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Codon that marks the end of a protein coding sequence

In molecular biology, a stop codon (or termination codon) is a codon (nucleotide triplet within messenger RNA) that signals the termination of the translation process of the current protein. Most codons in messenger RNA correspond to the addition of an amino acid to a growing polypeptide chain, which may ultimately become a protein; stop codons signal the termination of this process by binding release factors, which cause the ribosomal subunits to disassociate, releasing the amino acid chain. While start codons need nearby sequences or initiation factors to start translation, a stop codon alone is sufficient to initiate termination.

In 1986, convincing evidence was provided that selenocysteine (Sec) was incorporated co translationally. Moreover, the codon partially directing its incorporation in the polypeptide chain was identified as UGA also known as the opal termination codon. Different mechanisms for overriding the termination function of this codon have been identified in prokaryotes and in eukaryotes. A particular difference between these kingdoms is that cis elements seem restricted to the neighborhood of the UAG codon in prokaryotes while in eukaryotes this restriction is not present. Instead such locations seem disfavored albeit not prohibited. In 2003, a landmark paper described the identification of all known selenoproteins in humans: 25 in total. Similar analyses have been run for other organisms. The UAG codon can translate into pyrrolysine (Pyl) in a similar manner.

Distribution of stop codons within the genome of an organism is non random and can correlate with GC content. For example, the E. coli K 12 genome contains 2705 TAA (63%), 1257 TGA (29%), and 326 TAG (8%) stop codons (GC content 50.8%). Also the substrates for the stop codons release factor 1 or release factor 2 are strongly correlated to the abundance of stop codons.

Recognition of stop codons in bacteria have been associated with the so called 'tripeptide anticodon', a highly conserved amino acid motif in RF1 (PxT) and RF2 (SPF). Even though this is supported by structural studies, it was shown that the tripeptide anticodon hypothesis is an oversimplification.

Stop codons were historically given many different names, as they each corresponded to a distinct class of mutants that all behaved in a similar manner. These mutants were first isolated within bacteriophages (T4 and lambda), viruses that infect the bacteria Escherichia coli. Mutations in viral genes weakened their infectious ability, sometimes creating viruses that were able to infect and grow within only certain varieties of E. coli.

They were the first set of nonsense mutations to be discovered, isolated by Richard H. Epstein and Charles Steinberg and named after their friend and graduate Caltech student Harris Bernstein, whose last name means "amber" in German (cf. Bernstein). Viruses with amber mutations are characterized by their ability to infect only certain strains of bacteria, known as amber suppressors. These bacteria carry their own mutation that allows a recovery of function in the mutant viruses. For example, a mutation in the tRNA that recognizes the amber stop codon allows translation to "read through" the codon and produce a full length protein, thereby recovering the normal form of the protein and "suppressing" the amber mutation. Thus, amber mutants are an entire class of virus mutants that can grow in bacteria that contain amber suppressor mutations. Similar suppressors are known for ochre and opal stop codons as well. tRNA molecules carrying unnatural aminoacids have been designed to recognize the amber stop codon in bacterial RNA. This technology allows for incorporation of orthogonal aminoacids (such as p azidophenylalanine) at specific locations of the target protein.

It was the second stop codon mutation to be discovered. Reminiscent of the usual yellow orange brown color associated with amber, this second stop codon was given the name of "ochre", an orange reddish brown mineral pigment.

The third and last stop codon in the standard genetic code was discovered soon after, and corresponds to the nucleotide triplet "UGA". To continue matching with the theme of colored minerals, the third nonsense codon came to be known as "opal", which is a type of silica showing a variety of colors. eye disease, and neurodevelopmental disorders.

Hidden stops are non stop codons that would be read as stop codons if they were frameshifted +1 or −1. These prematurely terminate translation if the corresponding frame shift (such as due to a ribosomal RNA slip) occurs before the hidden stop. It is hypothesised that this decreases resource wastage on nonfunctional proteins and the production of potential cytotoxins. Researchers at Louisiana State University propose the ambush hypothesis, that hidden stops are selected for. Codons that can form hidden stops are used in genomes more frequently compared to synonymous codons that would otherwise code for the same amino acid. Unstable rRNA in an organism correlates with a higher frequency of hidden stops. However, this hypothesis could not be validated with a larger data set. Stop codons and hidden stops together are collectively referred as stop signals. Researchers at University of Memphis found that the ratios of the stop signals on the three reading frames of a genome (referred to as translation stop signals ratio or TSSR) of genetically related bacteria, despite their great differences in gene contents, are much alike. This nearly identical genomic TSSR value of genetically related bacteria may suggest that bacterial genome expansion is limited by their unique stop signals bias of that bacterial species.

Stop codon suppression or translational readthrough occurs when in translation a stop codon is interpreted as a sense codon, that is, when a (standard) amino acid is 'encoded' by the stop codon. Mutated tRNAs can be the cause of readthrough, but also certain nucleotide motifs close to the stop codon. Translational readthrough is very common in viruses and bacteria, and has also been found as a gene regulatory principle in humans, yeasts, bacteria and drosophila. This kind of endogenous translational readthrough constitutes a variation of the genetic code, because a stop codon codes for an amino acid. In the case of human malate dehydrogenase, the stop codon is read through with a frequency of about 4%. The amino acid inserted at the stop codon depends on the identity of the stop codon itself: Gln, Tyr, and Lys have been found for the UAA and UAG codons, while Cys, Trp, and Arg for the UGA codon have been identified by mass spectrometry. Extent of readthrough in mammals have widely variable extents, and can broadly diversify the proteome and affect cancer progression.

In 2010, when Craig Venter unveiled the first fully functioning, reproducing cell controlled by synthetic DNA he described how his team used frequent stop codons to create watermarks in RNA and DNA to help confirm the results were indeed synthetic (and not contaminated or otherwise), using it to encode authors' names and website addresses.