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fis is an E. coli gene encoding the Fis protein. The regulation of this gene is more complex than most other genes in the E. coli genome, as Fis is an important protein which regulates expression of other genes. It is supposed that fis is regulated by H-NS, IHF and CRP. It also regulates its own expression (autoregulation). Fis is one of the most abundant DNA binding proteins in Escherichia coli under nutrient-rich growth conditions.
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 SraC/RyeA RNA is a non-coding RNA that was discovered in E. coli during two large scale screens for RNAs. 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.
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.
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.
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 GlmY RNA family consists of a number of bacterial RNA genes of around 167 bases in length. The GlmY RNA gene is present in Escherichia coli, Shigella flexneri, Yersinia pestis and Salmonella species, where it is found between the yfhK and purL genes. It was originally predicted in a bioinformatic screen for novel ncRNAs in E. coli.
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, but undetectable during the stationary phase. 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 recognition site for RNA polymerase sigma factor σA.
Bacterial small RNAs are small RNAs produced by bacteria; they are 50- to 500-nucleotide non-coding RNA molecules, highly structured and containing several stem-loops. Numerous sRNAs have been identified using both computational analysis and laboratory-based techniques such as Northern blotting, microarrays and RNA-Seq in a number of bacterial species including Escherichia coli, the model pathogen Salmonella, the nitrogen-fixing alphaproteobacterium Sinorhizobium meliloti, marine cyanobacteria, Francisella tularensis, Streptococcus pyogenes, the pathogen Staphylococcus aureus, and the plant pathogen Xanthomonas oryzae pathovar oryzae. Bacterial sRNAs affect how genes are expressed within bacterial cells via interaction with mRNA or protein, and thus can affect a variety of bacterial functions like metabolism, virulence, environmental stress response, and structure.
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.
A toxin-antitoxin system consists of a "toxin" and a corresponding "antitoxin", usually encoded by closely linked genes. The toxin is usually a protein while the antitoxin can be a protein or an RNA. 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).
RdlD RNA is a family of small non-coding RNAs which repress the protein LdrD in a type I toxin-antitoxin system. It was discovered in Escherichia coli strain K-12 in a long direct repeat (LDR) named LDR-D. This locus encodes two products: a 35 amino acid peptide toxin (ldrD) and a 60 nucleotide RNA antitoxin. The 374nt toxin mRNA has a half-life of around 30 minutes while rdlD RNA has a half-life of only 2 minutes. This is in keeping with other type I toxin-antitoxin systems.
The SymE-SymR toxin-antitoxin system consists of a small symbiotic endonuclease toxin, SymE, and a non-coding RNA symbiotic RNA antitoxin, SymR, which inhibits SymE translation. SymE-SymR is a type I toxin-antitoxin system, and is under regulation by the antitoxin, SymR. The SymE-SymR complex is believed to play an important role in recycling damaged RNA and DNA. The relationship and corresponding structures of SymE and SymR provide insight into the mechanism of toxicity and overall role in prokaryotic systems.
The FlmA-FlmB toxin-antitoxin system consists of FlmB RNA, a family of non-coding RNAs and the protein toxin FlmA. The FlmB RNA transcript is 100 nucleotides in length and is homologous to sok RNA from the hok/sok system and fulfills the identical function as a post-segregational killing (PSK) mechanism.
Mycobacterium tuberculosis contains at least nine small RNA families in its genome. The small RNA (sRNA) 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 blot experiments. Secondary structures of the sRNAs were predicted using Mfold.
The TxpA/RatA toxin-antitoxin system was first identified in Bacillus subtilis. It consists of a non-coding 222nt sRNA called RatA and a protein toxin named TxpA.
An RNA thermometer is a temperature-sensitive non-coding RNA molecule which regulates gene expression. RNA thermometers often regulate genes required during either a heat shock or cold shock response, but have been implicated in other regulatory roles such as in pathogenicity and starvation.
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.
References
- ↑ Hershberg R, Altuvia S, Margalit H (April 2003). "A survey of small RNA-encoding genes in Escherichia coli". Nucleic Acids Research. 31 (7): 1813–1820. doi:10.1093/nar/gkg297. PMC 152812 . PMID 12654996.
- ↑ Rivas E, Klein RJ, Jones TA, Eddy SR (September 2001). "Computational identification of noncoding RNAs in E. coli by comparative genomics". Current Biology. 11 (17): 1369–1373. doi: 10.1016/S0960-9822(01)00401-8 . PMID 11553332. S2CID 5243194.
- ↑ Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner EG, Margalit H, Altuvia S (June 2001). "Novel small RNA-encoding genes in the intergenic regions of Escherichia coli". Current Biology. 11 (12): 941–950. doi: 10.1016/S0960-9822(01)00270-6 . PMID 11448770.
- ↑ Wassarman KM, Repoila F, Rosenow C, Storz G, Gottesman S (July 2001). "Identification of novel small RNAs using comparative genomics and microarrays". Genes & Development. 15 (13): 1637–1651. doi:10.1101/gad.901001. PMC 312727 . PMID 11445539.
- ↑ Guigueno A, Dassa J, Belin P, Boquet PL (February 2001). "Oversynthesis of a new Escherichia coli small RNA suppresses export toxicity of DsbA'-PhoA unfoldable periplasmic proteins". Journal of Bacteriology. 183 (4): 1147–1158. doi:10.1128/JB.183.4.1147-1158.2001. PMC 94987 . PMID 11157926.
- ↑ Sudo N, Soma A, Muto A, Iyoda S, Suh M, Kurihara N, Abe H, Tobe T, Ogura Y, Hayashi T, Kurokawa K, Ohnishi M, Sekine Y (2014-01-01). "A novel small regulatory RNA enhances cell motility in enterohemorrhagic Escherichia coli". The Journal of General and Applied Microbiology. 60 (1): 44–50. doi: 10.2323/jgam.60.44 . PMID 24646762.
- ↑ Guo Y, Quiroga C, Chen Q, McAnulty MJ, Benedik MJ, Wood TK, Wang X (June 2014). "RalR (a DNase) and RalA (a small RNA) form a type I toxin-antitoxin system in Escherichia coli". Nucleic Acids Research. 42 (10): 6448–6462. doi:10.1093/nar/gku279. PMC 4041452 . PMID 24748661.
- ↑ Rau MH, Bojanovič K, Nielsen AT, Long KS (December 2015). "Differential expression of small RNAs under chemical stress and fed-batch fermentation in E. coli". BMC Genomics. 16: 1051. doi: 10.1186/s12864-015-2231-8 . PMC 4676190 . PMID 26653712.
This article contains quotations from this source, which is available under the Creative Commons Attribution 4.0 International (CC BY 4.0) license. - ↑ Chen Z, Wang Y, Li Y, Li Y, Fu N, Ye J, Zhang H (April 2012). "Esre: a novel essential non-coding RNA in Escherichia coli". FEBS Letters. 586 (8): 1195–1200. doi:10.1016/j.febslet.2012.03.010. PMID 22575655. S2CID 43271507.
- ↑ Weel-Sneve R, Kristiansen KI, Odsbu I, Dalhus B, Booth J, Rognes T, Skarstad K, Bjørås M (2013). "Single transmembrane peptide DinQ modulates membrane-dependent activities". PLOS Genetics. 9 (2): e1003260. doi: 10.1371/journal.pgen.1003260 . PMC 3567139 . PMID 23408903.
