Growth-phase dependent gene regulation in the alpha-proteobacterium Rhodobacter sphaeroides. Cereibacter sphaeroides 2.4.1

Global transcriptome analyses at different stages of growth were applied to monitor growth phase-dependent gene expression in the alpha-proteobacterium Rhodobacter sphaeroides. Low aerated cultures with strong changes in levels of dissolved oxygen during growth, were compared to aerated cultures showing little variation in oxygen levels. Cells were in stationary phase for 12 h or for 57 h before dilution into fresh medium. The majority of genes (78-86%) were not differentially expressed across growth phases. Gene expression in outgrowth phase was strongly influenced by the length of the preceding stationary phase. After 57 h in stationary phase a much larger number of genes was induced after dilution, 39% of which are known to be controlled by the alternative sigma factors RpoHI and/or RpoHII. Growth experiments with mutant strains assign an important function in stationary phase and especially in outgrowth to these sigma factors and genes for both sigma factors showed growth phase-dependent expression. Besides the known consensus sequences for the RpoH sigma factors, some new consensus sequences were identified in subsets of growth phase-dependent genes. Genes for several predicted regulatory proteins exhibited growth phase-specific expression implying a role in growth phase adaptation in alpha-proteobacteria, which needs verification in the future. Overall design: RNA samples collected from R. sphaeroides 2.4.1 wild type cells in several growth phases were analyzed by two-color microarrays Please note that each sample represents biological triplicates.

本研究针对α-变形菌（alpha-proteobacterium）球形红杆菌（Rhodobacter sphaeroides）的不同生长阶段开展全局转录组分析，以监测其生长阶段依赖的基因表达模式。本研究将生长过程中溶解氧水平发生剧烈变化的低通气培养体系，与氧水平波动极小的正常通气培养体系进行对比。将稳定期培养12小时或57小时的菌体稀释接种至新鲜培养基。绝大多数基因（78%~86%）在不同生长阶段间未呈现差异表达。复苏生长阶段（outgrowth phase）的基因表达水平，显著受此前稳定期持续时长的调控。当菌体稳定期持续57小时后，稀释接种后会有更多基因被诱导表达，其中39%的基因已知由替代σ因子RpoHI和/或RpoHII调控。突变菌株生长实验证实，上述σ因子在稳定期，尤其是复苏生长阶段发挥关键调控功能；且两种σ因子的编码基因均呈现生长阶段依赖的表达模式。除了已知的RpoH家族σ因子结合共有保守序列外，本研究还在部分生长阶段依赖基因的调控区域中鉴定出全新的共有保守序列。多个预测的调控蛋白编码基因呈现生长阶段特异性表达，提示其在α-变形菌的生长阶段适应过程中发挥功能，该结论仍需后续实验验证。实验设计概况：采用双色微阵列技术，对球形红杆菌2.4.1野生型菌株多个生长阶段收集的RNA样本进行检测分析。请注意，每个样本均设置三次生物学重复。