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RyhB SodB
RyhB RNA is a 90 nucleotide RNA that down-regulates a set of iron-storage and iron-using proteins when iron is limiting; it is itself negatively regulated by the ferric uptake repressor protein, Fur (Ferric uptake regulator). Discovery The gene was independently identified in two screens, named RyhB by Wassarman ''et al''. and called SraI by Argaman ''et al''. and was found to be expressed only in stationary phase. Function and regulation RyhB RNA levels are inversely correlated with mRNA levels for the ''sdhCDAB'' operon, encoding succinate dehydrogenase, as well as five other genes previously shown to be positively regulated by Fur by an unknown mechanism. These include two other genes encoding enzymes in the tricarboxylic acid cycle, ''acnA'' and ''fumA'', two ferritin genes, ''ftnA'' and ''bfr'', and a gene for superoxide dismutase, ''sodB''. A number of other genes have been predicted computationally and verified as targets by microarray analysis: ''napF'', ''sodA'', ''cysE' ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
RyhB SodB
RyhB RNA is a 90 nucleotide RNA that down-regulates a set of iron-storage and iron-using proteins when iron is limiting; it is itself negatively regulated by the ferric uptake repressor protein, Fur (Ferric uptake regulator). Discovery The gene was independently identified in two screens, named RyhB by Wassarman ''et al''. and called SraI by Argaman ''et al''. and was found to be expressed only in stationary phase. Function and regulation RyhB RNA levels are inversely correlated with mRNA levels for the ''sdhCDAB'' operon, encoding succinate dehydrogenase, as well as five other genes previously shown to be positively regulated by Fur by an unknown mechanism. These include two other genes encoding enzymes in the tricarboxylic acid cycle, ''acnA'' and ''fumA'', two ferritin genes, ''ftnA'' and ''bfr'', and a gene for superoxide dismutase, ''sodB''. A number of other genes have been predicted computationally and verified as targets by microarray analysis: ''napF'', ''sodA'', ''cysE' ... [...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. col ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
RyeE RNA
The CyaR RNA (formerly known as RyeE RNA) non-coding RNA was identified in a large scale screen of ''Escherichia coli'' and was called candidate 14. The exact 5′ and 3′ ends of this RNA are uncertain. This gene lies between yegQ and orgK in ''E. coli''. This small RNA was shown to be bound by the Hfq protein. This RNA has been renamed as CyaR for (cyclic AMP-activated RNA). It has been shown that the CyaR RNA acts as a repressor of the porin OmpX. It has also been shown that ''cyaR'' expression is tightly controlled by the cyclic AMP receptor protein, CRP. A comparative genomics approach was able to detect and verify the additional targets ''ptsI'', ''sdhA'' and ''yobF''. See also * RydB RNA *RyhB RNA RyhB RNA is a 90 nucleotide RNA that down-regulates a set of iron-storage and iron-using proteins when iron is limiting; it is itself negatively regulated by the ferric uptake repressor protein, Fur ( Ferric uptake regulator). Discovery The gene ... * RyeB RNA References ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
RyeB RNA
The SdsR/RyeB RNA is a non-coding RNA that was identified in a large scale screen of ''E. coli''. The exact 5′ and 3′ ends of this RNA are uncertain. This RNA overlaps the SraC/RyeA RNA on the opposite strand suggesting that the two may act in a concerted manner. It is transcribed by general stress factor σs and is most highly expressed in stationary phase. SdsR/RyeB RNA interacts with Hfq. The homologous sRNA in ''S. enterica'' was shown to regulate synthesis of major porin OmpD. A study using ''Salmonella'' identified 20 targets of this sRNA including transcriptional regulator, CRP, global DNA-binding factors, StpA and HupB, the antibiotic transporter protein, TolC, and the RtsA/B two-component system (TCS), and validated their post-transcriptional control by SdsR/RyeB RNA. See also * RydB RNA *RyhB RNA *RyeE RNA The CyaR RNA (formerly known as RyeE RNA) non-coding RNA was identified in a large scale screen of ''Escherichia coli'' and was called candidate 14. The exac ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
RydB RNA
The RydB RNA is a non-coding RNA originally identified in ''E. coli'' in an RNA screen. This gene is only 67 nucleotides in length and is composed of a hairpin like structure. RydB lies between the ''ydiC'' and ''ydiH'' in ''E. coli''. Homologous RNA genes have been found in other species such as ''Shigella flexneri'' and ''Salmonella'' species. The molecular function of this RNA is unknown. See also *RyhB RNA *RyeB RNA *RyeE RNA The CyaR RNA (formerly known as RyeE RNA) non-coding RNA was identified in a large scale screen of ''Escherichia coli'' and was called candidate 14. The exact 5′ and 3′ ends of this RNA are uncertain. This gene lies between yegQ and orgK in '' ... References External links * Non-coding RNA {{molecular-cell-biology-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
HrrF RNA
HrrF RNA (''Haemophilus'' regulatory RNA responsive to iron Fe) is a small non-coding RNA involved in iron homeostasis in ''Haemophilus'' species. Orthologues exist only among other '' Pasteurellacae.'' Iron- regulated sRNAs JA01- JA04 were identified in related ''Aggregatibacte''r. It is an analog to PrrF and RyhB RNAs. HrrF is maximally expressed when iron levels are low. Ferric uptake regulator (Fur) binds upstream of the ''hrrF'' promoter. HrrF stability is not dependent on the RNA chaperone Hfq. RNA-seq has shown that HrrF targets are mRNAs of genes whose products are involved in molybdate uptake, deoxyribonucleotide synthesis, and amino acid synthesis. See also * NrrF RNA NrrF is a non-coding RNA which is regulated by the Ferric uptake regulator (Fur) protein in bacteria. This non-coding RNA was identified in ''Neisseria meningitidis'' and is involved in iron regulation of the succinate dehydrogenase genes sdhA an ... References Non-coding RNA {{mole ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
PrrF RNA
The PrrF RNAs are small non-coding RNAs involved in iron homeostasis and are encoded by all ''Pseudomonas'' species. The PrrF RNAs are analogs of the RyhB RNA, which is encoded by enteric bacteria. Expression of the PrrF RNAs is repressed by the ferric uptake regulator (Fur) when cells are grown in iron-replete conditions. Under iron limitation, the PrrF RNAs are expressed and act to negatively regulate several genes encoding iron-containing proteins, including SodB and succinate dehydrogenase. As such, PrrF regulation "spares" iron when this nutrient becomes scarce. PrrF and virulence In ''Pseudomonas aeruginosa'', the PrrF RNAs are required for the production of the Pseudomonas quinolone signal (PQS), a quorum sensing molecule that activates the expression of several virulence genes. The phenomenon is mediated by PrrF repressing the expression of enzymes that degrade anthranilic acid, which is the precursor for PQS synthesis. Due to this regulatory link with PQS, the PrrF RNAs ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Analogy (biology)
Convergent evolution is the independent evolution of similar features in species of different periods or epochs in time. Convergent evolution creates analogous structures that have similar form or function but were not present in the last common ancestor of those groups. The cladistic term for the same phenomenon is homoplasy. The recurrent evolution of flight is a classic example, as flying insects, birds, pterosaurs, and bats have independently evolved the useful capacity of flight. Functionally similar features that have arisen through convergent evolution are ''analogous'', whereas '' homologous'' structures or traits have a common origin but can have dissimilar functions. Bird, bat, and pterosaur wings are analogous structures, but their forelimbs are homologous, sharing an ancestral state despite serving different functions. The opposite of convergence is divergent evolution, where related species evolve different traits. Convergent evolution is similar to parallel evo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Comparative Genomics
Comparative genomics is a field of biological research in which the genomic features of different organisms are compared. The genomic features may include the DNA sequence, genes, gene order, regulatory sequences, and other genomic structural landmarks. In this branch of genomics, whole or large parts of genomes resulting from genome projects are compared to study basic biological similarities and differences as well as evolutionary relationships between organisms. The major principle of comparative genomics is that common features of two organisms will often be encoded within the DNA that is evolutionarily conserved between them. Therefore, comparative genomic approaches start with making some form of alignment of genome sequences and looking for orthologous sequences (sequences that share a common ancestry) in the aligned genomes and checking to what extent those sequences are conserved. Based on these, genome and molecular evolution are inferred and this may in turn be put in ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nucleotide
Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules within all life-forms on Earth. Nucleotides are obtained in the diet and are also synthesized from common nutrients by the liver. Nucleotides are composed of three subunit molecules: a nucleobase, a five-carbon sugar (ribose or deoxyribose), and a phosphate group consisting of one to three phosphates. The four nucleobases in DNA are guanine, adenine, cytosine and thymine; in RNA, uracil is used in place of thymine. Nucleotides also play a central role in metabolism at a fundamental, cellular level. They provide chemical energy—in the form of the nucleoside triphosphates, adenosine triphosphate (ATP), guanosine triphosphate (GTP), cytidine triphosphate (CTP) and uridine triphosphate (UTP)—throughout the cell for the many cellular func ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hfq Protein
The Hfq protein (also known as HF-I protein) encoded by the ''hfq'' gene was discovered in 1968 as an ''Escherichia coli'' host factor that was essential for replication of the bacteriophage Qβ. It is now clear that Hfq is an abundant bacterial RNA binding protein which has many important physiological roles that are usually mediated by interacting with Hfq binding sRNA. In ''E. coli'', Hfq mutants show multiple stress response related phenotypes. The Hfq protein is now known to regulate the translation of two major stress transcription factors ( σS (RpoS) and σE (RpoE) ) in Enterobacteria. It also regulates sRNA in ''Vibrio cholerae'', a specific example being MicX sRNA. In ''Salmonella typhimurium'', Hfq has been shown to be an essential virulence factor as its deletion attenuates the ability of ''S.typhimurium'' to invade epithelial cells, secrete virulence factors or survive in cultured macrophages. In ''Salmonella'', Hfq deletion mutants are also non motile and exhibit chro ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Microarray
A microarray is a multiplex lab-on-a-chip. Its purpose is to simultaneously detect the expression of thousands of genes from a sample (e.g. from a tissue). It is a two-dimensional array on a solid substrate—usually a glass slide or silicon thin-film cell—that assays (tests) large amounts of biological material using high-throughput screening miniaturized, multiplexed and parallel processing and detection methods. The concept and methodology of microarrays was first introduced and illustrated in antibody microarrays (also referred to as antibody matrix) by Tse Wen Chang in 1983 in a scientific publication and a series of patents. The "gene chip" industry started to grow significantly after the 1995 ''Science Magazine'' article by the Ron Davis and Pat Brown labs at Stanford University. With the establishment of companies, such as Affymetrix, Agilent, Applied Microarrays, Arrayjet, Illumina, and others, the technology of DNA microarrays has become the most sophisticated and ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
