Team:Imperial College London/Biobricks

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=Submitted 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>
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[[Image:II09_BBa.png|center|150px]]
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=Biobricks=
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{| style="color:#CCC; background-color:#325d97;" cellpadding="6" cellspacing="0" border="3"
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== Coding Sequences ==
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! Registry Code
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! Type
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! Sequence Description
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{{Imperial/09/BoxWhite|RcsB|<b>RcsB: Colanic acid global regulator</b><br>
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|- style="color:#333; background-color:#CCCCFF;" cellpadding="6" cellspacing="0" border="1"
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<i>Part BBa_K200000 </i>: [http://partsregistry.org/Part:BBa_K200000 <b>Link</b>]<br>
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<!----------------------------------------biobricks---------------------------------------->
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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. <br> Colanic acid is a heteropolymer containing glucose, galactose, fucose, and glucuronic acid. <br><br>
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| <partinfo>BBa_K200000 </partinfo>
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It is important to note that RcsB is a global regulator found in many Enterobacteria. In Salmonella, up to 38 genes were found to be up-regulated by RcsB including ftsZ which affects the rate of cell division. The majority of upregulated genes are associated with enhancing structural integrety and acid resistance. 22 genes were found to be downregualted by RcsB in the same microarray experiment.<br><br>}}
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| Coding
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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:#CCCCFF;" cellpadding="6" cellspacing="0" border="1"
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| <partinfo>BBa_K200001 </partinfo>
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| 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, this protects the DNA from cleavage.  
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|- style="color:#333; background-color:#CCCCFF;" cellpadding="6" cellspacing="0" border="1"
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| <partinfo>BBa_K200002 </partinfo>
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| Coding
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| '''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:#CCCCFF;" cellpadding="6" cellspacing="0" border="1"
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| <partinfo>BBa_K200003 </partinfo>
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| Coding
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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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|- style="color:#333; background-color:#CCCCFF;" cellpadding="6" cellspacing="0" border="1"
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| <partinfo>BBa_K200005 </partinfo>
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| Coding
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| '''OtsA''' is the first of two required in the conversion of glucose to [http://en.wikipedia.org/wiki/Trehalose trehalose].
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This enzyme catalyses the following reaction:
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{{Imperial/Box2|Dam|<b> Dam: DNA Adenine Methylase</b><br>
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UDP-glucose + D-glucose 6-phosphate -> UDP + alpha,alpha-trehalose 6-phosphate
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<i>Part BBa_K200001 </i>: [http://partsregistry.org/Part:BBa_K200001 <b>Link</b>]<br>
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|- style="color:#333; background-color:#CCCCFF;" cellpadding="6" cellspacing="0" border="1"
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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.<br><br>}}
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| <partinfo>BBa_K200006 </partinfo>
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<b>RcsB: Colanic acid global regulator</b><br>
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| Coding
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Part BBa_K200000 : [http://partsregistry.org/Part:BBa_K200000 Link]<br><br>
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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].  
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<b>Dam: DNA Adenine Methylase</b><br>
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This enzyme catalyses the following reaction:
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Part BBa_K200001 : [http://partsregistry.org/Part:BBa_K200001 Link]<br><br>
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<b>ygiV (B3023): Colanic acid global regulator </b><br>
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alpha,alpha-trehalose 6-phosphate + H2O -> alpha,alpha-trehalose + phosphate
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Part BBa_K200002 : [http://partsregistry.org/Part:BBa_K200002 Link]<br><br>
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|- style="color:#333; background-color:#CCCCFF;" cellpadding="6" cellspacing="0" border="1"
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<b>WaaL Ligase </b><br>
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| <partinfo>BBa_K200007 </partinfo>
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Part BBa_K200003 : [http://partsregistry.org/Part:BBa_K200003 Link]<br><br>
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| Coding
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<b>OtsA: Part 1 of 2 for trehalose producing enzymes </b><br>
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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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Part BBa_K200005 : [http://partsregistry.org/Part:BBa_K200005 Link]<br><br>
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|- style="color:#333; background-color:#CCCCFF;" cellpadding="6" cellspacing="0" border="1"
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<b>OtsB: Part 2 of 2 coding for trehalose producing enzymes </b><br>
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| <partinfo>BBa_K200008 </partinfo>
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Part BBa_K200006 : [http://partsregistry.org/Part:BBa_K200006 Link]<br><br>
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| Coding
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<b>Cellulase </b><br>
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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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Part BBa_K200007 : [http://partsregistry.org/Part:BBa_K200007 Link]<br><br>
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|- style="color:#333; background-color:#CCCCFF;" cellpadding="6" cellspacing="0" border="1"
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<b>PAH : Phenylalanine Hydroxylase </b><br>
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| <partinfo>BBa_K200009 </partinfo>
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Part BBa_K200008 : [http://partsregistry.org/Part:BBa_K200008 Link]<br><br>
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| Coding
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<b>Coding Sequence for the Restriction Enzyme DpnII </b><br>
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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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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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|- style="color:#333; background-color:#CCCCFF;" cellpadding="6" cellspacing="0" border="1"
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Part BBa_K200010 : [http://partsregistry.org/Part:BBa_K200010 Link]<br><br>
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| <partinfo>BBa_K200010 </partinfo>
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<b>Temperature Sensitive lamda cI Repressor  </b><br>
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| Coding
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Part BBa_K200011 : [http://partsregistry.org/Part:BBa_K200011 Link]<br><br>
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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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<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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|- style="color:#333; background-color:#CCCCFF;" cellpadding="6" cellspacing="0" border="1"
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| <partinfo>BBa_K200011 </partinfo>
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| Coding
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| 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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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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| <partinfo>BBa_K200012 </partinfo>
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| 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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|- style="color:#333; background-color:#CCCCFF;" cellpadding="6" cellspacing="0" border="1"
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|
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|}
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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

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