Genome-scale analysis of escherichia coli FNR reveals complex features of transcription factor binding.
Genome-scale analysis of escherichia coli FNR reveals complex features of transcription factor binding.
复制标题
DOI：
10.1371/journal.pgen.1003565
复制
发表时间：
2013-06
期刊：
影响因子：
4.5
通讯作者：
Kiley PJ
中科院分区：
文献类型：
--
作者：
Myers KS;Yan H;Ong IM;Chung D;Liang K;Tran F;Keleş S;Landick R;Kiley PJ
FNR 是一种经过充分研究的全局厌氧调节因子，在细菌中广泛保守。尽管 FNR 和厌氧作用在微生物生活方式中很重要，但在全基因组范围内影响其功能的因素却知之甚少。在这里，我们报告了 FNR 作用的功能基因组分析。我们发现许多靶位点上的 FNR 占用受到核样相关蛋白 (NAP) 的强烈影响，这些蛋白限制了对许多 FNR 结合位点的访问。在全基因组水平上，只有一部分预测的 FNR 结合位点在厌氧发酵条件下结合，并且许多似乎被 NAP H-NS、IHF 和 Fis 掩盖。在缺乏 H-NS 及其旁系同源物 StpA 的细胞中进行的类似测定显示，WT 菌株中 H-NS 结合位点的 FNR 占有率增加，表明基因组的大部分区域不容易与 FNR 结合。基因组可及性也可以解释我们的发现，即全基因组 FNR 占用率与结合位点的一致性匹配不相关，这表明 ChIP 信号的显着变化可归因于交联或免疫沉淀效率，而不是 FNR 位点结合亲和力的差异。 FNR ChIP-seq 峰与转录组数据的相关性表明，不到一半的 FNR 调节操纵子可归因于直接 FNR 结合。相反，FNR 结合一些启动子而不调节表达，可能需要改变条件特异性转录因子的活性。这种组合调节可能使大肠杆菌能够快速响应环境变化，并在哺乳动物肠道的厌氧但营养波动的环境中赋予生态优势。转录因子（TF）调节基因表达是适应环境变化的关键。我们对原型全局 TF（来自大肠杆菌的厌氧调节因子 FNR）进行了全面的基因组规模分析，得出了一些关于全基因组 FNR 结合的影响以及细菌调节子复杂结构的新颖且意想不到的见解。我们发现 NAP 的结合限制了 FNR 在部分位点的结合，这表明细菌基因组不能自由地进行 FNR 结合。我们发现，不到一半的预测 FNR 结合位点在体内被占据，这进一步挑战了单独使用生物信息学搜索来预测调节子结构的效用，从而加强了对 TF 结合进行实验测定的需要。通过将占用数据与转录组数据相关联，我们确认 FNR 作为厌氧的全局信号，但 FNR 调节子中某些操纵子的表达需要其他对替代环境刺激敏感的调节因子。因此，FNR 结合和调节似乎取决于染色体的核蛋白结构以及 FNR 与其他调节因子的组合结合。这两种现象都是真核生物中 TF 结合的典型现象。我们的结果表明它们也是细菌 TF 结合的特征。
FNR is a well-studied global regulator of anaerobiosis, which is widely conserved across bacteria. Despite the importance of FNR and anaerobiosis in microbial lifestyles, the factors that influence its function on a genome-wide scale are poorly understood. Here, we report a functional genomic analysis of FNR action. We find that FNR occupancy at many target sites is strongly influenced by nucleoid-associated proteins (NAPs) that restrict access to many FNR binding sites. At a genome-wide level, only a subset of predicted FNR binding sites were bound under anaerobic fermentative conditions and many appeared to be masked by the NAPs H-NS, IHF and Fis. Similar assays in cells lacking H-NS and its paralog StpA showed increased FNR occupancy at sites bound by H-NS in WT strains, indicating that large regions of the genome are not readily accessible for FNR binding. Genome accessibility may also explain our finding that genome-wide FNR occupancy did not correlate with the match to consensus at binding sites, suggesting that significant variation in ChIP signal was attributable to cross-linking or immunoprecipitation efficiency rather than differences in binding affinities for FNR sites. Correlation of FNR ChIP-seq peaks with transcriptomic data showed that less than half of the FNR-regulated operons could be attributed to direct FNR binding. Conversely, FNR bound some promoters without regulating expression presumably requiring changes in activity of condition-specific transcription factors. Such combinatorial regulation may allow Escherichia coli to respond rapidly to environmental changes and confer an ecological advantage in the anaerobic but nutrient-fluctuating environment of the mammalian gut. Regulation of gene expression by transcription factors (TFs) is key to adaptation to environmental changes. Our comprehensive, genome-scale analysis of a prototypical global TF, the anaerobic regulator FNR from Escherichia coli, leads to several novel and unanticipated insights into the influences on FNR binding genome-wide and the complex structure of bacterial regulons. We found that binding of NAPs restricts FNR binding at a subset of sites, suggesting that the bacterial genome is not freely accessible for FNR binding. Our finding that less than half of the predicted FNR binding sites were occupied in vivo further challenges the utility of using bioinformatic searches alone to predict regulon structure, reinforcing the need for experimental determination of TF binding. By correlating the occupancy data with transcriptomic data, we confirm that FNR serves as a global signal of anaerobiosis but expression of some operons in the FNR regulon require other regulators sensitive to alternative environmental stimuli. Thus, FNR binding and regulation appear to depend on both the nucleoprotein structure of the chromosome and on combinatorial binding of FNR with other regulators. Both of these phenomena are typical of TF binding in eukaryotes; our results establish that they are also features of bacterial TF binding.
登录
查看更多内容
影响因子：
46.9
作者：
Cho, Byung-Kwan;Zengler, Karsten;Qiu, Yu;Park, Young Seoub;Knight, Eric M.;Barrett, Christian L.;Gao, Yuan;Palsson, Bernhard O.
通讯作者：
Palsson, Bernhard O.
DOI：
10.1016/0005-2728(77)90197-9
发表时间：
1977-01-01
期刊：
BIOCHIMICA ET BIOPHYSICA ACTA
影响因子：
--
作者：
ANDREWS, S;COX, GB;GIBSON, F
通讯作者：
GIBSON, F
影响因子：
14.9
作者：
Chen Z;Lewis KA;Shultzaberger RK;Lyakhov IG;Zheng M;Doan B;Storz G;Schneider TD
通讯作者：
Schneider TD
影响因子：
3.2
作者：
Buchet, A;Eichler, K;Mandrand-Berthelot, MA
通讯作者：
Mandrand-Berthelot, MA
影响因子：
3.6
作者：
Browning, DF;Grainger, DC;Busby, SJW
通讯作者：
Busby, SJW