|
Hfq Binding SRNA
An Hfq binding sRNA is an sRNA that binds the bacterial RNA binding protein called Hfq. A number of bacterial small RNAs which have been shown to bind to Hfq have been characterised (see list). Many of these RNAs share a similar structure composed of three stem-loops. Several studies have expanded this list, and experimentally validated a total of 64 Hfq binding sRNA in ''Salmonella Typhimurium''. A transcriptome wide study on Hfq binding sites in ''Salmonella'' mapped 126 Hfq binding sites within sRNAs. Genomic SELEX has been used to show that Hfq binding RNAs are enriched in the sequence motif 5′-AAYAAYAA-3′. Genome-wide study identified 40 candidate Hfq-dependent sRNAs in plant pathogen ''Erwinia amylovora.'' 12 of them were confirmed by Northern blot. Bacterial Hfq binding sRNAs * DicF RNA * DsrA RNA * FnrS RNA * GadY RNA * GcvB RNA * IsrJ RNA * MicA RNA / SraD RNA * MicC RNA * MicF RNA * OmrA RNA / OmrB RNA / RygA RNA / RygB RNA / SraE RNA * OxyS RNA * Qrr RN ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gene
In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a basic unit of heredity and the molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protein-coding genes and noncoding genes. During gene expression, the DNA is first copied into RNA. The RNA can be directly functional or be the intermediate template for a protein that performs a function. The transmission of genes to an organism's offspring is the basis of the inheritance of phenotypic traits. These genes make up different DNA sequences called genotypes. Genotypes along with environmental and developmental factors determine what the phenotypes will be. Most biological traits are under the influence of polygenes (many different genes) as well as gen ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
GcvB RNA
The gcvB RNA gene encodes a small non-coding RNA involved in the regulation of a number of amino acid transport systems as well as amino acid biosynthetic genes. The GcvB gene is found in enteric bacteria such as ''Escherichia coli''. GcvB regulates genes by acting as an antisense binding partner of the mRNAs for each regulated gene. This binding is dependent on binding to a protein called Hfq. Transcription of the GcvB RNA is activated by the adjacent GcvA gene and repressed by the GcvR gene. A deletion of GcvB RNA from ''Y. pestis'' changed colony shape as well as reducing growth. It has been shown by gene deletion that GcvB is a regulator of acid resistance in ''E. coli''. GcvB enhances the ability of the bacterium to survive low pH by upregulating the levels of the alternate sigma factor RpoS. A polymeric form of GcvB has recently been identified. Interaction of GcvB with small RNA SroC triggers the degradation of GcvB by RNase E, lifting the GcvB-mediated mRNA repression of i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 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] |
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] |
RydC RNA
RydC is a bacterial non-coding RNA. RydC is thought to regulate a mRNA, yejABEF, which encodes an ABC transporter protein. RydC is known to bind the 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 RN ..., which causes a conformational change in the RNA molecule. The Hfq/RydC complex is then thought to bind to the target mRNA and induce its degradation. See also * RyfA RNA * RydB RNA * RybB RNA References Further reading * External links * Non-coding RNA {{molecular-cell-biology-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
RybB RNA
RybB is a small non-coding RNA was identified in a large scale screen of ''Escherichia coli''. The function of this short RNA has been studied using a transcriptomic approach and kinetic analyses of target mRNA decay ''in vivo''. RybB was identified as a factor that selectively accelerates the decay of multiple major omp mRNAs upon induction of the envelope stress response. This RNA has been shown to bind to the Hfq protein. In ''Salmonella'', direct interactions for RybB with the following targets have been verified experimentally: STM2391 (''fadL''), STM1070 (''ompA''), STM2267 (''ompC''), STM1572 (''ompD''), STM0999 (''ompF''), STM1473 (''ompN''), STM1995 (''ompS''), STM1732 (''ompW''), STM0413 (''tsx''), STM0687 (''ybfM'', ''chiP'') and STM1530. In ''Escherichia coli'', direct interactions for RybB with the following targets have been verified experimentally: b0805 (''fiu''), b0721 (''sdhC''), b2215 (''ompC''), b1256 (''ompW''), b2594 (''rluD'') and b0081 (''mraZ''). See also ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
RprA RNA
The RprA RNA gene encodes a 106 nucleotide regulatory non-coding RNA. Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA A) increased the translation of RpoS. As with DsrA, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. RprA also appears to bind to the RpoS leader. RprA is non-essential. Wasserman ''et al.'' demonstrated that this RNA is bound by the Hfq protein. Binding to Hfq alters the conformation of RprA. In the presence of Hfq the stability of RprA is influenced by the osmolarity of the cell, this is dependent on the endoribonuclease RNase E. It has been shown the RprA regulates the protein coding genes, called csgD, this protein encodes a stationary p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Regulator Of Motility And Amylovoran A
In molecular biology, the regulator of motility and amylovoran A (RmaA) gene is a bacterial non-coding RNA. It was discovered in genome-wide identification of Hfq binding sRNAs in plant pathogen ''Erwinia amylovora Fire blight, also written fireblight, is a contagious disease affecting apples, pears, and some other members of the family Rosaceae. It is a serious concern to apple and pear producers. Under optimal conditions, it can destroy an entire orchard ...''. Together with Hfq it positively controls motility and negatively controls the production of acidic exopolysaccharide amylovoran in ''E. amylovora''. References Non-coding RNA {{molecular-cell-biology-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Qrr RNA
Introduction Qrr (Quorum regulatory RNA) is a small non-coding RNA that is thought to be involved in the regulation of quorum sensing in ''Vibrio'' species. The use of small RNAs for vital functions like metabolism, infection cycling, and stress response is ubiquitous among bacteria. Qrr operates as part of a negative feedback loop which regulates the shift in cell state from that of low density populations to that in high density populations. This feedback system allows for rapid responses to changes in population cell density, eliminating the production of energy-costly molecules. It is believed that these RNAs, guided by a protein, Hfq protein, Hfq, can mediate the destabilization of the quorum-sensing master regulators LuxR/HapR/VanT mRNAs. This group of non-coding RNAs are trans-acting small RNAs (sRNAs) that bind via base pairing to the untranscribed domain of their Messenger RNA, mRNA targets. This binding results in degradation or stabilization, deciding their translation ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
OxyS RNA
OxyS RNA is a small non-coding RNA which is induced in response to oxidative stress in ''Escherichia coli''. This RNA acts as a global regulator to activate or repress the expression of as many as 40 genes, by an antisense mechanism, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages. Binding to Hfq alters the conformation of OxyS. The 109 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 biomolecule ... RNA is thought to be composed of three stem-loops. Target genes A number of additional targets were predicted and verified using microarray analysis. These are listed below: * yobF – confirmed by Northern analysis * yaiZ * rumA ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
OmrA-B RNA
The OmrA-B RNA gene family (also known as SraE RNA, RygA and RygB and OmrA and OmrB) is a pair of homologous OmpR-regulated small non-coding RNA that was discovered in ''E. coli'' during two large-scale screens. OmrA-B is highly abundant in stationary phase, but low levels could be detected in exponentially growing cells as well. RygB is adjacent to RygA a closely related RNA. These RNAs bind to the Hfq protein and regulate gene expression by antisense binding. They negatively regulate the expression of several genes encoding outer membrane proteins, including cirA, CsgD, fecA, fepA and ompT by binding in the vicinity of the Shine-Dalgarno sequence, suggesting the control of these targets is dependent on Hfq protein and RNase E. Taken together, these data suggest that OmrA-B participates in the regulation of outer membrane composition, responding to environmental conditions. Together with the RNA chaperone Hfq, OmrA-B positively controls bacterial motility and negatively cont ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
