Substrate recognition by Arg/Pro-rich insert domain in calcium/calmodulin-dependent protein kinase kinase for target protein kinases

Calcium/calmodulin-dependent protein kinase kinases (CaMKKs) activate CaMKI, CaMKIV, protein kinase B/Akt, and AMP-activated protein kinase (AMPK) by phosphorylating Thr residues in activation loops to mediate various Ca²⁺ -signaling pathways. Mammalian cells expressing CaMKKα and CaMKKβ lacking Arg/Pro-rich insert domain (RP-domain) sequences showed impaired phosphorylation of AMPKα, CaMKIα, and CaMKIV, whereas the autophosphorylation activities of CaMKK mutants remained intact and were similar to those of wild-type CaMKKs. Liver kinase B1 (LKB1, an AMPK kinase) complexed with STRAD and MO25 and was unable to phosphorylate CaMKIα and CaMKIV; however, mutant LKB1 with the RP-domain sequences of CaMKKα and CaMKKβ inserted between kinase subdomains II and III acquired CaMKIα and CaMKIV phosphorylating activity in vitro and in transfected cultured cells. Furthermore, ionomycin-induced phosphorylation of hemagglutinin (HA)-CaMKIα at Thr177, HA-CaMKIV at Thr196, and HA-AMPKα at Thr172 in transfected cells was significantly suppressed by cotransfection of kinase-dead mutants of CaMKK isoforms, but these dominant-negative effects were abrogated with RP-deletion mutants, suggesting that sequestration of substrate kinases by loss-of-function CaMKK mutants requires the RP-domain. This was confirmed by pulldown experiments that showed that dominant-negative mutants of CaMKKα and CaMKKβ interact with target kinases but not RP-deletion mutants. Taken together, these results clearly indicate that both CaMKK isoforms require the RP-domain to recognize downstream kinases to interact with and phosphorylate Thr residues in their activation loops. Thus, the RP-domain may be a promising target for specific CaMKK inhibitors.

The immunoreceptor SLAMF8 promotes the differentiation of follicular dendritic cell-dependent monocytic cells with B cell-activating ability

Follicular dendritic cells (FDCs) play a crucial role in generating high-affinity antibody-producing B cells during the germinal center (GC) reaction. Herein, we analyzed the altered gene expression profile of a mouse FDC line, FL-Y, following lymphotoxin β receptor stimulation, and observed increased Slam-family member 8 (Slamf8) mRNA expression. Forced Slamf8 expression and SLAMF8-Fc addition enhanced the ability of FL-Y cells to induce FDC-induced monocytic cell (FDMC) differentiation. FDMCs accelerated GC-phenotype proliferation in cultured B cells, suggesting that they are capable of promoting GC responses. Furthermore, a pulldown assay showed that SLAMF8-Fc could bind to SLAMF8-His. Overall, the homophilic interaction of SLAMF8 promotes FDMC differentiation and SLAMF8 might act as a novel regulator of GC responses by regulating FDMC differentiation.

Conformation-Dependent Reversible Interaction of Ca2+/Calmodulin-Dependent Protein Kinase Kinase with an Inhibitor, TIM-063

Ca²⁺/calmodulin-dependent protein kinase kinase (CaMKK), a Ca²⁺/CaM-dependent enzyme that phosphorylates and activates multifunctional kinases, including CaMKI, CaMKIV, protein kinase B/Akt, and 5'AMP-activated protein kinase, is involved in various Ca²⁺-signaling pathways in cells. Recently, we developed an ATP-competitive CaMKK inhibitor, TIM-063 (2-hydroxy-3-nitro-7H-benzo[de]benzo[4,5]imidazo[2,1-a]isoquinolin-7-one, Ohtsuka et al. Biochemistry 2020, 59, 1701-1710). To gain mechanistic insights into the interaction of CaMKK with TIM-063, we prepared TIM-063-coupled sepharose (TIM-127-sepharose) for association/dissociation analysis of the enzyme/inhibitor complex. CaMKKα/β in transfected COS-7 cells and in mouse brain extracts specifically bound to TIM-127-sepharose and dissociated following the addition of TIM-063 in a manner similar to that of recombinant GST-CaMKKα/β, which could bind to TIM-127-sepharose in a Ca²⁺/CaM-dependent fashion and dissociate from the sepharose following the addition of TIM-063 in a dose-dependent manner. In contrast to GST-CaMKKα, GST-CaMKKβ was able to weakly bind to TIM-127-sepharose in the presence of EGTA, probably due to the partially active conformation of recombinant GST-CaMKKβ without Ca²⁺/CaM-binding. These results suggested that the regulatory domain of CaMKKα prevented the inhibitor from interacting with the catalytic domain as the GST-CaMKKα mutant (residues 126-434) lacking the regulatory domain (residues 438-463) interacted with TIM-127-sepharose regardless of the presence or absence of Ca²⁺/CaM. Furthermore, CaMKKα bound to TIM-127-sepharose in the presence of Ca²⁺/CaM completely dissociated from TIM-127-sepharose following the addition of excess EGTA. These results indicated that TIM-063 interacted with and inhibited CaMKK in its active state but not in its autoinhibited state and that this interaction is likely reversible, depending on the concentration of intracellular Ca²⁺.

Oligomerization of Ca2+/calmodulin-dependent protein kinase kinase

Ca²⁺/calmodulin-dependent protein kinase kinases (CaMKKα and β) are regulatory kinases for multiple downstream kinases, including CaMKI, CaMKIV, PKB/Akt, and AMP-activated protein kinase (AMPK) through phosphorylation of each activation-loop Thr residue. In this report, we biochemically characterize the oligomeric structure of CaMKK isoforms through a heterologous expression system using COS-7 cells. Oligomerization of CaMKK isoforms was readily observed by treating CaMKK transfected cells with cell membrane permeable crosslinkers. In addition, His-tagged CaMKKα (His-CaMKKα) pulled down with FLAG-tagged CaMKKα (FLAG-CaMKKα) in transfected cells. The oligomerization of CaMKKα was confirmed by the fact that GST-CaMKKα/His-CaMKKα complex from transiently expressed COS-7 cells extracts was purified to near homogeneity by the sequential chromatography using glutathione-sepharose/Ni-sepharose and was observed in a Ca²⁺/CaM-independent manner by reciprocal pulldown assay, suggesting the direct interaction between monomeric CaMKKα. Furthermore, the His-CaMKKα kinase-dead mutant (D293A) complexed with FLAG-CaMKKα exhibited significant CaMKK activity, indicating the active CaMKKα multimeric complex. Collectively, these results suggest that CaMKKα can self-associate in the cells, constituting a catalytically active oligomer that might be important for the efficient activation of CaMKK-mediated intracellular signaling.

Terminal Sequence-Specific Interparticle Attraction between DNA Duplex-Carrying Polystyrene Microparticles in Aqueous Salt Solution Assessed by Optical Tweezers

The dispersion behavior of DNA duplex-carrying colloidal particles in aqueous high-salt solutions shows extraordinary selectivity against the duplex terminal sequence. We investigated the interparticle force between DNA duplex-carrying polystyrene (dsDNA-PS) microparticles in aqueous salt solutions and examined their behavior in relation to the duplex terminal sequences. Force-distance (F-D) curves for a pair of dsDNA-PS particles were recorded with a dual-beam optical tweezers system with the two optically trapped particles closely approaching each other. Interestingly, only 3-5% of the oligo-DNA strands on the dsDNA-PS particles formed a duplex with complementary DNAs, and the F-D curves showed a distinct specificity to the duplex terminal sequences in the interparticle force at a high-NaCl concentration; a clear attraction peak was observed in F-D curves only when the duplex terminal was a complementary base pair. The attractive strength reached 2.6 ± 0.5 pN at 500 mM NaCl and 4.3 ± 1.0 pN at 750 mM NaCl. By sharp contrast, no significant attraction occurred for the particles with mismatched duplex terminals even at 750 mM NaCl. Similar duplex terminal-specificity in the interparticle force was also confirmed for dsDNA-PS particles in divalent MgCl₂ solutions. Considering that the duplex terminal sequences on the dsDNA-PS particles showed only a negligible difference in their surface charges under identical salt conditions, we concluded that the interparticle attraction observed only for the dsDNA-PS particles with complementary duplex terminals is attributable to the salt-facilitated stacking interaction between the paired terminal nucleobases (i.e., blunt-end stacking) on the dsDNA-PS surfaces. Our results thus demonstrate the occurrence of a duplex terminal-specific interparticle force between dsDNA-PS particles under high-salt conditions.

Identification and Biochemical Characterization of High Mobility Group Protein 20A as a Novel Ca2+/S100A6 Target

During screening of protein-protein interactions, using human protein arrays carrying 19,676 recombinant glutathione s-transferase (GST)-fused human proteins, we identified the high-mobility protein group 20A (HMG20A) as a novel S100A6 binding partner. We confirmed the Ca²⁺-dependent interaction of HMG20A with S100A6 by the protein array method, biotinylated S100A6 overlay, and GST-pulldown assay in vitro and in transfected COS-7 cells. Co-immunoprecipitation of S100A6 with HMG20A from HeLa cells in a Ca²⁺-dependent manner revealed the physiological relevance of the S100A6/HMG20A interaction. In addition, HMG20A has the ability to interact with S100A1, S100A2, and S100B in a Ca²⁺-dependent manner, but not with S100A4, A11, A12, and calmodulin. S100A6 binding experiments using various HMG20A mutants revealed that Ca²⁺/S100A6 interacts with the C-terminal region (residues 311–342) of HMG20A with stoichiometric binding (HMG20A:S100A6 dimer = 1:1). This was confirmed by the fact that a GST-HMG20A mutant lacking the S100A6 binding region (residues 311–347, HMG20A-ΔC) failed to interact with endogenous S100A6 in transfected COS-7 cells, unlike wild-type HMG20A. Taken together, these results identify, for the first time, HMG20A as a target of Ca²⁺/S100 proteins, and may suggest a novel linkage between Ca²⁺/S100 protein signaling and HMG20A function, including in the regulation of neural differentiation.

Regulation of the tubulin polymerization-promoting protein by Ca2+/S100 proteins

To elucidate S100 protein-mediated signaling pathways, we attempted to identify novel binding partners for S100A2 by screening protein arrays carrying 19,676 recombinant glutathione S-transferase (GST)-fused human proteins with biotinylated S100A2. Among newly discovered putative S100A2 interactants, including TMLHE, TRH, RPL36, MRPS34, CDR2L, OIP5, and MED29, we identified and characterized the tubulin polymerization-promoting protein (TPPP) as a novel S100A2-binding protein. We confirmed the interaction of TPPP with Ca²⁺/S100A2 by multiple independent methods, including the protein array method, S100A2 overlay, and pulldown assay in vitro and in transfected COS-7 cells. Based on the results from the S100A2 overlay assay using various GST-TPPP mutants, the S100A2-binding region was identified in the C-terminal (residues 111-160) of the central core domain of a monomeric form of TPPP that is involved in TPPP dimerization. Chemical cross-linking experiments indicated that S100A2 suppresses dimer formation of His-tagged TPPP in a dose-dependent and a Ca²⁺-dependent manner. In addition to S100A2, TPPP dimerization is disrupted by other multiple S100 proteins, including S100A6 and S100B, in a Ca²⁺-dependent manner but not by S100A4. This is consistent with the fact that S100A6 and S100B, but not S100A4, are capable of interacting with GST-TPPP in the presence of Ca²⁺. Considering these results together, TPPP was identified as a novel target for S100A2, and it is a potential binding target for other multiple S100 proteins, including S100A6 and S100B. Direct binding of the S100 proteins with TPPP may cause disassembly of TPPP dimer formation in response to the increasing concentration of intracellular Ca²⁺, thus resulting in the regulation of the physiological function of TPPP, such as microtubule organization.

DNA Terminal-Specific Dispersion Behavior of Polystyrene Latex Microparticles Densely Covered with Oligo-DNA Strands Under High-Salt Conditions

We prepared microspheres densely covered with oligo-DNA strands by immobilizing amino-terminated oligo-DNA strands on the surface of carboxylate polystyrene latex (PS) particles via the amide bond formation. The obtained microspheres (ssDNA-PS) stably dispersed in neutral pH buffer containing high concentrations of NaCl. For the ssDNA-PS ≥1 μm diameter, only 3 - 5% of surface-immobilized oligo-DNA could form a duplex with the complementary strands. Nevertheless, the resulting ssDNA-PS showed a distinct duplex terminal dependency in their dispersion behavior under neutral pH and high NaCl conditions; the microspheres with fully-matched duplexes on the surface spontaneously aggregated in a non-crosslinking manner. By contrast, the microspheres with terminal-mismatched duplexes remained dispersed under the identical conditions. These results suggest that the micrometer-scale particles covered with oligo-DNA strands also have high susceptibility to a duplex terminal sequence in their dispersion property, similar to previously reported DNA-functionalized nanoparticles. This property could potentially be used in various applications including analytical purposes.

Development and Characterization of Novel Molecular Probes for Ca2+/Calmodulin-Dependent Protein Kinase Kinase, Derived from STO-609

Ca²⁺/calmodulin-dependent protein kinase kinase (CaMKK) activates particular multifunctional kinases, including CaMKI, CaMKIV, and 5'AMP-activated protein kinase (AMPK), resulting in the regulation of various Ca²⁺-dependent cellular processes, including neuronal, metabolic, and pathophysiological pathways. We developed and characterized a novel pan-CaMKK inhibitor, TIM-063 (2-hydroxy-3-nitro-7H-benzo[de]benzo[4,5]imidazo[2,1-a]isoquinolin-7-one) derived from STO-609 (7H-benzimidazo[2,1-a]benz[de]isoquinoline-7-one-3-carboxylic acid), and an inactive analogue (TIM-062) as molecular probes for the analysis of CaMKK-mediated cellular responses. Unlike STO-609, TIM-063 had an inhibitory activity against CaMKK isoforms (CaMKKα and CaMKKβ) with a similar potency (K_i = 0.35 μM for CaMKKα, and K_i = 0.2 μM for CaMKKβ) in vitro. Two TIM-063 analogues lacking a nitro group (TIM-062) or a hydroxy group (TIM-064) completely impaired CaMKK inhibitory activities, indicating that both substituents are necessary for the CaMKK inhibitory activity of TIM-063. Enzymatic analysis revealed that TIM-063 is an ATP-competitive inhibitor that directly targets the catalytic domain of CaMKK, similar to STO-609. TIM-063 suppressed the ionomycin-induced phosphorylation of exogenously expressed CaMKI, CaMKIV, and endogenous AMPKα in HeLa cells with an IC₅₀ of ∼0.3 μM, and it suppressed CaMKK isoform-mediated CaMKIV phosphorylation in transfected COS-7 cells. Thus, TIM-063, but not the inactive analogue (TIM-062), displayed cell permeability and the ability to inhibit CaMKK activity in cells. Taken together, these results indicate that TIM-063 could be a useful tool for the precise analysis of CaMKK-mediated signaling pathways and may be a promising lead compound for the development of therapeutic agents for the treatment of CaMKK-related diseases.

Phosphorylation and dephosphorylation of Ca2+/calmodulin-dependent protein kinase kinase β at Thr144 in HeLa cells

Ca2+/calmodulin-dependent protein kinase kinase β (CaMKKβ) acts as a regulatory kinase that phosphorylates and activates multiple downstream kinases including CaMKI, CaMKIV, 5'AMP-activated protein kinase (AMPK) and protein kinase B (PKB), resulting in regulation of wide variety of Ca2+-dependent physiological responses under normal and pathological conditions. CaMKKβ is regulated by Ca2+/calmodulin-binding, autophosphorylation, and transphosphorylation by multiple protein kinases including cAMP-dependent protein kinase (PKA). In this report, we found that phosphorylation of CaMKKβ is dynamically regulated by protein phosphatase/kinase system in HeLa cells. Global phosphoproteomic analysis revealed the constitutive phosphorylation at 8 Ser residues including Ser128, 132, and 136 in the N-terminal regulatory domain of rat CaMKKβ in unstimulated HeLa cells as well as inducible phosphorylation of Thr144 in the cells treated with a phosphatase inhibitor, okadaic acid (OA). Thr144 phosphorylation in CaMKKβ has shown to be rapidly induced by OA treatment in a time- and dose-dependent manner in transfected HeLa cells, indicating that Thr144 in CaMKKβ is maintained unphosphorylated state by protein phosphatase(s). We confirmed that in vitro dephosphorylation of pThr144 in CaMKKβ by protein phosphatase 2A and 1. We also found that the pharmacological inhibition of protein phosphatase(s) significantly induces CaMKKβ-phosphorylating activity (at Thr144) in HeLa cell lysates as well as in intact cells; however, it was unlikely that this activity was catalyzed by previously identified Thr144-kinases, such as AMPK and PKA. Taken together, these results suggest that the phosphorylation and dephosphorylation of Thr144 in CaMKKβ is dynamically regulated by multiple kinases/phosphatases signaling resulting in fine-tuning of the enzymatic property.

Photo-switching of blunt-end stacking between DNA strands immobilized on gold nanoparticles

End-to-end stacking of DNAs on gold nanoparticles was switched by terminal base pairing/unpairing triggered by the photo-isomerization of an azobenzene moiety nearby the DNA terminal.

Chemically Fueled Plasmon Switching of Gold Nanorods by Single-Base Pairing of Surface-Grafted DNA

The interactions between metal ions and biomolecules are crucial to various bioprocesses. Development of plasmon switching nanodevices that exploit these molecular interactions is of fundamental and technological interest. Here, we show plasmon switching based on rapid aggregation/dispersion of double-stranded DNA-modified gold nanorods (dsDNA-AuNRs) that exhibit colloidal behaviors depending on pairing/unpairing of the terminal bases. The dsDNA-AuNRs bearing a thymine-thymine (T-T) mismatch at the penultimate position undergo spontaneous non-cross-linking aggregation in the presence of Hg²⁺ due to T-Hg-T base pairing. Inversely, the subsequent addition of cysteine (Cys) gives rise to the removal of Hg²⁺ from the T-Hg-T base pair to reproduce the T-T mismatch, resulting in stable dispersion of the dsDNA-AuNRs. The chemical-responsive plasmon switch allows for the rapid and repeatable cycles at room temperature. The validity of the present method is further exemplified by developing another plasmon switch fueled by Ag⁺ and Cys by installing the Ag⁺-binding DNA sequence in the dsDNA-AuNR.

Effect of a saline flush technique for head and neck imaging in dual-energy CT: improvement of image quality and perivenous artefact reduction using virtual monochromatic imaging

AIM

To evaluate the effect of the saline flush (SF) technique on the depiction of lesions and the reduction of perivenous artefacts in the head and neck region using dual-energy computed tomography (CT) with virtual monochromatic imaging (VMI).

MATERIALS AND METHODS

Fifty patients with head and neck cancer were divided into two groups: group A, without a SF and group B, with a 30-ml SF. All images were acquired using fast kilovolt-switching CT (Revolution HD, GE Healthcare, Milwaukee, WI, USA). Contrast-to-noise ratios (CNRs) of the lesions were calculated at VMI energy levels ranging from 40 to 80 keV. Subjective analysis of overall image quality, delineation of lesions, and perivenous artefacts was conducted by two reviewers at both VMI energy level 40 keV and the optimal energy level (which showed optimal CNR by objective analysis).

RESULTS

Optimal energy level was 63 keV for group A and 61 keV for group B. At VMI energy levels ranging from 40 to 80 keV, the CNR was higher for group B. The highest subjective overall image quality was shown for group B at the optimal energy level (subjective image quality mean value, 3.40). Subjective delineation of lesions was comparable. The perivenous artefact score was significantly higher for group B (2.44 versus 2.74 [p<0.05] at 40 keV, 3.20 versus 3.46 [p<0.05] at the optimal energy level).

CONCLUSION

The SF technique results in an improvement of lesion CNR and a reduction of perivenous artefacts in VMI using duel-energy CT, especially at 40 keV.

Regulation of Ca2+/calmodulin-dependent protein kinase kinase β by cAMP signaling

BACKGROUND

Ca²⁺/calmodulin-dependent protein kinase kinase (CaMKK) is a pivotal activator of CaMKI, CaMKIV and 5'-AMP-activated protein kinase (AMPK), controlling Ca²⁺-dependent intracellular signaling including various neuronal, metabolic and pathophysiological responses. Recently, we demonstrated that CaMKKβ is feedback phosphorylated at Thr144 by the downstream AMPK, resulting in the conversion of CaMKKβ into Ca²⁺/CaM-dependent enzyme. However, the regulatory phosphorylation of CaMKKβ at Thr144 in intact cells and in vivo remains unclear.

METHODS

Anti-phosphoThr144 antibody was used to characterize the site-specific phosphorylation of CaMKKβ in immunoprecipitated samples from mouse cerebellum and in transfected mammalian cells that were treated with various agonists and protein kinase inhibitors. CaMKK activity assay and LC-MS/MS analysis were used for biochemical characterization of phosphorylated CaMKKβ.

RESULTS

Our data suggest that the phosphorylation of Thr144 in CaMKKβ is rapidly induced by cAMP/cAMP-dependent protein kinase (PKA) signaling in CaMKKβ-transfected HeLa cells, that is physiologically relevant in mouse cerebellum. We confirmed that the catalytic subunit of PKA was capable of directly phosphorylating CaMKKβ at Thr144 in vitro and in transfected cells. In addition, the basal phosphorylation of CaMKKβ at Thr144 in transfected HeLa cells was suppressed by AMPK inhibitor (compound C). PKA-catalyzed phosphorylation reduced the autonomous activity of CaMKKβ in vitro without significant effect on the Ca²⁺/CaM-dependent activity, resulting in the conversion of CaMKKβ into Ca²⁺/CaM-dependent enzyme.

CONCLUSION

cAMP/PKA signaling may confer Ca²⁺-dependency to the CaMKKβ-mediated signaling pathway through direct phosphorylation of Thr144 in intact cells.

GENERAL SIGNIFICANCE

Our results suggest a novel cross-talk between cAMP/PKA and Ca²⁺/CaM/CaMKKβ signaling through regulatory phosphorylation.

Interleukin 34 (IL-34) cell-surface localization regulated by the molecular chaperone 78-kDa glucose-regulated protein facilitates the differentiation of monocytic cells

Interleukin 34 (IL-34) constitutes a cytokine that shares a common receptor, colony-stimulating factor-1 receptor (CSF-1R), with CSF-1. We recently identified a novel type of monocytic cell termed follicular dendritic cell-induced monocytic cells (FDMCs), whose differentiation depended on CSF-1R signaling through the IL-34 produced from a follicular dendritic cell line, FL-Y. Here, we report the functional mechanisms of the IL-34-mediated CSF-1R signaling underlying FDMC differentiation. CRIPSR/Cas9-mediated knockout of the Il34 gene confirmed that the ability of FL-Y cells to induce FDMCs completely depends on the IL-34 expressed by FL-Y cells. Transwell culture experiments revealed that FDMC differentiation requires a signal from a membrane-anchored form of IL-34 on the FL-Y cell surface, but not from a secreted form, in a direct interaction between FDMC precursor cells and FL-Y cells. Furthermore, flow cytometric analysis using an anti-IL-34 antibody indicated that IL-34 was also expressed on the FL-Y cell surface. Thus, we explored proteins interacting with IL-34 in FL-Y cells. Mass spectrometry analysis and pulldown assay identified that IL-34 was associated with the molecular chaperone 78-kDa glucose-regulated protein (GRP78) in the plasma membrane fraction of FL-Y cells. Consistent with this finding, GRP78-heterozygous FL-Y cells expressed a lower level of IL-34 protein on their cell surface and exhibited a reduced competency to induce FDMC differentiation compared with the original FL-Y cells. These results indicated a novel GRP78-dependent localization and specific function of IL-34 in FL-Y cells related to monocytic cell differentiation.

Stochastic Binding Process of Blunt-End Stacking of DNA Molecules Observed by Atomic Force Microscopy

Hydrophobic attraction is often a physical origin of nonspecific and irreversible (uncontrollable) processes observed for colloidal and biological systems, such as aggregation, precipitation, and fouling with biomolecules. On the contrary, blunt-end stacking of complementary DNA duplex chain pairs, which is also mainly driven by hydrophobic interaction, is specific and stable enough to lead to self-assemblies of DNA nanostructures. To understand the reason behind these contradicting phenomena, we measured forces operating between two self-assembled monolayers of duplexed DNA molecules with blunt ends (DNA-SAMs) and analyzed their statistics. We found the high specificity and stability of blunt-end stacking that resulted in the high resemblance between the interaction forces measured on approaching and retracting. The other finding is on the stochastic formation process of blunt-end stacking, which appeared as a significant fluctuation of the interaction forces at separations smaller than 2.5 nm. Based on these results, we discuss the underlying mechanism of the specificity and stability of blunt-end stacking.

Directed Assembly of Gold Nanorods by Terminal-Base Pairing of Surface-Grafted DNA

Directed assemblies of anisotropic metal nanoparticles exhibit attractive physical and chemical properties. However, an effective methodology to prepare differently directed assemblies from the same anisotropic nanoparticles is not yet available. Gold nanorods (AuNRs) region-selectively modified with different DNA strands can form side-by-side (SBS) and end-to-end (ETE) assemblies in a non-crosslinking manner. When the complementary DNA is hybridized to the surface-bound DNA, stacking interaction between the blunt ends takes place in the designated regions. Such AuNRs assemble into highly ordered structures, assisted by capillary forces emerging on the substrate surface. Moreover, insertion of a mercury(II)-mediated thymine-thymine base pair into the periphery of the DNA layer allows selective formation of the SBS or ETE assemblies from the strictly identical AuNRs with or without mercury(II).

AMP-activated protein kinase-mediated feedback phosphorylation controls the Ca2+/calmodulin (CaM) dependence of Ca2+/CaM-dependent protein kinase kinase β

The Ca²⁺/calmodulin-dependent protein kinase kinase β (CaMKKβ)/5'-AMP-activated protein kinase (AMPK) phosphorylation cascade affects various Ca²⁺-dependent metabolic pathways and cancer growth. Unlike recombinant CaMKKβ that exhibits higher basal activity (autonomous activity), activation of the CaMKKβ/AMPK signaling pathway requires increased intracellular Ca²⁺ concentrations. Moreover, the Ca²⁺/CaM dependence of CaMKKβ appears to arise from multiple phosphorylation events, including autophosphorylation and activities furnished by other protein kinases. However, the effects of proximal downstream kinases on CaMKKβ activity have not yet been evaluated. Here, we demonstrate feedback phosphorylation of CaMKKβ at multiple residues by CaMKKβ-activated AMPK in addition to autophosphorylation in vitro, leading to reduced autonomous, but not Ca²⁺/CaM-activated, CaMKKβ activity. MS analysis and site-directed mutagenesis of AMPK phosphorylation sites in CaMKKβ indicated that Thr¹⁴⁴ phosphorylation by activated AMPK converts CaMKKβ into a Ca²⁺/CaM-dependent enzyme as shown by completely Ca²⁺/CaM-dependent CaMKK activity of a phosphomimetic T144E CaMKKβ mutant. CaMKKβ mutant analysis indicated that the C-terminal domain (residues 471-587), including the autoinhibitory region, plays an important role in stabilizing an inactive conformation in a Thr¹⁴⁴ phosphorylation-dependent manner. Furthermore, immunoblot analysis with anti-phospho-Thr¹⁴⁴ antibody revealed phosphorylation of Thr¹⁴⁴ in CaMKKβ in transfected COS-7 cells that was further enhanced by exogenous expression of AMPKα. These results indicate that AMPK-mediated feedback phosphorylation of CaMKKβ regulates the CaMKKβ/AMPK signaling cascade and may be physiologically important for intracellular maintenance of Ca²⁺-dependent AMPK activation by CaMKKβ.

Terminal-Specific Interaction between Double-Stranded DNA Layers: Colloidal Dispersion Behavior and Surface Force

Double-stranded DNA-grafted nanoparticles (dsDNA-NPs) exhibit a unique dispersion behavior under high-salt conditions depending on the pairing status of their outermost base pairs (pairing or unpairing). The dsDNA-NPs having complementary (i.e., pairing) outermost base pairs spontaneously aggregate under high-salt conditions, but not when their outermost base pairs are mismatched (unpairing). In this study, we used colloidal probe atomic force microscopy to examine how the outermost base pairs affect the interaction between the dsDNA-grafted layers (dsDNA layers). To precisely assess the subtle structural differences in the dsDNA layers, we developed a method for the formation of a homogenous dsDNA layer on gold surfaces using hairpin-shaped DNAs. Homogenous dsDNA layers having complementary (G-C) or mismatched (C-C) outermost base pairs were grafted onto the surfaces of colloidal probes and gold substrates. Force-distance curves measured in an aqueous medium under high-salt conditions revealed that the surface forces between the dsDNA layers were bilateral in nature and were governed by the outermost base pairs. Between complementary outermost dsDNA layers, the surface force changed from repulsive to attractive with an increase in the NaCl concentration (10-1000 mM). The attraction observed under high-salt conditions was attributed to the site-specific interaction proceeded only between complementary dsDNA terminals, the so-called blunt-end stacking. In fact, between mismatched outermost dsDNA layers, the repulsive force was mostly dominant within the same NaCl concentration range. Our results clearly revealed that the pairing status of the outermost base pairs has significant implications for the surface forces between dsDNA layers, leading to the unique dispersion behavior of dsDNA-NPs.

Rapid Naked-Eye Discrimination of Cytochrome P450 Genetic Polymorphism through Non-Crosslinking Aggregation of DNA-Functionalized Gold Nanoparticles

Involvement of single-nucleotide polymorphism (SNP) genotyping in healthcare should allow for more effective use of pharmacogenomics. However, user-friendly assays without the requirement of a special instrument still remain unavailable. This study describes naked-eye SNP discrimination in exon 5 of the human cytochrome P450 2C19 monooxygenase gene, CYP2C19*1 (the wild-type allele) and CYP2C19*2 (the variant allele with G681A point mutation). The present assay is composed of allele-specific single-base primer extension and salt-induced aggregation of DNA-modified gold nanoparticles (DNA-AuNPs). Genetic samples extracted from human hair roots are subjected to this assay. The results are verified by direct sequencing. This study should promise the prospective use of DNA-AuNPs in gene diagnosis.

Rapid Naked-Eye Discrimination of Cytochrome P450 Genetic Polymorphism through Non-Crosslinking Aggregation of DNA-Functionalized Gold Nanoparticles

The front cover artwork is provided by the group of Tohru Takarada at RIKEN (Japan). The image shows a colorimetric single‐nucleotide polymorphism (SNP) genotyping method that uses spontaneous aggregation of DNA‐modified gold nanoparticles (DNA–AuNPs) for the simple and rapid SNP genotyping of the human cytochrome P450 2C19 monooxygenase gene. For more details, read the full text of the Full Paper at p. 508.

Cover Picture: Rapid Naked-Eye Discrimination of Cytochrome P450 Genetic Polymorphism through Non-Crosslinking Aggregation of DNA-Functionalized Gold Nanoparticles (ChemistryOpen 6/2016)

The Front Cover picture shows a colorimetric single‐nucleotide polymorphism (SNP) genotyping method using spontaneous aggregation of DNA‐modified gold nanoparticles (DNA–AuNPs). Simple and rapid SNP genotyping of the human cytochrome P450 2C19 monooxygenase gene is reported. Allele‐specific single‐base primer extension using a fragment of the gene isolated from human hair roots, followed by salt‐induced aggregation of DNA–AuNPs, results in a rapid color change from red to blue or no color change, thereby allowing SNP discrimination by the naked eye. More information can be found in the Communication by T. Takarada and co‐workers on page 508 in Issue 6, 2016 (DOI: 10.1002/open.201600110).

Sulfobetaine-terminated PEG improves the qualities of an immunosensing surface

Poly(ethylene glycol) (PEG) possessing a sulfobetaine (SB) moiety at one end and a pentaethylenehexamine (N6) at the other end (SB-PEG-N6) was newly synthesized as a blocking agent for immunosensing surfaces. The N6 moiety strongly coordinates on gold surfaces, facilitating the tethering of the PEG chain to the sensor chip surface, and leaves the SB moiety free. Non-specific adsorption of bovine serum albumin (BSA) was analyzed on the SB-PEG-N6 tethered surface and compared with the methoxy-PEG-N6 (M-PEG-N6) tethered surface using a surface plasmon resonance (SPR) sensor. Non-specific BSA adsorption decreased with decreasing PEG chain length on the SB-PEG tethered chain surface. Non-specific adsorption of BSA decreased as ionic strength increased on SB-PEG-N6 surfaces; this phenomenon was completely opposite to that observed with an M-PEG-N6 tethered chain surface. The results show that SB moieties located close to the gold surface perform well with regard to protein rejection. Actually, low-molecular weight alkane thiol SB (SB-SH) showed minimum BSA adsorption. To evaluate protein recognition efficacy on a PEGylated surface, an antibody (IgG) immobilized surface was then constructed on a gold sensor chip using SB-PEG-N6 as the blocking agent. The specific protein recognition efficacy of SB-PEG-N6/IgG co-immobilized surfaces was higher than that obtained using SB-SH/IgG co-immobilized surfaces. We conclude that SB-terminated PEG exhibits the optimal qualities of a blocking agent, as it possesses both high suppression efficacy of nonspecific protein adsorption and specific protein recognition ability.

Differential AMP-activated Protein Kinase (AMPK) Recognition Mechanism of Ca2+/Calmodulin-dependent Protein Kinase Kinase Isoforms

Ca(2+)/calmodulin-dependent protein kinase kinase β (CaMKKβ) is a known activating kinase for AMP-activated protein kinase (AMPK). In vitro, CaMKKβ phosphorylates Thr(172) in the AMPKα subunit more efficiently than CaMKKα, with a lower Km (∼2 μm) for AMPK, whereas the CaMKIα phosphorylation efficiencies by both CaMKKs are indistinguishable. Here we found that subdomain VIII of CaMKK is involved in the discrimination of AMPK as a native substrate by measuring the activities of various CaMKKα/CaMKKβ chimera mutants. Site-directed mutagenesis analysis revealed that Leu(358) in CaMKKβ/Ile(322) in CaMKKα confer, at least in part, a distinct recognition of AMPK but not of CaMKIα.

Identification of striated muscle activator of Rho signaling (STARS) as a novel calmodulin target by a newly developed genome-wide screen

To search for novel target(s) of the Ca(2+)-signaling transducer, calmodulin (CaM), we performed a newly developed genome-wide CaM interaction screening of 19,676 GST-fused proteins expressed in human. We identified striated muscle activator of Rho signaling (STARS) as a novel CaM target and characterized its CaM binding ability and found that the Ca(2+)/CaM complex interacted stoichiometrically with the N-terminal region (Ala13-Gln35) of STARS in vitro as well as in living cells. Mutagenesis studies identified Ile20 and Trp33 as the essential hydrophobic residues in CaM anchoring. Furthermore, the CaM binding deficient mutant (Ile20Ala, Trp33Ala) of STARS further enhanced its stimulatory effect on SRF-dependent transcriptional activation. These results suggest a connection between Ca(2+)-signaling via excitation-contraction coupling and the regulation of STARS-mediated gene expression in muscles.

Modulation of Interparticle Distance in Discrete Gold Nanoparticle Dimers and Trimers by DNA Single-Base Pairing

Self-assembled structures of metallic nanoparticles with dynamically changeable interparticle distance hold promise for the regulation of collective physical properties. This paper describes gold nanoparticle dimers and trimers that exhibit spontaneous and reversible changes in interparticle distance. To exploit this property, a gold nanoparticle is modified with precisely one long DNA strand and approximately five short DNA strands. The long DNA serves to align the nanoparticles on a template DNA via hybridization, while the short DNAs function to induce the interparticle distance changes. The obtained dimer and trimer are characterized with gel electrophoresis, dynamic light scattering measurements, and transmission electron microscopy (TEM). When the complementary short DNA is added to form the fully matched duplexes on the particle surface in the presence of MgCl2 , spontaneous reduction of the interparticle distance is observed with TEM and cryo-electron microscopy. By contrast, when the terminal-mismatched DNA is added, no structural change occurs under the same conditions. Therefore, the single base pairing/unpairing at the outermost surface of the nanoparticle impacts the interparticle distance. This unique feature could be applied to the regulation of structures and properties of various DNA-functionalized nanoparticle assemblies.

Thermodynamics-based rational design of DNA block copolymers for quantitative detection of single-nucleotide polymorphisms by affinity capillary electrophoresis

Diblock copolymers composed of allele-specific oligodeoxyribonucleotide (ODN) and poly(ethylene glycol) (PEG) are used as an affinity probe of free-solution capillary electrophoresis to quantitatively detect single-base substitutions in genetic samples. During electrophoresis, the probe binds strongly to a wild-type single-stranded DNA analyte (WT) through hybridization, while it binds weakly to its single-base-mutated DNA analyte (MT) due to a mismatch. Complex formation with the probe augments the hydrodynamic friction of either analyte, thereby retarding its migration. The difference in affinity strength leads to separation of the WT, MT, and contaminants, including the PCR primers used for sample preparation. The optimal sequence of the probe's ODN segment is rationally determined in such a way that the binding constant between the ODN segment and MT at the capillary temperature is on the order of 10(6) M(-1). The validity of this guideline is verified using various chemically synthesized DNA analytes, as well as those derived from a bacterial genome. The peak area ratio of MT agrees well with its feed ratio, suggesting the prospective use of the present method in SNP allele frequency estimation.

DNA dangling-end-induced colloidal stabilization of gold nanoparticles for colorimetric single-nucleotide polymorphism genotyping

A single-nucleotide polymorphism (SNP) detection method was developed by combining single-base primer extension and salt-induced aggregation of gold nanoparticles densely functionalized with double-stranded DNA (dsDNA-AuNP). The dsDNA-AuNPs undergo rapid aggregation in a medium of high ionic strength, whereas particles having a single-base protrusion at the outermost surface disperse stably, allowing detection of a single-base difference in length by color changes. When SNP typing primers are used as analytes to hybridize to the single-stranded DNA on the AuNP surface, the resulting dsDNA-AuNP works as a visual indicator of single-base extension. A set of four extension reaction mixtures is prepared using each of ddNTPs and subsequently subjected to the aggregation assay. Three mixtures involving ddNTP that is not complementary to the SNP site in the target produce the aggregates that exhibit a purple color. In contrast, one mixture with the complementary ddNTP generates the single-base protrusion and appears red. This method could potentially be used in clinical diagnostics for personalized medicine.

CSF-1 receptor-mediated differentiation of a new type of monocytic cell with B cell-stimulating activity: its selective dependence on IL-34

With the use of a mouse FDC line, FL-Y, we have been analyzing roles for FDCs in controlling B cell fate in GCs. Beside these regulatory functions, we fortuitously found that FL-Y cells induced a new type of CD11b⁺ monocytic cells (F4/80⁺, Gr-1⁻, Ly6C⁻, I-A/E(-/lo), CD11c⁻, CD115⁺, CXCR4⁺, CCR2⁺, CX₃CR1⁻) when cultured with a Lin⁻c-kit⁺ population from mouse spleen cells. The developed CD11b⁺ cells shared a similar gene-expression profile to mononuclear phagocytes and were designated as FDMCs. Here, we describe characteristic immunological functions and the induction mechanism of FDMCs. Proliferation of anti-CD40 antibody-stimulated B cells was markedly accelerated in the presence of FDMCs. In addition, the FDMC-activated B cells efficiently acquired GC B cell-associated markers (Fas and GL-7). We observed an increase of FDMC-like cells in mice after immunization. On the other hand, FL-Y cells were found to produce CSF-1 as well as IL-34, both of which are known to induce development of macrophages and monocytes by binding to the common receptor, CSF-1R, expressed on the progenitors. However, we show that FL-Y-derived IL-34, but not CSF-1, was selectively responsible for FDMC generation using neutralizing antibodies and RNAi. We also confirmed that FDMC generation was strictly dependent on CSF-1R. To our knowledge, a CSF-1R-mediated differentiation process that is intrinsically specific for IL-34 has not been reported. Our results provide new insights into understanding the diversity of IL-34 and CSF-1 signaling pathways through CSF-1R.

Dumbbell-shaped DNA analytes amplified by polymerase chain reaction for robust single-nucleotide polymorphism genotyping by affinity capillary electrophoresis

A sample preparation method was developed for single-nucleotide polymorphism (SNP) genotyping based on hybridization between a single-stranded DNA (ssDNA) analyte and an allele-specific oligonucleotide (ASO) probe. When the SNP site is located in the stable secondary structure, the folding of this analyte imposes kinetic penalties on the hybridization with the ASO probe. To address this issue, the sequence of the ssDNA analyte was converted from the original one so that the analyte exhibited a clear dumbbell-shaped structure composed of two stem-loop moieties and an unfolded probe-binding site. The as-prepared analyte was structurally favorable for hybridization with the ASO probe, irrespective of the original sequence and secondary structure of the analyte. The sequence conversion was easily achieved by polymerase chain reaction using forward and reverse primers having an additional sequence at the 5'-terminus. These ssDNA analytes were subjected to affinity capillary electrophoresis using a diblock copolymer probe composed of an ASO segment and a poly(ethylene glycol) segment. The 70-base dumbbell-shaped analytes with a single-base difference were clearly separated within 12 min, although the original ones exhibited almost no separation due to the undesired folding of the probe-binding site. This sample preparation method should open up a wide range of applications for the ASO probes in genetic analysis.

In vitro substrate phosphorylation by Ca²⁺/calmodulin-dependent protein kinase kinase using guanosine-5'-triphosphate as a phosphate donor

Background

Ca²⁺/calmodulin-dependent protein kinase kinase (CaMKK) phosphorylates and activates particular downstream protein kinases — including CaMKI, CaMKIV, and AMPK— to stimulate multiple Ca²⁺-signal transduction pathways. To identify previously unidentified CaMKK substrates, we used various nucleotides as phosphate donors to develop and characterize an in vitro phosphorylation assay for CaMKK.

Results

Here, we found that the recombinant CaMKK isoforms were capable of utilizing Mg-GTP as a phosphate donor to phosphorylate the Thr residue in the activation-loop of CaMKIα (Thr¹⁷⁷) and of AMPK (Thr¹⁷²) in vitro. Kinetic analysis indicated that the K_m values of CaMKK isoforms for GTP (400-500 μM) were significantly higher than those for ATP (~15 μM), and a 2- to 4-fold decrease in V_max was observed with GTP. We also confirmed that an ATP competitive CaMKK inhibitor, STO-609, also competes with GTP to inhibit the activities of CaMKK isoforms. In addition, to detect enhanced CaMKI phosphorylation in brain extracts with Mg-GTP and recombinant CaMKKs, we found potential CaMKK substrates of ~45 kDa and ~35 kDa whose Ca²⁺/CaM-induced phosphorylation was inhibited by STO-609.

Conclusions

These results indicated that screens that use STO-609 as a CaMKK inhibitor and Mg-GTP as a CaMKK-dependent phosphate donor might be useful to identify previously unidentified downstream target substrates of CaMKK.

Quantitative SNP genotyping by affinity capillary electrophoresis using PEG-oligodeoxyribonucleotide block copolymers with electroosmotic flow

Quantitative SNP detection was demonstrated with an ACE using a PEG-oligodeoxyribonucleotide block copolymer (PEG-b-ODN) as a probe in the presence of an EOF. The probe's PEG segment with large molecular weight and small polydispersity yielded a high resolution in the separation of a chemically synthesized 60-base ssDNA (WT) and its single-base-substituted mutant (MT). A mixture of WT and MT was clearly separated within 10 min by simultaneously using two types of PEG-b-ODN probes whose ODN segments were complementary to WT and MT and whose PEG segments were of different lengths. The peak area ratio between WT and MT was in good agreement with the feed ratio. The averaged difference between the feed and observed ratio of MT was determined to be 0.23%, which is lower than that of any other methods. The ACE using the PEG-b-ODN probes in the presence of EOF could be utilized as a facile method for estimating SNP allele frequency in various research fields.