Genome-wide analysis of the general stress response in Bacillus subtilis
Genome-wide analysis of the general stress response in Bacillus subtilis
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DOI：
10.1046/j.1365-2958.2001.02534.x
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发表时间：
2001-08-01
影响因子：
3.6
通讯作者：
Youngman, P
中科院分区：
文献类型：
--
作者：
Price, CW;Fawcett, P;Youngman, P
细菌通过产生大量的一般应激蛋白来应对不同的生长限制应激。在枯草芽孢杆菌和相关革兰氏阳性病原体中，这种应答由sigma（B）转录因子控制。为了建立与一般应激反应相关的细胞功能的范围，我们比较了在诱导σ（B）活性的条件下野生型和突变型菌株的转录谱。代表B的超过3900个注释阅读帧的宏阵列。将枯草芽孢杆菌基因组与P-33标记的cDNA群体杂交，所述cDNA群体来源于（i）已经经受乙醇胁迫的野生型和sigB突变菌株;和（ii）其中sigma（B）表达受诱导型启动子控制的菌株。基于在三个独立实验中它们显著的sigma（B）依赖性表达，我们鉴定了127个基因作为sigma（B）调节子成员的主要候选基因。在这些基因中，有30个是以前已知的或通过其他方法推断为sigma（B）依赖性的。为了帮助分析97个新基因，我们构建了隐马尔可夫模型（HMM），识别可能的西格玛（B）识别序列之前的21个，为了测试HMM，并提供一个独立的验证杂交实验，我们映射的西格玛（B）依赖的消息为7个代表性基因。对于所有七个，消息的5'端位于典型的西格玛（B）识别序列附近，并且对于七个示例中的五个，这些已被HMM正确预测。最后，通过考虑它们与已知蛋白质的相似性，将所有127个基因产物分配到功能组。值得注意的是，具有直接保护功能的产品占少数。相反，一般的应激反应增加了已知的或预测的调节蛋白，转运控制溶质流入和Eflux，包括潜在的药物外排泵，和碳代谢，包膜功能和大分子周转的产品的相对信息水平。
Bacteria respond to diverse growth-limiting stresses by producing a large set of general stress proteins. In Bacillus subtilis and related Gram-positive pathogens, this response is governed by the sigma (B) transcription factor. To establish the range of cellular functions associated with the general stress response, we compared the transcriptional profiles of wild and mutant strains under conditions that induce sigma (B) activity. Macroarrays representing more than 3900 annotated reading frames of the B. subtilis genome were hybridized to P-33-labelled cDNA populations derived from (i) wild-type and sigB mutant strains that had been subjected to ethanol stress; and (ii) a strain in which sigma (B) expression was controlled by an inducible promoter. On the basis of their significant sigma (B)-dependent expression in three independent experiments, we identified 127 genes as prime candidates for members of the sigma (B) regulon. Of these genes, 30 were known previously or inferred to be sigma (B) dependent by other means. To assist in the analysis of the 97 new genes, we constructed hidden Markov models (HMM) that identified possible sigma (B) recognition sequences preceding 21 of them, To test the HMM and to provide an independent validation of the hybridization experiments, we mapped the sigma (B)-dependent messages for seven representative genes. For all seven, the 5' end of the message lay near typical sigma (B) recognition sequences, and these had been predicted correctly by the HMM for five of the seven examples. Lastly, all 127 gene products were assigned to functional groups by considering their similarity to known proteins. Notably, products with a direct protective function were in the minority. Instead, the general stress response increased relative message levels for known or predicted regulatory proteins, for transporters controlling solute influx and eff lux, including potential drug efflux pumps, and for products implicated in carbon metabolism, envelope function and macromolecular turnover.