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Yan C, Tao Y, Fan J, Dai J, Li S, Huang Q, Zhou R. Generation and characterization of two acid-resistant macrocin O-methyltransferase variants with a higher enzyme activity at 30 °C from Streptomyces fradiae. Comput Struct Biotechnol J 2024; 23:3232-3240. [PMID: 39257526 PMCID: PMC11384511 DOI: 10.1016/j.csbj.2024.08.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 08/07/2024] [Accepted: 08/20/2024] [Indexed: 09/12/2024] Open
Abstract
Tylosin is an important macrolide antibiotic produced by Streptomyces fradiae. In the biosynthesis of tylosin, macrocin O-methyltransferase TylF catalyzes the conversion of the side-product tylosin C (macrocin) to the primary component tylosin A (C/A conversion). This conversion is the rate-limiting step in the biosynthesis of tylosin, and affects the quality of the end product. To find a high activity and environment-adapted TylF enzyme, a TylF variant pool has been constructed via protein evolution approach in our previous study (Fan et al., 2023 [41]). In this study, the TylF variants with higher C/A conversion rates were expressed in E. coli and purified. The variants TylFY139F, TylFQ138H, F232Y and TylFT36S, V54A were shown to have a higher C/A conversion rate at 30 °C than that of TylF at 38 °C. Moreover, they had a greater acid resistance and showed more adaptable to the pH change during fermentation. Further protein structural and substrate-binding affinity analyses revealed that the T36S, V54A, Q138H, Y139F, and F232Y mutations enlarged the volume of the substrate-binding pocket, thereby increasing the affinity of enzyme variants for their substrates of SAM and macrocin, and decreasing the inhibition of SAH. Three of the TylF variants were overexpressed in the industrial tylosin-producing S. fradiae strain, and the recombinant strains showed the highest C/A conversion at 30 °C without heating up to 38 °C during the last 24 h of fermentation. This is of great energy-saving significance for tylosin industrial production.
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Affiliation(s)
- Chaoyue Yan
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Yujun Tao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Jingyan Fan
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou 311300, China
| | - Jun Dai
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- The HZAU-HVSEN Institute, Wuhan 430060, China
| | - Shuo Li
- The HZAU-HVSEN Institute, Wuhan 430060, China
| | - Qi Huang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- International Research Center for Animal Disease (Ministry of Science & Technology of China), Wuhan 430070, China
- The Cooperative Innovation Center of Sustainable Pig Production, Wuhan 430070, China
| | - Rui Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- International Research Center for Animal Disease (Ministry of Science & Technology of China), Wuhan 430070, China
- The Cooperative Innovation Center of Sustainable Pig Production, Wuhan 430070, China
- The HZAU-HVSEN Institute, Wuhan 430060, China
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2
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Janzing NBM, Niehoff M, Sander W, Senges CHR, Schäkermann S, Bandow JE. A metabolomics perspective on clorobiocin biosynthesis: discovery of bromobiocin and novel derivatives through LC-MS E-based molecular networking. Microbiol Spectr 2024; 12:e0042324. [PMID: 38864648 PMCID: PMC11218499 DOI: 10.1128/spectrum.00423-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 04/17/2024] [Indexed: 06/13/2024] Open
Abstract
Clorobiocin is a well-known, highly effective inhibitor of DNA gyrase belonging to the aminocoumarin antibiotics. To identify potentially novel derivatives of this natural product, we conducted an untargeted investigation of clorobiocin biosynthesis in the known producer Streptomyces roseochromogenes DS 12.976 using LC-MSE, molecular networking, and analysis of fragmentation spectra. Previously undescribed clorobiocin derivatives uncovered in this study include bromobiocin, a variant halogenated with bromine instead of chlorine, hydroxylated clorobiocin, carrying an additional hydroxyl group on its 5-methyl-pyrrole 2-carboxyl moiety, and two other derivatives with modifications on their 3-dimethylallyl 4-hydroxybenzoate moieties. Furthermore, we identified several compounds not previously considered clorobiocin pathway products, which provide new insights into the clorobiocin biosynthetic pathway. By supplementing the medium with different concentrations of potassium bromide, we confirmed that the clorobiocin halogenase can utilize bromine instead of chlorine. The reaction, however, is impeded such that non-halogenated clorobiocin derivatives accumulate. Preliminary assays indicate that the antibacterial activity of bromobioin against Bacillus subtilis and efflux-impaired Escherichia coli matches that of clorobiocin. Our findings emphasize that yet unexplored compounds can be discovered from established strains and biosynthetic gene clusters by means of metabolomics analysis and highlight the utility of LC-MSE-based methods to contribute to unraveling natural product biosynthetic pathways. IMPORTANCE The aminocoumarin clorobiocin is a well-known gyrase inhibitor produced by the gram-positive bacterium Streptomyces roseochromogenes DS 12.976. To gain a deeper understanding of the biosynthetic pathway of this complex composite of three chemically distinct entities and the product spectrum, we chose a metabolite-centric approach. Employing high-resolution LC-MSE analysis, we investigated the pathway products in extracted culture supernatants of the natural producer. Novel pathway products were identified that expand our understanding of three aspects of the biosynthetic pathway, namely the modification of the noviose, transfer and methylation of the pyrrole 2-carboxyl moiety, and halogenation. For the first time, brominated products were detected. Their levels and the levels of non-halogenated products increased in medium supplemented with KBr. Based on the presented data, we propose that the enzyme promiscuity contributes to a broad product spectrum.
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Affiliation(s)
- Niklas B. M. Janzing
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Maurice Niehoff
- Organic Chemistry II, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Wolfram Sander
- Organic Chemistry II, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Christoph H. R. Senges
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Sina Schäkermann
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Julia E. Bandow
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
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Fan J, Yao Z, Yan C, Hao M, Dai J, Zou W, Ni M, Li T, Li L, Li S, Liu J, Huang Q, Zhou R. Discovery of a highly efficient TylF methyltransferase via random mutagenesis for improving tylosin production. Comput Struct Biotechnol J 2023; 21:2759-2766. [PMID: 37181661 PMCID: PMC10172623 DOI: 10.1016/j.csbj.2023.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 04/11/2023] [Accepted: 04/11/2023] [Indexed: 05/16/2023] Open
Abstract
Macrolides are currently a class of extensively used antibiotics in human and animal medicine. Tylosin is not only one of the most important veterinary macrolides but also an indispensable material for the bio- and chemo-synthesis of new generations of macrolide antibiotics. Thus, improving its production yield is of great value. As the key rate-limiting enzyme catalyzing the terminal step of tylosin biosynthesis in Streptomyces fradiae (S. fradiae), TylF methyltransferase's catalytic activity directly affects tylosin yield. In this study, a tylF mutant library of S. fradiae SF-3 was constructed based on error-prone PCR technology. After two steps of screening in 24-well plates and conical flask fermentation and enzyme activity assay, a mutant strain was identified with higher TylF activity and tylosin yield. The mutation of tyrosine to phenylalanine is localized at the 139th amino acid residue on TylF (TylFY139F), and protein structure simulations demonstrated that this mutation changed the protein structure of TylF. Compared with wild-type protein TylF, TylFY139F exhibited higher enzymatic activity and thermostability. More importantly, the Y139 residue in TylF is a previously unidentified position required for TylF activity and tylosin production in S. fradiae, indicating the further potential to engineer the enzyme. These findings provide helpful information for the directed molecular evolution of this important enzyme and the genetic modification of tylosin-producing bacteria.
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Affiliation(s)
- Jingyan Fan
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhiming Yao
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Chaoyue Yan
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Meilin Hao
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Jun Dai
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Provincial Bioengineering Technology Research Center for Animal Health Products, Yingcheng 432400, China
- The HZAU-HVSEN Research Institute, Wuhan 430042, China
| | - Wenjin Zou
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Minghui Ni
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Tingting Li
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Lu Li
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- International Research Center for Animal Disease (Ministry of Science and Technology of China), Wuhan 430070, China
- Cooperative Innovation Center of Sustainable Pig Production, Wuhan 430070, China
| | - Shuo Li
- Hubei Provincial Bioengineering Technology Research Center for Animal Health Products, Yingcheng 432400, China
- The HZAU-HVSEN Research Institute, Wuhan 430042, China
| | - Jie Liu
- Hubei Provincial Bioengineering Technology Research Center for Animal Health Products, Yingcheng 432400, China
- The HZAU-HVSEN Research Institute, Wuhan 430042, China
| | - Qi Huang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- International Research Center for Animal Disease (Ministry of Science and Technology of China), Wuhan 430070, China
- Cooperative Innovation Center of Sustainable Pig Production, Wuhan 430070, China
- Correspondence to: College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
| | - Rui Zhou
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- International Research Center for Animal Disease (Ministry of Science and Technology of China), Wuhan 430070, China
- Cooperative Innovation Center of Sustainable Pig Production, Wuhan 430070, China
- The HZAU-HVSEN Research Institute, Wuhan 430042, China
- Correspondence to: College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
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Amariei DA, Pozhydaieva N, David B, Schneider P, Classen T, Gohlke H, Weiergräber OH, Pietruszka J. Enzymatic C3-Methylation of Indoles Using Methyltransferase PsmD─Crystal Structure, Catalytic Mechanism, and Preparative Applications. ACS Catal 2022. [DOI: 10.1021/acscatal.2c04240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Diana A. Amariei
- Institute of Bioorganic Chemistry & Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf in Forschungszentrum Jülich, Jülich 52426, Germany
| | - Nadiia Pozhydaieva
- Institute of Bioorganic Chemistry & Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf in Forschungszentrum Jülich, Jülich 52426, Germany
| | - Benoit David
- Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich, Jülich 52426, Germany
| | - Pascal Schneider
- Institute of Bioorganic Chemistry & Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf in Forschungszentrum Jülich, Jülich 52426, Germany
| | - Thomas Classen
- Institute of Bio- and Geosciences (IBG-1: Bioorganic Chemistry) & Bioeconomy Science Center (BioSC) Forschungszentrum Jülich, Jülich 52426, Germany
| | - Holger Gohlke
- Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich, Jülich 52426, Germany
- Institute for Pharmaceutical and Medicinal Chemistry & Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Oliver H. Weiergräber
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) & Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich 52425, Germany
| | - Jörg Pietruszka
- Institute of Bioorganic Chemistry & Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf in Forschungszentrum Jülich, Jülich 52426, Germany
- Institute of Bio- and Geosciences (IBG-1: Bioorganic Chemistry) & Bioeconomy Science Center (BioSC) Forschungszentrum Jülich, Jülich 52426, Germany
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5
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Abdelraheem E, Thair B, Varela RF, Jockmann E, Popadić D, Hailes HC, Ward JM, Iribarren AM, Lewkowicz ES, Andexer JN, Hagedoorn P, Hanefeld U. Methyltransferases: Functions and Applications. Chembiochem 2022; 23:e202200212. [PMID: 35691829 PMCID: PMC9539859 DOI: 10.1002/cbic.202200212] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/10/2022] [Indexed: 11/25/2022]
Abstract
In this review the current state-of-the-art of S-adenosylmethionine (SAM)-dependent methyltransferases and SAM are evaluated. Their structural classification and diversity is introduced and key mechanistic aspects presented which are then detailed further. Then, catalytic SAM as a target for drugs, and approaches to utilise SAM as a cofactor in synthesis are introduced with different supply and regeneration approaches evaluated. The use of SAM analogues are also described. Finally O-, N-, C- and S-MTs, their synthetic applications and potential for compound diversification is given.
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Affiliation(s)
- Eman Abdelraheem
- BiocatalysisDepartment of BiotechnologyDelft University of TechnologyVan der Maasweg 92629 HZDelft (TheNetherlands
| | - Benjamin Thair
- Department of ChemistryUniversity College London20 Gordon StreetLondonWC1H 0AJUK
| | - Romina Fernández Varela
- Laboratorio de Biotransformaciones y Química de Ácidos NucleicosUniversidad Nacional de QuilmesRoque S. Peña 352B1876BXDBernalArgentina
| | - Emely Jockmann
- Institute of Pharmaceutical SciencesUniversity of FreiburgAlbertstr. 2579104FreiburgGermany
| | - Désirée Popadić
- Institute of Pharmaceutical SciencesUniversity of FreiburgAlbertstr. 2579104FreiburgGermany
| | - Helen C. Hailes
- Department of ChemistryUniversity College London20 Gordon StreetLondonWC1H 0AJUK
| | - John M. Ward
- Department of Biochemical EngineeringBernard Katz BuildingUniversity College LondonLondonWC1E 6BTUK
| | - Adolfo M. Iribarren
- Laboratorio de Biotransformaciones y Química de Ácidos NucleicosUniversidad Nacional de QuilmesRoque S. Peña 352B1876BXDBernalArgentina
| | - Elizabeth S. Lewkowicz
- Laboratorio de Biotransformaciones y Química de Ácidos NucleicosUniversidad Nacional de QuilmesRoque S. Peña 352B1876BXDBernalArgentina
| | - Jennifer N. Andexer
- Institute of Pharmaceutical SciencesUniversity of FreiburgAlbertstr. 2579104FreiburgGermany
| | - Peter‐Leon Hagedoorn
- BiocatalysisDepartment of BiotechnologyDelft University of TechnologyVan der Maasweg 92629 HZDelft (TheNetherlands
| | - Ulf Hanefeld
- BiocatalysisDepartment of BiotechnologyDelft University of TechnologyVan der Maasweg 92629 HZDelft (TheNetherlands
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6
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Enzymatic characterization of three human RNA adenosine methyltransferases reveals diverse substrate affinities and reaction optima. J Biol Chem 2021; 296:100270. [PMID: 33428944 PMCID: PMC7948815 DOI: 10.1016/j.jbc.2021.100270] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/06/2021] [Accepted: 01/07/2021] [Indexed: 11/22/2022] Open
Abstract
RNA methylations of varied RNA species (mRNA, tRNA, rRNA, non-coding RNA) generate a range of modified nucleotides, including N6-methyladenosine. Here we study the enzymology of three human RNA methyltransferases that methylate the adenosine amino group in diverse contexts, when it is: the first transcribed nucleotide after the mRNA cap (PCIF1), at position 1832 of 18S rRNA (MettL5-Trm112 complex), and within a hairpin in the 3′ UTR of the S-adenosyl-l-methionine synthetase (MettL16). Among these three enzymes, the catalytic efficiency ranges from PCIF1, with the fastest turnover rate of >230 h−1 μM−1 on mRNA cap analog, down to MettL16, which has the lowest rate of ∼3 h−1 μM−1 acting on an RNA hairpin. Both PCIF1 and MettL5 have a binding affinity (Km) of ∼1 μM or less for both substrates of SAM and RNA, whereas MettL16 has significantly lower binding affinities for both (Km >0.4 mM for SAM and ∼10 μM for RNA). The three enzymes are active over a wide pH range (∼5.4–9.4) and have different preferences for ionic strength. Sodium chloride at 200 mM markedly diminished methylation activity of MettL5-Trm112 complex, whereas MettL16 had higher activity in the range of 200 to 500 mM NaCl. Zinc ion inhibited activities of all three enzymes. Together, these results illustrate the diversity of RNA adenosine methyltransferases in their enzymatic mechanisms and substrate specificities and underline the need for assay optimization in their study.
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Speciale I, Laugieri ME, Noel E, Lin S, Lowary TL, Molinaro A, Duncan GA, Agarkova IV, Garozzo D, Tonetti MG, Van Etten JL, De Castro C. Chlorovirus PBCV-1 protein A064R has three of the transferase activities necessary to synthesize its capsid protein N-linked glycans. Proc Natl Acad Sci U S A 2020; 117:28735-28742. [PMID: 33139538 PMCID: PMC7682578 DOI: 10.1073/pnas.2016626117] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Paramecium bursaria chlorella virus-1 (PBCV-1) is a large double-stranded DNA (dsDNA) virus that infects the unicellular green alga Chlorella variabilis NC64A. Unlike many other viruses, PBCV-1 encodes most, if not all, of the enzymes involved in the synthesis of the glycans attached to its major capsid protein. Importantly, these glycans differ from those reported from the three domains of life in terms of structure and asparagine location in the sequon of the protein. Previous data collected from 20 PBCV-1 spontaneous mutants (or antigenic variants) suggested that the a064r gene encodes a glycosyltransferase (GT) with three domains, each with a different function. Here, we demonstrate that: domain 1 is a β-l-rhamnosyltransferase; domain 2 is an α-l-rhamnosyltransferase resembling only bacterial proteins of unknown function, and domain 3 is a methyltransferase that methylates the C-2 hydroxyl group of the terminal α-l-rhamnose (Rha) unit. We also establish that methylation of the C-3 hydroxyl group of the terminal α-l-Rha is achieved by another virus-encoded protein A061L, which requires an O-2 methylated substrate. This study, thus, identifies two of the glycosyltransferase activities involved in the synthesis of the N-glycan of the viral major capsid protein in PBCV-1 and establishes that a single protein A064R possesses the three activities needed to synthetize the 2-OMe-α-l-Rha-(1→2)-β-l-Rha fragment. Remarkably, this fragment can be attached to any xylose unit.
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Affiliation(s)
- Immacolata Speciale
- Department of Chemical Sciences, University of Napoli Federico II, 80126 Napoli, Italy
- Department of Agricultural Sciences, University of Napoli Federico II, 80055 Portici NA, Italy
| | - Maria Elena Laugieri
- Department of Experimental Medicine and Center of Excellence for Biomedical Research, University of Genova, 16132 Genova, Italy
| | - Eric Noel
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE 68583-0900
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588-0118
| | - Sicheng Lin
- Department of Chemistry, University of Alberta, Gunning-Lemieux Chemistry Centre, Edmonton, AB T6G 2G2 , Canada
| | - Todd L Lowary
- Department of Chemistry, University of Alberta, Gunning-Lemieux Chemistry Centre, Edmonton, AB T6G 2G2 , Canada
- Institute of Biological Chemistry, Academia Sinica, Nangang, 11529 Taipei, Taiwan
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Napoli Federico II, 80126 Napoli, Italy
| | - Garry A Duncan
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE 68583-0900
| | - Irina V Agarkova
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE 68583-0900
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583-0722
| | - Domenico Garozzo
- CNR, Institute for Polymers, Composites and Biomaterials, 95126 Catania, Italy
| | - Michela G Tonetti
- Department of Experimental Medicine and Center of Excellence for Biomedical Research, University of Genova, 16132 Genova, Italy;
| | - James L Van Etten
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE 68583-0900;
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583-0722
| | - Cristina De Castro
- Department of Agricultural Sciences, University of Napoli Federico II, 80055 Portici NA, Italy;
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Medina A, Triviño J, Borges RJ, Millán C, Usón I, Sammito MD. ALEPH: a network-oriented approach for the generation of fragment-based libraries and for structure interpretation. Acta Crystallogr D Struct Biol 2020; 76:193-208. [PMID: 32133985 PMCID: PMC7057218 DOI: 10.1107/s2059798320001679] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 02/05/2020] [Indexed: 11/17/2022] Open
Abstract
The analysis of large structural databases reveals general features and relationships among proteins, providing useful insight. A different approach is required to characterize ubiquitous secondary-structure elements, where flexibility is essential in order to capture small local differences. The ALEPH software is optimized for the analysis and the extraction of small protein folds by relying on their geometry rather than on their sequence. The annotation of the structural variability of a given fold provides valuable information for fragment-based molecular-replacement methods, in which testing alternative model hypotheses can succeed in solving difficult structures when no homology models are available or are successful. ARCIMBOLDO_BORGES combines the use of composite secondary-structure elements as a search model with density modification and tracing to reveal the rest of the structure when both steps are successful. This phasing method relies on general fold libraries describing variations around a given pattern of β-sheets and helices extracted using ALEPH. The program introduces characteristic vectors defined from the main-chain atoms as a way to describe the geometrical properties of the structure. ALEPH encodes structural properties in a graph network, the exploration of which allows secondary-structure annotation, decomposition of a structure into small compact folds, generation of libraries of models representing a variation of a given fold and finally superposition of these folds onto a target structure. These functions are available through a graphical interface designed to interactively show the results of structure manipulation, annotation, fold decomposition, clustering and library generation. ALEPH can produce pictures of the graphs, structures and folds for publication purposes.
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Grants
- 790122 H2020 Marie Skłodowska-Curie Actions
- BES-2017-080368 Ministerio de Economía, Industria y Competitividad, Gobierno de España
- BES-2015-071397 Ministerio de Economía, Industria y Competitividad, Gobierno de España
- BIO2015-64216-P Ministerio de Economía, Industria y Competitividad, Gobierno de España
- BIO2013-49604-EXP Ministerio de Economía, Industria y Competitividad, Gobierno de España
- MDM2014-0435-01 Ministerio de Economía, Industria y Competitividad, Gobierno de España
- 16/24191-8 Fundação de Amparo à Pesquisa do Estado de São Paulo
- 17/13485-3 Fundação de Amparo à Pesquisa do Estado de São Paulo
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Affiliation(s)
- Ana Medina
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Josep Triviño
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Rafael J. Borges
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu-SP 18618-689, Brazil
| | - Claudia Millán
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Isabel Usón
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
- ICREA, Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys 23, 08003 Barcelona, Spain
| | - Massimo D. Sammito
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, England
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Biosynthesis of mycobacterial methylmannose polysaccharides requires a unique 1- O-methyltransferase specific for 3- O-methylated mannosides. Proc Natl Acad Sci U S A 2019; 116:835-844. [PMID: 30606802 DOI: 10.1073/pnas.1813450116] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Mycobacteria are a wide group of organisms that includes strict pathogens, such as Mycobacterium tuberculosis, as well as environmental species known as nontuberculous mycobacteria (NTM), some of which-namely Mycobacterium avium-are important opportunistic pathogens. In addition to a distinctive cell envelope mediating critical interactions with the host immune system and largely responsible for their formidable resistance to antimicrobials, mycobacteria synthesize rare intracellular polymethylated polysaccharides implicated in the modulation of fatty acid metabolism, thus critical players in cell envelope assembly. These are the 6-O-methylglucose lipopolysaccharides (MGLP) ubiquitously detected across the Mycobacterium genus, and the 3-O-methylmannose polysaccharides (MMP) identified only in NTM. The polymethylated nature of these polysaccharides renders the intervening methyltransferases essential for their optimal function. Although the knowledge of MGLP biogenesis is greater than that of MMP biosynthesis, the methyltransferases of both pathways remain uncharacterized. Here, we report the identification and characterization of a unique S-adenosyl-l-methionine-dependent sugar 1-O-methyltransferase (MeT1) from Mycobacterium hassiacum that specifically blocks the 1-OH position of 3,3'-di-O-methyl-4α-mannobiose, a probable early precursor of MMP, which we chemically synthesized. The high-resolution 3D structure of MeT1 in complex with its exhausted cofactor, S-adenosyl-l-homocysteine, together with mutagenesis studies and molecular docking simulations, unveiled the enzyme's reaction mechanism. The functional and structural properties of this unique sugar methyltransferase further our knowledge of MMP biosynthesis and provide important tools to dissect the role of MMP in NTM physiology and resilience.
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Starbird CA, Perry NA, Chen Q, Berndt S, Yamakawa I, Loukachevitch LV, Limbrick EM, Bachmann BO, Iverson TM, McCulloch KM. The Structure of the Bifunctional Everninomicin Biosynthetic Enzyme EvdMO1 Suggests Independent Activity of the Fused Methyltransferase-Oxidase Domains. Biochemistry 2018; 57:6827-6837. [PMID: 30525509 DOI: 10.1021/acs.biochem.8b00836] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Members of the orthosomycin family of natural products are decorated polysaccharides with potent antibiotic activity and complex biosynthetic pathways. The defining feature of the orthosomycins is an orthoester linkage between carbohydrate moieties that is necessary for antibiotic activity and is likely formed by a family of conserved oxygenases. Everninomicins are octasaccharide orthosomycins produced by Micromonospora carbonacea that have two orthoester linkages and a methylenedioxy bridge, three features whose formation logically requires oxidative chemistry. Correspondingly, the evd gene cluster encoding everninomicin D encodes two monofunctional nonheme iron, α-ketoglutarate-dependent oxygenases and one bifunctional enzyme with an N-terminal methyltransferase domain and a C-terminal oxygenase domain. To investigate whether the activities of these domains are linked in the bifunctional enzyme EvdMO1, we determined the structure of the N-terminal methyltransferase domain to 1.1 Å and that of the full-length protein to 3.35 Å resolution. Both domains of EvdMO1 adopt the canonical folds of their respective superfamilies and are connected by a short linker. Each domain's active site is oriented such that it faces away from the other domain, and there is no evidence of a channel connecting the two. Our results support EvdMO1 working as a bifunctional enzyme with independent catalytic activities.
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11
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Ongpipattanakul C, Nair SK. Molecular Basis for Autocatalytic Backbone N-Methylation in RiPP Natural Product Biosynthesis. ACS Chem Biol 2018; 13:2989-2999. [PMID: 30204409 DOI: 10.1021/acschembio.8b00668] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
N-methylation of nucleic acids, proteins, and peptides is a chemical modification with significant impact on biological regulation. Despite the simplicity of the structural change, N-methylation can influence diverse functions including epigenetics, protein complex formation, and microtubule stability. While there are limited examples of N-methylation of the α-amino group of bacterial and eukaryotic proteins, there are no examples of catalysts that carry out post-translation methylation of backbone amides in proteins or peptides. Recent studies have identified enzymes that catalyze backbone N-methylation on a peptide substrate, a reaction with little biochemical precedent, in a family of ribosomally synthesized natural products produced in basidiomycetes. Here, we describe the crystal structures of Dendrothele bispora dbOphMA, a methyltransferase that catalyzes multiple N-methylations on the peptide backbone. We further carry out biochemical studies of this catalyst to determine the molecular details that promote this unusual chemical transformation. The structural and biochemical framework described here could facilitate biotechnological applications of catalysts for the rapid production of backbone N-methylated peptides.
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12
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Rosa BA, Supali T, Gankpala L, Djuardi Y, Sartono E, Zhou Y, Fischer K, Martin J, Tyagi R, Bolay FK, Fischer PU, Yazdanbakhsh M, Mitreva M. Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia. MICROBIOME 2018; 6:33. [PMID: 29486796 PMCID: PMC6389212 DOI: 10.1186/s40168-018-0416-5] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 01/26/2018] [Indexed: 05/11/2023]
Abstract
BACKGROUND The human intestine and its microbiota is the most common infection site for soil-transmitted helminths (STHs), which affect the well-being of ~ 1.5 billion people worldwide. The complex cross-kingdom interactions are not well understood. RESULTS A cross-sectional analysis identified conserved microbial signatures positively or negatively associated with STH infections across Liberia and Indonesia, and longitudinal samples analysis from a double-blind randomized trial showed that the gut microbiota responds to deworming but does not transition closer to the uninfected state. The microbiomes of individuals able to self-clear the infection had more alike microbiome assemblages compared to individuals who remained infected. One bacterial taxon (Lachnospiracae) was negatively associated with infection in both countries, and 12 bacterial taxa were significantly associated with STH infection in both countries, including Olsenella (associated with reduced gut inflammation), which also significantly reduced in abundance following clearance of infection. Microbial community gene abundances were also affected by deworming. Functional categories identified as associated with STH infection included arachidonic acid metabolism; arachidonic acid is the precursor for pro-inflammatory leukotrienes that threaten helminth survival, and our findings suggest that some modulation of arachidonic acid activity in the STH-infected gut may occur through the increase of arachidonic acid metabolizing bacteria. CONCLUSIONS For the first time, we identify specific members of the gut microbiome that discriminate between moderately/heavily STH-infected and non-infected states across very diverse geographical regions using two different statistical methods. We also identify microbiome-encoded biological functions associated with the STH infections, which are associated potentially with STH survival strategies, and changes in the host environment. These results provide a novel insight of the cross-kingdom interactions in the human gut ecosystem by unlocking the microbiome assemblages at taxonomic, genetic, and functional levels so that advances towards key mechanistic studies can be made.
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Affiliation(s)
- Bruce A. Rosa
- McDonnell Genome Institute, Washington University, St. Louis, MO 63108 USA
| | - Taniawati Supali
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Lincoln Gankpala
- Public Health and Medical Research, National Public Health Institute of Liberia, Charlesville, Liberia
| | - Yenny Djuardi
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Erliyani Sartono
- Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - Yanjiao Zhou
- Microbial Genomics, The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | - Kerstin Fischer
- Department of Medicine, Washington University School of Medicine, St. Louis, MO USA
| | - John Martin
- McDonnell Genome Institute, Washington University, St. Louis, MO 63108 USA
| | - Rahul Tyagi
- McDonnell Genome Institute, Washington University, St. Louis, MO 63108 USA
| | - Fatorma K. Bolay
- Public Health and Medical Research, National Public Health Institute of Liberia, Charlesville, Liberia
| | - Peter U. Fischer
- Department of Medicine, Washington University School of Medicine, St. Louis, MO USA
| | - Maria Yazdanbakhsh
- Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - Makedonka Mitreva
- McDonnell Genome Institute, Washington University, St. Louis, MO 63108 USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO USA
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13
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Dai P, Wang CX, Gao H, Wang QZ, Tang XL, Chen GD, Hong K, Hu D, Yao XS. Characterization of Methyltransferase AlmCII in Chalcomycin Biosynthesis: The First TylF Family O-Methyltransferase Works on a 4'-Deoxysugar. Chembiochem 2017; 18:1510-1517. [PMID: 28488816 DOI: 10.1002/cbic.201700216] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Indexed: 11/11/2022]
Abstract
Sugar O-methylation is a ubiquitous modification in natural products and plays diverse roles. This realization has inspired many attempts to search for novel methyltransferases. Chalcomycins are a group of 16-membered macrolides containing two methylated sugars that require three methyltransferases for their biosynthesis. Here, we identified that AlmCII, a sugar O-methyltransferase belonging to the TylF family that was previously only known to methylate sugars with a 4'-hydroxy group, can methylate a 4',6'-dideoxysugar during the biosynthesis of chalcomycins. An in vitro enzymatic assay revealed that AlmCII is divalent metal-dependent with an optimal pH of 8.0 and optimal temperature of 42 °C. Moreover, the 3'-O-demethylated chalcomycins exhibit less than 6 % of the antibacterial activity of their parent compounds. This is the first report demonstrating that a TylF family O-methyltransferase can use a 4'-deoxy sugar as a substrate and highlighting the importance of this methylation for the antibacterial activity of chalcomycins.
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Affiliation(s)
- Ping Dai
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, No. 601 Huangpu Avenue, Guangzhou, 510632, P. R. China
| | - Chuan-Xi Wang
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, No. 601 Huangpu Avenue, Guangzhou, 510632, P. R. China
| | - Hao Gao
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, No. 601 Huangpu Avenue, Guangzhou, 510632, P. R. China
| | - Qiao-Zhen Wang
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, No. 601 Huangpu Avenue, Guangzhou, 510632, P. R. China
| | - Xiao-Long Tang
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, No. 601 Huangpu Avenue, Guangzhou, 510632, P. R. China
| | - Guo-Dong Chen
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, No. 601 Huangpu Avenue, Guangzhou, 510632, P. R. China
| | - Kui Hong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, No. 185 Donghu Road, Wuhan, 430071, P. R. China
| | - Dan Hu
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, No. 601 Huangpu Avenue, Guangzhou, 510632, P. R. China.,State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, No.345 Lingling Road, Shanghai, 200032, P. R. China
| | - Xin-Sheng Yao
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, No. 601 Huangpu Avenue, Guangzhou, 510632, P. R. China
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14
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Han L, Singh S, Thorson JS, Phillips GN. Loop dynamics of thymidine diphosphate-rhamnose 3'-O-methyltransferase (CalS11), an enzyme in calicheamicin biosynthesis. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2016; 3:012004. [PMID: 26958582 PMCID: PMC4760980 DOI: 10.1063/1.4941368] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 01/22/2016] [Indexed: 06/05/2023]
Abstract
Structure analysis and ensemble refinement of the apo-structure of thymidine diphosphate (TDP)-rhamnose 3'-O-methyltransferase reveal a gate for substrate entry and product release. TDP-rhamnose 3'-O-methyltransferase (CalS11) catalyses a 3'-O-methylation of TDP-rhamnose, an intermediate in the biosynthesis of enediyne antitumor antibiotic calicheamicin. CalS11 operates at the sugar nucleotide stage prior to glycosylation step. Here, we present the crystal structure of the apo form of CalS11 at 1.89 Å resolution. We propose that the L2 loop functions as a gate facilitating and/or providing specificity for substrate entry or promoting product release. Ensemble refinement analysis slightly improves the crystallographic refinement statistics and furthermore provides a compelling way to visualize the dynamic model of loop L2, supporting the understanding of its proposed role in catalysis.
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Affiliation(s)
- Lu Han
- Biosciences at Rice, Rice University , Houston, Texas 77005, USA
| | - Shanteri Singh
- Center for Pharmaceutical Research and Innovation, Pharmaceutical Sciences, University of Kentucky College of Pharmacy , Lexington, Kentucky 40536-0596, USA
| | - Jon S Thorson
- Center for Pharmaceutical Research and Innovation, Pharmaceutical Sciences, University of Kentucky College of Pharmacy , Lexington, Kentucky 40536-0596, USA
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15
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Oliva Chávez AS, Fairman JW, Felsheim RF, Nelson CM, Herron MJ, Higgins L, Burkhardt NY, Oliver JD, Markowski TW, Kurtti TJ, Edwards TE, Munderloh UG. An O-Methyltransferase Is Required for Infection of Tick Cells by Anaplasma phagocytophilum. PLoS Pathog 2015; 11:e1005248. [PMID: 26544981 PMCID: PMC4636158 DOI: 10.1371/journal.ppat.1005248] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 10/03/2015] [Indexed: 12/16/2022] Open
Abstract
Anaplasma phagocytophilum, the causative agent of Human Granulocytic Anaplasmosis (HGA), is an obligately intracellular α-proteobacterium that is transmitted by Ixodes spp ticks. However, the pathogen is not transovarially transmitted between tick generations and therefore needs to survive in both a mammalian host and the arthropod vector to complete its life cycle. To adapt to different environments, pathogens rely on differential gene expression as well as the modification of proteins and other molecules. Random transposon mutagenesis of A. phagocytophilum resulted in an insertion within the coding region of an o-methyltransferase (omt) family 3 gene. In wild-type bacteria, expression of omt was up-regulated during binding to tick cells (ISE6) at 2 hr post-inoculation, but nearly absent by 4 hr p.i. Gene disruption reduced bacterial binding to ISE6 cells, and the mutant bacteria that were able to enter the cells were arrested in their replication and development. Analyses of the proteomes of wild-type versus mutant bacteria during binding to ISE6 cells identified Major Surface Protein 4 (Msp4), but also hypothetical protein APH_0406, as the most differentially methylated. Importantly, two glutamic acid residues (the targets of the OMT) were methyl-modified in wild-type Msp4, whereas a single asparagine (not a target of the OMT) was methylated in APH_0406. In vitro methylation assays demonstrated that recombinant OMT specifically methylated Msp4. Towards a greater understanding of the overall structure and catalytic activity of the OMT, we solved the apo (PDB_ID:4OA8), the S-adenosine homocystein-bound (PDB_ID:4OA5), the SAH-Mn2+ bound (PDB_ID:4PCA), and SAM- Mn2+ bound (PDB_ID:4PCL) X-ray crystal structures of the enzyme. Here, we characterized a mutation in A. phagocytophilum that affected the ability of the bacteria to productively infect cells from its natural vector. Nevertheless, due to the lack of complementation, we cannot rule out secondary mutations. Since its discovery in 1994, Human Granulocytic Anaplasmosis (HGA) has become the second most commonly diagnosed tick-borne disease in the US, and it is gaining importance in several countries in Europe. HGA is caused by Anaplasma phagocytophilum, a bacterium transmitted by black-legged ticks and their relatives. Whereas several of the molecules and processes leading to infection of human cells have been identified, little is known about their counterparts in the tick. We analyzed the effects of a mutation in a gene encoding an o-methyltransferase that is involved in methylation of an outer membrane protein. The mutation of the OMT appears to be important for the ability of A. phagocytophilum to adhere to, invade, and replicate in tick cells. Several tests including binding assays, microscopic analysis of the infection cycle within tick cells, gene expression assays, and biochemical assays using recombinant OMT strongly suggested that the mutation of the o-methyltransferase gene arrested the growth and development of this bacterium within tick cells. Proteomic analyses identified several possible OMT substrates, and in vitro methylation assays using recombinant o-methyltransferase identified an outer membrane protein, Msp4, as a specifically methyl-modified target. Our results indicated that methylation was important for infection of tick cells by A. phagocytophilum, and suggested possible strategies to block transmission of this emerging pathogen. The solved crystal structure of the o-methyltransferase will further stimulate the search for small molecule inhibitors that could break the tick transmission cycle of A. phagocytophilum in nature.
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Affiliation(s)
- Adela S. Oliva Chávez
- Department of Entomology, University of Minnesota, Saint Paul, Minnesota, United States of America
- * E-mail:
| | - James W. Fairman
- Emerald Bio, Bainbridge Island, Washington, United States of America
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
| | - Roderick F. Felsheim
- Department of Entomology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Curtis M. Nelson
- Department of Entomology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Michael J. Herron
- Department of Entomology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - LeeAnn Higgins
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Nicole Y. Burkhardt
- Department of Entomology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Jonathan D. Oliver
- Department of Entomology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Todd W. Markowski
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Timothy J. Kurtti
- Department of Entomology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Thomas E. Edwards
- Emerald Bio, Bainbridge Island, Washington, United States of America
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
| | - Ulrike G. Munderloh
- Department of Entomology, University of Minnesota, Saint Paul, Minnesota, United States of America
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16
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Bernard SM, Akey DL, Tripathi A, Park SR, Konwerski JR, Anzai Y, Li S, Kato F, Sherman DH, Smith JL. Structural basis of substrate specificity and regiochemistry in the MycF/TylF family of sugar O-methyltransferases. ACS Chem Biol 2015; 10:1340-51. [PMID: 25692963 DOI: 10.1021/cb5009348] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Sugar moieties in natural products are frequently modified by O-methylation. In the biosynthesis of the macrolide antibiotic mycinamicin, methylation of a 6'-deoxyallose substituent occurs in a stepwise manner first at the 2'- and then the 3'-hydroxyl groups to produce the mycinose moiety in the final product. The timing and placement of the O-methylations impact final stage C-H functionalization reactions mediated by the P450 monooxygenase MycG. The structural basis of pathway ordering and substrate specificity is unknown. A series of crystal structures of MycF, the 3'-O-methyltransferase, including the free enzyme and complexes with S-adenosyl homocysteine (SAH), substrate, product, and unnatural substrates, show that SAM binding induces substantial ordering that creates the binding site for the natural substrate, and a bound metal ion positions the substrate for catalysis. A single amino acid substitution relaxed the 2'-methoxy specificity but retained regiospecificity. The engineered variant produced a new mycinamicin analog, demonstrating the utility of structural information to facilitate bioengineering approaches for the chemoenzymatic synthesis of complex small molecules containing modified sugars. Using the MycF substrate complex and the modeled substrate complex of a 4'-specific homologue, active site residues were identified that correlate with the 3' or 4' specificity of MycF family members and define the protein and substrate features that direct the regiochemistry of methyltransfer. This classification scheme will be useful in the annotation of new secondary metabolite pathways that utilize this family of enzymes.
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Affiliation(s)
- Steffen M. Bernard
- Chemical
Biology Doctoral Program, University of Michigan, Ann Arbor, Michigan 48109, United States
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - David L. Akey
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ashootosh Tripathi
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Sung Ryeol Park
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jamie R. Konwerski
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yojiro Anzai
- Faculty
of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Shengying Li
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Fumio Kato
- Faculty
of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - David H. Sherman
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Departments of Medicinal Chemistry, Chemistry, and Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Janet L. Smith
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department
of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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17
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Structure and mechanism of an antibiotics-synthesizing 3-hydroxykynurenine C-methyltransferase. Sci Rep 2015; 5:10100. [PMID: 25960001 PMCID: PMC4426599 DOI: 10.1038/srep10100] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 03/27/2015] [Indexed: 12/15/2022] Open
Abstract
Streptosporangium sibiricum SibL catalyzes the methyl transfer from S-adenosylmethionine (SAM) to 3-hydroxykynurenine (3-HK) to produce S-adenosylhomocysteine (SAH) and 3-hydroxy-4-methyl-kynurenine for sibiromycin biosynthesis. Here, we present the crystal structures of apo-form Ss-SibL, Ss-SibL/SAH binary complex and Ss-SibL/SAH/3-HK ternary complex. Ss-SibL is a homodimer. Each subunit comprises a helical N-terminal domain and a Rossmann-fold C-terminal domain. SAM (or SAH) binding alone results in domain movements, suggesting a two-step catalytic cycle. Analyses of the enzyme-ligand interactions and further mutant studies support a mechanism in which Tyr134 serves as the principal base in the transferase reaction of methyl group from SAM to 3-HK.
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18
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Larabi R, Abtouche S, Brahimi M. Theoretical study of methyl group transfer assisted by proton transfer reaction in the N-acylated imidates. J Mol Model 2014; 20:2302. [DOI: 10.1007/s00894-014-2302-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 05/12/2014] [Indexed: 11/28/2022]
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19
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Szeja W, Grynkiewicz G, Bieg T, Swierk P, Byczek A, Papaj K, Kitel R, Rusin A. Synthesis and cytotoxicity of 2,3-enopyranosyl C-linked conjugates of genistein. Molecules 2014; 19:7072-93. [PMID: 24886936 PMCID: PMC6271854 DOI: 10.3390/molecules19067072] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 05/23/2014] [Accepted: 05/23/2014] [Indexed: 11/16/2022] Open
Abstract
A series of glycoconjugates, derivatives of genistein containing a C-glycosylated carbohydrate moiety, were synthesized and their anticancer activity was tested in vitro in the human cell lines HCT 116 and DU 145. The target compounds 15–17 were synthesized by treating ω-bromoalkyl C-glycosides derived from l-rhamnal (1) with a tetrabutylammonium salt of genistein. The new, metabolically stable analogs of previously studied O-glycosidic genistein derivatives inhibited proliferation of cancer cell lines through inhibition of the cell cycle.
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Affiliation(s)
- Wieslaw Szeja
- Department of Chemistry, Biochemistry and Biotechnology, Silesian Technical University, Krzywoustego 8, 44-100 Gliwice, Poland.
| | | | - Tadeusz Bieg
- Department of Chemistry, Biochemistry and Biotechnology, Silesian Technical University, Krzywoustego 8, 44-100 Gliwice, Poland.
| | - Piotr Swierk
- Department of Chemistry, Biochemistry and Biotechnology, Silesian Technical University, Krzywoustego 8, 44-100 Gliwice, Poland.
| | - Anna Byczek
- Department of Chemistry, Biochemistry and Biotechnology, Silesian Technical University, Krzywoustego 8, 44-100 Gliwice, Poland.
| | - Katarzyna Papaj
- Department of Chemistry, Biochemistry and Biotechnology, Silesian Technical University, Krzywoustego 8, 44-100 Gliwice, Poland.
| | - Radosław Kitel
- Department of Chemistry, Biochemistry and Biotechnology, Silesian Technical University, Krzywoustego 8, 44-100 Gliwice, Poland.
| | - Aleksandra Rusin
- Maria Sklodowska-Curie Memorial Cancer Center & Institute of Oncology, Branch Gliwice, Wybrzeze AK 15, 44-100 Gliwice, Poland.
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20
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Zou XW, Liu YC, Hsu NS, Huang CJ, Lyu SY, Chan HC, Chang CY, Yeh HW, Lin KH, Wu CJ, Tsai MD, Li TL. Structure and mechanism of a nonhaem-iron SAM-dependent C-methyltransferase and its engineering to a hydratase and an O-methyltransferase. ACTA ACUST UNITED AC 2014; 70:1549-60. [PMID: 24914966 DOI: 10.1107/s1399004714005239] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 03/06/2014] [Indexed: 12/16/2022]
Abstract
In biological systems, methylation is most commonly performed by methyltransferases (MTs) using the electrophilic methyl source S-adenosyl-L-methionine (SAM) via the S(N)2 mechanism. (2S,3S)-β-Methylphenylalanine, a nonproteinogenic amino acid, is a building unit of the glycopeptide antibiotic mannopeptimycin. The gene product of mppJ from the mannopeptimycin-biosynthetic gene cluster is the MT that methylates the benzylic C atom of phenylpyruvate (Ppy) to give βMePpy. Although the benzylic C atom of Ppy is acidic, how its nucleophilicity is further enhanced to become an acceptor for C-methylation has not conclusively been determined. Here, a structural approach is used to address the mechanism of MppJ and to engineer it for new functions. The purified MppJ displays a turquoise colour, implying the presence of a metal ion. The crystal structures reveal MppJ to be the first ferric ion SAM-dependent MT. An additional four structures of binary and ternary complexes illustrate the molecular mechanism for the metal ion-dependent methyltransfer reaction. Overall, MppJ has a nonhaem iron centre that bind, orients and activates the α-ketoacid substrate and has developed a sandwiched bi-water device to avoid the formation of the unwanted reactive oxo-iron(IV) species during the C-methylation reaction. This discovery further prompted the conversion of the MT into a structurally/functionally unrelated new enzyme. Through stepwise mutagenesis and manipulation of coordination chemistry, MppJ was engineered to perform both Lewis acid-assisted hydration and/or O-methyltransfer reactions to give stereospecific new compounds. This process was validated by six crystal structures. The results reported in this study will facilitate the development and design of new biocatalysts for difficult-to-synthesize biochemicals.
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Affiliation(s)
- Xiao-Wei Zou
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Chen Liu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Ning-Shian Hsu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | | | - Syue-Yi Lyu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Hsiu-Chien Chan
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chin-Yuan Chang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Hsien-Wei Yeh
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Kuan-Hung Lin
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chang-Jer Wu
- Department of Food Science, National Taiwan Ocean University, Keelung 202, Taiwan
| | - Ming-Daw Tsai
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Tsung-Lin Li
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
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21
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Singh S, Chang A, Helmich KE, Bingman CA, Wrobel RL, Beebe ET, Makino SI, Aceti DJ, Dyer K, Hura GL, Sunkara M, Morris AJ, Phillips GN, Thorson JS. Structural and functional characterization of CalS11, a TDP-rhamnose 3'-O-methyltransferase involved in calicheamicin biosynthesis. ACS Chem Biol 2013; 8:1632-9. [PMID: 23662776 PMCID: PMC3875630 DOI: 10.1021/cb400068k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sugar methyltransferases (MTs) are an important class of tailoring enzymes that catalyze the transfer of a methyl group from S-adenosyl-l-methionine to sugar-based N-, C- and O-nucleophiles. While sugar N- and C-MTs involved in natural product biosynthesis have been found to act on sugar nucleotide substrates prior to a subsequent glycosyltransferase reaction, corresponding sugar O-methylation reactions studied thus far occur after the glycosyltransfer reaction. Herein we report the first in vitro characterization using (1)H-(13)C-gHSQC with isotopically labeled substrates and the X-ray structure determination at 1.55 Å resolution of the TDP-3'-O-rhamnose-methyltransferase CalS11 from Micromonospora echinospora. This study highlights a unique NMR-based methyltransferase assay, implicates CalS11 to be a metal- and general acid/base-dependent O-methyltransferase, and as a first crystal structure for a TDP-hexose-O-methyltransferase, presents a new template for mechanistic studies and/or 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, KY 40536-0596, USA
| | - Aram Chang
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Kate E. Helmich
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Craig A. Bingman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Russel L. Wrobel
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Emily T. Beebe
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Shin-Ichi Makino
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - David J. Aceti
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Kevin Dyer
- Physical Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley CA 94720, USA
| | - Greg L. Hura
- Physical Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley CA 94720, USA
| | - Manjula Sunkara
- Division of Cardiovascular Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Andrew J. Morris
- Division of Cardiovascular Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - George N. Phillips
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005, USA
| | - Jon S. Thorson
- Center for Pharmaceutical Research and Innovation, University of Kentucky College of Pharmacy, 789 South Limestone Street, Lexington, KY 40536-0596, USA
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22
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Tengg M, Stecher H, Remler P, Eiteljörg I, Schwab H, Gruber-Khadjawi M. Molecular characterization of the C-methyltransferase NovO of Streptomyces spheroides, a valuable enzyme for performing Friedel–Crafts alkylation. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.molcatb.2012.03.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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23
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Liscombe DK, Louie GV, Noel JP. Architectures, mechanisms and molecular evolution of natural product methyltransferases. Nat Prod Rep 2012; 29:1238-50. [PMID: 22850796 DOI: 10.1039/c2np20029e] [Citation(s) in RCA: 212] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The addition of a methyl moiety to a small chemical is a common transformation in the biosynthesis of natural products across all three domains of life. These methylation reactions are most often catalysed by S-adenosyl-L-methionine (SAM)-dependent methyltransferases (MTs). MTs are categorized based on the electron-rich, methyl accepting atom, usually O, N, C, or S. SAM-dependent natural product MTs (NPMTs) are responsible for the modification of a wide array of structurally distinct substrates, including signalling and host defense compounds, pigments, prosthetic groups, cofactors, cell membrane and cell wall components, and xenobiotics. Most notably, methylation modulates the bioavailability, bioactivity, and reactivity of acceptor molecules, and thus exerts a central role on the functional output of many metabolic pathways. Our current understanding of the structural enzymology of NPMTs groups these phylogenetically diverse enzymes into two MT-superfamily fold classes (class I and class III). Structural biology has also shed light on the catalytic mechanisms and molecular bases for substrate specificity for over fifty NPMTs. These biophysical-based approaches have contributed to our understanding of NPMT evolution, demonstrating how a widespread protein fold evolved to accommodate chemically diverse methyl acceptors and to catalyse disparate mechanisms suited to the physiochemical properties of the target substrates. This evolutionary diversity suggests that NPMTs may serve as starting points for generating new biocatalysts.
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Affiliation(s)
- David K Liscombe
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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24
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Shah SQ, Khan MR. Radiosynthesis of 99m Tc-labeled novobiocin dithiocarbamate complex as a potential Staphylococcus aureus infection radiotracer. RADIOCHEMISTRY 2012. [DOI: 10.1134/s1066362212030113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Singh S, Phillips GN, Thorson JS. The structural biology of enzymes involved in natural product glycosylation. Nat Prod Rep 2012; 29:1201-37. [PMID: 22688446 DOI: 10.1039/c2np20039b] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The glycosylation of microbial natural products often dramatically influences the biological and/or pharmacological activities of the parental metabolite. Over the past decade, crystal structures of several enzymes involved in the biosynthesis and attachment of novel sugars found appended to natural products have emerged. In many cases, these studies have paved the way to a better understanding of the corresponding enzyme mechanism of action and have served as a starting point for engineering variant enzymes to facilitate to production of differentially-glycosylated natural products. This review specifically summarizes the structural studies of bacterial enzymes involved in biosynthesis of novel sugar nucleotides.
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Affiliation(s)
- Shanteri Singh
- Laboratory for Biosynthetic Chemistry, Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
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26
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Lawson DM, Stevenson CEM. Structural and functional dissection of aminocoumarin antibiotic biosynthesis: a review. ACTA ACUST UNITED AC 2012; 13:125-33. [DOI: 10.1007/s10969-012-9138-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Accepted: 05/12/2012] [Indexed: 10/28/2022]
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27
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Akey DL, Li S, Konwerski JR, Confer LA, Bernard SM, Anzai Y, Kato F, Sherman DH, Smith JL. A new structural form in the SAM/metal-dependent o‑methyltransferase family: MycE from the mycinamicin biosynthetic pathway. J Mol Biol 2011; 413:438-50. [PMID: 21884704 PMCID: PMC3193595 DOI: 10.1016/j.jmb.2011.08.040] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Revised: 08/16/2011] [Accepted: 08/16/2011] [Indexed: 01/07/2023]
Abstract
O-linked methylation of sugar substituents is a common modification in the biosynthesis of many natural products and is catalyzed by multiple families of S-adenosyl-L-methionine (SAM or AdoMet)-dependent methyltransferases (MTs). Mycinamicins, potent antibiotics from Micromonospora griseorubida, can be methylated at two positions on a 6-deoxyallose substituent. The first methylation is catalyzed by MycE, a SAM- and metal-dependent MT. Crystal structures were determined for MycE bound to the product S-adenosyl-L-homocysteine (AdoHcy) and magnesium, both with and without the natural substrate mycinamicin VI. This represents the first structure of a natural product sugar MT in complex with its natural substrate. MycE is a tetramer of a two-domain polypeptide, comprising a C-terminal catalytic MT domain and an N-terminal auxiliary domain, which is important for quaternary assembly and for substrate binding. The symmetric MycE tetramer has a novel MT organization in which each of the four active sites is formed at the junction of three monomers within the tetramer. The active-site structure supports a mechanism in which a conserved histidine acts as a general base, and the metal ion helps to position the methyl acceptor and to stabilize a hydroxylate intermediate. A conserved tyrosine is suggested to support activity through interactions with the transferred methyl group from the SAM methyl donor. The structure of the free enzyme reveals a dramatic order-disorder transition in the active site relative to the S-adenosyl-L-homocysteine complexes, suggesting a mechanism for product/substrate exchange through concerted movement of five loops and the polypeptide C-terminus.
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Affiliation(s)
- David L. Akey
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
| | - Shengying Li
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
| | | | - Laura A. Confer
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109,Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Steffen M. Bernard
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109,Chemical Biology Doctoral Program, University of Michigan, Ann Arbor, MI 48109
| | - Yojiro Anzai
- Faculty of Pharmaceutical Sciences, Toho University 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Fumio Kato
- Faculty of Pharmaceutical Sciences, Toho University 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - David H. Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109,Departments of Medicinal Chemistry, Chemistry, Microbiology & Immunology, University of Michigan, Ann Arbor, MI 48109
| | - Janet L. Smith
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109,Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109,Correspondence: (734) 615-9564, Fax: (734) 763-6492
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28
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Niu S, Hu T, Li S, Xiao Y, Ma L, Zhang G, Zhang H, Yang X, Ju J, Zhang C. Characterization of a sugar-O-methyltransferase TiaS5 affords new Tiacumicin analogues with improved antibacterial properties and reveals substrate promiscuity. Chembiochem 2011; 12:1740-8. [PMID: 21633995 DOI: 10.1002/cbic.201100129] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Indexed: 12/18/2022]
Abstract
The 18-membered macrocyclic glycoside tiacumicin B, an RNA polymerase inhibitor, is of great therapeutic significance in treating Clostridium difficile infections. The recent characterization of the tiacumicin B biosynthetic gene cluster from Dactylosporangium aurantiacum subsp. hamdenensis NRRL 18085 revealed the functions of two glycosyltransferases, a C-methyltransferase, an acyltransferase, two cytochrome P450s, and a tailoring dihalogenase in tiacumicin biosynthesis. Here we report the genetic confirmation and biochemical characterization of TiaS5 as a sugar-O-methyltransferase, requisite for tiacumicin B biosynthesis. The tiaS5-inactivation mutant is capable of producing 14 tiacumicin analogues (11 of which are new), all lacking the 2'-O-methyl group on the internal rhamnose moiety. Notably, two tiacumicin analogues exhibit improved antibacterial properties. We have also biochemically verified TiaS5 as an S-adenosyl-L-methionine-dependent O-methyltransferase, requiring divalent metal ions for activity. Substrate probing revealed TiaS5 to be a promiscuous enzyme, recognizing 12 tiacumicin analogues. These findings unequivocally establish that TiaS5 functions as a 2'-O-methyltransferase and provide direct biochemical evidence that TiaS5-catalyzed methylation is a tailoring step after glycosyl coupling in tiacumicin B biosynthesis.
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Affiliation(s)
- Siwen Niu
- CAS Key Laboratory of Marine Bio-resources Sustainable Utilization, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
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29
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Abstract
Abstract
The radiosynthesis of 99mTc-Novobiocin (99mTc-NBN) complex and its suitability as a radiotracer for infection imaging was assessed. The radiochemical purity (RCP) of the 99mTc-NBN complex was determined using radio-TLC and radioactive HPLC and biodistribution was studied in artificially infected (A.I.) rats and rabbit, using single well gamma counter (SWGRC) interface with scalar count rate meter (SCRM) and Gamma Camera (γ-CM). The maximum RCP observed for the preparation having 2 mg of NBN, 111 MBq of sodium pertechnetate (Na99mTcO4) and 125 μL of SnF2 (1 μg/μL in 0.01 N HCl) at a pH 5.6 was 98.97±0.40% and remained stable >90% up to 120 min. The activity of the 99mTc-NBN in the infected muscle (TI) was significantly increased from 6.50±0.15 to 19.00±0.17% and decreased in the inflamed muscle (TII), normal muscle (NT), blood, liver, spleen, stomach and intestine within 120 min. The TI/NT and TII/NT ratios were 7.60±1.08 and 1.60±1.14. The Whole Body Static (WBS) images of A.I. rabbit were obtained at 30, 40, 50 and 60 min after the I.V. administration of 111 MBq of 99mTc-NBN to the A.I. rabbit. The stability in saline and serum, higher TI/NT, lower TII/NT ratios and WBS images confirmed the feasibility of the 99mTc-NBN complex as an infection imaging agent.
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Affiliation(s)
| | - M. R. Khan
- University of Peshawar, Phyotopharmaceutical & Neutraceuticals Researc, Peshawar, NWFP, Pakistan
| | - A. U. Khan
- Oncology and Radiotherapy Institute, Nuclear Medicine, Islamabad, Pakistan
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