Membrane targeting of the EF-hand containing calcium-sensing proteins CaBP7 and CaBP8

Structure-Function Diversity of Calcium-Binding Proteins (CaBPs): Key Roles in Cell Signalling and Disease

Calcium (Ca2+) signalling is a fundamental cellular process, essential for a wide range of physiological functions. It is regulated by various mechanisms, including a diverse family of Ca2+-binding proteins (CaBPs), which are structurally and functionally similar to calmodulin (CaM). The CaBP family consists of six members (CaBP1, CaBP2, CaBP4, CaBP5, CaBP7, and CaBP8), each exhibiting unique localisation, structural features, and functional roles. In this review, we provide a structure-function analysis of the CaBP family, highlighting the key similarities and differences both within the family and in comparison to CaM. It has been shown that CaBP1-5 share similar structural and interaction characteristics, while CaBP7 and CaBP8 form a distinct subfamily with unique properties. This review of current CaBP knowledge highlights the critical gaps in our understanding, as some CaBP members are less well characterised than others. We also examine pathogenic mutations within CaBPs and their functional impact, showing the need for further research to improve treatment options for associated disorders.

Calcium-Associated Proteins in Neuroregeneration

The dysregulation of intracellular calcium levels is a critical factor in neurodegeneration, leading to the aberrant activation of calcium-dependent processes and, ultimately, cell death. Ca2+ signals vary in magnitude, duration, and the type of neuron affected. A moderate Ca2+ concentration can initiate certain cellular repair pathways and promote neuroregeneration. While the peripheral nervous system exhibits an intrinsic regenerative capability, the central nervous system has limited self-repair potential. There is evidence that significant variations exist in evoked calcium responses and axonal regeneration among neurons, and individual differences in regenerative capacity are apparent even within the same type of neurons. Furthermore, some studies have shown that neuronal activity could serve as a potent regulator of this process. The spatio-temporal patterns of calcium dynamics are intricately controlled by a variety of proteins, including channels, ion pumps, enzymes, and various calcium-binding proteins, each of which can exert either positive or negative effects on neural repair, depending on the cellular context. In this concise review, we focus on several calcium-associated proteins such as CaM kinase II, GAP-43, oncomodulin, caldendrin, calneuron, and NCS-1 in order to elaborate on their roles in the intrinsic mechanisms governing neuronal regeneration following traumatic damage processes.

RREB1 regulates neuronal proteostasis and the microtubule network

Transcription factors play vital roles in neuron development; however, little is known about the role of these proteins in maintaining neuronal homeostasis. Here, we show that the transcription factor RREB1 (Ras-responsive element-binding protein 1) is essential for neuron survival in the mammalian brain. A spontaneous mouse mutation causing loss of a nervous system-enriched Rreb1 transcript is associated with progressive loss of cerebellar Purkinje cells and ataxia. Analysis of chromatin immunoprecipitation and sequencing, along with RNA sequencing data revealed dysregulation of RREB1 targets associated with the microtubule cytoskeleton. In agreement with the known role of microtubules in dendritic development, dendritic complexity was disrupted in Rreb1-deficient neurons. Analysis of sequencing data also suggested that RREB1 plays a role in the endomembrane system. Mutant Purkinje cells had fewer numbers of autophagosomes and lysosomes and contained P62- and ubiquitin-positive inclusions. Together, these studies demonstrate that RREB1 functions to maintain the microtubule network and proteostasis in mammalian neurons.

Mitosis, Focus on Calcium

The transformation of a single fertilised egg into an adult human consisting of tens of trillions of highly diverse cell types is a marvel of biology. The expansion is largely achieved by cell duplication through the process of mitosis. Mitosis is essential for normal growth, development, and tissue repair and is one of the most tightly regulated biological processes studied. This regulation is designed to ensure accurate segregation of chromosomes into each new daughter cell since errors in this process can lead to genetic imbalances, aneuploidy, that can lead to diseases including cancer. Understanding how mitosis operates and the molecular mechanisms that ensure its fidelity are therefore not only of significant intellectual value but provide unique insights into disease pathology. The purpose of this review is to revisit historical evidence that mitosis can be influenced by the ubiquitous second messenger calcium and to discuss this in the context of new findings revealing exciting new information about its role in cell division.

Full function of exon junction complex factor, Rbm8a, is critical for interneuron development

The formation of the nervous system requires a balance between proliferation, differentiation, and migration of neural progenitors (NPs). Mutations in genes regulating development impede neurogenesis and lead to neuropsychiatric diseases, including autism spectrum disorders (ASDs) and schizophrenia (SZ). Recently, mutations in nonsense-mediated mRNA decay genes have been associated with ASDs, intellectual disability (ID), and SZ. Here, we examine the function of a gene in the exon junction complex, Rbm8a, in the cortical development. When Rbm8a is selectively knocked out in neural stem cells, the resulting mice exhibit microcephaly, early postnatal lethality, and altered distribution of excitatory neurons in the neocortex. Moreover, Rbm8a haploinsufficiency in the central nervous system decreases cell proliferation in the ganglionic eminences. Parvalbumin+ and neuropeptide Y+ interneurons in the cortex are significantly reduced, and distribution of interneurons are altered. Consistently, neurons in the cortex of conditional knockout (cKO) mice show a significant decrease in GABA frequency. Transcriptomic analysis revealed differentially expressed genes enriched in telencephalon development and mitosis. To further investigate the role of Rbm8a in interneuron differentiation, conditional KO of Rbm8a in NKX2.1 interneuron progenitor cells reduces progenitor proliferation and alters interneuron distributions. Taken together, these data reveal a critical role of Rbm8a in interneuron development, and establish that perturbation of this gene leads to profound cortical deficits.

Calcium Sensors in Neuronal Function and Dysfunction

Calcium signaling in neurons as in other cell types can lead to varied changes in cellular function. Neuronal Ca²⁺ signaling processes have also become adapted to modulate the function of specific pathways over a wide variety of time domains and these can have effects on, for example, axon outgrowth, neuronal survival, and changes in synaptic strength. Ca²⁺ also plays a key role in synapses as the trigger for fast neurotransmitter release. Given its physiological importance, abnormalities in neuronal Ca²⁺ signaling potentially underlie many different neurological and neurodegenerative diseases. The mechanisms by which changes in intracellular Ca²⁺ concentration in neurons can bring about diverse responses is underpinned by the roles of ubiquitous or specialized neuronal Ca²⁺ sensors. It has been established that synaptotagmins have key functions in neurotransmitter release, and, in addition to calmodulin, other families of EF-hand-containing neuronal Ca²⁺ sensors, including the neuronal calcium sensor (NCS) and the calcium-binding protein (CaBP) families, play important physiological roles in neuronal Ca²⁺ signaling. It has become increasingly apparent that these various Ca²⁺ sensors may also be crucial for aspects of neuronal dysfunction and disease either indirectly or directly as a direct consequence of genetic variation or mutations. An understanding of the molecular basis for the regulation of the targets of the Ca²⁺ sensors and the physiological roles of each protein in identified neurons may contribute to future approaches to the development of treatments for a variety of human neuronal disorders.

Alternative splicing, expression and cellular localization of Calneuron-1 in the rat and human brain

Calneuron-1 and -2 are members of the neuronal calcium-binding protein family (nCaBP). They are transmembrane Calmodulin-like EF-hand Ca(2+)-sensors, and a function in the control of Golgi-to-plasma membrane vesicle trafficking has been assigned to both proteins. In this paper, we describe the distribution of Calneuron-1 in rat and human brains. We show that Calneuron-1 is ubiquitously expressed in all brain regions examined. The protein is most abundant in Purkinje cells of the cerebellum and principal neurons of the cortex and limbic brain whereas no expression in glial cells is apparent. In addition, we identify two novel splice isoforms of Calneuron-1 with extended N-termini. These isoforms are particular abundant in the cerebellum. Taken together, these data set grounds for a better understanding of the cellular function of Calneurons.

Modulation of phosphatidylinositol 4-phosphate levels by CaBP7 controls cytokinesis in mammalian cells

For more than 25 years, lysosomes have been known to cluster at the intercellular bridge during cytokinesis, but why has remained a mystery. This study provides evidence that phosphoinositide metabolism is important for this clustering and that lysosome activity is required for cytokinesis.

Calcium and phosphoinositide signaling regulate cell division in model systems, but their significance in mammalian cells is unclear. Calcium-binding protein-7 (CaBP7) is a phosphatidylinositol 4-kinaseIIIβ (PI4KIIIβ) inhibitor required during cytokinesis in mammalian cells, hinting at a link between these pathways. Here we characterize a novel association of CaBP7 with lysosomes that cluster at the intercellular bridge during cytokinesis in HeLa cells. We show that CaBP7 regulates lysosome clustering and that PI4KIIIβ is essential for normal cytokinesis. CaBP7 depletion induces lysosome mislocalization, extension of intercellular bridge lifetime, and cytokinesis failure. These data connect phosphoinositide and calcium pathways to lysosome localization and normal cytokinesis in mammalian cells.

Sense and specificity in neuronal calcium signalling

Changes in the intracellular free calcium concentration ([Ca²⁺]i) in neurons regulate many and varied aspects of neuronal function over time scales from microseconds to days. The mystery is how a single signalling ion can lead to such diverse and specific changes in cell function. This is partly due to aspects of the Ca²⁺ signal itself, including its magnitude, duration, localisation and persistent or oscillatory nature. The transduction of the Ca²⁺ signal requires Ca²⁺binding to various Ca²⁺ sensor proteins. The different properties of these sensors are important for differential signal processing and determine the physiological specificity of Ca(2+) signalling pathways. A major factor underlying the specific roles of particular Ca²⁺ sensor proteins is the nature of their interaction with target proteins and how this mediates unique patterns of regulation. We review here recent progress from structural analyses and from functional analyses in model organisms that have begun to reveal the rules that underlie Ca²⁺ sensor protein specificity for target interaction. We discuss three case studies exemplifying different aspects of Ca²⁺ sensor/target interaction. This article is part of a special issue titled the 13th European Symposium on Calcium.

Super-resolution microscopy of the neuronal calcium-binding proteins Calneuron-1 and Caldendrin

Calcium (Ca(2+)) signaling in neurons is mediated by plethora of calcium binding proteins with many of them belonging to the Calmodulin family of calcium sensors. Many studies have shown that the subcellular localization of neuronal EF-hand Ca(2+)-sensors is crucial for their cellular function. To overcome the resolution limit of classical fluorescence and confocal microscopy various imaging techniques have been developed recently that improve the resolution by an order of magnitude in all dimensions. This new microscope techniques make co-localization studies of Ca(2+)-binding proteins more reliable and help to get insights into the macromolecular organization of intracellular structures and signaling pathways beyond the diffraction limit of visible light.

Solution NMR structure of the Ca2+-bound N-terminal domain of CaBP7: a regulator of golgi trafficking

Calcium-binding protein 7 (CaBP7) is a member of the calmodulin (CaM) superfamily that harbors two high affinity EF-hand motifs and a C-terminal transmembrane domain. CaBP7 has been previously shown to interact with and modulate phosphatidylinositol 4-kinase III-β (PI4KIIIβ) activity in in vitro assays and affects vesicle transport in neurons when overexpressed. Here we show that the N-terminal domain (NTD) of CaBP7 is sufficient to mediate the interaction of CaBP7 with PI4KIIIβ. CaBP7 NTD encompasses the two high affinity Ca(2+) binding sites, and structural characterization through multiangle light scattering, circular dichroism, and NMR reveals unique properties for this domain. CaBP7 NTD binds specifically to Ca(2+) but not Mg(2+) and undergoes significant conformational changes in both secondary and tertiary structure upon Ca(2+) binding. The Ca(2+)-bound form of CaBP7 NTD is monomeric and exhibits an open conformation similar to that of CaM. Ca(2+)-bound CaBP7 NTD has a solvent-exposed hydrophobic surface that is more expansive than observed in CaM or CaBP1. Within this hydrophobic pocket, there is a significant reduction in the number of methionine residues that are conserved in CaM and CaBP1 and shown to be important for target recognition. In CaBP7 NTD, these residues are replaced with isoleucine and leucine residues with branched side chains that are intrinsically more rigid than the flexible methionine side chain. We propose that these differences in surface hydrophobicity, charge, and methionine content may be important in determining highly specific interactions of CaBP7 with target proteins, such as PI4KIIIβ.

Ca(2+) sensor proteins in dendritic spines: a race for Ca(2+)

Dendritic spines are believed to be micro-compartments of Ca²⁺ regulation. In a recent study, it was suggested that the ubiquitous and evolutionarily conserved Ca²⁺ sensor, calmodulin (CaM), is the first to intercept Ca²⁺ entering the spine and might be responsible for the fast decay of Ca²⁺ transients in spines. Neuronal calcium sensor (NCS) and neuronal calcium-binding protein (nCaBP) families consist of Ca²⁺ sensors with largely unknown synaptic functions despite an increasing number of interaction partners. Particularly how these sensors operate in spines in the presence of CaM has not been discussed in detail before. The limited Ca²⁺ resources and the existence of common targets create a highly competitive environment where Ca²⁺ sensors compete with each other for Ca²⁺ and target binding. In this review, we take a simple numerical approach to put forth possible scenarios and their impact on signaling via Ca²⁺ sensors of the NCS and nCaBP families. We also discuss the ways in which spine geometry and properties of ion channels, their kinetics and distribution, alter the spatio-temporal aspects of Ca²⁺ transients in dendritic spines, whose interplay with Ca²⁺ sensors in turn influences the race for Ca²⁺.

Evolution and functional diversity of the Calcium Binding Proteins (CaBPs)

The mammalian central nervous system (CNS) exhibits a remarkable ability to process, store, and transfer information. Key to these activities is the use of highly regulated and unique patterns of calcium signals encoded by calcium channels and decoded by families of specific calcium-sensing proteins. The largest family of eukaryotic calcium sensors is those related to the small EF-hand containing protein calmodulin (CaM). In order to maximize the usefulness of calcium as a signaling species and to permit the evolution and fine tuning of the mammalian CNS, families of related proteins have arisen that exhibit characteristic calcium binding properties and tissue-, cellular-, and sub-cellular distribution profiles. The Calcium Binding Proteins (CaBPs) represent one such family of vertebrate specific CaM like proteins that have emerged in recent years as important regulators of essential neuronal target proteins. Bioinformatic analyses indicate that the CaBPs consist of two subfamilies and that the ancestral members of these are CaBP1 and CaBP8. The CaBPs have distinct intracellular localizations based on different targeting mechanisms including a novel type-II transmembrane domain in CaBPs 7 and 8 (otherwise known as calneuron II and calneuron I, respectively). Recent work has led to the identification of new target interactions and possible functions for the CaBPs suggesting that they have multiple physiological roles with relevance for the normal functioning of the CNS.

Post-translational membrane insertion of tail-anchored transmembrane EF-hand Ca2+ sensor calneurons requires the TRC40/Asna1 protein chaperone

Calneuron-1 and -2 are neuronal EF-hand-type calcium sensor proteins that are prominently targeted to trans-Golgi network membranes and impose a calcium threshold at the Golgi for phosphatidylinositol 4-OH kinase IIIβ activation and the regulated local synthesis of phospholipids that are crucial for TGN-to-plasma membrane trafficking. In this study, we show that calneurons are nonclassical type II tail-anchored proteins that are post-translationally inserted into the endoplasmic reticulum membrane via an association of a 23-amino acid-long transmembrane domain (TMD) with the TRC40/Asna1 chaperone complex. Following trafficking to the Golgi, calneurons are probably retained in the TGN because of the length of the TMD and phosphatidylinositol 4-phosphate lipid binding. Both calneurons rapidly self-associate in vitro and in vivo via their TMD and EF-hand containing the N terminus. Although dimerization and potentially multimerization precludes TRC40/Asna1 binding and thereby membrane insertion, we found no evidence for a cytosolic pool of calneurons and could demonstrate that self-association of calneurons is restricted to membrane-inserted protein. The dimerization properties and the fact that they, unlike every other EF-hand calmodulin-like Ca(2+) sensor, are always associated with membranes of the secretory pathway, including vesicles and plasma membrane, suggests a high degree of spatial segregation for physiological target interactions.

Between promiscuity and specificity: novel roles of EF-hand calcium sensors in neuronal Ca2+ signalling

In recent years, substantial progress has been made towards an understanding of the physiological function of EF-hand calcium sensor proteins of the Calmodulin (CaM) superfamily in neurons. This deeper appreciation is based on the identification of novel target interactions, structural studies and the discovery of novel signalling mechanisms in protein trafficking and synaptic plasticity, in which CaM-like sensor proteins appear to play a role. However, not all interactions are of plausible physiological relevance and in many cases it is not yet clear how the CaM signaling network relates to the proposed function of other EF-hand sensors. In this review, we will summarize these findings and address some of the open questions on the functional role of EF-hand calcium binding proteins in neurons.

Determination of the membrane topology of the small EF-hand Ca2+-sensing proteins CaBP7 and CaBP8

The CaBPs represent a subfamily of small EF-hand containing calcium (Ca(2+))-sensing proteins related to calmodulin that regulate key ion channels in the mammalian nervous system. In a recent bioinformatic analyses we determined that CaBP7 and CaBP8 form an evolutionarily distinct branch within the CaBPs (also known as the calneurons) a finding that is consistent with earlier observations characterising a putative C-terminal transmembrane (TM) spanning helix in each of these proteins which is essential for their sub-cellular targeting to the Golgi apparatus and constitutive secretory vesicles. The C-terminal position of the predicted TM-helix suggests that CaBP7 and CaBP8 could be processed in a manner analogous to tail-anchored integral membrane proteins which exhibit the ability to insert across membranes post-translationally. In this study we have investigated the topology of CaBP7 and CaBP8 within cellular membranes through a combination of trypsin protection and epitope accessibility analyses. Our results indicate that the TM-helices of CaBP7 and CaBP8 insert fully across membranes such that their extreme C-termini are luminal. The observed type-II membrane topology is consistent with processing of CaBP7 and CaBP8 as true tail-anchored proteins. This targeting mechanism is distinct from any other calmodulin related Ca(2+)-sensor and conceivably underpins unique physiological functions of these proteins.

The diversity of calcium sensor proteins in the regulation of neuronal function

Calcium signaling in neurons as in other cell types mediates changes in gene expression, cell growth, development, survival, and cell death. However, neuronal Ca(2+) signaling processes have become adapted to modulate the function of other important pathways including axon outgrowth and changes in synaptic strength. Ca(2+) plays a key role as the trigger for fast neurotransmitter release. The ubiquitous Ca(2+) sensor calmodulin is involved in various aspects of neuronal regulation. The mechanisms by which changes in intracellular Ca(2+) concentration in neurons can bring about such diverse responses has, however, become a topic of widespread interest that has recently focused on the roles of specialized neuronal Ca(2+) sensors. In this article, we summarize synaptotagmins in neurotransmitter release, the neuronal roles of calmodulin, and the functional significance of the NCS and the CaBP/calneuron protein families of neuronal Ca(2+) sensors.

Bioinformatic analysis of CaBP/calneuron proteins reveals a family of highly conserved vertebrate Ca2+-binding proteins

Background

Ca²⁺-binding proteins are important for the transduction of Ca²⁺ signals into physiological outcomes. As in calmodulin many of the Ca²⁺-binding proteins bind Ca²⁺ through EF-hand motifs. Amongst the large number of EF-hand containing Ca²⁺-binding proteins are a subfamily expressed in neurons and retinal photoreceptors known as the CaBPs and the related calneuron proteins. These were suggested to be vertebrate specific but exactly which family members are expressed outside of mammalian species had not been examined.

Findings

We have carried out a bioinformatic analysis to determine when members of this family arose and the conserved aspects of the protein family. Sequences of human members of the family obtained from GenBank were used in Blast searches to identify corresponding proteins encoded in other species using searches of non-redundant proteins, genome sequences and mRNA sequences. Sequences were aligned and compared using ClustalW. Some families of Ca²⁺-binding proteins are known to show a progressive expansion in gene number as organisms increase in complexity. In contrast, the results for CaBPs and calneurons showed that a full complement of CaBPs and calneurons are present in the teleost fish Danio rerio and possibly in cartilaginous fish. These findings suggest that the entire family of genes may have arisen at the same time during vertebrate evolution. Certain members of the family (for example the short form of CaBP1 and calneuron 1) are highly conserved suggesting essential functional roles.

Conclusions

The findings support the designation of the calneurons as a distinct sub-family. While the gene number for CaBPs/calneurons does not increase, a distinctive evolutionary change in these proteins in vertebrates has been an increase in the number of splice variants present in mammals.

Role of neuronal Ca2+-sensor proteins in Golgi-cell-surface membrane traffic

The regulated local synthesis of PtdIns4P and PtdIns(4,5)P(2) is crucial for TGN (trans-Golgi network)-plasma membrane trafficking. The activity of PI4Kbeta (phosphoinositide 4-kinase IIIbeta) at the Golgi membrane is a first mandatory step in this process. In addition to PI4Kbeta activity, elevated Ca(2+) levels are also needed for the exit of vesicles from the TGN. The reason for this Ca(2+) requirement is at present unclear. In the present review, we discuss the role of neuronal Ca(2+)-sensor proteins in the regulation of PI4Kbeta and suggest that this regulation might impose a need for elevated Ca(2+) levels for a late step of vesicle assembly.

Neuronal calcium sensor proteins: emerging roles in membrane traffic and synaptic plasticity

Ca²⁺ plays a crucial role in the regulation of neuronal function. Recent work has revealed important functions for two families of neuronally expressed Ca²⁺ sensor proteins. These include roles in membrane traffic and in alterations in synaptic plasticity underlying changes in behaviour.

Calneuron I inhibits Ca(2+) channel activity in bovine chromaffin cells

Calneuron I (CalnI) is a calmodulin-like protein that contains two functional EF-hand motifs at the N-terminal and a hydrophobic segment at the C-terminal. CalnI was cloned from the adult rat cortex and fused with GFP at its N-terminal. When expressed in bovine chromaffin cells, wild-type CalnI was localized at the plasma membrane. However, a mutant that lacked the hydrophobic segment was localized in the cytosol and nucleus, while a Ca(2+)-binding-deficient mutant was found in the cytosol and at the plasma membrane. Evaluation using the whole-cell patch-clamp technique revealed that Ca(2+) currents were inhibited by both wild-type CalnI and the Ca(2+)-binding-deficient mutant. When the bovine N-type Ca(2+) channel was expressed in 293T cells, Ca(2+) currents were mostly inhibited by co-expression of CalnI, but not by the mutant without the hydrophobic tail. These results suggest that CalnI attenuates Ca(2+) channel activity and that its subcellular localization is important for this effect.

Calneurons provide a calcium threshold for trans-Golgi network to plasma membrane trafficking

Phosphatidylinositol 4-OH kinase IIIbeta (PI-4Kbeta) is involved in the regulated local synthesis of phospholipids that are crucial for trans-Golgi network (TGN)-to-plasma membrane trafficking. In this study, we show that the calcium sensor proteins calneuron-1 and calneuron-2 physically associate with PI-4Kbeta, inhibit the enzyme profoundly at resting and low calcium levels, and negatively interfere with Golgi-to-plasma membrane trafficking. At high calcium levels this inhibition is released and PI-4Kbeta is activated via a preferential association with neuronal calcium sensor-1 (NCS-1). In accord to its supposed function as a filter for subthreshold Golgi calcium transients, neuronal overexpression of calneuron-1 enlarges the size of the TGN caused by a build-up of vesicle proteins and reduces the number of axonal Piccolo-Bassoon transport vesicles, large dense core vesicles that carry a set of essential proteins for the formation of the presynaptic active zone during development. A corresponding protein knockdown has the opposite effect. The opposing roles of calneurons and NCS-1 provide a molecular switch to decode local calcium transients at the Golgi and impose a calcium threshold for PI-4Kbeta activity and vesicle trafficking.