Difference between revisions of "Part:BBa K844008"

(New page: __NOTOC__ <partinfo>BBa_K844001 short</partinfo> Spider silk subunit optimized to use a reduced set of tRNA codons (1 to 2 codons per amino acid); contains two elasticity domains and one...)
 
 
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__NOTOC__
 
__NOTOC__
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<partinfo>BBa_K844001 short</partinfo>
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<partinfo>BBa_K844008 short</partinfo>
  
 
Spider silk subunit optimized to use a reduced set of tRNA codons (1 to 2 codons per amino acid); contains  two elasticity domains and one strength domain, also contains 5’ Met (ATG) codon.
 
Spider silk subunit optimized to use a reduced set of tRNA codons (1 to 2 codons per amino acid); contains  two elasticity domains and one strength domain, also contains 5’ Met (ATG) codon.
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IMPORTANT NOTE: This part uses [https://parts.igem.org/Assembly_standard_23 Assembly Standard #23 (Silver Fusion)] scar sites, which the sequence data below and on composite parts using this part will not reflect this scar sequence (it shows [https://parts.igem.org/Assembly_standard_10 Assembly Standard #10] scars).
  
  
 
===Usage and Biology===
 
===Usage and Biology===
  
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This subunit is based on the 2E subunit from MaSp2 silk gene from Argiope aurantia The DNA sequence was altered from the native sequence so that each of the six amino acids in the silk subunit has either one or two codons representing it (example: all glycines are GGT or GGA in the DNA). See part [https://parts.igem.org/Part:BBa_K844004 BBa_K844004] for additional sequence details. This part contains an added Met (ATG) codon at the 5’ end and is designed for use as the first subunit in a longer spider silk construct. This part should be followed by numerous repeats of the K844004 silk subunit, and the silk coding region should end with a K844012 subunit, which contains a 10-Histidine tag and a double stop codon (TAATAA).
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This subunit is based on the 2E subunit from MaSp2 silk gene from ''Argiope aurantia'' The DNA sequence was altered from the native sequence so that each of the six amino acids in the silk subunit has either one or two codons representing it (example: all glycines are GGT or GGA in the DNA). See part [https://parts.igem.org/Part:BBa_K844004 BBa_K844004] for additional sequence details. This part contains an added Met (ATG) codon at the 5’ end and is designed for use as the first subunit in a longer spider silk construct. This part should be followed by numerous repeats of the [https://parts.igem.org/Part:BBa_K844004 BBa_K844004] silk subunit, and the silk coding region should end with a [https://parts.igem.org/Part:BBa_K844000 BBa_K844000] part, which contains a 10-Histidine tag and a double stop codon (TAATAA).
  
 
The silk subunit contains four main domains: two elasticity domains, a linker domain, and a strength domain. The elasticity domains contains sequences coding for beta-helices and beta-spiral in the protein; these structures increase the elasticity of the spider silk. The linker domain joins the strength and elasticity domains together. The strength domain will form beta-sheets and strengthen the silk fibers by cross-linking silk strands.
 
The silk subunit contains four main domains: two elasticity domains, a linker domain, and a strength domain. The elasticity domains contains sequences coding for beta-helices and beta-spiral in the protein; these structures increase the elasticity of the spider silk. The linker domain joins the strength and elasticity domains together. The strength domain will form beta-sheets and strengthen the silk fibers by cross-linking silk strands.
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===Silk Subunit Amino Acid Composition:===
 
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https://static.igem.org/mediawiki/parts/5/50/Silk_Subunit_U_Sequence_Composition.PNG
 
  
  
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[https://parts.igem.org/Part:BBa_K844004 BBa_K844004] – this spider silk subunit '''without''' the added Met (ATG) start codon at the 5’ end
 
[https://parts.igem.org/Part:BBa_K844004 BBa_K844004] – this spider silk subunit '''without''' the added Met (ATG) start codon at the 5’ end
  
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[https://parts.igem.org/Part:BBa_K844016 BBa_K844016] – this part is an expression unit containing this silk subunit fused to a 10x-His Tag. This protein generator is driven by a lactose/IPTG inducible promoter coupled with a RBS.
  
 
===References:===
 
===References:===
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<span class='h3bb'>Sequence and Features</span>
 
<span class='h3bb'>Sequence and Features</span>
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<partinfo>BBa_K844001 SequenceAndFeatures</partinfo>
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<partinfo>BBa_K844008 SequenceAndFeatures</partinfo>
  
  
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<!-- Uncomment this to enable Functional Parameter display
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===Functional Parameters===
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<partinfo>BBa_K844001 parameters</partinfo>
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==Functional Parameters: Austin_UTexas==
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<html>
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<body>
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<partinfo>BBa_K844008 parameters</partinfo>
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<h3><center>Burden Imposed by this Part:</center></h3>
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<figure>
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<div class = "center">
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<center><img src = "https://static.igem.org/mediawiki/parts/f/fa/T--Austin_Utexas--no_burden_icon.png" style = "width:160px;height:120px"></center>
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</div>
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<figcaption><center><b>Burden Value: 7.6 ± 11.5% </b></center></figcaption>
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</figure>
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<p> Burden is the percent reduction in the growth rate of <i>E. coli</i> cells transformed with a plasmid containing this BioBrick (± values are 95% confidence limits). This BioBrick did not exhibit a burden that was significantly greater than zero (i.e., it appears to have little to no impact on growth). Therefore, users can depend on this part to remain stable for many bacterial cell divisions and in large culture volumes. Refer to any one of the
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<a href="https://parts.igem.org/Part:BBa_K3174002">BBa_K3174002</a> - <a href="https://parts.igem.org/Part:BBa_K3174007">BBa_K3174007</a> pages for more information on the methods, an explanation of the sources of burden,  and other conclusions from a large-scale measurement project conducted by the <a href="http://2019.igem.org/Team:Austin_UTexas">2019 Austin_UTexas team</a>.</p>
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<p>This functional parameter was added by the <a href="https://2020.igem.org/Team:Austin_UTexas/Contribution">2020 Austin_UTexas team.</a></p>
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</body>
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</html>

Latest revision as of 22:45, 3 September 2020

Spider Silk 1x Subunit "B" (Balanced tRNA codon optimized) with Met (ATG) added

Spider silk subunit optimized to use a reduced set of tRNA codons (1 to 2 codons per amino acid); contains two elasticity domains and one strength domain, also contains 5’ Met (ATG) codon.

IMPORTANT NOTE: This part uses Assembly Standard #23 (Silver Fusion) scar sites, which the sequence data below and on composite parts using this part will not reflect this scar sequence (it shows Assembly Standard #10 scars).


Usage and Biology

This subunit is based on the 2E subunit from MaSp2 silk gene from Argiope aurantia The DNA sequence was altered from the native sequence so that each of the six amino acids in the silk subunit has either one or two codons representing it (example: all glycines are GGT or GGA in the DNA). See part BBa_K844004 for additional sequence details. This part contains an added Met (ATG) codon at the 5’ end and is designed for use as the first subunit in a longer spider silk construct. This part should be followed by numerous repeats of the BBa_K844004 silk subunit, and the silk coding region should end with a BBa_K844000 part, which contains a 10-Histidine tag and a double stop codon (TAATAA).

The silk subunit contains four main domains: two elasticity domains, a linker domain, and a strength domain. The elasticity domains contains sequences coding for beta-helices and beta-spiral in the protein; these structures increase the elasticity of the spider silk. The linker domain joins the strength and elasticity domains together. The strength domain will form beta-sheets and strengthen the silk fibers by cross-linking silk strands.


Related parts:

BBa_K844002 – the native 2E spider silk subunit with two elasticity domains and one strength domain (no sequence manipulation)

BBa_K844004 – this spider silk subunit without the added Met (ATG) start codon at the 5’ end

BBa_K844016 – this part is an expression unit containing this silk subunit fused to a 10x-His Tag. This protein generator is driven by a lactose/IPTG inducible promoter coupled with a RBS.

References:

Brooks AE, Stricker SM, Joshi SB, Kamerzell TJ, Middaugh CR, and Lewis RV. 2008. Properties of synthetic spider silk fibers based on Argiope aurantia MaSp2. Biomacromolecules 9:1506–10.


Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]



Functional Parameters: Austin_UTexas

BBa_K844008 parameters

Burden Imposed by this Part:

Burden Value: 7.6 ± 11.5%

Burden is the percent reduction in the growth rate of E. coli cells transformed with a plasmid containing this BioBrick (± values are 95% confidence limits). This BioBrick did not exhibit a burden that was significantly greater than zero (i.e., it appears to have little to no impact on growth). Therefore, users can depend on this part to remain stable for many bacterial cell divisions and in large culture volumes. Refer to any one of the BBa_K3174002 - BBa_K3174007 pages for more information on the methods, an explanation of the sources of burden, and other conclusions from a large-scale measurement project conducted by the 2019 Austin_UTexas team.

This functional parameter was added by the 2020 Austin_UTexas team.