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Normal Codon Behavior: fix typo

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'''Codon reassignment''' is the [[biological process]] via which the way the [[genetic code]] of a [[Cell (biology)|cell]] is read is changed as a response to the environment. Typically [[codons]], sets of three [[Messenger RNA|mRNA]] nucleotides, correspond to one specific [[amino acid]].<ref name=":14">{{Citation |last1=Alberts |first1=Bruce |title=From RNA to Protein |date=2002 |work=Molecular Biology of the Cell. 4th edition |url=https://www.ncbi.nlm.nih.gov/books/NBK26829/ |access-date=2025-02-17 |publisher=Garland Science |language=en |last2=Johnson |first2=Alexander |last3=Lewis |first3=Julian |last4=Raff |first4=Martin |last5=Roberts |first5=Keith |last6=Walter |first6=Peter}}</ref> Codon reassignment is the exception to this rule. When a codon is reassigned, it codes for a new amino acid.<ref name=":22">{{Cite journal |last1=Dumas |first1=Anaëlle |last2=Lercher |first2=Lukas |last3=Spicer |first3=Christopher D. |last4=Davis |first4=Benjamin G. |date=2014-12-01 |title=Designing logical codon reassignment – Expanding the chemistry in biology |journal=Chemical Science |language=en |volume=6 |issue=1 |pages=50–69 |doi=10.1039/C4SC01534G |pmid=28553457 |issn=2041-6539|pmc=5424465 }}</ref> This change in code can have immense consequences for the cell as [[protein]] structures are altered.

== Mechanics of Codon Reassignment ==

=== Normal Codon Behavior ===
[[File:Aminoacids_table.svg|thumb|266x266px|When read from the center out, this chart shows which amino acid a sequence of three nucleotides would normally code for. When codon reassignment occurs, the sequence of three nucleotides may code for a different amino acid.]]
[[Protein|Proteins]] are essential to life, performing many necessary cellular functions. Cells construct proteins with [[Amino acid|amino acids]] using [[DNA]] instructions. Typically, DNA is [[Transcription (biology)|transcribed]] into messenger RNA ([[Messenger RNA|mRNA]]) and the mRNA is [[Translation (biology)|translated]] into a sequence of amino acids.<ref name=":14" /> The complex that facilitates translation from mRNA to amino acid is called the [[ribosome]].<ref name=":14" /> Ribosomes hold and read mRNA in three nucleotide chunks called [[codons]]. Codons have a corresponding transport RNA ([[Transfer RNA|tRNA]]) that binds to the ribosome. tRNAs are responsible for bringing amino acids to the ribosome so they can be incorporated into the protein. Though each codon only codes for a single tRNA, a tRNA can represent multiple codons. This is because there are 64 possible codon combinations and 20 natural amino acids.<ref name=":14" /> Each tRNA codes for a single amino acid. Each amino acid is added to the growing chain of amino acids that will form the final protein. The initial chain of amino acids, also called the [[Protein structure|primary structure]] of the protein, determines the final shape and functional capacity of the protein.<ref name=":14" />

=== Reassigned Codon Behavior ===
When codon reassignment occurs, it is usually due to a change in tRNAs. A tRNA can be assigned to a new codon or the tRNA can be altered to pick up a different amino acid.<ref name=":02">{{Cite journal |last1=Pataskar |first1=A. |last2=Champagne |first2=J. |last3=Nagel |first3=R. |last4=Kenski |first4=J. |last5=Laos |first5=M. |last6=Michaux |first6=J. |last7=Pak |first7=H. S. |last8=Bleijerveld |first8=O. B. |last9=Mordente |first9=K. |last10=Navarro |first10=J. M. |last11=Blommaert |first11=N. |last12=Nielsen |first12=M. M. |last13=Lovecchio |first13=D. |last14=Stone |first14=E. |last15=Georgiou |first15=G. |last16=De Gooijer |first16=M. C. |last17=Van Tellingen |first17=O. |last18=Altelaar |first18=M. |last19=Joosten |first19=R. P. |last20=Perrakis |first20=A. |last21=Olweus |first21=J. |last22=Bassani-Sternberg |first22=M. |last23=Peeper |first23=D. S. |last24=Agami |first24=R. |date=2025-02-13 |title=Tryptophan depletion results in tryptophan-to-phenylalanine substitutants - PMC |journal=Nature |volume=603 |issue=7902 |pages=721–727 |doi=10.1038/s41586-022-04499-2 |pmid=35264796 |pmc=8942854 }}</ref> For the protein, this means either swapping one amino acid for another, or in the case of a stop codon, adding an amino acid where there was none before. Since the [[Protein structure|primary structure]] determines the functionality of a protein,<ref name=":14" /> changing even one amino acid in this way can drastically impact what the final protein is able to do.

== Examples of Codon Reassignment ==

=== Amino acid deficiencies ===
In [[bacteria]] and [[yeast]], codon reassignment can be caused by a shortage of required amino acids.<ref name=":02" /> Instead of halting protein production all together, tRNA molecules select another amino acid to add to the amino acid chain.<ref name=":02" /> This amino acid may have similar properties to the intended amino acid, or it may not. This may cause deformities in the proteins, making them less efficient or even nonfunctional. A hypothesis as to why this phenomenon persists despite the loss of efficiency is that it is preferable for the organism to have a worse version of the protein than to have no protein at all.<ref name=":02" />

In some human [[cancer]] cells, such as [[melanoma]] cells, a similar tactic is used. As an [[immune response]], to try and destroy the cancer, [[T cell|T cells]] release an [[enzyme]] that destroys the essential amino acid [[tryptophan]] within the cancer cells.<ref name=":02" /> This typically deprives the cancer of many key proteins, killing the cancer cells. However, some cancer cells are able to use codon reassignment to replace the [[tryptophan]] with a similar amino acid called [[phenylalanine]].<ref name=":02" /> This amino acid replacement and resulting functional protein allows the cancer cell to survive and continue dividing.

=== Alteration of tRNAs ===
In some [[Bacteriophage|bacteriophages]], tRNAs have been assigned to stop codons TAG and TGA to code for amino acids [[glutamine]] and [[tryptophan]] respectively.<ref name=":4">{{Cite journal |last1=Cook |first1=Ryan |last2=Telatin |first2=Andrea |last3=Bouras |first3=George |last4=Camargo |first4=Antonio Pedro |last5=Larralde |first5=Martin |last6=Edwards |first6=Robert A |last7=Adriaenssens |first7=Evelien M |date=2024-01-01 |title=Driving through stop signs: predicting stop codon reassignment improves functional annotation of bacteriophages |url=https://academic.oup.com/ismecommun/article/4/1/ycae079/7696150?login=false#468717066 |journal=ISME Communications |volume=4 |issue=1 |article-number=ycae079 |doi=10.1093/ismeco/ycae079 |pmid=38939532 |issn=2730-6151|pmc=11210395 }}</ref> The reasons for this codon reassignment are still being studied, it may be related to the [[infection]] process.<ref name=":4" />

Exposure to outside environmental factors can alter tRNA molecules enough to result in codon reassignment. For example, after being infected with a certain virus, rat liver cells can replace the amino acid [[selenocysteine]] with [[cysteine]], a structurally similar amino acid.<ref name=":02" />

== Implications of Codon Reassignment ==

=== Not-So Universal Genetic Code ===
It has been well documented that there are variations in [[genetic code]] within between [[Cell nucleus|nucleic]] DNA, [[Mitochondrion|mitochondrial]] DNA and [[chloroplast]] DNA.<ref name=":14" /><ref name=":5">{{Cite journal |last1=O'Sullivan |first1=Justin M |last2=Bernard Davenport |first2=J |last3=Tuite |first3=Mick F |date=2001-01-01 |title=Codon reassignment and the evolving genetic code: problems and pitfalls in post-genome analysis |url=https://www.sciencedirect.com/science/article/abs/pii/S0168952500021442 |journal=Trends in Genetics |volume=17 |issue=1 |pages=20–22 |doi=10.1016/S0168-9525(00)02144-2 |pmid=11163917 |issn=0168-9525|url-access=subscription }}</ref> However, it was previously thought that the genetic code was consistent across species within the nucleus. The existence of codon reassignment challenges this idea.<ref name=":5" /> The same codon may code for different amino acids in different species. Codon reassignment shows flexibility and adaptability within genetic code.

=== Potential Uses of Codon Reassignment ===
Artificial, synthetic, unnatural, or [[non-proteinogenic amino acids]] are used in research to help understand the construction and functionality of proteins.<ref name=":22" /> These artificial amino acids are also used in some medications.<ref name=":3">{{Cite journal |last1=McFeely |first1=Clinton A L |last2=Dods |first2=Kara K |last3=Patel |first3=Shivam S |last4=Hartman |first4=Matthew C T |date=2022-10-28 |title=Expansion of the genetic code through reassignment of redundant sense codons using fully modified tRNA |url=https://academic.oup.com/nar/article/50/19/11374/6775395?login=true |journal=Nucleic Acids Research |volume=50 |issue=19 |pages=11374–11386 |doi=10.1093/nar/gkac846 |pmid=36300637 |issn=0305-1048|pmc=9638912 }}</ref> Researchers normally use stop codons, which do not code for an amino acid, to insert these amino acids into proteins. Since there are only three stop codons, researchers were previously limited to using only one or two artificial amino acids.<ref name=":22" /><ref name=":3" /> There was also an option to use artificial tRNA molecules to insert artificial amino acids, but these artificial tRNA molecules are not as high quality as natural tRNA molecules, often making mistakes.<ref name=":3" /> The ability to reassign natural tRNA to artificial amino acids through codon reassignment unlocks many possibilities for this research. Since there are 64 possible combinations and only about 20 natural amino acids,<ref name=":14" /> this method would allow researchers to hypothetically insert 43 artificial amino acids into a protein, preserving one stop codon to complete the translation process properly. These advancements in genetic and protein manipulation may help scientists and doctors to deepen humanity's understanding of cellular functions and produce more effective and efficient medicines.<ref name=":22" /><ref name=":3" />

== See also ==

* [[Expanded genetic code]]
* [[Transcription (biology)]]
* [[Translation (biology)]]
* [[Gene expression]]
* [[Cancer genome sequencing]]

== References ==
{{Reflist}}

[[Category:Genetics]]
[[Category:Amino acids]]
[[Category:Biological processes]]
[[Category:Bacteria]]
[[Category:Yeasts]]
[[Category:Oncology]]

{{genetics-stub}}

Codon reassignment - История изменений

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ru>NOLA1982: /* Normal Codon Behavior */ fix typo