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  • metabolism
  • Extensive transcript changes also occurred for genes involved in carbohydrate metabolism, including multi-functional proteins and regulators putatively involved in pathogenesis. (nih.gov)
  • In the presence of toluene, menadione reduced TodS activity whereas toluene did not stimulate activity in the presence of menadione.The opposing effects of menadione on glucose and toluene metabolism may be partially responsible for the interwoven regulation of both catabolic pathways.This work provides mechanistic detail on how complex sensor kinases integrate different types of signal molecules. (nih.gov)
  • This regulation controls parts of the sulfur metabolism of marine bacteria. (wikipedia.org)
  • In some rhizobia, the nif genes are located on plasmids called 'sym plasmids' (sym = symbiosis) which contain genes related to nitrogen fixation and metabolism, while the chromosomes contain most of the housekeeping genes of the bacteria. (wikipedia.org)
  • genetics
  • In honoring Campbell, ASM officials cited his "exceptional insights and achievements in the field of molecular genetics - a career of groundbreaking research that has had a profound influence on several fields, including molecular cloning and gene therapy. (wikipedia.org)
  • Mutation
  • The reduced accumulation of Spa was reversed by mutation of the gene encoding aureolysin, while the reduced accumulation of FnbA was reversed by mutation of the sspABC operon. (nih.gov)
  • The architecture of a prototypical bacterial signaling circuit enables a single point mutation to confer novel network properties. (nih.gov)
  • Genetic
  • The bacterium Escherichia coli carries approximately 3000 genes, but this total repertoire describes its potential properties and, in reality, only a small subset of this genetic information is expressed at any given moment. (springer.com)
  • The dormant form of the lambda genome was called the 'prophage' Study of phage lambda over the next 50 years provided valuable insights into virus life cycles, the regulation and expression of genetic material, and the mechanism of integration and excision of genetic material into chromosomal locations. (wikipedia.org)
  • instead, non-genetic factors cause the organism's genes to behave (or "express themselves") differently. (wikipedia.org)
  • Shortly thereafter, a series of papers were published by Youssef Idaghdour and his colleagues looking at the role of environmental factors on gene expression throughout the genome where they found that only 5% of the variation in genomic expression was attributable to genetic factors (i.e. sequence variation in the genome) whereas, as much as half was due to the living environment of the individual, either urban or rural. (wikipedia.org)
  • Genetic expression is far from random, allowing the differentiation and specialization of different cell types with identical genomes. (wikipedia.org)
  • The most efficient way for an organism to regulate genetic expression is at the transcriptional level. (wikipedia.org)
  • promoter
  • By using fluorescent promoter reporters, we show that global regulation is growth rate dependent not only during steady state but also during dynamic changes in growth rate and can be quantified through two promoter‐specific parameters. (embopress.org)
  • We present a model‐based approach to quantitatively dissect simultaneous contributions from specific transcription factors and the global growth status to bacterial gene expression, based on parameter inference from GFP‐based promoter activity measurements. (embopress.org)
  • 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)
  • Verification of eQRNA/RNAz predictions by Northern hybridization and RACE mapping led to the identification of eight previously unknown genes, with recognizable promoter and termination signatures, expressing small transcripts. (wikipedia.org)
  • While characterizing the outer membrane porin ompC in E.coli, some of the ompC promoter clones observed were capable of repressing the expression of other membrane porin such as ompF. (wikipedia.org)
  • Expression of this fis operon is negatively regulated by Fis in vivo and purified Fis can prevent stable complex formation by RNA polymerase at the fis promoter in vitro. (wikipedia.org)
  • It has been found that a single gene can contain multiple promoter sites. (wikipedia.org)
  • DNA TATA box Pribnow box SOS box CAAT box CCAAT box Operator (biology) Upstream activation sequence RNA List of cis-regulatory RNA elements Polyadenylation signals, mRNA AU-rich element, mRNA Other Regulation of gene expression cis-regulatory module Gene regulatory network Operon Promoter Trans-acting factor Rfam Transterm Butler JE, Kadonaga JT (October 2002). (wikipedia.org)
  • Clusters
  • Engineering Streptomyces coelicolor for heterologous expression of secondary metabolite gene clusters. (nih.gov)
  • Removal of the four endogenous gene clusters (to yield M1146) resulted in a much simpler chromatogram with fewer peaks, and a lower and more stable baseline (Fig. 4). (nih.gov)
  • Consequently, when combined with liquid chromatography and mass spectrometry, these engineered strains are likely to markedly facilitate the discovery of new compounds from heterologously expressed gene clusters. (nih.gov)
  • Social genomics researchers have thus examined the role of social factors (e.g. isolation, rejection) on the expression of individual genes, or more commonly, clusters of many genes (i.e. gene profiles, or gene programs). (wikipedia.org)
  • polymerase
  • However, NMR studies show that in the DNA-bound state, two domains tumble separately and an REC-DBD interaction is transiently populated in solution.Reporter gene analyses of PmrA variants with altered interface residues suggest that the interface is not crucial for supporting gene expression.We propose that REC-DBD interdomain dynamics and the DBD-DBD interface help PmrA interact with RNA polymerase holoenzyme to activate downstream gene transcription. (nih.gov)
  • We propose that REC-DBD interdomain dynamics and the DBD-DBD interface help PmrA interact with RNA polymerase holoenzyme to activate downstream gene transcription. (nih.gov)
  • Only once this region has been bound with the appropriate set of TFs, and in the proper order, can RNA polymerase bind and begin transcribing the gene. (wikipedia.org)
  • protein
  • Importantly, we observed up-regulation of four genes encoding LPXTG proteins after 30 min of incubation in blood, including gbs0428, gbs1087 (fbsA) encoding a major receptor for fibrinogen, gbs1420 (bsp) which encodes a putative choline-binding protein, and gbs2018 (bibA) which encodes a protein that binds to human C4-binding protein and contributes to survival in human blood (Fig. 4A and Table 2). (nih.gov)
  • Highly potent dUTPase inhibition by a bacterial repressor protein reveals a novel mechanism for gene expression control. (nih.gov)
  • The last gene of the cluster encodes the fourth listerial GGDEF domain protein, PssE, that functions as an I-site c-di-GMP receptor essential for exopolysaccharide synthesis. (nih.gov)
  • HU is a small (10 kDa) bacterial histone-like protein that resembles the eukaryotic Histone H2B. (wikipedia.org)
  • In 2002, the first comprehensive proofs of multiple classes of riboswitches were published, including protein-free binding assays, and metabolite-binding riboswitches were established as a new mechanism of gene regulation. (wikipedia.org)
  • Fis has been deemed a bacterial chromatin architectural protein. (wikipedia.org)
  • riboswitches
  • Prior to the discovery of riboswitches, the mechanism by which some genes involved in multiple metabolic pathways were regulated remained mysterious. (wikipedia.org)
  • Riboswitches are often conceptually divided into two parts: an aptamer and an expression platform. (wikipedia.org)
  • mRNA
  • Later on, this transcript, denoted micF, was found to be an asRNA of ompF and capable of downregulating the expression of ompF under stress by forming a duplex with the ompF mRNA. (wikipedia.org)
  • Regions
  • Two complementary computational screens, eQRNA and RNAz, were used to search for novel sRNA-encoding genes in the intergenic regions IGRs of S. meliloti. (wikipedia.org)
  • Gene expression can be controlled through the action of repressor proteins that attach to silencer regions of the DNA. (wikipedia.org)
  • These data included conserved RNA secondary structures often found in the untranslated regions (UTRs) of the relevant genes and the success of procedures to create artificial small molecule-binding RNAs called aptamers. (wikipedia.org)
  • For example, comparative analysis of upstream regions of several genes expected to be co-regulated led to the description of the S-box (now the SAM-I riboswitch), the THI-box (a region within the TPP riboswitch), the RFN element (now the FMN riboswitch) and the B12-box (a part of the cobalamin riboswitch), and in some cases experimental demonstrations that they were involved in gene regulation via an unknown mechanism. (wikipedia.org)
  • Cis-regulatory elements (CREs) are regions of non-coding DNA which regulate the transcription of neighboring genes. (wikipedia.org)
  • genome sequence
  • Recently, an analysis of the R. equi 103 genome sequence revealed the presence of four potential catalase genes. (nih.gov)
  • The in silico analysis of the genome sequence of the R. equi 103 strain revealed the presence of four potential catalase genes, designated katA, katB, katC and katD. (nih.gov)
  • molecule
  • The aptamer directly binds the small molecule, and the expression platform undergoes structural changes in response to the changes in the aptamer. (wikipedia.org)
  • Expression platforms typically turn off gene expression in response to the small molecule, but some turn it on. (wikipedia.org)
  • The Latin prefix cis means "on this side", i.e. on the same molecule of DNA as the gene(s) to be transcribed. (wikipedia.org)
  • This DNA sequence is bound by the lac repressor, which, in turn, prevents transcription of the adjacent genes on the same DNA molecule. (wikipedia.org)
  • To summarize, cis-regulatory elements are present on the same molecule of DNA as the gene they regulate whereas trans-regulatory elements can regulate genes distant from the gene from which they were transcribed. (wikipedia.org)
  • regulatory
  • The genomic features may include the DNA sequence, genes, gene order, regulatory sequences, and other genomic structural landmarks. (wikipedia.org)
  • Rhodobacter capsulatus-a free-living anaerobic phototroph containing a transcriptional nif gene regulatory system. (wikipedia.org)
  • combined A repressive effect of Fis and previously characterized negative regulatory factors could be responsible to keep the gene silenced most of the time. (wikipedia.org)
  • In contrast, trans-regulatory elements are diffusible factors, usually proteins, that may modify the expression of genes distant from the gene that was originally transcribed to create them. (wikipedia.org)
  • enzyme
  • What is meant by the "one gene-one enzyme" hypothesis (Beadle and Tatum)? (brainscape.com)
  • The primary enzyme encoded by the nif genes is the nitrogenase complex which is in charge of converting atmospheric nitrogen (N2) to other nitrogen forms such as ammonia which the organism can use for various purposes. (wikipedia.org)
  • sequence
  • The DNA sequence in the region of the fusion between bla and tRNAArg5 genes is displayed above the plasmid map. (nih.gov)
  • Epigenetics is the study of heritable changes in gene function that do not involve changes in the DNA sequence. (wikipedia.org)
  • Examples of mechanisms that produce such changes are DNA methylation and histone modification, each of which alters how genes are expressed without altering the underlying DNA sequence. (wikipedia.org)
  • For example, small RNA viruses infecting animals (picornaviruses) and those infecting plants (cowpea mosaic virus) were compared and turned out to share significant sequence similarity and, in part, the order of their genes. (wikipedia.org)
  • transcripts
  • Most (83%) of the significantly altered transcripts were down-regulated after 30 minutes of incubation in blood, and all functional categories of genes were abundantly represented. (nih.gov)
  • However, riboswitch transcripts subsequently modulate the expression of a gene located elsewhere in the genome. (wikipedia.org)
  • organisms
  • The nif genes are genes encoding enzymes involved in the fixation of atmospheric nitrogen into a form of nitrogen available to living organisms. (wikipedia.org)
  • The expression and regulation of nif genes, while sharing common features in all or most of the nitrogen-fixing organisms in nature, have distinct characters and qualities that differ from one diazotroph to another. (wikipedia.org)
  • signals
  • It presents the cell with the signals that ultimately lead to gene regulation-the turning on or off of gene expression. (springer.com)
  • The active and inactive state of transcription factors in growing cells is usually directed by allosteric physicochemical signals or metabolites, which are in turn either produced in the cell or obtained from the environment by the activity of the products of effector genes. (nih.gov)
  • coordinate
  • Rhizobial adaptations to soil and plant cell environments require the coordinate expression of complex gene networks in which sRNAs are expected to participate. (wikipedia.org)
  • commonly
  • 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)
  • thus
  • Simultaneous specific and global regulation thus constitutes an additional-but often neglected-layer of complexity in gene expression. (embopress.org)
  • a) In a bifan motif, two TFs A and B, both regulate the expression of two different target genes C and D. Thus making the positions of the TFs to be symmetric, unlike in FFLs. (nih.gov)
  • These methods can also quickly uncover single-nucleotide polymorphisms, insertions and deletions by mapping unassembled reads against a well annotated reference genome, and thus provide a list of possible gene differences that may be the basis for any functional variation among strains. (wikipedia.org)
  • The lac operator is, thus, considered to "act in cis" on the regulation of the nearby genes. (wikipedia.org)
  • genomic
  • In 1986, the first comparative genomic study at a larger scale was published, comparing the genomes of varicella-zoster virus and Epstein-Barr virus that contained more than 100 genes each. (wikipedia.org)
  • phenotypic
  • For numerous reasons, including organizational maintenance, energy conservation, and generating phenotypic variance, it is important that genes are only expressed when they are needed. (wikipedia.org)
  • mechanism
  • The 1940s produced the first pictures of bacterial viruses using electron microscopy produced the first photos of bacterial viruses, and research on the mechanism of infection and reproduction dramatically increased. (wikipedia.org)
  • regulator
  • A simple regulon being a group of genes regulated by one regulator, and complex regulons, groups of genes regulated by the same set of two or more TFs. (nih.gov)
  • growth
  • Gene expression is regulated by specific transcriptional circuits but also by the global expression machinery as a function of growth. (embopress.org)
  • We show that growth rate can be used to predict the unregulated expression baseline of a gene, since growth rate dependence of global regulation occurs both in steady state and during transient changes in growth rate. (embopress.org)
  • HPLC chromatograms of supernatants of M145 and the quadruply deleted mutant M1146, and of the same strains containing the congocidine gene cluster (indicated as '+pCGC002') after growth in liquid GYM medium. (nih.gov)
  • infection
  • In conditions of social stress however, the up-regulation of pro-inflammatory gene expression prepares the body to better deal with bodily injury and bacterial infection which is more likely under conditions of social stress either through hostile human contact, or increased predatory vulnerability due to separation from the social group. (wikipedia.org)
  • Concurrently, the down-regulation of anti-viral gene expression leaves the individual more vulnerable to viral infection such as the flu and the common cold. (wikipedia.org)
  • Proteins
  • This gene encodes a member of the bicoid subfamily of the paired (PRD) homeobox family of proteins. (genecards.org)
  • Deposition of matricellular proteins modulates growth factor signaling and contributes to the spatial and temporal regulation of the reparative response. (jci.org)
  • More than twenty distinct IFN genes and proteins have been identified in animals, including humans. (wikipedia.org)
  • In addition, interferons induce production of hundreds of other proteins-known collectively as interferon-stimulated genes (ISGs)-that have roles in combating viruses and other actions produced by interferon. (wikipedia.org)
  • In the cells of extant organisms, the vast majority of the proteins present in the mitochondria (numbering approximately 1500 different types in mammals) are coded for by nuclear DNA, but the genes for some, if not most, of them are thought to have originally been of bacterial origin, having since been transferred to the eukaryotic nucleus during evolution. (wikipedia.org)
  • The operon contains two heat-shock genes, encoding inclusion body binding proteins A and B (IbpA/B), and is the most drastically upregulated operon under heat-shock in Escherichia coli. (wikipedia.org)
  • plasmids
  • The IncP-1 plasmid group (IncP plasmids in Escherichia coli) of which RK2 is a part has been described as "highly potent, self-transmissible, selfish DNA molecules with a complicated regulatory circuit" RK 2 was first isolated in connection with an outbreak of antibotic-resistant Pseudomonas aeruginosa and Klebsiella aerogenes in Birmingham in 1969, as one of a family of plasmids implicated in transfer of Ampicillin resistance between bacterial strains. (wikipedia.org)
  • In these plasmids most of the genes have been removed, leaving only genes essential for replication and one or more selectable markers. (wikipedia.org)
  • Minimal plasmids such as PFF1 are useful for studying the basic mechanisms of plasmid replication and copy number regulation, as there are less superfluous genetic elements which might affect the processes being studied. (wikipedia.org)
  • Broad-Host-Range Plasmids from Agricultural Soils Have IncP-1 Backbones with Diverse Accessory Genes", Appl Environ Microbiol. (wikipedia.org)
  • transcriptional
  • The mechanism whereby pRB activates hTR remains unknown though pRB is not known to interact directly in a specific fashion with DNA, relying instead on recruitment to genes through interaction with other transcriptional regulators including Sp1 and mdm2. (biomedcentral.com)
  • In addition, RK2 contains a set of potentially lethal (to the cell) genes, called kil genes, and a set of complementary transcriptional repressor genes, called kor (short for "kil-override") genes, which inactivate the kil genes. (wikipedia.org)
  • As promoters are typically immediately adjacent to the gene in question, positions in the promoter are designated relative to the transcriptional start site, where transcription of DNA begins for a particular gene (i.e., positions upstream are negative numbers counting back from -1, for example -100 is a position 100 base pairs upstream). (wikipedia.org)
  • Promoter
  • We have previously demonstrated that NF-Y and Sp1 interact with the human telomerase RNA (hTR) promoter and play a central role in its regulation. (biomedcentral.com)
  • The aim was to investigate possible roles for mdm2 in hTR promoter regulation. (biomedcentral.com)
  • Transient co-transfection experiments using an hTR promoter luciferase reporter construct show that hTR promoter activity is inhibited by over-expression of mdm2 in 5637 bladder carcinoma cells (p53 and pRB negative, low mdm2). (biomedcentral.com)
  • Titration of mdm2 was able to antagonise activation of hTR promoter activity mediated by pRB or Sp1 over-expression, although in the presence of pRB, mdm2 could not repress promoter activity below basal levels. (biomedcentral.com)
  • Elucidation of new regulators affecting hTR basal promoter activity in cancer cells provides a basis for future studies aimed at improving our understanding of the differential hTR expression between normal and cancer cells. (biomedcentral.com)
  • The previously identified core promoter region in the hTR gene has several features utilised by the basal RNA PolII transcription machinery, including one CCAAT-box and four Sp1 sites termed Sp1.1-Sp1.4. (biomedcentral.com)
  • In genetics, a promoter is a region of DNA that initiates transcription of a particular gene. (wikipedia.org)
  • enhancers
  • Promoters represent critical elements that can work in concert with other regulatory regions (enhancers, silencers, boundary elements/insulators) to direct the level of transcription of a given gene. (wikipedia.org)
  • locus
  • J A Kornacki, C H Chang, and D H Figurski: "kil-kor regulon of promiscuous plasmid RK2: structure, products, and regulation of two operons that constitute the kilE locus. (wikipedia.org)
  • Complementation, deletion, and recombination tests can be used to map out the rII gene locus by using T4. (wikipedia.org)
  • Promoters
  • These transcription factors have specific activator or repressor sequences of corresponding nucleotides that attach to specific promoters and regulate gene expression. (wikipedia.org)
  • 5'-XXXXXXXPPPPPPXXXXXXPPPPPPXXXXGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGXXXX-3' -35 -10 Gene to be transcribed for -10 sequence T A T A A T 77% 76% 60% 61% 56% 82% for -35 sequence T T G A C A 69% 79% 61% 56% 54% 54% Eukaryotic promoters are diverse and can be difficult to characterize, however, recent studies show that they are divided in more than 10 classes. (wikipedia.org)
  • viral infections
  • IFNs belonging to all three classes are important for fighting viral infections and for the regulation of the immune system. (wikipedia.org)
  • However, available evidence suggests that MYD88 is dispensable for human resistance to common viral infections and to all but a few pyogenic bacterial infections, demonstrating a major difference between mouse and human immune responses. (wikipedia.org)
  • binds
  • The essential replication system in RK2 consists of an origin of replication, oriV, and a gene, trfA, whose gene product, the TrfA protein, binds to and activates oriV. (wikipedia.org)
  • replication
  • These phenotypes were unexpectedly linked to mutations in the gene encoding a subunit of the Go-Ichi-Ni-San (GINS) complex, which is essential for DNA replication prior to cell division. (jci.org)
  • RK2 is approximately 60 kbp long and contains genes for replication, maintenance, conjugation and antibiotic resistance. (wikipedia.org)
  • The D period refers to the stage between the end of DNA replication and the splitting of the bacterial cell into two daughter cells. (wikipedia.org)
  • cell
  • Expression of type I and III IFNs can be induced in virtually all cell types upon recognition of viral components, especially nucleic acids, by cytoplasmic and endosomal receptors, whereas type II interferon is induced by cytokines such as IL-12, and its expression is restricted to immune cells such as T cells and NK cells. (wikipedia.org)
  • cells
  • The protein encoded by this gene is found in rod cells in the back of the eye and is essential for vision in low-light conditions. (genecards.org)
  • Nature Immunology, 2004;5:516 Lu L, Ikizawa K, Hu D, Werneck MBF, Wucherpfennig KW, Cantor H. Regulation of activated CD4+ T cells by NK cells via the Qa-1-NKG2A inhibitory pathway. (wikipedia.org)
  • mutant
  • Our subsequent experimental work focused upon practical applications of BOEC: their use for gene therapy, tissue engineering, assessment of mutant gene effect, and discovery of heterogeneity in endothelial biology. (jci.org)
  • Twenty-one tests were carried out on homozygous mutant animals, revealing one abnormality: male mutants had an increased susceptibility to bacterial infection. (wikipedia.org)
  • Transcription
  • Thus, investigation of the activating and repressive mechanisms of telomerase gene transcription has become an area of intense interest in cancer research. (biomedcentral.com)
  • For transcription to take place, the enzyme that synthesizes RNA, known as RNA polymerase, must attach to the DNA near a gene. (wikipedia.org)
  • response
  • HDAC3-deficient macrophages possessed decreased ability to activate inflammatory gene expression in response to LPS stimulation [ 13 ]. (hindawi.com)
  • Viral tropism for the decidua and placenta is then dependent on viral entry receptor expression in these tissues as well as on the maternal immune response to the virus. (jci.org)
  • major
  • they increase host defenses by up-regulating antigen presentation by virtue of increasing the expression of major histocompatibility complex (MHC) antigens. (wikipedia.org)