Parallel adaptive feedback enhances reliability of the Ca ²⁺ signaling system

Abstract

Despite large cell-to-cell variations in the concentrations of individual signaling proteins, cells transmit signals correctly. This phenomenon raises the question of what signaling systems do to prevent a predicted high failure rate. Here we combine quantitative modeling, RNA interference, and targeted selective reaction monitoring (SRM) mass spectrometry, and we show for the ubiquitous and fundamental calcium signaling system that cells monitor cytosolic and endoplasmic reticulum (ER) Ca 2+ levels and adjust in parallel the concentrations of the store-operated Ca 2+ influx mediator stromal interaction molecule (STIM), the plasma membrane Ca 2+ pump plasma membrane Ca-ATPase (PMCA), and the ER Ca 2+ pump sarco/ER Ca 2+ -ATPase (SERCA). Model calculations show that this combined parallel regulation in protein expression levels effectively stabilizes basal cytosolic and ER Ca 2+ levels and preserves receptor signaling. Our results demonstrate that, rather than directly controlling the relative level of signaling proteins in a forward regulation strategy, cells prevent transmission failure by sensing the state of the signaling pathway and using multiple parallel adaptive feedbacks.absolute quantification of calcium signaling proteins | targeted proteomics | compensation mechanisms in signal transduction networks | cell signaling | protein abundance profiling R ecent studies in mammalian cells and lower eukaryotes showed a significant variation in the expression level of individual proteins between genetically identical cells (1, 2). These variations-often exceeding a factor of 2-likely reflect noise in transcription, mRNA turnover, translation, and protein degradation. This cell-to-cell variability creates a fundamental problem for signal transduction because even small differences in the relative levels of signaling components along a pathway lead to a processive degradation of signal transmission and failed physiological responses. However, cells typically manage to transmit signals correctly, overcoming protein expression variations by unknown mechanisms.Ca 2+ signals regulate fundamental eukaryotic processes that range from secretion, muscle contraction, and memory formation to activation and differentiation of immune cells (3, 4). Our detailed knowledge of the Ca 2+ signaling system makes this pathway ideally suited to address the puzzling question of how signal transmission processes can tolerate large variations in the expression level of the underlying signaling components. We hypothesized that additional control principles must exist to explain how the otherwise well-understood Ca 2+ signaling system avoids failure and copes with large cell-to-cell variations in protein expression. To keep cells in a signaling-competent state, the Ca 2+ signaling system employs a system of pumps and channels to tightly balance Ca 2+ fluxes across the endoplasmic reticulum (ER) and plasma membrane (PM). The highly coordinated regulation of calcium homeostasis raises the questions of whether the pumps and channels are alway...

A Micropeptide Encoded by a Putative Long Noncoding RNA Regulates Muscle Performance

“…SR Ca 2+ levels were directly measured using T1ER as previously described (Abell et al, 2011; Tsai et al, 2014). See Extended Experimental Procedures for a more detailed protocol.…”

Changes in plasma membrane Ca-ATPase and stromal interacting molecule 1 expression levels for Ca2+ signaling in dystrophic mdx mouse muscle

“…8). To be consistent with parallel adaptive feedback, the tcSR of mdx muscle must have a lower [Ca 2ϩ ] than that in WT to induce an increase in PMCA protein expression and the lSR must maintain a [Ca 2ϩ ] that is similar in mdx and WT muscle to maintain a similar expression level of the SR Ca 2ϩ pump (1,8). A lower [Ca 2ϩ ] in the tcSR of mdx muscle is probably the result of the leaky Ca 2ϩ release channel on the tcSR (2).…”

“…It has been demonstrated that cells can continue to transmit signals correctly in the presence of higher or lower than normal resting [Ca 2ϩ ] and expression levels of the major Ca 2ϩ signaling proteins. Feedback mechanisms detect the [Ca 2ϩ ] of the external environment, cytoplasm, and internal Ca 2ϩ store, and protein expression levels of STIM1, PMCA, and the SR Ca 2ϩ pump are adapted in parallel (1). Evidence for a similar situation involving the Na ϩ -K ϩ ATPase, PMCA, SR Ca 2ϩ pump, and Na ϩ /Ca 2ϩ exchanger has been put forward from work in smooth muscle cells (28 (1), an increase in cytoplasmic [Ca 2ϩ ] will increase the expression of PMCA (Fig.…”

“…While somewhat controversial, [Ca 2ϩ ] levels at rest in dystrophic muscle are reportedly raised in mdx muscle, which may lead to variations in Ca 2ϩ regulatory protein expression level changes (1). In response to different [Ca 2ϩ ] levels, multiple adaptive feedback mechanisms adjust the levels of STIM1, PMCA, and sarco(endo)plasmic reticulum Ca 2ϩ -ATPase (SERCA: referred to as "SR Ca 2ϩ pump" in this study) in parallel to maintain Ca 2ϩ signaling (1). This process may be occurring in mdx muscle to maintain normal Ca 2ϩ signaling under the stress of its pathophysiological state.…”

Ca2+-dependent Transcriptional Control of Ca2+ Homeostasis

“…Consolidated evidence, as well as recent evidence, indicates that this group of proteins, with the mission to keep tight control of free Ca 2ϩ concentration, is in turn subjected to regulation by several mechanisms controlled by changes in free Ca 2ϩ concentration. In some cases, these self-regulatory processes involve parallel compensatory changes in several Ca 2ϩ regulatory proteins so that increases or decreases in intracellular stores and cytosolic Ca 2ϩ levels slowly adjust the concentrations of key signaling pathway components (3). In other cases, components of the homeostasis machinery are coordinately modified to respond to chronic pathological conditions as in end stages of heart failure (4,5) or in neurodegenerative processes.…”