Fluoride riboswitch: Difference between revisions
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== Discovery of the Fluoride Riboswitch == |
== Discovery of the Fluoride Riboswitch == |
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The identification of a fluoride-responsive riboswitch was accidently discovered when a compound contaminated with fluoride caused significant conformational changes to the non-coding crcB RNA motif during an in-line probing experiment.<ref name="Baker2012" /> The use of in-line probing was to help illuminate the secondary structure of the crcB RNA motif and its binding mechanisms to specific metabolites.<ref name="Regulski">{{cite journal|last=Regulski|first=EE|coauthors=Breaker RR|title=In-line probing analysis of riboswitches|journal=Methods molecular biology|month=2008|volume=419|page=53-67|pages=14|doi=10.1007/978-1-59745-033-1_4|pmid=18369975|url=http://www.ncbi.nlm.nih.gov/pubmed/18369975?dopt=Abstract&holding=npg|accessdate=24 February 2013}}</ref> The results of the probe showed the addition of increasing fluoride ion concentrations suppressing certain regions of spontaneous RNA cleavage and heightening other regions. These nucleotide regions in the crcB RNA motif play important roles in the aptamer binding region for fluoride.<ref name="Baker2012"/> Upon binding fluoride ions, the fluoride riboswitch showed regulation of downstream gene transcription.<ref name="science2011">{{cite news|title=How bacteria fight fluoride in toothpaste and in nature|url=http://www.sciencedaily.com/releases/2011/12/111222142450.htm|accessdate=24 February 2013|newspaper=ScienceDaily|date=2011, December 23}}</ref> These downstream genes transcribe fluoride sensitive enzymes such as enolase, pyrophosphatase, and a superfamily of CLC membrane proteins such as the crcB and ericF gene proteins.<ref name="Stockbridge2012">{{cite journal|last=Stockbridge|first=RB|coauthors=Lim HH, Otten R, Williams C, Shane T, Weinberg Z, Miller C|title=Fluoride resistance and transport by riboswitch-controlled CLC antiporters.|journal=Proc Natl Acad Sci U S A|date=18|year=2012|month=September|volume=109|issue=38|page=15289-94|pages=5|pmid=22949689|accessdate=25 February 2013}}</ref> The CLC proteins have been shown to function as fluoride transporters against fluoride toxicity.<ref name="Stockbridge2012"/> The ericF gene is a mutant version of the chloride channel gene that is less pervasive in bacteria but nonetheless found in the genome of S. mutans.<ref>{{cite journal|last=Breaker|first=R.R.|title=New Insight on the Response of Bacteria to Fluoride|journal=Caries Research|date=10|year=2012|month=February|volume=46|page=78-81|pages=3|doi=10.1159/000336397|url=http://www.karger.com/Article/Pdf/336397|accessdate=25 February 2013}}</ref> The ericF protein in particular carries specific amino acids in their channels that targets fluoride anions whereas the regular eric protein favored chloride over fluoride ions.<ref name="science2011" /> The CrcB proteins have been shown to be involved with chromosome condensation and camphor resistance<ref>{{cite journal|last=Hu|first=K.H.|coauthors=E. Liu, K. Dean, M. Gringras, W. DeGraff, N.J. Trun|title=Overproduction of three genes leads to camphor resistance and chromosome condensation in Escherichia coli.|journal=Genetics|year=1996|volume=143|page=1521-1532|pages=11|pmid=8844142|accessdate=25 February 2013}}</ref> but its existence in the CLC superfamily suggests that the CrcB proteins may also behave as fluoride transporters.<ref name="science2011" /> |
The identification of a fluoride-responsive riboswitch was accidently discovered when a compound contaminated with fluoride caused significant conformational changes to the non-coding crcB RNA motif during an in-line probing experiment.<ref name="Baker2012" /> The use of in-line probing was to help illuminate the secondary structure of the crcB RNA motif and its binding mechanisms to specific metabolites.<ref name="Regulski">{{cite journal|last=Regulski|first=EE|coauthors=Breaker RR|title=In-line probing analysis of riboswitches|journal=Methods molecular biology|month=2008|volume=419|page=53-67|pages=14|doi=10.1007/978-1-59745-033-1_4|pmid=18369975|url=http://www.ncbi.nlm.nih.gov/pubmed/18369975?dopt=Abstract&holding=npg|accessdate=24 February 2013}}</ref> The results of the probe showed the addition of increasing fluoride ion concentrations suppressing certain regions of spontaneous RNA cleavage and heightening other regions. These nucleotide regions in the crcB RNA motif play important roles in the aptamer binding region for fluoride.<ref name="Baker2012"/> |
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Upon binding fluoride ions, the fluoride riboswitch showed regulation of downstream gene transcription.<ref name="science2011">{{cite news|title=How bacteria fight fluoride in toothpaste and in nature|url=http://www.sciencedaily.com/releases/2011/12/111222142450.htm|accessdate=24 February 2013|newspaper=ScienceDaily|date=2011, December 23}}</ref> These downstream genes transcribe fluoride sensitive enzymes such as enolase, pyrophosphatase, and a superfamily of CLC membrane proteins such as the crcB and ericF gene proteins.<ref name="Stockbridge2012">{{cite journal|last=Stockbridge|first=RB|coauthors=Lim HH, Otten R, Williams C, Shane T, Weinberg Z, Miller C|title=Fluoride resistance and transport by riboswitch-controlled CLC antiporters.|journal=Proc Natl Acad Sci U S A|date=18|year=2012|month=September|volume=109|issue=38|page=15289-94|pages=5|pmid=22949689|accessdate=25 February 2013}}</ref> The CLC proteins have been shown to function as fluoride transporters against fluoride toxicity.<ref name="Stockbridge2012"/> The ericF gene is a mutant version of the chloride channel gene that is less pervasive in bacteria but nonetheless found in the genome of S. mutans.<ref>{{cite journal|last=Breaker|first=R.R.|title=New Insight on the Response of Bacteria to Fluoride|journal=Caries Research|date=10|year=2012|month=February|volume=46|page=78-81|pages=3|doi=10.1159/000336397|url=http://www.karger.com/Article/Pdf/336397|accessdate=25 February 2013}}</ref> The ericF protein in particular carries specific amino acids in their channels that targets fluoride anions whereas the regular eric protein favored chloride over fluoride ions.<ref name="science2011" /> The CrcB proteins have been shown to be involved with chromosome condensation and camphor resistance<ref>{{cite journal|last=Hu|first=K.H.|coauthors=E. Liu, K. Dean, M. Gringras, W. DeGraff, N.J. Trun|title=Overproduction of three genes leads to camphor resistance and chromosome condensation in Escherichia coli.|journal=Genetics|year=1996|volume=143|page=1521-1532|pages=11|pmid=8844142|accessdate=25 February 2013}}</ref> but its existence in the CLC superfamily suggests that the CrcB proteins may also behave as fluoride transporters.<ref name="science2011" /> |
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== Fluoride Riboswitch Structure == |
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The discovery of the fluoride riboswitch was surprising as both fluoride ions and the crcB RNA phosphate groups are negatively charged and should not be able to bind to one another.<ref name="science2011"/> Previous research came across this question in elucidating the cofactor thiamine pyrophosphate (TPP) riboswitch. The TPP riboswitch structure showed the assistance of two hydrated Mg2+ ions that help stabilize the connection between the phosphates of TPP and guanine bases of the RNA.<ref name="Serganov">{{cite journal|last=Serganov|first=A|coauthors=Polonskaia A, Phan AT, Breaker RR, Patel DJ|title=Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch.|journal=Nature|date=29|year=2006|month=June|volume=441|issue=7097|page=1167-71|pages=4|pmid=16728979|url=http://www.ncbi.nlm.nih.gov/pubmed/16728979|accessdate=25 February 2013}}</ref><ref name="Thore">{{cite journal|last=Thore|first=S|coauthors=Leibundgut M, Ban N|title=Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand.|journal=Science|date=26|year=2006|month=May|volume=312|issue=5777|page=1208-11|pages=3|pmid=16675665|accessdate=25 February 2013}}</ref> This guiding research help characterize the fluoride riboswitch’s own interactions with fluoride and its structure. Through in-line probing and mutational studies the fluoride riboswitch of the organism Thermotoga petrophila is recognized to have two helical stems adjoined by a helical loop with the capacity to become a pseudoknot.<ref name="Ren">{{cite journal|last=Ren|first=A|coauthors=Rajashankar KR, Patel DJ|title=Fluoride ion encapsulation by Mg2+ ions and phosphates in a fluoride riboswitch.|journal=Nature|date=13|year=2012|month=May|volume=486|issue=7401|page=85-9|pages=4|pmid=22678284|accessdate=25 February 2013}}</ref> The bound fluoride ligand is found to be located witin the center of the riboswitch fold, enclosed by three Mg2+ ions. The Mg2+ ions are octahedrally coordinated with five outer backbone phosphates and water molecules making a metabolite specific pocket for coordinating the fluoride ligand to bind. The placement of the Mg2+ ions cleverly positions the fluoride ion into the negatively charged crcB RNA scaffold.<ref name="Ren"/> |
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== Biological Significance == |
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In the earth’s crust, fluoride is the 13th most abundant element.<ref name="Baker2012"/> It is generally seen most pervasive in oral healthcare products and water.<ref name="science2011"/> The fluoride acts as a hardening agent with the enamel base on teeth, remineralizing and protecting them from harsh acids and bacteria in the oral cavity.<ref name="Wolfgang">{{cite journal|last=Wolfgang|first=Arnold|coauthors=Andreas Dorow, Stephanie Langenhorst, Zeno Gintner, Jolan Banoczy, Peter Gaengler|title=Effect of fluoride toothpastes on enamel demineralization|journal=BMC Oral Health|date=15|year=2006|month=June|volume=6|issue=8|doi=10.1186/1472-6831-6-8|pmid=16776820|accessdate=25 February 2013}}</ref> Additionally, its significance lies in the effect of the toxicity of fluoride at high concentrations to bacteria, especially those that cause dental caries. It has long been discovered that many species encapsulate a sensor system for toxic metals such as cadmium and silver.<ref name="Baker2012"/> However, a sensor system against fluoride has been elusive. The fluoride riboswitch elucidates the bacterial defense mechanism in counteracting against the toxicity of high concentrations of fluoride by regulating downstream genes of the riboswitch upon binding the fluoride ligand.<ref name="science2011"/> Further elucidating the mechanism of how bacteria protect itself from fluoride toxicity can help modify the mechanism to make smaller concentrations of fluoride even more lethal to bacteria. Additionally, the fluoride riboswitch and the downstream regulated genes can be potential targets for drug development in the future. Overall, these advancements will help towards making fluoride and future drugs strong protectors against oral health disease. |
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==References== |
==References== |
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<references/> |
<references/> |
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Revision as of 01:28, 25 February 2013
| crcB RNA motif | |
|---|---|
 Consensus secondary structure of crcB RNAs | |
| Identifiers | |
| Symbol | crcB RNA |
| Rfam | RF01734 |
| Other data | |
| RNA type | Cis-reg; riboswitch |
| Domain(s) | Prokaryota |
| PDB structures | PDBe |
The crcB RNA motif (now called the fluoride riboswitch) is a conserved RNA structure identified by bioinformatics in a wide variety of bacteria and archaea.[1] These RNAs were later shown to function as riboswitches that sense fluoride ions.[2] These "fluoride riboswitches" increase expression of downstream genes when fluoride levels are elevated, and the genes are proposed to help mitigate the toxic effects of very high levels of fluoride.
Many genes are presumed to be regulated by these fluoride riboswitches. Two of the most common encode proteins that are proposed to function by removing fluoride from the cell. These proteins are CrcB proteins and a fluoride-specific subtype of chloride channels referred to as EriC^F or ClC^F. ClC^F proteins have been shown to function as fluoride-specific fluoride/proton antiporters.[3]
The three dimensional structure of a fluoride riboswitch has been solved at atomic resolution by X-ray crystallography.[4]
Fluoride riboswitches are found in many organisms within the domains bacteria and archaea, indicating that many of these organisms sometimes encounter elevated levels of fluoride. Of particular interest is Streptococcus mutans, a major cause of dental caries. It has been shown that sodium fluoride has inhibited the growth rate of S. mutans using glucose as an energy and carbon source.[5] However, it is also noteworthy that many organisms that do not encounter fluoride in the human mouth carry fluoride riboswitches or resistance genes.
Discovery of the Fluoride Riboswitch
The identification of a fluoride-responsive riboswitch was accidently discovered when a compound contaminated with fluoride caused significant conformational changes to the non-coding crcB RNA motif during an in-line probing experiment.[2] The use of in-line probing was to help illuminate the secondary structure of the crcB RNA motif and its binding mechanisms to specific metabolites.[6] The results of the probe showed the addition of increasing fluoride ion concentrations suppressing certain regions of spontaneous RNA cleavage and heightening other regions. These nucleotide regions in the crcB RNA motif play important roles in the aptamer binding region for fluoride.[2]
Upon binding fluoride ions, the fluoride riboswitch showed regulation of downstream gene transcription.[7] These downstream genes transcribe fluoride sensitive enzymes such as enolase, pyrophosphatase, and a superfamily of CLC membrane proteins such as the crcB and ericF gene proteins.[8] The CLC proteins have been shown to function as fluoride transporters against fluoride toxicity.[8] The ericF gene is a mutant version of the chloride channel gene that is less pervasive in bacteria but nonetheless found in the genome of S. mutans.[9] The ericF protein in particular carries specific amino acids in their channels that targets fluoride anions whereas the regular eric protein favored chloride over fluoride ions.[7] The CrcB proteins have been shown to be involved with chromosome condensation and camphor resistance[10] but its existence in the CLC superfamily suggests that the CrcB proteins may also behave as fluoride transporters.[7]
Fluoride Riboswitch Structure
The discovery of the fluoride riboswitch was surprising as both fluoride ions and the crcB RNA phosphate groups are negatively charged and should not be able to bind to one another.[7] Previous research came across this question in elucidating the cofactor thiamine pyrophosphate (TPP) riboswitch. The TPP riboswitch structure showed the assistance of two hydrated Mg2+ ions that help stabilize the connection between the phosphates of TPP and guanine bases of the RNA.[11][12] This guiding research help characterize the fluoride riboswitch’s own interactions with fluoride and its structure. Through in-line probing and mutational studies the fluoride riboswitch of the organism Thermotoga petrophila is recognized to have two helical stems adjoined by a helical loop with the capacity to become a pseudoknot.[13] The bound fluoride ligand is found to be located witin the center of the riboswitch fold, enclosed by three Mg2+ ions. The Mg2+ ions are octahedrally coordinated with five outer backbone phosphates and water molecules making a metabolite specific pocket for coordinating the fluoride ligand to bind. The placement of the Mg2+ ions cleverly positions the fluoride ion into the negatively charged crcB RNA scaffold.[13]
Biological Significance
In the earth’s crust, fluoride is the 13th most abundant element.[2] It is generally seen most pervasive in oral healthcare products and water.[7] The fluoride acts as a hardening agent with the enamel base on teeth, remineralizing and protecting them from harsh acids and bacteria in the oral cavity.[14] Additionally, its significance lies in the effect of the toxicity of fluoride at high concentrations to bacteria, especially those that cause dental caries. It has long been discovered that many species encapsulate a sensor system for toxic metals such as cadmium and silver.[2] However, a sensor system against fluoride has been elusive. The fluoride riboswitch elucidates the bacterial defense mechanism in counteracting against the toxicity of high concentrations of fluoride by regulating downstream genes of the riboswitch upon binding the fluoride ligand.[7] Further elucidating the mechanism of how bacteria protect itself from fluoride toxicity can help modify the mechanism to make smaller concentrations of fluoride even more lethal to bacteria. Additionally, the fluoride riboswitch and the downstream regulated genes can be potential targets for drug development in the future. Overall, these advancements will help towards making fluoride and future drugs strong protectors against oral health disease.
References
- ^ Weinberg Z, Wang JX, Bogue J; et al. (2010). "Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea and their metagenomes". Genome Biol. 11 (3): R31. doi:10.1186/gb-2010-11-3-r31. PMC 2864571. PMID 20230605.
{{cite journal}}: Explicit use of et al. in:|author=(help); Unknown parameter|month=ignored (help)CS1 maint: multiple names: authors list (link) CS1 maint: unflagged free DOI (link) - ^ a b c d e Baker JL, Sudarsan N, Weinberg Z; et al. (2012). "Widespread genetic switches and toxicity resistance proteins for fluoride". Science. 335 (6065): 233–5. doi:10.1126/science.1215063. PMID 22194412.
{{cite journal}}: Explicit use of et al. in:|author=(help); Unknown parameter|month=ignored (help)CS1 maint: multiple names: authors list (link) - ^ Stockbridge RB, Lim HH, Otten R; et al. (2012). "Fluoride resistance and transport by riboswitch-controlled CLC antiporters". Proc. Natl. Acad. Sci. U.S.A. 109 (38): 15289–94. doi:10.1073/pnas.1210896109. PMID 22949689.
{{cite journal}}: Explicit use of et al. in:|author=(help); Unknown parameter|month=ignored (help)CS1 maint: multiple names: authors list (link) - ^ Ren A, Rajashankar KR, Patel DJ (2012). "Fluoride ion encapsulation by Mg2+ ions and phosphates in a fluoride riboswitch". Nature. 486 (7401): 85–9. doi:10.1038/nature11152. PMID 22678284.
{{cite journal}}: Unknown parameter|month=ignored (help)CS1 maint: multiple names: authors list (link) - ^ Yost, K G (1978). "Growth inhibition of Streptococcus mutans and Leuconostoc mesenteroides by sodium fluoride and ionic tin". Applied Environmental Microbiology. 5 (35): 920-924. PMID 655708. Retrieved 24 February 2013.
{{cite journal}}: More than one of|pages=and|page=specified (help); Unknown parameter|coauthors=ignored (|author=suggested) (help); Unknown parameter|month=ignored (help) - ^ Regulski, EE. "In-line probing analysis of riboswitches". Methods molecular biology. 419: 53-67. doi:10.1007/978-1-59745-033-1_4. PMID 18369975. Retrieved 24 February 2013.
{{cite journal}}: More than one of|pages=and|page=specified (help); Unknown parameter|coauthors=ignored (|author=suggested) (help); Unknown parameter|month=ignored (help) - ^ a b c d e f "How bacteria fight fluoride in toothpaste and in nature". ScienceDaily. 2011, December 23. Retrieved 24 February 2013.
{{cite news}}: Check|url=value (help); Check date values in:|date=(help); soft hyphen character in|url=at position 28 (help) - ^ a b Stockbridge, RB (18). "Fluoride resistance and transport by riboswitch-controlled CLC antiporters". Proc Natl Acad Sci U S A. 109 (38): 15289-94. PMID 22949689.
{{cite journal}}:|access-date=requires|url=(help); Check date values in:|date=and|year=/|date=mismatch (help); More than one of|pages=and|page=specified (help); Unknown parameter|coauthors=ignored (|author=suggested) (help); Unknown parameter|month=ignored (help) - ^ Breaker, R.R. (10). "New Insight on the Response of Bacteria to Fluoride". Caries Research. 46: 78-81. doi:10.1159/000336397. Retrieved 25 February 2013.
{{cite journal}}: Check date values in:|date=and|year=/|date=mismatch (help); More than one of|pages=and|page=specified (help); Unknown parameter|month=ignored (help) - ^ Hu, K.H. (1996). "Overproduction of three genes leads to camphor resistance and chromosome condensation in Escherichia coli". Genetics. 143: 1521-1532. PMID 8844142.
{{cite journal}}:|access-date=requires|url=(help); More than one of|pages=and|page=specified (help); Unknown parameter|coauthors=ignored (|author=suggested) (help) - ^ Serganov, A (29). "Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch". Nature. 441 (7097): 1167-71. PMID 16728979. Retrieved 25 February 2013.
{{cite journal}}: Check date values in:|date=and|year=/|date=mismatch (help); More than one of|pages=and|page=specified (help); Unknown parameter|coauthors=ignored (|author=suggested) (help); Unknown parameter|month=ignored (help) - ^ Thore, S (26). "Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand". Science. 312 (5777): 1208-11. PMID 16675665.
{{cite journal}}:|access-date=requires|url=(help); Check date values in:|date=and|year=/|date=mismatch (help); More than one of|pages=and|page=specified (help); Unknown parameter|coauthors=ignored (|author=suggested) (help); Unknown parameter|month=ignored (help) - ^ a b Ren, A (13). "Fluoride ion encapsulation by Mg2+ ions and phosphates in a fluoride riboswitch". Nature. 486 (7401): 85-9. PMID 22678284.
{{cite journal}}:|access-date=requires|url=(help); Check date values in:|date=and|year=/|date=mismatch (help); More than one of|pages=and|page=specified (help); Unknown parameter|coauthors=ignored (|author=suggested) (help); Unknown parameter|month=ignored (help) - ^ Wolfgang, Arnold (15). "Effect of fluoride toothpastes on enamel demineralization". BMC Oral Health. 6 (8). doi:10.1186/1472-6831-6-8. PMID 16776820.
{{cite journal}}:|access-date=requires|url=(help); Check date values in:|date=and|year=/|date=mismatch (help); Unknown parameter|coauthors=ignored (|author=suggested) (help); Unknown parameter|month=ignored (help)CS1 maint: unflagged free DOI (link)