"
Team:Costa Rica-TEC-UNA/Parts
From 2012.igem.org
ChaosPaladin (Talk | contribs) |
ChaosPaladin (Talk | contribs) |
||
| (6 intermediate revisions not shown) | |||
| Line 60: | Line 60: | ||
list-style: none; | list-style: none; | ||
float: left; | float: left; | ||
| - | font: bold 11px | + | font: bold 11px arial} |
#sddm li a | #sddm li a | ||
| Line 94: | Line 94: | ||
background: #FFFFFF; | background: #FFFFFF; | ||
color: #000000; | color: #000000; | ||
| - | font: 11px | + | font: 11px arial} |
#sddm div a:hover | #sddm div a:hover | ||
| Line 105: | Line 105: | ||
padding: 0; | padding: 0; | ||
font-family: seriff; | font-family: seriff; | ||
| - | font-size: | + | font-size: 13px; |
| - | background-color: # | + | background-color: #FFFFFF |
} | } | ||
</style> | </style> | ||
| Line 142: | Line 142: | ||
onmouseout="mclosetime()"> | onmouseout="mclosetime()"> | ||
<a href="https://2012.igem.org/Team:Costa_Rica-TEC-UNA/Parts">Parts Submitted to the registry</a> | <a href="https://2012.igem.org/Team:Costa_Rica-TEC-UNA/Parts">Parts Submitted to the registry</a> | ||
| - | |||
</div> | </div> | ||
</li> | </li> | ||
| Line 153: | Line 152: | ||
<a href="https://2012.igem.org/Team:Costa_Rica-TEC-UNA/Safety">Safety</a> | <a href="https://2012.igem.org/Team:Costa_Rica-TEC-UNA/Safety">Safety</a> | ||
<a href="https://2012.igem.org/Team:Costa_Rica-TEC-UNA/Attributions">Attributions</a> | <a href="https://2012.igem.org/Team:Costa_Rica-TEC-UNA/Attributions">Attributions</a> | ||
| + | <a href="https://2012.igem.org/Team:Costa_Rica-TEC-UNA/Human Practice">Human Practice</a> | ||
<a href="https://igem.org/Team.cgi?year=2012&team_name=Costa_Rica-TEC-UNA">Official team profile</a> | <a href="https://igem.org/Team.cgi?year=2012&team_name=Costa_Rica-TEC-UNA">Official team profile</a> | ||
| + | |||
</div> | </div> | ||
</li> | </li> | ||
| Line 160: | Line 161: | ||
</body> | </body> | ||
</html> | </html> | ||
| + | |||
== '''Biobricks designed''' == | == '''Biobricks designed''' == | ||
| - | <groupparts>iGEM012 Costa_Rica-TEC-UNA</groupparts> | + | == BBa_K836006 == |
| + | |||
| + | Lysis protein S from Enterobacteria phage lambda. This gene codifies for a protein that makes holes in the inner membrane of the bacterial cell. Between the RBS and the CDS a spacer consisting on a scar from a standard suffix and a prefix for CDS was inserted. | ||
| + | |||
| + | Source: http://www.uniprot.org/uniprot/P03705#section_seq it was optimized for ''R. opacus'' (avoiding standard restriction sites) | ||
| + | |||
| + | |||
| + | == Part:BBa_K836005 == | ||
| + | |||
| + | Lysozyme from Rhodococcus phage RER2. Protein involved in the peptidoglycan degradation of the bacterial cell wall. A RBS for Gram positive bacteria (SpoVG) was added at the beginning.A spacer was put between the RBS and the start codon which corresponds to the scar between a normal suffix and the prefix used for CDS to avoid RBS-CDS problems. The sequence has no termination codon since we rely on the double terminators of the scar formed during assembly of biobricks. | ||
| + | |||
| + | Source: http://www.uniprot.org/uniprot/G9FHW6) and then it was optimized for ''R. opacus'' (avoiding standard restriction sites). | ||
| + | |||
| + | |||
| + | == Part:BBa_K836007 == | ||
| + | |||
| + | Nitrilase regulator from R. rhodochrous. Protein in charge to regulate the expression of the genes put under control of nitA promoter. A spacer which consist of the scar left by the assembly of a normal suffix and a CDS prefix was inserted between RBS and CDS. The sequence has no termination codon since we rely on the double terminators of the scar formed during assembly of biobricks. | ||
| + | |||
| + | Source: The amino sequence was obtained from Uniprot (http://www.uniprot.org/uniprot/P72312) and then the condon usage was optimized for expression in ''R. opacus''. | ||
| + | |||
| + | |||
| + | == Part:BBa_K836008 == | ||
| + | |||
| + | nitA promoter. Promoter inducible by nitrile and similar agents. | ||
| + | |||
| + | Source: http://www.ncbi.nlm.nih.gov/nucleotide/346420896?report=genbank&log$=nuclalign&blast_rank=1&RID=W0SH1PA7016 | ||
| + | |||
| + | |||
| + | == Part:BBa_K836009 == | ||
| + | |||
| + | Lysis device for ''R. opacus''. Lysis construct based on the one presented by Berkeley's 2008 team BBa_K112022. It is based on the inducible expression of a lysozyme and lambda phage's holin in order to liberate internal products of the bacterial cell in an efficient way. The induction is achieved by the addition of nitrile or a similar agent since both genes are regulated by nitA promoter. Constitutive expression of nitR and a low constitutive expression of an antiholin are required to avoid undesired lysis. | ||
| + | |||
| + | Source: The majority of the parts where made by backtranslating a protein. Others are existing biobricks while some are promoters obtained from databases as NCBI. | ||
| + | |||
| + | |||
| + | == Part:BBa_K836002 == | ||
| + | |||
| + | O-acyltransferase WSD from ''Acinetobacter'' sp. This biobrick codifies for the protein DGAT (Diacylglycerol O-acyltransferase) which have dual activity, it can act as a wax ester synthase or as a diacylglycerol acyltransferase. In the latter case, its function consists in mediate the final step in TGAs synthesis using a fatty acyl-CoA and a DGA. This enzyme is vital in the storage and synthesis of lipids. Two transcriptional terminators (two biobricks BBa_B1006) were set at the end of the coding sequence. | ||
| + | |||
| + | Source: The amino sequence of this part was taken from Uniprot (wax-dgaT accesion Q8GGG1; http://www.uniprot.org/uniprot/Q8GGG1) and then codon optimization for ''R. opacus'' (avoiding restriction sites for the standard assembly method) | ||
| + | |||
| + | |||
| + | == Part:BBa_K836003 == | ||
| + | |||
| + | lipA from ''B. cepacia''. This biobrick codifies for the protein lipA from ''Burkholderia cepacia'' (''Pseudomonas cepacia'') which catalyzes the hydrolysis of triglycerides (Triacylglycerol + H2O = diacylglycerol + a carboxylate). In the presence of certain alcohols, it catalyzes the transesterification of TGAs to produce acyl esters and glycerol. | ||
| + | It has only one PTM (Post-Translational Modification) which consists in a sulfide bond between 234 and 314 aa. Calcium serves as a cofactor for this enzyme (1 ion per subunit). The native signal peptide was not modified. | ||
| + | The sequence of a transcriptional terminator (biobrick BBa_B1006) was set at the end of the coding sequence. | ||
| + | |||
| + | Source: The amino sequence of this part was taken from Uniprot (lipA accesion P22088; http://www.uniprot.org/uniprot/P22088) and then codon optimization for E. coli (avoiding restriction sites for the standard assembly method). | ||
| + | |||
| + | |||
| + | == Detailed parts == | ||
| + | |||
| + | <groupparts>iGEM012 Costa_Rica-TEC-UNA</groupparts> | ||
Latest revision as of 03:55, 27 September 2012
Biobricks designed
BBa_K836006
Lysis protein S from Enterobacteria phage lambda. This gene codifies for a protein that makes holes in the inner membrane of the bacterial cell. Between the RBS and the CDS a spacer consisting on a scar from a standard suffix and a prefix for CDS was inserted.
Source: http://www.uniprot.org/uniprot/P03705#section_seq it was optimized for R. opacus (avoiding standard restriction sites)
Part:BBa_K836005
Lysozyme from Rhodococcus phage RER2. Protein involved in the peptidoglycan degradation of the bacterial cell wall. A RBS for Gram positive bacteria (SpoVG) was added at the beginning.A spacer was put between the RBS and the start codon which corresponds to the scar between a normal suffix and the prefix used for CDS to avoid RBS-CDS problems. The sequence has no termination codon since we rely on the double terminators of the scar formed during assembly of biobricks.
Source: http://www.uniprot.org/uniprot/G9FHW6) and then it was optimized for R. opacus (avoiding standard restriction sites).
Part:BBa_K836007
Nitrilase regulator from R. rhodochrous. Protein in charge to regulate the expression of the genes put under control of nitA promoter. A spacer which consist of the scar left by the assembly of a normal suffix and a CDS prefix was inserted between RBS and CDS. The sequence has no termination codon since we rely on the double terminators of the scar formed during assembly of biobricks.
Source: The amino sequence was obtained from Uniprot (http://www.uniprot.org/uniprot/P72312) and then the condon usage was optimized for expression in R. opacus.
Part:BBa_K836008
nitA promoter. Promoter inducible by nitrile and similar agents.
Part:BBa_K836009
Lysis device for R. opacus. Lysis construct based on the one presented by Berkeley's 2008 team BBa_K112022. It is based on the inducible expression of a lysozyme and lambda phage's holin in order to liberate internal products of the bacterial cell in an efficient way. The induction is achieved by the addition of nitrile or a similar agent since both genes are regulated by nitA promoter. Constitutive expression of nitR and a low constitutive expression of an antiholin are required to avoid undesired lysis.
Source: The majority of the parts where made by backtranslating a protein. Others are existing biobricks while some are promoters obtained from databases as NCBI.
Part:BBa_K836002
O-acyltransferase WSD from Acinetobacter sp. This biobrick codifies for the protein DGAT (Diacylglycerol O-acyltransferase) which have dual activity, it can act as a wax ester synthase or as a diacylglycerol acyltransferase. In the latter case, its function consists in mediate the final step in TGAs synthesis using a fatty acyl-CoA and a DGA. This enzyme is vital in the storage and synthesis of lipids. Two transcriptional terminators (two biobricks BBa_B1006) were set at the end of the coding sequence.
Source: The amino sequence of this part was taken from Uniprot (wax-dgaT accesion Q8GGG1; http://www.uniprot.org/uniprot/Q8GGG1) and then codon optimization for R. opacus (avoiding restriction sites for the standard assembly method)
Part:BBa_K836003
lipA from B. cepacia. This biobrick codifies for the protein lipA from Burkholderia cepacia (Pseudomonas cepacia) which catalyzes the hydrolysis of triglycerides (Triacylglycerol + H2O = diacylglycerol + a carboxylate). In the presence of certain alcohols, it catalyzes the transesterification of TGAs to produce acyl esters and glycerol. It has only one PTM (Post-Translational Modification) which consists in a sulfide bond between 234 and 314 aa. Calcium serves as a cofactor for this enzyme (1 ion per subunit). The native signal peptide was not modified. The sequence of a transcriptional terminator (biobrick BBa_B1006) was set at the end of the coding sequence.
Source: The amino sequence of this part was taken from Uniprot (lipA accesion P22088; http://www.uniprot.org/uniprot/P22088) and then codon optimization for E. coli (avoiding restriction sites for the standard assembly method).
Detailed parts
<groupparts>iGEM012 Costa_Rica-TEC-UNA</groupparts>
