Structures and metal-ion-binding properties of the Ca2+-binding helix–loop–helix EF-hand motifs

Design, structures, and applications of an icosahedral artificial protein nanocage, TIP60

Many protein nanocages are polyhedral shapes with icosahedral symmetry owing to the geometric constraints defined by Euler's polyhedral theorem, which suggests that pentagonal faces play a key role in creating uniform structures. This principle has inspired a range of design approaches to create artificial protein nanocages. For example, this review mainly shows design, structures, and applications of TIP60, an artificially designed icosahedral protein nanocage produced through a fusion protein approach incorporating pentameric structures. Protein engineering techniques, such as chemical modifications and mutation strategies for TIP60, have successfully added properties useful for various applications, including drug delivery, nanoreactors, and hydrogels. Recent advances in computational protein design can enable precise structural customization. Therefore, the integration of rational design with targeted modifications is likely to become a powerful approach for developing functionalized proteins.

Soluble form of tumor necrosis factor-related apoptosis-inducing ligand interacts with S100P protein

Tumor Necrosis Factor (TNF)-Related Apoptosis-Inducing Ligand (TRAIL) is a therapeutically relevant protein belonging to the TNF superfamily. Both membrane-bound and soluble (sTRAIL) forms of TRAIL affect innate and adaptive immune responses. We recently showed that soluble TNF binds specific members of the S100 family of multifunctional calcium-binding proteins, leading to suppression of its cytotoxic activity (Int. J. Mol. Sci. 2022, 23(24), 15,956). To test the ability of S100 proteins to affect sTRAIL functioning, we used surface plasmon resonance spectroscopy, intrinsic fluorescence, chemical crosslinking, molecular modeling, site-directed mutagenesis, cytotoxicity assay, and bioinformatics to study interaction of human sTRAIL with human non-fused S100 proteins. Of the 21 S100 proteins examined, only S100P protein showed specific interaction with sTRAIL characterized by equilibrium dissociation constant, Kd, reaching (0.16 ± 0.07) μM. sTRAIL monomer binds dimeric S100P strictly in the presence of Ca2+, while sTRAIL trimer interacts with S100P dimer regardless of Ca2+. Site-directed mutagenesis confirmed involvement of the 'hinge' and C-terminal regions of S100P in the sTRAIL recognition, consistent with the structural modeling results. Bioinformatic analysis indicates dysregulation of TRAIL and S100P in various neoplasms. S100P lowers cytotoxicity of sTRAIL against human fibrosarcoma HT-1080 cells. The suppression of proapoptotic sTRAIL signaling by S100P protein may contribute to oncogenic effects of the latter.

Anatolian ground squirrel (Spermophilus xanthoprymnus) retina: Comparative expression of synaptophysin, NeuN, calbindin-D28k, parvalbumin, glial fibrillary acidic protein, and Iba-1 during pre-hibernation and hibernation

Hibernation induces significant molecular and cellular adaptations in the retina to maintain function under reduced metabolic conditions. This study aimed to investigate the expression of neuronal, synaptic, and glial markers in the retina of Spermophilus xanthoprymnus during pre-hibernation and hibernation periods using immunohistochemical staining. Synaptophysin expression, restricted to the inner plexiform layer (IPL) and outer plexiform layer (OPL) during pre-hibernation, significantly increased in both layers during hibernation, with additional expression observed in the outer nuclear layer. NeuN immunoreactivity remained unchanged in the ganglion cell layer (GCL) but increased notably in the INL during hibernation. Calbindin-D28k expression, prominent in the INL and plexiform layers during pre-hibernation, decreased markedly in hibernation. In contrast, parvalbumin expression increased across all retinal layers, except the photoreceptor layer, during hibernation. Glial fibrillary acidic protein (GFAP) expression, observed in the NFL and GCL, was significantly reduced during hibernation. Iba-1 immunoreactivity, sparse in the IPL and OPL during pre-hibernation, showed a pronounced increase in the IPL, OPL, and INL during hibernation periods. In conclusion, the expression of synaptophysin, NeuN, calbindin-D28k, parvalbumin, GFAP, and Iba-1 was investigated for the first time in the retina of the Anatolian ground squirrel during pre-hibernation and hibernation. This study reveals region-specific shifts in retinal marker expression during pre-hibernation and hibernation, providing a basis for future research into visual system adaptations and retinal plasticity under metabolic suppression.

Plant microRNAs enter the scene of calcium signaling

Recent studies have identified the miRNA391/1432/4376 superfamily (miR391S) in seed plants, which targets the 5' untranslated region (UTR) of mRNAs encoding autoinhibited Ca2+-ATPases (ACAs), a key component of calcium signaling. This superfamily includes miR391 in the Brassicaceae, miR4376 in the Solanaceae, and miR1432 in the Poaceae, all of which share a highly conserved 10-nucleotide (nt) core in their mature miRNA sequences. Notably, miR1432 in the Poaceae targets both ACA and mRNAs encoding calmodulin-like proteins, which are putative Ca2+ sensors. In this opinion article we highlight evidence revealing this miRNA superfamily's ancient origin, regulatory conservation, and sequence diversification linked to functional innovation. Consistent with the central role of calcium signaling, recent studies on Arabidopsis thaliana and rice suggest the broad implications of the ACA-targeting miRNAs in plant development, immunity, and abiotic stress responses.

CaV2.1 mediates presynaptic dysfunction induced by amyloid β oligomers

Synaptic dysfunction is an early pathological phenotype of Alzheimer's disease (AD) that is initiated by oligomers of amyloid β peptide (Aβos). Treatments aimed at correcting synaptic dysfunction could be beneficial in preventing disease progression, but mechanisms underlying Aβo-induced synaptic defects remain incompletely understood. Here, we uncover an epithelial sodium channel (ENaC) - CaV2.3 - protein kinase C (PKC) - glycogen synthase kinase-3β (GSK-3β) signal transduction pathway that is engaged by Aβos to enhance presynaptic CaV2.1 voltage-gated Ca2+ channel activity, resulting in pathological potentiation of action-potential-evoked synaptic vesicle exocytosis. We present evidence that the pathway is active in human APP transgenic mice in vivo and in human AD brains, and we show that either pharmacological CaV2.1 inhibition or genetic CaV2.1 haploinsufficiency is sufficient to restore normal neurotransmitter release. These findings reveal a previously unrecognized mechanism driving synaptic dysfunction in AD and identify multiple potentially tractable therapeutic targets.

Genome-Wide Characterization of CaM/CML Gene Family in Cabbage (Brassica oleracea var. capitata): Expression Profiling and Functional Implications During Hyaloperonospora parasitica Infection

Calmodulin (CaM) and calmodulin-like proteins (CMLs) are crucial for calcium signal transduction in plants. Although CaM/CML genes have been extensively studied in various plant species, research on these genes in Brassica oleracea is still limited. In this study, 14 BoCaM and 75 BoCML genes were identified in the B. oleracea genome through a genome-wide search. Phylogenetic analysis categorized these genes, along with their homologs in Arabidopsis and rice, into six distinct groups. All BoCaM/BoCML genes were unevenly distributed across the nine chromosomes of B. oleracea, with 52 of them lacking introns. Collinearity analysis revealed that CaM/CML genes in Arabidopsis are present in multiple copies in the B. oleracea genome. Moreover, the majority of BoCaM/BoCML genes exhibited distinct expression patterns across the different tissues, indicating their role in the growth and development of B. oleracea. A clustering heatmap of BoCaM/BoCML gene expression showed distinct patterns before and four days after Hyaloperonospora parasitica infection, dividing the genes into five groups based on their expression patterns. Notably, BoCML46-2 is significantly downregulated in both susceptible and resistant materials, suggesting that it plays an important role in responding to H. parasitica infection. This study conducted a comprehensive survey of the BoCaM/BoCML gene family in B. oleracea. It could serve as a theoretical foundation for further functional identification and utilization of family members and their role in the interaction between B. oleracea and H. parasitica.

Binding of Pro-Inflammatory Proteins S100A8 or S100A9 to Amyloid-β Peptide Suppresses Its Fibrillation

Human serum albumin (HSA) is a natural depot of amyloid-β peptide (Aβ), a key player in Alzheimer's disease (AD). HSA and pro-inflammatory Ca2+-binding proteins S100A8 and S100A9 are involved in Aβ metabolism and its deposition in the brain, serving as probable triggers and therapeutic targets in AD, but their interplay with regard to Aβ binding/fibrillation is unclear. To this end, here we explore the in vitro binding of Ca2+-bound S100A8 or S100A9 to monomeric Aβ and the influence of the S100 proteins on Aβ fibrillation. The equilibrium dissociation constants of the complexes of dimeric S100A8/S100A9 with Aβ40/42 estimated by biolayer interferometry are 1-5 µM. S100A8 and S100A9 interfere with HSA binding to Aβ. Thioflavin T assay and electron microscopy data show that micromolar S100A8/S100A9 inhibit Aβ40 fibrillation, and the inhibitory effect of S100A8 exceeds that for HSA. The competition for Aβ between HSA and S100A8/S100A9 may contribute to the Aβ-HSA imbalance in the pro-inflammatory conditions in AD.

Tuning the lanthanide binding tags for preferential actinide chelation: an all atom molecular dynamics study

The present study focuses on designing mutant peptides derived from the lanthanide binding tag (LBT) to enhance selectivity for trivalent actinide (An3+) ions over lanthanide (Ln3+) metal ions (M). The LBT is a short peptide consisting of only 17 amino acids, and is known for its high affinity towards Ln3+. LBT was modified by substituting hard-donor ligands like asparagine (ASN or N) and aspartic acid (ASP or D) with softer ligand cysteine (CYS or C) to create four mutant peptides: M-LBT (wild-type), M-N103C, M-D105C, and M-N103C-D105C. All atom molecular dynamics (MD) simulations were employed to analyze the binding dynamics and affinities of these mutants with Eu3+ and Am3+ as representatives for trivalent Ln and An ions, respectively. Hydrogen bond dynamics and short-range Coulomb interactions are evaluated from the equilibrium run for all the systems. The study utilized an enhanced sampling method, namely, well-tempered meta-dynamics (WT-MtD), to overcome sampling challenges and obtain converged free energy profiles for the metal-binding interactions. Our simulations studies indicate that both single and double mutations alter the coordination environment within the peptide's binding pocket, potentially increasing Am3+ selectivity over the Eu3+ ion. The binding of Eu3+ and Am3+ to LBT systems was analyzed, showing an unbinding energy barrier of ∼60 kJ mol-1 for the wild-type. The N103C variant increases the binding strength with a barrier over 100 kJ mol-1, while D105C shows a preference for Am3+ with a barrier around 70 kJ mol-1. The doubly mutated N103C-D105C variant favors Am3+ by more than 20 kJ mol-1. The findings suggest N103C for general chelation and N103C-D105C for preferential trivalent Ln/An separation. These insights contribute to the development of more effective and selective chelating agents for preferential actinide binding.

QM Investigation of Rare Earth Ion Interactions with First Hydration Shell Waters and Protein-Based Coordination Models

Conventional methods for extracting rare earth metals (REMs) from mined mineral ores are inefficient, expensive, and environmentally damaging. Recent discovery of lanmodulin (LanM), a protein that coordinates REMs with high-affinity and selectivity over competing ions, provides inspiration for new REM refinement methods. Here, we used quantum mechanical (QM) methods to investigate trivalent lanthanide cation (Ln3+) interactions with coordination systems representing bulk solvent water and protein binding sites. Energy decomposition analysis (EDA) showed differences in the energetic components of Ln3+ interaction with representatives of solvent (water, H2O) and protein binding sites (acetate, CH3COO-), highlighting the importance of accurate description of electrostatics and polarization in computational modeling of REM interactions with biological and bioinspired molecules. Relative binding free energies were obtained for Ln3+ with coordination complexes originating from binding sites in PDB structures of a lanthanum binding peptide (PDB entry 7CCO) and LanM, with explicit consideration of the first hydration shell waters, according to quasi-chemical theory (QCT). Beyond the first shell, the bulk solvent environment was represented with an implicit continuum model. Ln3+ interactions with (H2O)9 and both binding site models became more favorable, moving down the periodic series. This trend was more pronounced with the protein binding site models than with water, resulting in affinity increasing with periodic number, except for the last REM, Lu3+, which bound less favorably than the preceding element, Yb3+. Using the truncated 7CCO binding site model, the magnitude and trend of the experimental Ln3+ relative binding free energies for the whole 7CCO peptide were reproduced. Conversely, the previously reported experimental data for LanM show a preference for the earlier lanthanides; this is likely due to longer-range interactions and cooperative effects, which are not represented by the reduced models. Using the truncated 7CCO binding site model, the magnitude and trend of the experimental Ln3+ relative binding free energies for the whole 7CCO peptide were reproduced. In contrast to the previously reported experimental data for LanM, the peptide preferentially binds the earlier lanthanides. This difference likely arises due to longer-range interactions and cooperative effects not represented by the peptide. Further investigation of Ln3+ interactions with whole proteins using polarizable molecular mechanics models with explicit solvent is warranted to understand the influence of longer-ranged interactions, cooperativity, and bulk solvent. Nevertheless, the present work provides new insights into Ln3+ interactions with biomolecules and presents an effective computational platform for designing specific single-site REM binding peptides more efficiently.

Comprehensive in-silico characterization and expression pattern of calmodulin genes under various abiotic and biotic stresses in Indian mustard (Brassica juncea)

Calcium (Ca2⁺) as a secondary messenger has a multidimensional role, including the growth and development of plants and the adaptive response to stress conditions. Calmodulin (CaM), a calcium-binding protein, uniquely binds with these Ca2⁺ ions and transmits Ca2⁺ signals. Calmodulin proteins have been well-reported in various plants for playing a role in abiotic and biotic stress signaling; however, a comprehensive analysis of the CaM genes of Indian mustard (Brassica juncea) has not been studied much. This study reports their chromosome placements, phylogenetic relations, the presence of protein motifs and cis-acting elements, and their expression patterns under stress due to salt, heat, cadmium, Xanthomonas campestris, and Alternaria brassicae. We identified 23 BjCaM genes coding for eight BjCaM proteins possessing the signature EF-hand domains. Chromosome locations, intron-exon structure, and in-silico protein characterization pointed toward genetic diversification. Phylogenetic analysis revealed a close relationship with previously characterized CaM proteins from Arabidopsis and rice. Cis-acting elements in the promoter regions suggested the potential role of BjCaM candidates in hormone signaling and various stress-responsive regulatory mechanisms. qRT-PCR analysis showed differential expression patterns, of which BjCaM17 and BjCaM19 showed higher expression under all stresses. The seven selected BjCaM genes were sensitive to cadmium stress. Interestingly, despite translating to same protein, BjCaM15, BjCaM17, and BjCaM19 showed differential expressions under the same stresses. This research represents the first genome-wide analysis of calmodulin genes in Indian mustard, providing a valuable reference for decoding calcium signaling via calmodulin and its potential exploitation to improve crop resistance to stress conditions.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-025-01561-x.

Differential structural characteristics, physicochemical properties, and calcium-binding capabilities of annexin A2 wild-type versus E53A, E96A, D162A, E247A and D322A mutants

Annexin A2 (ANXA2) is a Ca2+-dependent multifunctional protein containing five Ca2+-binding domains, but their functional significance and difference remain unclear. Herein, glutamic acid (E) or aspartic acid (D) in five Ca2+-binding domains of canine ANXA2 (98.82 % and 96.76-99.41 % identical to ANXA2 from human and other mammals, respectively) was substituted by alanine (A) using site-directed mutagenesis. Recombinant ANXA2 wild-type (WT) and E53A, E96A, D162A, E247A and D322A mutants were constructed and expressed using a bacterial expression system followed by high-affinity purification using nickel-nitrilotriacetic acid (Ni-NTA) matrix. Efficacies of their expression and purification were confirmed by SDS-PAGE and Western blotting. Their amino acid sequences were verified by nanoLC-ESI-Qq-TOF tandem mass spectrometry. ATR-FTIR spectroscopy revealed that their secondary structure significantly differed (α-helix decreased but random coil increased in all mutants). Analyses of physicochemical properties revealed that molecular weight slightly decreased, whereas isoelectric point, aliphatic index, grand average of hydropathicity, electrostatic potential and molecular hydrophobicity potential slightly increased in all the mutants compared with WT. Interestingly, Ca2+-binding capability of these mutants (particularly E96A and D322A) significantly decreased from that of WT. In summary, secondary structure, physicochemical properties, and Ca2+-binding capability of E53A, E96A, D162A, E247A and D322A mutants of ANXA2 significantly differed from its WT, consistent with the loss of negatively charged E/D. In particular, E96A and D322A exhibited the lowest Ca2+-binding capability. These data and recombinant proteins would be useful for further investigations of the Ca2+-dependent functions of individual Ca2+-binding domains in ANXA2.

From rock to living systems: Lanthanides toxicity and biological interactions

Since the discovery of lanthanides, the expanding range of applications and the growing demand for lanthanides in different aspects of life have escalated their dispersion in the environment, raising concerns about their impact on the living world. This review explores the interaction between lanthanides and different groups of living organisms (bacteria, algae, lichens, plants, invertebrates, and low vertebrates), reflecting the current state of scientific knowledge. We have aimed to provide a comprehensive overview of relevant studies, highlight existing gaps, and suggest potential areas for future research to enhance the understanding of this topic.

Dynamics of AKAP/Calmodulin complex is largely driven by ionic occupancy state

AKAP79/150 is a scaffold protein found in dendritic spines and other neuronal compartments. It localizes and regulates phosphorylation by protein kinase A and C and is, in turn regulated by Ca2+, mediated by Calmodulin (CaM). Thus, the interaction of AKAP79/150 with CaM is of biological interest. A 2017 study used a peptide cross linking coupled to mass spectrometry (XLMS) to identify the CaM binding site on AKAP79/150 and subsequently solved an X-ray crystallography structure of CaM in complex with a short helical AKAP79/150 peptide. The XRD structure revealed an unusual mixed ionic occupancy state of CaM as bound to the AKAP79/150 peptide. In this molecular dynamics-based study, we have explored the motional modes of the CaM-AKAP helix complex under three ionic occupancy conditions. Our results indicate that the dynamics of this CaM backbone is largely dominated by the ionic occupancy state. We find that binding of the AKAP79/150 peptide to CaM is not preferentially stabilized in energetic terms in the Ca2+ state as compared to apo. However, the Mg2+ state is destabilized energetically as compared to the apo state. In addition, in the Ca2+ state, the AKAP79/150 peptide appears to be preferentially stabilized by additional hydrogen bonds. Our simulations suggest that further structural biology studies should be carried out, with a focus on driving the system equilibrium to full Ca2+ occupancy. NMR studies may be able to capture conformational states which are not seen in crystals.

Comparative studies of seafood and reptile α- and β-parvalbumins

Small calcium-binding proteins such as parvalbumins (PVs) are major seafood and fish allergens. However, the impact of structural changes on their capacity to bind IgE has not been studied in detail. Therefore, fish and reptilian PVs, as well as human α-PV, were selected for biochemical, structural, and IgE binding studies. Likely due to their high solubility, crystallization proved difficult, so additional techniques were used to promote crystallization of the proteins. Novel crystal structures were determined for human PV, cod allergen Gad m 1.0201, saltwater crocodile allergen Cro p 1.0101, and the α-PV from thornback ray. β-PVs are considered the major fish allergens, while α-PVs are rarely categorized as allergens. To explain these differences, the results of structural and IgE binding studies were combined. This approach allowed us to provide new insight into IgE binding epitopes present on PVs, focusing on cross-reactivity among the selected α- and β-PVs. In addition, we have shown that these proteins display remarkable thermal stability across a range of pH conditions, which is relevant in the case of food allergens and food processing. Moreover, it is shown that the presence of calcium cations is critical for stability of the studied PVs via their protein folding, which has an impact on the formation of IgE binding epitopes. These studies shows the stability of fish and reptile PV allergens, and it allows for further evaluation of their IgE cross-reactivity.

Homology-based identification and structural analysis of Pangasius hypophthalmus Annexins and Serine proteases to search molecules for wound healing applications

Chronic wounds and burns are a worldwide healthcare problem that erodes patients' well-being and healthcare systems. This silent and costly epidemic requires new, cost-efficient solutions to improve patients' physical and economic welfare. Eschar-degrading vegetal and bacterial proteases have been utilized as a solution. However, these proteins are evolutionarily far from those present in human wound healing. Serine protease (SP) and annexin (ANX) proteins interact within the skin healing process. A homology-based identification pipeline can help in discovering selective human SP and ANX analogs in the epithelial tissue of the fast-healing species, Pangasius hypophthalmus. In the present work, we found 14 candidates for RT-PCR in P. hypophthalmus using homology inference. The genetically detected candidates were then structurally and sequentially analyzed to understand their possible relation to SPs and ANXs involved in human wound healing. A total of six TBLASTN/BLASTX candidates (four SPs and two ANXs) were detected in P. hypophthalmus skin. Structural analysis revealed that all SP candidates resembled human KLK4, KLK5, KLK6, and KLK8, whereas all ANX only resembled human ANXA4. Structure and sequence analysis revealed high conservation of ANX Ca2+ binding sites (GDXD) and SP catalytic triad (HDS) motifs. In addition, structural analysis revealed that SP substrate selectivity position 186 was the main difference between human KLK5 and P. hypophthalmus SPs. These findings may allow the proposal and testing of more selective formulations, broadening treatments beyond debridement.

Synergistic effects of putative Ca2+-binding sites of calmodulin in fungal development, temperature stress and virulence of Aspergillus fumigatus

In pathogenic fungi, calcium-calmodulin-dependent serine-threonine-specific phosphatase calcineurin is involved in morphogenesis and virulence. Therefore, calcineurin and its tightly related protein complexes are attractive antifungal drug targets. However, there is limited knowledge available on the relationship between in vivo Ca2+-binding sites of calmodulin (CaM) and its functions in regulating stress responses, morphogenesis, and pathogenesis. In the current study, we demonstrated that calmodulin is required for hyphal growth, conidiation, and virulence in the human fungal pathogen, Aspergillus fumigatus. Site-directed mutations of calmodulin revealed that a single Ca2+-binding site mutation had no significant effect on A. fumigatus hyphal development, but multiple Ca2+-binding site mutations exhibited synergistic effects, especially when cultured at 42 °C, indicating that calmodulin function in response to temperature stress depends on its Ca2+-binding sites. Western blotting implied that mutations in Ca2+-binding sites caused highly degraded calmodulin fragments, suggesting that the loss of Ca2+-binding sites results in reduced protein stability. Moreover, normal intracellular calcium homeostasis and the nuclear translocation of the transcriptional factor CrzA are dependent on Ca2+-binding sites of AfCaM, demonstrating that Ca2+-binding sites of calmodulin are required for calcium signalling and its major transcription factor CrzA. Importantly, in situ mutations for four Ca2+-binding sites of calmodulin resulted in an almost complete loss of virulence in the Galleria mellonella wax moth model. This study shed more light on the functional characterization of putative calcium-binding sites of calmodulin in the morphogenesis and virulence of A. fumigatus, which enhances our understanding of calmodulin biological functions in cells of opportunistic fungal pathogens.

EPHB4-RASA1 Inhibition of PIEZO1 Ras Activation Drives Lymphatic Valvulogenesis

BACKGROUND

EPHB4 (ephrin receptor B4) and the RASA1 (p120 Ras GTPase-activating protein) are necessary for the development of lymphatic vessel (LV) valves. However, precisely how EPHB4 and RASA1 regulate LV valve development is unknown. In this study, we examine the mechanisms by which EPHB4 and RASA1 regulate the development of LV valves.

METHODS

We used LV-specific inducible EPHB4-deficient mice and EPHB4 knockin mice that express a form of EPHB4 that is unable to bind RASA1 yet retains protein tyrosine kinase activity (EPHB4 2YP) to study the role of EPHB4 and RASA1 in LV valve development in the embryo and LV valve maintenance in adults. We also used human dermal lymphatic endothelial cells in vitro to study the role of EPHB4 and RASA1 as regulators of LV valve specification induced by oscillatory shear stress, considered the trigger for LV valve specification in vivo.

RESULTS

LV valve specification, continued valve development postspecification, and LV valve maintenance were blocked upon induced loss of EPHB4 in LV. LV valve specification and maintenance were also impaired in EPHB4 2YP mice. Defects in LV valve development were reversed by inhibition of the Ras-MAPK (mitogen-activated protein kinase) signaling pathway. In human dermal lymphatic endothelial cells, loss of expression of EPHB4 or its ephrin b2 ligand, loss of expression of RASA1, and inhibition of physical interaction between EPHB4 and RASA1 resulted in dysregulated oscillatory shear stress-induced Ras-MAPK activation and impaired expression of LV specification markers that could be rescued by Ras-MAPK pathway inhibition. The same results were observed when human dermal lymphatic endothelial cells were stimulated with the Yoda1 agonist of the PIEZO1 oscillatory shear stress sensor. Although Yoda1 increased the number of LV valves when administered to wild-type embryos, it did not increase LV valve number when administered to EPHB4 2YP embryos.

CONCLUSIONS

EPHB4 is necessary for LV valve specification, continued valve development postspecification, and valve maintenance. LV valve specification requires physical interaction between EPHB4 and RASA1 to limit activation of the Ras-MAPK pathway in lymphatic endothelial cells. Specifically, EPHB4-RASA1 physical interaction is necessary to dampen Ras-MAPK activation induced through the PIEZO1 oscillatory shear stress sensor. These findings reveal the mechanism by which EPHB4 and RASA1 regulate the development of LV valves.

An AI-informed NMR structure reveals an extraordinary LETM1 F-EF-hand domain that functions as a two-way regulator of mitochondrial calcium

AlphaFold can accurately predict static protein structures but does not account for solvent conditions. Human leucine zipper EF-hand transmembrane protein-1 (LETM1) has one sequence-identifiable EF-hand but how calcium (Ca2+) affects structure and function remains enigmatic. Here, we used highly confident AlphaFold Cα predictions to guide nuclear Overhauser effect (NOE) assignments and structure calculation of the LETM1 EF-hand in the presence of Ca2+. The resultant NMR structure exposes pairing between a partial loop-helix and full helix-loop-helix, forming an unprecedented F-EF-hand with non-canonical Ca2+ coordination but enhanced hydrophobicity for protein interactions compared to calmodulin. The structure also reveals the basis for pH sensing at the link between canonical and partial EF-hands. Functionally, mutations that augmented or weakened Ca2+ binding increased or decreased matrix Ca2+, respectively, establishing F-EF as a two-way mitochondrial Ca2+ regulator. Thus, we show how to synergize AI prediction with NMR data, elucidating a solution-specific and extraordinary LETM1 F-EF-hand.

Can Physicochemical Properties Alter the Potency of Aeroallergens? Part 1 - Aeroallergen Protein Families

PURPOSE OF REVIEW

Respiratory allergies are non-communicable diseases caused by the hypersensitivity of the immune system to environmental aeroallergens. The culprits are aero-transported proteins eliciting respiratory symptoms in sensitized/allergic individuals. This review intends to provide a holistic overview on the categorization of aeroallergens into protein families (Part 1) and to exploit the impact of physicochemical properties on inhalant protein allergenicity (Part 2). This first part will focus particularly on aeroallergen organization into families and how this classification fits their physicochemical properties.

RECENT FINDINGS

Aeroallergen classification into protein families facilitates the identification of common physicochemical properties, thus aiding a better comprehension of known allergens, while predicting the behavior of novel ones. The available online databases gathering important features of aeroallergens are currently scarce. Information on distinct aeroallergen classification is still lacking, as data is dispersed and often outdated, hampering an efficient evaluation of new aeroallergens.

Cooperative folding as a molecular switch in an evolved antibody binder

Designing proteins with tunable activities from easily accessible external cues remains a biotechnological challenge. Here, we set out to create a small antibody-binding domain equipped with a molecular switch inspired by the allosteric response to calcium seen in naturally derived proteins like calmodulin. We have focused on one of the three domains of Protein G that show inherent affinity to antibodies. By combining a semi-rational protein design with directed evolution, we engineered novel variants containing a calcium-binding loop rendering the inherent antibody affinity calcium-dependent. The evolved variants resulted from a designed selection strategy subjecting them to negative and positive selection pressures focused on conditional antibody binding. Hence, these variants contains molecular "on/off" switches, controlling the target affinity towards antibody fragments simply by the presence or absence of calcium. From NMR spectroscopy we found that the molecular mechanism underlying the evolved switching behavior was a coupled calcium-binding and folding event where the target binding surface was intact and functional only in the presence of bound calcium. Notably, it was observed that the response to the employed selection pressures gave rise to the evolution of a cooperative folding mechanism. This observation illustrates why the cooperative folding reaction is an effective solution seen repeatedly in the natural evolution of fine-tuned macromolecular recognition. Engineering binding moieties to confer conditional target interaction has great potential due to the exquisite interaction control that is tunable to application requirements. Improved understanding of the molecular mechanisms behind regulated interactions is crucial to unlock how to engineer switchable proteins useful in a variety of biotechnological applications.

Defining physicochemical properties of urinary proteins that determine their inhibitory activities against calcium oxalate kidney stone formation

We have recently reported a set of urinary proteins that inhibited calcium oxalate (CaOx) stone development. However, physicochemical properties that determine their inhibitory activities remained unknown. Herein, human urinary proteins were chromatographically fractionated into 15 fractions and subjected to various CaOx crystal assays and identification by nanoLC-ESI-Qq-TOF MS/MS. Their physicochemical properties and crystal inhibitory activities were subjected to Pearson correlation analysis. The data showed that almost all urinary protein fractions had crystal inhibitory activities. Up to 128 proteins were identified from each fraction. Crystallization inhibitory activity correlated with percentages of Ca2+-binding proteins, stable proteins, polar amino acids, alpha helix, beta turn, and random coil, but inversely correlated with number of Ox2--binding motifs/protein and percentage of unstable proteins. Crystal aggregation inhibitory activity correlated with percentage of stable proteins but inversely correlated with percentage of unstable proteins. Crystal adhesion inhibitory activity correlated with percentage of stable proteins and GRAVY, but inversely correlated with pI, instability index and percentages of unstable proteins and positively charged amino acids. However, there was no correlation between crystal growth inhibitory activity and any physicochemical properties. In summary, some physicochemical properties of urinary proteins can determine and may be able to predict their CaOx stone inhibitory activities.

Role of Calcium in an Experimental Breast Cancer Model Induced by Radiation and Estrogen

Background: Breast cancer, a global health challenge, significantly impacts women worldwide, causing morbidity, disability, and mortality. Objectives: To analyze the role of genes encoding S100 calcium-binding proteins and their relationship with radiation as possible markers in breast carcinogenesis. Methods: The normal MCF-10F cell line was used to study the role of ionizing radiation and estrogen to induce distinct stages of malignancy giving rise to an in vitro experimental breast cancer model. Results: Analysis of an Affymetrix system revealed that the gene expression levels of the S100 calcium-binding protein P (S100P), the S100 calcium-binding protein A14 (S100A14), and the S100 calcium-binding protein A2 (S100A2) were greater in the Tumor2 than the non-tumorigenic Alpha3 or the tumorigenic Alpha5 cell lines; however, the S100 calcium-binding protein A8 (S100A8) and the S100 calcium-binding protein A9 (S100A9) expression levels were higher in A5 than T2 and A3 cell lines. A significant positive association was found between the estrogen receptor alpha gene (ESR1) and S100A14 in Basal and Her2 patients. The association between ESR1 and S100A8 and S100A9 expression levels was positive in Basal patients but negative in Her2, Luminal A, and Luminal B. S100P and S100A14 expression levels were higher in tumor tissues than in normal ones. The estrogen receptor status was positive in patients with high levels of the S10014 gene, but negative in S100A2, S100A8, and S100A9 expression levels. Conclusion: Cell dependence needs to be considered while designing new breast cancer treatments since gene signatures might vary depending on the type of tumor.

Genome-wide identification of CAMTA genes and their expression dependence on light and calcium signaling during seedling growth and development in mung bean

BACKGROUND

Calmodulin-binding transcription activator (CAMTA) is comprised of a group of transcription factors and plays an important role in the Ca2+ signaling pathway, mediating various molecular responses via interactions with other transcription factors and binding to the promoter region of specific genes. Mung beans (Vigna radiata) are one of the most commonly consumed commodities in Asia. To date, CAMTA proteins have not been characterized in this important crop plant.

RESULTS

Eight paralogous VrCAMTA genes were identified and found to be distributed on five of the 11 chromosomes. The proteins possessed CG-1 DNA-binding domains with bipartite NLS signals, ankyrin domains, CaM-binding IQ motifs, and CaM-binding domain (CaMBD). The 2 kb upstream regions of VrCAMTA genes contained sequence motifs of abscisic acid-responsive elements (ABRE) and ethylene-responsive elements (ERE), and binding sites for transcription factors of the bZIP and bHLH domains. Analysis of RNA-seq data from a public repository revealed ubiquitous expression of the VrCAMTA genes, as VrCAMTA1 was expressed at the highest level in seedling leaves, whereas VrCAMTA8 was expressed at the lowest level, which agreed with the RT-qPCR analysis performed on the first true leaves. On day four after leaf emergence, all VrCAMTA genes were upregulated, with VrCAMTA1 exhibiting the highest degree of upregulation. In darkness on day 4, upregulation was not observed in most VrCAMTA genes, except VrCAMTA7, for which a low degree of upregulation was found, whereas no difference was found in VrCAMTA8 expression between light and dark conditions. Treatment with calcium ionophores enhanced VrCAMTA expression under light and/or dark conditions at different times after leaf emergence, suggesting that calcium signaling is involved in the light-induced upregulation of VrCAMTA gene expression.

CONCLUSIONS

The expression dependence of nearly all VrCAMTA genes on light and calcium signaling suggests their possible differential but likely complementary roles during the early stages of mung bean growth and development.

A Deep Dive into the N-Terminus of STIM Proteins: Structure-Function Analysis and Evolutionary Significance of the Functional Domains

Calcium is an important second messenger that is involved in almost all cellular processes. Disruptions in the regulation of intracellular Ca2+ levels ([Ca2+]i) adversely impact normal physiological function and can contribute to various diseased conditions. STIM and Orai proteins play important roles in maintaining [Ca2+]i through store-operated Ca2+ entry (SOCE), with STIM being the primary regulatory protein that governs the function of Orai channels. STIM1 and STIM2 are single-pass ER-transmembrane proteins with their N- and C-termini located in the ER lumen and cytoplasm, respectively. The N-terminal EF-SAM domain of STIMs senses [Ca2+]ER changes, while the C-terminus mediates clustering in ER-PM junctions and gating of Orai1. ER-Ca2+ store depletion triggers activation of the STIM proteins, which involves their multimerization and clustering in ER-PM junctions, where they recruit and activate Orai1 channels. In this review, we will discuss the structure, organization, and function of EF-hand motifs and the SAM domain of STIM proteins in relation to those of other eukaryotic proteins.

Genome-wide identification of Rosa roxburghii CML family genes identifies an RrCML13-RrGGP2 interaction involved in calcium-mediated regulation of ascorbate biosynthesis

Calmodulin-like proteins (CMLs) are an essential family of calcium sensors involved in multiple Ca2+-mediated cellular processes in plants. Rosa roxburghii Tratt, known for the abundance of L-ascorbic acid (AsA) in its fruits, is widely distributed in calcium-rich soil of the karst region in southwestern China. The aim of this study was to identify key CMLs that respond to exogenous Ca2+ levels and regulate AsA biosynthesis in R. roxburghii. A genome-wide scan revealed the presence of 41 RrCML genes with 1-4 EF-hand motif (s) unevenly distributed across the 7 chromosomes of R. roxburghii. qRT-PCR analysis revealed that RrCML13, RrCML10, and RrCML36 responded significantly to exogenous Ca2+ treatment, and RrCML13 was positively correlated with GDP-L-galactose phosphorylase encoding gene (RrGGP2) expression and AsA content in the developing fruit. Overexpression of RrCML13 in fruits and roots significantly promoted the transcription of RrGGP2 and the accumulation of AsA, while virus-induced silencing of RrCML13 reduced the transcription of RrGGP2 and the content of AsA. Furthermore, Moreover, the yeast two-hybrid and bimolecular fluorescence complementation (BiFC) analysis confirmed the interaction between RrCML13 and RrGGP2 proteins, indicating that RrCML13 plays a regulatory role in calcium-mediated AsA biosynthesis. This study enhances our understanding of R. roxburghii CMLs and sheds light on the calcium-mediated regulation of AsA biosynthesis.

Ca2+ binding shifts dimeric dual oxidase's truncated EF-hand domain to monomer

Hydrogen peroxide, produced by Dual Oxidase (Duox), is essential for thyroid hormone synthesis. Duox activation involves Ca2+ binding to its EF-hand Domain (EFD), which contains two EF-hands (EFs). In this study, we characterized a truncated EFD using spectrometry, calorimetry, electrophoretic mobility, and gel filtration to obtain its Ca2+ binding thermodynamic and kinetics, as well as to assess the associated conformational changes. Our results revealed that its 2nd EF-hand (EF2) exhibits a strong exothermic Ca2+ binding (Ka = 107 M-1) while EF1 shows a weaker binding (Ka = 105 M-1), resulting in the burial of its negatively charged residues. The Ca2+ binding to EFD results in a stable structure with a melting temperature shifting from 67 to 99 °C and induces a structural transition from a dimeric to monomeric form. EF2 appears to play a role in dimer formation in its apo form, while the hydrophobic exposure of Ca2+-bound-EF1 is crucial for dimer formation in its holo form. The result is consistent with structures obtained from Cryo-EM, indicating that a stable structure of EFD with hydrophobic patches upon Ca2+ binding is vital for its Duox's domain-domain interaction for electron transfer.

Comparative Physiological and Transcriptomic Analyses of Oat (Avena sativa) Seedlings under Salt Stress Reveal Salt Tolerance Mechanisms

Soil salinity is a major abiotic stress limiting crop production globally. Oat (Avena sativa) is an annual cereal with a strong salt tolerance, a high yield, and nutritional quality, although the mechanisms underlying its salt stress response remain largely unknown. We examined the physiological and transcriptomic responses of A. sativa seedlings to salt stress in tolerant cultivar Qingyongjiu 195 and sensitive cultivar 709. Under salt stress, Qingyongjiu 195 maintained a higher photosynthetic efficiency, antioxidant enzymes activity, and leaf K+ accumulation but a lower Na+ uptake than 709. RNA-seq revealed 6616 differentially expressed genes (DEGs), including 4265 up- and 2351 downregulated. These were enriched in pathways like plant-pathogen interaction, phenylpropanoid biosynthesis, and MAPK signaling. We specifically highlight DEGs involved in photosynthesis (chlG, CP47 psbB, COX2, LHCB) and antioxidants (trxA, GroES). Qingyongjiu 195 also appeared to enhance K+ uptake via KAT1 and AKT2 and sequester Na+ in vacuoles via NHX2. Additionally, HKT restricted Na+ while promoting K+ transport to shoots, maintaining K+/Na+. The expression levels of CAX, ACA, CML, CaM, and CDPK in Qingyongjiu 195 were higher than those in 709. Oats regulated Ca2+ concentration through CAX and ACA after salt stress, decoded Ca2+ signals through CML, and then transferred Ca2+ signals to downstream receptors through the Ca2+ sensors CaM and CDPK, thereby activating K+/Na+ transporters, such as SOS1 and NHX, etc. Our results shed light on plant salt stress response mechanisms and provide transcriptomic resources for molecular breeding in improving salt tolerance in oats.

Lanmodulin's EF 2-3 Domain: Insights from Infrared Spectroscopy and Simulations

Lanmodulins are small, ∼110-residue proteins with four EF-hand motifs that demonstrate a picomolar affinity for lanthanide ions, making them efficient in the recovery and separation of these technologically important metals. In this study, we examine the thermodynamic and structural complexities of lanthanide ion binding to a 41-residue domain, EF 2-3, that constitutes the two highest-affinity metal-binding sites in the lanmodulin protein from Methylorubrum extorquens. Using a combination of circular dichroism (CD) spectroscopy, isothermal titration calorimetry (ITC), two-dimensional infrared (2D IR) spectroscopy, and molecular dynamics (MD) simulations, we characterize the metal binding capabilities of EF 2-3. ITC demonstrates that binding occurs between peptide and lanthanides with conditional dissociation constants (Kd) in the range 20-30 μM, with no significant differences in the Kd values for La3+, Eu3+, and Tb3+ at pH 7.4. In addition, CD spectroscopy suggests that only one binding site of EF 2-3 undergoes a significant conformational change in the presence of lanthanides. 2D IR spectroscopy demonstrates the presence of both mono- and bidentate binding configurations in EF 2-3 with all three lanthanides. MD simulations, supported by Eu3+ luminescence measurements, explore these results, suggesting a competition between water-lanthanide and carboxylate-lanthanide interactions in the EF 2-3 domain. These results underscore the role of the core helical bundle of the protein architecture in influencing binding affinities and communication between the metal-binding sites in the full-length protein.

Genome-Wide Identification of Members of the Soybean CBL Gene Family and Characterization of the Functional Role of GmCBL1 in Responses to Saline and Alkaline Stress

Calcium ions function as key messengers in the context of intracellular signal transduction. The ability of plants to respond to biotic and abiotic stressors is highly dependent on the calcineurin B-like protein (CBL) and CBL-interacting protein kinase (CIPK) signaling network. Here, a comprehensive effort was made to identify all members of the soybean CBL gene family, leading to the identification of 15 total genes distributed randomly across nine chromosomes, including 13 segmental duplicates. All the GmCBL gene subfamilies presented with similar gene structures and conserved motifs. Analyses of the expression of these genes in different tissues revealed that the majority of these GmCBLs were predominantly expressed in the roots. Significant GmCBL expression and activity increases were also observed in response to a range of stress-related treatments, including salt stress, alkaline stress, osmotic stress, or exposure to salicylic acid, brassinosteroids, or abscisic acid. Striking increases in GmCBL1 expression were observed in response to alkaline and salt stress. Subsequent analyses revealed that GmCBL1 was capable of enhancing soybean salt and alkali tolerance through the regulation of redox reactions. These results offer new insight into the complex mechanisms through which the soybean CBL gene family regulates the responses of these plants to environmental stressors, highlighting promising targets for efforts aimed at enhancing soybean stress tolerance.

PVALB Was Identified as an Independent Prognostic Factor for HCC Closely Related to Immunity, and Its Absence Accelerates Tumor Progression by Regulating NK Cell Infiltration

Purpose

Hepatocellular carcinoma is the most common primary liver cancer, with poor prognosis. Complex immune microenvironment of the liver is linked to the development of HCC. PVALB is a calcium-binding protein which has been described as a cancer suppressor gene in thyroid cancer and glioma. Nevertheless, the role of PVALB in HCC is unknown.

Materials and Methods

We obtained data from TCGA and GSE54236 datasets. MCP-counter, WGCNA and LASSO model were applied to identify PVALB. With UALCAN, MethSurv, and other websites, we probed the expression, methylation and survival of PVALB. LinkedOmics and GSEA were adopted for functional analysis, while TIMER, TISIDB, Kaplan-Meier plotter, TIDE databases were utilized to evaluate the relevance of PVALB to the tumor immune microenvironment and predict immunotherapy efficacy. TargetScan, DIANA, LncRNASNP2 databases and relevant experiments were employed to construct ceRNA network. Finally, molecular docking and drug sensitivity of PVALB were characterized by GeneMANIA, CTD, and so on.

Results

PVALB was recognized as a gene associated with HCC and NK cell. Its expression was down-regulated in HCC tissue, which lead to adverse prognosis. Besides, the hypomethylation of PVALB was related to its reduced expression. Notably, PVALB was tightly linked to immune, and its reduced expression attenuated the anticancer effect of NK cells via the Fas/FasL pathway, leading to a adverse outcome. The lnc-YY1AP1-3/hsa-miR-6735-5p/PVALB axis may regulate the PVALB expression. Finally, we found immunotherapy might be a viable treatment option.

Conclusion

In a word, PVALB is a prognostic indicator, whose low expression facilitates HCC progression by impacting NK cell infiltration.

Functional characterization of calmodulin-like proteins, CML13 and CML14, as novel light chains of Arabidopsis class VIII myosins

Myosins are important motor proteins that associate with the actin cytoskeleton. Structurally, myosins function as heteromeric complexes where smaller light chains, such as calmodulin (CaM), bind to isoleucine-glutamine (IQ) domains in the neck region to facilitate mechano-enzymatic activity. We recently identified Arabidopsis CaM-like (CML) proteins CML13 and CML14 as interactors of proteins containing multiple IQ domains, including a myosin VIII. Here, we demonstrate that CaM, CML13, and CML14 bind the neck region of all four Arabidopsis myosin VIII isoforms. Among CMLs tested for binding to myosins VIIIs, CaM, CML13, and CML14 gave the strongest signals using in planta split-luciferase protein interaction assays. In vitro, recombinant CaM, CML13, and CML14 showed specific, high-affinity, calcium-independent binding to the IQ domains of myosin VIIIs. CaM, CML13, and CML14 co-localized to plasma membrane-bound puncta when co-expressed with red fluorescent protein-myosin fusion proteins containing IQ and tail domains of myosin VIIIs. In vitro actin motility assays using recombinant myosin VIIIs demonstrated that CaM, CML13, and CML14 function as light chains. Suppression of CML13 or CML14 expression using RNA silencing resulted in a shortened-hypocotyl phenotype, similar to that observed in a quadruple myosin mutant, myosin viii4KO. Collectively, our data indicate that Arabidopsis CML13 and CML14 are novel myosin VIII light chains.

Back in time to the Gly-rich prototype of the phosphate binding elementary function

Binding of nucleotides and their derivatives is one of the most ancient elementary functions dating back to the Origin of Life. We review here the works considering one of the key elements in binding of (di)nucleotide-containing ligands - phosphate binding. We start from a brief discussion of major participants, conditions, and events in prebiotic evolution that resulted in the Origin of Life. Tracing back to the basic functions, including metal and phosphate binding, and, potentially, formation of primitive protein-protein interactions, we focus here on the phosphate binding. Critically assessing works on the structural, functional, and evolutionary aspects of phosphate binding, we perform a simple computational experiment reconstructing its most ancient and generic sequence prototype. The profiles of the phosphate binding signatures have been derived in form of position-specific scoring matrices (PSSMs), their peculiarities depending on the type of the ligands have been analyzed, and evolutionary connections between them have been delineated. Then, the apparent prototype that gave rise to all relevant phosphate-binding signatures had also been reconstructed. We show that two major signatures of the phosphate binding that discriminate between the binding of dinucleotide- and nucleotide-containing ligands are GxGxxG and GxxGxG, respectively. It appears that the signature archetypal for dinucleotide-containing ligands is more generic, and it can frequently bind phosphate groups in nucleotide-containing ligands as well. The reconstructed prototype's key signature GxGGxG underlies the role of glycine residues in providing flexibility and interactions necessary for binding the phosphate groups. The prototype also contains other ancient amino acids, valine, and alanine, showing versatility towards evolutionary design and functional diversification.

LanTERN: A Fluorescent Sensor That Specifically Responds to Lanthanides

Lanthanides, a series of 15 f-block elements, are crucial in modern technology, and their purification by conventional chemical means comes at a significant environmental cost. Synthetic biology offers promising solutions. However, progress in developing synthetic biology approaches is bottlenecked because it is challenging to measure lanthanide binding with current biochemical tools. Here we introduce LanTERN, a lanthanide-responsive fluorescent protein. LanTERN was designed based on GCaMP, a genetically encoded calcium indicator that couples the ion binding of four EF hand motifs to increased GFP fluorescence. We engineered eight mutations across the parent construct's four EF hand motifs to switch specificity from calcium to lanthanides. The resulting protein, LanTERN, directly converts the binding of 10 measured lanthanides to 14-fold or greater increased fluorescence. LanTERN development opens new avenues for creating improved lanthanide-binding proteins and biosensing systems.

Exploring the multifaceted role of RASGRP1 in disease: immune, neural, metabolic, and oncogenic perspectives

RAS guanyl releasing protein 1 (RASGRP1) is a guanine nucleotide exchange factor (GEF) characterized by the presence of a RAS superfamily GEF domain. It functions as a diacylglycerol (DAG)-regulated nucleotide exchange factor, specifically activating RAS through the exchange of bound GDP for GTP. Activation of RAS by RASGRP1 has a wide range of downstream effects at the cellular level. Thus, it is not surprising that many diseases are associated with RASGRP1 disorders. Here, we present an overview of the structure and function of RASGRP1, its crucial role in the development, expression, and regulation of immune cells, and its involvement in various signaling pathways. This review comprehensively explores the relationship between RASGRP1 and various diseases, elucidates the underlying molecular mechanisms of RASGRP1 in each disease, and identifies potential therapeutic targets. This study provides novel insights into the role of RASGRP1 in insulin secretion and highlights its potential as a therapeutic target for diabetes. The limitations and challenges associated with studying RASGRP1 in disease are also discussed.

Genome-wide analysis of the peanut CaM/CML gene family reveals that the AhCML69 gene is associated with resistance to Ralstonia solanacearum

BACKGROUND

Calmodulins (CaMs)/CaM-like proteins (CMLs) are crucial Ca2+-binding sensors that can decode and transduce Ca2+ signals during plant development and in response to various stimuli. The CaM/CML gene family has been characterized in many plant species, but this family has not yet been characterized and analyzed in peanut, especially for its functions in response to Ralstonia solanacearum. In this study, we performed a genome-wide analysis to analyze the CaM/CML genes and their functions in resistance to R. solanacearum.

RESULTS

Here, 67, 72, and 214 CaM/CML genes were identified from Arachis duranensis, Arachis ipaensis, and Arachis hypogaea, respectively. The genes were divided into nine subgroups (Groups I-IX) with relatively conserved exon‒intron structures and motif compositions. Gene duplication, which included whole-genome duplication, tandem repeats, scattered repeats, and unconnected repeats, produced approximately 81 pairs of homologous genes in the AhCaM/CML gene family. Allopolyploidization was the main reason for the greater number of AhCaM/CML members. The nonsynonymous (Ka) versus synonymous (Ks) substitution rates (less than 1.0) suggested that all homologous pairs underwent intensive purifying selection pressure during evolution. AhCML69 was constitutively expressed in different tissues of peanut plants and was involved in the response to R. solanacearum infection. The AhCML69 protein was localized in the cytoplasm and nucleus. Transient overexpression of AhCML69 in tobacco leaves increased resistance to R. solanacearum infection and induced the expression of defense-related genes, suggesting that AhCML69 is a positive regulator of disease resistance.

CONCLUSIONS

This study provides the first comprehensive analysis of the AhCaM/CML gene family and potential genetic resources for the molecular design and breeding of peanut bacterial wilt resistance.

Bioseparation of rare earth elements and high value-added biomaterials applications

Rare earth elements (REEs) are a group of critical minerals and extensively employed in new material manufacturing. However, separation of lanthanides is difficult because of their similar chemical natures. Current lanthanide leaching and separation methods require hazardous compounds, resulting in severe environmental concerns. Bioprocessing of lanthanides offers an emerging class of tools for REE separation due to mild leaching conditions and highly selective separation scenarios. In the course of biopreparation, engineered microbes not only dissolve REEs from ores but also allow for selective separation of the lanthanides. In this review, we present an overview of recent advances in microbes and proteins used for the biomanufacturing of lanthanides and discuss high value-added applications of REE-derived biomaterials. We begin by introducing the fundamental interactions between natural microbes and REEs. Then we discuss the rational design of chassis microbes for bioleaching and biosorption. We also highlight the investigations on REE binding proteins and their applications in the synthesis of high value-added biomaterials. Finally, future opportunities and challenges for the development of next generation lanthanide-binding biological systems are discussed.

Calcium homeostasis and signaling in plant immunity

Calcium (Ca2+) signaling consists of three steps: (1) initiation of a change in cellular Ca2+ concentration in response to a stimulus, (2) recognition of the change through direct binding of Ca2+ by its sensors, (3) transduction of the signal to elicit downstream responses. Recent studies have uncovered a central role for Ca2+ signaling in both layers of immune responses initiated by plasma membrane (PM) and intracellular receptors, respectively. These advances in our understanding are attributed to several lines of research, including invention of genetically-encoded Ca2+ reporters for the recording of intracellular Ca2+ signals, identification of Ca2+ channels and their gating mechanisms, and functional analysis of Ca2+ binding proteins (Ca2+ sensors). This review analyzes the recent literature that illustrates the importance of Ca2+ homeostasis and signaling in plant innate immunity, featuring intricate Ca2+dependent positive and negative regulations.

Imaging of plant calcium-sensor kinase conformation monitors real time calcium-dependent decoding in planta

Changes in cytosolic calcium (Ca2+) concentration are among the earliest reactions to a multitude of stress cues. While a plethora of Ca2+-permeable channels may generate distinct Ca2+ signatures and contribute to response specificities, the mechanisms by which Ca2+ signatures are decoded are poorly understood. Here, we developed a genetically encoded Förster resonance energy transfer (FRET)-based reporter that visualizes the conformational changes in Ca2+-dependent protein kinases (CDPKs/CPKs). We focused on two CDPKs with distinct Ca2+-sensitivities, highly Ca2+-sensitive Arabidopsis (Arabidopsis thaliana) AtCPK21 and rather Ca2+-insensitive AtCPK23, to report conformational changes accompanying kinase activation. In tobacco (Nicotiana tabacum) pollen tubes, which naturally display coordinated spatial and temporal Ca2+ fluctuations, CPK21-FRET, but not CPK23-FRET, reported oscillatory emission ratio changes mirroring cytosolic Ca2+ changes, pointing to the isoform-specific Ca2+-sensitivity and reversibility of the conformational change. In Arabidopsis guard cells, CPK21-FRET-monitored conformational dynamics suggest that CPK21 serves as a decoder of signal-specific Ca2+ signatures in response to abscisic acid and the flagellin peptide flg22. Based on these data, CDPK-FRET is a powerful approach for tackling real-time live-cell Ca2+ decoding in a multitude of plant developmental and stress responses.

Recognition of Aedes aegypti Mosquito Saliva Protein LTRIN by the Human Receptor LTβR for Controlling the Immune Response

Salivary proteins from mosquitoes have received significant attention lately due to their potential to develop therapeutic treatments or vaccines for mosquito-borne diseases. Here, we report the characterization of LTRIN (lymphotoxin beta receptor inhibitor), a salivary protein known to enhance the pathogenicity of ZIKV by interrupting the LTβR-initiated NF-κB signaling pathway and, therefore, diminish the immune responses. We demonstrated that the truncated C-terminal LTRIN (ΔLTRIN) is a dimeric protein with a stable alpha helix-dominant secondary structure, which possibly aids in withstanding the temperature fluctuations during blood-feeding events. ΔLTRIN possesses two Ca2+ binding EF-hand domains, with the second EF-hand motif playing a more significant role in interacting with LTβR. Additionally, we mapped the primary binding regions of ΔLTRIN on LTβR using hydrogen-deuterium exchange mass spectrometry (HDX-MS) and identified that 91QEKAHIAEHMDVPIDTSKMSEQELQFHY118 from the N-terminal of ΔLTRIN is the major interacting region. Together, our studies provide insight into the recognition of LTRIN by LTβR. This finding may aid in a future therapeutic and transmission-blocking vaccine development against ZIKV.

Calcium Signaling and the Response to Heat Shock in Crop Plants

Climate change and the increasing frequency of high temperature (HT) events are significant threats to global crop yields. To address this, a comprehensive understanding of how plants respond to heat shock (HS) is essential. Signaling pathways involving calcium (Ca2+), a versatile second messenger in plants, encode information through temporal and spatial variations in ion concentration. Ca2+ is detected by Ca2+-sensing effectors, including channels and binding proteins, which trigger specific cellular responses. At elevated temperatures, the cytosolic concentration of Ca2+ in plant cells increases rapidly, making Ca2+ signals the earliest response to HS. In this review, we discuss the crucial role of Ca2+ signaling in raising plant thermotolerance, and we explore its multifaceted contributions to various aspects of the plant HS response (HSR).

Calmodulin and calmodulin-like protein-mediated plant responses to biotic stresses

Plants have evolved a set of finely regulated mechanisms to respond to various biotic stresses. Transient changes in intracellular calcium (Ca2+ ) concentration have been well documented to act as cellular signals in coupling environmental stimuli to appropriate physiological responses with astonishing accuracy and specificity in plants. Calmodulins (CaMs) and calmodulin-like proteins (CMLs) are extensively characterized as important classes of Ca2+ sensors. The spatial-temporal coordination between Ca2+ transients, CaMs/CMLs and their target proteins is critical for plant responses to environmental stresses. Ca2+ -loaded CaMs/CMLs interact with and regulate a broad spectrum of target proteins, such as ion transporters (including channels, pumps, and antiporters), transcription factors, protein kinases, protein phosphatases, metabolic enzymes and proteins with unknown biological functions. This review focuses on mechanisms underlying how CaMs/CMLs are involved in the regulation of plant responses to diverse biotic stresses including pathogen infections and herbivore attacks. Recent discoveries of crucial functions of CaMs/CMLs and their target proteins in biotic stress resistance revealed through physiological, molecular, biochemical, and genetic analyses have been described, and intriguing insights into the CaM/CML-mediated regulatory network are proposed. Perspectives for future directions in understanding CaM/CML-mediated signalling pathways in plant responses to biotic stresses are discussed. The application of accumulated knowledge of CaM/CML-mediated signalling in biotic stress responses into crop cultivation would improve crop resistance to various biotic stresses and safeguard our food production in the future.

Calcium (Ca2+ ) sensors and MYC2 are crucial players during jasmonates-mediated abiotic stress tolerance in plants

Plants evolve stress-specific responses that sense changes in their external environmental conditions and develop various mechanisms for acclimatization and survival. Calcium (Ca2+ ) is an essential stress-sensing secondary messenger in plants. Ca2+ sensors, including calcium-dependent protein kinases (CDPKs), calmodulins (CaMs), CaM-like proteins (CMLs), and calcineurin B-like proteins (CBLs), are involved in jasmonates (JAs) signalling and biosynthesis. Moreover, JAs are phospholipid-derived phytohormones that control plant response to abiotic stresses. The JAs signalling pathway affects hormone-receptor gene transcription by binding to the basic helix-loop-helix (bHLH) transcription factor. MYC2 acts as a master regulator of JAs signalling module assimilated through various genes. The Ca2+ sensor CML regulates MYC2 and is involved in a distinct mechanism mediating JAs signalling during abiotic stresses. This review highlights the pivotal role of the Ca2+ sensors in JAs biosynthesis and MYC2-mediated JAs signalling during abiotic stresses in plants.

The neuronal calcium sensor NCS-1 regulates the phosphorylation state and activity of the Gα chaperone and GEF Ric-8A

The neuronal calcium sensor 1 (NCS-1), an EF-hand Ca2+ binding protein, and Ric-8A coregulate synapse number and probability of neurotransmitter release. Recently, the structures of Ric-8A bound to Gα have revealed how Ric-8A phosphorylation promotes Gα recognition and activity as a chaperone and guanine nucleotide exchange factor. However, the molecular mechanism by which NCS-1 regulates Ric-8A activity and its interaction with Gα subunits is not well understood. Given the interest in the NCS-1/Ric-8A complex as a therapeutic target in nervous system disorders, it is necessary to shed light on this molecular mechanism of action at atomic level. We have reconstituted NCS-1/Ric-8A complexes to conduct a multimodal approach and determine the sequence of Ca2+ signals and phosphorylation events that promote the interaction of Ric-8A with Gα. Our data show that the binding of NCS-1 and Gα to Ric-8A are mutually exclusive. Importantly, NCS-1 induces a structural rearrangement in Ric-8A that traps the protein in a conformational state that is inaccessible to casein kinase II-mediated phosphorylation, demonstrating one aspect of its negative regulation of Ric-8A-mediated G-protein signaling. Functional experiments indicate a loss of Ric-8A guanine nucleotide exchange factor (GEF) activity toward Gα when complexed with NCS-1, and restoration of nucleotide exchange activity upon increasing Ca2+ concentration. Finally, the high-resolution crystallographic data reported here define the NCS-1/Ric-8A interface and will allow the development of therapeutic synapse function regulators with improved activity and selectivity.

An EPHB4-RASA1 signaling complex inhibits shear stress-induced Ras-MAPK activation in lymphatic endothelial cells to promote the development of lymphatic vessel valves

EPHB4 is a receptor protein tyrosine kinase that is required for the development of lymphatic vessel (LV) valves. We show here that EPHB4 is necessary for the specification of LV valves, their continued development after specification, and the maintenance of LV valves in adult mice. EPHB4 promotes LV valve development by inhibiting the activation of the Ras-MAPK pathway in LV endothelial cells (LEC). For LV specification, this role for EPHB4 depends on its ability to interact physically with the p120 Ras-GTPase-activating protein (RASA1) that acts as a negative regulator of Ras. Through physical interaction, EPHB4 and RASA1 dampen oscillatory shear stress (OSS)-induced Ras-MAPK activation in LEC, which is required for LV specification. We identify the Piezo1 OSS sensor as a focus of EPHB4-RASA1 regulation of OSS-induced Ras-MAPK signaling mediated through physical interaction. These findings contribute to an understanding of the mechanism by which EPHB4, RASA1 and Ras regulate lymphatic valvulogenesis.

Centrins control chicken cone cell lipid droplet dynamics through lipid-droplet-localized SPDL1

As evolutionarily conserved organelles, lipid droplets (LDs) carry out numerous functions and have various subcellular localizations in different cell types and species. In avian cone cells, there is a single apically localized LD. We demonstrated that CIDEA (cell death inducing DFFA like effector a) and microtubules promote the formation of the single LD in chicken cone cells. Centrins, which are well-known centriole proteins, target to the cone cell LD via their C-terminal calcium-binding domains. Centrins localize on cone cell LDs with the help of SPDL1-L (spindle apparatus coiled-coil protein 1-L), a previously uncharacterized isoform of the kinetochore-associated dynein adaptor SPDL1. The loss of CETN3 or overexpression of a truncated CETN1 abrogates the apical localization of the cone cell LD. Simulation analysis showed that multiple LDs or a single mispositioned LD reduces the light sensitivity. Collectively, our findings identify a role of centrins in the regulation of cone cell LD localization, which is important for the light sensitivity of cone cells.

Solvation Behavior of Elastin-like Polypeptides in Divalent Metal Salt Solutions

The effects of CaCl2 and MgCl2 on the cloud point temperature of two different elastin-like polypeptides (ELPs) were studied using a combination of cloud point measurements, molecular dynamics simulations, and infrared spectroscopy. Changes in the cloud point for the ELPs in aqueous divalent metal cation solutions were primarily governed by two competing interactions: the cation-amide oxygen electrostatic interaction and the hydration of the cation. In particular, Ca2+ cations can more readily shed their hydration shells and directly contact two amide oxygens by the formation of ion bridges. By contrast, Mg2+ cations were more strongly hydrated and preferred to partition toward the amide oxygens along with their hydration shells. In fact, although hydrophilic ELP V5A2G3 was salted-out at low concentrations of MgCl2, it was salted-in at higher salt concentrations. By contrast, CaCl2 salted the ELP sharply out of solution at higher salt concentrations because of the bridging effect.

Enhanced Ca2+ binding to EF-hands through phosphorylation of conserved serine residues activates MpRBOHB and chitin-triggered ROS production

NADPH oxidases/RBOHs catalyze apoplastic ROS production and act as key signaling nodes, integrating multiple signal transduction pathways regulating plant development and stress responses. Although RBOHs have been suggested to be activated by Ca2+ binding and phosphorylation by various protein kinases, a mechanism linking Ca2+ binding and phosphorylation in the activity regulation remained elusive. Chitin-triggered ROS production required cytosolic Ca2+ elevation and Ca2+ binding to MpRBOHB in a liverwort Marchantia polymorpha. Heterologous expression analysis of truncated variants revealed that a segment of the N-terminal cytosolic region highly conserved among land plant RBOHs encompassing the two EF-hand motifs is essential for the activation of MpRBOHB. Within the conserved regulatory domain, we have identified two Ser residues whose phosphorylation is critical for the activation in planta. Isothermal titration calorimetry analyses revealed that phosphorylation of the two Ser residues increased the Ca2+ binding affinity of MpRBOHB, while Ca2+ binding is indispensable for the activation, even if the two Ser residues are phosphorylated. Our findings shed light on a mechanism through which phosphorylation potentiates the Ca2+ -dependent activation of MpRBOHB, emphasizing the pivotal role of Ca2+ binding in mediating the Ca2+ and phosphorylation-driven activation of MpRBOHB, which is likely to represent a fundamental mechanism conserved among land plant RBOHs.

Physiology of intracellular calcium buffering

Calcium signaling underlies much of physiology. Almost all the Ca2+ in the cytoplasm is bound to buffers, with typically only ∼1% being freely ionized at resting levels in most cells. Physiological Ca2+ buffers include small molecules and proteins, and experimentally Ca2+ indicators will also buffer calcium. The chemistry of interactions between Ca2+ and buffers determines the extent and speed of Ca2+ binding. The physiological effects of Ca2+ buffers are determined by the kinetics with which they bind Ca2+ and their mobility within the cell. The degree of buffering depends on factors such as the affinity for Ca2+, the Ca2+ concentration, and whether Ca2+ ions bind cooperatively. Buffering affects both the amplitude and time course of cytoplasmic Ca2+ signals as well as changes of Ca2+ concentration in organelles. It can also facilitate Ca2+ diffusion inside the cell. Ca2+ buffering affects synaptic transmission, muscle contraction, Ca2+ transport across epithelia, and the killing of bacteria. Saturation of buffers leads to synaptic facilitation and tetanic contraction in skeletal muscle and may play a role in inotropy in the heart. This review focuses on the link between buffer chemistry and function and how Ca2+ buffering affects normal physiology and the consequences of changes in disease. As well as summarizing what is known, we point out the many areas where further work is required.

Role of myristoylation in modulating PCaP1 interaction with calmodulin

Plasma membrane-associated Cation-binding Protein 1 (PCaP1) belongs to the plant-unique DREPP protein family with largely unknown biological functions but ascertained roles in plant development and calcium (Ca2+) signaling. PCaP1 is anchored to the plasma membrane via N-myristoylation and a polybasic cluster, and its N-terminal region can bind Ca2+/calmodulin (CaM). However, the molecular determinants of PCaP1-Ca2+-CaM interaction and the functional impact of myristoylation in the complex formation and Ca2+ sensitivity of CaM remained to be elucidated. Herein, we investigated the direct interaction between Arabidopsis PCaP1 (AtPCaP1) and CaM1 (AtCaM1) using both myristoylated and non-myristoylated peptides corresponding to the N-terminal region of AtPCaP1. ITC analysis showed that AtCaM1 forms a high affinity 1:1 complex with AtPCaP1 peptides and the interaction is strictly Ca2+-dependent. Spectroscopic and kinetic Ca2+ binding studies showed that the myristoylated peptide dramatically increased the Ca2+-binding affinity of AtCaM1 and slowed the Ca2+ dissociation rates from both the C- and N-lobes, thus suggesting that the myristoylation modulates the mechanism of AtPCaP1 recognition by AtCaM1. Furthermore, NMR and CD spectroscopy revealed that the structure of both the N- and C-lobes of Ca2+-AtCaM1 changes markedly in the presence of the myristoylated AtPCaP1 peptide, which assumes a helical structure in the final complex. Overall, our results indicate that AtPCaP1 biological function is strictly related to the presence of multiple ligands, i.e., the myristoyl moiety, Ca2+ ions and AtCaM1 and only a full characterization of their equilibria will allow for a complete molecular understanding of the putative role of PCaP1 as signal protein.

The Dictyostelium discoideum FimA protein, unlike yeast and plant fimbrins, is regulated by calcium similar to mammalian plastins

Plastins, also known as fimbrins, are highly conserved eukaryotic multidomain proteins that are involved in actin-bundling. They all contain four independently folded Calponin Homology-domains and an N-terminal headpiece that is comprised of two calcium-binding EF-hand motifs. Since calcium-binding has been shown to be integral to regulating the activity of the three mammalian plastin proteins, we decided to study the properties of the headpiece regions of fimbrins from the model plant Arabidopsis thaliana, the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe and the amoeba Dictyostelium discoideum. Of these protein domains only the FimA headpiece from the amoeba protein possesses calcium binding properties. Structural characterization of this protein domain by multidimensional NMR and site-directed mutagenesis studies indicates that this EF-hand region of FimA also contains a regulatory 'switch helix' that is essential to regulating the activity of the human L-plastin protein. Interestingly this regulatory helical region seems to be lacking in the plant and yeast proteins and in fimbrins from all other nonmotile systems. Typical calmodulin antagonists can displace the switch-helix from the FimA headpiece, suggesting that such drugs can deregulate the Ca2+-regulation of the actin-bunding in the amoeba, thereby making it a useful organism for drug screening against mammalian plastins.