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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.
Selenocysteine is the 21st proteinogenic amino acid. Selenoproteins contain selenocysteine residues. Selenocysteine is an analogue of the more common cysteine with selenium in place of the sulfur.
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.
Proteinogenic amino acids are amino acids that are incorporated biosynthetically into proteins during translation. The word "proteinogenic" means "protein creating". Throughout known life, there are 22 genetically encoded (proteinogenic) amino acids, 20 in the standard genetic code and an additional 2 that can be incorporated by special translation mechanisms.
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.
An expanded genetic code is an artificially modified genetic code in which one or more specific codons have been re-allocated to encode an amino acid that is not among the 22 common naturally-encoded proteinogenic amino acids.
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 pterobranchia mitochondrial code is a genetic code used by the mitochondrial genome of Rhabdopleura compacta (Pterobranchia). The Pterobranchia are one of the two groups in the Hemichordata which together with the Echinodermata and Chordata form the three major lineages of deuterostomes. AUA translates to isoleucine in Rhabdopleura as it does in the Echinodermata and Enteropneusta while AUA encodes methionine in the Chordata. The assignment of AGG to lysine is not found elsewhere in deuterostome mitochondria but it occurs in some taxa of Arthropoda. This code shares with many other mitochondrial codes the reassignment of the UGA STOP to tryptophan, and AGG and AGA to an amino acid other than arginine. The initiation codons in Rhabdopleura compacta are ATG and GTG.
The yeast mitochondrial code is a genetic code used by the mitochondrial genome of yeasts, notably Saccharomyces cerevisiae, Candida glabrata, Hansenula saturnus, and Kluyveromyces thermotolerans.
The mold, protozoan, and coelenterate mitochondrial code and the mycoplasma/spiroplasma code is the genetic code used by various organisms, in some cases with slight variations, notably the use of UGA as a tryptophan codon rather than a stop codon.
The invertebrate mitochondrial code is a genetic code used by the mitochondrial genome of invertebrates. Mitochondria contain their own DNA and reproduce independently from their host cell. Variation in translation of the mitochondrial genetic code occurs when DNA codons result in non-standard amino acids has been identified in invertebrates, most notably arthropods. This variation has been helpful as a tool to improve upon the phylogenetic tree of invertebrates, like flatworms.
The ascidian mitochondrial code is a genetic code found in the mitochondria of Ascidia.
The Condylostoma nuclear code is a genetic code used by the nuclear genome of the heterotrich ciliate Condylostoma magnum. This code, along with translation tables 27 and 31, is remarkable in that every one of the 64 possible codons can be a sense codon. Experimental evidence suggests that translation termination relies on context, specifically proximity to the poly(A) tail. Near such a tail, PABP could help terminate the protein by recruiting eRF1 and eRF3 to prevent the cognate tRNA from binding.
The Mesodinium nuclear code is a genetic code used by the nuclear genome of the ciliates Mesodinium and Myrionecta.
The Cephalodiscidae mitochondrial code is a genetic code used by the mitochondrial genome of Cephalodiscidae (Pterobranchia). The Pterobranchia are one of the two groups in the Hemichordata which together with the Echinodermata and Chordata form the major clades of deuterostomes.
The candidate phyla radiation is a large evolutionary radiation of bacterial lineages whose members are mostly uncultivated and only known from metagenomics and single cell sequencing. They have been described as nanobacteria or ultra-small bacteria due to their reduced size (nanometric) compared to other bacteria.
Gracilibacteria is a bacterial candidate phylum formerly known as GN02, BD1-5, or SN-2. It is part of the Candidate Phyla Radiation and the Patescibacteria group.
The Absconditabacterales genetic code translates UGA to glycine, and CGG and GCA to tryptophan, as determined by the codon assignment software Codetta; it was further shown that these recodings are associated with three special tRNAs with appropriate anticodons and tRNA identity elements. Codetta called the Absconditibacterales code for the following genome assemblies: GCA_002792495.1, GCA_001007975.1, GCA_003488625.1, GCA_003260355.1, GCA_003242865.1, GCA_000350285.1, GCA_002746475.1, GCA_007116275.1, GCA_007115995.1, GCA_002361595.1, GCA_000503875.1, GCA_003543185.1, GCA_002441085.1, and GCA_002791215.1. Review of the GTDB taxonomy system for the order Absconditabacterales left two questionable genome assemblies ; spot-checking these two genomes shows that they both have all three special tRNAs, suggesting that the code is universal across the order.
References
This article incorporates text from the United States National Library of Medicine, which is in the public domain. [5]
- ↑ Davis, James P.; Youssef, Noha H.; Elshahed, Mostafa S. (June 2009). "Assessment of the diversity, abundance, and ecological distribution of members of candidate division SR1 reveals a high level of phylogenetic diversity but limited morphotypic diversity". Applied and Environmental Microbiology. 75 (12): 4139–4148. Bibcode:2009ApEnM..75.4139D. doi:10.1128/AEM.00137-09. ISSN 1098-5336. PMC 2698373 . PMID 19395567.
- ↑ J. H. Campbell; O'P. Donoghue; A. G. Campbell; P. Schwientek; A. Sczyrba; T. Woyke; D. Söll; M. Podar (2 April 2013). "UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota". Proc Natl Acad Sci U S A. 110 (14): 5540–5. Bibcode:2013PNAS..110.5540C. doi: 10.1073/pnas.1303090110 . PMC 3619370 . PMID 23509275.
- ↑ Shulgina, Yekaterina; Eddy, Sean R. (9 November 2021). "A computational screen for alternative genetic codes in over 250,000 genomes". eLife. 10. doi: 10.7554/eLife.71402 . PMC 8629427 . PMID 34751130.
- ↑ Parks, Donovan H.; Chuvochina, Maria; Chaumeil, Pierre-Alain; Rinke, Christian; Mussig, Aaron J.; Hugenholtz, Philip (September 2020). "A complete domain-to-species taxonomy for Bacteria and Archaea". Nature Biotechnol. 38. doi:10.1038/s41587-020-0501-8. PMID 32341564.
- ↑ 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 19 March 2016.