What are archaebacteria: life's third domain or monoderm prokaryotes related to Gram‐positive bacteria? A new proposal for the classification of prokaryotic organisms

@article{Gupta1998WhatAA,
  title={What are archaebacteria: life's third domain or monoderm prokaryotes related to Gram‐positive bacteria? A new proposal for the classification of prokaryotic organisms},
  author={Radhey S. Gupta},
  journal={Molecular Microbiology},
  year={1998},
  volume={29}
}
The evolutionary relationship within prokaryotes is examined based on signature sequences (defined as conserved inserts or deletions shared by specific taxa) and phylogenies derived from different proteins. Archaebacteria are indicated as being monophyletic by a number of proteins related to the information transfer processes. In contrast, for several other highly conserved proteins, common signature sequences are present in archaebacteria and Gram‐positive bacteria, whereas Gram‐negative… 
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References

SHOWING 1-10 OF 43 REFERENCES
Protein-based phylogenies support a chimeric origin for the eukaryotic genome.
TLDR
The hypothesis of a chimeric origin for the eukaryotic cell nucleus formed from the fusion of an archaebacteria and a gram-negative bacteria is supported.
Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea
Protein sequences encoded in three complete bacterial genomes, those of Haemophilus influenzae, Mycoplasma genitalium and Synechocystis sp., and the first available archaeal genome sequence, that of
Sequencing of heat shock protein 70 (DnaK) homologs from Deinococcus proteolyticus and Thermomicrobium roseum and their integration in a protein-based phylogeny of prokaryotes
TLDR
Phylogenetic analysis of hsp70 sequences shows that all of the gram-negative eubacterial species examined to date form a monophyletic group, which calls into question the general validity of the currently favored three-domain dogma.
Evolutionary relationships among eubacterial groups as inferred from GroEL (chaperonin) sequence comparisons.
TLDR
The general observations suggest that GroEL proteins provide valuable evolutionary tools for defining evolutionary relationships among the eubacterial lineage of life.
Archaeal-eubacterial mergers in the origin of Eukarya: phylogenetic classification of life.
  • L. Margulis
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 1996
TLDR
Molecular biology, life-history, and fossil record evidence support the reunification of bacteria as Prokarya while subdividing Eukarya into uniquely defined subtaxa: Protoctista, Animalia, Fungi, and Plantae.
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
TLDR
It is proposed that a formal system of organisms be established in which above the level of kingdom there exists a new taxon called a "domain." Life on this planet would be seen as comprising three domains, the Bacteria, the Archaea, and the Eucarya, each containing two or more kingdoms.
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.
Archaea and the prokaryote-to-eukaryote transition.
TLDR
This review considers the cumulative knowledge about the Archaea in relationship to the Bacteria and Eucarya and the recent use of molecular phylogenetic approaches to reconstructing the tree of life.
...
...