Live dynamical tracking of slncRNA speckles in single E. coli cells reveals bursts of fluorescence degradation

We study synthetic fluorescent speckles in bacteria by encoding two types of synthetic long-non-coding RNA genes (slncRNA) that incorporate RNA-binding phage-coat-protein (RBP) binding sites downstream from a pT7 promoter in BL21 E. coli cells. For both slncRNAs studied, fluorescent speckles containing ~15-30 RBP-bound slncRNA molecules form in cell poles. Measurement of speckle fluorescence reveals both positive and negative bursts spaced by exponentially distributed periods of non-classified activity lasting 10 minutes on average. We identify positive events with transcriptional bursts, and term the negative events fluorescence degradation bursts. Our data indicates that negative bursts correspond to shedding of multiple slncRNAs back to cytoplasm. Finally, we composed a kinetic model that reproduced the negative bursts and showed that a multi-burst mechanism can reduce gene expression intrinsic noise. These results may have implications to transcriptional dynamics, synthetic speckle formation, and to the understanding of the regulatory role of intracellular phase-separated compartments.