Ecological Niche-Inspired Genome Mining Leads to the Discovery of Crop-Protecting Nonribosomal Lipopeptides Featuring a Transient Amino Acid Building Block

Abstract

Investigating the ecological context of microbial predator−prey interactions enables the identification of microorganisms, which produce multiple secondary metabolites to evade predation or to kill the predator. In addition, genome mining combined with molecular biology methods can be used to identify further biosynthetic gene clusters that yield new antimicrobials to fight the antimicrobial crisis. In contrast, classical screening-based approaches have limitations since they do not aim to unlock the entire biosynthetic potential of a given organism. Here, we describe the genomics-based identification of keanumycins A−C. These nonribosomal peptides enable bacteria of the genus Pseudomonas to evade amoebal predation. While being amoebicidal at a nanomolar level, these compounds also exhibit a strong antimycotic activity in particular against the devastating plant pathogen Botrytis cinerea and they drastically inhibit the infection of Hydrangea macrophylla leaves using only supernatants of Pseudomonas cultures. The structures of the keanumycins were fully elucidated through a combination of nuclear magnetic resonance, tandem mass spectrometry, and degradation experiments revealing an unprecedented terminal imine motif in keanumycin C extending the family of nonribosomal amino acids by a highly reactive building block. In addition, chemical synthesis unveiled the absolute configuration of the unusual dihydroxylated fatty acid of keanumycin A, which has not yet been reported for this lipodepsipeptide class. Finally, a detailed genome-wide microarray analysis of Candida albicans exposed to keanumycin A shed light on the mode-of-action of this potential natural product lead, which will aid the development of new pharmaceutical and agrochemical antifungals.

Assessing the Biosynthetic Inventory of the Biocontrol Fungus Trichoderma afroharzianum T22

“…For example, none of the five lipopeptide BGCs, which contain NRPSs with a characteristic N -terminal C domain, has been characterized or has homologous BGCs (Table ). A recent study has demonstrated the antifungal activity of bacterial lipopeptide keanumycins against plant pathogen Botrytis cinerea . These ThT22 lipopeptide BGCs may be a promising source for new antifungal agents.…”

“…A recent study has demonstrated the antifungal activity of bacterial lipopeptide keanumycins against plant pathogen Botrytis cinerea. 72 These ThT22 lipopeptide BGCs may be a promising source for new antifungal agents. In addition, the BGCs we have discussed so far all have a core biosynthetic gene that has been used as the hallmark for the genome mining of natural products.…”

Nonribosomal peptides protect Pseudomonas nunensis 4A2e from amoebal and nematodal predation

“…41,42 Structure elucidation of keanumycin D Our recent identication of keanumycins A-C proved to be helpful for structure elucidation of 1 (m/z 1122.5433 [M+H] + ). 22,43 Except for keanumycin C, all reported mycins are cyclic lipopeptides. Mild saponication 13 of 1 in MeOH led to the formation of compound with a mass increase of 32 Da (Fig.…”

“…QS1027 uses a combination of structurally related CLPs, keanumycins and jessenipeptin, to overcome grazing by the model social amoeba Dictyostelium discoideum. 22 Interestingly, it has been hypothesised that predation resistance is linked to phytopathogen-suppressive traits, opening potential application in agricultural systems. 23,24 A good example is the work on CLPs of the amphisin family.…”

Experiment ended

“…Đầu năm 2023, một tài tử đã khiến cho cả tạp chí khoa học lừng danh Nature phải sớm reo hò cổ vũ, huyên náo cả văn đàn học giới [1]. Nguyên do là từ một nghiên cứu mới xuất bản trên Tạp chí Hiệp hội Hóa học Mỹ (JACS) trong đó các nhà nghiên cứu đã phát hiện được một số hợp chất hóa học do vi khuẩn tổ hợp được, có sức mạnh hạ gục nhanh, tiêu diệt gọn nhiều loại nấm, bao gồm cả những loại gây thối hỏng hoa quả, thực phẩm [2].…”