User:Mitchell Long/Sandbox 1 - Revision history

Mitchell Long at 23:20, 17 November 2011

2011-11-17T23:20:40Z

←Older revision		Revision as of 23:20, 17 November 2011
Line 21:		Line 21:
	<p>'''Structure homology'''-There is a great deal of sequence homology and structural coservation between the α and β subunits. When superimposed over the barrels of the alpha and beta subunits with a deviation of 0.62Å for 42 equivalent α carbons. The region of the beta subunit that contains the 29 residue deletion with respect to the alpha subunit differs notably in arrangement<ref name=Fisher, A.J.>PMID: 7756289</ref> . In the alpha subunit, the α7a helix is straight and extends toward the beta subunit. The region involved with dimerization, helices α and β are exceptionally similar in superposition.		<p>'''Structure homology'''-There is a great deal of sequence homology and structural coservation between the α and β subunits. When superimposed over the barrels of the alpha and beta subunits with a deviation of 0.62Å for 42 equivalent α carbons. The region of the beta subunit that contains the 29 residue deletion with respect to the alpha subunit differs notably in arrangement<ref name=Fisher, A.J.>PMID: 7756289</ref> . In the alpha subunit, the α7a helix is straight and extends toward the beta subunit. The region involved with dimerization, helices α and β are exceptionally similar in superposition.
	</p>		</p>
-	<p>'''Active Site and Alpha Subunit'''-the <scene name='User:Mitchell_Long/Sandbox_1/Yellow_sheets/1'>flavin binding pocket</scene> of bacterial luciferase is a large open cavity that is accessible to solvent via an opening located at the C-terminal ends of the ǰ ~~strans~~ of the TIM-barrel structure. During the first step of the oxidation reaction, FMNH<sub>2</sub> binds to the flavin binding pocket and the enzyme undergoes a conformational change that blocks water in the surrounding environment from accessing both the excited peroxydihydroflavin intermediate. Next O<sub>2</sub> and a long chain aldehyde bind to the FMNH<sub>2</sub> luciferase complex and a two step oxidatino reaction occurs.	+	<p>'''Active Site and Alpha Subunit'''-the <scene name='User:Mitchell_Long/Sandbox_1/Yellow_sheets/1'>flavin binding pocket</scene> of bacterial luciferase is a large open cavity that is accessible to solvent via an opening located at the C-terminal ends of the ǰ strands of the TIM-barrel structure<ref Campbell, Z.T.>PMID: 19435287</ref>. During the first step of the oxidation reaction, FMNH<sub>2</sub> binds to the flavin binding pocket and the enzyme undergoes a conformational change that blocks water in the surrounding environment from accessing both the excited peroxydihydroflavin intermediate. Next, O<sub>2</sub> and a long chain aldehyde bind to the FMNH<sub>2</sub> luciferase complex and a two step oxidatino reaction occurs.
	.</p>		.</p>
	<scene name='User:Mitchell_Long/Sandbox_1/Hetero_translucent/1'>Heterodimer</scene>		<scene name='User:Mitchell_Long/Sandbox_1/Hetero_translucent/1'>Heterodimer</scene>

Mitchell Long at 23:18, 17 November 2011

2011-11-17T23:18:06Z

←Older revision		Revision as of 23:18, 17 November 2011
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	<p><scene name='User:Mitchell_Long/Sandbox_1/Phe272_tyr151_interface/1'>Phe 272 Tyr 151 interface</scene></p>		<p><scene name='User:Mitchell_Long/Sandbox_1/Phe272_tyr151_interface/1'>Phe 272 Tyr 151 interface</scene></p>

-	<p>'''The β subunit'''-The beta subunit is characterized as a necessary but non-catalytic subunit that stabilizes the catalytic &#~~495~~; subunit that is responsible for the oxidation reaction. The beta and alpha subunits are connected by a single interaction between the <scene name='User:Mitchell_Long/Sandbox_1/Phe272_tyr151_interface/1'>Phe 272 Tyr 151 interface</scene>	+	<p>'''The β subunit'''-The beta subunit is characterized as a necessary but non-catalytic subunit that stabilizes the catalytic α subunit that is responsible for the oxidation reaction. The beta and alpha subunits are connected by a single interaction between the <scene name='User:Mitchell_Long/Sandbox_1/Phe272_tyr151_interface/1'>Phe 272 Tyr 151 interface</scene>
	</p>		</p>

Mitchell Long at 23:16, 17 November 2011

2011-11-17T23:16:50Z

←Older revision		Revision as of 23:16, 17 November 2011
Line 6:		Line 6:

	==Mechanism==		==Mechanism==
-	Luciferase found in''''V. Harveyi'''' binds noncovalently to a reduced flavin mononucleotide cofactor, an aliphatic aldehyde and oxygen to yield oxidized flavin mononucleotide, water, and carboxylic acid. The reaction occurs in two steps forming a hydroxyflavin intermediate and ultimately results in the oxidation of the aldehyde and emission of photons	+	Luciferase found in''''V. Harveyi'''' binds noncovalently to a reduced flavin mononucleotide cofactor, an aliphatic aldehyde and oxygen to yield oxidized flavin mononucleotide, water, and carboxylic acid. The reaction occurs in two steps forming a hydroxyflavin intermediate and ultimately results in the oxidation of the aldehyde and emission of photons<ref Campbell, Z.T.>PMID: 19435287</ref>.
	<p>FMNH<sub>2</sub>+O<sub>2</sub>+RCHO→FMN+RCOOH+H<sub>2</sub>O+hv(490nm)</p>		<p>FMNH<sub>2</sub>+O<sub>2</sub>+RCHO→FMN+RCOOH+H<sub>2</sub>O+hv(490nm)</p>

Mitchell Long at 23:14, 17 November 2011

2011-11-17T23:14:51Z

←Older revision		Revision as of 23:14, 17 November 2011
Line 19:		Line 19:


-	<p>'''Structure homology'''-There is a great deal of sequence homology and structural coservation between the α and β subunits. When superimposed over the barrels of the alpha and beta subunits with a deviation of 0.62Å for 42 equivalent α carbons. The region of the beta subunit that contains the 29 residue deletion with respect to the alpha subunit differs notably in arrangement. In the alpha subunit, the α7a helix is straight and extends toward the beta subunit. The region involved with dimerization, helices α and β are exceptionally similar in superposition.	+	<p>'''Structure homology'''-There is a great deal of sequence homology and structural coservation between the α and β subunits. When superimposed over the barrels of the alpha and beta subunits with a deviation of 0.62Å for 42 equivalent α carbons. The region of the beta subunit that contains the 29 residue deletion with respect to the alpha subunit differs notably in arrangement<ref name=Fisher, A.J.>PMID: 7756289</ref> . In the alpha subunit, the α7a helix is straight and extends toward the beta subunit. The region involved with dimerization, helices α and β are exceptionally similar in superposition.
	</p>		</p>
	<p>'''Active Site and Alpha Subunit'''-the <scene name='User:Mitchell_Long/Sandbox_1/Yellow_sheets/1'>flavin binding pocket</scene> of bacterial luciferase is a large open cavity that is accessible to solvent via an opening located at the C-terminal ends of the ǰ strans of the TIM-barrel structure. During the first step of the oxidation reaction, FMNH<sub>2</sub> binds to the flavin binding pocket and the enzyme undergoes a conformational change that blocks water in the surrounding environment from accessing both the excited peroxydihydroflavin intermediate. Next O<sub>2</sub> and a long chain aldehyde bind to the FMNH<sub>2</sub> luciferase complex and a two step oxidatino reaction occurs.		<p>'''Active Site and Alpha Subunit'''-the <scene name='User:Mitchell_Long/Sandbox_1/Yellow_sheets/1'>flavin binding pocket</scene> of bacterial luciferase is a large open cavity that is accessible to solvent via an opening located at the C-terminal ends of the ǰ strans of the TIM-barrel structure. During the first step of the oxidation reaction, FMNH<sub>2</sub> binds to the flavin binding pocket and the enzyme undergoes a conformational change that blocks water in the surrounding environment from accessing both the excited peroxydihydroflavin intermediate. Next O<sub>2</sub> and a long chain aldehyde bind to the FMNH<sub>2</sub> luciferase complex and a two step oxidatino reaction occurs.

Mitchell Long at 23:12, 17 November 2011

2011-11-17T23:12:28Z

←Older revision		Revision as of 23:12, 17 November 2011
Line 19:		Line 19:


-	<p>'''Structure homology'''-There is a great deal of sequence homology and structural coservation between the α and β subunits. When superimposed over the barrels of the alpha and beta subunits with a deviation of 0.62Å for 42 equivalent α carbons. The region of the beta subunit that contains the 29 residue deletion with respect to the alpha subunit differs notably in arrangement. In the alpha subunit, the α7a helix is straight and extends toward the beta subunit. The region involved with dimerization, helices α and β ~~and the hairpin loop structure~~ are exceptionally similar in superposition.	+	<p>'''Structure homology'''-There is a great deal of sequence homology and structural coservation between the α and β subunits. When superimposed over the barrels of the alpha and beta subunits with a deviation of 0.62Å for 42 equivalent α carbons. The region of the beta subunit that contains the 29 residue deletion with respect to the alpha subunit differs notably in arrangement. In the alpha subunit, the α7a helix is straight and extends toward the beta subunit. The region involved with dimerization, helices α and β are exceptionally similar in superposition.
	</p>		</p>
	<p>'''Active Site and Alpha Subunit'''-the <scene name='User:Mitchell_Long/Sandbox_1/Yellow_sheets/1'>flavin binding pocket</scene> of bacterial luciferase is a large open cavity that is accessible to solvent via an opening located at the C-terminal ends of the ǰ strans of the TIM-barrel structure. During the first step of the oxidation reaction, FMNH<sub>2</sub> binds to the flavin binding pocket and the enzyme undergoes a conformational change that blocks water in the surrounding environment from accessing both the excited peroxydihydroflavin intermediate. Next O<sub>2</sub> and a long chain aldehyde bind to the FMNH<sub>2</sub> luciferase complex and a two step oxidatino reaction occurs.		<p>'''Active Site and Alpha Subunit'''-the <scene name='User:Mitchell_Long/Sandbox_1/Yellow_sheets/1'>flavin binding pocket</scene> of bacterial luciferase is a large open cavity that is accessible to solvent via an opening located at the C-terminal ends of the ǰ strans of the TIM-barrel structure. During the first step of the oxidation reaction, FMNH<sub>2</sub> binds to the flavin binding pocket and the enzyme undergoes a conformational change that blocks water in the surrounding environment from accessing both the excited peroxydihydroflavin intermediate. Next O<sub>2</sub> and a long chain aldehyde bind to the FMNH<sub>2</sub> luciferase complex and a two step oxidatino reaction occurs.
Line 32:		Line 32:


-	<p>'''Mobile Loop'''- ~~Phe2772~~-~~thr~~ 288	+	<p>'''Mobile Loop'''- Residues 272-288 on the α are known as the mobile loop. This portion of the alpha subunit contains a single residue that forms a salt bridge with the beta subunit and stabilizes the active site<ref Campbell, Z.T.>PMID: 19435287</ref>.
-	(β/α)<SUB>8</SUB> Barrel- The tertiary structure of the α and β subunits is very similar. both subunits fold into a single-domain eight-stranded β/α barrel motif. the two subunits assemble around a parallel four-helix bundle centered on a pseudo 2-fold axis that relates the alpha and beta subunits.	+	</p>
		+	<p>
		+	(β/α)<SUB>8</SUB> TIM Barrel- The tertiary structure of the α and β subunits is very similar. While both the alpha and beta subunits are similar, the alpha subunit contains an extra 29 residues that the beta lacks. Both subunits fold into a single-domain eight-stranded β/α barrel motif. the two subunits assemble around a parallel four-helix bundle centered on a pseudo 2-fold axis that relates the alpha and beta subunits<ref Campbell, Z.T.>PMID: 19435287</ref>.
	.</p>		.</p>
	</StructureSection>		</StructureSection>

Mitchell Long at 22:39, 17 November 2011

2011-11-17T22:39:36Z

←Older revision		Revision as of 22:39, 17 November 2011
Line 2:		Line 2:

	==Introduction==		==Introduction==
-	Luciferases are a class of enzymes that catalyze the oxidation of a long chain aliphatic aldehydes the emission of blue-green light. The luciferase found in ''''Vibrio harveyi'''' is a heterodimer that is composed of a catalytic α subunit and a homologous but noncatalytic β subunit~~<ref Campbell, Z.T.>PMID: 19435287</ref>~~. This reaction results in the formation of a carboxylic acid, reduced flavinmononucleotide and the emission of photons in the form of blue-green light. The catalytic α subunit houses the active site and is connected to the β subunit via a single interatcion between the mobile loop and the α subunit at α Phe 272 and Tyr 151 of the β subunit~~<ref Campbell, Z.T.>PMID: 19435287</ref>~~.	+	Luciferases are a class of enzymes that catalyze the oxidation of a long chain aliphatic aldehydes the emission of blue-green light. The luciferase found in ''''Vibrio harveyi'''' is a heterodimer that is composed of a catalytic α subunit and a homologous but noncatalytic β subunit. This reaction results in the formation of a carboxylic acid, reduced flavinmononucleotide and the emission of photons in the form of blue-green light. The catalytic α subunit houses the active site and is connected to the β subunit via a single interatcion between the mobile loop and the α subunit at α Phe 272 and Tyr 151 of the β subunit.


Line 9:		Line 9:
	<p>FMNH<sub>2</sub>+O<sub>2</sub>+RCHO→FMN+RCOOH+H<sub>2</sub>O+hv(490nm)</p>		<p>FMNH<sub>2</sub>+O<sub>2</sub>+RCHO→FMN+RCOOH+H<sub>2</sub>O+hv(490nm)</p>

-	The catalytic α subunit houses the FMN cofactor and is connected to the β subunit via a hairpin structure called the "<scene name='User:Mitchell_Long/Sandbox_1/Protease_labile_region/3'>Mobile loop</scene>." The organic substrate for bacterial luciferase in vivo is myristic aldehyde, although many aliphatic aldehydes of various lengths can induce bioluminescence in vitro<ref name=Waters, C.M.>PMID: 17015436</ref>. Oxygen is needed for light generation, no bioluminescent activity occurs in anaerobic conditions.	+	The catalytic α subunit houses the FMN cofactor and is connected to the β subunit via a hairpin structure called the "<scene name='User:Mitchell_Long/Sandbox_1/Protease_labile_region/3'>Mobile loop</scene>." The organic substrate for bacterial luciferase in vivo is myristic aldehyde, although many aliphatic aldehydes of various lengths can induce bioluminescence in vitro<ref name=Waters, C.M.>PMID: 17015436</ref>. Oxygen is needed for light generation, no bioluminescent activity occurs in anaerobic conditions<ref name=Waters, C.M.>PMID: 17015436</ref>.

	<p><scene name='User:Mitchell_Long/Sandbox_1/Luciferase_w_out_cofactor/1'>Luciferase with no bound cofactor</scene> </p>		<p><scene name='User:Mitchell_Long/Sandbox_1/Luciferase_w_out_cofactor/1'>Luciferase with no bound cofactor</scene> </p>
Line 43:		Line 43:

	==Quorum Sensing==		==Quorum Sensing==
-	In a process known as quorum sensing, bacteria communicate using secreted signal molecules called autoinducers(AIs). ''''V. harveyi'''' is a mesophilic, gram negative, rod shaped bacteria that can communicate with other bacteria via quorum sensing. Quorum-sensing bacteria alter gene expression in response to the accumulation of AIs, which reflects an increase in cell population density. This process is believed to provide bacteria a means to coordinately control the gene expression of the group, giving them multicellular characteristics~~<ref name=Waters, C.M.>PMID: 17015436</ref>~~. When bacteria reach a "quorum," their population has reached a density high enough to coordinate gene expression. Often, bacteria make and respond to multiple AIs. Vibrio harveyi, a free-living marine bacterium, produces at least three distinct AIs to control bioluminescence, biofilm formation, Type III Secretion (TTS), and protease production~~<ref name=Waters, C.M.>PMID: 17015436</ref>~~. When a bacterial population density is low, the LuxI gene is transcribed constitutively at basal level. The three V. harveyi AIs are HAI-1, an acyl homoserine lactone; AI-2, a furanosyl-borate-diester; and CAI-1, of unknown structure. When the population density reaches an adequate level, the conjugate receptor LuxR begins transcription. LuxR is the regulatory receptor, and when an AI binds the the LuxR receptor, transcription is turned on resulting in the production of more AI and the expression of other genes involved in quorum sensing. When '''V. harveyi''' reaches a high enough population density, it's quorum sensing genes are activated and the transcription of the genes that code for the luciferase enzyme ~~and results in bioluminescence~~.	+	In a process known as quorum sensing, bacteria communicate using secreted signal molecules called autoinducers(AIs). ''''V. harveyi'''' is a mesophilic, gram negative, rod shaped bacteria that can communicate with other bacteria via quorum sensing. Quorum-sensing bacteria alter gene expression in response to the accumulation of AIs, which reflects an increase in cell population density<ref name=Waters, C.M.>PMID: 17015436</ref>. This process is believed to provide bacteria a means to coordinately control the gene expression of the group, giving them multicellular characteristics. When bacteria reach a "quorum," their population has reached a density high enough to coordinate gene expression<ref name=Waters, C.M.>PMID: 17015436</ref>. Often, bacteria make and respond to multiple AIs. Vibrio harveyi, a free-living marine bacterium, produces at least three distinct AIs to control bioluminescence, biofilm formation, Type III Secretion (TTS), and protease production. When a bacterial population density is low, the LuxI gene is transcribed constitutively at basal level. The three V. harveyi AIs are HAI-1, an acyl homoserine lactone; AI-2, a furanosyl-borate-diester; and CAI-1, of unknown structure<ref name=Waters, C.M.>PMID: 17015436</ref>. When the population density reaches an adequate level, the conjugate receptor LuxR begins transcription. LuxR is the regulatory receptor, and when an AI binds the the LuxR receptor, transcription is turned on resulting in the production of more AI and the expression of other genes involved in quorum sensing. When '''V. harveyi''' reaches a high enough population density, it's quorum sensing genes are activated and the transcription of the genes that code for the luciferase enzyme.
	<ref Campbell, Z.T.>PMID: 19435287</ref>		<ref Campbell, Z.T.>PMID: 19435287</ref>
	<ref name=Waters, C.M.>PMID: 17015436</ref>		<ref name=Waters, C.M.>PMID: 17015436</ref>

Mitchell Long at 22:32, 17 November 2011

2011-11-17T22:32:35Z

←Older revision		Revision as of 22:32, 17 November 2011
Line 2:		Line 2:

	==Introduction==		==Introduction==
-	Luciferases are a class of enzymes that catalyze the oxidation of a long chain aliphatic aldehydes the emission of blue-green light. The luciferase found in ''''Vibrio harveyi'''' is a heterodimer that is composed of a catalytic α subunit and a homologous but noncatalytic β subunit. This reaction results in the formation of a carboxylic acid, reduced flavinmononucleotide and the emission of photons in the form of blue-green light. The catalytic α subunit houses the active site and is connected to the β subunit via a single interatcion between the mobile loop and the α subunit at α Phe 272 and Tyr 151 of the β subunit.	+	Luciferases are a class of enzymes that catalyze the oxidation of a long chain aliphatic aldehydes the emission of blue-green light. The luciferase found in ''''Vibrio harveyi'''' is a heterodimer that is composed of a catalytic α subunit and a homologous but noncatalytic β subunit<ref Campbell, Z.T.>PMID: 19435287</ref>. This reaction results in the formation of a carboxylic acid, reduced flavinmononucleotide and the emission of photons in the form of blue-green light. The catalytic α subunit houses the active site and is connected to the β subunit via a single interatcion between the mobile loop and the α subunit at α Phe 272 and Tyr 151 of the β subunit<ref Campbell, Z.T.>PMID: 19435287</ref>.


Line 9:		Line 9:
	<p>FMNH<sub>2</sub>+O<sub>2</sub>+RCHO→FMN+RCOOH+H<sub>2</sub>O+hv(490nm)</p>		<p>FMNH<sub>2</sub>+O<sub>2</sub>+RCHO→FMN+RCOOH+H<sub>2</sub>O+hv(490nm)</p>

-	The catalytic α subunit houses the FMN cofactor and is connected to the β subunit via a hairpin structure called the "<scene name='User:Mitchell_Long/Sandbox_1/Protease_labile_region/3'>Mobile loop</scene>." The organic substrate for bacterial luciferase in vivo is myristic aldehyde, although many aliphatic aldehydes of various lengths can induce bioluminescence in vitro. Oxygen is needed for light generation, no bioluminescent activity occurs in anaerobic conditions.	+	The catalytic α subunit houses the FMN cofactor and is connected to the β subunit via a hairpin structure called the "<scene name='User:Mitchell_Long/Sandbox_1/Protease_labile_region/3'>Mobile loop</scene>." The organic substrate for bacterial luciferase in vivo is myristic aldehyde, although many aliphatic aldehydes of various lengths can induce bioluminescence in vitro<ref name=Waters, C.M.>PMID: 17015436</ref>. Oxygen is needed for light generation, no bioluminescent activity occurs in anaerobic conditions.

	<p><scene name='User:Mitchell_Long/Sandbox_1/Luciferase_w_out_cofactor/1'>Luciferase with no bound cofactor</scene> </p>		<p><scene name='User:Mitchell_Long/Sandbox_1/Luciferase_w_out_cofactor/1'>Luciferase with no bound cofactor</scene> </p>
Line 43:		Line 43:

	==Quorum Sensing==		==Quorum Sensing==
-	In a process known as quorum sensing, bacteria communicate using secreted signal molecules called autoinducers(AIs). ''''V. harveyi'''' is a mesophilic, gram negative, rod shaped bacteria that can communicate with other bacteria via quorum sensing. Quorum-sensing bacteria alter gene expression in response to the accumulation of AIs, which reflects an increase in cell population density. This process is believed to provide bacteria a means to coordinately control the gene expression of the group, giving them multicellular characteristics. When bacteria reach a "quorum," their population has reached a density high enough to coordinate gene expression. Often, bacteria make and respond to multiple AIs. Vibrio harveyi, a free-living marine bacterium, produces at least three distinct AIs to control bioluminescence, biofilm formation, Type III Secretion (TTS), and protease production. When a bacterial population density is low, the LuxI gene is transcribed constitutively at basal level. The three V. harveyi AIs are HAI-1, an acyl homoserine lactone; AI-2, a furanosyl-borate-diester; and CAI-1, of unknown structure. When the population density reaches an adequate level, the conjugate receptor LuxR begins transcription. LuxR is the regulatory receptor, and when an AI binds the the LuxR receptor, transcription is turned on resulting in the production of more AI and the expression of other genes involved in quorum sensing. When '''V. harveyi''' reaches a high enough population density, it's quorum sensing genes are activated and the transcription of the genes that code for the luciferase enzyme.	+	In a process known as quorum sensing, bacteria communicate using secreted signal molecules called autoinducers(AIs). ''''V. harveyi'''' is a mesophilic, gram negative, rod shaped bacteria that can communicate with other bacteria via quorum sensing. Quorum-sensing bacteria alter gene expression in response to the accumulation of AIs, which reflects an increase in cell population density. This process is believed to provide bacteria a means to coordinately control the gene expression of the group, giving them multicellular characteristics<ref name=Waters, C.M.>PMID: 17015436</ref>. When bacteria reach a "quorum," their population has reached a density high enough to coordinate gene expression. Often, bacteria make and respond to multiple AIs. Vibrio harveyi, a free-living marine bacterium, produces at least three distinct AIs to control bioluminescence, biofilm formation, Type III Secretion (TTS), and protease production<ref name=Waters, C.M.>PMID: 17015436</ref>. When a bacterial population density is low, the LuxI gene is transcribed constitutively at basal level. The three V. harveyi AIs are HAI-1, an acyl homoserine lactone; AI-2, a furanosyl-borate-diester; and CAI-1, of unknown structure. When the population density reaches an adequate level, the conjugate receptor LuxR begins transcription. LuxR is the regulatory receptor, and when an AI binds the the LuxR receptor, transcription is turned on resulting in the production of more AI and the expression of other genes involved in quorum sensing. When '''V. harveyi''' reaches a high enough population density, it's quorum sensing genes are activated and the transcription of the genes that code for the luciferase enzyme and results in bioluminescence.
	<ref Campbell, Z.T.>PMID: 19435287</ref>		<ref Campbell, Z.T.>PMID: 19435287</ref>
	<ref name=Waters, C.M.>PMID: 17015436</ref>		<ref name=Waters, C.M.>PMID: 17015436</ref>

Mitchell Long at 22:22, 17 November 2011

2011-11-17T22:22:10Z

←Older revision		Revision as of 22:22, 17 November 2011
Line 44:		Line 44:
	==Quorum Sensing==		==Quorum Sensing==
	In a process known as quorum sensing, bacteria communicate using secreted signal molecules called autoinducers(AIs). ''''V. harveyi'''' is a mesophilic, gram negative, rod shaped bacteria that can communicate with other bacteria via quorum sensing. Quorum-sensing bacteria alter gene expression in response to the accumulation of AIs, which reflects an increase in cell population density. This process is believed to provide bacteria a means to coordinately control the gene expression of the group, giving them multicellular characteristics. When bacteria reach a "quorum," their population has reached a density high enough to coordinate gene expression. Often, bacteria make and respond to multiple AIs. Vibrio harveyi, a free-living marine bacterium, produces at least three distinct AIs to control bioluminescence, biofilm formation, Type III Secretion (TTS), and protease production. When a bacterial population density is low, the LuxI gene is transcribed constitutively at basal level. The three V. harveyi AIs are HAI-1, an acyl homoserine lactone; AI-2, a furanosyl-borate-diester; and CAI-1, of unknown structure. When the population density reaches an adequate level, the conjugate receptor LuxR begins transcription. LuxR is the regulatory receptor, and when an AI binds the the LuxR receptor, transcription is turned on resulting in the production of more AI and the expression of other genes involved in quorum sensing. When '''V. harveyi''' reaches a high enough population density, it's quorum sensing genes are activated and the transcription of the genes that code for the luciferase enzyme.		In a process known as quorum sensing, bacteria communicate using secreted signal molecules called autoinducers(AIs). ''''V. harveyi'''' is a mesophilic, gram negative, rod shaped bacteria that can communicate with other bacteria via quorum sensing. Quorum-sensing bacteria alter gene expression in response to the accumulation of AIs, which reflects an increase in cell population density. This process is believed to provide bacteria a means to coordinately control the gene expression of the group, giving them multicellular characteristics. When bacteria reach a "quorum," their population has reached a density high enough to coordinate gene expression. Often, bacteria make and respond to multiple AIs. Vibrio harveyi, a free-living marine bacterium, produces at least three distinct AIs to control bioluminescence, biofilm formation, Type III Secretion (TTS), and protease production. When a bacterial population density is low, the LuxI gene is transcribed constitutively at basal level. The three V. harveyi AIs are HAI-1, an acyl homoserine lactone; AI-2, a furanosyl-borate-diester; and CAI-1, of unknown structure. When the population density reaches an adequate level, the conjugate receptor LuxR begins transcription. LuxR is the regulatory receptor, and when an AI binds the the LuxR receptor, transcription is turned on resulting in the production of more AI and the expression of other genes involved in quorum sensing. When '''V. harveyi''' reaches a high enough population density, it's quorum sensing genes are activated and the transcription of the genes that code for the luciferase enzyme.
-	<ref Campbell Z.T.>PMID: 19435287</ref>	+	<ref Campbell, Z.T.>PMID: 19435287</ref>
	<ref name=Waters, C.M.>PMID: 17015436</ref>		<ref name=Waters, C.M.>PMID: 17015436</ref>
	<ref name=Fisher, A.J.>PMID: 7756289</ref>		<ref name=Fisher, A.J.>PMID: 7756289</ref>
	==References==		==References==
	{{Reflist}}		{{Reflist}}

Mitchell Long at 22:17, 17 November 2011

2011-11-17T22:17:47Z

←Older revision		Revision as of 22:17, 17 November 2011
Line 43:		Line 43:

	==Quorum Sensing==		==Quorum Sensing==
-	In a process known as quorum sensing, bacteria communicate using secreted signal molecules called autoinducers(AIs). ''''V. harveyi'''' is a mesophilic, gram negative, rod shaped bacteria that can communicate with other bacteria via quorum sensing. Quorum-sensing bacteria alter gene expression in response to the accumulation of AIs, which reflects an increase in cell population density. This process is believed to provide bacteria a means to coordinately control the gene expression of the group, giving them multicellular characteristics. When bacteria reach a "quorum," their population has reached a density high enough to coordinate gene expression. Often, bacteria make and respond to multiple AIs. Vibrio harveyi, a free-living marine bacterium, produces at least three distinct AIs to control bioluminescence, biofilm formation, Type III Secretion (TTS), and protease production. When a bacterial population density is low, the LuxI gene is transcribed constitutively at basal level. The three V. harveyi AIs are HAI-1, an acyl homoserine lactone; AI-2, a furanosyl-borate-diester; and CAI-1, of unknown structure. When the population density reaches an adequate level, the conjugate receptor LuxR begins transcription. LuxR is the regulatory receptor, and when an AI binds the the LuxR receptor, transcription is turned on resulting in the production of more AI and the expression of other genes involved in quorum sensing. When '''V. harveyi''' reaches a high enough population density, it's quorum sensing genes are activated and the transcription of the genes that code for the luciferase enzyme.	+	In a process known as quorum sensing, bacteria communicate using secreted signal molecules called autoinducers(AIs). ''''V. harveyi'''' is a mesophilic, gram negative, rod shaped bacteria that can communicate with other bacteria via quorum sensing. Quorum-sensing bacteria alter gene expression in response to the accumulation of AIs, which reflects an increase in cell population density. This process is believed to provide bacteria a means to coordinately control the gene expression of the group, giving them multicellular characteristics. When bacteria reach a "quorum," their population has reached a density high enough to coordinate gene expression. Often, bacteria make and respond to multiple AIs. Vibrio harveyi, a free-living marine bacterium, produces at least three distinct AIs to control bioluminescence, biofilm formation, Type III Secretion (TTS), and protease production. When a bacterial population density is low, the LuxI gene is transcribed constitutively at basal level. The three V. harveyi AIs are HAI-1, an acyl homoserine lactone; AI-2, a furanosyl-borate-diester; and CAI-1, of unknown structure. When the population density reaches an adequate level, the conjugate receptor LuxR begins transcription. LuxR is the regulatory receptor, and when an AI binds the the LuxR receptor, transcription is turned on resulting in the production of more AI and the expression of other genes involved in quorum sensing. When '''V. harveyi''' reaches a high enough population density, it's quorum sensing genes are activated and the transcription of the genes that code for the luciferase enzyme.
		+	<ref Campbell Z.T.>PMID: 19435287</ref>
		+	<ref name=Waters, C.M.>PMID: 17015436</ref>
		+	<ref name=Fisher, A.J.>PMID: 7756289</ref>
	==References==		==References==
	{{Reflist}}		{{Reflist}}

Mitchell Long at 21:54, 17 November 2011

2011-11-17T21:54:26Z

←Older revision		Revision as of 21:54, 17 November 2011
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	==Introduction==		==Introduction==
-	Luciferases are a class of enzymes that catalyze the oxidation of a long chain aliphatic aldehydes~~. This reaction results in the formation of a carboxylic acid and~~ the emission ~~of photons in the form~~ of blue-green light. The luciferase found in ''''Vibrio harveyi'''' is a heterodimer that is composed of a catalytic α subunit and a homologous but noncatalytic β subunit. The catalytic α subunit houses the ~~FMN cofactor~~ and is connected to the β subunit via a ~~hairpin structure called~~ the "mobile loop."	+	Luciferases are a class of enzymes that catalyze the oxidation of a long chain aliphatic aldehydes the emission of blue-green light. The luciferase found in ''''Vibrio harveyi'''' is a heterodimer that is composed of a catalytic α subunit and a homologous but noncatalytic β subunit. This reaction results in the formation of a carboxylic acid, reduced flavinmononucleotide and the emission of photons in the form of blue-green light. The catalytic α subunit houses the active site and is connected to the β subunit via a single interatcion between the mobile loop and the α subunit at α Phe 272 and Tyr 151 of the β subunit.


	==Mechanism==		==Mechanism==
-	Luciferase found in'''V. Harveyi''' binds noncovalently to a reduced flavin mononucleotide cofactor, an aliphatic aldehyde and oxygen to yield oxidized flavin mononucleotide, water, and carboxylic acid. The reaction occurs in two steps forming a hydroxyflavin intermediate and ultimately results in the oxidation of the aldehyde and emission of photons ~~in the form of blue green light.~~	+	Luciferase found in''''V. Harveyi'''' binds noncovalently to a reduced flavin mononucleotide cofactor, an aliphatic aldehyde and oxygen to yield oxidized flavin mononucleotide, water, and carboxylic acid. The reaction occurs in two steps forming a hydroxyflavin intermediate and ultimately results in the oxidation of the aldehyde and emission of photons
	<p>FMNH<sub>2</sub>+O<sub>2</sub>+RCHO→FMN+RCOOH+H<sub>2</sub>O+hv(490nm)</p>		<p>FMNH<sub>2</sub>+O<sub>2</sub>+RCHO→FMN+RCOOH+H<sub>2</sub>O+hv(490nm)</p>

-	The catalytic α subunit houses the FMN cofactor and is connected to the β subunit via a hairpin structure called the "<scene name='User:Mitchell_Long/Sandbox_1/Protease_labile_region/3'>Mobile loop</scene>." The organic substrate for bacterial luciferase in vivo is myristic aldehyde, although many aliphatic aldehydes of various lengths can induce bioluminescence in vitro.	+	The catalytic α subunit houses the FMN cofactor and is connected to the β subunit via a hairpin structure called the "<scene name='User:Mitchell_Long/Sandbox_1/Protease_labile_region/3'>Mobile loop</scene>." The organic substrate for bacterial luciferase in vivo is myristic aldehyde, although many aliphatic aldehydes of various lengths can induce bioluminescence in vitro. Oxygen is needed for light generation, no bioluminescent activity occurs in anaerobic conditions.
-	<scene name='User:Mitchell_Long/Sandbox_1/Luciferase_w_out_cofactor/1'>Luciferase with no bound cofactor</scene>	+
-		+	<p><scene name='User:Mitchell_Long/Sandbox_1/Luciferase_w_out_cofactor/1'>Luciferase with no bound cofactor</scene> </p>
	<p><scene name='User:Mitchell_Long/Sandbox_1/Hetero_fmn_complex/1'>Luciferase+FMN</scene></p>		<p><scene name='User:Mitchell_Long/Sandbox_1/Hetero_fmn_complex/1'>Luciferase+FMN</scene></p>
	<p><scene name='User:Mitchell_Long/Sandbox_1/Hetero_fmn_complex_translucent/1'>FMN Positioning</scene></p>		<p><scene name='User:Mitchell_Long/Sandbox_1/Hetero_fmn_complex_translucent/1'>FMN Positioning</scene></p>
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-	<p>'''Structure homology'''-There is a great deal of sequence homology and structural coservation between the α and β subunits. When superimposed over ~~eachother~~ the barrels of the alpha and beta subunits with a deviation of 0.62Å for 42 equivalent α carbons. The region of the beta subunit that contains the 29 residue deletion with respect to the alpha subunit differs notably in arrangement. In the alpha subunit, the α7a helix is straight and extends toward the beta subunit. The region involved with dimerization, helices α and β and the hairpin loop structure are exceptionally similar in superposition.	+	<p>'''Structure homology'''-There is a great deal of sequence homology and structural coservation between the α and β subunits. When superimposed over the barrels of the alpha and beta subunits with a deviation of 0.62Å for 42 equivalent α carbons. The region of the beta subunit that contains the 29 residue deletion with respect to the alpha subunit differs notably in arrangement. In the alpha subunit, the α7a helix is straight and extends toward the beta subunit. The region involved with dimerization, helices α and β and the hairpin loop structure are exceptionally similar in superposition.
	</p>		</p>
	<p>'''Active Site and Alpha Subunit'''-the <scene name='User:Mitchell_Long/Sandbox_1/Yellow_sheets/1'>flavin binding pocket</scene> of bacterial luciferase is a large open cavity that is accessible to solvent via an opening located at the C-terminal ends of the ǰ strans of the TIM-barrel structure. During the first step of the oxidation reaction, FMNH<sub>2</sub> binds to the flavin binding pocket and the enzyme undergoes a conformational change that blocks water in the surrounding environment from accessing both the excited peroxydihydroflavin intermediate. Next O<sub>2</sub> and a long chain aldehyde bind to the FMNH<sub>2</sub> luciferase complex and a two step oxidatino reaction occurs.		<p>'''Active Site and Alpha Subunit'''-the <scene name='User:Mitchell_Long/Sandbox_1/Yellow_sheets/1'>flavin binding pocket</scene> of bacterial luciferase is a large open cavity that is accessible to solvent via an opening located at the C-terminal ends of the ǰ strans of the TIM-barrel structure. During the first step of the oxidation reaction, FMNH<sub>2</sub> binds to the flavin binding pocket and the enzyme undergoes a conformational change that blocks water in the surrounding environment from accessing both the excited peroxydihydroflavin intermediate. Next O<sub>2</sub> and a long chain aldehyde bind to the FMNH<sub>2</sub> luciferase complex and a two step oxidatino reaction occurs.
	.</p>		.</p>
	<scene name='User:Mitchell_Long/Sandbox_1/Hetero_translucent/1'>Heterodimer</scene>		<scene name='User:Mitchell_Long/Sandbox_1/Hetero_translucent/1'>Heterodimer</scene>
-	<scene name='User:Mitchell_Long/Sandbox_1/Fmn_in_barrel/1'>FMN bound Heterodimer</scene>	+	<p><scene name='User:Mitchell_Long/Sandbox_1/Fmn_in_barrel/1'>FMN bound Heterodimer</scene></p>

		+	<p><scene name='User:Mitchell_Long/Sandbox_1/Phe272_tyr151_interface/1'>Phe 272 Tyr 151 interface</scene></p>

-		+	<p>'''The β subunit'''-The beta subunit is characterized as a necessary but non-catalytic subunit that stabilizes the catalytic ǯ subunit that is responsible for the oxidation reaction. The beta and alpha subunits are connected by a single interaction between the <scene name='User:Mitchell_Long/Sandbox_1/Phe272_tyr151_interface/1'>Phe 272 Tyr 151 interface</scene>
-	<p>'''The β subunit'''-The beta subunit is characterized as a necessary but non-catalytic subunit that stabilizes the catalytic ǯ subunit that is responsible for the oxidation reaction. ~~Both~~ subunits ~~share~~ a ~~great deal of homology~~	+
	</p>		</p>

Line 36:		Line 36:
	.</p>		.</p>
	</StructureSection>		</StructureSection>
-
-

	{{STRUCTURE_3fgc\| PDB=3fgc \| SCENE= }}		{{STRUCTURE_3fgc\| PDB=3fgc \| SCENE= }}
-
-

	==Applications In Biotechnology==		==Applications In Biotechnology==
Line 47:		Line 43:

	==Quorum Sensing==		==Quorum Sensing==
-	In a process known as quorum sensing, bacteria communicate using secreted signal molecules called autoinducers(AIs). '''V. harveyi''' is a mesophilic, gram negative, rod shaped bacteria that can communicate with other bacteria via quorum sensing. Quorum-sensing bacteria alter gene expression in response to the accumulation of AIs, which reflects an increase in cell population density. This process is believed to provide bacteria a means to coordinately control the gene expression of the group, giving them multicellular characteristics. When bacteria reach a "quorum," their population has reached a density high enough to coordinate gene expression. Often, bacteria make and respond to multiple AIs. Vibrio harveyi, a free-living marine bacterium, produces at least three distinct AIs to control bioluminescence, biofilm formation, Type III Secretion (TTS), and protease production. When a bacterial population density is low, the LuxI gene is transcribed constitutively at basal level. The three V. harveyi AIs are HAI-1, an acyl homoserine lactone; AI-2, a furanosyl-borate-diester; and CAI-1, of unknown structure. When the population density reaches an adequate level, the conjugate receptor LuxR begins transcription. LuxR is the regulatory receptor, and when an AI binds the the LuxR receptor, transcription is turned on resulting in the production of more AI and the expression of other genes involved in quorum sensing. When '''V. harveyi''' reaches a high enough population density, it's quorum sensing genes are activated and the transcription of the genes that code for the luciferase enzyme.	+	In a process known as quorum sensing, bacteria communicate using secreted signal molecules called autoinducers(AIs). ''''V. harveyi'''' is a mesophilic, gram negative, rod shaped bacteria that can communicate with other bacteria via quorum sensing. Quorum-sensing bacteria alter gene expression in response to the accumulation of AIs, which reflects an increase in cell population density. This process is believed to provide bacteria a means to coordinately control the gene expression of the group, giving them multicellular characteristics. When bacteria reach a "quorum," their population has reached a density high enough to coordinate gene expression. Often, bacteria make and respond to multiple AIs. Vibrio harveyi, a free-living marine bacterium, produces at least three distinct AIs to control bioluminescence, biofilm formation, Type III Secretion (TTS), and protease production. When a bacterial population density is low, the LuxI gene is transcribed constitutively at basal level. The three V. harveyi AIs are HAI-1, an acyl homoserine lactone; AI-2, a furanosyl-borate-diester; and CAI-1, of unknown structure. When the population density reaches an adequate level, the conjugate receptor LuxR begins transcription. LuxR is the regulatory receptor, and when an AI binds the the LuxR receptor, transcription is turned on resulting in the production of more AI and the expression of other genes involved in quorum sensing. When '''V. harveyi''' reaches a high enough population density, it's quorum sensing genes are activated and the transcription of the genes that code for the luciferase enzyme.
	==References==		==References==
	{{Reflist}}		{{Reflist}}