RpoE

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The gene rpoE (RNA polymerase, extracytoplasmic E) encodes the sigma factor sigma-24 (σ24, sigma E, or RpoE), a protein in Escherichia coli [1] and other species of bacteria. Depending on the bacterial species, this gene may be referred to as sigE. [2]

RpoE appears to be necessary for the exocytoplasmic stress response. E. coli mutants without rpoE cannot grow at high temperatures (that is, above 42 degrees C) [3] and show growth defects at lower temperatures, though this may be due to compensatory mutations. [4] In some bacterial species, such as Clostridium botulinum , this sigma factor may be necessary for sporulation. [5]

The stress response regulation activities of RpoE are modulated by the Hfq protein in E. coli. [6]

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The gene rpoS encodes the sigma factor sigma-38, a 37.8 kD protein in Escherichia coli. Sigma factors are proteins that regulate transcription in bacteria. Sigma factors can be activated in response to different environmental conditions. rpoS is transcribed in late exponential phase, and RpoS is the primary regulator of stationary phase genes. RpoS is a central regulator of the general stress response and operates in both a retroactive and a proactive manner: it not only allows the cell to survive environmental challenges, but it also prepares the cell for subsequent stresses (cross-protection). The transcriptional regulator CsgD is central to biofilm formation, controlling the expression of the curli structural and export proteins, and the diguanylate cyclase, adrA, which indirectly activates cellulose production. The rpoS gene most likely originated in the gammaproteobacteria.

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DicF RNA

DicF RNA is a non-coding RNA that is an antisense inhibitor of cell division gene ftsZ. DicF is bound by the Hfq protein which enhances its interaction with its targets. Pathogenic E. coli strains possess multiple copies of sRNA DicF in their genomes, while no-pathogenic strains do not.DicF and Hfq are both necessary to reduce FtsZ protein levels, leading to cell filamentation under anaerobic conditions.

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DsrA RNA

DsrA RNA is a non-coding RNA that regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation. The structures of DsrA and DsrA/rpoS complex were studied by NMR. The study concluded that the sRNA contains a dynamic conformational equilibrium for its second stem–loop which might be an important mechanism for DsrA to regulate the translations of its multiple target mRNAs.

GcvB RNA

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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 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.

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References

  1. Rouvière, PE; De Las Peñas, A; Mecsas, J; Lu, CZ; Rudd, KE; Gross, CA (1995). "rpoE, the gene encoding the second heat-shock sigma factor, sigma E, in Escherichia coli". The EMBO Journal. 14 (5): 1032–42. doi:10.1002/j.1460-2075.1995.tb07084.x. PMC   398175 . PMID   7889934.
  2. Jensen-Cain, DM; Quinn, FD (2001). "Differential expression of sigE by Mycobacterium tuberculosis during intracellular growth". Microbial Pathogenesis. 30 (5): 271–8. doi:10.1006/mpat.2001.0431. PMID   11373121.
  3. Hiratsu, K; Amemura, M; Nashimoto, H; Shinagawa, H; Makino, K (1995). "The rpoE gene of Escherichia coli, which encodes sigma E, is essential for bacterial growth at high temperature". Journal of Bacteriology. 177 (10): 2918–22. doi:10.1128/jb.177.10.2918-2922.1995. PMC   176969 . PMID   7751307.
  4. De Las Peñas, A; Connolly, L; Gross, CA (Nov 1997). "SigmaE is an essential sigma factor in Escherichia coli". Journal of Bacteriology. 179 (21): 6862–4. doi:10.1128/jb.179.21.6862-6864.1997. PMC   179621 . PMID   9352942.
  5. Kirk, DG; Zhang, Z; Korkeala, H; Lindström, M (2014). "Alternative sigma factors SigF, SigE, and SigG are essential for sporulation in Clostridium botulinum ATCC 3502". Applied and Environmental Microbiology. 80 (16): 5141–50. doi:10.1128/aem.01015-14. PMC   4135750 . PMID   24928875.
  6. De Las Peñas, A; Connolly, L; Gross, CA (Nov 1997). "SigmaE is an essential sigma factor in Escherichia coli". Journal of Bacteriology. 179 (21): 6862–4. doi:10.1128/jb.179.21.6862-6864.1997. PMC   179621 . PMID   9352942.