Remaining Challenges

The E. coli strains KRX Δalr ΔdadX and DH5α Δalr ΔdadX respectivly showed a strict dependance of D-alanine but as mentioned above the ratio of false-positive was slightly higher compared to the selection on the antibiotic selection using Chlormaphenicol and even on the negative plate some colony forming untis were obervable, while there were no on the LB plate containing 30 mg/L Chloramphenicol. This effect migth due to some revertants of the D-alanine auxotropy and the corresponding selection pressure.
Therefore the Revertants were analyzed by streking out an overnight culture of the strain DH5α Δalr ΔdadX and DH5α Δalr kan:dadX on normal LB and several dilution on LB medium containing 5 mM D-alanine. The same procedure was performed with the transformation approach. In both cases the nearly the same revertants rate of xx (overnight culture) and yy (Transformation) was estimated. Beside there was no significante difference between the revertion ratio of the strain DH5α Δalr ΔdadX and DH5α Δalr kan:dadX, so that an effect by some contamination could be excluded and so the additional colonies probably some revertants which are able to accumulate D-alanine in some way.
A possible explanation might be a point mutation in the coding sequence of the methionine repressor metJ (Kang et al., 2011). Under normal circumstances the MetJ represses all essential genes for the biosynthesis of L-methionin like metA, metB, metC, MetF, metE and metK as well as the genes of the metD operon by using S-adenosylmethionine (SAM) as cofactor, see Figure x below.

Bild Figure X:
It could be demonstrated that in the presence of L-methionine all genes affected are surpressed and no revertants are observable, and that the reversion could not be quantified in its absence, suggesting that there is an other methionin-repressible enzyme able to accumulate D-alanine in E. coli. The revertants formed in the absence of L-methionin showed a higher expression of the Cystathionin β-lyase and point mutations in the MetJ repressor like R42C. It could be shwon that a strict D-alanine auxotrophy can be restore by a plasmidar expression of the natural metJ repressor or the additional deletion of metC (Kang et al., 2011).
Up to now the antibiotic-free selection could be demonstrated only for normal plasmids like BBa_K1465401 as Backbone (3163 bp) and BBa_J04450 (RFP, 1069 bp), BBa_I13522 (GFP, 937 bp) respectivley resultin in a plasmid-size of 4232 bp and 4100 bp.

References

• Kang L, Shaw AC, Xu D, Xia W, Zhang J, Deng J, Wöldike HF, Liu Y, Su J. (2011) Upregulation of MetC is essential for D-alanine-independent growth of an alr/dadX-deficient Escherichia coli strain. Journal of bacteriology, vol. 193, pp. 1098 - 1106.