Qin Jingliang, Guo Han, Wu Xiaoxue, Ma Shuai, Zhang Xin, Yang Xiaofeng, Liu Bin, Feng Lu, Liu Huanhuan, Huang Di
Tianjin Key Laboratory of Microbial Functional Genomics, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China.
School of Biology and Biological Engineering, South China University of Technology, 382 East Outer Loop Road, University Park, Guangzhou 510006, China.
Microorganisms. 2024 Jul 31;12(8):1565. doi: 10.3390/microorganisms12081565.
Engineering acid-tolerant microbial strains is a cost-effective approach to overcoming acid stress during industrial fermentation. We previously constructed an acid-tolerant strain ( SC3124) with enhanced growth robustness and productivity under mildly acidic conditions by fine-tuning the expression of synthetic acid-tolerance module genes consisting of a proton-consuming acid resistance system (E), a periplasmic chaperone (B), and ROS scavengers (B, E). However, the precise acid-tolerance mechanism of SC3124 remained unclear. In this study, the growth of SC3124 under mild acid stress (pH 6.0) was determined. The final OD600 of SC3124 at pH 6.0 was 131% and 124% of that of the parent MG1655 at pH 6.8 and pH 6.0, respectively. Transcriptome analysis revealed the significant upregulation of the genes involved in oxidative phosphorylation, the tricarboxylic acid (TCA) cycle, and lysine-dependent acid-resistance system in SC3124 at pH 6.0. Subsequently, a weighted gene coexpression network analysis was performed to systematically determine the metabolic perturbations of SC3124 with mild acid treatment, and we extracted the gene modules highly associated with different acid traits. The results showed two biologically significant coexpression modules, and 263 hub genes were identified. Specifically, the genes involved in ATP-binding cassette (ABC) transporters, oxidative phosphorylation, the TCA cycle, amino acid metabolism, and purine metabolism were highly positively associated with mild acid stress responses. We propose that the overexpression of synthetic acid-tolerance genes leads to metabolic changes that confer mild acid stress resistance in . Integrated omics platforms provide valuable information for understanding the regulatory mechanisms of mild acid tolerance in and highlight the important roles of oxidative phosphorylation and ABC transporters in mild acid stress regulation. These findings offer novel insights to better the design of acid-tolerant chasses to synthesize value-added chemicals in a green and sustainable manner.
工程化耐酸微生物菌株是克服工业发酵过程中酸胁迫的一种经济有效的方法。我们之前通过微调由质子消耗型抗酸系统（E）、周质伴侣（B）和活性氧清除剂（B、E）组成的合成耐酸模块基因的表达，构建了一种在轻度酸性条件下具有增强生长稳健性和生产力的耐酸菌株（SC3124）。然而，SC3124的确切耐酸机制仍不清楚。在本研究中，测定了SC3124在轻度酸胁迫（pH 6.0）下的生长情况。SC3124在pH 6.0时的最终OD600分别是亲本MG1655在pH 6.8和pH 6.0时的131%和124%。转录组分析显示，在pH 6.0时，SC3124中参与氧化磷酸化、三羧酸（TCA）循环和赖氨酸依赖性抗酸系统的基因显著上调。随后，进行了加权基因共表达网络分析，以系统地确定轻度酸处理下SC3124的代谢扰动，并提取了与不同酸性状高度相关的基因模块。结果显示了两个具有生物学意义的共表达模块，并鉴定出263个枢纽基因。具体而言，参与ATP结合盒（ABC）转运蛋白、氧化磷酸化、TCA循环、氨基酸代谢和嘌呤代谢的基因与轻度酸胁迫反应高度正相关。我们提出，合成耐酸基因的过表达导致代谢变化，从而赋予对轻度酸胁迫的抗性。综合组学平台为理解对轻度酸耐受性的调控机制提供了有价值的信息，并突出了氧化磷酸化和ABC转运蛋白在轻度酸胁迫调控中的重要作用。这些发现为更好地设计耐酸底盘以绿色可持续方式合成增值化学品提供了新的见解。
