Acta Scientific Microbiology (ASMI) (ISSN: 2581-3226)

Research Article Volume 3 Issue 2

From FUCA To LUCA: A Theoretical Analysis on the Common Descent of Gene Families

Francisco Prosdocimi1* and Sávio Torres de Farias2,3

1Laboratório De Biologia Teórica E De Sistemas, Instituto De Bioquímica Médica Leopoldo De Meis, Universidade Federal Do Rio De Janeiro, Rio De Janeiro, Brasil
2Laboratório De Genética Evolutiva Paulo Leminsk, Departamento De Biologia Molecular, Universidade Federal Da Paraíba, João Pessoa, Paraíba, Brasil
3Departamento De Filosofia, Programa De Pós-Graduação Em Filosofia, Universidade Federal De Santa Catarina, Florianopólis, Santa Catarina, Brasil

*Corresponding Author: Francisco Prosdocimi, Laboratório De Biologia Teórica E De Sistemas, Instituto De Bioquímica Médica Leopoldo De Meis, Universidade Federal Do Rio De Janeiro, Rio De Janeiro, Brasil.

Received: December 12, 2019; Published: January 22, 2020

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Abstract

  Genes and gene trees have been extensively used to study the evolutionary relationships among populations, species, families and higher systematic clades of organisms. This brought modern Biology into a sophisticated level of understanding about the evolutionary relationships and diversification patterns that happened along the entire history of organismal evolution in Earth. Genes however have not been placed in the center of questions when one aims to unravel the evolutionary history of genes themselves. Thus, we still ignore whether Insulin share a more recent common ancestor to Hexokinase or DNA polymerase. This brought modern Genetics into a very poor level of understanding about sister group relationships that happened along the entire evolutionary history of genes. Many conceptual challenges must be overcome to allow this broader comprehension about gene evolution. Here we aim to clear the intellectual path in order to provide a fertile research program that will help geneticists to understand the deep ancestry and sister group relationships among different gene families (or orthologs). We aim to propose methods to study gene formation starting from the establishment of the genetic code in pre-cellular organisms like the FUCA (First Universal Common Ancestor) until the formation of the highly complex genome of LUCA (Last UCA), that harbors hundreds of genes families working coordinated into a cellular organism. The deep understanding of ancestral relationships among orthologs will certainly inspire biotechnological and biomedical approaches and allow a deep understanding about how Darwinian molecular evolution operates inside cells and before the appearance of cellular organisms.

Keywords: Ancestry of Orthologs; Ancestry of Gene Families; Gene Genealogy; FUCA; LUCA; Origins of Life; Gradualism; Evolutionary Biology

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References

  1. Penny D and Poole A. “The nature of the last universal common ancestor”. Current Opinion in Genetics and Development 9.6 (1999): 672-677.
  2. Forterre P and Philippe H. “The last universal common ancestor (LUCA), simple or complex?” The Biological Bulletin 196.3 (1999): 373-375.
  3. Delaye L., et al. “The last common ancestor: what's in a name?” Origins of Life and Evolution of Biospheres 35.6 (2005): 537-554. 
  4. Nasir A and Caetano-Anollés G. “A phylogenomic data-driven exploration of viral origins and evolution”. Science Advances 1.8 (2015): e1500527. 
  5. Woese CR., et al. “Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya”. Proceedings of the National Academy of Sciences of the United States of America 87.12 (1990): 4576-4579.
  6. Weiss MC., et al. “The physiology and habitat of the last universal common ancestor”. Nature Microbiology 1.9 (2016):16116. 
  7. Prosdocimi F., et al. “Two Dogmas for the Emergence of Biological Systems: Cell Theory and Self-Replication”. Preprints (2018a): 2018050445.
  8. Prosdocimi F., et al. “Conceptual challenges for the emergence of biological system: Cell Theory and Self-Replication”. Medical Hypotheses 119 (2018b): 79-83.
  9. Prosdocimi F. “Teleological Thought in Gene Naming: The Quest for an Evolutionary-Based Taxonomy and Systematics for Genes”. Journal of Phylogenetics and Evolutionary Biology 3.2 (2015): 152.
  10. Wain HM., et al. “Guidelines for human gene nomenclature”. Genomics 79.4 (2002): 464-470. 
  11. HGNC (HUGO gene nomenclature committee) website (2018).
  12. Jeffery CJ. “Moonlighting proteins”. Trends in Biochemical Sciences 24.1 (1999): 8-11. 
  13. Copley SD. “Moonlighting is mainstream: paradigm adjustment required”. Bioessays 34.7 (2012): 578-588. 
  14. Lanier KA., et al. “The Central Symbiosis of Molecular Biology: Molecules in Mutualism”. Journal of Molecular Evolution 85.1-2 (2017): 8-13.
  15. Vitas M and Dobovišek A. “In the Beginning was a Mutualism - On the Origin of Translation”. Origins of Life and Evolution of Biospheres 48.2 (2018): 223-243.
  16. Prosdocimi F., et al. “The First Universal Common Ancestor (FUCA) as the Earliest Ancestor of LUCA’s (Last UCA) Lineage. Chapter 3. In book: Evolution, Origin of Life, Concepts and Methods”. Pierre Pontarotti (Editor). Springer (2019). 
  17. Farias ST and Prosdocimi F. “A emergência dos sistemas biológicos: uma visão molecular da origem da vida”. Ed. ArtecomCiencia, 1ed (2019): 236.
  18. Farias ST., et al. “tRNA Core Hypothesis for the Transition from the RNA World to the Ribonucleoprotein World”. Life (Basel) 6.2 (2016): E15. 
  19. Darwin CR. “On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life”. London: John Murray (1859).
  20. Mayr E. “The Idea of Teleology”. Journal of the History of Ideas 53.1 (1992): 117-135. 
  21. Beadle GW and Tatum EL. “Genetic Control of Biochemical Reactions in Neurospora”. Proceedings of the National Academy of Sciences of the United States of America 27.11 (1941): 499-506.
  22. Henderson B and Martin A. “Bacterial virulence in the moonlight: multitasking bacterial moonlighting proteins are virulence determinants in infectious disease”. Infection and Immunity 79.9 (2011): 3476-3491.
  23. Jia B., et al. “Multifunctional enzymes in archaea: promiscuity and moonlight”. Extremophiles 17.2 (2013): 193-203.
  24. Gancedo C., et al. “The Expanding Landscape of Moonlighting Proteins in Yeasts”. Microbiology and Molecular Biology Reviews 80.3 (2016): 765-777.
  25. Jeffery CJ. “Protein moonlighting: what is it, and why is it important?” Philosophical Transactions of the Royal Society B: Biological Sciences 373.1738 (2018):  20160523.
  26. Kauffman S. “There Are More Uses For A Screwdriver Than You Can Calculate”. Cosmos and Culture 4.4 (2011). 
  27. Kruger K., et al. “Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena”. Cell 31.1 (1982): 147-157.
  28. Gilbert W. “The RNA world”. Nature 319 (1986): 618.
  29. Higgs PG and Lehman N. “The RNA World: molecular cooperation at the origins of life”. Nature Reviews Genetics 16.1 (2015): 7-17. 
  30. Lynch M and Force A. “The probability of duplicate gene preservation by subfunctionalization”. Genetics 154.1 (2000): 459-473.
  31. Massingham T., et al. “Analysing gene function after duplication”. Bioessays 23.10 (2001): 873-876.
  32. Farias ST., et al. “Viruses as a survival strategy in the armory of life”. HPLS 41 (2019): 45.
  33. Dawson NL., et al. “CATH: an expanded resource to predict protein function through structure and sequence”. Nucleic Acids Research 45.1 (2017): D289-D295.
  34. Murzin AG., et al. “SCOP: a structural classification of proteins database for the investigation of sequences and structures”. Journal of Molecular Biology 247.4 (1995): 536-540.
  35. Woese CR. “The universal ancestor”. Proceedings of the National Academy of Sciences 95.12 (1998) 6854-6859. 
  36. Hahn MW. “Distinguishing among evolutionary models for the maintenance of gene duplicates”. Journal of Heredity 100.5 (2009): 605-617. 
  37. Conant GC., et al. “Dosage, duplication, and diploidization: clarifying the interplay of multiple models for duplicate gene evolution over time”. Current Opinion in Plant Biology 19 (2014): 91-98.
  38. Freeling M., et al. “Fractionation and subfunctionalization following genome duplications: mechanisms that drive gene content and their consequences”. Current Opinion in Genetics and Development 35 (2015): 110-118. 
  39. Behe M. “Darwin’s black box: the biochemical challenge to evolution”. Free Press (1996).
  40. Shepherd JC. “Periodic correlations in DNA sequences and evidence suggesting their evolutionary origin in a comma-less genetic code”. Journal of Molecular Evolution 17.2 (1981): 94-102. 
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Citation

Citation: Francisco Prosdocimi and Sávio Torres de Farias. “From FUCA To LUCA: A Theoretical Analysis on the Common Descent of Gene Families". Acta Scientific Microbiology 3.2 (2020): 73-81.




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