Miramides A–D: Identification of Detoxin-like Depsipeptides after Heterologous Expression of a Hybrid NRPS-PKS Gene Cluster from Streptomyces mirabilis Lu17588

Abstract

Natural products derived from plants, fungi or bacteria have been used for years in the medicine, agriculture and food industries as they exhibit a variety of beneficial properties, such as antibiotic, antifungal, anticancer, herbicidal and immunosuppressive activities. Compared to synthetic compounds, natural products possess a greater chemical diversity, which is a reason why they are profitable templates for developing pharmaceutical drug candidates and ongoing research on them is inevitable. Performing heterologous expression with unknown gene clusters is the preferred method to activate gene clusters that are not expressed in the wild-type strain under laboratory conditions; thus, this method offers a way to discover new interesting metabolites. Here, we report the gene cluster assembly of a hybrid NRPS-PKS gene cluster from Streptomyces mirabilis Lu17588, which was heterologously expressed in Streptomyces albus Del14. Four new compounds were produced by the obtained strain, which were named miramides A–D. Isolation and structure elucidation revealed similarity of the isolated compounds to the known depsipeptides rimosamides/detoxins.

Bacterial natural product discovery by heterologous expression

“…License: CC BY-NC-ND 4.0 Accordingly, DNA synthesis or polymerase chain reaction (PCR) was used in 87% of the studies expressing only RiPPs (Han et al 2022;Zhang et al 2021;Wang et al 2023;Koos and Link 2019;Kaweewan, Nakagawa, and Kodani 2021;Bothwell et al 2021;Vermeulen et al 2022;Unno et al 2020;Ayikpoe et al 2022;Nguyen et al 2022;Bösch et al 2020;Mevaere et al 2018;Carson et al 2023 In fact, 80% of the studies aiming to express only PKS or NRPS used random library generation often in combination with assembly methods (Figure 3) (Libis et al 2022;Hashimoto et al 2021;Lasch et al 2021;Shi et al 2019;Yuet et al 2020;Liu et al 2021;Lasch, Stierhof, et al 2020;Gao et al 2023;S. H. Liu et al 2019;Lasch, Gummerlich, et al 2020;Paulus et al 2022;Wu et al 2019;Hover et al 2018;Myronovskyi et al 2018;Cheng et al 2023;Libis et al 2022). For example, the libraries generated for the discovery of cadasides, malacindins and miramides produced cosmids with portions of the desired BGCs.…”

“…For example, the libraries generated for the discovery of cadasides, malacindins and miramides produced cosmids with portions of the desired BGCs. The overlapping pieces of the BGCs were then assembled into a BAC by TAR cloning and integrated into the chromosome of the hosts (Paulus et al 2022;Hover et al 2018;Wu et al 2019). Moreover, recombination methods like Red/ET can be used to introduce a selective marker (Lasch et al 2021;Lasch, Stierhof, et al 2020;Shuai et al 2020) or insert integration machinery into the vector (Gummerlich et al 2020).…”

“…The most frequent approach (56%) was to prioritize novelty by expressing unusual BGCs found in rare and/or understudied bacteria, exemplified by the discovery of the lanthipeptide marinsedin from Marinicella sedimis (Han et al 2022), and by the discovery of 31 other compounds listed in SI Table S1 (Hashimoto et al 2021;Hao et al 2019;Zhang et al 2021;Lasch et al 2021;Enghiad et al 2021;Shi et al 2019;Yuet et al 2020;De Rond, Asay, and Moore 2021;Wang et al 2023;Liu et al 2021;Lasch, Stierhof, et al 2020;Li et al 2020;Myronovskyi et al 2018;Gao et al 2023;Cheng et al 2023;Koos and Link 2019;Kaweewan, Nakagawa, and Kodani 2021;S. H. Liu et al 2019;Shuai et al 2020;Lasch, Gummerlich, et al 2020;Paulus et al 2022;Bothwell et al 2021;Gummerlich et al 2020;Alberti et al 2019;Vermeulen et al 2022;Zhang et al 2021;Unno et al 2020).…”

“…License: CC BY-NC-ND 4.0 12 mentioned as reason, strains related to the source organism were used as host for expression in 28 other studies (Libis et al 2022;Hashimoto et al 2021;Lasch et al 2021;Enghiad et al 2021;Shi et al 2019;Liu et al 2021;Lasch, Stierhof, et al 2020;Li et al 2020;Myronovskyi et al 2018;Gao et al 2023;Cheng et al 2023;Kaweewan, Nakagawa, and Kodani 2021;S. H. Liu et al 2019;Shuai et al 2020;Lasch, Gummerlich, et al 2020;Paulus et al 2022;…”

Bacterial natural product discovery by heterologous expression

“…2A ). The most frequent approach (56%) was to prioritize novelty by expressing unusual BGCs found in rare and/or understudied bacteria, exemplified by the discovery of the lanthipeptide marinsedin from Marinicella sedimis (Han et al, 2022 ), and by the discovery of 31 other compounds listed in Supplemental Table S1 (Alberti et al, 2019 ; Bothwell et al, 2021 ; Cheng et al, 2023 ; De Rond et al, 2021 ; Enghiad et al, 2021 ; Gao et al, 2023 ; Gummerlich et al, 2020 ; Hao et al, 2019 ; Hashimoto et al, 2021 ; Kaweewan et al, 2021 ; Lasch et al, 2021 ; Lasch, Gummerlich, et al, 2020 , 2020 ; Li et al, 2020 ; S. H. Liu et al, 2019 ; Y. Liu et al, 2021 ; Myronovskyi et al, 2018 ; Paulus et al, 2022 ; Shi et al, 2019 ; Shuai et al, 2020 ; Unno et al, 2020 ; Vermeulen et al, 2022 ; X. Wang et al, 2023 ; Yuet et al, 2020 ; Y. Zhang et al, 2021 ; Y. Zhang et al, 2022 ).…”