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For: Di Giulio M. The late stage of genetic code structuring took place at a high temperature. Gene 2000;261:189-95. [PMID: 11164050 DOI: 10.1016/s0378-1119(00)00522-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Number Cited by Other Article(s)
1
Caldararo F, Di Giulio M. The genetic code is very close to a global optimum in a model of its origin taking into account both the partition energy of amino acids and their biosynthetic relationships. Biosystems 2022;214:104613. [DOI: 10.1016/j.biosystems.2022.104613] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/16/2022] [Accepted: 01/17/2022] [Indexed: 01/23/2023]
2
The Mutational Robustness of the Genetic Code and Codon Usage in Environmental Context: A Non-Extremophilic Preference? Life (Basel) 2021;11:life11080773. [PMID: 34440517 PMCID: PMC8398314 DOI: 10.3390/life11080773] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/23/2021] [Accepted: 07/28/2021] [Indexed: 12/12/2022]  Open
3
Phylogenetic analysis of mutational robustness based on codon usage supports that the standard genetic code does not prefer extreme environments. Sci Rep 2021;11:10963. [PMID: 34040064 PMCID: PMC8154912 DOI: 10.1038/s41598-021-90440-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/10/2021] [Indexed: 02/04/2023]  Open
4
Seligmann H, Warthi G. Natural pyrrolysine-biased translation of stop codons in mitochondrial peptides entirely coded by expanded codons. Biosystems 2020;196:104180. [PMID: 32534170 DOI: 10.1016/j.biosystems.2020.104180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/02/2020] [Accepted: 06/02/2020] [Indexed: 12/31/2022]
5
Seligmann H, Warthi G. Chimeric Translation for Mitochondrial Peptides: Regular and Expanded Codons. Comput Struct Biotechnol J 2019;17:1195-1202. [PMID: 31534643 PMCID: PMC6742854 DOI: 10.1016/j.csbj.2019.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/19/2019] [Accepted: 08/21/2019] [Indexed: 02/07/2023]  Open
6
Wolfenden R. Primordial chemistry and enzyme evolution in a hot environment. Cell Mol Life Sci 2014;71:2909-15. [PMID: 24623557 DOI: 10.1007/s00018-014-1587-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 02/06/2014] [Accepted: 02/12/2014] [Indexed: 11/25/2022]
7
Comparative analysis of barophily-related amino acid content in protein domains of Pyrococcus abyssi and Pyrococcus furiosus. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2013;2013:680436. [PMID: 24187517 PMCID: PMC3804272 DOI: 10.1155/2013/680436] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 08/21/2013] [Accepted: 08/23/2013] [Indexed: 11/17/2022]
8
Di Giulio M. The origin of the genetic code in the ocean abysses: new comparisons confirm old observations. J Theor Biol 2013;333:109-16. [PMID: 23727280 DOI: 10.1016/j.jtbi.2013.05.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 05/15/2013] [Accepted: 05/21/2013] [Indexed: 11/26/2022]
9
Putative mitochondrial polypeptides coded by expanded quadruplet codons, decoded by antisense tRNAs with unusual anticodons. Biosystems 2012;110:84-106. [DOI: 10.1016/j.biosystems.2012.09.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Revised: 09/20/2012] [Accepted: 09/26/2012] [Indexed: 11/19/2022]
10
El-Murr N, Maurel MC, Rihova M, Vergne J, Hervé G, Kato M, Kawamura K. Behavior of a hammerhead ribozyme in aqueous solution at medium to high temperatures. THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 2012;99:731-8. [PMID: 22915317 DOI: 10.1007/s00114-012-0954-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 07/17/2012] [Accepted: 07/19/2012] [Indexed: 11/28/2022]
11
Gao J, Wang W. Analysis of structural requirements for thermo-adaptation from orthologs in microbial genomes. ANN MICROBIOL 2012. [DOI: 10.1007/s13213-012-0420-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]  Open
12
Jestin JL, Kempf A. Optimization models and the structure of the genetic code. J Mol Evol 2009;69:452-7. [PMID: 19841850 DOI: 10.1007/s00239-009-9287-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Accepted: 09/18/2009] [Indexed: 11/29/2022]
13
Di Giulio M. A methanogen hosted the origin of the genetic code. J Theor Biol 2009;260:77-82. [DOI: 10.1016/j.jtbi.2009.05.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2009] [Revised: 05/26/2009] [Accepted: 05/29/2009] [Indexed: 11/17/2022]
14
Di Giulio M. The split genes of Nanoarchaeum equitans are an ancestral character. Gene 2008;421:20-6. [DOI: 10.1016/j.gene.2008.06.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2007] [Revised: 01/15/2008] [Accepted: 06/03/2008] [Indexed: 11/30/2022]
15
Glansdorff N, Xu Y, Labedan B. The last universal common ancestor: emergence, constitution and genetic legacy of an elusive forerunner. Biol Direct 2008;3:29. [PMID: 18613974 PMCID: PMC2478661 DOI: 10.1186/1745-6150-3-29] [Citation(s) in RCA: 186] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2008] [Accepted: 07/09/2008] [Indexed: 11/10/2022]  Open
16
Wang J, Ma BG, Zhang HY, Chen LL, Zhang SC. How does gene expression level contribute to thermophilic adaptation of prokaryotes? An exploration based on predictors. Gene 2008;421:32-6. [PMID: 18621118 DOI: 10.1016/j.gene.2008.06.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2008] [Revised: 06/16/2008] [Accepted: 06/17/2008] [Indexed: 11/17/2022]
17
Di Giulio M. The tree of life might be rooted in the branch leading to Nanoarchaeota. Gene 2007;401:108-13. [PMID: 17689206 DOI: 10.1016/j.gene.2007.07.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2007] [Revised: 06/29/2007] [Accepted: 07/04/2007] [Indexed: 11/30/2022]
18
Shimizu H, Yokobori SI, Ohkuri T, Yokogawa T, Nishikawa K, Yamagishi A. Extremely thermophilic translation system in the common ancestor commonote: ancestral mutants of Glycyl-tRNA synthetase from the extreme thermophile Thermus thermophilus. J Mol Biol 2007;369:1060-9. [PMID: 17477933 DOI: 10.1016/j.jmb.2007.04.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2006] [Revised: 03/29/2007] [Accepted: 04/02/2007] [Indexed: 11/16/2022]
19
Archetti M, Di Giulio M. The evolution of the genetic code took place in an anaerobic environment. J Theor Biol 2006;245:169-74. [PMID: 17078972 DOI: 10.1016/j.jtbi.2006.09.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2006] [Revised: 09/21/2006] [Accepted: 09/22/2006] [Indexed: 12/17/2022]
20
Vergne J, Cognet JAH, Szathmáry E, Maurel MC. In vitro selection of halo-thermophilic RNA reveals two families of resistant RNA. Gene 2006;371:182-93. [PMID: 16503099 DOI: 10.1016/j.gene.2005.11.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2005] [Revised: 11/09/2005] [Accepted: 11/17/2005] [Indexed: 11/29/2022]
21
Iwabata H, Watanabe K, Ohkuri T, Yokobori SI, Yamagishi A. Thermostability of ancestral mutants of Caldococcus noboribetus isocitrate dehydrogenase. FEMS Microbiol Lett 2005;243:393-8. [PMID: 15686840 DOI: 10.1016/j.femsle.2004.12.030] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2004] [Revised: 12/28/2004] [Accepted: 12/28/2004] [Indexed: 11/16/2022]  Open
22
Di Giulio M. Structuring of the genetic code took place at acidic pH. J Theor Biol 2005;237:219-26. [PMID: 15978625 DOI: 10.1016/j.jtbi.2005.04.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2005] [Accepted: 04/11/2005] [Indexed: 11/21/2022]
23
Di Giulio M. A comparison of proteins from Pyrococcus furiosus and Pyrococcus abyssi: barophily in the physicochemical properties of amino acids and in the genetic code. Gene 2005;346:1-6. [PMID: 15716096 DOI: 10.1016/j.gene.2004.10.008] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2004] [Revised: 05/30/2004] [Accepted: 10/05/2004] [Indexed: 11/26/2022]
24
Di Giulio M. The ocean abysses witnessed the origin of the genetic code. Gene 2005;346:7-12. [PMID: 15716095 DOI: 10.1016/j.gene.2004.07.045] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2004] [Accepted: 07/26/2004] [Indexed: 11/15/2022]
25
Di Giulio M. The origin of the genetic code: theories and their relationships, a review. Biosystems 2004;80:175-84. [PMID: 15823416 DOI: 10.1016/j.biosystems.2004.11.005] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2004] [Revised: 11/12/2004] [Accepted: 11/18/2004] [Indexed: 10/26/2022]
26
McCabe C, Galindo A, Cummings PT. Anomalies in the Solubility of Alkanes in Near-Critical Water. J Phys Chem B 2003. [DOI: 10.1021/jp0352332] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
27
Di Giulio M. The ancestor of the Bacteria domain was a hyperthermophile. J Theor Biol 2003;224:277-83. [PMID: 12941586 DOI: 10.1016/s0022-5193(03)00164-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
28
Trevors JT. Genetic material in the early evolution of bacteria. Microbiol Res 2003;158:1-6. [PMID: 12608574 DOI: 10.1078/0944-5013-00171] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
29
Di Giulio M. The universal ancestor was a thermophile or a hyperthermophile: tests and further evidence. J Theor Biol 2003;221:425-36. [PMID: 12642117 DOI: 10.1006/jtbi.2003.3197] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
30
Trevors JT. Early assembly of cellular life. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2003;81:201-17. [PMID: 12732262 DOI: 10.1016/s0079-6107(03)00018-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
31
Schneider D, Liu Y, Gerstein M, Engelman DM. Thermostability of membrane protein helix-helix interaction elucidated by statistical analysis. FEBS Lett 2002;532:231-6. [PMID: 12459496 DOI: 10.1016/s0014-5793(02)03687-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
32
Di Giulio M. The universal ancestor was a thermophile or a hyperthermophile. Gene 2001;281:11-7. [PMID: 11750123 DOI: 10.1016/s0378-1119(01)00781-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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