In Pseudomonas donghuensis SVBP6, isolated from an agricultural field, the well-conserved Gac-Rsm pathway upregulates biosynthesis of the antifungal compound 7-hydroxytropolone (7-HT). However, 7-HT does not fully explain the strain's Gac-Rsm-dependent antimicrobial activity. Here, we combined comparative transcriptomic, proteomic, and metabolomic approaches to identify novel GacS-dependent biosynthetic gene clusters (BGC) and/or extracellular specialized metabolites. Our data revealed a broad impact of GacS on gene expression and extracellular metabolite profile of SVBP6. At both the mRNA and polypeptide levels, specialized metabolism was the main affected functional category in the gacS mutant. The major extracellular MS/MS spectral families promoted by GacS were fatty acid amides, fatty acids, and alkaloids. GacS was required for the production of the antimicrobial compound pseudoiodinine and to activate expression of the corresponding BGC. We also detected GacS-dependent production of 2,3,4-trihydro-β-carboline-1-one, which may add to the antimicrobial arsenal of SVBP6. Furthermore, transcriptomics and proteomics pinpointed several GacS-activated BGCs that had escaped in silico genome mining tools. Altogether, comparative multi-omics analyses of gacS loss-of-function mutants in Pseudomonas isolates are a promising strategy to uncover bioactive metabolites and/or their BGCs. Discovery of novel natural products is important for harnessing the potential of microbiota to improve crop plant growth and health.

中文翻译：

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比较多组学调查揭示了东湖假单胞菌菌株 SVBP6 中 GacS 控制下的新型特化代谢物和生物合成基因簇


在从农田中分离的东湖假单胞菌 SVBP6 中，保守的 Gac-Rsm 通路上调了抗真菌化合物 7-羟基原油酮 （7-HT） 的生物合成。然而，7-HT 并不能完全解释该菌株的 Gac-Rsm 依赖性抗菌活性。在这里，我们结合了比较转录组学、蛋白质组学和代谢组学方法来鉴定新的 GacS 依赖性生物合成基因簇 （BGC） 和/或细胞外特化代谢物。我们的数据揭示了 GacS 对 SVBP6 基因表达和细胞外代谢物谱的广泛影响。在 mRNA 和多肽水平上，特化代谢是 gacS 突变体中主要受影响的功能类别。GacS 促进的主要细胞外 MS/MS 谱系是脂肪酸酰胺、脂肪酸和生物碱。GacS 是生产抗菌化合物假碘二氨酸和激活相应 BGC 表达所必需的。我们还检测到 2,3,4-三氢-β-咔啉-1-酮的 GacS 依赖性产生，这可能会增加 SVBP6 的抗菌库。此外，转录组学和蛋白质组学确定了几种在计算机基因组挖掘工具中逃逸的 GacS 激活的 BGC。总而言之，对假单胞菌分离株中 gacS 功能丧失突变体的比较多组学分析是揭示生物活性代谢物和/或其 BGC 的一种很有前途的策略。发现新的天然产物对于利用微生物群的潜力来改善作物生长和健康非常重要。