FnrS RNA

FnrS

Conserved secondary structure of FnrS RNA. The colour of nucleotides indicate their conservation within the family.
Identifiers
Symbol FnrS
Rfam RF01796
Other data
RNA type Gene
Domain(s) Enterobacteriaceae
SO {{{SO}}}

FnrS RNA is a family of Hfq-binding small RNA whose expression is upregulated in response to anaerobic conditions. It is named FnrS because its expression is strongly dependent on fumarate and nitrate reductase regulator (FNR), a direct oxygen availability sensor.[1][2]

A conserved intergenic region between genes ydaN and dbpA was predicted to encode an sRNA, adjacent to where another non-coding RNA (C0343) has been identified.[3] However, northern blot analysis of this 477bp sequence yielded no results.[4] A subsequent tiling array analysis sequencing Hfq-binding sRNA found that the Watson strand did indeed encode an sRNA.[1]

Gene regulation

FnrS has been shown to downregulate 32 different mRNAs in Enterobacteria, in 15 of these cases it does so by base-pairing with the mRNA transcript.[1] The majority of genes downregulated by FnrS are required for aerobic metabolism or the oxidative stress response.[2] Some of the genes downregulated by FnrS are:[1]

A study incorporating comparative target prediction and subsequent experimental verification of selected predictions, suggests that FnrS might be a more global regulator in Escherichia coli. It is predicted to control several transcription factors. These include the verified targets marA and IscR.[9] MarA activates genes involved in the resistance to superoxide,[10] which might not be necessary at the anaerobic conditions where FnrS is expressed. IscR regulates genes for iron-sulfur-cluster containing or biogenesis proteins.[11] FnrS might be involved in the observed O2 dependent expression of the IscR regulon.[11] Further targets of FnrS are nagZ and sdhA.[9]

There is also evidence to suggest that the expression of FnrS is regulated by the RcsCDB signalling system in Salmonella enterica.[12]

References

  1. 1 2 3 4 Durand S, Storz G (March 2010). "Reprogramming of anaerobic metabolism by the FnrS small RNA". Mol. Microbiol. 75 (5): 1215–31. PMC 2941437 Freely accessible. PMID 20070527. doi:10.1111/j.1365-2958.2010.07044.x. Retrieved 2010-08-04.
  2. 1 2 Boysen A, Møller-Jensen J, Kallipolitis B, Valentin-Hansen P, Overgaard M (April 2010). "Translational regulation of gene expression by an anaerobically induced small non-coding RNA in Escherichia coli". J. Biol. Chem. 285 (14): 10690–702. PMC 2856277 Freely accessible. PMID 20075074. doi:10.1074/jbc.M109.089755. Retrieved 2010-08-05.
  3. ↑ Tjaden B, Saxena RM, Stolyar S, Haynor DR, Kolker E, Rosenow C (September 2002). "Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays". Nucleic Acids Res. 30 (17): 3732–8. PMC 137427 Freely accessible. PMID 12202758. doi:10.1093/nar/gkf505. Retrieved 2010-08-05.
  4. ↑ Carter RJ, Dubchak I, Holbrook SR (October 2001). "A computational approach to identify genes for functional RNAs in genomic sequences". Nucleic Acids Res. 29 (19): 3928–38. PMC 60242 Freely accessible. PMID 11574674. doi:10.1093/nar/29.19.3928. Retrieved 2010-08-05.
  5. ↑ Poole RK, Gibson F, Wu G (April 1994). "The cydD gene product, component of a heterodimeric ABC transporter, is required for assembly of periplasmic cytochrome c and of cytochrome bd in Escherichia coli". FEMS Microbiol. Lett. 117 (2): 217–23. PMID 8181727. doi:10.1111/j.1574-6968.1994.tb06768.x.
  6. ↑ van der Rest ME, Frank C, Molenaar D (December 2000). "Functions of the membrane-associated and cytoplasmic malate dehydrogenases in the citric acid cycle of Escherichia coli". J. Bacteriol. 182 (24): 6892–9. PMC 94812 Freely accessible. PMID 11092847. doi:10.1128/jb.182.24.6892-6899.2000. Retrieved 2010-08-06.
  7. ↑ EntrezGene 944953
  8. ↑ EntrezGene 8872708
  9. 1 2 Wright PR, Richter AS, Papenfort K, Mann M, Vogel J, Hess WR, Backofen R, Georg J (2013). "Comparative genomics boosts target prediction for bacterial small RNAs.". Proc Natl Acad Sci U S A. 110 (37): E3487–E3496. PMC 3773804 Freely accessible. PMID 23980183. doi:10.1073/pnas.1303248110.
  10. ↑ Martin RG, Rosner JL (2011). "Promoter Discrimination at Class I MarA Regulon Promoters Mediated by Glutamic Acid 89 of the MarA Transcriptional Activator of Escherichia coli.". J Bacteriol. 193 (2): 506–15. PMC 3019838 Freely accessible. PMID 21097628. doi:10.1128/JB.00360-10.
  11. 1 2 Giel JL, Rodionov D, Liu M, Blattner FR, Kiley PJ (2006). "IscR-dependent gene expression links iron-sulphur cluster assembly to the control of O2-regulated genes in Escherichia coli.". Mol Microbiol. 60 (4): 1058–1075. PMID 16677314. doi:10.1111/j.1365-2958.2006.05160.x.
  12. ↑ Paradela A, Mariscotti JF, Navajas R, Ramos-Fernández A, Albar JP, García-Del Portillo F (2011). "Inverse regulation in the metabolic genes pckA and metE revealed by proteomic analysis of the Salmonella RcsCDB regulon.". J Proteome Res. 10 (8): 3386–98. PMID 21657791. doi:10.1021/pr101294v.

Further reading

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