Genomic Insights of Biosynthetic Potential from Actinoalloteichus caeruleus LHW52806, a Promising Actinomycete for Natural Product Discovery.

Abstract

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^T, 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.