Difference between revisions of "Part:BBa K3114008"
 
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<partinfo>BBa_K3114008 short</partinfo>
 
<partinfo>BBa_K3114008 short</partinfo>
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Chlorophyll B Reductase is a naturally occurring plant enzyme, encoded by the gene NYC1, which catalyzes the first step of chlorophyll b degradation (Horie et al. 2009). Specifically, chlorophyll b reductase converts chlorophyll b into 7-Hydroxymethyl Chlorophyll a.
 
  
  
 
===Usage and Biology===
 
===Usage and Biology===
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BBa_K3114008 is a golden gate compatible part which allows insertion of the NYC1 gene into genetic circuits to express the enzyme chlorophyll B reductase.
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Chlorophyll B Reductase is a naturally occurring plant enzyme, encoded by the gene NYC1, which catalyzes the first step of chlorophyll b degradation (Horie et al. 2009). With the cofactor NADPH, chlorophyll b reductase converts chlorophyll b into 7-Hydroxymethyl Chlorophyll a.
  
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==Collection of Parts==
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BBa_K3114008 is a golden gate compatible part which allows insertion of the NYC1 gene into genetic circuits to express the enzyme chlorophyll B reductase. In creating this part, iGEM Calgary wished to allow the golden gate cloning of this plant enzyme into <i>E.coli</i> for other teams to use in projects involving degradation of chlorophyll. This part was designed to be golden-gate compatible based on the Mo-Clo standard (Weber et al., 2011). It is also compatible with the BioBrick RFC[10] standard.
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This part was designed to be Golden Gate compatible with all of the other Golden Gate parts in iGEM Calgary's 2019 part collection including the following: <br/>
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1. DsbA signal peptide - Bba_K3114000 https://parts.igem.org/Part:BBa_K3114000<br/>
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This part is compatible with other golden gate parts created by iGEM Calgary including the following:
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2. MalE signal peptide - Bba_K3114001 https://parts.igem.org/Part:BBa_K3114001<br/>
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<ul>
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3. OmpA signal peptide - Bba_K3114002 https://parts.igem.org/Part:BBa_K3114002<br/>
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        <li>DsbA signal peptide [https://parts.igem.org/Part:BBa_K3114000 (BBa_K3114000)]</li>
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4. PhoA signal peptide - Bba_K3114003 https://parts.igem.org/Part:BBa_K3114003<br/>
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<li>MalE signal peptide [https://parts.igem.org/Part:BBa_K3114001 (BBa_K3114001)]</li>  
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5. Tat signal peptide - Bba_K3114004 https://parts.igem.org/Part:BBa_K3114004<br/>
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<li>OmpA signal peptide [https://parts.igem.org/Part:BBa_K3114002 (BBa_K3114002)]</li>  
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6. TorA signal peptide - Bba_K3114005 https://parts.igem.org/Part:BBa_K3114005<br/>
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<li>PhoA signal peptide [https://parts.igem.org/Part:BBa_K3114003 (BBa_K3114003)]</li>
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7. Double Terminator  - Bba_K3114013 https://parts.igem.org/Part:BBa_K3114013
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<li>TorA signal peptide [https://parts.igem.org/Part:BBa_K3114005 (BBa_K3114005)]</li>
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<li>YcbK signal peptide [https://parts.igem.org/Part:BBa_K3114004 (BBa_K3114004)]</li>
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        <li>Double Terminator  [https://parts.igem.org/Part:BBa_K3114013 (BBa_K3114013)]</li>
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        <li>Universal Spacer with 6XHis tag and Double Terminator [https://parts.igem.org/Part:BBa_K3114014 (BBa_k3114014)]</li>
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</ul>
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===Design===
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When designing this part and the rest of our collection, we were interested in creating parts that could be used in Golden Gate assembly right out of the distribution kit without the need to first domesticate them in a Golden Gate entry vector. As such, these parts are not compatible with the iGEM Type IIS RFC[1000] assembly standard because we included the BsaI restriction site and MoClo standard fusion site in the part’s sequence.
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As per the MoClo standard, the 5’ signal peptide fusion sequence included in this part is AATG, and the 5’ signal peptide fusion sequence is AGGT.
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[[Image:T--Calgary--MoClo1.png|900px|thumb|center|Figure 1. Fusion sites used in the MoClo standard for Golden Gate assembly (Weber et al., 2011).]]
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This part includes a start codon. A Gly-Gly spacer sequence was added to the end of the signal peptide sequence in order to ensure that the fused protein of interest will be in-frame following Golden Gate assembly.
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This sequence has been codon optimized for high expression in <i>E. coli</i>.
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===Sequences and Features===
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<partinfo>BBa_K3114008 SequenceAndFeatures</partinfo>
  
  
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Horie, Y., Ito, H., Kusaba, M., Tanaka, R., & Tanaka, A. (2009). Participation of chlorophyll b reductase in the initial step of the degradation of light-harvesting chlorophyll a/b-protein complexes in Arabidopsis. Journal of Biological Chemistry, 284(26), 17449-17456.
 
Horie, Y., Ito, H., Kusaba, M., Tanaka, R., & Tanaka, A. (2009). Participation of chlorophyll b reductase in the initial step of the degradation of light-harvesting chlorophyll a/b-protein complexes in Arabidopsis. Journal of Biological Chemistry, 284(26), 17449-17456.
  
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<span class='h3bb'>Sequence and Features</span>
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Weber, E., Engler, C., Gruetzner, R., Werner, S., & Marillonnet, S. (2011). A modular cloning system for standardized assembly of multigene constructs. <i>PLoS ONE</i>, 6(2). https://doi.org/10.1371/journal.pone.0016765
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<partinfo>BBa_K3114008 SequenceAndFeatures</partinfo>
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Latest revision as of 23:51, 18 October 2019


Chlorophyll B Reductase (CBR)


Usage and Biology

Chlorophyll B Reductase is a naturally occurring plant enzyme, encoded by the gene NYC1, which catalyzes the first step of chlorophyll b degradation (Horie et al. 2009). With the cofactor NADPH, chlorophyll b reductase converts chlorophyll b into 7-Hydroxymethyl Chlorophyll a.

BBa_K3114008 is a golden gate compatible part which allows insertion of the NYC1 gene into genetic circuits to express the enzyme chlorophyll B reductase. In creating this part, iGEM Calgary wished to allow the golden gate cloning of this plant enzyme into E.coli for other teams to use in projects involving degradation of chlorophyll. This part was designed to be golden-gate compatible based on the Mo-Clo standard (Weber et al., 2011). It is also compatible with the BioBrick RFC[10] standard.

This part is compatible with other golden gate parts created by iGEM Calgary including the following:


Design

When designing this part and the rest of our collection, we were interested in creating parts that could be used in Golden Gate assembly right out of the distribution kit without the need to first domesticate them in a Golden Gate entry vector. As such, these parts are not compatible with the iGEM Type IIS RFC[1000] assembly standard because we included the BsaI restriction site and MoClo standard fusion site in the part’s sequence.

As per the MoClo standard, the 5’ signal peptide fusion sequence included in this part is AATG, and the 5’ signal peptide fusion sequence is AGGT.

Figure 1. Fusion sites used in the MoClo standard for Golden Gate assembly (Weber et al., 2011).

This part includes a start codon. A Gly-Gly spacer sequence was added to the end of the signal peptide sequence in order to ensure that the fused protein of interest will be in-frame following Golden Gate assembly.

This sequence has been codon optimized for high expression in E. coli.



Sequences and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal XhoI site found at 4
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI site found at 1
    Illegal BsaI.rc site found at 1061


References

Horie, Y., Ito, H., Kusaba, M., Tanaka, R., & Tanaka, A. (2009). Participation of chlorophyll b reductase in the initial step of the degradation of light-harvesting chlorophyll a/b-protein complexes in Arabidopsis. Journal of Biological Chemistry, 284(26), 17449-17456.


Weber, E., Engler, C., Gruetzner, R., Werner, S., & Marillonnet, S. (2011). A modular cloning system for standardized assembly of multigene constructs. PLoS ONE, 6(2). https://doi.org/10.1371/journal.pone.0016765