Difference between revisions of "Part:BBa K3520008"
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| − | The signal for initiation of protein synthesis in bacteria | + | The signal for initiation of protein synthesis in bacteria consists of both an AUG codon and an rRNA sequence, which is called the “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 from the Flavobacterium species, in which 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] |
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=Athens 2020= | =Athens 2020= | ||
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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. | 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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=SOURCE OF THIS PART= | =SOURCE OF THIS PART= | ||
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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 | [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 | [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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Revision as of 03:19, 28 October 2020
Flavobacteria RBS
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]
Description
The signal for initiation of protein synthesis in bacteria consists of both an AUG codon and an rRNA sequence, which is called the “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 from the Flavobacterium species, in which 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