Buffer regulation of calcium puff sequences

IP3Rs puff along: A SNAPpy dance with IP3 and Ca2

Concerted openings of clustered inositol 1,4,5-trisphosphate receptors (IP3Rs) result in short, localized Ca2+ bursts, also called puffs, which are crucial regulators of Ca2+-dependent signaling processes. However, the processes regulating Ca2+ puff amplitude (average ∼0.5 ΔF/F0) and duration (at half-maximal; average ∼25-30 ms) have yet to be elucidated. A recent study in JBC by Smith and Taylor determined that Ca2+ puff amplitude is independent of IP3R cluster density and that the termination of IP3R Ca2+ puff is regulated by IP3 dissociation, illuminating the steps of this regulatory dance.

High rates of calcium-free diffusion in the cytosol of living cells

Calcium (Ca²⁺) is a universal second messenger that participates in the regulation of innumerous physiological processes. The way in which local elevations of the cytosolic Ca²⁺ concentration spread in space and time is key for the versatility of the signals. Ca²⁺ diffusion in the cytosol is hindered by its interaction with proteins that act as buffers. Depending on the concentrations and the kinetics of the interactions, there is a large range of values at which Ca²⁺ diffusion can proceed. Having reliable estimates of this range, particularly of its highest end, which corresponds to the ions free diffusion, is key to understand how the signals propagate. In this work, we present the first experimental results with which the Ca²⁺-free diffusion coefficient is directly quantified in the cytosol of living cells. By means of fluorescence correlation spectroscopy experiments performed in Xenopus laevis oocytes and in cells of Saccharomyces cerevisiae, we show that the ions can freely diffuse in the cytosol at a higher rate than previously thought.

Quantification of fluctuations from fluorescence correlation spectroscopy experiments in reaction-diffusion systems

Fluorescence correlation spectroscopy (FCS) is commonly used to estimate diffusion and reaction rates. In FCS the fluorescence coming from a small volume is recorded and the autocorrelation function (ACF) of the fluorescence fluctuations is computed. Scaling out the fluctuations due to the emission process, this ACF can be related to the ACF of the fluctuations in the number of observed fluorescent molecules. In this paper the ACF of the molecule number fluctuations is studied theoretically, with no approximations, for a reaction-diffusion system in which the fluorescence changes with binding and unbinding. Theoretical ACFs are usually derived assuming that fluctuations in the number of molecules of one species are instantaneously uncorrelated to those of the others and obey Poisson statistics. Under these assumptions, the ACF derived in this paper is characterized only by the diffusive timescale of the fluorescent species and its total weight is the inverse of the mean number of observed fluorescent molecules. The theory is then scrutinized in view of previous experimental results which, for a similar system, gave a different total weight and correct estimates of other diffusive timescales. The total weight mismatch is corrected by assuming that the variance of the number of fluorescent molecules depends on the variance of the particle numbers of the other species, as in the variance decomposition formula. Including the finite acquisition time in its computation, it is shown that the ACF depends on various timescales of the system and that its total weight coincides with the one obtained with the variance decomposition formula. This calculation implies that diffusion coefficients of nonobservable species can be estimated with FCS experiments performed in reaction-diffusion systems. Ways to proceed in future experiments are also discussed.

Simulation of calcium signaling in fine astrocytic processes: Effect of spatial properties on spontaneous activity

Astrocytes, a glial cell type of the central nervous system, have emerged as detectors and regulators of neuronal information processing. Astrocyte excitability resides in transient variations of free cytosolic calcium concentration over a range of temporal and spatial scales, from sub-microdomains to waves propagating throughout the cell. Despite extensive experimental approaches, it is not clear how these signals are transmitted to and integrated within an astrocyte. The localization of the main molecular actors and the geometry of the system, including the spatial organization of calcium channels IP3R, are deemed essential. However, as most calcium signals occur in astrocytic ramifications that are too fine to be resolved by conventional light microscopy, most of those spatial data are unknown and computational modeling remains the only methodology to study this issue. Here, we propose an IP3R-mediated calcium signaling model for dynamics in such small sub-cellular volumes. To account for the expected stochasticity and low copy numbers, our model is both spatially explicit and particle-based. Extensive simulations show that spontaneous calcium signals arise in the model via the interplay between excitability and stochasticity. The model reproduces the main forms of calcium signals and indicates that their frequency crucially depends on the spatial organization of the IP3R channels. Importantly, we show that two processes expressing exactly the same calcium channels can display different types of calcium signals depending on the spatial organization of the channels. Our model with realistic process volume and calcium concentrations successfully reproduces spontaneous calcium signals that we measured in calcium micro-domains with confocal microscopy and predicts that local variations of calcium indicators might contribute to the diversity of calcium signals observed in astrocytes. To our knowledge, this model is the first model suited to investigate calcium dynamics in fine astrocytic processes and to propose plausible mechanisms responsible for their variability.

Using two dyes to observe the competition of Ca2+ trapping mechanisms and their effect on intracellular Ca2+ signals

The specificity and universality of intracellular [Formula: see text] signals rely on the variety of spatio-temporal patterns that the [Formula: see text] concentration can display. [Formula: see text] liberation through inositol 1,4,5-trisphosphate receptors ([Formula: see text]) is key for this variety. In this paper, we study how the competition between buffers of different kinetics affects [Formula: see text] signals that involve [Formula: see text] release through [Formula: see text]. The study also provides insight into the underlying spatial distribution of the channels that participate in the signals. Previous works on the effects of [Formula: see text] buffers have drawn conclusions 'indirectly' by observing the [Formula: see text]-bound dye distributions in the presence of varying concentrations of exogenous buffers and using simulations to interpret the results. In this paper, we make visible the invisible by observing the signals simultaneously with two dyes, [Formula: see text] and [Formula: see text], each of which plays the role of a slow or fast [Formula: see text] buffer, respectively. Our observations obtained for different concentrations of [Formula: see text] highlight the dual role that fast buffers exert on the dynamics, either reducing the intracluster channel coupling or preventing channel inhibition and allowing the occurrence of relatively long cycles of [Formula: see text] release. Our experiments also show that signals with relatively high [Formula: see text] release rates remain localized in the presence of large [Formula: see text] concentrations, while the mean speed of the elicited waves increases. We interpret this as a consequence of the more effective uncoupling between [Formula: see text] clusters as the slow dye concentration increases. Combining the analysis of the experiments with numerical simulations, we also conclude that [Formula: see text] release not only occurs within the close vicinity of the centers of the clearly identifiable release sites ([Formula: see text] clusters) but there are also functional [Formula: see text] in between them.

Exact stochastic simulation of a calcium microdomain reveals the impact of Ca²⁺ fluctuations on IP₃R gating

In this study, we numerically analyzed the nonlinear Ca(2+)-dependent gating dynamics of a single, nonconducting inositol 1,4,5-trisphosphate receptor (IP₃R) channel, using an exact and fully stochastic simulation algorithm that includes channel gating, Ca(2+) buffering, and Ca(2+) diffusion. The IP₃R is a ubiquitous intracellular Ca(2+) release channel that plays an important role in the formation of complex spatiotemporal Ca(2+) signals such as waves and oscillations. Dynamic subfemtoliter Ca(2+) microdomains reveal low copy numbers of Ca(2+) ions, buffer molecules, and IP₃Rs, and stochastic fluctuations arising from molecular interactions and diffusion do not average out. In contrast to models treating calcium dynamics deterministically, the stochastic approach accounts for this molecular noise. We varied Ca(2+) diffusion coefficients and buffer reaction rates to tune the autocorrelation properties of Ca(2+) noise and found a distinct relation between the autocorrelation time τac, the mean channel open and close times, and the resulting IP₃R open probability PO. We observed an increased PO for shorter noise autocorrelation times, caused by increasing channel open times and decreasing close times. In a pure diffusion model the effects become apparent at elevated calcium concentrations, e.g., at [Ca(2+)] = 25 μM, τac = 0.082 ms, the IP₃R open probability increased by ≈20% and mean open times increased by ≈4 ms, compared to a zero noise model. We identified the inactivating Ca(2+) binding site of IP₃R subunits as the primarily noise-susceptible element of the De Young and Keizer model. Short Ca(2+) noise autocorrelation times decrease the probability of Ca(2+) association and consequently increase IPvR activity. These results suggest a functional role of local calcium noise properties on calcium-regulated target molecules such as the ubiquitous IP₃R. This finding may stimulate novel experimental approaches analyzing the role of calcium noise properties on microdomain behavior.

Frequency and relative prevalence of calcium blips and puffs in a model of small IP₃R clusters

In this work, we model the local calcium release from clusters with a few inositol 1,4,5-trisphosphate receptor (IP3R) channels, focusing on the stochastic process in which an open channel either triggers other channels to open (as a puff) or fails to cause any channel to open (as a blip). We show that there are linear relations for the interevent interval (including blips and puffs) and the first event latency against the inverse cluster size. However, nonlinearity is found for the interpuff interval and the first puff latency against the inverse cluster size. Furthermore, the simulations indicate that the blip fraction among all release events and the blip frequency are increasing with larger basal [Ca(2+)], with blips in turn giving a growing contribution to basal [Ca(2+)]. This result suggests that blips are not just lapses to trigger puffs, but they may also possess a biological function to contribute to the initiation of calcium waves by a preceding increase of basal [Ca(2+)] in cells that have small IP3R clusters.

Ca²⁺ images obtained in different experimental conditions shed light on the spatial distribution of IP₃ receptors that underlie Ca²⁺ puffs

Many intracellular Ca(2+) signals involve Ca(2+) release from the endoplasmic reticulum through inositol 1,4,5-trisphosphate receptors (IP3Rs). The open probability of IP3Rs depends on cytosolic Ca(2+) so that these signals involve Ca(2+)-induced Ca(2+)-release (CICR). IP3Rs are organized in clusters. The signals they mediate are observed using single-wavelength dyes and, often, a slow Ca(2+) buffer (EGTA) is added to disrupt CICR between clusters and keep the signals spatially restricted. It is assumed that the presence of the dye or of EGTA does not alter the intra-cluster Ca(2+) dynamics. In this paper we analyze this issue combining experiments and numerical simulations. We compare the properties of local signals known as puffs observed with different dyes and EGTA concentrations. We determine that although the dye or EGTA does not alter the intra-cluster dynamics, the set of observable events is different depending on the degree of inter-cluster uncoupling of the experiment. An analysis of the observations shows that the events that are missed for insufficient inter-cluster uncoupling are those of fastest amplitude growth rate. This agrees with a spatial organization in which the largest amplitude events correspond to clusters with densely packed active IP3Rs.