirdly, some distinctive post-PKS modification mechanisms that complete macrolactam antibiotic biosynthesis are summarized. Finally, future directions for creating new macrolactam compounds through engineered biosynthesis pathways are described.
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Affiliation(s)
- Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo, 152-8551, Japan.
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3
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Benninghaus L, Zagami L, Tassini G, Meyer F, Wendisch VF. γ-Glutamylation of Isopropylamine by Fermentation. Chembiochem 2024; 25:e202300608. [PMID: 37987374 DOI: 10.1002/cbic.202300608] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 11/22/2023]
Abstract
Glutamylation yields N-functionalized amino acids in several natural pathways. γ-Glutamylated amino acids may exhibit improved properties for their industrial application, e. g., as taste enhancers or in peptide drugs. γ-Glutamyl-isopropylamide (GIPA) can be synthesized from isopropylamine (IPA) and l-glutamate. In Pseudomonas sp. strain KIE171, GIPA is an intermediate in the biosynthesis of l-alaninol (2-amino-1-propanol), a precursor of the fluorochinolone antibiotic levofloxacin and of the chloroacetanilide herbicide metolachlor. In this study, fermentative production of GIPA with metabolically engineered Pseudomonas putida KT2440 using γ-glutamylmethylamide synthetase (GMAS) from Methylorubrum extorquens was established. Upon addition of IPA during growth with glycerol as carbon source in shake flasks, the recombinant strain produced up to 21.8 mM GIPA. In fed-batch bioreactor cultivations, GIPA accumulated to a titer of 11 g L-1 with a product yield of 0.11 g g-1 glycerol and a volumetric productivity of 0.24 g L-1 h-1 . To the best of our knowledge, this is the first fermentative production of GIPA.
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Affiliation(s)
- Leonie Benninghaus
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Laura Zagami
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Giulio Tassini
- School of Science Mathematics Physical and Natural Sciences, University of Florence, Piazza San Marco 4, 50121, Firenze, Italy
| | - Florian Meyer
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
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4
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Amino acid (acyl carrier protein) ligase-associated biosynthetic gene clusters reveal unexplored biosynthetic potential. Mol Genet Genomics 2023; 298:49-65. [PMID: 36271918 DOI: 10.1007/s00438-022-01962-7] [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: 05/04/2022] [Accepted: 10/09/2022] [Indexed: 01/10/2023]
Abstract
This study aimed to evaluate the postulated cellular function of a novel family of amino acid (acyl carrier protein) ligases (AALs) in natural product biosynthesis. Here, we analyzed the manually curated, putative, aal-associated natural product biosynthetic gene clusters (NP BGCs) using two computational platforms for NP prediction, antiSMASH-BiG-SCAPE-CORASON and DeepBGC. The detected BGCs included a diversity of type I polyketide/nonribosomal peptide (PKS/NRPS) hybrid BGCs, exemplified by the guadinomine BGC, which suggested a dedicated function of AALs in the biosynthesis of rare (2S)-aminomalonyl-ACP extension units. Besides modular PKS/NRPSs and NRPSs, AAL-associated BGCs were predicted to assemble arylpolyenes, ladderane lipids, phosphonates, aminoglycosides, β-lactones, and thioamides of both nonribosomal and ribosomal origins. Additionally, we revealed a frequent association of AALs with putative, seldom observed transglutaminase-like and BtrH-like transferases of the cysteine protease superfamily, which may form larger families of ACP-dependent amide bond catalysts used in NP synthesis. Our results disclosed an exceptional chemical novelty and biosynthetic potential of the AAL-associated BGCs in NP biosynthesis. The presented in silico evidence supports the initial hypothesis and provides an important foundation for future experimental studies aimed at discovering novel pharmaceutically relevant active compounds.
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Oxalactam A, a Novel Macrolactam with Potent Anti- Rhizoctonia solani Activity from the Endophytic Fungus Penicillium oxalicum. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27248811. [PMID: 36557941 PMCID: PMC9788486 DOI: 10.3390/molecules27248811] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022]
Abstract
A novel macrolactam named oxalactam A (1), three known dipeptides (2-4) as well as other known alkaloids (5-7) were obtained from the endophytic fungus Penicillium oxalicum, which was derived from the tuber of Icacina trichantha (Icacinaceae). All chemical structures were established based on spectroscopic data, chemical methods, ECD calculations, and 13C-DP4+ analysis. Among them, oxalactam A (1) is a 16-membered polyenic macrolactam bearing a new skeleton of 2,9-dimethyl-azacyclohexadecane core and exhibited potent anti-Rhizoctonia solani activity with a MIC value of 10 μg/mL in vitro. The plausible biosynthetic pathway of 1 was also proposed via the alanyl protecting mechanism. Notably, three dipeptides (2-4) were first identified from the endophytic fungus P. oxalicum and the NMR data of cyclo(L-Trp-L-Glu) (2) was reported for the first time. In addition, the binding interactions between compound 1 and the sterol 14α-demethylase enzyme (CYP51) were studied by molecular docking and dynamics technologies, and the results revealed that the 16-membered polyenic macrolactam could be a promising CYP51 inhibitor to develop as a new anti-Rhizoctonia solani fungicide.
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6
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Crystal structure of BtrK, a decarboxylase involved in the (S)-4-amino-2-hydroxybutyrate (AHBA) formation during butirosin biosynthesis. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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7
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Zhang H, Zhang C, Li Q, Ma J, Ju J. Metabolic Blockade-Based Genome Mining Reveals Lipochain-Linked Dihydro-β-alanine Synthetases Involved in Autucedine Biosynthesis. Org Lett 2022; 24:5535-5540. [PMID: 35876054 DOI: 10.1021/acs.orglett.2c01957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Huaran Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Rd., Nansha District, Guangzhou 511458, China
- College of Oceanology, University of Chinese Academy of Sciences, Qingdao 266400, China
| | - Chunyan Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Qinglian Li
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Rd., Nansha District, Guangzhou 511458, China
- College of Oceanology, University of Chinese Academy of Sciences, Qingdao 266400, China
| | - Junying Ma
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Rd., Nansha District, Guangzhou 511458, China
- College of Oceanology, University of Chinese Academy of Sciences, Qingdao 266400, China
| | - Jianhua Ju
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Rd., Nansha District, Guangzhou 511458, China
- College of Oceanology, University of Chinese Academy of Sciences, Qingdao 266400, China
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Abstract
Colchicine (1) is a bioactive plant alkaloid from Colchicum and Gloriosa species that is used as a pharmaceutical treatment for inflammatory diseases, including gouty arthritis and familial Mediterranean fever. The activity of this alkaloid is attributed to its ability to bind tubulin dimers and inhibit microtubule assembly, which not only promotes anti-inflammatory effects, but also makes colchicine a potent mitotic poison. The biochemical origins of colchicine biosynthesis have been investigated for over 50 years, but only recently has the underlying enzymatic machinery become clear. Here, we report the discovery of multiple pathway enzymes from Gloriosa superba that allows for the reconstitution of a complete metabolic route to 1. This includes three enzymes that process a previously established tropolone-containing intermediate into 1 via tailoring of the nitrogen atom. We further demonstrate the total biosynthesis of enantiopure (-)-1 from primary metabolites via heterologous production in a model plant, thus enabling future efforts for the metabolic engineering of this medicinal alkaloid. Additionally, our results provide insight into the timing and tissue specificity for the late stage modifications required in colchicine biosynthesis, which are likely connected to the biological functions for this class of medicinal alkaloids in native producing plants.
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Affiliation(s)
- Ryan S. Nett
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford, CA 94305, USA
| | - Elizabeth S. Sattely
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford, CA 94305, USA
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9
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Simunović V. Genomic and molecular evidence reveals novel pathways associated with cell surface polysaccharides in bacteria. FEMS Microbiol Ecol 2021; 97:6355432. [PMID: 34415013 DOI: 10.1093/femsec/fiab119] [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: 05/21/2021] [Accepted: 08/18/2021] [Indexed: 11/13/2022] Open
Abstract
Amino acid (acyl carrier protein) ligases (AALs) are a relatively new family of bacterial amino acid adenylating enzymes with unknown function(s). Here, genomic enzymology tools that employ sequence similarity networks and genome context analyses were used to hypothesize the metabolic function(s) of AALs. In over 50% of species, aal and its cognate acyl carrier protein (acp) genes, along with three more genes, formed a highly conserved AAL cassette. AAL cassettes were strongly associated with surface polysaccharide gene clusters in Proteobacteria and Actinobacteria, yet were prevalent among soil and rhizosphere-associated α- and β-Proteobacteria, including symbiotic α- and β-rhizobia and some Mycolata. Based on these associations, AAL cassettes were proposed to encode a noncanonical Acp-dependent polysaccharide modification route. Genomic-inferred predictions were substantiated by published experimental evidence, revealing a role for AAL cassettes in biosynthesis of biofilm-forming exopolysaccharide in pathogenic Burkholderia and expression of aal and acp genes in nitrogen-fixing Rhizobium bacteroids. Aal and acp genes were associated with dltBD-like homologs that modify cell wall teichoic acids with d-alanine, including in Paenibacillus and certain other bacteria. Characterization of pathways that involve AAL and Acp may lead to developing new plant and human disease-controlling agents as well as strains with improved nitrogen fixation capacity.
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10
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Balo AR, Tao L, Britt RD. Characterizing SPASM/twitch Domain-Containing Radical SAM Enzymes by EPR Spectroscopy. APPLIED MAGNETIC RESONANCE 2021; 53:809-820. [PMID: 35509369 PMCID: PMC9012708 DOI: 10.1007/s00723-021-01406-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/28/2021] [Accepted: 07/30/2021] [Indexed: 06/14/2023]
Abstract
Owing to their importance, diversity and abundance of generated paramagnetic species, radical S-adenosylmethionine (rSAM) enzymes have become popular targets for electron paramagnetic resonance (EPR) spectroscopic studies. In contrast to prototypic single-domain and thus single-[4Fe-4S]-containing rSAM enzymes, there is a large subfamily of rSAM enzymes with multiple domains and one or two additional iron-sulfur cluster(s) called the SPASM/twitch domain-containing rSAM enzymes. EPR spectroscopy is a powerful tool that allows for the observation of the iron-sulfur clusters as well as potentially trappable paramagnetic reaction intermediates. Here, we review continuous-wave and pulse EPR spectroscopic studies of SPASM/twitch domain-containing rSAM enzymes. Among these enzymes, we will review in greater depth four well-studied enzymes, BtrN, MoaA, PqqE, and SuiB. Towards establishing a functional consensus of the additional architecture in these enzymes, we describe the commonalities between these enzymes as observed by EPR spectroscopy.
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Affiliation(s)
- Aidin R. Balo
- Department of Chemistry, University of California, Davis, CA 95616 USA
| | - Lizhi Tao
- Department of Chemistry, University of California, Davis, CA 95616 USA
| | - R. David Britt
- Department of Chemistry, University of California, Davis, CA 95616 USA
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11
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He HY, Ryan KS. Glycine-derived nitronates bifurcate to O-methylation or denitrification in bacteria. Nat Chem 2021; 13:599-606. [PMID: 33782561 DOI: 10.1038/s41557-021-00656-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 02/08/2021] [Indexed: 02/01/2023]
Abstract
Natural products with rare functional groups are likely to be constructed by unique biosynthetic enzymes. One such rare functional group is the O-methyl nitronate, which can undergo [3 + 2] cycloaddition reactions with olefins in mild conditions. O-methyl nitronates are found in some natural products; however, how such O-methyl nitronates are assembled biosynthetically is unknown. Here we show that the assembly of the O-methyl nitronate in the natural product enteromycin carboxamide occurs via activation of glycine on a peptidyl carrier protein, followed by reaction with a diiron oxygenase to give a nitronate intermediate and then with a methyltransferase to give an O-methyl nitronate. Guided by the discovery of this pathway, we then identify related cryptic biosynthetic gene cassettes in other bacteria and show that these alternative gene cassettes can, instead, facilitate oxidative denitrification of glycine-derived nitronates. Altogether, our work reveals bifurcating pathways from a central glycine-derived nitronate intermediate in bacteria.
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Affiliation(s)
- Hai-Yan He
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia, Canada.,Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Katherine S Ryan
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia, Canada.
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12
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Li B, Deng X, Kim SH, Buhrow L, Tomchick DR, Phillips MA, Michael AJ. Alternative pathways utilize or circumvent putrescine for biosynthesis of putrescine-containing rhizoferrin. J Biol Chem 2020; 296:100146. [PMID: 33277357 PMCID: PMC7857480 DOI: 10.1074/jbc.ra120.016738] [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: 11/10/2020] [Revised: 12/02/2020] [Accepted: 12/04/2020] [Indexed: 11/23/2022] Open
Abstract
The siderophore rhizoferrin (N1,N4-dicitrylputrescine) is produced in fungi and bacteria to scavenge iron. Putrescine-producing bacterium Ralstonia pickettii synthesizes rhizoferrin and encodes a single nonribosomal peptide synthetase-independent siderophore (NIS) synthetase. From biosynthetic logic, we hypothesized that this single enzyme is sufficient for rhizoferrin biosynthesis. We confirmed this by expression of R. pickettii NIS synthetase in Escherichia coli, resulting in rhizoferrin production. This was further confirmed in vitro using the recombinant NIS synthetase, synthesizing rhizoferrin from putrescine and citrate. Heterologous expression of homologous lbtA from Legionella pneumophila, required for rhizoferrin biosynthesis in that species, produced siderophore activity in E. coli. Rhizoferrin is also synthesized by Francisella tularensis and Francisella novicida, but unlike R. pickettii or L. pneumophila, Francisella species lack putrescine biosynthetic pathways because of genomic decay. Francisella encodes a NIS synthetase FslA/FigA and an ornithine decarboxylase homolog FslC/FigC, required for rhizoferrin biosynthesis. Ornithine decarboxylase produces putrescine from ornithine, but we show here in vitro that FigA synthesizes N-citrylornithine, and FigC is an N-citrylornithine decarboxylase that together synthesize rhizoferrin without using putrescine. We co-expressed F. novicida figA and figC in E. coli and produced rhizoferrin. A 2.1 Å X-ray crystal structure of the FigC N-citrylornithine decarboxylase reveals how the larger substrate is accommodated and how active site residues have changed to recognize N-citrylornithine. FigC belongs to a new subfamily of alanine racemase-fold PLP-dependent decarboxylases that are not involved in polyamine biosynthesis. These data reveal a natural product biosynthetic workaround that evolved to bypass a missing precursor and re-establish it in the final structure.
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Affiliation(s)
- Bin Li
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Xiaoyi Deng
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Sok Ho Kim
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Leann Buhrow
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Diana R Tomchick
- Department of Biophysics, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Margaret A Phillips
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Anthony J Michael
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA.
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13
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Draelos MM, Thanapipatsiri A, Sucipto H, Yokoyama K. Cryptic phosphorylation in nucleoside natural product biosynthesis. Nat Chem Biol 2020; 17:213-221. [PMID: 33257873 PMCID: PMC7855722 DOI: 10.1038/s41589-020-00656-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 08/20/2020] [Indexed: 11/11/2022]
Abstract
Kinases are annotated in many nucleoside biosynthetic gene clusters (BGCs) but generally are considered responsible only for self-resistance. Here, we report an unexpected 2’-phosphorylation of nucleoside biosynthetic intermediates in the nikkomycin and polyoxin pathways. This phosphorylation is a unique cryptic modification as it is introduced in the third of seven steps during aminohexuronic acid (AHA) nucleoside biosynthesis, retained throughout the pathway’s duration, and is removed in the last step of the pathway. Bioinformatic analysis of reported nucleoside BGCs suggests the presence of cryptic phosphorylation in other pathways and the importance of functional characterization of kinases in nucleoside biosynthetic pathways in general. This study also functionally characterized all of the enzymes responsible for AHA biosynthesis and revealed that AHA is constructed via a unique oxidative C-C bond cleavage reaction. The results suggest a divergent biosynthetic mechanism for three classes of antifungal nucleoside natural products.
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Affiliation(s)
| | | | - Hilda Sucipto
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Kenichi Yokoyama
- Department of Chemistry, Duke University, Durham, NC, USA. .,Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA.
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14
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Reconstitution of polythioamide antibiotic backbone formation reveals unusual thiotemplated assembly strategy. Proc Natl Acad Sci U S A 2020; 117:8850-8858. [PMID: 32265283 PMCID: PMC7183216 DOI: 10.1073/pnas.1918759117] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Nonribosomal peptides (NRPs) are a vast class of natural products and an important source of therapeutics. Typically, these secondary metabolites are assembled by NRP synthetases (NRPSs) that function on substrates covalently linked to the enzyme by a thioester, in a process known as thiotemplated biosynthesis. Although NRPS-independent assembly pathways are known, all are nonthiotemplated. Here we report an NRPS-independent yet thiotemplated pathway for NRP biosynthesis and demonstrate that members of the ATP-grasp and cysteine protease families form the β-peptide backbone of an antibiotic. Armed with this knowledge, we provide genomic evidence that this noncanonical assembly pathway is widespread in bacteria. Our results will inspire future genome mining efforts for the discovery of potential therapeutics that otherwise would be overlooked. Closthioamide (CTA) is a rare example of a thioamide-containing nonribosomal peptide and is one of only a handful of secondary metabolites described from obligately anaerobic bacteria. Although the biosynthetic gene cluster responsible for CTA production and the thioamide synthetase that catalyzes sulfur incorporation were recently discovered, the logic for peptide backbone assembly has remained a mystery. Here, through the use of in vitro biochemical assays, we demonstrate that the amide backbone of CTA is assembled in an unusual thiotemplated pathway involving the cooperation of a transacylating member of the papain-like cysteine protease family and an iteratively acting ATP-grasp protein. Using the ATP-grasp protein as a bioinformatic handle, we identified hundreds of such thiotemplated yet nonribosomal peptide synthetase (NRPS)-independent biosynthetic gene clusters across diverse bacterial phyla. The data presented herein not only clarify the pathway for the biosynthesis of CTA, but also provide a foundation for the discovery of additional secondary metabolites produced by noncanonical biosynthetic pathways.
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15
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Abstract
In this chapter we describe different strategies for enzyme immobilization in biomimetic silica nanoparticles. Synthesis of this type of support is performed under mild and biocompatible conditions and has been proven suitable for the immobilization and stabilization of a range of enzymes and enzymatic systems in nanostructured particles. Immobilization occurs by entrapment while the silica matrix is formed via catalysis of a polyamine molecule and the presence of silicic acid. Parameters such as enzyme, polyamine molecule, or source of Si concentration have been tailored in order to maximize enzymatic loads, stabilities, and specific activities of the catalysts. We provide different approaches for the immobilization and co-immobilization of enzymes that could be potentially extensible to other biocatalysts.
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Affiliation(s)
- Erienne Jackson
- Laboratorio de Biotecnología, Facultad de Ingeniería, Universidad ORT Uruguay, Montevideo, Uruguay
| | - Sonali Correa
- Laboratorio de Biotecnología, Facultad de Ingeniería, Universidad ORT Uruguay, Montevideo, Uruguay
| | - Lorena Betancor
- Laboratorio de Biotecnología, Facultad de Ingeniería, Universidad ORT Uruguay, Montevideo, Uruguay.
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16
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Tang J, Ju Y, Gu Q, Xu J, Zhou H. Structural Insights into Substrate Recognition and Activity Regulation of the Key Decarboxylase SbnH in Staphyloferrin B Biosynthesis. J Mol Biol 2019; 431:4868-4881. [PMID: 31634470 DOI: 10.1016/j.jmb.2019.10.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/08/2019] [Accepted: 10/10/2019] [Indexed: 12/21/2022]
Abstract
Staphyloferrin B is a hydroxycarboxylate siderophore that is crucial for the invasion and virulence of Staphylococcus aureus in mammalian hosts where free iron ions are scarce. The assembly of staphyloferrin B involves four enzymatic steps, in which SbnH, a pyridoxal 5'-phosphate (PLP)-dependent decarboxylase, catalyzes the second step. Here, we report the X-ray crystal structures of S. aureus SbnH (SaSbnH) in complex with PLP, citrate, and the decarboxylation product citryl-diaminoethane (citryl-Dae). The overall structure of SaSbnH resembles those of the previously reported PLP-dependent amino acid decarboxylases, but the active site of SaSbnH showed unique structural features. Structural and mutagenesis analysis revealed that the citryl moiety of the substrate citryl-l-2,3-diaminopropionic acid (citryl-l-Dap) inserts into a narrow groove at the dimer interface of SaSbnH and forms hydrogen bonding interactions with both subunits. In the active site, a conserved lysine residue forms an aldimine linkage with the cofactor PLP, and a phenylalanine residue is essential for accommodating the l-configuration Dap of the substrate. Interestingly, the freestanding citrate molecule was found to bind to SaSbnH in a conformation inverse to that of the citryl group of citryl-Dae and efficiently inhibit SaSbnH. As an intermediate in the tricarboxylic acid (TCA) cycle, citrate is highly abundant in bacterial cells until iron depletion; thus, its inhibition of SaSbnH may serve as an iron-dependent regulatory mechanism in staphyloferrin B biosynthesis.
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Affiliation(s)
- Jieyu Tang
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China; Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Yingchen Ju
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China; Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Qiong Gu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jun Xu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Huihao Zhou
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China; Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.
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17
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Complete reconstitution of the diverse pathways of gentamicin B biosynthesis. Nat Chem Biol 2019; 15:295-303. [PMID: 30643280 PMCID: PMC6488028 DOI: 10.1038/s41589-018-0203-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 11/13/2018] [Indexed: 11/13/2022]
Abstract
Gentamicin B (GB), a valuable starting material for the preparation of the semisynthetic aminoglycoside antibiotic isepamicin, is produced in trace amounts by the wild-type Micromonospora echinospora. While the biosynthetic pathway to GB has remained obscure for decades, we have now identified three hidden pathways to GB production via seven hitherto unknown intermediates in M. echinospora. The narrow substrate specificity of a key glycosyltransferase and the C6′-amination enzymes, in combination with the weak and unsynchronized gene expression of the 2′-deamination enzymes, limit GB production in M. echinospora. The crystal structure of the aminotransferase involved in C6′-amination explains its substrate specificity. Some of the new intermediates displayed similar premature termination codon readthrough activity but with reduced toxicity compared to the natural aminoglycoside G418. This work not only led to the discovery of unknown biosynthetic routes to GB, but also demonstrated the potential to mine new aminoglycosides from nature for drug discovery.
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18
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Dunbar KL, Büttner H, Molloy EM, Dell M, Kumpfmüller J, Hertweck C. Genome Editing Reveals Novel Thiotemplated Assembly of Polythioamide Antibiotics in Anaerobic Bacteria. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807970] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kyle L. Dunbar
- Dept. of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology, HKI; Beutenbergstrasse 11a 07745 Jena Germany
| | - Hannah Büttner
- Dept. of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology, HKI; Beutenbergstrasse 11a 07745 Jena Germany
| | - Evelyn M. Molloy
- Dept. of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology, HKI; Beutenbergstrasse 11a 07745 Jena Germany
| | - Maria Dell
- Dept. of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology, HKI; Beutenbergstrasse 11a 07745 Jena Germany
| | - Jana Kumpfmüller
- Dept. of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology, HKI; Beutenbergstrasse 11a 07745 Jena Germany
| | - Christian Hertweck
- Dept. of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology, HKI; Beutenbergstrasse 11a 07745 Jena Germany
- Natural Product Chemistry; Friedrich Schiller University; 07743 Jena Germany
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19
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Dunbar KL, Büttner H, Molloy EM, Dell M, Kumpfmüller J, Hertweck C. Genome Editing Reveals Novel Thiotemplated Assembly of Polythioamide Antibiotics in Anaerobic Bacteria. Angew Chem Int Ed Engl 2018; 57:14080-14084. [PMID: 30193003 DOI: 10.1002/anie.201807970] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 08/23/2018] [Indexed: 12/18/2022]
Abstract
Closthioamide (CTA) is a unique symmetric nonribosomal peptide with six thioamide moieties that is produced by the Gram-positive obligate anaerobe Ruminiclostridium cellulolyticum. CTA displays potent inhibitory activity against important clinical pathogens, making it a promising drug candidate. Yet, the biosynthesis of this DNA gyrase-targeting antibiotic has remained enigmatic. Using a combination of genome mining, genome editing (targeted group II intron, CRISPR/Cas9), and heterologous expression, we show that CTA biosynthesis involves specialized enzymes for starter unit biosynthesis, amide bond formation, thionation, and dimerization. Surprisingly, CTA biosynthesis involves a novel thiotemplated peptide assembly line that markedly differs from known nonribosomal peptide synthetases. These findings provide the first insights into the biosynthesis of thioamide-containing nonribosomal peptides and offer a starting point for the discovery of related natural products.
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Affiliation(s)
- Kyle L Dunbar
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Hannah Büttner
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Evelyn M Molloy
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Maria Dell
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Jana Kumpfmüller
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Christian Hertweck
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany.,Natural Product Chemistry, Friedrich Schiller University, 07743, Jena, Germany
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20
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Wang KKA, Ng TL, Wang P, Huang Z, Balskus EP, van der Donk WA. Glutamic acid is a carrier for hydrazine during the biosyntheses of fosfazinomycin and kinamycin. Nat Commun 2018; 9:3687. [PMID: 30206228 PMCID: PMC6133997 DOI: 10.1038/s41467-018-06083-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 08/14/2018] [Indexed: 01/03/2023] Open
Abstract
Fosfazinomycin and kinamycin are natural products that contain nitrogen-nitrogen (N-N) bonds but that are otherwise structurally unrelated. Despite their considerable structural differences, their biosynthetic gene clusters share a set of genes predicted to facilitate N-N bond formation. In this study, we show that for both compounds, one of the nitrogen atoms in the N-N bond originates from nitrous acid. Furthermore, we show that for both compounds, an acetylhydrazine biosynthetic synthon is generated first and then funneled via a glutamyl carrier into the respective biosynthetic pathways. Therefore, unlike other pathways to N-N bond-containing natural products wherein the N-N bond is formed directly on a biosynthetic intermediate, during the biosyntheses of fosfazinomycin, kinamycin, and related compounds, the N-N bond is made in an independent pathway that forms a branch of a convergent route to structurally complex natural products.
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Affiliation(s)
- Kwo-Kwang A Wang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
| | - Tai L Ng
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, 02138, MA, USA
| | - Peng Wang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, 02138, MA, USA
- Red & Charline McCombs Institute for the Early Detection and Treatment of Cancer, University of Texas MD Anderson Cancer Center, Houston, 77030, TX, USA
| | - Zedu Huang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
- Department of Chemistry, Fudan University, Shanghai, 200438-6789, China
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, 02138, MA, USA.
| | - Wilfred A van der Donk
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA.
- Howard Hughes Medical Institute, Chevy Chase, 20815, MD, USA.
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21
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Park JW, Ban YH, Nam SJ, Cha SS, Yoon YJ. Biosynthetic pathways of aminoglycosides and their engineering. Curr Opin Biotechnol 2017; 48:33-41. [PMID: 28365471 DOI: 10.1016/j.copbio.2017.03.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 02/27/2017] [Accepted: 03/15/2017] [Indexed: 11/30/2022]
Abstract
Despite decades long clinical usage, aminoglycosides still remain a valuable pharmaceutical source for fighting Gram-negative bacterial pathogens, and their newly identified bioactivities are also renewing interest in this old class of antibiotics. As Nature's gift, some aminoglycosides possess natural defensive structural elements that can circumvent drug resistance mechanisms. Thus, a detailed understanding of aminoglycoside biosynthesis will enable us to apply Nature's biosynthetic strategy towards expanding structural diversity in order to produce novel and more robust aminoglycoside analogs. The engineered biosynthesis of novel aminoglycosides is required not only to develop effective therapeutics against the emerging 'superbugs' but also to reinvigorate antibiotic lead discovery in readiness for the emerging post-antibiotic era.
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Affiliation(s)
- Je Won Park
- School of Biosystem and Biomedical Science, Korea University, Seoul 02841, Republic of Korea
| | - Yeon Hee Ban
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Sun-Shin Cha
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Yeo Joon Yoon
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea.
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22
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Mechanisms of β-amino acid incorporation in polyketide macrolactam biosynthesis. Curr Opin Chem Biol 2016; 35:58-64. [DOI: 10.1016/j.cbpa.2016.08.030] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 06/30/2016] [Accepted: 08/26/2016] [Indexed: 12/11/2022]
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23
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Chang CY, Lohman JR, Cao H, Tan K, Rudolf JD, Ma M, Xu W, Bingman CA, Yennamalli RM, Bigelow L, Babnigg G, Yan X, Joachimiak A, Phillips GN, Shen B. Crystal Structures of SgcE6 and SgcC, the Two-Component Monooxygenase That Catalyzes Hydroxylation of a Carrier Protein-Tethered Substrate during the Biosynthesis of the Enediyne Antitumor Antibiotic C-1027 in Streptomyces globisporus. Biochemistry 2016; 55:5142-54. [PMID: 27560143 PMCID: PMC5024704 DOI: 10.1021/acs.biochem.6b00713] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
C-1027
is a chromoprotein enediyne antitumor antibiotic produced
by Streptomyces globisporus. In the last step of
biosynthesis of the (S)-3-chloro-5-hydroxy-β-tyrosine
moiety of the C-1027 enediyne chromophore, SgcE6 and SgcC compose
a two-component monooxygenase that hydroxylates the C-5 position of
(S)-3-chloro-β-tyrosine. This two-component
monooxygenase is remarkable for two reasons. (i) SgcE6 specifically
reacts with FAD and NADH, and (ii) SgcC is active with only the peptidyl
carrier protein (PCP)-tethered substrate. To address the molecular
details of substrate specificity, we determined the crystal structures
of SgcE6 and SgcC at 1.66 and 2.63 Å resolution, respectively.
SgcE6 shares a similar β-barrel fold with the class I HpaC-like
flavin reductases. A flexible loop near the active site of SgcE6 plays
a role in FAD binding, likely by providing sufficient space to accommodate
the AMP moiety of FAD, when compared to that of FMN-utilizing homologues.
SgcC shows structural similarity to a few other known FADH2-dependent monooxygenases and sheds light on some biochemically but
not structurally characterized homologues. The crystal structures
reported here provide insights into substrate specificity, and comparison
with homologues provides a catalytic mechanism of the two-component,
FADH2-dependent monooxygenase (SgcE6 and SgcC) that catalyzes
the hydroxylation of a PCP-tethered substrate.
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Affiliation(s)
- Chin-Yuan Chang
- Department of Chemistry, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Jeremy R Lohman
- Department of Chemistry, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Hongnan Cao
- BioScience at Rice and Department of Chemistry, Rice University , Houston, Texas 77251, United States
| | - Kemin Tan
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Jeffrey D Rudolf
- Department of Chemistry, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Ming Ma
- Department of Chemistry, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Weijun Xu
- BioScience at Rice and Department of Chemistry, Rice University , Houston, Texas 77251, United States
| | - Craig A Bingman
- Department of Biochemistry, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States
| | - Ragothaman M Yennamalli
- BioScience at Rice and Department of Chemistry, Rice University , Houston, Texas 77251, United States.,Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology , Waknaghat, Himachal Pradesh, India 173234
| | - Lance Bigelow
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Gyorgy Babnigg
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Xiaohui Yan
- Department of Chemistry, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - George N Phillips
- BioScience at Rice and Department of Chemistry, Rice University , Houston, Texas 77251, United States
| | - Ben Shen
- Department of Chemistry, The Scripps Research Institute , Jupiter, Florida 33458, United States
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24
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Struck AW, Bennett MR, Shepherd SA, Law BJC, Zhuo Y, Wong LS, Micklefield J. An Enzyme Cascade for Selective Modification of Tyrosine Residues in Structurally Diverse Peptides and Proteins. J Am Chem Soc 2016; 138:3038-45. [DOI: 10.1021/jacs.5b10928] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Anna-Winona Struck
- School of Chemistry and Manchester
Institute of Biotechnology, The University of Manchester, 131 Princess
Street, Manchester M1 7DN, United Kingdom
| | - Matthew R. Bennett
- School of Chemistry and Manchester
Institute of Biotechnology, The University of Manchester, 131 Princess
Street, Manchester M1 7DN, United Kingdom
| | - Sarah A. Shepherd
- School of Chemistry and Manchester
Institute of Biotechnology, The University of Manchester, 131 Princess
Street, Manchester M1 7DN, United Kingdom
| | - Brian J. C. Law
- School of Chemistry and Manchester
Institute of Biotechnology, The University of Manchester, 131 Princess
Street, Manchester M1 7DN, United Kingdom
| | - Ying Zhuo
- School of Chemistry and Manchester
Institute of Biotechnology, The University of Manchester, 131 Princess
Street, Manchester M1 7DN, United Kingdom
| | - Lu Shin Wong
- School of Chemistry and Manchester
Institute of Biotechnology, The University of Manchester, 131 Princess
Street, Manchester M1 7DN, United Kingdom
| | - Jason Micklefield
- School of Chemistry and Manchester
Institute of Biotechnology, The University of Manchester, 131 Princess
Street, Manchester M1 7DN, United Kingdom
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25
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Hong H, Samborskyy M, Lindner F, Leadlay PF. An Amidinohydrolase Provides the Missing Link in the Biosynthesis of Amino Marginolactone Antibiotics. Angew Chem Int Ed Engl 2016; 55:1118-23. [PMID: 26630438 PMCID: PMC4737276 DOI: 10.1002/anie.201509300] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Indexed: 01/23/2023]
Abstract
Desertomycin A is an aminopolyol polyketide containing a macrolactone ring. We have proposed that desertomycin A and similar compounds (marginolactones) are formed by polyketide synthases primed not with γ-aminobutanoyl-CoA but with 4-guanidinylbutanoyl-CoA, to avoid facile cyclization of the starter unit. This hypothesis requires that there be a final-stage de-amidination of the corresponding guanidino-substituted natural product, but no enzyme for such a process has been described. We have now identified candidate amidinohydrolase genes within the desertomycin and primycin clusters. Deletion of the putative desertomycin amidinohydrolase gene dstH in Streptomyces macronensis led to the accumulation of desertomycin B, the guanidino form of the antibiotic. Also, purified DstH efficiently catalyzed the in vitro conversion of desertomycin B into the A form. Hence this amidinohydrolase furnishes the missing link in this proposed naturally evolved example of protective-group chemistry.
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Affiliation(s)
- Hui Hong
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Markiyan Samborskyy
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Frederick Lindner
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
- Institut für Organische Chemie, Leibniz Universität Hannover, Schneiderberg 1 B, 30167, Hannover, Germany
| | - Peter F Leadlay
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.
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26
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Hong H, Samborskyy M, Lindner F, Leadlay PF. An Amidinohydrolase Provides the Missing Link in the Biosynthesis of Amino Marginolactone Antibiotics. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201509300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Hui Hong
- Department of Biochemistry; University of Cambridge; 80 Tennis Court Road Cambridge CB2 1GA UK
| | - Markiyan Samborskyy
- Department of Biochemistry; University of Cambridge; 80 Tennis Court Road Cambridge CB2 1GA UK
| | - Frederick Lindner
- Department of Biochemistry; University of Cambridge; 80 Tennis Court Road Cambridge CB2 1GA UK
- Institut für Organische Chemie; Leibniz Universität Hannover; Schneiderberg 1 B 30167 Hannover Germany
| | - Peter F. Leadlay
- Department of Biochemistry; University of Cambridge; 80 Tennis Court Road Cambridge CB2 1GA UK
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27
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Metabolic engineering of Escherichia coli for the biosynthesis of 2-pyrrolidone. Metab Eng Commun 2015; 3:1-7. [PMID: 29468109 PMCID: PMC5779725 DOI: 10.1016/j.meteno.2015.11.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 10/25/2015] [Accepted: 11/03/2015] [Indexed: 11/23/2022] Open
Abstract
2-Pyrrolidone is a valuable bulk chemical with myriad applications as a solvent, polymer precursor and active pharmaceutical intermediate. A novel 2-pyrrolidone synthase, ORF27, from Streptomyces aizunensis was identified to catalyze the ring closing dehydration of γ-aminobutyrate. ORF27's tendency to aggregate was resolved by expression at low temperature and fusion to the maltose binding protein (MBP). Recombinant Escherichia coli was metabolically engineered for the production of 2-pyrrolidone from glutamate by expressing both the genes encoding GadB, a glutamate decarboxylase, and ORF27. Incorporation of a GadB mutant lacking H465 and T466, GadB_ΔHT, improved the efficiency of one-pot 2-pyrrolidone biosynthesis in vivo. When the recombinant E. coli strain expressing the E. coli GadB_ΔHT mutant and the ORF27-MBP fusion was cultured in ZYM-5052 medium containing 9 g/L of l-glutamate, 7.7 g/L of l-glutamate was converted to 1.1 g/L of 2-pyrrolidone within 31 h, achieving 25% molar yield from the consumed substrate. ORF27 from Streptomyces aizunensis catalyzes formation of 2-pyrrolidone from γ-aminobutyrate. Recombinant Escherichia coli with GadB and ORF27 produces 2-pyrrolidone from glutamate. Engineered strain capable of producing 1.1 g/L of 2-pyrrolidone from 9 g/L of glutamate within 31 h.
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28
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Kudo F, Eguchi T. Aminoglycoside Antibiotics: New Insights into the Biosynthetic Machinery of Old Drugs. CHEM REC 2015; 16:4-18. [PMID: 26455715 DOI: 10.1002/tcr.201500210] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Indexed: 11/07/2022]
Abstract
2-Deoxystreptamine (2DOS) is the unique chemically stable aminocyclitol scaffold of clinically important aminoglycoside antibiotics such as neomycin, kanamycin, and gentamicin, which are produced by Actinomycetes. The 2DOS core can be decorated with various deoxyaminosugars to make structurally diverse pseudo-oligosaccharides. After the discovery of biosynthetic gene clusters for 2DOS-containing aminoglycoside antibiotics, the function of each biosynthetic enzyme has been extensively elucidated. The common biosynthetic intermediates 2DOS, paromamine and ribostamycin are constructed by conserved enzymes encoded in the gene clusters. The biosynthetic intermediates are then converted to characteristic architectures by unique enzymes encoded in each biosynthetic gene cluster. In this Personal Account, we summarize both common biosynthetic pathways and the pathways used for structural diversification.
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Affiliation(s)
- Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8551, Japan
| | - Tadashi Eguchi
- Department of Chemistry and Materials Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8551, Japan
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29
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Walker MC, van der Donk WA. The many roles of glutamate in metabolism. J Ind Microbiol Biotechnol 2015; 43:419-30. [PMID: 26323613 DOI: 10.1007/s10295-015-1665-y] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Accepted: 07/25/2015] [Indexed: 12/20/2022]
Abstract
The amino acid glutamate is a major metabolic hub in many organisms and as such is involved in diverse processes in addition to its role in protein synthesis. Nitrogen assimilation, nucleotide, amino acid, and cofactor biosynthesis, as well as secondary natural product formation all utilize glutamate in some manner. Glutamate also plays a role in the catabolism of certain amines. Understanding glutamate's role in these various processes can aid in genome mining for novel metabolic pathways or the engineering of pathways for bioremediation or chemical production of valuable compounds.
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Affiliation(s)
- Mark C Walker
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Wilfred A van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA.
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30
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Takeishi R, Kudo F, Numakura M, Eguchi T. Epimerization at C-3'' in butirosin biosynthesis by an NAD(+) -dependent dehydrogenase BtrE and an NADPH-dependent reductase BtrF. Chembiochem 2015; 16:487-95. [PMID: 25600434 DOI: 10.1002/cbic.201402612] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Indexed: 11/11/2022]
Abstract
Butirosin is an aminoglycoside antibiotic consisting two epimers at C-3'' of ribostamycin/xylostasin with a unique 4-amino-2-hydroxybutyrate moiety at C-1 of the aminocyclitol 2-deoxystreptamine (2DOS). To date, most of the enzymes encoded in the biosynthetic gene cluster for butirosin, from the producing strain Bacillus circulans, have been characterized. A few unknown functional proteins, including nicotinamide adenine dinucleotide cofactor-dependent dehydrogenase/reductase (BtrE and BtrF), are supposed to be involved in the epimerization at C-3'' of butirosin B/ribostamycin but remain to be characterized. Herein, the conversion of ribostamycin to xylsostasin by BtrE and BtrF in the presence of NAD(+) and NADPH was demonstrated. BtrE oxidized the C-3'' of ribostamycin with NAD(+) to yield 3''-oxoribostamycin. BtrF then reduced the generated 3''-oxoribostamycin with NADPH to produce xylostasin. This reaction step was the last piece of butirosin biosynthesis to be described.
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Affiliation(s)
- Ryohei Takeishi
- Department of Chemistry, Tokyo Institute of Technology, Okayama, Meguro-ku, Tokyo 152-8551 (Japan)
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31
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Ni X, Sun Z, Zhang H, He H, Ji Z, Xia H. Genetic engineering combined with random mutagenesis to enhance G418 production in Micromonospora echinospora. ACTA ACUST UNITED AC 2014; 41:1383-90. [DOI: 10.1007/s10295-014-1479-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 06/18/2014] [Indexed: 10/25/2022]
Abstract
Abstract
G418, produced by fermentation of Micromonospora echinospora, is an aminoglycoside antibiotic commonly used in genetic selection and maintenance of eukaryotic cells. Besides G418, M. echinospora produces many G418 analogs. As a result, the G418 product always contains impurities such as gentamicin C1, C1a, C2, C2a, gentamicin A and gentamicin X2. These impurities are less potent but more toxic than G418, but the purification of G418 is difficult because it has similar properties to its impurities. G418 is an intermediate in the gentamicin biosynthesis pathway. From G418 the pathway proceeds via successive dehydrogenation and aminotransferation at the C-6′ position to generate the gentamicin C complex, but genes responsible for these steps are still obscure. Through disruption of gacJ, which is deduced to encode a C-6′ dehydrogenase, the biosynthetic impurities gentamicin C1, C1a, C2 and C2a were all removed, and G418 became the main product of the gacJ disruption strain. These results demonstrated that gacJ is in charge of conversion of the 6′-OH of G418 into 6′-NH2. Disruption of gacJ not only eliminates the impurities seen in the original strain but also improves G418 titers by 15-fold. G418 production was further improved by 26.6 % through traditional random mutagenesis. Through the use of combined traditional and recombinant genetic techniques, we produced a strain from which most impurities were removed and G418 production was improved by 19 fold.
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Affiliation(s)
- Xianpu Ni
- grid.412561.5 0000000086454345 School of Life Science and Biopharmaceutics Shenyang Pharmaceutical University 110016 Shenyang Liaoning China
| | - Zhenpeng Sun
- grid.412561.5 0000000086454345 School of Life Science and Biopharmaceutics Shenyang Pharmaceutical University 110016 Shenyang Liaoning China
| | - Hongyu Zhang
- grid.412561.5 0000000086454345 School of Life Science and Biopharmaceutics Shenyang Pharmaceutical University 110016 Shenyang Liaoning China
| | - Han He
- grid.412561.5 0000000086454345 School of Life Science and Biopharmaceutics Shenyang Pharmaceutical University 110016 Shenyang Liaoning China
| | - Zhouxiang Ji
- grid.412561.5 0000000086454345 School of Life Science and Biopharmaceutics Shenyang Pharmaceutical University 110016 Shenyang Liaoning China
| | - Huanzhang Xia
- grid.412561.5 0000000086454345 School of Life Science and Biopharmaceutics Shenyang Pharmaceutical University 110016 Shenyang Liaoning China
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32
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Hong H, Fill T, Leadlay PF. A Common Origin for Guanidinobutanoate Starter Units in Antifungal Natural Products. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201308136] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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33
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Hong H, Fill T, Leadlay PF. A Common Origin for Guanidinobutanoate Starter Units in Antifungal Natural Products. Angew Chem Int Ed Engl 2013; 52:13096-9. [DOI: 10.1002/anie.201308136] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Indexed: 11/07/2022]
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34
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Park SR, Park JW, Ban YH, Sohng JK, Yoon YJ. 2-Deoxystreptamine-containing aminoglycoside antibiotics: Recent advances in the characterization and manipulation of their biosynthetic pathways. Nat Prod Rep 2013. [DOI: 10.1039/c2np20092a] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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35
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Shinohara Y, Kudo F, Eguchi T. A Natural Protecting Group Strategy To Carry an Amino Acid Starter Unit in the Biosynthesis of Macrolactam Polyketide Antibiotics. J Am Chem Soc 2011; 133:18134-7. [DOI: 10.1021/ja208927r] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yuji Shinohara
- Department of Chemistry and Materials Science and ‡Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Fumitaka Kudo
- Department of Chemistry and Materials Science and ‡Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Tadashi Eguchi
- Department of Chemistry and Materials Science and ‡Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan
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36
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Ni X, Li D, Yang L, Huang T, Li H, Xia H. Construction of kanamycin B overproducing strain by genetic engineering of Streptomyces tenebrarius. Appl Microbiol Biotechnol 2010; 89:723-31. [PMID: 20936279 DOI: 10.1007/s00253-010-2908-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Revised: 09/08/2010] [Accepted: 09/14/2010] [Indexed: 11/29/2022]
Abstract
Genetic engineering as an important approach to strain optimization has received wide recognition. Recent advances in the studies on the biosynthetic pathways and gene clusters of Streptomyces make stain optimization by genetic alteration possible. Kanamycin B is a key intermediate in the manufacture of the important medicines dibekacin and arbekacin, which belong to a class of antibiotics known as the aminoglycosides. Kanamycin could be prepared by carbamoylkanamycin B hydrolysis. However, carbamoylkanamycin B production in Streptomyces tenebrarius H6 is very low. Therefore, we tried to obtain high kanamycin B-producing strains that produced kanamycin B as a main component. In our work, aprD3 and aprD4 were clarified to be responsible for deoxygenation in apramycin and tobramycin biosynthesis. Based on this information, genes aprD3, aprQ (deduced apramycin biosynthetic gene), and aprD4 were disrupted to optimize the production of carbamoylkanamycin B. Compared with wild-type strain, mutant strain SPU313 (ΔaprD3, ΔaprQ, and ΔaprD4) produced carbamoylkanamycin B as a single antibiotic, whose production increased approximately fivefold. To construct a strain producing kanamycin B instead of carbamoylkanamycin B, the carbamoyl-transfer gene tacA was inactivated in strain SPU313. Mutant strain SPU314 (ΔaprD3, ΔaprQ, ΔaprD4, and ΔtacA) specifically produced kanamycin B, which was proven by LC-MS. This work demonstrated careful genetic engineering could significantly improve production and eliminate undesired products.
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Affiliation(s)
- Xianpu Ni
- Shenyang Pharmaceutical University, Liaoning, China
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37
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Wong LS, Janusz SJ, Sun S, Leggett GJ, Micklefield J. Nanoscale Biomolecular Structures on Self-Assembled Monolayers Generated from Modular Pegylated Disulfides. Chemistry 2010; 16:12234-43. [DOI: 10.1002/chem.200902439] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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38
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Wong LS, Okrasa K, Micklefield J. Site-selective immobilisation of functional enzymes on to polystyrene nanoparticles. Org Biomol Chem 2009; 8:782-7. [PMID: 20135034 DOI: 10.1039/b916773k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The immobilisation of proteins on to nanoparticles has a number of applications ranging from biocatalysis through to cellular delivery of biopharmaceuticals. Here we describe a phosphopantetheinyl transferase (Sfp)-catalysed method for immobilising proteins bearing a small 12-mer "ybbR" tag on to nanoparticles functionalised with coenzyme A. The Sfp-catalysed immobilisation of proteins on to nanoparticles is a highly efficient, single step reaction that proceeds under mild conditions and results in a homogeneous population of proteins that are covalently and site-specifically attached to the surface of the nanoparticles. Several enzymes of interest for biocatalysis, including an arylmalonate decarboxylase (AMDase) and a glutamate racemase (GluR), were immobilised on to nanoparticles using this approach. These enzymes retained their activity and showed high operational stability upon immobilisation.
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Affiliation(s)
- Lu Shin Wong
- School of Chemistry and Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester, UKM1 7DN
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39
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Abstract
Biosynthetic studies of aminoglycoside antibiotics have progressed remarkably during the last decade. Many biosynthetic gene clusters for aminoglycoside antibiotics including streptomycin, kanamycin, butirosin, neomycin and gentamicin have been identified to date. In addition, most butirosin and neomycin biosynthetic enzymes have been functionally characterized using recombinant proteins. Herein, we reanalyze biosynthetic genes for structurally related 2-deoxystreptamine (2DOS)-containing aminoglycosides, such as kanamycin, gentamicin and istamycin, based on genetic information including characterized biosynthetic enzymes in neomycin and butirosin biosynthetic pathways. These proposed enzymatic functions for uncharacterized enzymes are expected to support investigation of the complex biosynthetic pathways for this important class of antibiotics.
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Affiliation(s)
- Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
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40
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Zhang J, Blazecka PG, Bruendl MM, Huang Y. Ru-TsDPEN with formic acid/Hunig's base for asymmetric transfer hydrogenation, a practical synthesis of optically enriched N-propyl pantolactam. J Org Chem 2009; 74:1411-4. [PMID: 19105680 DOI: 10.1021/jo802380j] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Noyori-Ikariya catalysts, Ru-TsDPEN 1 or 2, in combination with HCOOH/Hunig's base (5:2) have been successfully utilized for catalytic asymmetric transfer hydrogenation of alpha-ketopantolactam, and optically enriched N-substituted pantolactam was prepared (S/C = 500, up to 95% ee and 99% conversion in HCOOH/Hunig's base condition). More than 2 kg of this key intermediate 9 has been synthesized efficiently with excellent chemical yield and chiral purity.
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Affiliation(s)
- Ji Zhang
- Research API, Pfizer Global Research & Development, Michigan Laboratories, Pfizer Inc., 2800 Plymouth Road, Ann Arbor, Michigan 48105, USA.
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41
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Abstract
Butirosin and neomycin belong to a family of clinically valuable 2-deoxystreptamine (2DOS)-containing aminoglycoside antibiotics. The biosynthetic gene clusters for butirosin and neomycin were identified in 2000 and in 2005, respectively. In recent years, most of the enzymes encoded in the gene clusters have been characterized, and thus almost all the biosynthetic steps leading to the final antibiotics have been understood. This knowledge could shed light on the complex biosynthetic pathways for other related structurally diverse aminoglycoside antibiotics. In this chapter, the enzymatic reactions in the biosynthesis of butirosin and neomycin are reviewed step by step.
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Affiliation(s)
- Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, Tokyo, Japan
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42
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43
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Llewellyn NM, Spencer JB. Chemoenzymatic acylation of aminoglycoside antibiotics. Chem Commun (Camb) 2008:3786-8. [PMID: 18685777 DOI: 10.1039/b802248h] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The chemoenzymatic installation of the clinically valuable (S)-4-amino-2-hydroxybutyryl side chain onto a number of 2-deoxystreptamine-containing aminoglycosides is described using the purified Bacillus circulans biosynthetic enzymes BtrH and BtrG in combination with a synthetic acyl-SNAC surrogate substrate.
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Affiliation(s)
- Nicholas M Llewellyn
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK.
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44
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Oakley AJ, Yamada T, Liu D, Coggan M, Clark AG, Board PG. The identification and structural characterization of C7orf24 as gamma-glutamyl cyclotransferase. An essential enzyme in the gamma-glutamyl cycle. J Biol Chem 2008; 283:22031-42. [PMID: 18515354 DOI: 10.1074/jbc.m803623200] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The hypothetical protein C7orf24 has been implicated as a cancer marker with a potential role in cell proliferation. We have identified C7orf24 as gamma-glutamyl cyclotransferase (GGCT) that catalyzes the formation of 5-oxoproline (pyroglutamic acid) from gamma-glutamyl dipeptides and potentially plays a significant role in glutathione homeostasis. In the present study we have identified the first cDNA clones encoding a gamma-glutamyl cyclotransferase. The GGCT gene is located on chromosome 7p14-15 and consists of four exons that span 8 kb. The primary sequence is 188 amino acids in length and is unlike any protein of known function. We crystallized functional recombinant gamma-glutamyl cyclotransferase and determined its structure at 1.7 A resolution. The enzyme is a dimer of 20,994-Da subunits. The topology of GGCT is unrelated to other enzymes associated with cyclotransferase-like activity. The fold was originally classified as "BtrG-like," a small family that only includes structures of hypothetical proteins from Mus musculus, Escherichia coli, Pyrococcus horikoshii, and Arabidopsis thaliana. Since this is the first member of this family with a defined function, we propose to refer to this structure as the gamma-glutamyl cyclotransferase fold. We have identified a potential active site pocket that contains a highly conserved glutamic acid (Glu(98)) and propose that it acts as a general acid/base in the reaction mechanism. Mutation of Glu(98) to Ala or Gln completely inactivates the enzyme without altering the overall fold.
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Affiliation(s)
- Aaron J Oakley
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
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45
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Leadlay P. Obituary: Jonathan B. Spencer (1960-2008). CHEMISTRY & BIOLOGY 2008; 15:424-426. [PMID: 18551814 DOI: 10.1016/j.chembiol.2008.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Affiliation(s)
- Peter Leadlay
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
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46
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Lin S, Van Lanen SG, Shen B. Characterization of the two-component, FAD-dependent monooxygenase SgcC that requires carrier protein-tethered substrates for the biosynthesis of the enediyne antitumor antibiotic C-1027. J Am Chem Soc 2008; 130:6616-23. [PMID: 18426211 DOI: 10.1021/ja710601d] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
C-1027 is a potent antitumor antibiotic composed of an apoprotein (CagA) and a reactive enediyne chromophore. The chromophore has four distinct chemical moieties, including an ( S)-3-chloro-5-hydroxy-beta-tyrosine moiety, the biosynthesis of which from l-alpha-tyrosine requires five proteins: SgcC, SgcC1, SgcC2, SgcC3, and SgcC4; a sixth protein, SgcC5, catalyzes the incorporation of this beta-amino acid moiety into C-1027. Biochemical characterization of SgcC has now revealed that (i) SgcC is a two-component, flavin adenine dinucleotide (FAD)-dependent monooxygenase, (ii) SgcC is only active with SgcC2 (peptidyl carrier protein)-tethered substrates, (iii) SgcC-catalyzed hydroxylation requires O 2 and FADH 2, the latter supplied by the C-1027 pathway-specific flavin reductase SgcE6 or Escherichia coli flavin reductase Fre, and (iv) SgcC efficiently catalyzes regioselective hydroxylation of 3-substituted beta-tyrosyl-S-SgcC2 analogues, including the chloro-, bromo-, iodo-, fluoro-, and methyl-substituted analogues, but does not accept 3-hydroxy-beta-tyrosyl-S-SgcC2 as a substrate. Together with the in vitro data for SgcC4, SgcC1, and SgcC3, the results establish that SgcC catalyzes the hydroxylation of ( S)-3-chloro-beta-tyrosyl-S-SgcC2 as the final step in the biosynthesis of the ( S)-3-chloro-5-hydroxy-beta-tyrosine moiety prior to incorporation into C-1027. SgcC now represents the first biochemically characterized two-component, FAD-dependent monooxygenase that acts on a carrier-protein-tethered aromatic substrate.
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Affiliation(s)
- Shuangjun Lin
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53705-2222, USA
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47
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Llewellyn NM, Li Y, Spencer JB. Biosynthesis of butirosin: transfer and deprotection of the unique amino acid side chain. ACTA ACUST UNITED AC 2007; 14:379-86. [PMID: 17462573 DOI: 10.1016/j.chembiol.2007.02.005] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2007] [Revised: 02/05/2007] [Accepted: 02/09/2007] [Indexed: 10/23/2022]
Abstract
Butirosin, an aminoglycoside antibiotic produced by Bacillus circulans, bears the unique (S)-4-amino-2-hydroxybutyrate (AHBA) side chain, which protects the antibiotic from several common resistance mechanisms. The AHBA side chain is advantageously incorporated into clinically valuable antibiotics such as amikacin and arbekacin by synthetic methods. Therefore, it is of significant interest to explore the biosynthetic origins of this useful moiety. We report here that the AHBA side chain of butirosin is transferred from the acyl carrier protein (ACP) BtrI to the parent aminoglycoside ribostamycin as a gamma-glutamylated dipeptide by the ACP:aminoglycoside acyltransferase BtrH. The protective gamma-glutamyl group is then cleaved by BtrG via an uncommon gamma-glutamyl cyclotransferase mechanism. The application of this pathway to the in vitro enzymatic production of novel AHBA-bearing aminoglycosides is explored with encouraging implications for the preparation of unnatural antibiotics via directed biosynthesis.
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Affiliation(s)
- Nicholas M Llewellyn
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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48
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Aramini JM, Huang YJ, Swapna GVT, Cort JR, Rajan PK, Xiao R, Shastry R, Acton TB, Liu J, Rost B, Kennedy MA, Montelione GT. Solution NMR structure of Escherichia coli ytfP expands the structural coverage of the UPF0131 protein domain family. Proteins 2007; 68:789-95. [PMID: 17523190 DOI: 10.1002/prot.21450] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- James M Aramini
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854, USA.
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49
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Kudo F, Fujii T, Kinoshita S, Eguchi T. Unique O-ribosylation in the biosynthesis of butirosin. Bioorg Med Chem 2007; 15:4360-8. [PMID: 17482823 DOI: 10.1016/j.bmc.2007.04.040] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2007] [Revised: 04/19/2007] [Accepted: 04/20/2007] [Indexed: 11/15/2022]
Abstract
Using a comparative genetics approach, one or more of the BtrA, BtrL, BtrP, and BtrV proteins encoded in the butirosin biosynthetic gene cluster (btr) from Bacillus circulans SANK72073 were identified as being responsible for an O-ribosylation process leading to the formation of ribostamycin, a key intermediate in this, and related antibiotic biosynthetic pathways. Functional analysis of the recombinantly expressed proteins revealed that both BtrL and BtrP were responsible for the ribosylation of neamine, using 5-phosphoribosyl-1-diphosphate (PRPP) as the ribosyl donor. Further detailed analysis indicated that this process occurs via two discrete steps: with BtrL first catalyzing the phosphoribosylaion of neamine to form 5''-phosphoribostamycin, followed by a BtrP-catalyzed dephosphorylation to generate ribostamycin. To the best of our knowledge, this is the first time that the functional characterization of a glycosyltransferase from an aminoglycoside biosynthetic gene cluster has been reported.
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Affiliation(s)
- Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan
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50
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Worthington AS, Burkart MD. The old is new again: asparagine oxidation in calcium-dependent antibiotic biosynthesis. ACS Chem Biol 2007; 2:152-4. [PMID: 17373761 DOI: 10.1021/cb700053g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Non-ribosomal peptides are built from both proteinogenic and non-proteinogenic amino acids. The latter resemble amino acids but contain modifications not found in proteins. The recent characterization of a non-heme Fe(2+) and alpha-ketoglutarate-dependent oxygenase that stereospecifically generates beta-hydroxyasparagine, an unnatural amino acid building block for the biosynthesis of calcium-dependent antibiotic, a lipopeptide antibiotic. This work improves our understanding of how these non-proteinogenic amino acids are synthesized.
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Affiliation(s)
- Andrew S Worthington
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0358, USA
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