1
|
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.
Collapse
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
| |
Collapse
|
2
|
Chisuga T, Murakami S, Miyanaga A, Kudo F, Eguchi T. Structure-Based Analysis of Transient Interactions between Ketosynthase-like Decarboxylase and Acyl Carrier Protein in a Loading Module of Modular Polyketide Synthase. ACS Chem Biol 2023; 18:1398-1404. [PMID: 37216195 DOI: 10.1021/acschembio.3c00151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Ketosynthase-like decarboxylase (KSQ) domains are widely distributed in the loading modules of modular type I polyketide synthases (PKSs) and catalyze the decarboxylation of the (alkyl-)malonyl unit bound to the acyl carrier protein (ACP) in the loading module for the construction of the PKS starter unit. Previously, we performed a structural and functional analysis of the GfsA KSQ domain involved in the biosynthesis of macrolide antibiotic FD-891. We furthermore revealed the recognition mechanism for the malonic acid thioester moiety of the malonyl-GfsA loading module ACP (ACPL) as a substrate. However, the exact recognition mechanism for the GfsA ACPL moiety remains unclear. Here, we present a structural basis for the interactions between the GfsA KSQ domain and GfsA ACPL. We determined the crystal structure of the GfsA KSQ-acyltransferase (AT) didomain in complex with ACPL (ACPL=KSQAT complex) by using a pantetheine crosslinking probe. We identified the key amino acid residues involved in the KSQ domain-ACPL interactions and confirmed the importance of these residues by mutational analysis. The binding mode of ACPL to the GfsA KSQ domain is similar to that of ACP to the ketosynthase domain in modular type I PKSs. Furthermore, comparing the ACPL=KSQAT complex structure with other full-length PKS module structures provides important insights into the overall architectures and conformational dynamics of the type I PKS modules.
Collapse
Affiliation(s)
- Taichi Chisuga
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-Okayama, Tokyo 152-8551, Japan
| | - Satoshi Murakami
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Akimasa Miyanaga
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-Okayama, Tokyo 152-8551, Japan
| | - Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-Okayama, Tokyo 152-8551, Japan
| | - Tadashi Eguchi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-Okayama, Tokyo 152-8551, Japan
| |
Collapse
|
3
|
Bertrand CDF, Martins R, Quintas-Nunes F, Reynolds-Brandão P, Crespo MTB, Nascimento FX. Saccharopolyspora sp. NFXS83 in Marine Biotechnological Applications: From Microalgae Growth Promotion to the Production of Secondary Metabolites. Microorganisms 2023; 11:microorganisms11040902. [PMID: 37110324 PMCID: PMC10145562 DOI: 10.3390/microorganisms11040902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023] Open
Abstract
Marine bacteria are a significant source of bioactive compounds for various biotechnological applications. Among these, actinomycetes have been found to produce a wide range of secondary metabolites of interest. Saccharopolyspora is one of the genera of actinomycetes that has been recognized as a potential source of these compounds. This study reports the characterization and genomic analysis of Saccharopolyspora sp. NFXS83, a marine bacterium isolated from seawater from the Sado estuary in Portugal. The NFXS83 strain produced multiple functional and stable extracellular enzymes under high-salt conditions, showed the ability to synthesize auxins such as indole-3-acetic acid, and produced diffusible secondary metabolites capable of inhibiting the growth of Staphylococcus aureus. Furthermore, when Phaeodactylum tricornutum was co-cultivated with strain NFXS83 a significant increase in microalgae cell count, cell size, auto-fluorescence, and fucoxanthin content was observed. Detailed analysis revealed the presence of clusters involved in the production of various secondary metabolites, including extracellular enzymes, antimicrobial compounds, terpenes, and carotenoids in the genome of strain NFXS83. Ultimately, these findings indicate that Saccharopolyspora sp. NFXS83 has a significant potential for a wide range of marine biotechnological applications.
Collapse
|
4
|
Kudo F, Kishikawa K, Tsuboi K, Kido T, Usui T, Hashimoto J, Shin-Ya K, Miyanaga A, Eguchi T. Acyltransferase Domain Exchange between Two Independent Type I Polyketide Synthases in the Same Producer Strain of Macrolide Antibiotics. Chembiochem 2023; 24:e202200670. [PMID: 36602093 DOI: 10.1002/cbic.202200670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/06/2023]
Abstract
Streptomyces graminofaciens A-8890 produces two macrolide antibiotics, FD-891 and virustomycin A, both of which show significant biological activity. In this study, we identified the virustomycin A biosynthetic gene cluster, which encodes type I polyketide synthases (PKSs), ethylmalonyl-CoA biosynthetic enzymes, methoxymalony-acyl carrier protein biosynthetic enzymes, and post-PKS modification enzymes. Next, we demonstrated that the acyltransferase domain can be exchanged between the Vsm PKSs and the PKSs involved in FD-891 biosynthesis (Gfs PKSs), without any supply problems of the unique extender units. We exchanged the malonyltransferase domain in the loading module of Gfs PKS with the ethylmalonyltransferase domain and the methoxymalonyltransferase domain of Vsm PKSs. Consequently, the expected two-carbon-elongated analog 26-ethyl-FD-891 was successfully produced with a titer comparable to FD-891 production by the wild type; however, exchange with the methoxymalonyltransferase domain did not produce any FD-891 analogs. Furthermore, 26-ethyl-FD-891 showed potent cytotoxic activity against HeLa cells, like natural FD-891.
Collapse
Affiliation(s)
- Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Meguro-ku, O-okayama, Tokyo, 152-8551, Japan
| | - Kosuke Kishikawa
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Meguro-ku, O-okayama, Tokyo, 152-8551, Japan
| | - Kazuma Tsuboi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Meguro-ku, O-okayama, Tokyo, 152-8551, Japan
| | - Takafusa Kido
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Meguro-ku, O-okayama, Tokyo, 152-8551, Japan
| | - Takeo Usui
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8572, Ibaraki, Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium (JBIC), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Akimasa Miyanaga
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Meguro-ku, O-okayama, Tokyo, 152-8551, Japan
| | - Tadashi Eguchi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Meguro-ku, O-okayama, Tokyo, 152-8551, Japan
| |
Collapse
|
5
|
Chisuga T, Nagai A, Miyanaga A, Goto E, Kishikawa K, Kudo F, Eguchi T. Structural Insight into the Reaction Mechanism of Ketosynthase-Like Decarboxylase in a Loading Module of Modular Polyketide Synthases. ACS Chem Biol 2022; 17:198-206. [PMID: 34985877 DOI: 10.1021/acschembio.1c00856] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Ketosynthase-like decarboxylase (KSQ) domains are widely distributed in the loading modules of modular polyketide synthases (PKSs) and are proposed to catalyze the decarboxylation of a malonyl or methylmalonyl unit for the construction of the PKS starter unit. KSQ domains have high sequence similarity to ketosynthase (KS) domains, which catalyze transacylation and decarboxylative condensation in polyketide and fatty acid biosynthesis, except that the catalytic Cys residue of KS domains is replaced by Gln in KSQ domains. Here, we present biochemical analyses of GfsA KSQ and CmiP4 KSQ, which are involved in the biosynthesis of FD-891 and cremimycin, respectively. In vitro analysis showed that these KSQ domains catalyze the decarboxylation of malonyl and methylmalonyl units. Furthermore, we determined the crystal structure of GfsA KSQ in complex with a malonyl thioester substrate analogue, which enabled identification of key amino acid residues involved in the decarboxylation reaction. The importance of these residues was confirmed by mutational analysis. On the basis of these findings, we propose a mechanism of the decarboxylation reaction catalyzed by GfsA KSQ. GfsA KSQ initiates decarboxylation by fixing the substrate in a suitable conformation for decarboxylation. The formation of enolate upon decarboxylation is assisted by two conserved threonine residues. Comparison of the structure of GfsA KSQ with those of KS domains suggests that the Gln residue in the active site of the KSQ domain mimics the acylated Cys residue in the active site of KS domains.
Collapse
Affiliation(s)
- Taichi Chisuga
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O̅okayama, Meguro-ku, Tokyo 152-8851, Japan
| | - Akira Nagai
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O̅okayama, Meguro-ku, Tokyo 152-8851, Japan
| | - Akimasa Miyanaga
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O̅okayama, Meguro-ku, Tokyo 152-8851, Japan
| | - Ena Goto
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O̅okayama, Meguro-ku, Tokyo 152-8851, Japan
| | - Kosuke Kishikawa
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O̅okayama, Meguro-ku, Tokyo 152-8851, Japan
| | - Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O̅okayama, Meguro-ku, Tokyo 152-8851, Japan
| | - Tadashi Eguchi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O̅okayama, Meguro-ku, Tokyo 152-8851, Japan
| |
Collapse
|
6
|
Iizaka Y, Arai R, Takahashi A, Ito M, Sakai M, Fukumoto A, Sherman DH, Anzai Y. Engineering Sequence and Selectivity of Late-Stage C-H Oxidation in the MycG Iterative Cytochrome P450. J Ind Microbiol Biotechnol 2021; 49:6372909. [PMID: 34543433 PMCID: PMC9113108 DOI: 10.1093/jimb/kuab069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/16/2021] [Indexed: 11/16/2022]
Abstract
MycG is a multifunctional P450 monooxygenase that catalyzes sequential hydroxylation and epoxidation or a single epoxidation in mycinamicin biosynthesis. In the mycinamicin-producing strain Micromonospora griseorubida A11725, very low-level accumulation of mycinamicin V generated by the initial C-14 allylic hydroxylation of MycG is observed due to its subsequent epoxidation to generate mycinamicin II, the terminal metabolite in this pathway. Herein, we investigated whether MycG can be engineered for production of the mycinamicin II intermediate as the predominant metabolite. Thus, mycG was subject to random mutagenesis and screening was conducted in Escherichia coli whole-cell assays. This enabled efficient identification of amino acid residues involved in reaction profile alterations, which included MycG R111Q/V358L, W44R, and V135G/E355K with enhanced monohydroxylation to accumulate mycinamicin V. The MycG V135G/E355K mutant generated 40-fold higher levels of mycinamicin V compared to wild-type M. griseorubida A11725. In addition, the E355K mutation showed improved ability to catalyze sequential hydroxylation and epoxidation with minimal mono-epoxidation product mycinamicin I compared to the wild-type enzyme. These approaches demonstrate the ability to selectively coordinate the catalytic activity of multifunctional P450s and efficiently produce the desired compounds.
Collapse
Affiliation(s)
- Yohei Iizaka
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba, Japan
| | - Ryusei Arai
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba, Japan
| | - Akari Takahashi
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba, Japan
| | - Mikino Ito
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba, Japan
| | - Miho Sakai
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba, Japan
| | - Atsushi Fukumoto
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba, Japan
| | - David H Sherman
- Life Sciences Institute, Department of Medicinal Chemistry, Chemistry, and Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Yojiro Anzai
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba, Japan
| |
Collapse
|
7
|
Iizaka Y, Sherman DH, Anzai Y. An overview of the cytochrome P450 enzymes that catalyze the same-site multistep oxidation reactions in biotechnologically relevant selected actinomycete strains. Appl Microbiol Biotechnol 2021; 105:2647-2661. [PMID: 33710358 DOI: 10.1007/s00253-021-11216-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 02/17/2021] [Accepted: 02/28/2021] [Indexed: 12/18/2022]
Abstract
Cytochrome P450 enzymes (P450s) are one of the major factors responsible for the diversity of metabolites produced through many biosynthetic and biodegradative processes in actinomycetes. P450s typically catalyze a single oxidative modification; however, several P450s have been identified with the unique ability to iteratively oxidize the same-site of the substrate. These P450s are capable of forming diverse compounds that affect biological processes, including alcohols, ketones, aldehydes, and carboxylic acids. Although further structural and functional studies are needed to elucidate the mechanisms that allow multistep oxidative modification, recent studies have revealed the enzymatic properties and reaction mechanisms of these P450s. This mini-review covers the current knowledge of P450s that catalyze the multistep oxidation reactions and contribute to the production of a wide variety of metabolites by selected actinomycete strains, along with insights into their application and utility. Understanding the characteristics of these remarkable enzymes will facilitate their utilization in biotechnological applications to create biologically active and other high-value compounds. KEY POINTS: • The multistep oxidation by P450s plays a key role in the diversity of metabolites. • The mechanisms that enable P450s to catalyze iterative oxidation remains unknown. • The effective use of P450s that iteratively oxidize the same-site is discussed.
Collapse
Affiliation(s)
- Yohei Iizaka
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba, 274-8510, Japan.
| | - David H Sherman
- Life Sciences Institute, Department of Medicinal Chemistry, Chemistry, and Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Yojiro Anzai
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba, 274-8510, Japan
| |
Collapse
|
8
|
Mnguni FC, Padayachee T, Chen W, Gront D, Yu JH, Nelson DR, Syed K. More P450s Are Involved in Secondary Metabolite Biosynthesis in Streptomyces Compared to Bacillus, Cyanobacteria, and Mycobacterium. Int J Mol Sci 2020; 21:ijms21134814. [PMID: 32646068 PMCID: PMC7369989 DOI: 10.3390/ijms21134814] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 02/11/2020] [Accepted: 02/13/2020] [Indexed: 12/18/2022] Open
Abstract
Unraveling the role of cytochrome P450 monooxygenases (CYPs/P450s), heme-thiolate proteins present in living and non-living entities, in secondary metabolite synthesis is gaining momentum. In this direction, in this study, we analyzed the genomes of 203 Streptomyces species for P450s and unraveled their association with secondary metabolism. Our analyses revealed the presence of 5460 P450s, grouped into 253 families and 698 subfamilies. The CYP107 family was found to be conserved and highly populated in Streptomyces and Bacillus species, indicating its key role in the synthesis of secondary metabolites. Streptomyces species had a higher number of P450s than Bacillus and cyanobacterial species. The average number of secondary metabolite biosynthetic gene clusters (BGCs) and the number of P450s located in BGCs were higher in Streptomyces species than in Bacillus, mycobacterial, and cyanobacterial species, corroborating the superior capacity of Streptomyces species for generating diverse secondary metabolites. Functional analysis via data mining confirmed that many Streptomyces P450s are involved in the biosynthesis of secondary metabolites. This study was the first of its kind to conduct a comparative analysis of P450s in such a large number (203) of Streptomyces species, revealing the P450s’ association with secondary metabolite synthesis in Streptomyces species. Future studies should include the selection of Streptomyces species with a higher number of P450s and BGCs and explore the biotechnological value of secondary metabolites they produce.
Collapse
Affiliation(s)
- Fanele Cabangile Mnguni
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (F.C.M.); (T.P.)
| | - Tiara Padayachee
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (F.C.M.); (T.P.)
| | - Wanping Chen
- Department of Molecular Microbiology and Genetics, University of Göttingen, 37077 Göttingen, Germany;
| | - Dominik Gront
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland;
| | - Jae-Hyuk Yu
- Department of Bacteriology, University of Wisconsin-Madison, 3155 MSB, 1550 Linden Drive, Madison, WI 53706, USA;
- Department of Systems Biotechnology, Konkuk University, Seoul 05029, Korea
| | - 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.)
| | - Khajamohiddin Syed
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (F.C.M.); (T.P.)
- Correspondence: (D.R.N.); (K.S.)
| |
Collapse
|
9
|
Belknap KC, Park CJ, Barth BM, Andam CP. Genome mining of biosynthetic and chemotherapeutic gene clusters in Streptomyces bacteria. Sci Rep 2020; 10:2003. [PMID: 32029878 PMCID: PMC7005152 DOI: 10.1038/s41598-020-58904-9] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 01/22/2020] [Indexed: 01/05/2023] Open
Abstract
Streptomyces bacteria are known for their prolific production of secondary metabolites, many of which have been widely used in human medicine, agriculture and animal health. To guide the effective prioritization of specific biosynthetic gene clusters (BGCs) for drug development and targeting the most prolific producer strains, knowledge about phylogenetic relationships of Streptomyces species, genome-wide diversity and distribution patterns of BGCs is critical. We used genomic and phylogenetic methods to elucidate the diversity of major classes of BGCs in 1,110 publicly available Streptomyces genomes. Genome mining of Streptomyces reveals high diversity of BGCs and variable distribution patterns in the Streptomyces phylogeny, even among very closely related strains. The most common BGCs are non-ribosomal peptide synthetases, type 1 polyketide synthases, terpenes, and lantipeptides. We also found that numerous Streptomyces species harbor BGCs known to encode antitumor compounds. We observed that strains that are considered the same species can vary tremendously in the BGCs they carry, suggesting that strain-level genome sequencing can uncover high levels of BGC diversity and potentially useful derivatives of any one compound. These findings suggest that a strain-level strategy for exploring secondary metabolites for clinical use provides an alternative or complementary approach to discovering novel pharmaceutical compounds from microbes.
Collapse
Affiliation(s)
- Kaitlyn C Belknap
- University of New Hampshire, Department of Molecular, Cellular and Biomedical Sciences, Durham, NH, 03824, USA
| | - Cooper J Park
- University of New Hampshire, Department of Molecular, Cellular and Biomedical Sciences, Durham, NH, 03824, USA
| | - Brian M Barth
- University of New Hampshire, Department of Molecular, Cellular and Biomedical Sciences, Durham, NH, 03824, USA
| | - Cheryl P Andam
- University of New Hampshire, Department of Molecular, Cellular and Biomedical Sciences, Durham, NH, 03824, USA.
| |
Collapse
|
10
|
Affiliation(s)
- Yujie Liang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road 38, Beijing 100191, China
| | - Jialiang Wei
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road 38, Beijing 100191, China
| | - Xu Qiu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road 38, Beijing 100191, China
| | - Ning Jiao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road 38, Beijing 100191, China
- State Key Laboratory of Organometallic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| |
Collapse
|
11
|
Vander Wood DA, Keatinge-Clay AT. The modules of trans-acyltransferase assembly lines redefined with a central acyl carrier protein. Proteins 2018. [PMID: 29524261 DOI: 10.1002/prot.25493] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Here, the term "module" is redefined for trans-acyltransferase (trans-AT) assembly lines to agree with how its domains cooperate and evolutionarily co-migrate. The key domain in both the polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) modules of assembly lines is the acyl carrier protein (ACP). ACPs not only relay growing acyl chains through the assembly line but also collaborate with enzymes in modules, both in cis and in trans, to add a specific chemical moiety. A ketosynthase (KS) downstream of ACP often plays the role of gatekeeper, ensuring that only a single intermediate generated by the enzymes of a module is passed downstream. Bioinformatic analysis of 526 ACPs from 33 characterized trans-AT assembly lines reveals ACPs from the same module type generally clade together, reflective of the co-evolution of these domains with their cognate enzymes. While KSs downstream of ACPs from the same module type generally also clade together, KSs upstream of ACPs do not-in disagreement with the traditional definition of a module. Beyond nomenclature, the presented analysis impacts our understanding of module function, the evolution of assembly lines, pathway prediction, and assembly line engineering.
Collapse
Affiliation(s)
- Drew A Vander Wood
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Adrian T Keatinge-Clay
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| |
Collapse
|
12
|
Kong C, Huang H, Xue Y, Liu Y, Peng Q, Liu Q, Xu Q, Zhu Q, Yin Y, Zhou X, Zhang Y, Cai M. Heterologous pathway assembly reveals molecular steps of fungal terreic acid biosynthesis. Sci Rep 2018; 8:2116. [PMID: 29391515 PMCID: PMC5794859 DOI: 10.1038/s41598-018-20514-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 01/19/2018] [Indexed: 12/11/2022] Open
Abstract
Terreic acid is a potential anticancer drug as it inhibits Bruton's tyrosine kinase; however, its biosynthetic molecular steps remain unclear. In this work, the individual reactions of terreic acid biosynthesis were determined by stepwise pathway assembly in a heterologous host, Pichia pastoris, on the basis of previous knockout studies in a native host, Aspergillus terreus. Polyketide synthase AtX was found to catalyze the formation of partially reduced polyketide 6-methylsalicylic acid, followed by 3-methylcatechol synthesis by salicylate 1-monooxygenase AtA-mediated decarboxylative hydroxylation of 6-methylsalicylic acid. Our results show that cytochrome P450 monooxygenase AtE hydroxylates 3-methylcatechol, thus producing the next product, 3-methyl-1,2,4-benzenetriol. A smaller putative cytochrome P450 monooxygenase, AtG, assists with this step. Then, AtD causes epoxidation and hydroxyl oxidation of 3-methyl-1,2,4-benzenetriol and produces a compound terremutin, via which the previously unknown function of AtD was identified as cyclooxygenation. The final step involves an oxidation reaction of a hydroxyl group by a glucose-methanol-choline oxidoreductase, AtC, which leads to the final product: terreic acid. Functions of AtD and AtG were determined for the first time. All the genes were reanalyzed and all intermediates and final products were isolated and identified. Our model fully defines the molecular steps and corrects previous results from the literature.
Collapse
Affiliation(s)
- Chuixing Kong
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Hezhou Huang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Ying Xue
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Yiqi Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Qiangqiang Peng
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Qi Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Qin Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Qiaoyun Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Ying Yin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Xiangshan Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
- Shanghai Collaborative Innovation Center for Biomanufacturing, 130 Meilong Road, Shanghai, 200237, China
| | - Menghao Cai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.
| |
Collapse
|
13
|
Miyanaga A, Takayanagi R, Furuya T, Kawamata A, Itagaki T, Iwabuchi Y, Kanoh N, Kudo F, Eguchi T. Substrate Recognition by a Dual-Function P450 Monooxygenase GfsF Involved in FD-891 Biosynthesis. Chembiochem 2017; 18:2179-2187. [PMID: 28869713 DOI: 10.1002/cbic.201700429] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Indexed: 12/22/2022]
Abstract
GfsF is a multifunctional P450 monooxygenase that catalyzes epoxidation and subsequent hydroxylation in the biosynthesis of macrolide polyketide FD-891. Here, we describe the biochemical and structural analysis of GfsF. To obtain the structural basis of a dual-function reaction, we determined the crystal structure of ligand-free GfsF, which revealed GfsF to have a predominantly hydrophobic substrate binding pocket. The docking models, in conjunction with the results of the enzymatic assay with substrate analogues and site-directed mutagenesis suggested two distinct substrate binding modes for epoxidation and hydroxylation reactions, which explained how GfsF regulates the order of two oxidative reactions. These findings provide new insights into the reaction mechanism of multifunctional P450 monooxygenases.
Collapse
Affiliation(s)
- Akimasa Miyanaga
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo, 152-8551, Japan
| | - Ryuichi Takayanagi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo, 152-8551, Japan
| | - Takashi Furuya
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo, 152-8551, Japan
| | - Ayano Kawamata
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Tomohiro Itagaki
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Yoshiharu Iwabuchi
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Naoki Kanoh
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo, 152-8551, Japan
| | - Tadashi Eguchi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo, 152-8551, Japan
| |
Collapse
|
14
|
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: 133] [Impact Index Per Article: 19.0] [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.
Collapse
Affiliation(s)
- Jeffrey D Rudolf
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | | | | | | |
Collapse
|
15
|
Iizaka Y, Takeda R, Senzaki Y, Fukumoto A, Anzai Y. Cytochrome P450 enzyme RosC catalyzes a multistep oxidation reaction to form the non-active compound 20-carboxyrosamicin. FEMS Microbiol Lett 2017; 364:3861254. [DOI: 10.1093/femsle/fnx110] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 06/01/2017] [Indexed: 11/14/2022] Open
|
16
|
Abstract
The enzymology of 135 assembly lines containing primarily cis-acyltransferase modules is comprehensively analyzed, with greater attention paid to less common phenomena. Diverse online transformations, in which the substrate and/or product of the reaction is an acyl chain bound to an acyl carrier protein, are classified so that unusual reactions can be compared and underlying assembly-line logic can emerge. As a complement to the chemistry surrounding the loading, extension, and offloading of assembly lines that construct primarily polyketide products, structural aspects of the assembly-line machinery itself are considered. This review of assembly-line phenomena, covering the literature up to 2017, should thus be informative to the modular polyketide synthase novice and expert alike.
Collapse
Affiliation(s)
- Adrian T Keatinge-Clay
- Department of Molecular Biosciences, The University of Texas at Austin , Austin, Texas 78712, United States
| |
Collapse
|
17
|
Zhang X, Li S. Expansion of chemical space for natural products by uncommon P450 reactions. Nat Prod Rep 2017; 34:1061-1089. [DOI: 10.1039/c7np00028f] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This review focuses on unusual P450 reactions related to new chemistry, skeleton construction, structure re-shaping, and protein–protein interactions in natural product biosynthesis, which play significant roles in chemical space expansion for natural products.
Collapse
Affiliation(s)
- Xingwang Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology
- CAS Key Laboratory of Biofuels at Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao
- China
| | - Shengying Li
- Shandong Provincial Key Laboratory of Synthetic Biology
- CAS Key Laboratory of Biofuels at Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao
- China
| |
Collapse
|
18
|
Liu X. Generate a bioactive natural product library by mining bacterial cytochrome P450 patterns. Synth Syst Biotechnol 2016; 1:95-108. [PMID: 29062932 PMCID: PMC5640691 DOI: 10.1016/j.synbio.2016.01.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 01/26/2016] [Indexed: 11/25/2022] Open
Abstract
The increased number of annotated bacterial genomes provides a vast resource for genome mining. Several bacterial natural products with epoxide groups have been identified as pre-mRNA spliceosome inhibitors and antitumor compounds through genome mining. These epoxide-containing natural products feature a common biosynthetic characteristic that cytochrome P450s (CYPs) and its patterns such as epoxidases are employed in the tailoring reactions. The tailoring enzyme patterns are essential to both biological activities and structural diversity of natural products, and can be used for enzyme pattern-based genome mining. Recent development of direct cloning, heterologous expression, manipulation of the biosynthetic pathways and the CRISPR-CAS9 system have provided molecular biology tools to turn on or pull out nascent biosynthetic gene clusters to generate a microbial natural product library. This review focuses on a library of epoxide-containing natural products and their associated CYPs, with the intention to provide strategies on diversifying the structures of CYP-catalyzed bioactive natural products. It is conceivable that a library of diversified bioactive natural products will be created by pattern-based genome mining, direct cloning and heterologous expression as well as the genomic manipulation.
Collapse
Affiliation(s)
- Xiangyang Liu
- UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| |
Collapse
|
19
|
Itagaki T, Kawamata A, Takeuchi M, Hamada K, Iwabuchi Y, Eguchi T, Kudo F, Usui T, Kanoh N. Synthesis and structure–activity relationship study of FD-891: importance of the side chain and C8–C9 epoxide for cytotoxic activity against cancer cells. J Antibiot (Tokyo) 2016; 69:287-93. [DOI: 10.1038/ja.2015.148] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 12/22/2015] [Accepted: 12/24/2015] [Indexed: 11/09/2022]
|
20
|
Kudo F, Kawamura K, Furuya T, Yamanishi H, Motegi A, Komatsubara A, Numakura M, Miyanaga A, Eguchi T. Parallel Post-Polyketide Synthase Modification Mechanism Involved in FD-891 Biosynthesis inStreptomyces graminofaciensA-8890. Chembiochem 2016; 17:233-8. [DOI: 10.1002/cbic.201500533] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Fumitaka Kudo
- Department of Chemistry; Tokyo Institute of Technology; 2-12-1 O-okayama Meguro-ku Tokyo 152-8551 Japan
| | - Koichi Kawamura
- Department of Chemistry; Tokyo Institute of Technology; 2-12-1 O-okayama Meguro-ku Tokyo 152-8551 Japan
| | - Takashi Furuya
- Department of Chemistry and Materials Science; Tokyo Institute of Technology; 2-12-1 O-okayama Meguro-ku Tokyo 152-8551 Japan
| | - Hiroto Yamanishi
- Department of Chemistry and Materials Science; Tokyo Institute of Technology; 2-12-1 O-okayama Meguro-ku Tokyo 152-8551 Japan
| | - Atsushi Motegi
- Department of Chemistry and Materials Science; Tokyo Institute of Technology; 2-12-1 O-okayama Meguro-ku Tokyo 152-8551 Japan
| | - Akiko Komatsubara
- Department of Chemistry; Tokyo Institute of Technology; 2-12-1 O-okayama Meguro-ku Tokyo 152-8551 Japan
| | - Mario Numakura
- Department of Chemistry; Tokyo Institute of Technology; 2-12-1 O-okayama Meguro-ku Tokyo 152-8551 Japan
| | - Akimasa Miyanaga
- Department of Chemistry; Tokyo Institute of Technology; 2-12-1 O-okayama Meguro-ku Tokyo 152-8551 Japan
| | - Tadashi Eguchi
- Department of Chemistry and Materials Science; Tokyo Institute of Technology; 2-12-1 O-okayama Meguro-ku Tokyo 152-8551 Japan
| |
Collapse
|
21
|
Cochrane RVK, Vederas JC. Highly selective but multifunctional oxygenases in secondary metabolism. Acc Chem Res 2014; 47:3148-61. [PMID: 25250512 DOI: 10.1021/ar500242c] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Biosynthesis of bioactive natural products frequently features oxidation at multiple sites. Starting from a relatively reduced chemical scaffold that is assembled by controlled polymerization of small precursors, for example, acetate or amino acids, a diverse range of redox reactions can generate very complex and highly oxygenated structures. Their formation often involves C-H activation reactions catalyzed by oxygenase enzymes, either monooxygenases or dioxygenases. The former category includes the cytochrome P450s and flavin-dependent oxygenases, whereas examples of the latter are the non-heme iron α-ketoglutarate-dependent oxygenases. Oxygenases can catalyze a plethora of reactions ranging from hydroxylations and epoxidations to dehydrogenations, cyclizations, and rearrangements. The specific transformations are usually possible only with the use of these enzymatic catalysts. Aside from the ability of oxygenases to specifically oxidize unactivated carbon skeletons, some have recently been demonstrated to possess a fascinating ability to catalyze multiple reactions in a highly ordered fashion at different sites starting with a single substrate molecule. In the past, oxygenases associated with secondary metabolite pathways were considered to be highly regio-, stereo-, and substrate specific, with one oxidizing enzyme encoded in the gene cluster corresponding to one oxidation location in the natural product itself. However, it is becoming progressively clear that this "one oxygenase, one oxidation site" relationship is not necessarily a valid assumption. Multifunctional oxidases are known to occur in higher plants, fungi, and bacteria. Natural product gene clusters that contain multifunctional oxidase enzymes are responsible for production of lovastatin (a cholesterol-lowering agent and precursor to simvastatin), scopolamine (an anticholinergic drug), and cytochalasin E (an angiogenesis inhibitor), among many others. As opposed to simply being substrate promiscuous, these enzymes show very high substrate specificity and catalyze several oxidative reactions in a single pathway, with each oxidation being a prerequisite for the next. The basis for their specificity and highly ordered sequence is not yet well understood. In the lovastatin pathway, LovA is a cytochrome P450 that introduces a double bond and a hydroxyl group. H6H is an α-ketoglutarate-dependent oxygenase that hydroxylates (-)-atropine and then closes the newly introduced oxygen onto a neighboring methylene to generate the epoxide of scopolamine. CcsB is a flavin-dependent Baeyer-Villigerase that converts a ketone to a carbonate by double oxidation, a reaction not possible without enzymes. Recent crystallographic studies of other multifunctional oxygenases, such as AurH, a cytochrome P450 from Streptomyces thioluteus involved in aureothin biosynthesis, have indicated a steric switch mechanism. After the initial hydroxylation reaction catalyzed by AurH, the enzyme is thought to undergo a substrate-induced conformational change. In this Account, advances in our knowledge of these fascinating multifunctional enzymes and their potential will be explored.
Collapse
Affiliation(s)
| | - John C. Vederas
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2 Canada
| |
Collapse
|
22
|
Kanoh N, Kawamata A, Itagaki T, Miyazaki Y, Yahata K, Kwon E, Iwabuchi Y. A Concise and Unified Strategy for Synthesis of the C1–C18 Macrolactone Fragments of FD-891, FD-892 and Their Analogues: Formal Total Synthesis of FD-891. Org Lett 2014; 16:5216-9. [DOI: 10.1021/ol502633j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Naoki Kanoh
- Graduate School of Pharmaceutical Sciences and ‡Research and Analytical Center
for Giant Molecules, Graduate School of Science, Tohoku University, 6-3
Aza-Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Ayano Kawamata
- Graduate School of Pharmaceutical Sciences and ‡Research and Analytical Center
for Giant Molecules, Graduate School of Science, Tohoku University, 6-3
Aza-Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Tomohiro Itagaki
- Graduate School of Pharmaceutical Sciences and ‡Research and Analytical Center
for Giant Molecules, Graduate School of Science, Tohoku University, 6-3
Aza-Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Yuta Miyazaki
- Graduate School of Pharmaceutical Sciences and ‡Research and Analytical Center
for Giant Molecules, Graduate School of Science, Tohoku University, 6-3
Aza-Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Kenzo Yahata
- Graduate School of Pharmaceutical Sciences and ‡Research and Analytical Center
for Giant Molecules, Graduate School of Science, Tohoku University, 6-3
Aza-Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Eunsang Kwon
- Graduate School of Pharmaceutical Sciences and ‡Research and Analytical Center
for Giant Molecules, Graduate School of Science, Tohoku University, 6-3
Aza-Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Yoshiharu Iwabuchi
- Graduate School of Pharmaceutical Sciences and ‡Research and Analytical Center
for Giant Molecules, Graduate School of Science, Tohoku University, 6-3
Aza-Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| |
Collapse
|
23
|
Spliceostatin hemiketal biosynthesis in Burkholderia spp. is catalyzed by an iron/α-ketoglutarate-dependent dioxygenase. Proc Natl Acad Sci U S A 2014; 111:E3376-85. [PMID: 25097259 DOI: 10.1073/pnas.1408300111] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Spliceostatins are potent spliceosome inhibitors biosynthesized by a hybrid nonribosomal peptide synthetase-polyketide synthase (NRPS-PKS) system of the trans-acyl transferase (AT) type. Burkholderia sp. FERM BP-3421 produces hemiketal spliceostatins, such as FR901464, as well as analogs containing a terminal carboxylic acid. We provide genetic and biochemical evidence for hemiketal biosynthesis by oxidative decarboxylation rather than the previously hypothesized Baeyer-Villiger oxidative release postulated to be catalyzed by a flavin-dependent monooxygenase (FMO) activity internal to the last module of the PKS. Inactivation of Fe(II)/α-ketoglutarate-dependent dioxygenase gene fr9P led to loss of hemiketal congeners, whereas the mutant was still able to produce all major carboxylic acid-type compounds. FMO mutants, on the other hand, produced both hemiketal and carboxylic acid analogs containing an exocyclic methylene instead of an epoxide, indicating that the FMO is involved in epoxidation rather than Baeyer-Villiger oxidation. Moreover, recombinant Fr9P enzyme was shown to catalyze hydroxylation to form β-hydroxy acids, which upon decarboxylation led to hemiketal FR901464. Finally, a third oxygenase activity encoded in the biosynthetic gene cluster, the cytochrome P450 monooxygenase Fr9R, was assigned as a 4-hydroxylase based on gene inactivation results. Identification and deletion of the gene involved in hemiketal formation allowed us to generate a strain--the dioxygenase fr9P(-) mutant--that accumulates only the carboxylic acid-type spliceostatins, which are as potent as the hemiketal analogs, when derivatized to increase cell permeability, but are chemically more stable.
Collapse
|
24
|
Krokida A, Delis C, Geisler K, Garagounis C, Tsikou D, Peña-Rodríguez LM, Katsarou D, Field B, Osbourn AE, Papadopoulou KK. A metabolic gene cluster in Lotus japonicus discloses novel enzyme functions and products in triterpene biosynthesis. THE NEW PHYTOLOGIST 2013; 200:675-690. [PMID: 23909862 DOI: 10.1111/nph.12414] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 06/20/2013] [Indexed: 05/03/2023]
Abstract
Genes for triterpene biosynthetic pathways exist as metabolic gene clusters in oat and Arabidopsis thaliana plants. We characterized the presence of an analogous gene cluster in the model legume Lotus japonicus. In the genomic regions flanking the oxidosqualene cyclase AMY2 gene, genes for two different classes of cytochrome P450 and a gene predicted to encode a reductase were identified. Functional characterization of the cluster genes was pursued by heterologous expression in Nicotiana benthamiana. The gene expression pattern was studied under different developmental and environmental conditions. The physiological role of the gene cluster in nodulation and plant development was studied in knockdown experiments. A novel triterpene structure, dihydrolupeol, was produced by AMY2. A new plant cytochrome P450, CYP71D353, which catalyses the formation of 20-hydroxybetulinic acid in a sequential three-step oxidation of 20-hydroxylupeol was characterized. The genes within the cluster are highly co-expressed during root and nodule development, in hormone-treated plants and under various environmental stresses. A transcriptional gene silencing mechanism that appears to be involved in the regulation of the cluster genes was also revealed. A tightly co-regulated cluster of functionally related genes is involved in legume triterpene biosynthesis, with a possible role in plant development.
Collapse
Affiliation(s)
- Afrodite Krokida
- Department of Biochemistry and Biotechnology, University of Thessaly, Ploutonos 26 & Aeolou Str., Larisa, 41221, Greece
| | - Costas Delis
- Department of Biochemistry and Biotechnology, University of Thessaly, Ploutonos 26 & Aeolou Str., Larisa, 41221, Greece
| | - Katrin Geisler
- Department of Metabolic Biology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK
| | - Constantine Garagounis
- Department of Biochemistry and Biotechnology, University of Thessaly, Ploutonos 26 & Aeolou Str., Larisa, 41221, Greece
| | - Daniela Tsikou
- Department of Biochemistry and Biotechnology, University of Thessaly, Ploutonos 26 & Aeolou Str., Larisa, 41221, Greece
| | - Luis M Peña-Rodríguez
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
| | - Dimitra Katsarou
- Department of Biochemistry and Biotechnology, University of Thessaly, Ploutonos 26 & Aeolou Str., Larisa, 41221, Greece
| | - Ben Field
- Department of Metabolic Biology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK
| | - Anne E Osbourn
- Department of Metabolic Biology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK
| | - Kalliope K Papadopoulou
- Department of Biochemistry and Biotechnology, University of Thessaly, Ploutonos 26 & Aeolou Str., Larisa, 41221, Greece
| |
Collapse
|
25
|
Geisler K, Hughes RK, Sainsbury F, Lomonossoff GP, Rejzek M, Fairhurst S, Olsen CE, Motawia MS, Melton RE, Hemmings AM, Bak S, Osbourn A. Biochemical analysis of a multifunctional cytochrome P450 (CYP51) enzyme required for synthesis of antimicrobial triterpenes in plants. Proc Natl Acad Sci U S A 2013; 110:E3360-7. [PMID: 23940321 PMCID: PMC3761579 DOI: 10.1073/pnas.1309157110] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Members of the cytochromes P450 superfamily (P450s) catalyze a huge variety of oxidation reactions in microbes and higher organisms. Most P450 families are highly divergent, but in contrast the cytochrome P450 14α-sterol demethylase (CYP51) family is one of the most ancient and conserved, catalyzing sterol 14α-demethylase reactions required for essential sterol synthesis across the fungal, animal, and plant kingdoms. Oats (Avena spp.) produce antimicrobial compounds, avenacins, that provide protection against disease. Avenacins are synthesized from the simple triterpene, β-amyrin. Previously we identified a gene encoding a member of the CYP51 family of cytochromes P450, AsCyp51H10 (also known as Saponin-deficient 2, Sad2), that is required for avenacin synthesis in a forward screen for avenacin-deficient oat mutants. sad2 mutants accumulate β-amyrin, suggesting that they are blocked early in the pathway. Here, using a transient plant expression system, we show that AsCYP51H10 is a multifunctional P450 capable of modifying both the C and D rings of the pentacyclic triterpene scaffold to give 12,13β-epoxy-3β,16β-dihydroxy-oleanane (12,13β-epoxy-16β-hydroxy-β-amyrin). Molecular modeling and docking experiments indicate that C16 hydroxylation is likely to precede C12,13 epoxidation. Our computational modeling, in combination with analysis of a suite of sad2 mutants, provides insights into the unusual catalytic behavior of AsCYP51H10 and its active site mutants. Fungal bioassays show that the C12,13 epoxy group is an important determinant of antifungal activity. Accordingly, the oat AsCYP51H10 enzyme has been recruited from primary metabolism and has acquired a different function compared to other characterized members of the plant CYP51 family--as a multifunctional stereo- and regio-specific hydroxylase in plant specialized metabolism.
Collapse
Affiliation(s)
- Katrin Geisler
- Departments of Metabolic Biology and
- Department of Plant and Environmental Sciences, VKR Research Centre Pro-Active Plants, Faculty of Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark; and
| | - Richard K. Hughes
- Biological Chemistry, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Frank Sainsbury
- Biological Chemistry, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | | | - Martin Rejzek
- Biological Chemistry, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Shirley Fairhurst
- Biological Chemistry, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Carl-Erik Olsen
- Department of Plant and Environmental Sciences, VKR Research Centre Pro-Active Plants, Faculty of Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark; and
| | - Mohammed Saddik Motawia
- Department of Plant and Environmental Sciences, VKR Research Centre Pro-Active Plants, Faculty of Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark; and
| | | | - Andrew M. Hemmings
- Schools of Chemistry and
- Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Søren Bak
- Department of Plant and Environmental Sciences, VKR Research Centre Pro-Active Plants, Faculty of Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark; and
| | | |
Collapse
|
26
|
Abstract
Diverse oxygenation patterns of natural products generated by secondary metabolic pathways in microorganisms and plants are largely achieved through the tailoring reactions catalysed by cytochrome P450 enzymes (P450s). P450s are a large family of oxidative hemoproteins found in all life forms from prokaryotes to humans. Understanding the reactivity and selectivity of these fascinating C-H bond-activating catalysts will advance their use in generating valuable pharmaceuticals and products for medicine, agriculture and industry. A major strength of this P450 group is its set of established enzyme-substrate relationships, the source of the most detailed knowledge on how P450 enzymes work. Engineering microbial-derived P450 enzymes to accommodate alternative substrates and add new functions continues to be an important near- and long-term practical goal driving the structural characterization of these molecules. Understanding the natural evolution of P450 structure-function should accelerate metabolic engineering and directed evolutionary approaches to enhance diversification of natural product structures and other biosynthetic applications.
Collapse
Affiliation(s)
- Larissa M. Podust
- Department of Pathology, Molecular Structure Group and Center for Discovery and Innovation in Parasitic Diseases (CDIPD), University of California San Francisco, San Francisco, California, 94158, USA. Fax: 415 502 8193; Tel: 415 514 1381;
| | - David H. Sherman
- Life Sciences Institute, Departments of Medicinal Chemistry, Chemistry, and Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan, 48109, USA. Fax: 734-615-3641; Tel: 734 615 9907;
| |
Collapse
|
27
|
Li S, Tietz DR, Rutaganira FU, Kells PM, Anzai Y, Kato F, Pochapsky TC, Sherman DH, Podust LM. Substrate recognition by the multifunctional cytochrome P450 MycG in mycinamicin hydroxylation and epoxidation reactions. J Biol Chem 2012; 287:37880-90. [PMID: 22952225 DOI: 10.1074/jbc.m112.410340] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The majority of characterized cytochrome P450 enzymes in actinomycete secondary metabolic pathways are strictly substrate-, regio-, and stereo-specific. Examples of multifunctional biosynthetic cytochromes P450 with broader substrate and regio-specificity are growing in number and are of particular interest for biosynthetic and chemoenzymatic applications. MycG is among the first P450 monooxygenases characterized that catalyzes both hydroxylation and epoxidation reactions in the final biosynthetic steps, leading to oxidative tailoring of the 16-membered ring macrolide antibiotic mycinamicin II in the actinomycete Micromonospora griseorubida. The ordering of steps to complete the biosynthetic process involves a complex substrate recognition pattern by the enzyme and interplay between three tailoring modifications as follows: glycosylation, methylation, and oxidation. To understand the catalytic properties of MycG, we structurally characterized the ligand-free enzyme and its complexes with three native metabolites. These include substrates mycinamicin IV and V and their biosynthetic precursor mycinamicin III, which carries the monomethoxy sugar javose instead of the dimethoxylated sugar mycinose. The two methoxy groups of mycinose serve as sensors that mediate initial recognition to discriminate between closely related substrates in the post-polyketide oxidative tailoring of mycinamicin metabolites. Because x-ray structures alone did not explain the mechanisms of macrolide hydroxylation and epoxidation, paramagnetic NMR relaxation measurements were conducted. Molecular modeling based on these data indicates that in solution substrate may penetrate the active site sufficiently to place the abstracted hydrogen atom of mycinamicin IV within 6 Å of the heme iron and ~4 Å of the oxygen of iron-ligated water.
Collapse
Affiliation(s)
- Shengying Li
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Function of cytochrome P450 enzymes MycCI and MycG in Micromonospora griseorubida, a producer of the macrolide antibiotic mycinamicin. Antimicrob Agents Chemother 2012; 56:3648-56. [PMID: 22547618 DOI: 10.1128/aac.06063-11] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The cytochrome P450 enzymes MycCI and MycG are encoded within the mycinamicin biosynthetic gene cluster and are involved in the biosynthesis of mycinamicin II (a 16-membered macrolide antibiotic produced by Micromonospora griseorubida). Based on recent enzymatic studies, MycCI is characterized as the C-21 methyl hydroxylase of mycinamicin VIII, while MycG is designated multifunctional P450, which catalyzes hydroxylation and also epoxidation at C-14 and C-12/13 on the macrolactone ring of mycinamicin. Here, we confirm the functions of MycCI and MycG in M. griseorubida. Protomycinolide IV and mycinamicin VIII accumulated in the culture broth of the mycCI disruption mutant; moreover, the mycCI gene fragment complemented the production of mycinamicin I and mycinamicin II, which are produced as major mycinamicins by the wild strain M. griseorubida A11725. The mycG disruption mutant did not produce mycinamicin I and mycinamicin II; however, mycinamicin IV accumulated in the culture broth. The mycG gene was located immediately downstream of the self-resistance gene myrB. The mycG gene under the control of mycGp complemented the production of mycinamicin I and mycinamicin II. Furthermore, the amount of mycinamicin II produced by the strain complemented with the mycG gene under the control of myrBp was approximately 2-fold higher than that produced by the wild strain. In M. griseorubida, MycG recognized mycinamicin IV, mycinamicin V, and also mycinamicin III as the substrates. Moreover, it catalyzed hydroxylation and also epoxidation at C-14 and C-12/13 on these intermediates. However, C-14 on mycinamicin I was not hydroxylated.
Collapse
|
29
|
Thibodeaux CJ, Chang WC, Liu HW. Enzymatic chemistry of cyclopropane, epoxide, and aziridine biosynthesis. Chem Rev 2012; 112:1681-709. [PMID: 22017381 PMCID: PMC3288687 DOI: 10.1021/cr200073d] [Citation(s) in RCA: 204] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Wei-chen Chang
- College of Pharmacy and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712
| | - Hung-wen Liu
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712
- College of Pharmacy and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712
| |
Collapse
|
30
|
Urlacher VB, Girhard M. Cytochrome P450 monooxygenases: an update on perspectives for synthetic application. Trends Biotechnol 2012; 30:26-36. [DOI: 10.1016/j.tibtech.2011.06.012] [Citation(s) in RCA: 342] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Revised: 06/10/2011] [Accepted: 06/16/2011] [Indexed: 01/14/2023]
|
31
|
Barriuso J, Nguyen DT, Li JWH, Roberts JN, MacNevin G, Chaytor JL, Marcus SL, Vederas JC, Ro DK. Double oxidation of the cyclic nonaketide dihydromonacolin L to monacolin J by a single cytochrome P450 monooxygenase, LovA. J Am Chem Soc 2011; 133:8078-81. [PMID: 21495633 DOI: 10.1021/ja201138v] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Lovastatin, a cyclic nonaketide from Aspergillus terreus, is a hypercholesterolemic agent and a precursor to simvastatin, a semi-synthetic cholesterol-lowering drug. The biosynthesis of the lovastatin backbone (dihydromonacolin L) and the final 2-methylbutyryl decoration have been fully characterized. However, it remains unclear how two central reactions are catalyzed, namely, introduction of the 4a,5-double bond and hydroxylation at C-8. A cytochrome P450 gene, lovA, clustered with polyketide synthase lovB, has been a prime candidate for these reactions, but inability to obtain LovA recombinant enzyme has impeded detailed biochemical analyses. The synthetic codon optimization and/or N-terminal peptide replacement of lovA allowed the lovA expression in yeast (Saccharomyces cerevisiae). Both in vivo feeding and in vitro enzyme assays showed that LovA catalyzed the conversion of dihydromonacolin L acid to monacolin L acid and monacolin J acid, two proposed pathway intermediates in the biosynthesis of lovastatin. LovA was demonstrated to catalyze the regio- and stereo-specific hydroxylation of monacolin L acid to yield monacolin J acid. These results demonstrate that LovA is the single enzyme that performs both of the two elusive oxidative reactions in the lovastatin biosynthesis.
Collapse
Affiliation(s)
- Jorge Barriuso
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary T2N 1N4, Canada
| | | | | | | | | | | | | | | | | |
Collapse
|