Diversity of the DNA Replication System in the Archaea Domain
Figure 1
Homologs for some key genes involved in archaeal DNA replication. Archaeal orders are phylogenetically organized following a rooted maximum likelihood tree of Archaea based on 53 concatenated ribosomal proteins [36]. The homology search was performed by RAST v4.0 (Rapid Annotation using Subsystem Technology), and the annotated data was viewed through the SEED viewer (http://www.theseed.org/). A total of 115 archaeal genome sequences were obtained from NCBI and uploaded into the RAST server. RAST annotation was performed using default parameters with the genetic code for Bacteria and Archaea. The replication proteins homologs were checked through the SEED subsystem DNA replication. Homology results of Thermococcus kodakaraensis KOD1, Pyrococcus furiosus DSM 3638, and Thermofilum pendens Hrk 5 were searched for replication protein homologs using BLAST (blastx v2.2.28+). Results with homology coverage of >80% and -values less than 0.001 were considered as real homologs. The results were also supplemented with data from literature reviews and BLAST searches. When indicated in the figure, zero (0) homologs means that no homolog was found for a specific gene by using the described methodology. Asterisks indicate that one or two of the analyzed microorganisms possess an exception for that specific feature. Exceptions noted are (feature/order) ORC1/CDC6/Thermoproteales, Thermofilum pendens Hrk5 (3 homologs), and Thermosphaera aggregans DSM11486 (2 homologs); ORC1/CDC6/Thermoplasmatales and Picrophilus torridus DSM 9790 (1 homolog); ORC1/CDC6/Methanomicrobiales and Methanoplanus petrolearius DSM11571 (4 homologs); ORC1/CDC6/Methanosarcinales and Methanosalsum zhilinae DSM4017 (4 homologs); GINS15/Thermoplasmatales and Thermoplasma acidophilum DSM1728 (1 homolog); GINS23/Desulfurococcales, Staphylothermus hellenicus DSM12710 (no homolog), and Staphylothermus marinus F1 (no homolog); GINS23/Thermococcales, Pyrococcus horikoshii OT3 (2 homologs), RPA/Thermoproteales, Thermofilum pendens Hrk5 (3 homologs), and Thermosphaera aggregans DSM11486 (1 homolog); RPA/Methanobacteriales and Methanothermus fervidus DSM2088 (no homolog); RPA/Archaeoglobales and Archaeoglobus fulgidus DSM4304 (1 homolog); MCM/Thermococcales and Thermococcus kodakaraensis KOD1 (3 homologs); MCM/Methanosarcinales and Methanosarcina acetivorans C2A (2 homologs); RFCS/Desulfurococcales and Hyperthermus butylicus DSM 5456 (2 homologs); RFCS/Halobacteriales and Haloquadratum walsbyi DSM16790 (1 homolog); RFCS/Methanosarcinales, Methanosaeta concilii CG6 (2 homologs), and Methanosaeta thermophila PT (2 homologs); PCNA/Desulfurococcales and Ignisphaera aggregans DSM17230 (1 homolog); PCNA/Sulfolobales and Metallosphaera cuprina Ar-4 (1 homolog); PCNA/Thermococcales, Pyrococcus horikoshii OT3 (2 homologs), and Thermococcus kodakaraensis KOD1 (2 homologs); PCNA/Methanococcales, Methanococcus maripaludis S2 (2 homologs), and Methanotorris igneus Kol5 (2 homologs). PolB/Thermoproteales, Caldivirga maquilingensis IC-167 (3 homologs), and Pyrobaculum calidifontis JCM 11548 (3 homologs); PolB/Desulfurococcales, Staphylothermus hellenicus DSM12710 (3 homologs), and Staphylothermus marinus F1 (3 homologs); PolB/Archaeoglobales, Archaeoglobus fulgidus DSM4304 (2 homologs); PolB/Halobacteriales, Halorhabdus utahensis DSM12940 (2 homologs); PolB/Methanosarcinales, Methanosaeta concilii GP6 (2 homologs); DP1/Methanosarcinales, Methanococcoides burtonii DSM6242 (2 homologs).
