Difference between revisions of "Part:BBa K3520008"
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__NOTOC__
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<partinfo>BBa_K3520008 short</partinfo>
  
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<b>Flavobacteria RBS
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<partinfo>BBa_K3520008 SequenceAndFeatures</partinfo>
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<br><br>
  
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<br/><br/>
  
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==Project-General==
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=Description=
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The current part is designed by iGEM Athens 2020 team during the project MORPHÆ. In this project Flavobacteriia were used to produce a non-cellular structurally coloured biomaterial which would require the secretion of a biomolecule that Flavobacteriia 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>
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The signal for initiation of protein synthesis in bacteria consist of both an AUG codon and an rRNA sequence which is called “Shine-Dalgarno sequence” and it is part of the RBS. This sequence is usually located 4 to 9 nucleotides upstream of the initiator AUG in many mRNAs and its exact sequence is 5’ AGGAGG 3’. The above information is very different to the Flavobacterium species where the most effective RBS sequence seems to be 5’ TAAAA 3’. This sequence is usually found 25 bases upstream of the AUG codon and it seems to show the higher expression level for proteins that come after it.The 3′ end of the 16S rRNA of Flavobacterium strains is 5′-CUGGAUCACCUCCUUUCUA-3′. This does include a sequence partially complementary to the sequence “TAAAA” found upstream of the open reading frames from various Flavobacterium strains.
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[2]
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=Athens 2020=
 +
<br>
 +
 
 +
The current 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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 +
 
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=SOURCE OF THIS PART=
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<br>
 +
The sources of the current promoter are the scientific publications below.
 +
<br><br>
 +
 
 +
=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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=REFERENCES=
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<br>
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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
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<!-- Add more about the biology of this part here
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===Usage and Biology===

Revision as of 01:17, 28 October 2020

Flavobacteria RBS


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


The signal for initiation of protein synthesis in bacteria consist of both an AUG codon and an rRNA sequence which is called “Shine-Dalgarno sequence” and it is part of the RBS. This sequence is usually located 4 to 9 nucleotides upstream of the initiator AUG in many mRNAs and its exact sequence is 5’ AGGAGG 3’. The above information is very different to the Flavobacterium species where the most effective RBS sequence seems to be 5’ TAAAA 3’. This sequence is usually found 25 bases upstream of the AUG codon and it seems to show the higher expression level for proteins that come after it.The 3′ end of the 16S rRNA of Flavobacterium strains is 5′-CUGGAUCACCUCCUUUCUA-3′. This does include a sequence partially complementary to the sequence “TAAAA” found upstream of the open reading frames from various Flavobacterium strains. [2]

Athens 2020


The current 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