Measuring Ca2+ inside intracellular organelles with luminescent and fluorescent aequorin-based sensors

Using Fluorescent GAP Indicators to Monitor ER Ca2

The endoplasmic reticulum (ER) is the main reservoir of Ca2+ of the cell. Accurate and quantitative measuring of Ca2+ dynamics within the lumen of the ER has been challenging. In the last decade a few genetically encoded Ca2+ indicators have been developed, including a family of fluorescent Ca2+ indicators, dubbed GFP-Aequorin Proteins (GAPs). They are based on the fusion of two jellyfish proteins, the green fluorescent protein (GFP) and the Ca2+-binding protein aequorin. GAP Ca2+ indicators exhibit a combination of several features: they are excitation ratiometric indicators, with reciprocal changes in the fluorescence excited at 405 and 470 nm, which is advantageous for imaging experiments; they exhibit a Hill coefficient of 1, which facilitates the calibration of the fluorescent signal into Ca2+ concentrations; they are insensible to variations in the Mg2+ concentrations or pH variations (in the 6.5-8.5 range); and, due to the lack of mammalian homologues, these proteins have a favorable expression in transgenic animals. A low Ca2+ affinity version of GAP, GAP3 (KD ≅ 489 µM), has been engineered to conform with the estimated [Ca2+] in the ER. GAP3 targeted to the lumen of the ER (erGAP3) can be utilized for imaging intraluminal Ca2+. The ratiometric measurements provide a quantitative method to assess accurate [Ca2+]ER, both dynamically and at rest. In addition, erGAP3 can be combined with synthetic cytosolic Ca2+ indicators to simultaneously monitor ER and cytosolic Ca2+. Here, we provide detailed methods to assess erGAP3 expression and to perform Ca2+ imaging, either restricted to the ER lumen, or simultaneously in the ER and the cytosol. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Detection of erGAP3 in the ER by immunofluorescence Basic Protocol 2: Monitoring ER Ca2+ Basic Protocol 3: Monitoring ER- and cytosolic-Ca2+ Support Protocol: Generation of a stable cell line expressing erGAP3.

In vitro and in vivo calibration of low affinity genetic Ca2+ indicators

Calcium is a universal intracellular messenger and proper Ca2+concentrations ([Ca2+]) both in the cytosol and in the lumen of cytoplasmic organelles are essential for cell functions. Ca2+ homeostasis is achieved by a delicate pump/leak balance both at the plasma membrane and at the endomembranes, and improper Ca2+ levels result in malfunction and disease. Selective intraorganellar Ca2+measurements are best achieved by using targeted genetically encoded Ca2+ indicators (GECIs) but to calibrate the luminal fluorescent signals into accurate [Ca2+] is challenging, especially in vivo, due to the difficulty to normalize and calibrate the fluorescent signal in various tissues or conditions. We report here a procedure to calibrate the ratiometric signal of GAP (GFP-Aequorin Protein) targeted to the endo-sarcoplasmic reticulum (ER/SR) into [Ca2+]ER/SR based on imaging of fluorescence after heating the tissue at 50-52 °C, since this value coincides with that obtained in the absence of Ca2+ (Rmin). Knowledge of the dynamic range (Rmax/Rmin) and the Ca2+-affinity (KD) of the indicator permits calculation of [Ca2+] by applying a simple algorithm. We have validated this procedure in vitro using several cell types (HeLa, HEK 293T and mouse astrocytes), as well as in vivo in Drosophila. Moreover, this methodology is applicable to other low Ca2+ affinity green and red GECIs.

The evolution of organellar calcium mapping technologies

Intracellular Ca2+ fluxes are dynamically controlled by the co-involvement of multiple organellar pools of stored Ca2+. Endolysosomes are emerging as physiologically critical, yet underexplored, sources and sinks of intracellular Ca2+. Delineating the role of organelles in Ca2+ signaling has relied on chemical fluorescent probes and electrophysiological strategies. However, the acidic endolysosomal environment presents unique issues, which preclude the use of traditional chemical reporter strategies to map lumenal Ca2+. Here, we broadly address the current state of knowledge about organellar Ca2+ pools. We then outline the application of traditional probes, and their sensing paradigms. We then discuss how a new generation of probes overcomes the limitations of traditional Ca2+probes, emphasizing their ability to offer critical insights into endolysosomal Ca2+, and its feedback with other organellar pools.

Shaped by leaky ER: Homeostatic Ca2+ fluxes

At any moment in time, cells coordinate and balance their calcium ion (Ca²⁺) fluxes. The term ‘Ca²⁺ homeostasis’ suggests that balancing resting Ca²⁺ levels is a rather static process. However, direct ER Ca²⁺ imaging shows that resting Ca²⁺ levels are maintained by surprisingly dynamic Ca²⁺ fluxes between the ER Ca²⁺ store, the cytosol, and the extracellular space. The data show that the ER Ca²⁺ leak, continuously fed by the high-energy consuming SERCA, is a fundamental driver of resting Ca²⁺ dynamics. Based on simplistic Ca²⁺ toolkit models, we discuss how the ER Ca²⁺ leak could contribute to evolutionarily conserved Ca²⁺ phenomena such as Ca²⁺ entry, ER Ca²⁺ release, and Ca²⁺ oscillations.

Association of Sonic Hedgehog with the extracellular matrix requires its zinc-coordination center

Background

Sonic Hedgehog (Shh) has a catalytic cleft characteristic for zinc metallopeptidases and has significant sequence similarities with some bacterial peptidoglycan metallopeptidases defining a subgroup within the M15A family that, besides having the characteristic zinc coordination motif, can bind two calcium ions. Extracellular matrix (ECM) components in animals include heparan-sulfate proteoglycans, which are analogs of bacterial peptidoglycan and are involved in the extracellular distribution of Shh.

Results

We found that the zinc-coordination center of Shh is required for its association to the ECM as well as for non-cell autonomous signaling. Association with the ECM requires the presence of at least 0.1 μM zinc and is prevented by mutations affecting critical conserved catalytical residues. Consistent with the presence of a conserved calcium binding domain, we find that extracellular calcium inhibits ECM association of Shh.

Conclusions

Our results indicate that the putative intrinsic peptidase activity of Shh is required for non-cell autonomous signaling, possibly by enzymatically altering ECM characteristics.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12860-021-00359-5.

Na+ controls hypoxic signalling by the mitochondrial respiratory chain

All metazoans depend on the consumption of O2 by the mitochondrial oxidative phosphorylation system (OXPHOS) to produce energy. In addition, the OXPHOS uses O2 to produce reactive oxygen species that can drive cell adaptations1-4, a phenomenon that occurs in hypoxia4-8 and whose precise mechanism remains unknown. Ca2+ is the best known ion that acts as a second messenger9, yet the role ascribed to Na+ is to serve as a mere mediator of membrane potential10. Here we show that Na+ acts as a second messenger that regulates OXPHOS function and the production of reactive oxygen species by modulating the fluidity of the inner mitochondrial membrane. A conformational shift in mitochondrial complex I during acute hypoxia11 drives acidification of the matrix and the release of free Ca2+ from calcium phosphate (CaP) precipitates. The concomitant activation of the mitochondrial Na+/Ca2+ exchanger promotes the import of Na+ into the matrix. Na+ interacts with phospholipids, reducing inner mitochondrial membrane fluidity and the mobility of free ubiquinone between complex II and complex III, but not inside supercomplexes. As a consequence, superoxide is produced at complex III. The inhibition of Na+ import through the Na+/Ca2+ exchanger is sufficient to block this pathway, preventing adaptation to hypoxia. These results reveal that Na+ controls OXPHOS function and redox signalling through an unexpected interaction with phospholipids, with profound consequences for cellular metabolism.

A Single Silicon Nanowire-Based Ratiometric Biosensor for Ca2+ at Various Locations in a Neuron

Ionic calcium (Ca²⁺) is an important second messenger in cells, particularly in the neuron. A deficiency or excess of Ca²⁺ would lead to neuronal apoptosis and further injury to the brain. For accurate analysis of intracellular Ca²⁺, a single silicon nanowire (SiNW)-based ratiometric biosensor was constructed by simultaneously anchoring Ru(bpy)₂(mcbpy-O-Su-ester)(PF₆)₂, as a reference molecule, and Fluo-3, as a response molecule, onto the surface of a single SiNW. The SiNW-based biosensor exhibits high sensitivity and favorable selectivity for detecting Ca²⁺. With the assistance of a micromanipulator and laser scanning confocal microscope, two single SiNW sensors were placed in the body and the neurites of an individual neuron to detect Ca²⁺. The difference between the concentrations of Ca²⁺ in the body and neurites was identified. The results from the present study provide new insights into Ca²⁺ in neurons at a high spatial resolution, and the strategy used in this study provides a new opportunity to investigate cellular metabolism by combining the advantages of a single-cell detection technique and physiology.

Sarcoplasmic reticulum Ca2+ decreases with age and correlates with the decline in muscle function in Drosophila

Sarcopenia, the loss of muscle mass and strength associated with age, has been linked to impairment of the cytosolic Ca2+ peak that triggers muscle contraction, but mechanistic details remain unknown. Here we explore the hypothesis that a reduction in sarcoplasmic reticulum (SR) Ca2+ concentration ([Ca2+]SR) is at the origin of this loss of Ca2+ homeostasis. We engineered Drosophila melanogaster to express the Ca2+ indicator GAP3 targeted to muscle SR, and we developed a new method to calibrate the signal into [Ca2+]SRin vivo [Ca2+]SR fell with age from ∼600 µM to 50 µM in close correlation with muscle function, which declined monotonically when [Ca2+]SR was <400 µM. [Ca2+]SR results from the pump-leak steady state at the SR membrane. However, changes in expression of the sarco/endoplasmic reticulum Ca2+-ATPase (SERCA) pump and of the ryanodine receptor leak were too modest to explain the large changes seen in [Ca2+]SR Instead, these changes are compatible with increased leakiness through the ryanodine receptor as the main determinant of the [Ca2+]SR decline in aging muscle. In contrast, there were no changes in endoplasmic reticulum [Ca2+] with age in brain neurons.This article has an associated First Person interview with the first author of the paper.

Imaging of Endoplasmic Reticulum Ca2+ in the Intact Pituitary Gland of Transgenic Mice Expressing a Low Affinity Ca2+ Indicator

The adenohypophysis contains five secretory cell types (somatotrophs, lactotrophs, thyrotrophs, corticotrophs, and gonadotrophs), each secreting a different hormone, and controlled by different hypothalamic releasing hormones (HRHs). Exocytic secretion is regulated by cytosolic Ca²⁺ signals ([Ca²⁺]_C), which can be generated either by Ca²⁺ entry through the plasma membrane and/or by Ca²⁺ release from the endoplasmic reticulum (ER). In addition, Ca²⁺ entry signals can eventually be amplified by ER release via calcium-induced calcium release (CICR). We have investigated the contribution of ER Ca²⁺ release to the action of physiological agonists in pituitary gland. Changes of [Ca²⁺] in the ER ([Ca²⁺]_ER) were measured with the genetically encoded low-affinity Ca²⁺ sensor GAP3 targeted to the ER. We used a transgenic mouse strain that expressed erGAP3 driven by a ubiquitous promoter. Virtually all the pituitary cells were positive for the sensor. In order to mimick the physiological environment, intact pituitary glands or acute slices from the transgenic mouse were used to image [Ca²⁺]_ER. [Ca²⁺]_C was measured simultaneously with Rhod-2. Luteinizing hormone-releasing hormone (LHRH) or thyrotropin releasing hormone (TRH), two agonists known to elicit intracellular Ca²⁺ mobilization, provoked robust decreases of [Ca²⁺]_ER and concomitant rises of [Ca²⁺]_C. A smaller fraction of cells responded to thyrotropin releasing hormone (TRH). By contrast, depolarization with high K⁺ triggered a rise of [Ca²⁺]_C without a decrease of [Ca²⁺]_ER, indicating that the calcium-induced calcium-release (CICR) via ryanodine receptor amplification mechanism is not present in these cells. Our results show the potential of transgenic ER Ca²⁺ indicators as novel tools to explore intraorganellar Ca²⁺ dynamics in pituitary gland in situ.

Genetic analyses uncover pleiotropic compensatory roles for Drosophila Nucleobindin-1 in inositol trisphosphate-mediated intracellular calcium homeostasis

Nucleobindin-1 is an EF-hand calcium-binding protein with a distinctive profile, predominantly localized to the Golgi in insect and wide-ranging vertebrate cell types, alike. Its putative involvements in intracellular calcium (Ca²⁺) homeostasis have never been phenotypically characterized in any model organism. We have analyzed an adult-viable mutant that completely disrupts the G protein α-subunit binding and activating (GBA) motif of Drosophila Nucleobindin-1 (dmNUCB1). Such disruption does not manifest any obvious fitness-related, morphological/developmental, or behavioral abnormalities. A single copy of this mutation or the knockdown of dmnucb1 in restricted sets of cells variously rescues pleiotropic mutant phenotypes arising from impaired inositol 1,4,5-trisphosphate receptor (IP3R) activity (in turn depleting cytoplasmic Ca²⁺ levels across diverse tissue types). Additionally, altered dmNUCB1 expression or function considerably reverses lifespan and mobility improvements effected by IP3R mutants, in a Drosophila model of amyotrophic lateral sclerosis. Homology modeling-based analyses further predict a high degree of conformational conservation in Drosophila, of biochemically validated structural determinants in the GBA motif that specify in vertebrates, the unconventional Ca²⁺-regulated interaction of NUCB1 with Gαi subunits. The broad implications of our findings are hypothetically discussed, regarding potential roles for NUCB1 in GBA-mediated, Golgi-associated Ca²⁺ signaling, in health and disease.

Caffeine chelates calcium in the lumen of the endoplasmic reticulum

Cytosolic Ca²⁺ signals are often amplified by massive calcium release from the endoplasmic reticulum (ER). This calcium-induced calcium release (CICR) occurs by activation of an ER Ca²⁺ channel, the ryanodine receptor (RyR), which is facilitated by both cytosolic- and ER Ca²⁺ levels. Caffeine sensitizes RyR to Ca²⁺ and promotes ER Ca²⁺ release at basal cytosolic Ca²⁺ levels. This outcome is frequently used as a readout for the presence of CICR. By monitoring ER luminal Ca²⁺ with the low-affinity genetic Ca²⁺ probe erGAP3, we find here that application of 50 mM caffeine rapidly reduces the Ca²⁺ content of the ER in HeLa cells by ∼50%. Interestingly, this apparent ER Ca²⁺ release does not go along with the expected cytosolic Ca²⁺ increase. These results can be explained by Ca²⁺ chelation by caffeine inside the ER. Ca²⁺-overloaded mitochondria also display a drop of the matrix Ca²⁺ concentration upon caffeine addition. In contrast, in the cytosol, with a low free Ca²⁺ concentration (10^-7 M), no chelation is observed. Expression of RyR3 sensitizes the responses to caffeine with effects both in the ER (increase in Ca²⁺ release) and in the cytosol (increase in Ca²⁺ peak) at low caffeine concentrations (0.3-1 mM) that have no effects in control cells. Our results illustrate the fact that simultaneous monitoring of both cytosolic- and ER Ca²⁺ are necessary to understand the action of caffeine and raise concerns against the use of high concentrations of caffeine as a readout of the presence of CICR.

Assessment of cytosolic free calcium changes during ceramide-induced cell death in MDA-MB-231 breast cancer cells expressing the calcium sensor GCaMP6m

Alterations in Ca²⁺ signaling can regulate key cancer hallmarks such as proliferation, invasiveness and resistance to cell death. Changes in the regulation of intracellular Ca²⁺ and specific components of Ca²⁺ influx are a feature of several cancers and/or cancer subtypes, including the basal-like breast cancer subtype, which has a poor prognosis. The development of genetically encoded calcium indicators, such as GCaMP6, represents an opportunity to measure changes in intracellular free Ca²⁺ during processes relevant to breast cancer progression that occur over long periods (e.g. hours), such as cell death. This study describes the development of a MDA-MB-231 breast cancer cell line stably expressing GCaMP6m. The cell line retained the key features of this aggressive basal-like breast cancer cell line. Using this model, we defined alterations in relative cytosolic free Ca²⁺ ([Ca²⁺]_CYT) when the cells were treated with C2-ceramide. Cell death was measured simultaneously via assessment of propidium iodide permeability. Treatment with ceramide produced delayed and heterogeneous sustained increases in [Ca²⁺]_CYT. Where cell death occurred, [Ca²⁺]_CYT increases preceded cell death. The sustained increases in [Ca²⁺]_CYT were not related to the rapid morphological changes induced by ceramide. Silencing of the plasma membrane Ca²⁺ ATPase isoform 1 (PMCA1) was associated with an augmentation in ceramide-induced increases in [Ca²⁺]_CYT and also cell death. This work demonstrates the utility of GCaMP6 Ca²⁺ indicators for investigating [Ca²⁺]_CYT changes in breast cancer cells during events relevant to tumor progression, which occur over hours rather than minutes.