Cell–cell signaling in microorganisms is still poorly characterized. In this Methods paper, we describe a genetic procedure for detecting cell-nonautonomous genetic effects, and in particular cell–cell signaling, termed the chimeric colony assay (CCA). The CCA measures the effect of a gene on a biological response in a neighboring cell. This assay can measure cell autonomy for range of biological activities including transcript or protein accumulation, subcellular localization, and cell differentiation. To date, the CCA has been used exclusively to investigate colony patterning in the budding yeast Saccharomyces cerevisiae. To demonstrate the wider potential of the assay, we applied this assay to two other systems: the effect of Grr1 on glucose repression of GAL1 transcription in yeast and the effect of rpsL on stop-codon translational readthrough in Escherichia coli. We also describe variations of the standard CCA that address specific aspects of cell–cell signaling, and we delineate essential controls for this assay. Finally, we discuss complementary approaches to the CCA. Taken together, this Methods paper demonstrates how genetic assays can reveal and explore the roles of cell–cell signaling in microbial processes.

微生物中的细胞间信号传导仍未得到充分表征。在这篇方法论文中，我们描述了一种用于检测细胞非自主遗传效应，特别是细胞间信号传导的遗传程序，称为嵌合菌落测定 (CCA)。CCA 测量基因对邻近细胞生物反应的影响。该测定可以测量一系列生物活动的细胞自主性，包括转录物或蛋白质积累、亚细胞定位和细胞分化。迄今为止，CCA 已专门用于研究芽殖酵母酿酒酵母中的菌落模式。为了证明该测定的更广泛潜力，我们将该测定应用于其他两个系统：Grr1 对GAL1葡萄糖抑制的影响酵母中的转录和 rpsL 对大肠杆菌中终止密码子翻译通读的影响。我们还描述了标准 CCA 的变体，这些变体解决了细胞间信号传导的特定方面，并且我们描述了该测定的基本控制。最后，我们讨论了 CCA 的补充方法。总之，这篇方法论文展示了基因检测如何揭示和探索细胞间信号转导在微生物过程中的作用。