Fawcett P, Eichenberger P, Losick R, Youngman P
Millennium Pharmaceuticals, Cambridge MA, 02138; Harvard University, Department of Molecular and Cellular Biology, Cambridge, MA, 01238, USA.
Proc Natl Acad Sci U S A. 2000 Jul 5;97(14):8063-8. doi: 10.1073/pnas.140209597.
Spore formation by Bacillus subtilis is governed by global changes in gene transcription. We used nylon-substrate DNA arrays representing approximately 96% of the predicted open reading frames in the B. subtilis chromosome to compare the pattern of transcripts from wild-type cells with the pattern from cells mutant for the sporulation transcription factors Spo0A or final sigma(F). We found 520 genes whose transcript levels were at least 3-fold dependent on Spo0A but not on final sigma(F), and an additional 66 genes whose transcript levels were dependent upon both regulatory proteins. Two strategies were used to help assign genes to the direct control of a particular developmental regulatory protein. In one approach, we analyzed the effects on global gene expression of artificially producing a constitutively active form of Spo0A during growth. In a second approach, Hidden Markov models were used to identify promoters likely to be activated by Spo0A, final sigma(F), or a third sporulation transcription factor, final sigma(E). In addition to detecting known sporulation genes, we identified many genes of unknown function whose patterns of expression and regulation suggest that they could be involved in sporulation. Disruption of two such newly identified genes, yabP and yabQ, blocked sporulation at a late stage.
枯草芽孢杆菌的孢子形成受基因转录的全局变化调控。我们使用了代表枯草芽孢杆菌染色体中约96%预测开放阅读框的尼龙基质DNA阵列，来比较野生型细胞的转录本模式与孢子形成转录因子Spo0A或最终σ因子（F）突变细胞的转录本模式。我们发现520个基因的转录水平至少3倍依赖于Spo0A而不依赖于最终σ因子（F），另外还有66个基因的转录水平依赖于这两种调节蛋白。我们采用了两种策略来帮助将基因分配到特定发育调节蛋白的直接控制之下。在一种方法中，我们分析了在生长过程中人工产生组成型活性形式的Spo0A对全局基因表达的影响。在第二种方法中，使用隐马尔可夫模型来识别可能被Spo0A、最终σ因子（F）或第三个孢子形成转录因子最终σ因子（E）激活的启动子。除了检测已知的孢子形成基因外，我们还鉴定了许多功能未知的基因，它们的表达和调控模式表明它们可能参与孢子形成。破坏两个新鉴定的基因yabP和yabQ会在后期阻断孢子形成。
