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Current problems in the field

The genetic code engineering and expansion is still marginally represented in the whole SynBio  and biological sciences in general, although this research was established already two decades ago. This can be overcome only if some serious issues (which are vastly neglected by the current major protagonists in the field) are going to be addressed systematically.

These are (a) the volume (scale) of production (the whole field is in fact at "shaking flask" stage; rescaling to e.g. 200 l culture is necessary). For that we need (b) metabolic engineering as a simple addition of chemically synthesized noncanonical amino acids (ncAAs) in cell culture can have only academic significance. Thus, the ncAAs have to be synthesized (in worst case) from simple precursors, ideally from the glucose.

Overall quality of o-pairs/engineered enzymes  (c) is demonstrated best by our recent paper (Nehring, Budisa, Wiltschi,  PloSOne 7, e31992).  Although these facts are generally ignored (or have played down) by the current main protagonists in the field, the problem of bad / lousy quality of the orthogonal enzymes/components remains. Furthermore, the most important problem is the near-cognate decoding, i.e. near-cognate recognition of amber, opal and quadruplet codons is sometimes so strong that orthogonal pair cannot completely outcompete the ncAAs incorporation (according to Dieter Söll).

To make a "real" engineering the genetic code / expansion, we also need (d) robust strains and concomitant evolution and selection procedures (to generate them) as well as paradigm shift from single proteins to proteomes . The introduction of novel amino acids is generally possible at the level of single recombinant proteins whereas the generation of chemically distinct (and robust) proteomes is still not generally possible (SeMet is only known example).

Last but not least, our research has great potential to yield new concepts and technological solutions with favorable effects on the whole society. Examples include the creation of novel and emergent features of protein translation (codon emancipation) as well as of cellular genetics and physiology (genetic firewall) which is relevant among others for novel biosafety and biosecurity strategies as discussed in “Vision” section (“Parallel Biological World with a Genetic Firewall”).


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