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Titolo:
The Archaea monophyly issue: A phylogeny of translational elongation factor G(2) sequences inferred from an optimized selection of alignment positions
Autore:
Cammarano, P; Creti, R; Sanangelantoni, AM; Palm, P;
Indirizzi:
Univ Rome La Sapienza 1, Policlin Umberto I, Dipt Biotecnol Cellulari & Ematol, Sez Genet Mol,Ist Pasteur Fdn Cenci Bolognetti, I-00161 Rome, Italy Univ Rome La Sapienza 1 Rome Italy I-00161 lognetti, I-00161 Rome, Italy Univ Pavia, Dipartimento Genet & Microbiol A Buzzati Traverso, I-27100 Pavia, Italy Univ Pavia Pavia Italy I-27100 A Buzzati Traverso, I-27100 Pavia, Italy Max Planck Inst Biochem, D-8033 Martinsried, Germany Max Planck Inst Biochem Martinsried Germany D-8033 Martinsried, Germany
Titolo Testata:
JOURNAL OF MOLECULAR EVOLUTION
fascicolo: 4, volume: 49, anno: 1999,
pagine: 524 - 537
SICI:
0022-2844(199910)49:4<524:TAMIAP>2.0.ZU;2-Z
Fonte:
ISI
Lingua:
ENG
Soggetto:
DUPLICATED GENES; DIPHTHERIA-TOXIN; UNIVERSAL TREE; EUKARYOTES; PROKARYOTES; DIVERSITY; EVOLUTION; ORIGIN; DOMAIN; ROOT;
Keywords:
elongation factor G(2); BLAST/FASTA; sequence alignment; insertion elements; phylogeny; Archaea; protein evolution;
Tipo documento:
Article
Natura:
Periodico
Settore Disciplinare:
Agriculture,Biology & Environmental Sciences
Life Sciences
Citazioni:
33
Recensione:
Indirizzi per estratti:
Indirizzo: Cammarano, P Univ Rome La Sapienza 1, Policlin Umberto I, Dipt Biotecnol Cellulari & Ematol, Sez Genet Mol,Ist Pasteur Fdn Cenci Bolognetti, Viale Regina Elena 324, I-00161 Rome, Italy Univ Rome La Sapienza 1 Viale Regina Elena 324 Rome Italy I-00161
Citazione:
P. Cammarano et al., "The Archaea monophyly issue: A phylogeny of translational elongation factor G(2) sequences inferred from an optimized selection of alignment positions", J MOL EVOL, 49(4), 1999, pp. 524-537

Abstract

A global alignment of EF-G(2) sequences was corrected by reference to protein structure. The selection of characters eligible for construction of phylogenetic trees was optimized by searching for regions arising from the artifactual matching of sequence segments unique to different phylogenetic domains. The spurious matchings were identified by comparing all sections of the global alignment with a comprehensive inventory of significant binary alignments obtained by BLAST probing of the DNA and protein databases with representative EF-G(2) sequences. In three discrete alignment blocks tone in domain II and two in domain (IV), the alignment of the bacterial sequences with those of Archaea-Eucarya was not retrieved by database probing with EF-G(2) sequences, and no EF-G homologue of the EF-2 sequence segments was detected by using partial EF-G(2) sequences as probes in BLAST/FASTA searches. The two domain IV regions (one of which comprises the ADP-ribosylatable site of EF-2) are almost certainly due to the artifactual alignment of insertion segments that are unique to Bacteria and to Archaea-Eucarya. Phylogenetic trees have been constructed from the global alignment after deselectingpositions encompassing the unretrieved, spuriously aligned regions, as well as positions arising from misalignment of the G' and G" subdomain insertion segments flanking the "fifth" consensus motif of the G domain (AE varsson, 1995). The results show inconsistencies between trees inferred by alternative methods and alternative (DNA and protein) data sets with regard to Archaea being a monophyletic or paraphyletic grouping. Both maximum-likelihood and maximum-parsimony methods do not allow discrimination (by log-likelihood difference and difference in number of inferred substitutions) between the conflicting (monophyletic vs. paraphyletic Archaea) topologies, No specific EF-2 insertions (or terminal accretions) supporting a crenarchaeal-eucaryal clade are detectable in the new EF-G(2) sequence alignment.

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Documento generato il 01/04/20 alle ore 22:58:35