Quantitative Proteomics for the Comprehensive Analysis of Stress Responses of Lactobacillus paracasei subsp. <i>paracasei</i> F19

Lactic acid bacteria are broadly employed as starter cultures in the manufacture of foods. Upon technological preparation, they are confronted with drying stress that amalgamates numerous stress conditions resulting in losses of fitness and survival. To better understand and differentiate physiological stress responses, discover general and specific markers for the investigated stress conditions, and predict optimal preconditioning for starter cultures, we performed a comprehensive genomic and quantitative proteomic analysis of a commonly used model system, Lactobacillus paracasei subsp. paracasei TMW 1.1434 (isogenic with F19) under 11 typical stress conditions, including among others oxidative, osmotic, pH, and pressure stress. We identified and quantified >1900 proteins in triplicate analyses, representing 65% of all genes encoded in the genome. The identified genes were thoroughly annotated in terms of subcellular localization prediction and biological functions, suggesting unbiased and comprehensive proteome coverage. In total, 427 proteins were significantly differentially expressed in at least one condition. Most notably, our analysis suggests that optimal preconditioning toward drying was predicted to be alkaline and high-pressure stress preconditioning. Taken together, we believe the presented strategy may serve as a prototypic example for the analysis and utility of employing quantitative-mass-spectrometry-based proteomics to study bacterial physiology.乳酸菌（Lactic acid bacteria）被广泛用作食品制造过程中的发酵剂（starter cultures）。在工业化制备流程中，这类菌株会遭遇整合了多种胁迫条件的干燥胁迫（drying stress），进而导致其活力与存活率下降。为了更深入地解析并区分生理胁迫响应、发掘目标胁迫条件的通用与特异性标志物，并预测发酵剂菌株的最优预适应处理（preconditioning）方案，本研究针对常用模式菌株——副干酪乳杆菌副干酪亚种Lactobacillus paracasei subsp. paracasei TMW 1.1434（与F19为同基因株）在11种典型胁迫条件（包括氧化胁迫、渗透胁迫、pH胁迫及压力胁迫等）下的样本开展了全面的基因组学与定量蛋白质组学分析。通过三次重复实验分析，我们共鉴定并定量了超过1900种蛋白质，覆盖该菌株基因组编码基因的65%。针对所鉴定的蛋白质，我们从亚细胞定位预测与生物学功能两个维度进行了详尽注释，证明本研究实现了无偏倚且全面的蛋白质组覆盖。总计有427种蛋白质在至少一种胁迫条件下呈现显著差异表达。尤为重要的是，本研究分析结果显示，用于提升干燥胁迫抗性的最优预适应处理方案为碱性胁迫与高压胁迫预适应。综上，本研究提出的分析策略可作为基于定量质谱的蛋白质组学（quantitative-mass-spectrometry-based proteomics）技术用于细菌生理学研究的典型范例。