B Site (b + site)

Distribution by Scientific Domains


Selected Abstracts


Phosphorylation of NF-,B proteins by cyclic GMP-dependent kinase

FEBS JOURNAL, Issue 10 2003
A noncanonical pathway to NF-, B activation
The transcription factor NF-,B is activated in cellular stress responses. This requires rapid regulation of its function, which is accomplished, in part, by various modes of phosphorylation. Even though diverse DNA binding subunits of NF-,B proteins may transactivate from distinct recognition sequences, the differential regulation of transcription from the large number of NF-,B responsive sites in various gene promoters and enhancers has been incompletely understood. The cyclic GMP-dependent kinase (PKG) is an important mediator of signal transduction that may induce gene expression through cAMP response element binding protein (CREB) and through other, yet undefined, mechanisms. We have previously characterized a signal transduction pathway that leads to activation-induced cell death in T-lymphocytes and involves the activation of PKG. Here we demonstrate that the NF-,B proteins p65, p49 (also called p52), and p50 are specific substrates for this kinase. PKG dose-dependently increases the transactivating activity of p65 from the NF-,B consensus sequence. It also mediates dose-dependently an increase in transcriptional activity by p49 or p50 from a unique CCAAT/enhance binding protein (C/EBP)-associated NF-,B site, but not from the consensus site. Phosphorylation of p65, p50, or p49 does not alter their subcellular distribution. Because the release of cytosolic p65/p50 heterodimers into the nucleus is by itself insufficient to differentiate all the numerous NF-,B promoter sequences, phosphorylation of the DNA-binding subunits reveals a form of differential regulation of NF-,B activity and it implies a novel pathway for PKG-induced gene transcription. These observations may bear on mechanisms of programmed cell death in T-lymphocytes. They may also be relevant to ongoing efforts to induce cancer cell apoptosis through activation of PKG. [source]


Early pyrotechnology in the Near East: Experimental lime-plaster production at the Pre-Pottery Neolithic B site of Kfar HaHoresh, Israel

GEOARCHAEOLOGY: AN INTERNATIONAL JOURNAL, Issue 6 2008
Y. Goren
A characteristic hallmark of the Pre-Pottery Neolithic B (PPNB) in the southern Levant was the extensive use of lime plaster for architectural and other purposes. Yet no obvious kilns have been identified in archaeological contexts. Here we present details of an experimental pit-kiln modeling lime-plaster production based on observed burnt stone accumulations in pits at the PPNB site of Kfar HaHoresh in the lower Galilee. The experimental kiln was loaded in layers with ,500 kg of limestone (pebbles and stones) and ,1000 kg of fuel (branches and dung). Fired for 24 hours, and reaching a maximum 870C, the kiln yielded almost 250 kg of quicklime (calcium oxide, CaO). Micromorphological samples, general observations, and scaled plan view drawings made immediately following and nine years after ignition demonstrate that the original shape of the kiln and residual quicklime within and around it rapidly dissipated through bioturbation, trampling by animals, erosion, rain, and exposure to the elements. This could account for the seeming absence of kilns within sites, although they were probably located close to where lime-plaster was applied, given the unstable nature and toxic effects of handling quicklime. Calculations of the manpower and fuel involved indicate that PPNB lime-plaster production may have been less labor intensive and less detrimental to the environment than previously portrayed. 2008 Wiley Periodicals, Inc. [source]


CXCR7 is inducible by HTLV-1 Tax and promotes growth and survival of HTLV-1-infected T cells

INTERNATIONAL JOURNAL OF CANCER, Issue 9 2009
Zhe Jin
Abstract Human T-lymphotropic virus type 1 (HTLV-1), the etiological agent of adult T-cell leukemia (ATL), encodes the potent transcriptional activator Tax, which is required for HTLV-1-induced immortalization of T cells. CXCR7 is an atypical chemokine receptor frequently expressed by tumor cells and known to promote cell growth and survival. We found that HTLV-1-immortalized T cells expressing Tax consistently expressed CXCR7. Induction of Tax in JPX-9 upregulated CXCR7. Wild-type Tax efficiently activated the CXCR7 promoter via a proximal NF-,B site, while a mutant Tax selectively defective in NF-,B activation did not. CCX754, a synthetic CXCR7 antagonist, inhibited cell growth and increased apoptosis of HTLV-1-immortalized T cells. Knockdown of CXCR7 by small interfering RNA also reduced cell growth. Stable expression of CXCR7 in a CXCR7-negative ATL cell line promoted cell growth and survival. Taken together, CXCR7 is inducible by Tax and may play an important role in HTLV-1-induced immortalization of T cells by promoting growth and survival of HTLV-1-infected T cells. 2009 UICC [source]


Candidate cis -elements for human renin gene expression in the promoter region

JOURNAL OF CELLULAR BIOCHEMISTRY, Issue 2 2004
Tadashi Konoshita
Abstract The regulation of renin gene expression, the rate-limiting enzyme of the system, is thought to be fundamental to the total system. Previously, we mapped six putative cis -elements in the promoter region of the human renin gene with nuclear proteins from human chorionic cells and human renal cortex by DNase I protection assay (footprint A,F). Each footprint contains Ets motif like site (A), HOXPBX recognition sequence (B), unknown sequence as DNA binding consensus (C), CRE (D), COUP-TFII (ARP-1) motif like site (E), and AGE3 like site (F). Footprint D has been characterized by means of functional studies as the genuine human renin gene CRE interacting with CREB in cooperation with the site of footprint B. To obtain further clues to the specific expression in the promoter region, these putative cis -elements were conducted to a consensus-specific binding assay to compare renin-producing and non-renin-producing cells by EMSA and electromobility super-shift assay. Different sequence-specific DNA/protein binding was obtained among the different cell lines with footprint B site, with COUP-TFII (ARP-1) motif like site and possibly with footprint F site. The results implicate these putative cis -elements and each corresponding trans -factor in the specific expression of the human renin gene in the promoter region. Further functional characterization of these elements would provide important data for a better understanding of human renin gene expression. 2004 Wiley-Liss, Inc. [source]


Structures of 6H perovskites Ba3CaSb2O9 and Ba3SrSb2O9 determined by synchrotron X-ray diffraction, neutron powder diffraction and ab initio calculations

ACTA CRYSTALLOGRAPHICA SECTION B, Issue 2 2008
Budwy Rowda
The structures of the 6H perovskites Ba3B2+Sb5+2O9, B = Ca and Sr, have been solved and refined using synchrotron X-ray and neutron powder diffraction data. Ba3CaSb2O9 and Ba3SrSb2O9 have monoclinic C2/c and triclinic space-group symmetries, respectively, while Ba3MgSb2O9 has ideal hexagonal P63/mmc space-group symmetry. The symmetry-lowering distortions are a consequence of internal `chemical pressure' owing to the increasing effective ionic radius of the alkaline-earth cation in the perovskite B site from Mg2+ (0.72,) to Ca2+ (1.00,) to Sr2+ (1.18,). Increasing the effective ionic radius further to Ba2+ (1.35,) leads to decomposition at room temperature. The driving force behind the transition from P63/mmc to C2/c is the need to alleviate underbonding of Ba2+ cations in the perovskite A site via octahedral rotations, while the transition from C2/c to is driven by the need to regularize the shape of the Sb2O9 face-sharing octahedral dimers. Ab initio geometry-optimization calculations were used to find a triclinic starting model for Ba3SrSb2O9. [source]


Monoclinic PZN-8%PT [Pb(Zn0.3066Nb0.6133Ti0.08)O3] at 4,K

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 12 2007
Jennifer S. Forrester
The structure of the relaxor ferroelectric Pb(Zn0.3066Nb0.6133Ti0.08)O3 (lead zinc niobium titanium trioxide), known as PZN-8%PT, was determined at 4,K from very high resolution neutron powder diffraction data. The material is known for its extraordinary piezoelectric properties, which are closely linked to the structure. Pseudo-cubic lattice parameters have led to considerable controversy over the symmetry of the structure. We find the structure to be monoclinic in the space group Cm (No. 8), with the Zn, Nb and Ti cations sharing the octahedrally coordinated B site (site symmetry m, special position 2a) and Pb occupying the 12-coordinate A site (site symmetry m, special position 2a). O atoms occupy a disorted octahedron around the B site (site symmetry m and special position 2a, and site symmetry 1 and general position 4b). Atomic coordinates have been determined for the first time, allowing the direction of spontaneous polarization to be visualized. [source]


The history of sweet taste: not exactly a piece of cake

JOURNAL OF MOLECULAR RECOGNITION, Issue 3 2006
Pierandrea Temussi
Abstract Understanding the molecular bases of sweet taste is of crucial importance not only in biotechnology but also for its medical implications, since an increasing number of people is affected by food-related diseases like, diabetes, hyperlipemia, caries, that are more or less directly linked to the secondary effects of sugar intake. Despite the interest paid to the field, it is only through the recent identification and functional expression of the receptor for sweet taste that new perspectives have been opened, drastically changing our approach to the development of new sweeteners. We shall give an overview of the field starting from the early days up to discussing the newest developments. After a review of early models of the active site, the mechanisms of interaction of small and macromolecular sweet molecules will be examined in the light of accurate modeling of the sweet taste receptor. The analysis of the homology models of all possible dimers allowed by combinations of the human T1R2 and T1R3 sequences of the sweet receptor and the closed (A) and open (B) conformations of the mGluR1 glutamate receptor shows that only ,type B' sites, either T1R2(B) and T1R3(B), can host the majority of small molecular weight sweeteners. Simultaneous binding to the A and B sites is not possible with two large sweeteners but is possible with a small molecule in site A and a large one in site B. This observation accounted for the first time for the peculiar phenomenon of synergy between some sweeteners. In addition to these two sites, the models showed an external binding site that can host sweet proteins. Copyright 2006 John Wiley & Sons, Ltd. [source]


Transcription factors NF-,B and Sp1 are major determinants of the basal promoter activity of the rat GD3-synthase gene

JOURNAL OF NEUROCHEMISTRY, Issue 2002
G. Zeng
GD3-synthase is one of the key sialyltransferases responsible for synthesis of ganglioside GD3, the substrate for initiation of the ,b' and ,c' series ganglioside synthesis. We have previously cloned the rat GD3-synthase gene promoter, and preliminary characterization has identified a minimal 0.5-kb region that has a strong basal promoter activity, and is GC-rich and has no CAAT or TATA boxes. In this study, we showed that the Sp1 and NF-,B sites in this region significantly contributed to basal GD3-synthase promoter activity. When either the Sp1 or NF-,B sites were deleted, a 50% decrease in promoter activity was observed. The same results were obtained by a decoy strategy using oligonucleotides containing the Sp1 or NF-,B sites. The binding to the Sp1 and NF-,B sites was confirmed by electrophoretic mobility shift assay (EMSA), competition and supershift EMSA. In addition, cell-type specific activation of the promoter was also determined. The promoter was highly activated in the GD3-expressing F-11 cells while repressed in NG-108 cells in which GD3 is almost undetectable. An additional band of NF-,B family was identified only in the F-11 nuclear extract using the NF-,B consensus probe by EMSA. DNA pull-down assays were further carried out to screen proteins that bound to the promoter including the basal region and the potential negative-regulatory region between ,526 and ,769. More than 10 major binding proteins were pulled down, some of which were present only in the F-11 or NG-108 nuclear extracts. Our data demonstrate that NF-,B and Sp1 are the major determinants for the basal promoter activity and some factors such as NF-,B may be involved in cell type-specific expression of the gene. [source]


Metal-ion dependence of the active-site conformation of the translesion DNA polymerase Dpo4 from Sulfolobus solfataricus

ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 9 2010
Adriana Irimia
Crystal structures of a binary Mg2+ -form Dpo4,DNA complex with 1,N2 -etheno-dG in the template strand as well as of ternary Mg2+ -form Dpo4,DNA,dCTP/dGTP complexes with 8-oxoG in the template strand have been determined. Comparison of their conformations and active-site geometries with those of the corresponding Ca2+ -form complexes revealed that the DNA and polymerase undergo subtle changes as a result of the catalytically more active Mg2+ occupying both the A and B sites. [source]


NF-,B activation in development and progression of cancer

CANCER SCIENCE, Issue 3 2007
Jun-ichiro Inoue
Nuclear factor-,, (NF-,B) binds specifically to NF-,B-binding sites (,B sites, 5,-GGGRNNYYCC-3,; R, purine; Y, pyrimidine; N, any nucleotide) present in enhancer regions of various genes. Binding of various cytokines, growth factors and pathogen-associated molecular patterns to specific receptors activates NF-,B and expression of genes that play critical roles in inflammation, innate and acquired immunity, bone remodeling and generation of skin appendices. Activation of NF-,B is also involved in cancer development and progression. NF-,B is activated in cells that become malignant tumors and in cells that are recruited to and constitute the tumor microenvironment. In the latter scenario, the TLR-TRAF6-NF-kB pathways seem to play major roles, and NF-,B activation results in production of cytokines, which in turn induce NF-,B activation in premalignant cells, leading to expression of genes involved abnormal growth and malignancy. Furthermore, NF-,B activation is involved in bone metastasis. Osteoclasts, whose generation requires the RANK-TRAF6-NF-,B pathways, release various growth factors stored in bone, which results in creation of microenvironment suitable for proliferation and colonization of cancer cells. Therefore, NF-,B and molecules involved its activation, such as TRAF6, are attractive targets for therapeutic strategies against cancer. (Cancer Sci 2007; 98: 268,274) [source]


The history of sweet taste: not exactly a piece of cake

JOURNAL OF MOLECULAR RECOGNITION, Issue 3 2006
Pierandrea Temussi
Abstract Understanding the molecular bases of sweet taste is of crucial importance not only in biotechnology but also for its medical implications, since an increasing number of people is affected by food-related diseases like, diabetes, hyperlipemia, caries, that are more or less directly linked to the secondary effects of sugar intake. Despite the interest paid to the field, it is only through the recent identification and functional expression of the receptor for sweet taste that new perspectives have been opened, drastically changing our approach to the development of new sweeteners. We shall give an overview of the field starting from the early days up to discussing the newest developments. After a review of early models of the active site, the mechanisms of interaction of small and macromolecular sweet molecules will be examined in the light of accurate modeling of the sweet taste receptor. The analysis of the homology models of all possible dimers allowed by combinations of the human T1R2 and T1R3 sequences of the sweet receptor and the closed (A) and open (B) conformations of the mGluR1 glutamate receptor shows that only ,type B' sites, either T1R2(B) and T1R3(B), can host the majority of small molecular weight sweeteners. Simultaneous binding to the A and B sites is not possible with two large sweeteners but is possible with a small molecule in site A and a large one in site B. This observation accounted for the first time for the peculiar phenomenon of synergy between some sweeteners. In addition to these two sites, the models showed an external binding site that can host sweet proteins. Copyright 2006 John Wiley & Sons, Ltd. [source]