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Sun H, Kong R, Zhu D, Lu M, Ji Q, Liew CW, Lescar J, Zhong G, Liang ZX. Products of the iterative polyketide synthases in 9- and 10-membered enediyne biosynthesis. Chem Commun (Camb) 2009:7399-401. [PMID: 20024241 DOI: 10.1039/b916751j] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The iterative polyketide synthases from the biosynthetic pathways of three enediyne natural products were examined. The results established the all-trans conjugated pentadecaheptanene as the only major product shared by the PKSs. The experiments further revealed some intrinsic differences among the PKSs by demonstrating the formation of different by-products.
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Affiliation(s)
- Huihua Sun
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
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52
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Horsman GP, Van Lanen SG, Shen B. Iterative type I polyketide synthases for enediyne core biosynthesis. Methods Enzymol 2009; 459:97-112. [PMID: 19362637 DOI: 10.1016/s0076-6879(09)04605-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Enediyne natural products are extremely potent antitumor antibiotics with a remarkable core structure consisting of two acetylenic groups conjugated to a double bond within either a 9- or 10-membered ring. Biosynthesis of this fascinating scaffold is catalyzed in part by an unusual iterative type I polyketide synthase, PKSE, that is shared among all enediyne biosynthetic pathways whose gene clusters have been sequenced to date. The PKSE is unusual in two main respects: (1) it contains an acyl carrier protein (ACP) domain with no sequence homology to any known proteins, and (2) it is self-phosphopantetheinylated by an integrated phosphopantetheinyl transferase (PPTase) domain. The unusual domain architecture and biochemistry of the PKSE hold promise both for the rapid identification of new enediyne natural products and for obtaining fundamental catalytic insights into enediyne biosynthesis. This chapter describes methods for rapid PCR-based classification of conserved enediyne biosynthetic genes, heterologous production of 9-membered PKSE proteins and isolation of the resulting polyene product, and in vitro characterization of the PKSE ACP domain.
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Affiliation(s)
- Geoffrey P Horsman
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
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54
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Kotaka M, Kong R, Qureshi I, Ho QS, Sun H, Liew CW, Goh LP, Cheung P, Mu Y, Lescar J, Liang ZX. Structure and catalytic mechanism of the thioesterase CalE7 in enediyne biosynthesis. J Biol Chem 2009; 284:15739-49. [PMID: 19357082 PMCID: PMC2708871 DOI: 10.1074/jbc.m809669200] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2008] [Revised: 03/19/2009] [Indexed: 11/06/2022] Open
Abstract
The biosynthesis of the enediyne moiety of the antitumor natural product calicheamicin involves an iterative polyketide synthase (CalE8) and other ancillary enzymes. In the proposed mechanism for the early stage of 10-membered enediyne biosynthesis, CalE8 produces a carbonyl-conjugated polyene with the assistance of a putative thioesterase (CalE7). We have determined the x-ray crystal structure of CalE7 and found that the subunit adopts a hotdog fold with an elongated and kinked substrate-binding channel embedded between two subunits. The 1.75-A crystal structure revealed that CalE7 does not contain a critical catalytic residue (Glu or Asp) conserved in other hotdog fold thioesterases. Based on biochemical and site-directed mutagenesis studies, we proposed a catalytic mechanism in which the conserved Arg(37) plays a crucial role in the hydrolysis of the thioester bond, and that Tyr(29) and a hydrogen-bonded water network assist the decarboxylation of the beta-ketocarboxylic acid intermediate. Moreover, computational docking suggested that the substrate-binding channel binds a polyene substrate that contains a single cis double bond at the C4/C5 position, raising the possibility that the C4=C5 double bond in the enediyne moiety could be generated by the iterative polyketide synthase. Together, the results revealed a hotdog fold thioesterase distinct from the common type I and type II thioesterases associated with polyketide biosynthesis and provided interesting insight into the enediyne biosynthetic mechanism.
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Affiliation(s)
- Masayo Kotaka
- From the School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Rong Kong
- From the School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Insaf Qureshi
- From the School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Qin Shi Ho
- From the School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Huihua Sun
- From the School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Chong Wai Liew
- From the School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Lan Pei Goh
- From the School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Peter Cheung
- From the School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Yuguang Mu
- From the School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Julien Lescar
- From the School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Zhao-Xun Liang
- From the School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
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56
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Hu Y, Al-Mestarihi A, Grimes CL, Kahne D, Bachmann BO. A unifying nitrososynthase involved in nitrosugar biosynthesis. J Am Chem Soc 2009; 130:15756-7. [PMID: 18983146 DOI: 10.1021/ja8051415] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Herein we describe the cloning, functional expression and initial characterization of ORF36 from Micromonospora carbonacae var. africana and rubN8 from Streptomyces achromogenes var. rubradiris. The purified enzymes play the same role, the double-oxidation of TDP-evernosamine to TDP-evernitrosose in the everninomycin and rubradirin pathways, respectively.
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Affiliation(s)
- Yunfeng Hu
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
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57
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Olano C, Méndez C, Salas JA. Antitumor compounds from actinomycetes: from gene clusters to new derivatives by combinatorial biosynthesis. Nat Prod Rep 2009; 26:628-60. [PMID: 19387499 DOI: 10.1039/b822528a] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Covering: up to October 2008. Antitumor compounds produced by actinomycetes and novel derivatives generated by combinatorial biosynthesis are reviewed (with 318 references cited.) The different structural groups for which the relevant gene clusters have been isolated and characterized are reviewed, with a description of the strategies used for the generation of the novel derivatives and the activities of these compounds against tumor cell lines.
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Affiliation(s)
- Carlos Olano
- Departamento de Biología Funcional and Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A.), Universidad de Oviedo, 33006, Oviedo, Spain
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58
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McCoy JG, Johnson HD, Singh S, Bingman CA, Lei IK, Thorson JS, Phillips GN. Structural characterization of CalO2: a putative orsellinic acid P450 oxidase in the calicheamicin biosynthetic pathway. Proteins 2009; 74:50-60. [PMID: 18561189 DOI: 10.1002/prot.22131] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Although bacterial iterative Type I polyketide synthases are now known to participate in the biosynthesis of a small set of diverse natural products, the subsequent downstream modification of the resulting polyketide products remains poorly understood. Toward this goal, we report the X-ray structure determination at 2.5 A resolution and preliminary characterization of the putative orsellenic acid P450 oxidase (CalO2) involved in calicheamicin biosynthesis. These studies represent the first crystal structure for a P450 involved in modifying a bacterial iterative Type I polyketide product and suggest the CalO2-catalyzed step may occur after CalO3-catalyzed iodination and may also require a coenzyme A- (CoA) or acyl carrier protein- (ACP) bound substrate. Docking studies also reveal a putative docking site within CalO2 for the CLM orsellinic acid synthase (CalO5) ACP domain which involves a well-ordered helix along the CalO2 active site cavity that is unique compared with other P450 structures.
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Affiliation(s)
- Jason G McCoy
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706-1544, USA
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59
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Wang L, Hu Y, Zhang Y, Wang S, Cui Z, Bao Y, Jiang W, Hong B. Role of sgcR3 in positive regulation of enediyne antibiotic C-1027 production of Streptomyces globisporus C-1027. BMC Microbiol 2009; 9:14. [PMID: 19159491 PMCID: PMC2657911 DOI: 10.1186/1471-2180-9-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2008] [Accepted: 01/22/2009] [Indexed: 12/03/2022] Open
Abstract
Background C-1027, produced by Streptomyces globisporus C-1027, is one of the most potent antitumoral agents. The biosynthetic gene cluster of C-1027, previously cloned and sequenced, contains at least three putative regulatory genes, i.e. sgcR1, sgcR2 and sgcR3. The predicted gene products of these genes share sequence similarities to StrR, regulators of AraC/XylS family and TylR. The purpose of this study was to investigate the role of sgcR3 in C-1027 biosynthesis. Results Overexpression of sgcR3 in S. globisporus C-1027 resulted in a 30–40% increase in C-1027 production. Consistent with this, disruption of sgcR3 abolished C-1027 production. Complementation of the sgcR3-disrupted strain R3KO with intact sgcR3 gene could restore C-1027 production. The results from real time RT-PCR analysis in R3KO mutant and wild type strain indicated that not only transcripts of biosynthetic structural genes such as sgcA1 and sgcC4, but also putative regulatory genes, sgcR1 and sgcR2, were significantly decreased in R3KO mutant. The cross-complementation studies showed that sgcR1R2 could functionally complement sgcR3 disruption in trans. Purified N-terminal His10-tagged SgcR3 showed specific DNA-binding activity to the promoter region of sgcR1R2. Conclusion The role of SgcR3 has been proved to be a positive regulator of C-1027 biosynthesis in S. globisporus C-1027. SgcR3 occupies a higher level than SgcR1 and SgcR2 in the regulatory hierarchy that controls C-1027 production and activates the transcription of sgcR1 and sgcR2 by binding directly to the promoter region of sgcR1R2.
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Affiliation(s)
- Lifei Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China.
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60
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Johnson HD, Thorson JS. Characterization of CalE10, the N-oxidase involved in calicheamicin hydroxyaminosugar formation. J Am Chem Soc 2008; 130:17662-3. [PMID: 19055330 PMCID: PMC2704561 DOI: 10.1021/ja807557a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
As the first in vitro characterization of a sugar N-oxidase, this study establishes CalE10 as the key oxidase involved in calicheamicin hydroxylamino glycoside formation. This study confirms that oxidation occurs at the sugar nucleotide stage prior to glycosyltransfer, and substrate specificity studies reveal CalE10-catalyzed oxidation to be regiospecific and to present trace amounts of the corresponding nitrosugar in vitro. This work also sets a precedent for the future study of other N-oxidases involved in hydroxylamino-, nitroso-, and/or nitrosugar formation.
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Affiliation(s)
- Heather D. Johnson
- Division of Pharmaceutical Sciences and University of Wisconsin National Drug Discovery Group, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Jon S. Thorson
- Division of Pharmaceutical Sciences and University of Wisconsin National Drug Discovery Group, University of Wisconsin-Madison, Madison, Wisconsin 53706
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61
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Zhang C, Bitto E, Goff RD, Singh S, Bingman CA, Griffith BR, Albermann C, Phillips GN, Thorson JS. Biochemical and structural insights of the early glycosylation steps in calicheamicin biosynthesis. CHEMISTRY & BIOLOGY 2008; 15:842-53. [PMID: 18721755 PMCID: PMC2965851 DOI: 10.1016/j.chembiol.2008.06.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2008] [Revised: 06/12/2008] [Accepted: 06/20/2008] [Indexed: 10/21/2022]
Abstract
The enediyne antibiotic calicheamicin (CLM) gamma(1)(I) is a prominent antitumor agent that is targeted to DNA by a novel aryltetrasaccharide comprised of an aromatic unit and four unusual carbohydrates. Herein we report the heterologous expression and the biochemical characterization of the two "internal" glycosyltransferases CalG3 and CalG2 and the structural elucidation of an enediyne glycosyltransferase (CalG3). In conjunction with the previous characterization of the "external" CLM GTs CalG1 and CalG4, this study completes the functional assignment of all four CLM GTs, extends the utility of enediyne GT-catalyzed reaction reversibility, and presents conclusive evidence of a sequential glycosylation pathway in CLM biosynthesis. This work also reveals the common GT-B structural fold can now be extended to include enediyne GTs.
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Affiliation(s)
- Changsheng Zhang
- Laboratory for Biosynthetic Chemistry, Pharmaceutical Sciences Division, School of Pharmacy, UW-National Cooperative Drug Discovery Group Program, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705-2222, USA
| | - Eduard Bitto
- Department of Biochemistry, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53706-1544, USA
| | - Randal D. Goff
- Laboratory for Biosynthetic Chemistry, Pharmaceutical Sciences Division, School of Pharmacy, UW-National Cooperative Drug Discovery Group Program, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705-2222, USA
| | - Shanteri Singh
- Laboratory for Biosynthetic Chemistry, Pharmaceutical Sciences Division, School of Pharmacy, UW-National Cooperative Drug Discovery Group Program, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705-2222, USA
| | - Craig A. Bingman
- Department of Biochemistry, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53706-1544, USA
| | - Byron R. Griffith
- Laboratory for Biosynthetic Chemistry, Pharmaceutical Sciences Division, School of Pharmacy, UW-National Cooperative Drug Discovery Group Program, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705-2222, USA
| | - Christoph Albermann
- Laboratory for Biosynthetic Chemistry, Pharmaceutical Sciences Division, School of Pharmacy, UW-National Cooperative Drug Discovery Group Program, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705-2222, USA
| | - George N. Phillips
- Department of Biochemistry, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53706-1544, USA
| | - Jon S. Thorson
- Laboratory for Biosynthetic Chemistry, Pharmaceutical Sciences Division, School of Pharmacy, UW-National Cooperative Drug Discovery Group Program, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705-2222, USA
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62
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Kong R, Goh LP, Liew CW, Ho QS, Murugan E, Li B, Tang K, Liang ZX. Characterization of a carbonyl-conjugated polyene precursor in 10-membered enediyne biosynthesis. J Am Chem Soc 2008; 130:8142-3. [PMID: 18529057 DOI: 10.1021/ja8019643] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have characterized a linear carbonyl-conjugated polyene generated by the iterative polyketide synthase (CalE8) involved in the biosynthesis of the 10-membered enediyne core of calicheamicin. The results provide insight into the mysterious biosynthetic mechanism of the unique enediyne. The carbonyl-conjugated polyene differs from the precursor for 9-membered enediyne, suggesting that the divergence of enediyne biosynthesis starts at the PKS stage.
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Affiliation(s)
- Rong Kong
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
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63
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Timmons SC, Thorson JS. Increasing carbohydrate diversity via amine oxidation: aminosugar, hydroxyaminosugar, nitrososugar, and nitrosugar biosynthesis in bacteria. Curr Opin Chem Biol 2008; 12:297-305. [PMID: 18424273 PMCID: PMC2517148 DOI: 10.1016/j.cbpa.2008.03.017] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2008] [Revised: 03/19/2008] [Accepted: 03/19/2008] [Indexed: 12/14/2022]
Abstract
Bacterial secondary metabolites often contain carbohydrate attachments that play a significant role in conferring biological activity. A small proportion of these bioactive sugars are derived from aminosugar oxidation to ultimately provide hydroxyaminosugars, nitrososugars, and nitrosugars. Recent advances in the elucidation of hydroxyaminosugar-, nitrososugar-, and nitrosugar-containing natural product gene clusters have enabled the proposal of biosynthetic pathways, the in vitro characterization of aminosugar oxidases, and the structure determination of key enzymes. This article focuses upon the key enzymatic transformations in aminosugar, hydroxyaminosugar, nitrososugar, and nitrosugar biosynthesis, as well as the unique chemical reactivity of alkoxyaminosugars, with a particular focus upon developments within the past two years.
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Affiliation(s)
- Shannon C. Timmons
- Laboratory for Biosynthetic Chemistry, Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705; University of Wisconsin National Cooperative Drug Discovery Group Program
| | - Jon S. Thorson
- Laboratory for Biosynthetic Chemistry, Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705; University of Wisconsin National Cooperative Drug Discovery Group Program
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