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  • 1
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    Crystal structure of the GlnZ-DraG complex reveals a different form of PII-target interaction [Biophysics and Computational Biology] (2011)
    National Academy of Sciences
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    Publication Date: 2011-11-23
    Description: Nitrogen metabolism in bacteria and archaea is regulated by a ubiquitous class of proteins belonging to the PIIfamily. PII proteins act as sensors of cellular nitrogen, carbon, and energy levels, and they control the activities of a wide range of target proteins by protein-protein interaction. The sensing mechanism relies on conformational changes induced by the binding of small molecules to PII and also by PII posttranslational modifications. In the diazotrophic bacterium Azospirillum brasilense, high levels of extracellular ammonium inactivate the nitrogenase regulatory enzyme DraG by relocalizing it from the cytoplasm to the cell membrane. Membrane localization of DraG occurs through the formation of a ternary complex in which the PII protein GlnZ interacts simultaneously with DraG and the ammonia channel AmtB. Here we describe the crystal structure of the GlnZ-DraG complex at 2.1 Å resolution, and confirm the physiological relevance of the structural data by site-directed mutagenesis. In contrast to other known PII complexes, the majority of contacts with the target protein do not involve the T-loop region of PII. Hence this structure identifies a different mode of PII interaction with a target protein and demonstrates the potential for PII proteins to interact simultaneously with two different targets. A structural model of the AmtB-GlnZ-DraG ternary complex is presented. The results explain how the intracellular levels of ATP, ADP, and 2-oxoglutarate regulate the interaction between these three proteins and how DraG discriminates GlnZ from its close paralogue GlnB.
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    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 2
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    Arabidopsis cryptochrome 2 (CRY2) functions by the photoactivation mechanism distinct from the tryptophan (trp) triad-dependent photoreduction [Plant Biology] (2011)
    National Academy of Sciences
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    Publication Date: 2011-12-21
    Description: Cryptochromes are blue-light receptors mediating various light responses in plants and animals. The photochemical mechanism of cryptochromes is not well understood. It has been proposed that photoactivation of cryptochromes involves the blue-light–dependent photoreduction of flavin adenine dinucleotide via the electron transport chain composed of three evolutionarily conserved tryptophan residues known as the “trp triad.” We investigated this hypothesis by analyzing the photochemical and physiological activities of Arabidopsis cryptochrome 2 (CRY2) mutations altered in each of the three trp-triad residues. We found that all trp-triad mutations of CRY2 tested lost photoreduction activity in vitro but retained the physiological and biochemical activities in vivo. Some of the trp-triad mutations of CRY2 remained responsive to blue light; others, such as CRY2W374A, became constitutively active. In contrast to wild-type CRY2, which undergoes blue-light–dependent interaction with the CRY2-signaling proteins SUPPRESSOR OF PHYA 1 (SPA1) and cryptochrome-interaction basic helix–loop–helix 1 (CIB1), the constitutively active CRY2W374A interacts with SPA1 and CIB1 constitutively. These results support the hypothesis that cryptochromes mediate blue-light responses via a photochemistry distinct from trp-triad–dependent photoreduction and that the trp-triad residues are evolutionarily conserved in the photolyase/cryptochrome superfamily for reasons of structural integrity rather than for photochemistry per se.
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  • 3
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    Lethal mitochondrial cardiomyopathy in a hypomorphic Med30 mouse mutant is ameliorated by ketogenic diet [Genetics] (2011)
    National Academy of Sciences
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    Publication Date: 2011-12-07
    Description: Deficiencies of subunits of the transcriptional regulatory complex Mediator generally result in embryonic lethality, precluding study of its physiological function. Here we describe a missense mutation in Med30 causing progressive cardiomyopathy in homozygous mice that, although viable during lactation, show precipitous lethality 2–3 wk after weaning. Expression profiling reveals pleiotropic changes in transcription of cardiac genes required for oxidative phosphorylation and mitochondrial integrity. Weaning mice to a ketogenic diet extends viability to 8.5 wk. Thus, we establish a mechanistic connection between Mediator and induction of a metabolic program for oxidative phosphorylation and fatty acid oxidation, in which lethal cardiomyopathy is mitigated by dietary intervention.
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  • 4
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    Large area and structured epitaxial graphene produced by confinement controlled sublimation of silicon carbide [Physics] (2011)
    National Academy of Sciences
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    Publication Date: 2011-10-12
    Description: After the pioneering investigations into graphene-based electronics at Georgia Tech, great strides have been made developing epitaxial graphene on silicon carbide (EG) as a new electronic material. EG has not only demonstrated its potential for large scale applications, it also has become an important material for fundamental two-dimensional electron gas physics. It was long known that graphene mono and multilayers grow on SiC crystals at high temperatures in ultrahigh vacuum. At these temperatures, silicon sublimes from the surface and the carbon rich surface layer transforms to graphene. However the quality of the graphene produced in ultrahigh vacuum is poor due to the high sublimation rates at relatively low temperatures. The Georgia Tech team developed growth methods involving encapsulating the SiC crystals in graphite enclosures, thereby sequestering the evaporated silicon and bringing growth process closer to equilibrium. In this confinement controlled sublimation (CCS) process, very high-quality graphene is grown on both polar faces of the SiC crystals. Since 2003, over 50 publications used CCS grown graphene, where it is known as the “furnace grown” graphene. Graphene multilayers grown on the carbon-terminated face of SiC, using the CCS method, were shown to consist of decoupled high mobility graphene layers. The CCS method is now applied on structured silicon carbide surfaces to produce high mobility nano-patterned graphene structures thereby demonstrating that EG is a viable contender for next-generation electronics. Here we present for the first time the CCS method that outperforms other epitaxial graphene production methods.
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  • 5
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    Large-scale, spatially-explicit test of the refuge strategy for delaying insecticide resistance [Agricultural Sciences] (2012)
    National Academy of Sciences
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    Publication Date: 2012-01-18
    Description: The refuge strategy is used worldwide to delay the evolution of pest resistance to insecticides that are either sprayed or produced by transgenic Bacillus thuringiensis (Bt) crops. This strategy is based on the idea that refuges of host plants where pests are not exposed to an insecticide promote survival of susceptible pests. Despite widespread adoption of this approach, large-scale tests of the refuge strategy have been problematic. Here we tested the refuge strategy with 8 y of data on refuges and resistance to the insecticide pyriproxyfen in 84 populations of the sweetpotato whitefly (Bemisia tabaci) from cotton fields in central Arizona. We found that spatial variation in resistance to pyriproxyfen within each year was not affected by refuges of melons or alfalfa near cotton fields. However, resistance was negatively associated with the area of cotton refuges and positively associated with the area of cotton treated with pyriproxyfen. A statistical model based on the first 4 y of data, incorporating the spatial distribution of cotton treated and not treated with pyriproxyfen, adequately predicted the spatial variation in resistance observed in the last 4 y of the study, confirming that cotton refuges delayed resistance and treated cotton fields accelerated resistance. By providing a systematic assessment of the effectiveness of refuges and the scale of their effects, the spatially explicit approach applied here could be useful for testing and improving the refuge strategy in other crop–pest systems.
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  • 6
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    Slug-dependent BRCA1 repression [Medical Sciences] (2012)
    National Academy of Sciences
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    Publication Date: 2012-10-10
    Description: Slug (Snail2) plays critical roles in regulating the epithelial–mesenchymal transition (EMT) programs operative during development and disease. However, the means by which Slug activity is controlled remain unclear. Herein we identify an unrecognized canonical Wnt/GSK3β/β-Trcp1 axis that controls Slug activity. In the absence of Wnt signaling, Slug is phosphorylated by...
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  • 7
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    Bacterial chemoreceptor arrays are hexagonally packed trimers of receptor dimers networked by rings of kinase and coupling proteins [Biochemistry] (2012)
    National Academy of Sciences
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    Publication Date: 2012-03-07
    Description: Chemoreceptor arrays are supramolecular transmembrane machines of unknown structure that allow bacteria to sense their surroundings and respond by chemotaxis. We have combined X-ray crystallography of purified proteins with electron cryotomography of native arrays inside cells to reveal the arrangement of the component transmembrane receptors, histidine kinases (CheA) and CheW coupling proteins. Trimers of receptor dimers lie at the vertices of a hexagonal lattice in a “two-facing-two” configuration surrounding a ring of alternating CheA regulatory domains (P5) and CheW couplers. Whereas the CheA kinase domains (P4) project downward below the ring, the CheA dimerization domains (P3) link neighboring rings to form an extended, stable array. This highly interconnected protein architecture underlies the remarkable sensitivity and cooperative nature of transmembrane signaling in bacterial chemotaxis.
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  • 8
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    Axin2 promotes colon carcinoma progression [Medical Sciences] (2012)
    National Academy of Sciences
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    Publication Date: 2012-07-11
    Description: Aberrant activation of canonical Wingless-type MMTV integration site family (Wnt) signaling is pathognomonic of colorectal cancers (CRC) harboring functional mutations in either adenomatous polyposis coli or β-catenin. Coincident with Wnt cascade activation, CRCs also up-regulate the expression of Wnt pathway feedback inhibitors, particularly the putative tumor suppressor, Axin2. Because Axin2 serves as a negative regulator of canonical Wnt signaling in normal cells, recent attention has focused on the utility of increasing Axin2 levels in CRCs as a means to slow tumor progression. However, rather than functioning as a tumor suppressor, we demonstrate that Axin2 acts as a potent promoter of carcinoma behavior by up-regulating the activity of the transcriptional repressor, Snail1, inducing a functional epithelial-mesenchymal transition (EMT) program and driving metastatic activity. Silencing Axin2 expression decreases Snail1 activity, reverses EMT, and inhibits CRC invasive and metastatic activities in concert with global effects on the Wnt-regulated cancer cell transcriptome. The further identification of Axin2 and nuclear Snail1 proteins at the invasive front of human CRCs supports a revised model wherein Axin2 acts as a potent tumor promoter in vivo.
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  • 9
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    Opposite regulation of TRPML1 by PIP2 isoforms [Neuroscience] (2012)
    National Academy of Sciences
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    Publication Date: 2012-07-11
    Description: Phosphoinositides serve as address labels for recruiting peripheral cytoplasmic proteins to specific subcellular compartments, and as endogenous factors for modulating the activity of integral membrane proteins. Phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) is a plasma-membrane (PM)–specific phosphoinositide and a positive cofactor required for the activity of most PM channels and transporters. This requirement for phosphoinositide cofactors has been proposed to prevent PM channel/transporter activity during passage through the biosynthetic/secretory and endocytic pathways. To determine whether intracellularly localized channels are similarly “inactivated” at the PM, we studied PIP2 modulation of intracellular TRPML1 channels. TRPML1 channels are primarily localized in lysosomes, but can also be detected temporarily in the PM upon lysosomal exocytosis. By directly patch-clamping isolated lysosomes, we previously found that lysosomal, but not PM-localized, TRPML1 is active with PI(3,5)P2, a lysosome-specific PIP2, as the underlying positive cofactor. Here we found that “silent” PM-localized TRPML1 could be activated by depleting PI(4,5)P2 levels and/or by adding PI(3,5)P2 to inside-out membrane patches. Unlike PM channels, surface-expressed TRPML1 underwent a unique and characteristic run-up upon patch excision, and was potently inhibited by a low micromolar concentration of PI(4,5)P2. Conversely, depletion of PI(4,5)P2 by either depolarization-induced activation or chemically induced translocation of 5′-phosphatase potentiated whole-cell TRPML1 currents. PI(3,5)P2 activation and PI(4,5)P2 inhibition of TRPML1 were mediated by distinct basic amino acid residues in a common PIP2-interacting domain. Thus, PI(4,5)P2 may serve as a negative cofactor for intracellular channels such as TRPML1. Based on these results, we propose that phosphoinositide regulation sets compartment-specific activity codes for membrane channels and transporters.
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  • 10
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    Role of DKK2 in glucose metabolism [Pharmacology] (2012)
    National Academy of Sciences
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    Publication Date: 2012-07-11
    Description: Mutations in Wnt receptor LRP5/6 and polymorphism in Wnt-regulated transcription factor TCF7L2 are associated with dysregulation of glucose metabolism. However, it is not clear whether Wnt antagonist Dickkopf (Dkk) has a significant role in the regulation of glucose metabolism. Here, we identified small-molecule inhibitors of Wnt antagonist Dkk through molecular modeling, computation-based virtual screens, and biological assays. One of the Dkk inhibitors reduced basal blood-glucose concentrations and improved glucose tolerance in mice. This Dkk inhibitor appeared to act through DKK2 because the inhibitor exerted no additional effects on glucose metabolism in the Dkk2−/− mice. Our study of Dkk2−/− mice showed that DKK2 deficiency was associated with increased hepatic glycogen accumulation and decreased hepatic glucose output. DKK2 deficiency did not cause in increase in insulin production but resulted in increased Wnt activity and GLP1 production in the intestines. Given that the Dkk inhibitor improved glucose tolerance in a murine model of type 2 diabetes (db/db), we suggest that DKK2 may be a potential therapeutic target for treating type 2 diabetes.
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