Counterbalancing Regulation in Response Memory of a Positively Autoregulated Two-Component System

Abstract

Fluctuations in nutrient availability often result in recurrent exposures to the same stimulus conditions. The ability to memorize the past event and use the "memory" to make adjustments to current behaviors can lead to a more efficient adaptation to the recurring stimulus. A short-term phenotypic memory can be conferred via carryover of the response proteins to facilitate the recurrent response, but the additional accumulation of response proteins can lead to a deviation from response homeostasis. We used the Escherichia coli PhoB/PhoR two-component system (TCS) as a model system to study how cells cope with the recurrence of environmental phosphate (Pi) starvation conditions. We discovered that "memory" of prior Pi starvation can exert distinct effects through two regulatory pathways, the TCS signaling pathway and the stress response pathway. Although carryover of TCS proteins can lead to higher initial levels of transcription factor PhoB and a faster initial response in prestarved cells than in cells not starved, the response enhancement can be overcome by an earlier and greater repression of promoter activity in prestarved cells due to the memory of the stress response. The repression counterbalances the carryover of the response proteins, leading to a homeostatic response whether or not cells are prestimulated. A computational model based on sigma factor competition was developed to understand the memory of stress response and to predict the homeostasis of other PhoB-regulated response proteins. Our insight into the history-dependent PhoBR response may provide a general understanding of how TCSs respond to recurring stimuli and adapt to fluctuating environmental conditions. IMPORTANCE Bacterial cells in their natural environments experience scenarios that are far more complex than are typically replicated in laboratory experiments. The architectures of signaling systems and the integration of multiple adaptive pathways have evolved to deal with such complexity. In this study, we examined the molecular "memory" that is generated by previous exposure to stimulus. Under our experimental conditions, activating effects of autoregulated two-component signaling and inhibitory effects of the stress response counterbalanced the transcriptional output to approach response homeostasis whether or not cells had been preexposed to stimulus. Modeling allows prediction of response behavior in different scenarios and demonstrates both the robustness of the system output and its sensitivity to historical parameters such as timing and levels of exposure to stimuli.

Control of the phoBR Regulon in Escherichia coli

“…In an alternate (or supplementary) mechanism, the PstSCAB transporter may also signal P i sufficiency to PhoR through a process in which its conformation is sensitive to intracellular P i levels by binding P i at a low-affinity, cytoplasm-accessible site. The answers to some of these questions have been provided through careful biochemical experiments, mathematical modeling of the signaling reactions, and bioinformatic analysis (73,74,77,87,(153)(154)(155)(156). For example, it has been shown through quantitative Western blotting that the concentrations of PhoB and PhoR under P i -limited growth conditions are ∼9.3 μM and 1 μM, respectively (77).…”

“…This memory model suggests that cells should accumulate higher levels of Pho regulon proteins if they have previously been starved of phosphate. However, this is not observed (154). To explain this robust behavior for the Pho system, Gao and Stock again employed sophisticated modeling of response kinetics, with the assessment of promoter activities to show that there exists a counterbalancing negative regulation to bring about output homeostasis (154).…”

“…However, this is not observed (154). To explain this robust behavior for the Pho system, Gao and Stock again employed sophisticated modeling of response kinetics, with the assessment of promoter activities to show that there exists a counterbalancing negative regulation to bring about output homeostasis (154). This phenotypic memory seemed to be dependent upon the induction of σ s , although the exact mechanism remains unknown.…”

Learning from Adversity?

“…However, the "memory" of starvation fades as the duration of the intervening period of P i abundance increases. Rong Gao, Ann Stock, and colleagues have revisited the phenomenon of P i starvation and hysteresis in more detail, with intriguing results (8). The present work is the latest in a series of studies by Gao and Stock (6, 9-11) that combine clever analyses of experimental data with computer modeling to explore the in vivo performance of PhoRB.…”

“…What happens with a more complex exposure history? The experiments reported by Gao et al (8) reasonably examined populations rather than single cells. Could circumstances in which cycles of starvation and abundance lead to bistability have been overlooked, particularly if the positive and negative regulatory effects were not precisely balanced?…”