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Article ; Online: Biosynthesis of indole diterpenes: a reconstitution approach in a heterologous host.

Ozaki, Taro / Minami, Atsushi / Oikawa, Hideaki

2023 Volume 40, Issue 1, Page(s) 202–213

Abstract: Covering: 2013 to 2022In this review, we provide an overview elucidating the biosynthetic pathway and heterologous production of fungal indole diterpenes (IDTs). Based on the studies of six IDT biosynthesis, we extracted nature's strategy: (1) two-stage ... ...

Abstract	Covering: 2013 to 2022In this review, we provide an overview elucidating the biosynthetic pathway and heterologous production of fungal indole diterpenes (IDTs). Based on the studies of six IDT biosynthesis, we extracted nature's strategy: (1) two-stage synthesis for the core scaffold and platform intermediates, and (2) late-stage modifications for installing an additional cyclic system on the indole ring. Herein, we describe reconstitution studies applying this strategy to the synthesis of highly elaborated IDTs. We also discuss its potential for future biosynthetic engineering.
MeSH term(s)	Indoles/metabolism ; Diterpenes/metabolism ; Biosynthetic Pathways
Chemical Substances	Indoles ; Diterpenes
Language	English
Publishing date	2023-01-25
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2002546-4
ISSN	1460-4752 ; 0265-0568
ISSN (online)	1460-4752
ISSN	0265-0568
DOI	10.1039/d2np00031h
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Article ; Online: Development and characterization of microsatellite markers for Ardisia japonica (Primulaceae), an evergreen clonal dwarf shrub

Minami, Atsushi / Sugawara, Hayato / Nishimura, Taisuke

Journal of Forest Research. 2023 May 04, v. 28, no. 3 p.212-216

2023

Abstract: Microsatellite markers were first developed for Ardisia japonica (Primulaceae), an evergreen clonal shrub that commonly grows in the understory of various types of temperate forests in East Asia. Of the 69 primer pairs designed based on genomic sequence ... ...

Abstract	Microsatellite markers were first developed for Ardisia japonica (Primulaceae), an evergreen clonal shrub that commonly grows in the understory of various types of temperate forests in East Asia. Of the 69 primer pairs designed based on genomic sequence data, 13 pairs showed clear microsatellite peaks and allelic polymorphisms with tetraploidy in ramets from two populations. Ramets were successfully assigned to multilocus lineages (genets) using microsatellite markers. The number of alleles per locus ranged from 3 to 8, and the observed heterozygosity ranged from 0.468 to 0.881. These will be useful for the assignment of genets and for investigating the genet-level population genetics and ecology of the understory clonal shrub.
Keywords	Ardisia ; clones ; forests ; heterozygosity ; loci ; microsatellite repeats ; population genetics ; research ; shrubs ; tetraploidy ; understory ; East Asia ; Clonal plant ; polyploidy ; microsatellite marker ; Ardisia japonica
Language	English
Dates of publication	2023-0504
Size	p. 212-216.
Publishing place	Taylor & Francis
Document type	Article ; Online
ZDB-ID	2104467-3
ISSN	1610-7403 ; 1341-6979
ISSN (online)	1610-7403
ISSN	1341-6979
DOI	10.1080/13416979.2022.2149058
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Article ; Online: Recent advances in the biosynthesis of ribosomally synthesized and posttranslationally modified peptides of fungal origin.

Ozaki, Taro / Minami, Atsushi / Oikawa, Hideaki

The Journal of antibiotics

2022 Volume 76, Issue 1, Page(s) 3–13

Abstract: Ribosomally synthesized and posttranslationally modified peptides (RiPPs) are growing class of natural products with potent biological activities. Although the core scaffolds of RiPPs are composed of proteinogenic amino acids, remarkable structural ... ...

Abstract	Ribosomally synthesized and posttranslationally modified peptides (RiPPs) are growing class of natural products with potent biological activities. Although the core scaffolds of RiPPs are composed of proteinogenic amino acids, remarkable structural diversity is generated through posttranslational modifications (PTMs) of precursor peptides. In addition, ribosomal origin of biosynthetic precursors enables supply of its analogs through genetic approach such as site-directed mutagenesis on corresponding genes. As PTM enzymes often exhibit substrate tolerance, RiPP biosynthetic machineries are considered as efficient tools for generation of unique peptide derivatives. RiPP pathways are distributed among all domains of life and those derived from bacteria and plants have been known for decades. In contrast, fungal RiPPs (F-RiPPs) have fewer examples. Amatoxins and omphalotins are F-RiPPs produced by Basidiomycota fungi. In the biosynthesis of these compounds, macrocyclization by prolyl oligopeptidase homologs and N-methylations of back bone amides have been characterized, respectively. Ustiloxins and related compounds are another group of F-RiPPs with characteristic macrocyclic ethers. UstYa family proteins, which are fungi-specific putative oxidases, have been identified as common proteins involved in PTMs of these compounds. Despite a limited number of characterized examples, recent progress in sequencing of fungal genomes indicated that a number of RiPP pathways are hidden in fungal resources, making F-RiPPs as attractive target for genome mining studies while more detailed understandings of key biosynthetic enzymes are still necessary. This review seeks to describe recent advances on the F-RiPP biosynthesis with slight emphasis on the function of UstYa family proteins.
MeSH term(s)	Ribosomes/genetics ; Peptides/chemistry ; Genes, Fungal ; Biological Products/chemistry ; Protein Processing, Post-Translational
Chemical Substances	Peptides ; Biological Products
Language	English
Publishing date	2022-11-24
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	390800-8
ISSN	1881-1469 ; 0021-8820 ; 0368-3532
ISSN (online)	1881-1469
ISSN	0021-8820 ; 0368-3532
DOI	10.1038/s41429-022-00576-w
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Article ; Online: Biosynthetic machineries of anthraquinones and bisanthraquinones in Talaromyces islandicus.

Fukaya, Mitsunori / Ozaki, Taro / Minami, Atsushi / Oikawa, Hideaki

Bioscience, biotechnology, and biochemistry

2022 Volume 86, Issue 4, Page(s) 435–443

Abstract: Talaromyces islandicus is a unique fungus that produces more than 20 numbers of anthraquinones (AQs) and their dimeric natural products, bisanthraquinones (BQs). These compounds share a 9,10-anthracenedione core derived from emodin. The biosynthetic ... ...

Abstract	Talaromyces islandicus is a unique fungus that produces more than 20 numbers of anthraquinones (AQs) and their dimeric natural products, bisanthraquinones (BQs). These compounds share a 9,10-anthracenedione core derived from emodin. The biosynthetic pathway of emodin has been firmly established, while that of other AQs and BQs is still unclear. In this study, we identified the biosynthetic gene clusters for chrysophanol and skyrin. The function of key modification enzymes was examined by performing biotransformation experiments and in vitro enzymatic reactions with emodin and its derivatives, allowing us to propose a mechanism for the modification reactions. The present study provides insight into the biosynthesis of AQs and BQs in T. islandicus.
MeSH term(s)	Anthraquinones/metabolism ; Biotransformation ; Emodin ; Talaromyces/metabolism
Chemical Substances	Anthraquinones ; Emodin (KA46RNI6HN)
Language	English
Publishing date	2022-02-15
Publishing country	England
Document type	Journal Article
ZDB-ID	1106450-x
ISSN	1347-6947 ; 0916-8451
ISSN (online)	1347-6947
ISSN	0916-8451
DOI	10.1093/bbb/zbac009
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Article ; Online: Bioinformatics-Guided Reconstitution of Biosynthetic Machineries of Fungal Eremophilane Sesquiterpenes.

Sato, Yoshiro / Shi, Xinge / Ye, Ying / Domon, Saori / Takino, Junya / Ozaki, Taro / Liu, Chengwei / Oikawa, Hideaki / Minami, Atsushi

ACS chemical biology

2024 Volume 19, Issue 4, Page(s) 861–865

Abstract: Eremophilanes exhibit diverse biological activities and chemical structures. This study reports the bioinformatics-guided reconstitution of the biosynthetic machinery of fungal eremophilanes, eremofortin C and sporogen-AO1, to elucidate their ... ...

Abstract	Eremophilanes exhibit diverse biological activities and chemical structures. This study reports the bioinformatics-guided reconstitution of the biosynthetic machinery of fungal eremophilanes, eremofortin C and sporogen-AO1, to elucidate their biosynthetic pathways. Their biosyntheses include P450-catalyzed multistep oxidation and enzyme-catalyzed isomerization by the DUF3237 family protein. Successful characterization of six P450s enabled us to discuss the functions of eremophilane P450s in putative eremophilane biosynthetic gene clusters, providing opportunities to understand the oxidative modification pathways of fungal eremophilanes.
MeSH term(s)	Oxidation-Reduction ; Polycyclic Sesquiterpenes ; Sesquiterpenes/chemistry ; Fungi/chemistry ; Fungi/metabolism ; Biosynthetic Pathways ; Computational Biology/methods
Chemical Substances	Polycyclic Sesquiterpenes ; Sesquiterpenes
Language	English
Publishing date	2024-04-03
Publishing country	United States
Document type	Journal Article
ISSN	1554-8937
ISSN (online)	1554-8937
DOI	10.1021/acschembio.4c00040
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Article ; Online: Predicting the chemical space of fungal polyketides by phylogeny-based bioinformatics analysis of polyketide synthase-nonribosomal peptide synthetase and its modification enzymes.

Minami, Atsushi / Ugai, Takahiro / Ozaki, Taro / Oikawa, Hideaki

Scientific reports

2020 Volume 10, Issue 1, Page(s) 13556

Abstract: Fungal polyketide synthase (PKS)-nonribosomal peptide synthetase (NRPS) hybrids are key enzymes for synthesizing structurally diverse hybrid natural products (NPs) with characteristic biological activities. Predicting their chemical space is of ... ...

Abstract	Fungal polyketide synthase (PKS)-nonribosomal peptide synthetase (NRPS) hybrids are key enzymes for synthesizing structurally diverse hybrid natural products (NPs) with characteristic biological activities. Predicting their chemical space is of particular importance in the field of natural product chemistry. However, the unexplored programming rule of the PKS module has prevented prediction of its chemical structure based on amino acid sequences. Here, we conducted a phylogenetic analysis of 884 PKS-NRPS hybrids and a modification enzyme analysis of the corresponding biosynthetic gene cluster, revealing a hidden relationship between its genealogy and core structures. This unexpected result allowed us to predict 18 biosynthetic gene cluster (BGC) groups producing known carbon skeletons (number of BGCs; 489) and 11 uncharacterized BGC groups (171). The limited number of carbon skeletons suggests that fungi tend to select PK skeletons for survival during their evolution. The possible involvement of a horizontal gene transfer event leading to the diverse distribution of PKS-NRPS genes among fungal species is also proposed. This study provides insight into the chemical space of fungal PKs and the distribution of their biosynthetic gene clusters.
MeSH term(s)	Computational Biology/methods ; Fungi/genetics ; Fungi/metabolism ; Multigene Family ; Peptide Synthases/genetics ; Peptide Synthases/metabolism ; Phylogeny ; Polyketide Synthases/genetics ; Polyketide Synthases/metabolism ; Polyketides/chemistry ; Polyketides/metabolism
Chemical Substances	Polyketides ; Polyketide Synthases (79956-01-7) ; Peptide Synthases (EC 6.3.2.-) ; non-ribosomal peptide synthase (EC 6.3.2.-)
Language	English
Publishing date	2020-08-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-020-70177-w
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Article ; Online: Total synthesis of alkaloids using both chemical and biochemical methods.

Tanifuji, Ryo / Minami, Atsushi / Oguri, Hiroki / Oikawa, Hideaki

Natural product reports

2020 Volume 37, Issue 8, Page(s) 1098–1121

Abstract: Covering: 2000 to 2019Rapid access to genomic data has facilitated the identification of the biosynthetic enzyme genes of alkaloid natural products and elucidation of their biosynthetic pathways. Enzymes for the rapid construction of molecular scaffolds ... ...

Abstract	Covering: 2000 to 2019Rapid access to genomic data has facilitated the identification of the biosynthetic enzyme genes of alkaloid natural products and elucidation of their biosynthetic pathways. Enzymes for the rapid construction of molecular scaffolds and versatile modifications during the late-stage biosynthesis of complex molecular skeletons constitute unique features of biosynthetic machineries. For example, enzymes involved in an alkaloid biosynthesis. In this review, we discuss three types of useful enzymes and enzymatic reactions that have been found in the biosynthetic studies of several alkaloids, and discuss their applications for the total synthesis of natural alkaloids and their derivatives. The selected examples include a single non-ribosomal peptide synthetase SfmC that catalyzes key Pictet-Spengler reactions, which construct a characteristic tetrahydroisoquinoline skeleton in antitumor antibiotics such as saframycin, prenylation-oxidative modification enzymes involved in the biosynthesis of fungal tremorgenic mycotoxins such as penitrem as well as versatile Diels-Alderases recently discovered in the biosynthesis of plant monoterpene indole alkaloids of iboga and aspidosperma type.
MeSH term(s)	Alkaloids/biosynthesis ; Alkaloids/chemical synthesis ; Anti-Bacterial Agents/biosynthesis ; Anti-Bacterial Agents/chemical synthesis ; Biological Products/chemical synthesis ; Biological Products/metabolism ; Biosynthetic Pathways ; Catalysis ; Peptide Synthases/metabolism
Chemical Substances	Alkaloids ; Anti-Bacterial Agents ; Biological Products ; Peptide Synthases (EC 6.3.2.-) ; non-ribosomal peptide synthase (EC 6.3.2.-)
Language	English
Publishing date	2020-03-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2002546-4
ISSN	1460-4752 ; 0265-0568
ISSN (online)	1460-4752
ISSN	0265-0568
DOI	10.1039/c9np00073a
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Article: Total synthesis of alkaloids using both chemical and biochemical methods

Tanifuji, Ryo / Minami, Atsushi / Oguri, Hiroki / Oikawa, Hideaki

Natural product reports. 2020 Aug. 19, v. 37, no. 8

2020

Abstract: Rapid access to genomic data has facilitated the identification of the biosynthetic enzyme genes of alkaloid natural products and elucidation of their biosynthetic pathways. Enzymes for the rapid construction of molecular scaffolds and versatile ... ...

Abstract	Rapid access to genomic data has facilitated the identification of the biosynthetic enzyme genes of alkaloid natural products and elucidation of their biosynthetic pathways. Enzymes for the rapid construction of molecular scaffolds and versatile modifications during the late-stage biosynthesis of complex molecular skeletons constitute unique features of biosynthetic machineries. For example, enzymes involved in an alkaloid biosynthesis. In this review, we discuss three types of useful enzymes and enzymatic reactions that have been found in the biosynthetic studies of several alkaloids, and discuss their applications for the total synthesis of natural alkaloids and their derivatives. The selected examples include a single non-ribosomal peptide synthetase SfmC that catalyzes key Pictet–Spengler reactions, which construct a characteristic tetrahydroisoquinoline skeleton in antitumor antibiotics such as saframycin, prenylation–oxidative modification enzymes involved in the biosynthesis of fungal tremorgenic mycotoxins such as penitrem as well as versatile Diels-Alderases recently discovered in the biosynthesis of plant monoterpene indole alkaloids of iboga and aspidosperma type.
Keywords	biosynthesis ; enzymes ; fungi ; genomics ; monoterpenoids ; mycotoxins ; nonribosomal peptides
Language	English
Dates of publication	2020-0819
Size	p. 1098-1121.
Publishing place	The Royal Society of Chemistry
Document type	Article
ZDB-ID	2002546-4
ISSN	1460-4752 ; 0265-0568
ISSN (online)	1460-4752
ISSN	0265-0568
DOI	10.1039/c9np00073a
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Article ; Online: Structure and biosynthesis of the ribosomal lipopeptide antibiotic albopeptins.

Oikawa, Hideaki / Mizunoue, Yusuke / Nakamura, Takemichi / Fukushi, Eri / Yulu, Jiang / Ozaki, Taro / Minami, Atsushi

Bioscience, biotechnology, and biochemistry

2022 Volume 86, Issue 6, Page(s) 717–723

Abstract: Albopeptins produced by Streptomyces albofaciens JC-82-120 were isolated as effective antibiotics for plant pathogenetic disease in 1986. However, their unusual physicochemical properties hampered the determination of their chemical structures. In this ... ...

Abstract	Albopeptins produced by Streptomyces albofaciens JC-82-120 were isolated as effective antibiotics for plant pathogenetic disease in 1986. However, their unusual physicochemical properties hampered the determination of their chemical structures. In this report, we describe our efforts to elucidate their structures. Initially, the structure of an unusual C13-fatty acid with an N-hydroxyguanidyl group was determined using degradation and chemical synthesis. After the linear portion of the octapeptide core was constructed based on the 2D-NMR data, the final assembly of the unusual structure, including the sulfoxide bridge, was achieved through the analysis of detailed NMR data. The proposed structure of albopeptin B was supported by MS/MS data, which also enabled us to determine the structure of 5 albopeptin family members. Bioinformatics analysis of the genomic data of the producer strain further led us to propose that their biosynthetic pathway is similar to the ribosomally derived lanthipeptides possessing a long-chain fatty acid.
MeSH term(s)	Anti-Bacterial Agents/chemistry ; Biosynthetic Pathways/genetics ; Fatty Acids ; Lipopeptides ; Multigene Family ; Tandem Mass Spectrometry
Chemical Substances	Anti-Bacterial Agents ; Fatty Acids ; Lipopeptides
Language	English
Publishing date	2022-03-13
Publishing country	England
Document type	Journal Article
ZDB-ID	1106450-x
ISSN	1347-6947 ; 0916-8451
ISSN (online)	1347-6947
ISSN	0916-8451
DOI	10.1093/bbb/zbac039
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Article: Recent advances of Diels-Alderases involved in natural product biosynthesis.

Minami, Atsushi / Oikawa, Hideaki

The Journal of antibiotics

2016 Volume 69, Issue 7, Page(s) 500–506

Abstract: Frequent occurrence of [4+2] adducts in the secondary metabolites suggested involvement of Diels-Alderases (DAases) in their biosynthesis. However, a limited number of DAases were reported before early 2000s. Advancements in whole-genome sequencing and ... ...

Abstract	Frequent occurrence of [4+2] adducts in the secondary metabolites suggested involvement of Diels-Alderases (DAases) in their biosynthesis. However, a limited number of DAases were reported before early 2000s. Advancements in whole-genome sequencing and searching tool of the biosynthetic gene clusters of the secondary metabolites facilitate the identification of plausible DAases. Thus, during past 5 years, nine DAases have been characterized by genetic and biochemical analyses. These include a detailed functional analysis of SpnF that solely catalyzes [4+2] cycloaddition, a structural analysis of spirotetramate-forming enzyme PyrI4 complexed with the corresponding cycloadduct, and DAases catalyzing decalin formation and macrocyclic pyridine formation. Together with decalin-forming enzymes and macrocyclic pyridine-forming enzymes, these results provided sufficient data to discuss catalytic mechanism of DAases and nature's strategy for molecular diversification of linear chain intermediates derived from polyketide and ribosomal peptide biosynthetic machinery.
MeSH term(s)	Biological Products/metabolism ; Cycloaddition Reaction ; Intramolecular Oxidoreductases/chemistry ; Intramolecular Oxidoreductases/metabolism ; Multienzyme Complexes/chemistry ; Multienzyme Complexes/metabolism ; Naphthalenes/chemistry ; Naphthalenes/metabolism ; Polyketide Synthases/chemistry ; Polyketide Synthases/metabolism
Chemical Substances	Biological Products ; Multienzyme Complexes ; Naphthalenes ; macrophomate synthase ; Polyketide Synthases (79956-01-7) ; decalin (88451Q4XYF) ; Intramolecular Oxidoreductases (EC 5.3.-) ; solanapyrone synthase (EC 5.3.99.-)
Language	English
Publishing date	2016-06-15
Publishing country	Japan
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	390800-8
ISSN	1881-1469 ; 0021-8820 ; 0368-3532
ISSN (online)	1881-1469
ISSN	0021-8820 ; 0368-3532
DOI	10.1038/ja.2016.67
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