Skip to main content

Genetic Redundancies and Their Evolutionary Maintenance

  • Chapter
  • First Online:
Evolutionary Systems Biology

Part of the book series: Advances in Experimental Medicine and Biology ((volume 751))

Abstract

Genetic redundancy refers to the common phenomenon that deleting or mutating a gene from a genome has minimal or no impact on the phenotype or fitness of the organism because of functional compensation conferred by one or more other genes. Here I summarize studies of functional redundancies between duplicate genes and those among metabolic reactions that respectively represent genetic redundancies at the individual gene level and at the systems level. I discuss the prevalence of genetic redundancies in a genome, evolutionary origins of these redundancies, and mechanisms responsible for their stable maintenance. I show that genetic redundancies are highly abundant. While some of them may be evolutionarily transient, many are stable. The majority of the stable redundancies are likely to have been selectively kept, not because of their potential benefits in regard to future deleterious mutations, but because of their actual benefits at present or in the recent past. The rest are probably preserved by selection on nonredundant pleiotropic functions. The studies summarized here illustrate the utility of systems analysis for understanding evolutionary phenomena and the importance of evolutionary thinking in uncovering the functions and origins of systemic properties.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Austin CP, Battey JF, Bradley A, et al. (2004) The knockout mouse project. Nat Genet 36: 921–924

    Article  PubMed  CAS  Google Scholar 

  2. Chen S, Zhang YE, Long M (2010) New genes in Drosophila quickly become essential. Science 330:1682–1685

    Article  PubMed  CAS  Google Scholar 

  3. Conant GC, Wagner A (2004) Duplicate genes and robustness to transient gene knock-downs in Caenorhabditis elegans. Proc Biol Sci 271:89–96

    Article  PubMed  Google Scholar 

  4. Cooke J, Nowak MA, Boerlijst M, Maynard-Smith J (1997) Evolutionary origins and maintenance of redundant gene expression during metazoan development. Trends Genet 13:360–364

    Article  PubMed  CAS  Google Scholar 

  5. de Visser JA, Hermisson J, Wagner GP, et al. (2003) Perspective: evolution and detection of genetic robustness. Evolution 57:1959–1972

    Article  PubMed  Google Scholar 

  6. Dean EJ, Davis JC, Davis RW, Petrov DA (2008) Pervasive and persistent redundancy among duplicated genes in yeast. PLoS Genet 4:e1000113

    Article  PubMed  Google Scholar 

  7. DeLuna A, Springer M, Kirschner MW, Kishony R (2010) Need-based up-regulation of protein levels in response to deletion of their duplicate genes. PLoS Biol 8:e1000347

    Article  PubMed  Google Scholar 

  8. DeLuna A, Vetsigian K, Shoresh N, Hegreness M, Colon-Gonzalez M, Chao S, Kishony R (2008) Exposing the fitness contribution of duplicated genes. Nat Genet 40:676–681

    Article  PubMed  CAS  Google Scholar 

  9. Deutschbauer AM, Jaramillo DF, Proctor M, Kumm J, Hillenmeyer ME, Davis RW, Nislow C, Giaever G (2005) Mechanisms of haploinsufficiency revealed by genome-wide profiling in yeast. Genetics 169:1915–1925

    Article  PubMed  CAS  Google Scholar 

  10. Duarte NC, Herrgard MJ, Palsson BO (2004) Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res 14:1298–1309

    Article  PubMed  CAS  Google Scholar 

  11. Edwards JS, Ibarra RU, Palsson BO (2001) In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat Biotechnol 19:125–130

    Article  PubMed  CAS  Google Scholar 

  12. Famili I, Forster J, Nielsen J, Palsson BO (2003) Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network. Proc Natl Acad Sci USA 100:13134–13139

    Article  PubMed  CAS  Google Scholar 

  13. Feldman I, Rzhetsky A, Vitkup D (2008) Network properties of genes harboring inherited disease mutations. Proc Natl Acad Sci USA 105:4323–4328

    Article  PubMed  CAS  Google Scholar 

  14. Fong SS, Burgard AP, Herring CD, Knight EM, Blattner FR, Maranas CD, Palsson BO (2005) In silico design and adaptive evolution of Escherichia coli for production of lactic acid. Biotechnol Bioeng 91:643–648

    Article  PubMed  CAS  Google Scholar 

  15. Fong SS, Palsson BO (2004) Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes. Nat Genet 36:1056–1058

    Article  PubMed  CAS  Google Scholar 

  16. Gogarten JP, Doolittle WF, Lawrence JG (2002) Prokaryotic evolution in light of gene transfer. Mol Biol Evol 19:2226–2238

    Article  PubMed  CAS  Google Scholar 

  17. Gu Z, Steinmetz LM, Gu X, Scharfe C, Davis RW, Li WH (2003) Role of duplicate genes in genetic robustness against null mutations. Nature 421:63–66

    Article  PubMed  CAS  Google Scholar 

  18. Hanada K, Kuromori T, Myouga F, Toyoda T, Li WH, Shinozaki K (2009) Evolutionary persistence of functional compensation by duplicate genes in Arabidopsis. Genome Biol Evol 1:409–414

    Article  PubMed  Google Scholar 

  19. Harrison R, Papp B, Pal C, Oliver SG, Delneri D (2007) Plasticity of genetic interactions in metabolic networks of yeast. Proc Natl Acad Sci USA 104:2307–2312

    Article  PubMed  CAS  Google Scholar 

  20. Hartman JL, Garvik B, Hartwell L (2001) Principles for the buffering of genetic variation. Science 291:1001–1004

    Article  PubMed  CAS  Google Scholar 

  21. He X, Qian W, Wang Z, Li Y, Zhang J (2010) Prevalent positive epistasis in Escherichia coli and Saccharomyces cerevisiae metabolic networks. Nat Genet 42:272–276

    Article  PubMed  CAS  Google Scholar 

  22. He X, Zhang J (2005) Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution. Genetics 169:1157–1164

    Article  PubMed  Google Scholar 

  23. He X, Zhang J (2006a) Higher duplicability of less important genes in yeast genomes. Mol Biol Evol 23:144–151

    Article  PubMed  CAS  Google Scholar 

  24. He X, Zhang J (2006b) Transcriptional reprogramming and backup between duplicate genes: is it a genome-wide phenomenon? Genetics 172:1363–1367

    Article  PubMed  Google Scholar 

  25. He X, Zhang J (2006c) Why do hubs tend to be essential in protein networks? PLoS Genet 2:e88

    Article  PubMed  Google Scholar 

  26. Hsiao TL, Vitkup D (2008) Role of duplicate genes in robustness against deleterious human mutations. PLoS Genet 4:e1000014

    Article  PubMed  Google Scholar 

  27. Ibarra RU, Edwards JS, Palsson BO (2002) Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 420:186–189

    Article  PubMed  CAS  Google Scholar 

  28. Joyner AL, Herrup K, Auerbach BA, Davis CA, Rossant J (1991) Subtle cerebellar phenotype in mice homozygous for a targeted deletion of the En-2 homeobox. Science 251:1239–1243

    Article  PubMed  CAS  Google Scholar 

  29. Kafri R, Bar-Even A, Pilpel Y (2005) Transcription control reprogramming in genetic backup circuits. Nat Genet 37:295–299

    Article  PubMed  CAS  Google Scholar 

  30. Kandror O, DeLeon A, Goldberg AL (2002) Trehalose synthesis is induced upon exposure of Escherichia coli to cold and is essential for viability at low temperatures. Proc Natl Acad Sci U S A 99:9727–9732

    Article  PubMed  CAS  Google Scholar 

  31. Kim DU, Hayles J, Kim D, et al. (2010) Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe. Nat Biotechnol 28:617–623

    Article  PubMed  CAS  Google Scholar 

  32. Kondrashov FA, Koonin EV (2004) A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. Trends Genet 20:287–290

    Article  PubMed  CAS  Google Scholar 

  33. Lenski RE, Barrick JE, Ofria C (2006) Balancing robustness and evolvability. PLoS Biol 4:e428

    Google Scholar 

  34. Lercher MJ, Pal C (2008) Integration of horizontally transferred genes into regulatory interaction networks takes many million years. Mol Biol Evol 25:559–567

    Article  PubMed  CAS  Google Scholar 

  35. Liang H, Li WH (2007) Gene essentiality, gene duplicability and protein connectivity in human and mouse. Trends Genet 23:375–378

    Article  PubMed  CAS  Google Scholar 

  36. Liang H, Li WH (2009) Functional compensation by duplicated genes in mouse. Trends Genet 25:441–442

    Article  PubMed  Google Scholar 

  37. Liao BY, Scott NM, Zhang J (2006) Impacts of gene essentiality, expression pattern, and gene compactness on the evolutionary rate of mammalian proteins. Mol Biol Evol 23:2072–2080

    Article  PubMed  CAS  Google Scholar 

  38. Liao BY, Zhang J (2007) Mouse duplicate genes are as essential as singletons. Trends Genet 23:378–381

    Article  PubMed  CAS  Google Scholar 

  39. Lynch M, Conery JS (2000) The evolutionary fate and consequences of duplicate genes. Science 290:1151–1155

    Article  PubMed  CAS  Google Scholar 

  40. Makino T, Hokamp K, McLysaght A (2009) The complex relationship of gene duplication and essentiality. Trends Genet 25:152–155

    Article  PubMed  CAS  Google Scholar 

  41. Musso G, Costanzo M, Huangfu M, et al. (2008) The extensive and condition-dependent nature of epistasis among whole-genome duplicates in yeast. Genome Res 18:1092–1099

    Article  PubMed  CAS  Google Scholar 

  42. Nowak MA, Boerlijst MC, Cooke J, Smith JM (1997) Evolution of genetic redundancy. Nature 388:167–171

    Article  PubMed  CAS  Google Scholar 

  43. Papp B, Pal C, Hurst LD (2003) Dosage sensitivity and the evolution of gene families in yeast. Nature 424:194–197

    Article  PubMed  CAS  Google Scholar 

  44. Parenteau J, Durand M, Morin G, Gagnon J, Lucier JF, Wellinger RJ, Chabot B, Abou Elela S (2011) Introns within ribosomal protein genes regulate the production and function of yeast ribosomes. Cell 147:320–331

    Article  PubMed  CAS  Google Scholar 

  45. Price ND, Reed JL, Palsson BO (2004) Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat Rev Microbiol 2:886–897

    Article  PubMed  CAS  Google Scholar 

  46. Qian W, Liao BY, Chang AY, Zhang J (2010) Maintenance of duplicate genes and their functional redundancy by reduced expression. Trends Genet 26:425–430

    Article  PubMed  CAS  Google Scholar 

  47. Saga Y, Yagi T, Ikawa Y, Sakakura T, Aizawa S (1992) Mice develop normally without tenascin. Genes Dev 6:1821–1831

    Article  PubMed  CAS  Google Scholar 

  48. Segre D, Vitkup D, Church GM (2002) Analysis of optimality in natural and perturbed metabolic networks. Proc Natl Acad Sci USA 99:15112–15117

    Article  PubMed  CAS  Google Scholar 

  49. Snitkin ES, Dudley AM, Janse DM, Wong K, Church GM, Segre D (2008) Model-driven analysis of experimentally determined growth phenotypes for 465 yeast gene deletion mutants under 16 different conditions. Genome Biol 9:R140

    Article  PubMed  Google Scholar 

  50. Soyer OS, Pfeiffer T (2010) Evolution under fluctuating environments explains observed robustness in metabolic networks. PLoS Comput Biol 6:e1000907

    Article  PubMed  Google Scholar 

  51. Tautz D (1992) Redundancies, development and the flow of information. Bioessays 14: 263–266

    Article  PubMed  CAS  Google Scholar 

  52. Thomas JH (1993) Thinking about genetic redundancy. Trends Genet 9:395–399

    Article  PubMed  CAS  Google Scholar 

  53. Tischler J, Lehner B, Chen N, Fraser AG (2006) Combinatorial RNA interference in Caenorhabditis elegans reveals that redundancy between gene duplicates can be maintained for more than 80 million years of evolution. Genome Biol 7:R69

    Article  PubMed  Google Scholar 

  54. Vavouri T, Semple JI, Lehner B (2008) Widespread conservation of genetic redundancy during a billion years of eukaryotic evolution. Trends Genet 24:485–488

    Article  PubMed  CAS  Google Scholar 

  55. Wagner A (2000a) Robustness against mutations in genetic networks of yeast. Nat Genet 24:355–361

    Article  PubMed  CAS  Google Scholar 

  56. Wagner A (2000b) The role of population size, pleiotropy and fitness effects of mutations in the evolution of overlapping gene functions. Genetics 154:1389–1401

    PubMed  CAS  Google Scholar 

  57. Wagner A (2005a) Distributed robustness versus redundancy as causes of mutational robustness. Bioessays 27:176–188

    Article  PubMed  CAS  Google Scholar 

  58. Wagner A (2005b) Energy constraints on the evolution of gene expression. Mol Biol Evol 22:1365–1374

    Article  PubMed  CAS  Google Scholar 

  59. Wagner A (2005c) Robustness and Evolvability in Living Systems. Princeton University Press, Princeton, NJ

    Google Scholar 

  60. Wagner GP, Zhang J (2011) The pleiotropic structure of the genotype-phenotype map: the evolvability of complex organisms. Nat Rev Genet 12:204–213

    Article  PubMed  CAS  Google Scholar 

  61. Wang Z, Zhang J (2009) Abundant indispensable redundancies in cellular metabolic networks. Genome Biol Evol 1:23–33

    Article  PubMed  Google Scholar 

  62. Zhang J (2003) Evolution by gene duplication: an update. Trends Eco Evol 18:292–298

    Article  Google Scholar 

Download references

Acknowledgments

I thank my former and current students, especially Xionglei He, Ben-Yang Liao, Zhi Wang, and Wenfeng Qian, for their contributions to several studies summarized here. Wenfeng Qian also assisted in the preparation of Fig. 13.1 and Table 13.1. Research in my laboratory has been supported by the U.S. National Institutes of Health.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Jianzhi Zhang .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer Science+Business Media, LLC

About this chapter

Cite this chapter

Zhang, J. (2012). Genetic Redundancies and Their Evolutionary Maintenance. In: Soyer, O. (eds) Evolutionary Systems Biology. Advances in Experimental Medicine and Biology, vol 751. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-3567-9_13

Download citation

Publish with us

Policies and ethics