- -

The causes of epistasis

RiuNet: Repositorio Institucional de la Universidad Politécnica de Valencia

Compartir/Enviar a

Citas

Estadísticas

  • Estadisticas de Uso

The causes of epistasis

Mostrar el registro completo del ítem

De Visser, JAGM.; Cooper, TF.; Elena Fito, SF. (2011). The causes of epistasis. Proceedings of the Royal Society B: Biological Sciences. 278(1725):3617-3624. https://doi.org/10.1098/rspb.2011.1537

Por favor, use este identificador para citar o enlazar este ítem: http://hdl.handle.net/10251/83307

Ficheros en el ítem

Metadatos del ítem

Título: The causes of epistasis
Autor: de Visser, J. Arjan G. M. Cooper, Tim F. Elena Fito, Santiago Fco
Entidad UPV: Universitat Politècnica de València. Instituto Universitario Mixto de Biología Molecular y Celular de Plantas - Institut Universitari Mixt de Biologia Molecular i Cel·lular de Plantes
Fecha difusión:
Resumen:
[EN] Since Bateson's discovery that genes can suppress the phenotypic effects of other genes, gene interactions-called epistasis-have been the topic of a vast research effort. Systems and developmental biologists study ...[+]
Palabras clave: Epistasis , Pleiotropy , Robustness , Evolvability
Derechos de uso: Reserva de todos los derechos
Fuente:
Proceedings of the Royal Society B: Biological Sciences. (issn: 0962-8452 )
DOI: 10.1098/rspb.2011.1537
Editorial:
Royal Society, The
Versión del editor: http://doi.org/10.1098/rspb.2011.1537
Código del Proyecto:
info:eu-repo/grantAgreement/EC/FP7/225167/EU/Evolutionary microfluidics/
info:eu-repo/grantAgreement/NSF//0844355/US/Collaborative Research: Understanding the basis of interactions between adaptive mutations and their environment/
Agradecimientos:
We thank Fons Debets, Ryszard Korona, Alexey Kondrashov, Joachim Krug, Sijmen Schoustra and an anonymous reviewer for constructive comments, and funds from the European Union Seventh Framework Programme (FP7/2007-2013) ...[+]
Tipo: Artículo

References

Costanzo, M., Baryshnikova, A., Bellay, J., Kim, Y., Spear, E. D., Sevier, C. S., … Mostafavi, S. (2010). The Genetic Landscape of a Cell. Science, 327(5964), 425-431. doi:10.1126/science.1180823

Moore, J. H., & Williams, S. M. (2005). Traversing the conceptual divide between biological and statistical epistasis: systems biology and a more modern synthesis. BioEssays, 27(6), 637-646. doi:10.1002/bies.20236

Phillips, P. C. (2008). Epistasis — the essential role of gene interactions in the structure and evolution of genetic systems. Nature Reviews Genetics, 9(11), 855-867. doi:10.1038/nrg2452 [+]
Costanzo, M., Baryshnikova, A., Bellay, J., Kim, Y., Spear, E. D., Sevier, C. S., … Mostafavi, S. (2010). The Genetic Landscape of a Cell. Science, 327(5964), 425-431. doi:10.1126/science.1180823

Moore, J. H., & Williams, S. M. (2005). Traversing the conceptual divide between biological and statistical epistasis: systems biology and a more modern synthesis. BioEssays, 27(6), 637-646. doi:10.1002/bies.20236

Phillips, P. C. (2008). Epistasis — the essential role of gene interactions in the structure and evolution of genetic systems. Nature Reviews Genetics, 9(11), 855-867. doi:10.1038/nrg2452

Azevedo, R. B. R., Lohaus, R., Srinivasan, S., Dang, K. K., & Burch, C. L. (2006). Sexual reproduction selects for robustness and negative epistasis in artificial gene networks. Nature, 440(7080), 87-90. doi:10.1038/nature04488

Desai, M. M., Weissman, D., & Feldman, M. W. (2007). Evolution Can Favor Antagonistic Epistasis. Genetics, 177(2), 1001-1010. doi:10.1534/genetics.107.075812

Gros, P.-A., Le Nagard, H., & Tenaillon, O. (2009). The Evolution of Epistasis and Its Links With Genetic Robustness, Complexity and Drift in a Phenotypic Model of Adaptation. Genetics, 182(1), 277-293. doi:10.1534/genetics.108.099127

Liberman, U., & Feldman, M. (2008). On the evolution of epistasis III: The haploid case with mutation. Theoretical Population Biology, 73(2), 307-316. doi:10.1016/j.tpb.2007.11.010

Liberman, U., & Feldman, M. W. (2005). On the evolution of epistasis I: diploids under selection. Theoretical Population Biology, 67(3), 141-160. doi:10.1016/j.tpb.2004.11.001

Liberman, U., Puniyani, A., & Feldman, M. W. (2007). On the evolution of epistasis II: A generalized Wright–Kimura framework. Theoretical Population Biology, 71(2), 230-238. doi:10.1016/j.tpb.2006.10.002

Martin, O. C., & Wagner, A. (2009). Effects of Recombination on Complex Regulatory Circuits. Genetics, 183(2), 673-684. doi:10.1534/genetics.109.104174

Misevic, D., Ofria, C., & Lenski, R. E. (2005). Sexual reproduction reshapes the genetic architecture of digital organisms. Proceedings of the Royal Society B: Biological Sciences, 273(1585), 457-464. doi:10.1098/rspb.2005.3338

Bateson W. Saunders E. R. Punnett R. C.& Hurst C. C.. 1905 Reports to the Evolution Committee of the Royal Society Report II. London UK: Harrison and Sons.

Fisher, R. A. (1919). XV.—The Correlation between Relatives on the Supposition of Mendelian Inheritance. Transactions of the Royal Society of Edinburgh, 52(2), 399-433. doi:10.1017/s0080456800012163

Kondrashov, F. A., & Kondrashov, A. S. (2001). Multidimensional epistasis and the disadvantage of sex. Proceedings of the National Academy of Sciences, 98(21), 12089-12092. doi:10.1073/pnas.211214298

Barton, N. H. (1995). A general model for the evolution of recombination. Genetical Research, 65(2), 123-144. doi:10.1017/s0016672300033140

Kondrashov, A. S. (1988). Deleterious mutations and the evolution of sexual reproduction. Nature, 336(6198), 435-440. doi:10.1038/336435a0

De Visser, J. A. G. M., & Elena, S. F. (2007). The evolution of sex: empirical insights into the roles of epistasis and drift. Nature Reviews Genetics, 8(2), 139-149. doi:10.1038/nrg1985

Kouyos, R. D., Silander, O. K., & Bonhoeffer, S. (2007). Epistasis between deleterious mutations and the evolution of recombination. Trends in Ecology & Evolution, 22(6), 308-315. doi:10.1016/j.tree.2007.02.014

The effect of sex and deleterious mutations on fitness in Chlamydomonas. (1996). Proceedings of the Royal Society of London. Series B: Biological Sciences, 263(1367), 193-200. doi:10.1098/rspb.1996.0031

Salathe, P., & Ebert, D. (2003). The effects of parasitism and inbreeding on the competitive ability in Daphnia magna: evidence for synergistic epistasis. Journal of Evolutionary Biology, 16(5), 976-985. doi:10.1046/j.1420-9101.2003.00582.x

Jasnos, L., & Korona, R. (2007). Epistatic buffering of fitness loss in yeast double deletion strains. Nature Genetics, 39(4), 550-554. doi:10.1038/ng1986

Lenski, R. E., Ofria, C., Collier, T. C., & Adami, C. (1999). Genome complexity, robustness and genetic interactions in digital organisms. Nature, 400(6745), 661-664. doi:10.1038/23245

Maisnier-Patin, S., Roth, J. R., Fredriksson, Å., Nyström, T., Berg, O. G., & Andersson, D. I. (2005). Genomic buffering mitigates the effects of deleterious mutations in bacteria. Nature Genetics, 37(12), 1376-1379. doi:10.1038/ng1676

Sanjuan, R., Moya, A., & Elena, S. F. (2004). The contribution of epistasis to the architecture of fitness in an RNA virus. Proceedings of the National Academy of Sciences, 101(43), 15376-15379. doi:10.1073/pnas.0404125101

Zeyl, C. (2005). The Number of Mutations Selected During Adaptation in a Laboratory Population of Saccharomyces cerevisiae. Genetics, 169(4), 1825-1831. doi:10.1534/genetics.104.027102

Peña, M. de la, Elena, S. F., & Moya, A. (2000). EFFECT OF DELETERIOUS MUTATION-ACCUMULATION ON THE FITNESS OF RNA BACTERIOPHAGE MS2. Evolution, 54(2), 686. doi:10.1554/0014-3820(2000)054[0686:eodmao]2.0.co;2

De Visser, J. A. G. M., Hoekstra, R. F., & van den Ende, H. (1997). Test of Interaction Between Genetic Markers That Affect Fitness in Aspergillus niger. Evolution, 51(5), 1499. doi:10.2307/2411202

Elena, S. F. (1999). Little Evidence for Synergism Among Deleterious Mutations in a Nonsegmented RNA Virus. Journal of Molecular Evolution, 49(5), 703-707. doi:10.1007/pl00000082

Elena, S. F., & Lenski, R. E. (1997). Test of synergistic interactions among deleterious mutations in bacteria. Nature, 390(6658), 395-398. doi:10.1038/37108

Hall, D. W., Agan, M., & Pope, S. C. (2010). Fitness Epistasis among 6 Biosynthetic Loci in the Budding Yeast Saccharomyces cerevisiae. Journal of Heredity, 101(Supplement 1), S75-S84. doi:10.1093/jhered/esq007

Kelly, J. K. (2005). Epistasis in Monkeyflowers. Genetics, 171(4), 1917-1931. doi:10.1534/genetics.105.041525

Segrè, D., DeLuna, A., Church, G. M., & Kishony, R. (2004). Modular epistasis in yeast metabolism. Nature Genetics, 37(1), 77-83. doi:10.1038/ng1489

He, X., Qian, W., Wang, Z., Li, Y., & Zhang, J. (2010). Prevalent positive epistasis in Escherichia coli and Saccharomyces cerevisiae metabolic networks. Nature Genetics, 42(3), 272-276. doi:10.1038/ng.524

Carneiro, M., & Hartl, D. L. (2009). Adaptive landscapes and protein evolution. Proceedings of the National Academy of Sciences, 107(suppl_1), 1747-1751. doi:10.1073/pnas.0906192106

Franke, J., Klözer, A., de Visser, J. A. G. M., & Krug, J. (2011). Evolutionary Accessibility of Mutational Pathways. PLoS Computational Biology, 7(8), e1002134. doi:10.1371/journal.pcbi.1002134

Weinreich, D. M. (2006). Darwinian Evolution Can Follow Only Very Few Mutational Paths to Fitter Proteins. Science, 312(5770), 111-114. doi:10.1126/science.1123539

Lunzer, M. (2005). The Biochemical Architecture of an Ancient Adaptive Landscape. Science, 310(5747), 499-501. doi:10.1126/science.1115649

O’Maille, P. E., Malone, A., Dellas, N., Andes Hess, B., Smentek, L., Sheehan, I., … Noel, J. P. (2008). Quantitative exploration of the catalytic landscape separating divergent plant sesquiterpene synthases. Nature Chemical Biology, 4(10), 617-623. doi:10.1038/nchembio.113

Lozovsky, E. R., Chookajorn, T., Brown, K. M., Imwong, M., Shaw, P. J., Kamchonwongpaisan, S., … Hartl, D. L. (2009). Stepwise acquisition of pyrimethamine resistance in the malaria parasite. Proceedings of the National Academy of Sciences, 106(29), 12025-12030. doi:10.1073/pnas.0905922106

De Visser, J. A. G. M., Park, S., & Krug, J. (2009). Exploring the Effect of Sex on Empirical Fitness Landscapes. The American Naturalist, 174(S1), S15-S30. doi:10.1086/599081

Khan, A. I., Dinh, D. M., Schneider, D., Lenski, R. E., & Cooper, T. F. (2011). Negative Epistasis Between Beneficial Mutations in an Evolving Bacterial Population. Science, 332(6034), 1193-1196. doi:10.1126/science.1203801

Chou, H.-H., Chiu, H.-C., Delaney, N. F., Segre, D., & Marx, C. J. (2011). Diminishing Returns Epistasis Among Beneficial Mutations Decelerates Adaptation. Science, 332(6034), 1190-1192. doi:10.1126/science.1203799

Da Silva, J., Coetzer, M., Nedellec, R., Pastore, C., & Mosier, D. E. (2010). Fitness Epistasis and Constraints on Adaptation in a Human Immunodeficiency Virus Type 1 Protein Region. Genetics, 185(1), 293-303. doi:10.1534/genetics.109.112458

Hinkley, T., Martins, J., Chappey, C., Haddad, M., Stawiski, E., Whitcomb, J. M., … Bonhoeffer, S. (2011). A systems analysis of mutational effects in HIV-1 protease and reverse transcriptase. Nature Genetics, 43(5), 487-489. doi:10.1038/ng.795

Kvitek, D. J., & Sherlock, G. (2011). Reciprocal Sign Epistasis between Frequently Experimentally Evolved Adaptive Mutations Causes a Rugged Fitness Landscape. PLoS Genetics, 7(4), e1002056. doi:10.1371/journal.pgen.1002056

MacLean, R. C., Perron, G. G., & Gardner, A. (2010). Diminishing Returns From Beneficial Mutations and Pervasive Epistasis Shape the Fitness Landscape for Rifampicin Resistance in Pseudomonas aeruginosa. Genetics, 186(4), 1345-1354. doi:10.1534/genetics.110.123083

Rokyta, D. R., Joyce, P., Caudle, S. B., Miller, C., Beisel, C. J., & Wichman, H. A. (2011). Epistasis between Beneficial Mutations and the Phenotype-to-Fitness Map for a ssDNA Virus. PLoS Genetics, 7(6), e1002075. doi:10.1371/journal.pgen.1002075

Salverda, M. L. M., Dellus, E., Gorter, F. A., Debets, A. J. M., van der Oost, J., Hoekstra, R. F., … de Visser, J. A. G. M. (2011). Initial Mutations Direct Alternative Pathways of Protein Evolution. PLoS Genetics, 7(3), e1001321. doi:10.1371/journal.pgen.1001321

Hayashi, Y., Aita, T., Toyota, H., Husimi, Y., Urabe, I., & Yomo, T. (2006). Experimental Rugged Fitness Landscape in Protein Sequence Space. PLoS ONE, 1(1), e96. doi:10.1371/journal.pone.0000096

De Visser, J. A. G., & Lenski, R. E. (2002). BMC Evolutionary Biology, 2(1), 19. doi:10.1186/1471-2148-2-19

Kryazhimskiy, S., Tkacik, G., & Plotkin, J. B. (2009). The dynamics of adaptation on correlated fitness landscapes. Proceedings of the National Academy of Sciences, 106(44), 18638-18643. doi:10.1073/pnas.0905497106

Lehner, B. (2011). Molecular mechanisms of epistasis within and between genes. Trends in Genetics, 27(8), 323-331. doi:10.1016/j.tig.2011.05.007

Feist, A. M., Henry, C. S., Reed, J. L., Krummenacker, M., Joyce, A. R., Karp, P. D., … Palsson, B. Ø. (2007). A genome‐scale metabolic reconstruction for Escherichia coli K‐12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Molecular Systems Biology, 3(1), 121. doi:10.1038/msb4100155

Szappanos, B., Kovács, K., Szamecz, B., Honti, F., Costanzo, M., Baryshnikova, A., … Papp, B. (2011). An integrated approach to characterize genetic interaction networks in yeast metabolism. Nature Genetics, 43(7), 656-662. doi:10.1038/ng.846

Dean, A. M., Dykhuizen, D. E., & Hartl, D. L. (1986). Fitness as a function of β-galactosidase activity in Escherichia coli. Genetical Research, 48(1), 1-8. doi:10.1017/s0016672300024587

Trindade, S., Sousa, A., Xavier, K. B., Dionisio, F., Ferreira, M. G., & Gordo, I. (2009). Positive Epistasis Drives the Acquisition of Multidrug Resistance. PLoS Genetics, 5(7), e1000578. doi:10.1371/journal.pgen.1000578

Agrawal, A. F., & Whitlock, M. C. (2010). Environmental duress and epistasis: how does stress affect the strength of selection on new mutations? Trends in Ecology & Evolution, 25(8), 450-458. doi:10.1016/j.tree.2010.05.003

Bonhoeffer, S. (2004). Evidence for Positive Epistasis in HIV-1. Science, 306(5701), 1547-1550. doi:10.1126/science.1101786

Burch, C. L., & Chao, L. (2004). Epistasis and Its Relationship to Canalization in the RNA Virus φ6. Genetics, 167(2), 559-567. doi:10.1534/genetics.103.021196

Martin, G., Elena, S. F., & Lenormand, T. (2007). Distributions of epistasis in microbes fit predictions from a fitness landscape model. Nature Genetics, 39(4), 555-560. doi:10.1038/ng1998

DePristo, M. A., Weinreich, D. M., & Hartl, D. L. (2005). Missense meanderings in sequence space: a biophysical view of protein evolution. Nature Reviews Genetics, 6(9), 678-687. doi:10.1038/nrg1672

Wang, X., Minasov, G., & Shoichet, B. K. (2002). Evolution of an Antibiotic Resistance Enzyme Constrained by Stability and Activity Trade-offs. Journal of Molecular Biology, 320(1), 85-95. doi:10.1016/s0022-2836(02)00400-x

Björkman, J. (2000). Effects of Environment on Compensatory Mutations to Ameliorate Costs of Antibiotic Resistance. Science, 287(5457), 1479-1482. doi:10.1126/science.287.5457.1479

Lenski, R. E. (1988). Experimental Studies of Pleiotropy and Epistasis in Escherichia coli. II. Compensation for Maldaptive Effects Associated with Resistance to Virus T4. Evolution, 42(3), 433. doi:10.2307/2409029

Schoustra, S. E., Debets, A. J. M., Slakhorst, M., & Hoekstra, R. F. (2007). Mitotic Recombination Accelerates Adaptation in the Fungus Aspergillus nidulans. PLoS Genetics, 3(4), e68. doi:10.1371/journal.pgen.0030068

MacLean, R. C., Bell, G., & Rainey, P. B. (2004). The evolution of a pleiotropic fitness tradeoff in Pseudomonas fluorescens. Proceedings of the National Academy of Sciences, 101(21), 8072-8077. doi:10.1073/pnas.0307195101

Cooper, T. F., Ostrowski, E. A., & Travisano, M. (2007). A NEGATIVE RELATIONSHIP BETWEEN MUTATION PLEIOTROPY AND FITNESS EFFECT IN YEAST. Evolution, 61(6), 1495-1499. doi:10.1111/j.1558-5646.2007.00109.x

Poon, A., & Chao, L. (2005). The Rate of Compensatory Mutation in the DNA Bacteriophage φX174. Genetics, 170(3), 989-999. doi:10.1534/genetics.104.039438

Remold, S. K., & Lenski, R. E. (2004). Pervasive joint influence of epistasis and plasticity on mutational effects in Escherichia coli. Nature Genetics, 36(4), 423-426. doi:10.1038/ng1324

Crow, J. F., & Kimura, M. (1979). Efficiency of truncation selection. Proceedings of the National Academy of Sciences, 76(1), 396-399. doi:10.1073/pnas.76.1.396

Hamilton, W. D., Axelrod, R., & Tanese, R. (1990). Sexual reproduction as an adaptation to resist parasites (a review). Proceedings of the National Academy of Sciences, 87(9), 3566-3573. doi:10.1073/pnas.87.9.3566

Jasnos, L., Tomala, K., Paczesniak, D., & Korona, R. (2008). Interactions Between Stressful Environment and Gene Deletions Alleviate the Expected Average Loss of Fitness in Yeast. Genetics, 178(4), 2105-2111. doi:10.1534/genetics.107.084533

Kishony, R., & Leibler, S. (2003). Journal of Biology, 2(2), 14. doi:10.1186/1475-4924-2-14

Yeh, P. J., Hegreness, M. J., Aiden, A. P., & Kishony, R. (2009). Drug interactions and the evolution of antibiotic resistance. Nature Reviews Microbiology, 7(6), 460-466. doi:10.1038/nrmicro2133

Cooper, T. F., & Lenski, R. E. (2010). Experimental evolution with E. coli in diverse resource environments. I. Fluctuating environments promote divergence of replicate populations. BMC Evolutionary Biology, 10(1), 11. doi:10.1186/1471-2148-10-11

Korona, R., Nakatsu, C. H., Forney, L. J., & Lenski, R. E. (1994). Evidence for multiple adaptive peaks from populations of bacteria evolving in a structured habitat. Proceedings of the National Academy of Sciences, 91(19), 9037-9041. doi:10.1073/pnas.91.19.9037

Rozen, D. E., Habets, M. G. J. L., Handel, A., & de Visser, J. A. G. M. (2008). Heterogeneous Adaptive Trajectories of Small Populations on Complex Fitness Landscapes. PLoS ONE, 3(3), e1715. doi:10.1371/journal.pone.0001715

Kashtan, N., & Alon, U. (2005). Spontaneous evolution of modularity and network motifs. Proceedings of the National Academy of Sciences, 102(39), 13773-13778. doi:10.1073/pnas.0503610102

De Visser, J. A. G. M., Hermisson, J., Wagner, G. P., Meyers, L. A., Bagheri-Chaichian, H., Blanchard, J. L., … Whitlock, M. C. (2003). PERSPECTIVE:EVOLUTION AND DETECTION OF GENETIC ROBUSTNESS. Evolution, 57(9), 1959. doi:10.1554/02-750r

Wilke, C. O., & Christoph, A. (2001). Interaction between directional epistasis and average mutational effects. Proceedings of the Royal Society of London. Series B: Biological Sciences, 268(1475), 1469-1474. doi:10.1098/rspb.2001.1690

Sanjuan, R., & Elena, S. F. (2006). Epistasis correlates to genomic complexity. Proceedings of the National Academy of Sciences, 103(39), 14402-14405. doi:10.1073/pnas.0604543103

Sanjuán, R., & Nebot, M. R. (2008). A Network Model for the Correlation between Epistasis and Genomic Complexity. PLoS ONE, 3(7), e2663. doi:10.1371/journal.pone.0002663

Lynch, M., & Conery, J. S. (2003). The Origins of Genome Complexity. Science, 302(5649), 1401-1404. doi:10.1126/science.1089370

Wilke, C. O., Wang, J. L., Ofria, C., Lenski, R. E., & Adami, C. (2001). Evolution of digital organisms at high mutation rates leads to survival of the flattest. Nature, 412(6844), 331-333. doi:10.1038/35085569

Weinreich, D. M., & Chao, L. (2005). RAPID EVOLUTIONARY ESCAPE BY LARGE POPULATIONS FROM LOCAL FITNESS PEAKS IS LIKELY IN NATURE. Evolution, 59(6), 1175-1182. doi:10.1111/j.0014-3820.2005.tb01769.x

Wagner, G. P., Pavlicev, M., & Cheverud, J. M. (2007). The road to modularity. Nature Reviews Genetics, 8(12), 921-931. doi:10.1038/nrg2267

Watson, R. A., Weinreich, D. M., & Wakeley, J. (2010). GENOME STRUCTURE AND THE BENEFIT OF SEX. Evolution, 65(2), 523-536. doi:10.1111/j.1558-5646.2010.01144.x

Hayden, E. J., Ferrada, E., & Wagner, A. (2011). Cryptic genetic variation promotes rapid evolutionary adaptation in an RNA enzyme. Nature, 474(7349), 92-95. doi:10.1038/nature10083

[-]

recommendations

 

Este ítem aparece en la(s) siguiente(s) colección(ones)

Mostrar el registro completo del ítem