Neoabyssomicins A–C, polycyclic macrolactones from the deep-sea derived Streptomyces koyangensis SCSIO 5802

Song, Yongxiang; Li, Qinglian; Qin, Fengxiang; Sun, Changli; Liang, Hao; Wei, Xiaoyi; Wong, Nai-Kei; Li, Ye; Zhang, Yun; Shao, Mingwei; Ju, Jianhua

doi:10.1016/j.tet.2017.07.034

Cited by 36 publications

(84 citation statements)

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“…Abyssomicin C exhibits promising antibacterial activities against a number of Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA) [ 2 ] and Mycobacterium tuberculosis [ 3 ]. Motivated in part by these important revelations, biosynthetic studies and bacterial activity screening programs have recently unveiled several new members of the abyssomicin family [ 4 – 10 ]. The abyssomicin class of natural products contains two related subfamilies (type I and type II) [ 10 ].…”

Section: Introductionmentioning

confidence: 99%

Characterization and heterologous expression of the neoabyssomicin/abyssomicin biosynthetic gene cluster from Streptomyces koyangensis SCSIO 5802

Jiang

et al. 2018

Microb Cell Fact

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BackgroundThe deep-sea-derived microbe Streptomyces koyangensis SCSIO 5802 produces neoabyssomicins A–B (1–2) and abyssomicins 2 (3) and 4 (4). Neoabyssomicin A (1) augments human immunodeficiency virus-1 (HIV-1) replication whereas abyssomicin 2 (3) selectively reactivates latent HIV and is also active against Gram-positive pathogens including methicillin-resistant Staphylococcus aureus (MRSA). Structurally, neoabyssomicins A–B constitute a new subtype within the abyssomicin family and feature unique structural traits characteristic of extremely interesting biosynthetic transformations.ResultsIn this work, the biosynthetic gene cluster (BGC) for the neoabyssomicins and abyssomicins, composed of 28 opening reading frames, was identified in S. koyangensis SCSIO 5802, and its role in neoabyssomicin/abyssomicin biosynthesis was confirmed via gene inactivation and heterologous expression experiments. Bioinformatics and genomics analyses enabled us to propose a biosynthetic pathway for neoabyssomicin/abyssomicin biosynthesis. Similarly, a protective export system by which both types of compounds are secreted from the S. koyangensis producer was identified, as was a four-component ABC transporter-based import system central to neoabyssomicin/abyssomicin biosynthesis. Furthermore, two regulatory genes, abmI and abmH, were unambiguously shown to be positive regulators of neoabyssomicin/abyssomicin biosynthesis. Consistent with their roles as positive regulatory genes, the overexpression of abmI and abmH (independent of each other) was shown to improve neoabyssomicin/abyssomicin titers.ConclusionsThese studies provide new insight into the biosynthesis of the abyssomicin class of natural products, and highlight important exploitable features of its BGC for future efforts. Elucidation of the neoabyssomicin/abyssomicin BGC now enables combinatorial biosynthetic initiatives aimed at improving both the titers and pharmaceutical properties of these important natural products-based drug leads.Electronic supplementary materialThe online version of this article (10.1186/s12934-018-0875-1) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Characterization and heterologous expression of the neoabyssomicin/abyssomicin biosynthetic gene cluster from Streptomyces koyangensis SCSIO 5802

Jiang

et al. 2018

Microb Cell Fact

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“…26 Table S11. The abyssomicin biosynthetic gene cluster from S. koyangensis SCSIO 5802 (modified from Song et al, 2017). 27- 28 Table S12.…”

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confidence: 99%

“…In maroon font appear those genes that appear both in aby and abs BGCs, in light brown those genes that appear both in aby and abm BGCs and in yellow those genes that appear both in abs and abm BGCs. (Song et al, 2017) MG243704 2, 4, neo-A, neo-B, neo-C, neo-D, neo-E, neo-F, neo-G, neo-2 Table S2. Isolation details of the abyssomicin producers isolated from aquatic environments.…”

Section: -25mentioning

confidence: 99%

“…MS100047 Isolated on a VER01 agar plate from a sediment sample collected in the South China Sea at 28 °C. (Huang et al, 2016) Streptomyces koyangensis SCSIO 5802 Isolated from a sediment sample collected from the South China Sea at a depth of -3536 m. (Song et al, 2017) Table S77. Predicted functions of ORFs surrounding AbyU homolog from Streptomyces sp.…”

Section: Isolation Details Referencementioning

confidence: 99%

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Out of the Abyss: Genome and Metagenome Mining Reveals Unexpected Environmental Distribution of Abyssomicins

et al. 2020

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ContentsPage Figure S1.Habitat distribution of the metagenomes analysed for the presence of AbyU, AbmU and AbsU. 2 Figure S2.Taxonomic profile at the phylum level of ten marine (1-10), ten terrestrial (11-20) and ten Diels-Alderase positive (21-30) metagenomes. These metagenomes were randomly selected from the 3027 metagenomes analysed. The ten Diels-Alderase positive were six terrestrial (21-26), one Arthropoda-associated (27) and three plant-associated (28-30). Only the most abundant phyla are shown. Numbers above each bar plot indicate metagenome size (Mb).3 Figure S3. Taxonomic profile at the order level of ten marine (1-10), ten terrestrial (11-20) and ten Diels-Alderase positive (21-30) metagenomes. These metagenomes were randomly selected from the 3027 metagenomes analysed. The ten Diels-Alderase positive were six terrestrial (21-26), one Arthropoda-associated (27) and three plant-associated (28-30).

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“…Finally, the last abyssomicins discovered were synthesised by the soil Streptomyces sp. LC-6-2 (Wang et al, 2017a) and the marine S. koyangensis SCSIO 5802 (Huang et al, 2018;Song et al, 2017) (Table S1).…”

Section: Introductionmentioning

confidence: 99%

Out of the abyss: Genome and metagenome mining reveals unexpected environmental distribution of abyssomicins

Iglesias

Latorre-Pérez²,

Stach

et al. 2019

Preprint

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AbstractNatural products have traditionally been discovered through the screening of culturable microbial isolates from all sort of environments. The sequencing revolution allowed the identification of dozens of biosynthetic gene clusters (BGCs) within single bacterial genomes, either from cultured or uncultured strains. However, we are still far from fully exploiting the microbial reservoir, as most of the species are non-model organisms with complex regulatory systems and yet recalcitrant to be engineered. Today, genomic and metagenomic data produced by laboratories worldwide covering the most different natural and artificial environments on Earth, are an invaluable source of raw information from which natural product biosynthesis can be accessed. In the present work, we describe the environmental distribution and evolution of the abyssomicin BGC through the analysis of publicly available genomic and metagenomic data. Our results demonstrate that the selection of a pathway-specific enzyme to direct the genome mining is an excellent strategy that led to the identification of 74 new Diels-Alderase homologs and unveiled a surprising prevalence of the abyssomicin BGC within terrestrial habitats, mainly soil and plant-associated, where we have identified five complete and 12 partial new abyssomicin BGCs and 23 new potential abyssomicin BGCs. Our results strongly support the potential of genome and metagenome mining as a key preliminary tool to inform bioprospecting strategies aiming at the identification of new bioactive compounds such as -but not restricted to-abyssomicins.

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Neoabyssomicins A–C, polycyclic macrolactones from the deep-sea derived Streptomyces koyangensis SCSIO 5802

Cited by 36 publications

References 32 publications

Characterization and heterologous expression of the neoabyssomicin/abyssomicin biosynthetic gene cluster from Streptomyces koyangensis SCSIO 5802

Characterization and heterologous expression of the neoabyssomicin/abyssomicin biosynthetic gene cluster from Streptomyces koyangensis SCSIO 5802

Out of the Abyss: Genome and Metagenome Mining Reveals Unexpected Environmental Distribution of Abyssomicins

Out of the abyss: Genome and metagenome mining reveals unexpected environmental distribution of abyssomicins

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