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Xu Z, Tian P. Rethinking Biosynthesis of Aclacinomycin A. Molecules 2023; 28:molecules28062761. [PMID: 36985733 PMCID: PMC10054333 DOI: 10.3390/molecules28062761] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/01/2023] [Accepted: 03/06/2023] [Indexed: 03/22/2023] Open
Abstract
Aclacinomycin A (ACM-A) is an anthracycline antitumor agent widely used in clinical practice. The current industrial production of ACM-A relies primarily on chemical synthesis and microbial fermentation. However, chemical synthesis involves multiple reactions which give rise to high production costs and environmental pollution. Microbial fermentation is a sustainable strategy, yet the current fermentation yield is too low to satisfy market demand. Hence, strain improvement is highly desirable, and tremendous endeavors have been made to decipher biosynthesis pathways and modify key enzymes. In this review, we comprehensively describe the reported biosynthesis pathways, key enzymes, and, especially, catalytic mechanisms. In addition, we come up with strategies to uncover unknown enzymes and improve the activities of rate-limiting enzymes. Overall, this review aims to provide valuable insights for complete biosynthesis of ACM-A.
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2
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Yang L, Zhou H, Chen G, Li H, Yang D, Pan L. Expression and Purification of Glycosyltransferase DnmS from Streptomyces peucetius ATCC 27952 and Study on Catalytic Characterization of Its Reverse Glycosyltransferase Reaction. Microorganisms 2023; 11:microorganisms11030762. [PMID: 36985335 PMCID: PMC10058486 DOI: 10.3390/microorganisms11030762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023] Open
Abstract
Anthracyclines are an important class of natural antitumor drugs. They have a conservative aromatic tetracycline backbone that is substituted with different deoxyglucoses. The deoxyglucoses are crucial for the biological activity of many bacterial natural products after the proper modification from glycosyltransferases (GTs). The difficulty in obtaining highly purified active GTs has prevented biochemical studies on natural product GTs. In this paper, a new Escherichia coli fusion plasmid pGro7′, which introduces the Streptomyces coelicolor chaperone genes groEL1, groES and groEL2, was constructed. The glycosyltransferase DnmS from Streptomyces peucetius ATCC 27952 was co-expressed with the plasmid pGro7′, and unprecedented high-efficiency and soluble expression of DnmS in the E. coli expression system was realized. Subsequently, the reverse glycosylation reaction characteristics of DnmS and DnmQ were verified. We found that DnmS and DnmQ had the highest enzyme activity when they participated in the reaction at the same time. These studies provide a strategy for the soluble expression of GTs in Streptomyces and confirm the reversibility of the catalytic reaction of GTs. This provides a powerful method for the production of active anthracyclines and to enhance the diversity of natural products.
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Affiliation(s)
- Liyan Yang
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning 530007, China
| | - Huimin Zhou
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning 530007, China
| | - Guiguang Chen
- College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Hongliang Li
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning 530007, China
| | - Dengfeng Yang
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning 530007, China
- Institute of Biology, Guangxi Academy of Sciences, Nanning 530007, China
- Correspondence: (D.Y.); (L.P.)
| | - Lixia Pan
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning 530007, China
- College of Food and Quality Engineering, Nanning University, Nanning 530200, China
- Correspondence: (D.Y.); (L.P.)
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3
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Mohideen FI, Nguyen LH, Richard JD, Ouadhi S, Kwan DH. In Vitro Reconstitution of the dTDP-l-Daunosamine Biosynthetic Pathway Provides Insights into Anthracycline Glycosylation. ACS Chem Biol 2022; 17:3331-3340. [PMID: 34751552 DOI: 10.1021/acschembio.1c00646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Many small molecule natural products are decorated with sugar moieties that are essential for their biological activity. A considerable number of natural product glycosides and their derivatives are clinically important therapeutics. Anthracyclines like daunorubicin and doxorubicin are examples of valuable glycosylated natural products used in medicine as potent anticancer agents. The sugar moiety, l-daunosamine (a highly modified deoxyhexose), plays a key role in the bioactivity of these molecules as evidenced by semisynthetic anthracycline derivatives such as epirubicin, wherein alteration in the configuration of a single stereocenter of the sugar unit generates a chemotherapeutic drug with lower cardiotoxicity. The nucleotide activated sugar donor that provides the l-daunosamine group for attachment to the natural product scaffold in the biosynthesis of these anthracyclines is dTDP-l-daunosamine. In an in vitro system, we have reconstituted the enzymes in the daunorubicin/doxorubicin pathway involved in the biosynthesis of dTDP-l-daunosamine. Through the study of the enzymatic steps in this reconstituted pathway, we have gained several insights into the assembly of this precursor including the identification of a major bottleneck and competing reactions. We carried out kinetic analysis of the aminotransferase that catalyzes a limiting step of the pathway. Our in vitro reconstituted pathway also provided a platform to test the combinatorial enzymatic synthesis of other dTDP-activated deoxyhexoses as potential tools for "glycodiversification" of natural products. To this end, we replaced the stereospecific ketoreductase that acts in the last step of dTDP-l-daunosamine biosynthesis with an enzyme from a heterologous pathway with opposite stereospecificity and found that it is active in the in vitro pathway, demonstrating the potential for the enzymatic synthesis of nucleotide-activated sugars with regio- and stereospecific tailoring.
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Affiliation(s)
- F Ifthiha Mohideen
- Department of Biology, Centre for Applied Synthetic Biology, and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec, Canada H4B 1R6.,PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Quebec City, Quebec, Canada G1V 0A6
| | - Lan Huong Nguyen
- Department of Biology, Centre for Applied Synthetic Biology, and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec, Canada H4B 1R6.,PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Quebec City, Quebec, Canada G1V 0A6
| | - Joël D Richard
- Department of Biology, Centre for Applied Synthetic Biology, and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec, Canada H4B 1R6
| | - Sara Ouadhi
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Quebec City, Quebec, Canada G1V 0A6.,Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec, Canada, H4B 1R6
| | - David H Kwan
- Department of Biology, Centre for Applied Synthetic Biology, and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec, Canada H4B 1R6.,PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Quebec City, Quebec, Canada G1V 0A6.,Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec, Canada, H4B 1R6
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4
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Carretero-Molina D, Ortiz-López FJ, Gren T, Oves-Costales D, Martín J, Román-Hurtado F, Sparholt Jørgensen T, de la Cruz M, Díaz C, Vicente F, Blin K, Reyes F, Weber T, Genilloud O. Discovery of gargantulides B and C, new 52-membered macrolactones from Amycolatopsis sp. Complete absolute stereochemistry of the gargantulide family. Org Chem Front 2022. [DOI: 10.1039/d1qo01480c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Gargantulides B and C are among the most complex bacterial polyketides discovered so far. A combination of NMR and genome-based bioinformatics analyses allowed us to complete and revise the absolute stereochemistry of the entire gargantulide family.
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Affiliation(s)
- Daniel Carretero-Molina
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Francisco Javier Ortiz-López
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Tetiana Gren
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, building 220, 2800 Kgs. Lyngby, Denmark
| | - Daniel Oves-Costales
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Jesús Martín
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Fernando Román-Hurtado
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Tue Sparholt Jørgensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, building 220, 2800 Kgs. Lyngby, Denmark
| | - Mercedes de la Cruz
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Caridad Díaz
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Francisca Vicente
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Kai Blin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, building 220, 2800 Kgs. Lyngby, Denmark
| | - Fernando Reyes
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, building 220, 2800 Kgs. Lyngby, Denmark
| | - Olga Genilloud
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
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Hulst MB, Grocholski T, Neefjes JJC, van Wezel GP, Metsä-Ketelä M. Anthracyclines: biosynthesis, engineering and clinical applications. Nat Prod Rep 2021; 39:814-841. [PMID: 34951423 DOI: 10.1039/d1np00059d] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Covering: January 1995 to June 2021Anthracyclines are glycosylated microbial natural products that harbour potent antiproliferative activities. Doxorubicin has been widely used as an anticancer agent in the clinic for several decades, but its use is restricted due to severe side-effects such as cardiotoxicity. Recent studies into the mode-of-action of anthracyclines have revealed that effective cardiotoxicity-free anthracyclines can be generated by focusing on histone eviction activity, instead of canonical topoisomerase II poisoning leading to double strand breaks in DNA. These developments have coincided with an increased understanding of the biosynthesis of anthracyclines, which has allowed generation of novel compound libraries by metabolic engineering and combinatorial biosynthesis. Coupled to the continued discovery of new congeners from rare Actinobacteria, a better understanding of the biology of Streptomyces and improved production methodologies, the stage is set for the development of novel anthracyclines that can finally surpass doxorubicin at the forefront of cancer chemotherapy.
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Affiliation(s)
- Mandy B Hulst
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.
| | - Thadee Grocholski
- Department of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - Jacques J C Neefjes
- Department of Cell and Chemical Biology and Oncode Institute, Leiden University Medical Centre, Leiden, The Netherlands
| | - Gilles P van Wezel
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.
| | - Mikko Metsä-Ketelä
- Department of Life Technologies, University of Turku, FIN-20014 Turku, Finland
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6
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Brown KV, Wandi BN, Metsä-Ketelä M, Nybo SE. Pathway Engineering of Anthracyclines: Blazing Trails in Natural Product Glycodiversification. J Org Chem 2020; 85:12012-12023. [PMID: 32938175 DOI: 10.1021/acs.joc.0c01863] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The anthracyclines are structurally diverse anticancer natural products that bind to DNA and poison the topoisomerase II-DNA complex in cancer cells. Rational modifications in the deoxysugar functionality are especially advantageous for synthesizing drugs with improved potency. Combinatorial biosynthesis of glycosyltransferases and deoxysugar synthesis enzymes is indispensable for the generation of glycodiversified anthracyclines. This Synopsis considers recent advances in glycosyltransferase structural biology and site-directed mutagenesis, pathway engineering, and deoxysugar combinatorial biosynthesis with a focus on the generation of "new-to-nature" anthracycline analogues.
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Affiliation(s)
- Katelyn V Brown
- Department of Pharmaceutical Sciences, College of Pharmacy, Ferris State University, Big Rapids, Michigan 49307, United States
| | - Benjamin Nji Wandi
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland
| | - Mikko Metsä-Ketelä
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland
| | - S Eric Nybo
- Department of Pharmaceutical Sciences, College of Pharmacy, Ferris State University, Big Rapids, Michigan 49307, United States
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7
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Costa OYA, de Hollander M, Pijl A, Liu B, Kuramae EE. Cultivation-independent and cultivation-dependent metagenomes reveal genetic and enzymatic potential of microbial community involved in the degradation of a complex microbial polymer. MICROBIOME 2020; 8:76. [PMID: 32482164 PMCID: PMC7265232 DOI: 10.1186/s40168-020-00836-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 03/31/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Cultivation-independent methods, including metagenomics, are tools for the exploration and discovery of biotechnological compounds produced by microbes in natural environments. Glycoside hydrolases (GHs) enzymes are extremely desired and important in the industry of production for goods and biofuel and removal of problematic biofilms and exopolysaccharide (EPS). Biofilms and EPS are complex, requiring a wide range of enzymes for a complete degradation. The aim of this study was to identify potential GH microbial producers and GH genes with biotechnological potential, using EPS-complex structure (WH15EPS) of Acidobacteria Granulicella sp. strain WH15 as an enrichment factor, in cultivation-independent and cultivation-dependent methods. We performed stable isotope probing (SIP) combined with metagenomics on topsoil litter amended with WH15EPS and coupled solid culture-EPS amended medium with metagenomics. RESULTS SIP metagenome analysis of the soil litter demonstrated that phyla Proteobacteria, Actinobacteria, Acidobacteria, and Planctomycetes were the most abundant in WH15EPS amended and unamended treatments. The enrichment cultures in solid culture medium coupled to metagenomics demonstrated an enrichment in Proteobacteria, and the metagenome assembly of this enrichment cultures resulted in 4 metagenome-assembled genomes (MAGs) of microbes with low identity (42-86%) to known microorganisms. Among all carbohydrate-active enzymes (CAZymes) retrieved genes, glycoside transferase (GT) was the most abundant family, either in culture-independent or culture-based metagenome datasets. Within the glycoside hydrolases (GHs), GH13 was the most abundant family in both metagenome datasets. In the "heavy" fraction of the culture-independent metagenome SIP dataset, GH109 (α-N-acetylgalactosaminidases), GH117 (agarases), GH50 (agarases), GH32 (invertases and inulinases), GH17 (endoglucanases), and GH71 (mutanases) families were more abundant in comparison with the controls. Those GH families are affiliated to microorganism that are probably capable to degrade WH15EPS and potentially applicable for biofilm deconstruction. Subsequent in culture-based metagenome, the assembled 4 MAGs (unclassified Proteobacteria) also contained GH families of interest, involving mannosidases, lysozymes, galactosidases, and chitinases. CONCLUSIONS We demonstrated that functional diversity induced by the presence of WH15EPS in both culture-independent and culture-dependent approaches was enriched in GHs, such as amylases and endoglucanases that could be applied in chemical, pharmaceutical, and food industrial sectors. Furthermore, WH15EPS may be used for the investigation and isolation of yet unknown taxa, such as unclassified Proteobacteria and Planctomycetes, increasing the number of current cultured bacterial representatives with potential biotechnological traits. Video Abstract.
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Affiliation(s)
- Ohana Y A Costa
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, Netherlands
- Institute of Biology (IBL), Leiden University, Leiden, The Netherlands
| | - Mattias de Hollander
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, Netherlands
| | - Agata Pijl
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, Netherlands
| | - Binbin Liu
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, Hebei, China.
| | - Eiko E Kuramae
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, Netherlands.
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Mrudulakumari Vasudevan U, Lee EY. Flavonoids, terpenoids, and polyketide antibiotics: Role of glycosylation and biocatalytic tactics in engineering glycosylation. Biotechnol Adv 2020; 41:107550. [PMID: 32360984 DOI: 10.1016/j.biotechadv.2020.107550] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/19/2020] [Accepted: 04/24/2020] [Indexed: 02/07/2023]
Abstract
Flavonoids, terpenoids, and polyketides are structurally diverse secondary metabolites used widely as pharmaceuticals and nutraceuticals. Most of these molecules exist in nature as glycosides, in which sugar residues act as a decisive factor in their architectural complexity and bioactivity. Engineering glycosylation through selective trimming or extension of the sugar residues in these molecules is a prerequisite to their commercial production as well to creating novel derivatives with specialized functions. Traditional chemical glycosylation methods are tedious and can offer only limited end-product diversity. New in vitro and in vivo biocatalytic tools have emerged as outstanding platforms for engineering glycosylation in these three classes of secondary metabolites to create a large repertoire of versatile glycoprofiles. As knowledge has increased about secondary metabolite-associated promiscuous glycosyltransferases and sugar biosynthetic machinery, along with phenomenal progress in combinatorial biosynthesis, reliable industrial production of unnatural secondary metabolites has gained momentum in recent years. This review highlights the significant role of sugar residues in naturally occurring flavonoids, terpenoids, and polyketide antibiotics. General biocatalytic tools used to alter the identity and pattern of sugar molecules are described, followed by a detailed illustration of diverse strategies used in the past decade to engineer glycosylation of these valuable metabolites, exemplified with commercialized products and patents. By addressing the challenges involved in current bio catalytic methods and considering the perspectives portrayed in this review, exceptional drugs, flavors, and aromas from these small molecules could come to dominate the natural-product industry.
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Affiliation(s)
| | - Eun Yeol Lee
- Department of Chemical Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea.
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Yeo WL, Heng E, Tan LL, Lim YW, Ching KC, Tsai DJ, Jhang YW, Lauderdale TL, Shia KS, Zhao H, Ang EL, Zhang MM, Lim YH, Wong FT. Biosynthetic engineering of the antifungal, anti-MRSA auroramycin. Microb Cell Fact 2020; 19:3. [PMID: 31906943 PMCID: PMC6943886 DOI: 10.1186/s12934-019-1274-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 12/21/2019] [Indexed: 12/12/2022] Open
Abstract
Using an established CRISPR-Cas mediated genome editing technique for streptomycetes, we explored the combinatorial biosynthesis potential of the auroramycin biosynthetic gene cluster in Streptomyces roseosporous. Auroramycin is a potent anti-MRSA polyene macrolactam. In addition, auroramycin has antifungal activities, which is unique among structurally similar polyene macrolactams, such as incednine and silvalactam. In this work, we employed different engineering strategies to target glycosylation and acylation biosynthetic machineries within its recently elucidated biosynthetic pathway. Auroramycin analogs with variations in C-, N- methylation, hydroxylation and extender units incorporation were produced and characterized. By comparing the bioactivity profiles of five of these analogs, we determined that unique disaccharide motif of auroramycin is essential for its antimicrobial bioactivity. We further demonstrated that C-methylation of the 3, 5-epi-lemonose unit, which is unique among structurally similar polyene macrolactams, is key to its antifungal activity.
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Affiliation(s)
- Wan Lin Yeo
- Metabolic Engineering, Functional Molecules & Polymers, Institute of Chemical and Engineering Sciences, A*STAR, Biopolis, Singapore
| | - Elena Heng
- Molecular Engineering Laboratory, Institute of Bioengineering and Nanotechnology, A*STAR, Biopolis, Singapore
| | - Lee Ling Tan
- Molecular Engineering Laboratory, Institute of Bioengineering and Nanotechnology, A*STAR, Biopolis, Singapore
| | - Yi Wee Lim
- Integrated Bio & Organic Chemistry, Functional Molecules & Polymers, Institute of Chemical and Engineering Sciences, A*STAR, Biopolis, Singapore
| | - Kuan Chieh Ching
- Integrated Bio & Organic Chemistry, Functional Molecules & Polymers, Institute of Chemical and Engineering Sciences, A*STAR, Biopolis, Singapore
| | - De-Juin Tsai
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes (NHRI), Zhunan, Miaoli, Taiwan
| | - Yi Wun Jhang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes (NHRI), Zhunan, Miaoli, Taiwan
| | - Tsai-Ling Lauderdale
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes (NHRI), Zhunan, Miaoli, Taiwan
| | - Kak-Shan Shia
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes (NHRI), Zhunan, Miaoli, Taiwan
| | - Huimin Zhao
- Departments of Chemical and Biomolecular Engineering, Chemistry, Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Ee Lui Ang
- Metabolic Engineering, Functional Molecules & Polymers, Institute of Chemical and Engineering Sciences, A*STAR, Biopolis, Singapore
| | - Mingzi M Zhang
- Metabolic Engineering, Functional Molecules & Polymers, Institute of Chemical and Engineering Sciences, A*STAR, Biopolis, Singapore.,Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Yee Hwee Lim
- Integrated Bio & Organic Chemistry, Functional Molecules & Polymers, Institute of Chemical and Engineering Sciences, A*STAR, Biopolis, Singapore.
| | - Fong T Wong
- Molecular Engineering Laboratory, Institute of Bioengineering and Nanotechnology, A*STAR, Biopolis, Singapore.
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10
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Greule A, Stok JE, De Voss JJ, Cryle MJ. Unrivalled diversity: the many roles and reactions of bacterial cytochromes P450 in secondary metabolism. Nat Prod Rep 2019; 35:757-791. [PMID: 29667657 DOI: 10.1039/c7np00063d] [Citation(s) in RCA: 140] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Covering: 2000 up to 2018 The cytochromes P450 (P450s) are a superfamily of heme-containing monooxygenases that perform diverse catalytic roles in many species, including bacteria. The P450 superfamily is widely known for the hydroxylation of unactivated C-H bonds, but the diversity of reactions that P450s can perform vastly exceeds this undoubtedly impressive chemical transformation. Within bacteria, P450s play important roles in many biosynthetic and biodegradative processes that span a wide range of secondary metabolite pathways and present diverse chemical transformations. In this review, we aim to provide an overview of the range of chemical transformations that P450 enzymes can catalyse within bacterial secondary metabolism, with the intention to provide an important resource to aid in understanding of the potential roles of P450 enzymes within newly identified bacterial biosynthetic pathways.
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Affiliation(s)
- Anja Greule
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia. and EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
| | - Jeanette E Stok
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia.
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia.
| | - Max J Cryle
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia. and EMBL Australia, Monash University, Clayton, Victoria 3800, Australia and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.
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11
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Siitonen V, Nji Wandi B, Törmänen AP, Metsä-Ketelä M. Enzymatic Synthesis of the C-Glycosidic Moiety of Nogalamycin R. ACS Chem Biol 2018; 13:2433-2437. [PMID: 30114358 PMCID: PMC6203184 DOI: 10.1021/acschembio.8b00658] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Carbohydrate moieties are essential for the biological activity of anthracycline anticancer agents such as nogalamycin, which contains l-nogalose and l-nogalamine units. The former of these is attached through a canonical O-glycosidic linkage, but the latter is connected via an unusual dual linkage composed of C-C and O-glycosidic bonds. In this work, we have utilized enzyme immobilization techniques and synthesized l-rhodosamine-thymidine diphosphate (TDP) from α-d-glucose-1-TDP using seven enzymes. In a second step, we assembled the dual linkage system by attaching the aminosugar to an anthracycline aglycone acceptor using the glycosyl transferase SnogD and the α-ketoglutarate dependent oxygenase SnoK. Furthermore, our work indicates that the auxiliary P450-type protein SnogN facilitating glycosylation is surprisingly associated with attachment of the neutral sugar l-nogalose rather than the aminosugar l-nogalamine in nogalamycin biosynthesis.
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Affiliation(s)
- Vilja Siitonen
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland
| | - Benjamin Nji Wandi
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland
| | | | - Mikko Metsä-Ketelä
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland
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12
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Cooperative Involvement of Glycosyltransferases in the Transfer of Amino Sugars during the Biosynthesis of the Macrolactam Sipanmycin by Streptomyces sp. Strain CS149. Appl Environ Microbiol 2018; 84:AEM.01462-18. [PMID: 30006405 DOI: 10.1128/aem.01462-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 07/11/2018] [Indexed: 12/22/2022] Open
Abstract
Macrolactams comprise a family of natural compounds with important bioactivities, such as antibiotic, antifungal, and antiproliferative activities. Sipanmycins A and B are two novel members of this family, with two sugar moieties attached to the aglycon. In the related macrolactam vicenistatin, the sugar moiety has been proven to be essential for cytotoxicity. In this work, the gene cluster responsible for the biosynthesis of sipanmycins (sip cluster) in Streptomyces sp. strain CS149 is described and the steps involved in the glycosylation of the final compounds unraveled. Also, the cooperation of two different glycosyltransferases in each glycosylation step is demonstrated. Additionally, the essential role of SipO2 as an auxiliary protein in the incorporation of the second deoxy sugar is addressed. In light of the results obtained by the generation of mutant strains and in silico characterization of the sip cluster, a biosynthetic pathway for sipanmycins and the two deoxy sugars attached is proposed. Finally, the importance of the hydroxyl group at C-10 of the macrolactam ring and the sugar moieties for cytotoxicity and antibiotic activity of sipanmycins is shown.IMPORTANCE The rapid emergence of infectious diseases and multiresistant pathogens has increased the necessity for new bioactive compounds; thus, novel strategies have to be developed to find them. Actinomycetes isolated in symbiosis with insects have attracted attention in recent years as producers of metabolites with important bioactivities. Sipanmycins are glycosylated macrolactams produced by Streptomyces sp. CS149, isolated from leaf-cutting ants, and show potent cytotoxic activity. Here, we characterize the sip cluster and propose a biosynthetic pathway for sipanmycins. As far as we know, it is the first time that the cooperation between two different glycosyltransferases is demonstrated to be strictly necessary for the incorporation of the same sugar. Also, a third protein with homology to P450 monooxygenases, SipO2, is shown to be essential in the second glycosylation step, forming a complex with the glycosyltransferase pair SipS9-SipS14.
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13
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Harrus D, Kellokumpu S, Glumoff T. Crystal structures of eukaryote glycosyltransferases reveal biologically relevant enzyme homooligomers. Cell Mol Life Sci 2018; 75:833-848. [PMID: 28932871 PMCID: PMC11105277 DOI: 10.1007/s00018-017-2659-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 08/24/2017] [Accepted: 09/13/2017] [Indexed: 12/31/2022]
Abstract
Glycosyltransferases (GTases) transfer sugar moieties to proteins, lipids or existing glycan or polysaccharide molecules. GTases form an important group of enzymes in the Golgi, where the synthesis and modification of glycoproteins and glycolipids take place. Golgi GTases are almost invariably type II integral membrane proteins, with the C-terminal globular catalytic domain residing in the Golgi lumen. The enzymes themselves are divided into 103 families based on their sequence homology. There is an abundance of published crystal structures of GTase catalytic domains deposited in the Protein Data Bank (PDB). All of these represent either of the two main characteristic structural folds, GT-A or GT-B, or present a variation thereof. Since GTases can function as homomeric or heteromeric complexes in vivo, we have summarized the structural features of the dimerization interfaces in crystal structures of GTases, as well as considered the biochemical data available for these enzymes. For this review, we have considered all 898 GTase crystal structures in the Protein Data Bank and highlight the dimer formation characteristics of various GTases based on 24 selected structures.
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Affiliation(s)
- Deborah Harrus
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, PO Box 5400, 90014, Oulu, Finland
| | - Sakari Kellokumpu
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, PO Box 5400, 90014, Oulu, Finland
| | - Tuomo Glumoff
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, PO Box 5400, 90014, Oulu, Finland.
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14
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Salem SM, Weidenbach S, Rohr J. Two Cooperative Glycosyltransferases Are Responsible for the Sugar Diversity of Saquayamycins Isolated from Streptomyces sp. KY 40-1. ACS Chem Biol 2017; 12:2529-2534. [PMID: 28892347 DOI: 10.1021/acschembio.7b00453] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Glycosyltransferases are key enzymes involved in the biosynthesis of valuable natural products providing an excellent drug-tailoring tool. Herein, we report the identification of two cooperative glycosyltransferases from the sqn gene cluster directing the biosynthesis of saquayamycins in Streptomyces sp. KY40-1: SqnG1 and SqnG2. Gene inactivation of sqnG1 leads to 50-fold decrease in saquayamycin production, while inactivation of sqnG2 leads to complete production loss, suggesting that SqnG2 acts as dual O- and C-glycosyltransferase. Gene inactivation of a third putative glycosyltransferase-encoding gene, sqnG3, does not affect saquayamycin production in a major way, suggesting that SqnG3 has no or a supportive role in glycosylation. The data indicate that SqnG1 and SqnG2 are solely and possibly cooperatively responsible for the sugar diversity observed in saquayamycins 1-7. This is the first evidence of a glycosyltransferase system showing codependence to achieve dual O- and C-glycosyltransferase activity, utilizing NDP-activated d-olivose, l-rhodinose, as well as an unusual amino sugar, presumably 3,6-dideoxy-l-idosamine.
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Affiliation(s)
- Shaimaa M. Salem
- Department of Pharmaceutical
Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Stevi Weidenbach
- Department of Pharmaceutical
Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Jürgen Rohr
- Department of Pharmaceutical
Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
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15
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Rudolf JD, Chang CY, Ma M, Shen B. Cytochromes P450 for natural product biosynthesis in Streptomyces: sequence, structure, and function. Nat Prod Rep 2017; 34:1141-1172. [PMID: 28758170 PMCID: PMC5585785 DOI: 10.1039/c7np00034k] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: up to January 2017Cytochrome P450 enzymes (P450s) are some of the most exquisite and versatile biocatalysts found in nature. In addition to their well-known roles in steroid biosynthesis and drug metabolism in humans, P450s are key players in natural product biosynthetic pathways. Natural products, the most chemically and structurally diverse small molecules known, require an extensive collection of P450s to accept and functionalize their unique scaffolds. In this review, we survey the current catalytic landscape of P450s within the Streptomyces genus, one of the most prolific producers of natural products, and comprehensively summarize the functionally characterized P450s from Streptomyces. A sequence similarity network of >8500 P450s revealed insights into the sequence-function relationships of these oxygen-dependent metalloenzymes. Although only ∼2.4% and <0.4% of streptomycete P450s have been functionally and structurally characterized, respectively, the study of streptomycete P450s involved in the biosynthesis of natural products has revealed their diverse roles in nature, expanded their catalytic repertoire, created structural and mechanistic paradigms, and exposed their potential for biomedical and biotechnological applications. Continued study of these remarkable enzymes will undoubtedly expose their true complement of chemical and biological capabilities.
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Affiliation(s)
- Jeffrey D Rudolf
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
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16
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Engineered jadomycin analogues with altered sugar moieties revealing JadS as a substrate flexible O-glycosyltransferase. Appl Microbiol Biotechnol 2017; 101:5291-5300. [PMID: 28429060 DOI: 10.1007/s00253-017-8256-y] [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: 01/23/2017] [Revised: 03/12/2017] [Accepted: 03/16/2017] [Indexed: 12/29/2022]
Abstract
Glycosyltransferases (GTs)-mediated glycodiversification studies have drawn significant attention recently, with the goal of generating bioactive compounds with improved pharmacological properties by diversifying the appended sugars. The key to achieving glycodiversification is to identify natural and/or engineered flexible GTs capable of acting upon a broad range of substrates. Here, we report the use of a combinatorial biosynthetic approach to probe the substrate flexibility of JadS, the GT in jadomycin biosynthesis, towards different non-native NDP-sugar substrates, enabling us to identify six jadomycin B analogues with different sugar moieties. Further structural engineering by precursor-directed biosynthesis allowed us to obtain 11 new jadomycin analogues. Our results for the first time show that JadS is a flexible O-GT that can utilize both L- and D- sugars as donor substrates, and tolerate structural changes at the C2, C4 and C6 positions of the sugar moiety. JadS may be further exploited to generate novel glycosylated jadomycin molecules in future glycodiversification studies.
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17
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Wu H, Li W, Xin C, Zhang C, Wang Y, Ren S, Ren M, Zhao W, Yuan L, Xu Z, Yuan H, Geng M, Zhang L, Weaver DT, Zhang B. In vivo investigation to the macrolide-glycosylating enzyme pair DesVII/DesVIII in Saccharopolyspora erythraea. Appl Microbiol Biotechnol 2015; 100:2257-66. [PMID: 26552796 DOI: 10.1007/s00253-015-7036-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 09/07/2015] [Accepted: 09/17/2015] [Indexed: 11/25/2022]
Abstract
Glycosyltransferase DesVII and its auxiliary partner DesVIII from Streptomyces venezulae, homologs of EryCIII and EryCII in Saccharopolyspora erythraea, have previously been demonstrated to be flexible on their substrates in vitro. Herein, we investigated their in vivo function by interspecies complementation in the mutant strains of Sac. erythraea A226. As desVII and desVIII were concomitantly expressed in the ΔeryCIII mutant, the erythromycin A (Er-A) production was restored. Interestingly, co-expression of desVII and desVIII in the ΔeryBV mutant exhibited an increased Er-A yield by 15 % in comparison to A226. Hence, DesVII/DesVIII not only replaced EryCIII to upload D-desosamine to C5 position of 3-O-mycarosyl erythronolide B (MEB) but also in vivo attached L-mycarose, not D-desosamine to C3 position of erythronolide B (EB) with a higher activity than EryBV. Furthermore, expression of desVII in ΔeryCIII and ΔeryBV-CIII partially restored the Er-A production; however, no Er-A was detected while desVII was expressed in ΔeryBV. It was implicated that DesVII coupled with EryCII to form the DesVII/EryCII complex for attaching above two deoxysugars in the absence of EryCIII in Sac. erythraea. In addition, when desVII and desVIII were co-expressed in ΔeryBV-CII, Er-A was recovered with a lower yield than ΔeryBV-CIII. Our study presents an opportunity with Sac. erythraea as a cell factory for macrolide glycodiversification.
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Affiliation(s)
- Hang Wu
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Weiwei Li
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Chen Xin
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Congming Zhang
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Yansheng Wang
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Shaohua Ren
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Min Ren
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Wei Zhao
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Li Yuan
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Zhongdong Xu
- School of Life Sciences, Hefei Normal University, Hefei, 230601, China
| | - Hualing Yuan
- School of Life Sciences, Hefei Normal University, Hefei, 230601, China
| | - Ming Geng
- School of Life Sciences, Hefei Normal University, Hefei, 230601, China
| | - Lixin Zhang
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China. .,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - David T Weaver
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China.
| | - Buchang Zhang
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China.
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18
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Liang DM, Liu JH, Wu H, Wang BB, Zhu HJ, Qiao JJ. Glycosyltransferases: mechanisms and applications in natural product development. Chem Soc Rev 2015; 44:8350-74. [DOI: 10.1039/c5cs00600g] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Glycosylation reactions mainly catalyzed by glycosyltransferases (Gts) occur almost everywhere in the biosphere, and always play crucial roles in vital processes.
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Affiliation(s)
- Dong-Mei Liang
- Department of Pharmaceutical Engineering
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Jia-Heng Liu
- Department of Pharmaceutical Engineering
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Hao Wu
- Department of Pharmaceutical Engineering
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Bin-Bin Wang
- Department of Pharmaceutical Engineering
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Hong-Ji Zhu
- Department of Pharmaceutical Engineering
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Jian-Jun Qiao
- Department of Pharmaceutical Engineering
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
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19
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Gloster TM. Advances in understanding glycosyltransferases from a structural perspective. Curr Opin Struct Biol 2014; 28:131-41. [PMID: 25240227 PMCID: PMC4330554 DOI: 10.1016/j.sbi.2014.08.012] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Accepted: 08/20/2014] [Indexed: 01/23/2023]
Abstract
Glycosyltransferases are the enzymes that catalyse glycosidic bond formation. Structural and kinetic studies are important for understanding function. Bacterial oligosaccharyltransferase structure aids understanding of N-linked glycosylation. Structure of human O-GlcNAc transferase gives mechanistic insights. Landmark structure of cellulose synthase membrane protein complex.
Glycosyltransferases (GTs), the enzymes that catalyse glycosidic bond formation, create a diverse range of saccharides and glycoconjugates in nature. Understanding GTs at the molecular level, through structural and kinetic studies, is important for gaining insights into their function. In addition, this understanding can help identify those enzymes which are involved in diseases, or that could be engineered to synthesize biologically or medically relevant molecules. This review describes how structural data, obtained in the last 3–4 years, have contributed to our understanding of the mechanisms of action and specificity of GTs. Particular highlights include the structure of a bacterial oligosaccharyltransferase, which provides insights into N-linked glycosylation, the structure of the human O-GlcNAc transferase, and the structure of a bacterial integral membrane protein complex that catalyses the synthesis of cellulose, the most abundant organic molecule in the biosphere.
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Affiliation(s)
- Tracey M Gloster
- Biomedical Sciences Research Complex, North Haugh, University of St Andrews, St Andrews, Fife KY16 9ST, UK.
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20
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Isiorho EA, Jeon BS, Kim NH, Liu HW, Keatinge-Clay AT. Structural studies of the spinosyn forosaminyltransferase, SpnP. Biochemistry 2014; 53:4292-301. [PMID: 24945604 PMCID: PMC4095934 DOI: 10.1021/bi5003629] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Spinosyns A and D (spinosad) are complex polyketide natural products biosynthesized through the cooperation of a modular polyketide synthase and several tailoring enzymes. SpnP catalyzes the final tailoring step, transferring forosamine from a TDP-D-forosamine donor substrate to a spinosyn pseudoaglycone acceptor substrate. Sequence analysis indicated that SpnP belongs to a small group of glycosyltransferases (GTs) that require an auxiliary protein for activation. However, unlike other GTs in this subgroup, no putative auxiliary protein gene could be located in the biosynthetic gene cluster. To learn more about SpnP, the structures of SpnP and its complex with TDP were determined to 2.50 and 3.15 Å resolution, respectively. Binding of TDP causes the reordering of several residues in the donor substrate pocket. SpnP possesses a structural feature that has only been previously observed in the related glycosyltransferase EryCIII, in which it mediates association with the auxiliary protein EryCII. This motif, H-X-R-X5-D-X5-R-X12-20-D-P-X3-W-L-X12-18-E-X4-G, may be predictive of glycosyltransferases that interact with an auxiliary protein. A reverse glycosyl transfer assay demonstrated that SpnP possesses measurable activity in the absence of an auxiliary protein. Our data suggest that SpnP can bind its donor substrate by itself but that the glycosyl transfer reaction is facilitated by an auxiliary protein that aids in the correct folding of a flexible loop surrounding the pseudoaglycone acceptor substrate-binding pocket.
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Affiliation(s)
- Eta A Isiorho
- Division of Medicinal Chemistry, College of Pharmacy, and ‡Department of Chemistry and Biochemistry, The University of Texas at Austin , Austin, Texas 78712, United States
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21
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Tracking down biotransformation to the genetic level: identification of a highly flexible glycosyltransferase from Saccharothrix espanaensis. Appl Environ Microbiol 2013; 79:5224-32. [PMID: 23793643 DOI: 10.1128/aem.01652-13] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Saccharothrix espanaensis is a member of the order Actinomycetales. The genome of the strain has been sequenced recently, revealing 106 glycosyltransferase genes. In this paper, we report the detection of a glycosyltransferase from Saccharothrix espanaensis which is able to rhamnosylate different phenolic compounds targeting different positions of the molecules. The gene encoding the flexible glycosyltransferase is not located close to a natural product biosynthetic gene cluster. Therefore, the native function of this enzyme might be not the biosynthesis of a secondary metabolite but the glycosylation of internal and external natural products as part of a defense mechanism.
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22
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Abstract
Cytochrome P450 enzymes primarily catalyze mixed-function oxidation reactions, plus some reductions and rearrangements of oxygenated species, e.g. prostaglandins. Most of these reactions can be rationalized in a paradigm involving Compound I, a high-valent iron-oxygen complex (FeO(3+)), to explain seemingly unusual reactions, including ring couplings, ring expansion and contraction, and fusion of substrates. Most P450s interact with flavoenzymes or iron-sulfur proteins to receive electrons from NAD(P)H. In some cases, P450s are fused to protein partners. Other P450s catalyze non-redox isomerization reactions. A number of permutations on the P450 theme reveal the diversity of cytochrome P450 form and function.
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Affiliation(s)
- F Peter Guengerich
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA.
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23
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Role of PelF in pel polysaccharide biosynthesis in Pseudomonas aeruginosa. Appl Environ Microbiol 2013; 79:2968-78. [PMID: 23435893 DOI: 10.1128/aem.03666-12] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas aeruginosa produces three exopolysaccharides, Psl, Pel, and alginate, that play vital roles in biofilm formation. Pel is a glucose-rich, cellulose-like exopolysaccharide. The essential Pel biosynthesis proteins are encoded by seven genes, pelA to pelG. Bioinformatics analysis suggests that PelF is a cytosolic glycosyltransferase. Here, experimental evidence was provided to support this PelF function. A UDP-glucose dehydrogenase-based assay was developed to quantify UDP-glucose. UDP-glucose was proposed as the substrate for PelF. The isogenic pelF deletion mutant accumulated 1.8 times more UDP-glucose in its cytosol than the wild type. This suggested that PelF, which was found localized in the cystosol, uses UDP-glucose as substrate. Additionally, in vitro experiments confirmed that PelF uses UDP-glucose as substrate. To analyze the functional roles of conserved residues in PelF, site-directed mutagenesis was performed. The presence of the EX7E motif is characteristic for various glycosyltransferase families, and in PelF, E405/E413 are the conserved residues in this motif. Replacement of E405 with A resulted in a reduction of PelF activity to 30.35% ± 3.15% (mean ± standard deviation) of the wild-type level, whereas replacement of the second E, E413, with A did not produce a significant change in the activity of PelF. Moreover, replacement of both E residues did not result in a loss of PelF function, but replacement of the conserved R325 or K330 with A resulted in a complete loss of PelF activity. Overall, our data show that PelF is a soluble glycosyltransferase that uses UDP-glucose as the substrate for Pel synthesis and that conserved residues R325 and K330 are important for the activity of PelF.
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24
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Davidsen JM, Bartley DM, Townsend CA. Non-ribosomal propeptide precursor in nocardicin A biosynthesis predicted from adenylation domain specificity dependent on the MbtH family protein NocI. J Am Chem Soc 2013; 135:1749-59. [PMID: 23330869 DOI: 10.1021/ja307710d] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Nocardicin A is a monocyclic β-lactam isolated from the actinomycete Nocardia uniformis that shows moderate antibiotic activity against a broad spectrum of gram-negative bacteria. The monobactams are of renewed interest due to emerging gram-negative strains resistant to clinically available penicillins and cephalosporins. Like isopenicillin N, nocardicin A has a tripeptide core of non-ribosomal origin. Paradoxically, the nocardicin A gene cluster encodes two non-ribosomal peptide synthetases (NRPSs), NocA and NocB, predicted to encode five modules pointing to a pentapeptide precursor in nocardicin A biosynthesis, unless module skipping or other nonlinear reactions are occurring. Previous radiochemical incorporation experiments and bioinformatic analyses predict the incorporation of p-hydroxy-L-phenylglycine (L-pHPG) into positions 1, 3, and 5 and L-serine into position 4. No prediction could be made for position 2. Multidomain constructs of each module were heterologous expressed in Escherichia coli for determination of the adenylation domain (A-domain) substrate specificity using the ATP/PPi exchange assay. Three of the five A-domains, from modules 1, 2, and 4, required the addition of stoichiometric amounts of MbtH family protein NocI to detect exchange activity. On the basis of these analyses, the predicted product of the NocA and NocB NRPSs is L-pHPG-L-Arg-D-pHPG-L-Ser-L-pHPG, a pentapeptide. Despite being flanked by non-proteinogenic amino acids, proteolysis of this pentapeptide by trypsin yields two fragments from cleavage at the C terminus of the L-Arg residue. Thus, a proteolytic step is likely involved in the biosynthesis of nocardicin A, a rare but precedented editing event in the formation of non-ribosomal natural products that is supported by the identification of trypsin-encoding genes in N. uniformis.
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Affiliation(s)
- Jeanne M Davidsen
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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25
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Claesson M, Siitonen V, Dobritzsch D, Metsä-Ketelä M, Schneider G. Crystal structure of the glycosyltransferase SnogD from the biosynthetic pathway of nogalamycin in Streptomyces nogalater. FEBS J 2012; 279:3251-63. [PMID: 22804797 DOI: 10.1111/j.1742-4658.2012.08711.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The glycosyltransferase SnogD from Streptomyces nogalater transfers a nogalamine moiety to the metabolic intermediate 3',4'-demethoxynogalose-1-hydroxynogalamycinone during the final steps of biosynthesis of the aromatic polyketide nogalamycin. The crystal structure of recombinant SnogD, as an apo-enzyme and with a bound nucleotide, 2-deoxyuridine-5'-diphosphate, was determined to 2.6 Å resolution. Reductive methylation of SnogD was crucial for reproducible preparation of diffraction quality crystals due to creation of an additional intermolecular salt bridge between methylated lysine residue Lys384 and Glu374* from an adjacent molecule in the crystal lattice. SnogD is a dimer both in solution and in the crystal, and the enzyme subunit displays a fold characteristic of the GT-B family of glycosyltransferases. Binding of the nucleotide is associated with rearrangement of two active-site loops. Site-directed mutagenesis shows that two active-site histidine residues, His25 and His301, are critical for the glycosyltransferase activities of SnogD both in vivo and in vitro. The crystal structures and the functional data are consistent with a role for His301 in binding of the diphosphate group of the sugar donor substrate, and a function of His25 as a catalytic base in the glycosyl transfer reaction.
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Affiliation(s)
- Magnus Claesson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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