In recent years, there has been a growing interest in modulating the performance of probiotic, mainly Lactic Acid Bacteria (LAB), in the field of probiotic food. Attenuation, induced by sub-lethal stresses, delays the probiotic metabolism, and induces a metabolic shift as survival strategy. In this paper, RNA sequencing was used to uncover the transcriptional regulation in ATCC 393 after ultrasound-induced attenuation. Six (T) and 8 (ST) min of sonication induced a significant differential expression of 742 and 409 genes, respectively. We identified 198 up-regulated and 321 down-regulated genes in T, and similarly 321 up-regulated and 249 down-regulated in ST. These results revealed a strong defensive response at 6 min, followed by adaptation at 8 min. Ultrasound attenuation modified the expression of genes related to a series of crucial biomolecular processes including membrane transport, carbohydrate and purine metabolism, phage-related genes, and translation. Specifically, genes encoding PTS transporters and genes involved in the glycolytic pathway and pyruvate metabolism were up-regulated, indicating an increased need for energy supply, as also suggested by an increase in the transcription of purine biosynthetic genes. Instead, protein translation, a high-energy process, was inhibited with the down-regulation of ribosomal protein biosynthetic genes. Moreover, phage-related genes were down-regulated suggesting a tight transcriptional control on DNA structure. The observed phenomena highlight the cell need of ATP to cope with the multiple ultrasound stresses and the activation of processes to stabilize and preserve the DNA structure. Our work demonstrates that ultrasound has remarkable effects on the tested strain and elucidates the involvement of different pathways in its defensive stress-response and in the modification of its phenotype.

中文翻译：

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转录组分析揭示干酪乳杆菌 ATCC 393 响应超声应激的差异基因表达模式


近年来，在益生菌食品领域，人们对调节益生菌（主要是乳酸菌（LAB））的性能越来越感兴趣。由亚致死应激诱导的减毒会延迟益生菌的代谢，并诱导代谢转变作为生存策略。在本文中，RNA 测序用于揭示超声诱导衰减后 ATCC 393 中的转录调控。 6 分钟 (T) 和 8 分钟 (ST) 超声处理分别诱导 742 个和 409 个基因的显着差异表达。我们在 T 中鉴定出 198 个上调基因和 321 个下调基因，在 ST 中鉴定出类似的 321 个上调基因和 249 个下调基因。这些结果显示出 6 分钟时出现强烈的防御反应，随后在 8 分钟时出现适应。超声衰减改变了与一系列关键生物分子过程相关的基因表达，包括膜运输、碳水化合物和嘌呤代谢、噬菌体相关基因和翻译。具体来说，编码 PTS 转运蛋白的基因以及参与糖酵解途径和丙酮酸代谢的基因上调，表明对能量供应的需求增加，嘌呤生物合成基因转录的增加也表明了这一点。相反，蛋白质翻译这一高能过程因核糖体蛋白质生物合成基因的下调而受到抑制。此外，噬菌体相关基因下调，表明 DNA 结构受到严格的转录控制。观察到的现象强调了细胞需要 ATP 来应对多重超声应力以及激活稳定和保存 DNA 结构的过程。 我们的工作表明，超声波对测试菌株具有显着影响，并阐明了不同途径参与其防御性应激反应及其表型修饰的过程。