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Results for “Origin Recognition Complex”

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At least 775 records · Page 43Linked to original sources

PubMed1995

RNA-protein interactions directed by the 3' end of human rhinovirus genomic RNA.

The replication of a picornavirus genomic RNA is a template-specific process involving the recognition of viral RNAs as target replication templates for the membrane-bound viral replication initiation complex. The virus-encoded RNA-dependent RNA polymerase, 3Dpol, is a major component of the replication complex; however, when supplied with a primed template, 3Dpol is capable of copying polyadenylated RNAs which are not of viral origin. Therefore, there must be some other molecular mechanism to direct the specific assembly of the replication initiation complex at the 3' end of viral genomic RNAs, presumably involving cis-acting binding determinants within the 3' noncoding region (3' NCR). This report describes the use of an in vitro UV cross-linking assay to identify proteins which interact with the 3' NCR of human rhinovirus 14 RNA. A cellular protein(s) was identified in cytoplasmic extracts from human rhinovirus 14-infected cells which had a marked binding preference for RNAs containing the rhinovirus 3' NCR sequence. This protein(s) showed reduced cross-linking efficiency for a 3' NCR with an engineered deletion. Virus recovered from RNA transfections with in vitro transcribed RNA containing the same 3' NCR deletion demonstrated a defective replication phenotype in vivo. Cross-linking experiments with RNAs containing the poliovirus 3' NCR and cytoplasmic extracts from poliovirus-infected cells produced an RNA-protein complex with indistinguishable electrophoretic properties, suggesting that the appearance of the cellular protein(s) may be a common phenomenon of picornavirus infection. We suggest that the observed cellular protein(s) is sequestered or modified as a result of rhinovirus or poliovirus infection and is utilized in viral RNA replication, perhaps by binding to the 3' NCR as a prerequisite for replication complex assembly at the 3' end of the viral genomic RNA.

Base Sequence↗

PubMed2006

Surfactant protein D augments bacterial association but attenuates major histocompatibility complex class II presentation of bacterial antigens.

Surfactant protein D (SP-D) is a secreted pattern recognition molecule associated with lung surfactant and mediates the clearance of pathogens in multiple ways. SP-D is an established part of the innate immune system, but it also modulates the adaptive immune response by interacting with both antigen-presenting cells and T cells. In a previous study, antigen presentation by bone marrow-derived dendritic cells was enhanced by SP-D. As dendritic cell function varies depending on the tissue of origin, we extended these studies to antigen-presenting cells isolated from mouse lung. Flow cytometric studies showed that SP-D binds calcium dependently and specifically to lung CD11c-positive cells. Opsonization of fluorescently labeled Escherichia coli by SP-D enhanced uptake by lung dendritic cells. SP-D facilitated the association of E. coli and antigen-presenting cells by increasing the frequency of CD11+ cells associated with E. coli by up to 10-fold. In contrast to the effect on bone marrow-derived dendritic cells, SP-D decreased the antigen presentation of ovalbumin, expressed in E. coli, to ovalbumin-specific major histocompatibility complex class II-specific T-cell hybridomas by 30-50%. The reduction of antigen presentation did not depend on whether the dendritic cells were isolated from the lungs of nonstimulated mice or mice that had been exposed to LPS aerosols. Our results show that SP-D increases the opsonization of pathogens, but decreases the antigen presentation by lung dendritic cells, and thereby, potentially dampens the activation of T cells and an adaptive immune response against bacterial antigens--during both steady-state conditions and inflammation.

Animals↗

PubMed2006

Natural products from marine organisms and their associated microbes.

The marine environment is distinguished by unique groups of organisms being the source of a wide array of fascinating structures. The enormous biodiversity of marine habitats is mirrored by the molecular diversity of secondary metabolites found in marine animals, plants and microbes. The recognition that many marine invertebrates contain endo- and epibiotic microorganisms and that some invertebrate-derived natural products are structurally related to bacterial metabolites suggests a microbial origin for some of these compounds. Other marine natural products, however, are clearly located in invertebrate tissue and microbial involvement in the biosynthetic process seems unlikely. The complexity of associations in marine organisms, especially in sponges, bryozoans and tunicates, makes it extremely difficult to definitively state the biosynthetic source of many marine natural products or to deduce their ecological significance. Whereas many symbiotic marine microorganisms cannot be isolated and cultured, numerous epi- and endobiotic marine fungi produce novel secondary metabolites in laboratory cultures. The potent biological activity of many marine natural products is of relevance for their ecological function but is also the basis of their biomedical importance.

Animals↗

PubMed2006

Aptamers targeted to an RNA hairpin show improved specificity compared to that of complementary oligonucleotides.

Aptamers interacting with RNA hairpins through loop-loop (so-called kissing) interactions have been described as an alternative to antisense oligomers for the recognition of RNA hairpins. R06, an RNA aptamer, was previously shown to form a kissing complex with the TAR (trans-activating responsive) hairpin of HIV-1 RNA (Ducongé and Toulmé (1999) RNA 5, 1605). We derived a chimeric locked nucleic acid (LNA)/DNA aptamer from R06 that retains the binding properties of the originally selected R06 aptamer. We demonstrated that this LNA/DNA aptamer competes with a peptide of the retroviral protein Tat for binding to TAR, even though the binding sites of the two ligands do not overlap each other. This suggests that upon binding, the aptamer TAR adopts a conformation that is no longer appropriate for Tat association. In contrast, a LNA/DNA antisense oligomer, which exhibits the same binding constant and displays the same base-pairing potential as the chimeric aptamer, does not compete with Tat. Moreover, we showed that the LNA/DNA aptamer is a more specific TAR binder than the LNA/DNA antisense sequence. These results demonstrate the benefit of reading the three-dimensional shape of an RNA target rather than its primary sequence for the design of highly specific oligonucleotides.

Aptamers, Nucleotide↗

PubMed1992

Nuclear respiratory factor 1 activation sites in genes encoding the gamma-subunit of ATP synthase, eukaryotic initiation factor 2 alpha, and tyrosine aminotransferase. Specific interaction of purified NRF-1 with multiple target genes.

Transcription factor nuclear respiratory factor 1 (NRF-1) was originally identified as an activator of the cytochrome c gene and subsequently found to stimulate transcription through specific sites in other nuclear genes whose products function in the mitochondria. These include subunits of the cytochrome oxidase and reductase complexes and a component of the mitochondrial DNA replication machinery. Here we establish that a functional recognition site for NRF-1 is present in the ATP synthase gamma-subunit gene extending the proposed respiratory role of NRF-1 to complex V. In addition, biologically active NRF-1 sites are found in genes encoding the eukaryotic translation initiation factor 2 alpha-subunit and tyrosine aminotransferase, both of which participate in the rate-limiting step of their respective pathways of protein biosynthesis and tyrosine catabolism. The recognition sites from each of these genes form identical complexes with NRF-1 as established by competition binding assays, methylation interference footprinting, and UV-induced DNA cross-linking. Cloned oligomers of each NRF-1 binding site also stimulate the activity of a truncated cytochrome c promoter in transfected cells. The NRF-1 binding activities for the various target sites copurified approximately 33,000-fold and resided in a single protein of 68 kDa. These observations further support a role for NRF-1 in the expression of nuclear respiratory genes and suggest it may help coordinate respiratory metabolism with other biosynthetic and degradative pathways.

Animals↗

PubMed1995

Modular structure of genes encoding multifunctional peptide synthetases required for non-ribosomal peptide synthesis.

Peptide synthetases are large multienzyme complexes that catalyze the non-ribosomal synthesis of a structurally diverse family of bioactive peptides. They possess a multidomain structure and employ the thiotemplate mechanism to activate, modify and link together by amide or ester bonds the constituent amino acids of the peptide product. The domains, which represent the functional building units of peptide synthetases, appear to act as independent enzymes whose specific linkage order forms the protein-template that defines the sequence of the incorporated amino acids. Two types of domains have been characterized in peptide synthetases of bacterial and fungal origin: type I comprises about 600 amino acids and contains at least two modules involved in substrate recognition, adenylation and thioester formation, whereas type II domains carry in addition an insertion of about 430 amino acids that may function as a N-methyltransferase module. The role of other genes associated with bacterial operons encoding peptide synthetases is also discussed.

Amino Acid Sequence↗

PubMed2005

Hox genes and their candidate downstream targets in the developing central nervous system.

1. Homeobox (Hox) genes were originally discovered in the fruit fly Drosophila, where they function through a conserved homeodomain as transcriptional regulators to control embryonic morphogenesis. Since then over 1000 homeodomain proteins have been identified in several species. In vertebrates, 39 Hox genes have been identified as homologs of the original Drosophila complex, and like their Drosophila counterparts they are organized within chromosomal clusters. Vertebrate Hox genes have also been shown to play a critical role in embryonic development as transcriptional regulators. 2. Both the Drosophila and vertebrate Hox genes have been shown to interact with various cofactors, such as the TALE homeodomain proteins, in recognition of consensus sequences within regulatory elements of their target genes. These protein-protein interactions are believed to contribute to enhancing the specificity of target gene recognition in a cell-type or tissue- dependent manner. The regulatory activity of a particular Hox protein on a specific regulatory element is highly variable and dependent on its interacting partners within the transcriptional complex. 3. In vertebrates, Hox genes display spatially restricted patterns of expression within the developing CNS, both along the anterioposterior and dorsoventral axis of the embryo. Their restricted gene expression is suggestive of a regulatory role in patterning of the CNS, as well as in cell specification. Determining the precise function of individual Hox genes in CNS morphogenesis through classical mutational analyses is complicated due to functional redundancy between Hox genes. 4. Understanding the precise mechanisms through which Hox genes mediate embryonic morphogenesis requires the identification of their downstream target genes. Although Hox genes have been implicated in the regulation of several pathways, few target genes have been shown to be under their direct regulatory control. Development of methodologies used for the isolation of target genes and for the analysis of putative targets will be beneficial in establishing the genetic pathways controlled by Hox factors. 5. Within the developing CNS various cell adhesion molecules and signaling molecules have been identified as candidate downstream target genes of Hox proteins. These targets play a role in processes such as cell migration and differentiation, and are implicated in contributing to neuronal processes such as plasticity and/or specification. Hence, Hox genes not only play a role in patterning of the CNS during early development, but may also contribute to cell specification and identity.

Animals↗

PubMed2000

A local training and pruning approach for neural networks.

The training of neural networks using the extended Kalman filter (EKF) algorithm is plagued by the drawback of high computational complexity and storage requirement that may become prohibitive even for networks of moderate size. In this paper, we present a local EKF training and pruning approach that can solve this problem. In particular, the by-products obtained along with the local EKF training can be utilized to measure the importance of the network weights. Comparing with the original global approach, the proposed local EKF training and pruning approach results in a much lower computational complexity and storage requirement. Hence, it is more practical in solving real world problems. The performance of the proposed algorithm is demonstrated on one medium- and one large-scale problems, namely, sunspot data prediction and handwritten digit recognition.

Algorithms↗

PubMed2005

Multiple cases of striking genetic similarity between alternate electric fish signal morphs in sympatry.

Striking trait polymorphisms are worthy of study in natural populations because they can often shed light on processes of phenotypic divergence and specialization, adaptive evolution, and (in some cases) the early stages of speciation. We examined patterns of genetic variation within and between populations of mormyrid fishes that are morphologically cryptic in sympatry but produce alternate types of electric organ discharge (EOD). Other species in a large group containing a clade of these morphologically cryptic EOD types produce stereotyped, species-typical EOD waveforms thought to function in mate recognition. First, for six populations from Gabon's Brienomyrus species flock, we confirm that forms of electric fish that exhibit distinctive morphologies and unique EOD waveforms (i.e., good reference species) are reproductively isolated from coexisting congeners. These sympatric species deviate from genetic panmixia across five microsatellite loci. Given this result, we examined three focal pairs of syntopic and morphologically cryptic EOD waveform types that are notable exceptions to the pattern of robust genetic partitioning among unique waveform classes within assemblages. These exceptional pairs constitute a monophyletic group within the Brienomyrus flock known as the magnostipes complex. One member of each pair (type I) produces a head-negative EOD, while the other member (either type II or type III, depending on location) produces a longer duration EOD differing in waveform from type I. We show that signal development in these pairs begins with juveniles of all magnostipes-complex morphs emitting head-positive EODs resembling those of type II adults. Divergence of EOD waveforms occurs with growth such that there are two discrete and fixed signal types in morphologically indistinguishable adults at each of several localities. Strong microsatellite partitioning between allopatric samples of any of these morphologically cryptic signal types suggests that geographically isolated populations are genetically decoupled from one another. By contrast, sympatric morphs appear genetically identical across microsatellite loci in Mouvanga Creek and the Okano River and only very weakly diverged, if at all, in the Ivindo River. Our results for the magnostipes complex fail to detect species boundaries between the focal morphs and are, instead, fully consistent with the existence of relatively stable signal dimorphisms at each of several different localities. No mechanism for the maintenance of this electrical polymorphism is suggested by the known natural history of the magnostipes complex. Despite a lack of evidence for genetic differentiation, the possibility of incipient sympatric speciation between morphs (especially type I and type II within the Ivindo River) merits further testing due to behavioral and neurobiological lines of evidence implying a general role for stereotyped EOD waveforms in species recognition. We discuss alternative hypotheses concerning the origins, stability, and evolutionary significance of these intriguing electrical morphs in light of geographical patterns of population structure and signal variation.

Action Potentials↗

PubMed1981

Self recognition in allogeneic radiation bone marrow chimeras. A radiation-resistant host element dictates the self specificity and immune response gene phenotype of T-helper cells.

The specificity of the self-recognition repertoire in fully allogeneic (A {arrow} B), semiallogeneic (A {arrow} A x B and A x B {arrow} A), and double donor (A + B {arrow} A) radiation bone marrow chimeras was assessed by the ability of their spleen cells to generate in vitro primary plaque-forming cell (PFC) responses to trinitrophenyl- keyhole limpet hemocyanin. In contrast to spleen cells from semiallogeneic and double donor chimeras, intact spleen cells from fully allogeneic BI0 {arrow} B10.A and B10.A {arrow} B10 chimeras were not capable of generating responses to trinitrophenyl (TNP)-keyhole limpet hemocyanin. However, cultures containing a mixture of both B10 {arrow} B10.A and B10.A {arrow} B10 spleen cells did respond, demonstrating that all the cell populations required for the in vitro generation of T-dependent PFC responses were able to differentiate into functional competence in a fully allogeneic major histocompatibility complex (MHC) environment. The self recognition repertoire of T-helper cells from fully allogeneic A {arrow} B chimeras was determined to be specific for the recognition of host, not donor, MHC determinants in that they were able to collaborate with cells expressing only host MHC determinants but not with cells expressing only donor MHC determinants, even though the functional lymphocytes in these chimeras were shown to be of donor origin. Experiments utilizing double donor A + B {arrow} A chimeras further demonstrated that the ability of chimeric T cells to recognize allogeneic MHC determinants as self structures was a function of a radiation-resistant host element and not simply a consequence of the tolerization of T cell precursors to allogeneic MHC determinants, because strain A lymphocytes isolated from A + B {arrow} A chimeras were tolerant to both A and B MHC determinants but were restricted to the self recognition of syngeneic host type A MHC determinants. Finally, the Ir gene phenotype expressed by B10 {arrow} B10.A and B10.A {arrow} B10 chimeric lymphocytes was determined by their ability to function in the Ir gene controlled response to TNP-poly-L-(Tyr,Glu)-poly-D,L-Ala-poly- L-Lys [(T,G)-A--L]. The ability of lymphocytes to function in TNP-(T,G)-A--L responses was not determined by their genotype but rather paralleled the specificity of their self recognition repertoire for high responder (H-2 (b)) determinants. The possible degeneracy of the MHC-specific self recognition repertoire is discussed, and a model is proposed for Ir gene regulation in which expression of Ir gene function by lymphocytes is an antigen-nonspecific consequence of the specificity and cross-reactivity of their self recognition repertoire.

Animals↗

PubMed2002

Population coding of shape in area V4.

Shape is represented in the visual system by patterns of activity across populations of neurons. We studied the population code for shape in area V4 of macaque monkeys, which is part of the ventral (object-related) pathway in primate visual cortex. We have previously found that many macaque V4 neurons are tuned for the curvature and object-centered position of boundary fragments (such as 'concavity on the right'). Here we tested the hypothesis that populations of such cells represent complete shapes as aggregates of boundary fragments. To estimate the population representation of a given shape, we scaled each cell's tuning peak by its response to that shape, summed across cells and smoothed. The resulting population response surface contained 3-8 peaks that represented major boundary features and could be used to reconstruct (approximately) the original shape. This exemplifies how a multi-peaked neural population response can represent a complex stimulus in terms of its constituent elements.

Action Potentials↗

PubMed1999

Monoterpene synthases of loblolly pine (Pinus taeda) produce pinene isomers and enantiomers.

The turpentine fraction of conifer oleoresin is a complex mixture of monoterpene olefins and plays important roles in defense and in the mediation of chemical communication between conifer hosts and insect predators. The stereochemistry of the turpentine monoterpenes is critical in these interactions, influencing host recognition, toxicity, and potency of derived pheromones, and the stereochemical composition of these compounds lends insight into their biogenetic origin, with implications for the numbers and types of enzymes responsible and their corresponding genes. Analysis of the oleoresin from several tissues of loblolly pine (Pinus taeda) showed the derived turpentine to consist mainly of (+)-(3R:5R)-alpha-pinene and (-)-(3S:5S)-beta-pinene. Cell-free extracts from xylem tissue yielded three monoterpene synthases which together account for the monoterpene isomer and enantiomer content of the turpentine of this tissue. The major products of these enzymes, produced from the universal precursor of monoterpenes, geranyl diphosphate, were shown to be (+)-alpha-pinene, (-)-alpha-pinene, and (-)-beta-pinene, respectively. In most properties (molecular mass of approximately 60 kDa, K(m) for geranyl diphosphate of 3 microM, requirement for monovalent and divalent cations), these enzymes resemble other monoterpene synthases from conifer species.

Animals↗

PubMed2002

EVH1 domains: structure, function and interactions.

Drosophila enabled/vasodilator-stimulated phosphoprotein homology 1 (EVH1) domains are 115 residue protein-protein interaction modules which provide essential links for their host proteins to various signal transduction pathways. Many EVH1-containing proteins are associated closely with actin-based structures and are involved in re-organization of the actin cytoskeleton. EVH1 domains are also present in proteins enriched in neuronal tissue, thus implicating them as potential mediators of synaptic plasticity, linking them to memory formation and learning. Like Src homology 3, WW and GYF domains and profilin, EVH1 domains recognize and bind specific proline-rich sequences (PRSs). The binding is of low affinity, but tightly regulated by the high specificity encoded into residues in the protein:peptide interface. In general, a small (3-6 residue) 'core' PRS in the target protein binds a 'recognition pocket' on the domain surface. Further affinity- and specificity-increasing interactions are then formed between additional domain epitopes and peptide 'core-flanking' residues. The three-dimensional structures of EVH1:peptide complexes now reveal, in great detail, some of the most important features of these interactions and allow us to better understand the origins of specificity, ligand orientation and sequence degeneracy of target peptides, in low affinity signalling complexes.

Amino Acid Sequence↗

PubMed1999

The SH3 domains of endophilin and amphiphysin bind to the proline-rich region of synaptojanin 1 at distinct sites that display an unconventional binding specificity.

The proline-rich domain of synaptojanin 1, a synaptic protein with phosphatidylinositol phosphatase activity, binds to amphiphysin and to a family of recently discovered proteins known as the SH3p4/8/13, the SH3-GL, or the endophilin family. These interactions are mediated by SH3 domains and are believed to play a regulatory role in synaptic vesicle recycling. We have precisely mapped the target peptides on human synaptojanin that are recognized by the SH3 domains of endophilins and amphiphysin and proven that they are distinct. By a combination of different approaches, selection of phage displayed peptide libraries, substitution analyses of peptides synthesized on cellulose membranes, and a peptide scan spanning a 252-residue long synaptojanin fragment, we have concluded that amphiphysin binds to two sites, PIRPSR and PTIPPR, whereas endophilin has a distinct preferred binding site, PKRPPPPR. The comparison of the results obtained by phage display and substitution analysis permitted the identification of proline and arginine at positions 4 and 6 in the PIRPSR and PTIPPR target sequence as the major determinants of the recognition specificity mediated by the SH3 domain of amphiphysin 1. More complex is the structural rationalization of the preferred endophilin ligands where SH3 binding cannot be easily interpreted in the framework of the "classical" type I or type II SH3 binding models. Our results suggest that the binding repertoire of SH3 domains may be more complex than originally predicted.

Adaptor Proteins, Signal Transducing↗

PubMed1997

cis elements that contribute to geminivirus transcriptional regulation and the efficiency of DNA replication.

The A genomic component of the geminivirus tomato golden mosaic virus (TGMV) contains a 5' intergenic sequence that includes the overlapping AL61 promoter and positive-strand origin of DNA replication. The TGMV AL1 protein negatively regulates its own transcription and mediates origin recognition by binding to a repeated motif shared by the AL61 promoter and the viral origin. We examined a series of truncated or mutated 5' intergenic regions in transient expression and replication assay to identify other DNA sequences that contribute to TGMV promoter and origin function. These experiments revealed that negative regulation of the AL61 promoter is complex, involving multiple cis-acting sequences and the AL1 and AL4 proteins, which acted through different DNA elements. We also found that mutation of the TATA box motif in the AL61 promoter reduced overall transcriptional activity and AL1-mediated repression, confirming the importance of this sequence in promoter function. Mutation of a G-box consensus sequence was highly detrimental to AL61 transcription and abolished AL1 sensitivity, suggesting that AL1 interferes with transcriptional activation. Cotransfection experiments showed that the TATA box and G-box motif mutations also impaired viral DNA replication in the presence of a wild-type origin but had no effect in its absence, demonstrating that these transcriptional motifs also function as replication efficiency elements.

Base Sequence↗

PubMedDate not supplied

A critical analysis of the current interpretation of immune diseases. Arguments for a more pathological classification.

Based on the new acquisitions of knowledge on the immune network and on the regulating mechanisms of the immune system, the paper presents an original and at the same time a more pathophysiological classification of immune diseases according to: 1. the functionality stage (input--or antigen presentation, central--integrative, and output--effector), and 2. the immune ligand involved (immunoglobulin or Ti complex). From these new concepts it results that the main feature of the immune system reactivity is the antigen recognition. The authors bring arguments in favour of the assertion that immunity--characterized by recognition--is equal with autoimmunity--characterized by autorecognition, i.e., recognition of the self antigens. From this statement it ensues that: 1. an immune disease is a disease of internal regulation of the immune network, i.e., of the relationships between idiotypes and anti-idiotypes, and 2. any immune disease is an autoimmune disease, meaning that the pathogenetic significance of the so-called "autoimmune diseases" and of the "hypersensitivity diseases" is the same.

Autoimmune Diseases↗

PubMed1980

[Computer analysis of the vectorcardiogram].

A computer method analysing Frank VCG recorded on rest and on exertion, is presented. Electrical noises due to exercise are eliminated by averaging 8 complexes. The pattern-recognition of every wave is carried out by analysing a particular function obtained by translating the X, Y, Z leads on the line joining the T-P, P-Q, ST and subsequent T-P segment. The following parameters are evaluated: maximal and mean vector, linear, areolar and tangential (our original method) spatial velocity, half-area vector, area described by the spatial vector and oriented according to X, Y, Z polarity.

Diagnosis, Computer-Assisted↗

PubMedDate not supplied

Theoretical conformational investigation of thrombin-fibrinogen recognition complex.

Theoretical conformational investigation of the thrombin-fibrinogen recognition complex was fulfilled. At first preliminary study was carried out using space-filling molecular models. At the next stage computer simulation was conducted. For this purpose a package of programs for the theoretical conformational analysis of two interacting molecules has been developed in the framework of atom-atom potentials. The package contains an original algorithm for constructing initial approximation based on assumption that the structure of the complex is determined mainly by the ligand-ligand attraction and Van-der-Vaals repulsion. Complex structure with considerable binding energy was obtained. Molecules of that structure are bound mainly by four oppositely charged pairs of side chain groups. The beta -loop of thrombin in the complex is shown to undergo essential structural transformations. A hypothesis is suggested that this transformation may influence active sites allosterically. Some ways and mechanisms of this influence are discussed as well as an approach to its calculation.

Computer Simulation↗