Rate of environmental change determines stress response specificity

Abstract

Cells use general stress response pathways to activate diverse target genes in response to a variety of stresses. However, general stress responses coexist with more specific pathways that are activated by individual stresses, provoking the fundamental question of whether and how cells control the generality or specificity of their response to a particular stress. Here we address this issue using quantitative time-lapse microscopy of the Bacillus subtilis environmental stress response, mediated by σ B . We analyzed σ B activation in response to stresses such as salt and ethanol imposed at varying rates of increase. Dynamically, σ B responded to these stresses with a single adaptive activity pulse, whose amplitude depended on the rate at which the stress increased. This rate-responsive behavior can be understood from mathematical modeling of a key negative feedback loop in the underlying regulatory circuit. Using RNAseq we analyzed the effects of both rapid and gradual increases of ethanol and salt stress across the genome. Because of the rate responsiveness of σ B activation, salt and ethanol regulons overlap under rapid, but not gradual, increases in stress. Thus, the cell responds specifically to individual stresses that appear gradually, while using σ B to broaden the cellular response under more rapidly deteriorating conditions. Such dynamic control of specificity could be a critical function of other general stress response pathways.systems biology | single-cell dynamics | computational biology C ells must respond to, and anticipate, a wide range of stresses that occur on multiple timescales. For this purpose, many species use general stress response pathways, which activate a diverse set of target regulons in response to a variety of stresses. For example, in mammals, p53 is activated by DNA damage (1-4) and hypoxia (5, 6), among others, and activates genes that impact cell cycle progression (7), DNA repair (8, 9), apoptosis, and angiogenesis (10, 11). In yeast, Msn2/4 responds to nutritional stress (12), as well as to salt (13), calcium (14), heat, and other stresses (15). Bacteria also contain general stress response pathways, including the alternative sigma factors RpoS in Escherichia coli (16) and σ B in Bacillus subtilis (17).It has been proposed that general stress response pathways enable cells to cross-protect, by anticipating stresses that may not be present at the moment, but are likely to occur soon (18). For example, preexposure to specific stresses is known to enhance bacterial resistance to different stresses applied subsequently (19)(20)(21). This raises a basic question: How do cells determine when to use the general stress response rather than activating more specific individual pathways?The σ B -mediated general stress response of B. subtilis provides an ideal model system to address these issues. σ B is activated by diverse stresses through a well-characterized and conserved transcriptional and posttranscriptional circuit mechanism (17). In response to stress, it activates ∼200 target ge...

The γ-Aminobutyrate Permease GabP Serves as the Third Proline Transporter of Bacillus subtilis

“…Transcription of opuE is strongly induced in response to both sudden and sustained increases in the external osmolarity, a process that is mediated by SigA-and SigB-type promoters (16,23,24). Data derived from transcriptional profiling experiments suggest that it is also under the positive control of the central carbon metabolism regulatory protein CcpA (79).…”

“…OpuE also operates as a recapturing device for newly synthesized proline that is released from B. subtilis grown under high-salinity conditions, probably in an effort by the cell to fine-tune turgor (22). Expression of opuE is osmotically inducible (16,23,24), but there is no stimulation of opuE expression in response to proline availability.…”

“…Conversely, not only can the proline import activity of OpuE withstand salt stress, but also it is actually increased in response to high osmo-larity (38). Underlying these characteristics of the PutP-and OpuE-mediated proline import are influences that result from the different transcriptional profile of the putBCP and opuE genes in response to proline availability in the growth medium and its osmolarity (10,16,23,24). However, posttranscriptional effects of high salinity on the transport activity of PutP and OpuE are also noticeable (10,16).…”

Single-Cell Analysis of the Dps Response to Oxidative Stress

“…For each microcolony, the fluorescence intensity curves were fitted with the best-fitting polynomial (degree 5), and the maximum of this function was considered to be the maximum fluorescence intensity. Dps production activity is defined as the rate of mCherry protein production (32,34,38,43). The duration of Dps production was calculated as the time from the beginning of the exposure to H 2 O 2 .…”

“…In addition, it is unknown how the dynamics of Dps production are affected when the concentration of stressor is varied, a question that is central to the ability of a cell to respond appropriately to changes in its environment. Clear insights into these biological processes require recently developed single-cell technologies to overcome the limitations of bulk experiments, allowing for the quantification of the cell-to-cell variability in a population as well as the characterization of the dynamics of stress responses (28)(29)(30)(31)(32)(33)(34).…”