Departamento de Biología, Universidad Autónoma de Madrid, C/Darwin, 2, 28049 Madrid Spain.
BMC Genomics. 2014 Mar 26;15:237. doi: 10.1186/1471-2164-15-237.
AmrZ, a RHH transcriptional regulator, regulates motility and alginate production in pseudomonads. Expression of amrZ depends on the environmental stress sigma factor AlgU. amrZ and algU mutants have been shown to be impaired in environmental fitness in different pseudomonads with different lifestyles. Considering the importance of AmrZ for the ecological fitness of pseudomonads and taking advantage of the full sequencing and annotation of the Pseudomonas fluorescens F113 genome, we have carried out a ChIP-seq analysis from a pool of eight independent ChIP assays in order to determine the AmrZ binding sites and its implication in the regulation of genes involved in environmental adaption.
154 enriched regions (AmrZ binding sites) were detected in this analysis, being 76% of them located in putative promoter regions. 18 of these peaks were validated in an independent ChIP assay by qPCR. The 154 peaks were assigned to genes involved in several functional classes such as motility and chemotaxis, iron homeostasis, and signal transduction and transcriptional regulators, including genes encoding proteins implicated in the turn-over of c-diGMP. A putative AmrZ binding site was also observed by aligning the 154 regions with the MEME software. This motif was present in 75% of the peaks and was similar to that described in the amrZ and algD promoters in P. aeruginosa. We have analyzed the role of AmrZ in the regulation of iron uptake genes, to find that AmrZ represses their expression under iron limiting conditions.
The results presented here show that AmrZ is an important global transcriptional regulator involved in environmental sensing and adaption. It is also a new partner in the complex iron homeostasis regulation.
AmrZ 是一种 RHH 转录调节因子，调节假单胞菌的运动性和藻酸盐产生。amrZ 的表达依赖于环境应激 sigma 因子 AlgU。amrZ 和 algU 突变体在不同生活方式的不同假单胞菌中表现出环境适应性降低。考虑到 AmrZ 对假单胞菌生态适应性的重要性，并且利用荧光假单胞菌 F113 基因组的完整测序和注释，我们进行了 ChIP-seq 分析，从八个独立的 ChIP 实验中进行了分析，以确定 AmrZ 结合位点及其在调节参与环境适应的基因中的作用。
在这项分析中，检测到 154 个富集区域（AmrZ 结合位点），其中 76%位于假定启动子区域。这些峰中有 18 个在独立的 ChIP 实验中通过 qPCR 得到了验证。这 154 个峰被分配到涉及几个功能类别的基因，如运动性和趋化性、铁稳态和信号转导以及转录调节因子，包括编码与 c-diGMP 周转相关的蛋白质的基因。通过将这 154 个区域与 MEME 软件对齐，还观察到一个假定的 AmrZ 结合位点。该基序存在于 75%的峰中，与铜绿假单胞菌中 amrZ 和 algD 启动子中描述的基序相似。我们分析了 AmrZ 在调节铁摄取基因表达中的作用，发现 AmrZ 在缺铁条件下抑制其表达。
这里呈现的结果表明，AmrZ 是一种重要的全局性转录调节因子，参与环境感应和适应。它也是铁稳态调节复杂网络中的一个新伙伴。
