Biosynthesis of depsides and related natural products from fungi and lichens.

Ji, Q., Matsuda, Y.*

Asian J. Org. Chem. submitted (Invited review)

Involvement of a noncanonical polyketide synthase−nonribosomal peptide synthetase hybrid in the biosynthesis of sterol-C4-methyl oxidase inhibitor PF1163A.

Ji, Q., Wei, X., Liu, S., Matsuda, Y.*

Org. Lett. accepted (2024) [Link] [BGC]

iResNetDM: An interpretable deep learning approach for four types of DNA methylation modification prediction.

Yang, Z., Shao, W., Matsuda, Y., Song, L.

Comput. Struct. Biotechnol. J. in press (2024) [Link]

Concise synthesis of cyctetryptomycin A and B enabled by Zr-catalyzed dimerization.

Yu, L., Ogawa, H., Li, S., Cheung, T.L., Liu, W., Yan, D., Matsuda, Y., Kobayashi, Y., Guo, Z., Ikeda, K., Hamlin, T.A., Yamazaki, K., Qian, P.-Y., Nakamura, H.

Angew. Chem. Int. Ed. 63, e202414295 (2024) [Link]

Structural and computational insights into the noncanonical aromatization in fungal polyketide biosynthesis.

Wang, H., Peng, C., Chen, X.-X., Wang, H.-Y., Yang, R., Xiang, H., Hu, Q.-F., Liu, L., Chung, L.W.,* Matsuda, Y.,* Wang, W.-G.*

ACS Catal. 14, 10796-10805 (2024) [Link] [BGC]

Discovery of fungal onoceroid triterpenoids through domainless enzyme-targeted global genome mining.

Tang, J., Matsuda, Y.*

Nat. Commun. 15, 4312 (2024) [Link] [BGC1] [BGC2] [BGC3] [BGC4]

ChemRxiv DOI: 10.26434/chemrxiv-2023-f0z8n [Link]

Methyltransferase domain-focused genome mining for fungal polyketide synthases.

Yan, D., Matsuda, Y.*

Small Methods 8, 2400107 (2024) [Link] [BGC]

Special issue "30th anniversary of the Department of Biology and Chemistry, City University of Hong Kong."

Production of non-natural 5-methylorsellinate-derived meroterpenoids in Aspergillus oryzae.

Tang, J., Zhang, Y., Matsuda, Y.*

Beilstein J. Org. Chem. 20, 638-644 (2024) [Link]

Thematic issue "Young investigators in natural products chemistry, biosynthesis, and enzymology."

Mechanism behind the programmed biosynthesis of heterotrimeric fungal depside thielavin A.

Ji, Q., Xiang, H., Wang, W.-G.,* Matsuda, Y.*

Angew. Chem. Int. Ed. 63, e202402663 (2024) [Link] [BGC1] [BGC2]

Global genome mining-driven discovery of an unusual biosynthetic logic for fungal polyketide–terpenoid hybrids.

Yan, D., Matsuda, Y.*

Chem. Sci. 15, 3011-3017 (2024) [Link] [BGC1] [BGC2] [BGC3]

Genomics-driven derivatization of the bioactive fungal sesterterpenoid variecolin: Creation of an unnatural analogue with improved anticancer properties.

Yan, D., Arakelyan, J., Wan, T., Raina, R., Chan, T. K., Ahn, D., Kushnarev, V., Cheung, T. K., Chan, H. C., Choi, I., Ho, P. Y., Hu, F., Kim, Y., Lau, H. L., Law, Y. L., Leung, C. S., Tong, C. Y., Wong, K. K., Yim, W. L., Karnaukhov, N. S., Kong, R. Y. C.,* Babak, M. V.,* Matsuda, Y.*

Acta Pharm. Sin. B. 14, 421-432 (2024) [Link] [BGC]

ChemRxiv DOI: 10.33774/chemrxiv-2021-x171c [Link]

This work was performed for the iGEM 2021 Competition. See our wiki and presentation video.

Dissection of the catalytic mechanisms of transmembrane terpene cyclases involved in fungal meroterpenoid biosynthesis.

Tang, J., Matsuda, Y.*

Angew. Chem. Int. Ed. 62, e202306046 (2023) [Link]

Ketoreductase domain-catalyzed polyketide chain release in fungal alkyl salicylaldehyde biosynthesis.

Yang, R., Feng, J., Xiang, H., Cheng, B., Shao, L.-D., Li, Y.-P., Wang, H., Hu, Q.-F., Xiao, W.-L.,* Matsuda, Y.,* Wang, W.-G.*

J. Am. Chem. Soc. 145, 11293-11300 (2023) [Link] [BGC]

Biosynthetic characterization, heterologous production, and genomics-guided discovery of GABA-containing fungal heptapeptides.

Wei, X., Chan, T. K., Kong, C. T. D., Matsuda, Y.* 

J. Nat. Prod. 86, 416-422 (2023) [Link] [BGC1] [BGC2]

Selected as ACS Editors' Choice.

Universal strategy to develop fluorogenic probes for lysine deacylase/demethylase activity and application in discriminating demethylation states.

Wei, W., Zhang, J., Xu, Z., Liu, Z., Huang, C., Cheng, K., Meng, L., Matsuda, Y., Hao, Q., Zhang, H., Sun, H.

ACS Sens. 8, 28-39 (2023) [Link]

Depside bond formation by the starter-unit acyltransferase domain of a fungal polyketide synthase.

Chen, L., Wei, X., Matsuda, Y.*

J. Am. Chem. Soc. 144, 19225-19230 (2022) [Link] [BGC]

Biosynthetic elucidation and structural revision of brevione E: Characterization of the key dioxygenase for pathway branching from setosusin biosynthesis.

Yan, D., Matsuda, Y.*

Angew. Chem. Int. Ed. 61, e202210938 (2022) [Link] [BGC]

Discovery of branching meroterpenoid biosynthetic pathways in Aspergillus insuetus: Involvement of two terpene cyclases with distinct cyclization modes.

Tang, J., Matsuda, Y.*

Chem. Sci. 13, 10361-10369 (2022) [Link] [BGC1] [BGC2]

Aspcandine: A pyrrolobenzazepine alkaloid synthesized by a fungal nonribosomal peptide synthetase-polyketide synthase hybrid.

Chen, L., Tang, J.-W., Liu, Y. Y., Matsuda, Y.*

Org. Lett. 24, 4816-4819 (2022) [Link] [BGC]

Recent advances in heterologous production of natural products using Aspergillus oryzae.

Dong, J., Li, M., Xiao, Z., Hu, M., Matsuda, Y.,* Wang, W.*

Synth. Biol. J. 3, 1126-1149 (2022) [Link]

Branching and converging pathways in fungal natural product biosynthesis.

Wei, X., Wang, W.-G., Matsuda, Y.*

Fungal Biol. Biotechnol. 9, 6 (2022) [Link]

Biocatalytic and chemical derivatization of fungal meroditerpenoid chevalone E.

Xiao, Z.-H., Dong, J.-Y., Li, A., Dai, J.-M., Li, Y.-P., Hu, Q.-F., Shao, L.-D.,* Matsuda, Y.,* Wang, W.-G.*

Org. Chem. Front. 9, 1837-1843 (2022) [Link] [BGC1] [BGC2]

Molecular and computational bases for spirofuranone formation in setosusin biosynthesis.

Wei, X.,† Matsuyama, T.,† Sato, H.,* Yan, D., Chan, P. M., Miyamoto, K., Uchiyama, M.,* Matsuda, Y.*

J. Am. Chem. Soc. 143, 17708-17715 (2021) [Link] [BGC]

Molecular insights into the endoperoxide formation by Fe(II)/α-KG-dependent oxygenase NvfI.

Mori, T., Zhai, R., Ushimaru, R., Matsuda, Y., Abe, I.

Nat. Commun. 12, 4417 (2021) [Link] [Press Release (in Japanese)] [Behind the paper] [BGC]

Recommended in Faculty Opinions.

Structural basis for isomerization reactions in fungal tetrahydroxanthone biosynthesis and diversification.

Yang, J., Mori, T.,* Wei, X., Matsuda, Y.,* Abe, I.*

Angew. Chem. Int. Ed. 60, 19458-19465 (2021) [Link] [BGC1] [BGC2]

Selected as Hot Paper.

Heterologous biosynthesis of tetrahydroxanthone dimers: Determination of key factors for selective or divergent synthesis.

Wei, X., Chen, X., Chen, L., Yan, D., Wang, W.-G., Matsuda, Y.*

J. Nat. Prod. 84, 1544-1549 (2021) [Link] [BGC]

Genome mining-driven discovery of 5-methylorsellinate-derived meroterpenoids from Aspergillus funiculosus.

Yan, D., Matsuda, Y.*

Org. Lett. 23, 3211-3215 (2021) [Link] [BGC]

One polyketide synthase, two distinct products: Trans-acting enzyme-controlled product divergence in calbistrin biosynthesis.

Tao, H., Mori, T., Wei, X., Matsuda, Y.,* Abe, I.*
Angew. Chem. Int. Ed. 60, 8851-8858 (2021) [Link] [Press Release (in Japanese)] [BGC]

Selected as Very Important Paper. Selected as Cover Picture.

Discovery of pyranoviolin A and its biosynthetic gene cluster in Aspergillus violaceofuscus.

Wei, X., Chen, L., Tang, J.-W., Matsuda, Y.*

Front. Microbiol. 11, 562063 (2020) [Link] [BGC]

BODI-Pt, a green-light-activatable and carboplatin-based platinum(IV) anticancer prodrug with enhanced activation and cytotoxicity.

Yao, H., Chen, S., Deng, Z., Tse, M.-K., Matsuda, Y., Zhu, G.

Inorg. Chem. 59, 11823-11833 (2020) [Link]

Structural diversification of andiconin-derived natural products by α-ketoglutarate-dependent dioxygenases.

Bai, T., Matsuda, Y.,* Tao, H., Mori, T., Zhang, Y., Abe, I.*

Org. Lett. 22, 4311-4315 (2020) [Link] [BGC]

Molecular basis for the biosynthesis of an unusual chain-fused polyketide, gregatin A.

Wang, W.-G.,* Wang, H., Du, L.-Q., Li, M., Chen, L., Yu, J., Cheng, G.-G., Zhan, M.-T., Hu, Q.-F., Zhang, L., Yao, M., Matsuda, Y.*

J. Am. Chem. Soc. 142, 8464-8472 (2020) [Link] [BGC]

Unraveling the fungal strategy for tetrahydroxanthone biosynthesis and diversification.

Wei, X., Matsuda, Y.*

Org. Lett. 22, 1919-1923 (2020) [Link] [BGC1] [BGC2]

Genome mining for fungal polyketide-diterpenoid hybrids: Discovery of key terpene cyclases and multifunctional P450s for structural diversification.

Wang, W.-G.,* Du, L.-Q., Sheng, S.-L., Li, A., Li, Y.-P., Cheng, G.-G., Li, G.-P., Sun, G., Hu, Q., Matsuda, Y.*

Org. Chem. Front. 6, 571-578 (2019) [Link] [BGC1] [BGC2]

Selected as Inside front cover.

Elucidation and heterologous reconstitution of chrodrimanin B biosynthesis.

Bai, T., Quan, Z., Zhai, R., Awakawa, T., Matsuda, Y.,* Abe, I*

Org. Lett. 20, 7504-7508 (2018) [Link] [BGC]

Genetic characterization of neosartorin biosynthesis provides insight into heterodimeric natural product generation.

Matsuda, Y.,* Gotfredsen, C.H., Larsen, T.O.*

Org. Lett. 20, 7197-7200 (2018) [Link] [BGC]

Structural and computational bases for dramatic skeletal rearrangement in anditomin biosynthesis.

Nakashima, Y.,† Mitsuhashi, T.,† Matsuda, Y.,† Senda, M., Sato, H., Yamazaki, M., Uchiyama, M., Senda, T., Abe, I. 

J. Am. Chem. Soc. 140, 9743-9750 (2018) [Link] [BGC]

Novofumigatonin biosynthesis involves a non-heme iron-dependent endoperoxide isomerase for orthoester formation.

Matsuda, Y.,* Bai, T., Phippen, C.B.W., Nødvig, C.S., Kjærbølling, I., Vesth, T.C., Andersen, M.R., Mortensen, U.H., Gotfredsen, C.H., Abe, I.,* Larsen, T.O.*

Nat. Commun. 9, 2587 (2018) [Link] [Behind the paper] [BGC]

Recommended in F1000.

Unique chemistry of non-heme iron enzymes in fungal biosynthetic pathways.

Nakamura, H., Matsuda, Y.,* Abe, I.*

Nat. Prod. Rep. 35, 633-645 (2018) [Link]

Selected as Front cover.

Complete biosynthetic pathways of ascofuranone and ascochlorin in Acremonium egyptiacum.

Araki, Y., Awakawa, T., Matsuzaki, M., Cho, R., Matsuda, Y., Hoshino, S., Shinohara, Y., Yamamoto, M., Kido, Y., Inaoka, D.K., Nagamune, K., Ito, K., Abe, I., Kita, K.

Proc. Natl. Acad. Sci. USA, 116, 8269-8274 (2019) [Link] [Press Release] [BGC]

Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species.

Kjærbølling, I., Vesth, T.C., Frisvad, J.C., Nybo, J.L., Theobald, S., Kuo, A., Bowyer, P., Matsuda, Y., Mondo, S., Lyhne, E.K., Kogle, M.E., Clum, A., Lipzen, A.M., Salamov, A.A., Ngan, C.Y., Daum, C.G., Chiniquy, J., Barry, K.W., LaButti, K.M., Haridas, S., Simmons, B.A., Magnuson, J.K., Mortensen, U.H., Larsen, T.O., Grigoriev, I.V., Baker, S.E., Andersen, M.R.

Proc. Natl. Acad. Sci. USA 115, E753-E761 (2018) [Link]

Molecular basis for the unusual ring reconstruction in fungal meroterpenoid biogenesis.

Mori, T., Iwabichi, T., Hoshino, S., Wang, H., Matsuda, Y., Abe, I.

Nat. Chem. Biol. 13, 1066-1073 (2017) [Link] [Press Release] [BGC]

Discovery of key dioxygenases that diverged the paraherquonin and acetoxydehydroaustin pathways in Penicillium brasilianum.

Matsuda, Y., Iwabuchi, T., Fujimoto, T., Awakawa, T., Nakashima, Y., Mori, T., Zhang, H., Hayashi, F., Abe, I.

J. Am. Chem. Soc. 138, 12671-12677 (2016) [Link] [BGC]

Genome-based discovery of an unprecedented cyclization mode in fungal sesterterpenoid biosynthesis.

Okada, M.,† Matsuda, Y.,† Mitsuhashi, T., Hoshino, S., Mori, T., Nakagawa, K., Quan, Z., Qin, B., Zhang, H., Hayashi, F., Kawaide, H., Abe, I.

J. Am. Chem. Soc. 138, 10011-10018 (2016) [Link] [BGC]

Highlighted in JACS Spotlight.

Astellifadiene: Structure determination by NMR spectroscopy and crystalline sponge method, and elucidation of its biosynthesis.

Matsuda, Y., Mitsuhashi, T., Lee, S., Hoshino, M., Mori, T., Okada, M., Zhang, H., Hayashi, F., Fujita, M., Abe, I.

Angew. Chem. Int. Ed. 55, 5785-5788 (2016) [Link] [BGC]

Biosynthesis of LL‐Z1272β: Discovery of a new member of NRPS‐like enzymes for aryl‐aldehyde formation.

Li, C., Matsuda, Y., Gao, H., Hu, D., Yao, X.S., Abe, I.

ChemBioChem 17, 904-907 (2016) [Link] [BGC]

Cytochrome P450 for citreohybridonol synthesis: Oxidative derivatization of the andrastin scaffold.

Matsuda, Y., Quan, Z., Mitsuhashi, T., Li, C., Abe, I.

Org. Lett. 18, 296-299 (2016) [Link] [BGC]

Unusual chemistries in fungal meroterpenoid biosynthesis.

Matsuda, Y., Awakawa, T., Mori, T., Abe, I.

Curr. Opin. Chem. Biol. 31, 1-7 (2016) [Link]

Biosynthesis of fungal meroterpenoids.

Matsuda, Y., Abe, I.

Nat. Prod. Rep. 33, 26-53 (2016) [Link]

An unusual chimeric diterpene synthase from Emericella variecolor and its functional conversion to a sesterterpene synthase by domain swapping.

Qin, B.,† Matsuda, Y.,† Mori, T., Okada, M., Quan, Z., Mitsuhashi, T., Wakimoto, T., Abe, I.

Angew. Chem. Int. Ed. 55, 1658-1661 (2016) [Link] [Press Release] [BGC]

Selected as Cover Picture.

Molecular basis for stellatic acid biosynthesis: A genome mining approach for discovery of sesterterpene synthases.

Matsuda, Y., Mitsuhashi, T., Quan, Z., Abe, I.

Org. Lett. 17, 4644-4647 (2015) [Link] [BGC]

Uncovering the unusual D-ring construction in terretonin biosynthesis by collaboration of a multifunctional cytochrome P450 and a unique isomerase.

Matsuda, Y., Iwabuchi, T., Wakimoto, T., Awakawa, T., Abe, I.

J. Am. Chem. Soc. 137, 3393–3401 (2015) [Link] [BGC]

Complete biosynthetic pathway of anditomin: Nature’s sophisticated synthetic route to a complex fungal meroterpenoid.

Matsuda, Y., Wakimoto, T., Mori, T., Awakawa, T., Abe, I.

J. Am. Chem. Soc. 136, 15326-15336 (2014) [Link] [BGC]

Selected as Cover Art. Highlighted in JACS Spotlight. Recommended in F1000.

Spiro-ring formation is catalyzed by a multifunctional dioxygenase in austinol biosynthesis.

Matsuda, Y., Awakawa, T., Wakimoto, T., Abe, I.

J. Am. Chem. Soc. 135, 10962-10965 (2013) [Link] [BGC1] [BGC2]

Reconstituted biosynthesis of fungal meroterpenoid andrastin A.

Matsuda, Y., Awakawa, T., Abe, I.

Tetrahedron 69, 8199-8204 (2013) [Link] [BGC]

Terretonin biosynthesis requires methylation as essential step for cyclization.

Matsuda, Y., Awakawa, T., Itoh, T., Wakimoto, T., Kushiro, T., Fujii, I., Ebizuka, Y., Abe, I.

ChemBioChem 13, 1738-1741 (2012) [Link] [BGC]

Reconstitution of a fungal meroterpenoid biosynthesis reveals the involvement of a novel family of terpene cyclases.

Itoh, T., Tokunaga, K., Matsuda, Y., Fujii, I., Abe, I., Ebizuka, Y., Kushiro, T.

Nature Chem. 2, 858-864 (2010) [Link] [BGC]

Highlighted in NEWS AND VIEWS. Recommended in F1000.

Functional analysis of transmembrane terpene cyclases involved in fungal meroterpenoid biosynthesis.

Tang, J., Matsuda, Y.*

In Methods Enzymol., Elsevier, Vol. 699, Chapter 16, pp. 445-478 (2024) [Link]

Fungal meroterpenoids.

Matsuda, Y., Abe, I.

In Comprehensive Natural Products III: Chemistry and Biology, Elsevier, Vol. 1, Chapter 14, pp. 445-478 (2020) [Link]

Meroterpenoids.

Matsuda, Y., Abe, I.

In Biosynthesis and Molecular Genetics of Fungal Secondary Metabolites, Springer, Chapter 13, pp. 289-301 (2014) [Link]