Sandbox Reserved 402 - Revision history

Clarence Barnes at 14:53, 2 May 2011

Clarence Barnes — Mon, 02 May 2011 14:53:33 GMT

←Older revision		Revision as of 14:53, 2 May 2011
Line 6:		Line 6:
	== Guanine Riboswitch ==		== Guanine Riboswitch ==
	'''		'''
-	Riboswitches are highly conserved metabolite binding domains that are present in the 5'-UTR of certain mRNAs in bacteria which can act in the absence of protein cofactors. Riboswitches have been found to be broadly distributed among all forms of life, but all most frequently found in bacteria. These structural elements bind specific metabolites in the aptamer (binding site) domain that results in allosteric rearrangement in the adjacent expression platform that interacts with RNA elements to regulate gene expression associated with biosythesis and transport. In bacteria, riboswitches account for the regulation of 2% of the genes, thus making them attractive for genetic research.	+	Riboswitches are highly conserved metabolite binding domains that are present in the 5'-untranslated region (5'-UTR) of certain mRNAs in bacteria which can act in the absence of protein cofactors. Riboswitches have been found to be broadly distributed among all forms of life, but all most frequently found in bacteria. These structural elements bind specific metabolites in the aptamer (binding site) domain that results in allosteric rearrangement in the adjacent expression platform that interacts with RNA elements to regulate gene expression associated with biosythesis and transport. In bacteria, riboswitches account for the regulation of 2% of the genes, thus making them attractive for genetic research.
-	Within the bacterium, Bacillus subtilus, the guanine riboswitch is found. The <scene name='Sandbox_Reserved_402/Initial_structure_with_bases/2'>guanine riboswitch</scene> operates by the binding of a guanine, hypoxanthine, or xanthine to the aptamer domain. Through allosteric effects the aptamer then changes the conformation of the expression platform which results in the premature termination of transcription. Thus, the guanine riboswitch has two distinct conformations in which it operates: a metabolite bound and metabolite-free folds, involving the alternative base-pairing of the regulatory RNA region.<ref>PMID: 15610857 </ref>	+	Within the bacterium, ''Bacillus subtilus'', the guanine riboswitch is found. The <scene name='Sandbox_Reserved_402/Initial_structure_with_bases/2'>guanine riboswitch</scene> operates by the binding of a guanine, hypoxanthine, or xanthine to the aptamer domain. Through allosteric effects the aptamer then changes the conformation of the expression platform which results in the premature termination of transcription. Thus, the guanine riboswitch has two distinct conformations in which it operates: a metabolite bound and metabolite-free folds, involving the alternative base-pairing of the regulatory RNA region.<ref>PMID: 15610857 </ref>

Clarence Barnes at 16:57, 28 April 2011

Clarence Barnes — Thu, 28 Apr 2011 16:57:49 GMT

←Older revision		Revision as of 16:57, 28 April 2011
Line 11:		Line 11:

	== Riboswitch Structure ==		== Riboswitch Structure ==
-	The guanine riboswitch is comprised of three helices which are labeled P1, P2, and P3 which connect to form a junction. It is within this junction that ligand binding occurs. When the g-riboswitch-guanine complex is formed the kissing interactions of two hairpin loops force P2 and P3 to align in a parallel fashion and form hydrogen bonds. The <scene name='Sandbox_Reserved_402/Binding_site/1'>ligand</scene> is bound to the junction within the guanine riboswitch via several hydrogen bonds to nucleotides U22, U47, U51, C74. Due to the compactness of the binding site the ligand must utilize the induced-fit binding mechanism. <ref>PMID: 17175531 </ref>	+	The guanine riboswitch is comprised of three helices which are labeled P1, P2, and P3 which connect to form a junction. It is within this junction that ligand binding occurs. When the g-riboswitch-guanine complex is formed the kissing interactions of two hairpin loops force P2 and P3 to align in a parallel fashion and form hydrogen bonds. The <scene name='Sandbox_Reserved_402/Binding_site/2'>ligand</scene> is bound to the junction within the guanine riboswitch via several hydrogen bonds to nucleotides U22, U47, U51, C74. Due to the compactness of the binding site the ligand must utilize the induced-fit binding mechanism. <ref>PMID: 17175531 </ref>

Clarence Barnes at 23:28, 24 April 2011

Clarence Barnes — Sun, 24 Apr 2011 23:28:05 GMT

←Older revision		Revision as of 23:28, 24 April 2011
Line 6:		Line 6:
	== Guanine Riboswitch ==		== Guanine Riboswitch ==
	'''		'''
-	Riboswitches are highly conserved metabolite binding domains that are present in the 5'-UTR of certain mRNAs in bacteria which can act in the absence of protein cofactors. Riboswitches have been found to be broadly distributed among all forms of life, but all most frequently found in bacteria. ~~In the bacterium, Bacilus subtilus, riboswitches account for the regulation of 2% of the genes, thus making them attractive for genetic research.~~ These structural elements bind specific metabolites in the aptamer (binding site) domain that results in allosteric rearrangement in the adjacent expression platform that interacts with RNA elements to regulate gene expression associated with biosythesis and transport.	+	Riboswitches are highly conserved metabolite binding domains that are present in the 5'-UTR of certain mRNAs in bacteria which can act in the absence of protein cofactors. Riboswitches have been found to be broadly distributed among all forms of life, but all most frequently found in bacteria. These structural elements bind specific metabolites in the aptamer (binding site) domain that results in allosteric rearrangement in the adjacent expression platform that interacts with RNA elements to regulate gene expression associated with biosythesis and transport. In bacteria, riboswitches account for the regulation of 2% of the genes, thus making them attractive for genetic research.
-	The <scene name='Sandbox_Reserved_402/Initial_structure_with_bases/2'>guanine riboswitch</scene> operates by the binding of a guanine, hypoxanthine, or xanthine to the aptamer domain. Through allosteric effects the aptamer then changes the conformation of the expression platform which results in the premature termination of transcription. Thus, the guanine riboswitch has two distinct conformations in which it operates: a metabolite bound and metabolite-free folds, involving the alternative base-pairing of the regulatory RNA region.<ref>PMID: 15610857 </ref>	+	Within the bacterium, Bacillus subtilus, the guanine riboswitch is found. The <scene name='Sandbox_Reserved_402/Initial_structure_with_bases/2'>guanine riboswitch</scene> operates by the binding of a guanine, hypoxanthine, or xanthine to the aptamer domain. Through allosteric effects the aptamer then changes the conformation of the expression platform which results in the premature termination of transcription. Thus, the guanine riboswitch has two distinct conformations in which it operates: a metabolite bound and metabolite-free folds, involving the alternative base-pairing of the regulatory RNA region.<ref>PMID: 15610857 </ref>


Line 19:		Line 19:
	Metabolite-binding riboswitches are triggered if a high concentration of the metabolite is present within the cell. Under these conditions, the metabolite will interact with the aptamer domain, with high affinity and selectivity, which will then stabilize the metabolite bound fold in the nascent RNA, and in so doing prevents the formation of the metabolite-free fold. This typically results in the stabilization or disruption of a regulatory hairpin, which prematurely terminates transcription or sequesters the ribosome-binding site, thereby regulating gene expression. In the absence of the metabolite when the 5’-UTR is transcribed the riboswitch folds into the metabolite-free fold which does not interfere with the expression of the adjacent open reading frame.		Metabolite-binding riboswitches are triggered if a high concentration of the metabolite is present within the cell. Under these conditions, the metabolite will interact with the aptamer domain, with high affinity and selectivity, which will then stabilize the metabolite bound fold in the nascent RNA, and in so doing prevents the formation of the metabolite-free fold. This typically results in the stabilization or disruption of a regulatory hairpin, which prematurely terminates transcription or sequesters the ribosome-binding site, thereby regulating gene expression. In the absence of the metabolite when the 5’-UTR is transcribed the riboswitch folds into the metabolite-free fold which does not interfere with the expression of the adjacent open reading frame.
	In Bacillus subtilis, the 5'-UTR of xpt-pbuX mRNA binds guanine with high precision to down regulate the expression of genes by forming transcription terminator structures. Due to the mechanism and function of riboswitches, they are an attractive target for drug development. <ref>PMID: 15610857 </ref>		In Bacillus subtilis, the 5'-UTR of xpt-pbuX mRNA binds guanine with high precision to down regulate the expression of genes by forming transcription terminator structures. Due to the mechanism and function of riboswitches, they are an attractive target for drug development. <ref>PMID: 15610857 </ref>
		+
		+
		+
		+	== References ==
		+
		+
		+	<references/>

Clarence Barnes at 23:18, 24 April 2011

Clarence Barnes — Sun, 24 Apr 2011 23:18:35 GMT

←Older revision		Revision as of 23:18, 24 April 2011
Line 6:		Line 6:
	== Guanine Riboswitch ==		== Guanine Riboswitch ==
	'''		'''
-	Riboswitches are highly conserved metabolite binding domains that are present in the 5'-UTR of certain mRNAs in bacteria. These structural elements bind specific metabolites in the aptamer (binding site) domain that results in allosteric rearrangement in the adjacent expression platform that interacts with RNA elements to regulate gene expression associated with biosythesis and transport.The <scene name='Sandbox_Reserved_402/Initial_structure_with_bases/2'>guanine riboswitch</scene> operates by the binding of a ~~metabolite~~ to the aptamer domain ~~which is highly conserved~~. Through allosteric effects the aptamer then changes the conformation of the expression platform which results in the premature termination of transcription~~, inhibition of translation initiation, or mRNA self-cleavage~~. Thus, ~~riboswitches have~~ two distinct conformations in which ~~they operate~~: a metabolite bound and metabolite-free folds, involving the alternative base-pairing of the regulatory RNA region.<ref>PMID: 15610857 </ref>	+	Riboswitches are highly conserved metabolite binding domains that are present in the 5'-UTR of certain mRNAs in bacteria which can act in the absence of protein cofactors. Riboswitches have been found to be broadly distributed among all forms of life, but all most frequently found in bacteria. In the bacterium, Bacilus subtilus, riboswitches account for the regulation of 2% of the genes, thus making them attractive for genetic research. These structural elements bind specific metabolites in the aptamer (binding site) domain that results in allosteric rearrangement in the adjacent expression platform that interacts with RNA elements to regulate gene expression associated with biosythesis and transport.
		+	The <scene name='Sandbox_Reserved_402/Initial_structure_with_bases/2'>guanine riboswitch</scene> operates by the binding of a guanine, hypoxanthine, or xanthine to the aptamer domain. Through allosteric effects the aptamer then changes the conformation of the expression platform which results in the premature termination of transcription. Thus, the guanine riboswitch has two distinct conformations in which it operates: a metabolite bound and metabolite-free folds, involving the alternative base-pairing of the regulatory RNA region.<ref>PMID: 15610857 </ref>


Line 17:		Line 18:

	Metabolite-binding riboswitches are triggered if a high concentration of the metabolite is present within the cell. Under these conditions, the metabolite will interact with the aptamer domain, with high affinity and selectivity, which will then stabilize the metabolite bound fold in the nascent RNA, and in so doing prevents the formation of the metabolite-free fold. This typically results in the stabilization or disruption of a regulatory hairpin, which prematurely terminates transcription or sequesters the ribosome-binding site, thereby regulating gene expression. In the absence of the metabolite when the 5’-UTR is transcribed the riboswitch folds into the metabolite-free fold which does not interfere with the expression of the adjacent open reading frame.		Metabolite-binding riboswitches are triggered if a high concentration of the metabolite is present within the cell. Under these conditions, the metabolite will interact with the aptamer domain, with high affinity and selectivity, which will then stabilize the metabolite bound fold in the nascent RNA, and in so doing prevents the formation of the metabolite-free fold. This typically results in the stabilization or disruption of a regulatory hairpin, which prematurely terminates transcription or sequesters the ribosome-binding site, thereby regulating gene expression. In the absence of the metabolite when the 5’-UTR is transcribed the riboswitch folds into the metabolite-free fold which does not interfere with the expression of the adjacent open reading frame.
-	In Bacillus subtilis, the 5'-UTR of xpt-pbuX mRNA binds guanine with high precision to down regulate the expression of genes by forming transcription terminator structures. ~~<ref>PMID: 15610857 </ref>~~	+	In Bacillus subtilis, the 5'-UTR of xpt-pbuX mRNA binds guanine with high precision to down regulate the expression of genes by forming transcription terminator structures. Due to the mechanism and function of riboswitches, they are an attractive target for drug development. <ref>PMID: 15610857 </ref>
-		+
-	~~[[Image:Mechanism_of_action_of_guanine riboswitch.jpg\|thumb\|350px\|left\|Mechanism~~ of ~~Action~~ for ~~Guanine Riboswitch~~.<ref> ~~Mechanism of Action of Tetanospasmin (Catherine Wakeman) [image on the internet]. 2005[updated 2005 August 30; cited 2011 Apr 24]. Available from~~: ~~http://en.wikipedia.org/wiki/File:Mechanism_of_action_of_tetanospasmin.gif~~</ref>]]	+

Clarence Barnes at 17:09, 24 April 2011

Clarence Barnes — Sun, 24 Apr 2011 17:09:58 GMT

←Older revision		Revision as of 17:09, 24 April 2011
Line 19:		Line 19:
	In Bacillus subtilis, the 5'-UTR of xpt-pbuX mRNA binds guanine with high precision to down regulate the expression of genes by forming transcription terminator structures. <ref>PMID: 15610857 </ref>		In Bacillus subtilis, the 5'-UTR of xpt-pbuX mRNA binds guanine with high precision to down regulate the expression of genes by forming transcription terminator structures. <ref>PMID: 15610857 </ref>

-	[[Image:~~Mechanism_of_action_of_tetanospasmin~~.jpg\|thumb\|350px\|left\|Mechanism of Action for ~~Tetanospasmin~~.<ref> Mechanism of Action of Tetanospasmin (~~Dr. Arnab K Rana~~) [image on the internet]. 2005[updated 2005 ~~Dec 26~~; cited 2011 Apr 20]. Available from: http://en.wikipedia.org/wiki/File:Mechanism_of_action_of_tetanospasmin.gif</ref>]]	+	[[Image:Mechanism_of_action_of_guanine riboswitch.jpg\|thumb\|350px\|left\|Mechanism of Action for Guanine Riboswitch.<ref> Mechanism of Action of Tetanospasmin (Catherine Wakeman) [image on the internet]. 2005[updated 2005 August 30; cited 2011 Apr 24]. Available from: http://en.wikipedia.org/wiki/File:Mechanism_of_action_of_tetanospasmin.gif</ref>]]

Clarence Barnes at 17:02, 24 April 2011

Clarence Barnes — Sun, 24 Apr 2011 17:02:46 GMT

←Older revision		Revision as of 17:02, 24 April 2011
Line 19:		Line 19:
	In Bacillus subtilis, the 5'-UTR of xpt-pbuX mRNA binds guanine with high precision to down regulate the expression of genes by forming transcription terminator structures. <ref>PMID: 15610857 </ref>		In Bacillus subtilis, the 5'-UTR of xpt-pbuX mRNA binds guanine with high precision to down regulate the expression of genes by forming transcription terminator structures. <ref>PMID: 15610857 </ref>

-	[[Image:~~guanine mechanism~~.jpg]]	+	[[Image:Mechanism_of_action_of_tetanospasmin.jpg\|thumb\|350px\|left\|Mechanism of Action for Tetanospasmin.<ref> Mechanism of Action of Tetanospasmin (Dr. Arnab K Rana) [image on the internet]. 2005[updated 2005 Dec 26; cited 2011 Apr 20]. Available from: http://en.wikipedia.org/wiki/File:Mechanism_of_action_of_tetanospasmin.gif</ref>]]

Clarence Barnes at 16:53, 24 April 2011

Clarence Barnes — Sun, 24 Apr 2011 16:53:40 GMT

←Older revision		Revision as of 16:53, 24 April 2011
Line 18:		Line 18:
	Metabolite-binding riboswitches are triggered if a high concentration of the metabolite is present within the cell. Under these conditions, the metabolite will interact with the aptamer domain, with high affinity and selectivity, which will then stabilize the metabolite bound fold in the nascent RNA, and in so doing prevents the formation of the metabolite-free fold. This typically results in the stabilization or disruption of a regulatory hairpin, which prematurely terminates transcription or sequesters the ribosome-binding site, thereby regulating gene expression. In the absence of the metabolite when the 5’-UTR is transcribed the riboswitch folds into the metabolite-free fold which does not interfere with the expression of the adjacent open reading frame.		Metabolite-binding riboswitches are triggered if a high concentration of the metabolite is present within the cell. Under these conditions, the metabolite will interact with the aptamer domain, with high affinity and selectivity, which will then stabilize the metabolite bound fold in the nascent RNA, and in so doing prevents the formation of the metabolite-free fold. This typically results in the stabilization or disruption of a regulatory hairpin, which prematurely terminates transcription or sequesters the ribosome-binding site, thereby regulating gene expression. In the absence of the metabolite when the 5’-UTR is transcribed the riboswitch folds into the metabolite-free fold which does not interfere with the expression of the adjacent open reading frame.
	In Bacillus subtilis, the 5'-UTR of xpt-pbuX mRNA binds guanine with high precision to down regulate the expression of genes by forming transcription terminator structures. <ref>PMID: 15610857 </ref>		In Bacillus subtilis, the 5'-UTR of xpt-pbuX mRNA binds guanine with high precision to down regulate the expression of genes by forming transcription terminator structures. <ref>PMID: 15610857 </ref>
		+
		+	[[Image:guanine mechanism.jpg]]

Clarence Barnes at 03:00, 24 April 2011

Clarence Barnes — Sun, 24 Apr 2011 03:00:38 GMT

←Older revision		Revision as of 03:00, 24 April 2011
Line 2:		Line 2:
	{{Template:Sandbox_Reserved_JMeans}}		{{Template:Sandbox_Reserved_JMeans}}
	<!-- PLEASE ADD YOUR CONTENT BELOW HERE -->		<!-- PLEASE ADD YOUR CONTENT BELOW HERE -->
-	<Structure load='1Y27' size='400' frame='true' align='right' caption='Guanine Riboswitch' scene='Insert optional scene name here' />	+	<Structure load='1Y27' size='400' frame='true' align='right' caption='Guanine-Riboswitch-Guanine complex' scene='Insert optional scene name here' />
	'''		'''
	== Guanine Riboswitch ==		== Guanine Riboswitch ==
Line 17:		Line 17:

	Metabolite-binding riboswitches are triggered if a high concentration of the metabolite is present within the cell. Under these conditions, the metabolite will interact with the aptamer domain, with high affinity and selectivity, which will then stabilize the metabolite bound fold in the nascent RNA, and in so doing prevents the formation of the metabolite-free fold. This typically results in the stabilization or disruption of a regulatory hairpin, which prematurely terminates transcription or sequesters the ribosome-binding site, thereby regulating gene expression. In the absence of the metabolite when the 5’-UTR is transcribed the riboswitch folds into the metabolite-free fold which does not interfere with the expression of the adjacent open reading frame.		Metabolite-binding riboswitches are triggered if a high concentration of the metabolite is present within the cell. Under these conditions, the metabolite will interact with the aptamer domain, with high affinity and selectivity, which will then stabilize the metabolite bound fold in the nascent RNA, and in so doing prevents the formation of the metabolite-free fold. This typically results in the stabilization or disruption of a regulatory hairpin, which prematurely terminates transcription or sequesters the ribosome-binding site, thereby regulating gene expression. In the absence of the metabolite when the 5’-UTR is transcribed the riboswitch folds into the metabolite-free fold which does not interfere with the expression of the adjacent open reading frame.
-	In Bacillus subtilis, the 5'-UTR of xpt-pbuX mRNA binds guanine with high precision to down-regulate the expression of genes by forming transcription terminator structures.	+	In Bacillus subtilis, the 5'-UTR of xpt-pbuX mRNA binds guanine with high precision to down regulate the expression of genes by forming transcription terminator structures. <ref>PMID: 15610857 </ref>

Clarence Barnes at 02:24, 24 April 2011

Clarence Barnes — Sun, 24 Apr 2011 02:24:51 GMT

←Older revision		Revision as of 02:24, 24 April 2011
Line 10:		Line 10:

	== Riboswitch Structure ==		== Riboswitch Structure ==
		+	The guanine riboswitch is comprised of three helices which are labeled P1, P2, and P3 which connect to form a junction. It is within this junction that ligand binding occurs. When the g-riboswitch-guanine complex is formed the kissing interactions of two hairpin loops force P2 and P3 to align in a parallel fashion and form hydrogen bonds. The <scene name='Sandbox_Reserved_402/Binding_site/1'>ligand</scene> is bound to the junction within the guanine riboswitch via several hydrogen bonds to nucleotides U22, U47, U51, C74. Due to the compactness of the binding site the ligand must utilize the induced-fit binding mechanism. <ref>PMID: 17175531 </ref>
		+


		+	== Regulation Mechanism ==

-		+	Metabolite-binding riboswitches are triggered if a high concentration of the metabolite is present within the cell. Under these conditions, the metabolite will interact with the aptamer domain, with high affinity and selectivity, which will then stabilize the metabolite bound fold in the nascent RNA, and in so doing prevents the formation of the metabolite-free fold. This typically results in the stabilization or disruption of a regulatory hairpin, which prematurely terminates transcription or sequesters the ribosome-binding site, thereby regulating gene expression. In the absence of the metabolite when the 5’-UTR is transcribed the riboswitch folds into the metabolite-free fold which does not interfere with the expression of the adjacent open reading frame.
-		+
-		+
-		+
	In Bacillus subtilis, the 5'-UTR of xpt-pbuX mRNA binds guanine with high precision to down-regulate the expression of genes by forming transcription terminator structures.		In Bacillus subtilis, the 5'-UTR of xpt-pbuX mRNA binds guanine with high precision to down-regulate the expression of genes by forming transcription terminator structures.

Clarence Barnes at 01:45, 24 April 2011

Clarence Barnes — Sun, 24 Apr 2011 01:45:24 GMT

←Older revision		Revision as of 01:45, 24 April 2011
Line 6:		Line 6:
	== Guanine Riboswitch ==		== Guanine Riboswitch ==
	'''		'''
-	Riboswitches are highly conserved metabolite binding domains that are present in the 5'-UTR of certain mRNAs in bacteria. These structural elements bind specific metabolites in the aptamer (binding site) domain that results in allosteric rearrangement in the adjacent expression platform that interacts with RNA elements to regulate gene expression associated with biosythesis and transport.The <scene name='Sandbox_Reserved_402/Initial_structure_with_bases/1'>guanine riboswitch</scene> operates by the binding of a metabolite to the aptamer domain which is highly conserved. Through allosteric effects the aptamer then changes the conformation of the expression platform which results in the premature termination of transcription, inhibition of translation initiation, or mRNA self-cleavage. Thus, riboswitches have two distinct conformations in which they operate: a metabolite bound and metabolite-free folds, involving the alternative base-pairing of the regulatory RNA region.<ref>PMID: 15610857 </ref>	+	Riboswitches are highly conserved metabolite binding domains that are present in the 5'-UTR of certain mRNAs in bacteria. These structural elements bind specific metabolites in the aptamer (binding site) domain that results in allosteric rearrangement in the adjacent expression platform that interacts with RNA elements to regulate gene expression associated with biosythesis and transport.The <scene name='Sandbox_Reserved_402/Initial_structure_with_bases/2'>guanine riboswitch</scene> operates by the binding of a metabolite to the aptamer domain which is highly conserved. Through allosteric effects the aptamer then changes the conformation of the expression platform which results in the premature termination of transcription, inhibition of translation initiation, or mRNA self-cleavage. Thus, riboswitches have two distinct conformations in which they operate: a metabolite bound and metabolite-free folds, involving the alternative base-pairing of the regulatory RNA region.<ref>PMID: 15610857 </ref>