Ultrasensitivity and noise propagation in a synthetic transcriptional cascade

Abstract

The precise nature of information flow through a biological network, which is governed by factors such as response sensitivities and noise propagation, greatly affects the operation of biological systems. Quantitative analysis of these properties is often difficult in naturally occurring systems but can be greatly facilitated by studying simple synthetic networks. Here, we report the construction of synthetic transcriptional cascades comprising one, two, and three repression stages. These model systems enable us to analyze sensitivity and noise propagation as a function of network complexity. We demonstrate experimentally steady-state switching behavior that becomes sharper with longer cascades. The regulatory mechanisms that confer this ultrasensitive response both attenuate and amplify phenotypical variations depending on the system's input conditions. Although noise attenuation allows the cascade to act as a low-pass filter by rejecting short-lived perturbations in input conditions, noise amplification results in loss of synchrony among a cell population. The experimental results demonstrating the above network properties correlate well with simulations of a simple mathematical model of the system. gene regulation ͉ gene network ͉ low-pass filter ͉ stochastic R egulatory cascades are ubiquitous in biological systems. For example, Escherichia coli and Saccharomyces cerevisiae regulatory networks contain transcriptional cascades with two or more stages (1-3). Many signal transduction programs and protein kinase pathways also take advantage of cascaded processes to regulate activities within living cells (4-6). In general, regulatory cascades exhibit several important features (7-8). Protein cascades provide an ultrasensitive ''all-or-none'' response to graded inputs where very small changes in input stimuli switch the output between low and high levels (9-10). Cascades direct temporal programs of successive gene expression as observed in the formation of flagella in E. coli (11), sporulation in budding yeast (12), or regulatory pathways that control bacterial cell cycle (13). In multicellular organisms, such as Drosophila and sea urchin, developmental programs require elaborate temporal ordering of events, often orchestrated by cascaded processes (14-15).Regulatory cascades are frequently found within more complex networks that incorporate additional control mechanisms [i.e., feed forward loops (3, 16), feedback (17), checkpoints (18), and single-input modules (3)]. A valuable approach to studying the properties of recurring network motifs is to decouple them as much as possible from other genetic regulatory elements (19-21). Examining network behavior in model systems can help discover the valuable properties and limitations of these motifs. Recent experimental studies of two-stage transcriptional cascades have examined quantitatively their steady-state sensitivity, § temporal programming (1), and noise properties (23). In addition, ultrasensitivity and attenuation of noise in longer cascades have been analyze...

Distinct noise-controlling roles of multiple negative feedback mechanisms in a prokaryotic operon system

“…Austin et al [21] lent more support to this hypothesis by showing that noise frequency content (spectra) is determined by the underlying gene circuit structure, establishing a mapping between the two. In a similar vein, synthetic transcriptional cascades of varying length were constructed in E.coli (Figure 1c) to explore the effect of cascade length on noise and sensitivity of the network's response [11].…”

“…On the other hand, the length of the cascade has minor effect on noise propagation for low and high output states [11].…”

“…More recent work on transcriptional cascades indicate that noise can propagate from upstream to downstream components, further decomposing the internal noise of a specific molecular species into an intrinsic noise part and a propagated noise part [10][11][12]. The intrinsic noise part is primarily determined by the component's copy number, while its propagated counterpart is determined by the total noise of upstream, internally connected components within the cascade [13].…”

“…(1) a two-stage protein cascade shown in Figure 3a where protein A acts as a transcriptional activator for protein B [28]; (2) Previous studies have showed that noise can be transmitted from upstream components to downstream ones in a biochemical cascade [10][11][12]. This means in the absence of extrinsic noise, the total noise of a downstream molecule is made up of its intrinsic noise (primarily as a consequence of its low copy number) and propagated noise coming from its immediate upstream species.…”

Synthetic circuits, devices and modules

“…The construction of such higher-order genetic circuits and devices has allowed the synthetic biologists to challenge more difficult works, such as output of specific signal mode (Kemmer et al, 2010), noise control (Hooshangi et al, 2005;Murphy et al, 2010), biological counters (Friedland et al, 2009) and circadian clocks (Danino et al, 2010). Given the broad applications of these genetic circuits and devices, it is crucial to develop more useful devices that operate effectively inside living cells.…”