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Du Y, Thanapipatsiri A, Yokoyama K. Biosynthesis and Genome Mining Potentials of Nucleoside Natural Products. Chembiochem 2023; 24:e202300342. [PMID: 37357819 PMCID: PMC10530009 DOI: 10.1002/cbic.202300342] [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: 05/05/2023] [Revised: 06/20/2023] [Accepted: 06/22/2023] [Indexed: 06/27/2023]
Abstract
Nucleoside natural products show diverse biological activities and serve as leads for various application purposes, including human and veterinary medicine and agriculture. Studies in the past decade revealed that these nucleosides are biosynthesized through divergent mechanisms, in which early steps of the pathways can be classified into two types (C5' oxidation and C5' radical extension), while the structural diversity is created by downstream tailoring enzymes. Based on this biosynthetic logic, we investigated the genome mining discovery potentials of these nucleosides using the two enzymes representing the two types of C5' modifications: LipL-type α-ketoglutarate (α-KG) and Fe-dependent oxygenases and NikJ-type radical S-adenosyl-L-methionine (SAM) enzymes. The results suggest that this approach allows discovery of putative nucleoside biosynthetic gene clusters (BGCs) and the prediction of the core nucleoside structures. The results also revealed the distribution of these pathways in nature and implied the possibility of future genome mining discovery of novel nucleoside natural products.
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Affiliation(s)
- Yanan Du
- Department of Biochemistry, Duke University School of Medicine, 307 Research Drive, Durham, NC 27710, USA
| | - Anyarat Thanapipatsiri
- Department of Biochemistry, Duke University School of Medicine, 307 Research Drive, Durham, NC 27710, USA
| | - Kenichi Yokoyama
- Department of Biochemistry, Duke University School of Medicine, 307 Research Drive, Durham, NC 27710, USA
- Department of Chemistry, Duke University, 307 Research Drive, Durham, NC 27710, USA
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2
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Lee YH, Hou X, Chen R, Feng J, Liu X, Ruszczycky MW, Gao JM, Wang B, Zhou J, Liu HW. Radical S-Adenosyl Methionine Enzyme BlsE Catalyzes a Radical-Mediated 1,2-Diol Dehydration during the Biosynthesis of Blasticidin S. J Am Chem Soc 2022; 144:4478-4486. [PMID: 35238201 DOI: 10.1021/jacs.1c12010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The biosynthesis of blasticidin S has drawn attention due to the participation of the radical S-adenosyl methionine (SAM) enzyme BlsE. The original assignment of BlsE as a radical-mediated, redox-neutral decarboxylase is unusual because this reaction appears to serve no biosynthetic purpose and would need to be reversed by a subsequent carboxylation step. Furthermore, with the exception of BlsE, all other radical SAM decarboxylases reported to date are oxidative in nature. Careful analysis of the BlsE reaction, however, demonstrates that BlsE is not a decarboxylase but instead a lyase that catalyzes the dehydration of cytosylglucuronic acid (CGA) to form cytosyl-4'-keto-3'-deoxy-d-glucuronic acid, which can rapidly decarboxylate nonenzymatically in vitro. Analysis of substrate isotopologs, fluorinated analogues, as well as computational models based on X-ray crystal structures of the BlsE·SAM (2.09 Å) and BlsE·SAM·CGA (2.62 Å) complexes suggests that BlsE catalysis likely proceeds via direct elimination of water from the CGA C4' α-hydroxyalkyl radical as opposed to 1,2-migration of the C3'-hydroxyl prior to dehydration. Biosynthetic and mechanistic implications of the revised assignment of BlsE are discussed.
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Affiliation(s)
- Yu-Hsuan Lee
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Xueli Hou
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, Shaanxi China.,State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ridao Chen
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States.,State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Jianqiang Feng
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xiao Liu
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States.,School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Mark W Ruszczycky
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jin-Ming Gao
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, Shaanxi China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Jiahai Zhou
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Hung-Wen Liu
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States.,Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
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3
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Zhang WH, Wang F, Wang YL, You S, Pan HX, Tang GL. Identification and Characterization of Enzymes Catalyzing Early Steps in Miharamycin and Amipurimycin Biosynthesis. Org Lett 2021; 23:8761-8765. [PMID: 34747180 DOI: 10.1021/acs.orglett.1c03254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The biochemical elucidation of the early biosynthetic pathways of miharamycins and amipurimycin revealed the roles of several enzymes, which include GMP hydrolase, represented by MihD/ApmD, and hypothetical proteins, MihI/ApmI, unexpectedly exhibiting the dual function of the guanylglucuronic acid assembly and GMP cleavage. In addition, MihE, a carbonyl reductase that functions on the C2 branch of high-carbon sugars, and MihF, a rare guanine O-methyltransferase, were also functionally verified.
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Affiliation(s)
- Wen-He Zhang
- School of Life Sciences and Biopharmaceuticals, Shenyang Pharmaceutical University, Benxi 117004, China
| | - Fei Wang
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences (CAS), Hangzhou 310024, China
| | - Yi-Lin Wang
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences (CAS), Hangzhou 310024, China
| | - Song You
- School of Life Sciences and Biopharmaceuticals, Shenyang Pharmaceutical University, Benxi 117004, China
| | - Hai-Xue Pan
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences (CAS), Hangzhou 310024, China
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of CAS, CAS, Shanghai 200032, China
| | - Gong-Li Tang
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences (CAS), Hangzhou 310024, China
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of CAS, CAS, Shanghai 200032, China
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4
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Kang M, Doddapaneni K, Sarni S, Heppner Z, Wysocki V, Wu Z. Solution structure of the nucleotide hydrolase BlsM: Implication of its substrate specificity. Protein Sci 2021; 29:1760-1773. [PMID: 31876335 DOI: 10.1002/pro.3812] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 12/17/2019] [Accepted: 12/21/2019] [Indexed: 11/06/2022]
Abstract
Biosynthesis of the peptidyl nucleoside antifungal agent blasticidin S in Streptomyces griseochromogenes requires the hydrolytic function of a nucleotide hydrolase, BlsM, to excise the free cytosine from the 5'-monophosphate cytosine nucleotide. In addition to its hydrolytic activity, interestingly, BlsM has also been shown to possess a novel cytidine deaminase activity, converting cytidine, and deoxycytidine to uridine and deoxyuridine. To gain insight into the substrate specificity of BlsM and the mechanism by which it performs these dual function, the solution structure of BlsM was determined by multi-dimensional nuclear magnetic resonance approaches. BlsM displays a nucleoside deoxyribosyltransferase-like dimeric topology, with each monomer consisting of a five-stranded β-sheet that is sandwiched by five α-helixes. Compared with the purine nucleotide hydrolase RCL, each monomer of BlsM has a smaller active site pocket, enclosed by a group of conserved hydrophobic residues from both monomers. The smaller size of active site is consistent with its substrate specificity for a pyrimidine, whereas a much more open active site, as in RCL might be required to accommodate a larger purine ring. In addition, BlsM confers its substrate specificity for a ribosyl-nucleotide through a key residue, Phe19. When mutated to a tyrosine, F19Y reverses its substrate preference. While significantly impaired in its hydrolytic capability, F19Y exhibited a pronounced deaminase activity on CMP, presumably due to an altered substrate orientation as a result of a steric clash between the 2'-hydroxyl of CMP and the ζ-OH group of F19Y. Finally, Glu105 appears to be critical for the dual function of BlsM.
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Affiliation(s)
- Minhee Kang
- Chemistry and Biochemistry Department, Ohio State University, Columbus, Ohio
| | - Kiran Doddapaneni
- Chemistry and Biochemistry Department, Ohio State University, Columbus, Ohio
| | - Samantha Sarni
- Chemistry and Biochemistry Department, Ohio State University, Columbus, Ohio
| | - Zach Heppner
- Chemistry and Biochemistry Department, Ohio State University, Columbus, Ohio
| | - Vicki Wysocki
- Chemistry and Biochemistry Department, Ohio State University, Columbus, Ohio
| | - Zhengrong Wu
- Chemistry and Biochemistry Department, Ohio State University, Columbus, Ohio
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5
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McErlean M, Liu X, Cui Z, Gust B, Van Lanen SG. Identification and characterization of enzymes involved in the biosynthesis of pyrimidine nucleoside antibiotics. Nat Prod Rep 2021; 38:1362-1407. [PMID: 33404015 DOI: 10.1039/d0np00064g] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: up to September 2020 Hundreds of nucleoside-based natural products have been isolated from various microorganisms, several of which have been utilized in agriculture as pesticides and herbicides, in medicine as therapeutics for cancer and infectious disease, and as molecular probes to study biological processes. Natural products consisting of structural modifications of each of the canonical nucleosides have been discovered, ranging from simple modifications such as single-step alkylations or acylations to highly elaborate modifications that dramatically alter the nucleoside scaffold and require multiple enzyme-catalyzed reactions. A vast amount of genomic information has been uncovered the past two decades, which has subsequently allowed the first opportunity to interrogate the chemically intriguing enzymatic transformations for the latter type of modifications. This review highlights (i) the discovery and potential applications of structurally complex pyrimidine nucleoside antibiotics for which genetic information is known, (ii) the established reactions that convert the canonical pyrimidine into a new nucleoside scaffold, and (iii) the important tailoring reactions that impart further structural complexity to these molecules.
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Affiliation(s)
- M McErlean
- Department of Pharmaceutical Science, College of Pharmacy, University of Kentucky, USA.
| | - X Liu
- Department of Pharmaceutical Science, College of Pharmacy, University of Kentucky, USA.
| | - Z Cui
- Department of Pharmaceutical Science, College of Pharmacy, University of Kentucky, USA.
| | - B Gust
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, Germany
| | - S G Van Lanen
- Department of Pharmaceutical Science, College of Pharmacy, University of Kentucky, USA.
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6
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Niu G, Zheng J, Tan H. Biosynthesis and combinatorial biosynthesis of antifungal nucleoside antibiotics. SCIENCE CHINA-LIFE SCIENCES 2017; 60:939-947. [DOI: 10.1007/s11427-017-9116-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 05/08/2017] [Indexed: 11/28/2022]
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7
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Niu G, Tan H. Nucleoside antibiotics: biosynthesis, regulation, and biotechnology. Trends Microbiol 2015; 23:110-9. [DOI: 10.1016/j.tim.2014.10.007] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 10/15/2014] [Accepted: 10/22/2014] [Indexed: 11/30/2022]
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8
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Zhao G, Wu G, Zhang Y, Liu G, Han T, Deng Z, He X. Structure of the N-glycosidase MilB in complex with hydroxymethyl CMP reveals its Arg23 specifically recognizes the substrate and controls its entry. Nucleic Acids Res 2014; 42:8115-24. [PMID: 24920828 PMCID: PMC4081090 DOI: 10.1093/nar/gku486] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
5-Hydroxymethylcytosine (5hmC) is present in T-even phage and mammalian DNA as well as some nucleoside antibiotics, including mildiomycin and bacimethrin, during whose synthesis 5hmC is produced by the hydrolysis of 5-hydroxymethyl cytidine 5′-monophosphate (hmCMP) by an N-glycosidase MilB. Recently, the MilB–CMP complex structure revealed its substrate specificity for CMP over dCMP. However, hmCMP instead of CMP is the preferred substrate for MilB as supported by that its KM for CMP is ∼27-fold higher than that for hmCMP. Here, we determined the crystal structures of MilB and its catalytically inactive E103A mutant in complex with hmCMP. In the structure of the complex, Phe22 and Arg23 are positioned in a cage-like active site resembling the binding pocket for the flipped 5-methylcytosine (5mC) in eukaryotic 5mC-binding proteins. Van der Waals interaction between the benzene ring of Phe22 and the pyrimidine ring of hmCMP stabilizes its binding. Remarkably, upon hmCMP binding, the guanidinium group of Arg23 was bent ∼65° toward hmCMP to recognize its 5-hydroxymethyl group, inducing semi-closure of the cage-like pocket. Mutagenesis studies of Arg23 and bioinformatics analysis demonstrate that the positively charged Arg/Lys at this site is critical for the specific recognition of the 5-hydroxymethyl group of hmCMP.
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Affiliation(s)
- Gong Zhao
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Geng Wu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Yan Zhang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Guang Liu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Tiesheng Han
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Xinyi He
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
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9
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Sikowitz MD, Cooper L, Begley TP, Kaminski PA, Ealick SE. Reversal of the substrate specificity of CMP N-glycosidase to dCMP. Biochemistry 2013; 52:4037-47. [PMID: 23659472 PMCID: PMC3750073 DOI: 10.1021/bi400316p] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
MilB is a CMP hydrolase involved in the early steps of biosynthesis of the antifungal compound mildiomycin. An enzyme from the bacimethrin biosynthetic pathway, BcmB, is closely related to MilB in both sequence and function. These two enzymes belong to the nucleoside 2'-deoxyribosyltransferase (NDT) superfamily. NDTs catalyze N-glycosidic bond cleavage of 2'-deoxynucleosides via a covalent 2-deoxyribosyl-enzyme intermediate. Conservation of key active site residues suggests that members of the NDT superfamily share a common mechanism; however, the enzymes differ in their substrate preferences. Substrates vary in the type of nucleobase, the presence or absence of a 2'-hydroxyl group, and the presence or absence of a 5'-phosphate group. We have determined the structures of MilB and BcmB and compared them to previously determined structures of NDT superfamily members. The comparisons reveal how these enzymes differentiate between ribosyl and deoxyribosyl nucleotides or nucleosides and among different nucleobases. The 1.6 Å structure of the MilB-CMP complex reveals an active site feature that is not obvious from comparisons of sequence alone. MilB and BcmB that prefer substrates containing 2'-ribosyl groups have a phenylalanine positioned in the active site, whereas NDT family members with a preference for 2'-deoxyribosyl groups have a tyrosine residue. Further studies show that the phenylalanine is critical for the specificity of MilB and BcmB toward CMP, and mutation of this phenylalanine residue to tyrosine results in a 1000-fold reversal of substrate specificity from CMP to dCMP.
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Affiliation(s)
- Megan D. Sikowitz
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
| | - Lisa Cooper
- Department of Chemistry, Texas A&M University, College Station, Texas 77843
| | - Tadhg P. Begley
- Department of Chemistry, Texas A&M University, College Station, Texas 77843
| | | | - Steven E. Ealick
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853,To whom correspondence should be addressed at the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853. Telephone: (607) 255-7961. Fax: (607) 255-1227.
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10
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Streptomyces lividans blasticidin S deaminase and its application in engineering a blasticidin S-producing strain for ease of genetic manipulation. Appl Environ Microbiol 2013; 79:2349-57. [PMID: 23377931 DOI: 10.1128/aem.03254-12] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Blasticidin S is a peptidyl nucleoside antibiotic produced by Streptomyces griseochromogenes that exhibits strong fungicidal activity. To circumvent an effective DNA uptake barrier system in the native producer and investigate its biosynthesis in vivo, the blasticidin S biosynthetic gene cluster (bls) was engrafted to the chromosome of Streptomyces lividans. However, the resulting mutant, LL2, produced the inactive deaminohydroxyblasticidin S instead of blasticidin S. Subsequently, a blasticidin S deaminase (SLBSD, for S. lividans blasticidin S deaminase) was identified in S. lividans and shown to govern this in vivo conversion. Purified SLBSD was found to be capable of transforming blasticidin S to deaminohydroxyblasticidin S in vitro. It also catalyzed deamination of the cytosine moiety of cytosylglucuronic acid, an intermediate in blasticidin S biosynthesis. Disruption of the SLBSD gene in S. lividans LL2 led to successful production of active blasticidin S in the resultant mutant, S. lividans WJ2. To demonstrate the easy manipulation of the blasticidin S biosynthetic gene cluster, blsE, blsF, and blsL, encoding a predicted radical S-adenosylmethionine (SAM) protein, an unknown protein, and a guanidino methyltransferase, were individually inactivated to access their role in blasticidin S biosynthesis.
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Wu J, Li L, Deng Z, Zabriskie TM, He X. Analysis of the Mildiomycin Biosynthesis Gene Cluster in Streptoverticillum remofaciens ZJU5119 and Characterization of MilC, a Hydroxymethyl cytosyl-glucuronic Acid Synthase. Chembiochem 2012; 13:1613-21. [DOI: 10.1002/cbic.201200173] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Indexed: 11/08/2022]
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12
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Characterization of the amicetin biosynthesis gene cluster from Streptomyces vinaceusdrappus NRRL 2363 implicates two alternative strategies for amide bond formation. Appl Environ Microbiol 2012; 78:2393-401. [PMID: 22267658 DOI: 10.1128/aem.07185-11] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Amicetin, an antibacterial and antiviral agent, belongs to a group of disaccharide nucleoside antibiotics featuring an α-(1→4)-glycoside bond in the disaccharide moiety. In this study, the amicetin biosynthesis gene cluster was cloned from Streptomyces vinaceusdrappus NRRL 2363 and localized on a 37-kb contiguous DNA region. Heterologous expression of the amicetin biosynthesis gene cluster in Streptomyces lividans TK64 resulted in the production of amicetin and its analogues, thereby confirming the identity of the ami gene cluster. In silico sequence analysis revealed that 21 genes were putatively involved in amicetin biosynthesis, including 3 for regulation and transportation, 10 for disaccharide biosynthesis, and 8 for the formation of the amicetin skeleton by the linkage of cytosine, p-aminobenzoic acid (PABA), and the terminal (+)-α-methylserine moieties. The inactivation of the benzoate coenzyme A (benzoate-CoA) ligase gene amiL and the N-acetyltransferase gene amiF led to two mutants that accumulated the same two compounds, cytosamine and 4-acetamido-3-hydroxybenzoic acid. These data indicated that AmiF functioned as an amide synthethase to link cytosine and PABA. The inactivation of amiR, encoding an acyl-CoA-acyl carrier protein transacylase, resulted in the production of plicacetin and norplicacetin, indicating AmiR to be responsible for attachment of the terminal methylserine moiety to form another amide bond. These findings implicated two alternative strategies for amide bond formation in amicetin biosynthesis.
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Doddapaneni K, Zahurancik W, Haushalter A, Yuan C, Jackman J, Wu Z. RCL hydrolyzes 2'-deoxyribonucleoside 5'-monophosphate via formation of a reaction intermediate. Biochemistry 2011; 50:4712-9. [PMID: 21510673 DOI: 10.1021/bi101742z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
RCL is an enzyme that catalyzes the N-glycosidic bond cleavage of purine 2'-deoxyribonucleoside 5'-monophosphates. Recently, the structures of both free wild type and GMP-bound mutant complex have been determined by multidimensional NMR, revealing a doubly wound α/β protein existing in a symmetric homodimer. In this work, we investigated the catalytic mechanism by rational site-directed mutagenesis, steady-state and pre-steady-state kinetics, ITC binding analysis, methanolysis, and NMR study. First, we provide kinetic evidence in support of the structural studies that RCL functions in a dimeric form, with an apparent dissociation constant around 0.5 μM in the presence of substrate dGMP. Second, among the eight residues under investigation, the highly conserved Glu93 is absolutely critical and Tyr13 is also important likely contributing to the chemical step, whereas Ser117 from the neighboring subunit and Ser87 could be the key residues for the phosphate group recognition. Lastly, we demonstrate by methanolysis study that the catalytic reaction proceeds via the formation of a reaction intermediate, which is subsequently hydrolyzed by solvent nucleophile resulting in the formation of normal product deoxyribose monophosphate (dR5P) or methoylated-dR5P. In conclusion, the current study provides mechanistic insights into a new class of nucleotide hydrolase, which resembles nucleoside 2'-deoxyribosyltransferases structurally and functionally but also possesses clear distinction.
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Affiliation(s)
- Kiran Doddapaneni
- Biochemistry Department, Ohio State University, Columbus, OH 43210, USA
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14
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Yang Y, Padilla A, Zhang C, Labesse G, Kaminski PA. Structural characterization of the mammalian deoxynucleotide N-hydrolase Rcl and its stabilizing interactions with two inhibitors. J Mol Biol 2009; 394:435-47. [PMID: 19822152 DOI: 10.1016/j.jmb.2009.10.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2009] [Revised: 09/25/2009] [Accepted: 10/06/2009] [Indexed: 11/25/2022]
Abstract
The gene Rcl encodes a deoxynucleoside 5'-monophosphate N-glycosidase that catalyzes the hydrolysis of the N-glycosidic bond of the nucleotide to give deoxyribose 5-phosphate and a nucleobase, preferentially a purine. This enzyme is over-expressed in several cancers, and its rate of expression is correlated to the degree of aggressiveness of tumors, which makes it a new and attractive therapeutic target. We describe here its structural characterization in the presence of two inhibitory substrate mimics. One of these ligands corresponds to the monophosphorylated form of acyclovir, which is used in the clinic. This study reveals an important ligand-induced stabilization of the dimer structure of the enzyme. The original structural features of Rcl will be helpful for designing new inhibitors.
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Affiliation(s)
- Yinshan Yang
- CNRS, UMR5048, Centre de Biochimie Structurale, Montpellier, France
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15
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Li L, Xu Z, Xu X, Wu J, Zhang Y, He X, Zabriskie TM, Deng Z. The mildiomycin biosynthesis: initial steps for sequential generation of 5-hydroxymethylcytidine 5'-monophosphate and 5-hydroxymethylcytosine in Streptoverticillium rimofaciens ZJU5119. Chembiochem 2008; 9:1286-94. [PMID: 18412191 DOI: 10.1002/cbic.200800008] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Mildiomycin (MIL) is a peptidyl nucleoside antibiotic with strong activity against powdery mildew disease of plants. We have cloned the MIL biosynthetic gene cluster in Streptoverticillum rimofaciens ZJU5119 and shown that this organism also produces the related antifungal compound, deshydroxymethyl mildiomycin (dHM-MIL). A cosmid genomic library was screened for a putative nucleotide hydrolase gene that is related to blsM from the blasticidin S cluster. Six cosmids were identified that contained a 3.5 kb DNA fragment that harbors a homologue of blsM. The sequence of the fragment revealed two open-reading frames that are likely to function in MIL formation: milA is a CMP hydroxymethylase gene and milB is the homologue of the CMP hydrolase gene blsM. Insertional disruption of milA abolished the production of MIL but not dHM-MIL, whereas a milB knockout strain did not produce either of the peptidyl nucleosides. Recombinant MilA was produced in E. coli and shown to specifically introduce a C-5 hydroxymethyl group on CMP, but it did not accept cytosine or dCMP as a substrate. MilB was also expressed and purified from E. coli and shown to efficiently hydrolyze both hydroxymethyl-CMP (HMCMP) and could accept CMP as an alternative substrate. The ratio of free HMC and cytosine released by MilB was ca. 9:1 in in vitro assays, and is consistent with the higher levels of MIL compared to dHM-MIL that are produced by Streptoverticillum rimofaciens.
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Affiliation(s)
- Li Li
- Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai 200030, China
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Ghiorghi YK, Zeller KI, Dang CV, Kaminski PA. The c-Myc target gene Rcl (C6orf108) encodes a novel enzyme, deoxynucleoside 5'-monophosphate N-glycosidase. J Biol Chem 2007; 282:8150-6. [PMID: 17234634 DOI: 10.1074/jbc.m610648200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
RCL is a c-Myc target with tumorigenic potential. Genome annotation predicted that RCL belonged to the N-deoxyribosyltransferase family. However, its putative relationship to this class of enzymes did not lead to its precise biochemical function. The purified native or N-terminal His-tagged recombinant rat RCL protein expressed in Escherichia coli exhibits the same enzyme activity, deoxynucleoside 5'-monophosphate N-glycosidase, never before described. dGMP appears to be the best substrate. RCL opens a new route in the nucleotide catabolic pathways by cleaving the N-glycosidic bond of deoxynucleoside 5'-monophosphates to yield two reaction products, deoxyribose 5-phosphate and purine or pyrimidine base. Biochemical studies show marked differences in the terms of the structure and catalytic mechanism between RCL and of its closest enzyme family neighbor, N-deoxyribosyltransferase. The reaction products of this novel enzyme activity have been implicated in purine or pyrimidine salvage, glycolysis, and angiogenesis, and hence are all highly relevant for tumorigenesis.
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Affiliation(s)
- Yoan Konto Ghiorghi
- Unité de Chimie Organique, CNRS Unité de Recherche Associée 2128, Institut Pasteur, 25-28 Rue du Dr. Roux, 75724 Paris Cedex 15, France
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