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Al-Fahad AJ, Al-Fageeh MB, Kharbatia NM, Sioud S, Mahadevan R. Metabolically engineered recombinant Saccharomyces cerevisiae for the production of 2-Deoxy- scyllo-inosose (2-DOI). Metab Eng Commun 2020; 11:e00134. [PMID: 32670790 PMCID: PMC7348060 DOI: 10.1016/j.mec.2020.e00134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 05/22/2020] [Accepted: 05/23/2020] [Indexed: 01/12/2023] Open
Abstract
Saccharomyces cerevisiae is a versatile industrial host for chemical production and has been engineered to produce efficiently many valuable compounds. 2-Deoxy-scyllo-inosose (2-DOI) is an important precursor for the biosynthesis of 2-deoxystreptamine-containing aminoglycosides antibiotics and benzenoid metabolites. Bacterial and cyanobacterial strains have been metabolically engineered to generate 2-DOI; nevertheless, the production of 2-DOI using a yeast host has not been reported. Here, we have metabolically engineered a series of CEN.PK yeast strains to produce 2-DOI using a synthetically yeast codon-optimized btrC gene from Bacillus circulans. The expression of the 2-Deoxy-scyllo-inosose synthase (2-DOIS) gene was successfully achieved via an expression vector and through chromosomal integration at a high-expression locus. In addition, the production of 2-DOI was further investigated for the CEN.PK knockout strains of phosphoglucose isomerase (Δpgi1), D-glucose-6-phosphate dehydrogenase (Δzwf1) and a double mutant (Δpgi1, Δzwf1) in a medium consisting of 2% fructose and 0.05% glucose as a carbon source. We have found that all the recombinant strains are capable of producing 2-DOI and reducing it into scyllo-quercitol and (-)-vibo-quercitol. Comparatively, the high production of 2-DOI and its analogs was observed for the recombinant CEN.PK-btrC carrying the multicopy btrC-expression vector. GC/MS analysis of culture filtrates of this strain showed 11 times higher response in EIC for the m/z 479 (methyloxime-tetra-TMS derivative of 2-DOI) than the YP-btrC recombinant that has only a single copy of btrC expression cassette integrated into the genomic DNA of the CEN.PK strain. The knockout strains namely Δpgi1-btrC and Δpgi1Δzwf1-btrC, that are transformed with the btrC-expression plasmids, have inactive Pgi1 and produced only traces of the compounds. In contrast, Δzwf1-btrC recombinant which has intact pgi1 yielded relatively higher amount of the carbocyclic compounds. Additionally, 1H-NMR analysis of samples showed slow consumption of fructose and no accumulation of 2-DOI and the quercitols in the culture broth of the recombinant CEN.PK-btrC suggesting that S. cerevisiae is capable of assimilating 2-DOI.
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Affiliation(s)
- Ahmed J Al-Fahad
- National Center of Biotechnology, King Abdulaziz City for Science and Technology (KACST), Riyadh, 11442, Saudi Arabia
| | - Mohamed B Al-Fageeh
- National Center of Biotechnology, King Abdulaziz City for Science and Technology (KACST), Riyadh, 11442, Saudi Arabia
| | - Najeh M Kharbatia
- Analytical Chemistry Core Laboratory, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Salim Sioud
- Analytical Chemistry Core Laboratory, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada
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Bai X, Meng D, Wei X, Zhou X, Lu F, You C. Facile synthesis of (-)-vibo-quercitol from maltodextrin via an in vitro synthetic enzymatic biosystem. Biotechnol Bioeng 2019; 116:2710-2719. [PMID: 31237686 DOI: 10.1002/bit.27096] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 06/17/2019] [Accepted: 06/19/2019] [Indexed: 11/09/2022]
Abstract
(-)-vibo-Quercitol (VQ: 1L-1,2,4/3,5-cyclohexanepentol), a form of deoxyinositol, is an alternative chiral building block in the synthesis of bioactive compounds to control diabetes. In this study, an adenosine triphosphate-free in vitro synthetic enzymatic biosystem composed of five enzymes (including one enzyme for NADH regeneration) was constructed to produce VQ from maltodextrin in one-pot. After optimization of reaction conditions, 7.6 g/L VQ was produced from 10 g/L maltodextrin with a product yield (mol/mol) of 77%, and 25.3 g/L VQ with a purity of 87% was produced from 50 g/L maltodextrin through simple scaling up of this nonfermentative enzymatic biosystem. Therefore, this study provides an economical and environmentally friendly method for the envisioned quercitol biosynthesis.
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Affiliation(s)
- Xue Bai
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Bioengineering, Tianjin University of Science and Technology, Tianjin, People's Republic of China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China
| | - Dongdong Meng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China
| | - Xinlei Wei
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China
| | - Xigui Zhou
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Bioengineering, Tianjin University of Science and Technology, Tianjin, People's Republic of China
| | - Chun You
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China
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3
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Lim JH, Hwang HH, Lee NJ, Lee JW, Seo EG, Son HB, Kim HJ, Yoon YJ, Park JW. Enhanced Biosynthesis of 2-Deoxy- scyllo-inosose in Metabolically Engineered Bacillus subtilis Recombinants. Front Microbiol 2018; 9:2333. [PMID: 30319595 PMCID: PMC6170601 DOI: 10.3389/fmicb.2018.02333] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 09/11/2018] [Indexed: 11/19/2022] Open
Abstract
2-Deoxy-scyllo-inosose (DOI) has been a valuable starting natural product for the manufacture of pharmaceuticals or chemical engineering resources such as pyranose catechol. DOI synthase, which uses glucose-6-phosphate (Glc6P) as a substrate for DOI biosynthesis, is indispensably involved in the initial stage of the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics including butirosin, gentamicin, kanamycin, and tobramycin. A number of metabolically engineered recombinant strains of Bacillus subtilis were constructed here; either one or both genes pgi and pgcA that encode Glc6p isomerase and phosphoglucomutase, respectively, was (or were) disrupted in the sugar metabolic pathway of the host. After that, three different DOI synthase–encoding genes, which were artificially synthesized according to the codon preference of the B. subtilis host, were separately introduced into the engineered recombinants. The expression of a natural btrC gene, encoding DOI synthase in butirosin-producing B. circulans, in the heterologous host B. subtilis (BSDOI-2) generated approximately 2.3 g/L DOI, whereas expression of an artificially codon-optimized tobC gene, derived from tobramycin-producing Streptomyces tenebrarius, into the recombinant of B. subtilis (BSDOI-15) in which both genes pgi and pgcA are disrupted significantly enhanced the DOI titer: up to 37.2 g/L. Fed-batch fermentation by the BSDOI-15 recombinant using glycerol and glucose as a dual carbon source yielded the highest DOI titer (38.0 g/L). The development of engineered microbial cell factories empowered through convergence of metabolic engineering and synthetic biology should enable mass production of DOI. Thus, strain BSDOI-15 will surely be a useful contributor to the industrial manufacturing of various kinds of DOI-based pharmaceuticals and fine chemicals.
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Affiliation(s)
- Joo Hyun Lim
- Department of Integrated Biomedical and Life Sciences, Graduate School, Korea University, Seoul, South Korea
| | - Hyun Ha Hwang
- Department of Integrated Biomedical and Life Sciences, Graduate School, Korea University, Seoul, South Korea
| | - Na Joon Lee
- Department of Integrated Biomedical and Life Sciences, Graduate School, Korea University, Seoul, South Korea
| | - Jae Woo Lee
- Department of Integrated Biomedical and Life Sciences, Graduate School, Korea University, Seoul, South Korea
| | - Eun Gyo Seo
- Department of Integrated Biomedical and Life Sciences, Graduate School, Korea University, Seoul, South Korea
| | - Hye Bin Son
- Department of Integrated Biomedical and Life Sciences, Graduate School, Korea University, Seoul, South Korea
| | - Hye Ji Kim
- Department of Integrated Biomedical and Life Sciences, Graduate School, Korea University, Seoul, South Korea
| | - Yeo Joon Yoon
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, South Korea
| | - Je Won Park
- Department of Integrated Biomedical and Life Sciences, Graduate School, Korea University, Seoul, South Korea.,School of Biosystem and Biomedical Science, Korea University, Seoul, South Korea
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Watanabe S, Ozawa H, Kato H, Nimura-Matsune K, Hirayama T, Kudo F, Eguchi T, Kakinuma K, Yoshikawa H. Carbon-free production of 2-deoxy-scyllo-inosose (DOI) in cyanobacterium Synechococcus elongatus PCC 7942. Biosci Biotechnol Biochem 2018; 82:161-165. [PMID: 29297252 DOI: 10.1080/09168451.2017.1411777] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Owing to their photosynthetic capabilities, there is increasing interest in utilizing cyanobacteria to convert solar energy into biomass. 2-Deoxy-scyllo-inosose (DOI) is a valuable starting material for the benzene-free synthesis of catechol and other benzenoids. DOI synthase (DOIS) is responsible for the formation of DOI from d-glucose-6-phosphate (G6P) in the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics such as neomycin and butirosin. DOI fermentation using a recombinant Escherichia coli strain has been reported, although a carbon source is necessary for high-yield DOI production. We constructed DOI-producing cyanobacteria toward carbon-free and sustainable DOI production. A DOIS gene derived from the butirosin producer strain Bacillus circulans (btrC) was introduced and expressed in the cyanobacterium Synechococcus elongatus PCC 7942. We ultimately succeeded in producing 400 mg/L of DOI in S. elongatus without using a carbon source. DOI production by cyanobacteria represents a novel and efficient approach for producing benzenoids from G6P synthesized by photosynthesis.
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Affiliation(s)
- Satoru Watanabe
- a Department of Bioscience , Tokyo University of Agriculture , Tokyo , Japan
| | - Hiroaki Ozawa
- a Department of Bioscience , Tokyo University of Agriculture , Tokyo , Japan
| | - Hiroaki Kato
- a Department of Bioscience , Tokyo University of Agriculture , Tokyo , Japan
| | | | - Toshifumi Hirayama
- b Department of Chemistry , Tokyo Institute of Technology , Tokyo , Japan
| | - Fumitaka Kudo
- b Department of Chemistry , Tokyo Institute of Technology , Tokyo , Japan
| | - Tadashi Eguchi
- b Department of Chemistry , Tokyo Institute of Technology , Tokyo , Japan
| | - Katsumi Kakinuma
- b Department of Chemistry , Tokyo Institute of Technology , Tokyo , Japan
| | - Hirofumi Yoshikawa
- a Department of Bioscience , Tokyo University of Agriculture , Tokyo , Japan
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Ara S, Yamazaki H, Takaku H. Isolation of 2-deoxy-scyllo-inosose (DOI)-assimilating yeasts and cloning and characterization of the DOI reductase gene of Cryptococcus podzolicus ND1. J Biosci Bioeng 2017; 125:397-406. [PMID: 29183694 DOI: 10.1016/j.jbiosc.2017.10.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 10/29/2017] [Accepted: 10/31/2017] [Indexed: 10/18/2022]
Abstract
2-Deoxy-scyllo-inosose (DOI) is the first intermediate in the 2-deoxystreptamine-containing aminoglycoside antibiotic biosynthesis pathway and has a six-membered carbocycle structure. DOI is a valuable material because it is easily converted to aromatic compounds and carbasugar derivatives. In this study, we isolated yeast strains capable of assimilating DOI as a carbon source. One of the strains, Cryptococcus podzolicus ND1, mainly converted DOI to scyllo-quercitol and (-)-vibo-quercitol, which is a valuable compound used as an antihypoglycemia agent and as a heat storage material. An NADH-dependent DOI reductase coding gene, DOIR, from C. podzolicus ND1 was cloned and successfully overexpressed in Escherichia coli. The purified protein catalyzed the irreversible reduction of DOI with NADH and converted DOI into (-)-vibo-quercitol. The enzyme had an optimal pH of 8.5 and optimal temperature of 35°C, respectively. The kcat of this enzyme was 9.98 s-1, and the Km values for DOI and NADH were 4.38 and 0.24 mM, respectively. The enzyme showed a strong preference for NADH and showed no activity with NADPH. Multiple-alignment analysis of DOI reductase revealed that it belongs to the GFO_IDH_MocA protein family and is an inositol dehydrogenase homolog in other fungi, such as Cryptococcus gattii, and bacteria, such as Bacillus subtilis. This is the first identification of a DOI-assimilating yeast and a gene involved in DOI metabolism in fungi.
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Affiliation(s)
- Satoshi Ara
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Higashijima 265-1, Niigata 956-8603, Japan
| | - Harutake Yamazaki
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Higashijima 265-1, Niigata 956-8603, Japan
| | - Hiroaki Takaku
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Higashijima 265-1, Niigata 956-8603, Japan.
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6
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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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7
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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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Kean KM, Codding SJ, Asamizu S, Mahmud T, Karplus PA. Structure of a sedoheptulose 7-phosphate cyclase: ValA from Streptomyces hygroscopicus. Biochemistry 2014; 53:4250-60. [PMID: 24832673 PMCID: PMC4095911 DOI: 10.1021/bi5003508] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Sedoheptulose 7-phosphate cyclases
(SH7PCs) encompass three enzymes
involved in producing the core cyclitol structures of pseudoglycosides
and similar bioactive natural products. One such enzyme is ValA from Streptomyces hygroscopicus subsp. jinggangensis 5008, which makes 2-epi-5-epi-valiolone as part of the biosynthesis
of the agricultural antifungal agent validamycin A. We present, as
the first SH7PC structure, the 2.1 Å resolution crystal structure
of ValA in complex with NAD+ and Zn2+ cofactors.
ValA has a fold and active site organization resembling those of the
sugar phosphate cyclase dehydroquinate synthase (DHQS) and contains
two notable, previously unrecognized interactions between NAD+ and Asp side chains conserved in all sugar phosphate cyclases
that may influence catalysis. Because the domains of ValA adopt a
nearly closed conformation even though no sugar substrate is present,
comparisons with a ligand-bound DHQS provide a model for aspects of
substrate binding. One striking active site difference is a loop that
adopts a distinct conformation as a result of an Asp → Asn
change with respect to DHQS and alters the identity and orientation
of a key Arg residue. This and other active site differences in ValA
are mostly localized to areas where the ValA substrate differs from
that of DHQS. Sequence comparisons with a second SH7PC making a product
with distinct stereochemistry lead us to postulate that the product
stereochemistry of a given SH7PC is not the result of events taking
place during catalysis but is accomplished by selective binding of
either the α or β pyranose anomer of the substrate.
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Affiliation(s)
- Kelsey M Kean
- Department of Biochemistry and Biophysics, Oregon State University , 2011 ALS Building, Corvallis, Oregon 97331-7305, United States
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Genes Encoding Carbocycle-Forming Enzymes Involved in Aminoglycoside Biosynthesis in Deep-Sea Environmental DNA. Biosci Biotechnol Biochem 2014; 74:1102-5. [DOI: 10.1271/bbb.90901] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Differences in the Roles of a Glutamine Amidotransferase Subunit of Pyridoxal 5'-Phosphate Synthase betweenBacillus circulansandBacillus subtilis. Biosci Biotechnol Biochem 2014; 77:1481-5. [DOI: 10.1271/bbb.130132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Ruszczycky MW, Ogasawara Y, Liu HW. Radical SAM enzymes in the biosynthesis of sugar-containing natural products. BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1824:1231-44. [PMID: 22172915 PMCID: PMC3438383 DOI: 10.1016/j.bbapap.2011.11.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 11/28/2011] [Indexed: 11/24/2022]
Abstract
Carbohydrates play a key role in the biological activity of numerous natural products. In many instances their biosynthesis requires radical mediated rearrangements, some of which are catalyzed by radical SAM enzymes. BtrN is one such enzyme responsible for the dehydrogenation of a secondary alcohol in the biosynthesis of 2-deoxystreptamine. DesII is another example that catalyzes a deamination reaction necessary for the net C4 deoxygenation of a glucose derivative en route to desosamine formation. BtrN and DesII represent the two most extensively characterized radical SAM enzymes involved in carbohydrate biosynthesis. In this review, we summarize the biosynthetic roles of these two enzymes, their mechanisms of catalysis, the questions that have arisen during these investigations and the insight they can offer for furthering our understanding of radical SAM enzymology. This article is part of a Special Issue entitled: Radical SAM enzymes and Radical Enzymology.
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Affiliation(s)
- Mark W. Ruszczycky
- Division of Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX 78712, USA Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Yasushi Ogasawara
- Division of Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX 78712, USA Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Hung-wen Liu
- Division of Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX 78712, USA Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
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Asamizu S, Xie P, Brumsted CJ, Flatt PM, Mahmud T. Evolutionary divergence of sedoheptulose 7-phosphate cyclases leads to several distinct cyclic products. J Am Chem Soc 2012; 134:12219-29. [PMID: 22741921 DOI: 10.1021/ja3041866] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sedoheptulose 7-phosphate cyclases are enzymes that utilize the pentose phosphate pathway intermediate, sedoheptulose 7-phosphate, to generate cyclic precursors of many bioactive natural products, such as the antidiabetic drug acarbose, the crop protectant validamycin, and the natural sunscreens mycosporine-like amino acids. These proteins are phylogenetically related to the dehydroquinate (DHQ) synthases from the shikimate pathway and are part of the more recently recognized superfamily of sugar phosphate cyclases, which includes DHQ synthases, aminoDHQ synthases, and 2-deoxy-scyllo-inosose synthases. Through genome mining and biochemical studies, we identified yet another subset of DHQS-like proteins in the actinomycete Actinosynnema mirum and the myxobacterium Stigmatella aurantiaca DW4/3-1. These enzymes catalyze the conversion of sedoheptulose 7-phosphate to 2-epi-valiolone, which is predicted to be an alternative precursor for aminocyclitol biosynthesis. Comparative bioinformatics and biochemical analyses of these proteins with 2-epi-5-epi-valiolone synthases (EEVS) and desmethyl-4-deoxygadusol synthases (DDGS) provided further insights into their genetic diversity, conserved amino acid sequences, and plausible catalytic mechanisms. The results further highlight the uniquely diverse DHQS-like sugar phosphate cyclases, which may provide new tools for chemoenzymatic, stereospecific synthesis of various cyclic molecules.
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Affiliation(s)
- Shumpei Asamizu
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon 97331-3507, USA
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de Mendonça JD, Adachi O, Rosado LA, Ducati RG, Santos DS, Basso LA. Kinetic mechanism determination and analysis of metal requirement of dehydroquinate synthase from Mycobacterium tuberculosis H37Rv: an essential step in the function-based rational design of anti-TB drugs. MOLECULAR BIOSYSTEMS 2010; 7:119-28. [PMID: 20978656 DOI: 10.1039/c0mb00085j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The number of new cases of tuberculosis (TB) arising each year is increasing globally. Migration, socio-economic deprivation, HIV co-infection and the emergence of drug-resistant strains of Mycobacterium tuberculosis, the main causative agent of TB in humans, have all contributed to the increasing number of TB cases worldwide. Proteins that are essential to the pathogen survival and absent in the host, such as enzymes of the shikimate pathway, are attractive targets to the development of new anti-TB drugs. Here we describe the metal requirement and kinetic mechanism determination of M. tuberculosis dehydroquinate synthase (MtDHQS). True steady-state kinetic parameters determination and ligand binding data suggested that the MtDHQS-catalyzed chemical reaction follows a rapid-equilibrium random mechanism. Treatment with EDTA abolished completely the activity of MtDHQS, and addition of Co(2+) and Zn(2+) led to, respectively, full and partial recovery of the enzyme activity. Excess Zn(2+) inhibited the MtDHQS activity, and isotitration microcalorimetry data revealed two sequential binding sites, which is consistent with the existence of a secondary inhibitory site. We also report measurements of metal concentrations by inductively coupled plasma atomic emission spectrometry. The constants of the cyclic reduction and oxidation of NAD(+) and NADH, respectively, during the reaction of MtDHQS was monitored by a stopped-flow instrument, under single-turnover experimental conditions. These results provide a better understanding of the mode of action of MtDHQS that should be useful to guide the rational (function-based) design of inhibitors of this enzyme that can be further evaluated as anti-TB drugs.
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Affiliation(s)
- Jordana Dutra de Mendonça
- Centro de Pesquisas em Biologia Molecular e Funcional, Instituto Nacional de Ciência e Tecnologia em Tuberculose, Pontifícia Universidade Católica do Rio Grande do Sul, 6681/92-A Av Ipiranga, 90619-900, Porto Alegre, RS, Brazil
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Kurumbang N, Liou K, Sohng J. Biosynthesis of paromamine derivatives in engineeredEscherichia coliby heterologous expression. J Appl Microbiol 2010; 108:1780-8. [DOI: 10.1111/j.1365-2672.2009.04582.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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15
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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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Nepal KK, Oh TJ, Sohng JK. Heterologous production of paromamine in Streptomyces lividans TK24 using kanamycin biosynthetic genes from Streptomyces kanamyceticus ATCC12853. Mol Cells 2009; 27:601-8. [PMID: 19466609 DOI: 10.1007/s10059-009-0080-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2009] [Revised: 03/26/2009] [Accepted: 03/30/2009] [Indexed: 10/20/2022] Open
Abstract
The 2-deoxystreptamine and paromamine are two key intermediates in kanamycin biosynthesis. In the present study, pSK-2 and pSK-7 recombinant plasmids were constructed with two combinations of genes: kanABK and kanABKF and kacA respectively from kanamycin producer Streptomyces kanamyceticus ATCC12853. These plasmids were heterologously expressed into Streptomyces lividans TK24 independently and generated two recombinant strains named S. lividans Sk-2/SL and S. lividans SK-7/SL, respectively. ESI/ MS and ESI-LC/MS analysis of the metabolite from S. lividans SK-2/SL showed that the compound had a molecular mass of 163 [M + H]+, which corresponds to that of 2-deoxystreptamine. ESI/MS and MS/MS analysis of metabolites from S. lividans SK-7/SL demonstrated the production of paromamine with a molecular mass of 324 [M + H]+. In this study, we report the production of paromamine in a heterologous host for the first time. This study will evoke to explore complete biosynthetic pathways of kanamycin and related aminoglycoside antibiotics.
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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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18
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Yokoyama K, Ohmori D, Kudo F, Eguchi T. Mechanistic Study on the Reaction of a Radical SAM Dehydrogenase BtrN by Electron Paramagnetic Resonance Spectroscopy. Biochemistry 2008; 47:8950-60. [DOI: 10.1021/bi800509x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kenichi Yokoyama
- Department of Chemistry and Department of Chemistry and Materials Science, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan, and Department of Chemistry, Juntendo University, Inba, Chiba 270-1695, Japan
| | - Daijiro Ohmori
- Department of Chemistry and Department of Chemistry and Materials Science, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan, and Department of Chemistry, Juntendo University, Inba, Chiba 270-1695, Japan
| | - Fumitaka Kudo
- Department of Chemistry and Department of Chemistry and Materials Science, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan, and Department of Chemistry, Juntendo University, Inba, Chiba 270-1695, Japan
| | - Tadashi Eguchi
- Department of Chemistry and Department of Chemistry and Materials Science, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan, and Department of Chemistry, Juntendo University, Inba, Chiba 270-1695, Japan
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19
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Kim JY, Suh JW, Kang SH, Phan TH, Park SH, Kwon HJ. Gene inactivation study of gntE reveals its role in the first step of pseudotrisaccharide modifications in gentamicin biosynthesis. Biochem Biophys Res Commun 2008; 372:730-4. [PMID: 18533111 DOI: 10.1016/j.bbrc.2008.05.133] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2008] [Accepted: 05/20/2008] [Indexed: 11/16/2022]
Abstract
A gene inactivation study was performed on gntE, a member of the gentamicin biosynthetic gene cluster in Micromonospora echinospora. Computer-aided homology analysis predicts a methyltransferase-related cobalamin-binding domain and a radical S-adenosylmethionine domain in GntE. It is also found that there is no gntE homolog within other aminoglycoside biosynthetic gene clusters. Inactivation of gntE was achieved in both M. echinospora ATCC 15835 and a gentamicin high-producer GMC106. High-performance liquid chromatographic analysis, coupled with mass spectrometry, revealed that gntE mutants accumulated gentamicin A2 and its derivative with a methyl group installed on the glucoamine moiety. This result substantiated that GntE participates in the first step of pseudotrisaccharide modifications in gentamicin biosynthesis, though the catalytic nature of this unusual oxidoreductase/methyltransferase candidate is not resolved. The present gene inactivation study also demonstrates that targeted genetic engineering can be applied to produce specific gentamicin structures and potentially new gentamicin derivatives in M. echinospora.
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Affiliation(s)
- Jin-Yong Kim
- Department of Biological Science, Division of Bioscience and Bioinformatics, Myongji University, Yongin 449-728, Republic of Korea
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20
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Nango E, Kumasaka T, Hirayama T, Tanaka N, Eguchi T. Structure of 2-deoxy-scyllo-inosose synthase, a key enzyme in the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics, in complex with a mechanism-based inhibitor and NAD+. Proteins 2008; 70:517-27. [PMID: 17879343 DOI: 10.1002/prot.21526] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A key enzyme in the biosynthesis of clinically important aminoglycoside antibiotics is 2-deoxy-scyllo-inosose synthase (DOIS), which catalyzes carbocycle formation from D-glucose-6-phosphate to 2-deoxy-scyllo-inosose through a multistep reaction. This reaction mechanism is similar to the catalysis by dehydroquinate synthase (DHQS) of the cyclization of 3-deoxy-D-arabino-heputulosonate-7-phosphate to dehydroquinate in the shikimate pathway, but significant dissimilarity between these enzymes is also known, particularly in the stereochemistry of the phosphate elimination reaction and the cyclization. Here, the crystal structures of DOIS from Bacillus circulans and its complex with the substrate analog inhibitor carbaglucose-6-phosphate, NAD+, and Co2+ have been determined to provide structural insights into the reaction mechanism. The complex structure shows that an active site exists between the N-terminal and C-terminal domains and that the inhibitor coordinates a cobalt ion in this site. Two subunits exist as a dimer in the asymmetric unit. The two active sites of the dimer were observed to be different. One contains a dephosphorylated compound derived from the inhibitor and the other includes the inhibitor without change. The present study suggested that phosphate elimination proceeds through syn-elimination assisted by Glu 243 and the aldol condensation proceeds via a boat conformation. Also discussed are significant similarities and dissimilarities between DOIS and DHQS, particularly in terms of the structure at the active site and the reaction mechanism.
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Affiliation(s)
- Eriko Nango
- Department of Chemistry, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan
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21
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Kogure T, Wakisaka N, Takaku H, Takagi M. Efficient production of 2-deoxy-scyllo-inosose from d-glucose by metabolically engineered recombinant Escherichia coli. J Biotechnol 2007; 129:502-9. [PMID: 17368605 DOI: 10.1016/j.jbiotec.2007.01.016] [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: 10/28/2006] [Revised: 01/09/2007] [Accepted: 01/22/2007] [Indexed: 11/26/2022]
Abstract
2-Deoxy-scyllo-inosose (DOI) is a six-membered carbocycle formed from d-glucose-6-phosphate catalyzed by 2-deoxy-scyllo-inosose synthase (DOIS), a key enzyme in the biosynthesis of 2-deoxystreptamine-containing aminocyclitol antibiotics. DOI is valuable as a starting material for the benzene-free synthesis of catechol and other benzenoids. We constructed a series of metabolically engineered Escherichia coli strains by introducing a DOIS gene (btrC) from Bacillus circulans and disrupting genes for phosphoglucose isomerase, d-glucose-6-phosphate dehydrogenase, and phosphoglucomutase (pgi, zwf and pgm, respectively). It was found that deletion of the pgi gene, pgi and zwf genes, pgi and pgm genes, or all pgi, zwf and pgm genes significantly improved DOI production by recombinant E. coli in 2YTG medium (3% glucose) up to 7.4, 6.1, 11.6, and 8.4 g l(-1), respectively, compared with that achieved by wild-type recombinant E. coli (1.5 g l(-1)). Moreover, E. coli mutants with disrupted pgi, zwf and pgm genes showed strongly enhanced DOI productivity of up to 29.5 g l(-1) (99% yield) in the presence of mannitol as a supplemental carbon source. These results demonstrated that DOI production by metabolically engineered recombinant E. coli may provide a novel, efficient approach to the production of benzenoids from renewable d-glucose.
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Affiliation(s)
- Takahisa Kogure
- Faculty of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Higashijima 265-1, Niitsu, Niigata 956-8603, Japan
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22
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Wu X, Flatt PM, Schlörke O, Zeeck A, Dairi T, Mahmud T. A comparative analysis of the sugar phosphate cyclase superfamily involved in primary and secondary metabolism. Chembiochem 2007; 8:239-48. [PMID: 17195255 PMCID: PMC3127856 DOI: 10.1002/cbic.200600446] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Sugar phosphate cyclases (SPCs) catalyze the cyclization of sugar phosphates to produce a variety of cyclitol intermediates that serve as the building blocks of many primary metabolites, for example, aromatic amino acids, and clinically relevant secondary metabolites, for example, aminocyclitol/aminoglycoside and ansamycin antibiotics. Feeding experiments with isotopically labeled cyclitols revealed that cetoniacytone A, a unique C(7)N-aminocyclitol antibiotic isolated from an insect endophytic Actinomyces sp., is derived from 2-epi-5-epi-valiolone, a product of SPC. By using heterologous probes from the 2-epi-5-epi-valiolone synthase class of SPCs, an SPC homologue gene, cetA, was isolated from the cetoniacytone producer. cetA is closely related to BE-orf9 found in the BE-40644 biosynthetic gene cluster from Actinoplanes sp. strain A40644. Recombinant expression of cetA and BE-orf9 and biochemical characterization of the gene products confirmed their function as 2-epi-5-epi-valiolone synthases. Further phylogenetic analysis of SPC sequences revealed a new clade of SPCs that might regulate the biosynthesis of a novel set of secondary metabolites.
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Affiliation(s)
- Xiumei Wu
- Genetics Program, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97331-2212, USA
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23
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Hirayama T, Kudo F, Huang Z, Eguchi T. Role of glutamate 243 in the active site of 2-deoxy-scyllo-inosose synthase from Bacillus circulans. Bioorg Med Chem 2007; 15:418-23. [PMID: 17035031 DOI: 10.1016/j.bmc.2006.09.042] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2006] [Revised: 09/19/2006] [Accepted: 09/21/2006] [Indexed: 11/18/2022]
Abstract
2-Deoxy-scyllo-inosose (DOI) synthase is involved in the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics and catalyzes the carbocyclic formation from d-glucose-6-phosphate (G-6-P) into DOI. The reaction mechanism is proposed to be similar to that of dehydroquinate (DHQ) synthase in the shikimate pathway, and includes oxidation of C-4, beta-elimination of phosphate, reduction of C-4, ring opening, and intramolecular aldol cyclization. To investigate the reaction mechanism of DOI synthase, site-directed mutational analysis of three presumable catalytically important amino acids of DOI synthase derived from the butirosin producer Bacillus circulans (BtrC) was carried out. Steady state and pre-steady state kinetic analysis suggested that E243 of BtrC is catalytically involved in the phosphate elimination step. Further analysis of the mutant E243Q of BtrC using substrate analogue, glucose-6-phosphonate, clearly confirmed that E243 was responsible to abstract a proton at C-5 in G-6-P and set off phosphate elimination. This glutamate residue is completely conserved in all DOI synthases identified so far and the corresponding amino acid of DHQ synthase is completely conserved as asparagine. Therefore, this characteristic glutamate residue of DOI synthase is a key determinant to distinguish the reaction mechanism between DOI synthase and DHQ synthase as well as primary sequence.
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Affiliation(s)
- Toshifumi Hirayama
- Department of Chemistry and Materials Science, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan
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24
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Flatt PM, Mahmud T. Biosynthesis of aminocyclitol-aminoglycoside antibiotics and related compounds. Nat Prod Rep 2006; 24:358-92. [PMID: 17390001 DOI: 10.1039/b603816f] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This review covers the biosynthesis of aminocyclitol-aminoglycoside antibiotics and related compounds, particularly from the molecular genetic perspectives. 195 references are cited.
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Affiliation(s)
- Patricia M Flatt
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507, USA
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25
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Llewellyn NM, Spencer JB. Biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics. Nat Prod Rep 2006; 23:864-74. [PMID: 17119636 DOI: 10.1039/b604709m] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The 2-deoxystreptamine-containing aminoglycosides are an important class of clinically valuable antibiotics. A deep understanding of the biosynthesis of these natural products is required to enable efforts to rationally manipulate and engineer the biological production of novel aminoglycosides. This review discusses the development of our biosynthetic knowledge over the past half-century, with emphasis on the relatively recent contributions of molecular biology to the elucidation of these biosynthetic pathways.
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Affiliation(s)
- Nicholas M Llewellyn
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UKCB2 1EW.
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26
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Kudo F, Yamamoto Y, Yokoyama K, Eguchi T, Kakinuma K. Biosynthesis of 2-Deoxystreptamine by Three Crucial Enzymes in Streptomyces fradiae NBRC 12773. J Antibiot (Tokyo) 2005; 58:766-74. [PMID: 16506694 DOI: 10.1038/ja.2005.104] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
NeoA, B, and C encoded in the neomycin biosynthetic gene cluster have been enzymatically confirmed to be responsible to the formation of 2-deoxystreptamine (DOS) in Streptomyces fradiae. NeoC was functionally characterized as 2-deoxy-scyllo-inosose synthase, which catalyzes the carbocycle formation from D-glucose-6-phosphate to 2-deoxy-scyllo-inosose. Further, NeoA appeared to catalyze the oxidation of 2-deoxy-scyllo-inosamine (DOIA) with NAD(P)+ forming 3-amino-2,3-dideoxy-scyllo-inosose (amino-DOI). Consequently, NeoA was characterized as 2-deoxy-scyllo-inosamine dehydrogenase. Finally, amino-DOI produced by NeoA from DOIA was transformed into DOS by NeoB. Since NeoB (Neo6) was also reported to be L-glutamine:2-deoxy-scyllo-inosose aminotransferase, all the enzymes in the DOS biosynthesis were characterized for the first time.
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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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27
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Nango E, Kumasaka T, Sato T, Tanaka N, Kakinuma K, Eguchi T. Crystallization and X-ray analysis of 2-deoxy-scyllo-inosose synthase, the key enzyme in the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:709-11. [PMID: 16511136 PMCID: PMC1952460 DOI: 10.1107/s1744309105018841] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2005] [Accepted: 06/14/2005] [Indexed: 11/10/2022]
Abstract
A recombinant 2-deoxy-scyllo-inosose synthase from Bacillus circulans has been crystallized at 277 K using PEG 4000 as precipitant. The diffraction pattern of the crystal extends to 2.30 A resolution at 100 K using synchrotron radiation at the Photon Factory. The crystals are monoclinic and belong to space group P2(1), with unit-cell parameters a = 80.5, b = 70.4, c = 83.0 A, beta = 117.8 degrees. The presence of two molecules per asymmetric unit gives a crystal volume per protein weight (VM) of 2.89 A3 Da(-1) and a solvent constant of 57.4% by volume.
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Affiliation(s)
- Eriko Nango
- Department of Chemistry, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Takashi Kumasaka
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Takao Sato
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Nobuo Tanaka
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Katsumi Kakinuma
- Department of Chemistry, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Tadashi Eguchi
- Department of Chemistry and Materials Science, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan
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Busscher GF, Rutjes FPJT, van Delft FL. 2-Deoxystreptamine: central scaffold of aminoglycoside antibiotics. Chem Rev 2005; 105:775-91. [PMID: 15755076 DOI: 10.1021/cr0404085] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Guuske F Busscher
- IMM Organic Chemistry, Radboud University Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
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29
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Huang Z, Kakinuma K, Eguchi T. Stereospecificity of hydride transfer in NAD+-catalyzed 2-deoxy-scyllo-inosose synthase, the key enzyme in the biosynthesis of 2-deoxystreptamine-containing aminocyclitol antibiotics. Bioorg Chem 2004; 33:82-9. [PMID: 15788164 DOI: 10.1016/j.bioorg.2004.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2004] [Revised: 09/21/2004] [Accepted: 09/21/2004] [Indexed: 12/01/2022]
Abstract
The key enzyme in the biosynthesis of clinically important aminocyclitol antibiotics is 2-deoxy-scyllo-inosose synthase (DOIS), which converts ubiquitous d-glucose 6-phosphate (G-6-P) into the specific carbocycle, 2-deoxy-scyllo-inosose with an aid of NAD(+)-NADH recycling. The NAD(+)-dependent first step of the DOIS reaction was examined in detail by the use of 6-phosphonate and 6-homophosphonate analogs of G-6-P. Both analogs showed competitive inhibition against the DOIS reaction with K(i) values of 1.3 and 2.8 mM, respectively, due to their inability for the subsequent phosphate elimination. Based on the direct spectrophotometric observation of NADH formed by the hydride transfer from 6-phosphonate to NAD(+), the stereospecificity of the hydride transfer in the DOIS reaction was analyzed with 6-[4-(2)H]phosphonate and was found to be pro-R specific.
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Affiliation(s)
- Zhen Huang
- Department of Chemistry and Materials Science, Tokyo Institute of Technology, O-okayama, Japan
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30
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Yamauchi N, Ueoka H, Kamada N, Murae T. Resemblance of Carbocycle Formation from Carbohydrates between Archaea and Eucarya/Eubacteria. Biosynthesis of Calditol, the Characteristic Lipid-Content Molecule inSulfolobus acidocaldarius. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2004. [DOI: 10.1246/bcsj.77.771] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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31
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Nango E, Kudo F, Eguchi T, Kakinuma K. Reaction Stereochemistry of 2-Deoxy-scyllo-inosose Synthase, the Key Enzyme in the Biosynthesis of 2-Deoxystreptamine. CHEM LETT 2003. [DOI: 10.1246/cl.2003.438] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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32
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Eguchi T, Sasaki S, Huang Z, Kakinuma K. Importance of specific hydrogen-bond donor-acceptor interactions for the key carbocycle-forming reaction catalyzed by 2-deoxy-scyllo-inosose synthase in the biosynthesis of 2-deoxystreptamine-containing aminocyclitol antibiotics. J Org Chem 2002; 67:3979-84. [PMID: 12054929 DOI: 10.1021/jo011107n] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A crucial enzyme in the biosynthesis of the 2-deoxystreptamine aglycon of clinically important aminocyclitol antibiotics is 2-deoxy-scyllo-inosose synthase (DOIS), which converts ubiquitous D-glucose 6-phosphate (G-6-P) into the specific carbocycle 2-deoxy-scyllo-inosose. Among all the oxygenated carbons of the substrate, C-1, -4, -5, and -6 are directly involved in the chemical transformation. To get insight into the roles of C-2 and C-3 hydroxy groups, 2-deoxy-2-fluoro-, 3-deoxy-3-fluoro-, 2-amino-2-deoxy-, and 3-amino-3-deoxy-D-glucose 6-phosphates (2-F-G-6-P, 3-F-G-6-P, 2-NH(2)-G-6-P, and 3-NH(2)-G-6-P, respectively) were subjected to the DOIS reaction as probe, since a fluorine substituent generally acts as a hydrogen-bond acceptor, and an ammonium functionality derived physiologically from an amino group as a hydrogen-bond donor. Among those tested, 2-F-G-6-P and 3-NH(2)-G-6-P were used as substrates by DOIS and were converted into the corresponding deoxyfluoro- and aminodeoxy-scyllo-inososes, respectively. In contrast, 3-F-G-6-P and 2-NH(2)-G-6-P were inactive in the cyclization reaction. Clearly, DOIS recognizes the G-6-P substrate through specific hydrogen-bonding interactions, i.e., through a hydrogen-donating group for C-2 and an accepting group for C-3 of the substrate. Modeling of DOIS based on the structure of evolutionary-related dehydroquinate synthase is also described.
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Affiliation(s)
- Tadashi Eguchi
- Department of Chemistry and Materials Science, Tokyo Institute of Technology, O-okayama, Meguro-ku 152-8551, Japan.
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33
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Yu J, Spencer JB. Convenient synthesis of 2-deoxy-scyllo-inosose and 2-deoxy-scyllo-inosamine: two key intermediates on the biosynthetic pathway to aminoglycoside antibiotics. Tetrahedron Lett 2001. [DOI: 10.1016/s0040-4039(01)00612-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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34
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Watanabe K, Mie T, Ichihara A, Oikawa H, Honma M. Detailed reaction mechanism of macrophomate synthase. Extraordinary enzyme catalyzing five-step transformation from 2-pyrones to benzoates. J Biol Chem 2000; 275:38393-401. [PMID: 10984474 DOI: 10.1074/jbc.m003119200] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Macrophomate synthase from the fungus Macrophoma commelinae IFO 9570 is a Mg(II)-dependent dimeric enzyme that catalyzes an extraordinary, complex five-step chemical transformation from 2-pyrone and oxalacetate to benzoate involving decarboxylation, C-C bond formation, and dehydration. The catalytic mechanism of the whole pathway was investigated in three separate chemical steps. In the first decarboxylation step, the enzyme loses oxalacetate decarboxylation activity upon incubation with EDTA. Activity is fully restored by addition of Mg(II) and is not restored with other divalent metal cations. The dissociation constant of 0.93 x 10(-)(7) for Mg(II) and atomic absorption analysis established a 1:1 stoichiometric complex. Inhibition of pyruvate formation with 2-pyrone revealed that the actual product in the first step is a pyruvate enolate, which undergoes C-C bond formation in the presence of 2-pyrone. Incubation of substrate analogs provided aberrant adducts that were produced via C-C bond formation and rearrangement. This strongly indicates that the second step is two C-C bond formations, affording a bicyclic intermediate. Based on the stereospecificity, involvement of a Diels-Alder reaction at the second step is proposed. Incubation of the stereospecifically deuterium-labeled malate with 2-pyrones in the presence of malate dehydrogenase provided information for the stereochemical course of the reaction catalyzed by macrophomate synthase, indicating that the first decarboxylation provides pyruvate (Z)-[3-(2)H]enolate and that dehydration at the final step occurs with anti-elimination accompanied by concomitant decarboxylation. Examination of kinetic parameters in the individual steps suggests that the third step is the rate-determining step of the overall transformation.
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Affiliation(s)
- K Watanabe
- Department of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
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35
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Oikawa H, Yagi K, Ohashi S, Watanabe K, Mie T, Ichihara A, Honma M, Kobayashi K. Potent inhibition of macrophomate synthase by reaction intermediate analogs. Biosci Biotechnol Biochem 2000; 64:2368-79. [PMID: 11193404 DOI: 10.1271/bbb.64.2368] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Potent inhibitors for macrophomate synthase, which has recently been found to catalyze a highly unusual five-step chemical transformation, were explored. Among 11 oxalacetate analogs tested, only three analogs had moderate to relatively strong inhibitory activities (I50 1.3-8.1 mM). On the other hand, among 35 bicyclic intermediate analogs synthesized, two diacids were found to be the most potent inhibitors (I50 0.80, 0.84 mM) which had a much higher affinity than that of the natural substrate 2-pyrone. (-)-Enantiomers of the diacids showed 30 times stronger activity (I50 0.34, 0.41 mM) than (+)-ones. The I50/Km values (0.20, 0.24) showed their potent inhibitions. Competitive inhibitions were observed in two representative inhibitors.
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Affiliation(s)
- H Oikawa
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan.
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Kakinuma K, Nango E, Kudo F, Matsushima Y, Eguchi T. An expeditious chemo-enzymatic route from glucose to catechol by the use of 2-deoxy-scyllo-inosose synthase. Tetrahedron Lett 2000. [DOI: 10.1016/s0040-4039(00)00064-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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