Institute of Basic Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tennodai, Tsukuba, Ibaraki, Japan.
PLoS One. 2011 Apr 26;6(4):e19172. doi: 10.1371/journal.pone.0019172.
The bacterial nucleoid contains several hundred kinds of nucleoid-associated proteins (NAPs), which play critical roles in genome functions such as transcription and replication. Several NAPs, such as Hu and H-NS in Escherichia coli, have so far been identified.
METHODOLOGY/PRINCIPAL FINDINGS: Log- and stationary-phase cells of E. coli, Pseudomonas aeruginosa, Bacillus subtilis, and Staphylococcus aureus were lysed in spermidine solutions. Nucleoids were collected by sucrose gradient centrifugation, and their protein constituents analyzed by liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). Over 200 proteins were identified in each species. Envelope and soluble protein fractions were also identified. By using these data sets, we obtained lists of contaminant-subtracted proteins enriched in the nucleoid fractions (csNAP lists). The lists do not cover all of the NAPs, but included Hu regardless of the growth phases and species. In addition, the csNAP lists of each species suggested that the bacterial nucleoid is equipped with the species-specific set of global regulators, oxidation-reduction enzymes, and fatty acid synthases. This implies bacteria individually developed nucleoid associated proteins toward obtaining similar characteristics.
CONCLUSIONS/SIGNIFICANCE: Ours is the first study to reveal hundreds of NAPs in the bacterial nucleoid, and the obtained data set enabled us to overview some important features of the nucleoid. Several implications obtained from the present proteomic study may make it a landmark for the future functional and evolutionary study of the bacterial nucleoid.
细菌拟核包含数百种核相关蛋白（NAPs），这些蛋白在转录和复制等基因组功能中发挥着关键作用。迄今为止，已经鉴定出几种 NAPs，如大肠杆菌中的 Hu 和 H-NS。
方法/主要发现：对数期和稳定期的大肠杆菌、铜绿假单胞菌、枯草芽孢杆菌和金黄色葡萄球菌细胞在亚精胺溶液中裂解。通过蔗糖梯度离心收集核体，并通过液相色谱-质谱/质谱（LC-MS/MS）分析其蛋白质成分。在每个物种中鉴定出超过 200 种蛋白质。还鉴定了包膜和可溶性蛋白部分。使用这些数据集，我们获得了在核体部分富集的去除污染物的蛋白质列表（csNAP 列表）。该列表并未涵盖所有 NAPs，但无论生长阶段和物种如何，均包含 Hu。此外，每个物种的 csNAP 列表表明，细菌拟核配备了特定于物种的全局调控因子、氧化还原酶和脂肪酸合酶。这意味着细菌各自开发了针对获得相似特征的核相关蛋白。
结论/意义：这是首次揭示细菌拟核中数百种 NAPs 的研究，获得的数据集使我们能够概述拟核的一些重要特征。本蛋白质组学研究得出的一些推论可能使其成为未来细菌拟核功能和进化研究的里程碑。
