The selection of growth media is a very important consideration of any cell-based proteomics experiment. Alterations thereof may result in differences in basal proteomes simply due to disparities in the metabolite composition of the media. We investigate the effect of growth media on the proteomes of three microorganisms, specifically E. coli, S. cerevisiae, and S. pombe, using tandem mass tag (TMT)-based quantitative proteomics. We compared the protein abundance profiles of these microorganisms propagated in two distinct growth media that are commonly used for the respective organism. Our sample preparation strategy included SP3 bead-assisted protein isolation and digestion. In addition, we assembled a replicate set of samples in which we altered the proteolytic digestion from sequential treatment with LysC and trypsin to only LysC. Despite differences in peptides identified and a drop in quantified proteins, the results were similar between the two datasets for all three microorganisms. Approximately 10% of the proteins of each respective microorganism were significantly altered in each dataset. As expected, gene ontology analysis revealed that the majority of differentially expressed proteins are implicated in metabolism. These data emphasize further the importance and the potential consequences of growth media selection.

Significance

Various microorganisms are used as model systems throughout in biological studies, including proteomics-based investigations. The growth conditions of these organisms are of utmost importance, of which one major consideration is the choice of growth media. We hypothesize that growth media selection has a considerable impact on the baseline proteome of a given microorganism. To test this hypothesis, we used tandem mass tag (TMT)-based quantitative multiplexed proteomics to profile the proteomes of E. coli, S. cerevisiae, and S. pombe each grown in two different, yet common, growth media for the respective species. Our data show that approximately 10% of the proteins of each respective microorganism were significantly altered and that many of the differentially expressed proteins are implicated in metabolism. We provide several datasets which are potentially valuable for growth media selection with respect to downstream biochemical analysis.

中文翻译：

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生长培养基的选择改变了三种模式微生物的蛋白质组谱

生长培养基的选择是任何基于细胞的蛋白质组学实验的一个非常重要的考虑因素。其改变可能仅由于培养基代谢物组成的差异而导致基础蛋白质组的差异。我们研究了生长培养基对三种微生物蛋白质组的影响，特别是大肠杆菌、酿酒酵母和庞贝酵母。，使用基于串联质量标签 (TMT) 的定量蛋白质组学。我们比较了这些微生物在两种不同的生长培养基中繁殖的蛋白质丰度分布，这两种培养基通常用于各自的生物体。我们的样品制备策略包括 SP3 微珠辅助蛋白质分离和消化。此外，我们组装了一组重复的样品，其中我们将蛋白水解消化从用 LysC 和胰蛋白酶的顺序处理改变为仅 LysC。尽管鉴定的肽存在差异并且定量蛋白质有所下降，但所有三种微生物的两个数据集之间的结果相似。在每个数据集中，每种微生物的大约 10% 的蛋白质发生了显着变化。正如预期的那样，基因本体分析表明，大多数差异表达的蛋白质与代谢有关。这些数据进一步强调了生长培养基选择的重要性和潜在后果。

意义

各种微生物在生物学研究中被用作模型系统，包括基于蛋白质组学的研究。这些生物的生长条件至关重要，其中一个主要考虑因素是生长培养基的选择。我们假设生长培养基的选择对给定微生物的基线蛋白质组有相当大的影响。为了验证这一假设，我们使用基于串联质量标签 (TMT) 的定量多重蛋白质组学来分析大肠杆菌、酿酒酵母和庞贝酵母的蛋白质组每种都在各自物种的两种不同但常见的生长培养基中生长。我们的数据表明，每种微生物中大约 10% 的蛋白质发生了显着改变，并且许多差异表达的蛋白质与新陈代谢有关。我们提供了几个数据集，这些数据集对于下游生化分析的生长培养基选择具有潜在价值。