Team:Imperial College London/Biobricks

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=Submitted BioBricks=
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=Biobricks=
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Imperial College iGEM 2009's uploaded BioBricks section on the Parts Registry can be found [http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2009&group=Imperial%20College%20London here].<br><br>
<!--template:---------------------------------------------------------------------------->
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{| style="color:#CCC; background-color:#3D5089;" cellpadding="6" cellspacing="0" border="1"
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{| style="color:#CCC; background-color:#325d97;" cellpadding="6" cellspacing="0" border="3"
! Registry Code
! Registry Code
! Type
! Type
! Sequence Description
! Sequence Description
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|- style="color:#333; background-color:#BCD2EE;" cellpadding="6" cellspacing="0" border="1"
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|- style="color:#333; background-color:#CCCCFF;" cellpadding="6" cellspacing="0" border="1"
<!----------------------------------------biobricks---------------------------------------->
<!----------------------------------------biobricks---------------------------------------->
| <partinfo>BBa_K200000 </partinfo>
| <partinfo>BBa_K200000 </partinfo>
| Coding
| Coding
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| '''RcsB''' is a receiver protein in a two component phosphorelay system, which acts as a positive regulator of a number of genes including capsule genes responsible for colanic acid production. This is via the activation of the ugd/cps operon which is required for capsule synthesis.  
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| '''RcsB''' is a receiver protein which acts as a positive regulator of a number of genes including capsule genes responsible for colanic acid production.
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|- style="color:#333; background-color:#BCD2EE;" cellpadding="6" cellspacing="0" border="1"
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|- style="color:#333; background-color:#CCCCFF;" cellpadding="6" cellspacing="0" border="1"
| <partinfo>BBa_K200001 </partinfo>
| <partinfo>BBa_K200001 </partinfo>
| Coding
| Coding
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| '''Dam (DNA Adenine Methylase)''' The methylase encoded by the dam gene ([http://en.wikipedia.org/wiki/Dam_(methylase) Dam methylase]) transfers a methyl group from S-adenosylmethionine to the N6 position of the adenine residues in the sequence GATC. When methylation occurs in the recognition site of a particular group of restriction endonuclease including MboI, this protects the DNA from cleavage.  
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| '''Dam (DNA Adenine Methylase)''' The methylase encoded by the dam gene ([http://en.wikipedia.org/wiki/Dam_(methylase) Dam methylase]) transfers a methyl group from S-adenosylmethionine to the N6 position of the adenine residues in the sequence GATC, this protects the DNA from cleavage.  
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|- style="color:#333; background-color:#BCD2EE;" cellpadding="6" cellspacing="0" border="1"
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|- style="color:#333; background-color:#CCCCFF;" cellpadding="6" cellspacing="0" border="1"
| <partinfo>BBa_K200002 </partinfo>
| <partinfo>BBa_K200002 </partinfo>
| Coding
| Coding
| '''Colanic acid global regulator''' ygiV (B3023) increases the production of colanic acid further in conjunction with RcsB by acting as a repressor for mcbR/yncC promoter. YncC/mcbR normally repress colanic acid overproduction so as to increase biofilm formation.  
| '''Colanic acid global regulator''' ygiV (B3023) increases the production of colanic acid further in conjunction with RcsB by acting as a repressor for mcbR/yncC promoter. YncC/mcbR normally repress colanic acid overproduction so as to increase biofilm formation.  
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|- style="color:#333; background-color:#BCD2EE;" cellpadding="6" cellspacing="0" border="1"
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|- style="color:#333; background-color:#CCCCFF;" cellpadding="6" cellspacing="0" border="1"
| <partinfo>BBa_K200003 </partinfo>
| <partinfo>BBa_K200003 </partinfo>
| Coding
| Coding
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| '''Waal Ligase''' is an enzyme responsible for the ligation of an O-antigen to the core oligosaccharide in the Gram-negative bacterium's outer membrane.  
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| '''Waal Ligase''' is an enzyme responsible for the ligation of an [http://en.wikipedia.org/wiki/O_antigen#O-antigen O-antigen] to the core [http://en.wikipedia.org/wiki/Oligosaccharide oligosaccharide] in the Gram-negative bacterium's outer membrane.  
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Unlike other exopolysaccharides, colanic acid does not naturally bind to the cell surface but rather forms a thick mesh between cells. While Waal Ligase usually links the O-antigen to the core oligosaccharide, in K-12 it links colanic acid to the core oligosaccharide.
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|- style="color:#333; background-color:#CCCCFF;" cellpadding="6" cellspacing="0" border="1"
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|- style="color:#333; background-color:#BCD2EE;" cellpadding="6" cellspacing="0" border="1"
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| <partinfo>BBa_K200005 </partinfo>
| <partinfo>BBa_K200005 </partinfo>
| Coding
| Coding
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| '''OtsA''' is the first of two required in the conversion of glucose to trehalose.  
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| '''OtsA''' is the first of two required in the conversion of glucose to [http://en.wikipedia.org/wiki/Trehalose trehalose].  
This enzyme catalyses the following reaction:  
This enzyme catalyses the following reaction:  
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UDP-glucose + D-glucose 6-phosphate -> UDP + alpha,alpha-trehalose 6-phosphate  
UDP-glucose + D-glucose 6-phosphate -> UDP + alpha,alpha-trehalose 6-phosphate  
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|- style="color:#333; background-color:#BCD2EE;" cellpadding="6" cellspacing="0" border="1"
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|- style="color:#333; background-color:#CCCCFF;" cellpadding="6" cellspacing="0" border="1"
| <partinfo>BBa_K200006 </partinfo>
| <partinfo>BBa_K200006 </partinfo>
| Coding
| Coding
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| '''OtsB''' This enzyme is the second of two required for the conversion of glucose to trehalose.  
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| '''OtsB''' This enzyme is the second of two required for the conversion of glucose to [http://en.wikipedia.org/wiki/Trehalose trehalose].  
This enzyme catalyses the following reaction:  
This enzyme catalyses the following reaction:  
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alpha,alpha-trehalose 6-phosphate + H2O -> alpha,alpha-trehalose + phosphate  
alpha,alpha-trehalose 6-phosphate + H2O -> alpha,alpha-trehalose + phosphate  
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|- style="color:#333; background-color:#BCD2EE;" cellpadding="6" cellspacing="0" border="1"
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|- style="color:#333; background-color:#CCCCFF;" cellpadding="6" cellspacing="0" border="1"
| <partinfo>BBa_K200007 </partinfo>
| <partinfo>BBa_K200007 </partinfo>
| Coding
| Coding
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| '''Cellulase''' mainly catalyses the reactions that changes crystalline cellulose to cellobiose and then finally to glucose. It also catalyses, to a small extent, the break down of carboxymethyl cellulose. This cellulase is protease resistant.  
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| [http://en.wikipedia.org/wiki/Cellulase '''Cellulase'''] mainly catalyses the reactions that changes crystalline [http://en.wikipedia.org/wiki/Cellulose cellulose] to [http://en.wikipedia.org/wiki/Cellobiose cellobiose] and then finally to glucose. This cellulase is protease resistant.  
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|- style="color:#333; background-color:#BCD2EE;" cellpadding="6" cellspacing="0" border="1"
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|- style="color:#333; background-color:#CCCCFF;" cellpadding="6" cellspacing="0" border="1"
| <partinfo>BBa_K200008 </partinfo>
| <partinfo>BBa_K200008 </partinfo>
| Coding
| Coding
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| '''Phenylalanine hydroxylase ''' is the enzyme that breaks down [http://en.wikipedia.org/wiki/Phenylalanine phenylalanine] to [http://en.wikipedia.org/wiki/Tyrosine tyrosine]. Deficiency of this enzyme activity results in the autosomal recessive disorder [http://en.wikipedia.org/wiki/Phenylketonuria phenylketonuria].  
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| [http://en.wikipedia.org/wiki/Phenylalanine_hydroxylase '''Phenylalanine hydroxylase'''] is the enzyme that breaks down [http://en.wikipedia.org/wiki/Phenylalanine phenylalanine] to [http://en.wikipedia.org/wiki/Tyrosine tyrosine]. Deficiency of this enzyme activity results in the autosomal recessive disorder [http://en.wikipedia.org/wiki/Phenylketonuria phenylketonuria].  
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|- style="color:#333; background-color:#BCD2EE;" cellpadding="6" cellspacing="0" border="1"
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|- style="color:#333; background-color:#CCCCFF;" cellpadding="6" cellspacing="0" border="1"
| <partinfo>BBa_K200009 </partinfo>
| <partinfo>BBa_K200009 </partinfo>
| Coding
| Coding
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| '''Restriction enzyme DpnII ''' is a Type II restriction enzyme that recognises the sequence GATC.  Its activity can be blocked by dam methylation.
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| '''Restriction enzyme [http://www.thelabrat.com/restriction/DpnII.shtml DpnII] ''' is a Type II restriction enzyme that recognises the sequence GATC.  Its activity can be blocked by dam methylation.
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The working temperature is 37°C.
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|- style="color:#333; background-color:#BCD2EE;" cellpadding="6" cellspacing="0" border="1"
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|- style="color:#333; background-color:#CCCCFF;" cellpadding="6" cellspacing="0" border="1"
| <partinfo>BBa_K200010 </partinfo>
| <partinfo>BBa_K200010 </partinfo>
| Coding
| Coding
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| '''Restriction enzyme TaqI ''' is a Type II restriction enzyme that recognises the sequence TCGA. Its activity can be blocked by dam methylation.
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| '''Restriction enzyme [http://www.thelabrat.com/restriction/TaqI.shtml TaqI] ''' is a Type II restriction enzyme that recognises the sequence TCGA. Its activity can be blocked by dam methylation.  
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The working temperature is 65°C.  
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|- style="color:#333; background-color:#BCD2EE;" cellpadding="6" cellspacing="0" border="1"
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|- style="color:#333; background-color:#CCCCFF;" cellpadding="6" cellspacing="0" border="1"
| <partinfo>BBa_K200011 </partinfo>
| <partinfo>BBa_K200011 </partinfo>
| Coding
| Coding
| This '''Lamda cI repressor ''' has a cI857 mutation that results in denaturation of the repressor when the temperature is raised from 30 to 42°C, thereby allowing lambda promoter expression.
| This '''Lamda cI repressor ''' has a cI857 mutation that results in denaturation of the repressor when the temperature is raised from 30 to 42°C, thereby allowing lambda promoter expression.
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The repressor normally negatively regulates the expression of genes from the bacteriophage lambda pL and pR promoters. This repressive action is strongest at 30°C.
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When the temperature is raised, typically to 42°C, the functionality of the protein is lost and the cI repressor is no longer able to bind to the operators on its promoter. Therefore, lambda promoter expression increases.  
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|- style="color:#333; background-color:#CCCCFF;" cellpadding="6" cellspacing="0" border="1"
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However, when the temperature is raised, typically to 42°C, the functionality of the protein is lost and the cI repressor is no longer able to bind to the operators on its promoter. Therefore, lambda promoter expression increases.  
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|- style="color:#333; background-color:#BCD2EE;" cellpadding="6" cellspacing="0" border="1"
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| <partinfo>BBa_K200012 </partinfo>
| <partinfo>BBa_K200012 </partinfo>
| Regulatory
| Regulatory
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| '''Lambda promoter (cIts responsive)  ''' is different from the common lambda promoter in that it is able to be repressed by the temperature sensitive cI protein (BBa_K200011). When it is not being repressed after 42°C induction, it acts as a strong promoter
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| '''Lambda promoter (cIts responsive)  ''' is different from the common lambda promoter in that it is able to be repressed by the temperature sensitive cI protein (BBa_K200011). When it is not being repressed after 42°C induction, it acts as a strong promoter.
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|- style="color:#333; background-color:#CCCCFF;" cellpadding="6" cellspacing="0" border="1"
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It has been shown through lysis experiments that this lambda promoter can be stringently repressed by the cI protein at temperatures up to 30°C. At temperatures higher than 30°C, the cI repressor is progressively thermally denatured and no longer able to bind to the promoter operator regions. Therefore, promoter activity is induced.  
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== Coding Sequences ==
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Part BBa_K200009 : [http://partsregistry.org/Part:BBa_K200009 Link]<br><br>
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<b>Coding sequence for the Restriction Enzyme TaqI </b><br>
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Part BBa_K200010 : [http://partsregistry.org/Part:BBa_K200010 Link]<br><br>
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<b>Temperature Sensitive lamda cI Repressor  </b><br>
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Part BBa_K200011 : [http://partsregistry.org/Part:BBa_K200011 Link]<br><br>
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<b>Lambda Promoter (cIts responsive) </b><br>
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Part BBa_K200012 : [http://partsregistry.org/Part:BBa_K200012 Link]<br><br>
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-->
-->
{{Imperial/09/TemplateBottom}}
{{Imperial/09/TemplateBottom}}

Latest revision as of 11:41, 15 September 2009

Submitted BioBricks

Imperial College iGEM 2009's uploaded BioBricks section on the Parts Registry can be found [http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2009&group=Imperial%20College%20London here].

Registry Code Type Sequence Description
Coding RcsB is a receiver protein which acts as a positive regulator of a number of genes including capsule genes responsible for colanic acid production.
Coding Dam (DNA Adenine Methylase) The methylase encoded by the dam gene ([http://en.wikipedia.org/wiki/Dam_(methylase) Dam methylase]) transfers a methyl group from S-adenosylmethionine to the N6 position of the adenine residues in the sequence GATC, this protects the DNA from cleavage.
Coding Colanic acid global regulator ygiV (B3023) increases the production of colanic acid further in conjunction with RcsB by acting as a repressor for mcbR/yncC promoter. YncC/mcbR normally repress colanic acid overproduction so as to increase biofilm formation.
Coding Waal Ligase is an enzyme responsible for the ligation of an [http://en.wikipedia.org/wiki/O_antigen#O-antigen O-antigen] to the core [http://en.wikipedia.org/wiki/Oligosaccharide oligosaccharide] in the Gram-negative bacterium's outer membrane.
Coding OtsA is the first of two required in the conversion of glucose to [http://en.wikipedia.org/wiki/Trehalose trehalose].

This enzyme catalyses the following reaction:

UDP-glucose + D-glucose 6-phosphate -> UDP + alpha,alpha-trehalose 6-phosphate

Coding OtsB This enzyme is the second of two required for the conversion of glucose to [http://en.wikipedia.org/wiki/Trehalose trehalose].

This enzyme catalyses the following reaction:

alpha,alpha-trehalose 6-phosphate + H2O -> alpha,alpha-trehalose + phosphate

Coding [http://en.wikipedia.org/wiki/Cellulase Cellulase] mainly catalyses the reactions that changes crystalline [http://en.wikipedia.org/wiki/Cellulose cellulose] to [http://en.wikipedia.org/wiki/Cellobiose cellobiose] and then finally to glucose. This cellulase is protease resistant.
Coding [http://en.wikipedia.org/wiki/Phenylalanine_hydroxylase Phenylalanine hydroxylase] is the enzyme that breaks down [http://en.wikipedia.org/wiki/Phenylalanine phenylalanine] to [http://en.wikipedia.org/wiki/Tyrosine tyrosine]. Deficiency of this enzyme activity results in the autosomal recessive disorder [http://en.wikipedia.org/wiki/Phenylketonuria phenylketonuria].
Coding Restriction enzyme [http://www.thelabrat.com/restriction/DpnII.shtml DpnII] is a Type II restriction enzyme that recognises the sequence GATC. Its activity can be blocked by dam methylation.
Coding Restriction enzyme [http://www.thelabrat.com/restriction/TaqI.shtml TaqI] is a Type II restriction enzyme that recognises the sequence TCGA. Its activity can be blocked by dam methylation.
Coding This Lamda cI repressor has a cI857 mutation that results in denaturation of the repressor when the temperature is raised from 30 to 42°C, thereby allowing lambda promoter expression.

When the temperature is raised, typically to 42°C, the functionality of the protein is lost and the cI repressor is no longer able to bind to the operators on its promoter. Therefore, lambda promoter expression increases.

Regulatory Lambda promoter (cIts responsive) is different from the common lambda promoter in that it is able to be repressed by the temperature sensitive cI protein (BBa_K200011). When it is not being repressed after 42°C induction, it acts as a strong promoter.

Mr. Gene   Geneart   Clontech   Giant Microbes

Retrieved from "http://2009.igem.org/Team:Imperial_College_London/Biobricks"