Evolutionary Tuning of Protein Expression Levels of a Positively Autoregulated Two-Component System

Abstract

Cellular adaptation relies on the development of proper regulatory schemes for accurate control of gene expression levels in response to environmental cues. Over- or under-expression can lead to diminished cell fitness due to increased costs or insufficient benefits. Positive autoregulation is a common regulatory scheme that controls protein expression levels and gives rise to essential features in diverse signaling systems, yet its roles in cell fitness are less understood. It remains largely unknown how much protein expression is ‘appropriate’ for optimal cell fitness under specific extracellular conditions and how the dynamic environment shapes the regulatory scheme to reach appropriate expression levels. Here, we investigate the correlation of cell fitness and output response with protein expression levels of the E. coli PhoB/PhoR two-component system (TCS). In response to phosphate (Pi)-depletion, the PhoB/PhoR system activates genes involved in phosphorus assimilation as well as genes encoding themselves, similarly to many other positively autoregulated TCSs. We developed a bacteria competition assay in continuous cultures and discovered that different Pi conditions have conflicting requirements of protein expression levels for optimal cell fitness. Pi-replete conditions favored cells with low levels of PhoB/PhoR while Pi-deplete conditions selected for cells with high levels of PhoB/PhoR. These two levels matched PhoB/PhoR concentrations achieved via positive autoregulation in wild-type cells under Pi-replete and -deplete conditions, respectively. The fitness optimum correlates with the wild-type expression level, above which the phosphorylation output saturates, thus further increase in expression presumably provides no additional benefits. Laboratory evolution experiments further indicate that cells with non-ideal protein levels can evolve toward the optimal levels with diverse mutational strategies. Our results suggest that the natural protein expression levels and feedback regulatory schemes of TCSs are evolved to match the phosphorylation output of the system, which is determined by intrinsic activities of TCS proteins.

Ca 2+ -Induced Two-Component System CvsSR Regulates the Type III Secretion System and the Extracytoplasmic Function Sigma Factor AlgU in Pseudomonas syringae pv. tomato DC3000

“…It is not uncommon for TCSs to tune expression of genes. For example, in Salmonella enterica, PhoPQ tunes expression of the effector steA during osmotic stress, and PhoBR tunes expression of itself in E. coli according to environmental phosphate concentrations (69,70). If CvsSR tunes expression of hrpRS, then it is conceivable that deletion of cvsS or cvsR may cause only subtle changes T3SS and T3E deployment that do not affect the HR but could still influence pathogenesis.…”

Learning from Adversity?

“…This remarkable, but not perfect, homeostasis of Pho system output strongly suggests that the observed response was nearly optimal. The convergence of Pho responses from different starting points is particularly striking because Gao and Stock previously also demonstrated that the autoregulated amounts of PhoRB signaling proteins generated under conditions of various degrees of P i starvation provide optimal fitness (9).…”

“…The pho response exhibits just such heterogeneity in the artificial circumstance represented by cells that lack PhoR and activate PhoB by inefficient cross talk from a nonpartner sensor kinase (14). On the other hand, when E. coli bacteria with the wild-type PhoRB system are starved once for P i , the population response is homogeneous and bistability is not seen (9). What happens with a more complex exposure history?…”

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

“…different environmental conditions (1)(2)(3). The ever-changing environments constantly challenge cells to optimize strategies to prevail under fluctuating conditions.…”

“…It has been demonstrated that different levels of PhoBR under different Pi conditions provide near-maximal fitness under the respective conditions. The importance of this was underscored by the finding that challenging cells with unfavorable PhoBR levels led to diverse homeostatic efforts to mediate optimal expression levels through acquisition of mutations (3). Maintaining expression optimality appears to be a strong evolutionary force to select the positive autoregulatory scheme for adaptation to different Pi conditions.…”