van Kessel STR416 v JV55

Microarray data for study "The master regulators AphA and LuxR control the Vibrio harveyi quorum-sensing regulon: analysis of their individual and combined effects". Bacteria use a chemical communication process called quorum sensing to control transitions between individual and group behaviors. In the Vibrio harveyi quorum-sensing circuit, two master transcription factors AphA and LuxR coordinate the quorum-sensing response. Here we show that AphA regulates 167 genes, LuxR regulates 625 genes, and they co-regulate 77 genes. LuxR strongly controls genes both at low-cell-density and high-cell-density, suggesting it is the major quorum-sensing regulator. By contrast, AphA is absent at high-cell-density, and acts to fine-tune quorum-sensing gene expression at low-cell-density. We examined two loci as case studies of co-regulation by AphA and LuxR. First, AphA and LuxR directly regulate expression of the genes encoding the quorum regulatory small RNAs Qrr2, Qrr3, and Qrr4, the consequence of which is a specifically timed transition between the individual and the group lifestyle. Second, AphA and LuxR repress type III secretion system genes but at different times and to different extents. The consequence of this regulation is that type III secretion is restricted to a peak at mid-cell-density. Thus, asymmetric production of AphA and LuxR coupled with differences in their strength and timing of target gene regulation generates a precise temporal pattern of gene expression. Triplicate biological samples of Vibrio harveyi strains STR416 and JV55 were hybridized to Agilent arrays (Amadid design ID: 021087), and one experiment was a control dye-swap, for a total of four experiments in this array set.

本数据集对应研究课题《主调控因子AphA与LuxR调控哈维弧菌群体感应调控子（quorum-sensing regulon）：单独与联合作用解析》的微阵列（Microarray）数据。细菌借助被称为群体感应（quorum sensing）的化学通信过程，调控个体与群体行为模式间的转换。在哈维弧菌的群体感应信号通路中，两种主转录因子（master transcription factors）AphA与LuxR协同调控群体感应应答反应。本研究显示，AphA调控167个基因，LuxR调控625个基因，二者共同调控77个基因。LuxR可在低细胞密度与高细胞密度条件下均强力调控靶基因，提示其为群体感应通路的核心调控因子。与之相对，AphA在高细胞密度条件下不表达，仅在低细胞密度时发挥微调群体感应基因表达的作用。我们选取两个基因座作为AphA与LuxR共同调控的案例展开研究：其一，AphA与LuxR直接调控编码群体感应调控小RNA Qrr2、Qrr3及Qrr4的基因表达，该调控的结果是实现个体与群体生活模式间的精准时序转换；其二，AphA与LuxR均会抑制III型分泌系统（type III secretion system）基因的表达，但二者的作用时序与调控强度各不相同，该调控模式使得III型分泌仅在中细胞密度条件下达到峰值。综上，AphA与LuxR的不对称表达，结合二者在靶基因调控强度与时序上的差异，共同塑造了精准的基因表达时序模式。将哈维弧菌菌株STR416与JV55的三份生物学重复样本与安捷伦（Agilent）芯片（Amadid设计编号：021087）进行杂交，其中一组实验采用了对照染料互换（dye-swap）设计，本芯片数据集总计包含4组实验。