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Escherichia Coli SRNA
''Escherichia coli'' contains a number of small RNAs located in intergenic regions of its genome. The presence of at least 55 of these has been verified experimentally. 275 potential sRNA-encoding loci were identified computationally using the QRNA program. These loci will include false positives, so the number of sRNA genes in ''E. coli'' is likely to be less than 275. A computational screen based on promoter sequences recognised by the sigma factor sigma 70 and on Rho-independent terminators predicted 24 putative sRNA genes, 14 of these were verified experimentally by northern blotting. The experimentally verified sRNAs included the well characterised sRNAs RprA and RyhB. Many of the sRNAs identified in this screen, including RprA, RyhB, SraB and SraL, are only expressed in the stationary phase of bacterial cell growth. A screen for sRNA genes based on homology to ''Salmonella'' and ''Klebsiella'' identified 59 candidate sRNA genes. From this set of candidate genes, micro ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Escherichia Coli
''Escherichia coli'' (),Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. also known as ''E. coli'' (), is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus '' Escherichia'' that is commonly found in the lower intestine of warm-blooded organisms. Most ''E. coli'' strains are harmless, but some serotypes ( EPEC, ETEC etc.) can cause serious food poisoning in their hosts, and are occasionally responsible for food contamination incidents that prompt product recalls. Most strains do not cause disease in humans and are part of the normal microbiota of the gut; such strains are harmless or even beneficial to humans (although these strains tend to be less studied than the pathogenic ones). For example, some strains of ''E. coli'' benefit their hosts by producing vitamin K2 or by preventing the colonization of the intestine by pathogenic bacteria. These mutually beneficial relationships between ''E ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Klebsiella
''Klebsiella'' is a genus of Gram-negative, oxidase-negative, rod-shaped bacteria with a prominent polysaccharide-based capsule. ''Klebsiella'' species are found everywhere in nature. This is thought to be due to distinct sublineages developing specific niche adaptations, with associated biochemical adaptations which make them better suited to a particular environment. They can be found in water, soil, plants, insects and other animals including humans. ''Klebsiella'' is named after German-Swiss microbiologist Edwin Klebs (1834–1913). Carl Friedlander described ''Klebsiella'' bacillus which is why it was termed Friedlander bacillus for many years. The members of the genus ''Klebsiella'' are a part of the human and animal's normal flora in the nose, mouth and intestines. The species of ''Klebsiella'' are all gram-negative and usually non-motile. They tend to be shorter and thicker when compared to others in the family Enterobacteriaceae. The cells are rods in shape and gen ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bacteroides Thetaiotaomicron SRNA
The ''Bacteroides thetaiotaomicron'' genome contains hundreds of small RNAs (sRNAs), discovered through RNA sequencing. These include canonical housekeeping RNA species such as the 6S RNA (SsrS), tmRNA (SsrA), M1 RNA (RnpB) and 4.5S RNA (Ffs) as well as several hundred cis and trans encoded small RNAs. More than 20 candidates have been validated with northern blots and the structures of several members have been characterized through ''in silico'' analyses and chemical probing experiments. Two ''B. thetaiotaomicron'' sRNAs that have been functionally characterized are RteR and GibS. RteR is a 78 nucleotide (nt) long sRNA that is conserved in closely related species and likely serves as a repressor of a transposon operon. Analyses based on secondary structure conservation, taking into consideration nucleotide covariation and in-vitro chemical probing have revealed a structure that consists of a 5’ hairpin and a Rho-independent terminator that are separated by an 8 nt sequ ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bacillus Subtilis BSR SRNAs
In a screen of the ''Bacillus subtilis'' genome for genes encoding ncRNAs, Saito et al. focused on 123 intergenic regions (IGRs) over 500 base pairs in length, the authors analyzed expression from these regions. Seven IGRs termed bsrC, bsrD, bsrE, bsrF, bsrG, bsrH and bsrI expressed RNAs smaller than 380 nt. All the small RNAs except BsrD RNA were expressed in transformed ''Escherichia coli'' cells harboring a plasmid with PCR-amplified IGRs of ''B. subtilis'', indicating that their own promoters independently express small RNAs. Under non-stressed condition, depletion of the genes for the small RNAs did not affect growth. Although their functions are unknown, gene expression profiles at several time points showed that most of the genes except for bsrD were expressed during the vegetative phase (4–6 h), but undetectable during the stationary phase (8 h). Mapping the 5' ends of the 6 small RNAs revealed that the genes for BsrE, BsrF, BsrG, BsrH, and BsrI RNAs are preceded by a re ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Pseudomonas SRNA
''Pseudomonas'' sRNA are non-coding RNAs (ncRNA) that were predicted by the bioinformatics, bioinformatic program SRNApredict2. This program identifies putative sRNAs by searching for co-localization of genetic features commonly associated with sRNA-encoding genes and the gene expression, expression of the predicted sRNAs was subsequently confirmed by Northern blot analysis. These sRNAs have been shown to be conservation (genetics), conserved across several ''pseudomonas'' species but their function is yet to be determined. Using Tet-Trap genetic approach RNA thermometer, RNAT genes post-transcriptionally regulated by temperature upshift were identified: ''ptxS'' (implicated in virulence) and PA5194. See also *Bacillus subtilis BSR sRNAs, ''Bacillus subtilis'' sRNA *C. elegans small RNAs, ''Caenorhabditis elegans'' sRNA *Mycobacterium tuberculosis sRNA, ''Mycobacterium tuberculosis'' sRNA *Bacteroides thetaiotaomicron sRNA, ''Bacteroides thetaiotaomicron'' sRNA *NrsZ small RNA *Aspo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Mycobacterium Tuberculosis SRNA
''Mycobacterium tuberculosis'' contains at least nine bacterial small RNA, small RNA families in its genome. The small RNA (sRNA) families were identified through RNomics – the direct analysis of RNA molecules isolated from cell culture, cultures of ''Mycobacterium tuberculosis''. The sRNAs were characterised through Rapid Amplification of cDNA Ends, RACE mapping and Northern blot experiments. Secondary structures of the sRNAs were predicted using Mfold. sRNAPredict2 – a bioinformatics tool – suggested 56 putative sRNAs in ''M. tuberculosis'', though these have yet to be verified experimentally. Hfq protein homologues have yet to be found in ''M. tuberculosis''; an alternative pathway – potentially involving conserved cytosine, C-rich motifs – has been theorised to enable trans-acting sRNA functionality. sRNAs were shown to have important physiology, physiological roles in ''M. tuberculosis''. Overexpression of G2 sRNA, for example, prevented growth of ''M. tuberculosis' ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
DinQ-agrB Toxin-antitoxin System
The ''dinQ-agrB'' type I toxin-antitoxin (TA) system was initially identified in ''Escherichia coli''. This type I TA system is induced by the bacterial DNA damage response system known as the SOS response system. ''dinQ'' ''dinQ'', DNA-damage-inducible protein Q produces two major transcripts, only one, however, +44, is actively translated. Translation is initiated using the unusual GUG start codon and results in a 27 amino acid peptide. Plasmid-based expression of C-terminal triple FLAG-tagged ''dinQ'' located DinQ in the inner-membrane of ''E. coli''. Overexpression of ''dinQ'' led to reduced survival, loss of transmembrane electrical polarity and reduced intracellular ATP concentrations. ''agrA'' and ''agrB'' ''agrA'' and ''agrB'' are two small RNAs, 84 ribonucleotides long, named due to their position in the '' E. coli'' genome (arsR-gor region gene A and B). 31 ribonucleotides at the 5'-end of ''agrA'' and ''agrB'' show partial sequence complementarity within the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
CC-BY Icon
A Creative Commons (CC) license is one of several public copyright licenses that enable the free distribution of an otherwise copyrighted "work".A "work" is any creative material made by a person. A painting, a graphic, a book, a song/lyrics to a song, or a photograph of almost anything are all examples of "works". A CC license is used when an author wants to give other people the right to share, use, and build upon a work that the author has created. CC provides an author flexibility (for example, they might choose to allow only non-commercial uses of a given work) and protects the people who use or redistribute an author's work from concerns of copyright infringement as long as they abide by the conditions that are specified in the license by which the author distributes the work. There are several types of Creative Commons licenses. Each license differs by several combinations that condition the terms of distribution. They were initially released on December 16, 2002, by ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Toxin-antitoxin System
A toxin-antitoxin system is a set of two or more closely linked genes that together encode both a "toxin" protein and a corresponding "antitoxin". Toxin-antitoxin systems are widely distributed in prokaryotes, and organisms often have them in multiple copies. When these systems are contained on plasmids – transferable genetic elements – they ensure that only the daughter cells that inherit the plasmid survive after cell division. If the plasmid is absent in a daughter cell, the unstable antitoxin is degraded and the stable toxic protein kills the new cell; this is known as 'post-segregational killing' (PSK). Toxin-antitoxin systems are typically classified according to how the antitoxin neutralises the toxin. In a type I toxin-antitoxin system, the translation of messenger RNA (mRNA) that encodes the toxin is inhibited by the binding of a small non-coding RNA antitoxin that binds the toxin mRNA. The toxic protein in a type II system is inhibited post-translationally ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Endonuclease
Endonucleases are enzymes that cleave the phosphodiester bond within a polynucleotide chain. Some, such as deoxyribonuclease I, cut DNA relatively nonspecifically (without regard to sequence), while many, typically called restriction endonucleases or restriction enzymes, cleave only at very specific nucleotide sequences. Endonucleases differ from exonucleases, which cleave the ends of recognition sequences instead of the middle (endo) portion. Some enzymes known as "exo-endonucleases", however, are not limited to either nuclease function, displaying qualities that are both endo- and exo-like. Evidence suggests that endonuclease activity experiences a lag compared to exonuclease activity. Restriction enzymes are endonucleases from eubacteria and archaea that recognize a specific DNA sequence. The nucleotide sequence recognized for cleavage by a restriction enzyme is called the restriction site. Typically, a restriction site will be a palindromic sequence about four to six nucleot ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sigma 38
The gene ''rpoS'' (RNA polymerase, sigma S, also called katF) encodes the sigma factor ''sigma-38'' (σ38, or RpoS), a 37.8 kD protein in ''Escherichia coli''. Sigma factors are proteins that regulate transcription in bacteria. Sigma factors can be activated in response to different environmental conditions. ''rpoS'' is transcribed in late exponential phase, and RpoS is the primary regulator of stationary phase genes. RpoS is a central regulator of the general stress response and operates in both a retroactive and a proactive manner: it not only allows the cell to survive environmental challenges, but it also prepares the cell for subsequent stresses (cross-protection). The transcriptional regulator CsgD is central to biofilm formation, controlling the expression of the curli structural and export proteins, and the diguanylate cyclase, adrA, which indirectly activates cellulose production. The ''rpoS'' gene most likely originated in the gammaproteobacteria. Environmental signa ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
