Hecker Michael, Antelmann Haike, Büttner Knut, Bernhardt Jörg
Institute of Microbiology, Ernst-Moritz-Arndt-University of Greifswald, Greifswald, Germany.
Proteomics. 2008 Dec;8(23-24):4958-75. doi: 10.1002/pmic.200800278.
In this review, we demonstrate the power of gel-based proteomics to address physiological questions of bacteria. Although gel-based proteomics covers a subpopulation of proteins only, fundamental issues of a bacterial cell such as almost all metabolic pathways or the main signatures of stress and starvation responses can be analyzed. The analysis of the synthesis pattern of single proteins, e.g., in response to environmental changes, requires gel-based proteomics because only this technique can compare protein synthesis and amount in the same 2-D gel. Moreover, highly sophisticated software packages facilitate the analysis of the regulation of the main metabolic enzymes or the stress/starvation responses, PTMs, protein damage/repair, and degradation and finally protein secretion mechanisms at a proteome-wide scale. The challenge of proteomics whose panorama view shows events never seen before is to select the most interesting issues for detailed follow up studies. This "road map of proteomics" from proteome data via new hypothesis and finally novel molecular mechanisms should lead to exciting information on bacterial physiology. However, many proteins escape detection by gel-based procedures, such as membrane or low abundance proteins. The smart combination of gel-free and gel-based approaches is the "state of the art" for physiological proteomics of bacteria.
在本综述中，我们展示了基于凝胶的蛋白质组学在解决细菌生理学问题方面的强大作用。尽管基于凝胶的蛋白质组学仅涵盖蛋白质亚群，但细菌细胞的基本问题，如几乎所有代谢途径或应激和饥饿反应的主要特征，均可进行分析。分析单一蛋白质的合成模式，例如响应环境变化时的合成模式，需要基于凝胶的蛋白质组学，因为只有该技术能够在同一二维凝胶中比较蛋白质合成及含量。此外，高度复杂的软件包有助于在蛋白质组范围内分析主要代谢酶的调控或应激/饥饿反应、翻译后修饰、蛋白质损伤/修复及降解，最终还有蛋白质分泌机制。蛋白质组学全景展示了前所未见的事件，其面临的挑战在于选择最有趣的问题进行详细的后续研究。这条从蛋白质组数据出发，经新假设，最终到新分子机制的“蛋白质组学路线图”应能带来有关细菌生理学的激动人心的信息。然而，许多蛋白质难以通过基于凝胶的方法检测到，如膜蛋白或低丰度蛋白。无凝胶和基于凝胶方法的巧妙结合是细菌生理学蛋白质组学的“最新技术水平”。
