Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanology, Shenzhen University, Shenzhen, Guangdong, China.
Kodikos Labs, Lyon, France.
Microb Biotechnol. 2024 Nov;17(11):e70059. doi: 10.1111/1751-7915.70059.
In Pseudomonas putida KT2440, a prime chassis for biotechnology, the clustered distribution of glucose catabolism genes and four related transcription factors (TFs) may facilitate the tight regulation of glucose catabolism. However, the genes under the direct control of these TFs remain unidentified, leaving their regulatory roles elusive. Furthermore, the carbon source gluconate was metabolised similarly to glucose in KT2440, but the responses of these catabolic and TF genes to gluconate were unclear. Here, these mysteries were unravelled through multi-omics analysis integrated with physiological studies. First, we found that the expression of these catabolic and TF genes were significantly induced by both glucose and gluconate in KT2440. The independent responses of these genes to glucose and gluconate were differentiated in the gcd deletion mutant. We then defined the regulon of GnuR, one of the four related TFs, and discovered that GnuR directly repressed the expression of catabolic genes involved in the Entner-Doudoroff and the peripheral glucose and gluconate metabolism pathways. These results were further confirmed by physiological studies. Finally, a regulatory mode of an incoherent feedforward loop involving GnuR is proposed.
在恶臭假单胞菌 KT2440 中，葡萄糖分解代谢基因簇和四个相关转录因子 (TF) 的聚集分布可能有助于对葡萄糖分解代谢进行严格的调控。然而，这些 TF 直接控制的基因仍未被识别，其调控作用仍难以捉摸。此外，碳源葡糖酸盐在 KT2440 中的代谢方式与葡萄糖相似，但这些分解代谢和 TF 基因对葡糖酸盐的反应尚不清楚。在这里，通过多组学分析与生理研究相结合，揭示了这些奥秘。首先，我们发现这些分解代谢和 TF 基因在 KT2440 中均被葡萄糖和葡糖酸盐显著诱导。gcd 缺失突变体中这些基因对葡萄糖和葡糖酸盐的独立反应有所不同。然后，我们定义了四个相关 TF 之一 GnuR 的调控组，并发现 GnuR 直接抑制了参与 Entner-Doudoroff 和周边葡萄糖和葡糖酸盐代谢途径的分解代谢基因的表达。这些结果通过生理研究得到了进一步证实。最后，提出了一个涉及 GnuR 的非相干前馈环的调控模式。
