Coding
SerA

Part:BBa_K2086001

Designed by: Daniel Dooling   Group: iGEM16_UNebraska-Lincoln   (2016-10-13)
Revision as of 22:05, 16 October 2016 by Dannyhdooling (Talk | contribs) (→‎SerA Supplementation)


Serine Repeat Antigen (SerA)

The E. coli serA gene encodes the D-3-phosphoglycerate dehydrogenase, which catalyzes the first committed step in the biosynthesis of serine. Serine is an essential amino acid for E. coli growth in minimal medium. Deletion of the serA gene leads to a serine auxotroph, which can be rescued either by the expression of a protein with the same catalytic activity as SerA or by the addition of serine in the growth media.


Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BamHI site found at 293
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Biology and Our Application

Figure 1: The serine biosynthesis pathway. Provided by: EcoCyc, a member of the BioCyc database collection http://ecocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=SERSYN-PWY&show-citations=NIL

Serine is an amino acid produced in E. coli K12 through the metabolic pathway shown in Figure 1. The SerA gene codes for D-3-Phosphoglycerate Dehydrogenase, the enzyme responsible for catalyzing the committed step of serine biosynthesis. Without SerA, E. coli are unable to grow without sufficient supplementation of other amino acids [1].

Taking advantage of the bacteria's dependence on serine, we planned to create a safety kill switch by controlling the production of the amino acid. By obtaining an auxotrophic strain missing the SerA strain (JW2880 [2]) we were able to create a complement SerA plasmid to rescue the strain when grown in media without supplementary amino acids.

[1]. PAULA D. RAVNIKAR AND RONALD L. SOMERVILLE: Genetic Characterization of a Highly Efficient Alternate Pathway of Serine Biosynthesis in Escherichia coli. http://jb.asm.org/content/169/6/2611.full.pdf

[2] Coli Generic Stock Center: JW2880. http://cgsc.biology.yale.edu/Strain.php?ID=108515

Isolation from Genomic DNA

SerA Supplementation

Figure 1: Fermentation of E. coli KRXwith BBa_K863005 (ECOL) in an Infors Labfors Bioreactor, scale: 3 L, [http://2012.igem.org/Team:Bielefeld-Germany/Protocols/Materials#Autoinduction_medium autoinduction medium] + 60 µg/mL chloramphenicol, 37 °C, pH 7, agitation on cascade to hold pO2 at 50 %, OD600 measured every 30 minutes.
Figure 1: Fermentation of E. coli KRXwith BBa_K863005 (ECOL) in an Infors Labfors Bioreactor, scale: 3 L, [http://2012.igem.org/Team:Bielefeld-Germany/Protocols/Materials#Autoinduction_medium autoinduction medium] + 60 µg/mL chloramphenicol, 37 °C, pH 7, agitation on cascade to hold pO2 at 50 %, OD600 measured every 30 minutes.

Our SerA gene was used in our experiment as part of our composite kill switch: BBa_K2086002. In this composite part, the SerA gene is only expressed in a high-nitrate environment.

Plasmid Synthesis

Figure 3: The gel electrophoresis results of the two components of our SerA plasmid

After testing, we were able to synthesize a basic SerA ORF plasmid, biobrick compatible with a wide variety of plasmids, promoters, and ribosome binding sites. In Figure 3, you can see the results of our gel electrophoresis, used to ligate the two components of our plasmid:

  • pSB1C3 : 2070 bp
  • SerA : 1233 bp


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Categories
//biosafety
//biosafety/semantic_containment
Parameters
None