Archaeal genetics — the third way

  title={Archaeal genetics — the third way},
  author={Thorsten Allers and Moshe Mevarech},
  journal={Nature Reviews Genetics},
For decades, archaea were misclassified as bacteria because of their prokaryotic morphology. Molecular phylogeny eventually revealed that archaea, like bacteria and eukaryotes, are a fundamentally distinct domain of life. Genome analyses have confirmed that archaea share many features with eukaryotes, particularly in information processing, and therefore can serve as streamlined models for understanding eukaryotic biology. Biochemists and structural biologists have embraced the study of archaea… 
Genetic technologies for Archaea.
Archaeal Communities: The Microbial Phylogenomic Frontier
Phylogenomic investigations reveal the complex evolutionary history of Archaea, overturning longstanding views of the history of life and determining the basis for living in extreme environments.
Genomic studies of uncultivated archaea
Genetic studies of uncultivated archaea are reviewed within a framework of the phylogenetic diversity and ecological distribution of this domain to reveal considerable heterogeneity among archaeal strains.
Archaea — timeline of the third domain
This Review charts the 'archaea movement', from its genesis through to key findings that illustrate just how strongly the field has built on new knowledge to advance the understanding not only of the Archaea, but of biology as a whole.
Archaeal DNA replication and repair.
Haloferax volcanii—a model archaeon for studying DNA replication and repair
This review will focus on DNA replication and DNA repair pathways in H. volcanii, how this work has advanced the knowledge of archaeal cellular biology, and how it may deepen the understanding of bacterial and eukaryotic processes.
Information Processing Differences Between Archaea and Eukaraya — Implications for Homologs and the Myth of Eukaryogenesis
It is shown how the key molecular features surrounding DNA replication, transcription, and translation are fundamentally distinct in eukarya despite superficial similarities to prokaryotes, particularly archaea.
Model organisms for genetics in the domain Archaea: methanogens, halophiles, Thermococcales and Sulfolobales.
This review presents the advantages and disadvantages of working with each archaeal group, gives an overview of their different genetic systems, and direct the neophyte archaeologist to the most appropriate model organism.
Archaeal phylogenomics provides evidence in support of a methanogenic origin of the Archaea and a thaumarchaeal origin for the eukaryotes
A machine-learning approach to identify 3537 discrete orthologue protein sequence groups distributed across all available archaeal genomes is developed and proposed and provided evidence for a methanogenic origin of the Archaea and evidence in support of an origin for Eukarya either within or as sisters to the Thaumarchaea.
Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes
An overview of state-of-the-art cultivation-independent genomics approaches is provided, and how these methods were used to obtain draft genome sequences of several novel members of the TACK superphylum are demonstrated, including Lokiarchaeum, two representatives of the Miscellaneous Crenarchaeotal Group (Bathyarchaeota), and a Kor Archaeum-related lineage.


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
Archaea and the prokaryote-to-eukaryote transition.
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.
Archeal DNA replication: eukaryal proteins in a bacterial context.
In this review the current knowledge of the mechanisms governing DNA replication in archaea is summarized and the similarities and differences of those of bacteria and eukarya are highlighted.
The unique features of glycolytic pathways in Archaea.
The structure and function of the archaeal glycolytic routes, the participating enzymes and their regulation are re-evaluated by means of integrating results from biochemical and genetic studies with recently obtained comparative and functional genomics data.
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
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.
Phylogenetic structure of the prokaryotic domain: The primary kingdoms
  • C. Woese, G. Fox
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 1977
A phylogenetic analysis based upon ribosomal RNA sequence characterization reveals that living systems represent one of three aboriginal lines of descent: the eubacteria, comprising all typical bacteria, the archaebacteria, and the urkaryotes, now represented in the cytoplasmic component of eukaryotic cells.
How big is the iceberg of which organellar genes in nuclear genomes are but the tip?
Evidence for and against the notion that there is a core of never-exchanged genes shared by all genomes, from which the "true" organismal tree can be deduced, are discussed.
Archaea and Their Potential Role in Human Disease
It is puzzling that despite being one of the most numerous and ubiquitous life forms on earth, no member of the domain Archaea has been described as a human pathogen.
Bacterial mode of replication with eukaryotic-like machinery in a hyperthermophilic archaeon.
The replication origin in three Pyrococcus species was found to be highly conserved, and several eukaryotic-like DNA replication genes were clustered around it, and the chromosomal region containing the replication terminus was a hot spot of genome shuffling.