Literature DB >> 15716095

The ocean abysses witnessed the origin of the genetic code.

Massimo Di Giulio1.   

Abstract

The comparison of proteins from a non-barophilous and a barophilous organism makes it possible to define the barophily ranks of amino acids. The correlation of these ranks with the number of codons attributed to amino acids in the genetic code, together with another straightforward argument based on an optimisation percentage of a barophily index (BI) (easily defined by barophily ranks) which can be associated to the genetic code table, suggest that the genetic code originated under high hydrostatic pressure. Moreover, as the BI value can be calculated for the sequence of any protein, it also makes it possible to define the BI for the genetic code if the number of codons attributed to the amino acids in the code is assumed to be the frequency with which the amino acids appeared in ancestral proteins. Finally, sampling the BI variable between many non-barophile organisms and from many proteins of a single non-barophile organism leads to the conclusion that the BI value of the genetic code is not typical of these organisms. Whereas, since the genetic code BI value is statistically higher than that of these non-barophile organisms, it supports the hypothesis that genetic code structuring took place under high hydrostatic pressure.

Mesh:

Year:  2004        PMID: 15716095     DOI: 10.1016/j.gene.2004.07.045

Source DB:  PubMed          Journal:  Gene        ISSN: 0378-1119            Impact factor:   3.688


  8 in total

Review 1.  Optimization models and the structure of the genetic code.

Authors:  J L Jestin; A Kempf
Journal:  J Mol Evol       Date:  2009-10-20       Impact factor: 2.395

2.  Important role of hydrophobic interactions in high-pressure adaptation of proteins.

Authors:  D A Afonnikov; K E Medvedev; K V Gunbin; N A Kolchanov
Journal:  Dokl Biochem Biophys       Date:  2011-07-03       Impact factor: 0.788

3.  Behavior of a hammerhead ribozyme in aqueous solution at medium to high temperatures.

Authors:  Nizar El-Murr; Marie-Christine Maurel; Martina Rihova; Jacques Vergne; Guy Hervé; Mikio Kato; Kunio Kawamura
Journal:  Naturwissenschaften       Date:  2012-08-23

4.  The indefinable term 'prokaryote' and the polyphyletic origin of genes.

Authors:  Massimo Di Giulio
Journal:  J Genet       Date:  2017-06       Impact factor: 1.166

5.  Molecular evolution of the hyperthermophilic archaea of the Pyrococcus genus: analysis of adaptation to different environmental conditions.

Authors:  Konstantin V Gunbin; Dmitry A Afonnikov; Nikolay A Kolchanov
Journal:  BMC Genomics       Date:  2009-12-30       Impact factor: 3.969

6.  Phylogenetic analysis of mutational robustness based on codon usage supports that the standard genetic code does not prefer extreme environments.

Authors:  Ádám Radványi; Ádám Kun
Journal:  Sci Rep       Date:  2021-05-26       Impact factor: 4.379

7.  The first genomic and proteomic characterization of a deep-sea sulfate reducer: insights into the piezophilic lifestyle of Desulfovibrio piezophilus.

Authors:  Nathalie Pradel; Boyang Ji; Grégory Gimenez; Emmanuel Talla; Patricia Lenoble; Marc Garel; Christian Tamburini; Patrick Fourquet; Régine Lebrun; Philippe Bertin; Yann Denis; Matthieu Pophillat; Valérie Barbe; Bernard Ollivier; Alain Dolla
Journal:  PLoS One       Date:  2013-01-30       Impact factor: 3.240

8.  Comparative analysis of barophily-related amino acid content in protein domains of Pyrococcus abyssi and Pyrococcus furiosus.

Authors:  Liudmila S Yafremava; Massimo Di Giulio; Gustavo Caetano-Anollés
Journal:  Archaea       Date:  2013-09-26       Impact factor: 3.273

  8 in total

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