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Evolutionary capacitance

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993:(especially trans regulatory expression) when removed. Singleton and duplicate capacitors both largely represent instances of incomplete functional redundancy; differentially expressed paralogs of duplicate capacitors continue some functionality of the original gene, and the protein-protein interaction complexes within which singleton capacitors reside largely exhibit overlapping functionality. In general the phenotypic capacitors identified by knockouts in yeast are genes expressed in several key regulatory areas which, while non-lethal when removed, do not have enough redundancy to maintain complete functionality. The concept of functional redundancy may also be involved in the high number of synthetic-lethal interactions which capacitor genes participate in. When a gene has its functionality resumed by a paralog or functional analog, its removal is not inherently lethal, however when the gene and its redundancy are removed, the result is lethality. 956: 36: 591: 972:), while duplicate capacitors are more highly connected and tend to interact with multiple large complexes. The gene ontologies of singleton and duplicate capacitors also differ notably. Singleton capacitors are concentrated in the categories of DNA maintenance and organization, response to stimuli, and RNA transcription and localization, whereas duplicate capacitors are concentrated in the categories of 578: 848:, in matched and strains in a variety of stressful environments. Sometimes the strain grows faster, sometimes : this depends on the genetic background of the strain, suggesting that taps into pre-existing cryptic genetic variation. Mathematical models suggest that may have evolved, as an evolutionary capacitor, to promote 1001:
Computational simulations of knockouts in complex gene interaction networks have demonstrated that many, and possibly all expressed genes have the potential to reveal phenotypic variation of some kind when removed, and that previously identified capacitor genes are simply especially strong examples.
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elsewhere in the genome; most capacitors identified in yeast are either singleton genes, or have historical paralogs from which they have diverged substantially in terms of expression. Singleton and duplicate capacitors largely exhibit disjoint behavior in the interactome. Singleton capacitors are
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at various levels of the genome. Coding regions that are necessary for the synthesis of key proteins which do not have paralogs elsewhere in the genome are lethal when removed. Conversely, coding regions with many paralogs or strongly expressed paralogs have a minimal effect on overall expression
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or genomic regions which function as evolutionary capacitors. When a gene is knocked out, and its removal reveals phenotypic variation that was not previously observable, that gene is functioning as a phenotypic capacitor. If any of the variation is adaptive, it is functioning as an evolutionary
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to new environmental conditions. Switching rates may be a function of stress, making genetic variation more likely to affect the phenotype at times when it is most likely to be useful for adaptation. In addition, strongly deleterious variation may be purged while in a partially cryptic state, so
919:. Unlike the chromatin regulators, the removal of genes which code for metabolic enzymes does not have a consistent effect on the difference in expression between species, with different enzyme knockouts either increasing, decreasing, or not significantly affecting the expression difference. 746:. It has been proposed that the presence of chaperones may, by providing additional robustness to errors in folding, allow the exploration of a larger set of genotypes. When chaperones are overworked at times of environmental stress, this may "switch on" previously cryptic genetic variation. 772:). This was thought to prove that the new phenotypes depended on pre-existing cryptic genetic variation that had merely been revealed. More recent evidence suggests that these data might be explained by new mutations caused by the reactivation of formally dormant 951:
observed for its expressed protein. However, proteins with the highest amount of interactions have reduced phenotypic capacitance, possibly due to increased duplication of regions coding these proteins in the genome, reducing the effect of a single knockout.
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Similar transient increases in error rates can evolve emergently in the absence of a "widget" like . The primary advantage of a -like widget is to facilitate the subsequent evolution of lower error rates once genetic assimilation has occurred.
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Switches that turn robustness to phenotypic rather than genetic variation on and off do not fit the capacitance analogy, as their presence does not cause variation to accumulate over time. They have instead been called phenotypic stabilizers.
658:. After that, the rest of variation, most of which is presumably deleterious, can be switched off, leaving the population with a newly evolved advantageous trait, but no long-term handicap. For evolutionary capacitance to increase 859:, mimicking the effects of , than would be expected from mutation bias or than are observed in other taxa that do not form the prion. These observations are compatible with acting as an evolutionary capacitor in the wild. 922:
Broader knockout samples in yeast have identified at least 300 genes which, when absent, increase morphological variation between yeast individuals. These capacitor genes predominantly occupy a few key domains in
654:. An evolutionary capacitor is a molecular switch mechanism that can "toggle" genetic variation between hidden and revealed states. If some subset of newly revealed variation is adaptive, it becomes fixed by 840:
form (). When is present, this depletes the amount of normal Sup35p available. As a result, the rate of errors in which translation continues beyond a stop codon increases from about 0.3% to about 1%.
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Specchia V; Piacentini L; Tritto P; Fanti L; D’Alessandro R; Palumbo G; Pimpinelli S; Bozzetti MP (2010). "Hsp90 prevents phenotypic variation by suppressing the mutagenic activity of transposons".
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perform side reactions. Similarly, binding proteins may spend some proportion of their time bound to off-target proteins. These reactions or interactions may be of no consequence to current
764:, a broad range of different phenotypes are seen, where the identity of the phenotype depends on the genetic background. Also, a recent study on the model insect, the red flour beetle 307: 681:
about the extent to which capacitance might contribute to evolution in natural populations. The possibility of evolutionary capacitance is considered to be part of the
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resistance. In populations exposed only to ampicillin, such mutations may be present in a minority of members since there is not fitness cost (i.e. are within the
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effect. But when the system is disturbed (perhaps by stress), robustness breaks down, and the variation has phenotypic effects and is subject to the full force of
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Matsumura, I; Ellington, AD (Jan 12, 2001). "In vitro evolution of beta-glucuronidase into a beta-galactosidase proceeds through non-specific intermediates".
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Singleton capacitors (light blue) are generally part of large complexes, while duplicate capacitors (dark blue) often interact with several major complexes.
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regulating genes increases the differences in expression between yeast species. The majority of the variation in protein expression is attributable to
727:). This represents cryptic genetic variation since if the population is newly exposed to cefotaxime, the minority members will exhibit some resistance. 711:
but under altered conditions, may provide the starting point for adaptive evolution. For example, several mutations in the antibiotic resistance gene
2427: 349: 1906:"The Spontaneous Appearance Rate of the Yeast Prion PSI+ and Its Implications for the Evolution of the Evolvability Properties of the PSI+ System" 1767:
Firoozan M, Grant CM, Duarte JA, Tuite MF (1991). "Quantitation of readthrough of termination codons in yeast using a novel gene fusion assay".
55: 776:. However, this finding regarding transposable elements may be dependent on the strong nature of the Hsp90 knockdown used in that experiment. 768:, showed that Hsp90 impairment revealed a new phenotype, reduced-eye phenotype, which was stably inherited without further HSP90 inhibition ( 536: 483: 939:, and response to stimuli such as stress. More generally, capacitor genes are likely to express proteins which act as network hubs in the 615: 344: 175: 1390:
Mohamed, MF; Hollfelder, F (Jan 2013). "Efficient, crosswise catalytic promiscuity among enzymes that catalyze phosphoryl transfer".
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cryptic variation that remains is more likely to be adaptive than random mutations are. Capacitance can help cross "valleys" in the
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can act as an evolutionary capacitor by breaking up allele combinations with phenotypic effects that normally cancel out.
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Nobuhiko Tokuriki; Dan S. Tawfik (2009). "Chaperonin overexpression promotes genetic variation and enzyme evolution".
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The hypothesis that chaperones can act as evolutionary capacitors is closely associated with the heat shock protein
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True HL, Lindquist SL (2000). "A yeast prion provides a mechanism for genetic variation and phenotypic diversity".
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interactions. The confidence that a specific gene acts as a phenotypic capacitor is correlated with the number of
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is the storage and release of variation, just as electric capacitors store and release charge. Living systems are
448: 423: 403: 383: 60: 2323:"The consequences of rare sexual reproduction by means of selfing in an otherwise clonally reproducing species" 1242:"Cryptic genetic variation can make "irreducible complexity" a common mode of adaptation in sexual populations" 1002:
Capacitance, then, is simply a feature of complex gene networks that arises in conjunction with canalization.
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Bergman A, Siegal ML (July 2003). "Evolutionary capacitance as a general feature of complex gene networks".
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appears more frequently in response to environmental stress. In yeast, more stop codon disappearances are
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Kazuo Takahashi (2013). "Multiple capacitors for natural genetic variation in Drosophila melanogaster".
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The mechanism of phenotypic capacitor genes in yeast appears to be closely related to the modalities of
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in this way, the switching rate should not be faster than the timescale of genetic assimilation.
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Masel J, Bergman A (2003). "The evolution of the evolvability properties of the yeast prion ".
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Mario A. Fares; Mario X. Ruiz-González; Andrés Moya; Santiago F. Elena; Eladio Barrio (2002).
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Deficiency in at least 15 different genes reveals cryptic variation in wing morphology in
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Rutherford SL, Lindquist S (1998). "Hsp90 as a capacitor for morphological evolution".
1367: 1342: 1266: 1241: 1214: 1189: 1107: 1080: 317: 220: 1443: 1426: 2416: 2111: 1753: 1541: 1307: 1151: 1134: 1052: 924: 871: 856: 837: 468: 140: 1890: 1796: 1168: 2403: 1847: 1702: 1592: 1338: 1324: 1237: 1185: 1076: 1030: 892: 849: 799: 659: 488: 473: 257: 252: 170: 2307: 2172:"Chromatin regulators as capacitors of interspecies variations in gene expression" 836:
to stop correctly at the ends of proteins. Sup35p comes in a normal form () and a
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mutations can be thought of as cryptic when they are present overwhelmingly in
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Itay Tirosh; Sharon Reikhav; Nadejda Sigal; Yael Assia; Naama Barkai (2010).
2096:"The Evolution of Reversible Switches in the Presence of Irreversible Mimics" 1097: 915:
effects, suggesting that trans-regulatory processes are strongly involved in
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population by creating homozygotes. Facultative sex that takes the form of
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Vamsi K Gangaraju; Hang Yin; Molly M Weiner; Jianquan Wang; Xiao A Huang;
1533: 577: 2221:"Network hubs buffer environmental variation in Saccharomyces cerevisiae" 1014: 521: 120: 2291: 2187: 1737: 1576: 2395: 704: 2156: 1257: 1831: 1661:"Endosymbiotic bacteria: GroEL buffers against deleterious mutations" 1427:"Catalytic promiscuity and the evolution of new enzymatic activities" 821: 1685: 1660: 1290: 2387: 1627: 1525: 954: 895:, and could even improve the flight capability of an individual. 785: 755: 742:. The need to fold proteins correctly is a big restriction on the 1190:"Cryptic Genetic Variation Is Enriched for Potential Adaptations" 844:
This can lead to different growth rates, and sometimes different
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Tyedmers J, Madariaga ML, Lindquist S (2008). Weissman J (ed.).
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most often part of highly interconnected complexes (such as the
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Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics
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to mutations. This means that living systems accumulate
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Lancaster, Alex K.; Masel, Joanna (September 2009).
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can act as an evolutionary capacitor in a primarily
1904:Lancaster AK, Bardill JP, True HL, Masel J (2010). 1499: 1497: 1291:"Do We Need an Extended Evolutionary Synthesis?" 2006:"The conversion of 3′ UTRs into coding regions" 758:. When Hsp90 is downregulated in the fruit fly 2219:Levy SF, Siegal ML (2008). 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This can increase 656:genetic assimilation 414:Evolutionary ecology 28:Evolutionary biology 2376:American Naturalist 2292:10.1038/nature01765 2284:2003Natur.424..549B 2188:10.1038/msb.2010.84 1824:2000Natur.407..477T 1738:10.1038/nature08009 1730:2009Natur.459..668T 1677:2002Natur.417..398F 1577:10.1038/nature08739 1569:2010Natur.463..662S 1518:1998Natur.396..336R 766:Tribolium castaneum 516:Social implications 504:Universal Darwinism 494:Island biogeography 429:Evolutionary ethics 394:Ecological genetics 340:Molecular evolution 278:Transitional fossil 106:Population genetics 22:Part of a series on 2151:(435): 1356–1365. 1347:Trends in Genetics 974:protein metabolism 961: 699:enzyme promiscuity 693:Enzyme promiscuity 547:Theistic evolution 479:Selective breeding 191:Parallel evolution 156:Adaptive radiation 2278:(6948): 549–552. 2157:10.1111/mec.12091 2145:Molecular Ecology 1818:(6803): 477–483. 1724:(7247): 668–673. 1512:(6709): 336–342. 1301:(12): 2743–2749. 1258:10.1111/evo.12517 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1084: 1071: 1009: 1000: 987: 962: 921: 917:canalization 902: 893:aerodynamics 886: 879:capacitor. 870: 861: 854: 850:evolvability 846:morphologies 843: 832:and causing 820: 806:Yeast prion 800:evolvability 789: 783: 759: 753: 734: 702: 687: 676: 664: 660:evolvability 635: 634: 489:Sociobiology 474:Paleontology 322: 258:Biogeography 253:Biodiversity 171:Coextinction 161:Co-operation 136:Polymorphism 61:Introduction 2231:(1): e264. 1085:BMC Biology 1048:Epigenetics 1031:outcrossing 997:Simulations 978:endocytosis 941:interactome 883:Fruit Flies 834:translation 830:stop codons 713:B-lactamase 499:Systematics 308:Renaissance 186:Convergence 176:Contingency 166:Coevolution 2417:Categories 1608:Haifan Lin 1064:References 984:Redundancy 937:cell cycle 794:increases 738:assist in 736:Chaperones 731:Chaperones 721:ampicillin 717:cefotaxime 715:introduce 667:adaptation 648:phenotypic 273:Cladistics 196:Extinction 181:Divergence 151:Speciation 131:Adaptation 45:John Gould 2433:Selection 2100:Evolution 1863:Evolution 1754:205216739 1542:204996106 1295:Evolution 1246:Evolution 1139:Evolution 1011:Recessive 909:chromatin 679:consensus 532:Dysgenics 248:Phylogeny 146:Gene flow 116:Diversity 111:Variation 2357:21888925 2300:12891357 2257:18986213 2206:21119629 2130:19486147 2081:30282033 2040:17099057 1991:19067491 1940:19917766 1910:Genetics 1891:30954684 1883:12940355 1840:11028992 1797:42869007 1746:19494908 1695:12024205 1646:21186352 1610:(2011). 1585:20062045 1488:11124909 1453:10099128 1412:22885024 1377:19717203 1317:17924956 1276:25178652 1224:16387877 1194:Genetics 1169:13150906 1161:17683428 1117:24228631 1077:Masel, J 1037:See also 965:paralogs 857:in-frame 596:Category 522:Eugenics 364:timeline 345:Evo-devo 303:Overview 121:Mutation 83:Evidence 78:Glossary 2404:5505336 2396:2460915 2348:3218209 2280:Bibcode 2248:2577700 2197:3010112 2121:2770902 2031:1808353 1982:2586387 1931:2828720 1848:4411231 1820:Bibcode 1789:1905859 1726:Bibcode 1703:4368351 1673:Bibcode 1637:3443399 1593:4429205 1565:Bibcode 1534:9845070 1514:Bibcode 1368:2770586 1339:Masel J 1325:2703146 1267:4258170 1215:1456269 1108:3849687 1091:: 103. 1027:asexual 1023:selfing 709:fitness 705:enzymes 88:History 71:Outline 2402:  2394:  2355:  2345:  2308:775036 2306:  2298:  2272:Nature 2255:  2245:  2204:  2194:  2128:  2118:  2079:  2038:  2028:  1989:  1979:  1938:  1928:  1889:  1881:  1846:  1838:  1812:Nature 1795:  1787:  1752:  1744:  1718:Nature 1701:  1693:  1665:Nature 1644:  1634:  1591:  1583:  1557:Nature 1540:  1532:  1506:Nature 1486:  1451:  1410:  1375:  1365:  1323:  1315:  1274:  1264:  1222:  1212:  1167:  1159:  1115:  1105:  822:Sup35p 810:": --> 640:robust 594:  318:Darwin 2400:S2CID 2392:JSTOR 2304:S2CID 1887:S2CID 1844:S2CID 1793:S2CID 1769:Yeast 1750:S2CID 1699:S2CID 1589:S2CID 1538:S2CID 1321:S2CID 1165:S2CID 913:trans 905:yeast 899:Yeast 876:genes 838:prion 826:yeast 824:is a 786:GroEL 780:GroEL 756:Hsp90 750:Hsp90 56:Index 2353:PMID 2296:PMID 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Index

Evolutionary biology

Darwin's finches
John Gould
Index
Introduction
Main
Outline
Glossary
Evidence
History
Population genetics
Variation
Diversity
Mutation
Natural selection
Adaptation
Polymorphism
Genetic drift
Gene flow
Speciation
Adaptive radiation
Co-operation
Coevolution
Coextinction
Contingency
Divergence
Convergence
Parallel evolution
Extinction

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