FnrS RNA

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]

FnrS
Conserved secondary structure of FnrS RNA. The colour of nucleotides indicate their conservation within the family.
Identifiers
SymbolFnrS
RfamRF01796
Other data
RNA typeGene
Domain(s)Enterobacteriaceae
PDB structuresPDBe

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. Durand S, Storz G (March 2010). "Reprogramming of anaerobic metabolism by the FnrS small RNA". Mol. Microbiol. 75 (5): 1215–1231. doi:10.1111/j.1365-2958.2010.07044.x. PMC 2941437. PMID 20070527.
  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): 10690–10702. doi:10.1074/jbc.M109.089755. PMC 2856277. PMID 20075074. 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): 3732–3738. doi:10.1093/nar/gkf505. PMC 137427. PMID 12202758.
  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): 3928–3938. doi:10.1093/nar/29.19.3928. PMC 60242. PMID 11574674.
  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): 217–223. doi:10.1111/j.1574-6968.1994.tb06768.x. PMID 8181727.
  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): 6892–6899. doi:10.1128/jb.182.24.6892-6899.2000. PMC 94812. PMID 11092847.
  7. EntrezGene 944953
  8. EntrezGene 8872708
  9. 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. Bibcode:2013PNAS..110E3487W. doi:10.1073/pnas.1303248110. PMC 3773804. PMID 23980183.
  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): 506–515. doi:10.1128/JB.00360-10. PMC 3019838. PMID 21097628.
  11. 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. doi:10.1111/j.1365-2958.2006.05160.x. PMID 16677314. S2CID 16807119.
  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): 3386–3398. doi:10.1021/pr101294v. PMID 21657791.

Further reading
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