Hong Hui, Zhang Die, Lin Hou-Wen, Li Lei
College of Food Science and Engineering, Shanghai Ocean University, Shanghai, 201200, People's Republic of China.
Marine Drug Integrated Innovation Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, People's Republic of China.
Biochem Genet. 2025 Jul 24. doi: 10.1007/s10528-025-11195-z.
Actinoalloteichus caeruleus, the type species of the rare actinomycete genus Actinoalloteichus, was found to produce various classes of bioactive compounds including bipyridine, β-carboline and cyclolipopeptides. Although the chemistry of natural products from A. caeruleus has been well studied over the past two decades, the complete genomes of this talent species along with its secondary metabolic potential was poorly reported. In this work, the complete genome sequence of Actinoalloteichus sp. LHW52806, the only producer of Marinacarboline glucuronic and Cyanogripeptides, was sequenced and the biosynthetic potential was investigated by a genome mining approach. Genomic analyses indicate a circular chromosome consisting of 6,184,314 bp with a G + C content of 72.27%. The dDDH and ANI values based on genome sequences between strain LHW52806 and the type strain, Actinoalloteichus caeruleus NRRL B-2194, were 93.1% and 99.2%, respectively, confirmed the species assignment. Combined analysis using antiSMASH and PRISM identified 27 biosynthetic gene clusters (BGCs) responsible for secondary metabolite. Among these, only 10 BGCs exhibited high similarities to known clusters in the MIBIG database. The remaining clusters are predicted to synthesize novel natural products, encompassing nonribosomal peptides (NRPs), polyketides (PKs), lassopeptides, lantibiotics, and guanidinotides, suggesting substantial biosynthetic potential. The candidate BGC for β-carboline alkaloids was identified in the genome and a biosynthetic pathway of marinacarboline glucuronic was proposed. Guided by the bioinformatic analysis on the BGCs, a series of polycyclic tetramate macrolactams (PTMs) was found by LC-MS in the fermentation extracts of A. caeruleus LHW52806, with 30,31-dihydrofrontalamide A (DHFA) isolated and identified. These findings advance comprehension of secondary metabolite biosynthesis in A. caeruleus, while simultaneously establishing a foundation for novel natural products discovery.
天蓝放线异壁放线菌（Actinoalloteichus caeruleus）是稀有放线菌属Actinoalloteichus的模式种，被发现能产生多种生物活性化合物，包括联吡啶、β-咔啉和环脂肽。尽管在过去二十年里对天蓝放线异壁放线菌的天然产物化学进行了深入研究，但关于这个有价值的菌种的完整基因组及其次生代谢潜力的报道却很少。在这项工作中，对Marinacarboline葡萄糖醛酸和氰基握肽的唯一产生菌天蓝放线异壁放线菌LHW52806进行了全基因组测序，并通过基因组挖掘方法研究了其生物合成潜力。基因组分析表明，该菌有一个由6,184,314 bp组成的环状染色体，G + C含量为72.27%。基于菌株LHW52806与模式菌株天蓝放线异壁放线菌NRRL B - 2194之间的基因组序列计算的dDDH和ANI值分别为93.1%和99.2%，证实了该菌种的分类。使用antiSMASH和PRISM进行的联合分析鉴定出27个负责次生代谢产物的生物合成基因簇（BGC）。其中，只有10个BGC与MIBIG数据库中的已知簇具有高度相似性。其余的簇预计能合成新型天然产物，包括非核糖体肽（NRP）、聚酮化合物（PK）、lassopeptide、羊毛硫抗生素和胍基核苷酸，这表明其具有巨大的生物合成潜力。在基因组中鉴定出了β-咔啉生物碱的候选BGC，并提出了Marinacarboline葡萄糖醛酸的生物合成途径。在BGCs的生物信息学分析指导下，通过液相色谱 - 质谱法在天蓝放线异壁放线菌LHW52806的发酵提取物中发现了一系列多环四酰胺大环内酯（PTM），并分离鉴定出了30,31 - 二氢前胡酰胺A（DHFA）。这些发现增进了对天蓝放线异壁放线菌次生代谢产物生物合成的理解，同时为新型天然产物的发现奠定了基础。
