Propagation of global resource fluctuations in a cell

To understand the full breadth of the physiological implications of random fluctuations, of crucial importance is the quantitative evaluation of the "noise" propagating through the cascade of downstream gene expression. In particular, we investigate the effects of RNA polymerase (RNAp) level fluctuations on the cell-to-cell variations in the reporter gene expression. For a quantitative assay of gene expression, we use the YFP-fused T7 RNAp plasmid system, which is designed to selectively transcribe the dual chromosomal reporter genes encoding the fluorescent protein CFP and mCherry. The expression of T7 RNAp itself is controlled by anhydrotetracycline (aTc) via its own trans- and cis-regulatory elements, TetR and the operator sequence tetO. For a measure of noise level we employ the coefficient of variation (CV) in fluorescence intensity, and measure the (co)variance for the dual reporter genes while varying both the average level and CV of RNAp expression. The total noise in reporter gene expression is decomposed into intrinsic and extrinsic contributions from RNAp noise. In addition to the "intrinsic" noise caused by random arrival of transcription and translation events, the fluctuating RNAp level gives rise to a major source of "extrinsic" noise for the downstream gene expression. With increased RNAp expression, both the intrinsic and extrinsic noise decreases but the relative contribution of extrinsic noise becomes more prevalent. Cell-to-cell variation in RNAp expression level rarely contributes to the intrinsic noise whereas it significantly elevates the extrinsic noise. Based on our observations, we propose a novel strategy for modulating the genetic noise by way of regulated global resources and identify the biochemical characteristics that determine the tunability of the genetic circuits in general. A particular emphasis is placed on the epigenetic control of phenotypic switching from which we discuss the design principles for scalable synthetic biological devices, accessible to experimentation or evolutionary selection