Overview of Archaea

Archaea were separated from Eubacteria after discovery of their specifics in cell outer membrane that usually not affected by common antibiotics. Phylogenetic analysis introduced by Karl Wöese supported this separation. Presently, only two phyla Crenarchaeota and Euryarchaeota include the valid representatives. Another three phyla that were proposed based on the sequence analysis of environmental samples, do not contain validly published species, and for this reason they are not included in this review. The phylum Euryarchaeota currently includes eight classes and ten orders, while the Crenarchaeota phylum contains the only class with five orders. Members of the phyla Crenarchaeota have two or three family B and no family D DNA polymerases, but members of the Euryarchaeota contain the only family B polymerases and the only family D polymerases, and it is still not clear, which is the main functional enzyme in the replication process. In this article, we are present an update and comparative analysis for this domain, discussing unique features of this group and Evolution, estimating their physiology within the matrix of physic-chemical factors, and outlining future perspectives in their study. Rules of the diagonal for the diagrams with all Archaea are presented and discussed.

[1]  W. Doolittle,et al.  Gene duplications in evolution of archaeal family B DNA polymerases , 1997, Journal of bacteriology.

[2]  Z. Kelman,et al.  Multiple origins of replication in archaea. , 2004, Trends in microbiology.

[3]  T. Schafer.  Metabolism of hyperthermophiles , 2022 .

[4]  T. Cavalier-smith,et al.  The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. , 2002, International journal of systematic and evolutionary microbiology.

[5]  C R Woese,et al.  An archaeal genomic signature. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[6]  Z. Kelman,et al.  The diverse spectrum of sliding clamp interacting proteins , 2003, FEBS letters.

[7]  T. Cavalier-smith.  The Origin of Eukaryote and Archaebacterial Cells , 1987, Annals of the New York Academy of Sciences.

[8]  J. Braman,et al.  PCR fidelity of pfu DNA polymerase and other thermostable DNA polymerases. , 1996, Nucleic acids research.

[9]  P. Albrecht,et al.  Polar Lipids of Archaebacteria in Sediments and Petroleums , 1982, Science.

[10]  K. Mullis,et al.  Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. , 1986, Cold Spring Harbor symposia on quantitative biology.

[11]  Z. Kelman,et al.  ARCHAEAL DNA REPLICATION: Eukaryal , 2003 .

[12]  K. Mullis,et al.  Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. , 1988, Science.

[13]  T. Kunkel,et al.  The Y-family of DNA polymerases. , 2001, Molecular cell.

[14]  J. Ito,et al.  Compilation and alignment of DNA polymerase sequences. , 1991, Nucleic acids research.

[15]  M. Esaka,et al.  Gene Cloning and Polymerase Chain Reaction with Proliferating Cell Nuclear Antigen from Thermococcus kodakaraensis KOD1 , 2002, Bioscience, biotechnology, and biochemistry.

[16]  Y. Kawarabayasi,et al.  Three Proliferating Cell Nuclear Antigen-Like Proteins Found in the Hyperthermophilic Archaeon Aeropyrum pernix: Interactions with the Two DNA Polymerases , 2002, Journal of bacteriology.

[17]  H. Doi,et al.  A novel DNA polymerase in the hyperthermophilic archaeon, Pyrococcus furiosus: gene cloning, expression, and characterization , 1997, Genes to cells : devoted to molecular & cellular mechanisms.

[18]  Y. Ishino,et al.  Two Family B DNA Polymerases from Aeropyrum pernix, an Aerobic Hyperthermophilic Crenarchaeote , 1999, Journal of bacteriology.

[19]  E. Pikuta,et al.  Microbial Extremophiles at the Limits of Life , 2007, Critical reviews in microbiology.

[20]  J. Kuriyan,et al.  Motors and switches: AAA+ machines within the replisome , 2002, Nature Reviews Molecular Cell Biology.

[21]  P. Haug,et al.  Traces of archaebacteria in ancient sediments , 1986 .

[22]  Y. Ishino,et al.  Archaeal DNA replication: identifying the pieces to solve a puzzle. , 1999, Genetics.

[23]  Michael Albers,et al.  Elucidation of an Archaeal Replication Protein Network to Generate Enhanced PCR Enzymes* , 2002, The Journal of Biological Chemistry.

[24]  G. Church,et al.  Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics , 1997, Journal of bacteriology.

[25]  M. O’Donnell,et al.  The ring-type polymerase sliding clamp family , 2001, Genome Biology.

[26]  M. Albà,et al.  Replicative DNA polymerases , 2001, Genome Biology.

[27]  U. Hübscher,et al.  Replication factor C from the hyperthermophilic archaeon Pyrococcus abyssi does not need ATP hydrolysis for clamp-loading and contains a functionally conserved RFC PCNA-binding domain. , 2002, Journal of molecular biology.

[28]  R. Woodgate,et al.  Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4): an archaeal DinB-like DNA polymerase with lesion-bypass properties akin to eukaryotic poleta. , 2001, Nucleic acids research.

[29]  D. Gelfand,et al.  Reverse transcription and DNA amplification by a Thermus thermophilus DNA polymerase. , 1991, Biochemistry.

[30]  G. Maga,et al.  DNA Polymerases: Discovery, Characterization and Functions in Cellular DNA Transactions , 2010 .

[31]  C. Sensen,et al.  Two DNA polymerase sliding clamps from the thermophilic archaeon Sulfolobus solfataricus. , 1999, Journal of molecular biology.

[32]  D. Wigley,et al.  Biochemical characterisation of the clamp/clamp loader proteins from the euryarchaeon Archaeoglobus fulgidus. , 2002, Nucleic acids research.

[33]  H. Toh,et al.  Biochemical Analysis of Replication Factor C from the Hyperthermophilic Archaeon Pyrococcus furiosus , 2001, Journal of bacteriology.

[34]  D. Shoemaker,et al.  High-fidelity amplification using a thermostable DNA polymerase isolated from Pyrococcus furiosus. , 1991, Gene.