ProteinsProteinAffinityTranscriptionMRNAsHelicaseSmall RNAsGenomeNegative-strand RNA virusesEIF4ETranscriptsMolecularNucleotideSubunitPolymerase IICell proliferationMiRNAsSynthesisMessenger RNAMediateRegulatesMetabolismVirusesInfluenzaPost-transcriptional modificationsGuanosineLncRNAsEndonucleasePhysiologicalStabilityReplicationCharacterizationComplexesSubunitsEnzymeAntisenseGene expressionMechanismPhosphorylationYeastCytoplasmicInterferenceImmunoprecipitationStructural basisTranslationalGranules
Proteins12
- The ProQ/FinO family of RNA binding proteins mediate sRNA-directed gene regulation throughout gram-negative bacteria. (nature.com)
- Here, we investigate the structural basis for RNA recognition by ProQ/FinO proteins, through the crystal structure of the ProQ/FinO domain of the Legionella pneumophila DNA uptake regulator, RocC, bound to the transcriptional terminator of its primary partner, the sRNA RocR. (nature.com)
- More recently, the application of RNA-seq technologies has enabled the elucidation of the biological partners and targets of several ProQ/FinO family proteins. (nature.com)
- Insight into how these proteins recognize their cognate RNAs initiated with FinO. (nature.com)
- Heterogeneous population of RNA granules serve as motile units to translocate, store, translate, and degrade mRNAs in the dendrites contain cis -elements and trans -acting factors such as RNA-binding proteins and microRNAs to convey stimulus-, transcript-specific local translation. (frontiersin.org)
- 4E-binding proteins (4E-BPs) block the interaction of eIF4E with eIF4G to negatively regulate the formation of the eIF4F complex. (biosyn.com)
- Nuclear mRNA transcripts acquire a protein coat composed of cap- and RNA-binding proteins that allow nuclear export and dictate the functional program of cytoplasmic mRNAs ( Moore, 2005 ). (rupress.org)
- Proteins that specifically bind to RNA CAPS and form nuclear cap binding protein complexes. (bvsalud.org)
- A heterodimeric protein complex of RNA cap-binding proteins which binds with high affinity to the 5' MRNA CAP STRUCTURE. (bvsalud.org)
- Additional links to NCBI resources are provided for human noncoding RNAs and repeated DNA elements and for proteins of interest from other species. (cshlpress.com)
- However, many enzymes can bind to different combinations of proteins to form groups (or 'complexes') with a variety of three-dimensional shapes, so there may be a variety of enzyme complexes in the solution. (elifesciences.org)
- Among these, three U4/U6·U5 snRNP proteins (hBrr2, hPrp4, and hPrp31) copurified with CBC in an RNA-independent fashion, suggesting that a significant fraction of CBC forms a complex with the U4/U6·U5 snRNP and that the activity of CBC might be associated with snRNP recruitment to pre-mRNA. (iucc.ac.il)
Protein28
- sRNAs usually work by pairing with target mRNAs, often with the assistance of protein partners called RNA chaperones. (nature.com)
- The eponymous FinO protein was discovered as a regulator of F plasmid conjugation nearly 50 years ago, and acts to bind a single partner sRNA called FinP to stabilize FinP and facilitate its interactions with its antisense partner, the mRNA encoding the major F plasmid transcription factor, TraJ 5 . (nature.com)
- Similarly, a minimal ProQ/FinO domain protein, NMB1681, has been shown to bind a range of structured RNAs in Neisseria meningitidis 15 . (nature.com)
- Here we report a class of mRNA granules in human neuronal processes that are enriched in the nuclear cap-binding protein complex (CBC) and exon junction complex (EJC) core components, Y14 and eIF4AIII. (frontiersin.org)
- The existence of mRNAs retaining both nuclear cap binding protein and EJC in the distal sites of neuronal processes suggests that some localized mRNAs have not yet undergone the "very first translation," which contribute to the spatio-temporal regulation of gene expression. (frontiersin.org)
- The S1 subunit (PDB I.D-6VSB) of the spike protein being reported to acts as receptor binding domain (RBD), binding to ACE-2 receptor with higher affinity. (ijpsonline.com)
- Mass spectrometry combined with X-ray crystallography allows the characterization of cap protein interactions. (biosyn.com)
- The RNA helicase eIF4A and the scaffold protein eukaryotic translation initiation factor 4G (eIF4G) and the capping protein eIF4E are part of the complex that loads the mRNAs onto the 40 S ribosomal subunit, together with eIF3. (biosyn.com)
- Different classes of RNA granules share some protein components and may use similar mechanisms to regulate mRNA translation/decay. (rupress.org)
- The Cusack group uses X-ray crystallography and cryo electron-microscopy (cryoEM) to study the structural biology of protein-RNA complexes involved in RNA virus replication, innate immunity and cellular RNA metabolism. (embl.org)
- Phosphorylation of eIF4E on serine 209 regulates the affinity of this protein for the 7 methyl GTP cap and/or RNA. (affbiotech.com)
- Recognizes and binds the 7-methylguanosine-containing mRNA cap during an early step in the initiation of protein synthesis and facilitates ribosome binding by inducing the unwinding of the mRNAs secondary structures. (affbiotech.com)
- Phosphorylation increases the ability of the protein to bind to mRNA caps and to form the eIF4F complex. (affbiotech.com)
- Electrophoretic mobility shift analysis detected a protein that binds specifically to a DNA motif encompassing the cap site. (nebraska.edu)
- Based on competitive DNA binding studies with mutated oligonucleotides, it was determined that bases from -5 to -2 and +4 to +11 are critical for protein binding. (nebraska.edu)
- consequently, this motif is referred to as the cap site diad element (CSDE) and the cognate factor as the cap site-binding protein (CSBP). (nebraska.edu)
- These results indicate that a negative regulatory element centered at the GPHα gene cap site and its cognate DNA-binding protein make a significant contribution to the production of α-subunit in a variety of tumor tissues. (nebraska.edu)
- MucR binds multiple target sites in the promoter of its own gene and is a heat-stable protein: Is MucR a H-NS-like protein? (cnr.it)
- In this study, we provide the first evidence that MucR from Brucella abortus binds more than one target site in the promoter region of its own gene, suggesting a molecular mechanism by which this protein represses its own expression. (cnr.it)
- Homo sapiens CGG triplet repeat binding protein 1 (CGGBP1), transcript variant 1, mRNA. (dbcls.jp)
- The decapping reaction was initiated by adding 30 L capped 32P-labeled 29 nt RNA substrate at 1.5 concentration in decapping reaction buffer to 60 L 3 protein + inhibitor at 4C. (abic2004.org)
- Poly(A) binding protein (PABPC1) normally stimulates mRNA translation by interacting with several translation initiation factors bound to the 5'- end of mRNAs. (expasy.org)
- The interaction between PABPC1 and eIF4G forms a protein bridge between 5'- and 3'-ends, enhancing cap binding by eIF4E and RNA binding by eIF4G and PABPC1. (expasy.org)
- After phenol/chloroform -extraction of the eluate protein and RNA-containing phases are precipitated and subjected to analysis. (sysy.com)
- mRNA cap-binding component of the eukaryotic translation initiation factor 3 (eIF-3) complex, a complex required for several steps in the initiation of protein synthesis of a specialized repertoire of mRNAs. (expasy.org)
- mRNA cap-binding component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis of a specialized repertoire of mRNAs and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome. (expasy.org)
- Influenza virus neuraminidase (NA) can act as a receptor-binding protein, a role commonly attributed to hemagglutinin (HA). (cdc.gov)
- Taken together, our findings provide new insights into the molecular mechanisms underlying the ability of NA to function as a binding protein. (cdc.gov)
Affinity4
- When used with the Vaccinia Capping System, (NEB # M2080 ) these reagents enable affinity tagging of RNA triphosphate ends. (neb.com)
- PABP binding to poly(A) increases PABP's affinity to eIF4G and the affinity of eIF4E for the cap as well. (biosyn.com)
- Human ANP32A IDD transiently binds to the 627 domain, exploiting multivalency to maximise affinity. (nature.com)
- We show that RAM selects the RNMT active site conformations that are optimal for binding of substrates (AdoMet and the cap), thus enhancing their affinity. (dundee.ac.uk)
Transcription7
- Transcription (genetics) Five-prime cap Gross CH, Shuman S (September 1998). (wikipedia.org)
- Most cytoplasmic-replicating negative-strand RNA viruses (NSVs) initiate genome transcription by cap snatching. (wur.nl)
- Altogether, the results implicate a more complex situation in which, besides PB, additional cytoplasmic sources are used during transcription/cap snatching of cytoplasmic-replicating and segmented NSVs. (wur.nl)
- Bacterial RNA polymerase (RNA Pol) can initiate transcription in vitro by accepting nucleotide metabolites capped with flavin adenine dinucleotide (FAD), uridine diphosphate glucose (UDP-Glc), and uridine diphosphate N-acetylglucosamine (UDP-GlcNAc). (biosyn.com)
- Our goal is to understand the molecular mechanisms whereby the genomic RNA of influenza-like viruses is, on the one hand, the template for transcription and replication of the viral genome by its RNA-dependent RNA polymerase and, on the other hand, an Achilles' heel, whose recognition as non-self can trigger an innate immune response to counter the viral infection. (embl.org)
- These studies are being extended to viral RNPs (the physiological RNA synthesis units) to understand the behaviour of the viral nucleoprotein during replication and transcription and to include host factors important for viral replication. (embl.org)
- Mammalian forms of the transcription repressor, Kaiso, can reportedly bind methylated DNA and non-methylated CTGCNA motifs. (biologists.com)
MRNAs5
- The source of host mRNAs from which the cytoplasmic NSVs snatch capped-RNA leader sequences has remained elusive. (wur.nl)
- The 5'- terminal ends of cellular mRNAs contain an m7GpppN cap, in which N can be any nucleotide. (biosyn.com)
- eIF4E binds to the 7 methyl GTP cap structure of eukaryotic mRNAs. (affbiotech.com)
- The eIF-3 complex specifically targets and initiates translation of a subset of mRNAs involved in cell proliferation, including cell cycling, differentiation and apoptosis, and uses different modes of RNA stem-loop binding to exert either translational activation or repression. (expasy.org)
- In the eIF-3 complex, EIF3D specifically recognizes and binds the 7-methylguanosine cap of a subset of mRNAs. (expasy.org)
Helicase1
- The cell counters RNA viruses with innate immune pattern-recognition receptors, such as the RNA helicase RIG-I, which recognise particular viral RNA structural motifs (e.g. 5′ triphosphate-dsRNA) as non-self, thus activating a signalling pathway leading to interferon production and establishment of the anti-viral state. (embl.org)
Small RNAs1
- Small RNAs (sRNAs) control a variety of physiological responses across bacterial species 1 . (nature.com)
Genome3
- Its genome consist of single-stranded plus sense RNA which is capped at 5' end and polyadenylated at 3' end[ 6 , 7 ]. (ijpsonline.com)
- The Lassa virus nucleoprotein coats the viral genome to make a template for RNA synthesis. (hal.science)
- The nucleoprotein plays critical roles in viral RNA replication and genome assembly, and nucleozin was shown to block replication of H1N1, H3N2, and H5N1 viruses in cell culture experiments and also to protect mice from lethal challenge with highly pathogenic avian influenza virus A H5N1. (drugdiscoveryopinion.com)
Negative-strand RNA viruses1
- We have extended our work on viral polymerases to those of other segmented negative-strand RNA viruses such as the large order of Bunyavirales . (embl.org)
EIF4E8
- Ribavirin competitively inhibits the binding of eIF4E to the m7G RNA cap. (haematologica.org)
- studied the interaction of synthetic N7-substituted GMP cap anlogs with the eIF4E mononucleotide binding site. (biosyn.com)
- The Kds of guanosine triphosphate (GTP), GMP, and cap derivatives interactions with eIF4E were determined. (biosyn.com)
- Figure 3 shows molecular models of the cystal structure of eIF4E, in complex with the cap m7GpppA, and a 4EBP1 peptide. (biosyn.com)
- Component of the CYFIP1-EIF4E-FMR1 complex which binds to the mRNA cap and mediates translational repression. (affbiotech.com)
- In the CYFIP1-EIF4E-FMR1 complex this subunit mediates the binding to the mRNA cap. (affbiotech.com)
- Whether translation initiation factor 4E (eIF4E), the mRNA cap binding and rate-limiting factor required for translation, is a target for cytotoxicity and cell death induced by cadmium , a human carcinogen, was investigated. (cdc.gov)
- Similarly, specific silencing of the expression of the eIF4E gene, caused by a small interfering RNA, resulted in significant cytotoxicity and cell death. (cdc.gov)
Transcripts9
- MicroRNAs (miRNAs) are small regulatory non-coding RNAs, resulting from the cleavage of long primary transcripts (pri-miRNAs) in the nucleus by the Microprocessor complex generating precursors (pre-miRNAs) that are then exported to the cytoplasm and processed into mature miRNAs. (mdpi.com)
- Contributes to the stability and delivery of capped primary miRNA transcripts to the primary miRNA processing complex containing DGCR8 and RNASEN, thereby playing a role in RNA-mediated gene silencing (RNAi) by miRNAs. (genetex.com)
- During in vivo cap-donor competition experiments, TSWV used transcripts destined to PB and SG, but also functional transcripts engaged in translation. (wur.nl)
- Capped (m27,3-GpppRNA) and decapped (pRNA) transcripts were resolved by high-resolution SDS-PAGE and quantified by autoradiography. (abic2004.org)
- Transcripts containing analogs 12C15 at the 5 terminus were incubated for 15 or 30 min with Dcp1/2, then the reaction Deruxtecan was quenched, and capped versus decapped (and uncapped) transcripts were separated by gel electrophoresis then quantified by autoradiography. (abic2004.org)
- All RNA transcripts capped with diastereomers of compound 12 were degraded significantly faster than those capped with an unmodified ARCA analog (Fig. 6). (abic2004.org)
- 2007). Cap analog 13, which introduces a methylene bridge into the O-to-S modified two-headed cap, is cleaved from RNA at a rate similar to the unmodified m27,3-band represents capped transcripts whereas band represents a mixture of decapped and uncapped transcripts. (abic2004.org)
- Time points were quenched by addition of excess EDTA, RNA was separated from m7GDP product by thin layer chromatography, and the fraction of capped versus decapped transcripts was quantified using a GE Typhoon scanner and ImageQuant as previously described (Deshmukh et al. (abic2004.org)
- The RNA guanine-N7 methyltransferase (RNMT) in complex with RNMT-Activating Miniprotein (RAM) catalyses the formation of a N7-methylated guanosine cap structure on the 5' end of nascent RNA polymerase II transcripts. (dundee.ac.uk)
Molecular6
- The only specific molecular function known is the catalysis of the reaction: a 5′-end triphospho-(purine-ribonucleotide) in mRNA + H2O = a 5′-end diphospho-(purine-ribonucleoside) in mRNA + phosphate RTPases cleave the 5′-terminal γ-β phosphoanhydride bond of nascent messenger RNA molecules, enabling the addition of a five-prime cap as part of post-transcriptional modifications. (wikipedia.org)
- in 2007, showed that mass spectrometry allows the measurement of the apparent gas-phase equilibrium dissociation constants (Kd) values for the specific molecular binding events. (biosyn.com)
- Molecular formula of common RNA modifications. (beds.ac.uk)
- Potential binding sites for nucleozin on the influenza nucleoprotein were also predicted using molecular docking models. (drugdiscoveryopinion.com)
- Molecular function: RNA binding. (expasy.org)
- Molecular function: mRNA cap binding. (expasy.org)
Nucleotide2
- The structure reveals specific recognition of the 3' nucleotide of the terminator by a conserved pocket involving a β-turn-α-helix motif, while the hairpin portion of the terminator is recognized by a conserved α-helical N-cap motif. (nature.com)
- Epigenetics refers to heritable changes in gene expression without changing the nucleotide sequence of the gene, including DNA methylation, histone modifications, and RNA modifications. (beds.ac.uk)
Subunit3
- Telomerase synthesizes chromosome-capping telomeric repeats using an active site in telomerase reverse transcriptase (TERT) and an integral RNA subunit template. (elifesciences.org)
- Overall, this work defines human telomerase DNA binding and synthesis properties at single-molecule level and establishes conserved telomerase subunit architecture from single-celled organisms to humans. (elifesciences.org)
- EIF3J is a labile subunit that binds to the eIF-3 complex via EIF3B. (expasy.org)
Polymerase II1
- The nuclear cap-binding complex (CBC) binds to the 7-methyl guanosine cap present on every RNA polymerase II transcript. (iucc.ac.il)
Cell proliferation2
- Acts as a mediator between the cap-binding complex (CBC) and the primary microRNAs (miRNAs) processing machinery during cell proliferation. (genetex.com)
- Messenger RNA (mRNA) regulates cell proliferation. (biosyn.com)
MiRNAs1
- Some miRNAs are hosted in pri-miRNAs annotated as long non-coding RNAs (lncRNAs) and defined as MIRHGs (for miRNA Host Genes). (mdpi.com)
Synthesis1
Messenger RNA1
- We review the relationship between different classes of these granules and discuss how spatial organization regulates messenger RNA translation/decay. (rupress.org)
Mediate1
- The mRNA cap protects the primary transcript from exonucleases and recruits cap-binding complexes that mediate RNA processing, export and translation. (dundee.ac.uk)
Regulates1
- The RNA gate region regulates mRNA cap recognition to prevent promiscuous mRNA-binding before assembly of eif3d into the full eukaryotic translation initiation factor 3 (eIF-3) complex. (expasy.org)
Metabolism1
- Not only is m7G involved in the normal physiological metabolism of RNA, but recent research also shows that m7G and related regulators appear to be considerably dysregulated in tumors [ 12 ]. (beds.ac.uk)
Viruses4
- Enteroviruses are a group of single-stranded sense RNA viruses that commonly cause infections, especially in infants and children. (medscape.com)
- Enteroviruses belong to the Picornaviridae (small RNA viruses) family. (medscape.com)
- Using the A/Puerto Rico/8/34 backbone, we generated a comprehensive panel of recombinant A(H3N2) viruses that have different NAs but shared an HA that displays poor binding to red blood cells (RBCs). (cdc.gov)
- Additionally, 31 viruses contained mutations that may reduce susceptibility to inhibitors of neuraminidase (NA) (n=20) or cap-dependent endonuclease (CEN) (n=11). (cdc.gov)
Influenza1
- The observed binding mode is maintained in the context of heterotrimeric influenza polymerase, placing ANP32A in the immediate vicinity of known host-adaptive PB2 mutants. (nature.com)
Post-transcriptional modifications1
- M7G modification, known as one of the common post-transcriptional modifications of RNA, is present in many different types of RNAs. (beds.ac.uk)
Guanosine1
- mRNA guanylyltransferase then adds a backwards guanosine monophosphate (GMP) group from GTP, generating pyrophosphate, and mRNA (guanine-N7-)-methyltransferase methylates the guanine to form the final 5′-cap structure. (wikipedia.org)
LncRNAs1
- BACKGROUND: Emerging evidence indicates that long noncoding RNAs (lncRNAs) are important regulators of various biological processes, and their expression can be altered following certain pathological conditions, including central nervous system injury. (bvsalud.org)
Endonuclease1
- In collaboration with various pharmaceutical companies, we continue to work on cap-binding, endonuclease (Omoto et al . (embl.org)
Physiological1
- With the accurate identification of m7G modifications within RNAs, their functional roles in the regulation of gene expression and different physiological functions have been revealed. (beds.ac.uk)
Stability1
- This result was surprising since our previous Deruxtecan studies on sulfur-modified cap analogs suggested that introduction of two nonbridging sulfur atoms in the phosphate chain should increase or have a neutral effect on cap analog stability (Grudzien-Nogalska et al. (abic2004.org)
Replication2
- In parallel, we are doing the same for viral replication, which is unprimed and occurs in two-steps via an intermediate complementary RNA (cRNA). (embl.org)
- Replication of IAV is carried out by the RNA-dependent RNA viral polymerase that functions as a heterotrimeric complex, formed from separate components PA, PB1 and PB2. (nature.com)
Characterization1
- NA-binding was observed when a virus preparation contained approximately 10% of NA variants with either T148I or T439R, highlighting the benefit of using deep sequencing in virus characterization. (cdc.gov)
Complexes1
- Surprisingly, telomerase reconstitutions yielded heterogeneous DNA-bound TERT monomer and dimer complexes in relative amounts that varied with assembly and purification method. (elifesciences.org)
Subunits1
- Spike glycoprotein has two subunits, S1-responsible for its binding to host cell membrane receptors and S2-responsible for the fusion of viral and host cellular membrane[ 8 , 11 ]. (ijpsonline.com)
Enzyme2
- The enzyme polynucleotide 5′-phosphatase (RNA 5′-triphosphatase, RTPase, EC 3.1.3.33) is an enzyme that catalyzes the reaction a 5′-phosphopolynucleotide + H2O ⇌ {\displaystyle \rightleftharpoons } a polynucleotide + phosphate This enzyme belongs to the family of hydrolases, specifically those acting on phosphoric monoester bonds. (wikipedia.org)
- It had previously been suggested that TERT is only an active enzyme when it is bound to another TERT molecule, but Wu et al. (elifesciences.org)
Antisense1
- Another plasmid-encoded ProQ/FinO family member, FopA, has also been shown to interact with a single antisense RNA 11 . (nature.com)
Gene expression3
- RNA transport and regulated local translation play critically important roles in spatially restricting gene expression in neurons. (frontiersin.org)
- Cytoplasmic RNA granules in germ cells (polar and germinal granules), somatic cells (stress granules and processing bodies), and neurons (neuronal granules) have emerged as important players in the posttranscriptional regulation of gene expression. (rupress.org)
- The detection of RNA modifications is fundamental to the study of m7G modifications in the regulation of gene expression. (beds.ac.uk)
Mechanism3
- Most patients in this study did have a reduction in ENT1 RNA levels post treatment, indicating a likely acquired mechanism of drug resistance. (haematologica.org)
- Nature 2014) and proposed a mechanism of how cap-snatching is performed (Reich et al . (embl.org)
- A study shows that it also binds the 'cap' structure of cellular messenger RNAs and directs immune evasion using a novel mechanism. (hal.science)
Phosphorylation1
- Mitogenic stimulation leads to binding and activation of a complex composed of MTOR and RPTOR, leading to phosphorylation and release of RPS6KB1 and binding of EIF4B to eIF-3. (expasy.org)
Yeast1
- recently reported a method called CapQuant that allows the identification of cap-like RNAs in bacteria, virusus, yeast and human tissues. (biosyn.com)
Cytoplasmic1
- Earlier reports have pointed towards cytoplasmic-RNA processing bodies (P body, PB), although several questions have remained unsolved. (wur.nl)
Interference3
- 2062 : 127-145 Global Identification of Human Exosome Substrates Using RNA Interference and RNA Sequencing. (genetex.com)
- fucosyltransferase VI and can be inhibited by an RNA interference -based approach JOURNAL Int. J. Biochem. (dbcls.jp)
- GeneRIF: ISCA1, ISCA2, and IBA57 were depleted by RNA interference . (dbcls.jp)
Immunoprecipitation1
- High-throughput sequencing refers to the use of antibody immunoprecipitation or chemical methods to accurately locate the site of m7G modification in RNA. (beds.ac.uk)
Structural basis1
- Our identification of the first small molecule inhibitor of Dcp2 should be instrumental in future studies aimed at understanding the structural basis of RNA decapping and may provide insight toward the development of novel therapeutically relevant decapping inhibitors. (abic2004.org)
Translational1
- Biological process: cap-dependent translational initiation. (expasy.org)
Granules1
- Morphological descriptions of RNA granules originated with Metschnikoff (1865) , who described dark staining granules at one pole within Miastor metraloas (fly) larvae. (rupress.org)