Ca
2+
is one of the most important messengers. It transmits signals inside living cells and takes part in intercellular coordination. The dynamics of the Ca
2+
concentration shows a transition from ...elemental, stochastic events to global events like waves and oscillations. This transition renders it an ideal tool for studying basic concepts of pattern formation, especially since access to the most important experimental parameters is given. Ca
2+
dynamics in living cells has been a major topic of biophysical modelling in the last 15 years. Modelling has reached the level of predictive power. The theoretical analysis of waves provided new insight into the mechanisms of Ca
2+
signaling and led to new concepts of analysis of wave equations with concentration dependent diffusion and novel wave bifurcations. Modelling of oscillations provided understanding especially of complex oscillations and allowed to extract information about the underlying cellular parameters and mechanisms. The investigation of the stochastic aspects of intracellular Ca
2+
dynamics demonstrated the fundamental role of fluctuations arising from the control of the release channel by Ca
2+
and IP
3
. This review presents an overview of current theoretical research on Ca
2+
dynamics in living cells driven by the inositol 1,4,5-trisphosphate receptor channel.
Cells relay a plethora of extracellular signals to specific cellular responses by using only a few second messengers, such as cAMP. To explain signaling specificity, cAMP-degrading phosphodiesterases ...(PDEs) have been suggested to confine cAMP to distinct cellular compartments. However, measured rates of fast cAMP diffusion and slow PDE activity render cAMP compartmentalization essentially impossible. Using fluorescence spectroscopy, we show that, contrary to earlier data, cAMP at physiological concentrations is predominantly bound to cAMP binding sites and, thus, immobile. Binding and unbinding results in largely reduced cAMP dynamics, which we term “buffered diffusion.” With a large fraction of cAMP being buffered, PDEs can create nanometer-size domains of low cAMP concentrations. Using FRET-cAMP nanorulers, we directly map cAMP gradients at the nanoscale around PDE molecules and the areas of resulting downstream activation of cAMP-dependent protein kinase (PKA). Our study reveals that spatiotemporal cAMP signaling is under precise control of nanometer-size domains shaped by PDEs that gate activation of downstream effectors.
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•Under basal conditions, most cAMP in cells is bound and its free concentration is low•Individual phosphodiesterases create nanometer-size domains of even lower cAMP•In such nanodomains, cAMP targets are protected from cAMP signals•Receptor stimuli increase cAMP to flood nanodomains and trigger downstream effects
Mapping cAMP dynamics and concentrations in live cells reveals how maintaining low levels of free second messengers enables formation of nanometer-sized signaling compartments.
G protein-coupled receptors (GPCRs) relay extracellular stimuli into specific cellular functions. Cells express many different GPCRs, but all these GPCRs signal to only a few second messengers such ...as cAMP. It is largely unknown how cells distinguish between signals triggered by different GPCRs to orchestrate their complex functions. Here, we demonstrate that individual GPCRs signal via receptor-associated independent cAMP nanodomains (RAINs) that constitute self-sufficient, independent cell signaling units. Low concentrations of glucagon-like peptide 1 (GLP-1) and isoproterenol exclusively generate highly localized cAMP pools around GLP-1- and β2-adrenergic receptors, respectively, which are protected from cAMP originating from other receptors and cell compartments. Mapping local cAMP concentrations with engineered GPCR nanorulers reveals gradients over only tens of nanometers that define the size of individual RAINs. The coexistence of many such RAINs allows a single cell to operate thousands of independent cellular signals simultaneously, rather than function as a simple “on/off” switch.
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•Receptors signal via receptor-associated independent cAMP nanodomains (RAINs)•RAINs constitute entirely self-sufficient, independent cell signaling units•When receptors are strongly stimulated, RAINs may fuse, and bulk cAMP increases•Cells may use thousands of independent RAINs to orchestrate signaling specificity
GPCRs signal via localized regions of cAMP that do not mix, leading to action of independent on/off switches rather than coupling via a shared pool of signaling molecules.
The fidelity of intracellular signaling hinges on the organization of dynamic activity architectures. Spatial compartmentation was first proposed over 30 years ago to explain how diverse G ...protein-coupled receptors achieve specificity despite converging on a ubiquitous messenger, cyclic adenosine monophosphate (cAMP). However, the mechanisms responsible for spatially constraining this diffusible messenger remain elusive. Here, we reveal that the type I regulatory subunit of cAMP-dependent protein kinase (PKA), RIα, undergoes liquid-liquid phase separation (LLPS) as a function of cAMP signaling to form biomolecular condensates enriched in cAMP and PKA activity, critical for effective cAMP compartmentation. We further show that a PKA fusion oncoprotein associated with an atypical liver cancer potently blocks RIα LLPS and induces aberrant cAMP signaling. Loss of RIα LLPS in normal cells increases cell proliferation and induces cell transformation. Our work reveals LLPS as a principal organizer of signaling compartments and highlights the pathological consequences of dysregulating this activity architecture.
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•PKA RIα undergoes liquid-liquid phase separation in response to cAMP dynamics•RIα condensates dynamically sequester cAMP and retain high PKA activity•RIα phase separation is necessary for effective cAMP compartmentation•A PKA oncoprotein disrupts RIα bodies, leading to aberrant signaling and growth
cAMP-responsive condensate formation by PKA’s RIα subunit controls local signaling, and disruption of phase separation in this context contributes to tumorigenesis.
Cell motility driven by actin polymerization is pivotal to the development and survival of organisms and individual cells. Motile cells plated on flat substrates form membrane protrusions called ...lamellipodia. The protrusions repeatedly appear and retract in all directions. If a lamellipodium is stabilized and lasts for some time, it can take over the lead and determine the direction of cell motion. Protrusions traveling along the cell perimeter have also been observed. Their initiation is in some situations the effect of the dynamics of the pathway linking plasma membrane receptors to actin filament nucleation, e.g. in chemotaxis. However, lamellipodia are also formed in many cells incessantly during motion with a constant state of the signaling pathways upstream from nucleation promoting factors (NPFs), or spontaneously in resting cells. These observations strongly suggest protrusion formation can also be a consequence of the dynamics downstream from NPFs, with signaling setting the dynamic regime but not initiating the formation of individual protrusions. A quantitative mechanism for this kind of lamellipodium dynamics has not been suggested yet. Here, we present a model exhibiting excitable actin network dynamics. Individual lamellipodia form due to random supercritical filament nucleation events amplified by autocatalytic branching. They last for about 30 seconds to many minutes and are terminated by filament bundling, severing and capping. We show the relevance of the model mechanism for experimentally observed protrusion dynamics by reproducing in very good approximation the repetitive protrusion formation measured by Burnette et al. with respect to the velocities of leading edge protrusion and retrograde flow, oscillation amplitudes, periods and shape, as well as the phase relation between protrusion and retrograde flow. Our modeling results agree with the mechanism of actin bundle formation during lamellipodium retraction suggested by Burnette et al. and Koestler et al.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The cell cycle is among the most basic phenomena in biology. Despite advances in single‐cell analysis, dynamics and topology of the cell cycle in high‐dimensional gene expression space remain largely ...unknown. We developed a linear analysis of transcriptome data which reveals that cells move along a planar circular trajectory in transcriptome space during the cycle. Non‐cycling gene expression adds a third dimension causing helical motion on a cylinder. We find in immortalized cell lines that cell cycle transcriptome dynamics occur largely independently from other cellular processes. We offer a simple method (“Revelio”) to order unsynchronized cells in time. Precise removal of cell cycle effects from the data becomes a straightforward operation. The shape of the trajectory implies that each gene is upregulated only once during the cycle, and only two dynamic components represented by groups of genes drive transcriptome dynamics. It indicates that the cell cycle has evolved to minimize changes of transcriptional activity and the related regulatory effort. This design principle of the cell cycle may be of relevance to many other cellular differentiation processes.
Synopsis
Deep single‐cell RNA sequencing of asynchronous immortalized cycling cells is leveraged to analyze the cell cycle in highdimensional gene expression space. Principles of dynamical systems theory are utilized to define a cell cycle trajectory and to seek for underlying design principles.
The cell cycle corresponds to a 2D circular trajectory in gene expression space, which suggests minimization of changes of gene expression velocity in this space (minimization of “acceleration”) as a general design principle of the cell cycle.
Cell cycle gene expression in immortalized cell lines is largely uncoupled from other biological processes.
A novel linear analysis of single‐cell data that orders unsynchronized proliferating cells in time and surgically removes cell cycle effects.
Deep single‐cell RNA sequencing of asynchronous immortalized cycling cells is leveraged to analyze the cell cycle in high‐dimensional gene expression space. Principles of dynamical systems theory are utilized to define a cell cycle trajectory and to seek for underlying design principles.
I present a stochastic model for intracellular Ca(2+) oscillations. The model starts from stochastic binding and dissociation of Ca(2+) to binding sites on a single subunit of the IP(3)-receptor ...channel but is capable of simulating large numbers of clusters for many oscillation periods too. I find oscillations with variable periods ranging from 17 s to 120 s and a standard deviation well in the experimentally observed range. Long period oscillations can be perceived as nucleation phenomenon and can be observed for a large variety of single channel dynamics. Their period depends on the geometric characteristics of the cluster array. Short periods are in the range of the time scale of channel dynamics. Both long and short period oscillations occur for parameters with a nonoscillatory deterministic regime.
Usually, the occurrence of random cell behavior is appointed to small copy numbers of molecules involved in the stochastic process. Recently, we demonstrated for a variety of cell types that ...intracellular Ca2+ oscillations are sequences of random spikes despite the involvement of many molecules in spike generation. This randomness arises from the stochastic state transitions of individual Ca2+ release channels and does not average out due to the existence of steep concentration gradients. The system is hierarchical due to the structural levels channel--channel cluster--cell and a corresponding strength of coupling. Concentration gradients introduce microdomains which couple channels of a cluster strongly. But they couple clusters only weakly; too weak to establish deterministic behavior on cell level. Here, we present a multi-scale modelling concept for stochastic hierarchical systems. It simulates active molecules individually as Markov chains and their coupling by deterministic diffusion. Thus, we are able to follow the consequences of random single molecule state changes up to the signal on cell level. To demonstrate the potential of the method, we simulate a variety of experiments. Comparisons of simulated and experimental data of spontaneous oscillations in astrocytes emphasize the role of spatial concentration gradients in Ca2+ signalling. Analysis of extensive simulations indicates that frequency encoding described by the relation between average and standard deviation of interspike intervals is surprisingly robust. This robustness is a property of the random spiking mechanism and not a result of control.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Calcium puffs are local transient Ca2+ releases from internal Ca2+ stores such as the endoplasmic reticulum or the sarcoplasmic reticulum. Such release occurs through a cluster of inositol ...1,4,5-trisphosphate receptors (IP3Rs). Based on the IP3R model (which is determined by fitting to stationary single-channel data) and nonstationary single-channel data, we construct a new IP3R model that includes time-dependent rates of mode switches. A point-source model of Ca2+ puffs is then constructed based on the new IP3R model and is solved by a hybrid Gillespie method with adaptive timing. Model results show that a relatively slow recovery of an IP3R from Ca2+ inhibition is necessary to reproduce most of the experimental outcomes, especially the nonexponential interpuff interval distributions. The number of receptors in a cluster could be severely underestimated when the recovery is sufficiently slow. Furthermore, we find that, as the number of IP3Rs increases, the average duration of puffs initially increases but then becomes saturated, whereas the average decay time keeps increasing linearly. This gives rise to the observed asymmetric puff shape.
Ca²⁺ is a universal second messenger in eukaryotic cells transmitting information through sequences of concentration spikes. A prominent mechanism to generate these spikes involves Ca²⁺ release from ...the endoplasmic reticulum Ca²⁺ store via inositol 1,4,5-trisphosphate (IP₃)-sensitive channels. Puffs are elemental events of IP₃-induced Ca²⁺ release through single clusters of channels. Intracellular Ca²⁺ dynamics are a stochastic system, but a complete stochastic theory has not been developed yet. We formulate the theory in terms of interpuff interval and puff duration distributions because, unlike the properties of individual channels, they can be measured in vivo. Our theory reproduces the typical spectrum of Ca²⁺ signals like puffs, spiking, and bursting in analytically treatable test cases as well as in more realistic simulations. We find conditions for spiking and calculate interspike interval (ISI) distributions. Signal form, average ISI and ISI distributions depend sensitively on the details of cluster properties and their spatial arrangement. In contrast to that, the relation between the average and the standard deviation of ISIs does not depend on cluster properties and cluster arrangement and is robust with respect to cell variability. It is controlled by the global feedback processes in the Ca²⁺ signaling pathway (e.g., via IP₃-3-kinase or endoplasmic reticulum depletion). That relation is essential for pathway function because it ensures frequency encoding despite the randomness of ISIs and determines the maximal spike train information content. Hence, we find a division of tasks between global feedbacks and local cluster properties that guarantees robustness of function while maintaining sensitivity of control of the average ISI.
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