Codon tricks

In most prokaryotes (bacteria and archaea), translation begins on the nascent mRNA before transcription of the mRNA is complete. This creates a number of opportunities for prokaryotes to use various codon tricks for improved regulation.
 * In an attenuation system, the ribosome must stall during the translation of a short, nonfunctional peptide called a leader peptide in order to prevent attenuation and let transcription of the downstream operon to continue. Attenuation systems are common upstream of amino acid biosynthesis operons, with stalling occuring at codons encoding tryptophan to regulate the trp operon (see trp operon), histidine to regulate the his operon, and so on. Because leader peptides are very short, and rather divergent, they are regularly missed in genome annotation. See Attenuator_(genetics).
 * In the prfB gene encoding peptide chain release factor 2 (RF-2), in most bacteria, the ribosome stalls shortly after the beginning of translation at a UGA codon. Both release factors recognize UAA, RF-1 recognizes UAG as well, but only RF-2 recognizes and terminates translation at a UGA codon. Translation to produce more RF-2 can occur, through a +1 programmed frameshift, only when RF-2 itself is in short supply.
 * Stop codons can be recoded to make amino acids beyond the twenty common amino acids. Selenocysteine (see Wikipedia::Selenocysteine) is incorporated at special UGA codons, usually with the aid of a signal from secondary structure that forms in the mRNA. The much rarer pyrrolysine (see Wikipedia::Pyrrolysine) is encoded at a few UAG codons. Selenoproteins typically are recognized by UGA codons that break an otherwise open reading frame such that homologous proteins can be found with cysteine residues aligning to the UGA codon position.Known post-translationally modified amino acids (> 300) greatly outnumber known unusual amino acids incorporated during translation (2), and there may be few if any analogs to selenocysteine and pyrrolysine left to discover.
 * Because the genetic code is degenerate, with most amino acids encoded by several different codons, the choice of codon for a particular amino acid can affect the relative abundance of its cognate tRNA. Highly expressed proteins show signatures of codon adaptation, the result of natural selection to the more abundant tRNAs of the host organism.
 * Tryptophan codons are rare in general, but are particularly rare in enzymes that encode the enzymes of tryptophan biosynthesis. The scarcity of trp codons in the trp operon can help a bacterium survive a tryptophan starvation crisis.
 * Restriction/modification systems, a defense against phage and other invasive DNA, can cause their cognate sequences to become rare over time in host genomes. The effect is especially easy to detect for shorter recognition sites, such as 4 base pair sites in Helicobacter pylori. These skews, of course, affect codon frequencies.