Difference between revisions of "Part:BBa K3520007"

 
 
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<partinfo>BBa_K3520007 short</partinfo>
 
<partinfo>BBa_K3520007 short</partinfo>
  
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<partinfo>BBa_K3520007 SequenceAndFeatures</partinfo>
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<br><br>
  
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<!-- Add more about the biology of this part here
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<br/><br/>
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===Usage and Biology===
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<!-- -->
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=Description=
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<span class='h3bb'>Sequence and Features</span>
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<br>
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<partinfo>BBa_K3520007 SequenceAndFeatures</partinfo>
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ompA is a constitutive promoter found in bacteria of the Bacteroidetes phylum. Bacteroidetes' promoters are generally characterised by a certain motif, upstream of the ORF. The motif, that constitutes part of the ompA promoter as well, is TTG at the -33 region and TAnnTTTG at the -7 region. The -33 region has proven to be necessary for maximum expression[2], while the -7 region plays an important role in maximizing promoter activity [1].
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The ompA promoter is highly efficient in Flavobacteria, but functions poorly in E. coli. Thus, it has a potent ability to drive the expression of heterologous genes [1]. The promoter observed in Flavobacterium strains indicates a preference in A in the +1 region. [2]
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<br><br>
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=Athens 2020=
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<br>
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This part is designed by iGEM Athens 2020 team during the project MORPHÆ. In this project, Flavobacteria were used to produce a non-cellular structurally coloured biomaterial which would require the secretion of a biomolecule that Flavobacteria do not normally secrete. Our hypothesis is that the formed matrix will have a structure similar to that of the biofilm and thus, it will provide the material with macroscopically the same colouration properties as the biofilm.
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<br><br>
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=SOURCE OF THIS PART=
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<br>
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The sources of the current promoter are the scientific publications below.
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<br><br>
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=Useful Links:=
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<br>
  
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NCBI taxonomy:<br /><br />
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https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=28448&lvl=3&lin=f&keep=1&srchmode=1&unlock<br /><br />
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GenBank link:<br /><br />
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https://www.ncbi.nlm.nih.gov/nuccore/X54676.1<br /><br />
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Codon optimisation bank:<br /><br />
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http://genomes.urv.es/OPTIMIZER/?fbclid=IwAR0ALbP_C8UVY4itvYdNX8b5KYYUM5ulQojz8UJAK6Zj5llobNNxE-jYmXQ<br /><br />
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Codon optimization table:<br /><br />
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https://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=376686&fbclid=IwAR0gwwrIarZsiYhWvHPc2BKy-iB_2OM-DPB5I2HYJZwBNiasmlLXWK87PwM<br /><br />
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<br><br>
  
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<!-- Uncomment this to enable Functional Parameter display
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=REFERENCES=
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===Functional Parameters===
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<br>
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<partinfo>BBa_K3520007 parameters</partinfo>
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[1] Chen, S., Kaufman, M., Bagdasarian, M., Bates, A., & Walker, E. (2010). Development of an efficient expression system for Flavobacterium strains. Gene, 458(1-2), 1-10. doi: 10.1016/j.gene.2010.02.006
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[2] Chen, S., Bagdasarian, M., Kaufman, M., & Walker, E. (2006). Characterization of Strong Promoters from an Environmental Flavobacterium hibernum Strain by Using a Green Fluorescent Protein-Based Reporter System. Applied And Environmental Microbiology, 73(4), 1089-1100. doi: 10.1128/aem.01577-06

Latest revision as of 03:16, 28 October 2020


Promoter ompA for Flavobacteriia


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]





Description


ompA is a constitutive promoter found in bacteria of the Bacteroidetes phylum. Bacteroidetes' promoters are generally characterised by a certain motif, upstream of the ORF. The motif, that constitutes part of the ompA promoter as well, is TTG at the -33 region and TAnnTTTG at the -7 region. The -33 region has proven to be necessary for maximum expression[2], while the -7 region plays an important role in maximizing promoter activity [1]. The ompA promoter is highly efficient in Flavobacteria, but functions poorly in E. coli. Thus, it has a potent ability to drive the expression of heterologous genes [1]. The promoter observed in Flavobacterium strains indicates a preference in A in the +1 region. [2]

Athens 2020


This part is designed by iGEM Athens 2020 team during the project MORPHÆ. In this project, Flavobacteria were used to produce a non-cellular structurally coloured biomaterial which would require the secretion of a biomolecule that Flavobacteria do not normally secrete. Our hypothesis is that the formed matrix will have a structure similar to that of the biofilm and thus, it will provide the material with macroscopically the same colouration properties as the biofilm.


SOURCE OF THIS PART


The sources of the current promoter are the scientific publications below.

Useful Links:


NCBI taxonomy:

https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=28448&lvl=3&lin=f&keep=1&srchmode=1&unlock

GenBank link:

https://www.ncbi.nlm.nih.gov/nuccore/X54676.1

Codon optimisation bank:

http://genomes.urv.es/OPTIMIZER/?fbclid=IwAR0ALbP_C8UVY4itvYdNX8b5KYYUM5ulQojz8UJAK6Zj5llobNNxE-jYmXQ

Codon optimization table:

https://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=376686&fbclid=IwAR0gwwrIarZsiYhWvHPc2BKy-iB_2OM-DPB5I2HYJZwBNiasmlLXWK87PwM



REFERENCES


[1] Chen, S., Kaufman, M., Bagdasarian, M., Bates, A., & Walker, E. (2010). Development of an efficient expression system for Flavobacterium strains. Gene, 458(1-2), 1-10. doi: 10.1016/j.gene.2010.02.006 [2] Chen, S., Bagdasarian, M., Kaufman, M., & Walker, E. (2006). Characterization of Strong Promoters from an Environmental Flavobacterium hibernum Strain by Using a Green Fluorescent Protein-Based Reporter System. Applied And Environmental Microbiology, 73(4), 1089-1100. doi: 10.1128/aem.01577-06