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词条 FnrS RNA
释义

  1. Gene regulation

  2. References

  3. Further reading

  4. External links

{{Infobox rfam
| Name = FnrS
| image = FnrS SScons.png
| width =
| caption = Conserved secondary structure of FnrS RNA. The colour of nucleotides indicate their conservation within the family.
| Symbol = FnrS
| AltSymbols =
| Rfam = RF01796
| RNA_type = Gene
| Tax_domain = Enterobacteriaceae
}}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]

  • adhP - an alcohol dehydrogenase involved in metabolism
  • cydD - zinc sensitive ATP-binding component of cytochrome-related transport[5]
  • mqo - membrane associated malate:quinone oxidoreductase which operates in the citric acid cycle[6]
  • sodB/A - a superoxide dismutase which aids with oxygen stress resistance[7]
  • ygiW - a hypothetical outer membrane protein[8]

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 {{cite journal |vauthors=Durand S, Storz G |title=Reprogramming of anaerobic metabolism by the FnrS small RNA |journal=Mol. Microbiol. |volume=75 |issue=5 |pages=1215–31 |date=March 2010 |pmid=20070527 |doi=10.1111/j.1365-2958.2010.07044.x |url=http://www3.interscience.wiley.com/resolve/openurl?genre=article&sid=nlm:pubmed&issn=0950-382X&date=2010&volume=75&issue=5&spage=1215 |accessdate=2010-08-04 |pmc=2941437}}{{dead link|date=February 2019|bot=medic}}{{cbignore|bot=medic}}
2. ^1 {{cite journal |vauthors=Boysen A, Møller-Jensen J, Kallipolitis B, Valentin-Hansen P, Overgaard M |title=Translational regulation of gene expression by an anaerobically induced small non-coding RNA in Escherichia coli |journal=J. Biol. Chem. |volume=285 |issue=14 |pages=10690–702 |date=April 2010 |pmid=20075074 |doi=10.1074/jbc.M109.089755 |url=http://www.jbc.org/cgi/pmidlookup?view=long&pmid=20075074 |accessdate=2010-08-05 |pmc=2856277}}
3. ^{{cite journal |vauthors=Tjaden B, Saxena RM, Stolyar S, Haynor DR, Kolker E, Rosenow C |title=Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays |journal=Nucleic Acids Res. |volume=30 |issue=17 |pages=3732–8 |date=September 2002 |pmid=12202758 |pmc=137427 |doi= 10.1093/nar/gkf505|url=http://nar.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=12202758 |accessdate=2010-08-05}}
4. ^{{cite journal |vauthors=Carter RJ, Dubchak I, Holbrook SR |title=A computational approach to identify genes for functional RNAs in genomic sequences |journal=Nucleic Acids Res. |volume=29 |issue=19 |pages=3928–38 |date=October 2001 |pmid=11574674 |pmc=60242 |doi= 10.1093/nar/29.19.3928|url=http://nar.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=11574674 |accessdate=2010-08-05}}
5. ^{{cite journal |vauthors=Poole RK, Gibson F, Wu G |title=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 |journal=FEMS Microbiol. Lett. |volume=117 |issue=2 |pages=217–23 |date=April 1994 |pmid=8181727 |doi= 10.1111/j.1574-6968.1994.tb06768.x|url= }}
6. ^{{cite journal |vauthors=van der Rest ME, Frank C, Molenaar D |title=Functions of the membrane-associated and cytoplasmic malate dehydrogenases in the citric acid cycle of Escherichia coli |journal=J. Bacteriol. |volume=182 |issue=24 |pages=6892–9 |date=December 2000 |pmid=11092847 |pmc=94812 |doi= 10.1128/jb.182.24.6892-6899.2000|url=http://jb.asm.org/cgi/pmidlookup?view=long&pmid=11092847 |accessdate=2010-08-06}}
7. ^{{EntrezGene|944953}}
8. ^{{EntrezGene|8872708}}
9. ^1 {{cite journal |vauthors=Wright PR, Richter AS, Papenfort K, Mann M, Vogel J, Hess WR, Backofen R, Georg J |title=Comparative genomics boosts target prediction for bacterial small RNAs. |journal=Proc Natl Acad Sci U S A |volume= 110|issue= 37|pages=E3487–E3496|year=2013 |pmid=23980183 |doi=10.1073/pnas.1303248110 |pmc=3773804}}
10. ^{{cite journal |vauthors=Martin RG, Rosner JL |title=Promoter Discrimination at Class I MarA Regulon Promoters Mediated by Glutamic Acid 89 of the MarA Transcriptional Activator of Escherichia coli. |journal=J Bacteriol |volume= 193|issue= 2|pages=506–15|year=2011 |pmid=21097628 |doi=10.1128/JB.00360-10 |pmc=3019838}}
11. ^1 {{cite journal |vauthors=Giel JL, Rodionov D, Liu M, Blattner FR, Kiley PJ |title=IscR-dependent gene expression links iron-sulphur cluster assembly to the control of O2-regulated genes in Escherichia coli. |journal=Mol Microbiol |volume= 60|issue= 4|pages=1058–1075|year=2006 |pmid=16677314 |doi=10.1111/j.1365-2958.2006.05160.x}}
12. ^{{cite journal |vauthors=Paradela A, Mariscotti JF, Navajas R, Ramos-Fernández A, Albar JP, García-Del Portillo F |title=Inverse regulation in the metabolic genes pckA and metE revealed by proteomic analysis of the Salmonella RcsCDB regulon. |journal=J Proteome Res |volume= 10|issue= 8|pages= 3386–98|year=2011 |pmid=21657791 |doi=10.1021/pr101294v}}

Further reading

{{refbegin}}
  • {{cite journal |vauthors=Bohn C, Rigoulay C, Chabelskaya S |title=Experimental discovery of small RNAs in Staphylococcus aureus reveals a riboregulator of central metabolism |journal=Nucleic Acids Res |volume= 38|issue= 19|pages= 6620–36|date=May 2010 |pmid=20511587 |doi=10.1093/nar/gkq462 |url=http://nar.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=20511587 |accessdate=2010-08-05 |pmc=2965222|display-authors=etal}}
  • {{cite journal |vauthors=Silveira AC, Robertson KL, Lin B |title=Identification of non-coding RNAs in environmental vibrios |journal=Microbiology |volume=156 |issue=Pt 8 |pages=2452–8 |date=August 2010 |pmid=20447992 |doi=10.1099/mic.0.039149-0 |url= |display-authors=etal}}
{{refend}}

External links

  • {{Rfam|id=RF01796|name=Fumarate/nitrate reductase regulator sRNA}}

1 : Non-coding RNA
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