Bacterial gene expression is orchestrated by numerous transcription factors (TFs). Elucidating how gene expression is regulated is fundamental to understanding bacterial physiology and engineering it for practical use. In this study, a machine-learning approach was applied to uncover the genome-scale transcriptional regulatory network (TRN) in Pseudomonas putida KT2440, an important organism for bioproduction. We performed independent component analysis of a compendium of 321 high-quality gene expression profiles, which were previously published or newly generated in this study. We identified 84 groups of independently modulated genes (iModulons) that explain 75.7% of the total variance in the compendium. With these iModulons, we (i) expand our understanding of the regulatory functions of 39 iModulon associated TFs (e.g., HexR, Zur) by systematic comparison with 1993 previously reported TF-gene interactions; (ii) outline transcriptional changes after the transition from the exponential growth to stationary phases; (iii) capture group of genes required for utilizing diverse carbon sources and increased stationary response with slower growth rates; (iv) unveil multiple evolutionary strategies of transcriptome reallocation to achieve fast growth rates; and (v) define an osmotic stimulon, which includes the Type VI secretion system, as coordination of multiple iModulon activity changes. Taken together, this study provides the first quantitative genome-scale TRN for P. putida KT2440 and a basis for a comprehensive understanding of its complex transcriptome changes in a variety of physiological states.

细菌基因表达由众多转录因子 (TF) 协调。阐明如何调节基因表达对于理解细菌生理学并将其工程化以供实际使用至关重要。在这项研究中，应用机器学习方法来揭示恶臭假单胞菌中的基因组规模转录调控网络 (TRN)KT2440，一种重要的生物生产有机体。我们对之前发表或在本研究中新生成的 321 个高质量基因表达谱进行了独立成分分析。我们确定了 84 组独立调节的基因 (iModulons)，它们解释了纲要中总变异的 75.7%。通过这些 iModulon，我们 (i) 通过与 1993 年先前报道的 TF 基因相互作用的系统比较，扩展了我们对 39 个 iModulon 相关 TF（例如，HexR、Zur）的调节功能的理解；(ii) 概述从指数增长到稳定期过渡后的转录变化；(iii) 捕获利用不同碳源所需的一组基因，并以较慢的生长速率增加固定响应；(iv) 揭示转录组重新分配的多种进化策略，以实现快速增长；(v) 定义一个渗透刺激，包括 VI 型分泌系统，作为多个 iModulon 活动的协调变化。总之，这项研究提供了第一个定量基因组规模的 TRN恶臭假单胞菌KT2440是全面了解其在多种生理状态下复杂转录组变化的基础。