Molecular signatures for the Crenarchaeota and the Thaumarchaeota

@article{Gupta2010MolecularSF,
  title={Molecular signatures for the Crenarchaeota and the Thaumarchaeota},
  author={Radhey S. Gupta and Ali Miraj Shami},
  journal={Antonie van Leeuwenhoek},
  year={2010},
  volume={99},
  pages={133-157}
}
Crenarchaeotes found in mesophilic marine environments were recently placed into a new phylum of Archaea called the Thaumarchaeota. However, very few molecular characteristics of this new phylum are currently known which can be used to distinguish them from the Crenarchaeota. In addition, their relationships to deep-branching archaeal lineages are unclear. We report here detailed analyses of protein sequences from Crenarchaeota and Thaumarchaeota that have identified many conserved signature… 
Phylogeny and molecular signatures for the phylum Thermotogae and its subgroups
TLDR
Detailed phylogenetic analyses on Thermotogae species based on concatenated sequences for many ribosomal as well as other conserved proteins that identify a number of distinct clades within this phylum are reported.
Molecular signatures for the phylum Synergistetes and some of its subclades
TLDR
Identification of 32 CSIs in widely distributed proteins that provide novel molecular markers that distinguish the species of the phylum Synergistetes from all other bacteria suggest novel targets for evolutionary, genetic and biochemical studies on these bacteria as well as for the identification of additional species belonging to this phylum in different environments.
Co-occurence of Crenarchaeota, Thermoplasmata and methanogens in anaerobic sludge digesters
TLDR
It is shown here that Crenarchaeotes coexist with methanogens and are particularly abundant when Arch I lineage (also called WSA2 by Hugenholtz) is dominant in digesters, and Thermoplasmata were detected when Cren Archaeota were present.
The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology
Protein based molecular markers provide reliable means to understand prokaryotic phylogeny and support Darwinian mode of evolution
TLDR
Evidence is provided that although LGT is an important evolutionary force, it does not mask the tree-like branching pattern of prokaryotes or understanding of their evolutionary relationships, as well as novel and highly specific means for identification of different groups of microbes and for taxonomical and biochemical studies.
Tropical Aquatic Archaea Show Environment-Specific Community Composition
TLDR
The results show strong environment-specific community structuring in tropical aquatic Archaea, as previously seen for Bacteria.
Phylogeny and Taxonomy of Archaea: A Comparison of the Whole-Genome-Based CVTree Approach with 16S rRNA Sequence Analysis
TLDR
A tripartite comparison of Archaea phylogeny and taxonomy at and above the rank order is reported, and the whole-genome-based and alignment-free CVTree helped to determine the taxonomic position of some newly sequenced genomes without proper lineage information.
DE DE LAS ARQUEAS AERÓBICAS
TLDR
A morphological comparison of the ATP synthase of these organisms with the rest of the family of rotary ATPases (F- and V-ATPases) as well as a topological analysis of this enzymatic complex based on the function of each of the subunits that comprise it.
Microbial systematics in the post-genomics era
TLDR
Two kinds of molecular markers consisting of conserved indels in protein sequences and whole proteins that are specific for different groups that are proving particularly valuable in defining different prokaryotic groups in clear molecular terms and in understanding their interrelationships are described.
...
...

References

SHOWING 1-10 OF 107 REFERENCES
Protein signatures (molecular synapomorphies) that are distinctive characteristics of the major cyanobacterial clades.
  • Radhey S. Gupta
  • Biology
    International journal of systematic and evolutionary microbiology
  • 2009
TLDR
The unique presence of these molecular signatures in all available sequences from the indicated groups of cyanobacteria, but not in any other cyanob bacteria, indicates that these synapomorphies provide novel and potentially useful means for circumscription of several important taxonomic clades of cyanOBacteria in more definitive terms.
Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota
TLDR
It is shown that these mesophilic archaea are different from hyperthermophilic Crenarchaeota and branch deeper than was previously assumed, and should be considered as a third archaeal phylum, which the authors propose to name Thaum archaeota.
Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis
TLDR
All methanogenic archaea form a monophyletic group exclusive of other archaea and that this lineage likely evolved from Archaeoglobus, particularly regarding the origin of methanogenesis.
Diversity and abundance of Korarchaeota in terrestrial hot springs of Iceland and Kamchatka
TLDR
It is shown that Korarchaeota represent only a minor fraction of the microbial community in hot springs; however, in some cases they constitute up to 7% of all Archaea.
Nanoarchaea: representatives of a novel archaeal phylum or a fast-evolving euryarchaeal lineage related to Thermococcales?
TLDR
It is indicated that the placement of N. equitans in archaeal phylogenies on the basis of ribosomal protein concatenation may be strongly biased by the coupled effect of its above-average evolutionary rate and lateral gene transfers.
A korarchaeal genome reveals insights into the evolution of the Archaea
TLDR
The initial characterization of a member of the Korarchaeota with the proposed name, “Candidatus Kor Archaeum cryptofilum,” which exhibits an ultrathin filamentous morphology is reported, suggesting that the organism relies on a simple mode of peptide fermentation for carbon and energy and lacks the ability to synthesize de novo purines, CoA, and several other cofactors.
An archaeal genomic signature.
TLDR
This communication uses the completed genomes from four major euryarchaeal taxa to define a genomic signature for the Euryarchaeota and, by extension, the Archaea as a whole.
A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont
TLDR
The cultivation of a new nanosized hyperthermophilic archaeon from a submarine hot vent is reported, which will provide insight into the evolution of thermophily, of tiny genomes and of interspecies communication.
Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences.
Phylogenetic analysis of ribosomal RNA sequences obtained from uncultivated organisms of a hot spring in Yellowstone National Park reveals several novel groups of Archaea, many of which diverged from
Protein Phylogenies and Signature Sequences: A Reappraisal of Evolutionary Relationships among Archaebacteria, Eubacteria, and Eukaryotes
TLDR
Evidence from indels supports the view that the archaebacteria probably evolved from gram-positive bacteria and suggests that this evolution occurred in response to antibiotic selection pressures, and an alternative model of microbial evolution based on the use of indels of conserved proteins and the morphological features of prokaryotic organisms is proposed.
...
...