��Pix Up-regulates Na+/H+ Exchanger 3 through a Shank2-mediated Protein-Protein Interaction

Na⁺/H⁺ exchanger 3 (NHE3) plays an important role in neutral Na⁺ transport in mammalian epithelial cells. The Rho family of small GTPases and the PDZ (PSD-95/discs large/ZO-1) domain-based adaptor Shank2 are known to regulate the membrane expression and activity of NHE3. In this study we examined the role of βPix, a guanine nucleotide exchange factor for the Rho GTPase and a strong binding partner to Shank2, in NHE3 regulation using integrated molecular and physiological approaches. Immunoprecipitation and pulldown assays revealed that NHE3, Shank2, and βPix form a macromolecular complex when expressed heterologously in mammalian cells as well as endogenously in rat colon, kidney, and pancreas. In addition, these proteins co-segregated at the apical surface of rat colonic epithelial cells, as detected by immunofluorescence staining. When expressed in PS120/NHE3 cells, βPix increased membrane expression and basal activity of NHE3. Interestingly, the effects of βPix on NHE3 were abolished by cotransfection with dominant-negative Shank2 mutants and by treatment with Clostridium difficile toxin B, a Rho GTPase inhibitor, indicating that Shank2 and Rho GTPases are involved in βPix-mediated NHE3 regulation. Knockdown of endogenous βPix by RNA interference decreased Shank2-induced increase of NHE3 membrane expression in HEK 293T cells. These results indicate that βPix up-regulates NHE3 membrane expression and activity by Shank2-mediated protein-protein interaction and by activating Rho GTPases in the apical regions of epithelial cells.     

From Genotype �� Environment Interaction to Gene �� Environment Interaction

Historically in plant breeding a large number of statistical models has been developed and used for studying genotype × environment interaction. These models have helped plant breeders to assess the stability of economically important traits and to predict the performance of newly developed genotypes evaluated under varying environmental conditions. In the last decade, the use of relatively low numbers of markers has facilitated the mapping of chromosome regions associated with phenotypic variability (e.g., QTL mapping) and, to a lesser extent, revealed the differetial response of these chromosome regions across environments (i.e., QTL × environment interaction). QTL technology has been useful for marker-assisted selection of simple traits; however, it has not been efficient for predicting complex traits affected by a large number of loci. Recently the appearance of cheap, abundant markers has made it possible to saturate the genome with high density markers and use marker information to predict genomic breeding values, thus increasing the precision of genetic value prediction over that achieved with the traditional use of pedigree information. Genomic data also allow assessing chromosome regions through marker effects and studying the pattern of covariablity of marker effects across differential environmental conditions. In this review, we outline the most important models for assessing genotype × environment interaction, QTL × environment interaction, and marker effect (gene) × environment interaction. Since analyzing genetic and genomic data is one of the most challenging statistical problems researchers currently face, different models from different areas of statistical research must be attempted in order to make significant progress in understanding genetic effects and their interaction with environment.     

Prolyl Oligopeptidase Enhances α-Synuclein Dimerization via Direct Protein-Protein Interaction

Prolyl oligopeptidase (PREP) accelerates the aggregation of α-synuclein (aSyn), a key protein involved in development of Parkinson disease and other synucleinopathies. PREP inhibitors reduce aSyn aggregation, but the mechanism has remained unknown. We have now used protein-fragment complementation assays (PCA) and microscale thermophoresis in parallel to show that PREP interacts directly with aSyn in both intact cells and in a cell-free system. Using split luciferase-based PCA, we first showed that PREP enhances the formation of soluble aSyn dimers in live Neuro-2A neuroblastoma cells. A PREP inhibitor, KYP-2047, reduced aSyn dimerization in PREP-expressing cells but not in cells lacking PREP expression. aSyn dimerization was also enhanced by PREP(S554A), an enzymatically inactive PREP mutant, but this was not affected by KYP-2047. PCA and microscale thermophoresis studies showed that aSyn interacts with both PREP and PREP(S554A) with low micromolar affinity. Neither the proline-rich, C-terminal domain of aSyn nor the hydrolytic activity of PREP was required for the interaction with PREP. Our results show that PREP binds directly to aSyn to enhance its dimerization and may thus serve as a nucleation point for aSyn aggregation. Native gel analysis showed that KYP-2047 shifts PREP to a compact monomeric form with reduced ability to promote aSyn nucleation. As PREP inhibition also enhances autophagic clearance of aSyn, PREP inhibitors may reduce accumulation of aSyn inclusions via a dual mechanism and are thus a novel therapeutic candidate for synucleinopathies. Our results also suggest that PREP has other cellular functions in addition to its peptidase activity.     

Investigations of �� Initiator Protein-mediated Interaction between Replication Origins �� and �� of the Plasmid R6K

A typical plasmid replicon of Escherichia coli, such as ori γ of R6K, contains tandem iterons (iterated initiator protein binding sites), an AT-rich region that melts upon initiator-iteron interaction, two binding sites for the bacterial initiator protein DnaA, and a binding site for the DNA-bending protein IHF. R6K also contains two structurally atypical origins called α and β that are located on either side of γ and contain a single and a half-iteron, respectively. Individually, these sites do not bind to initiator protein π but access it by DNA looping-mediated interaction with the seven π-bound γ iterons. The π protein exists in 2 interconvertible forms: inert dimers and active monomers. Initiator dimers generally function as negative regulators of replication by promoting iteron pairing (“handcuffing”) between pairs of replicons that turn off both origins. Contrary to this existing paradigm, here we show that both the dimeric and the monomeric π are necessary for ori α-driven plasmid maintenance. Furthermore, efficient looping interaction between α and γ or between 2 γ iterons in vitro also required both forms of π. Why does α-γ iteron pairing promote α activation rather than repression? We show that a weak, transitory α-γ interaction at the iteron pairs was essential for α-driven plasmid maintenance. Swapping the α iteron with one of γ without changing the original sequence context that caused enhanced looping in vitro caused a significant inhibition of α-mediated plasmid maintenance. Therefore, the affinity of α iteron for π-bound γ and not the sequence context determined whether the origin was activated or repressed.     

Evidence That Integrin ��IIb��3-dependent Interaction of Mast Cells with Fibrinogen Exacerbates Chronic Inflammation

Integrin αIIbβ3 is expressed in mast cells as well as in megakaryocytes/platelets. A recent study has shown that surface expression levels of integrin αVβ3 are elevated in integrin αIIb-deficient bone marrow-derived mast cells (BMMCs) as compared with wild-type (WT) counterparts, but the underlying mechanism remains obscure. Here we demonstrate by transducing integrin αIIb into integrin αIIb-deficient BMMCs that surface expression levels of integrin αVβ3 are inversely related to those of integrin αIIbβ3. Thus, competitive association of integrin β3 with integrin αIIb or integrin αV determines surface expression levels of integrin αIIbβ3 or αVβ3 in mast cells. We compared WT and integrin αIIb-deficient BMMCs as well as integrin αIIb-deficient BMMCs transduced with integrin αIIb(WT) or non-functional αIIb(D163A) mutant and found that enhancement of proliferation, degranulation, cytokine production, and migration of BMMCs through interaction with fibrinogen (FB) depended on integrin αIIbβ3. In addition, elevated surface expression of integrin αVβ3 failed to compensate for loss of FB-associated functions in integrin αIIb-deficient BMMCs while enhancing adhesion to vitronectin or von Willebrand factor. Importantly, integrin αIIb deficiency strongly suppressed chronic inflammation with the remarkable increase of mast cells induced by continuous intraperitoneal administration of FB, although it did not affect acute allergic responses or mast cell numbers in tissues in steady states. Interestingly, soluble FB promoted cytokine production of BMMCs in response to Staphylococcus aureus with FB-binding capacity, through integrin αIIbβ3-dependent recognition of this pathogen. Collectively, integrin αIIbβ3 in mast cells plays an important part in FB-associated, chronic inflammation and innate immune responses.     

A Small Molecule That Inhibits the Interaction of Paxillin and ��4 Integrin Inhibits Accumulation of Mononuclear Leukocytes at a Site of Inflammation

Extracellular antagonists of α4 integrin are an effective therapy for several autoimmune and inflammatory diseases; however, these agents that directly block ligand binding may exhibit mechanism-based toxicities. Inhibition of α4 integrin signaling by mutations of α4 that block paxillin binding inhibits inflammation while limiting mechanism-based toxicities. Here, we test a pharmacological approach by identifying small molecules that inhibit the α4 integrin-paxillin interaction. By screening a large (∼40,000-compound) chemical library, we identified a noncytotoxic inhibitor of this interaction that impaired integrin α4-mediated but not αLβ2-mediated Jurkat T cell migration. The identified compound had no effect on α4-mediated migration in cells bearing the α4(Y991A) mutation that disrupts the α4-paxillin interaction, establishing the specificity of its action. Administration of this compound to mice led to impaired recruitment of mononuclear leukocytes to a site of inflammation in vivo, whereas an isomer that does not inhibit the α4-paxillin interaction had no effect on α4-mediated cell migration, cell spreading, or recruitment of leukocytes to an inflammatory site. Thus, a small molecule inhibitor that interferes with α4 integrin signaling reduces α4-mediated T cell migration in vivo, thus providing proof of principle for inhibition of α4 integrin signaling as a target for the pharmacological reduction of inflammation.     

Neurotoxicity of Alzheimer's disease A�� peptides is induced by small changes in the A��42 to A��40 ratio

The amyloid peptides Aβ₄₀ and Aβ₄₂ of Alzheimer's disease are thought to contribute differentially to the disease process. Although Aβ₄₂ seems more pathogenic than Aβ₄₀, the reason for this is not well understood. We show here that small alterations in the Aβ₄₂:Aβ₄₀ ratio dramatically affect the biophysical and biological properties of the Aβ mixtures reflected in their aggregation kinetics, the morphology of the resulting amyloid fibrils and synaptic function tested in vitro and in vivo. A minor increase in the Aβ₄₂:Aβ₄₀ ratio stabilizes toxic oligomeric species with intermediate conformations. The initial toxic impact of these Aβ species is synaptic in nature, but this can spread into the cells leading to neuronal cell death. The fact that the relative ratio of Aβ peptides is more crucial than the absolute amounts of peptides for the induction of neurotoxic conformations has important implications for anti‐amyloid therapy. Our work also suggests the dynamic nature of the equilibrium between toxic and non‐toxic intermediates.     

Analysis of Cynandione A’s Anti-Ischemic Stroke Effects from Pathways and Protein-Protein Interactome

Ischemic stroke is the third leading cause of death in the world. Our previous study found that cynandione A (CYNA), the main component from the root of Cynanchum bungei, exhibits anti-ischemic stroke activity. In this work, we investigated the therapeutic mechanisms of CYNA to ischemic stroke at protein network level. First, PC12 cells and cerebellar granule neurons were prepared to validate the effects of CYNA against glutamate injury. Our experiments suggested that CYNA could dose-dependently mitigate glutamate-induced neurons neurotoxicity and inhibit glutamate-induced upregulation of KHSRP and HMGB1, further confirming the neuroprotective effects of CYNA in vivo. Then, on the pathway sub-networks, which present biological processes that can be impacted directly or in periphery nodes by drugs via their targets, we found that CYNA regulates 11 pathways associated with the biological process of thrombotic or embolic occlusion of a cerebral artery. Meanwhile, by defining a network-based anti-ischemic stroke effect score, we showed that CYNA has a significantly higher effect score than random counterparts, which suggests a synergistic effect of CYNA to ischemic stroke. This study may shed new lights on the study of network based pharmacology.     

Allele-specific Effects of Human Deafness ��-Actin Mutations (DFNA20/26) on the Actin/Cofilin Interaction

Auditory hair cell function requires proper assembly and regulation of the nonmuscle gamma isoactin-rich cytoskeleton, and six point mutations in this isoactin cause a type of delayed onset autosomal dominant nonsyndromic progressive hearing loss, DFNA20/26. The molecular basis underlying this actin-dependent hearing loss is unknown. To address this problem, the mutations have been introduced into yeast actin, and their effects on actin function were assessed in vivo and in vitro. Because we previously showed that polymerization was unaffected in five of the six mutants, we have focused on proteins that regulate actin, in particular cofilin, which severs F-actin and sequesters actin monomers. The mutations do not affect the interaction of cofilin with G-actin. However, T89I and V370A mutant F-actins are much more susceptible to cofilin disassembly than WT filaments in vitro. Conversely, P332A filaments demonstrate enhanced resistance. Wild type actin solutions containing T89I, K118M, or P332A mutant actins at mole fractions similar to those found in the hair cell respond in vitro toward cofilin in a manner proportional to the level of the mutant present. Finally, depression of cofilin action in vivo by elimination of the cofilin-activating protein, Aip1p, rescues the inability to grow on glycerol caused by K118M, T278I, P332A, and V370A. These results suggest that a filament instability caused by these mutations can be balanced by decreasing a system in vivo that promotes increased filament turnover. Such mutant-dependent filament destabilization could easily result in hair cell malfunction leading to the late-onset hearing loss observed in these patients.Our ability to perceive sounds hinges on the proper functioning of a highly specialized group of cells, called hair cells, which are housed in the cochlea of the inner ear. Their actin cytoskeleton plays a vital role in the ability of these cells to transduce mechanical stimuli into electrical responses (1). The columnar auditory hair cell consists of three actin-rich components (2). First are the three graded rows of finger-like projections from the apical surface of the cell referred to as stereocilia. These protrusions, comprised predominantly of bundles of actin filaments, are surrounded by the cellular membrane (3, 4). Sound-generated pressure waves in the cochlear fluid displace the basilar membrane, which in turn forces the stereocilia into the overlaying tectorial membrane, resulting in their mechanical deformation. Deflection of the stereocilia results in the opening of mechanoelectrical transduction ion channels residing on the stereocilia and ultimately triggers the initiation of a nerve impulse, which is relayed by the auditory nerve to the brain for interpretation (5).Normal development, functioning, and maintenance of hair cell structures depend on tight regulation of the hair cell cytoskeleton as it controls the height and width of the stereociliary bundles. Each stereocilium inserts into the second actin-rich structure, the cuticular plate, a web-like arrangement of actin filaments and associated actin-binding proteins located just beneath the basal surface of the stereocilia (3, 6). This fibrous matrix produces a foundation into which the stereocilia are anchored, and it furnishes physical support for maintaining the stereociliary bundles in their upright positions. Finally, the zonula adherens contains a thick band of actin filaments which encircles each hair cell. Its function is to both unite the hair cells with the surrounding matrix of epithelial cells and provide tension across the cuticular plate in a manner analogous to the springs found on a trampoline. Based on actin involvement in cochlear cell function, it is not surprising that mutations in the components of these filamentous networks cause deafness.In the majority of non-muscle cells in the body, the predominant actin isoform is β-nonmuscle actin with smaller amounts of γ-nonmuscle isoactin also present (7). These two isoforms differ at only 4 of the 375 amino acid residues in the protein. The N terminus of β-actin has three Asp residues, whereas that of γ-actin has three Glu residues. The other difference occurs at position 10; Val in β-actin is substituted by Ile in γ-actin. In the hair cell, however, γ-nonmuscle actin is the major form comprising about 75% of the total actin in the cell based on immunological studies with actin isoform-specific antibodies (8, 9).Six point mutations in the coding region of the γ-nonmuscle actin gene (ACT1G) have been shown to cause a subtype of autosomal dominant nonsyndromic progressive sensorineural hearing loss designated DNFA20/26 (10–12). Patients carrying these mutations hear fine until their teens and twenties. Typically at this point the patients demonstrate marked decreases in their ability to hear high frequency sounds ranging from 4 to 8 kHz. As the patient ages the initial high frequency of hearing loss spreads over a broader range of frequencies (250 Hz to 8 kHz) until the overall loss becomes profound.Until recently nothing was known about how the biochemical effects of these actin mutations might ultimately lead to hearing loss. To address this problem, we devised a model system in which we introduced these six point mutations into their corresponding positions in yeast actin whose sequence is 90% identical to that of γ-nonmuscle isoactin. Furthermore, each of the mutation sites in γ-nonmuscle actin is identical to the corresponding site in yeast actin. This system allows for the analysis of these mutation effects in vivo and for the purification of enough of the mutant proteins to assess their biochemical and biophysical properties. Although these mutations produced allele-specific effects in yeast cells harboring them, the purified mutant actins, with one exception, V370A, displayed polymerization characteristics virtually identical to those of WT yeast actin (13). The lack of apparent gross polymerization defects associated with these mutant actins suggested that, instead, the deafness associated with them might result from misregulation of cytoskeletal dynamics because of altered interactions with one or more of the battery of actin-binding proteins known to control cytoskeletal function and dynamics.The actin filament is a polar structure (14, 15) with a barbed end, the preferred end for actin monomer addition, and a pointed end, which is the predominant end for monomer dissociation from the filament (16). This polarity is translated to each monomer, with the barbed end defined by subdomains 1 and 3 of the actin and the pointed end by subdomains 2 and 4 (Fig. 1). Four of the six mutations, K118M, T278I, P332A, and V370A, are in positions that could affect the barbed end surface, which interfaces with the pointed end of the next lower monomer in the filament strand (15). Moreover, three of the mutations, T89I and K118M and V370A, are predicted to be part of the actin surface comprising the tight and weak binding sites, respectively, for the actin-binding protein cofilin (17).Open in a separate windowFIGURE 1.Locations of the six γ-actin deafness mutations in yeast. A, front view of the crystal structure of the yeast actin monomer (63), modified from Protein Data Bank code 1YAG using Swiss-PdbViewer Version 4.01. The positions of the mutations are modeled in space-fill and color-highlighted as follows: T89I, orange; K118M, red; P264L, blue; T278I, green; P332A purple; cyan, V370A. ATP is modeled in ball-stick and colored in Corey-Pauling-Koltun. Numbers denote the actin subdomains, and N and C mark the respective termini. B, model illustrating the longitudinal contacts between two neighboring monomers within the same filament strand based on the Holmes filament model (15). Each monomer is labeled as in panel A with regard to the mutations, ADP, and subdomains. The red dashed circle denotes the general vicinity on the actin surface to which cofilin binds (21, 41, 42).Cofilin is a small, 15–21-kDa actin-binding protein that, depending on its concentration, can sequester actin monomers (18, 19), sever/disassemble actin filaments (20–24), and promote filament nucleation by stabilizing spontaneously forming actin nuclei (25, 26). Cofilin plays an essential role in the regulation of actin cytoskeletal dynamics (18, 27–31) and is found in cochlear cells (neibank.nei.nih.gov). Cofilin-dependent filament scission/disassembly results from its disruption of both lateral (24, 32) and longitudinal (21) contacts between neighboring monomers within the filament. Thus, an actin mutation which results in destabilization of monomer-monomer interfaces or alters the cofilin binding site might make the filament more susceptible to cofilin severing. An alternative function of cofilin that might be affected by these mutations is its ability to bind to either ATP monomers being added to the barbed end of the filament or ADP-actin monomers being released from the pointed end of the filament (23, 33, 34). Altered binding could lead to altered degrees of monomer sequestration by the cofilin ultimately affecting filament length and polymer dynamics.In this study we have assessed the ability of yeast actins carrying the deafness-causing actin mutations to interact with yeast cofilin in vitro. Based on our results in vitro, which demonstrated allele-specific altered actin-cofilin interactions, we then dampened cofilin function in vivo to determine whether altered regulation of the mutant actins by cofilin was responsible for the glycerol phenotypes associated with these mutations in vivo in yeast (13).     

Genetic Map of Bacteriophage α

Temperature-sensitive mutants of phage alpha were obtained by means of various mutagens and assigned to 25 complementation groups. Temperature-sensitive mutants belonging to 21 complementation groups and a mutant giving turbid plaques were used to perform two- and three-factor crosses. Seventeen of the cistrons and the turbid mutant were shown to belong to the same linear linkage group, which showed no signs of circularity. The remaining four unlinked cistrons showed peculiarities in their recombination properties. Genes which are known to be expressed earlier apear to be grouped together in a terminal segment of the linkage group.     

Hydrophilicity Matching – A Potential Prerequisite for the Formation of Protein-Protein Complexes in the Cell

A binding event between two proteins typically consists of a diffusional search of binding partners for one another, followed by a specific recognition of the compatible binding sites resulting in the formation of the complex. However, it is unclear how binding partners find each other in the context of the crowded, constantly fluctuating, and interaction-rich cellular environment. Here we examine the non-specific component of protein-protein interactions, which refers to those physicochemical properties of the binding partners that are independent of the exact details of their binding sites, but which can affect their localization or diffusional search for one another. We show that, for a large set of high-resolution experimental 3D structures of binary, transient protein complexes taken from the DOCKGROUND database, the binding partners display a surprising, statistically significant similarity in terms of their total hydration free energies normalized by a size-dependent variable. We hypothesize that colocalization of binding partners, even within individual cellular compartments such as the cytoplasm, may be influenced by their relative hydrophilicity, potentially in response to local hydrophilic gradients.