Escherichia coli sRNA
Encyclopedia
Escherichia coli
contains a number of small RNAs
located in intergenic region
s of its genome
. The presence of at least 55 of these has been verfied 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 (Sigma 38
).
Escherichia coli
Escherichia coli is a Gram-negative, rod-shaped bacterium that is commonly found in the lower intestine of warm-blooded organisms . Most E. coli strains are harmless, but some serotypes can cause serious food poisoning in humans, and are occasionally responsible for product recalls...
contains a number of small RNAs
Bacterial small RNA
Bacterial small RNAs are small non-coding RNA molecules produced by bacteria, they are highly structured and contain several stem-loops...
located in intergenic region
Intergenic region
An Intergenic region is a stretch of DNA sequences located between clusters of genes that contain few or no genes. Occasionally some intergenic DNA acts to control genes nearby, but most of it has no currently known function...
s of its genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
. The presence of at least 55 of these has been verfied experimentally. 275 potential sRNA-encoding loci
Locus (genetics)
In the fields of genetics and genetic computation, a locus is the specific location of a gene or DNA sequence on a chromosome. A variant of the DNA sequence at a given locus is called an allele. The ordered list of loci known for a particular genome is called a genetic map...
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 factor
A sigma factor is a bacterial transcription initiation factor that enables specific binding of RNA polymerase to gene promoters. Different sigma factors are activated in response to different environmental conditions...
sigma 70 and on Rho
Rho factor
A ρ factor is a prokaryotic protein involved in the termination of transcription.Rho factor is an essential transcription protein in prokaryotes. In Escherichia coli, it is a ~275 kD hexamer of identical subunits. Each subunit has an RNA-binding domain and an ATP-hydrolysis domain...
-independent terminators
Termination factor
Termination is part of the process of transcribing RNA. In eukaryotes, a termination factor is required to release the newly made RNA from the transcription complex...
predicted 24 putative sRNA genes, 14 of these were verified experimentally by northern blotting. The experimentally verified sRNAs included the well characterised sRNAs RprA
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...
and RyhB
RyhB RNA
RyhB RNA is a 90 nucleotide non-coding 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 . This ncRNA gene was independently identified in two screens, named RyhB by Wasserman et...
. Many of the sRNAs identified in this screen, including RprA, RyhB, SraB
SraB RNA
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...
and SraL, are only expressed in the stationary phase of bacterial cell growth. A screen for sRNA genes based on homology
Homology (biology)
Homology forms the basis of organization for comparative biology. In 1843, Richard Owen defined homology as "the same organ in different animals under every variety of form and function". Organs as different as a bat's wing, a seal's flipper, a cat's paw and a human hand have a common underlying...
to Salmonella
Salmonella
Salmonella is a genus of rod-shaped, Gram-negative, non-spore-forming, predominantly motile enterobacteria with diameters around 0.7 to 1.5 µm, lengths from 2 to 5 µm, and flagella which grade in all directions . They are chemoorganotrophs, obtaining their energy from oxidation and reduction...
and Klebsiella
Klebsiella
Klebsiella is a genus of non-motile, Gram-negative, oxidase-negative, rod-shaped bacteria with a prominent polysaccharide-based capsule. It is named after the German microbiologist Edwin Klebs...
identified 59 candidate sRNA genes. From this set of candidate genes, microarray
Microarray
A microarray is a multiplex lab-on-a-chip. It is a 2D array on a solid substrate that assays large amounts of biological material using high-throughput screening methods.Types of microarrays include:...
analysis and northern blotting confirmed the existence of 17 previously undescribed sRNAs, many of which bind to the chaperone protein Hfq
Hfq protein
The Hfq 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. Usually mediated by...
and regulate the translation of RpoS (Sigma 38
Sigma 38
Sigma factors are proteins that regulate transcription in bacteria. Sigma factors can be activated in response to different environmental conditions. The gene rpoS encodes sigma-38 , a 37.8 kD protein in Escherichia coli. rpoS is transcribed in late exponential phase, and RpoS is the primary...
).
See also
- Mycobacterium tuberculosis sRNAMycobacterium tuberculosis sRNAMycobactierum tuberculosis contains at least nine small RNA families in its genome. The small RNA families were identified through RNomics - the direct analysis of RNA molecules isolated from cultures of Mycobacterium tuberculosis. The sRNAs were characterised through RACE mapping and Northern...
- Pseudomonas sRNAPseudomonas sRNAPseudomonas sRNA are non-coding RNAs that were predicted by the bioinformatic program SRNApredict2. This program identifies putative sRNAs by searching for co-localization of genetic features commonly associated with sRNA-encoding genes and the expression of the predicted sRNAs was subsequently...
- Bacillus subtilis BSR sRNAsBacillus subtilis BSR sRNAsIn a screen of the Bacillus subtilis genome for genes encoding ncRNAs, Saito et al. focused on 123 intergenic regions over 500 bp 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...
- Caenorhabditis elegans sRNAC. elegans small RNAsSmall RNAs have been identified within the C. elegans genome and comparative genomics has shown that they are conserved across several nematode species. These sRNAs contain a characteristic 2,2,7-trimethylguanosine cap structure that identifies them as non-coding RNAs that have a functional role...
- List of RNA structure prediction software