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The genetic code is the set of rules used by living cells to translate information encoded within genetic material into proteins. Translation is accomplished by the ribosome, which links proteinogenic amino acids in an order specified by messenger RNA (mRNA), using transfer RNA (tRNA) molecules to carry amino acids and to read the mRNA three nucleotides at a time. The genetic code is highly similar among all organisms and can be expressed in a simple table with 64 entries.
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.
In biology, translation is the process in living cells in which proteins are produced using RNA molecules as templates. The generated protein is a sequence of amino acids. This sequence is determined by the sequence of nucleotides in the RNA. The nucleotides are considered three at a time. Each such triple results in addition of one specific amino acid to the protein being generated. The matching from nucleotide triple to amino acid is called the genetic code. The translation is performed by a large complex of functional RNA and proteins called ribosomes. The entire process is called gene expression.
In genetics, a nonsense mutation is a point mutation in a sequence of DNA that results in a nonsense codon, or a premature stop codon in the transcribed mRNA, and leads to a truncated, incomplete, and possibly nonfunctional protein product. Nonsense mutations are not always harmful; the functional effect of a nonsense mutation depends on many aspects, such as the location of the stop codon within the coding DNA. For example, the effect of a nonsense mutation depends on the proximity of the nonsense mutation to the original stop codon, and the degree to which functional subdomains of the protein are affected. As nonsense mutations leads to premature termination of polypeptide chains; they are also called chain termination mutations.
The start codon is the first codon of a messenger RNA (mRNA) transcript translated by a ribosome. The start codon always codes for methionine in eukaryotes and archaea and a N-formylmethionine (fMet) in bacteria, mitochondria and plastids.
Eukaryotic translation termination factor1 (eRF1), also referred to as TB3-1 or SUP45L1, is a protein that is encoded by the ERF1 gene. In Eukaryotes, eRF1 is an essential protein involved in stop codon recognition in translation, termination of translation, and nonsense mediated mRNA decay via the SURF complex.
Karyorelictea is a class of ciliates in the subphylum Postciliodesmatophora. Most species are members of the microbenthos community, that is, microscopic organisms found in the marine interstitial habitat, though one genus, Loxodes, is found in freshwater.
A codon table can be used to translate a genetic code into a sequence of amino acids. The standard genetic code is traditionally represented as an RNA codon table, because when proteins are made in a cell by ribosomes, it is messenger RNA (mRNA) that directs protein synthesis. The mRNA sequence is determined by the sequence of genomic DNA. In this context, the standard genetic code is referred to as translation table 1. It can also be represented in a DNA codon table. The DNA codons in such tables occur on the sense DNA strand and are arranged in a 5′-to-3′ direction. Different tables with alternate codons are used depending on the source of the genetic code, such as from a cell nucleus, mitochondrion, plastid, or hydrogenosome.
The ciliate, dasycladacean and Hexamita nuclear code is a genetic code used by certain ciliate, dasycladacean and Hexamita species.
The euplotid nuclear code is the genetic code used by Euplotidae. The euplotid code is a socalled "symmetrical code", which results from the symmetrical distribution of the codons. This symmetry allows for arythmic exploration of the codon distribution. In 2013, shCherbak and Makukov, reported that "the patterns are shown to match the criteria of an intelligent signal."
The candidate division SR1 and gracilibacteria code is used in two groups of uncultivated bacteria found in marine and fresh-water environments and in the intestines and oral cavities of mammals among others. The difference to the standard and the bacterial code is that UGA represents an additional glycine codon and does not code for termination. A survey of many genomes with the codon assignment software Codetta, analyzed through the GTDB taxonomy system shows that this genetic code is limited to the Patescibacteria order BD1-5, not what are now termed Gracilibacteria, and that the SR1 genome assembly GCA_000350285.1 for which the table 25 code was originally defined is actually using the Absconditibacterales genetic code and has the associated three special recoding tRNAs. Thus this code may now be better named the "BD1-5 code".
The alternative flatworm mitochondrial code is a genetic code found in the mitochondria of Platyhelminthes and Nematodes.
The chlorophycean mitochondrial code is a genetic code found in the mitochondria of Chlorophyceae.
The pachysolen tannophilus nuclear code is a genetic code found in the ascomycete fungus Pachysolen tannophilus.
The karyorelictid nuclear code is a genetic code used by the nuclear genome of the Karyorelictea ciliate Parduczia sp. This code, along with translation tables 28 and 31, is remarkable in that every one of the 64 possible codons can be a sense codon. Translation termination probably relies on context, specifically proximity to the poly(A) tail.
The Mesodinium nuclear code is a genetic code used by the nuclear genome of the ciliates Mesodinium and Myrionecta.
Condylostoma is a genus of unicellular ciliate protists, belonging to the class Heterotrichea.
The Blastocrithidia nuclear code is a genetic code used by the nuclear genome of the trypanosomatid genus Blastocrithidia. This code, along with translation tables 27 and 28, is remarkable in that every one of the 64 possible codons can be a sense codon.
Parduczia is a genus of karyorelict ciliates in the family Geleiidae.
References
This article incorporates text from the United States National Library of Medicine, which is in the public domain. [2]
- ↑ Heaphy, Stephen M.; Mariotti, Marco; Gladyshev, Vadim N.; Atkins, John F.; Baranov, Pavel V. (2016-11-01). "Novel Ciliate Genetic Code Variants Including the Reassignment of All Three Stop Codons to Sense Codons in Condylostoma magnum". Molecular Biology and Evolution. 33 (11): 2885–2889. doi:10.1093/molbev/msw166. ISSN 0737-4038. PMC 5062323 . PMID 27501944.
- 1 2 Elzanowski A, Ostell J, Leipe D, Soussov V. "The Genetic Codes". Taxonomy browser. National Center for Biotechnology Information (NCBI), U.S. National Library of Medicine. Retrieved 18 November 2016.
- ↑ Swart, Estienne Carl; Serra, Valentina; Petroni, Giulio; Nowacki, Mariusz (2016). "Genetic Codes with No Dedicated Stop Codon: Context-Dependent Translation Termination". Cell. 166 (3): 691–702. doi:10.1016/j.cell.2016.06.020. PMC 4967479 . PMID 27426948.