Does the Ribosome Challenge our Understanding of the RNA World?

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• 作者：Anthony M. Poole ; Daniel C. Jeffares ; Marc P. Hoeppner…
• 关键词：RNA world ; Ribosome ; Polymer transition ; Darwinian evolution ; Chemical evolution ; Translation
• 刊名：Journal of Molecular Evolution
• 出版年：2016
• 出版时间：January 2016
• 年：2016
• 卷：82
• 期：1
• 页码：1-4
• 全文大小：333 KB
• 参考文献：Albery WJ, Knowles JR (1976) Evolution of enzyme function and the development of catalytic efficiency. Biochemistry 15:5631PubMed CrossRef
  Ardell DH (1998) On error minimization in a sequential origin of the standard genetic code. J Mol Evol 47:1PubMed CrossRef
  Attwater J, Wochner A, Holliger P (2013) In-ice evolution of RNA polymerase ribozyme activity. Nat Chem 5:1011PubMed PubMedCentral CrossRef
  Bernhardt HS, Tate WP (2010) The transition from noncoded to coded protein synthesis: did coding mRNAs arise from stability-enhancing binding partners to tRNA? Biol Direct 5:16PubMed PubMedCentral CrossRef
  Bowman JC, Hud NV, Williams LD (2015) The ribosome challenge to the RNA world. J Mol Evol 80:143PubMed CrossRef
  Doudna JA, Lorsch JR (2005) Ribozyme catalysis: not different, just worse. Nat Struct Mol Biol 12:395PubMed CrossRef
  Freeland SJ, Hurst LD (1998) The genetic code is one in a million. J Mol Evol 47:238PubMed CrossRef
  Freeland SJ, Knight RD, Landweber LF, Hurst LD (2000) Early fixation of an optimal genetic code. Mol Biol Evol 17:511PubMed CrossRef
  Gardner PP, Bateman A, Poole AM (2010) SnoPatrol: how many snoRNA genes are there? J Biol 9:4PubMed PubMedCentral CrossRef
  Goldman AD, Bernhard TM, Dolzhenko E, Landweber LF (2013) LUCApedia: a database for the study of ancient life. Nucleic Acids Res 41:D1079PubMed PubMedCentral CrossRef
  Harris JK, Kelley ST, Spiegelman GB, Pace NR (2003) The genetic core of the universal ancestor. Genome Res 13:407PubMed PubMedCentral CrossRef
  Hasegawa M, Yano T, Miyata T (1984) Evolutionary implications of error amplification in the self-replicating and protein-synthesizing machinery. J Mol Evol 20:77PubMed CrossRef
  Hoeppner MP, Poole AM (2012) Comparative genomics of eukaryotic small nucleolar RNAs reveals deep evolutionary ancestry amidst ongoing intragenomic mobility. BMC Evol Biol 12:183PubMed PubMedCentral CrossRef
  Hoeppner MP, Gardner PP, Poole AM (2012) Comparative analysis of RNA families reveals distinct repertoires for each domain of life. PLoS Comput Biol 8:e1002752PubMed PubMedCentral CrossRef
  Hud NV, Cafferty BJ, Krishnamurthy R, Williams LD (2013) The origin of RNA and “my grandfather’s axe”. Chem Biol 20:466PubMed CrossRef
  Jeffares DC, Poole AM, Penny D (1998) Relics from the RNA world. J Mol Evol 46:18PubMed CrossRef
  Koonin EV, Mushegian AR, Bork P (1996) Non-orthologous gene displacement. Trends Genet 12:334PubMed CrossRef
  Lehman N (2013) Origin of life: Cold-hearted RNA heats up life. Nat Chem 5:987PubMed CrossRef
  Noller HF (2004) The driving force for molecular evolution of translation. RNA 10:1833PubMed PubMedCentral CrossRef
  Penny D, Zhong B (2014) Two fundamental questions about protein evolution. Biochimie. doi:10.​1016/​j.​biochi.​2014.​10.​020 PubMed
  Penny D, Hoeppner MP, Poole AM, Jeffares DC (2009) An overview of the introns-first theory. J Mol Evol 69:527PubMed CrossRef
  Poole AM, Logan DT (2005) Modern mRNA proofreading and repair: clues that the last universal common ancestor possessed an RNA genome? Mol Biol Evol 22:1444PubMed CrossRef
  Poole AM, Jeffares DC, Penny D (1998) The path from the RNA world. J Mol Evol 46:1PubMed CrossRef
  Poole A, Jeffares D, Penny D (1999) Early evolution: prokaryotes, the new kids on the block. BioEssays 21:880PubMed CrossRef
  Steitz TA (1998) A mechanism for all polymerases. Nature 391:231PubMed CrossRef
  Vetsigian K, Woese C, Goldenfeld N (2006) Collective evolution and the genetic code. Proc Natl Acad Sci USA 103:10696PubMed PubMedCentral CrossRef
  
• 作者单位：Anthony M. Poole (1)
  Daniel C. Jeffares (2)
  Marc P. Hoeppner (3)
  David Penny (4)
  
  1. Biomolecular Interaction Centre & School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
  2. Department of Genetics, Evolution & Environment, University College London, London, UK
  3. Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
  4. Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
  
• 刊物类别：Biomedical and Life Sciences
• 刊物主题：Life Sciences
  Cell Biology
  Microbiology
  Plant Sciences
  
• 出版者：Springer New York
• ISSN：1432-1432

文摘

In a recent article published in these pages, Bowman and colleagues propose that the ribosome represents a challenge to the RNA world model, a long-standing framework to explain the origin of DNA and genetically encoded proteins from a hypothetical RNA-based system. Specifically, they outline a scenario for the emergence and subsequent coevolution of the peptidyl transferase centre (PTC) of the ribosome with non-templated peptide products of this RNA through chemical evolution. They also propose that the PTC would have predated the emergence of enzymatic RNA replication, and that this in turn indicates that the RNA world never existed. We and others have previously incorporated non-templated peptide production as an early stage in the evolution of protein synthesis, which we would count as a chemical process, in agreement with Bowman and colleagues’ model. However, their model raises an important question: to what extent could early protein synthesis and its products have evolved in the absence of Darwinian processes? We argue that evolution of the early ribosome requires Darwinian evolution, and that, while chemical evolution could give rise to peptidyl transferase activity, it is insufficient for subsequent improvement of a proto-PTC, or for ongoing coevolution of the proto-PTC with its early non-templated peptide products. We conclude that it is difficult to preclude the involvement of replicative processes, themselves subject to Darwinian evolution, from the evolution of the PTC. Finally, Bowman et al. call into question current models for the RNA to protein transition. We show that the difficulty that Bowman et al. have with this scenario is down to a misreading of our previous work. Keywords RNA world Ribosome Polymer transition Darwinian evolution Chemical evolution Translation