Kim Min-Seon, Selvaraj Baskar, Yeo Hee-Tae, Park Jun-Su, Lee Jae Wook, Park Jin-Soo
Center for Natural Product Systems Biology, Institute of Natural Product, Korea Institute of Science and Technology, Gangneung, 25451, Republic of Korea.
Center for Natural Product Efficacy Optimization, Institute of Natural Product, Korea Institute of Science and Technology, Gangneung, 25451, Republic of Korea.
Microb Cell Fact. 2025 Jan 10;24(1):14. doi: 10.1186/s12934-024-02641-5.
Genome mining is a promising avenue for expanding the repertoire of microbial natural products, which are important for drug development. This approach involves predicting genetically encoded small molecules by examining bacterial genomes via accumulated knowledge of microbial biosynthesis. However, it is also important that the microbes produce the predicted molecule in practice. Here, we introduce an endophytic Streptomyces sp. N50, which was isolated from the medicinal plant Selaginella tamariscina. Upon sequencing its entire genome, 33 biosynthetic gene clusters (BGCs) were identified in a chromosome and a megaplasmid. Subsequent genome mining revealed that the new 15-deoxynaphthomycin could be produced due to the presence of an enoyl reductase domain, which is absent in the known BGC of naphthomycin, a type of ansamycin antibiotics. In addition, the engineered strain with the introduction of the global regulatory gene afsR2 into N50 successfully produced 15-deoxynaphthomycins. Furthermore, molecular network analysis via MS/MS selectively confirmed the presence of additional sulfur-containing 15-deoxynaphthomycin congeners. Eventually, six new 15-deoxynaphthomycins were isolated and elucidated from the engineered strain N50. This family of compounds is known to exhibit various biological activities. Also, the presence of quinone moieties in these compounds, which are known to activate NRF2, they were tested for their ability to activate NRF2. Among the new compounds, three (1, 5, and 6) activated the antioxidant NRF2-ARE signaling pathway. Treatment with these compounds significantly elevated NRF2 levels in HepG2 cells and further induced the expression of NRF2 target genes associated with the antioxidant response. This study suggests that the combination of genome mining, gene engineering and molecular networking is helpful for generating new small molecules as pharmaceutical candidates from microorganisms.
基因组挖掘是拓展微生物天然产物库的一条有前景的途径，而微生物天然产物对药物开发很重要。这种方法通过利用微生物生物合成的积累知识检查细菌基因组来预测基因编码的小分子。然而，微生物在实际中产生预测的分子也很重要。在此，我们介绍一种从药用植物卷柏中分离出的内生链霉菌N50。对其全基因组测序后，在一条染色体和一个大质粒中鉴定出33个生物合成基因簇（BGCs）。随后的基因组挖掘表明，由于存在一个烯酰还原酶结构域，可能会产生新的15 - 脱氧萘霉素，而在已知的萘霉素（一种安莎霉素类抗生素）的BGC中不存在该结构域。此外，将全局调控基因afsR2引入N50得到的工程菌株成功产生了15 - 脱氧萘霉素。此外，通过MS/MS进行的分子网络分析选择性地证实了额外含硫的15 - 脱氧萘霉素同系物的存在。最终，从工程菌株N50中分离并鉴定出六种新的15 - 脱氧萘霉素。已知该类化合物具有多种生物活性。而且，这些化合物中存在已知可激活NRF2 的醌部分，因此测试了它们激活NRF2 的能力。在新化合物中，有三种（1、5和6）激活了抗氧化剂NRF2 - ARE信号通路。用这些化合物处理显著提高了HepG2细胞中的NRF2水平，并进一步诱导了与抗氧化反应相关的NRF2靶基因的表达。这项研究表明，基因组挖掘、基因工程和分子网络相结合有助于从微生物中产生新的小分子作为药物候选物。
