• metabolism
  • The novel antiterminator structure consists of two small hairpins with highly conserved terminal loop residues, both features being essential for successful antitermination.Despite the unrelatedness of the species in which they are found, the majority of the ANTAR-associated genes are thematically related to nitrogen management.These data suggest that the central tenets for gene regulation by ANTAR antitermination occur widely in nature to specifically control nitrogen metabolism. (nih.gov)
  • These data suggest that the central tenets for gene regulation by ANTAR antitermination occur widely in nature to specifically control nitrogen metabolism. (nih.gov)
  • Regulation of carbon metabolism in the mollicutes and its relation to virulence. (asmscience.org)
  • Trigger enzymes: bifunctional proteins active in metabolism and in controlling gene expression. (asmscience.org)
  • encode
  • Although MG1655 does not encode a T7 RNA polymerase gene, the pde genes were expressed from a fortuitous promoter at sufficiently high levels to partially restore the swimming defect of MG1655 ΔyhjH in semi-solid agar. (nih.gov)
  • Proteins called 'CRISPR-associated genes' (cas genes) encode cellular machinery that cuts exogenous DNA into small fragments and inserts them into a CRISPR repeat locus. (wikipedia.org)
  • While identifying these small RNAs, her lab discovered that some of these small RNAs encode small proteins that had previously been overlooked because they are not detected in many traditional biochemical assays and the corresponding genes are poorly annotated. (wikipedia.org)
  • pathogens
  • Recent studies have revealed that viruses and bacterial pathogens exploit the host ubiquitination pathways to gain entry and to aid their survival/replication inside host cells. (frontiersin.org)
  • This review will summarize recent developments in understanding the biochemical and structural mechanisms utilized by bacterial pathogens to interact with the host ubiquitination pathways. (frontiersin.org)
  • In this chapter, we provide an overview on these mechanisms and discuss the relevance of trigger enzymes for virulence gene expression in bacterial pathogens. (asmscience.org)
  • degradation
  • Interaction of Bpa with the proteasome stimulates proteosomal peptidase and casein degradation activity, which suggests Bpa could play a role in the removal of non-native or damaged proteins by influencing the conformation of the proteasome complex upon interaction. (uniprot.org)
  • The story started with a search for a non-lysosomal pathway for protein degradation. (frontiersin.org)
  • Binding can occur either through the blocking of transcription (in the case of gene-binding), the degradation of the mRNA transcript (e.g. by small interfering RNA (siRNA)) or RNase-H dependent antisense), or through the blocking of either mRNA translation, pre-mRNA splicing sites, or nuclease cleavage sites used for maturation of other functional RNAs, including miRNA (e.g. by morpholino oligos or other RNase-H independent antisense). (wikipedia.org)
  • RNA interference (RNAi) is a means of silencing genes by way of mRNA degradation. (wikipedia.org)
  • mutations
  • p>Describes annotations that are concluded from looking at variations or changes in a gene product such as mutations or abnormal levels and includes techniques such as knockouts, overexpression, anti-sense experiments and use of specific protein inhibitors. (uniprot.org)
  • Through the analysis of per circadian mutants and additional mutations on Drosophila clock genes, a model encompassing positive and negative autoregulatory feedback loops of transcription and translation has been proposed. (wikipedia.org)
  • RNAs
  • Furthermore, bioinformatic searches using this conserved antiterminator motif identified many new ANTAR target RNAs in phylogenetically diverse bacterial species, some comprising complex regulons. (nih.gov)
  • Gene knockdown by this method is achieved by introducing small double-stranded interfering RNAs (siRNA) into the cytoplasm. (wikipedia.org)
  • When this CRISPR region of DNA is expressed by the cell, the small RNAs produced from the exogenous DNA inserts serve as a template sequence that other Cas proteins use to silence this same exogenous sequence. (wikipedia.org)
  • residues
  • Ubiquitination is a post-translational modification in which one or more 76 amino acid polypeptide ubiquitin molecules are covalently linked to the lysine residues of target proteins. (frontiersin.org)
  • transcriptional
  • The integration host factor (IHF), a dimer of closely related chains which is suggested to function in genetic recombination as well as in translational and transcriptional control is found in Enterobacteria and viral proteins including the African swine fever virus protein A104R (or LMW5-AR). (wikipedia.org)
  • Chromosome
  • The structure of the bacterial chromosome can be considered at several different levels. (springer.com)
  • However, the analogy with protein structure should not be carried too far, because the three-dimensional structure of the chromosome appears to be dynamic in its organization and its structural fluctuations may go beyond the kinds of statistical perturbations expected in proteins. (springer.com)
  • As a result of his interest in gene regulation in mammalian cells, Riggs became curious about X chromosome inactivation, in which one of the two copies of the X chromosome present in a female mammal is inactivated. (wikipedia.org)
  • defense
  • Involved in regulation of pathogen-specific host defense of activated macrophages. (genecards.org)
  • These sequences play a key role in a bacterial defense system, and form the basis of a technology known as CRISPR/Cas9 that effectively and specifically changes genes within organisms. (wikipedia.org)
  • amino
  • Finally, with the help of a ubiquitin-protein ligase, E3, a covalent bond is formed between the C-terminus of ubiquitin and the ε-amino group of a lysine residue on the protein substrate. (frontiersin.org)
  • Feedback and allosteric mechanisms ensure that all twenty amino acids are maintained in sufficient amounts for protein synthesis and other processes. (wikipedia.org)
  • Dr. Storz's research interests include the characterization of small non-coding RNA and small proteins of 50 amino acids or less. (wikipedia.org)
  • binds
  • Following elution, the protein readily binds DNA, indicating the protein's high affinity for DNA. (wikipedia.org)
  • Her research group demonstrated that one such small protein, AcrZ, binds to the multidrug efflux pump protein AcrB to affect its ability to export certain classes of antibiotics. (wikipedia.org)
  • Diguanylate
  • Genome-wide genetic and biochemical analyses of c-di-GMP signaling pathways revealed that L. monocytogenes has three GGDEF domain proteins, DgcA (Lmo1911), DgcB (Lmo1912) and DgcC (Lmo2174), that possess diguanylate cyclase activity, and three EAL domain proteins, PdeB (Lmo0131), PdeC (Lmo1914) and PdeD (Lmo0111), that possess c-di-GMP phosphodiesterase activity. (nih.gov)
  • Deletion of all phosphodiesterase genes (ΔpdeB/C/D) or expression of a heterologous diguanylate cyclase stimulated production of a previously unknown exopolysaccharide. (nih.gov)
  • viral
  • Most alphaviruses lose the peripheral protein E3, but in Semliki viruses it remains associated with the viral surface. (wikipedia.org)
  • expression
  • The mechanism for RNA recognition by ANTAR regulators of gene expression. (nih.gov)
  • Virulence gene expression serves two main functions, growth in/on the host, and the acquisition of nutrients. (asmscience.org)
  • Therefore, it is obvious that nutrient availability is important to control expression of virulence genes. (asmscience.org)
  • Enzymes that have a second (so-called moonlighting) function in the regulation of gene expression are collectively referred to as trigger enzymes. (asmscience.org)
  • Gene knockdown is an experimental technique by which the expression of one or more of an organism's genes are reduced. (wikipedia.org)
  • In a transient knockdown, the binding of this oligonucleotide to the active gene or its transcripts causes decreased expression through a variety of processes. (wikipedia.org)
  • structural
  • in these processes, bacterial DNA binding proteins have an architectural role, maintaining structural integrity as transcription, recombination, replication, or any other DNA-dependent process proceeds. (wikipedia.org)
  • The four non-structural protein genes are encoded in the 5′ two-thirds of the genome, while the three structural proteins are translated from a subgenomic mRNA colinear with the 3′ one-third of the genome. (wikipedia.org)
  • synthesis
  • The c-di-GMP produced by this enzyme up-regulates poly-GlcNAc production as well as the biofilm synthesis protein PgaD, although c-di-GMP is probably not the main inducing principle. (uniprot.org)
  • The synthesis of this exopolysaccharide was attributed to the pssA-E (lmo0527-0531) gene cluster. (nih.gov)
  • deletion
  • Mutation in this gene results in deletion of the DAG binding-like motif and causes a recessive ataxia. (genecards.org)
  • Interaction
  • We speculated that in order to bind an RNA target that presents two similar surfaces for interaction, the protein component is also likely to form a dimer or higher ordered oligomeric state to recognize the RNA substrate. (nih.gov)
  • species
  • Despite the unrelatedness of the species in which they are found, the majority of the ANTAR-associated genes are thematically related to nitrogen management. (nih.gov)
  • monomers
  • D) The theoretical molar masses for monomers of EutV protein variants are listed alongside experimentally observed values. (nih.gov)
  • The E1-E2 heterodimers form one-to-one contacts between the E2 protein and the nucleocapsid monomers. (wikipedia.org)
  • suggests
  • Dimerization of ANTAR-containing proteins.A) Comparison of size exclusion chromatography profiles (Superdex-75 column) for ANTARcc (blue), ANTAR (green) and protein calibration standards (grey) suggests a dimeric state for ANTARcc and ANTAR. (nih.gov)
  • coli
  • Riggs and Itakura collaborated with Herbert Boyer at Genentech, and used recombinant DNA technology to become the first to produce a human protein in E. coli. (wikipedia.org)
  • strand
  • The use of DNA binding domains to target tethered functional protein domains (for example double strand endonucleases and DNA methylases ) or bait moieties in two-hybrid experiments to defined sites on DNA is now routine. (wikipedia.org)
  • pathways
  • Following bacterial infection promotes NADH oxidase activity by association with CYBA thereby affecting TLR2 signaling and probably other TLR-NOX pathways. (genecards.org)
  • substrate
  • The ANTAR protein dimerizes and associates with its substrate RNA in response to signal-induced phosphorylation. (nih.gov)
  • commonly
  • section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein. (uniprot.org)
  • The exopolysaccharide also greatly enhances bacterial tolerance to commonly used disinfectants as well as desiccation, which may contribute to survival of L. monocytogenes on contaminated food products and in food-processing facilities. (nih.gov)
  • target
  • a href='/help/protein_existence' target='_top'>More. (uniprot.org)
  • a href='/help/gene_ontology' target='_top'>More. (uniprot.org)
  • a href='/help/gene_name' target='_top'>More. (uniprot.org)
  • The first description of what would later be called CRISPR was from Osaka University researcher Yoshizumi Ishino in 1987, who accidentally cloned part of a CRISPR together with the iap gene, the target of interest. (wikipedia.org)
  • found
  • Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. (genecards.org)
  • HU-type proteins have been found in a variety of eubacteria, cyanobacteria and archaebacteria, and are also encoded in the chloroplast genome of some algae. (wikipedia.org)
  • Cell
  • The c-di-GMP-inducible exopolysaccharide causes cell aggregation in minimal medium and impairs bacterial migration in semi-solid agar, however, it does not promote biofilm formation on abiotic surfaces. (nih.gov)
  • By delivering the Cas9 nuclease complexed with a synthetic guide RNA (gRNA) into a cell, the cell's genome can be cut at a desired location, allowing existing genes to be removed and/or new ones added. (wikipedia.org)
  • Research
  • Bacillus amyloliquefaciens is the source of a natural antibiotic protein barnase (a ribonuclease), alpha amylase used in starch hydrolysis, the protease subtilisin used with detergents, and the BamH1 restriction enzyme used in DNA research. (wikipedia.org)
  • In C. elegans research, the availability of tools such as the Ahringer RNAi Library give laboratories a way of testing many genes in a variety of experimental backgrounds. (wikipedia.org)
  • FUNCTION
  • Since bacterial binding proteins have a diversity of functions, it has been difficult to develop a common function for all of them. (wikipedia.org)
  • The most direct use of transient knockdowns is for learning about a gene that has been sequenced, but has an unknown or incompletely known function. (wikipedia.org)
  • RNAi in organisms such as C. elegans and Drosophila melanogaster provides a quick and inexpensive means of investigating gene function. (wikipedia.org)
  • strain
  • PDE activities of the L. monocytogenes proteins PdeB-D.A: Restoration of motility in semi-solid (0.25%) agar of strain MG1655 ΔyhjH by L. monocytogenes PdeB, PdeC and PdeD is indicative of their c-di-GMP PDE activities. (nih.gov)
  • cluster
  • A major addition to the understanding of CRISPR came with Jansen's observation that the prokaryote repeat cluster was accompanied by a set of homologous genes that make up CRISPR-associated systems or cas genes. (wikipedia.org)