AND Heavy Metals

AND Sugar'

CzrA-ArsR AND GATE

HEAVY-METAL AND

This construct was designed to function as a logic gate, an AND to be specific. This is due to the way the CzrA-ArsR promoter was designed. We used a system that sensed heavy metals in Bacillus subtilis, which was originally designed by the iGEM Newcastle team 2009 (Newcastle University iGEM team 2009). This system consists of a fused promoter, which includes both ArsR and CzrA binding sites. Arar and CzrA are metal sensing repressors. They both respond to cadmium, however silver, arsenic, or copper induces ArsR and zinc, cobalt, or nickel induces CzrA as well (Moore CM, Helmann JD. Metal ion homeostasis in Bacillus subtilis. Curr Opin Microbiol. 2005 Apr;8(2):188-95.). If we use two different metals, specific for each repressor we will have an AND gate. Besides Newcastle’s 2009 design, we designed two different fused promoters with the same binding sites but in different order to try different combinations that could make the system more efficient.


To obtain our final construct we required the following Biological Parts:


Obtained from the registry:
[http://partsregistry.org/Part:BBa_K143001 BBa_K143001 (AmyE 5’)]
[http://partsregistry.org/Part:BBa_K143002 BBa_K143002] (AmyE 3’)
[http://partsregistry.org/Part:BBa_E1010 BBa_E1010 (RFP)]
[http://partsregistry.org/Part:BBa_B0014 BBa_B0014 (Terminator)]
[http://partsregistry.org/wiki/index.php?title=Part:BBa_C0179 BBa_C0179 (LasR)]


Synthesis Products:
CzrA-AsR 99
CzrA-AsR 98
CzrA-AsR 97
RBS-CI


Obtained from Margarita Salas Ph.D.’s Group:
P4 from phage phi29 from plasmid pRMn25.


Omega cassette from plasmid pHP45Ω.

We designed the following primers to add the RBS site to BBa_C0179, BBa_E100 and P4.

LASR_2.0_seq_registry
UPPER 5'-3'
PREFIJO+RBS+ESPACIADOR+LASR
GTTTCTTCGAATTCGCGGCCGCTTCTAGAG AAAGGTGGTGAA TACTAG atggccttggttgac

LOWER 5'-3'
SUFIJO+LASR_
GTTTCTTCCTGCAGCGGCCGCTACTAGTATTATTA ttattagagagtaat

RFP
UPPER 5'-3'
PREFIX+RBS+SPACER+RFP
GTTTCTTCGAATTCGCGGCCGCTTCTAGAG AAAGGTGGTGAA TACTAG ATGGCTTCCTCCGAA

LOWER 5'-3'
SUFIX+RFP
GTTTCTTCCTGCAGCGGCCGCTACTAGTA TTATTAAGCACCGGT

P4
PREFIX+RBS+SPACER+P4
UPPER
GTTTCTTCGAATTCGCGGCCGCTTCTAGAG AAAGGTGGTGAA TACTAG ATGCCTAAAACACAA

SUFIX+P4
LOWER 5'-3'
GTTTCTTCCTGCAGCGGCCGCTACTAGTATTATTA CTACACCATACTTTT


This metal AND team had to build the following construct:

The other AND (pBad/pXyl) team was in charge of building this part.

So we obtain the final product:

After the Regional Jamboree, we continued working very hard, and our work has paid off, these our new results: Amy,98,P4,CI,RFP,TT
Amy99,P4,CI,RFP,TT
Also we feel very proud and excited because we finally have one complete AND gate =D !!!!
AMY,97,P4,CI,RFP,TT,OMEGA,AMY3

AmyE 5’_ArsR/CzrA 97-99, P4_CI, RFP_Terminator, P4_CI_RFP_Terminator and AmyE 5’_CzrA/ArsR 99-97_P4CI_RFP_Terminator

ARABINOSE-XYLOSE AND GATE

SWEET AND

This construct was designed to function as a AND logic gate. This is due to the way the pBad/pXyl promoter was designed. We used a system that sensed l-arabinose in E.coli which was originally designed by Amelia Hardjasa and used by iGEM09_British_Columbia1,2. In the absence of arabinose, the repressor protein AraC (BBa_C0080) binds to the AraI1 operator site of pBAD and the upstream operator site AraO2, blocking transcription1. In the presence of arabinose, AraC binds to it and changes its conformation such that it interacts with the AraI1 and AraI2 operator sites, permitting transcription1. We also used a promoter inducible by xylose that has been designed for high expression in B.subtilis which was originally designed by James Chappell and used by iGEM08_Imperial_College. Xylose does not induce the promoter xylose directly, but requires the transcriptional regulator XylR (BBa_K143036). Our system consists in a fused promoter which includes both AraC and XylR binding sites. AraC and XylR are l-arabinose and xylose sensing, respectively, repressors. In this way, if we use these two inputs, each specific for each repressor we will have an AND gate.
To obtain our final construct we required the following Biological Parts:


Obtained from the Registry:
[http://partsregistry.org/Part:BBa_K143001 BBa_K143001 (AmyE 5’)]
[http://partsregistry.org/Part:BBa_K143002 BBa_K143002 (AmyE 3’)]
[http://partsregistry.org/Part:BBa_E1010 BBa_E1010 (RFP)]
[http://partsregistry.org/Part:BBa_B0014 BBa_B0014 (Terminator)]
[http://partsregistry.org/wiki/index.php/Part:BBa_C0080 BBa_C0080 (AraC)]

Synthesis Products:
pBad/pXyl promoter
RBS XylR

Obtained from Margarita Salas Ph.D.’s Group:
A3 from phage phi29 from plasmid pFRC54.

Omega cassette from plasmid pHP45Ω.

We designed the following primers to add the RBS site to BBa_E1010 (RFP) and BBa_C0080 (AraC):
RFP
UPPER 5'-3'
PREFIX+RBS+SPACER+RFP
GTTTCTTCGAATTCGCGGCCGCTTCTAGAG AAAGGTGGTGAA TACTAG ATGGCTTCCTCCGAA
LOWER 5'-3'
SUFIX+RFP
GTTTCTTCCTGCAGCGGCCGCTACTAGTA TTATTAAGCACCGGT

ARAC without LVA
UPPER 5'-3'
PREFIX+RBS+SPACER+ARAC
GTTTCTTCGAATTCGCGGCCGCTTCTAGAG AAAGGTGGTGAA TACTAG ATGGCTGAAGCGCAA
LOWER 5'-3'
SUFIX+ARAC
GTTTCTTCCTGCAGCGGCCGCTACTAGTATTATTA CAACTTGACGGCTAC

We also designed the following primers to obtain A3 from phage phi29 from plasmid pFRC54 and Omega cassette from plasmid pHP45Ω:

A3
UPPER 5'-3'
PREFIX+A3
5' GTTTCTTCGAATTCGCGGCCGCTTCTAGAG taactttttgcaaga 3'
LOWER 5'-3'
SUFIX+A3
5'GTTTCTTCCTGCAGCGGCCGCTACTAGTA ctacttaattatacc 3'


OMEGA CASSETTE
PREFIX+OMEGA CASSETTE(45 bp)
5' GTTTCTTCGAATTCGCGGCCGCTTCTAGAG CCGGGGATCCGGTGA 3'

SUFIX+OMEGA CASSETTE (44 bp)
5' GTTTCTTCCTGCAGCGGCCGCTACTAGTA CCGGGGATCCGGTGA 3'


This arabinose-xylose AND team had to build the following constructs:

The other AND (heavy metals) team was in charge of building this part.

RFP_Terminator

So we could obtain the final product:

What we have up now is:

AmyE 5’_pBad/pXyl, pVeg_RBS_XylR, Omega cassette_AmyE 3’, RBS_AraC_Omega cassette_AmyE 3’

We are working hard to obtain these last two constructs in order to finish it:

pVeg_RBS_XylR_RBS_AraC_Omega cassette_AmyE 3’, AmyE 5’_pBad/pXyl_RBS_P4/LasR_RBS_CI_RBS_RFP_Double Terminador

Please see our wetlab notebook in the clicking the following image:

AND Heavy Metals Notebook

AND Sugar Notebook'

References

[1] Schlief, R. (2000). Regulation of the L-arabinose operon of Escherichia coli. Trends in Genetics. 16(12):559-565.
[2] Khlebnikov A, Datsenko KA, Skaug T, Wanner BL, and Keasling JD. (2001). Homogeneous expression of the PBAD promoter in Escherichia coli by constitutive expression of the low-affinity high-capacity AraE transporter. Microbiology. 147(12):3241-7.