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Ushimaru R. Unusual Enzymatic C-C Bond Formation and Cleavage Reactions during Natural Product Biosynthesis. Chem Pharm Bull (Tokyo) 2024; 72:241-247. [PMID: 38432903 DOI: 10.1248/cpb.c23-00889] [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] [Indexed: 03/05/2024]
Abstract
Natural products from plants and microorganisms provide a valuable reservoir of pharmaceutical compounds. C-C bond formation and cleavage are crucial events during natural product biosynthesis, playing pivotal roles in generating diverse and intricate chemical structures that are essential for biological functions. This review summarizes our recent findings regarding biosynthetic enzymes that catalyze unconventional C-C bond formation and cleavage reactions during natural product biosynthesis.
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Affiliation(s)
- Richiro Ushimaru
- Graduate School of Pharmaceutical Sciences, The University of Tokyo
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo
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2
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Nguyen KU, Zhang Y, Liu Q, Zhang R, Jin X, Taniguchi M, Miller ES, Lindsey JS. Tolyporphins-Exotic Tetrapyrrole Pigments in a Cyanobacterium-A Review. Molecules 2023; 28:6132. [PMID: 37630384 PMCID: PMC10459692 DOI: 10.3390/molecules28166132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/11/2023] [Accepted: 08/13/2023] [Indexed: 08/27/2023] Open
Abstract
Tolyporphins were discovered some 30 years ago as part of a global search for antineoplastic compounds from cyanobacteria. To date, the culture HT-58-2, comprised of a cyanobacterium-microbial consortium, is the sole known producer of tolyporphins. Eighteen tolyporphins are now known-each is a free base tetrapyrrole macrocycle with a dioxobacteriochlorin (14), oxochlorin (3), or porphyrin (1) chromophore. Each compound displays two, three, or four open β-pyrrole positions and two, one, or zero appended C-glycoside (or -OH or -OAc) groups, respectively; the appended groups form part of a geminal disubstitution motif flanking the oxo moiety in the pyrroline ring. The distinct structures and repertoire of tolyporphins stand alone in the large pigments-of-life family. Efforts to understand the cyanobacterial origin, biosynthetic pathways, structural diversity, physiological roles, and potential pharmacological properties of tolyporphins have attracted a broad spectrum of researchers from diverse scientific areas. The identification of putative biosynthetic gene clusters in the HT-58-2 cyanobacterial genome and accompanying studies suggest a new biosynthetic paradigm in the tetrapyrrole arena. The present review provides a comprehensive treatment of the rich science concerning tolyporphins.
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Affiliation(s)
- Kathy-Uyen Nguyen
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA; (K.-U.N.); (Y.Z.); (Q.L.); (R.Z.); (X.J.); (M.T.)
| | - Yunlong Zhang
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA; (K.-U.N.); (Y.Z.); (Q.L.); (R.Z.); (X.J.); (M.T.)
| | - Qihui Liu
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA; (K.-U.N.); (Y.Z.); (Q.L.); (R.Z.); (X.J.); (M.T.)
| | - Ran Zhang
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA; (K.-U.N.); (Y.Z.); (Q.L.); (R.Z.); (X.J.); (M.T.)
| | - Xiaohe Jin
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA; (K.-U.N.); (Y.Z.); (Q.L.); (R.Z.); (X.J.); (M.T.)
| | - Masahiko Taniguchi
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA; (K.-U.N.); (Y.Z.); (Q.L.); (R.Z.); (X.J.); (M.T.)
| | - Eric S. Miller
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695-7612, USA;
| | - Jonathan S. Lindsey
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA; (K.-U.N.); (Y.Z.); (Q.L.); (R.Z.); (X.J.); (M.T.)
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Ushimaru R, Lyu J, Abe I. Diverse enzymatic chemistry for propionate side chain cleavages in tetrapyrrole biosynthesis. J Ind Microbiol Biotechnol 2023; 50:kuad016. [PMID: 37422437 PMCID: PMC10548856 DOI: 10.1093/jimb/kuad016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 07/07/2023] [Indexed: 07/10/2023]
Abstract
Tetrapyrroles represent a unique class of natural products that possess diverse chemical architectures and exhibit a broad range of biological functions. Accordingly, they attract keen attention from the natural product community. Many metal-chelating tetrapyrroles serve as enzyme cofactors essential for life, while certain organisms produce metal-free porphyrin metabolites with biological activities potentially beneficial for the producing organisms and for human use. The unique properties of tetrapyrrole natural products derive from their extensively modified and highly conjugated macrocyclic core structures. Most of these various tetrapyrrole natural products biosynthetically originate from a branching point precursor, uroporphyrinogen III, which contains propionate and acetate side chains on its macrocycle. Over the past few decades, many modification enzymes with unique catalytic activities, and the diverse enzymatic chemistries employed to cleave the propionate side chains from the macrocycles, have been identified. In this review, we highlight the tetrapyrrole biosynthetic enzymes required for the propionate side chain removal processes and discuss their various chemical mechanisms. ONE-SENTENCE SUMMARY This mini-review describes various enzymes involved in the propionate side chain cleavages during the biosynthesis of tetrapyrrole cofactors and secondary metabolites.
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Affiliation(s)
- Richiro Ushimaru
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Jiaqi Lyu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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Taniguchi M, Bocian DF, Holten D, Lindsey JS. Beyond green with synthetic chlorophylls – Connecting structural features with spectral properties. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C: PHOTOCHEMISTRY REVIEWS 2022. [DOI: 10.1016/j.jphotochemrev.2022.100513] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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Abstract
Covering: 2020This review covers the literature published in 2020 for marine natural products (MNPs), with 757 citations (747 for the period January to December 2020) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1407 in 420 papers for 2020), together with the relevant biological activities, source organisms and country of origin. Pertinent reviews, biosynthetic studies, first syntheses, and syntheses that led to the revision of structures or stereochemistries, have been included. A meta analysis of bioactivity data relating to new MNPs reported over the last five years is also presented.
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Affiliation(s)
- Anthony R Carroll
- School of Environment and Science, Griffith University, Gold Coast, Australia. .,Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia
| | - Brent R Copp
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | - Rohan A Davis
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia.,School of Enivironment and Science, Griffith University, Brisbane, Australia
| | - Robert A Keyzers
- Centre for Biodiscovery, School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington, New Zealand
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Jin X, Zhang Y, Zhang R, Nguyen KU, Lindsey JS, Miller ES. Identification of Putative Biosynthetic Gene Clusters for Tolyporphins in Multiple Filamentous Cyanobacteria. Life (Basel) 2021; 11:758. [PMID: 34440502 PMCID: PMC8401325 DOI: 10.3390/life11080758] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 07/21/2021] [Accepted: 07/26/2021] [Indexed: 01/23/2023] Open
Abstract
Tolyporphins A-R are unusual tetrapyrrole macrocycles produced by the non-axenic filamentous cyanobacterium HT-58-2. A putative biosynthetic gene cluster for biosynthesis of tolyporphins (here termed BGC-1) was previously identified in the genome of HT-58-2. Here, homology searching of BGC-1 in HT-58-2 led to identification of similar BGCs in seven other filamentous cyanobacteria, including strains Nostoc sp. 106C, Nostoc sp. RF31YmG, Nostoc sp. FACHB-892, Brasilonema octagenarum UFV-OR1, Brasilonema octagenarum UFV-E1, Brasilonema sennae CENA114 and Oculatella sp. LEGE 06141, suggesting their potential for tolyporphins production. A similar gene cluster (BGC-2) also was identified unexpectedly in HT-58-2. Tolyporphins BGCs were not identified in unicellular cyanobacteria. Phylogenetic analysis based on 16S rRNA and a common component of the BGCs, TolD, points to a close evolutionary history between each strain and their respective tolyporphins BGC. Though identified with putative tolyporphins BGCs, examination of pigments extracted from three cyanobacteria has not revealed the presence of tolyporphins. Overall, the identification of BGCs and potential producers of tolyporphins presents a collection of candidate cyanobacteria for genetic and biochemical analysis pertaining to these unusual tetrapyrrole macrocycles.
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Affiliation(s)
- Xiaohe Jin
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA; (X.J.); (Y.Z.); (R.Z.); (K.-U.N.)
| | - Yunlong Zhang
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA; (X.J.); (Y.Z.); (R.Z.); (K.-U.N.)
| | - Ran Zhang
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA; (X.J.); (Y.Z.); (R.Z.); (K.-U.N.)
| | - Kathy-Uyen Nguyen
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA; (X.J.); (Y.Z.); (R.Z.); (K.-U.N.)
| | - Jonathan S. Lindsey
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA; (X.J.); (Y.Z.); (R.Z.); (K.-U.N.)
| | - Eric S. Miller
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695-7615, USA
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Sollert C, Kocsi D, Jane RT, Orthaber A, Borbas KE. C-glycosylated pyrroles and their application in dipyrromethane and porphyrin synthesis. J PORPHYR PHTHALOCYA 2021. [DOI: 10.1142/s1088424621500723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Pyrrole C-glycosylated in either the 2- or the 3-position could be prepared by the acid-catalyzed reaction between trichloroacetimidate glycosyl donors and pyrrole, or [Formula: see text]-phenyl-tri?uoroacetimidate glucosyl donor and [Formula: see text]-TIPS pyrrole, respectively. Pyrroles carrying glucose, mannose, galactose and lactose in the 2-position, and glucose in the 3-position were obtained. The configurations of the products could be assigned using a combination of 1D and 2D NMR spectroscopy. A number of undesired background reactions yielding a variety of stereo- and regioisomers were identified; in several cases these could be eliminated. Glycosylpyrroles could be incorporated into mono- and diglycosylated dipyrromethanes, a diglycosylated BODIPY dye, and a monoglycosylated Zn(II) porphyrin without damaging the sugar unit.
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Affiliation(s)
- Carina Sollert
- Department of Chemistry, Ångström Laboratory, Box 523, Uppsala University, 75120 Uppsala, Sweden
| | - Daniel Kocsi
- Department of Chemistry, Ångström Laboratory, Box 523, Uppsala University, 75120 Uppsala, Sweden
| | - Reuben T. Jane
- Department of Chemistry, Ångström Laboratory, Box 523, Uppsala University, 75120 Uppsala, Sweden
| | - Andreas Orthaber
- Department of Chemistry, Ångström Laboratory, Box 523, Uppsala University, 75120 Uppsala, Sweden
| | - K. Eszter Borbas
- Department of Chemistry, Ångström Laboratory, Box 523, Uppsala University, 75120 Uppsala, Sweden
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Nguyen KU, Zhang R, Taniguchi M, Lindsey JS. Fluorescence Assay for Tolyporphins Amidst Abundant Chlorophyll in Crude Cyanobacterial Extracts. Photochem Photobiol 2021; 97:1507-1515. [PMID: 34152600 DOI: 10.1111/php.13474] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 06/17/2021] [Indexed: 11/30/2022]
Abstract
Tolyporphins are distinctive tetrapyrrole natural products found singularly in a filamentous cyanobacterial-microbial holobiont (termed HT-58-2) from Micronesia. The absorption and fluorescence features of tolyporphins resemble those of chlorophyll a, complicating direct analysis of culture samples. Treatment of the crude (unfractionated) organic extract (CH2 Cl2 /2-propanol, 1:1) of HT-58-2 cultures with NaBH4 in methanol causes reduction of the peripheral ketone auxochromes, whereupon tolyporphins (predominantly 7,17-dioxobacteriochlorins) exhibit a bathochromic shift (λabs ~ 676 → ~ 700 nm) and chlorophyll a (a 131 -oxochlorin) exhibits a hypsochromic shift (λabs 665 → 634 nm). Fluorescence excitation spectroscopy (at 368 and 491 nm with λem 710 nm) enabled detection of reduced tolyporphins amidst abundant reduced chlorophyll a (1:19 ratio), a detection sensitivity >5 times that without reduction. The resulting assay combines simple sample preparation from non-axenic cultures at microscale quantities (2 mL, 2 μm), absence of any fractionation procedures, and fluorescence detection. Tolyporphins were readily detected in cultures of HT-58-2 at reasonable growth periods in the absence of environmental stressors, which was not possible previously.
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Affiliation(s)
- Kathy-Uyen Nguyen
- Department of Chemistry, North Carolina State University, Raleigh, NC
| | - Ran Zhang
- Department of Chemistry, North Carolina State University, Raleigh, NC
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Natural Product Gene Clusters in the Filamentous Nostocales Cyanobacterium HT-58-2. Life (Basel) 2021; 11:life11040356. [PMID: 33919559 PMCID: PMC8073705 DOI: 10.3390/life11040356] [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: 03/14/2021] [Revised: 04/12/2021] [Accepted: 04/15/2021] [Indexed: 12/15/2022] Open
Abstract
Cyanobacteria are known as rich repositories of natural products. One cyanobacterial-microbial consortium (isolate HT-58-2) is known to produce two fundamentally new classes of natural products: the tetrapyrrole pigments tolyporphins A–R, and the diterpenoid compounds tolypodiol, 6-deoxytolypodiol, and 11-hydroxytolypodiol. The genome (7.85 Mbp) of the Nostocales cyanobacterium HT-58-2 was annotated previously for tetrapyrrole biosynthesis genes, which led to the identification of a putative biosynthetic gene cluster (BGC) for tolyporphins. Here, bioinformatics tools have been employed to annotate the genome more broadly in an effort to identify pathways for the biosynthesis of tolypodiols as well as other natural products. A putative BGC (15 genes) for tolypodiols has been identified. Four BGCs have been identified for the biosynthesis of other natural products. Two BGCs related to nitrogen fixation may be relevant, given the association of nitrogen stress with production of tolyporphins. The results point to the rich biosynthetic capacity of the HT-58-2 cyanobacterium beyond the production of tolyporphins and tolypodiols.
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O'Donnell TJ, Gurr JR, Dai J, Taniguchi M, Williams PG, Lindsey JS. Tolyporphins A–R, unusual tetrapyrrole macrocycles in a cyanobacterium from Micronesia, assessed quantitatively from the culture HT-58-2. NEW J CHEM 2021. [DOI: 10.1039/d1nj02108g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Tolyporphins A–R are the newest additions to the family of native tetrapyrroles. LC-MS-dMRM and absorption spectroscopy have been employed for analysis of mixtures containing the 18 distinctive natural products.
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Affiliation(s)
| | - Joshua R. Gurr
- Department of Chemistry
- University of Hawaii at Manoa
- Honolulu
- USA
| | - Jingqiu Dai
- Department of Chemistry
- University of Hawaii at Manoa
- Honolulu
- USA
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Abstract
Tolyporphins, relatively new members of the pigments of life family found in a cyanobacterium, differ in the chromophores, pyrroline substituents, and stereochemistry, yet likely all derive from uroporphyrinogen III.
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Gurr JR, O’Donnell TJ, Luo Y, Yoshida WY, Hall ML, Mayer AM, Sun R, Williams PG. 6-Deoxy- and 11-Hydroxytolypodiols: Meroterpenoids from the Cyanobacterium HT-58-2. JOURNAL OF NATURAL PRODUCTS 2020; 83:1691-1695. [PMID: 32282204 PMCID: PMC7246299 DOI: 10.1021/acs.jnatprod.9b00844] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Chemical investigation of cyanobacterial strain HT-58-2, which most closely aligns with the genus Brasilomena, has led to the isolation of two compounds related to tolypodiol. The structures and absolute configuration of 6-deoxytolypodiol (1) and 11-hydroxytolypodiol (2) were elucidated by spectroscopic and spectrometric analysis. While tolypodiol previously showed anti-inflammatory activity in a mouse ear edema assay, only 2 reduced in vitro thromboxane B2 and superoxide anion (O2-) generation from Escherichia coli lipopolysaccharide-activated rat neonatal microglia to any appreciable degree.
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Affiliation(s)
- Joshua R. Gurr
- Department of Chemistry, University of Hawaii at Manoa, 2545 McCarthy Mall, Honolulu, HI 96822
| | - Timothy J. O’Donnell
- Department of Chemistry, University of Hawaii at Manoa, 2545 McCarthy Mall, Honolulu, HI 96822
| | - Yuheng Luo
- Department of Chemistry, University of Hawaii at Manoa, 2545 McCarthy Mall, Honolulu, HI 96822
| | - Wesley Y. Yoshida
- Department of Chemistry, University of Hawaii at Manoa, 2545 McCarthy Mall, Honolulu, HI 96822
| | - Mary L. Hall
- Department of Pharmacology, College of Graduate Studies Medicine, Midwestern University, 555 31 Street, Downers Grove, IL 60515
| | - Alejandro M.S. Mayer
- Department of Pharmacology, College of Graduate Studies Medicine, Midwestern University, 555 31 Street, Downers Grove, IL 60515
| | - Rui Sun
- Department of Chemistry, University of Hawaii at Manoa, 2545 McCarthy Mall, Honolulu, HI 96822
| | - Philip G. Williams
- Department of Chemistry, University of Hawaii at Manoa, 2545 McCarthy Mall, Honolulu, HI 96822
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