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{{Short description|Genetic process}}
{{Distinguish|Neofunctionalism}}

[[File:Neofunctionalization after a gene duplication event.png|thumb|Neofunctionalization is the process by which a gene acquires a new function after a gene duplication event. The figure shows that once a gene duplication event has occurred one gene copy retains the original ancestral function (represented by the green paralog), while the other acquires mutations that allow it to diverge and develop a new function (represented by the blue paralog).]]
'''Neofunctionalization''', one of the possible outcomes of [[functional divergence]], occurs when one gene copy, or [[paralog]], takes on a totally new function after a [[gene duplication]] event. Neofunctionalization is an adaptive mutation process; meaning one of the gene copies must mutate to develop a function that was not present in the ancestral gene.<ref>{{cite journal | vauthors = Kleinjan DA, Bancewicz RM, Gautier P, Dahm R, Schonthaler HB, Damante G, Seawright A, Hever AM, Yeyati PL, van Heyningen V, Coutinho P | display-authors = 6 | title = Subfunctionalization of duplicated zebrafish pax6 genes by cis-regulatory divergence | journal = PLOS Genetics | volume = 4 | issue = 2 | pages = e29 | date = February 2008 | pmid = 18282108 | pmc = 2242813 | doi = 10.1371/journal.pgen.0040029 | doi-access = free }}</ref><ref name="Liberles_2005">{{cite journal | vauthors = Rastogi S, Liberles DA | title = Subfunctionalization of duplicated genes as a transition state to neofunctionalization | journal = BMC Evolutionary Biology | volume = 5 | issue = 1 | pages = 28 | date = April 2005 | pmid = 15831095 | pmc = 1112588 | doi = 10.1186/1471-2148-5-28 | doi-access = free }}</ref><ref name="Antonarakis_2007">{{cite journal | vauthors = Conrad B, Antonarakis SE | title = Gene duplication: a drive for phenotypic diversity and cause of human disease | journal = Annual Review of Genomics and Human Genetics | volume = 8 | pages = 17–35 | year = 2007 | pmid = 17386002 | doi = 10.1146/annurev.genom.8.021307.110233 }}</ref> In other words, one of the duplicates retains its original function, while the other accumulates molecular changes such that, in time, it can perform a different task.<ref>{{cite book | vauthors = [[Susumu Ohno|Ohno]] | title = Evolution by Gene Duplication. | location = New York, Heidelberg, Berlin | publisher = Springer-Verlag | date = 1970 | pages = 59–87 | isbn = 978-3-540-05225-8 }}</ref>

==The process==
The process of neofunctionalization begins with a [[gene duplication]] event, which is thought to occur as a defense mechanism against the accumulation of deleterious mutations.<ref name="De_Smet_2012">{{cite journal | vauthors = De Smet R, Van de Peer Y | title = Redundancy and rewiring of genetic networks following genome-wide duplication events | journal = Current Opinion in Plant Biology | volume = 15 | issue = 2 | pages = 168–76 | date = April 2012 | pmid = 22305522 | doi = 10.1016/j.pbi.2012.01.003 }}</ref><ref name="Graur_2000">{{cite book | vauthors = Graur D, Li WH |title=Fundamentals of molecular evolution |date=2000 |publisher=Sinauer Associates |location=Sunderland, Mass. |isbn=978-0-87893-266-5 |edition= 2nd }}</ref><ref name="pmid20080574">{{cite journal | vauthors = Amoutzias GD, He Y, Gordon J, Mossialos D, Oliver SG, Van de Peer Y | title = Posttranslational regulation impacts the fate of duplicated genes | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 107 | issue = 7 | pages = 2967–71 | date = February 2010 | pmid = 20080574 | pmc = 2840353 | doi = 10.1073/pnas.0911603107 | bibcode = 2010PNAS..107.2967A | doi-access = free }}</ref> Following the gene duplication event there are two identical copies of the ancestral gene performing exactly the same function. This redundancy allows one of the copies to take on a new function. In the event that the new function is advantageous, natural selection positively selects for it and the new mutation becomes fixed in the population.<ref name="Antonarakis_2007"/><ref name="Innan_2009">{{cite journal | vauthors = Innan H | title = Population genetic models of duplicated genes | journal = Genetica | volume = 137 | issue = 1 | pages = 19–37 | date = September 2009 | pmid = 19266289 | doi = 10.1007/s10709-009-9355-1 | s2cid = 31795158 }}</ref>
The occurrence of neofunctionalization can most often be attributed to changes in the coding region or changes in the regulatory elements of a gene.<ref name="Graur_2000" /> It is much more rare to see major changes in protein function, such as subunit structure or substrate and ligand affinity, as a result of neofunctionalization.<ref name="Graur_2000"/>

==Selective constraints==

Neofunctionalization is also commonly referred to as "mutation during non-functionality" or "mutation during redundancy".<ref>{{cite book | vauthors = Hughes AL |title=Adaptive evolution of genes and genomes |date=1999 |publisher=Oxford University Press |location=New York |isbn=978-0-19-511626-7}}</ref> Regardless of if the mutation arises after non-functionality of a gene or due to redundant gene copies, the important aspect is that in both scenarios one copy of the duplicated gene is freed from selective constraints and by chance acquires a new function which is then improved by natural selection.<ref name="Graur_2000"/> This process is thought to occur very rarely in evolution for two major reasons. The first reason is that functional changes typically require a large number of amino acid changes; which has a low probability of occurrence. Secondly, because deleterious mutations occur much more frequently than advantageous mutations in evolution, the likelihood that gene function is lost over time (i.e. pseudogenization) is far greater than the likelihood of the emergence of a new gene function. <ref name="Graur_2000" /><ref name="Innan_2009"/>
Walsh discovered that the relative probability of neofunctionalization is determined by the selective advantage and the relative rate of advantageous mutations.<ref name="Lynch_2000">{{cite journal | vauthors = Lynch M, Force A | title = The probability of duplicate gene preservation by subfunctionalization | journal = Genetics | volume = 154 | issue = 1 | pages = 459–73 | date = January 2000 | doi = 10.1093/genetics/154.1.459 | pmid = 10629003 | pmc = 1460895 | url = https://www.genetics.org/content/154/1/459 }}</ref> This was proven in his derivation of the relative probability of neofunctionalization to pseudogenization, which is given by: <math>\frac{\rho\,\!S-1}{1 - e^s}</math> where ρ is the ratio of advantageous mutation rate to null mutation rate and S is the population selection 4NeS (Ne: [[effective population size]] S: selection intensity).<ref name="Lynch_2000"/>

==Classical model==
In 1936, [[Hermann Joseph Muller|Muller]] originally proposed neofunctionalization as a possible outcome of a gene duplication event.<ref>{{cite journal | vauthors = [[Hermann Joseph Muller|Muller HJ]] | title = Bar duplication | journal = Science | volume = 83 | issue = 2161 | pages = 528–30 | date = May 1936 | pmid = 17806465 | doi = 10.1126/science.83.2161.528-a | bibcode = 1936Sci....83..528M | s2cid = 5426313 }}</ref> In 1970, [[Susumu Ohno|Ohno]] suggested that neofunctionalization was the only evolutionary mechanism that gave rise to new gene functions in a population.<ref name="Graur_2000"/> He also believed that neofunctionalization was the only alternative to pseudogenization.<ref name="Liberles_2005"/> [[Tomoko Ohta|Ohta]] (1987) was among the first to suggest that other mechanisms may exist for the preservation of duplicated genes in the population.<ref name="Graur_2000"/> Today, subfunctionalization is a widely accepted alternative fixation process for gene duplicates in the population and is currently the only other possible outcome of functional divergence.<ref name="Liberles_2005"/>

==Neosubfunctionalization==
Neosubfunctionalization occurs when neofunctionalization is the result of [[subfunctionalization]]. In other words, once a gene duplication event occurs forming paralogs that after an evolutionary period subfunctionalize, one gene copy continues on this evolutionary journey and accumulates mutations that give rise to a new function.<ref name="Graur_2000"/><ref name="He_2005">{{cite journal | vauthors = He X, Zhang J | title = Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution | journal = Genetics | volume = 169 | issue = 2 | pages = 1157–64 | date = February 2005 | pmid = 15654095 | pmc = 1449125 | doi = 10.1534/genetics.104.037051 }}</ref> Some believe that neofunctionalization is the end stage for all subfunctionalized genes. For instance, according to Rastogi and Liberles "Neofunctionalization is the terminal fate of all duplicate gene copies retained in the genome and subfunctionlization merely exist as a transient state to preserve the duplicate gene copy."<ref name="Liberles_2005"/> The results of their study become punctuated as population size increases.

==Examples==


The evolution of the [[antifreeze protein]] in the Antarctic [[eelpout|zoarcid]] fish ''[[Lycodichthys]] dearborni'' provides a prime example of neofunctionalization after gene duplication. In the case of the Antarctic zoarcid fish type III antifreeze protein gene (AFPIII; {{UniProt|P12102}}) diverged from a paralogous copy of [[sialic acid]] synthase (SAS) gene.<ref name="Deng_2010">{{cite journal | vauthors = Deng C, Cheng CH, Ye H, He X, Chen L | title = Evolution of an antifreeze protein by neofunctionalization under escape from adaptive conflict | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 107 | issue = 50 | pages = 21593–8 | date = December 2010 | pmid = 21115821 | pmc = 3003108 | doi = 10.1073/pnas.1007883107 | doi-access = free | bibcode = 2010PNAS..10721593D }}</ref> The ancestral SAS gene was found to have both sialic acid synthase and rudimentary ice-binding functionalities. After duplication one of the paralogs began to accumulate mutations that lead to the replacement of SAS domains of the gene allowing for further development and optimization of the antifreeze functionality.<ref name="Deng_2010"/> The new gene is now capable of noncolligative freezing-point depression, and thus is neofunctionalized.<ref name="Deng_2010"/> This specialization allows Antarctic zoarcid fish to survive in the frigid temperatures of the Antarctic Seas.

Another example concerns the [[Vertebrate visual opsin|light-sensitive opsin proteins in vertebrate eyes]] that allow them to see different wavelengths of light. Extant vertebrates typically have four [[cone cell|cone]] opsin classes (LWS, SWS1, SWS2, and Rh2) as well as one [[rod cell|rod]] opsin class ([[rhodopsin]], Rh1), all of which were inherited from early vertebrate ancestors. These five classes of vertebrate visual opsins emerged through a series of gene duplications beginning with LWS and ending with Rh1.<ref name="HuntCarvalho2009">{{cite journal | vauthors = Hunt DM, Carvalho LS, Cowing JA, Davies WL | title = Evolution and spectral tuning of visual pigments in birds and mammals | journal = Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences | volume = 364 | issue = 1531 | pages = 2941–2955 | date = October 2009 | pmid = 19720655 | pmc = 2781856 | doi = 10.1098/rstb.2009.0044 }}</ref><ref name="TreziseCollin2005">{{cite journal | vauthors = Trezise AE, Collin SP | title = Opsins: evolution in waiting | journal = Current Biology | volume = 15 | issue = 19 | pages = R794–R796 | date = October 2005 | pmid = 16213808 | doi = 10.1016/j.cub.2005.09.025 | doi-access = free | bibcode = 2005CBio...15.R794T }}</ref>

==Model limitations==
Limitations exist in neofunctionalization as a model for functional divergence primarily because:
#the amount of nucleotide changes giving rise to a new function must be very minimal; making the probability for [[Pseudogene|pseudogenization]] much higher than neofunctionalization after a gene duplication event.<ref name="Graur_2000" />
#After a gene duplication event both copies may be subjected to selective pressure equivalent to that constraining the ancestral gene; meaning that neither copy is available for neofunctionalization.<ref name="Graur_2000" />
#In many cases positive Darwinian selection presents a more parsimonious explanation for the divergence of multigene families.<ref name="Graur_2000" />

== See also ==
* [[Subfunctionalization]]

== References ==
{{Reflist}}

[[Category:Genetics]]

Neofunctionalization - История изменений

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