15N Stable Isotope Labeling and Comparative Metabolomics Facilitates Genome Mining in Cultured Cyanobacteria
15N Stable Isotope Labeling and Comparative Metabolomics Facilitates Genome Mining in Cultured Cyanobacteria
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DOI：
10.1021/acschembio.9b00993
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发表时间：
2020-03-20
影响因子：
4
通讯作者：
Orjala, Jimmy E.
中科院分区：
文献类型：
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作者：
May, Daniel S.;Crnkovic, Camila M.;Orjala, Jimmy E.
随着基因组挖掘成为鉴定细菌天然产物的一种更广泛使用的方法，将生物合成基因粉尘与其同源次生代谢物相匹配的挑战变得更加明显。AntiSMASH等生物信息学平台在利用遗传信息预测化学结构方面取得了很大进展，但预测的结构往往是不完整的。这使得用质谱法鉴定预测的化合物变得复杂。蓝藻产生的次生代谢物为弥合这一差距提供了独特的机会。培养的蓝藻将化学定义的培养基中提供的无机氮纳入所有含氮的次生代谢物中。因此，用N-1(5)标记硝酸盐的稳定同位素标记和随后的比较代谢组学可以用于将生物合成基因粉尘与其细胞提取物中的同源化合物相匹配。通过对Nostoc sp. UIC 10630的基因组测序分析，鉴定出6个生物合成基因粉尘，预测它们编码产生至少含有一个氮原子的次级代谢物。对N-1(5)标记和未标记的细胞提取物进行比较代谢组学分析，发现四种含氮化合物含有与生物合成基因簇中预测的氮原子数量相同的氮原子。4个化合物中有2个为新的次级代谢物，其结构经NMR、HRESIMS和MS/MS鉴定。
As genome mining becomes a more widely used approach to identify bacterial natural products, the challenge of matching biosynthetic gene dusters to their cognate secondary metabolites has become more apparent. Bioinformatic platforms such as AntiSMASH have made great progress in predicting chemical structures from genetic information, however the predicted structures are often incomplete. This complicates identifying the predicted compounds by mass spectrometry. Secondary metabolites produced by cyanobacteria represent a unique opportunity for bridging this gap. Cultured cyanobacteria incorporate inorganic nitrogen provided in chemically defined media into all nitrogen-containing secondary metabolites. Thus, stable isotope labeling with N-1(5) labeled nitrate and subsequent comparative metabolomics can be used to match biosynthetic gene dusters to their cognate compounds in cell extracts. Analysis of the sequenced genome of Nostoc sp. UIC 10630 identified six biosynthetic gene dusters predicted to encode the production of a secondary metabolite with at least one nitrogen atom. Comparative metabolomic analysis of the N-1(5) labeled and unlabeled cell extracts revealed four nitrogen containing compounds that contained the same number of nitrogen atoms as were predicted in the biosynthetic gene clusters. Two of the four compounds were new secondary metabolites, and their structures were elucidated by NMR, HRESIMS, and MS/MS.