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Meng Y, Tao S, Wu XY, Huang SH, Hong R. Nitroso-Ene-type Cyclization Toward Diversified Synthesis of Amino Deoxysugars: A Proof of Concept. Org Lett 2023; 25:1929-1934. [PMID: 36913431 DOI: 10.1021/acs.orglett.3c00461] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
Amino deoxysugars are abundant in nature and play an important role in various biological functions, promoting numerous efforts to synthesize their structurally unique motifs. In this report, a de novo approach from a readily available lactic acid derivative is devised to construct several amino deoxysugars embedded in natural products, featuring a novel nitroso-ene-type cyclization to introduce a nitrogen atom into the carbon framework. This efficient synthesis provides an unprecedented synthetic route to explore the nitroso-ene cyclization to accumulate intriguing amino deoxysugars.
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Affiliation(s)
- Yuan Meng
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai 200444, People's Republic of China
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, People's Republic of China
| | - Shunan Tao
- School of Environmental and Chemical Engineering, Shanghai Institute of Technology, Shanghai 201418, People's Republic of China
| | - Xiao-Yu Wu
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai 200444, People's Republic of China
| | - Sha-Hua Huang
- School of Environmental and Chemical Engineering, Shanghai Institute of Technology, Shanghai 201418, People's Republic of China
| | - Ran Hong
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, People's Republic of China
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2
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You C, Zhang Y, Xu Y, Xu P, Li Z, Li H, Huang S, Chen Z, Li J, Xu HE, Jiang Y. Structural basis for motilin and erythromycin recognition by motilin receptor. SCIENCE ADVANCES 2023; 9:eade9020. [PMID: 36921049 PMCID: PMC10017046 DOI: 10.1126/sciadv.ade9020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
Motilin is an endogenous peptide hormone almost exclusively expressed in the human gastrointestinal (GI) tract. It activates the motilin receptor (MTLR), a class A G protein-coupled receptor (GPCR), and stimulates GI motility. To our knowledge, MTLR is the first GPCR reported to be activated by macrolide antibiotics, such as erythromycin. It has attracted extensive attention as a potential drug target for GI disorders. We report two structures of Gq-coupled human MTLR bound to motilin and erythromycin. Our structures reveal the recognition mechanism of both ligands and explain the specificity of motilin and ghrelin, a related gut peptide hormone, for their respective receptors. These structures also provide the basis for understanding the different recognition modes of erythromycin by MTLR and ribosome. These findings provide a framework for understanding the physiological regulation of MTLR and guiding drug design targeting MTLR for the treatment of GI motility disorders.
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Affiliation(s)
- Chongzhao You
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yumu Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Youwei Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Peiyu Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Zhen Li
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
| | - Huadong Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Sijie Huang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Zecai Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingru Li
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
| | - H. Eric Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
- Lingang Laboratory, Shanghai 200031, China
| | - Yi Jiang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Lingang Laboratory, Shanghai 200031, China
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3
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Cárdenas-Fernández M, Sinclair O, Ward JM. Novel transaminases from thermophiles: from discovery to application. Microb Biotechnol 2021; 15:305-317. [PMID: 34713952 PMCID: PMC8719814 DOI: 10.1111/1751-7915.13940] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 01/26/2023] Open
Abstract
Transaminases (TAs) are promising biocatalysts for chiral amine synthesis; however, only few thermophilic TAs have been described to date. In this work, a genome mining approach was taken to seek novel TAs from nine thermophilic microorganisms. TA sequences were identified from their respective genome sequences and their Pfam were predicted confirming that TAs class I–II are the most abundant (50%), followed by class III (26%), V (16%), IV (8%) and VI (1%). The percentage of open reading frames (ORFs) that are TAs ranges from 0.689% in Thermococcus litoralis to 0.424% in Sulfolobus solfataricus. A total of 94 putative TAs were successfully cloned and expressed into E. coli, showing mostly good expression levels when using a chemical chaperone media containing d‐sorbitol. Kinetic and end‐point colorimetric assays with different amino donors–acceptors confirmed TAs activity allowing for initial exploration of the substrate scope. Stereoselective and non‐stereoselective serine‐TAs were selected for the synthesis of hydroxypyruvate (HPA). Low HPA reaction yields were observed with four non‐stereoselective serine‐TAs, whilst two stereoselective serine‐TAs showed significantly higher yields. Coupling serine‐TA reactions to a transketolase to yield l‐erythrulose (Ery) substantially increased serine conversion into HPA. Combining both stereoselective serine‐TAs and transketolase using the inexpensive racemic D/L‐serine led to high Ery yield (82%). Thermal characterization of stereoselective serine‐TAs confirmed they have excellent thermostability up to 60°C and high optimum temperatures.
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Affiliation(s)
- Max Cárdenas-Fernández
- Department of Biochemical Engineering, University College London, Gower St, WC1E 6BT, London, UK.,School of Biosciences, University of Kent, CT2 7NJ, Kent, UK
| | - Oliver Sinclair
- Department of Biochemical Engineering, University College London, Gower St, WC1E 6BT, London, UK
| | - John M Ward
- Department of Biochemical Engineering, University College London, Gower St, WC1E 6BT, London, UK
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4
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Seltzner CA, Ferek JD, Thoden JB, Holden HM. Characterization of an aminotransferase from Acanthamoeba polyphaga Mimivirus. Protein Sci 2021; 30:1882-1894. [PMID: 34076307 DOI: 10.1002/pro.4139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 01/03/2023]
Abstract
Acanthamoeba polyphaga Mimivirus, a complex virus that infects amoeba, was first reported in 2003. It is now known that its DNA genome encodes for nearly 1,000 proteins including enzymes that are required for the biosynthesis of the unusual sugar 4-amino-4,6-dideoxy-d-glucose, also known as d-viosamine. As observed in some bacteria, the pathway for the production of this sugar initiates with a nucleotide-linked sugar, which in the Mimivirus is thought to be UDP-d-glucose. The enzyme required for the installment of the amino group at the C-4' position of the pyranosyl moiety is encoded in the Mimivirus by the L136 gene. Here, we describe a structural and functional analysis of this pyridoxal 5'-phosphate-dependent enzyme, referred to as L136. For this analysis, three high-resolution X-ray structures were determined: the wildtype enzyme/pyridoxamine 5'-phosphate/dTDP complex and the site-directed mutant variant K185A in the presence of either UDP-4-amino-4,6-dideoxy-d-glucose or dTDP-4-amino-4,6-dideoxy-d-glucose. Additionally, the kinetic parameters of the enzyme utilizing either UDP-d-glucose or dTDP-d-glucose were measured and demonstrated that L136 is efficient with both substrates. This is in sharp contrast to the structurally related DesI from Streptomyces venezuelae, whose three-dimensional architecture was previously reported by this laboratory. As determined in this investigation, DesI shows a profound preference in its catalytic efficiency for the dTDP-linked sugar substrate. This difference can be explained in part by a hydrophobic patch in DesI that is missing in L136. Notably, the structure of L136 reported here represents the first three-dimensional model for a virally encoded PLP-dependent enzyme and thus provides new information on sugar aminotransferases in general.
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Affiliation(s)
- Chase A Seltzner
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Justin D Ferek
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - James B Thoden
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Hazel M Holden
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
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5
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Sridharan AP, Sugitha T, Karthikeyan G, Nakkeeran S, Sivakumar U. Metabolites of Trichoderma longibrachiatum EF5 inhibits soil borne pathogen, Macrophomina phaseolina by triggering amino sugar metabolism. Microb Pathog 2020; 150:104714. [PMID: 33383148 DOI: 10.1016/j.micpath.2020.104714] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 01/07/2023]
Abstract
An endophytic fungal antagonist Trichoderma longibrachiatum EF5 exhibited biocontrol activity against a soil-borne fungal pathogen Macrophomina phaseolina. Under dual co-culture, T. longibrachiatum EF5 showed 58% inhibition against M. phaseolina. Crude soluble metabolites (SMs) extracted from EF5 exhibited biocontrol activity (61%), which is more significant than the cell-free extract. Dual culture of both T. longibrachiatum EF5 and M. phaseolina displayed entangled mycelial structures and retarded hyphal growth. The metabolites responsible for antibiosis and pathogenic activity profiled through GC-MS revealed a total of 131 SMs from axenic culture and upon the interaction of T. longibrachiatum EF5 and M. phaseolina. Interestingly, potential plant-growth-promoting and antimicrobial compounds such as 1- pentanol, 1-hexanol, myristonyl pantothenate, bisabolol, d-Alanine, and diethyl trisulphide were unique with T. longibrachiatum EF5. Few compounds that were not observed or produced minimally under axenic culture were increased during their interaction (e.g., 1,6-anhydro-á-d-Glucopyranose and 5-heptyl dihydro-2(3H)-Furanone), suggesting antimicrobial action against the pathogen. This study also unraveled the induction of amino sugar metabolism when T. longibrachiatum EF5 interacts with M. phaseolina, which is responsible for colonization and counterfeiting the pathogen. Hence T. longibrachiatum EF5 could be a potential biocontrol agent employed for defense priming and plant growth promotion.
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Affiliation(s)
- A P Sridharan
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - Thangappan Sugitha
- Biocatalysts Laboratory, Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - G Karthikeyan
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - S Nakkeeran
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - Uthandi Sivakumar
- Biocatalysts Laboratory, Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, 641003, India.
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6
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Fick RJ, Horowitz S, McDole BG, Clay MC, Mehl RA, Al-Hashimi HM, Scheiner S, Trievel RC. Structural and Functional Characterization of Sulfonium Carbon-Oxygen Hydrogen Bonding in the Deoxyamino Sugar Methyltransferase TylM1. Biochemistry 2019; 58:2152-2159. [PMID: 30810306 DOI: 10.1021/acs.biochem.8b01141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The N-methyltransferase TylM1 from Streptomyces fradiae catalyzes the final step in the biosynthesis of the deoxyamino sugar mycaminose, a substituent of the antibiotic tylosin. The high-resolution crystal structure of TylM1 bound to the methyl donor S-adenosylmethionine (AdoMet) illustrates a network of carbon-oxygen (CH···O) hydrogen bonds between the substrate's sulfonium cation and residues within the active site. These interactions include hydrogen bonds between the methyl and methylene groups of the AdoMet sulfonium cation and the hydroxyl groups of Tyr14 and Ser120 in the enzyme. To examine the functions of these interactions, we generated Tyr14 to phenylalanine (Y14F) and Ser120 to alanine (S120A) mutations to selectively ablate the CH···O hydrogen bonding to AdoMet. The TylM1 S120A mutant exhibited a modest decrease in its catalytic efficiency relative to that of the wild type (WT) enzyme, whereas the Y14F mutation resulted in an approximately 30-fold decrease in catalytic efficiency. In contrast, site-specific substitution of Tyr14 by the noncanonical amino acid p-aminophenylalanine partially restored activity comparable to that of the WT enzyme. Correlatively, quantum mechanical calculations of the activation barrier energies of WT TylM1 and the Tyr14 mutants suggest that substitutions that abrogate hydrogen bonding with the AdoMet methyl group impair methyl transfer. Together, these results offer insights into roles of CH···O hydrogen bonding in modulating the catalytic efficiency of TylM1.
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Affiliation(s)
- Robert J Fick
- Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Scott Horowitz
- Department of Chemistry and Biochemistry, Knoebel Institute for Healthy Aging , University of Denver , Denver , Colorado 80208 , United States
| | - Brandon G McDole
- Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Mary C Clay
- Department of Biochemistry , Duke University , Durham , North Carolina 27710 , United States
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics , Oregon State University , Corvallis , Oregon 97331 , United States
| | - Hashim M Al-Hashimi
- Department of Biochemistry , Duke University , Durham , North Carolina 27710 , United States
| | - Steve Scheiner
- Department of Chemistry and Biochemistry , Utah State University , Logan , Utah 84322 , United States
| | - Raymond C Trievel
- Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
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7
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Kitamura K, Ando Y, Matsumoto T, Suzuki K. Total Synthesis of Aryl C-Glycoside Natural Products: Strategies and Tactics. Chem Rev 2017; 118:1495-1598. [DOI: 10.1021/acs.chemrev.7b00380] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kei Kitamura
- Department
of Applied Chemistry for Environment, School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337, Japan
| | - Yoshio Ando
- Department
of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Takashi Matsumoto
- School
of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1
Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Keisuke Suzuki
- Department
of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan
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8
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Matsushima Y, Kino J. A versatile route to 2,4,6-trideoxy-4-aminohexoses: Stereoselective syntheses of d -vicenisamine and its epimers via iodocyclization of carbamate. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.10.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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9
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Wang F, Singh S, Xu W, Helmich KE, Miller MD, Cao H, Bingman CA, Thorson JS, Phillips GN. Structural Basis for the Stereochemical Control of Amine Installation in Nucleotide Sugar Aminotransferases. ACS Chem Biol 2015; 10:2048-56. [PMID: 26023720 DOI: 10.1021/acschembio.5b00244] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sugar aminotransferases (SATs) are an important class of tailoring enzymes that catalyze the 5'-pyridoxal phosphate (PLP)-dependent stereo- and regiospecific installation of an amino group from an amino acid donor (typically L-Glu or L-Gln) to a corresponding ketosugar nucleotide acceptor. Herein we report the strategic structural study of two homologous C4 SATs (Micromonospora echinospora CalS13 and Escherichia coli WecE) that utilize identical substrates but differ in their stereochemistry of aminotransfer. This study reveals for the first time a new mode of SAT sugar nucleotide binding and, in conjunction with previously reported SAT structural studies, provides the basis from which to propose a universal model for SAT stereo- and regiochemical control of amine installation. Specifically, the universal model put forth highlights catalytic divergence to derive solely from distinctions within nucleotide sugar orientation upon binding within a relatively fixed SAT active site where the available ligand bound structures of the three out of four representative C3 and C4 SAT examples provide a basis for the overall model. Importantly, this study presents a new predictive model to support SAT functional annotation, biochemical study and rational engineering.
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Affiliation(s)
| | - Shanteri Singh
- Center
for Pharmaceutical Research and Innovation, University of Kentucky College of Pharmacy, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | | | - Kate E. Helmich
- Department
of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | | | | | - Craig A. Bingman
- Department
of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Jon S. Thorson
- Center
for Pharmaceutical Research and Innovation, University of Kentucky College of Pharmacy, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - George N. Phillips
- Department
of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
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10
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Rebets Y, Tokovenko B, Lushchyk I, Rückert C, Zaburannyi N, Bechthold A, Kalinowski J, Luzhetskyy A. Complete genome sequence of producer of the glycopeptide antibiotic Aculeximycin Kutzneria albida DSM 43870T, a representative of minor genus of Pseudonocardiaceae. BMC Genomics 2014; 15:885. [PMID: 25301375 PMCID: PMC4210621 DOI: 10.1186/1471-2164-15-885] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 10/03/2014] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Kutzneria is a representative of a rarely observed genus of the family Pseudonocardiaceae. Kutzneria species were initially placed in the Streptosporangiaceae genus and later reconsidered to be an independent genus of the Pseudonocardiaceae. Kutzneria albida is one of the eight known members of the genus. This strain is a unique producer of the glycosylated polyole macrolide aculeximycin which is active against both bacteria and fungi. Kutzneria albida genome sequencing and analysis allow a deeper understanding of evolution of this genus of Pseudonocardiaceae, provide new insight in the phylogeny of the genus, as well as decipher the hidden secondary metabolic potential of these rare actinobacteria. RESULTS To explore the biosynthetic potential of Kutzneria albida to its full extent, the complete genome was sequenced. With a size of 9,874,926 bp, coding for 8,822 genes, it stands alongside other Pseudonocardiaceae with large circular genomes. Genome analysis revealed 46 gene clusters potentially encoding secondary metabolite biosynthesis pathways. Two large genomic islands were identified, containing regions most enriched with secondary metabolism gene clusters. Large parts of this secondary metabolism "clustome" are dedicated to siderophores production. CONCLUSIONS Kutzneria albida is the first species of the genus Kutzneria with a completely sequenced genome. Genome sequencing allowed identifying the gene cluster responsible for the biosynthesis of aculeximycin, one of the largest known oligosaccharide-macrolide antibiotics. Moreover, the genome revealed 45 additional putative secondary metabolite gene clusters, suggesting a huge biosynthetic potential, which makes Kutzneria albida a very rich source of natural products. Comparison of the Kutzneria albida genome to genomes of other actinobacteria clearly shows its close relations with Pseudonocardiaceae in line with the taxonomic position of the genus.
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Affiliation(s)
- Yuriy Rebets
- />Helmholtz-Institute for Pharmaceutical Research Saarland, Saarland University Campus, Building C2.3, 66123 Saarbrücken, Germany
| | - Bogdan Tokovenko
- />Helmholtz-Institute for Pharmaceutical Research Saarland, Saarland University Campus, Building C2.3, 66123 Saarbrücken, Germany
| | - Igor Lushchyk
- />Helmholtz-Institute for Pharmaceutical Research Saarland, Saarland University Campus, Building C2.3, 66123 Saarbrücken, Germany
| | - Christian Rückert
- />Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Nestor Zaburannyi
- />Helmholtz-Institute for Pharmaceutical Research Saarland, Saarland University Campus, Building C2.3, 66123 Saarbrücken, Germany
| | - Andreas Bechthold
- />Institut für Pharmazeutische Biologie und Biotechnologie, Albert-Ludwigs Universität, Stefan-Meier-Strasse 19, 79104 Freiburg, Germany
| | - Jörn Kalinowski
- />Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Andriy Luzhetskyy
- />Helmholtz-Institute for Pharmaceutical Research Saarland, Saarland University Campus, Building C2.3, 66123 Saarbrücken, Germany
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11
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Deoxysugar pathway interchange for erythromycin analogues heterologously produced through Escherichia coli. Metab Eng 2013; 20:92-100. [PMID: 24060454 DOI: 10.1016/j.ymben.2013.09.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 08/30/2013] [Accepted: 09/11/2013] [Indexed: 01/16/2023]
Abstract
The overall erythromycin biosynthetic pathway can be sub-divided into macrocyclic polyketide formation and polyketide tailoring to produce the final bioactive molecule. In this study, the native deoxysugar tailoring reactions were exchanged for the purpose of demonstrating the production of alternative final erythromycin compounds. Both the d-desosamine and l-mycarose deoxysugar pathways were replaced with the alternative d-mycaminose and d-olivose pathways to produce new erythromycin analogues through the Escherichia coli heterologous system. Both analogues exhibited bioactivity against multiple antibiotic-resistant Bacillus subtilis strains. Besides demonstrating an intrinsic flexibility for the biosynthetic system to accommodate alternative tailoring pathways, the results offer an initial attempt to leverage the E. coli platform for erythromycin analogue production.
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12
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Identification of the incednine biosynthetic gene cluster: characterization of novel β-glutamate-β-decarboxylase IdnL3. J Antibiot (Tokyo) 2013; 66:691-9. [DOI: 10.1038/ja.2013.76] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 06/11/2013] [Accepted: 06/21/2013] [Indexed: 12/18/2022]
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13
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Lin CI, McCarty RM, Liu HW. The biosynthesis of nitrogen-, sulfur-, and high-carbon chain-containing sugars. Chem Soc Rev 2013; 42:4377-407. [PMID: 23348524 PMCID: PMC3641179 DOI: 10.1039/c2cs35438a] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Carbohydrates serve many structural and functional roles in biology. While the majority of monosaccharides are characterized by the chemical composition (CH2O)n, modifications including deoxygenation, C-alkylation, amination, O- and N-methylation, which are characteristic of many sugar appendages of secondary metabolites, are not uncommon. Interestingly, some sugar molecules are formed via modifications including amine oxidation, sulfur incorporation, and "high-carbon" chain attachment. Most of these unusual sugars have been identified over the past several decades as components of microbially produced natural products, although a few high-carbon sugars are also found in the lipooligosaccharides of the outer cell walls of Gram-negative bacteria. Despite their broad distribution in nature, these sugars are considered "rare" due to their relative scarcity. The biosynthetic steps that underlie their formation continue to perplex researchers to this day and many questions regarding key transformations remain unanswered. This review will focus on our current understanding of the biosynthesis of unusual sugars bearing oxidized amine substituents, thio-functional groups, and high-carbon chains.
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Affiliation(s)
| | | | - Hung-wen Liu
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712
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14
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Nebot J, Romea P, Urpí F. Stereoselective synthesis of protected 3-amino-3,6-dideoxyaminosugars. Org Biomol Chem 2012; 10:6395-403. [DOI: 10.1039/c2ob25793a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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15
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Romo AJ, Liu HW. Mechanisms and structures of vitamin B(6)-dependent enzymes involved in deoxy sugar biosynthesis. BIOCHIMICA ET BIOPHYSICA ACTA 2011; 1814:1534-47. [PMID: 21315852 PMCID: PMC3115481 DOI: 10.1016/j.bbapap.2011.02.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Revised: 01/08/2011] [Accepted: 02/01/2011] [Indexed: 10/18/2022]
Abstract
PLP is well-regarded for its role as a coenzyme in a number of diverse enzymatic reactions. Transamination, deoxygenation, and aldol reactions mediated by PLP-dependent enzymes enliven and enrich deoxy sugar biosynthesis, endowing these compounds with unique structures and contributing to their roles as determinants of biological activity in many natural products. The importance of deoxy aminosugars in natural product biosynthesis has spurred several recent structural investigations of sugar aminotransferases. The structure of a PMP-dependent enzyme catalyzing the C-3 deoxygenation reaction in the biosynthesis of ascarylose was also determined. These studies, and the crystal structures they have provided, offer a wealth of new insights regarding the enzymology of PLP/PMP-dependent enzymes in deoxy sugar biosynthesis. In this review, we consider these recent achievements in the structural biology of deoxy sugar biosynthetic enzymes and the important implications they hold for understanding enzyme catalysis and natural product biosynthesis in general. This article is part of a Special Issue entitled: Pyridoxal Phosphate Enzymology.
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Affiliation(s)
- Anthony J. Romo
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712
| | - Hung-wen Liu
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712
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16
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Carney AE, Holden HM. Molecular architecture of TylM1 from Streptomyces fradiae: an N,N-dimethyltransferase involved in the production of dTDP-D-mycaminose. Biochemistry 2011; 50:780-7. [PMID: 21142177 DOI: 10.1021/bi101733y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
d-Mycaminose is an unusual dideoxy sugar found attached to the antibiotic tylosin, a commonly used veterinarian therapeutic. It is synthesized by the Gram-positive bacterium Streptomyces fradiae as a dTDP-linked sugar. The last step in its biosynthesis involves the dimethylation of the hexose C-3' amino group by an S-adenosylmethionine (SAM) dependent enzyme referred to as TylM1. Here we report two high-resolution X-ray structures of TylM1, one in which the enzyme contains bound SAM and dTDP-phenol and the second in which the protein is complexed with S-adenosylhomocysteine (SAH) and dTDP-3-amino-3,6-dideoxyglucose, its natural substrate. Combined, these two structures, solved to 1.35 and 1.79 Å resolution, respectively, show the orientations of SAM and the dTDP-linked sugar substrate within the active site region. Specifically, the C-3' amino group of the hexose is in the correct position for an in-line attack at the reactive methyl group of SAM. Both Tyr 14 and Arg 241 serve to anchor the dTDP-linked sugar to the protein. To test the role of His 123 in catalysis, two site-directed mutant proteins were constructed, H123A and H123N. Both mutant proteins retained catalytic activity, albeit with reduced rates. Specifically, the k(cat)/K(m) was reduced to 1.8% and 0.37% for the H123A and H123N mutant proteins, respectively. High-resolution X-ray models showed that the observed perturbations in the kinetic constants were not due to major changes in their three-dimensional folds. Most likely the proton on the C-3' amino group is transferred to one of the water molecules lining the active site pocket as catalysis proceeds.
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Affiliation(s)
- Amanda E Carney
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
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17
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Matsushima Y, Kino J. Synthesis ofN-Bz-Protected D-Daunosamine and D-Ristosamine by Silica Gel Promoted Intramolecular Conjugate Addition of Trichloroacetimidates obtained from Osmundalactone and Its Epimer. European J Org Chem 2010. [DOI: 10.1002/ejoc.200901402] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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18
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Olano C, Méndez C, Salas JA. Post-PKS tailoring steps in natural product-producing actinomycetes from the perspective of combinatorial biosynthesis. Nat Prod Rep 2010; 27:571-616. [DOI: 10.1039/b911956f] [Citation(s) in RCA: 134] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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19
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Planchon S, Desvaux M, Chafsey I, Chambon C, Leroy S, Hébraud M, Talon R. Comparative subproteome analyses of planktonic and sessile Staphylococcus xylosus C2a: new insight in cell physiology of a coagulase-negative Staphylococcus in biofilm. J Proteome Res 2009; 8:1797-809. [PMID: 19253936 DOI: 10.1021/pr8004056] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Staphylococcus xylosus is a Gram-positive bacterium found on the skin of mammals and frequently isolated from food plants and fermented cheese or meat. To gain further insight in protein determinants involved in biofilm formation by this coagulase-negative Staphylococcus, a comparative proteomic analysis between planktonic and sessile cells was performed. With the use of a protocol previously developed, protein patterns of the cytoplasmic and cell envelope fractions were compared by 2-DE. Following protein identification by MALDI-TOF mass spectrometry and bioinformatic analyses, this study revealed differences in expression levels of 89 distinct proteins with 55 up-expressed and 34 down-expressed proteins in biofilm compared to planktonic cells. Most proteins differentially expressed were related to nitrogen and carbon metabolisms. Besides amino acid biosynthesis and protein translation, protein determinants related to protein secretion were up-expressed in biofilm, suggesting a more active protein trafficking in sessile cells. While up-expression of several enzymes involved in pentose phosphate and glycolytic pathways was observed in biofilm, connections with unexpected metabolic routes were further unravelled. Indeed, this proteomic analysis allowed identifying novel proteins that could be involved in a previously uncovered exopolysaccharide biosynthetic pathway in S. xylosus as well as several enzymes related to polyketide biosynthesis. This findings are particularly relevant considering exopolysaccharide production in S. xylosus is ica-independent contrary to coagulase-negative model strain Staphylococcus epidermidis RP62A.
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Affiliation(s)
- Stella Planchon
- INRA, UR454 Microbiologie, F-63122 Saint-Genès Champanelle, France
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20
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Identification of functionally clustered nystatin-like biosynthetic genes in a rare actinomycetes, Pseudonocardia autotrophica. J Ind Microbiol Biotechnol 2009; 36:1425-34. [PMID: 19697072 DOI: 10.1007/s10295-009-0629-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2009] [Accepted: 07/27/2009] [Indexed: 02/07/2023]
Abstract
The polyene antibiotics, including nystatin, pimaricin, amphotericin, and candicidin, comprise a family of very valuable antifungal polyketide compounds, and they are typically produced by soil actinomycetes. Previously, using a polyene cytochrome P450 hydroxylase-specific genome screening strategy, Pseudonocardia autotrophica KCTC9441 was determined to contain genes potentially encoding polyene biosynthesis. Here, sequence information of an approximately 125.7-kb contiguous DNA region in five overlapping cosmids isolated from the P. autotrophica KCTC9441 genomic library revealed a total of 23 open reading frames, which are presumably involved in the biosynthesis of a nystatin-like compound tentatively named NPP. The deduced roles for six multi-modular polyketide synthase (PKS) catalytic domains were found to be highly homologous to those of previously identified nystatin biosynthetic genes. Low NPP productivity suggests that the functionally clustered NPP biosynthetic pathway genes are tightly regulated in P. autotrophica. Disruption of a NPP PKS gene completely abolished both NPP biosynthesis and antifungal activity against Candida albicans, suggesting that polyene-specific genome screening may constitute an efficient method for isolation of potentially valuable previously identified polyene genes and compounds from various rare actinomycetes widespread in nature.
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21
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Abstract
Many bioactive compounds contain as part of their molecules one or more deoxysugar units. Their presence in the final compound is generally necessary for biological activity. These sugars derive from common monosaccharides, like d-glucose, which have lost one or more hydroxyl groups (monodeoxysugars, dideoxysugars, trideoxysugars) during their biosynthesis. These deoxysugars are transferred to the final molecule by the action of a glycosyltransferase. Here, we first summarize the different biosynthetic steps required for the generation of the different families of deoxysugars, including those containing extra methyl or amino groups, or tailoring modifications of the glycosylated compounds. We then give examples of several strategies for modification of the glycosylation pattern of a given bioactive compound: inactivation of genes involved in the biosynthesis of deoxysugars; heterologous expression of genes for the biosynthesis or transfer of a specific deoxysugar; and combinatorial biosynthesis (including the use of gene cassette plasmids). Finally, we report techniques for the isolation and detection of the new glycosylated derivatives generated using these strategies.
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Affiliation(s)
- Felipe Lombó
- Departamento de Biología Funcional and Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, Oviedo, Spain
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22
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Thoden JB, Schäffer C, Messner P, Holden HM. Structural analysis of QdtB, an aminotransferase required for the biosynthesis of dTDP-3-acetamido-3,6-dideoxy-alpha-D-glucose. Biochemistry 2009; 48:1553-61. [PMID: 19178182 DOI: 10.1021/bi8022015] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
3-Acetamido-3,6-dideoxy-alpha-d-glucose or Quip3NAc is an unusual deoxyamino sugar found in the O-antigens of some Gram-negative bacteria and in the S-layers of Gram-positive bacteria. It is synthesized in these organisms as a dTDP-linked sugar via the action of five enzymes. The focus of this investigation is on QdtB from Thermoanaerobacterium thermosaccharolyticum E207-71, a PLP-dependent aminotransferase that catalyzes the penultimate step in the production of dTDP-Quip3NAc. For this analysis, the enzyme was crystallized in the presence of its product, dTDP-Quip3N, and the structure was solved and refined to 2.15 A resolution. QdtB is a dimer, and its overall fold places it into the well-characterized aspartate aminotransferase superfamily. Electron density corresponding to the bound product reveals the presence of a Schiff base between C-4' of the PLP cofactor and the amino nitrogen of the sugar. Those amino acid side chains involved in binding the dTDP-sugar into the active site include Tyr 183, His 309, and Tyr 310 from subunit 1 and Lys 219 from subunit 2. Notably there is a decided lack of interactions between the pyranosyl C-4' hydroxyl of the dTDP-sugar and the protein. In keeping with this observation, we show that QdtB can also turn over dTDP-3-acetamido-3,6-dideoxy-alpha-d-galactose. This investigation represents the first structural analysis of a sugar-modifying aminotransferase with a bound product in its active site that functions at the C-3' rather than the C-4' position of the hexose.
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Affiliation(s)
- James B Thoden
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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23
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Johnson HD, Thorson JS. Characterization of CalE10, the N-oxidase involved in calicheamicin hydroxyaminosugar formation. J Am Chem Soc 2008; 130:17662-3. [PMID: 19055330 PMCID: PMC2704561 DOI: 10.1021/ja807557a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
As the first in vitro characterization of a sugar N-oxidase, this study establishes CalE10 as the key oxidase involved in calicheamicin hydroxylamino glycoside formation. This study confirms that oxidation occurs at the sugar nucleotide stage prior to glycosyltransfer, and substrate specificity studies reveal CalE10-catalyzed oxidation to be regiospecific and to present trace amounts of the corresponding nitrosugar in vitro. This work also sets a precedent for the future study of other N-oxidases involved in hydroxylamino-, nitroso-, and/or nitrosugar formation.
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Affiliation(s)
- Heather D. Johnson
- Division of Pharmaceutical Sciences and University of Wisconsin National Drug Discovery Group, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Jon S. Thorson
- Division of Pharmaceutical Sciences and University of Wisconsin National Drug Discovery Group, University of Wisconsin-Madison, Madison, Wisconsin 53706
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24
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Timmons SC, Thorson JS. Increasing carbohydrate diversity via amine oxidation: aminosugar, hydroxyaminosugar, nitrososugar, and nitrosugar biosynthesis in bacteria. Curr Opin Chem Biol 2008; 12:297-305. [PMID: 18424273 PMCID: PMC2517148 DOI: 10.1016/j.cbpa.2008.03.017] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2008] [Revised: 03/19/2008] [Accepted: 03/19/2008] [Indexed: 12/14/2022]
Abstract
Bacterial secondary metabolites often contain carbohydrate attachments that play a significant role in conferring biological activity. A small proportion of these bioactive sugars are derived from aminosugar oxidation to ultimately provide hydroxyaminosugars, nitrososugars, and nitrosugars. Recent advances in the elucidation of hydroxyaminosugar-, nitrososugar-, and nitrosugar-containing natural product gene clusters have enabled the proposal of biosynthetic pathways, the in vitro characterization of aminosugar oxidases, and the structure determination of key enzymes. This article focuses upon the key enzymatic transformations in aminosugar, hydroxyaminosugar, nitrososugar, and nitrosugar biosynthesis, as well as the unique chemical reactivity of alkoxyaminosugars, with a particular focus upon developments within the past two years.
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Affiliation(s)
- Shannon C. Timmons
- Laboratory for Biosynthetic Chemistry, Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705; University of Wisconsin National Cooperative Drug Discovery Group Program
| | - Jon S. Thorson
- Laboratory for Biosynthetic Chemistry, Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705; University of Wisconsin National Cooperative Drug Discovery Group Program
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25
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Forsberg LS, Carlson RW. Structural characterization of the primary O-antigenic polysaccharide of the Rhizobium leguminosarum 3841 lipopolysaccharide and identification of a new 3-acetimidoylamino-3-deoxyhexuronic acid glycosyl component: a unique O-methylated glycan of uniform size, containing 6-deoxy-3-O-methyl-D-talose, n-acetylquinovosamine, and rhizoaminuronic acid (3-acetimidoylamino-3-deoxy-D-gluco-hexuronic acid). J Biol Chem 2008; 283:16037-50. [PMID: 18387959 DOI: 10.1074/jbc.m709615200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Rhizobium are Gram-negative bacteria that survive intracellularly, within host membrane-derived plant cell compartments called symbiosomes. Within the symbiosomes the bacteria differentiate to bacteroids, the active form that carries out nitrogen fixation. The progression from free-living bacteria to bacteroid is characterized by physiological and morphological changes at the bacterial surface, a phase shift with an altered array of cell surface glycoconjugates. Lipopolysaccharides undergo structural changes upon differentiation from the free living to the bacteroid (intracellular) form. The array of carbohydrate structures carried on lipopolysaccharides confer resistance to plant defense mechanisms and may serve as signals that trigger the plant to allow the infection to proceed. We have determined the structure of the major O-polysaccharide (OPS) isolated from free living Rhizobium leguminosarum 3841, a symbiont of Pisum sativum, using chemical methods, mass spectrometry, and NMR spectroscopy analysis. The OPS is composed of several unusual glycosyl residues, including 6-deoxy-3-O-methyl-d-talose and 2-acetamido-2deoxy-l-quinovosamine. In addition, a new glycosyl residue, 3-acetimidoylamino-3-deoxy-d-gluco-hexuronic acid was identified and characterized, a novel hexosaminuronic acid that does not have an amino group at the 2-position. The OPS is composed of three to four tetrasaccharide repeating units of -->4)-beta-dGlcp3NAmA-(1-->4)-[2-O-Ac-3-O-Me-alpha-d-6dTalp-(1-->3)]-alpha-l-Fucp-(1-->3)-alpha-l-QuipNAc-(1-->. The unique 3-amino hexuronate residue, rhizoaminuronic acid, is an attractive candidate for selective inhibition of OPS synthesis.
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Affiliation(s)
- L Scott Forsberg
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30605, USA
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26
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Matsushima Y, Kino J. Intramolecular conjugate addition of γ- and δ-trichloroacetimidoyloxy-α,β-unsaturated esters in an acyclic system. Tetrahedron 2008. [DOI: 10.1016/j.tet.2008.02.061] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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27
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Abstract
The exosporium of Bacillus anthracis spores consists of a basal layer and an external hair-like nap. The nap is composed primarily of the glycoprotein BclA, which contains a collagen-like region with multiple copies of a pentasaccharide side chain. This oligosaccharide possesses an unusual terminal sugar called anthrose, followed by three rhamnose residues and a protein-bound N-acetylgalactosamine. Based on the structure of anthrose, we proposed an enzymatic pathway for its biosynthesis. Examination of the B. anthracis genome revealed six contiguous genes that could encode the predicted anthrose biosynthetic enzymes. These genes are transcribed in the same direction and appear to form two operons. We introduced mutations into the B. anthracis chromosome that either delete the promoter of the putative upstream, four-gene operon or delete selected genes in both putative operons. Spores produced by strains carrying mutations in the upstream operon completely lacked or contained much less anthrose, indicating that this operon is required for anthrose biosynthesis. In contrast, inactivation of the downstream, two-gene operon did not alter anthrose content. Additional experiments confirmed the organization of the anthrose operon and indicated that it is transcribed from a sigma(E)-specific promoter. Finally, we demonstrated that anthrose biosynthesis is not restricted to B. anthracis as previously suggested.
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28
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Burgie ES, Holden HM. Molecular architecture of DesI: a key enzyme in the biosynthesis of desosamine. Biochemistry 2007; 46:8999-9006. [PMID: 17630700 PMCID: PMC2528198 DOI: 10.1021/bi700751d] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Desosamine is a 3-(dimethylamino)-3,4,6-trideoxyhexose found, for example, in such macrolide antibiotics as erthyromycin, azithromycin, and clarithromycin. The efficacies of these macrolide antibiotics are markedly reduced in the absence of desosamine. In the bacterium Streptomyces venezuelae, six enzymes are required for the production of dTDP-desosamine. The focus of this X-ray crystallographic analysis is the third enzyme in the pathway, a PLP-dependent aminotransferase referred to as DesI. The structure of DesI was solved in complex with its product, dTDP-4-amino-4,6-dideoxyglucose, to a nominal resolution of 2.1 A. Each subunit of the dimeric enzyme contains 12 alpha-helices and 14 beta-strands. Three cis-peptides are observed in each subunit, Phe 330, Pro 332, and Pro 339. The two active sites of the enzyme are located in clefts at the subunit/subunit interface. Electron density corresponding to the bound product clearly demonstrates a covalent bond between the amino group of the product and C-4' of the PLP cofactor. Interestingly, there are no hydrogen-bonding interactions between the protein and the dideoxyglucosyl group of the product (within 3.2 A). The only other sugar-modifying aminotransferase whose structure is known in the presence of product is PseC from Helicobacter pylori. This enzyme, as opposed to DesI, catalyzes amino transfer to the axial position of the sugar. A superposition of the two active sites for these proteins reveals that the major differences in ligand binding occur in the orientations of the deoxyglucosyl and phosphoryl groups. Indeed, the nearly 180 degrees difference in hexose orientation explains the equatorial versus axial amino transfer exhibited by DesI and PseC, respectively.
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Affiliation(s)
| | - Hazel M. Holden
- To whom correspondence should be addressed. FAX: 608−262−1319 PHONE: 608−262−4988
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29
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Chung YS, Kim DH, Seo WM, Lee HC, Liou K, Oh TJ, Sohng JK. Enzymatic synthesis of dTDP-4-amino-4,6-dideoxy-D-glucose using GerB (dTDP-4-keto-6-deoxy-D-glucose aminotransferase). Carbohydr Res 2007; 342:1412-8. [PMID: 17532307 DOI: 10.1016/j.carres.2007.04.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2007] [Accepted: 04/11/2007] [Indexed: 11/27/2022]
Abstract
Over-expressed GerB (dTDP-4-keto-6-deoxy-d-glucose aminotransferase) of Streptomyces sp. GERI-155 was used in the enzymatic synthesis of dTDP-4-amino-4,6-dideoxy-D-glucose (2) from dTDP-4-keto-6-deoxy-D-glucose (1). [Carbohydrate structure: see text]. Five enzymes including dTMP kinase (TMK), acetate kinase (ACK), dTDP-glucose synthase (TGS), dTDP-glucose 4,6-dehydratase (DH), and dTDP-4-keto-6-deoxy-d-glucose aminotransferase (GerB) were used to synthesize 2 on a large scale from glucose-1-phosphate and TMP. A conversion yield of up to 57% was obtained by HPLC peak integration given a reaction time of 270min. After purification by two successive preparative HPLC systems, the final product was identified by HPLC and then analyzed by (1)H, (13)C, (1)H-(1)H COSY NMR spectrometry.
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Affiliation(s)
- Young Soo Chung
- Genechem Inc., 59-5 Jang-dong, Yuseong-gu, Daejeon 305-343, South Korea
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30
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Moretti R, Thorson JS. Enhancing the latent nucleotide triphosphate flexibility of the glucose-1-phosphate thymidylyltransferase RmlA. J Biol Chem 2007; 282:16942-7. [PMID: 17434871 DOI: 10.1074/jbc.m701951200] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nucleotidyltransferases are central to nearly all glycosylation-dependent processes and have been used extensively for the chemoenzymatic synthesis of sugar nucleotides. The determination of the NTP specificity of the model thymidylyltransferase RmlA revealed RmlA to utilize all eight naturally occurring NTPs with varying levels of catalytic efficiency, even in the presence of nonnative sugar-1-phosphates. Guided by structural models, active site engineering of RmlA led to alterations of the inherent pyrimidine/purine bias by up to three orders of magnitude. This study sets the stage for engineering single universal nucleotidyltransferases and also provides new catalysts for the synthesis of novel nucleotide diphosphosugars.
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Affiliation(s)
- Rocco Moretti
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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31
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McNally DJ, Schoenhofen IC, Mulrooney EF, Whitfield DM, Vinogradov E, Lam JS, Logan SM, Brisson JR. Identification of labile UDP-ketosugars in Helicobacter pylori, Campylobacter jejuni and Pseudomonas aeruginosa: key metabolites used to make glycan virulence factors. Chembiochem 2007; 7:1865-8. [PMID: 17031886 DOI: 10.1002/cbic.200600298] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- David J McNally
- National Research Council of Canada-Institute for Biological Sciences, Ottawa ON, K1A 0R6, Canada.
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32
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Lee HY, Khosla C. Bioassay-guided evolution of glycosylated macrolide antibiotics in Escherichia coli. PLoS Biol 2007; 5:e45. [PMID: 17298179 PMCID: PMC1790958 DOI: 10.1371/journal.pbio.0050045] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2006] [Accepted: 12/13/2006] [Indexed: 11/19/2022] Open
Abstract
Macrolide antibiotics such as erythromycin are clinically important polyketide natural products. We have engineered a recombinant strain of Escherichia coli that produces small but measurable quantities of the bioactive macrolide 6-deoxyerythromycin D. Bioassay-guided evolution of this strain led to the identification of an antibiotic-overproducing mutation in the mycarose biosynthesis and transfer pathway that was detectable via a colony-based screening assay. This high-throughput assay was then used to evolve second-generation mutants capable of enhanced precursor-directed biosynthesis of macrolide antibiotics. The availability of a screen for macrolide biosynthesis in E. coli offers a fundamentally new approach in dissecting modular megasynthase mechanisms as well as engineering antibiotics with novel pharmacological properties.
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Affiliation(s)
- Ho Young Lee
- Department of Chemistry, Stanford University, Stanford, California, United States of America
| | - Chaitan Khosla
- Department of Chemistry, Stanford University, Stanford, California, United States of America
- Department of Chemical Engineering, Stanford University, Stanford, California, United States of America
- * To whom correspondence should be addressed. E-mail:
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33
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Gao Q, Zhang C, Blanchard S, Thorson JS. Deciphering indolocarbazole and enediyne aminodideoxypentose biosynthesis through comparative genomics: insights from the AT2433 biosynthetic locus. ACTA ACUST UNITED AC 2006; 13:733-43. [PMID: 16873021 DOI: 10.1016/j.chembiol.2006.05.009] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2006] [Revised: 04/28/2006] [Accepted: 05/04/2006] [Indexed: 11/19/2022]
Abstract
AT2433, an indolocarbazole antitumor antibiotic, is structurally distinguished by its aminodideoxypentose-containing disaccharide and asymmetrically halogenated N-methylated aglycon. Cloning and sequence analysis of AT2433 gene cluster and comparison of this locus with that encoding for rebeccamycin and the gene cluster encoding calicheamicin present an opportunity to study the aminodideoxypentose biosynthesis via comparative genomics. The locus was confirmed via in vitro biochemical characterization of two methyltransferases--one common to AT2433 and rebeccamycin, the other unique to AT2433--as well as via heterologous expression and in vivo bioconversion experiments using the AT2433 N-glycosyltransferase. Preliminary studies of substrate tolerance for these three enzymes reveal the potential to expand upon the enzymatic diversification of indolocarbazoles. Moreover, this work sets the stage for future studies regarding the origins of the indolocarbazole maleimide nitrogen and indolocarbazole asymmetry.
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Affiliation(s)
- Qunjie Gao
- Laboratory for Biosynthetic Chemistry, Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, 53705, USA
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34
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Matsushima Y, Kino J. An intramolecular conjugate addition of γ-trichloroacetimidoyloxy-α,β-unsaturated esters: a very concise route to daunosamine, acosamine, ristosamine and 3-epi-daunosamine precursors. Tetrahedron Lett 2006. [DOI: 10.1016/j.tetlet.2006.09.164] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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35
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36
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Matsushima Y, Kino J. A new simple route to deoxyamino sugars from non-sugar material: synthesis of d-tolyposamine and 4-epi-d-tolyposamine and formal synthesis of d-vicenisamine. Tetrahedron Lett 2005. [DOI: 10.1016/j.tetlet.2005.09.195] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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37
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Obhi RK, Creuzenet C. Biochemical characterization of the Campylobacter jejuni Cj1294, a novel UDP-4-keto-6-deoxy-GlcNAc aminotransferase that generates UDP-4-amino-4,6-dideoxy-GalNAc. J Biol Chem 2005; 280:20902-8. [PMID: 15790564 DOI: 10.1074/jbc.m413832200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Campylobacter jejuni produces multiple glycoproteins whose glycans contain 4-amino 6-deoxy sugars or their derivatives, such as diacetamidobacillosamine or pseudaminic acid. Because the proteoglycans contribute to bacterial virulence and their constitutive sugars are not commonly found in humans, inhibitors developed against the enzymes that are responsible for their biosynthesis could be novel therapeutic targets to fight this important food-borne pathogen. The biosynthesis of diacetamidobacillosamine is anticipated to involve a sugar nucleotide C6 dehydratase, a C4 aminotransferase and an acetyltransferase. We have identified a set of genes (cj1293, cj1294, and cj1298) potentially encoding one of each enzymatic activity, and demonstrated earlier that Cj1293 was a UDP-GlcNAc-specific C6 dehydratase. Others have shown that Cj1293 was involved in protein glycosylation. Here, we report on our investigation of the potential activity of Cj1294 as a sugar nucleotide C4 aminotransferase. Our biochemical characterization of overexpressed and purified protein shows that Cj1294 is a pyridoxal phosphate-dependent aminotransferase specific for UDP-4-keto-6-deoxy-GlcNAc that uses preferentially glutamic acid as an amino donor. A detailed physicokinetic study of Cj1294 was performed to determine the K(m) of 1.28 +/- 0.2 mm and k(cat) of 11.5 +/- 1.3 min(-1). Also, two residues essential for protein stability and activity, Arg(228) and Lys(181), respectively, were identified by site-directed mutagenesis. Finally, we demonstrated by NMR analysis of purified reaction product that Cj1294 produces UDP-4-amino-4,6-dideoxy-GalNAc. These results indicate that Cj1294 is involved in the biosynthesis of diacetamidofucosamine, a C4 epimer of diacetamidobacillosamine not yet described in C. jejuni proteoglycans, suggesting that the composition of C. jejuni proteoglycans is more variable than anticipated.
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Affiliation(s)
- Ravinder Kaur Obhi
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario N6A 5C1, Canada
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Liu W, Nonaka K, Nie L, Zhang J, Christenson SD, Bae J, Van Lanen SG, Zazopoulos E, Farnet CM, Yang CF, Shen B. The Neocarzinostatin Biosynthetic Gene Cluster from Streptomyces carzinostaticus ATCC 15944 Involving Two Iterative Type I Polyketide Synthases. ACTA ACUST UNITED AC 2005; 12:293-302. [PMID: 15797213 DOI: 10.1016/j.chembiol.2004.12.013] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2004] [Revised: 12/16/2004] [Accepted: 01/12/2005] [Indexed: 10/25/2022]
Abstract
The biosynthetic gene cluster for the enediyne antitumor antibiotic neocarzinostatin (NCS) was localized to 130 kb continuous DNA from Streptomyces carzinostaticus ATCC15944 and confirmed by gene inactivation. DNA sequence analysis of 92 kb of the cloned region revealed 68 open reading frames (ORFs), 47 of which were determined to constitute the NCS cluster. Sequence analysis of the genes within the NCS cluster suggested dNDP-D-mannose as a precursor for the deoxy aminosugar, revealed two distinct type I polyketide synthases (PKSs), and supported a convergent model for NCS chromophore biosynthesis from the deoxy aminosugar, naphthoic acid, and enediyne core building blocks. These findings shed light into deoxysugar biosynthesis, further support the iterative type I PKS paradigm for enediyne core biosynthesis, and unveil a mechanism for microbial polycyclic aromatic polyketide biosynthesis by an iterative type I PKS.
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Affiliation(s)
- Wen Liu
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
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