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Huo T, Zhao X, Cheng Z, Wei J, Zhu M, Dou X, Jiao N. Late-stage modification of bioactive compounds: Improving druggability through efficient molecular editing. Acta Pharm Sin B 2024; 14:1030-1076. [PMID: 38487004 PMCID: PMC10935128 DOI: 10.1016/j.apsb.2023.11.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/14/2023] [Accepted: 11/13/2023] [Indexed: 03/17/2024] Open
Abstract
Synthetic chemistry plays an indispensable role in drug discovery, contributing to hit compounds identification, lead compounds optimization, candidate drugs preparation, and so on. As Nobel Prize laureate James Black emphasized, "the most fruitful basis for the discovery of a new drug is to start with an old drug"1. Late-stage modification or functionalization of drugs, natural products and bioactive compounds have garnered significant interest due to its ability to introduce diverse elements into bioactive compounds promptly. Such modifications alter the chemical space and physiochemical properties of these compounds, ultimately influencing their potency and druggability. To enrich a toolbox of chemical modification methods for drug discovery, this review focuses on the incorporation of halogen, oxygen, and nitrogen-the ubiquitous elements in pharmacophore components of the marketed drugs-through late-stage modification in recent two decades, and discusses the state and challenges faced in these fields. We also emphasize that increasing cooperation between chemists and pharmacists may be conducive to the rapid discovery of new activities of the functionalized molecules. Ultimately, we hope this review would serve as a valuable resource, facilitating the application of late-stage modification in the construction of novel molecules and inspiring innovative concepts for designing and building new drugs.
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Affiliation(s)
- Tongyu Huo
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xinyi Zhao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Zengrui Cheng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Jialiang Wei
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
- Changping Laboratory, Beijing 102206, China
| | - Minghui Zhu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xiaodong Dou
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Ning Jiao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
- Changping Laboratory, Beijing 102206, China
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, East China Normal University, Shanghai 200062, China
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2
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Adhikari A, Shakya S, Shrestha S, Aryal D, Timalsina KP, Dhakal D, Khatri Y, Parajuli N. Biocatalytic role of cytochrome P450s to produce antibiotics: A review. Biotechnol Bioeng 2023; 120:3465-3492. [PMID: 37691185 DOI: 10.1002/bit.28548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 08/15/2023] [Accepted: 08/26/2023] [Indexed: 09/12/2023]
Abstract
Cytochrome P450s belong to a family of heme-binding monooxygenases, which catalyze regio- and stereospecific functionalisation of C-H, C-C, and C-N bonds, including heteroatom oxidation, oxidative C-C bond cleavages, and nitrene transfer. P450s are considered useful biocatalysts for the production of pharmaceutical products, fine chemicals, and bioremediating agents. Despite having tremendous biotechnological potential, being heme-monooxygenases, P450s require either autologous or heterologous redox partner(s) to perform chemical transformations. Randomly distributed P450s throughout a bacterial genome and devoid of particular redox partners in natural products biosynthetic gene clusters (BGCs) showed an extra challenge to reveal their pharmaceutical potential. However, continuous efforts have been made to understand their involvement in antibiotic biosynthesis and their modification, and this review focused on such BGCs. Here, particularly, we have discussed the role of P450s involved in the production of macrolides and aminocoumarin antibiotics, nonribosomal peptide (NRPSs) antibiotics, ribosomally synthesized and post-translationally modified peptide (RiPPs) antibiotics, and others. Several reactions catalyzed by P450s, as well as the role of their redox partners involved in the BGCs of various antibiotics and their derivatives, have been primarily addressed in this review, which would be useful in further exploration of P450s for the biosynthesis of new therapeutics.
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Affiliation(s)
- Anup Adhikari
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Sajan Shakya
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Shreesti Shrestha
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Dipa Aryal
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Kavi Prasad Timalsina
- Department of Biotechnology, National College, Tribhuvan University, Kathmandu, Nepal
| | - Dipesh Dhakal
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida, USA
| | | | - Niranjan Parajuli
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
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3
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Malinga NA, Nzuza N, Padayachee T, Syed PR, Karpoormath R, Gront D, Nelson DR, Syed K. An Unprecedented Number of Cytochrome P450s Are Involved in Secondary Metabolism in Salinispora Species. Microorganisms 2022; 10:microorganisms10050871. [PMID: 35630316 PMCID: PMC9143469 DOI: 10.3390/microorganisms10050871] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/15/2022] [Accepted: 04/19/2022] [Indexed: 01/04/2023] Open
Abstract
Cytochrome P450 monooxygenases (CYPs/P450s) are heme thiolate proteins present in species across the biological kingdoms. By virtue of their broad substrate promiscuity and regio- and stereo-selectivity, these enzymes enhance or attribute diversity to secondary metabolites. Actinomycetes species are well-known producers of secondary metabolites, especially Salinispora species. Despite the importance of P450s, a comprehensive comparative analysis of P450s and their role in secondary metabolism in Salinispora species is not reported. We therefore analyzed P450s in 126 strains from three different species Salinispora arenicola, S. pacifica, and S. tropica. The study revealed the presence of 2643 P450s that can be grouped into 45 families and 103 subfamilies. CYP107 and CYP125 families are conserved, and CYP105 and CYP107 families are bloomed (a P450 family with many members) across Salinispora species. Analysis of P450s that are part of secondary metabolite biosynthetic gene clusters (smBGCs) revealed Salinispora species have an unprecedented number of P450s (1236 P450s-47%) part of smBGCs compared to other bacterial species belonging to the genera Streptomyces (23%) and Mycobacterium (11%), phyla Cyanobacteria (8%) and Firmicutes (18%) and the classes Alphaproteobacteria (2%) and Gammaproteobacteria (18%). A peculiar characteristic of up to six P450s in smBGCs was observed in Salinispora species. Future characterization Salinispora species P450s and their smBGCs have the potential for discovering novel secondary metabolites.
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Affiliation(s)
- Nsikelelo Allison Malinga
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (N.A.M.); (N.N.); (T.P.)
| | - Nomfundo Nzuza
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (N.A.M.); (N.N.); (T.P.)
| | - Tiara Padayachee
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (N.A.M.); (N.N.); (T.P.)
| | - Puleng Rosinah Syed
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (P.R.S.); (R.K.)
| | - Rajshekhar Karpoormath
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (P.R.S.); (R.K.)
| | - Dominik Gront
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland;
| | - David R. Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Correspondence: (D.R.N.); (K.S.); Tel.: +19-014-488-303 (D.R.N.); +27-035-902-6857 (K.S.)
| | - Khajamohiddin Syed
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (N.A.M.); (N.N.); (T.P.)
- Correspondence: (D.R.N.); (K.S.); Tel.: +19-014-488-303 (D.R.N.); +27-035-902-6857 (K.S.)
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Liu Z, Xu J, Liu H, Wang Y. Engineered EryF hydroxylase improving heterologous polyketide erythronolide B production in Escherichia coli. Microb Biotechnol 2022; 15:1598-1609. [PMID: 35174640 PMCID: PMC9049603 DOI: 10.1111/1751-7915.14000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 12/22/2021] [Indexed: 11/27/2022] Open
Abstract
In the last two decades, the production of complex polyketides such as erythromycin and its precursor 6-deoxyerythronolide B (6-dEB) was demonstrated feasible in Escherichia coli. Although the heterologous production of polyketide skeleton 6-dEB has reached 210 mg l-1 in E. coli, the yield of its post-modification products erythromycins remains to be improved. Cytochrome P450EryF catalyses the C6 hydroxylation of 6-dEB to form erythronolide B (EB), which is the initial rate-limiting modification in a multi-step pathway to convert 6-dEB into erythromycin. Here, we engineered hydroxylase EryF to improve the production of heterologous polyketide EB in E. coli. By comparative analysis of various versions of P450EryFs, we confirmed the optimal SaEryF for the biosynthesis of EB. Further mutation of SaEryF based on the crystal structure of SaEryF and homology modelling of AcEryF and AeEryF afforded the enhancement of EB production. The designed mutant of SaEryF, I379V, achieved the yield of 131 mg l-1 EB, which was fourfold to that produced by wild-type SaEryF. Moreover, the combined mutagenesis of multiple residues led to further boost the EB concentration by another 41%, which laid the foundation for efficient heterologous biosynthesis of erythromycin or other complex polyketides.
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Affiliation(s)
- Zhifeng Liu
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Jianlin Xu
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.,University of Chinese Academy of Sciences, Beijing, 100039, China.,State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Haili Liu
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yong Wang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
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5
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Teshima A, Kondo H, Tanaka Y, Nindita Y, Misaki Y, Konaka Y, Itakura Y, Tonokawa T, Kinashi H, Arakawa K. Substrate specificity of two cytochrome P450 monooxygenases involved in lankamycin biosynthesis. Biosci Biotechnol Biochem 2021; 85:115-125. [PMID: 33577670 DOI: 10.1093/bbb/zbaa063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 10/14/2020] [Indexed: 11/13/2022]
Abstract
To elucidate the gross lankamycin biosynthetic pathway including two cytochrome P450 monooxygenases, LkmK and LkmF, we constructed two double mutants of P450 genes in combination with glycosyltransferase genes, lkmL and lkmI. An aglycon 8,15-dideoxylankanolide, a possible substrate for LkmK, was prepared from an lkmK-lkmL double mutant, while a monoglycoside 3-O-l-arcanosyl-8-deoxylankanolide, a substrate for LkmF, was from an lkmF-lkmI double mutant. Bioconversion of lankamycin derivatives was performed in the Escherichia coli recombinant for LkmK and the Streptomyces lividans recombinant for LkmF, respectively. LkmK catalyzes the C-15 hydroxylation on all 15-deoxy derivatives, including 8,15-dideoxylankanolide (a possible substrate), 8,15-dideoxylankamycin, and 15-deoxylankamycin, suggesting the relaxed substrate specificity of LkmK. On the other hand, LkmF hydroxylates the C-8 methine of 3-O-l-anosyl-8-deoxylankanolide. Other 8-deoxy lankamycin/lankanolide derivatives were not oxidized, suggesting the importance of a C-3 l-arcanosyl moiety for substrate recognition by LkmF in lankamycin biosynthesis. Thus, LkmF has a strict substrate specificity in lankamycin biosynthesis.
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Affiliation(s)
- Aiko Teshima
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Hiroshima, Japan.,Hiroshima Research Center for Healthy Aging (HiHA), Hiroshima University, Hiroshima, Japan
| | - Hisashi Kondo
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Hiroshima, Japan
| | - Yu Tanaka
- Hiroshima Research Center for Healthy Aging (HiHA), Hiroshima University, Hiroshima, Japan.,Unit of Biotechnology, Division of Biological and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Yosi Nindita
- Hiroshima Research Center for Healthy Aging (HiHA), Hiroshima University, Hiroshima, Japan.,Unit of Biotechnology, Division of Biological and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Yuya Misaki
- Hiroshima Research Center for Healthy Aging (HiHA), Hiroshima University, Hiroshima, Japan.,Unit of Biotechnology, Division of Biological and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Yuji Konaka
- Faculty of Engineering, Hiroshima University, Hiroshima, Japan
| | | | | | - Haruyasu Kinashi
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Hiroshima, Japan
| | - Kenji Arakawa
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Hiroshima, Japan.,Hiroshima Research Center for Healthy Aging (HiHA), Hiroshima University, Hiroshima, Japan.,Unit of Biotechnology, Division of Biological and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
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6
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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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7
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Abstract
The atomistic change of C( sp3)-H to C( sp3)-O can have a profound impact on the physical and biological properties of small molecules. Traditionally, chemical synthesis has relied on pre-existing functionality to install new functionality, and directed approaches to C-H oxidation are an extension of this logic. The impact of developing undirected C-H oxidation reactions with controlled site-selectivity is that scientists gain the ability to diversify complex structures at sites remote from existing functionality, without having to carry out individual de novo syntheses. This Perspective offers a historical view of why, as recently as 2007, it was thought that the differences between aliphatic C-H bonds of the same bond type (for example, 2° aliphatic) were not large enough to distinguish them preparatively with small-molecule catalysis in the absence of directing groups or molecular recognition elements. We give an account of the discovery of Fe(PDP)-catalyzed non-directed aliphatic C-H hydroxylations and how the electronic, steric, and stereoelectronic rules for predicting site-selectivity that emerged have affected a shift in how the chemical community views the reactivity among these bonds. The discovery that site-selectivity could be altered by tuning the catalyst [i.e., Fe(CF3-PDP)] with no changes to the substrate or reaction now gives scientists the ability to exert control on the site of oxidation on a range of functionally and topologically diverse compounds. Collectively, these findings have made possible the emerging area of late-stage C-H functionalizations for streamlining synthesis and derivatizing complex molecules.
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Affiliation(s)
- M. Christina White
- Roger Adams Laboratory, Department of Chemistry, University of Illinois
at Urbana—Champaign, Urbana, Illinois 61801, United States
| | - Jinpeng Zhao
- Roger Adams Laboratory, Department of Chemistry, University of Illinois
at Urbana—Champaign, Urbana, Illinois 61801, United States
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Filling the Gaps in the Kirromycin Biosynthesis: Deciphering the Role of Genes Involved in Ethylmalonyl-CoA Supply and Tailoring Reactions. Sci Rep 2018; 8:3230. [PMID: 29459765 PMCID: PMC5818483 DOI: 10.1038/s41598-018-21507-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 02/06/2018] [Indexed: 11/08/2022] Open
Abstract
Kirromycin is the main product of the soil-dwelling Streptomyces collinus Tü 365. The elucidation of the biosynthetic pathway revealed that the antibiotic is synthesised via a unique combination of trans-/cis-AT type I polyketide synthases and non-ribosomal peptide synthetases (PKS I/NRPS). This was the first example of an assembly line integrating the three biosynthetic principles in one pathway. However, information about other enzymes involved in kirromycin biosynthesis remained scarce. In this study, genes encoding tailoring enzymes KirM, KirHVI, KirOI, and KirOII, and the putative crotonyl-CoA reductase/carboxylase KirN were deleted, complemented, and the emerged products analysed by HPLC-HRMS and MS/MS. Derivatives were identified in mutants ΔkirM, ΔkirHVI, ΔkirOI, and ΔkirOII. The products of ΔkirOI, ΔkirOII, and kirHVI were subjected to 2D-NMR for structure elucidation. Our results enabled functional assignment of those enzymes, demonstrating their involvement in kirromycin tailoring. In the ΔkirN mutant, the production of kirromycin was significantly decreased. The obtained data enabled us to clarify the putative roles of the studied enzymes, ultimately allowing us to fill many of the missing gaps in the biosynthesis of the complex antibiotic. Furthermore, this collection of mutants can serve as a toolbox for generation of new kirromycins.
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9
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Yu D, Xu F, Shao L, Zhan J. A specific cytochrome P450 hydroxylase in herboxidiene biosynthesis. Bioorg Med Chem Lett 2014; 24:4511-4514. [DOI: 10.1016/j.bmcl.2014.07.078] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 07/25/2014] [Accepted: 07/29/2014] [Indexed: 10/24/2022]
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10
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Deoxysugar pathway interchange for erythromycin analogues heterologously produced through Escherichia coli. Metab Eng 2013; 20:92-100. [PMID: 24060454 DOI: 10.1016/j.ymben.2013.09.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 08/30/2013] [Accepted: 09/11/2013] [Indexed: 01/16/2023]
Abstract
The overall erythromycin biosynthetic pathway can be sub-divided into macrocyclic polyketide formation and polyketide tailoring to produce the final bioactive molecule. In this study, the native deoxysugar tailoring reactions were exchanged for the purpose of demonstrating the production of alternative final erythromycin compounds. Both the d-desosamine and l-mycarose deoxysugar pathways were replaced with the alternative d-mycaminose and d-olivose pathways to produce new erythromycin analogues through the Escherichia coli heterologous system. Both analogues exhibited bioactivity against multiple antibiotic-resistant Bacillus subtilis strains. Besides demonstrating an intrinsic flexibility for the biosynthetic system to accommodate alternative tailoring pathways, the results offer an initial attempt to leverage the E. coli platform for erythromycin analogue production.
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11
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Müller R, Wink J. Future potential for anti-infectives from bacteria - how to exploit biodiversity and genomic potential. Int J Med Microbiol 2013; 304:3-13. [PMID: 24119567 DOI: 10.1016/j.ijmm.2013.09.004] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The early stages of antibiotic development include the identification of novel hit compounds. Since actinomycetes and myxobacteria are still the most important natural sources of active metabolites, we provide an overview on these producers and discuss three of the most promising approaches toward finding novel anti-infectives from microorganisms. These are defined as the use of biodiversity to find novel producers, the variation of culture conditions and induction of silent genes, and the exploitation of the genomic potential of producers via "genome mining". Challenges that exist beyond compound discovery are outlined in the last section.
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Affiliation(s)
- Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), P.O. Box 151150, 66041 Saarbrücken, Germany; Helmholtz Centre for Infectious Research (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Joachim Wink
- Helmholtz Centre for Infectious Research (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany.
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12
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Capturing Linear Intermediates and C-Terminal Variants during Maturation of the Thiopeptide GE2270. ACTA ACUST UNITED AC 2013; 20:1067-77. [DOI: 10.1016/j.chembiol.2013.07.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 07/05/2013] [Accepted: 07/10/2013] [Indexed: 11/18/2022]
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13
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Sezutsu H, Le Goff G, Feyereisen R. Origins of P450 diversity. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120428. [PMID: 23297351 DOI: 10.1098/rstb.2012.0428] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The P450 enzymes maintain a conserved P450 fold despite a considerable variation in sequence. The P450 family even includes proteins that lack the single conserved cysteine and are therefore no longer haem-thiolate proteins. The mechanisms of successive gene duplications leading to large families in plants and animals are well established. Comparisons of P450 CYP gene clusters in related species illustrate the rapid changes in CYPome sizes. Examples of CYP copy number variation with effects on fitness are emerging, and these provide an opportunity to study the proximal causes of duplication or pseudogenization. Birth and death models can explain the proliferation of CYP genes that is amply illustrated by the sequence of every new genome. Thus, the distribution of P450 diversity within the CYPome of plants and animals, a few families with many genes (P450 blooms) and many families with few genes, follows similar power laws in both groups. A closer look at some families with few genes shows that these, often single member families, are not stable during evolution. The enzymatic prowess of P450 may predispose them to switch back and forth between metabolism of critical structural or signal molecules and metabolism dedicated to environmental response.
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Affiliation(s)
- Hideki Sezutsu
- National Institute of Agrobiological Sciences, 1-2 Ohwashi, Tsukuba, Ibaraki 3058634, Japan
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14
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Wilson MC, Gulder TAM, Mahmud T, Moore BS. Shared biosynthesis of the saliniketals and rifamycins in Salinispora arenicola is controlled by the sare1259-encoded cytochrome P450. J Am Chem Soc 2011; 132:12757-65. [PMID: 20726561 DOI: 10.1021/ja105891a] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Saliniketals A and B are unusual polyketides from the marine actinomycete Salinispora arenicola that inhibit ornithine decarboxylase induction. The structural similarities between the saliniketals and the ansa chain of the potent rifamycin antibiotics, which co-occur in the fermentation broth, suggest a common origin between the two compound classes. Using PCR-directed mutagenesis, chemical complementation studies, and stable isotope feeding experiments, we showed that the saliniketals are byproducts of the rifamycin biosynthetic pathway diverging at the stage of 34a-deoxyrifamycin W. Our results suggest that a single enzyme, the cytochrome P450 monooxygenase encoded by sare1259, catalyzes multiple oxidative rearrangement reactions on 34a-deoxyrifamyin W to yield both the saliniketal and rifamycin structural classes.
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Affiliation(s)
- Micheal C Wilson
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0204, USA
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15
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Diez B, Mellado E, Rodriguez M, Fouces R, Barredo JL. Recombinant microorganisms for industrial production of antibiotics. Biotechnol Bioeng 2009; 55:216-26. [PMID: 18636459 DOI: 10.1002/(sici)1097-0290(19970705)55:1<216::aid-bit22>3.0.co;2-i] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The enhancement of industrial antibiotic yield has been achieved through technological innovations and traditional strain improvement programs based on random mutation and screening. The development of recombinant DNA techniques and their application to antibiotic producing microorganisms has allowed yield increments and the design of biosynthetic pathways giving rise to new antibiotics. Genetic manipulations of the cephalosporin producing fungus Cephalosporium acremonium have included yield improvements, accomplished increasing biosynthetic gene dosage or enhancing oxygen uptake, and new biosynthetic capacities as 7-aminocephalosporanic acid (7-ACA) or penicillin G production. Similarly, in Penicillium chrysogenum, the industrial penicillin producing fungus, heterologous expression of cephalosporin biosynthetic genes has led to the biosynthesis of adipyl-7-aminodeacetoxycephalosporanic acid (adipyl-7-ADCA) and adipyl-7-ACA, compounds that can be transformed into the economically relevant 7-ADCA and 7-ACA intermediates. Escherichia coli expression of the genes encoding D-amino acid oxidase and cephalosporin acylase activities has simplified the bioconversion of cephalosporin C into 7-ACA, eliminating the use of organic solvents. The genetic manipulation of antibiotic producing actinomycetes has allowed productivity increments and the development of new hybrid antibiotics. A legal framework has been developed for the confined manipulation of genetically modified organisms.
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Affiliation(s)
- B Diez
- Laboratorio de Ingeniería Genética, Antibióticos S. A. U., 24080 León, Spain
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16
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Adrio JL, Demain AL. Recombinant organisms for production of industrial products. Bioeng Bugs 2009; 1:116-31. [PMID: 21326937 DOI: 10.4161/bbug.1.2.10484] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Revised: 10/30/2009] [Accepted: 11/02/2009] [Indexed: 11/19/2022] Open
Abstract
A revolution in industrial microbiology was sparked by the discoveries of ther double-stranded structure of DNA and the development of recombinant DNA technology. Traditional industrial microbiology was merged with molecular biology to yield improved recombinant processes for the industrial production of primary and secondary metabolites, protein biopharmaceuticals and industrial enzymes. Novel genetic techniques such as metabolic engineering, combinatorial biosynthesis and molecular breeding techniques and their modifications are contributing greatly to the development of improved industrial processes. In addition, functional genomics, proteomics and metabolomics are being exploited for the discovery of novel valuable small molecules for medicine as well as enzymes for catalysis. The sequencing of industrial microbal genomes is being carried out which bodes well for future process improvement and discovery of new industrial products.
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Affiliation(s)
- Jose-Luis Adrio
- NeuronBioPharma, S.A., Parque Tecnologico de Ciencias de la Salud, Edificio BIC, Armilla, Granada, Spain
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17
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Prior JE, Shokati T, Christians U, Gill RT. Identification and characterization of a bacterial cytochrome P450 for the metabolism of diclofenac. Appl Microbiol Biotechnol 2009; 85:625-33. [PMID: 19636551 DOI: 10.1007/s00253-009-2135-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2009] [Revised: 07/06/2009] [Accepted: 07/07/2009] [Indexed: 10/20/2022]
Abstract
The bacterium Actinoplanes sp. ATCC 53771 is known to perform drug metabolism of several xenobiotics similarly to humans. We identified a cytochrome P450 enzyme from this strain, CYP107E4, and expressed it in Escherichia coli using the pET101 vector. The purified enzyme showed the characteristic reduced-CO difference spectra with a peak at 450 nm, indicating the protein is produced in the active form with proper heme incorporation. The CYP107E4 enzyme was found to bind the drug diclofenac. Using redox enzymes from spinach, the reconstituted system is able to produce hydroxylated metabolites of diclofenac. Production of the human 4'-hydroxydiclofenac metabolite by CYP107E4 was confirmed, and a second hydroxylated metabolite was also produced.
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Affiliation(s)
- Jamie E Prior
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80309, USA
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18
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Furuya T, Nishi T, Shibata D, Suzuki H, Ohta D, Kino K. Characterization of orphan monooxygenases by rapid substrate screening using FT-ICR mass spectrometry. ACTA ACUST UNITED AC 2008; 15:563-72. [PMID: 18559267 DOI: 10.1016/j.chembiol.2008.05.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2008] [Revised: 04/29/2008] [Accepted: 05/02/2008] [Indexed: 11/26/2022]
Abstract
Characterization of orphan enzymes, for which the catalytic functions and actual substrates are still not elucidated, is a significant challenge in the postgenomic era. Here, we describe a general strategy for exploring the catalytic potentials of orphan monooxygenases based on direct infusion analysis by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR/MS). Eight cytochromes P450 from Bacillus subtilis were recombinantly expressed in Escherichia coli and subjected to a reconstitution system containing appropriate electron transfer components and many potential substrates. The reaction mixtures were directly analyzed using FT-ICR/MS, and substrates of the putative enzymes were readily identified from the mass spectral data. This allowed identification of previously unreported CYP109B1 substrates and the functional assignment of two putative cytochromes P450, CYP107J1 and CYP134A1. The FT-ICR/MS-based approach can be easily applied to large-scale screening with the aid of the extremely high mass resolution and accuracy.
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Affiliation(s)
- Toshiki Furuya
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, Tokyo, Japan
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19
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Sasaki M, Tsuchido T, Matsumura Y. Molecular cloning and characterization of cytochrome P450 and ferredoxin genes involved in bisphenol A degradation in Sphingomonas bisphenolicum strain AO1. J Appl Microbiol 2008; 105:1158-69. [PMID: 18492046 DOI: 10.1111/j.1365-2672.2008.03843.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS To clone and characterize the genes bisdA and bisdB, encoding Ferredoxin(bisd) (Fd(bisd)) and cytochrome P450(bisd) (P450(bisd)), respectively, from the bisphenol A (BPA) degrading Sphingomonas bisphenolicum strain AO1. METHODS AND RESULTS The 3.7 kb region containing bisdA and bisdB was cloned by genome walking and colony hybridization. The deduced N-terminal amino acid sequences of bisdA and bisdB were consistent with those of Fd(bisd) and P450(bisd) proteins characterized in our previous report. Two transposase genes, tnpA1 and tnpA2, were also located upstream and downstream of bisdAB. From amino acid sequence analysis, P450(bisd) has two conserved regions corresponding to the oxygen and heme binding regions of the bacterial cytochrome P450 family. Fd(bisd) was similar to putidaredoxin-type [2Fe-2S] ferredoxins. Escherichia coli BL21 (DE3) cells bearing bisdB- and bisdAB-recombinant pET19b were able to degrade BPA. A spontaneous mutant, strain AO1L, which was unable to degrade BPA, was isolated from the stock culture, and it was confirmed that strain AO1L had no bisdAB region. CONCLUSIONS P450(bisd) monooxygenase sytem, encoded by bisdAB, is one system required for BPA hydroxylation in S. bisphenolicum strain AO1. SIGNIFICANCE AND IMPACT OF THE STUDY Our results indicate that bisdAB are key genes for BPA degradation in S. bisphenolicum strain AO1.
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Affiliation(s)
- M Sasaki
- Department of Life Science and Biotechnology, Kansai University, Suita, Osaka, Japan
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20
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TW Chu D. Section Review Anti-infectives: Recent developments in 14- and 15-membered macrolides. Expert Opin Investig Drugs 2008. [DOI: 10.1517/13543784.4.2.65] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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21
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Demain AL, Adrio JL. Strain improvement for production of pharmaceuticals and other microbial metabolites by fermentation. PROGRESS IN DRUG RESEARCH. FORTSCHRITTE DER ARZNEIMITTELFORSCHUNG. PROGRES DES RECHERCHES PHARMACEUTIQUES 2008; 65:251-289. [PMID: 18084918 DOI: 10.1007/978-3-7643-8117-2_7] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Microbes have been good to us. They have given us thousands of valuable products with novel structures and activities. In nature, they only produce tiny amounts of these secondary metabolic products as a matter of survival. Thus, these metabolites are not overproduced in nature, but they must be overproduced in the pharmaceutical industry. Genetic manipulations are used in industry to obtain strains that produce hundreds or thousands of times more than that produced by the originally isolated strain. These strain improvement programs traditionally employ mutagenesis followed by screening or selection; this is known as 'brute-force' technology. Today, they are supplemented by modern strategic technologies developed via advances in molecular biology, recombinant DNA technology, and genetics. The progress in strain improvement has increased fermentation productivity and decreased costs tremendously. These genetic programs also serve other goals such as the elimination of undesirable products or analogs, discovery of new antibiotics, and deciphering of biosynthetic pathways.
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Affiliation(s)
- Arnold L Demain
- Research Institute for Scientists Emeriti (RISE), HS-330, Drew University, Madison, NJ 07940 USA.
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22
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Zhang C, Fu Q, Albermann C, Li L, Thorson JS. The in vitro characterization of the erythronolide mycarosyltransferase EryBV and its utility in macrolide diversification. Chembiochem 2007; 8:385-90. [PMID: 17262863 DOI: 10.1002/cbic.200600509] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Changsheng Zhang
- Laboratory for Biosynthetic Chemistry, University of Wisconsin, National Cooperative Drug Discovery Group, Pharmaceutical Sciences Division, School of Pharmacy, Madison, WI 53705, USA
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23
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Arakawa K, Kodama K, Tatsuno S, Ide S, Kinashi H. Analysis of the loading and hydroxylation steps in lankamycin biosynthesis in Streptomyces rochei. Antimicrob Agents Chemother 2006; 50:1946-52. [PMID: 16723550 PMCID: PMC1479134 DOI: 10.1128/aac.00016-06] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The biosynthetic gene cluster of lankamycin (LM), a 14-member macrolide antibiotic, is encoded on the 210-kb linear plasmid pSLA2-L in Streptomyces rochei 7434AN4. LM contains a 3-hydroxy-2-butyl group at the C-13 position, which is different from an ethyl group in erythromycin. The following two possibilities could be considered for the origin of this starter moiety of LM biosynthesis: (i) an extra module exists in the biosynthetic gene cluster and loads an additional acetate molecule, or (ii) 3-hydroxy-2-butyrate or its equivalent is loaded and incorporated as a starter. The former possibility was eliminated by the complete sequencing of pSLA2-L, which showed no extra module. On the other hand, the latter was confirmed by incorporation of deuterium in [3-(2)H]dl-isoleucine into the C-14 position of LM. The timing of hydroxylation reactions at the C-15 and C-8 positions of LM was studied by constructing disruptants of two P450 hydroxylase genes, lkmF (orf26) and lkmK (orf37). The lkmF disruptant produced 8-deoxylankamycin, while the lkmK disruptant produced both 15-deoxylankamycin and 8,15-dideoxylankamycin. These results clearly showed that LkmF is a C-8 hydroxylase and LkmK is a C-15 hydroxylase in LM biosynthesis and in addition suggested the order of hydroxylation steps; namely, hydroxylation may occur at first at C-15 by LkmK and then at C-8 by LkmF.
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Affiliation(s)
- Kenji Arakawa
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Japan
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24
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Fischbach MA, Walsh CT. Assembly-Line Enzymology for Polyketide and Nonribosomal Peptide Antibiotics: Logic, Machinery, and Mechanisms. Chem Rev 2006; 106:3468-96. [PMID: 16895337 DOI: 10.1021/cr0503097] [Citation(s) in RCA: 1062] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michael A Fischbach
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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Abstract
Although microorganisms are extremely good in presenting us with an amazing array of valuable products, they usually produce them only in amounts that they need for their own benefit; thus, they tend not to overproduce their metabolites. In strain improvement programs, a strain producing a high titer is usually the desired goal. Genetics has had a long history of contributing to the production of microbial products. The tremendous increases in fermentation productivity and the resulting decreases in costs have come about mainly by mutagenesis and screening/selection for higher producing microbial strains and the application of recombinant DNA technology.
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Affiliation(s)
- Jose L Adrio
- Department of Biotechnology, Puleva Biotech, S.A., Granada, Spain.
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26
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A journey across the sequential development of macrolides and ketolides related to erythromycin. Tetrahedron 2006. [DOI: 10.1016/j.tet.2005.11.064] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Xu J, Wan E, Kim CJ, Floss HG, Mahmud T. Identification of tailoring genes involved in the modification of the polyketide backbone of rifamycin B by Amycolatopsis mediterranei S699. MICROBIOLOGY-SGM 2005; 151:2515-2528. [PMID: 16079331 DOI: 10.1099/mic.0.28138-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Rifamycin B biosynthesis by Amycolatopsis mediterranei S699 involves a number of unusual modification reactions in the formation of the unique polyketide backbone and decoration of the molecule. A number of genes believed to be involved in the tailoring of rifamycin B were investigated and the results confirmed that the formation of the naphthalene ring moiety of rifamycin takes place during the polyketide chain extension and is catalysed by Rif-Orf19, a 3-(3-hydroxyphenyl)propionate hydroxylase-like protein. The cytochrome P450-dependent monooxygenase encoded by rif-orf5 is required for the conversion of the Delta12, 29 olefinic bond in the polyketide backbone of rifamycin W into the ketal moiety of rifamycin B. Furthermore, Rif-Orf3 may be involved in the regulation of rifamycin B production, as its knock-out mutant produced about 40 % more rifamycin B than the wild-type. The work also revealed that many of the genes located in the cluster are not involved in rifamycin biosynthesis, but might be evolutionary remnants carried over from an ancestral lineage.
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Affiliation(s)
- Jun Xu
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195-1700, USA
| | - Eva Wan
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331-3507, USA
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195-1700, USA
| | - Chang-Joon Kim
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195-1700, USA
| | - Heinz G Floss
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195-1700, USA
| | - Taifo Mahmud
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331-3507, USA
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195-1700, USA
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28
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Cooper SM, Laosripaiboon W, Rahman AS, Hothersall J, El-Sayed AK, Winfield C, Crosby J, Cox RJ, Simpson TJ, Thomas CM. Shift to Pseudomonic Acid B Production in P. fluorescens NCIMB10586 by Mutation of Mupirocin Tailoring Genes mupO, mupU, mupV, and macpE. ACTA ACUST UNITED AC 2005; 12:825-33. [PMID: 16039529 DOI: 10.1016/j.chembiol.2005.05.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2004] [Revised: 04/11/2005] [Accepted: 05/16/2005] [Indexed: 10/25/2022]
Abstract
Mupirocin, a polyketide-derived antibiotic from Pseudomonas fluorescens NCIMB10586, is a mixture of pseudomonic acids (PA) that target isoleucyl-tRNA synthase. The mup gene cluster encodes both type I polyketide synthases and monofunctional enzymes that should play a role during the conversion of the product of the polyketide synthase into the active antibiotic (tailoring). By in-frame deletion analysis of selected tailoring open-reading frames we show that mupQ, mupS, mupT, and mupW are essential for mupirocin production, whereas mupO, mupU, mupV, and macpE are essential for production of PA-A but not PA-B. Therefore, PA-B is not simply produced by hydroxylation of PA-A but is either a precursor of PA-A or a shunt product. In the mupW mutant, a new metabolite lacking the tetrahydropyran ring is produced, implicating mupW in oxidation of the 16-methyl group.
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Affiliation(s)
- Sian M Cooper
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
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29
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Peirú S, Menzella HG, Rodríguez E, Carney J, Gramajo H. Production of the potent antibacterial polyketide erythromycin C in Escherichia coli. Appl Environ Microbiol 2005; 71:2539-47. [PMID: 15870344 PMCID: PMC1087553 DOI: 10.1128/aem.71.5.2539-2547.2005] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An Escherichia coli strain capable of producing the potent antibiotic erythromycin C (Ery C) was developed by expressing 17 new heterologous genes in a 6-deoxyerythronolide B (6dEB) producer strain. The megalomicin gene cluster was used as the source for the construction of two artificial operons that contained the genes encoding the deoxysugar biosynthetic and tailoring enzymes necessary to convert 6dEB to Ery C. The reconstructed mycarose operon contained the seven genes coding for the enzymes that convert glucose-1-phosphate (G-1-P) to TDP-L-mycarose, a 6dEB mycarosyl transferase, and a 6dEB 6-hydroxylase. The activity of the pathway was confirmed by demonstrating conversion of exogenous 6dEB to 3-O-alpha-mycarosylerythronolide B (MEB). The reconstructed desosamine operon contained the six genes necessary to convert TDP-4-keto-6-deoxyglucose, an intermediate formed in the mycarose pathway, to TDP-D-desosamine, a desosamine transferase, a 6dEB 12-hydroxylase, and the rRNA methyltransferase ErmE; the last was required to confer resistance to the host cell upon production of mature macrolide antibiotics. The activity of this pathway was demonstrated by conversion of MEB to Ery C. When the mycarose and desosamine operons were expressed in an E. coli strain engineered to synthesize 6dEB, Ery C and Ery D were produced. The successful production of Ery C in E. coli shows the potentiality of this model microorganism to synthesize novel 6-deoxysugars and to produce bioactive glycosylated compounds and also establishes the basis for the future use of E. coli both in the production of new glycosylated polyketides and for the generation of novel bioactive compounds through combinatorial biosynthesis.
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Affiliation(s)
- Salvador Peirú
- Microbiology Division, IBR (Instituto de Biología Molecular y Celular de Rosario), Consejo Nacional de Investigaciones Científicas ye Técnicas, Universidad Nacional de Rosario, Suipacha 531, Argentina
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30
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Affiliation(s)
- Leonard Katz
- Kosan Biosciences, Incorporated, 3832 Bay Center Place, Hayward, California 94545, USA.
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32
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He J, Müller M, Hertweck C. Formation of the aureothin tetrahydrofuran ring by a bifunctional cytochrome p450 monooxygenase. J Am Chem Soc 2005; 126:16742-3. [PMID: 15612710 DOI: 10.1021/ja046104h] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The polyketide antibiotic aureothin, produced by Streptomyces thioluteus, is equipped with a rare exomethylene-tetrahydrofuran moiety. Cloning, heterologous expression, and inactivation experiments reveal that AurH, a bifunctional cytochrome P450 monooxygenase, is required and sufficient for the stereoselective synthesis of the furan ring, involving the subsequent formation of two new C-O bonds.
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Affiliation(s)
- Jing He
- Hans-Knöll-Institute for Natural Products Research, Beutenbergstrasse 11a, 07745 Jena, Germany
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Olano C, Moss SJ, Braña AF, Sheridan RM, Math V, Weston AJ, Méndez C, Leadlay PF, Wilkinson B, Salas JA. Biosynthesis of the angiogenesis inhibitor borrelidin by Streptomyces parvulus Tü4055: insights into nitrile formation. Mol Microbiol 2005; 52:1745-56. [PMID: 15186422 DOI: 10.1111/j.1365-2958.2004.04090.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The 18-membered polyketide macrolide borrelidin exhibits a number of important biological activities, including potent angiogenesis inhibition. This has prompted two recent total syntheses as well as the cloning of the biosynthetic gene cluster from Streptomyces parvulus Tü4055. Borrelidin possesses some unusual structural characteristics, including a cyclopentane carboxylic acid moiety at C17 and a nitrile moiety at C12 of the macrocyclic ring. Nitrile groups are relatively rare in nature, and little is known of their biosynthesis during secondary metabolism. The nitrile group of borrelidin is shown here to arise from the methyl group of a methylmalonyl-CoA extender unit incorporated during polyketide chain extension. Insertional inactivation of two genes in the borrelidin gene cluster, borI (coding for a cytochrome P450 monooxygenase) and borJ (coding for an aminotransferase), generated borrelidin non-producing mutants. These mutants accumulated different compounds lacking the C12 nitrile moiety, with the product of the borI-minus mutant (12-desnitrile-12-methyl-borrelidin) possessing a methyl group and that of the borJ-minus mutant (12-desnitrile-12-carboxyl-borrelidin) a carboxyl group at C12. The former but not the latter was converted into borrelidin when biotransformed by an S. parvulus mutant that is deficient in the biosynthesis of the borrelidin starter unit. This suggests that 12-desnitrile-12-methyl-borrelidin is a competent biosynthetic intermediate, whereas the carboxylated derivative is a shunt metabolite. Bioconversion of 12-desnitrile-12-methyl-borrelidin into borrelidin was also achieved in a heterologous system co-expressing borI and borJ in Streptomyces albus J1074. This bioconversion was more efficient when borK, which is believed to encode a dehydrogenase, was simultaneously expressed with borI and borJ. On the basis of these findings, a pathway is proposed for the formation of the nitrile moiety during borrelidin biosynthesis.
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Affiliation(s)
- Carlos Olano
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, 33006 Oviedo, Spain
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34
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Affiliation(s)
- Robert McDaniel
- Kosan Biosciences, 3832 Bay Center Place, Hayward, California 94545, USA.
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35
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Brikun IA, Reeves AR, Cernota WH, Luu MB, Weber JM. The erythromycin biosynthetic gene cluster of Aeromicrobium erythreum. J Ind Microbiol Biotechnol 2004; 31:335-44. [PMID: 15257441 DOI: 10.1007/s10295-004-0154-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2004] [Accepted: 06/11/2004] [Indexed: 11/25/2022]
Abstract
The erythromycin-biosynthetic (ery) gene cluster of Aeromicrobium erythreum was cloned and characterized. The 55.4-kb cluster contains 25 ery genes. Homologues were found for each gene in the previously characterized ery gene cluster from Saccharopolyspora erythraea. In addition, four new predicted ery genes were identified. Two of the new predicted genes, coding for a phosphopantetheinyl transferase (eryP) and a type II thioesterase (eryTII), were internal to the ery cluster. The other two new genes, coding for a thymidine 5'-diphosphate-glucose synthase (eryDI) and a MarR-family transcriptional repressor (ery-ORF25), were found at the two ends of the ery cluster. A knockout in eryDI showed it to be essential for erythromycin biosynthesis. The gene order of the two ery clusters was conserved within a core region of 15 contiguous genes, with the exception of IS1136 which was not found in the A. erythreum cluster. Beyond the core region, gene shuffling had occurred between the two sides of the cluster. The flanking regions of the two ery clusters were not alike in the type of genes found.
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Affiliation(s)
- Igor A Brikun
- Fermalogic Inc., 2201 W. Campbell Park Drive, Chicago, IL 60612, USA
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36
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Parajuli N, Basnet DB, Chan Lee H, Sohng JK, Liou K. Genome analyses of Streptomyces peucetius ATCC 27952 for the identification and comparison of cytochrome P450 complement with other Streptomyces. Arch Biochem Biophys 2004; 425:233-41. [PMID: 15111132 DOI: 10.1016/j.abb.2004.03.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2004] [Revised: 03/04/2004] [Indexed: 10/26/2022]
Abstract
We have determined the genome sequence of 8.7 Mb chromosome of Streptomyces peucetius ATCC 27952, which produces clinically important anthracycline chemotherapeutic agents of the polyketide class of antibiotics, daunorubicin and doxorubicin. The cytochrome P450 (CYP) superfamily is represented by 19 sequences in the S. peucetius. Among those, 15 code for functional genes, whereas the remaining four are pseudo genes. CYPs from S. peucetius are phylogenetically close to those of Streptomyces amermitilis. Four CYPs are associated with modular PKS of avermectin and two with doxorubicin biosynthetic gene cluster. CYP252A1 is the new family found in S. peucetius, which shares 38% identity to CYP51 from Streptomyces coelicolor A3 (2). Nine CYPs from S. peucetius are found in the cluster containing various regulatory genes including rar operon, conserved in S. coelicolor A3 (2) and Streptomyces griseus. Although two ferredoxins and four ferredoxin reductases have been identified so far, only one ferredoxin reductase was found in the cluster of CYP147F1 in S. peucetius. To date, 174 CYPs have been described from 45 Streptomyces species in all searchable databases. However, only 18 CYPs are clustered with ferredoxin. The comparative study of cytochrome P450s, ferredoxins, and ferredoxin reductases should be useful for the future development and manipulation of antibiotic biosynthetic pathways.
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Affiliation(s)
- Niranjan Parajuli
- Institute of Biomolecule Reconstruction, Sun Moon University, Asan, 336-708, Republic of Korea
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37
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Lei L, Waterman MR, Fulco AJ, Kelly SL, Lamb DC. Availability of specific reductases controls the temporal activity of the cytochrome P450 complement of Streptomyces coelicolor A3(2). Proc Natl Acad Sci U S A 2004; 101:494-9. [PMID: 14704268 PMCID: PMC327175 DOI: 10.1073/pnas.2435922100] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2003] [Indexed: 11/18/2022] Open
Abstract
The annotated genome of Streptomyces coelicolor A3(2) revealed 18 cytosolic cytochromes P450 (CYPs) with six ferredoxin (fdx) proteins and two soluble ferredoxin reductases (fpr), their putative electron transport proteins. mRNA expression was observed for all 18 CYPs throughout growth and secondary metabolism, from 3 h after spore germination, and all CYP proteins examined also were present. Expression of members of the fdx complement was detected from the same time point, yet both fpr were detected only at 12 h. Six-hour exposure to dimethylbenzanthracene and benzo[a]pyrene xenobiotics resulted in the absence of some CYP mRNAs and expression of a specific fpr, FR2. This finding and the expression pattern during growth suggested that CYP activity may be regulated by availability of specific reductases. To test this proposal, we expressed in Escherichia coli and purified to homogeneity five CYPs: CYP105D5 (involved in xenobiotic metabolism) and CYP154A1, CYP154C1, CYP158A1, and CYP158A2 (putatively involved in secondary metabolism). Also the two soluble fpr (FR2 and FR3) proposed to shuttle electrons by means of fdx were purified, and specific interactions were observed so that FR2 preferentially reduced CYP105D5 (>90% reduction) compared with the other CYPs (>20% reduction), whereas FR3 preferentially reduced the other CYPs (>85% reduction) compared with CYP105D5 (>10%). Furthermore FR2 was shown to efficiently bind CYP105D5 and drive benzo[a]pyrene hydroxylation in contrast to FR3. These data show that control of CYP activity in S. coelicolor A3(2) involves specific interactions with fpr and their availability during the life cycle and, after xenobiotic exposure, represents a unique mechanism for regulating CYP function.
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Affiliation(s)
- Li Lei
- Wolfson Laboratory of P450 Biodiversity, Institute of Biological Sciences, University of Wales Aberystwyth, Aberystwyth, Wales SY23 3DA, United Kingdom
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38
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Affiliation(s)
- Pawan Kumar
- Department of Chemical Engineering, Stanford University, California 94305, USA
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39
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He J, Hertweck C. Iteration as Programmed Event during Polyketide Assembly; Molecular Analysis of the Aureothin Biosynthesis Gene Cluster. ACTA ACUST UNITED AC 2003; 10:1225-32. [PMID: 14700630 DOI: 10.1016/j.chembiol.2003.11.009] [Citation(s) in RCA: 137] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Analysis of the type I modular polyketide synthase (PKS) involved in the biosynthesis of the rare nitroaryl polyketide metabolite aureothin (aur) from Streptomyces thioluteus HKI-227 has revealed only four modules to catalyze the five polyketide chain extensions required. By heterologous expression of the aur PKS cluster, direct evidence was obtained that these modules were sufficient to support aureothin biosynthesis. It appears that one module catalyzes two successive cycles of chain extension, one of the first examples of a PKS in which such iteration or "stuttering" is required to produce the normal polyketide product. In addition, lack of a specified loading domain implicates a novel PKS priming mechanism involving the unique p-nitrobenzoate starter unit. The 27 kb aur gene cluster also encodes a novel N-oxidase, which may represent the first member of a new family of such enzymes.
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Affiliation(s)
- Jing He
- Hans-Knoell-Institute for Natural Products Research, Department of Bioorganic Synthesis, Beutenbergstr 11a, D-07745 Jena, Germany
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40
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Paradkar A, Trefzer A, Chakraburtty R, Stassi D. Streptomyces genetics: a genomic perspective. Crit Rev Biotechnol 2003; 23:1-27. [PMID: 12693442 DOI: 10.1080/713609296] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Streptomycetes are gram-positive, soil-inhabiting bacteria of the order Actinomycetales. These organisms exhibit an unusual, developmentally complex life cycle and produce many economically important secondary metabolites, such as antibiotics, immunosuppressants, insecticides, and anti-tumor agents. Streptomyces species have been the subject of genetic investigation for over 50 years, with many studies focusing on the developmental cycle and the production of secondary metabolites. This information provides a solid foundation for the application of structural and functional genomics to the actinomycetes. The complete DNA sequence of the model organism, Streptomyces coelicolor M145, has been published recently, with others expected to follow soon. As more genomic sequences become available, the rational genetic manipulation of these organisms to elucidate metabolic and regulatory networks, to increase the production of commercially important compounds, and to create novel secondary metabolites will be greatly facilitated. This review presents the current state of the field of genomics as it is being applied to the actinomycetes.
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Affiliation(s)
- Ashish Paradkar
- Small Molecule Discovery, Diversa Corporation, 4955 Directors Place, San Diego, CA 92121, USA
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41
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Vanden Boom TJ. Recent developments in the molecular genetics of the erythromycin-producing organism Saccharopolyspora erythraea. ADVANCES IN APPLIED MICROBIOLOGY 2003; 47:79-111. [PMID: 12876795 DOI: 10.1016/s0065-2164(00)47002-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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42
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Hu Z, Pfeifer BA, Chao E, Murli S, Kealey J, Carney JR, Ashley G, Khosla C, Hutchinson CR. A specific role of the Saccharopolyspora erythraea thioesterase II gene in the function of modular polyketide synthases. MICROBIOLOGY (READING, ENGLAND) 2003; 149:2213-2225. [PMID: 12904561 DOI: 10.1099/mic.0.26015-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Bacterial modular polyketide synthase (PKS) genes are commonly associated with another gene that encodes a thioesterase II (TEII) believed to remove aberrantly loaded substrates from the PKS. Co-expression of the Saccharopolyspora erythraea ery-ORF5 TEII and eryA genes encoding 6-deoxyerythronolide B synthase (DEBS) in Streptomyces hosts eliminated or significantly lowered production of 8,8'-deoxyoleandolide [15-nor-6-deoxyerythronolide B (15-nor-6dEB)], which arises from an acetate instead of a propionate starter unit. Disruption of the TEII gene in an industrial Sac. erythraea strain caused a notable amount of 15-norerythromycins to be produced by utilization of an acetate instead of a propionate starter unit and also resulted in moderately lowered production of erythromycin compared with the amount produced by the parental strain. A similar behaviour of the TEII gene was observed in Escherichia coli strains that produce 6dEB and 15-methyl-6dEB. Direct biochemical analysis showed that the ery-ORF5 TEII enzyme favours hydrolysis of acetyl groups bound to the loading acyl carrier protein domain (ACP(L)) of DEBS. These results point to a clear role of the TEII enzyme, i.e. removal of a specific type of acyl group from the ACP(L) domain of the DEBS1 loading module.
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Affiliation(s)
- Zhihao Hu
- Kosan Biosciences, Hayward, CA 94545, USA
| | - Blaine A Pfeifer
- Department of Chemical Engineering, Chemistry and Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Elizabeth Chao
- Department of Chemical Engineering, Chemistry and Biochemistry, Stanford University, Stanford, CA 94305, USA
| | | | - Jim Kealey
- Kosan Biosciences, Hayward, CA 94545, USA
| | | | | | - Chaitan Khosla
- Department of Chemical Engineering, Chemistry and Biochemistry, Stanford University, Stanford, CA 94305, USA
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43
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Lamb DC, Ikeda H, Nelson DR, Ishikawa J, Skaug T, Jackson C, Omura S, Waterman MR, Kelly SL. Cytochrome p450 complement (CYPome) of the avermectin-producer Streptomyces avermitilis and comparison to that of Streptomyces coelicolor A3(2). Biochem Biophys Res Commun 2003; 307:610-9. [PMID: 12893267 DOI: 10.1016/s0006-291x(03)01231-2] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The genus Streptomyces produces about two-thirds of naturally occurring antibiotics and a wide array of other secondary metabolites, including antihelminthic agents, antitumor agents, antifungal agents, and herbicides. The newly completed genome sequence of the avermectin-producing bacterium Streptomyces avermitilis contains 33 cytochromes p450 (CYPs), many more than the 18 observed in Streptomyces coelicolor A3(2). Some of the likely metabolic functions are reported together with their genomic location and bioinformatic analysis. Seven entirely new CYP families were found together with close homologues of some forms observed in S. coelicolor A3(2). The presence of unusual CYP forms associated with conservons is revealed and of these, CYP157 forms in both S. avermitilis and S. coelicolor A3(2) deviate from the previously accepted rule for an EXXR motif within the K-helix of CYPs. Amongst this range of CYPs are forms associated with avermectin, filipin, geosmin, and pentalenolactone biosynthesis as well as unknown pathways of secondary metabolism.
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Affiliation(s)
- David C Lamb
- Institute of Biological Sciences, University of Wales Aberystwyth, Aberystwyth, UK.
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44
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Abstract
Hybrid antibiotics that do not occur in nature have been obtained by combining structural genes of antibiotic producers. Some of these substances were effective against pathogenic microorganisms resistant against antibiotics produced by the parent strains. The majority of hybrid antibiotics were obtained by combining genes encoding polyketide synthases. Hybrid peptides with new biological properties have also been synthesized.
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Affiliation(s)
- V Bĕhal
- Institute of Microbiology, Academy of Sciences of the Czech Republic, 142 20 Prague, Czechia.
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45
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Podust LM, Kim Y, Arase M, Neely BA, Beck BJ, Bach H, Sherman DH, Lamb DC, Kelly SL, Waterman MR. The 1.92-A structure of Streptomyces coelicolor A3(2) CYP154C1. A new monooxygenase that functionalizes macrolide ring systems. J Biol Chem 2003; 278:12214-21. [PMID: 12519772 DOI: 10.1074/jbc.m212210200] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Evolutionary links between cytochrome P450 monooxygenases, a superfamily of extraordinarily divergent heme-thiolate proteins catalyzing a wide array of NADPH/NADH- and O(2)-dependent reactions, are becoming better understood because of availability of an increasing number of fully sequenced genomes. Among other reactions, P450s catalyze the site-specific oxidation of the precursors to macrolide antibiotics in the genus Streptomyces introducing regiochemical diversity into the macrolide ring system, thereby significantly increasing antibiotic activity. Developing effective uses for Streptomyces enzymes in biosynthetic processes and bioremediation requires identification and engineering of additional monooxygenases with activities toward a diverse array of small molecules. To elucidate the molecular basis for substrate specificity of oxidative enzymes toward macrolide antibiotics, the x-ray structure of CYP154C1 from Streptomyces coelicolor A3(2) was determined (Protein Data Bank code ). Relocation of certain common P450 secondary structure elements, along with a novel structural feature involving an additional beta-strand transforming the five-stranded beta-sheet into a six-stranded variant, creates an open cleft-shaped substrate-binding site between the two P450 domains. High sequence similarity to macrolide monooxygenases from other microbial species translates into catalytic activity of CYP154C1 toward both 12- and 14-membered ring macrolactones in vitro.
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Affiliation(s)
- Larissa M Podust
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA.
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Trefzer A, Pelzer S, Schimana J, Stockert S, Bihlmaier C, Fiedler HP, Welzel K, Vente A, Bechthold A. Biosynthetic gene cluster of simocyclinone, a natural multihybrid antibiotic. Antimicrob Agents Chemother 2002; 46:1174-82. [PMID: 11959542 PMCID: PMC127163 DOI: 10.1128/aac.46.5.1174-1182.2002] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The entire simocyclinone biosynthetic cluster (sim gene cluster) from the producer Streptomyces antibioticus Tü6040 was identified on six overlapping cosmids (1N1, 5J10, 2L16, 2P6, 4G22, and 1K3). In total, 80.7 kb of DNA from these cosmids was sequenced, and the analysis revealed 49 complete open reading frames (ORFs). These ORFs include genes responsible for the formation and attachment of four different moieties originating from at least three different pools of primary metabolites. Also in the sim gene cluster, four ORFs were detected that resemble putative regulatory and export functions. Based on the putative function of the gene products, a model for simocyclinone D8 biosynthesis was proposed. Biosynthetic mutants were generated by insertional gene inactivation experiments, and culture extracts of these mutants were analyzed by high-performance liquid chromatography. Production of simocyclinone D8 was clearly detectable in the wild-type strain but was not detectable in the mutant strains. This indicated that indeed the sim gene cluster had been cloned.
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Affiliation(s)
- A Trefzer
- Pharmazeutische Biologie, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
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47
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Gaisser S, Lill R, Staunton J, Méndez C, Salas J, Leadlay PF. Parallel pathways for oxidation of 14-membered polyketide macrolactones in Saccharopolyspora erythraea. Mol Microbiol 2002; 44:771-81. [PMID: 11994157 DOI: 10.1046/j.1365-2958.2002.02910.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The glycosyltransferases OleG1 and OleG2 and the cytochrome P450 oxidase OleP from the oleandomycin biosynthetic gene cluster of Streptomyces antibioticus have been expressed, either separately or from artificial gene cassettes, in strains of Saccharopolyspora erythraea blocked in erythromycin biosynthesis, to investigate their potential for the production of diverse novel macrolides from erythronolide precursors. OleP was found to oxidize 6-deoxyerythronolide B, but not erythronolide B. However, OleP did oxidize derivatives of erythronolide B in which a neutral sugar is attached at C-3. The oxidized products 3-O-mycarosyl-8a-hydroxyerythronolide B, 3-O-mycarosyl-8,8a-epoxyerythronolide B, 6-deoxy-8-hydroxyerythronolide B and the olefin 6-deoxy-8,8a-dehydroerythronolide B were all isolated and their structures determined. When oleP and the mycarosyltransferase eryBV were co-expressed in a gene cassette, 3-O-mycarosyl-6-deoxy-8,8a-dihydroxyerythronolide B was directly obtained. When oleG2 was co-expressed in a gene cassette together with oleP, 6-deoxyerythronolide B was converted into a mixture of 3-O-rhamnosyl-6-deoxy-8,8a-dehydroerythronolide B and 3-O-rhamnosyl-6-deoxy-8,8a-dihydroxyerythronolide B, confirming previous reports that OleG2 can transfer rhamnose, and confirming that oxidation by OleP and attachment of the neutral sugar to the aglycone can occur in either order. Similarly, four different 3-O-mycarosylerythronolides were found to be substrates for the desosaminyltransferase OleG1. These results provide additional insight into the nature of the intermediates in OleP-mediated oxidation, and suggest that oleandomycin biosynthesis might follow parallel pathways in which epoxidation either precedes or follows attachment of the neutral sugar.
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48
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Weitnauer G, Gaisser S, Kellenberger L, Leadlay PF, Bechthold A. Analysis of a C-methyltransferase gene (aviG1) involved in avilamycin biosynthesis in Streptomyces viridochromogenes Tü57 and complementation of a Saccharopolyspora erythraea eryBIII mutant by aviG1. MICROBIOLOGY (READING, ENGLAND) 2002; 148:373-379. [PMID: 11832501 DOI: 10.1099/00221287-148-2-373] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Streptomyces viridochromogenes Tü57 is the principal producer of avilamycin A. aviG1, a putative methyltransferase gene, was detected in the avilamycin biosynthetic gene cluster. To determine the function of aviG1, a targeted gene inactivation experiment was performed. The resulting chromosomal mutant, carrying an in-frame deletion in aviG1, was deficient in avilamycin production. aviG1 was used to complement an eryBIII mutant of the erythromycin A producer Saccharopolyspora erythraea [Gaisser, S., Bohm, G. A., Doumith, M., Raynal, M. C., Dhillon, N., Cortes, J. & Leadlay, P. F. (1998). Mol Gen Genet 258, 78-88]. The presence of erythromycin A in the culture supernatant of the complemented mutant indicated that L-mycarose biosynthesis could be restored and that AviG1 could take over the function of the C-methyltransferase EryBIII.
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Affiliation(s)
- G Weitnauer
- Albert-Ludwigs-Universität Freiburg, Institut für Pharmazeutische Biologie, Stefan-Meier Str. 19, 79104 Freiburg, Germany1
| | - S Gaisser
- Cambridge Centre for Molecular Recognition and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK2
| | - L Kellenberger
- Cambridge Centre for Molecular Recognition and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK2
| | - P F Leadlay
- Cambridge Centre for Molecular Recognition and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK2
| | - A Bechthold
- Albert-Ludwigs-Universität Freiburg, Institut für Pharmazeutische Biologie, Stefan-Meier Str. 19, 79104 Freiburg, Germany1
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Abstract
Metabolic engineering is the science that combines systematic analysis of metabolic and other pathways with molecular biological techniques to improve cellular properties by designing and implementing rational genetic modifications. As such, metabolic engineering deals with the measurement of metabolic fluxes and elucidation of their control as determinants of metabolic function and cell physiology. A novel aspect of metabolic engineering is that it departs from the traditional reductionist paradigm of cellular metabolism, taking instead a holistic view. In this sense, metabolic engineering is well suited as a framework for the analysis of genome-wide differential gene expression data, in combination with data on protein content and in vivo metabolic fluxes. The insights of the integrated view of metabolism generated by metabolic engineering will have profound implications in biotechnological applications, as well as in devising rational strategies for target selection for screening candidate drugs or designing gene therapies. In this article we review basic concepts of metabolic engineering and provide examples of applications in the production of primary and secondary metabolites, improving cellular properties, and biomedical engineering.
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Affiliation(s)
- M Koffas
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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50
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Paitan Y, Orr E, Ron EZ, Rosenberg E. An unusual beta-ketoacyl:acyl carrier protein synthase and acyltransferase motifs in TaK, a putative protein required for biosynthesis of the antibiotic TA in Myxococcus xanthus. FEMS Microbiol Lett 2001; 203:191-7. [PMID: 11583847 DOI: 10.1111/j.1574-6968.2001.tb10840.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The antibiotic TA of Myxococcus xanthus is produced by a type-I polyketide synthase mechanism. Previous studies have indicated that TA genes are clustered within a 36-kb region. The chemical structure of TA indicates the need for several post-modification steps, which are introduced to form the final bioactive molecule. These include three C-methylations, an O-methylation and a specific hydroxylation. In this study, we describe the genetic analysis of taK, encoding a specific polyketide beta-ketoacyl:acyl carrier protein synthase, which contains an unusual beta-ketoacyl synthase and acyltransferase motifs and is likely to be involved in antibiotic TA post-modification. Functional analysis of this beta-ketoacyl:acyl carrier protein synthase by specific gene disruption suggests that it is essential for the production of an active TA molecule.
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Affiliation(s)
- Y Paitan
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
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