M Di Giulio

Summary

Affiliation: Institute of Genetics and Biophysics
Country: Italy

Publications

  1. ncbi tRNA creation by hairpin duplication
    Jeremy Widmann
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
    J Mol Evol 61:524-30. 2005
  2. ncbi Structuring of the genetic code took place at acidic pH
    Massimo Di Giulio
    Institute of Genetics and Biophysics Adriano Buzzati Traverso, CNR, Via G Marconi 10, 80125 Naples, Napoli, Italy
    J Theor Biol 237:219-26. 2005
  3. ncbi An extension of the coevolution theory of the origin of the genetic code
    Massimo Di Giulio
    Laboratory for Molecular Evolution, Institute of Genetics and Biophysics Adriano Buzzati Traverso, CNR, Via P Castellino, 111, 80131 Naples, Napoli, Italy
    Biol Direct 3:37. 2008
  4. ncbi The split genes of Nanoarchaeum equitans are an ancestral character
    Massimo Di Giulio
    Laboratory for Molecular Evolution, Institute of Genetics and Biophysics Adriano Buzzati Traverso, CNR, Via P Castellino, 111, 80131 Naples, Napoli, Italy
    Gene 421:20-6. 2008
  5. ncbi Permuted tRNA genes of Cyanidioschyzon merolae, the origin of the tRNA molecule and the root of the Eukarya domain
    Massimo Di Giulio
    Laboratory for Molecular Evolution, Institute of Genetics and Biophysics Adriano Buzzati Traverso, CNR, Via P Castellino, 111, 80131 Naples, Napoli, Italy
    J Theor Biol 253:587-92. 2008
  6. ncbi A comparison among the models proposed to explain the origin of the tRNA molecule: A synthesis
    Massimo Di Giulio
    Institute of Genetics and Biophysics, Adriano Buzzati Travers, CNR, Naples, Napoli, Italy
    J Mol Evol 69:1-9. 2009
  7. ncbi The close relationship between the biosynthetic families of amino acids and the organisation of the genetic code
    Massimo Di Giulio
    Institute of Genetics and Biophysics Adriano Buzzati Traverso, CNR, Naples, Napoli, Italy
    Gene 435:9-12. 2009
  8. ncbi A methanogen hosted the origin of the genetic code
    Massimo Di Giulio
    Institute of Genetics and Biophysics Adriano Buzzati Traverso, CNR, Naples, Napoli, Italy
    J Theor Biol 260:77-82. 2009
  9. ncbi The tree of life might be rooted in the branch leading to Nanoarchaeota
    Massimo Di Giulio
    Institute of Genetics and Biophysics Adriano Buzzati Traverso, CNR, Via P Castellino, 111, 80131 Naples, Napoli, Italy
    Gene 401:108-13. 2007
  10. ncbi The universal ancestor and the ancestors of Archaea and Bacteria were anaerobes whereas the ancestor of the Eukarya domain was an aerobe
    M Di Giulio
    Laboratory of Molecular Evolution, Institute of Genetics and Biophysics Adriano Buzzati Traverso, CNR, Naples, Napoli, Italy
    J Evol Biol 20:543-8. 2007

Collaborators

Detail Information

Publications43

  1. ncbi tRNA creation by hairpin duplication
    Jeremy Widmann
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
    J Mol Evol 61:524-30. 2005
    ..These results support the hypothesis that the modern tRNA cloverleaf arose from a single hairpin duplication prior to the divergence of modern tRNA specificities and the three domains of life...
  2. ncbi Structuring of the genetic code took place at acidic pH
    Massimo Di Giulio
    Institute of Genetics and Biophysics Adriano Buzzati Traverso, CNR, Via G Marconi 10, 80125 Naples, Napoli, Italy
    J Theor Biol 237:219-26. 2005
    ....
  3. ncbi An extension of the coevolution theory of the origin of the genetic code
    Massimo Di Giulio
    Laboratory for Molecular Evolution, Institute of Genetics and Biophysics Adriano Buzzati Traverso, CNR, Via P Castellino, 111, 80131 Naples, Napoli, Italy
    Biol Direct 3:37. 2008
    ....
  4. ncbi The split genes of Nanoarchaeum equitans are an ancestral character
    Massimo Di Giulio
    Laboratory for Molecular Evolution, Institute of Genetics and Biophysics Adriano Buzzati Traverso, CNR, Via P Castellino, 111, 80131 Naples, Napoli, Italy
    Gene 421:20-6. 2008
    ..Furthermore, it would seem that hyperthermophily is also an ancestral trait because it is linked to a split gene in N. equitans...
  5. ncbi Permuted tRNA genes of Cyanidioschyzon merolae, the origin of the tRNA molecule and the root of the Eukarya domain
    Massimo Di Giulio
    Laboratory for Molecular Evolution, Institute of Genetics and Biophysics Adriano Buzzati Traverso, CNR, Via P Castellino, 111, 80131 Naples, Napoli, Italy
    J Theor Biol 253:587-92. 2008
    ..merolae belongs are the first line of divergence...
  6. ncbi A comparison among the models proposed to explain the origin of the tRNA molecule: A synthesis
    Massimo Di Giulio
    Institute of Genetics and Biophysics, Adriano Buzzati Travers, CNR, Naples, Napoli, Italy
    J Mol Evol 69:1-9. 2009
    ..These might be the witnesses of the transition stage predicted by the model through which the evolution of the tRNA molecule passed, thus providing considerable corroboration for this model...
  7. ncbi The close relationship between the biosynthetic families of amino acids and the organisation of the genetic code
    Massimo Di Giulio
    Institute of Genetics and Biophysics Adriano Buzzati Traverso, CNR, Naples, Napoli, Italy
    Gene 435:9-12. 2009
    ....
  8. ncbi A methanogen hosted the origin of the genetic code
    Massimo Di Giulio
    Institute of Genetics and Biophysics Adriano Buzzati Traverso, CNR, Naples, Napoli, Italy
    J Theor Biol 260:77-82. 2009
    ..This might indicate that the genetic code evolved in a methanogenic 'organism'...
  9. ncbi The tree of life might be rooted in the branch leading to Nanoarchaeota
    Massimo Di Giulio
    Institute of Genetics and Biophysics Adriano Buzzati Traverso, CNR, Via P Castellino, 111, 80131 Naples, Napoli, Italy
    Gene 401:108-13. 2007
    ..Moreover, the late appearance of DNA coinciding with the rooting of the universal phylogenetic tree would make the genome of N. equitans a witness to this fundamental event...
  10. ncbi The universal ancestor and the ancestors of Archaea and Bacteria were anaerobes whereas the ancestor of the Eukarya domain was an aerobe
    M Di Giulio
    Laboratory of Molecular Evolution, Institute of Genetics and Biophysics Adriano Buzzati Traverso, CNR, Naples, Napoli, Italy
    J Evol Biol 20:543-8. 2007
    ..These observations seem to falsify the hypothesis that the LUCA was an aerobe and help to identify better the environment in which the first organisms lived...
  11. ncbi The non-monophyletic origin of the tRNA molecule and the origin of genes only after the evolutionary stage of the last universal common ancestor (LUCA)
    Massimo Di Giulio
    Institute of Genetics and Biophysics Adriano Buzzati Traverso, CNR, Via P Castellino 111, 80131 Naples, Napoli, Italy
    J Theor Biol 240:343-52. 2006
    ..Finally, the characteristic of the indivisibility of homology that these polyphyletic origins seem to remove at the sequence level is discussed...
  12. ncbi Formal proof that the split genes of tRNAs of Nanoarchaeum equitans are an ancestral character
    Massimo Di Giulio
    Laboratory for Molecular Evolution, Institute of Genetics and Biophysics Adriano Buzzati Traverso, CNR, Via P Castellino, 111, 80131, Naples, Italy
    J Mol Evol 69:505-11. 2009
    ..The other regards when the genes of tRNAs originated, reaching the conclusion that the origin of these genes is polyphyletic, i.e. not monophyletic and hence contrary to the assumptions of the current paradigm...
  13. ncbi Biological evidence against the panspermia theory
    Massimo Di Giulio
    Laboratory for Molecular Evolution, Institute of Genetics and Biophysics Adriano Buzzati Traverso, CNR, Via P Castellino 111, 80131 Naples, Napoli, Italy
    J Theor Biol 266:569-72. 2010
    ....
  14. ncbi The origin of genes could be polyphyletic
    Massimo Di Giulio
    Laboratory for Molecular Evolution, Institute of Genetics and Biophysics Adriano Buzzati Traverso, CNR, Via P Castellino, 111, 80131 Naples, Napoli, Italy
    Gene 426:39-46. 2008
    ..These motifs, and also genes, might have evolved late on, thus making their polyphyletic origin likely...
  15. ncbi The late stage of genetic code structuring took place at a high temperature
    M Di Giulio
    International Institute of Genetics and Biophysics, CNR, Via G Marconi 10, 80125 Naples, Napoli, Italy
    Gene 261:189-95. 2000
    ..These observations seem to support the hypothesis that the origin of life might have taken place at a high temperature...
  16. ncbi Physicochemical optimization in the genetic code origin as the number of codified amino acids increases
    M Di Giulio
    International Institute of Genetics and Biophysics, CNR, Via G Marconi 10, 80125 Naples, Napoli, Italy
    J Mol Evol 49:1-10. 1999
    ..The results are therefore discussed in the context of the various theories proposed to explain genetic code origin...
  17. ncbi The historical factor: the biosynthetic relationships between amino acids and their physicochemical properties in the origin of the genetic code
    M Di Giulio
    International Institute of Genetics and Biophysics, CNR, Via G Marconi 10, 80125 Naples, Napoli, Italy
    J Mol Evol 46:615-21. 1998
    ..The results are therefore discussed in the context of the different theories proposed to explain the origin of the genetic code...
  18. ncbi The non-universality of the genetic code: the universal ancestor was a progenote
    M Di Giulio
    International Institute of Genetics and Biophysics, CNR, Via G Marconi 10, 80125 Naples, Italy
    J Theor Biol 209:345-9. 2001
    ..This, in turn, appears to imply that the last universal common ancestor was a progenote. Finally, the implications that the finding of this pathway has for the stereochemical theory of genetic code origin are discussed...
  19. ncbi On the relationships between the genetic code coevolution hypothesis and the physicochemical hypothesis
    M Di Giulio
    International Institute of Genetics and Biophysics, CNR Via G Marconi 10, Napoli, Italy
    Z Naturforsch C 46:305-12. 1991
    ..It is furthermore pointed out that the two evolutionary hypothesis might be aspects of the same selective pressure, and thus difficult to differentiate...
  20. ncbi The level and landscape of optimization in the origin of the genetic code
    M Di Giulio
    International Institute of Genetics and Biophysics, CNR, Via G Marconi 10, 80125 Naples, Napoli, Italy
    J Mol Evol 52:372-82. 2001
    ....
  21. ncbi The universal ancestor and the ancestor of bacteria were hyperthermophiles
    Massimo Di Giulio
    Adriano Buzzati Traverso Institute of Genetics and Biophysics, CNR, Via G Marconi 10, 80125 Naples, Italy
    J Mol Evol 57:721-30. 2003
    ..These conclusions are thus more easily understood under the hypothesis that the origin of life took place at a high temperature...
  22. ncbi The robust statistical bases of the coevolution theory of genetic code origin
    M Di Giulio
    International Institute of Genetics and Biophysics, CNR, Via G Marconi 10, 80125 Naples, Napoli, Italy
    J Mol Evol 50:258-63. 2000
    ..This observation seems to provide particularly strong support to the coevolution theory...
  23. ncbi The non-monophyletic origin of the tRNA molecule
    M Di Giulio
    International Institute of Genetics and Biophysics, CNR, Via G Marconi 10, 80125 Naples, Italy
    J Theor Biol 197:403-14. 1999
    ....
  24. ncbi The last universal common ancestor (LUCA) and the ancestors of archaea and bacteria were progenotes
    Massimo Di Giulio
    Laboratory for Molecular Evolution, Institute of Genetics and Biophysics Adriano Buzzati Traverso, CNR, Via P Castellino, 111, 80131, Naples, Italy
    J Mol Evol 72:119-26. 2011
    ..These conclusions are in disagreement with commonly held beliefs...
  25. ncbi The universal ancestor lived in a thermophilic or hyperthermophilic environment
    M Di Giulio
    International Institute of Genetics and Biophysics, CNR, Via G Marconi 10, Naples, Napoli, 80125, Italy
    J Theor Biol 203:203-13. 2000
    ..This finding is also supported by some tRNA ancestral sequences. The main conclusion of this analysis is that if the LUCA was a progenote then the origin of life might have taken place at a high temperature...
  26. ncbi A blind empiricism against the coevolution theory of the origin of the genetic code
    M Di Giulio
    International Institute of Genetics and Biophysics, CNR, Via G Marconi 10, 80125 Naples, Italy
    J Mol Evol 53:724-32. 2001
    ....
  27. ncbi The origin of the genetic code: theories and their relationships, a review
    Massimo Di Giulio
    Institute of Genetics and Biophysics Adriano Buzzati-Traverso, CNR, Naples, Italy
    Biosystems 80:175-84. 2005
    ..Finally, I discuss the question of why a given number of synonymous codons was attributed to the amino acids in the genetic code...
  28. ncbi Genetic code origin: are the pathways of type Glu-tRNA(Gln) --> Gln-tRNA(Gln) molecular fossils or not?
    Massimo Di Giulio
    International Institute of Genetics and Biophysics, CNR, Via G Marconi 10, 80125 Naples, Italy
    J Mol Evol 55:616-22. 2002
    ..Comments on the different interpretations of these pathways found in the literature are also provided...
  29. ncbi The universal ancestor was a thermophile or a hyperthermophile: tests and further evidence
    Massimo Di Giulio
    Institute of Genetics and Biophysics Adriano Buzzati Traverso CNR, Via G Marconi 10, 80125 Naples, Napoli, Italy
    J Theor Biol 221:425-36. 2003
    ..These conclusions are easier to interpret in the light of the hypotheses that see the origin of life taking place at a high temperature...
  30. ncbi The ancestor of the Bacteria domain was a hyperthermophile
    Massimo Di Giulio
    Institute of Genetics and Biophysics Adriano Buzzati Traverso, CNR, Via G Marconi 10, Naples 80125, Napoli, Italy
    J Theor Biol 224:277-83. 2003
    ..These findings consolidate the hypothesis that the ancestor of the Bacteria domain was a hyperthermophile and, more generally, that the last universal common ancestor might also have been one...
  31. ncbi The origin of protein synthesis: on some molecular fossils identified through comparison of protein sequences
    M Di Giulio
    International Institute of Genetics and Biophysics, CNR, Naples, Napoli, Italy
    Biosystems 39:159-69. 1996
    ..Therefore, the pre-CoA (and/or CoA) and the tRNA-like molecules were able to use this enzyme ambiguity for a certain period, thus giving weight to the scheme of evolutionary transitions mentioned above...
  32. ncbi The origin of the genetic code cannot be studied using measurements based on the PAM matrix because this matrix reflects the code itself, making any such analyses tautologous
    M Di Giulio
    International Institute of Genetics and Biophysics, CNR, Via G Marconi 10, 80125 Naples, Napoli, Italy
    J Theor Biol 208:141-4. 2001
    ....
  33. ncbi The universal ancestor was a thermophile or a hyperthermophile
    M Di Giulio
    International Institute of Genetics and Biophysics, CNR, Via G Marconi 10, 80125 Naples, Italy
    Gene 281:11-7. 2001
    ..The thermophily index of all the reconstructed ancestral sequences of the LUCA belongs to the set of the thermophile/hyperthermophile sequences, thus supporting the hypotheses that see the LUCA as a thermophile or a hyperthermophile...
  34. ncbi The origin of the tRNA molecule: implications for the origin of protein synthesis
    Massimo Di Giulio
    International Institute of Genetics and Biophysics, Adriano Buzzati Traverso, CNR, Via G Marconi 10, Naples, Napoli 80125, Italy
    J Theor Biol 226:89-93. 2004
    ..Finally, some strong historical evidence is provided to corroborate the model...
  35. ncbi The evidence that the tree of life is not rooted within the Archaea is unreliable: a reply to Skophammer et al
    Massimo Di Giulio
    Laboratory of Molecular Evolution, Institute of Genetics and Biophysics Adriano Buzzati Traverso, CNR, Via P Castellino, 111, 80131 Naples, Napoli, Italy
    Gene 394:105-6. 2007
    ..I have observed that an alignment used in their analysis is not reliable and that, therefore, their conclusions are unjustified...
  36. ncbi The early phases of genetic code origin: conjectures on the evolution of coded catalysis
    Massimo Di Giulio
    Institute of Genetics and Biophysics Adriano Buzzati Traverso, CNR, Naples, Napoli, Italy
    Orig Life Evol Biosph 33:479-89. 2003
    ..Some aspects of the model here discussed might be rendered real by the transfer-messenger RNA molecule (tmRNA) which is here considered a molecular fossil of ancestral protein synthesis...
  37. ncbi A comparison of proteins from Pyrococcus furiosus and Pyrococcus abyssi: barophily in the physicochemical properties of amino acids and in the genetic code
    Massimo Di Giulio
    Institute of Genetics and Biophysics Adriano Buzzati Traverso, CNR, Via G Marconi 10, 80125 Naples, Napoli, Italy
    Gene 346:1-6. 2005
    ....
  38. ncbi On the RNA world: evidence in favor of an early ribonucleopeptide world
    M Di Giulio
    International Institute of Genetics and Biophysics, CNR, Napoli, Italy
    J Mol Evol 45:571-8. 1997
    ..Finally, the appearance of the genetic code in the late phase of the ribonucleopeptide world is discussed...
  39. ncbi The ocean abysses witnessed the origin of the genetic code
    Massimo Di Giulio
    Institute of Genetics and Biophysics Adriano Buzzati Traverso, CNR, Via G Marconi 10, 80125 Naples, Napoli, Italy
    Gene 346:7-12. 2005
    ..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...
  40. ncbi Nanoarchaeum equitans is a living fossil
    Massimo Di Giulio
    J Theor Biol 242:257-60. 2006
  41. ncbi The first lines of divergence in the Bacteria domain were the hyperthermophilic organisms, the Thermotogales and the Aquificales, and not the mesophilic Planctomycetales
    Sacha Barion
    Department of Animal Biology and Genetics, University of Florence, via Romana 17 19, 50125 Florence, Italy
    Biosystems 87:13-9. 2007
    ..This strengthens the hypothesis that the last universal common ancestor might have been a hyperthermophilic 'organism' and that, more generally, life might have originated at high temperature...
  42. ncbi The evolution of the genetic code took place in an anaerobic environment
    Marco Archetti
    Department of Zoology, Oxford University, South Parks Road, OX1 3PS Oxford, UK
    J Theor Biol 245:169-74. 2007
    ..This result is discussed in the framework of hypotheses suggested to explain the timing of the evolutionary appearance of the aerobic metabolism...
  43. ncbi The basal phylogenetic position of Nanoarchaeum equitans (Nanoarchaeota)
    Sergio Branciamore
    Department of Animal Biology and Genetics, University of Florence, via Romana 17 19, 50125 Florence, Italy
    Front Biosci 13:6886-92. 2008
    ..However, our analysis is unable to be equally as clear on the phylogenetic position of Methanopyrus kandleri...