A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
Escherichia coli K12
Materials or substances used in the composition of traditional medical remedies. The use of this term in MeSH was formerly restricted to historical articles or those concerned with traditional medicine, but it can also refer to homeopathic remedies. Nosodes are specific types of homeopathic remedies prepared from causal agents or disease products.
Molecular Sequence Data
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
Gene Expression Regulation, Bacterial
Amino Acid Sequence
One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to OXYGEN: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or PHOTOTROPHY (via light reaction); for chemotrophs by their source of chemical energy: CHEMOLITHOTROPHY (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for CARBON; NITROGEN; etc.; HETEROTROPHY (from organic sources) or AUTOTROPHY (from CARBON DIOXIDE). They can also be classified by whether or not they stain (based on the structure of their CELL WALLS) with CRYSTAL VIOLET dye: gram-negative or gram-positive.
Escherichia coli O157
A verocytotoxin-producing serogroup belonging to the O subfamily of Escherichia coli which has been shown to cause severe food-borne disease. A strain from this serogroup, serotype H7, which produces SHIGA TOXINS, has been linked to human disease outbreaks resulting from contamination of foods by E. coli O157 from bovine origin.
Adhesins, Escherichia coli
Bacterial Outer Membrane Proteins
Meningitis, Escherichia coli
A form of gram-negative meningitis that tends to occur in neonates, in association with anatomical abnormalities (which feature communication between the meninges and cutaneous structures) or as OPPORTUNISTIC INFECTIONS in association with IMMUNOLOGIC DEFICIENCY SYNDROMES. In premature neonates the clinical presentation may be limited to ANOREXIA; VOMITING; lethargy; or respiratory distress. Full-term infants may have as additional features FEVER; SEIZURES; and bulging of the anterior fontanelle. (From Menkes, Textbook of Child Neurology, 5th ed, pp398-400)
Genetic Complementation Test
Sequence Analysis, DNA
Sequence Homology, Amino Acid
Any liquid or solid preparation made specifically for the growth, storage, or transport of microorganisms or other types of cells. The variety of media that exist allow for the culturing of specific microorganisms and cell types, such as differential media, selective media, test media, and defined media. Solid media consist of liquid media that have been solidified with an agent such as AGAR or GELATIN.
Enterotoxigenic Escherichia coli
Strains of ESCHERICHIA COLI that produce or contain at least one member of either heat-labile or heat-stable ENTEROTOXINS. The organisms colonize the mucosal surface of the small intestine and elaborate their enterotoxins causing DIARRHEA. They are mainly associated with tropical and developing countries and affect susceptible travelers to those places.
Thin, hairlike appendages, 1 to 20 microns in length and often occurring in large numbers, present on the cells of gram-negative bacteria, particularly Enterobacteriaceae and Neisseria. Unlike flagella, they do not possess motility, but being protein (pilin) in nature, they possess antigenic and hemagglutinating properties. They are of medical importance because some fimbriae mediate the attachment of bacteria to cells via adhesins (ADHESINS, BACTERIAL). Bacterial fimbriae refer to common pili, to be distinguished from the preferred use of "pili", which is confined to sex pili (PILI, SEX).
A parasexual process in BACTERIA; ALGAE; FUNGI; and ciliate EUKARYOTA for achieving exchange of chromosome material during fusion of two cells. In bacteria, this is a uni-directional transfer of genetic material; in protozoa it is a bi-directional exchange. In algae and fungi, it is a form of sexual reproduction, with the union of male and female gametes.
Electrophoresis, Polyacrylamide Gel
The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
Drug Resistance, Microbial
Shiga-Toxigenic Escherichia coli
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
Enteropathogenic Escherichia coli
Strains of ESCHERICHIA COLI characterized by attaching-and-effacing histopathology. These strains of bacteria intimately adhere to the epithelial cell membrane and show effacement of microvilli. In developed countries they are associated with INFANTILE DIARRHEA and infantile GASTROENTERITIS and, in contrast to ETEC strains, do not produce ENDOTOXINS.
DNA Restriction Enzymes
Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.
DNA Transposable Elements
Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.
Recombinant Fusion Proteins
An antibiotic first isolated from cultures of Streptomyces venequelae in 1947 but now produced synthetically. It has a relatively simple structure and was the first broad-spectrum antibiotic to be discovered. It acts by interfering with bacterial protein synthesis and is mainly bacteriostatic. (From Martindale, The Extra Pharmacopoeia, 29th ed, p106)
Escherichia coli Vaccines
The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).
The phenomenon by which a temperate phage incorporates itself into the DNA of a bacterial host, establishing a kind of symbiotic relation between PROPHAGE and bacterium which results in the perpetuation of the prophage in all the descendants of the bacterium. Upon induction (VIRUS ACTIVATION) by various agents, such as ultraviolet radiation, the phage is released, which then becomes virulent and lyses the bacterium.
Enterohemorrhagic Escherichia coli
Uropathogenic Escherichia coli
Membrane Transport Proteins
Sequence Homology, Nucleic Acid
An envelope of loose gel surrounding a bacterial cell which is associated with the virulence of pathogenic bacteria. Some capsules have a well-defined border, whereas others form a slime layer that trails off into the medium. Most capsules consist of relatively simple polysaccharides but there are some bacteria whose capsules are made of polypeptides.
Polymerase Chain Reaction
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
DNA-Directed RNA Polymerases
Enzymes that catalyze DNA template-directed extension of the 3'-end of an RNA strand one nucleotide at a time. They can initiate a chain de novo. In eukaryotes, three forms of the enzyme have been distinguished on the basis of sensitivity to alpha-amanitin, and the type of RNA synthesized. (From Enzyme Nomenclature, 1992).
Promoter Regions, Genetic
Nucleic Acid Conformation
Periplasmic Binding Proteins
A family of gram-negative, facultatively anaerobic, rod-shaped bacteria that do not form endospores. Its organisms are distributed worldwide with some being saprophytes and others being plant and animal parasites. Many species are of considerable economic importance due to their pathogenic effects on agriculture and livestock.
Open Reading Frames
Mutagenesis where the mutation is caused by the introduction of foreign DNA sequences into a gene or extragenic sequence. This may occur spontaneously in vivo or be experimentally induced in vivo or in vitro. Proviral DNA insertions into or adjacent to a cellular proto-oncogene can interrupt GENETIC TRANSLATION of the coding sequences or interfere with recognition of regulatory elements and cause unregulated expression of the proto-oncogene resulting in tumor formation.
The class of all enzymes catalyzing oxidoreduction reactions. The substrate that is oxidized is regarded as a hydrogen donor. The systematic name is based on donor:acceptor oxidoreductase. The recommended name will be dehydrogenase, wherever this is possible; as an alternative, reductase can be used. Oxidase is only used in cases where O2 is the acceptor. (Enzyme Nomenclature, 1992, p9)
Colony Count, Microbial
Enumeration by direct count of viable, isolated bacterial, archaeal, or fungal CELLS or SPORES capable of growth on solid CULTURE MEDIA. The method is used routinely by environmental microbiologists for quantifying organisms in AIR; FOOD; and WATER; by clinicians for measuring patients' microbial load; and in antimicrobial drug testing.
Microbial Sensitivity Tests
Urinary Tract Infections
Shiga Toxin 1
SOS Response (Genetics)
An error-prone mechanism or set of functions for repairing damaged microbial DNA. SOS functions (a concept reputedly derived from the SOS of the international distress signal) are involved in DNA repair and mutagenesis, in cell division inhibition, in recovery of normal physiological conditions after DNA repair, and possibly in cell death when DNA damage is extensive.
A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).
Those components of an organism that determine its capacity to cause disease but are not required for its viability per se. Two classes have been characterized: TOXINS, BIOLOGICAL and surface adhesion molecules that effect the ability of the microorganism to invade and colonize a host. (From Davis et al., Microbiology, 4th ed. p486)
Nucleic Acid Hybridization
Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)
The small RNA molecules, 73-80 nucleotides long, that function during translation (TRANSLATION, GENETIC) to align AMINO ACIDS at the RIBOSOMES in a sequence determined by the mRNA (RNA, MESSENGER). There are about 30 different transfer RNAs. Each recognizes a specific CODON set on the mRNA through its own ANTICODON and as aminoacyl tRNAs (RNA, TRANSFER, AMINO ACYL), each carries a specific amino acid to the ribosome to add to the elongating peptide chains.
Rec A Recombinases
A family of recombinases initially identified in BACTERIA. They catalyze the ATP-driven exchange of DNA strands in GENETIC RECOMBINATION. The product of the reaction consists of a duplex and a displaced single-stranded loop, which has the shape of the letter D and is therefore called a D-loop structure.
Protein Structure, Tertiary
The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.
Mutation process that restores the wild-type PHENOTYPE in an organism possessing a mutationally altered GENOTYPE. The second "suppressor" mutation may be on a different gene, on the same gene but located at a distance from the site of the primary mutation, or in extrachromosomal genes (EXTRACHROMOSOMAL INHERITANCE).
Drug Resistance, Bacterial
That portion of the electromagnetic spectrum immediately below the visible range and extending into the x-ray frequencies. The longer wavelengths (near-UV or biotic or vital rays) are necessary for the endogenous synthesis of vitamin D and are also called antirachitic rays; the shorter, ionizing wavelengths (far-UV or abiotic or extravital rays) are viricidal, bactericidal, mutagenic, and carcinogenic and are used as disinfectants.
Shiga Toxin 2
The lipopolysaccharide-protein somatic antigens, usually from gram-negative bacteria, important in the serological classification of enteric bacilli. The O-specific chains determine the specificity of the O antigens of a given serotype. O antigens are the immunodominant part of the lipopolysaccharide molecule in the intact bacterial cell. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)
A chemical reaction in which an electron is transferred from one molecule to another. The electron-donating molecule is the reducing agent or reductant; the electron-accepting molecule is the oxidizing agent or oxidant. Reducing and oxidizing agents function as conjugate reductant-oxidant pairs or redox pairs (Lehninger, Principles of Biochemistry, 1982, p471).
A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)
A class of toxins that inhibit protein synthesis by blocking the interaction of ribosomal RNA; (RNA, RIBOSOMAL) with PEPTIDE ELONGATION FACTORS. They include SHIGA TOXIN which is produced by SHIGELLA DYSENTERIAE and a variety of shiga-like toxins that are produced by pathologic strains of ESCHERICHIA COLI such as ESCHERICHIA COLI O157.
Cell-surface components or appendages of bacteria that facilitate adhesion (BACTERIAL ADHESION) to other cells or to inanimate surfaces. Most fimbriae (FIMBRIAE, BACTERIAL) of gram-negative bacteria function as adhesins, but in many cases it is a minor subunit protein at the tip of the fimbriae that is the actual adhesin. In gram-positive bacteria, a protein or polysaccharide surface layer serves as the specific adhesin. What is sometimes called polymeric adhesin (BIOFILMS) is distinct from protein adhesin.
Microscopy using an electron beam, instead of light, to visualize the sample, thereby allowing much greater magnification. The interactions of ELECTRONS with specimens are used to provide information about the fine structure of that specimen. In TRANSMISSION ELECTRON MICROSCOPY the reactions of the electrons that are transmitted through the specimen are imaged. In SCANNING ELECTRON MICROSCOPY an electron beam falls at a non-normal angle on the specimen and the image is derived from the reactions occurring above the plane of the specimen.
A genus of gram-negative, facultatively anaerobic, rod-shaped bacteria that utilizes citrate as a sole carbon source. It is pathogenic for humans, causing enteric fevers, gastroenteritis, and bacteremia. Food poisoning is the most common clinical manifestation. Organisms within this genus are separated on the basis of antigenic characteristics, sugar fermentation patterns, and bacteriophage susceptibility.
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
Porins are protein molecules that were originally found in the outer membrane of GRAM-NEGATIVE BACTERIA and that form multi-meric channels for the passive DIFFUSION of WATER; IONS; or other small molecules. Porins are present in bacterial CELL WALLS, as well as in plant, fungal, mammalian and other vertebrate CELL MEMBRANES and MITOCHONDRIAL MEMBRANES.
Any of various animals that constitute the family Suidae and comprise stout-bodied, short-legged omnivorous mammals with thick skin, usually covered with coarse bristles, a rather long mobile snout, and small tail. Included are the genera Babyrousa, Phacochoerus (wart hogs), and Sus, the latter containing the domestic pig (see SUS SCROFA).
The reconstruction of a continuous two-stranded DNA molecule without mismatch from a molecule which contained damaged regions. The major repair mechanisms are excision repair, in which defective regions in one strand are excised and resynthesized using the complementary base pairing information in the intact strand; photoreactivation repair, in which the lethal and mutagenic effects of ultraviolet light are eliminated; and post-replication repair, in which the primary lesions are not repaired, but the gaps in one daughter duplex are filled in by incorporation of portions of the other (undamaged) daughter duplex. Excision repair and post-replication repair are sometimes referred to as "dark repair" because they do not require light.
Biological Transport, Active
Integration Host Factors
Lipid-containing polysaccharides which are endotoxins and important group-specific antigens. They are often derived from the cell wall of gram-negative bacteria and induce immunoglobulin secretion. The lipopolysaccharide molecule consists of three parts: LIPID A, core polysaccharide, and O-specific chains (O ANTIGENS). When derived from Escherichia coli, lipopolysaccharides serve as polyclonal B-cell mitogens commonly used in laboratory immunology. (From Dorland, 28th ed)
Protein Structure, Secondary
In bioinformatics EcoCyc is a biological database for the bacterium Escherichia coli K-12. The EcoCyc project performs ... coli genome, and of E. coli transcriptional regulation, transporters, and metabolic pathways. EcoCyc contains written summaries ... EcoCyc is also a description of the genome and cellular networks of E. coli that supports scientists to carry out computational ... Karp PD, Riley M, Paley SM, Pelligrini-Toole A (1996). "EcoCyc: an encyclopedia of Escherichia coli genes and metabolism". ...
Pseudomonas aeruginosa PAO1 has 33 proteins with GGDEF domains, Escherichia coli K-12 has 19, and Vibrio cholerae O1 has 41. In ... The GGDEF domain was first identified in the regulatory protein, PleD of the bacterium Caulobacter crescentus. It was later ... PleD is responsible for turning off flagellum rotations and inhibiting motility before genome replication begins and also for ... Jenal U, Malone J (2006). "Mechanisms of cyclic-di-GMP signaling in bacteria". Annual Review of Genetics. 40: 385-407. doi: ...
"Escherichia coli str. K-12 substr. MG1655, complete genome [Genbank Accession Number: U00096]". GenBank. NCBI. Retrieved 2013- ... These mutants were first isolated within bacteriophages (T4 and lambda), viruses that infect the bacteria Escherichia coli. ... For example, the E. coli K-12 genome contains 2705 TAA (63%), 1257 TGA (29%), and 326 TAG (8%) stop codons (GC content 50.8%). ... is one step forward for engineering an omnipotent release factor in bacteria Escherichia coli". Journal of Biological Chemistry ...
Escherichia coli in molecular biology
E. coli was one of the first organisms to have its genome sequenced; the complete genome of E. coli K-12 was published by ... "Gene recombination in the bacterium Escherichia coli". J. Bacteriol. 53: 673-684. doi:10.1128/jb.53.6.673-684.1947.. ... coli K-12 with agents such as nitrogen mustard, ultra-violet radiation, X-ray etc. An extensive list of Escherichia coli K-12 ... Main article: Escherichia coli § Diversity. Escherichia coli is one of the most diverse bacterial species, with several ...
"Environmental regulation of the fim switch controlling type 1 fimbrial phase variation in Escherichia coli K-12: effects of ... The promoter region of the genome can move from one copy of a gene to another through homologous recombination. This occurs ... Many bacterial species can utilize inversion to change the expression of certain genes for the benefit of the bacterium during ... "Slipped strand mispairing can function as a phase variation mechanism in Escherichia coli". J Bacteriol. 185 (23): 6990-6994. ...
E. coli was one of the first organisms to have its genome sequenced; the complete genome of E. coli K12 was published by ... coli O157:H7, the Shiga toxin-producing strain of E. coli. E. coli encompasses an enormous population of bacteria that exhibit ... coli interaction database EcoGene (genome database and website dedicated to Escherichia coli K-12 substrain MG1655) EcoSal ... "Clean Genome. E.coli", where 15% of the genome of the parental strain (E. coli K-12 MG1655) were removed to aid in molecular ...
"An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)". Genome Biology. 4 (9): R54. doi:10.1186/gb-2003-4-9- ... "A functional update of the Escherichia coli K-12 genome". Genome Biology. 2 (9): RESEARCH0035. doi:10.1186/gb-2001-2-9- ... Bacteria (/bækˈtɪəriə/ (. listen); common noun bacteria, singular bacterium) are a type of biological cell. They constitute a ... This is achievable in some well-studied bacteria, with models of Escherichia coli metabolism now being produced and tested.[197 ...
E. Coli Metabolome Database
... coli strain K12, MG1655). Escherichia coli is perhaps the best studied bacterium on earth and has served as the "model microbe ... The ECMDB is essentially an E. coli "omics" encyclopedia containing detailed data on E. coli's genome, proteome and its ... coli, in general. In particular, under the "About" tab, a section called "E. coli numbers and stats" contains hundreds of ... online database of small molecule metabolites found in or produced by Escherichia coli (E. ...
Bakteria, kamusi elezo huru
"An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)". Genome Biol. 4 (9): R54. doi:10.1186/gb-2003-4-9-r54 ... "Global organization of metabolic fluxes in the bacterium Escherichia coli". Nature 427 (6977): 839-43. doi:10.1038/nature02289 ... "A functional update of the Escherichia coli K-12 genome". Genome Biology 2 (9): RESEARCH0035. doi:10.1186/gb-2001-2-9- ... Hali hii inaweza kufikiwa katika baadhi ya bakteria ambao wametafitiwa vizuri, wenye maumbo ya umetaboli wa Escherichia coli ...
Italy and infects Escherichia coli K-12. Recently, a number of genetically related phages were isolated, infecting Silicibacter ... Bacteria serve as natural hosts. There is currently only one species in this genus: the type species Escherichia virus N4. ... All the phages of this genus are strictly virulent and contain a linear dsDNA genome (with terminal repeats) in the range of 70 ... Bacteria serve as the natural host. Transmission routes are passive diffusion. A remarkable feature of this clade of phages is ...
2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection". Molecular Systems ... "The essential genome of a bacterium". Molecular Systems Biology. 7: 528. doi:10.1038/msb.2011.58. PMC 3202797. PMID 21878915. ... August 2004). "Systematic mutagenesis of the Escherichia coli genome". Journal of Bacteriology. 186 (15): 4921-30. doi:10.1128/ ... "The Genome-Wide Interaction Network of Nutrient Stress Genes in Escherichia coli". mBio. 7 (6). doi:10.1128/mBio.01714-16. ISSN ...
September 1997). "The complete genome sequence of Escherichia coli K-12". Science. 277 (5331): 1453-62. doi:10.1126/science. ... most parasitic bacteria have reduced genomes as their hosts supply many if not most nutrients, so that their genome does not ... While the E. coli genome is roughly 4.6Mb in length, in comparison the Human genome is much larger with a size of approximately ... Genome evolution is the process by which a genome changes in structure (sequence) or size over time. The study of genome ...
2006). "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110". Mol. Syst. Biol. 2 (1): 2006.0007 ... coli for intergenic regions of high sequence identity (sequence conservation) with the genomes of closely related bacteria ( ... Addiction module TisB-IstR toxin-antitoxin system Rudd KE (1999). "Novel intergenic repeats of Escherichia coli K-12". Res. ... Rudd KE (1999). "Novel intergenic repeats of Escherichia coli K-12". Res. Microbiol. 150 (9-10): 653-664. doi:10.1016/S0923- ...
Bakteria, kamusi elezo huru
"An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)". Genome Biol. 4 (9): R54. doi:10.1186/gb-2003-4-9-r54 ... "Global organization of metabolic fluxes in the bacterium Escherichia coli". Nature 427 (6977): 839-43. doi:10.1038/nature02289 ... "A functional update of the Escherichia coli K-12 genome". Genome Biology 2 (9): RESEARCH0035. doi:10.1186/gb-2001-2-9- ... Genome.gov. Iliwekwa mnamo 2021-03-30. *↑ Denamur E, Matic I (2006). "Evolution of mutation rates in bacteria". Mol Microbiol ...
List of sequenced bacterial genomes
1997). "The complete genome sequence of Escherichia coli K-12". Science. 277 (5331): 1453-74. doi:10.1126/science.277.5331.1453 ... 2001). "The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403". Genome Res. 11 (5): ... insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157". Nucleic Acids Res. 30 (20): 4432 ... 2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot-2005". Nucleic Acids Res. 34 (1): 1-9. doi:10.1093 ...
"An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)". Genome Biol. 4 (9): R54. doi:10.1186/gb-2003-4-9-r54 ... Yeates TO, Kerfeld CA, Heinhorst S, Cannon GC, Shively JM (August 2008). "Protein-based organelles in bacteria: carboxysomes ... Mowbray J, Moses V (June 1976). "The tentative identification in Escherichia coli of a multienzyme complex with glycolytic ... In eukaryotes the genome is held within the cell nucleus, which is separated from the cytosol by nuclear pores that block the ...
Bacterial, archaeal and plant plastid code
"The complete genome sequence of Escherichia coli K-12". Science. 277 (5331): 1453-62. doi:10.1126/science.277.5331.1453. PMID ... In Escherichia coli, UUG is estimated to serve as initiator for about 3% of the bacterium's proteins. CUG is known to function ... "The Complete Genome Sequence of Escherichia coli K-12". Science. 277 (5331): 1453-1462. doi:10.1126/science.277.5331.1453. PMID ... "The cloning and sequence analysis of the aspC and tyrB genes from Escherichia coli K12. Comparison of the primary structures of ...
In bacteria, an estimated 250-400 genes are essential for Escherichia coli and Bacillus subtilis, which is less than 10% of ... 2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection". Molecular Systems ... "Bacillus subtilis and Escherichia coli essential genes and minimal cell factories after one decade of genome engineering". ... Prokaryotes (bacteria and archaea) typically store their genomes on a single large, circular chromosome. Similarly, some ...
LdrD-RdlD toxin-antitoxin system
June 1996). "A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage ... "Abundance of type I toxin-antitoxin systems in bacteria: searches for new candidates and discovery of novel families". Nucleic ... It was discovered in Escherichia coli strain K-12 in a long direct repeat (LDR) named LDR-D. This locus encodes two products: a ... Four long direct repeat (LDR) sequences were identified during genetic sequencing of a 718kb segment of the E. coli genome. One ...
The GalP/H+ symporter is the galactose permease from the galP gene of the Escherichia coli genome. Galactose is an alternate ... coli and in other bacteria. E. coli has a well-studied GltS glutamate/Na+ symporter that aids in the uptake of glutamate into ... glucose and their molecular analogues by Escherichia coli K12. Biochem. J. 162, 309-320. 2. McDonald, T. P., Walmsley, A. R. ... 3. McDonald, T. P. and Henderson, P. J. F. (2001) Cysteine residues in the D-galactose-H+ symport protein of Escherichia coli: ...
For instance, when the complete genome of the bacterium Escherichia coli was finally completed in 1997, it was presented with a ... "The complete genome sequence of Escherichia coli K-12". Science. 277 (5331): 1453-62. doi:10.1126/science.277.5331.1453. PMID ... "Escherichia coli K-12 substr. MG1655 oriC". biocyc.org. EcoCyc. Retrieved 4 April 2021. For historical reasons, the numbering ... Often this point is the origin of replication, although for E. coli it is the origin of transfer during conjugation. Hence, the ...
Universal stress protein
... coli (Strain K-12). Consequently, much is known about the USP domains in bacteria. In E. coli there are six families of USP ... demonstrated in Escherichia coli that USPs are involved in actions such as adhesion and motility. The researchers, through ... UspA is the most commonly studied USP due to its widespread presence within bacterial genomes. UspA is especially implicated in ... Diez A (2002). "The universal stress protein A of Escherichia coli is required for resistance to DNA damaging agents and is ...
Xenoma, a enciclopedia libre
"The Complete Genome Sequence of Escherichia coli K-12". Science 277 (5331): 1453-1462. PMID 9278503. doi:10.1126/science. ... Bacteria Solibacter usitatus (cepa Ellin 6076) 9.970.000 10Mb  Ameba Polychaos dubium ("Amoeba" dubia) 670.000.000.000 ... The International Silkworm Genome (2008). "The genome of a lepidopteran model insect, the silkworm Bombyx mori". Insect ... e a bacteria Esherichia coli. As novas tecnoloxías de secuenciación, como a secuenciación paralela masiva abren a posibilidade ...
... a virus that infects bacteria by highjacking the bacteria's own replication machinery, in Escherichia coli. By using a genetic ... Saito H, Uchida H (June 1977). "Initiation of the DNA replication of bacteriophage lambda in Escherichia coli K12". Journal of ... In the Archaea genome, the gene for GrpE is located upstream of the gene for DnaK which, is upstream of the gene for DnaJ. Out ... A grpE mutant of Escherichia coli is more resistant to heat than the wild-type. J Gen Microbiol. 1990;136(5):797-801. doi: ...
... is a database of the regulatory network of gene expression in Escherichia coli K-12. RegulonDB also models the ... In bacteria, such as E. coli, genes, are regulated by sequence elements in promoters and related binding sites). RegulonDB ... The TFs binding sites are physical DNA sites recognized by transcription factors within a genome, including enhancer, upstream ... transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)". Nucleic ...
Геном - Вікіпедія
Frederick R. Blattner; Guy Plunkett III (1997). The Complete Genome Sequence of Escherichia coli K-12. Science 277 (5331): 1453 ... genetic engineering in bacteria using homologous recombination. Current Protocols in Molecular Biology. Chapter 1: Unit 1.16. ... Escherichia coli 4,600,000 4.6Mb 4288  Бактерія - ціанобактеріїя Prochlorococcus[en] spp. (1.7 Mb) 1,700,000 1.7Mb 1884 ... The International Silkworm Genome (2008). The genome of a lepidopteran model insect, the silkworm Bombyx mori. Insect ...
... proteomic as well metabolomic data on Escherichia coli. Escherichia coli (strain K12) is perhaps the best-studied bacterium on ... Rudd, K.E. (2000). "EcoGene: a genome sequence database for Escherichia coli K-12". Nucleic Acids Res. 28 (1): 60-64. doi: ... relational database to coordinate and facilitate in silico modeling of Escherichia coli". Nucleic Acids Res. 32 (Database issue ... E.coli BLAST Sundararaj, S; Guo A; Habibi-Nazhad B; Rouani M; Stothard P; Ellison M; Wishart DS. (2004). "The CyberCell ...
Horizontal gene transfer
Biel SW, Hartl DL (June 1983). "Evolution of transposons: natural selection for Tn5 in Escherichia coli K12". Genetics. 103 (4 ... The role of virus and bacteriophages in HGT in bacteria, suggests that TP-containing genomes could be a vehicle of inter- ... 2013), endosymbiotic bacteria, and intracellular parasitic bacteria. In some cases, even TEs facilitate transport for other TEs ... Genes responsible for antibiotic resistance in one species of bacteria can be transferred to another species of bacteria ...
Genome sequence of Shimia str. SK013, a representative of the Roseobacter group isolated from marine sediment (Journal Article)...
... escherichia-coli k-12; sp-nov.; emended description; rna genes; bacteria; system; clade; identification; annotation. ... of Energy Joint Genome Institute, Walnut Creek, CA (United States). Genome Biology Program; King Abdulaziz Univ., Jeddah (Saudi ... of Energy Joint Genome Institute, Walnut Creek, CA (United States). Genome Biology Program ... Journal Article: Genome sequence of Shimia str. SK013, a representative of the Roseobacter group isolated from marine sediment ...
Bacteria - Wikipedia
"An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)". Genome Biology. 4 (9): R54. doi:10.1186/gb-2003-4-9- ... "A functional update of the Escherichia coli K-12 genome". Genome Biology. 2 (9): RESEARCH0035. doi:10.1186/gb-2001-2-9- ... Bacteria (/bækˈtɪəriə/ (. listen); common noun bacteria, singular bacterium) are a type of biological cell. They constitute a ... This is achievable in some well-studied bacteria, with models of Escherichia coli metabolism now being produced and tested.[197 ...
Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing...
1997) The complete genome sequence of Escherichia coli K-12. Science 277:1453-1462. ... Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing ... Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing ... 2006) Escherichia coli K-12: A cooperatively developed annotation snapshot-2005. Nucleic Acids Res 34:1-9. ...
KEGG GENOME: Escherichia coli K-12 BW2952
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia. Data source. GenBank ( ... sequencing reveals regulatory mutations and recombinational events in the widely used MC4100 lineage of Escherichia coli K-12. ... Escherichia coli K-12 BW2952. Definition. Escherichia coli BW2952 (K-12 MC41000 with placMu50 fusion). ... Escherichia coli K-12 BW2952. Genome info. Pathway map. Brite hierarchy. Module. Genome map. Blast. Taxonomy. ...
The complete genomic sequence of Nocardia farcinica IFM 10152 | PNAS
Escherichia coli O-157; k-12, E. coli K-12; gsul, Geobacter sulfurreducens; linn, Listeria innocua; mlot, Mesorhizobium loti; ... Comparative Study. To characterize the N. farcinica genome, we first compared it with the genomes of closely related bacteria. ... Genome Sequencing and Assembly. The nucleotide sequence of the N. farcinica IFM 10152 genome was determined by a whole-genome ... Correlation between paralog content and genome size in various bacteria: atum, Agrobacterium tumefaciens; bjap, Bradyrhizobium ...
UniProt/SWISS-PROT: AMY2 ECOLI
"Highly accurate genome sequences of Escherichia coli K-12 strains RT MG1655 and W3110."; RL Mol. Syst. Biol. 2:E1-E5(2006). RN ... Escherichia coli (strain K12). OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; OC Enterobacteriaceae; ... "A 460-kb DNA sequence of the Escherichia coli K-12 genome RT corresponding to the 40.1-50.0 min region on the linkage map."; RL ... "The complete genome sequence of Escherichia coli K-12."; RL Science 277:1453-1462(1997). RN  RP NUCLEOTIDE SEQUENCE [LARGE ...
Escherichia coli in molecular biology - Wikipedia
E. coli was one of the first organisms to have its genome sequenced; the complete genome of E. coli K-12 was published by ... "Gene recombination in the bacterium Escherichia coli". J. Bacteriol. 53: 673-684. doi:10.1128/jb.53.6.673-684.1947. E. coli ... coli K-12 with agents such as nitrogen mustard, ultra-violet radiation, X-ray etc. An extensive list of Escherichia coli K-12 ... "The complete genome sequence of Escherichia coli K-12". Science. 277 (5331): 1453-1462. doi:10.1126/science.277.5331.1453. PMID ...
Escherichia coli by Emma Blackwood on Prezi
K12) genome was completed in 1997 by Blattner, Plunkett and colegues. Genetics Prokaryotic Bacteria Proteobacteria ... The complete genome sequence of Escherichia coli K-12. Science. 277: p 1453 -1462.. 5. Brown, A. D, Berg, C. H.. 1974. Temporal ... Transcript of Escherichia coli. Category Domain Phylum Class Order Family Genus Species Taxonomy Escherichia coli Gram Negative ... Escherichia coli from the family Enterobacteriaceae Gram Negative Rod Bacteria With Fimbrae and sometimes Pili, inclusion ...
Ecological Significance of Microdiversity: Identical 16S rRNA Gene Sequences Can Be Found in Bacteria with Highly Divergent...
Escherichia coli K-12 and O157:H7 differ not only in genome size (by 0.89 Mb) but also in a considerable number of chromosomal ... The complete genome sequence of Escherichia coli K-12. Science 277:1453-1462. ... Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409:529-533. ... The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature 423:81-86. ...
Bacteria - wikidoc
"A functional update of the Escherichia coli K-12 genome". Genome Biol. 2 (9): RESEARCH0035. PMID 11574054.. CS1 maint: Multiple ... "An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)". Genome Biol. 4 (9): R54. PMID 12952533. doi:10.1186/ ... This is achievable in some well-studied bacteria, with models of Escherichia coli metabolism now being produced and tested.[145 ... Bacteria (singular: bacterium) are unicellular microorganisms. Typically a few micrometres in length, bacteria have a wide ...
HOGENOM: ECOW3 1 PE1013
CC Escherichia coli str. K-12 substr. W3110 chromosome, complete genome. CC chromosome, complete sequence. CC -!- GENE_FAMILY: ... 3, Last annotation update) DE (ECOW3_1.PE1013). OS ESCHERICHIA COLI STR. K-12 SUBSTR. W3110. OC Bacteria; Proteobacteria; ... Gammaproteobacteria; Enterobacteriales; OC Enterobacteriaceae; Escherichia. OX NCBI_TaxID=316407; RN  RP -.; RG -.; RL -.; ...
EcoCyc: Encyclopedia of E. coli Genes and Metabolism
... and regulatory network of Escherichia coli and provides extensive bioinformatics tools. ... The EcoCyc database describes the genome, metabolic pathways, ... is a scientific database for the bacterium Escherichia coli K- ... Comparative Genome Analysis. Multiple comparative analysis tools are available in this website.. Learn More ... 2017), "EcoCyc: reflecting new knowledge about Escherichia coli K-12", Nucleic Acids Research 45:D543-50. ...
Selection-driven cost-efficiency optimization of transcripts modulates gene evolutionary rate in bacteria | Genome Biology |...
Through analysis of 1320 bacterial genomes, we show that bacterial genes are subject to multi-objective selection-driven ... Elucidation of the transcription unit architecture of the Escherichia coli K-12 MG1655 genome. Nat Biotechnol. 2009;27:1043-9. ... correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome. ... The energetics of Escherichia coli during aerobic growth in continuous culture. Eur J Biochem. 1976;67:115-22.View Article ...
Frontiers | Epigenome Engineering in Cancer: Fairytale or a Realistic Path to the Clinic? | Oncology
... growing field of epigenome engineering has opened new grounds for improving epigenetic therapy in view of reducing the genome- ... growing field of epigenome engineering has opened new grounds for improving epigenetic therapy in view of reducing the genome- ... which may result in the over-expression of undesirable parts of the genome. The emerging and rapidly ... which may result in the over-expression of undesirable parts of the genome. The emerging and rapidly ...
Prediction of lipoprotein signal peptides in Gram-negative bacteria
ibpB - Small heat shock protein IbpB - Escherichia coli (strain K12 / DH10B) - ibpB gene & protein
Genome annotation databases. Ensembl bacterial and archaeal genome annotation project. More...EnsemblBacteriai. ACB04732; ... cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia › ... sp,B1X9B6,IBPB_ECODH Small heat shock protein IbpB OS=Escherichia coli (strain K12 / DH10B) OX=316385 GN=ibpB PE=3 SV=1 ... Escherichia coli (strain K12 / DH10B). ,p>This subsection of the ,a href="http://www.uniprot.org/help/names_and_taxonomy_ ...
uspB - Universal stress protein B - Escherichia coli (strain K12 / DH10B) - uspB gene & protein
Genome annotation databases. Ensembl bacterial and archaeal genome annotation project. More...EnsemblBacteriai. ACB04547; ... cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia › ... sp,B1X7U9,USPB_ECODH Universal stress protein B OS=Escherichia coli (strain K12 / DH10B) OX=316385 GN=uspB PE=3 SV=1 ... Escherichia coli (strain K12 / DH10B). ,p>This subsection of the ,a href="http://www.uniprot.org/help/names_and_taxonomy_ ...
ActionBioscience - promoting bioscience literacy
Escherichia coli K-12 and O157:H7 could probably exchange such genes with relative ease, but a bacterium and an archaeon ... At minimum, 17% of the K-12 genome has been borrowed since these two bacteria split from a common ancestor around 100 million ... On a broader level, a now famous comparison of Escherichia coli K-12 to Salmonella enterica (another species of bacterium often ... Comparing two bacteria from the same species reveals major differences.9 For example, Escherichia coli is a common gut ...
Evolutionary dynamics of small RNAs in 27 Escherichia coli and Shigella genomes
They are best characterized in Escherichia coli K-12 MG1655, where 83 sRNAs constitute nearly 2% of the gene complement. Most ... are widespread in bacteria and play critical roles in regulating physiological processes. ... We identify core (encoded in all 27 genomes) and variable sRNAs; more than two-thirds of the E. coli K-12 MG1655 sRNAs are core ... Small RNAs (sRNAs) are widespread in bacteria and play critical roles in regulating physiological processes. They are best ...
Genome-Wide Prediction of Nucleosome Occupancy in Maize Reveals Plant Chromatin Structural Features at Genes and Other Elements...
K12-MG1655; downloaded in January 2012 from ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/Escherichia_coli_K_12_substr__ ... S1, E and F). Similarly, the NOL values for the Escherichia coli genome (Supplemental Fig. S1G) resembled those of the ... Annotation of the Maize Genome on a New Public Genome Browser, Genomaize. We produced a publicly available B73 genome browser, ... 1A) but is not seen for NOL scores of noneukaryotic genomes such as maize mitochondria, maize plastid, or E. coli (Table I; ...
An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR) | Genome Biology | Full Text
Constraint-based models of Escherichia coli K-12 MG1655 have been developed and used to study the bacteriums metabolism and ... An expanded genome-scale metabolic model of E. coli (iJR904 GSM/GPR) has been reconstructed which includes 904 genes and 931 ... E. coli iJR904 has improved capabilities over iJE660a. iJR904 is a more complete and chemically accurate description of E. coli ... The most comprehensive E. coli model to date (E. coli iJE660a GSM) accounts for 660 genes and includes 627 unique biochemical ...
Nanopore DNA Sequencing and Genome Assembly on the International Space Station | Scientific Reports
Samples contained equimolar mixtures of genomic DNA from lambda bacteriophage, Escherichia coli (strain K12, MG1655) and Mus ... coli genome, ~48.5 kb lambda genome, and a representative M. musculus sequence (the ~16.3 kb mitochondrial genome), at 100%, ... coli genome from raw reads yielded a single contig comprising 99.9% of the genome at 98.6% consensus pairwise identity. ... a bacterium (Escherichia coli), and a model mammalian organism, the mouse (Mus musculus). In parallel, we performed control ...
Genome Sequence of the Chemolithoautotrophic Nitrite-Oxidizing Bacterium Nitrobacter winogradskyi Nb-255 | Applied and...
The roles of the polytopic membrane proteins NarK, NarU and NirC in Escherichia coli K-12: two nitrate and three nitrite ... Genome Sequence of the Chemolithoautotrophic Nitrite-Oxidizing Bacterium Nitrobacter winogradskyi Nb-255. Shawn R. Starkenburg ... Here we present the analysis of the first complete genome sequence from a nitrite-oxidizing bacterium, N. winogradskyi Nb-255. ... Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea. J. ...
Functional and evolutionary implications of gene orthology. - PubMed - NCBI
... the bacterium Escherichia coli K12 (a); and the archaeon Haloarcula marismortui (b). In this analysis, these are termed the ... master genomes. For all proteins encoded in each of the master genomes, a BLASTP search was carried out against the protein ... Escherichia coli and Pseudomonas aeruginosa). They are based on comparisons of Gene Ontology annotations backed by experimental ... The BLASTP score for each BBH was normalized by the self-hit score in the master genome and converted into distance using the ...
Differences in possible TCA cycle replenishing pathways in purple non-sulfur bacteria possessing glyoxylate pathway |...
Ornston LN, Ornston MK (1969) Regulation of glyoxylate metabolism in Escherichia coli K-12. J Bacteriol 98:1098-1108Google ... Multiple genome sequences reveal adaptations of a phototrophic bacterium to sediment microenvironments. Proc Natl Acad Sci USA ... Brock M, Maerker C, Schutz A, Volker U, Buckel W (2002) Oxidation of propionate to pyruvate in Escherichia coli. Involvement of ... Molina I, Pellicer MT, Badia J, Aguilar J, Baldoma L (1994) Molecular characterization of Escherichia coli malate synthase G: ...
Bacteria Nanoparticle Interactions
... we are also looking at an organism-level response to bacteria with the model bacterium, Escherichia coli, K12. We have looked ... The genome and metabolome of E. coli are well known the system level response to nanoparticle toxicity can be studies by ... Silver Nanoparticle enhanced Silver Ion Stress Response in Escherichia coli K12. Jonathan McQuillan1, Heidi Goenaga Infante, ... Whole-Cell Escherichia coli-based Bio-Sensor Assay for dual Zinc Oxide Nanoparticle Toxicity Mechanisms. Jonathan Mcquillan and ...
Dynamic Distribution of SeqA Protein across the Chromosome of Escherichia coli K-12 | mBio
... coli genome bound by SeqA at time point A (A) and the entire E. coli genome (B) were compared. The data show that, in vivo, a ... In Escherichia coli K-12, the single replication origin oriC is a well-characterized target for SeqA, which binds to multiple ... In the bacterium Escherichia coli, chromosome replication initiates bidirectionally from a single locus, oriC, and terminates ... coli genome in the form of a genome atlas. (A) SeqA binding signal generated using unsynchronized cultures of E. coli (time ...
GenesStrainsSequenceStrainMG1655OrganismEnterobacteriaceaeAnnotationGenomicMetabolismWhole-genomeModel bacteriumO157ArchaeaMolecularProteinsOrganismsSalmonellaMicrobiologyShigellaChromosome replicationPathogenic bacteriaMetabolic ModelGram-NegativeNCBIProkaryotic genomesSpeciesTranscriptionalBacterial and archaeal genomesReplicationGenomicsProtein-coding seGenus1997PutativePathwayOrganizationAnalysis2001GeneticBiologyRecombinantPathogensGeneticsNucleic Acids RePhysiologicalTranscriptionPhageFlexneriDifferent genomesMicrobial GenomesEukaryotic genomesCharacterizationBL21PseudomonasAgrobacterium tumefaciens C58LaboratoryClosely related bacteriaCellular
- The genome analysis revealed the presence of genes for a dimethylsulfoniopropionate lyase, demethylase and the trimethylamine methyltransferase ( mttB ) as well as genes for nitrate, nitrite and dimethyl sulfoxide reduction. (osti.gov)
- Nearly all animal life is dependent on bacteria for survival as only bacteria and some archaea possess the genes and enzymes necessary to synthesize vitamin B 12 , also known as cobalamin , and provide it through the food chain. (wikipedia.org)
- RT "Subdivision of flagellar region III of the Escherichia coli and RT Salmonella typhimurium chromosomes and identification of two RT additional flagellar genes. (genome.jp)
- EcoCyc contains written summaries of E. coli genes, distilled from over 36,000 scientific articles. (wikipedia.org)
- Escherichia coli K-12 and O157:H7 differ not only in genome size (by 0.89 Mb) but also in a considerable number of chromosomal genes. (asm.org)
- Twenty-five percent of the genes present in the enterohemorrhagic organism E. coli O157:H7 are not found in the nonpathogenic organism E. coli K-12, whereas 12% of the genes in the latter organism are absent in the former organism ( 9 , 39 ). (asm.org)
- The most comprehensive E. coli model to date ( E. coli i JE660a GSM) accounts for 660 genes and includes 627 unique biochemical reactions. (biomedcentral.com)
- An expanded genome-scale metabolic model of E. coli ( i JR904 GSM/GPR) has been reconstructed which includes 904 genes and 931 unique biochemical reactions. (biomedcentral.com)
- Through analysis of 1320 bacterial genomes, we show that bacterial genes are subject to multi-objective selection-driven optimization of codon use. (biomedcentral.com)
- Bacteria that utilize strategy 1 do not have tRNA genes harbouring an A residue at position 34 in the anticodon (A 34 NN), and therefore codons in transcripts with U in the third position (NNU 3 ) are read by G 34 NN tRNAs via G:U base pairing. (biomedcentral.com)
- A genome houses all the genes in an organism, and a 'catalogue' of these genes is obtained by sequencing the organism's DNA. (actionbioscience.org)
- Finally, we present evidence that more than 80% of genes targeted by Hfq-associated core sRNAs have been transferred within the E. coli-Shigella clade, and that most of these genes have been transferred intact. (nih.gov)
- The inability of N. winogradskyi to grow on C 6 molecules is consistent with the genome sequence, which lacks genes for complete Embden-Meyerhof and Entner-Doudoroff pathways, and active uptake of sugars. (asm.org)
- Approximately 10% of the N. winogradskyi genome codes for genes involved in transport and secretion, including the presence of transporters for various organic-nitrogen molecules. (asm.org)
- Our first generation array targets genes from Escherichia coli strains K12 and CFT073, Enterococcus faecalis and Staphylococcus aureus. (mendeley.com)
- Novel phosphotransferase system genes revealed by bacterial genome analysis: unique, putative fructose- and glucoside-specific systems. (nih.gov)
- many families of similar genes within E. coli are also evident. (sciencemag.org)
- Availability of the complete set of genes also enables global approaches to biological function in living cells ( 4 ) and has led to new ways of looking at the evolutionary history of bacteria ( 5 ). (sciencemag.org)
- 1] "Cloning and sequencing of two genes from Staphylococcus carnosus coding for glucose-specific PTS and their expression in Escherichia coli K-12. (tcdb.org)
- The phosphodiesterase PdeH was identified as a key regulator of motility in Escherichia coli , while deletions of any of the other 12 genes encoding potential phosphodiesterases did not interfere with motility. (asm.org)
- For example, the genomes of Escherichia coli K-12 strains contain genes encoding a total of 29 proteins harboring a GGDEF and/or EAL domain, the catalytic units of DGC and PDE enzyme activities, respectively ( 6 ). (asm.org)
- Genome-scale metabolic models (GEMs) computationally describe gene-protein-reaction associations for entire metabolic genes in an organism, and can be simulated to predict metabolic fluxes for various systems-level metabolic studies. (springer.com)
- The present invention relates to a recombinant E. coli exhibiting a complex phenotype, comprising one or more RNA polymerase subunit genes, one or more functional genes, and, optionally, one or more transcription factors from a heterologous prokaryote. (freepatentsonline.com)
- 2002). "Genome-wide screening for trait conferring genes using DNA microarrays. (freepatentsonline.com)
- Genome comparisons showed that the phages with Stx-like toxin genes have closely related genome sequences ( 40 , 71 , 72 ). (asm.org)
- The genome of strain Rue61a contains numerous genes associated with osmoprotection, and a high number of genes coding for transporters. (biomedcentral.com)
- Genome analyses indicated that soil isolates like strains TC1 and FB24 have a large number of genes encoding stress-related proteins. (biomedcentral.com)
- We developed an automated computational pipeline for identification of r-protein genes and applied it to 995 completely sequenced bacterial and 87 archaeal genomes available in the RefSeq database. (pubmedcentralcanada.ca)
- In bacteria and archaea, genes encoding r-proteins are organized in genomic clusters that include several partially conserved operons and are often called ribosomal superoperons  ,  . (pubmedcentralcanada.ca)
- However, some of the r-protein genes are difficult targets for automatic annotation in sequenced genomes because they are short and compositionally biased. (pubmedcentralcanada.ca)
- Because a significant fraction of essential E. coli genes are preserved throughout the bacterial kingdom, alternative oligonucleotide primers for specific E. coli detection are not easily identified. (biomedcentral.com)
- Global regulators control a vast number of genes, which must be physically separated on the genome and belong to different metabolic pathways [ 6 ]. (biomedcentral.com)
- This comprised an exhaustive reconstruction process based on experimental information, analysis of genome sequence, manual re-annotation of metabolic genes, and in-depth refinement. (biomedcentral.com)
- Shigella shares many genes with ''Escherichia coli'', especially those of E. coli K12 strain MG1655. (kenyon.edu)
- Determination of the whole genome sequence allows comparison with genes of other psychrophiles and mesophiles. (biomedcentral.com)
- Additionally, we are working in collaboration with Dr. Julio Collado-Vides lab to develop analysis tools which can be used to map global expression data from E. coli to information such as: operon organization, promoter and regulatory signals upstream of individual genes, and comparisons of the set of affected genes with known and putative transcriptional factors in E.coli. (davidson.edu)
- EcoGene is a collection of information about the genes, proteins, and intergenic regions of the E. coli K-12 genome and proteome accumulated during years of sequence analysis and literature surveys by Kenn Rudd and his collaborators: Mary Berlyn of the E. coli Genetic Stock Center, Amos Bairoch of SWISS-PROT, and Antoine Danchin and Ivan Mozser of Colibri. (davidson.edu)
- These data allow new approaches for the identification of pathogen-specific regions of the genome and thereby may direct the identification of new virulence genes. (asm.org)
- The integration of DNA segments containing clusters of virulence genes has lead to the evolution of pathogenic bacteria from nonpathogenic ancestors. (asm.org)
- These genes are highly conserved among bacterial genomes and are known to serve as anchor points for temperate phages ( 16 ). (asm.org)
- Based on the observation that many PAI are inserted into the genome adjacent to a tRNA gene, we systematically scanned tRNA genes and compared the tRNA-associated regions of a pathogen and its nonpathogenic relative. (asm.org)
- 2008) Genes, Genomes and Genomics. (g-language.org)
- Executing the script should generate a vector of the RSCU values of all codons (omitting start and stop codons) for a collection of all protein-coding genes in each genome. (g-language.org)
- Annotation of the genome of an organism entails identification of genes, the boundaries of genes in terms of precise start and end sites, and description of the gene products. (sri.com)
- An accurate and up-to-date description of E.coli K-12 genes is of particular importance to the scientific community because experimentally determined properties of its gene products provide fundamental information for annotation of innumerable genes of other organisms. (sri.com)
- Identification of DNA Methyltransferase Genes in Human Pathogenic Bacteria by Comparative Genomics Indian Journal of Microbiology, 56, 134-141. (unam.mx)
- Genome sequence analysis revealed homologs of nitrite reductase genes nirK and nirBD and siderophore synthesis genes for Agrobacterium tumefaciens , as well as homologs of nitrite reductase genes nirBD and phosphatase genes phoA and appA in E. coli , whose contribution to phytostimulation will require experimental assessment. (apsnet.org)
- Like E. coli C, it forms plaques when infected with bacteriophage Ã‰Â¸X174 and carries genes needed for the utilization of 5-carbon sugar alcohol xylitol. (imedpub.com)
- Complex organisms have a larger genome (our Ec dataset contains ~4000 genes, the Vv one ~28000). (unitn.it)
- Using bioinformatics and homology of conserved L-arabinose transporter genes shared in Escherichia coli K12 ( E. coli ) and S . Tm, we aimed to create a S . Tm mutant strain unable to obtain L-arabinose from it environment. (diva-portal.org)
- The genome exhibits the backbone and island mosaic structure of E. coli pathogens, albeit with much less horizontally transferred DNA and lacking 357 genes present in E. coli . (asm.org)
- Genes essential for phage maintenance and replication are encoded on approximately 50% of the genome, while most of the remaining genes are of unknown function nor is it known if these annotated hypothetical genes are even expressed. (ufl.edu)
- This study used Change Mediated Antigen Technology (CMAT)™ and 2D-PAGE, in combination with RT-qPCR, to identify Stx phage genes that are expressed in E. coli during the lysogenic cycle. (ufl.edu)
- Conservation of these genes in this phage genome, and other Stx phages where they have been identified as present, indicates their importance in the phage/lysogen life cycle, with possible implications for the biology and pathogenicity of the bacterial host. (ufl.edu)
- With modifications to just 18 genes, the researchers bred E. coli bacteria to Making colored bacterial film sounds like a fun project, but it's also a demonstration for some important future applications Here are six home remedies to prevent and treat UTI (Urinary Tract Infections). (meisten-verliebt.com)
- The goal of this group project has been to coordinate and bring up-to-date information on all genes of Escherichia coli K-12. (mblwhoilibrary.org)
- In particular, insight into the metabolic capabilities of these bacteria can be obtained from the construction and analysis of metabolic models generated from the inventory of genes with function in metabolism. (biomedcentral.com)
- His biggest contributions are to a second year course on bacterial genes and genomes, and a third year course on bacterial gene regulation. (birmingham.ac.uk)
- Steve Busby's work concerns the mechanisms by which the expression of different genes is regulated in bacteria. (birmingham.ac.uk)
- Thirty-eight percent of the E. coli genes have no known function. (icr.org)
- Most of the emphasis has been on how similar genes are in man and bacteria, with little attention to the differences. (icr.org)
- For example, a recent study analyzed the base-pair substitutions (BPSs) that arose in Escherichia coli strains that had been subjected to long-term evolution studies ( 3 ). (pnas.org)
- RT "Highly accurate genome sequences of Escherichia coli K-12 strains RT MG1655 and W3110. (genome.jp)
- For pathogenic bacteria it is well established that even phylogenetically identical strains or species can exhibit distinct ecophysiological properties. (asm.org)
- However, the genomes of certain phylogenetically identical strains exhibit profound differences. (asm.org)
- Escherichia coli is one of the most diverse bacterial species, with several pathogenic strains with different symptoms and with only 20% of the genome common to all strains. (wikipedia.org)
-  Furthermore, from the evolutionary point of view, the members of genus Shigella ( dysenteriae , flexneri , boydii , sonnei ) are actually E. coli strains "in disguise" (i.e. (wikipedia.org)
- Four of the many E. coli strains (K-12, B, C, and W) are thought of as model organism strains. (wikipedia.org)
-  Due to the lack of specific record-keeping, the "pedigree" of strains was not available and had to be inferred by consulting lab-book and records in order to set up the E. coli Genetic Stock Centre at Yale by Barbara Bachmann . (wikipedia.org)
-  The different strains have been derived through treating E. coli K-12 with agents such as nitrogen mustard, ultra-violet radiation, X-ray etc. (wikipedia.org)
- When tested with organisms at varying phylogenetic distances from the four target strains, the array detected orthologs for the majority of targeted gene families present in bacteria belonging to the same taxonomic family. (mendeley.com)
- Pathogenic E. coli strains are responsible for infections of the enteric, urinary, pulmonary, and nervous systems. (sciencemag.org)
- Using this metabolic map, the analysis of genetic potential for functioning of tricarboxylic acid cycle replenishment pathways was carried out for seven strains of purple non-sulfur bacterium Rhodopseudomonas palustris . (springer.com)
- As expected, the metabolic diversity and niche specialization of the environmental Arthrobacter strains is reflected in their genomes. (biomedcentral.com)
- 9) Another area of research surrounding 'Klebsiella pneumoniae' is learning about its presence in different regions of the world and understanding each of the different strains of the bacteria. (kenyon.edu)
- from E. coli, several Shigella strains are able to ferment lactose after cultivation. (biomedcentral.com)
- The occurrence of unilateral flagellar phase variation was previously demonstrated in Escherichia coli strains carrying the non- fliC flagellin-specifying locus flk . (asm.org)
- A general model for flagellar phase variation in flk -positive E. coli strains can be expressed as fliC off + flkA on → fliC on + flkA none . (asm.org)
- In addition, a comparison of the genome sequences of the two strains showed that BL21 possesses two mutations in the promoter region of iclR and rare codons are present in arcA implying a lower tRNA acceptance. (biomedcentral.com)
- The genome size of Bacillus cereus strains varies from 5.5 to 6.3 Mb, and great diversity is seen in the number and organization of the chromosomes. (asmscience.org)
- Chromosome transfer and Hfr formation by F in rec + and recA strains of E. coli K-12. (springer.com)
- Enumeration and identification ofIS3 elements in E. coli strains. (microbiologyresearch.org)
- Availability of the complete genome sequence of two K-12 strains allows comparison of their genotypes and mutant status of alleles. (sri.com)
- Plant-beneficial effects of bacteria are often underestimated, especially for well-studied strains associated with pathogenicity or originating from other environments. (apsnet.org)
- During 1960-1975, three different strains of E. coli , E. coli K-12, E. coli B and E. coli C have been used worldwide to develop microbial genetics [ 6 , 7 ]. (imedpub.com)
- Shigella strains are unusual among enteric bacteria in their ability to gain access to the epithelial cell cytosol, where they replicate and spread directly into adjacent cells. (asm.org)
- Although most Escherichia coli (E. coli) bacteria are harmless, certain pathogenic strains can infect the human intestinal tract The animation illustrates how a pathogenic E. coli bacterium uses a series of proteins to attach itself to a human intestinal epithelial cell Escherichia coli, ou E.Coli est une bactérie naturellement présente dans la flore intestinale. (meisten-verliebt.com)
- Most E. coli strains are harmless, but some serotypes can cause serious. (meisten-verliebt.com)
- Genome sequence of Shimia str. (osti.gov)
- The nucleotide sequence of the N. farcinica IFM 10152 genome was determined by a whole-genome shotgun strategy. (pnas.org)
- RT "A 460-kb DNA sequence of the Escherichia coli K-12 genome RT corresponding to the 40.1-50.0 min region on the linkage map. (genome.jp)
- RT "The complete genome sequence of Escherichia coli K-12. (genome.jp)
- This annotation provides sequence-based comprehensive coverage across the entire genome, including repetitive genomic regions typically excluded from experimental genomics data. (plantphysiol.org)
- The knowledge of a complete genome sequence holds the potential to reveal the 'blueprints' for cellular life. (biomedcentral.com)
- The genome sequence contains the information to propagate the living system, and this information exists as open reading frames (ORFs) and regulatory information. (biomedcentral.com)
- The 4,639,221-base pair sequence of Escherichia coli K-12 is presented. (sciencemag.org)
- The genome also contains insertion sequence (IS) elements, phage remnants, and many other patches of unusual composition indicating genome plasticity through horizontal transfer. (sciencemag.org)
- The availability of the complete sequence of E. coli should stimulate further research toward a more complete understanding of this important experimental, medical, and industrial organism. (sciencemag.org)
- Therefore, we evaluated the selection pressure on MI in terms of the protein sequence diversity for all the protein-coding sequences in E. coli . (pubmedcentralcanada.ca)
- However, these two phages are dissimilar in genome size, genome features, and DNA sequence in comparison with phages of the other genera of the Myoviridae family, such as the T4-like phages ( 85 ). (asm.org)
- Complete genome sequence and metabolic potential of the quinaldine-degrading bacterium Arthrobacter sp. (biomedcentral.com)
- The genome sequence of the sea-ice bacterium Psychromonas ingrahamii 37, which grows exponentially at -12C, may reveal features that help to explain how this extreme psychrophile is able to grow at such low temperatures. (biomedcentral.com)
- Based on annotation of proteins by sequence similarity, (1) P. ingrahamii has a large number (61) of regulators of cyclic GDP, suggesting that this bacterium produces an extracellular polysaccharide that may help sequester water or lower the freezing point in the vicinity of the cell. (biomedcentral.com)
- Genome sequence of the probiotic bacterium Bifidobacterium animalis subsp. (google.ca)
- The DNA sequence of 168 promoter regions (-50 to +10) for Escherichia coli RNA polymerase were compiled. (psu.edu)
- Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. (psu.edu)
- RT "Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. (univ-lyon1.fr)
- Finishing is the process of improving the quality and utility of a draft genome sequence. (biomedcentral.com)
- Close vicinity of IS1 integration sites in the leader sequence of the gal operon of E. coli. (microbiologyresearch.org)
- Deoxyribonucleic acid sequence homologies among bacterial insertion sequence elements and genomes of various organisms. (microbiologyresearch.org)
- Distribution of the insertion sequence IS1 in Gram-negative bacteria. (microbiologyresearch.org)
- The dif resolvase locus of the Escherichia coli chromosome can be replaced by a 33-bp sequence, but function depends on location. (ebi.ac.uk)
- We determined the complete genome sequence of Shigella flexneri serotype 2a strain 2457T (4,599,354 bp). (asm.org)
- RT "Sequence of minutes 4-25 of Escherichia coli. (sourceforge.net)
- Do Genome DNA Sequence Data Better Support Descent with Natural Variation or Independent Origins? (icr.org)
- In 1997 scientists reported the complete 4,639,221 base DNA sequence of E. coli (Blattner, et al. (icr.org)
- The complete nucleotide sequence of the tdc region of Escherichia coli. (ecmdb.ca)
- OS Escherichia coli (strain K12). (genome.jp)
- Current Research Highlight van Summeren-Wesenhagen and Marienhagen have developed a platform strain of E.Coli utilizing the ability of E. Coli to readily take up plasmids and it's viability in the lab. (prezi.com)
- More than 500 E. coli strain databases are available via the change organism database link (upper right corner). (ecocyc.org)
- An extensive list of Escherichia coli K-12 strain derivatives and their individual construction, genotypes, phenotypes, plasmids and phage information can be viewed at Ecoliwiki . (wikipedia.org)
- A second common laboratory strain is the B strain, whose history is less straightforward and the first naming of the strain as E. coli B was by Delbrück and Luria in 1942 in their study of bacteriophages T1 and T7. (wikipedia.org)
- Samples contained equimolar mixtures of genomic DNA from lambda bacteriophage, Escherichia coli (strain K12, MG1655) and Mus musculus (female BALB/c mouse). (nature.com)
- For instance, a number of phages have been isolated from the notorious E. coli strain O157:H7, which is an important and well-known human pathogen in uncooked and contaminated food ( 20 ) that may cause serious complications of bloody diarrhea, thrombotic thrombocytopenic purpura (TTP), and hemolytic-uremic syndrome (HUS) ( 58 ). (asm.org)
- AR1, a lytic phage that can efficiently infect the E. coli O157:H7 strain, was identified from the stool of cows by Ronner and Cliver in 1990 ( 70 ). (asm.org)
- The genome provides insight into the molecular basis of the versatility and robustness of this environmental Arthrobacter strain. (biomedcentral.com)
- Colibri provides a complete dataset of DNA and protein sequences derived from the paradigm strain E. coli K-12, linked to the relevant annotations and functional assignments. (vifabio.de)
- This can be explained by the lower flux through several CO 2 producing pathways in the E. coli K12 Δ arcA Δ iclR double knockout strain. (biomedcentral.com)
- Finally, in E. coli BL21 (DE3), ArcA and IclR are poorly expressed, explaining the similar fluxes observed compared to the Δ arcA Δ iclR strain. (biomedcentral.com)
- Mashko, S. 2010-03-23 00:00:00 MG1655 of Escherichia coli K-12 is frequently used in metabolic engineering as the wild-type strain. (deepdyve.com)
- Nevertheless, Lederberg and Tatum, working at Yale University, chose to make another attempt using a common laboratory strain of bacteria, Escherichia coli K-12, as their experimental system. (springer.com)
- Effects of temperature, agitation, and donor strain on chromosome transfer in E. coli K-12. (springer.com)
- For this analysis, we compared genome data of two S. enterica serovars, i.e., serovars Typhi and Typhimurium, with genome data of a nonpathogenic strain of Escherichia coli K-12 ( 3 ) and enterohemorrhagic E. coli (EHEC) O157:H7 ( 25 ). (asm.org)
- This entry contains MatP (YcbG), which is a component of the MatP/MatS site-specific system that organises the Ter macrodomain (MD) in Escherichia coli (strain K12) and related enterobacteria during replication of the chromosome. (ebi.ac.uk)
- Growth curve of E. coli C is similar to that of the pathogenic Gram positive strain Streptococcus pneumoniae (Sp). (imedpub.com)
- We identified 22 E. coli RS218-derived genomic islands (RDIs), using a comparative genome analysis of meningitis-causing E. coli K1 strain RS218 (O18:K1:H7) and laboratory K-12 strain MG1655. (ovid.com)
- The 2457T genome was also compared with that of a recently sequenced S. flexneri 2a strain, 301. (asm.org)
- Whole-genome sequencing showed that the K. pneumoniae strain had genotype ST15 and confirmed the presence of the mcr-1 gene on a 33,303-kb transferable plasmid of incompatibility group IncX4 ( Technical Appendix ). (cdc.gov)
- EcoCyc is a scientific database for the bacterium Escherichia coli K-12 MG1655. (ecocyc.org)
- Constraint-based models of Escherichia coli K-12 MG1655 have been developed and used to study the bacterium's metabolism and phenotypic behavior. (biomedcentral.com)
- They are best characterized in Escherichia coli K-12 MG1655, where 83 sRNAs constitute nearly 2% of the gene complement. (nih.gov)
- more than two-thirds of the E. coli K-12 MG1655 sRNAs are core, whereas the others show patterns of presence and absence that are principally due to genetic loss, not duplication or lateral genetic transfer. (nih.gov)
- This study investigates the physiological and metabolic consequences of arcA and iclR deletions on E. coli K12 MG1655 under glucose abundant and limiting conditions and compares the results with the metabolic characteristics of E. coli BL21 (DE3). (biomedcentral.com)
- In this work, the substitution of two loci in the genome of MG1655 with the recovery of the wild-type phenotype was accomplished. (deepdyve.com)
- Parallel to this procedure, a spontaneous ValR mutant of E. coli MG1655 yielding colonies of maximal size on M9 medium with glucose in the presence of L-Val (50 μg/ml) was isolated. (deepdyve.com)
- Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655. (ucsd.edu)
- Here, we perform a genome-scale reconstruction of the OxyR, SoxR, and SoxS regulons in Escherichia coli K-12 MG1655. (ucsd.edu)
- The MG1655 chromosome is shown as a circle and the locations of oriC (at the genome map position of 84.6 min), datA (at 94.6 min), DARS1 (at 17.5 min), DARS2 (at 64.0 min), and terC / dif (around 36 min) are indicated. (frontiersin.org)
- MG1655, complete genome. (g-language.org)
- Multi-organism Genome Browser image generated by Pathway Tools. (ecocyc.org)
- Because of its extraordinary position as a preferred model in biochemical genetics, molecular biology, and biotechnology, E. coli K-12 was the earliest organism to be suggested as a candidate for whole genome sequencing ( 1 , 2 ). (sciencemag.org)
- Aside from the physical chemistry measurements of nanoparticle fate, we are also looking at an organism-level response to bacteria with the model bacterium, Escherichia coli, K12. (exeter.ac.uk)
- Availability of complete genome sequences provides the opportunity to search all of the proteins of the organisms for similarities and differences that might have bearing on the ability of the organism to grow at low temperatures. (biomedcentral.com)
- grep -A 2 ORGANISM g-language-1.8.13/share/genomes/ecoli.gbk ORGANISM Escherichia coli str. (g-language.org)
- Insa exista anumite tulpini ale bacteriei care sunt nocive pentru organism si provoaca infectii bacteriene Escherichia coli (E. coli) is a bacteria that is found in the intestines of both humans and animals. (meisten-verliebt.com)
- This single-celled organism is also important in industry, where it is used to make bread, beer, wine, enzymes, and pharmaceuticals.The Saccharomyces cerevisiae genome is approximately 12 Mb, organized in 16 chromosomes. (sitelinks.info)
- 1: Bacteria 2: Proteobacteria 3: Gammaproteobacteria 4: Enterobacteriales 5: Enterobacteriaceae 6: Escherichia. (g-language.org)
- Genome Annotation and Analysis. (pnas.org)
- The pipeline employs curated seed alignments of r-proteins to run position-specific scoring matrix (PSSM)-based BLAST searches against six-frame genome translations, mitigating possible gene annotation errors. (pubmedcentralcanada.ca)
- These alignments, available for download, can be used as search profiles to improve genome annotation of r-proteins and for further comparative genomics studies. (pubmedcentralcanada.ca)
- CyanoBase provides an easy way of accessing the sequences and all-inclusive annotation data on the structures of the cyanobacterial genomes. (vifabio.de)
- The Entrez Protein Clusters database contains annotation information, publications, structures and analysis tools for related protein sequences encoded by complete genomes. (re3data.org)
- Genomic sequencing reveals regulatory mutations and recombinational events in the widely used MC4100 lineage of Escherichia coli K-12. (genome.jp)
- Similarly, genomic fingerprinting ( 48 , 50 , 57 ) and analysis of fosmid libraries of DNA fragments from marine samples ( 6 ) have indicated that nonpathogenic bacteria with identical 16S rRNA gene sequences but distinctly different genomes coexist in natural ecosystems ( 46 ). (asm.org)
- i JR904 will help to outline the genotype-phenotype relationship for E. coli K-12, as it can account for genomic, transcriptomic, proteomic and fluxomic data simultaneously. (biomedcentral.com)
- Comparative genomic analysis of AR1 and four other completely sequenced T4-like genomes (RB32, RB69, T4, and JS98) indicated that they share a well-organized and highly conserved core genome, particularly in the regions encoding DNA replication and virion structural proteins. (asm.org)
- Its purpose is to collate and integrate various aspects of the genomic information from E. coli, the paradigm of Gram-negative bacteria. (vifabio.de)
- We performed a comparative genome analysis of Salmonella enterica serovars Typhi and Typhimurium and Escherichia coli and scanned tRNA loci for the presence of species-specific, horizontally acquired genomic elements. (asm.org)
- 4. Bellanger X, Payot S, Leblond-Bourget N, Guedon G. Conjugative and mobilizable genomic islands in bacteria: evolution and diversity. (prolekarniky.cz)
- The backbone of our work is the design and expansion of the RegulonDB database, with knowledge of the genetic regulation in Escherichia coli K-12 extracted by curators, both from classical experiments and from High-Throughput (HT) post-genomic methods. (unam.mx)
- i JR904 is a more complete and chemically accurate description of E. coli metabolism than i JE660a. (biomedcentral.com)
- A constraint-based model of E. coli metabolism can accomplish this and serve as a model centric database. (biomedcentral.com)
- We have used an in silico analysis to identify seven gene products of central metabolism (glycolysis, pentose phosphate pathway, TCA cycle, electron transport system) essential for aerobic growth of E. coli on glucose minimal media, and 15 gene products essential for anaerobic growth on glucose minimal media. (biomedcentral.com)
- We found that computational models of E. coli metabolism based on physicochemical constraints can be used to interpret mutant behavior. (biomedcentral.com)
- As the techniques for genome sequencing and relevant omics analyses continue to evolve, the quality and application scopes of GEMs have also expanded accordingly, and together they have contributed to better understanding of metabolism in various organisms. (springer.com)
- In addition, it can be useful to optimize the metabolism of other halophilic bacteria for metabolite production. (biomedcentral.com)
- EcoCyc describes all known pathways of E. coli small-molecule metabolism. (davidson.edu)
- Do lifestyles influence the presence of promiscuous enzymes in bacteria and Archaea metabolism? (unam.mx)
- The experimental approach may use reporter loci that are not representative of the whole genome and necessarily incorporates assumptions about the expression and neutrality of the mutant phenotypes. (pnas.org)
- High-throughput whole-genome sequencing allows some of these limitations to be overcome. (pnas.org)
- The mutation-accumulation (MA) strategy combined with whole-genome sequencing overcomes many of these limitations. (pnas.org)
- In combination with whole-genome amplification, the array detects femtogram concentrations of purified DNA, either spiked in to an aerosol sample background, or in combinations from one or more of the four target organisms. (mendeley.com)
- Phenotypic screening of Escherichia coli K-12 Tn5 insertion libraries, using whole-genome oligonucleotide microarrays. (nih.gov)
- We are looking at array transcriptome analysis of the whole genome as well as metabolome response over time course experiments to establish the nature of the response and the route to cell death. (exeter.ac.uk)
- Whole-genome shotgun assembly (WGA) is the process of constructing a draft assembly of a genome from whole-genome shotgun reads (WGS). (biomedcentral.com)
- Executing the script should generate a vector of start and end positions, G+C content, and the relative abundance values of 16 dinucleotides for a whole genome region, as shown in http://www.pnas.org/content/96/16/9184/F1.large.jpg . (g-language.org)
- The molecular mechanisms and physiological consequences of oxidative stress: Lessons from a model bacterium. (prolekare.cz)
- There is a particular opportunity to apply systems-level tools developed for the model bacterium Escherichia coli to study the evolution and function of symbiotic bacteria which are metabolically specialised to overproduce specific nutrients for their host and, remarkably, have a gene complement that is a subset of the E. coli genome. (biomedcentral.com)
- We report the genome organization and analysis of the first completely sequenced T4-like phage, AR1, of Escherichia coli O157:H7. (asm.org)
- The 167,435-bp AR1 genome is currently the largest among all the sequenced E. coli O157:H7 phages. (asm.org)
- The major pathogenic factor of E. coli O157:H7 is the Shiga toxin (Stx), encoded by Stx-producing temperate phages ( 24 ). (asm.org)
- The genomes of 12 E. coli O157:H7 phages have been sequenced completely and published in the NCBI genome database. (asm.org)
- Two other sequenced lytic phages, Rv5 and WV8, are the only two known E. coli O157:H7 lytic phages which belong to the Myoviridae phage family ( 53 , 54 ). (asm.org)
- Escherichia coli O157:H7 is a major food-borne infectious pathogen that causes diarrhea, hemorrhagic colitis, and hemolytic uremic syndrome. (psu.edu)
- OS Escherichia coli O157:H7. (univ-lyon1.fr)
- People: When people are infected with E. coli O157:H7, they shed the bacteria in their waste. (meisten-verliebt.com)
- These evolutionary domains are called Bacteria and Archaea . (wikipedia.org)
- For about 3 billion years, most organisms were microscopic, and bacteria and archaea were the dominant forms of life. (wikipedia.org)
- The most recent common ancestor of bacteria and archaea was probably a hyperthermophile that lived about 2.5 billion-3.2 billion years ago. (wikipedia.org)
- Bacteria were also involved in the second great evolutionary divergence, that of the archaea and eukaryotes. (wikipedia.org)
- Here, eukaryotes resulted from the entering of ancient bacteria into endosymbiotic associations with the ancestors of eukaryotic cells, which were themselves possibly related to the Archaea. (wikipedia.org)
- Most striking is the discovery of the archaea ( image B ). 1 These are simple organisms that, to look at them, are indistinguishable from bacteria ( image C ). 2 Before the prototype tree of life was built in 1977, it was thought that life had two major branches, the eukaryotes (e.g., plants, animals & fungi) and the prokaryotes (bacteria, and what are now known as archaea). (actionbioscience.org)
- But despite appearances, archaea and bacteria are as different from one another as either is from eukaryotes. (actionbioscience.org)
- Which features of the archaea, bacteria, and eukaryotes can be traced to LUCA? (actionbioscience.org)
- 3 The question they are asking is, "which features of the archaea, bacteria and eukaryotes can be traced back to their common ancestor, LUCA? (actionbioscience.org)
- Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea. (nih.gov)
- Since the first GEM for Haemophilus influenzae was reported in 1999, advances have been made to develop and simulate GEMs for an increasing number of organisms across bacteria, archaea, and eukarya. (springer.com)
- GEMs for 434, 40, and 117 taxonomic families of bacteria ( light blue ), archaea ( light purple ), and eukarya ( pink ), respectively, are marked in the phylogenetic tree. (springer.com)
- Archaeal and bacterial ribosomes contain more than 50 proteins, including 34 that are universally conserved in the three domains of cellular life (bacteria, archaea, and eukaryotes). (pubmedcentralcanada.ca)
- 23 r-proteins are bacteria-specific, 1 r-protein is archaea-specific and 11 r-proteins are eukaryotes-specific  . (pubmedcentralcanada.ca)
- Here we report a comprehensive reannotation of r-proteins in genomes of 995 bacteria and 87 archaea and discuss trends of their distribution across the different branches of life and patterns in their evolution. (pubmedcentralcanada.ca)
- This defence system directly degrades invading genetic material and is present in almost all archaea and many bacteria. (vifabio.de)
- Dissecting the protein architecture of DNA-binding transcription factors in bacteria and archaea Microbiology, 163, 1167-1178. (unam.mx)
- A combination of cultivation-based methods with a molecular biological approach was used to investigate whether planktonic bacteria with identical 16S rRNA gene sequences can represent distinct eco- and genotypes. (asm.org)
- The genome will serve as a model to study the cellular and molecular processes that control nitrite oxidation and its interaction with other nitrogen-cycling processes. (asm.org)
- Genome sequencing and bioinformatics are producing detailed lists of the molecular components contained in many prokaryotic organisms. (biomedcentral.com)
- This is the first time that a molecular mechanism for flagellar phase variation has been reported for E. coli . (asm.org)
- Research in Steve Busby's lab is concerned with understanding the molecular mechanisms that control gene expression in bacteria, with particular attention to studying the regulation of transcription initiation in Escherichia coli . (birmingham.ac.uk)
- Molecular characterization of the tdc operon of Escherichia coli K-12. (ecmdb.ca)
- The 5-subunit Bam complex is responsible for the assembly and insertion of beta-barrel proteins into the OM of E. coli . (ecocyc.org)
- Eukaryotic genomes consist of DNA that is packaged together with histone proteins into chromatin. (plantphysiol.org)
- For all proteins encoded in each of the master genomes, a BLASTP search was carried out against the protein sequences from 573 representative bacterial and archaeal genomes, and for the most similar proteins (that is, the best hits), a reciprocal BLASTP search was carried out to identify BBHs. (nih.gov)
- Sequencing and analysis of its genome revealed a single circular chromosome of 3,402,093 bp encoding 3,143 predicted proteins. (asm.org)
- A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome. (harvard.edu)
- To analyze the roles of E. coli phosphodiesterases, we demonstrated that most of these proteins are expressed under laboratory conditions. (asm.org)
- Contributing to an explanation for this enormous multiplicity and diversity is the observation that most bacteria contain multiple representatives, often a few tens, of these proteins ( 3 ). (asm.org)
- Briefly, position-specific scoring matrices (PSSMs) for 56 bacterial and 71 archaeal r-proteins  ,  ( Table S1 ) were used to screen completely sequenced prokaryotic genomes ( Table S2 ) translated in six frames. (pubmedcentralcanada.ca)
- Identification of beta-Lactamases and beta-Lactam-Related Proteins in Human Pathogenic Bacteria using a Computational Search Approach Current Microbiology, 74, 915-920. (unam.mx)
- Many proteins and RNA's were similar from one life form to another, even between bacteria and man. (icr.org)
- In comparison to Haemophilus, Synechocystis, and Mycoplasma bacteria, of the 4,288 coded proteins in E. coli, there are only 111 proteins (2.6%) in common with these three eubacteria. (icr.org)
- Although the term bacteria traditionally included all prokaryotes, the scientific classification changed after the discovery in the 1990s that prokaryotes consist of two very different groups of organisms that evolved from an ancient common ancestor . (wikipedia.org)
- commonly abbreviated E. coli ) is a Gram-negative gammaproteobacterium commonly found in the lower intestine of warm-blooded organisms (endotherms). (wikipedia.org)
- Genome sequences, especially those of well-studied experimental organisms, help to integrate a vast resource of biological knowledge and serve as a guide for further experimentation. (sciencemag.org)
- [ 7 ] Bacteria are vital in recycling nutrients, with many of the stages in nutrient cycles dependent on these organisms, such as the fixation of nitrogen from the atmosphere and putrefaction . (omicsgroup.org)
- Si la plupart des souches de cette bactérie sont sans danger pour la santé, certaines sont à l'origine d'infections intestinales ou urinaires qui peuvent être graves Escherichia coli (commonly abbreviated E. coli) is a Gram-negative, rod-shaped bacterium that is commonly found in the lower intestine of warm-blooded organisms (endotherms). (meisten-verliebt.com)
- Constraints-based modelling using FBA has been applied to a variety of organisms, from E. coli to humans [ 7 , 8 ] and various symbiotic bacteria [ 9 , 10 ] including B. aphidicola . (biomedcentral.com)
- At the root are three major divisions of true bacteria: 'old' bacteria (archaebacteria), and organisms with nuclei including plants, fungi, and animals. (icr.org)
- On the other hand, if there were independent origins for major kinds of animals, then a large portion of the genome should be original, unique sequences not present in other kinds of organisms. (icr.org)
- RT "Organization of the Escherichia coli and Salmonella typhimurium RT chromosomes between flagellar regions IIIa and IIIb, including a large RT non-coding region. (genome.jp)
- 2004. Cell-to-cell signaling in Escherichia coli and Salmonella enterica. (prezi.com)
- however, bacteria were considered primitive and pre-cellular and received little attention before 1944, when Avery, Macleod and McCarty demonstrated that DNA was the genetic material using Salmonella typhimurium , following which Escherichia coli was used for linkage mapping studies. (wikipedia.org)
- Genome-Based Identification of Chromosomal Regions Specific for Salmonella spp. (asm.org)
- A comparative analysis of the surrounding areas of all tRNA sequences in the genomes of E. coli and Salmonella was performed. (asm.org)
- The project highlights Salmonella enterica subspecies enterica serovar Typhimurium ( S . Tm)'s ability to metabolize simple sugars released from dead commensal bacteria, by using the p BAD (araBAD promoter) system as a reporter of L-arabinose availability. (diva-portal.org)
- An important aspect is the use of Natural language processing (NLP) to enrich knowledge extraction strategies that shall allow us to expand the biocuration to other bacteria such as Salmonella , and other few more bacteria. (unam.mx)
- Here, we apply phylogenetic and network analyses to investigate the evolutionary processes and principles that govern sRNA gene distribution in 27 E. coli and Shigella genomes. (nih.gov)
- We present evidence that variable sRNAs are less tightly integrated into cellular genetic regulatory networks than are the core sRNAs, and that Hfq facilitates posttranscriptional cross talk between the E. coli-Shigella core and variable genomes. (nih.gov)
- Our data are consistent with Shigella being phylogenetically indistinguishable from E. coli . (asm.org)
- In common with other enteric bacteria, Shigella survives the proteases and acids of the intestinal tract by uncertain means. (asm.org)
- In the bacterium Escherichia coli , chromosome replication initiates bidirectionally from a single locus, oriC , and terminates at the diametrically opposed ter region ( 1 ). (asm.org)
- In Escherichia coli , chromosome replication is initiated from oriC by the DnaA initiator protein associated with ATP. (frontiersin.org)
- In Escherichia coli chromosome replication is initiated from a single origin, oriC , and proceeds bi-directionally until the two replication forks meet at terminus of replication ( terC ). (frontiersin.org)
- Chromosome replication and segregation are intimately linked and tightly controlled to ensure that daughter cells each receive a complete copy of the genome. (ebi.ac.uk)
-  Although the vast majority of these bacteria are rendered harmless by the protective effects of the immune system , and a few are beneficial , some are pathogenic bacteria and cause infectious diseases , including cholera , syphilis , anthrax , leprosy and bubonic plague . (wikidoc.org)
- Pathogenic bacteria specifically produce flagella to promote colonization and invasion of mucosa ( 27 ). (asm.org)
- A quantitative metabolic model for E. coli K-12 derived from EcoCyc is available. (ecocyc.org)
- Since the first genome-scale metabolic model (GEM) of Haemophilus influenzae RD was reported in 1999 [ 1 ], GEM reconstruction has been established as one of the major modeling approaches for systems-level metabolic studies. (springer.com)
- For this purpose, the construction of a robust and high-quality genome-based metabolic model of C. salexigens was approached. (biomedcentral.com)
- We generated and validated a high quality genome-based C. salexigens metabolic model ( i FP764). (biomedcentral.com)
- Reconstruction of a genome-scale metabolic model for this model photo-synthetic bacterium is one of the main goals of the current study. (biomedcentral.com)
- Flagellar antigen, also known as H antigen, is one of the major antigens in gram-negative bacteria. (asm.org)
- Palchaudhuri S, Mundigala H, Kurtovic E, Palchaudhuri A, Biswas A (2017) Avirulent Gram-negative Bacteria E. coli K-12 or E. coli C Compared with Gram-positive Virulent Diplococcic Streptoccocus pneumoniae . (imedpub.com)
- Resistance to colistin in gram-negative bacteria stems mainly from structural modifications of bacterial lipopolysaccharide. (cdc.gov)
- Currently, 2074 complete bacterial genomes from the NCBI RefSeq project are accessible via EcoGene-RefSeq. (vifabio.de)
- We present RASTA-Bacteria, an automated method allowing quick and reliable identification of TA loci in sequenced prokaryotic genomes, whether they are annotated open reading frames or not. (beds.ac.uk)
- Most bacteria have not been characterised, and only about 27 percent of the bacterial phyla have species that can be grown in the laboratory. (wikipedia.org)
- However, several species of bacteria are pathogenic and cause infectious diseases , including cholera , syphilis , anthrax , leprosy , and bubonic plague . (wikipedia.org)
- However, most of these bacteria have not been characterized, and only about half of the phyla of bacteria have species that can be cultured in the laboratory . (wikidoc.org)
- In 1885, Theodor Escherich , a German pediatrician, first discovered this species in the feces of healthy individuals and called it Bacterium coli commune because it is found in the colon and early classifications of Prokaryotes placed these in a handful of genera based on their shape and motility (at that time Ernst Haeckel 's classification of Bacteria in the kingdom Monera was in place  ). (wikipedia.org)
- All the results were compared with the results for another purple non-sulfur bacterium, Rhodobacter capsulatus SB1003 and species-specific differences were clarified. (springer.com)
- The complete genome sequences of five environmental Arthrobacter species are available. (biomedcentral.com)
- Most bacteria have not been characterized, and only about half of the phyla of bacteria have species that can be grown in the laboratory. (omicsgroup.org)
- A total of 15 bacterial species were screened for the presence of the Escherichia coli K12 insertion sequences IS1, IS2 and IS3 by Southern blotting and DNA hybridization. (microbiologyresearch.org)
- The EcoCyc project performs literature-based curation of the E. coli genome, and of E. coli transcriptional regulation, transporters, and metabolic pathways. (wikipedia.org)
- frvR putative transcriptional regulator FrvR [Escherichia coli str. (nih.gov)
- The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12. (nih.gov)
- Dr. Adhya and his team have demonstrated transcriptional regulation both at the level of initiation by activators and repressors and at the level of elongation by terminators and antiterminators in the gal operon, which encodes enzymes of D-galactose metabolims in Escherichia coli . (cancer.gov)
- Three transcription factors (TFs), OxyR, SoxR, and SoxS, play a critical role in transcriptional regulation of the defense system for oxidative stress in bacteria. (ucsd.edu)
- 5. Zheng M, Wang X, Templeton LJ, Smulski DR, LaRossa RA, Storz G. DNA microarray-mediated transcriptional profiling of the Escherichia coli response to hydrogen peroxide. (prolekare.cz)
Bacterial and archaeal genomes1
- Systematic analysis of gene neighborhoods shows that ribosomal superoperons are the largest partially conserved gene arrays in bacterial and archaeal genomes  ,  . (pubmedcentralcanada.ca)
- In this report, we analyze spontaneous mutations accumulated over thousands of generations by wild-type Escherichia coli and a derivative defective in mismatch repair (MMR), the primary pathway for correcting replication errors. (pnas.org)
- In Escherichia coli K-12, the single replication origin oriC is a well-characterized target for SeqA, which binds to multiple hemi-methylated GATC sequences immediately after replication has initiated. (asm.org)
- IMPORTANCE DNA replication in bacteria is a highly regulated process. (asm.org)
- Functional Genomics of E. coli characterizing the genome of E. coli by measuring the expression level of every gene under a variety of environmental and genetic conditions. (davidson.edu)
- Genomics, Biological Features, and Biotechnological Applications of Escherichia coli B: "Is B for better? (google.ca)
- TMIC is funded by Genome Alberta , Genome British Columbia , and Genome Canada , a not-for-profit organization that is leading Canada's national genomics strategy with $900 million in funding from the federal government. (ecmdb.ca)
- Therefore, selection might significantly influence protein-coding sequences in terms of the transcription-associated mutability per transcription event under stress to improve the survival of Escherichia coli . (pubmedcentralcanada.ca)
- Publication of the Entire E. coli (K12) genome was completed in 1997 by Blattner, Plunkett and colegues. (prezi.com)
- Nace así la bioinformática de la regulación genómica microbiana, con predicciones y análisis del genoma completo de Escherichia coli , con la publicación en Science en 1997 del genoma de dicha bacteria. (unam.mx)
- 1997), a common bacterium in our intestines. (icr.org)
- The tool successfully confirmed all reported TA systems, and spotted new putative loci upon screening of sequenced genomes. (beds.ac.uk)
- Distribution of putative xenogeneic silencers in prokaryote genomes Computational Biology and Chemistry, 58, 167-172. (unam.mx)
- During the projects course of time it was discovered that L-arabinose transporters are not a shared gene trait between E. coli and S . Tm, and that putative L-arabinose transporter orthologues may exists in the S . Tm genome. (diva-portal.org)
- Finally, similar central metabolic fluxes were observed in E. coli K12 Δ arcA Δ iclR compared to the industrially relevant E. coli BL21 (DE3), especially with respect to the pentose pathway, the glyoxylate pathway, and the TCA fluxes. (biomedcentral.com)
- MetaCy c contains the E. coli pathways of EcoCyc, plus additional pathways that have been gathered from a variety of literature and on-line sources, with citations to the source of each pathway. (davidson.edu)
- In Charlebois R (ed), Organization of the Prokaryotic Genome . (asmscience.org)
- The structural organization of oriC, datA, DARS1 , and DARS2 were found conserved among 59 fully sequenced E. coli genomes, with differences primarily in the non-functional spacer regions between key protein binding sites. (frontiersin.org)
- Chromosome organization and segregation in bacteria. (ebi.ac.uk)
- Genome analysis revealed the presence of a flagellum ( fla1 ) and a type IV pilus biogenesis, which is speculated to be a prerequisite for biofilm formation. (osti.gov)
- In conclusion, the genome analysis of Shimia str. (osti.gov)
- EcoCyc provides several genome-scale visualization tools to aid in the analysis of omics data, such as by painting gene expression or metabolomics data onto the full regulatory network of E. coli. (wikipedia.org)
- Analysis of 16S rRNA gene sequences has become the primary approach for studying the natural occurrence and distribution of bacteria in a culture-independent manner ( 3 ). (asm.org)
- Analysis of genome-scale proton balancing shows how the flux of protons into and out of the medium is important for maximizing cellular growth. (biomedcentral.com)
- In this analysis, these are termed the 'master' genomes. (nih.gov)
- Analysis of the Escherichia coli genome. (nih.gov)
- 2] "Genome analysis of the meat starter culture bacterium Staphylococcus carnosus TM300. (tcdb.org)
- This server is constructed around a database dedicated to the analysis of the genome of Escherichia coli: Colibri. (vifabio.de)
- This tutorial shows sample Perl scripts for retrieving taxonomic information, multiple genome analysis, reconstructing gene tree, calculating statistics for a genome or a gene. (g-language.org)
- G-language Genome Analysis Environment v.1.8.13 http://www.g-language.org/ Please cite: Arakawa K. et al. (g-language.org)
- This is a snapshot analysis based on the most recent genome sequences of two E.coli K-12 bacteria. (sri.com)
- Titok, M. 2004-10-07 00:00:00 Based on the results of matings with interrupted conjugation and analysis of marker joint inheritance frequencies, distances between 26 genetic determinants were estimated and a genetic map of Pseudomonas mendocina bacteria was constructed. (deepdyve.com)
- This systems-level analysis predicts that the fragility of the bacterial metabolic network renders the symbiotic bacterium intolerant of drastic environmental fluctuations, whilst the coupling of histidine production to growth prevents the bacterium from exploiting host nutrients without reciprocating. (biomedcentral.com)
- Despite this, informed hypotheses can be constructed from systems-level in silico analysis of those bacteria for which full genome sequences are available. (biomedcentral.com)
- Crea la Sociedad Mexicana de Ciencias Genómicas (2001-2004), y es designado Director del Centro de Ciencias Genómicas de la UNAM (2005-2009), tomando la responsabilidad del período inicial de una de las instituciones pioneras de la genómica y la bioinformática en nuestro país. (unam.mx)
- 1987). "Genetic-Engineering of Ethanol-Production in Escherichia-coli. (freepatentsonline.com)
- 1989 . Physical and genetic maps of the genome of the heterocyst-forming cyanobacterium Anabaena sp. (asmscience.org)
- Conjugation and genetic recombination in Escherichia coli K-12. (springer.com)
- Comparison of Metabolic Pathways in Escherichia coli by Using Genetic Algorithms Computational and Structural Biotechnology Journal, 13, 277-285. (unam.mx)
- Recombinant of E. coli K-12 and E. coli C formed in vivo by genetic cross linkage. (imedpub.com)
- In the genetic system of Cairns and Foster, a nongrowing population of an E. coli lac frameshift mutant appears to specifically accumulate Lac + revertants when starved on medium including lactose (adaptive mutation). (genetics.org)
- The E.coli bacteria was specifically chosen due to its natural ability to retain the genetic information of viruses. (meisten-verliebt.com)
- E. coli C is very small in size (~1 μm), K-12 is long (2.5 μm) but the recombinant E. coli HF4714 is more like E. coli K-12 in size. (imedpub.com)
- The Nan cluster among bacteria is confined to human pathogens and commensals conferring them the ability to utilize a ubiquitous carbon source in mucus rich surfaces of the human body. (biomedcentral.com)
- The genome sequences of many important bacterial pathogens as well as of nonpathogenic relatives are now available or will be completed in the near future. (asm.org)
- PAI of various pathogens share several characteristics, such as a base composition different from that of the host genome. (asm.org)
- Sexuality and the Genetics of Bacteria. (springer.com)
Nucleic Acids Re1
- 2017), "EcoCyc: reflecting new knowledge about Escherichia coli K-12" , Nucleic Acids Research 45:D543-50. (ecocyc.org)
- SK013 offered first insights into specific physiological and phenotypic adaptation mechanisms of Roseobacter -affiliated bacteria to the benthic environment. (osti.gov)
- Small RNAs (sRNAs) are widespread in bacteria and play critical roles in regulating physiological processes. (nih.gov)
- The N. winogradskyi genome provides new insight into the phylogenetic identity and physiological capabilities of nitrite-oxidizing bacteria. (asm.org)
- The genome and metabolome of E. coli are well known the system level response to nanoparticle toxicity can be studies by looking at the gene transcription response and the metabolome response over time. (exeter.ac.uk)
- Nonrandom transcription-associated mutagenesis under stress should improve the survival of E. coli . (pubmedcentralcanada.ca)
- The larger numbers of mutations on the nontranscribed strand are partly but not solely attributable to the activity of the transcription-coupled DNA repair system, which acts on the transcribed strand, in E. coli  . (pubmedcentralcanada.ca)
- Since all 10 prophages in E. coli K-12 carry only a small number of promoters, the altered occupancy of RpoZ-defective RNAP and of transcripts might represent transcription initiated from as-yet-unidentified host promoters. (asm.org)
- Functional prediction of hypothetical transcription factors of Escherichia coli K-12 based on expression data Computational and Structural Biotechnology Journal, 16, 157-166. (unam.mx)
- Working with Escherichia coli K-12, over the past 25 years, the lab has elucidated some of the basic rules of promoter recognition by RNA polymerase and some of the fundamental mechanisms by which transcription activators function (see reviews listed below). (birmingham.ac.uk)
- The work with RNA polymerase has focused on the roles of the alpha and sigma subunits, whilst the work on transcription activation has developed from studies of the cyclic AMP receptor protein (known as CRP or CAP), which have established a paradigm for understanding transcription activation in bacteria. (birmingham.ac.uk)
- From protecting E. coli against phage infection to the promise of gene therapy: How does Cascade do it? (ecocyc.org)
- CRISPR features may be exploited for typing purposes, ecological and epidemiological studies, and also for enhancing phage resistance in bacteria. (asmscience.org)
- The extent of the impact of CRISPR on phage genomes is perhaps best illustrated by extensive genome recombination events observed in environmental phage populations in response to CRISPR. (asmscience.org)
- המובאת כאן היא שיטה פשוטה ליצירת ספריית ההכנסה transposon בצפיפות גבוהה ב- Escherichia coli או שיגלה flexneri באמצעות קוניוגציה. (jove.com)
- This fact supports the idea that PAI could have been laterally transferred by phages into different genomes (for a review, see reference 4 ). (asm.org)
- Available genomes include plants and viruses as well as organelles and microbial genomes. (re3data.org)
- The nucleosome is a fundamental structural and functional chromatin unit that affects nearly all DNA-templated events in eukaryotic genomes. (plantphysiol.org)
- Empirical data on nucleosome distribution have been valuable in determining the chromatin landscape of eukaryotic genomes. (plantphysiol.org)
- PEP aims at the exploration of the diversity of eukaryotic genomes in a systematic, comprehensive and integrated way. (re3data.org)
- Chemical characterization of biodegradative threonine dehydratases from two enteric bacteria. (ecmdb.ca)
- Both phenomena presumably result in a reduced ArcA and IclR synthesis in BL21, which contributes to the similar physiology as observed in E. coli K12 Δ arcA Δ iclR . (biomedcentral.com)
- General Information: Pseudomonas stutzeri is a nonfluorescent denitrifying bacterium widely distributed in the environment. (up.ac.za)
- Bacteria belonging to the Pseudomonas group are common inhabitants of soil and water and can also be found on the surfaces of plants and animals. (up.ac.za)
- Pseudomonas bacteria are found in nature in a biofilm or in planktonic form. (up.ac.za)
- Pseudomonas bacteria are renowned for their metabolic versatility as they can grow under a variety of growth conditions and do not need any organic growth factors. (up.ac.za)
Agrobacterium tumefaciens C581
- We assessed the impact of seed inoculation with the emblematic bacterial models Agrobacterium tumefaciens C58 (plasmid-cured) or Escherichia coli K-12 on maize seedlings in nonsterile soil. (apsnet.org)
- E. Coli can be grown and cultured very easily in a laboratory setting and thus has been intensively studied for over 60 years. (prezi.com)
- This argues that E. coli possesses several phosphodiesterases that are inactive under laboratory conditions because they lack appropriate input signals. (asm.org)
- Selection of laboratory wild-type phenotype from natural isolates of Escherichia coli in chemostats. (prolekare.cz)
Closely related bacteria3
- In many cases phylogenetically closely related bacteria (whose 16S rRNA sequences differ by between 2.7 and 0.3%) have been detected in the same freshwater, marine, or soil habitat ( 19 , 32 , 43 , 56 ). (asm.org)
- Accordingly, phylogenetically closely related bacteria coexisting in the same habitat occupy distinct ecological niches ( 19 , 32 , 43 , 56 ). (asm.org)
- 1 million deaths per year from dysentery and diarrhea and have a lifestyle that is markedly different from those of closely related bacteria, including Escherichia coli . (asm.org)
- EcoCyc is also a description of the genome and cellular networks of E. coli that supports scientists to carry out computational analyses. (wikipedia.org)
- In particular, c-di-GMP controls important cellular and behavioral processes in a wide range of bacteria, including motility and chemotaxis, surface colonization and the formation of communities, virulence and persistence, and cell cycle progression (for reviews, see references 1 to 3 ). (asm.org)
- E. coli can cause urinary tract infections, neonatal meningitis, and many different intestinal diseases, usually by attaching to the host cell and introducing toxins that disrupt normal cellular processes. (up.ac.za)
- This study advances understanding of not only the regulatory role of omega subunit in the functions of RNAP but also the regulatory interplay between prophages and the host E. coli for adjustment of cellular physiology to a variety of environments in nature. (asm.org)