Which is the most conserved group of proteins? Homology-orthology, paralogy, xenology, and the fusion of independent lineages

@article{Gogarten2004WhichIT,
  title={Which is the most conserved group of proteins? Homology-orthology, paralogy, xenology, and the fusion of independent lineages},
  author={Johann Peter Gogarten},
  journal={Journal of Molecular Evolution},
  year={2004},
  volume={39},
  pages={541-543}
}
  • J. Gogarten
  • Published 1 November 1994
  • Biology
  • Journal of Molecular Evolution
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TLDR
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References

SHOWING 1-10 OF 18 REFERENCES
Evolution of antibiotic resistance genes: the DNA sequence of a kanamycin resistance gene from Staphylococcus aureus.
TLDR
The kanamycin resistance gene from Staphylococcus aureus has been sequenced and its structure compared with similar genes isolated from Streptomyces fradiae and from two transposons, originally isolated from Klebsiella pneumoniae and Salmonella typhimurium, respectively, suggest that homologous genes of this type be called xenologous.
Evolution of HSP70 gene and its implications regarding relationships between archaebacteria, eubacteria, and eukaryotes
TLDR
Detailed phylogenetic analyses of HSP70 sequence data provide evidence that archaebacteria are not monophyletic and show a close evolutionary linkage with the gram-positive eubacteria, and results do not support the traditionalarchaebacterial tree, where a close relationship between arch aebacterial and eukaryotic homologs is observed.
Evolution of the vacuolar H+-ATPase: implications for the origin of eukaryotes.
TLDR
It is reported that the same vacuolar H-ATPase subunits are approximately equal to 50% identical to the alpha and beta subunits, respectively, of the sulfur-metabolizing Sulfolobus acidocaldarius, an archaebacterium (Archaeobacterium).
Cloning and sequencing of the gene encoding glutamine synthetase I from the archaeum Pyrococcus woesei: anomalous phylogenies inferred from analysis of archaeal and bacterial glutamine synthetase I sequences
TLDR
The possibility is presented that the GSI gene arose among the archaea and was then laterally transferred from some early methanogen to a Thermotoga-like organism.
Protein splicing converts the yeast TFP1 gene product to the 69-kD subunit of the vacuolar H(+)-adenosine triphosphatase.
TLDR
Evidence is presented that both the 69-kilodalton (kD) catalytic subunit of the vacuolar proton-translocating adenosine triphosphatase (H(+)-ATPase) and a 50-kD protein are obtained from a single translation product that is cleaved to release the 50- kD protein and spliced to form the 69 -kD subunit.
Evolution of the glutamine synthetase gene, one of the oldest existing and functioning genes.
TLDR
It is suggested that GS genes are one of the oldest existing and functioning genes in the history of gene evolution and that GSI genes should also exist in eukaryotes.
Horizontal transfer of ATPase genes--the tree of life becomes a net of life.
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