Team:Costa Rica-TEC-UNA/Parts

From 2012.igem.org

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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.

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>

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-        <a href="https://igem.org/Team.cgi?year=2012&team_name=Costa_Rica-TEC-UNA">Official team profile</a>
          <a href="https://2012.igem.org/Team:Costa_Rica-TEC-UNA/Team">Team Members and Advisors</a>
          </div>
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          <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/Modeling">Modeling</a>
          </div>
      </li>
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          <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/Human Practice">Human Practice</a>
+        <a href="https://igem.org/Team.cgi?year=2012&team_name=Costa_Rica-TEC-UNA">Official team profile</a>
          </div>
      </li>
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-An important aspect of the iGEM competition is the use and creation of standard  biological parts. Each team will make new parts during iGEM and will place them in the [http://partsregistry.org Registry of Standard Biological Parts]. The iGEM software provides an easy way to present the parts your team has created . The "groupparts" tag will generate a table with all of the parts that your team adds to your team sandbox.  Note that if you want to document a part you need to document it on the [http://partsregistry.org Registry], not on your team wiki.
-Remember that the goal of proper part documentation is to describe and define a part such that it can be used without a need to refer to the primary literature. The next iGEM team should be able to read your documentation and be able to use the part successfully. Also, you should provide proper references to acknowledge previous authors and to provide for  users who wish to know more.
+== '''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.
+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>
+                                <groupparts>iGEM012 Costa_Rica-TEC-UNA</groupparts>