Stop codon
In molecular biology, a stop codon is a codon 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.
Properties
Standard codons
In the standard genetic code, there are three different termination codons:Alternative stop codons
There are variations on the standard genetic code, and alternative stop codons have been found in the mitochondrial genomes of vertebrates, Scenedesmus obliquus, and Thraustochytrium.| Amino-acid biochemical properties | Nonpolar | Polar | Basic | Acidic | Termination: stop codon |
Reassigned stop codons
The nuclear genetic code is flexible as illustrated by variant genetic codes that reassign standard stop codons to amino acids.Translation
In 2007, the UGA codon was identified as the codon coding for selenocysteine and found in 25 selenoproteins located in the active site of the protein. Translation of this codon is enabled by the proximity of the SECIS element.The UAG codon can translate into pyrrolysine in a similar manner.
Genomic distribution
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, 1257 TGA, and 326 TAG stop codons. Also the substrates for the stop codons release factor 1 or release factor 2 are strongly correlated to the abundance of stop codons. Large scale study of bacteria with a broad range of GC-contents shows that while the frequency of occurrence of TAA is negatively correlated to the GC-content and the frequency of occurrence of TGA is positively correlated to the GC-content, the frequency of occurrence of the TAG stop codon, which is often the minimally used stop codon in a genome, is not influenced by the GC-content.Recognition
Recognition of stop codons in bacteria have been associated with the so-called 'tripeptide anticodon', a highly conserved amino acid motif in RF1 and RF2. Even though this is supported by structural studies, it was shown that the tripeptide anticodon hypothesis is an oversimplification.Nomenclature
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, 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.''amber'' mutations (UAG)
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.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.
''ochre'' mutations (UAA)
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", a orange-reddish-brown mineral pigment.Ochre mutant viruses had a property similar to amber mutants in that they recovered infectious ability within certain suppressor strains of bacteria. The set of ochre suppressors was distinct from amber suppressors, so ochre mutants were inferred to correspond to a different nucleotide triplet. Through a series of mutation experiments comparing these mutants with each other and other known amino acid codons, Sydney Brenner concluded that the amber and ochre mutations corresponded to the nucleotide triplets "UAG" and "UAA".
''opal'' or ''umber'' mutations (UGA)
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. Nonsense mutations that created this premature stop codon were later called opal mutations or umber mutations.
Mutations
Nonsense
are changes in DNA sequence that introduce a premature stop codon, causing any resulting protein to be abnormally shortened. This often causes a loss of function in the protein, as critical parts of the amino acid chain are no longer created. Because of this terminology, stop codons have also been referred to as nonsense codons.Nonstop
A nonstop mutation is a point mutation that occurs within a stop codon. Nonstop mutations cause the continued translation of an mRNA strand into what should be an untranslated region. Most polypeptides resulting from a gene with a nonstop mutation are nonfunctional due to their extreme length.Nonstop mutations differ from nonsense mutations in that they do not create a stop codon but, instead, delete one. Nonstop mutations also differ from missense mutations, which are point mutations where a single nucleotide is changed to cause replacement by a different amino acid.
Nonstop mutations have been linked with several congenital diseases including congenital adrenal hyperplasia, variable anterior segment dysgenesis, cystic fibrosis and mitochondrial neurogastrointestinal encephalomyopathy.
Hidden stops
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 occurs before the hidden stop. It is hypothesised that this decreases resource waste 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.This hypothesis however 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 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.