| SraC/RyeA RNA | |
|---|---|
 Predicted secondary structure and sequence conservation of SraC_RyeA | |
| Identifiers | |
| Symbol | SraC_RyeA |
| Rfam | RF00101 |
| Other data | |
| RNA type | Gene; sRNA |
| Domain(s) | Bacteria |
| SO | 0000655 |
| PDB structures | PDBe |
The SraC/RyeA RNA is a non-coding RNA that was discovered in E. coli during two large scale screens for RNAs. [1] [2] The function of this RNA is currently unknown. This RNA overlaps the SdsR/RyeB RNA on the opposite strand suggesting that the two RNAs may act in a concerted manner.
Prokaryotic translation is the process by which messenger RNA is translated into proteins in prokaryotes.
The 245 nucleotide sRNA of Escherichia coli, CsrC, was discovered using a genetic screen for factors that regulate glycogen biosynthesis. CsrC RNA binds multiple copies of CsrA, a protein that post-transcriptionally regulates central carbon flux, biofilm formation and motility in E. coli. CsrC antagonises the regulatory effects of CsrA, presumably by sequestering this protein. The discovery of CsrC is intriguing, in that a similar sRNA, CsrB, performs essentially the same function. Both sRNAs possess similar imperfect repeat sequences, primarily localised in the loops of predicted hairpins, which may serve as CsrA binding elements. Transcription of csrC increases as the culture approaches the stationary phase of growth and is indirectly activated by CsrA via the response regulator UvrY [1]. This RNA was also discovered in E. coli during a large scale screen [2]. The gene called SraK, was highly abundant in stationary phase, but low levels could be detected in exponentially growing cells as well [2].
The OmrA-B RNA gene family 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.
Sib RNA refers to a group of related non-coding RNA. They were originally named QUAD RNA after they were discovered as four repeat elements in Escherichia coli intergenic regions. The family was later renamed Sib when it was discovered that the number of repeats is variable in other species and in other E. coli strains.
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 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.
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.
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 CyaR 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. 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.
The ryfA RNA gene is a non-coding RNA present in E. coli, Shigella flexneri and Salmonella species where it is found between the ydaN and dbpA genes. These RNA genes are about 300 nucleotides in length. The function of this RNA is unknown.
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.
The SraB RNA is a small non-coding RNA discovered in E. coli during a large scale experimental screen. The 14 novel RNAs discovered were named 'sra' for small RNA, examples include SraC, SraD and SraG. This ncRNA was found to be expressed only in stationary phase. The exact function of this RNA is unknown but it has been shown to affect survival of Salmonella enterica to antibiotic administration in egg albumin. The authors suggest this may be due to SraB regulating a response to components in albumin.
The MicA RNA is a small non-coding RNA that was discovered in E. coli during a large scale screen. Expression of SraD is highly abundant in stationary phase, but low levels could be detected in exponentially growing cells as well.
SraG is a small non-coding RNA (ncRNA). It is the functional product of a gene which is not translated into protein.
In molecular biology the ArcZ RNA is a small non-coding RNA (ncRNA). It is the functional product of a gene which is not translated into protein. ArcZ is an Hfq binding RNA that functions as an antisense regulator of a number of protein coding genes.
GlmZ is a small non-coding RNA (ncRNA). It is the functional product of a gene which is not translated into protein.
The yybP-ykoY leader RNA element was originally discovered in E. coli during a large scale screen and was named SraF. This family was later found to exist upstream of related families of protein genes in many bacteria, including the yybP and ykoY genes in B. subtilis. The specific functions of these proteins are unknown, but this structured RNA element may be involved in their genetic regulation as a riboswitch. The yybP-ykoY element was later proposed to be manganese-responsive after another associated family of genes, YebN/MntP, was shown to encode Mn2+ efflux pumps in several bacteria. Genetic data and a crystal structure confirmed that yybp-ykoY is a manganese riboswitch that directly binds Mn2+
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 . 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.
The TisB-IstR toxin-antitoxin system is the first known toxin-antitoxin system which is induced by the SOS response in response to DNA damage.
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, microarray analysis and northern blotting confirmed the existence of 17 previously undescribed sRNAs, many of which bind to the chaperone protein Hfq and regulate the translation of RpoS. UptR sRNA transcribed from the uptR gene is implicated in suppressing extracytoplasmic toxicity by reducing the amount of membrane-bound toxic hybrid protein.
The SraL RNA, also known as RyjA, is a small non-coding RNA discovered in E. coli, and later in Salmonella Tiphimurium. This ncRNA was found to be expressed only in stationary phase. It may possibly play a role in Salmonella virulence. The major stationary phase regulator RpoS is transcriptionally regulating SraL and directly binds to the sraL gene promoter. SraL down-regulates the expression of the ribosome-associated chaperone Trigger Factor (TF), which is involved in the folding of the newly synthesised cystolic proteins.
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