I know that by now this is old new but I heard that a cell that used a synthetic pair of nucleotides, called X and Y, have been made. My question was, how did the cell understand the X and Y nucleotides during translation and how was it even represented in mRNA? It must have been represented differently, possibly using X and Y nucleotides only. That's the only way I can think of that causes the cell to make 172 amino acids instead of the usual 20. By the way I read this in the Discover magazine, January issue.
The altered E Coli still only made use of the regular 20 amino acids (presumably).
Looking at the original citation, Malyshev et al didn't characterize the RNA in their altered E Coli at all. All they did was add free X and Y to the E Coli's growth medium and add a gene to the E Coli that expressed an
algal nucleotide triphosphate transporter. Malyshev et al then demonstrated that replication (copying of the DNA) proceeds normally and in such a way as to preserve the X and Y content.
So no information as to whether any of the products downstream from the DNA (ie mRNA, proteins, etc) were affected by their modifications.