Lee Pat S, Shaw Leah B, Choe Leila H, Mehra Amit, Hatzimanikatis Vassily, Lee Kelvin H
Department of Chemical Engineering Cornell University, 120 Olin Hall, Ithaca, New York 14853, USA.
Biotechnol Bioeng. 2003 Dec 30;84(7):834-41. doi: 10.1002/bit.10841.
There is a need for improved appreciation of the importance of genome-wide mRNA and protein expression measurements and their role in understanding translation and in relation to genome-wide mathematical frameworks for gene expression regulation. We investigated the use of a high-density microarray technique for mRNA expression analysis and a two-dimensional protein electrophoresis-tandem mass spectrometry method for protein analysis to monitor changes in gene expression. We applied these analytical tools in the context of an environmental perturbation of Escherichia coli cells-the addition of varying amounts of IPTG. We also tested the application of these tools to the study of a genetic perturbation of Escherichia coli cells-the ability of certain strains to hypersecrete the hemolysin protein. We observed a lack of correspondence between mRNA and protein expression profiles. Although our data do not include measurements on all expressed genes (because the ability to measure protein expression profiles is limiting), we observed that the qualitative and quantitative behavior of the measurements of a subset of expressed genes is similar to the behavior of the entire system. The change in observed average mRNA and protein amplification factors for 77 and 52 genes coincided with the observed change in mRNA amplification factor for the entire system. Furthermore, we found that the use of relative changes in expression could be used to elucidate mechanisms of gene expression regulation for the system studied, even when measurements were made on a small subset of the system.
需要更好地认识全基因组mRNA和蛋白质表达测量的重要性，以及它们在理解翻译过程中，以及在与全基因组基因表达调控数学框架相关方面所起的作用。我们研究了利用高密度微阵列技术进行mRNA表达分析，以及利用二维蛋白质电泳-串联质谱法进行蛋白质分析，以监测基因表达的变化。我们在对大肠杆菌细胞进行环境扰动（添加不同量的异丙基-β-D-硫代半乳糖苷（IPTG））的背景下应用了这些分析工具。我们还测试了将这些工具应用于对大肠杆菌细胞进行基因扰动的研究——某些菌株超分泌溶血素蛋白的能力。我们观察到mRNA和蛋白质表达谱之间缺乏对应关系。虽然我们的数据并不包括对所有表达基因的测量（因为测量蛋白质表达谱的能力有限），但我们观察到，一部分表达基因测量的定性和定量行为与整个系统的行为相似。77个基因和52个基因观察到的平均mRNA和蛋白质扩增因子的变化与整个系统观察到的mRNA扩增因子的变化一致。此外，我们发现，即使是对系统的一小部分进行测量，使用表达的相对变化也可用于阐明所研究系统的基因表达调控机制。
