Literature DB >> 22191510

An exit cavity was crucial to the polymerase activity of the early ribosome.

George E Fox1, Quyen Tran, Ada Yonath.   

Abstract

The emergence of an RNA entity capable of synthesizing peptides was a key prebiotic development. It is hypothesized that a precursor of the modern ribosomal exit tunnel was associated with this RNA entity (e.g., "protoribosome" or "bonding entity") from the earliest time and played an essential role. Various compounds that can bind and activate amino acids, including extremely short RNA chains carrying amino acids, and possibly di- or tripeptides, would have associated with the internal cavity of the protoribosome. This cavity hosts the site for peptide bond formation and adjacent to it a relatively elongated feature that could have evolved to the modern ribosomal exit tunnel, as it is wide enough to allow passage of an oligopeptide. When two of the compounds carrying amino acids or di- or tripeptides (to which we refer, for simplicity, as small aminoacylated RNAs) were in proximity within the heart of the protoribosome, a peptide bond could form spontaneously. The growing peptide would enter the nearby cavity and would not disrupt the attachment of the substrates to the protoribosome or interfere with the subsequent attachment of additional small aminoacylated RNAs. Additionally, the presence of the peptide in the cavity would increase the lifetime of the oligopeptide in the protoribosome. Thus, subsequent addition of another amino acid would be more likely than detachment from the protoribosome, and synthesis could continue. The early ability to synthesize peptides may have resulted in an abbreviated RNA World.

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Year:  2011        PMID: 22191510      PMCID: PMC3264961          DOI: 10.1089/ast.2011.0692

Source DB:  PubMed          Journal:  Astrobiology        ISSN: 1557-8070            Impact factor:   4.335


  28 in total

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Authors:  B M Rode
Journal:  Peptides       Date:  1999       Impact factor: 3.750

Review 2.  Ribosomal tolerance and peptide bond formation.

Authors:  Ada Yonath
Journal:  Biol Chem       Date:  2003 Oct-Nov       Impact factor: 3.915

Review 3.  Ribosomal crystallography: peptide bond formation and its inhibition.

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Journal:  Biopolymers       Date:  2003-09       Impact factor: 2.505

Review 4.  Antibiotics targeting ribosomes: resistance, selectivity, synergism and cellular regulation.

Authors:  Ada Yonath
Journal:  Annu Rev Biochem       Date:  2005       Impact factor: 23.643

Review 5.  Symmetry at the active site of the ribosome: structural and functional implications.

Authors:  Ilana Agmon; Anat Bashan; Raz Zarivach; Ada Yonath
Journal:  Biol Chem       Date:  2005-09       Impact factor: 3.915

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Journal:  Nat Struct Mol Biol       Date:  2005-11-20       Impact factor: 15.369

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Authors:  C R Woese; G E Fox
Journal:  J Mol Evol       Date:  1977-09-20       Impact factor: 2.395

Review 8.  Atomic structures at last: the ribosome in 2000.

Authors:  V Ramakrishnan; P B Moore
Journal:  Curr Opin Struct Biol       Date:  2001-04       Impact factor: 6.809

9.  Carbonyl sulfide-mediated prebiotic formation of peptides.

Authors:  Luke Leman; Leslie Orgel; M Reza Ghadiri
Journal:  Science       Date:  2004-10-08       Impact factor: 47.728

10.  Self-sustained replication of an RNA enzyme.

Authors:  Tracey A Lincoln; Gerald F Joyce
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  16 in total

1.  History of the ribosome and the origin of translation.

Authors:  Anton S Petrov; Burak Gulen; Ashlyn M Norris; Nicholas A Kovacs; Chad R Bernier; Kathryn A Lanier; George E Fox; Stephen C Harvey; Roger M Wartell; Nicholas V Hud; Loren Dean Williams
Journal:  Proc Natl Acad Sci U S A       Date:  2015-11-30       Impact factor: 11.205

Review 2.  The ribosome challenge to the RNA world.

Authors:  Jessica C Bowman; Nicholas V Hud; Loren Dean Williams
Journal:  J Mol Evol       Date:  2015-03-05       Impact factor: 2.395

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4.  Evolution of the ribosome at atomic resolution.

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Journal:  Proc Natl Acad Sci U S A       Date:  2014-06-30       Impact factor: 11.205

5.  The Origin(s) of Cell(s): Pre-Darwinian Evolution from FUCAs to LUCA : To Carl Woese (1928-2012), for his Conceptual Breakthrough of Cellular Evolution.

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Journal:  J Mol Evol       Date:  2021-06-25       Impact factor: 2.395

6.  Ancient Systems of Sodium/Potassium Homeostasis as Predecessors of Membrane Bioenergetics.

Authors:  D V Dibrova; M Y Galperin; E V Koonin; A Y Mulkidjanian
Journal:  Biochemistry (Mosc)       Date:  2015-05       Impact factor: 2.487

7.  Origin of life: protoribosome forms peptide bonds and links RNA and protein dominated worlds.

Authors:  Tanaya Bose; Gil Fridkin; Chen Davidovich; Miri Krupkin; Nikita Dinger; Alla H Falkovich; Yoav Peleg; Ilana Agmon; Anat Bashan; Ada Yonath
Journal:  Nucleic Acids Res       Date:  2022-02-28       Impact factor: 16.971

Review 8.  Systems protobiology: origin of life in lipid catalytic networks.

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Journal:  J R Soc Interface       Date:  2018-07       Impact factor: 4.118

9.  The drive to life on wet and icy worlds.

Authors:  Michael J Russell; Laura M Barge; Rohit Bhartia; Dylan Bocanegra; Paul J Bracher; Elbert Branscomb; Richard Kidd; Shawn McGlynn; David H Meier; Wolfgang Nitschke; Takazo Shibuya; Steve Vance; Lauren White; Isik Kanik
Journal:  Astrobiology       Date:  2014-04-03       Impact factor: 4.335

Review 10.  How amino acids and peptides shaped the RNA world.

Authors:  Peter T S van der Gulik; Dave Speijer
Journal:  Life (Basel)       Date:  2015-01-19
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