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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.
A tunicate is an exclusively marine invertebrate animal, a member of the subphylum Tunicata. This grouping is part of the Chordata, a phylum which includes all animals with dorsal nerve cords and notochords. The subphylum was at one time called Urochordata, and the term urochordates is still sometimes used for these animals. They are the only chordates that have lost their myomeric segmentation, with the possible exception of the seriation of the gill slits. However, doliolids still display segmentation of the muscle bands.
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.
Mitochondrial translational release factor 1, also known as MTRF1 is a human gene.
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.
Pyura praeputialis is an intertidal and shallow water species of tunicate. It is one of three species of "cunjevoi" in Australasia. It is the first reported species of marine organism to create a "foam-nest" for its larvae.
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 vertebrate mitochondrial code is the genetic code found in the mitochondria of all vertebrata.
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 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 echinoderm and flatworm mitochondrial code is a genetic code used by the mitochondria of certain echinoderm and flatworm species.
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 trematode mitochondrial code is a genetic code found in the mitochondria of Trematoda.
The Scenedesmus obliquusmitochondrial code is a genetic code found in the mitochondria of Scenedesmus obliquus, a species of green algae.
The Thraustochytrium mitochondrial code is a genetic code found in the mitochondria of the labyrinthulid protist Thraustochytrium aureum. The mitochondrial genome was sequenced by the Organelle Genome Megasequencing Program.
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.
References
This article incorporates text from the United States National Library of Medicine, which is in the public domain. [7]
- ↑ Durrheim GA, Corfield VA, Harley EH, Ricketts MH (1993). "Nucleotide sequence of cytochrome oxidase (subunit III) from the mitochondrion of the tunicate Pyura stolonifera: evidence that AGR encodes glycine". Nucleic Acids Research. 21 (15): 3587–8. doi:10.1093/nar/21.15.3587. PMC 331473 . PMID 8393993.
- ↑ Yokobori S, Ueda T, Watanabe K (January 1993). "Codons AGA and AGG are read as glycine in ascidian mitochondria". Journal of Molecular Evolution. 36 (1): 1–8. Bibcode:1993JMolE..36....1Y. doi:10.1007/bf02407301. PMID 8381878. S2CID 12603691.
- ↑ Kondow A, Suzuki T, Yokobori S, Ueda T, Watanabe K (June 1999). "An extra tRNAGly(U*CU) found in ascidian mitochondria responsible for decoding non-universal codons AGA/AGG as glycine". Nucleic Acids Research. 27 (12): 2554–9. doi:10.1093/nar/27.12.2554. PMC 148460 . PMID 10352185.
- ↑ Yokobori S, Ueda T, Feldmaier-Fuchs G, Pääbo S, Ueshima R, Kondow A, Nishikawa K, Watanabe K (December 1999). "Complete DNA sequence of the mitochondrial genome of the ascidian Halocynthia roretzi (Chordata, Urochordata)". Genetics. 153 (4): 1851–62. doi:10.1093/genetics/153.4.1851. PMC 1460873 . PMID 10581290.
- 1 2 Yokobori S, Watanabe Y, Oshima T (November 2003). "Mitochondrial genome of Ciona savignyi (Urochordata, Ascidiacea, Enterogona): comparison of gene arrangement and tRNA genes with Halocynthia roretzi mitochondrial genome". Journal of Molecular Evolution. 57 (5): 574–87. Bibcode:2003JMolE..57..574Y. doi:10.1007/s00239-003-2511-9. PMID 14738316. S2CID 19474615.
- ↑ Gissi C, Pesole G (2003). "Transcript mapping and genome annotation of ascidian mtDNA using EST data". Genome Research. 13 (9): 2203–12. doi:10.1101/gr.1227803. PMC 403730 . PMID 12915488.
- ↑ 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 5 June 2016.
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